~ubuntu-branches/ubuntu/trusty/travis/trusty-proposed : revision 4

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/*****************************************************************************

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TRAVIS - Trajectory Analyzer and Visualizer

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This program is free software: you can redistribute it and/or modify

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it under the terms of the GNU General Public License as published by

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the Free Software Foundation, either version 3 of the License, or

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(at your option) any later version.

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This program is distributed in the hope that it will be useful,

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but WITHOUT ANY WARRANTY; without even the implied warranty of

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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

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GNU General Public License for more details.

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You should have received a copy of the GNU General Public License

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along with this program. If not, see <http://www.gnu.org/licenses/>.

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*****************************************************************************/

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#include "travis.h"

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#include "tools.h"

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#include "database.h"

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#include "statistics.h"

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#include "maintools.h"

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#include <float.h>

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#include "dacf.h"

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#include "lmwrapper.h"

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#include "cluster.h"

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#ifdef TARGET_WINDOWS

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#include <windows.h>

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#include <direct.h>

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#endif

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#ifdef TARGET_LINUX

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#include <unistd.h>

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#endif

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/***************************************************************************************************************

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********************** Beginn Quellcode ***********************************************************************

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***************************************************************************************************************/

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int main(int argc, const char *argv[])

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{

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BTIN;

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// FILE *fff;

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FILE *a, *tfi;

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char buf[256], buf2[64], buf3[256], *p, *q;

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int ti, ti2, ti3, cc, cc2, ticomb, tic_r, tic_o;

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int z0, z, z2, z3, z4, z5, z6, z7, zr, zs, zi;

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int z1a, z1t, z2a, z2t;

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CxIntArray *a1, *a2;

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CAtomGroup *g1, *g2;

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int tia[3];

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CxVector3 vec0, vec1, vec2, vec3, vec4, vec5, vecv, vecc;

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CxMatrix3 mat;

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double tf, tf2, tfr, tf3, tf4, tfs;

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double c0, c1, r;

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double *pd;

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float *pf;

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CMolecule *m, *tm;

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CSingleMolecule *sm, *smfix, *sm2, *tsm;

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char tc;

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unsigned long t0, t1, eta;

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int showinterval;

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CObservation *o;

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C3DF *tempSDF;

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C3DF *temp3DF;

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CDF *tdf;

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int sic;

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// CxIntArray tempwa, *twa; // "Tempor�res "W"ord-"A"rray

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CxIntArray templa, *tla;

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CxDoubleArray **apfa; // "A"rray von "P"ointern auf "F"loat-"A"rrays

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double *tda; // "T"empor�res "D"ouble-"Array"

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CxByteArray **apba;

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CxVec3Array tempvel;

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CAtomGroup *atgr, *ag;

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struct tm *today;

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time_t ltime;

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bool secondmolrun, tb;

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int multicounter;

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char multibuf[64];

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long fpos, fpos2;

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CMolBondGroup *bg;

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CMolBond *bond;

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CxFloatArray tempfa, tempfa2, *ptfa;

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CxFloatArray *ptfa2, *ptfa3;

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CGrace *gc, *gc2;

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CFFT *fft/*, *fft2*/;

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C2DF *temp2df, *tempc2df, **temp2dfa;

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// CNbSet *nbset;

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CConditionGroup *cg;

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// CNbSearch *nbs;

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int *tpi;

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bool ReactSecondRun;

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unsigned long tul;

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CAutoCorrelation *ac;

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CDACFSub *dacfsub;

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CMicroHetObservation *mho;

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g_bSaxonize = false;

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g_bUnknownElements = false;

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g_iStartTime = 0;

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g_bSMode = false;

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g_bNoColor = false;

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g_iColorIntensity = 1;

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g_bNPT = true; // Nur anfaenglich

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g_sNPTFile[0] = 0;

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g_fNPTFile = NULL;

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g_fBoxX = 0;

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g_fBoxY = 0;

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g_fBoxZ = 0;

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g_bVerbose = false;

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g_bClusterAnalysis = false;

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g_bNeedMoleculeWrap = false;

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g_bDipoleDefined = false;

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g_bDipolGrimme = false;

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g_bVoidSDF = false;

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g_fTimestepLength = 0;

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// mprintf("\"%s\"\n\"%d\"\n\"%s\"\n",RemovePath(__FILE__),__LINE__,__PRETTY_FUNCTION__);

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/* CClusterAnalysis *can;

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can = new CClusterAnalysis();

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for (z=0;z<15;z++)

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{

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can->AddCluster();

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can->AddParticle(rand()%20,rand()%20,rand()%20);

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}

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can->BuildTree();

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can->DumpAgr("C:\\Software\\test.csv");

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gets(buf);

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return 0;*/

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/* int maj, min;

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CreateTicks(0,540,maj,min);

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return 0;*/

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/* CExtendedCondition *ec;

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ec = new CExtendedCondition();

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ec->m_fD[0] = 1;

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ec->m_fA[0] = 1;

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ec->m_fD[1] = 2;

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ec->m_fA[1] = 1;

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ec->m_fD[2] = 2;

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ec->m_fA[2] = 0;

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if (!ec->Evaluate())

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{

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printf("Fail.\n");

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// return 0;

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}

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printf("%G * d + %G * a %c %G.\n",ec->m_fX,ec->m_fY,ec->m_bLarger?'>':'<',ec->m_fZ);

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return 0;*/

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/* CLMWrapper w;

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double *px, *py, *pp, r, integral;

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px = new double[100];

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py = new double[100];

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pp = new double[6];

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pp[0] = 1;

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pp[1] = -0.001;

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pp[2] = 1;

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pp[3] = -0.01;

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pp[4] = 1;

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pp[5] = -0.0001;

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for (z=0;z<100;z++)

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{

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px[z] = z;

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py[z] = 0.2 * exp(-0.004 * z) + 0.3 * exp(-0.05 * z) + 0.5 * exp(-0.15 * z) + 0.1 * exp(-0.1 * z);

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}

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w.Fit_TriExp(100,px,py,pp,r,integral);

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return 0;*/

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/* C3DF *df3;

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df3 = new C3DF();

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df3->m_fMinVal[0] = -100;

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df3->m_fMaxVal[0] = 100;

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df3->m_fMinVal[1] = -100;

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df3->m_fMaxVal[1] = 100;

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df3->m_fMinVal[2] = -100;

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df3->m_fMaxVal[2] = 100;

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df3->m_iRes[0] = 101;

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df3->m_iRes[1] = 101;

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df3->m_iRes[2] = 101;

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df3->Create();

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for (z=0;z<101;z++)

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for (z2=0;z2<101;z2++)

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for (z3=0;z3<101;z3++)

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if (sqrt(pow(z-50,2)+pow(z2-50,2)+pow(z3-50,2)) < 30)

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df3->AddToBin(CxVector3(z-50,z2-50,z3-50));

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df3->WritePLT("","C:\\test.plt","",true);

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df3->WriteCube("","C:\\test.cube","",true);

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return 0;*/

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/* CDF *mdf;

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mdf = new CDF();

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mdf->m_fMinVal = 0;

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mdf->m_fMaxVal = 1;

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mdf->m_iResolution = 20;

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mdf->Create(true);

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srand(time(NULL));

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for (z=0;z<1000000;z++)

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mdf->AddToBin(z/999999.0);

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mdf->Write("","D:\\Software\\out.csv","");

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return 0;*/

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/* CAutoCorrelation *ac;

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ac = new CAutoCorrelation();

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#define N 23

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ac->Init(N,N,false);

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ptfa = new CxFloatArray();

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ptfa->SetSize(N);

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ptfa2 = new CxFloatArray();

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ptfa2->SetSize(N);

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for (z=0;z<N;z++)

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ptfa->SetAt(z,sin(z/1.3)*exp(-0.01*z));

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ac->AutoCorrelate(ptfa,ptfa2);

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mprintf("Classic:\n");

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for (z=0;z<N;z++)

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mprintf("%02d: %.10f\n",z,ptfa2->GetAt(z));

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ac->Init(N,N,true);

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for (z=0;z<N;z++)

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ptfa->SetAt(z,sin(z/1.3)*exp(-0.01*z));

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ac->AutoCorrelate(ptfa,ptfa2);

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mprintf("\nFFT:\n");

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for (z=0;z<N;z++)

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mprintf("%02d: %.10f\n",z,ptfa2->GetAt(z));

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gets(buf);

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return 0;*/

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/* fft = new CFFT();

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fft->PrepareFFT_R2C(300);

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for (z=0;z<300;z++)

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{

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fft->m_pInput[z*2] = sin(z/3.1) * exp(-10.0/z);

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fft->m_pInput[z*2+1] = sin(z/2.7+1.0) * exp(-2.0/z);

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}

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fft->DoFFT();

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for (z=0;z<300;z++)

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mprintf("%03d: % 10.6f % 10.6f\n",z+1,fft->m_pOutput[z*2],fft->m_pOutput[z*2+1]);

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gets(buf);

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return 0;*/

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/* CxVector3 v1, v2, v3, v;

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v1 = CxVector3(0,0,0);

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v2 = CxVector3(1,0,0);

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v3 = CxVector3(1,1,0);

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v = PointFromRAD(v1,v2,v3,3,3.1415926/2,3.1415926/2);

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v.Dump();

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gets(buf);

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return 0;*/

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/* fft = new CFFT();

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fft->PrepareFFT_C2C(20);

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for (z=0;z<20;z++)

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{

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if (z < 20)

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{

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fft->m_pInput[2*z] = sin(2*z*17.89) * exp(-0.1*z*2);

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fft->m_pInput[2*z+1] = sin((2*z+1)*17.89) * exp(-0.1*(2*z+1));

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} else

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{

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fft->m_pInput[2*z] = 0;

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fft->m_pInput[2*z+1] = 0;

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}

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printf("%2d: % f + I * % f\n",z+1,fft->m_pInput[2*z],fft->m_pInput[2*z+1]);

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}

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printf("Transforming...\n");

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fft->DoFFT();

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for (z=0;z<20;z++)

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printf("%2d: % f + I * % f\n",z+1,fft->m_pOutput[2*z],fft->m_pOutput[2*z+1]);

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gets(buf);

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return 0;*/

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/* vec0 = CxVector3(-4.20694017, 9.48010063, -2.43410969);

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vec1 = CxVector3(0.159780025, -0.360321045, 0.0924463272);

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tf = DotP(vec0,vec1);

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tf2 = Angle_Deg(vec0,vec1);

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printf("DotP: %f, Length 1: %f, Length 2: %f, DotP/Length1/Length2: %.10f, Angle: %.10f\n",tf,vec0.GetLength(),vec1.GetLength(),tf/vec0.GetLength()/vec1.GetLength(),tf2);

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printf("acos(1)=%f, acos(-1)=%f\n",acos(1.0f),acos(-1.0f));

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return 0;*/

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/* CxVector3 a1, a2, a3;

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a1 = CxVector3(0,1.0,0);

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a2 = CxVector3(0,-1.0,0.0001);

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a3 = CxVector3(1.0,0,0);

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mprintf("Dihedral = %.3f\n",Dihedral(a1,a2,a3,false));

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getchar();

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return 0;*/

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apfa = NULL;

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tda = NULL;

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// g_pNbAll = NULL;

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// g_iMaxMSDDepth = 0;

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350

AddElementData();

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try { g_sExeName = new char[strlen(argv[0])+1]; } catch(...) { g_sExeName = NULL; }

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if (g_sExeName == NULL) NewException((double)(strlen(argv[0])+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

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355

strcpy(g_sExeName,argv[0]);

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357

GetTravisPath();

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359

g_bAbortAnalysis = true;

360

g_bBetaFeatures = false;

361

362

InstallSignalHandler();

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InitColor();

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366

g_pLogFile = OpenFileWrite("travis.log",true);

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368

showinterval = 1;

369

370

srand(time(NULL));

371

372

tul = 256;

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#ifdef TARGET_WINDOWS

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g_sHomeDir = getenv("APPDATA");

375

if (GetComputerName(buf,&tul))

376

{

377

try { g_sHostName = new char[strlen(buf)+1]; } catch(...) { g_sHostName = NULL; }

378

if (g_sHostName == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

379

380

strcpy(g_sHostName,buf);

381

} else g_sHostName = NULL;

382

383

g_sWorkingDir = _getcwd(NULL,1024);

384

#elif defined(TARGET_LINUX)

385

g_sHomeDir = getenv("HOME");

386

buf[0] = 0;

387

if (gethostname(buf,256)==0)

388

{

389

try { g_sHostName = new char[strlen(buf)+1]; } catch(...) { g_sHostName = NULL; }

390

if (g_sHostName == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

391

392

strcpy(g_sHostName,buf);

393

} else g_sHostName = NULL;

394

395

g_sWorkingDir = getcwd(NULL,1024);

396

#else

397

g_sHomeDir = NULL;

398

g_sHostName = NULL;

399

g_sWorkingDir = NULL;

400

#endif

401

402

try { g_pDatabase = new CDatabase(); } catch(...) { g_pDatabase = NULL; }

403

if (g_pDatabase == NULL) NewException((double)sizeof(CDatabase),__FILE__,__LINE__,__PRETTY_FUNCTION__);

404

405

406

// LoadSettings(argv[0]);

407

408

/* CGrace *g = new CGrace();

409

410

g->m_fMinValX = 1.37;

411

g->m_fMaxValX = 2.53;

412

g->m_fMinValY = 225;

413

g->m_fMaxValY = 8337;

414

g->MakeTicks();

415

416

printf("X: %f - %f Ticks %f\nY: %f - %f Ticks %f\n",g->m_fMinRangeX,g->m_fMaxRangeX,g->m_fTickMajorX,g->m_fMinRangeY,g->m_fMaxRangeY,g->m_fTickMajorY);

417

*/

418

419

/* CDatabaseTable *dt = new CDatabaseTable();

420

421

dt->AddInt(0,0,12345);

422

dt->AddInt(1,1,123456);

423

dt->AddInt(2,2,123);

424

dt->AddInt(3,3,1);

425

dt->AddInt(4,4,123456789);

426

427

dt->AddDouble(1,0,13.45);

428

dt->AddDouble(2,1,3.199);

429

dt->AddDouble(3,2,1367.4597);

430

dt->AddDouble(4,3,13.45);

431

dt->AddDouble(0,4,1.45);

432

433

dt->AddString(2,0,"Hallo!");

434

dt->AddString(3,1,"Hiu");

435

dt->AddString(4,2,"Hallo Welt!");

436

dt->AddString(0,3,"Dies ist ein Test");

437

dt->AddString(1,4,"^^");

438

439

dt->AddBool(3,0,true);

440

dt->AddBool(4,1,false);

441

dt->AddBool(0,2,true);

442

dt->AddBool(1,3,false);

443

dt->AddBool(2,4,true);

444

445

dt->DumpTable();

446

a = fopen("table.dat","wt");

447

dt->DumpOutputFile(a);

448

fclose(a);

449

450

return 0;*/

451

452

g_bMiddleAvg = true;

453

g_bVFHisto = false;

454

g_bUseVelocities = false;

455

g_bUseForces = false;

456

// g_bKeepNbCount = false;

457

// g_bRefEnvAtomwise = false;

458

g_bWriteAtomwise = false;

459

g_fBondFactor = 1.15f;

460

g_fVelPercentage = 0.95f;

461

g_fForcePercentage = 0.95f;

462

g_fPos = NULL;

463

g_fVel = NULL;

464

g_fForce = NULL;

465

g_iRefSystemDim = 0;

466

g_iFixMol = -1;

467

g_fInputFile = NULL;

468

g_fInput = NULL;

469

g_fSaveCondFile = NULL;

470

g_bSaveCondSnapshot = false;

471

g_bScanVelocities = false;

472

g_bSilentProgress = false;

473

ReactSecondRun = false;

474

g_bCreateRevSDF = false;

475

g_bDeriv = false;

476

477

ParsePassiveArgs(argc,argv);

478

479

InitAnalyses();

480

481

WriteHeader();

482

483

if (g_bDipolGrimme)

484

{

485

if (argc < 3)

486

DipolGrimme(NULL);

487

else DipolGrimme(argv[2]);

488

return 0;

489

}

490

491

if (!ParseArgs(argc,argv))

492

goto _ende;

493

494

if (strlen(g_sInputTraj) == 0)

495

{

496

eprintf("No trajectory file specified.\n");

497

mprintf("Please use the -p flag to specify an input trajectory in the command line.\n\n");

498

mprintf(" Enter the file name of the trajectory file to open: [Quit] ");

499

myget(buf);

500

mprintf("\n");

501

if (strlen(buf)==0)

502

{

503

CommandLineHelp();

504

goto _ende;

505

}

506

strcpy(g_sInputTraj,buf);

507

}

508

509

if (!DetermineTrajFormat())

510

goto _ende;

511

512

g_bInputRedirected = false;

513

if (g_sInputFile != NULL)

514

{

515

g_fInputFile = fopen(g_sInputFile,"rt");

516

if (g_fInputFile == NULL)

517

{

518

eprintf("Could not open input file \"%s\".\n",g_sInputFile);

519

goto _ende;

520

}

521

g_bInputRedirected = true;

522

}

523

524

if (IsTTY(stdin) && (!g_bInputRedirected))

525

{

526

g_fInput = OpenFileWrite("input.txt",true);

527

g_bInputRedirected = false;

528

inpprintf("! TRAVIS input file\n! Created with TRAVIS version compiled at %s %s\n",__DATE__,__TIME__);

529

530

time(&ltime);

531

today = localtime(&ltime);

532

strcpy(buf,asctime(today));

533

buf[strlen(buf)-1] = 0;

534

inpprintf("! Input file written at %s.\n",buf);

535

536

} else g_bInputRedirected = true;

537

538

if (g_sInputTraj[0] != 0)

539

{

540

mprintf("Opening position trajectory %s ...",g_sInputTraj);

541

if (!FileExist(g_sInputTraj))

542

{

543

eprintf("\nError. File does not exist or cannot be read.\n");

544

goto _ende;

545

}

546

}

547

if (g_sInputVel[0] != 0)

548

{

549

mprintf("Opening velocity trajectory %s ...",g_sInputVel);

550

if (!FileExist(g_sInputVel))

551

{

552

eprintf("\nError. File does not exist or cannot be read.\n");

553

goto _ende;

554

}

555

}

556

if (g_sInputForce[0] != 0)

557

{

558

mprintf("Opening Force Trajectory %s ...",g_sInputForce);

559

if (!FileExist(g_sInputForce))

560

{

561

eprintf("\nError. File does not exist or cannot be read.\n");

562

goto _ende;

563

}

564

}

565

mprintf("\n");

566

if (g_sInputTraj[0] == 0)

567

{

568

eprintf("Error: No trajectory file specified.\n");

569

goto _ende;

570

}

571

g_fPos = fopen(g_sInputTraj,"rt");

572

if (g_fPos == NULL)

573

{

574

eprintf("Error. Could not open \"%s\".\n",g_sInputTraj);

575

goto _ende;

576

}

577

578

if (!g_TimeStep.ReadTimestep(g_fPos,true))

579

{

580

eprintf("\nError reading first time step from trajectory. Leaving.\n");

581

goto _ende;

582

}

583

584

g_TimeStep.CalcMinMax();

585

586

// fgetpos(g_fPos,&fpos);

587

fpos = ftell(g_fPos);

588

fseek(g_fPos,0,SEEK_END);

589

fpos2 = ftell(g_fPos);

590

// fgetpos(g_fPos,&fpos2);

591

fclose(g_fPos);

592

593

if (fpos2 < 0)

594

{

595

mprintf("\nCould not determine trajectory file size.\n\n");

596

g_iTrajSteps = -1;

597

} else

598

{

599

g_iTrajSteps = fpos2/fpos;

600

mprintf("\nTrajectory contains approximately %d time steps (file size %s).\n\n",g_iTrajSteps,FormatBytes(fpos2));

601

}

602

603

g_iGesAtomCount = g_TimeStep.m_iGesAtomCount;

604

605

if (g_iGesAtomCount == 0)

606

{

607

eprintf("\n\nNo atoms found. This is probably not what you want. Leaving.\n");

608

goto _ende;

609

}

610

611

g_iGesVirtAtomCount = g_iGesAtomCount;

612

g_TimeStep.AddAtoms();

613

if (g_bUnknownElements)

614

mprintf("\n");

615

616

SortAtoms();

617

mprintf(WHITE,"%d atoms in the system: ",g_iGesAtomCount);

618

for (z=0;z<g_oaAtoms.GetSize();z++)

619

{

620

mprintf("%dx %s",((CAtom*)g_oaAtoms[z])->m_iCount,((CAtom*)g_oaAtoms[z])->m_sName);

621

if (z < (int)g_oaAtoms.GetSize()-1)

622

mprintf(", ");

623

}

624

mprintf("\n\n");

625

mprintf("System extent: X = { %+5.0f .. %+5.0f pm }, dX = %.0f pm\n",g_TimeStep.m_vMin[0],g_TimeStep.m_vMax[0],g_TimeStep.m_vMax[0]-g_TimeStep.m_vMin[0]);

626

mprintf(" (in step 1) Y = { %+5.0f .. %+5.0f pm }, dY = %.0f pm\n",g_TimeStep.m_vMin[1],g_TimeStep.m_vMax[1],g_TimeStep.m_vMax[1]-g_TimeStep.m_vMin[1]);

627

mprintf(" Z = { %+5.0f .. %+5.0f pm }, dZ = %.0f pm\n",g_TimeStep.m_vMin[2],g_TimeStep.m_vMax[2],g_TimeStep.m_vMax[2]-g_TimeStep.m_vMin[2]);

628

629

g_iVirtAtomType = (unsigned char)g_oaAtoms.GetSize();

630

631

xAddAtom("#");

632

633

/****************************/

634

635

if (!GatherInfos())

636

goto _ende;

637

638

/************** Beginn Analyse **************/

639

640

g_iStartTime = time(NULL);

641

642

if (g_iMaxStep != -1)

643

{

644

g_iTrajSteps = g_iMaxStep;

645

} else

646

{

647

if (g_iTrajSteps != -1)

648

{

649

g_iTrajSteps -= g_iBeginStep;

650

if (g_iTrajSteps < 1)

651

g_iTrajSteps = 1;

652

}

653

}

654

655

if (g_bResp || g_bFFGen)

656

goto _ende;

657

658

g_iStepHistory = 3;

659

multicounter = 0;

660

661

_multiintervalstart:

662

if (g_bMultiInterval)

663

{

664

g_iBeginStep = g_laMultiIntervalStart[multicounter];

665

g_iScanNbhStart = g_iBeginStep;

666

g_iMaxStep = g_laMultiIntervalEnd[multicounter] - g_laMultiIntervalStart[multicounter] + 1;

667

g_iScanNbhSteps = g_iMaxStep;

668

mprintf(YELLOW,"***********************************************\n");

669

mprintf(YELLOW,"*** Interval %2d (%6d - %6d) starting. ***\n",multicounter+1,g_laMultiIntervalStart[multicounter]+1,g_laMultiIntervalEnd[multicounter]+1);

670

mprintf(YELLOW,"***********************************************\n\n");

671

sprintf(multibuf,"_I%d_%d-%d",multicounter+1,g_laMultiIntervalStart[multicounter],g_laMultiIntervalEnd[multicounter]);

672

} else multibuf[0] = 0;

673

674

mprintf(WHITE,">>> Initialization >>>\n\n");

675

676

g_bAbortAnalysis = false;

677

678

g_fPos = fopen(g_sInputTraj,"rb"); // Eingabedatei erneut oeffnen

679

if (g_fPos == NULL)

680

{

681

eprintf("\nError. Input Trajectory suddenly vanished ^^\n");

682

goto _ende;

683

}

684

if ((g_bNPT) && (g_sNPTFile[0] != 0))

685

{

686

g_fNPTFile = fopen(g_sNPTFile,"rt");

687

if (g_fNPTFile == NULL)

688

{

689

eprintf("\nCould not open cell vector file.\n");

690

goto _ende;

691

}

692

}

693

if (g_iBeginStep != 0)

694

{

695

mprintf("Fast-forwarding to step %d...\n",g_iBeginStep+1);

696

mprintf(WHITE," [");

697

for (z=0;z<g_iBeginStep;z++)

698

{

699

if (fmod(z,g_iBeginStep/50.0) < 1.0)

700

mprintf(WHITE,"#");

701

if (!g_TimeStep.SkipTimestep(g_fPos))

702

{

703

eprintf("\nError: Unexpected end of position trajectory.\n");

704

goto _ende;

705

}

706

if ((g_bNPT) && (g_sNPTFile[0] != 0))

707

fgets(buf,256,g_fNPTFile);

708

}

709

mprintf(WHITE,"]\n");

710

g_iFastForwardPos = ftell(g_fPos);

711

mprintf(" Step %d begins at offset %lu (%.1f MB).\n\n",g_iBeginStep+1,g_iFastForwardPos,g_iFastForwardPos/1024.0/1024.0);

712

}

713

// fclose(g_fPos);

714

// g_fPos = fopen(g_sInputTraj,"rb");

715

// mprintf("Seek: %d.\n",g_iFastForwardPos);

716

// fseek(g_fPos,g_iFastForwardPos,SEEK_SET);

717

718

g_TimeStep.ReadTimestep(g_fPos,true);

719

if ((g_bNPT) && (g_sNPTFile[0] != 0))

720

{

721

g_TimeStep.ReadCellVector(g_fNPTFile);

722

fclose(g_fNPTFile);

723

}

724

fclose(g_fPos);

725

g_TimeStep.CalcCenters();

726

727

if (g_bPeriodic)

728

g_TimeStep.UniteMolecules(false);

729

730

if (g_bScanVelocities)

731

{

732

mprintf(WHITE,"\n>>> Pre-Analysis for velocity distribution >>>\n\n");

733

734

g_fPos = fopen(g_sInputTraj,"rt"); // Eingabedatei erneut Oeffnen

735

if (g_fPos == NULL)

736

{

737

eprintf("Error. Input Trajectory suddenly vanished ^^\n");

738

return 0;

739

}

740

g_iSteps = 0; // Der Zaehler der Zeitschritte

741

if (g_iScanVelStart != 0)

742

{

743

mprintf("Fast-forwarding to step %d...\n",g_iScanVelStart+1);

744

mprintf(WHITE," [");

745

for (z=0;z<g_iScanVelStart;z++)

746

{

747

if (fmod(z,g_iScanVelStart/60.0) < 1.0)

748

mprintf(WHITE,"#");

749

if (!g_TimeStep.SkipTimestep(g_fPos))

750

break;

751

}

752

mprintf(WHITE,"]\n");

753

}

754

755

while (!feof(g_fPos)) // Zeitschritt fuer Zeitschritt die Trajektorie durchgehen

756

{

757

if (!g_TimeStep.ReadTimestep(g_fPos,false))

758

goto _endvel;

759

if (g_TimeStep.m_iGesAtomCount == 0)

760

goto _endvel;

761

762

g_TimeStep.CalcCenters();

763

764

if ((g_iSteps % 4) == 0)

765

{

766

if ((g_iSteps % 200) == 0)

767

mprintf("\nStep %6d...",g_iSteps);

768

else mprintf(".");

769

}

770

771

g_iSteps++;

772

773

if ((g_iScanVelSteps > 0) && ((int)g_iSteps >= g_iScanVelSteps))

774

break;

775

}

776

_endvel:

777

778

fclose(g_fPos);

779

780

mprintf(WHITE,"\n<<< End of Pre-Analysis for velocity distribution <<<\n\n");

781

} // END IF g_bScanVelocities

782

783

784

if (g_bSaveRefEnv && (g_iNbhMode == 1))

785

{

786

mprintf("Creating statical neighborhood...\n");

787

g_pNbSet->Scan((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[g_iSaveRefMol]],&g_TimeStep,true);

788

if (g_bSaveRefWithEnv)

789

{

790

mprintf("Adding reference molecule to neighborhood...\n");

791

g_pNbSet->AddMolecule(g_iFixMol,g_iSaveRefMol);

792

}

793

mprintf("\n");

794

g_pNbSet->Dump();

795

mprintf("\n");

796

}

797

798

if (g_bVACF && g_bGlobalVACF)

799

{

800

mprintf("Initializing Global Velocity Autocorrelation Function...\n");

801

g_pGlobalVACF->Create();

802

803

if (!g_bVACFCacheMode)

804

{

805

if (g_pGlobalVACF->m_iSize > g_iStepHistory)

806

g_iStepHistory = g_pGlobalVACF->m_iSize;

807

} else

808

{

809

mprintf(" VACF Cache: Trying to allocate %s of memory...\n",FormatBytes((double)g_iGesAtomCount*g_iTrajSteps*3.1*sizeof(float)));

810

for (z=0;z<g_iGesAtomCount;z++)

811

{

812

try { ptfa = new CxFloatArray(); } catch(...) { ptfa = NULL; }

813

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

814

815

if (g_iTrajSteps != -1)

816

{

817

ptfa->SetMaxSize((long)(g_iTrajSteps*3.1));

818

ptfa->SetGrow((long)(g_iTrajSteps*0.1));

819

} else ptfa->SetGrow(1000);

820

g_pGlobalVACF->m_oaCache.Add(ptfa);

821

}

822

}

823

}

824

825

if (g_bSaveCondSnapshot)

826

g_fSaveCondFile = OpenFileWrite("savecondition.xyz",true);

827

828

for (z=0;z<g_oaObserv.GetSize();z++)

829

{

830

mprintf("Initializing Observation %d...\n",z+1);

831

o = (CObservation*)g_oaObserv[z];

832

833

if (g_bAggregation)

834

{

835

mprintf(" Creating Aggregation Functions (%d value sets)...\n",o->m_pDACF->m_oaSubDACFs.GetSize());

836

for (z2=0;z2<o->m_pDACF->m_oaSubDACFs.GetSize();z2++)

837

{

838

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[z2];

839

if (g_bDLDisp)

840

{

841

try { dacfsub->m_pDLDisp = new C2DF(); } catch(...) { dacfsub->m_pDLDisp = NULL; }

842

if (dacfsub->m_pDLDisp == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

843

844

dacfsub->m_pDLDisp->m_iRes[0] = o->m_pDACF->m_iLifetimeRes;

845

dacfsub->m_pDLDisp->m_fMinVal[0] = 0.0f;

846

dacfsub->m_pDLDisp->m_fMaxVal[0] = o->m_pDACF->m_fLargestLifetime;

847

dacfsub->m_pDLDisp->m_iRes[1] = o->m_pDACF->m_iDisplacementRes;

848

dacfsub->m_pDLDisp->m_fMinVal[1] = 0.0f;

849

dacfsub->m_pDLDisp->m_fMaxVal[1] = o->m_pDACF->m_fLargestDisplacement;

850

dacfsub->m_pDLDisp->Create();

851

dacfsub->m_pDLDisp->SetLabelX("Lifetime [ps]");

852

dacfsub->m_pDLDisp->SetLabelY("Displacement [pm]");

853

}

854

855

if (g_bDDisp)

856

{

857

try { dacfsub->m_pDDisp = new CDF(); } catch(...) { dacfsub->m_pDDisp = NULL; }

858

if (dacfsub->m_pDDisp == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

859

860

dacfsub->m_pDDisp->m_iResolution = o->m_pDACF->m_iDisplacementRes;

861

dacfsub->m_pDDisp->m_fMinVal = 0.0f;

862

dacfsub->m_pDDisp->m_fMaxVal = o->m_pDACF->m_fLargestDisplacement;

863

dacfsub->m_pDDisp->SetLabelX("Dimer displacement [pm]");

864

dacfsub->m_pDDisp->SetLabelY("Occurrence");

865

dacfsub->m_pDDisp->Create();

866

}

867

868

if (g_bDLDF)

869

{

870

try { dacfsub->m_pDLDF = new CDF(); } catch(...) { dacfsub->m_pDLDF = NULL; }

871

if (dacfsub->m_pDLDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

872

873

dacfsub->m_pDLDF->m_bLeft = true;

874

dacfsub->m_pDLDF->m_iResolution = o->m_pDACF->m_iLifetimeRes;

875

dacfsub->m_pDLDF->m_fMinVal = 0.0f;

876

dacfsub->m_pDLDF->m_fMaxVal = o->m_pDACF->m_fLargestLifetime;

877

dacfsub->m_pDLDF->SetLabelX("Tau [ps]");

878

dacfsub->m_pDLDF->SetLabelY("Occurrence");

879

dacfsub->m_pDLDF->Create();

880

}

881

882

if (g_bDACF)

883

{

884

try { dacfsub->m_pDACF = new CDF(); } catch(...) { dacfsub->m_pDACF = NULL; }

885

if (dacfsub->m_pDACF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

886

887

dacfsub->m_pDACF->m_bLeft = true;

888

dacfsub->m_pDACF->m_iResolution = o->m_pDACF->m_iDACFRes;

889

dacfsub->m_pDACF->m_fMinVal = 0;

890

dacfsub->m_pDACF->m_fMaxVal = o->m_pDACF->m_iDACFRes * g_fTimestepLength / 1000.0;

891

dacfsub->m_pDACF->SetLabelX("Tau [ps]");

892

dacfsub->m_pDACF->SetLabelY("Occurrence");

893

dacfsub->m_pDACF->Create();

894

}

895

896

try { dacfsub->m_pNDF = new CDF(); } catch(...) { dacfsub->m_pNDF = NULL; }

897

if (dacfsub->m_pNDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

898

899

dacfsub->m_pNDF->m_iResolution = ((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+1;

900

dacfsub->m_pNDF->m_fMinVal = 0.0f;

901

dacfsub->m_pNDF->m_fMaxVal = ((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+1;

902

dacfsub->m_pNDF->Create();

903

}

904

}

905

906

if (g_bSDF)

907

{

908

mprintf(" Creating SDF...\n");

909

o->m_pSDF->m_pSDF->m_fMinVal[0] = -o->m_pSDF->m_fRadius;

910

o->m_pSDF->m_pSDF->m_fMaxVal[0] = o->m_pSDF->m_fRadius;

911

o->m_pSDF->m_pSDF->m_fMinVal[1] = -o->m_pSDF->m_fRadius;

912

o->m_pSDF->m_pSDF->m_fMaxVal[1] = o->m_pSDF->m_fRadius;

913

o->m_pSDF->m_pSDF->m_fMinVal[2] = -o->m_pSDF->m_fRadius;

914

o->m_pSDF->m_pSDF->m_fMaxVal[2] = o->m_pSDF->m_fRadius;

915

o->m_pSDF->m_pSDF->m_iRes[0] = o->m_pSDF->m_iResolution;

916

o->m_pSDF->m_pSDF->m_iRes[1] = o->m_pSDF->m_iResolution;

917

o->m_pSDF->m_pSDF->m_iRes[2] = o->m_pSDF->m_iResolution;

918

o->m_pSDF->m_pSDF->m_iHistogramRes = o->m_pSDF->m_iHistogramRes;

919

o->m_pSDF->m_pSDF->Create();

920

// mprintf("Observation %d: Creating %d VecArrays.\n",z+1,o->m_iShowMolCount);

921

922

try { o->m_pSDF->m_vaData = new CxVec3Array[o->m_iShowMolCount]; } catch(...) { o->m_pSDF->m_vaData = NULL; }

923

if (o->m_pSDF->m_vaData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxVec3Array),__FILE__,__LINE__,__PRETTY_FUNCTION__);

924

925

if (o->m_pSDF->m_bVdWSpheres)

926

{

927

try { o->m_pSDF->m_faRadius = new CxFloatArray[o->m_iShowMolCount]; } catch(...) { o->m_pSDF->m_faRadius = NULL; }

928

if (o->m_pSDF->m_faRadius == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

929

}

930

931

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

932

{

933

try { o->m_pSDF->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pSDF->m_baDataEnabled = NULL; }

934

if (o->m_pSDF->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

935

}

936

}

937

938

if (g_bRDyn)

939

{

940

mprintf(" Creating Reorientation Dynamics...\n");

941

o->m_pRDyn->m_pRDyn->m_fMinVal = 0;

942

o->m_pRDyn->m_pRDyn->m_fMaxVal = o->m_pRDyn->m_iDepth * g_fTimestepLength / 1000.0f;

943

o->m_pRDyn->m_pRDyn->m_iResolution = o->m_pRDyn->m_iDepth/o->m_pRDyn->m_iStride;

944

o->m_pRDyn->m_pRDyn->SetLabelX("Tau [ps]");

945

o->m_pRDyn->m_pRDyn->SetLabelY("Vector autocorrelation");

946

o->m_pRDyn->m_pRDyn->Create();

947

if (g_bRDynCacheMode)

948

{

949

if (g_iTrajSteps != -1)

950

mprintf(" RDyn Cache: Trying to allocate %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pRDyn->m_iCombinations*g_iTrajSteps/g_iStride*3.1*sizeof(float)));

951

else mprintf(" RDyn Cache: Trying to allocate %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pRDyn->m_iCombinations*10000/g_iStride*3.1*sizeof(float)));

952

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pRDyn->m_iCombinations;z2++)

953

{

954

try { ptfa = new CxFloatArray(); } catch(...) { ptfa = NULL; }

955

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

956

957

if (g_iTrajSteps != -1)

958

{

959

ptfa->SetMaxSize((long)(g_iTrajSteps/g_iStride*3.3));

960

ptfa->SetGrow((long)(g_iTrajSteps/g_iStride*0.3));

961

} else ptfa->SetGrow(10000);

962

o->m_pRDyn->m_oaCache.Add(ptfa);

963

}

964

} else

965

{

966

try { o->m_pRDyn->m_pCount = new double[o->m_pRDyn->m_pRDyn->m_iResolution]; } catch(...) { o->m_pRDyn->m_pCount = NULL; }

967

if (o->m_pRDyn->m_pCount == NULL) NewException((double)o->m_pRDyn->m_pRDyn->m_iResolution*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

968

969

for (z2=0;z2<o->m_pRDyn->m_pRDyn->m_iResolution;z2++)

970

o->m_pRDyn->m_pCount[z2] = 0;

971

if (!g_bRDynCacheMode)

972

{

973

if (o->m_pRDyn->m_iDepth > g_iStepHistory)

974

g_iStepHistory = o->m_pRDyn->m_iDepth;

975

}

976

}

977

}

978

979

if (g_bVHDF)

980

{

981

mprintf(" Creating VHCF...\n");

982

o->m_pVHDF->m_pVHDF->m_fMinVal[0] = o->m_pVHDF->m_fMinDist;

983

o->m_pVHDF->m_pVHDF->m_fMaxVal[0] = o->m_pVHDF->m_fMaxDist;

984

o->m_pVHDF->m_pVHDF->m_iRes[0] = o->m_pVHDF->m_iResolution;

985

o->m_pVHDF->m_pVHDF->m_fMinVal[1] = 0.0;

986

o->m_pVHDF->m_pVHDF->m_fMaxVal[1] = o->m_pVHDF->m_iDepth * g_fTimestepLength / 1000.0f;

987

o->m_pVHDF->m_pVHDF->m_iRes[1] = o->m_pVHDF->m_iDepth / o->m_pVHDF->m_iStride;

988

o->m_pVHDF->m_pVHDF->Create();

989

990

try { o->m_pVHDF->m_pCount = new double[o->m_pVHDF->m_pVHDF->m_iRes[1]]; } catch(...) { o->m_pVHDF->m_pCount = NULL; }

991

if (o->m_pVHDF->m_pCount == NULL) NewException((double)o->m_pVHDF->m_pVHDF->m_iRes[1]*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

992

993

for (z0=0;z0<o->m_pVHDF->m_pVHDF->m_iRes[1];z0++)

994

o->m_pVHDF->m_pCount[z0] = 0;

995

o->m_pVHDF->m_pVHDF->SetLabelX("Distance [pm]");

996

o->m_pVHDF->m_pVHDF->SetLabelY("Tau [ps]");

997

if (o->m_pVHDF->m_iDepth > g_iStepHistory)

998

g_iStepHistory = o->m_pVHDF->m_iDepth;

999

}

1000

1001

if (g_bNbAnalysis)

1002

{

1003

mprintf(" Creating Neighborhood Analysis...\n");

1004

1005

try { o->m_pNbAnalysis->m_pNPFCount = new CDF(); } catch(...) { o->m_pNbAnalysis->m_pNPFCount = NULL; }

1006

if (o->m_pNbAnalysis->m_pNPFCount == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1007

1008

o->m_pNbAnalysis->m_pNPFCount->m_fMinVal = o->m_pNbAnalysis->m_fMinDist;

1009

o->m_pNbAnalysis->m_pNPFCount->m_fMaxVal = o->m_pNbAnalysis->m_fMaxDist;

1010

o->m_pNbAnalysis->m_pNPFCount->m_iResolution = o->m_pNbAnalysis->m_iResolution;

1011

1012

o->m_pNbAnalysis->m_pNPFCount->Create();

1013

1014

try { tdf = new CDF(); } catch(...) { tdf = NULL; }

1015

if (tdf == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1016

1017

tdf->m_fMinVal = o->m_pNbAnalysis->m_fMinDist;

1018

tdf->m_fMaxVal = o->m_pNbAnalysis->m_fMaxDist;

1019

tdf->m_iResolution = o->m_pNbAnalysis->m_iResolution;

1020

tdf->SetLabelX("Distance [pm]");

1021

tdf->SetLabelY("Occurrence");

1022

tdf->Create();

1023

o->m_pNbAnalysis->m_oaNPF.Add(tdf);

1024

1025

for (z2=0;z2<=o->m_pNbAnalysis->m_iNbCount;z2++)

1026

{

1027

try { tdf = new CDF(); } catch(...) { tdf = NULL; }

1028

if (tdf == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1029

1030

tdf->m_fMinVal = o->m_pNbAnalysis->m_fMinDist;

1031

tdf->m_fMaxVal = o->m_pNbAnalysis->m_fMaxDist;

1032

tdf->m_iResolution = o->m_pNbAnalysis->m_iResolution;

1033

tdf->SetLabelX("Distance [pm]");

1034

tdf->SetLabelY("Occurrence");

1035

tdf->Create();

1036

o->m_pNbAnalysis->m_oaDF.Add(tdf);

1037

1038

try { tdf = new CDF(); } catch(...) { tdf = NULL; }

1039

if (tdf == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1040

1041

tdf->m_fMinVal = o->m_pNbAnalysis->m_fMinDist;

1042

tdf->m_fMaxVal = o->m_pNbAnalysis->m_fMaxDist;

1043

tdf->m_iResolution = o->m_pNbAnalysis->m_iResolution;

1044

tdf->SetLabelX("Distance [pm]");

1045

tdf->SetLabelY("Occurrence");

1046

tdf->Create();

1047

o->m_pNbAnalysis->m_oaNPF.Add(tdf);

1048

}

1049

}

1050

1051

for (z0=0;z0<g_iCDFChannels;z0++)

1052

{

1053

if (g_bRDF && (o->m_pRDF[z0] != NULL))

1054

{

1055

mprintf(" Creating RDF...\n");

1056

o->m_pRDF[z0]->m_pRDF->m_fMinVal = o->m_pRDF[z0]->m_fMinDist;

1057

o->m_pRDF[z0]->m_pRDF->m_fMaxVal = o->m_pRDF[z0]->m_fMaxDist;

1058

o->m_pRDF[z0]->m_pRDF->m_iResolution = o->m_pRDF[z0]->m_iResolution;

1059

o->m_pRDF[z0]->m_pRDF->m_iHistogramRes = o->m_pRDF[z0]->m_iHistogramRes;

1060

o->m_pRDF[z0]->m_pRDF->SetLabelX("Distance [pm]");

1061

o->m_pRDF[z0]->m_pRDF->SetLabelY("g(r)");

1062

1063

if (o->m_bObsCertain && o->m_bDecompDist)

1064

{

1065

o->m_pRDF[z0]->m_pRDF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1066

1067

/* try { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti = new char*[o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize()]; } catch(...) { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti = NULL; }

1068

if (o->m_pRDF[z0]->m_pRDF->m_sLabelMulti == NULL) NewException((double)o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize()*sizeof(char*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1069

1070

for (z=0;z<o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize();z++)

1071

{

1072

try { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] = new char[128]; } catch(...) { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] = NULL; }

1073

if (o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] == NULL) NewException((double)128*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1074

}

1075

*/

1076

for (z=0;z<o->m_waObsRefList.GetSize();z++)

1077

{

1078

for (z2=0;z2<o->m_waObsShowList.GetSize();z2++)

1079

{

1080

if ((o->m_waObsRefList.GetSize() > 1) && (o->m_waObsShowList.GetSize() > 1))

1081

sprintf(buf,"RM%d-OM%d",o->m_waObsRefList[z]+1,o->m_waObsShowList[z2]+1);

1082

else if (o->m_waObsRefList.GetSize() > 1)

1083

sprintf(buf,"RM%d",o->m_waObsRefList[z]+1);

1084

else

1085

sprintf(buf,"OM%d",o->m_waObsShowList[z2]+1);

1086

1087

o->m_pRDF[z0]->m_pRDF->SetLabelMulti(z*o->m_waObsShowList.GetSize()+z2,buf);

1088

}

1089

}

1090

} else if (o->m_bDecompType)

1091

{

1092

m = (CMolecule*)g_oaMolecules[g_iFixMol];

1093

o->m_waDecompTypeRefOffs.SetSize(g_iGesVirtAtomCount);

1094

for (z=0;z<o->m_pRDF[z0]->m_oaVectors.GetSize()/2;z++)

1095

{

1096

ag = (CAtomGroup*)o->m_pRDF[z0]->m_oaVectors[z*2];

1097

for (z2=0;z2<ag->m_baRealAtomType.GetSize();z2++)

1098

{

1099

for (z3=0;z3<o->m_waDecompTypeRefList.GetSize();z3++)

1100

if (o->m_waDecompTypeRefList[z3] == ag->m_baRealAtomType[z2])

1101

goto _decomptype1;

1102

z3 = o->m_waDecompTypeRefList.GetSize();

1103

o->m_waDecompTypeRefList.Add(ag->m_baRealAtomType[z2]);

1104

_decomptype1:

1105

for (z4=0;z4<m->m_laSingleMolIndex.GetSize();z4++)

1106

{

1107

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z4]];

1108

for (z5=0;z5<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z5++)

1109

o->m_waDecompTypeRefOffs[((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z5))] = z3;

1110

}

1111

}

1112

}

1113

1114

if (o->m_bOthers)

1115

m = (CMolecule*)g_oaMolecules[o->m_iShowMol];

1116

else m = (CMolecule*)g_oaMolecules[g_iFixMol];

1117

o->m_waDecompTypeObsOffs.SetSize(g_iGesVirtAtomCount);

1118

for (z=0;z<o->m_pRDF[z0]->m_oaVectors.GetSize()/2;z++)

1119

{

1120

ag = (CAtomGroup*)o->m_pRDF[z0]->m_oaVectors[z*2+1];

1121

for (z2=0;z2<ag->m_baRealAtomType.GetSize();z2++)

1122

{

1123

for (z3=0;z3<o->m_waDecompTypeObsList.GetSize();z3++)

1124

if (o->m_waDecompTypeObsList[z3] == ag->m_baRealAtomType[z2])

1125

goto _decomptype2;

1126

z3 = o->m_waDecompTypeObsList.GetSize();

1127

o->m_waDecompTypeObsList.Add(ag->m_baRealAtomType[z2]);

1128

_decomptype2:

1129

for (z4=0;z4<m->m_laSingleMolIndex.GetSize();z4++)

1130

{

1131

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z4]];

1132

for (z5=0;z5<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z5++)

1133

o->m_waDecompTypeObsOffs[((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z5))] = z3;

1134

}

1135

}

1136

}

1137

1138

o->m_pRDF[z0]->m_pRDF->CreateMulti(o->m_waDecompTypeRefList.GetSize()*o->m_waDecompTypeObsList.GetSize());

1139

1140

/* try { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti = new char*[o->m_waDecompTypeRefList.GetSize()*o->m_waDecompTypeObsList.GetSize()]; } catch(...) { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti = NULL; }

1141

if (o->m_pRDF[z0]->m_pRDF->m_sLabelMulti == NULL) NewException((double)o->m_waDecompTypeRefList.GetSize()*o->m_waDecompTypeObsList.GetSize()*sizeof(char*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1142

1143

for (z=0;z<o->m_waDecompTypeRefList.GetSize()*o->m_waDecompTypeObsList.GetSize();z++)

1144

{

1145

try { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] = new char[128]; } catch(...) { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] = NULL; }

1146

if (o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] == NULL) NewException((double)128*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1147

}*/

1148

1149

for (z=0;z<o->m_waDecompTypeRefList.GetSize();z++)

1150

{

1151

for (z2=0;z2<o->m_waDecompTypeObsList.GetSize();z2++)

1152

{

1153

sprintf(buf,"%s-%s",((CAtom*)g_oaAtoms[o->m_waDecompTypeRefList[z]])->m_sName,((CAtom*)g_oaAtoms[o->m_waDecompTypeObsList[z2]])->m_sName);

1154

o->m_pRDF[z0]->m_pRDF->SetLabelMulti(z*o->m_waDecompTypeObsList.GetSize()+z2,buf);

1155

}

1156

}

1157

} else o->m_pRDF[z0]->m_pRDF->Create();

1158

1159

if (o->m_bSecondShowMol && (z0 == 1))

1160

{

1161

try { o->m_pRDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pRDF[z0]->m_faData = NULL; }

1162

if (o->m_pRDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1163

1164

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1165

{

1166

try { o->m_pRDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pRDF[z0]->m_baDataEnabled = NULL; }

1167

if (o->m_pRDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1168

}

1169

} else

1170

{

1171

try { o->m_pRDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pRDF[z0]->m_faData = NULL; }

1172

if (o->m_pRDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1173

1174

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1175

{

1176

try { o->m_pRDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pRDF[z0]->m_baDataEnabled = NULL; }

1177

if (o->m_pRDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1178

}

1179

}

1180

if (o->m_bTimeDev)

1181

{

1182

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1183

{

1184

try { o->m_pRDF[z0]->m_fDist = new FILE*[1]; } catch(...) { o->m_pRDF[z0]->m_fDist = NULL; }

1185

if (o->m_pRDF[z0]->m_fDist == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1186

1187

sprintf(buf,"rdf_timedev_%s%s.csv",o->m_pRDF[z0]->m_sName,multibuf);

1188

o->m_pRDF[z0]->m_fDist[0] = OpenFileWrite(buf,true);

1189

} else

1190

{

1191

try { o->m_pRDF[z0]->m_fDist = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pRDF[z0]->m_fDist = NULL; }

1192

if (o->m_pRDF[z0]->m_fDist == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1193

1194

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1195

{

1196

sprintf(buf,"rdf_timedev_%s_ref%d%s.csv",o->m_pRDF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1197

o->m_pRDF[z0]->m_fDist[z2] = OpenFileWrite(buf,true);

1198

}

1199

}

1200

if (o->m_bCombinedPlot)

1201

{

1202

// mprintf("Combined: Reflist %d, Showlist %d, Combinations %d, Steps %d.\n",o->m_waSaveRefList.GetSize(),o->m_waSaveShowList.GetSize(),o->m_pRDF[z0]->m_iCombinations,g_iTrajSteps);

1203

1204

try { o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot = NULL; }

1205

if (o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1206

1207

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetTitle("Combined distance time development/histogram");

1208

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetSubTitle(o->m_pRDF[z0]->m_sShortName);

1209

// smfix = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]];

1210

// sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[0]];

1211

// o->m_pRDF[z0]->BuildAtomList(smfix,sm,sm,&templa);

1212

mprintf(" Trying to reserve %s of memory for combined plot...\n",FormatBytes((double)sizeof(double)*o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pRDF[z0]->m_iCombinations*g_iTrajSteps/g_iStride));

1213

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1214

{

1215

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1216

{

1217

/* for (z4=0;z4<templa.GetSize()/2;z4++)

1218

{

1219

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->AddDataset();

1220

sprintf(buf,"%s[%d] %s%d - %s[%d] %s%d",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,o->m_waSaveRefList[z2]+1,((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[g_waAtomElement[templa[z4*2]]]])->m_sName,g_waAtomMolNumber[templa[z4*2]]+1,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName,o->m_waSaveShowList[z3]+1,((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex[g_waAtomElement[templa[z4*2+1]]]])->m_sName,g_waAtomMolNumber[templa[z4*2+1]]+1);

1221

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetDatasetName(buf);

1222

if (g_iTrajSteps != -1)

1223

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize() *g_iTrajSteps);

1224

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize() *100);

1225

if (o->m_bCombinedGreyMode)

1226

{

1227

ti = o->m_iCombinedGreyMin + ((z4+z3*o->m_pRDF[z0]->m_iCombinations+z2*o->m_pRDF[z0]->m_iCombinations*o->m_waSaveShowList.GetSize())%o->m_iCombinedGreyShades)*(o->m_iCombinedGreyMax-o->m_iCombinedGreyMin)/o->m_iCombinedGreyShades;

1228

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_iLineColor = ti*0x10000 + ti*0x100 + ti;

1229

}

1230

}*/

1231

1232

ti2 = 0;

1233

for (z4=0;z4<o->m_pRDF[z0]->m_oaVectors.GetSize()/2;z4++)

1234

{

1235

g1 = (CAtomGroup*)o->m_pRDF[z0]->m_oaVectors[z4*2];

1236

for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)

1237

{

1238

a1 = (CxIntArray*)g1->m_oaAtoms[z1t];

1239

for (z1a=0;z1a<a1->GetSize();z1a++)

1240

{

1241

g2 = (CAtomGroup*)o->m_pRDF[z0]->m_oaVectors[z4*2+1];

1242

for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)

1243

{

1244

a2 = (CxIntArray*)g2->m_oaAtoms[z2t];

1245

for (z2a=0;z2a<a2->GetSize();z2a++)

1246

{

1247

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->AddDataset();

1248

if (o->m_bOthers)

1249

sprintf(buf,"%s[%d] %s%d - %s[%d] %s%d",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,o->m_waSaveRefList[z2]+1,((CAtom*)g_oaAtoms[g1->m_baRealAtomType[z1t]])->m_sName,a1->GetAt(z1a)+1,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName,o->m_waSaveShowList[z3]+1,((CAtom*)g_oaAtoms[g2->m_baRealAtomType[z2t]])->m_sName,a2->GetAt(z2a)+1);

1250

else sprintf(buf,"%s[%d] %s%d - %s%d",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,o->m_waSaveRefList[z2]+1,((CAtom*)g_oaAtoms[g1->m_baRealAtomType[z1t]])->m_sName,a1->GetAt(z1a)+1,((CAtom*)g_oaAtoms[g2->m_baRealAtomType[z2t]])->m_sName,a2->GetAt(z2a)+1);

1251

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetDatasetName(buf);

1252

if (g_iTrajSteps != -1)

1253

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()/**o->m_pRDF[z0]->m_iCombinations*/ *g_iTrajSteps/g_iStride);

1254

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()/**o->m_pRDF[z0]->m_iCombinations*/ *100);

1255

if (o->m_bCombinedGreyMode)

1256

{

1257

ti = o->m_iCombinedGreyMin + ((ti2+z3*o->m_pRDF[z0]->m_iCombinations+z2*o->m_pRDF[z0]->m_iCombinations*o->m_waSaveShowList.GetSize())%o->m_iCombinedGreyShades)*(o->m_iCombinedGreyMax-o->m_iCombinedGreyMin)/o->m_iCombinedGreyShades;

1258

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1259

}

1260

ti2++;

1261

/* if (o->m_pRDF[z0]->m_iRefOrSec[0])

1262

vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));

1263

else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));

1264

if (o->m_pRDF[z0]->m_iRefOrSec[1])

1265

vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));

1266

else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));

1267

*/ // mprintf("Vector z=%d, z1t=%d, z1a=%d, z2t=%d, z2a=%d.\n",z,z1t,z1a,z2t,z2a);

1268

}

1269

}

1270

}

1271

}

1272

}

1273

1274

}

1275

}

1276

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetLabelX("Time [ps] / g(r)");

1277

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetLabelY("Distance [pm]");

1278

}

1279

} // END IF TIMEDEV

1280

1281

if (o->m_bTimeDiff)

1282

o->CreateTimeDiff(o->m_pRDF[z0]->m_pRDF,o->m_pRDF[z0]->m_iCombinations);

1283

1284

if (g_bDeriv)

1285

o->m_pDipDF[z0]->InitDeriv();

1286

} // END IF RDF

1287

1288

if (g_bADF && (o->m_pADF[z0] != NULL))

1289

{

1290

mprintf(" Creating ADF...\n");

1291

o->m_pADF[z0]->m_pADF->m_fMinVal = o->m_pADF[z0]->m_fMinAngle;

1292

o->m_pADF[z0]->m_pADF->m_fMaxVal = o->m_pADF[z0]->m_fMaxAngle;

1293

o->m_pADF[z0]->m_pADF->m_iResolution = o->m_pADF[z0]->m_iResolution;

1294

o->m_pADF[z0]->m_pADF->m_iHistogramRes = o->m_pADF[z0]->m_iHistogramRes;

1295

if (o->m_pADF[z0]->m_bCosine)

1296

o->m_pADF[z0]->m_pADF->SetLabelX("Cos(angle)");

1297

else o->m_pADF[z0]->m_pADF->SetLabelX("Angle (degree)");

1298

o->m_pADF[z0]->m_pADF->SetLabelY("Occurrence");

1299

if (o->m_bObsCertain && o->m_bDecompDist)

1300

o->m_pADF[z0]->m_pADF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1301

else o->m_pADF[z0]->m_pADF->Create();

1302

if (o->m_bSecondShowMol && (z0 == 1))

1303

{

1304

try { o->m_pADF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pADF[z0]->m_faData = NULL; }

1305

if (o->m_pADF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1306

1307

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1308

{

1309

try { o->m_pADF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pADF[z0]->m_baDataEnabled = NULL; }

1310

if (o->m_pADF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1311

}

1312

} else

1313

{

1314

try { o->m_pADF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pADF[z0]->m_faData = NULL; }

1315

if (o->m_pADF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1316

1317

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1318

{

1319

try { o->m_pADF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pADF[z0]->m_baDataEnabled = NULL; }

1320

if (o->m_pADF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1321

}

1322

}

1323

if (o->m_bTimeDev)

1324

{

1325

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1326

{

1327

try { o->m_pADF[z0]->m_fAngle = new FILE*[1]; } catch(...) { o->m_pADF[z0]->m_fAngle = NULL; }

1328

if (o->m_pADF[z0]->m_fAngle == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1329

1330

sprintf(buf,"adf_timedev_%s%s.csv",o->m_pADF[z0]->m_sName,multibuf);

1331

o->m_pADF[z0]->m_fAngle[0] = OpenFileWrite(buf,true);

1332

} else

1333

{

1334

try { o->m_pADF[z0]->m_fAngle = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pADF[z0]->m_fAngle = NULL; }

1335

if (o->m_pADF[z0]->m_fAngle == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1336

1337

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1338

{

1339

sprintf(buf,"adf_timedev_%s_ref%d%s.csv",o->m_pADF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1340

o->m_pADF[z0]->m_fAngle[z2] = OpenFileWrite(buf,true);

1341

}

1342

}

1343

if (o->m_bCombinedPlot)

1344

{

1345

try { o->m_pADF[z0]->m_pADF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pADF[z0]->m_pADF->m_pCombinedPlot = NULL; }

1346

if (o->m_pADF[z0]->m_pADF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1347

1348

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetTitle("Combined angle time development/histogram");

1349

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetSubTitle(o->m_pADF[z0]->m_sShortName);

1350

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1351

{

1352

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1353

{

1354

for (z4=0;z4<o->m_pADF[z0]->m_iCombinations;z4++)

1355

{

1356

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->AddDataset();

1357

if (g_iTrajSteps != -1)

1358

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pADF[z0]->m_iCombinations*g_iTrajSteps);

1359

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pADF[z0]->m_iCombinations*100);

1360

if (o->m_bCombinedGreyMode)

1361

{

1362

ti = o->m_iCombinedGreyMin + ((z4+z3*o->m_pADF[z0]->m_iCombinations+z2*o->m_pADF[z0]->m_iCombinations*o->m_waSaveShowList.GetSize())%o->m_iCombinedGreyShades)*(o->m_iCombinedGreyMax-o->m_iCombinedGreyMin)/o->m_iCombinedGreyShades;

1363

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1364

}

1365

// o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetSetLineWidth((z2*o->m_waSaveRefList.GetSize()+z3)*o->m_pADF[z0]->m_iCombinations+z4,2.0f);

1366

}

1367

}

1368

}

1369

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetLabelX("Time [ps] / ADF(r)");

1370

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetLabelY("Angle [Degree]");

1371

}

1372

} // END IF TIMEDEV

1373

1374

if (o->m_bTimeDiff)

1375

o->CreateTimeDiff(o->m_pADF[z0]->m_pADF,o->m_pADF[z0]->m_iCombinations);

1376

1377

if (g_bDeriv)

1378

o->m_pDipDF[z0]->InitDeriv();

1379

} // END IF ADF

1380

1381

if (g_bDipDF && (o->m_pDipDF[z0] != NULL))

1382

{

1383

mprintf(" Creating DipDF...\n");

1384

o->m_pDipDF[z0]->m_pDipoleDF->m_fMinVal = o->m_pDipDF[z0]->m_fDipoleMin;

1385

o->m_pDipDF[z0]->m_pDipoleDF->m_fMaxVal = o->m_pDipDF[z0]->m_fDipoleMax;

1386

o->m_pDipDF[z0]->m_pDipoleDF->m_iResolution = o->m_pDipDF[z0]->m_iResolution;

1387

o->m_pDipDF[z0]->m_pDipoleDF->m_iHistogramRes = o->m_pDipDF[z0]->m_iHistogramRes;

1388

o->m_pDipDF[z0]->m_pDipoleDF->SetLabelX("Dipole moment (Debye)");

1389

o->m_pDipDF[z0]->m_pDipoleDF->SetLabelY("Occurrence");

1390

if (o->m_bObsCertain && o->m_bDecompDist)

1391

o->m_pDipDF[z0]->m_pDipoleDF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1392

else o->m_pDipDF[z0]->m_pDipoleDF->Create();

1393

if (o->m_bSecondShowMol && (z0 == 1))

1394

{

1395

try { o->m_pDipDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pDipDF[z0]->m_faData = NULL; }

1396

if (o->m_pDipDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1397

1398

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1399

{

1400

try { o->m_pDipDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pDipDF[z0]->m_baDataEnabled = NULL; }

1401

if (o->m_pDipDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1402

}

1403

} else

1404

{

1405

try { o->m_pDipDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pDipDF[z0]->m_faData = NULL; }

1406

if (o->m_pDipDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1407

1408

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1409

{

1410

try { o->m_pDipDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pDipDF[z0]->m_baDataEnabled = NULL; }

1411

if (o->m_pDipDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1412

}

1413

}

1414

if (o->m_bTimeDev)

1415

{

1416

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1417

{

1418

try { o->m_pDipDF[z0]->m_fDipole = new FILE*[1]; } catch(...) { o->m_pDipDF[z0]->m_fDipole = NULL; }

1419

if (o->m_pDipDF[z0]->m_fDipole == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1420

1421

sprintf(buf,"dipole_timedev_%s%s.csv",o->m_pDipDF[z0]->m_sName,multibuf);

1422

o->m_pDipDF[z0]->m_fDipole[0] = OpenFileWrite(buf,true);

1423

} else

1424

{

1425

try { o->m_pDipDF[z0]->m_fDipole = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pDipDF[z0]->m_fDipole = NULL; }

1426

if (o->m_pDipDF[z0]->m_fDipole == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1427

1428

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1429

{

1430

sprintf(buf,"dipole_timedev_%s_ref%d%s.csv",o->m_pDipDF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1431

o->m_pDipDF[z0]->m_fDipole[z2] = OpenFileWrite(buf,true);

1432

}

1433

}

1434

if (o->m_bCombinedPlot)

1435

{

1436

try { o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot = NULL; }

1437

if (o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1438

1439

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetTitle("Combined dipole moment time development/histogram");

1440

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetSubTitle(o->m_pDipDF[z0]->m_sShortName);

1441

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1442

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1443

{

1444

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->AddDataset();

1445

if (g_iTrajSteps != -1)

1446

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*g_iTrajSteps);

1447

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*100);

1448

if (o->m_bCombinedGreyMode)

1449

{

1450

ti = o->m_iCombinedGreyMin + ((z3+z2*o->m_waSaveShowList.GetSize())%o->m_iCombinedGreyShades)*(o->m_iCombinedGreyMax-o->m_iCombinedGreyMin)/o->m_iCombinedGreyShades;

1451

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1452

}

1453

}

1454

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetLabelX("Time [ps] / DipDF(r)");

1455

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetLabelY("Dipole moment [Debye]");

1456

}

1457

} // END IF TIMEDEV

1458

1459

if (o->m_bTimeDiff)

1460

o->CreateTimeDiff(o->m_pDipDF[z0]->m_pDipoleDF,1);

1461

1462

if (g_bDeriv)

1463

o->m_pDipDF[z0]->InitDeriv();

1464

} // END IF DIPOLE

1465

1466

if (g_bVDF && (o->m_pVDF[z0] != NULL))

1467

{

1468

mprintf(" Creating VDF...\n");

1469

o->m_pVDF[z0]->m_pVDF->m_fMinVal = o->m_pVDF[z0]->m_fMinSpeed;

1470

o->m_pVDF[z0]->m_pVDF->m_fMaxVal = o->m_pVDF[z0]->m_fMaxSpeed;

1471

o->m_pVDF[z0]->m_pVDF->m_iResolution = o->m_pVDF[z0]->m_iResolution;

1472

o->m_pVDF[z0]->m_pVDF->m_iHistogramRes = o->m_pVDF[z0]->m_iHistogramRes;

1473

o->m_pVDF[z0]->m_pVDF->SetLabelX("Velocity [pm/ps]");

1474

o->m_pVDF[z0]->m_pVDF->SetLabelY("Occurrence");

1475

if (o->m_bObsCertain && o->m_bDecompDist)

1476

o->m_pVDF[z0]->m_pVDF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1477

else o->m_pVDF[z0]->m_pVDF->Create();

1478

if (o->m_bSecondShowMol && (z0 == 1))

1479

{

1480

try { o->m_pVDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pVDF[z0]->m_faData = NULL; }

1481

if (o->m_pVDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1482

1483

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1484

{

1485

try { o->m_pVDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pVDF[z0]->m_baDataEnabled = NULL; }

1486

if (o->m_pVDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1487

}

1488

} else

1489

{

1490

try { o->m_pVDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pVDF[z0]->m_faData = NULL; }

1491

if (o->m_pVDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1492

1493

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1494

{

1495

try { o->m_pVDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pVDF[z0]->m_baDataEnabled = NULL; }

1496

if (o->m_pVDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1497

}

1498

}

1499

if (o->m_bTimeDev)

1500

{

1501

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1502

{

1503

try { o->m_pVDF[z0]->m_fSpeed = new FILE*[1]; } catch(...) { o->m_pVDF[z0]->m_fSpeed = NULL; }

1504

if (o->m_pVDF[z0]->m_fSpeed == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1505

1506

sprintf(buf,"vdf_timedev_%s%s.csv",o->m_pVDF[z0]->m_sName,multibuf);

1507

o->m_pVDF[z0]->m_fSpeed[0] = OpenFileWrite(buf,true);

1508

} else

1509

{

1510

try { o->m_pVDF[z0]->m_fSpeed = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pVDF[z0]->m_fSpeed = NULL; }

1511

if (o->m_pVDF[z0]->m_fSpeed == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1512

1513

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1514

{

1515

sprintf(buf,"vdf_timedev_%s_ref%d%s.csv",o->m_pVDF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1516

o->m_pVDF[z0]->m_fSpeed[z2] = OpenFileWrite(buf,true);

1517

}

1518

}

1519

if (o->m_bCombinedPlot)

1520

{

1521

try { o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot = NULL; }

1522

if (o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1523

1524

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetTitle("Combined velocity time development/histogram");

1525

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetSubTitle(o->m_pVDF[z0]->m_sShortName);

1526

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1527

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1528

for (z4=0;z4<o->m_pVDF[z0]->m_iCombinations;z4++)

1529

{

1530

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->AddDataset();

1531

if (g_iTrajSteps != -1)

1532

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pVDF[z0]->m_iCombinations*g_iTrajSteps);

1533

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pVDF[z0]->m_iCombinations*100);

1534

if (o->m_bCombinedGreyMode)

1535

{

1536

ti = o->m_iCombinedGreyMin + ((z4+z3*o->m_pVDF[z0]->m_iCombinations+z2*o->m_pVDF[z0]->m_iCombinations*o->m_waSaveShowList.GetSize())%o->m_iCombinedGreyShades)*(o->m_iCombinedGreyMax-o->m_iCombinedGreyMin)/o->m_iCombinedGreyShades;

1537

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1538

}

1539

// o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetSetLineWidth(z2*o->m_waSaveRefList.GetSize()+z3,3.0f);

1540

}

1541

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetLabelX("Time [ps] / VDF(r)");

1542

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetLabelY("Velocity [pm/ps]");

1543

}

1544

} // END IF TIMEDEV

1545

1546

if (o->m_bTimeDiff)

1547

o->CreateTimeDiff(o->m_pVDF[z0]->m_pVDF,o->m_pVDF[z0]->m_iCombinations);

1548

1549

if (g_bDeriv)

1550

o->m_pVDF[z0]->InitDeriv();

1551

} // END IF VDF

1552

1553

if (g_bDDF && (o->m_pDDF[z0] != NULL))

1554

{

1555

mprintf(" Creating DDF...\n");

1556

o->m_pDDF[z0]->m_pDDF->m_fMinVal = o->m_pDDF[z0]->m_fMinAngle;

1557

o->m_pDDF[z0]->m_pDDF->m_fMaxVal = o->m_pDDF[z0]->m_fMaxAngle;

1558

o->m_pDDF[z0]->m_pDDF->m_iResolution = o->m_pDDF[z0]->m_iResolution;

1559

o->m_pDDF[z0]->m_pDDF->m_iHistogramRes = o->m_pDDF[z0]->m_iHistogramRes;

1560

if (o->m_pDDF[z0]->m_bCosine)

1561

o->m_pDDF[z0]->m_pDDF->SetLabelX("Cos(Dihedral Angle)");

1562

else o->m_pDDF[z0]->m_pDDF->SetLabelX("Dihedral Angle (Degree)");

1563

o->m_pDDF[z0]->m_pDDF->SetLabelY("Occurrence");

1564

if (o->m_bObsCertain && o->m_bDecompDist)

1565

o->m_pDDF[z0]->m_pDDF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1566

else o->m_pDDF[z0]->m_pDDF->Create();

1567

if (o->m_bSecondShowMol && (z0 == 1))

1568

{

1569

try { o->m_pDDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pDDF[z0]->m_faData = NULL; }

1570

if (o->m_pDDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1571

1572

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1573

{

1574

try { o->m_pDDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pDDF[z0]->m_baDataEnabled = NULL; }

1575

if (o->m_pDDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1576

}

1577

} else

1578

{

1579

try { o->m_pDDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pDDF[z0]->m_faData = NULL; }

1580

if (o->m_pDDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1581

1582

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1583

{

1584

try { o->m_pDDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pDDF[z0]->m_baDataEnabled = NULL; }

1585

if (o->m_pDDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1586

}

1587

1588

if (o->m_pDDF[z0]->m_bRotate)

1589

{

1590

for (z2=0;z2<o->m_iShowMolCount * ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() * o->m_pDDF[z0]->m_iCombinations;z2++)

1591

{

1592

o->m_pDDF[z0]->m_faLastData.Add(0);

1593

o->m_pDDF[z0]->m_laRotation.Add(0);

1594

}

1595

}

1596

}

1597

if (o->m_bTimeDev)

1598

{

1599

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1600

{

1601

try { o->m_pDDF[z0]->m_fAngle = new FILE*[1]; } catch(...) { o->m_pDDF[z0]->m_fAngle = NULL; }

1602

if (o->m_pDDF[z0]->m_fAngle == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1603

1604

sprintf(buf,"ddf_timedev_%s%s.csv",o->m_pDDF[z0]->m_sName,multibuf);

1605

o->m_pDDF[z0]->m_fAngle[0] = OpenFileWrite(buf,true);

1606

} else

1607

{

1608

try { o->m_pDDF[z0]->m_fAngle = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pDDF[z0]->m_fAngle = NULL; }

1609

if (o->m_pDDF[z0]->m_fAngle == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1610

1611

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1612

{

1613

sprintf(buf,"ddf_timedev_%s_ref%d%s.csv",o->m_pDDF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1614

o->m_pDDF[z0]->m_fAngle[z2] = OpenFileWrite(buf,true);

1615

}

1616

}

1617

if (o->m_bCombinedPlot)

1618

{

1619

try { o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot = NULL; }

1620

if (o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1621

1622

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetTitle("Combined dihedral time development/histogram");

1623

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetSubTitle(o->m_pDDF[z0]->m_sShortName);

1624

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1625

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1626

for (z4=0;z4<o->m_pDDF[z0]->m_iCombinations;z4++)

1627

{

1628

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->AddDataset();

1629

if (g_iTrajSteps != -1)

1630

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pDDF[z0]->m_iCombinations*g_iTrajSteps);

1631

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pDDF[z0]->m_iCombinations*100);

1632

if (o->m_bCombinedGreyMode)

1633

{

1634

ti = o->m_iCombinedGreyMin + ((z4+z3*o->m_pDDF[z0]->m_iCombinations+z2*o->m_pDDF[z0]->m_iCombinations*o->m_waSaveShowList.GetSize())%o->m_iCombinedGreyShades)*(o->m_iCombinedGreyMax-o->m_iCombinedGreyMin)/o->m_iCombinedGreyShades;

1635

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1636

}

1637

// o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetSetLineWidth((z2*o->m_waSaveRefList.GetSize()+z3)*o->m_pDDF[z0]->m_iCombinations+z4,2.0f);

1638

}

1639

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetLabelX("Time [ps] / DDF(r)");

1640

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetLabelY("Dihedral [Degree]");

1641

}

1642

} // END IF TIMEDEV

1643

1644

if (o->m_bTimeDiff)

1645

o->CreateTimeDiff(o->m_pDDF[z0]->m_pDDF,o->m_pDDF[z0]->m_iCombinations);

1646

1647

if (g_bDeriv)

1648

o->m_pDDF[z0]->InitDeriv();

1649

} // END IF DDF

1650

} // END FOR z0

1651

1652

if (g_bCDF)

1653

{

1654

mprintf(" Creating CDF...\n");

1655

if (g_iCDFChannels == 2)

1656

{

1657

try { o->m_pCDF->m_p2DF = new C2DF(); } catch(...) { o->m_pCDF->m_p2DF = NULL; }

1658

if (o->m_pCDF->m_p2DF == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1659

1660

buf[0] = 0;

1661

for (z2=0;z2<2;z2++)

1662

{

1663

o->m_pCDF->m_p2DF->m_iRes[z2] = o->m_pCDF->m_iResolution[z2];

1664

switch(g_iObsChannel[z2])

1665

{

1666

case 0:

1667

strcat(buf,"_rdf");

1668

strcat(buf,o->m_pRDF[z2]->m_sShortName);

1669

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pRDF[z2]->m_fMinDist;

1670

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pRDF[z2]->m_fMaxDist;

1671

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pRDF[z2]->m_pRDF;

1672

break;

1673

case 1:

1674

strcat(buf,"_adf");

1675

strcat(buf,o->m_pADF[z2]->m_sShortName);

1676

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pADF[z2]->m_fMinAngle;

1677

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pADF[z2]->m_fMaxAngle;

1678

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pADF[z2]->m_pADF;

1679

break;

1680

case 2:

1681

strcat(buf,"_ddf");

1682

strcat(buf,o->m_pDDF[z2]->m_sShortName);

1683

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pDDF[z2]->m_fMinAngle;

1684

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pDDF[z2]->m_fMaxAngle;

1685

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pDDF[z2]->m_pDDF;

1686

break;

1687

case 3:

1688

strcat(buf,"_dipole");

1689

strcat(buf,o->m_pDipDF[z2]->m_sShortName);

1690

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pDipDF[z2]->m_fDipoleMin;

1691

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pDipDF[z2]->m_fDipoleMax;

1692

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pDipDF[z2]->m_pDipoleDF;

1693

break;

1694

case 4:

1695

strcat(buf,"_vdf");

1696

strcat(buf,o->m_pVDF[z2]->m_sShortName);

1697

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pVDF[z2]->m_fMinSpeed;

1698

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pVDF[z2]->m_fMaxSpeed;

1699

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pVDF[z2]->m_pVDF;

1700

break;

1701

}

1702

}

1703

o->m_pCDF->m_p2DF->m_iHistogramRes = o->m_pCDF->m_iHistogramRes;

1704

o->m_pCDF->m_p2DF->Create();

1705

switch(g_iObsChannel[0])

1706

{

1707

case 0:

1708

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[0]->m_sShortName);

1709

o->m_pCDF->m_p2DF->SetLabelX(buf2);

1710

break;

1711

case 1:

1712

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[0]->m_sShortName);

1713

o->m_pCDF->m_p2DF->SetLabelX(buf2);

1714

break;

1715

case 2:

1716

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[0]->m_sShortName);

1717

o->m_pCDF->m_p2DF->SetLabelX(buf2);

1718

break;

1719

case 3:

1720

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[0]->m_sShortName);

1721

o->m_pCDF->m_p2DF->SetLabelX(buf2);

1722

break;

1723

case 4:

1724

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[0]->m_sShortName);

1725

o->m_pCDF->m_p2DF->SetLabelX(buf2);

1726

break;

1727

}

1728

switch(g_iObsChannel[1])

1729

{

1730

case 0:

1731

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[1]->m_sShortName);

1732

o->m_pCDF->m_p2DF->SetLabelY(buf2);

1733

break;

1734

case 1:

1735

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[1]->m_sShortName);

1736

o->m_pCDF->m_p2DF->SetLabelY(buf2);

1737

break;

1738

case 2:

1739

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[1]->m_sShortName);

1740

o->m_pCDF->m_p2DF->SetLabelY(buf2);

1741

break;

1742

case 3:

1743

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[1]->m_sShortName);

1744

o->m_pCDF->m_p2DF->SetLabelY(buf2);

1745

break;

1746

case 4:

1747

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[1]->m_sShortName);

1748

o->m_pCDF->m_p2DF->SetLabelY(buf2);

1749

break;

1750

}

1751

} // END IF CHANNELS == 2

1752

1753

if (g_iCDFChannels == 3)

1754

{

1755

try { o->m_pCDF->m_p3DF = new C3DF(); } catch(...) { o->m_pCDF->m_p3DF = NULL; }

1756

if (o->m_pCDF->m_p3DF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1757

1758

buf[0] = 0;

1759

for (z2=0;z2<g_iCDFChannels;z2++)

1760

{

1761

o->m_pCDF->m_p3DF->m_iRes[z2] = o->m_pCDF->m_iResolution[z2];

1762

switch(g_iObsChannel[z2])

1763

{

1764

case 0:

1765

strcat(buf,"_rdf");

1766

strcat(buf,o->m_pRDF[z2]->m_sShortName);

1767

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pRDF[z2]->m_fMinDist;

1768

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pRDF[z2]->m_fMaxDist;

1769

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pRDF[z2]->m_pRDF;

1770

break;

1771

case 1:

1772

strcat(buf,"_adf");

1773

strcat(buf,o->m_pADF[z2]->m_sShortName);

1774

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pADF[z2]->m_fMinAngle;

1775

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pADF[z2]->m_fMaxAngle;

1776

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pADF[z2]->m_pADF;

1777

break;

1778

case 2:

1779

strcat(buf,"_ddf");

1780

strcat(buf,o->m_pDDF[z2]->m_sShortName);

1781

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pDDF[z2]->m_fMinAngle;

1782

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pDDF[z2]->m_fMaxAngle;

1783

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pDDF[z2]->m_pDDF;

1784

break;

1785

case 3:

1786

strcat(buf,"_dipole");

1787

strcat(buf,o->m_pDipDF[z2]->m_sShortName);

1788

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pDipDF[z2]->m_fDipoleMin;

1789

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pDipDF[z2]->m_fDipoleMax;

1790

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pDipDF[z2]->m_pDipoleDF;

1791

break;

1792

case 4:

1793

strcat(buf,"_vdf");

1794

strcat(buf,o->m_pVDF[z2]->m_sShortName);

1795

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pVDF[z2]->m_fMinSpeed;

1796

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pVDF[z2]->m_fMaxSpeed;

1797

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pVDF[z2]->m_pVDF;

1798

break;

1799

}

1800

}

1801

o->m_pCDF->m_p3DF->m_iHistogramRes = o->m_pCDF->m_iHistogramRes;

1802

o->m_pCDF->m_p3DF->Create();

1803

switch(g_iObsChannel[0])

1804

{

1805

case 0:

1806

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[0]->m_sShortName);

1807

o->m_pCDF->m_p3DF->SetLabelX(buf2);

1808

break;

1809

case 1:

1810

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[0]->m_sShortName);

1811

o->m_pCDF->m_p3DF->SetLabelX(buf2);

1812

break;

1813

case 2:

1814

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[0]->m_sShortName);

1815

o->m_pCDF->m_p3DF->SetLabelX(buf2);

1816

break;

1817

case 3:

1818

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[0]->m_sShortName);

1819

o->m_pCDF->m_p3DF->SetLabelX(buf2);

1820

break;

1821

case 4:

1822

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[0]->m_sShortName);

1823

o->m_pCDF->m_p3DF->SetLabelX(buf2);

1824

break;

1825

}

1826

switch(g_iObsChannel[1])

1827

{

1828

case 0:

1829

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[1]->m_sShortName);

1830

o->m_pCDF->m_p3DF->SetLabelY(buf2);

1831

break;

1832

case 1:

1833

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[1]->m_sShortName);

1834

o->m_pCDF->m_p3DF->SetLabelY(buf2);

1835

break;

1836

case 2:

1837

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[1]->m_sShortName);

1838

o->m_pCDF->m_p3DF->SetLabelY(buf2);

1839

break;

1840

case 3:

1841

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[1]->m_sShortName);

1842

o->m_pCDF->m_p3DF->SetLabelY(buf2);

1843

break;

1844

case 4:

1845

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[1]->m_sShortName);

1846

o->m_pCDF->m_p3DF->SetLabelY(buf2);

1847

break;

1848

}

1849

switch(g_iObsChannel[2])

1850

{

1851

case 0:

1852

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[2]->m_sShortName);

1853

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

1854

break;

1855

case 1:

1856

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[2]->m_sShortName);

1857

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

1858

break;

1859

case 2:

1860

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[2]->m_sShortName);

1861

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

1862

break;

1863

case 3:

1864

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[2]->m_sShortName);

1865

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

1866

break;

1867

case 4:

1868

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[2]->m_sShortName);

1869

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

1870

break;

1871

}

1872

1873

// Fuer jede C3DF noch die 3 C2DFs erzeugen

1874

for (z3=0;z3<3;z3++)

1875

{

1876

try { o->m_pCDF->m_p3DF->m_p2DF[z3] = new C2DF(); } catch(...) { o->m_pCDF->m_p3DF->m_p2DF[z3] = NULL; }

1877

if (o->m_pCDF->m_p3DF->m_p2DF[z3] == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1878

1879

buf3[0] = 0;

1880

switch(z3)

1881

{

1882

case 0:

1883

tia[0] = 0;

1884

tia[1] = 1;

1885

break;

1886

case 1:

1887

tia[0] = 0;

1888

tia[1] = 2;

1889

break;

1890

case 2:

1891

tia[0] = 1;

1892

tia[1] = 2;

1893

break;

1894

}

1895

for (z2=0;z2<2;z2++)

1896

{

1897

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_iRes[z2] = o->m_pCDF->m_iResolution[tia[z2]];

1898

switch(g_iObsChannel[tia[z2]])

1899

{

1900

case 0:

1901

strcat(buf3,"_rdf");

1902

strcat(buf3,o->m_pRDF[tia[z2]]->m_sShortName);

1903

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pRDF[tia[z2]]->m_fMinDist;

1904

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pRDF[tia[z2]]->m_fMaxDist;

1905

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pRDF[tia[z2]]->m_pRDF;

1906

break;

1907

case 1:

1908

strcat(buf3,"_adf");

1909

strcat(buf3,o->m_pADF[tia[z2]]->m_sShortName);

1910

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pADF[tia[z2]]->m_fMinAngle;

1911

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pADF[tia[z2]]->m_fMaxAngle;

1912

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pADF[tia[z2]]->m_pADF;

1913

break;

1914

case 2:

1915

strcat(buf3,"_ddf");

1916

strcat(buf3,o->m_pDDF[tia[z2]]->m_sShortName);

1917

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pDDF[tia[z2]]->m_fMinAngle;

1918

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pDDF[tia[z2]]->m_fMaxAngle;

1919

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pDDF[tia[z2]]->m_pDDF;

1920

break;

1921

case 3:

1922

strcat(buf3,"_dipole");

1923

strcat(buf3,o->m_pDipDF[tia[z2]]->m_sShortName);

1924

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pDipDF[tia[z2]]->m_fDipoleMin;

1925

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pDipDF[tia[z2]]->m_fDipoleMax;

1926

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pDipDF[tia[z2]]->m_pDipoleDF;

1927

break;

1928

case 4:

1929

strcat(buf3,"_vdf");

1930

strcat(buf3,o->m_pVDF[tia[z2]]->m_sShortName);

1931

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pVDF[tia[z2]]->m_fMinSpeed;

1932

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pVDF[tia[z2]]->m_fMaxSpeed;

1933

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pVDF[tia[z2]]->m_pVDF;

1934

break;

1935

}

1936

}

1937

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_iHistogramRes = o->m_pCDF->m_iHistogramRes;

1938

o->m_pCDF->m_p3DF->m_p2DF[z3]->Create();

1939

switch(g_iObsChannel[tia[0]])

1940

{

1941

case 0:

1942

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[tia[0]]->m_sShortName);

1943

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

1944

break;

1945

case 1:

1946

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[tia[0]]->m_sShortName);

1947

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

1948

break;

1949

case 2:

1950

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[tia[0]]->m_sShortName);

1951

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

1952

break;

1953

case 3:

1954

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[tia[0]]->m_sShortName);

1955

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

1956

break;

1957

case 4:

1958

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[tia[0]]->m_sShortName);

1959

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

1960

break;

1961

}

1962

switch(g_iObsChannel[tia[1]])

1963

{

1964

case 0:

1965

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[tia[1]]->m_sShortName);

1966

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

1967

break;

1968

case 1:

1969

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[tia[1]]->m_sShortName);

1970

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

1971

break;

1972

case 2:

1973

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[tia[1]]->m_sShortName);

1974

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

1975

break;

1976

case 3:

1977

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[tia[1]]->m_sShortName);

1978

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

1979

break;

1980

case 4:

1981

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[tia[1]]->m_sShortName);

1982

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

1983

break;

1984

}

1985

try { o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName = new char[strlen(buf3)+1]; } catch(...) { o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName = NULL; }

1986

if (o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName == NULL) NewException((double)(strlen(buf3)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1987

1988

strcpy(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName,buf3);

1989

sprintf(buf3,"cdf_2");

1990

strcat(buf3,o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName);

1991

1992

try { o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName = new char[strlen(buf3)+1]; } catch(...) { o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName = NULL; }

1993

if (o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName == NULL) NewException((double)(strlen(buf3)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1994

1995

strcpy(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,buf3);

1996

} // END FOR z3

1997

} // END IF CHANNELS == 3

1998

1999

try { o->m_pCDF->m_sShortName = new char[strlen(buf)+1]; } catch(...) { o->m_pCDF->m_sShortName = NULL; }

2000

if (o->m_pCDF->m_sShortName == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2001

2002

strcpy(o->m_pCDF->m_sShortName,buf);

2003

sprintf(buf,"cdf_%d",g_iCDFChannels);

2004

strcat(buf,o->m_pCDF->m_sShortName);

2005

2006

try { o->m_pCDF->m_sName = new char[strlen(buf)+1]; } catch(...) { o->m_pCDF->m_sName = NULL; }

2007

if (o->m_pCDF->m_sName == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2008

2009

strcpy(o->m_pCDF->m_sName,buf);

2010

if (o->m_pCDF->m_bDumpDat)

2011

{

2012

sprintf(buf,"cdfdump_%dd%s%s.csv",g_iCDFChannels,o->m_pCDF->m_sShortName,multibuf);

2013

o->m_pCDF->m_fDump = OpenFileWrite(buf,true);

2014

fprintf(o->m_pCDF->m_fDump,"# step; RM; OM1; OM2; channels\n");

2015

}

2016

if (o->m_bTimeDev)

2017

{

2018

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

2019

{

2020

try { o->m_pCDF->m_fTimeDev = new FILE*[1]; } catch(...) { o->m_pCDF->m_fTimeDev = NULL; }

2021

if (o->m_pCDF->m_fTimeDev == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2022

2023

sprintf(buf,"cdf_timedev_%dd%s%s.csv",g_iCDFChannels,o->m_pCDF->m_sShortName,multibuf);

2024

o->m_pCDF->m_fTimeDev[0] = OpenFileWrite(buf,true);

2025

} else

2026

{

2027

try { o->m_pCDF->m_fTimeDev = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pCDF->m_fTimeDev = NULL; }

2028

if (o->m_pCDF->m_fTimeDev == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2029

2030

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

2031

{

2032

sprintf(buf,"cdf_timedev_%dd%s_ref%d%s.csv",g_iCDFChannels,o->m_pCDF->m_sShortName,z2+1,multibuf);

2033

o->m_pCDF->m_fTimeDev[z2] = OpenFileWrite(buf,true);

2034

}

2035

}

2036

if (o->m_pCDF->m_bTDAnimation)

2037

{

2038

try { o->m_pCDF->m_pTDAPlot = new CGrace(); } catch(...) { o->m_pCDF->m_pTDAPlot = NULL; }

2039

if (o->m_pCDF->m_pTDAPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2040

2041

o->m_pCDF->m_pTDAPlot->SetTitle("CDF Time Development");

2042

o->m_pCDF->m_pTDAPlot->SetSubTitle(&o->m_pCDF->m_sShortName[1]);

2043

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

2044

{

2045

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

2046

{

2047

for (z4=0;z4<o->m_pCDF->m_iCombinationsEnabled;z4++)

2048

{

2049

o->m_pCDF->m_pTDAPlot->AddDataset();

2050

if (g_iTrajSteps != -1)

2051

o->m_pCDF->m_pTDAPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled*g_iTrajSteps);

2052

o->m_pCDF->m_pTDAPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled*100);

2053

}

2054

}

2055

}

2056

o->m_pCDF->m_pTDAPlot->SetRangeX(o->m_pCDF->m_p2DF->m_fMinVal[0],o->m_pCDF->m_p2DF->m_fMaxVal[0]);

2057

o->m_pCDF->m_pTDAPlot->SetRangeY(o->m_pCDF->m_p2DF->m_fMinVal[1],o->m_pCDF->m_p2DF->m_fMaxVal[1]);

2058

o->m_pCDF->m_pTDAPlot->MakeTicks();

2059

o->m_pCDF->m_pTDAPlot->SetLabelX(o->m_pCDF->m_p2DF->m_sLabelX);

2060

o->m_pCDF->m_pTDAPlot->SetLabelY(o->m_pCDF->m_p2DF->m_sLabelY);

2061

}

2062

}

2063

} // END IF CDF

2064

2065

if (g_bVACF)

2066

{

2067

mprintf(" Creating VACF...\n");

2068

o->m_pVACF->Create();

2069

if (g_bVACFCacheMode)

2070

{

2071

mprintf(" VACF Cache: Trying to allocate %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes*g_iTrajSteps*3.1*sizeof(float)));

2072

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes;z2++)

2073

{

2074

try { ptfa = new CxFloatArray(); } catch(...) { ptfa = NULL; }

2075

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2076

2077

if (g_iTrajSteps != -1)

2078

{

2079

ptfa->SetMaxSize((long)(g_iTrajSteps*3.1));

2080

ptfa->SetGrow((long)(g_iTrajSteps*0.1));

2081

} else ptfa->SetGrow(1000);

2082

o->m_pVACF->m_oaCache.Add(ptfa);

2083

}

2084

} else

2085

{

2086

if (o->m_pVACF->m_iSize > g_iStepHistory)

2087

g_iStepHistory = o->m_pVACF->m_iSize;

2088

}

2089

}

2090

2091

if (g_bDipACF)

2092

{

2093

mprintf(" Creating DipACF...\n");

2094

o->m_pDipACF->Create();

2095

}

2096

2097

if (g_bMSD)

2098

{

2099

mprintf(" Creating MSD...\n");

2100

o->m_pMSD->m_pMSD->m_fMinVal = 0.0f;

2101

o->m_pMSD->m_pMSD->m_fMaxVal = o->m_pMSD->m_iResolution*g_fTimestepLength*g_iStride/1000.0;

2102

o->m_pMSD->m_pMSD->m_iResolution = o->m_pMSD->m_iResolution/o->m_pMSD->m_iStride;

2103

o->m_pMSD->m_pMSD->Create();

2104

if (g_bMSDCacheMode)

2105

{

2106

mprintf(" MSD Cache: Trying to reserve %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms*g_iTrajSteps/g_iStride*3.1*sizeof(float)));

2107

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms;z2++)

2108

{

2109

try { ptfa = new CxFloatArray(); } catch(...) { ptfa = NULL; }

2110

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2111

2112

if (g_iTrajSteps != -1)

2113

{

2114

ptfa->SetMaxSize((long)(g_iTrajSteps/g_iStride*3.1));

2115

ptfa->SetGrow((long)(g_iTrajSteps/g_iStride*0.1));

2116

} else ptfa->SetGrow(1000);

2117

o->m_pMSD->m_oaCache.Add(ptfa);

2118

}

2119

if (o->m_pMSD->m_bSplit)

2120

{

2121

mprintf(" MSD Split: Trying to reserve %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms*o->m_pMSD->m_iResolution/o->m_pMSD->m_iStride*sizeof(double)));

2122

try { o->m_pMSD->m_pSplitMSD = new CAF*[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms]; } catch(...) { o->m_pMSD->m_pSplitMSD = NULL; }

2123

if (o->m_pMSD->m_pSplitMSD == NULL) NewException((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms*sizeof(CAF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2124

2125

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms;z2++)

2126

{

2127

try { o->m_pMSD->m_pSplitMSD[z2] = new CAF(); } catch(...) { o->m_pMSD->m_pSplitMSD[z2] = NULL; }

2128

if (o->m_pMSD->m_pSplitMSD[z2] == NULL) NewException((double)sizeof(CAF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2129

2130

o->m_pMSD->m_pSplitMSD[z2]->m_fMinVal = 0.0f;

2131

o->m_pMSD->m_pSplitMSD[z2]->m_fMaxVal = o->m_pMSD->m_iResolution*g_fTimestepLength/1000.0;

2132

o->m_pMSD->m_pSplitMSD[z2]->m_iResolution = o->m_pMSD->m_iResolution/o->m_pMSD->m_iStride;

2133

o->m_pMSD->m_pSplitMSD[z2]->Create();

2134

}

2135

}

2136

} else

2137

{

2138

if (!g_bMSDCacheMode)

2139

{

2140

if (o->m_pMSD->m_iResolution > g_iStepHistory)

2141

g_iStepHistory = o->m_pMSD->m_iResolution;

2142

}

2143

}

2144

}

2145

2146

if (g_bRevSDF)

2147

{

2148

mprintf(" Creating Pseudo SDF...\n");

2149

o->m_pRevSDF->m_p2DF->m_fMinVal[0] = -o->m_pRevSDF->m_fRadius;

2150

o->m_pRevSDF->m_p2DF->m_fMaxVal[0] = o->m_pRevSDF->m_fRadius;

2151

o->m_pRevSDF->m_p2DF->m_fMinVal[1] = -o->m_pRevSDF->m_fRadius;

2152

o->m_pRevSDF->m_p2DF->m_fMaxVal[1] = o->m_pRevSDF->m_fRadius;

2153

o->m_pRevSDF->m_p2DF->m_iRes[0] = o->m_pRevSDF->m_iResolution;

2154

o->m_pRevSDF->m_p2DF->m_iRes[1] = o->m_pRevSDF->m_iResolution;

2155

o->m_pRevSDF->m_p2DF->SetLabelX("X [pm]");

2156

o->m_pRevSDF->m_p2DF->SetLabelY("Y [pm]");

2157

o->m_pRevSDF->m_p2DF->m_iHistogramRes = o->m_pRevSDF->m_iHistogramRes;

2158

o->m_pRevSDF->m_p2DF->Create();

2159

2160

try { o->m_pRevSDF->m_vaData = new CxVec3Array[o->m_iShowMolCount]; } catch(...) { o->m_pRevSDF->m_vaData = NULL; }

2161

if (o->m_pRevSDF->m_vaData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxVec3Array),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2162

}

2163

}

2164

2165

if (g_bBondACF)

2166

{

2167

mprintf(" Creating BondACF...\n");

2168

for (z=0;z<g_oaSingleMolecules.GetSize();z++)

2169

{

2170

sm = (CSingleMolecule*)g_oaSingleMolecules[z];

2171

for (z2=0;z2<sm->m_oaBondGroups.GetSize();z2++)

2172

{

2173

bg = (CMolBondGroup*)sm->m_oaBondGroups[z2];

2174

for (z3=0;z3<bg->m_oaBonds.GetSize();z3++)

2175

{

2176

if (g_iTrajSteps != -1)

2177

{

2178

((CMolBond*)bg->m_oaBonds[z3])->m_faData.SetMaxSize(g_iTrajSteps);

2179

((CMolBond*)bg->m_oaBonds[z3])->m_faData.SetGrow(g_iTrajSteps/10);

2180

} else ((CMolBond*)bg->m_oaBonds[z3])->m_faData.SetGrow(10000);

2181

}

2182

}

2183

}

2184

}

2185

2186

if (g_bClusterAnalysis)

2187

{

2188

mprintf(" Creating Cluster Analysis...\n");

2189

g_pClusterAnalysis->Create();

2190

}

2191

2192

if (g_bMicroHet)

2193

{

2194

mprintf(" Creating Microheterogeneity Analysis...\n");

2195

g_pMicroHet->Create();

2196

}

2197

2198

if (g_iRefSystemDim == 3)

2199

g_pRefMol.SetSize(((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes);

2200

if ((g_iRefSystemDim == 3) && !g_bMiddleAvg) // Einfach das erstbeste Molekuel als Referenz nehmen

2201

{

2202

mprintf("Creating reference molecule from first time step...");

2203

g_TimeStep.CalcCenters();

2204

vec1 = g_TimeStep.m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]])->m_oaAtomOffset[g_iFixAtomType[0]])->GetAt(g_iFixAtom[0])];

2205

vec2 = g_TimeStep.m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]])->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])];

2206

vec3 = g_TimeStep.m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]])->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])];

2207

vec2 -= vec1;

2208

vec3 -= vec1;

2209

mat.MatUltra(vec2,vec3);

2210

cc = 0;

2211

// Jeden Atomtyp des Zielmolekuels durchgehen

2212

for (z3=0;z3<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z3++)

2213

{

2214

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z3];z4++)

2215

{

2216

vec2 = g_TimeStep.m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]])->m_oaAtomOffset[z3])->GetAt(z4)];

2217

vec2 -= vec1;

2218

g_pRefMol[cc] = mat * vec2;

2219

cc++;

2220

}

2221

}

2222

mprintf("Done.\n");

2223

} // Ende Referenzbestimmung

2224

2225

unsigned int *g_pSwapMatrix;

2226

2227

if (g_iSwapAtoms)

2228

{

2229

mprintf("Creating Reference Molecule Swap Matrix...\n");

2230

2231

try { g_pSwapMatrix = new unsigned int[((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes]; } catch(...) { g_pSwapMatrix = NULL; }

2232

if (g_pSwapMatrix == NULL) NewException((double)((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes*sizeof(unsigned int),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2233

2234

for (z=0;z<((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes;z++)

2235

g_pSwapMatrix[z] = 0;

2236

}

2237

2238

g_iCurrentTimeStep = -1;

2239

g_iNextTimeStep = -1;

2240

g_iLastTimeStep = -1;

2241

2242

try { g_pTempTimestep = new CTimeStep(); } catch(...) { g_pTempTimestep = NULL; }

2243

if (g_pTempTimestep == NULL) NewException((double)sizeof(CTimeStep),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2244

2245

if ((g_bSaveRefEnv) && (g_iNbhMode == 3))

2246

{

2247

mprintf(WHITE,"\n>>> Pre-analysis for neighborhood search >>>\n");

2248

2249

g_fPos = fopen(g_sInputTraj,"rt"); // Eingabedatei erneut Oeffnen

2250

if (g_fPos == NULL)

2251

{

2252

eprintf("\nError. Input Trajectory suddenly vanished ^^\n");

2253

return 0;

2254

}

2255

g_iSteps = 0; // Der Zaehler der Zeitschritte

2256

if (g_iScanNbhStart != 0)

2257

{

2258

mprintf("\nFast-forwarding to step %d...\n",g_iScanNbhStart+1);

2259

mprintf(WHITE," [");

2260

for (z=0;z<g_iScanNbhStart;z++)

2261

{

2262

if (fmod(z,g_iScanNbhStart/60.0) < 1.0)

2263

mprintf(WHITE,"#");

2264

if (!g_TimeStep.SkipTimestep(g_fPos))

2265

break;

2266

}

2267

mprintf(WHITE,"]\n");

2268

}

2269

while (!feof(g_fPos)) // Zeitschritt fuer Zeitschritt die Trajektorie durchgehen

2270

{

2271

for (z=0;z<(g_iScanNbhStride-1);z++)

2272

if (!g_TimeStep.SkipTimestep(g_fPos))

2273

goto _endnbs;

2274

if (!g_TimeStep.ReadTimestep(g_fPos,false))

2275

goto _endnbs;

2276

if (g_TimeStep.m_iGesAtomCount == 0)

2277

goto _endnbs;

2278

// g_TimeStep.m_vaCoords.SetSize(g_iGesVirtAtomCount);

2279

// g_TimeStep.UniteMolecules();

2280

// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

2281

g_TimeStep.CalcCenters();

2282

2283

if ((g_iSteps % (4*g_iScanNbhStride)) == 0)

2284

{

2285

if ((g_iSteps % (200*g_iScanNbhStride)) == 0)

2286

mprintf("\nStep %6d...",g_iSteps);

2287

else mprintf(".");

2288

}

2289

2290

g_iSteps+=g_iScanNbhStride;

2291

2292

// vec1 = g_TimeStep.m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[g_iSaveRefMol]])->m_oaAtomOffset[g_iFixAtomType[0]])->GetAt(g_iFixAtom[0])];

2293

2294

// g_TimeStep.CenterPos(vec1);

2295

2296

// if (g_bFold)

2297

// g_TimeStep.FoldMolecules();

2298

2299

// for (z=0;z<g_oaNbSearches.GetSize();z++)

2300

g_pNbSet->Scan((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[g_iSaveRefMol]],&g_TimeStep,g_bFold);

2301

2302

if ((g_iScanNbhSteps > 0) && ((int)g_iSteps >= g_iScanNbhSteps))

2303

break;

2304

}

2305

_endnbs:

2306

2307

fclose(g_fPos);

2308

mprintf(WHITE,"\n\n<<< Neighborhood search done <<<\n");

2309

// for (z0=0;z0<g_oaNbSearches.GetSize();z0++)

2310

{

2311

mprintf(YELLOW,"\n*** Choose Neighbors\n");

2312

// nbset = (CNbSet*)g_oaNbSearches[z0];

2313

// Sort Neighbors after time they have been neighbors

2314

for (z=0;z<g_pNbSet->m_oaConditionGroups.GetSize();z++)

2315

{

2316

if (g_pNbSet->m_oaConditionGroups[z] == NULL)

2317

continue;

2318

cg = (CConditionGroup*)g_pNbSet->m_oaConditionGroups[z];

2319

2320

try { tpi = new int[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize()]; } catch(...) { tpi = NULL; }

2321

if (tpi == NULL) NewException((double)((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize()*sizeof(int),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2322

2323

for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)

2324

{

2325

cg->m_bAlwaysTrue[z2] = false;

2326

tpi[z2] = -1;

2327

}

2328

ti3 = 0;

2329

for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)

2330

{

2331

ti = 0;

2332

for (z3=z2;z3<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z3++)

2333

{

2334

for (z4=0;z4<z2;z4++)

2335

if (tpi[z4] == z3)

2336

goto _nbhave;

2337

if (cg->m_iPassCounter[z3] > ti)

2338

{

2339

ti = cg->m_iPassCounter[z3];

2340

ti2 = z3;

2341

}

2342

_nbhave:;

2343

}

2344

if (ti == 0)

2345

break;

2346

ti3++;

2347

tpi[z2] = ti2;

2348

}

2349

mprintf(WHITE,"\n Molecule type %s. %d neighbors found in total:\n",((CMolecule*)g_oaMolecules[z])->m_sName,ti3);

2350

for (z2=0;z2<ti3;z2++)

2351

mprintf(" %2d.) Molecule %3d (%8.4f percent of the time, %d hits)\n",z2+1,tpi[z2]+1,((double)cg->m_iPassCounter[tpi[z2]])*g_iScanNbhStride/g_iSteps*100.0,cg->m_iPassCounter[tpi[z2]]);

2352

2353

if (ti3 != 0)

2354

{

2355

z3 = AskUnsignedInteger("\nUse how many of the frequentiest neighbors for molecule %s? [%d] ",ti3,((CMolecule*)g_oaMolecules[z])->m_sName,ti3);

2356

for (z2=0;z2<z3;z2++)

2357

cg->m_bAlwaysTrue[tpi[z2]] = true;

2358

}

2359

2360

delete[] tpi;

2361

cg->m_bInactive = true;

2362

}

2363

}

2364

mprintf("\n");

2365

// for (z0=0;z0<g_oaNbSearches.GetSize();z0++)

2366

if (g_bSaveRefWithEnv)

2367

{

2368

mprintf("Adding reference molecule to neighborhood...\n");

2369

g_pNbSet->AddMolecule(g_iFixMol,g_iSaveRefMol);

2370

}

2371

2372

g_pNbSet->Reset();

2373

g_pNbSet->Dump();

2374

}

2375

2376

if (g_bVFDF)

2377

{

2378

g_iVFCorrCount = 0;

2379

for (z=0;z<g_oaMolecules.GetSize();z++)

2380

{

2381

for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_baAtomIndex.GetSize();z2++)

2382

{

2383

sprintf(buf,"vfcorr_%s_%s%s.dat",((CMolecule*)g_oaMolecules[z])->m_sName,((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[z])->m_baAtomIndex[z2]])->m_sName,multibuf);

2384

// FreeFileName(buf);

2385

g_fVFCorr[g_iVFCorrCount] = OpenFileWrite(buf,true);

2386

g_iVFCorrCount++;

2387

}

2388

}

2389

}

2390

2391

if (g_bReact)

2392

{

2393

g_pReact->Create();

2394

g_pReact->InitMolecules(&g_TimeStep);

2395

}

2396

2397

if (g_bSaveRefEnv)

2398

{

2399

mprintf("\n");

2400

sprintf(g_sRefEnv,"refenv_%s.%d.",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1);

2401

/* for (z=0;z<g_oaMolecules.GetSize();z++)

2402

if (g_pNbAll->m_waMolCount[z] != 0)

2403

{

2404

sprintf(buf2,"%dx%s.",g_pNbAll->m_waMolCount[z],((CMolecule*)g_oaMolecules[z])->m_sName);

2405

strcat(g_sRefEnv,buf2);

2406

}*/

2407

/* if (!g_bDynamicNeighbor)

2408

strcat(g_sRefEnv,"static.");

2409

if (g_bRefEnvCenter)

2410

strcat(g_sRefEnv,"center.");

2411

if (g_bRefEnvFix)

2412

strcat(g_sRefEnv,"fix.");

2413

if (g_bScanNeighbors)

2414

strcat(g_sRefEnv,"scannb.");*/

2415

strcat(g_sRefEnv,multibuf);

2416

strcat(g_sRefEnv,"xyz");

2417

mprintf(">>> Saving reference environment as %s\n",g_sRefEnv);

2418

// FreeFileName(g_sRefEnv);

2419

g_fRefEnv = OpenFileWrite(g_sRefEnv,true);

2420

mprintf("\n");

2421

}

2422

2423

if (g_bCutCluster)

2424

{

2425

mprintf("\n");

2426

sprintf(g_sRefEnv,"cluster_%s.",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);

2427

/* for (z=0;z<g_oaMolecules.GetSize();z++)

2428

if (g_pNbAll->m_waMolCount[z] != 0)

2429

{

2430

sprintf(buf2,"%dx%s.",g_pNbAll->m_waMolCount[z],((CMolecule*)g_oaMolecules[z])->m_sName);

2431

strcat(g_sRefEnv,buf2);

2432

}*/

2433

/* if (g_bRefEnvCenter)

2434

strcat(g_sRefEnv,"center.");

2435

if (g_bRefEnvFix)

2436

strcat(g_sRefEnv,"fix.");*/

2437

strcat(g_sRefEnv,multibuf);

2438

strcat(g_sRefEnv,"xyz");

2439

mprintf(">>> Saving cluster list as %s\n",g_sRefEnv);

2440

// FreeFileName(g_sRefEnv);

2441

g_fRefEnv = OpenFileWrite(g_sRefEnv,true);

2442

mprintf("\n");

2443

}

2444

2445

if (g_bSaveJustTraj)

2446

{

2447

strcpy(buf,g_sInputTraj);

2448

p = strrchr(buf,'/');

2449

q = strrchr(buf,'\\');

2450

if (q > p)

2451

p = q;

2452

if (p == NULL)

2453

p = buf;

2454

else p++;

2455

strcpy(buf2,p);

2456

p = strrchr(buf2,'.');

2457

if (p != NULL)

2458

*p = 0;

2459

strcat(buf2,multibuf);

2460

strcat(buf2,"_out.xyz");

2461

// FreeFileName(buf);

2462

// sprintf(buf,"traj_out.xyz");

2463

mprintf("Saving processed trajectory as %s ...\n",buf2);

2464

g_fSaveJustTraj = OpenFileWrite(buf2,true);

2465

}

2466

2467

mprintf(WHITE,"\n<<< End of Initialization <<<\n\n");

2468

2469

_beginmain:

2470

if (ReactSecondRun)

2471

mprintf(WHITE,"\n### Starting Second Pass ###\n");

2472

else mprintf(WHITE,"\n### Starting Main Analysis ###\n");

2473

2474

#ifdef TARGET_LINUX

2475

if (!g_bMultiInterval || (multicounter == 0))

2476

{

2477

mprintf(WHITE,"\nHint: ");

2478

mprintf("Press CTRL+C once to softly interrupt analysis and still write the results.\n");

2479

mprintf(" Creating an empty file named EXIT (\"touch EXIT\") has the same effect.\n");

2480

}

2481

#endif

2482

2483

g_fPos = fopen(g_sInputTraj,"rb");

2484

if (g_fPos == NULL)

2485

{

2486

eprintf("\nCould not open position trajectory.\n");

2487

goto _ende;

2488

}

2489

if ((g_bNPT) && (g_sNPTFile[0] != 0))

2490

{

2491

g_fNPTFile = fopen(g_sNPTFile,"rt");

2492

if (g_fNPTFile == NULL)

2493

{

2494

eprintf("\nCould not open cell vector file.\n");

2495

goto _ende;

2496

}

2497

}

2498

2499

if (g_bUseVelocities && (g_sInputVel[0] != 0))

2500

{

2501

g_fVel = fopen(g_sInputVel,"rt");

2502

if (g_fVel == NULL)

2503

{

2504

eprintf("\nCould not open velocity trajectory.\n");

2505

goto _ende;

2506

}

2507

}

2508

if (g_bUseForces && (g_sInputForce[0] != 0))

2509

{

2510

g_fForce = fopen(g_sInputForce,"rt");

2511

if (g_fForce == NULL)

2512

{

2513

eprintf("\nCould not open force trajectory.\n");

2514

goto _ende;

2515

}

2516

}

2517

2518

// fff = fopen("dipole.txt","wt");

2519

2520

if (g_iBeginStep != 0)

2521

{

2522

mprintf("\nFast-forwarding to step %d...\n",g_iBeginStep+1);

2523

// mprintf("Seek: %d.\n",g_iFastForwardPos);

2524

fseek(g_fPos,g_iFastForwardPos,SEEK_SET);

2525

if ((g_fVel != NULL) || (g_fForce != NULL) || ((g_bNPT) && (g_sNPTFile[0] != 0)))

2526

{

2527

mprintf(WHITE," [");

2528

for (z=0;z<g_iBeginStep;z++)

2529

{

2530

/* if (!g_TimeStep.SkipTimestep(g_fPos))

2531

{

2532

eprintf("Error. Unexpected end of position trajectory.\n");

2533

goto _endmainloop;

2534

}*/

2535

if (fmod(z,g_iBeginStep/60.0) < 1.0)

2536

mprintf(WHITE,"#");

2537

if (g_fVel != NULL)

2538

if (!g_TimeStep.SkipTimestep(g_fVel))

2539

{

2540

eprintf("Error. Unexpected end of velocity trajectory.\n");

2541

goto _endmainloop;

2542

}

2543

if (g_fForce != NULL)

2544

if (!g_TimeStep.SkipTimestep(g_fForce))

2545

{

2546

eprintf("Error. Unexpected end of force trajectory.\n");

2547

goto _endmainloop;

2548

}

2549

if (((g_bNPT) && (g_sNPTFile[0] != 0)))

2550

fgets(buf,256,g_fNPTFile);

2551

}

2552

mprintf(WHITE,"]\n");

2553

}

2554

}

2555

2556

g_oaTimeSteps.SetSize(g_iStepHistory);

2557

for (z=0;z<g_iStepHistory;z++)

2558

g_oaTimeSteps[z] = NULL;

2559

2560

g_iSteps = 0; // Der Zaehler der Zeitschritte

2561

g_iCurrentTimeStep = 0;

2562

t0 = time(NULL);

2563

g_iClusterPos = 0;

2564

sic = 0;

2565

g_iSaveCondCount = 0;

2566

2567

try { apfa = new CxDoubleArray*[g_iCDFChannels]; } catch(...) { apfa = NULL; }

2568

if (apfa == NULL) NewException((double)g_iCDFChannels*sizeof(CxDoubleArray*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2569

2570

try { apba = new CxByteArray*[g_iCDFChannels]; } catch(...) { apba = NULL; }

2571

if (apba == NULL) NewException((double)g_iCDFChannels*sizeof(CxByteArray*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2572

2573

try { tda = new double[g_iCDFChannels]; } catch(...) { tda = NULL; }

2574

if (tda == NULL) NewException((double)g_iCDFChannels*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2575

2576

if (g_bDeriv)

2577

{

2578

g_iDerivNext = 2;

2579

g_iDerivCurr = 1;

2580

g_iDerivLast = 0;

2581

}

2582

2583

2584

/*****************************************************************************

2585

*************** Beginn Hauptschleife *****************************************

2586

*****************************************************************************/

2587

2588

g_iLastTimeStep = -1;

2589

g_iDotCounter = 0;

2590

g_bStepSkipped = false;

2591

g_iFirstStepSkipped = -1;

2592

2593

while (true) // Zeitschritt fuer Zeitschritt die Trajektorie durchgehen

2594

{

2595

if (feof(g_fPos))

2596

{

2597

mprintf("\nEnd of trajectory file reached.\n");

2598

break;

2599

}

2600

if (g_bAbortAnalysis)

2601

{

2602

mprintf("\nAnalysis aborted by user.\n");

2603

break;

2604

}

2605

g_iCurrentTimeStep++;

2606

if (g_iCurrentTimeStep >= g_iStepHistory)

2607

g_iCurrentTimeStep = 0;

2608

2609

if (g_bDeriv)

2610

{

2611

g_iDerivNext++;

2612

if (g_iDerivNext > 2)

2613

g_iDerivNext = 0;

2614

g_iDerivCurr++;

2615

if (g_iDerivCurr > 2)

2616

g_iDerivCurr = 0;

2617

g_iDerivLast++;

2618

if (g_iDerivLast > 2)

2619

g_iDerivLast = 0;

2620

}

2621

2622

for (z=0;z<(g_iStride-1);z++)

2623

{

2624

if (!g_TimeStep.SkipTimestep(g_fPos))

2625

{

2626

if (!feof(g_fPos))

2627

eprintf("\nError while skipping time step %d.\n",g_iSteps+z+1);

2628

goto _endmainloop;

2629

}

2630

if (((g_bNPT) && (g_sNPTFile[0] != 0)))

2631

fgets(buf,256,g_fNPTFile);

2632

if (g_fVel != NULL)

2633

if (!g_TimeStep.SkipTimestep(g_fVel))

2634

{

2635

eprintf("\nError while skipping velocity time step %d.\n",g_iSteps+z+1);

2636

goto _endmainloop;

2637

}

2638

if (g_fForce != NULL)

2639

if (!g_TimeStep.SkipTimestep(g_fForce))

2640

{

2641

eprintf("\nError while skipping force time step %d.\n",g_iSteps+z+1);

2642

goto _endmainloop;

2643

}

2644

}

2645

_readagain:

2646

if (g_bUseVelocities || g_bUseForces)

2647

{

2648

if (GetTimeStep(-1) == NULL)

2649

{

2650

try { *GetTimeStepAddress(-1) = new CTimeStep(); } catch(...) { *GetTimeStepAddress(-1) = NULL; }

2651

if (*GetTimeStepAddress(-1) == NULL) NewException((double)sizeof(CTimeStep),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2652

}

2653

if (!GetTimeStep(-1)->ReadTimestep(g_fPos,false))

2654

{

2655

if (feof(g_fPos))

2656

{

2657

mprintf("\nEnd of Trajectory File reached.\n");

2658

break;

2659

}

2660

eprintf("\nError while reading time step %d.\n",g_iSteps+1);

2661

goto _endmainloop;

2662

}

2663

if (((g_bNPT) && (g_sNPTFile[0] != 0)))

2664

GetTimeStep(-1)->ReadCellVector(g_fNPTFile);

2665

if (g_bSkipDoubleSteps)

2666

{

2667

if (GetTimeStep(-1)->ExtractNumber(g_iNumberPos) <= g_iLastTimeStep)

2668

{

2669

if (!g_bStepSkipped)

2670

{

2671

g_bStepSkipped = true;

2672

g_iFirstStepSkipped = GetTimeStep(-1)->ExtractNumber(g_iNumberPos);

2673

mprintf("\nSkipping:");

2674

}

2675

mprintf("*");

2676

goto _readagain;

2677

} else if (g_iFirstStepSkipped != -1)

2678

{

2679

if (g_iFirstStepSkipped == GetTimeStep(-1)->ExtractNumber(g_iNumberPos))

2680

mprintf("\nRepeated step %d skipped.",g_iFirstStepSkipped);

2681

else mprintf("\nRepeated steps %d-%d skipped.",g_iFirstStepSkipped,GetTimeStep(-1)->ExtractNumber(g_iNumberPos));

2682

g_iDotCounter = 0;

2683

g_iFirstStepSkipped = -1;

2684

}

2685

if (GetTimeStep(-1)->ExtractNumber(g_iNumberPos) > g_iLastTimeStep)

2686

g_iLastTimeStep = GetTimeStep(-1)->ExtractNumber(g_iNumberPos);

2687

}

2688

if (GetTimeStep(-1)->m_iGesAtomCount == 0)

2689

{

2690

eprintf("\nError: Atom count = 0 at time step %d.\n",g_iSteps+1);

2691

goto _endmainloop;

2692

}

2693

GetTimeStep(-1)->UniteMolecules(false);

2694

if (g_bRemoveCOM)

2695

GetTimeStep(-1)->CenterCOM();

2696

GetTimeStep(-1)->CalcCenters();

2697

if (g_bDipole)

2698

{

2699

if (g_bWannier)

2700

GetTimeStep(-1)->ScanWannier(false);

2701

GetTimeStep(-1)->CalcDipoles();

2702

}

2703

} else

2704

{

2705

if (GetTimeStep(0) == NULL)

2706

{

2707

try { *GetTimeStepAddress(0) = new CTimeStep(); } catch(...) { *GetTimeStepAddress(0) = NULL; }

2708

if (*GetTimeStepAddress(0) == NULL) NewException((double)sizeof(CTimeStep),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2709

}

2710

if (!GetTimeStep(0)->ReadTimestep(g_fPos,false))

2711

{

2712

if (feof(g_fPos))

2713

{

2714

mprintf("\nEnd of trajectory file reached.\n");

2715

break;

2716

}

2717

eprintf("\nError while reading time step %d.\n",g_iSteps+1);

2718

goto _endmainloop;

2719

}

2720

if (((g_bNPT) && (g_sNPTFile[0] != 0)))

2721

GetTimeStep(0)->ReadCellVector(g_fNPTFile);

2722

if (g_bSkipDoubleSteps)

2723

{

2724

if (GetTimeStep(0)->ExtractNumber(g_iNumberPos) <= g_iLastTimeStep)

2725

{

2726

// mprintf("\n[Skip %d/%d]",GetTimeStep(0)->ExtractNumber(),g_iLastTimeStep);

2727

if (!g_bStepSkipped)

2728

{

2729

g_bStepSkipped = true;

2730

g_iFirstStepSkipped = GetTimeStep(0)->ExtractNumber(g_iNumberPos);

2731

mprintf("\nSkipping:");

2732

}

2733

mprintf("*");

2734

goto _readagain;

2735

} else if (g_iFirstStepSkipped != -1)

2736

{

2737

if (g_iFirstStepSkipped == GetTimeStep(0)->ExtractNumber(g_iNumberPos))

2738

mprintf("\nRepeated step %d skipped.",g_iFirstStepSkipped);

2739

else mprintf("\nRepeated steps %d-%d skipped.",g_iFirstStepSkipped,GetTimeStep(0)->ExtractNumber(g_iNumberPos));

2740

g_iDotCounter = 0;

2741

g_iFirstStepSkipped = -1;

2742

}

2743

// mprintf("\nNumber %d.",GetTimeStep(0)->ExtractNumber());

2744

if (GetTimeStep(0)->ExtractNumber(g_iNumberPos) > g_iLastTimeStep)

2745

g_iLastTimeStep = GetTimeStep(0)->ExtractNumber(g_iNumberPos);

2746

}

2747

if (GetTimeStep(0)->m_iGesAtomCount == 0)

2748

{

2749

eprintf("\nError: Atom count = 0 at time step %d.\n",g_iSteps+1);

2750

goto _endmainloop;

2751

}

2752

if (!g_bSaveCoordsUnchanged)

2753

{

2754

GetTimeStep(0)->UniteMolecules(false);

2755

if (g_bRemoveCOM)

2756

GetTimeStep(0)->CenterCOM();

2757

}

2758

GetTimeStep(0)->CalcCenters();

2759

if (g_bDipole)

2760

{

2761

if (g_bWannier)

2762

GetTimeStep(0)->ScanWannier(false);

2763

GetTimeStep(0)->CalcDipoles();

2764

}

2765

}

2766

g_bWarnUnsteady = false;

2767

2768

if (((g_iSteps-(sic*g_iStride*50)) % (showinterval*g_iStride)) == 0)

2769

{

2770

if ((g_iSteps == 0) || g_bStepSkipped)

2771

{

2772

g_bStepSkipped = false;

2773

if (!g_bSilentProgress)

2774

mprintf("\nStep %6d ",g_iSteps);

2775

}

2776

if (g_bAsciiArt && (!g_bSilentProgress))

2777

{

2778

tc = g_oAsciiArt.GetChar();

2779

if (tc == 0)

2780

{

2781

if ((g_iSteps != 0) && (g_iTrajSteps != -1))

2782

{

2783

if ((time(NULL) - t0) > 5)

2784

{

2785

eta = (unsigned long)(((double)time(NULL) - t0) / g_iSteps * ((double)max(long(0),(((g_iMaxStep > 0)?g_iMaxStep:g_iTrajSteps) - ((long)g_iSteps)))));

2786

FormatTime(eta,buf);

2787

mprintf(" ETA %s",buf);

2788

}

2789

}

2790

mprintf("\nStep %6d ",g_iSteps);

2791

if (g_iSteps != 0)

2792

g_oAsciiArt.NewLine();

2793

} else mprintf("%c",tc);

2794

} else

2795

{

2796

if (g_iDotCounter >= 50)

2797

{

2798

g_iDotCounter = 0;

2799

if (!g_bSilentProgress)

2800

{

2801

if ((g_iSteps != 0) && (g_iTrajSteps != -1))

2802

{

2803

if ((time(NULL) - t0) > 5)

2804

{

2805

eta = (unsigned long)(((double)time(NULL) - t0) / g_iSteps * ((double)max(long(0),g_iTrajSteps - ((long)g_iSteps))));

2806

FormatTime(eta,buf);

2807

mprintf(" ETA %s",buf);

2808

}

2809

}

2810

mprintf("\nStep %6d ",g_iSteps);

2811

}

2812

}

2813

g_iDotCounter++;

2814

if (!g_bSilentProgress)

2815

mprintf(".");

2816

}

2817

if (FileExist("EXIT"))

2818

{

2819

mprintf("\n\n*** File \"EXIT\" detected. Aborting analys. ***\n\n");

2820

remove("EXIT");

2821

break;

2822

}

2823

}

2824

2825

if ((int)g_iSteps == /*showinterval**/g_iStride*50)

2826

{

2827

t1 = time(NULL);

2828

if (t1 == t0)

2829

showinterval = 20;

2830

else showinterval = (int)(20.0f/(t1-t0));

2831

if (showinterval == 0)

2832

showinterval = 1;

2833

sic = 1;

2834

}

2835

2836

g_iSteps += g_iStride;

2837

2838

if (GetTimeStep(0)==NULL)

2839

continue;

2840

2841

if ((g_bUseVelocities || g_bUseForces) && (GetTimeStep(1)==NULL))

2842

continue;

2843

2844

if (g_bUseVelocities)

2845

{

2846

if (g_fVel == NULL)

2847

{

2848

CalcVelocities();

2849

} else if (!GetTimeStep(-1)->ReadTimestepVel(g_fVel))

2850

{

2851

eprintf("\nError reading velocity time step %d.\n",g_iSteps+1);

2852

goto _endmainloop;

2853

}

2854

}

2855

if (g_bUseForces)

2856

{

2857

if (g_fForce == NULL)

2858

{

2859

CalcForces();

2860

} else if (!GetTimeStep(-1)->ReadTimestepForce(g_fForce))

2861

{

2862

eprintf("\nError reading force time step %d.\n",g_iSteps+1);

2863

goto _endmainloop;

2864

}

2865

}

2866

2867

if (g_bCutCluster)

2868

{

2869

if (((int)g_iSteps/g_iStride) >= g_iClusterSteps)

2870

break;

2871

if (g_iClusterPos >= g_iClusterCount)

2872

break;

2873

if (g_iaClusterSteps[g_iClusterPos] != (g_iSteps/g_iStride))

2874

continue;

2875

}

2876

2877

2878

if (g_bUnwrap && ((int)g_iSteps > g_iStride))

2879

// Nicht im ersten Schritt

2880

{

2881

for (z=0;z<g_oaMolecules.GetSize();z++)

2882

{

2883

m = (CMolecule*)g_oaMolecules[z];

2884

for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)

2885

{

2886

if (m->m_baAtomIndex[z3] != g_iVirtAtomType)

2887

continue;

2888

for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)

2889

{

2890

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];

2891

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][0] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][0] > g_fBoxX/2.0f)

2892

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][0] -= g_fBoxX;

2893

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][0] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][0] < -g_fBoxX/2.0f)

2894

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][0] += g_fBoxX;

2895

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][1] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][1] > g_fBoxY/2.0f)

2896

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][1] -= g_fBoxY;

2897

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][1] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][1] < -g_fBoxY/2.0f)

2898

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][1] += g_fBoxY;

2899

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][2] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][2] > g_fBoxZ/2.0f)

2900

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][2] -= g_fBoxZ;

2901

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][2] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][2] < -g_fBoxZ/2.0f)

2902

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][2] += g_fBoxZ;

2903

}

2904

}

2905

}

2906

}

2907

2908

if (g_bMSD)

2909

{

2910

g_pT2Timestep = GetTimeStep(0);

2911

for (z0=0;z0<g_oaObserv.GetSize();z0++)

2912

{

2913

ti2 = 0;

2914

o = (CObservation*)g_oaObserv[z0];

2915

if (g_bMSDCacheMode)

2916

{

2917

for (z2=0;z2<o->m_pMSD->m_pAtomGroup->m_oaAtoms.GetSize();z2++)

2918

for (z3=0;z3<((CxIntArray*)o->m_pMSD->m_pAtomGroup->m_oaAtoms[z2])->GetSize();z3++)

2919

for (z4=0;z4<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z4++)

2920

{

2921

ti = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z4]])->m_oaAtomOffset[o->m_pMSD->m_pAtomGroup->m_baAtomType[z2]])->GetAt(((CxIntArray*)o->m_pMSD->m_pAtomGroup->m_oaAtoms[z2])->GetAt(z3));

2922

((CxFloatArray*)o->m_pMSD->m_oaCache[ti2])->Add(g_pT2Timestep->m_vaCoords[ti][0]);

2923

((CxFloatArray*)o->m_pMSD->m_oaCache[ti2])->Add(g_pT2Timestep->m_vaCoords[ti][1]);

2924

((CxFloatArray*)o->m_pMSD->m_oaCache[ti2++])->Add(g_pT2Timestep->m_vaCoords[ti][2]);

2925

}

2926

} else

2927

{

2928

for (z=0;z<o->m_pMSD->m_iResolution/o->m_pMSD->m_iStride;z++)

2929

{

2930

g_pTempTimestep = GetTimeStep(z*o->m_pMSD->m_iStride);

2931

if (g_pTempTimestep == NULL)

2932

continue;

2933

for (z2=0;z2<o->m_pMSD->m_pAtomGroup->m_oaAtoms.GetSize();z2++)

2934

for (z3=0;z3<((CxIntArray*)o->m_pMSD->m_pAtomGroup->m_oaAtoms[z2])->GetSize();z3++)

2935

for (z4=0;z4<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z4++)

2936

{

2937

ti = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z4]])->m_oaAtomOffset[o->m_pMSD->m_pAtomGroup->m_baAtomType[z2]])->GetAt(((CxIntArray*)o->m_pMSD->m_pAtomGroup->m_oaAtoms[z2])->GetAt(z3));

2938

o->m_pMSD->m_pMSD->AddToBin_Index(z,(double)(pow(g_pTempTimestep->m_vaCoords[ti][0]-g_pT2Timestep->m_vaCoords[ti][0],2)+pow(g_pTempTimestep->m_vaCoords[ti][1]-g_pT2Timestep->m_vaCoords[ti][1],2)+pow(g_pTempTimestep->m_vaCoords[ti][2]-g_pT2Timestep->m_vaCoords[ti][2],2)));

2939

}

2940

}

2941

}

2942

}

2943

} // END IF MSD

2944

2945

if (g_bSaveJustTraj)

2946

{

2947

g_pTempTimestep->CopyFrom(GetTimeStep(0));

2948

2949

if (g_bSaveJustCenter && (!g_bSaveCoordsUnchanged))

2950

{

2951

vec0 = g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iSaveJustMol])->m_laSingleMolIndex[g_iSaveJustSM]])->m_oaAtomOffset[g_iSaveJustAtomType])->GetAt(g_iSaveJustAtom)];

2952

g_pTempTimestep->CenterPos(vec0);

2953

}

2954

2955

if (g_bFold && (!g_bSaveCoordsUnchanged))

2956

{

2957

if (g_bFoldAtomwise)

2958

g_pTempTimestep->FoldAtoms();

2959

else g_pTempTimestep->FoldMolecules();

2960

}

2961

2962

if (!g_bCenterZero && (!g_bSaveCoordsUnchanged))

2963

g_pTempTimestep->CenterPos(CxVector3(-g_fBoxX/2,-g_fBoxY/2,-g_fBoxZ/2));

2964

2965

fprintf(g_fSaveJustTraj," %d\n",(int)g_iSaveGesAtoms);

2966

if (g_pTempTimestep->m_pComment != NULL)

2967

fprintf(g_fSaveJustTraj,"%s\n",g_pTempTimestep->m_pComment);

2968

else fprintf(g_fSaveJustTraj,"\n");

2969

if (g_bWriteAtomwise)

2970

{

2971

for (z7=0;z7<g_oaAtoms.GetSize();z7++)

2972

{

2973

for (z3=0;z3<g_oaSaveMolecules.GetSize();z3++)

2974

{

2975

atgr = (CAtomGroup*)g_oaSaveMolecules[z3];

2976

for (z6=0;z6<atgr->m_pMolecule->m_laSingleMolIndex.GetSize();z6++)

2977

{

2978

for (z4=0;z4<atgr->m_baAtomType.GetSize();z4++)

2979

{

2980

if (atgr->m_baRealAtomType[z4] != z7)

2981

continue;

2982

tla = (CxIntArray*)atgr->m_oaAtoms[z4];

2983

for (z5=0;z5<tla->GetSize();z5++)

2984

{

2985

vec0 = g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[atgr->m_pMolecule->m_laSingleMolIndex[z6]])->m_oaAtomOffset[atgr->m_baAtomType[z4]])->GetAt(tla->GetAt(z5))];

2986

if (g_bUnwrap)

2987

vec0 += g_vaUnwrapArray[atgr->m_pMolecule->m_laSingleMolIndex[z6]];

2988

if (atgr->m_baRealAtomType[z4] == g_iVirtAtomType)

2989

{

2990

if (g_bSaveVirtAtoms)

2991

fprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CVirtualAtom*)g_oaVirtualAtoms[atgr->m_pMolecule->m_laVirtualAtoms[tla->GetAt(z5)]])->m_sLabel,vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

2992

} else fprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[atgr->m_baRealAtomType[z4]])->m_sName,vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

2993

}

2994

}

2995

}

2996

}

2997

}

2998

} else

2999

{

3000

for (z3=0;z3<g_oaSaveMolecules.GetSize();z3++)

3001

{

3002

atgr = (CAtomGroup*)g_oaSaveMolecules[z3];

3003

for (z6=0;z6<atgr->m_pMolecule->m_laSingleMolIndex.GetSize();z6++)

3004

{

3005

for (z4=0;z4<atgr->m_baAtomType.GetSize();z4++)

3006

{

3007

tla = (CxIntArray*)atgr->m_oaAtoms[z4];

3008

for (z5=0;z5<tla->GetSize();z5++)

3009

{

3010

vec0 = g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[atgr->m_pMolecule->m_laSingleMolIndex[z6]])->m_oaAtomOffset[atgr->m_baAtomType[z4]])->GetAt(tla->GetAt(z5))];

3011

if (g_bUnwrap)

3012

vec0 += g_vaUnwrapArray[atgr->m_pMolecule->m_laSingleMolIndex[z6]];

3013

if (atgr->m_baRealAtomType[z4] == g_iVirtAtomType)

3014

{

3015

if (g_bSaveVirtAtoms)

3016

fprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CVirtualAtom*)g_oaVirtualAtoms[atgr->m_pMolecule->m_laVirtualAtoms[tla->GetAt(z5)]])->m_sLabel,vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

3017

} else fprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[atgr->m_baRealAtomType[z4]])->m_sName,vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

3018

}

3019

}

3020

}

3021

}

3022

}

3023

}

3024

3025

if (g_bBondACF)

3026

{

3027

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3028

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

3029

{

3030

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

3031

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

3032

{

3033

bond = (CMolBond*)sm->m_oaBonds[z3];

3034

bond->m_faData.Add(VecDist(g_pTempTimestep->m_vaCoords[bond->m_iAtomOffset[0]],g_pTempTimestep->m_vaCoords[bond->m_iAtomOffset[1]]));

3035

}

3036

}

3037

}

3038

3039

if (g_bKeepUnfoldedCoords)

3040

GetTimeStep(0)->m_vaCoords_Unfolded.CopyFrom(&GetTimeStep(0)->m_vaCoords);

3041

3042

if (g_bAggregation || g_bNbExchange)

3043

{

3044

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3045

3046

for (z0=0;z0<g_oaObserv.GetSize();z0++)

3047

{

3048

o = (CObservation*)g_oaObserv[z0];

3049

for (zs=0;zs<o->m_pDACF->m_oaSubDACFs.GetSize();zs++)

3050

{

3051

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[zs];

3052

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize();z2++)

3053

dacfsub->m_pCondition->m_iPassCounter[z2] = 0;

3054

}

3055

}

3056

for (z0=0;z0<g_oaObserv.GetSize();z0++)

3057

{

3058

o = (CObservation*)g_oaObserv[z0];

3059

3060

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_pDACF->m_iFirstMol])->m_laSingleMolIndex.GetSize();z2++)

3061

{

3062

smfix = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_pDACF->m_iFirstMol])->m_laSingleMolIndex[z2]];

3063

3064

o->m_pDACF->m_pCondition->PreScanNeighborhoodAllOM(g_pTempTimestep,smfix,g_bPeriodic);

3065

3066

for (zs=0;zs<o->m_pDACF->m_oaSubDACFs.GetSize();zs++)

3067

{

3068

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[zs];

3069

3070

dacfsub->m_pCondition->CopyResults(o->m_pDACF->m_pCondition);

3071

dacfsub->m_pCondition->m_bAnyPassed = false;

3072

dacfsub->m_pCondition->ReScan(smfix);

3073

if (dacfsub->m_pCondition->m_bAnyPassed)

3074

dacfsub->m_pCondition->m_iRMPassCounter[z2]++;

3075

3076

if (g_bDACF)

3077

o->m_pDACF->UpdateDACFSub(z2,g_pTempTimestep,dacfsub);

3078

3079

if (g_bNbExchange)

3080

o->m_pDACF->UpdateNbEx(z2,g_pTempTimestep,dacfsub);

3081

} // END FOR ZS

3082

} // END FOR Z2

3083

} // END FOR Z0

3084

for (z0=0;z0<g_oaObserv.GetSize();z0++)

3085

{

3086

o = (CObservation*)g_oaObserv[z0];

3087

for (zs=0;zs<o->m_pDACF->m_oaSubDACFs.GetSize();zs++)

3088

{

3089

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[zs];

3090

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize();z2++)

3091

if (dacfsub->m_pCondition->m_iPassCounter[z2] != 0)

3092

dacfsub->m_pCondition->m_iOMPassCounter[z2]++;

3093

}

3094

}

3095

} // END IF AGGREGATION OR NBEX

3096

3097

if (g_bRDyn)

3098

{

3099

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3100

for (z6=0;z6<g_oaObserv.GetSize();z6++)

3101

{

3102

o = (CObservation*)g_oaObserv[z6];

3103

ti = 0;

3104

for (z3=0;z3<o->m_iShowMolCount;z3++) // Alle anderen Molekuele durchgehen

3105

{

3106

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z3]];

3107

3108

if (o->m_pRDyn->m_iVecType == 0)

3109

{

3110

o->m_pRDyn->BuildAtomList(sm,&templa);

3111

for (z4=0;z4<templa.GetSize();z4+=3)

3112

{

3113

if (o->m_pRDyn->m_bOrtho)

3114

{

3115

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

3116

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

3117

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

3118

vec1 = CrossP(vec2-vec0,vec3-vec0);

3119

} else

3120

{

3121

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

3122

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

3123

vec1 = vec2-vec0;

3124

}

3125

vec1.Normalize();

3126

if (g_bRDynCacheMode)

3127

{

3128

((CxFloatArray*)o->m_pRDyn->m_oaCache[ti])->Add(vec1[0]);

3129

((CxFloatArray*)o->m_pRDyn->m_oaCache[ti])->Add(vec1[1]);

3130

((CxFloatArray*)o->m_pRDyn->m_oaCache[ti])->Add(vec1[2]);

3131

ti++;

3132

} else

3133

{

3134

for (z=0;z<o->m_pRDyn->m_iDepth/o->m_pRDyn->m_iStride;z++)

3135

{

3136

g_pT2Timestep = GetTimeStep(z*o->m_pRDyn->m_iStride);

3137

if (g_pT2Timestep == NULL)

3138

continue;

3139

if (o->m_pRDyn->m_bOrtho)

3140

{

3141

vec4 = g_pT2Timestep->m_vaCoords[templa[z4]];

3142

vec3 = g_pT2Timestep->m_vaCoords[templa[z4+1]];

3143

vec5 = g_pT2Timestep->m_vaCoords[templa[z4+2]];

3144

vec2 = CrossP(vec3-vec4,vec5-vec4);

3145

} else

3146

{

3147

vec4 = g_pT2Timestep->m_vaCoords[templa[z4]];

3148

vec3 = g_pT2Timestep->m_vaCoords[templa[z4+1]];

3149

vec2 = vec3-vec4;

3150

}

3151

vec2.Normalize();

3152

o->m_pRDyn->m_pRDyn->AddToBin_Int(z,DotP(vec1,vec2));

3153

o->m_pRDyn->m_pCount[z]++;

3154

}

3155

}

3156

}

3157

} else if (o->m_pRDyn->m_iVecType == 1)

3158

{

3159

vec1 = sm->m_vDipole;

3160

((CxFloatArray*)o->m_pRDyn->m_oaCache[ti])->Add(vec1[0]);

3161

((CxFloatArray*)o->m_pRDyn->m_oaCache[ti])->Add(vec1[1]);

3162

((CxFloatArray*)o->m_pRDyn->m_oaCache[ti])->Add(vec1[2]);

3163

3164

// if (z3 == 0)

3165

// fprintf(fff,"%f, %f, %f\n",vec1[0],vec1[1],vec1[2]);

3166

3167

ti++;

3168

} // END VECTYPE

3169

}

3170

}

3171

} // END IF RDYN

3172

3173

if (g_bVACF)

3174

{

3175

g_pT2Timestep = GetTimeStep(0);

3176

// mprintf("\nStep=%d, adding.",g_iSteps);

3177

if (g_bGlobalVACF)

3178

{

3179

if (g_bVACFCacheMode)

3180

{

3181

for (z2=0;z2<g_iGesAtomCount;z2++)

3182

{

3183

// mprintf("Global: Step %d, Atom %d: %.4ff | %.4ff | %.4ff\n",g_iSteps,z2+1,g_pT2Timestep->m_vaVelocities[z2][0],g_pT2Timestep->m_vaVelocities[z2][1],g_pT2Timestep->m_vaVelocities[z2][2]);

3184

((CxFloatArray*)g_pGlobalVACF->m_oaCache[z2])->Add(g_pT2Timestep->m_vaVelocities[z2][0]);

3185

((CxFloatArray*)g_pGlobalVACF->m_oaCache[z2])->Add(g_pT2Timestep->m_vaVelocities[z2][1]);

3186

((CxFloatArray*)g_pGlobalVACF->m_oaCache[z2])->Add(g_pT2Timestep->m_vaVelocities[z2][2]);

3187

}

3188

} else

3189

{

3190

for (z=0;z<g_pGlobalVACF->m_iSize;z++)

3191

{

3192

g_pTempTimestep = GetTimeStep(z);

3193

if (g_pTempTimestep == NULL)

3194

continue;

3195

if (g_pTempTimestep->m_vaVelocities.GetSize() == 0)

3196

continue;

3197

pd = &g_pGlobalVACF->m_pData[z];

3198

g_pGlobalVACF->m_pCounter[z] += g_iGesAtomCount;

3199

for (z2=0;z2<g_iGesAtomCount;z2++)

3200

*pd += DotP(g_pTempTimestep->m_vaVelocities[z2],g_pT2Timestep->m_vaVelocities[z2]);

3201

}

3202

}

3203

}

3204

for (z6=0;z6<g_oaObserv.GetSize();z6++)

3205

{

3206

o = (CObservation*)g_oaObserv[z6];

3207

for (z3=0;z3<o->m_iShowMolCount;z3++) // Alle anderen Molekuele durchgehen

3208

{

3209

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z3]];

3210

o->m_pVACF->BuildAtomList(sm,&templa);

3211

for (z4=0;z4<templa.GetSize();z4++)

3212

{

3213

if (g_bVACFCacheMode)

3214

{

3215

ti = templa[z4];

3216

((CxFloatArray*)o->m_pVACF->m_oaCache[z3*o->m_pVACF->m_iShowAtomGes+z4])->Add(g_pT2Timestep->m_vaVelocities[ti][0]);

3217

((CxFloatArray*)o->m_pVACF->m_oaCache[z3*o->m_pVACF->m_iShowAtomGes+z4])->Add(g_pT2Timestep->m_vaVelocities[ti][1]);

3218

((CxFloatArray*)o->m_pVACF->m_oaCache[z3*o->m_pVACF->m_iShowAtomGes+z4])->Add(g_pT2Timestep->m_vaVelocities[ti][2]);

3219

// mprintf("%d*%d+%d=%d\n",z3,o->m_pVACF->m_iShowAtomGes,z4,z3*o->m_pVACF->m_iShowAtomGes+z4);

3220

// mprintf("Lokal: Step %d, Atom %d: %.4ff | %.4ff | %.4ff\n",g_iSteps,ti+1,g_pT2Timestep->m_vaVelocities[ti][0],g_pT2Timestep->m_vaVelocities[ti][1],g_pT2Timestep->m_vaVelocities[ti][2]);

3221

// mprintf("Step %d: Obs %d, Mol %d, Atom %d: Index %d.\n",g_iStepHistory,z6+1,z3+1,z4+1,ti+1);

3222

} else

3223

{

3224

o->m_pVACF->m_pCounter[z5] += o->m_pVACF->m_iShowAtomGes;

3225

for (z5=0;z5<o->m_pVACF->m_iSize;z5++)

3226

{

3227

g_pTempTimestep = GetTimeStep(z5);

3228

if (g_pTempTimestep == NULL)

3229

continue;

3230

if (g_pTempTimestep->m_vaVelocities.GetSize() == 0)

3231

continue;

3232

o->m_pVACF->m_pData[z5] += DotP(g_pTempTimestep->m_vaVelocities[templa[z4]],g_pT2Timestep->m_vaVelocities[templa[z4]]);

3233

}

3234

}

3235

}

3236

}

3237

}

3238

} // END IF VACF

3239

3240

if (g_bReact)

3241

{

3242

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3243

if (ReactSecondRun)

3244

{

3245

g_pReact->WriteTrajec(g_pTempTimestep);

3246

} else

3247

{

3248

g_pReact->ScanBonds(g_pTempTimestep,false);

3249

}

3250

}

3251

3252

if (g_bNbAnalysis)

3253

{

3254

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3255

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize();z2++)

3256

{

3257

smfix = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]];

3258

for (z6=0;z6<g_oaObserv.GetSize();z6++)

3259

{

3260

o = (CObservation*)g_oaObserv[z6];

3261

o->m_pNbAnalysis->m_pNbSearch->ScanAllOM(smfix,g_pTempTimestep,g_bPeriodic);

3262

o->m_pNbAnalysis->AnalyzeStep();

3263

}

3264

}

3265

}

3266

3267

if (g_bNbExchange)

3268

{

3269

}

3270

3271

if (g_bClusterAnalysis)

3272

{

3273

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3274

g_pClusterAnalysis->Process(g_pTempTimestep);

3275

}

3276

3277

if (g_bMicroHet)

3278

{

3279

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3280

g_pTempTimestep->FoldAtomsPositive();

3281

g_pMicroHet->Process(g_pTempTimestep);

3282

}

3283

3284

if (g_bVoro)

3285

{

3286

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3287

g_pTempTimestep->FoldAtomsPositive();

3288

g_pVoroWrapper->Build(g_pTempTimestep);

3289

}

3290

3291

if (g_bVoid)

3292

{

3293

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3294

g_pTempTimestep->FoldAtomsPositive();

3295

g_pVoroAnalysis->Step(g_pTempTimestep);

3296

}

3297

3298

if ((!g_bCDF) && (!g_bRDF) && (!g_bSDF) && (!g_bVoidSDF) && (!g_bADF) && (!g_bDDF) && (!g_bVDF) && (!g_bDipDF) && (!g_bCutCluster) && (!g_bSaveRefEnv) && (!g_bVHDF) && (!g_bRevSDF) && (!g_bCond))

3299

goto _endstep;

3300

3301

if (g_bVoid)

3302

{

3303

if (g_bVoidSDF && g_pVoroAnalysis->m_bEmptySpaceSDF && g_pVoroAnalysis->m_bNewEmptyMode)

3304

{

3305

g_pVoroAnalysis->m_pTempSDF->Clear();

3306

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3307

g_pTempTimestep->FoldAtomsPositive();

3308

for (z3=0;z3<g_iGesAtomCount;z3++)

3309

{

3310

vec0 = g_pTempTimestep->m_vaCoords[z3];

3311

g_pVoroAnalysis->m_pTempSDF->AddToBin_SphereWrap(vec0,g_faVdWRadius[z3]);

3312

}

3313

// g_pVoroAnalysis->m_pTempSDF->WritePLT("","bla.plt","",true);

3314

}

3315

}

3316

3317

tfr = 9999.0;

3318

3319

if (g_iFixMol == -1)

3320

goto _norefmol;

3321

3322

for (z6=0;z6<g_oaObserv.GetSize();z6++)

3323

{

3324

o = (CObservation*)g_oaObserv[z6];

3325

if (o->m_pConditions != NULL)

3326

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z2++)

3327

o->m_pConditions->m_iPassCounter[z2] = 0;

3328

}

3329

3330

// Jedes Festhalte-Molekuel mal im Ursprung liegen lassen

3331

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize();z2++)

3332

{

3333

if (g_bDoubleBox && (z2 >= ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()/g_iDoubleBoxFactor))

3334

continue;

3335

3336

smfix = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]];

3337

3338

if (g_bCutCluster)

3339

{

3340

if (g_iaClusterMol[g_iClusterPos] != z2)

3341

continue;

3342

g_iClusterPos++;

3343

if (g_iClusterPos >= g_iClusterCount)

3344

break;

3345

}

3346

3347

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3348

3349

/* for (z3=0;z3<g_iGesAtomCount;z3++)

3350

{

3351

mprintf("\nAtom %4d: ",z3);

3352

g_pTempTimestep->m_vaCoords[z3].Dump();

3353

}*/

3354

3355

vecc = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[0]])->GetAt(g_iFixAtom[0])];

3356

3357

/* mprintf("\n\n%d, %d, vecc: ",g_iFixAtomType[0],g_iFixAtom[0]);

3358

vecc.Dump();

3359

mprintf("\n\n");*/

3360

3361

if ((g_bCutCluster && !g_bRefEnvCenter) || (g_bSaveRefEnv && (!g_bRefEnvCenter) && (z2==g_iSaveRefMol)))

3362

{

3363

if (g_bFold)

3364

{

3365

g_pTempTimestep->CenterPos(vecc);

3366

if (g_bFoldAtomwise)

3367

g_pTempTimestep->FoldAtoms();

3368

else g_pTempTimestep->FoldMolecules();

3369

vec2 = -1.0f * vecc;

3370

g_pTempTimestep->CenterPos(vec2);

3371

}

3372

if (g_bCutCluster || (g_iNbhMode == 2))

3373

{

3374

g_pNbSet->Reset();

3375

if (g_bCutCluster)

3376

g_pNbSet->ResetAlwaysTrue();

3377

g_pNbSet->Scan(smfix,g_pTempTimestep,g_bPeriodic);

3378

if (g_bSaveRefWithEnv)

3379

g_pNbSet->AddMolecule(g_iFixMol,z2);

3380

}

3381

g_pTempTimestep->WriteTimestepNb(g_fRefEnv,g_pNbSet);

3382

if (g_bTDO)

3383

{

3384

if (g_laTDOSteps.Contains(g_iSteps-1))

3385

{

3386

sprintf(buf,"tdo_%s_%d_%06lu%s.xyz",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_iSteps-1,multibuf);

3387

mprintf("\nSaving TDO step as %s.\n",buf);

3388

tfi = OpenFileWrite(buf,true);

3389

g_pTempTimestep->WriteTimestepNb(tfi,g_pNbSet);

3390

fclose(tfi);

3391

}

3392

}

3393

}

3394

3395

// Legt vecc genau in den Ursprung des Koordinatensystems

3396

g_pTempTimestep->CenterPos(vecc);

3397

3398

/* if (vecc.GetLength() > 100000.0f)

3399

{

3400

eprintf("*** Centerpos Error (fixmol=%d, z2=%d, type=%d, atom=%d, offset=%d): ",g_iFixMol,z2,g_iFixAtomType[0],g_iFixAtom[0],((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[0]])->GetAt(g_iFixAtom[0]));

3401

vecc.Dump();

3402

mprintf("\n");

3403

}*/

3404

3405

if (g_bFold)

3406

{

3407

if (g_bFoldAtomwise)

3408

g_pTempTimestep->FoldAtoms();

3409

else g_pTempTimestep->FoldMolecules();

3410

}

3411

3412

if ((g_bCutCluster && g_bRefEnvCenter && (!g_bRefEnvFix)) || (g_bSaveRefEnv && g_bRefEnvCenter && (!g_bRefEnvFix) && (z2==g_iSaveRefMol)))

3413

{

3414

if (g_bCutCluster || (g_iNbhMode == 2))

3415

{

3416

g_pNbSet->Reset();

3417

if (g_bCutCluster)

3418

g_pNbSet->ResetAlwaysTrue();

3419

g_pNbSet->Scan(smfix,g_pTempTimestep,g_bPeriodic);

3420

if (g_bSaveRefWithEnv)

3421

g_pNbSet->AddMolecule(g_iFixMol,z2);

3422

}

3423

if (!g_bCenterZero)

3424

g_pTempTimestep->CenterPos(CxVector3(-g_fBoxX/2,-g_fBoxY/2,-g_fBoxZ/2));

3425

g_pTempTimestep->WriteTimestepNb(g_fRefEnv,g_pNbSet);

3426

if (g_bTDO)

3427

{

3428

if (g_laTDOSteps.Contains(g_iSteps-1))

3429

{

3430

sprintf(buf,"tdo_%s_%d_%06lu%s.xyz",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_iSteps-1,multibuf);

3431

mprintf("\nSaving TDO step as %s.\n",buf);

3432

tfi = OpenFileWrite(buf,true);

3433

g_pTempTimestep->WriteTimestepNb(tfi,g_pNbSet);

3434

fclose(tfi);

3435

}

3436

}

3437

}

3438

3439

if (g_bSDF || g_bVoidSDF || g_bSVDF || g_bSFDF || g_bAvg || ((g_bSaveRefEnv || g_bCutCluster) && g_bRefEnvCenter && g_bRefEnvFix)) // Wir brauchen ein neues Koordinatensystem und eine Drehmatrix

3440

{

3441

vec2 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])];

3442

vec3 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])];

3443

mat.MatUltra(vec2,vec3); // Dies erstellt uns die Drehmatrix

3444

g_pTempTimestep->Transform(mat);

3445

}

3446

3447

if ((g_bCutCluster && g_bRefEnvCenter && g_bRefEnvFix) || (g_bSaveRefEnv && g_bRefEnvCenter && g_bRefEnvFix && (z2==g_iSaveRefMol)))

3448

{

3449

if (g_bCutCluster || (g_iNbhMode == 2))

3450

{

3451

g_pNbSet->Reset();

3452

if (g_bCutCluster)

3453

g_pNbSet->ResetAlwaysTrue();

3454

g_pNbSet->Scan(smfix,g_pTempTimestep,g_bPeriodic);

3455

if (g_bSaveRefWithEnv)

3456

g_pNbSet->AddMolecule(g_iFixMol,z2);

3457

}

3458

if (!g_bCenterZero)

3459

g_pTempTimestep->CenterPos(CxVector3(-g_fBoxX/2,-g_fBoxY/2,-g_fBoxZ/2));

3460

g_pTempTimestep->WriteTimestepNb(g_fRefEnv,g_pNbSet);

3461

3462

if (g_bTDO)

3463

{

3464

if (g_laTDOSteps.Contains(g_iSteps-1))

3465

{

3466

sprintf(buf,"tdo_%s_%d_%06lu%s.xyz",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_iSteps-1,multibuf);

3467

mprintf("\nSaving TDO step as %s.\n",buf);

3468

tfi = OpenFileWrite(buf,true);

3469

g_pTempTimestep->WriteTimestepNb(tfi,g_pNbSet);

3470

fclose(tfi);

3471

}

3472

}

3473

}

3474

3475

/***************************************************************************************************************************/

3476

3477

if (g_bVoidSDF)

3478

{

3479

if (g_pVoroAnalysis->m_bEmptySpaceSDF)

3480

{

3481

if (!g_pVoroAnalysis->m_bNewEmptyMode)

3482

{

3483

g_pVoroAnalysis->m_pTempSDF->Clear();

3484

3485

for (z3=0;z3<g_oaMolecules.GetSize();z3++)

3486

{

3487

tm = (CMolecule*)g_oaMolecules[z3];

3488

for (z4=0;z4<tm->m_laSingleMolIndex.GetSize();z4++)

3489

{

3490

if (!g_pVoroAnalysis->m_bEmptySpaceSDF_RefMol)

3491

if ((z3 == g_iFixMol) && (z4 == z2))

3492

continue;

3493

3494

tsm = (CSingleMolecule*)g_oaSingleMolecules[tm->m_laSingleMolIndex[z4]];

3495

3496

for (z5=0;z5<tsm->m_oaAtomOffset.GetSize();z5++)

3497

{

3498

if (tm->m_baAtomIndex[z5] == g_iVirtAtomType)

3499

continue;

3500

3501

for (z6=0;z6<((CxIntArray*)tsm->m_oaAtomOffset[z5])->GetSize();z6++)

3502

{

3503

vec0 = g_pTempTimestep->m_vaCoords[((CxIntArray*)tsm->m_oaAtomOffset[z5])->GetAt(z6)];

3504

3505

g_pVoroAnalysis->m_pTempSDF->AddToBin_Sphere(vec0,g_faVdWRadius[((CxIntArray*)tsm->m_oaAtomOffset[z5])->GetAt(z6)]);

3506

}

3507

}

3508

}

3509

}

3510

g_pVoroAnalysis->BinEmptySDF_New(&mat,&vecc);

3511

} else

3512

{

3513

g_pVoroAnalysis->BinEmptySDF();

3514

}

3515

}

3516

3517

if (g_pVoroAnalysis->m_bSphereHoleSDF)

3518

{

3519

g_pVoroAnalysis->BinSphereHoleSDF(&mat,&vecc);

3520

}

3521

}

3522

3523

if (g_bDipDF || g_bRevSDF || g_bVHDF || g_bRDF || g_bSDF || g_bSVDF || g_bSFDF || g_bADF || g_bDDF || g_bVDF || g_bCond)

3524

{

3525

for (z6=0;z6<g_oaObserv.GetSize();z6++)

3526

{

3527

o = (CObservation*)g_oaObserv[z6];

3528

ti2 = o->m_waSaveRefList.GetPosition(z2);

3529

3530

if (o->m_bObsCertain)

3531

{

3532

if (!o->m_waObsRefList.Contains(z2))

3533

continue;

3534

tic_r = o->m_waObsRefList.GetPosition(z2);

3535

}

3536

3537

if (g_bUseVelocities)

3538

{

3539

tempvel.CopyFrom(&g_pTempTimestep->m_vaVelocities);

3540

if (o->m_bVelocityRelToRef)

3541

{

3542

vecv = g_pTempTimestep->m_vaVelocities[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[0]])->GetAt(g_iFixAtom[0])];

3543

for (z3=0;z3<g_iGesVirtAtomCount;z3++)

3544

tempvel[z3] -= vecv;

3545

}

3546

}

3547

3548

if ((g_bCDF) && (o->m_bTimeDev) && (ti2 != -1))

3549

{

3550

if (o->m_bSaveSeparateFiles)

3551

fprintf(o->m_pCDF->m_fTimeDev[ti2],"%d",(int)g_iSteps);

3552

else if (ti2 == 0)

3553

fprintf(o->m_pCDF->m_fTimeDev[0],"%d",(int)g_iSteps);

3554

}

3555

3556

for (zr=0;zr<g_iCDFChannels;zr++)

3557

{

3558

if (g_bRDF && (o->m_pRDF[zr] != NULL))

3559

{

3560

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

3561

o->m_pRDF[zr]->m_faData[z3].RemoveAll_KeepSize();

3562

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

3563

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

3564

o->m_pRDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

3565

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

3566

{

3567

if (o->m_bSaveSeparateFiles)

3568

fprintf(o->m_pRDF[zr]->m_fDist[ti2],"%d",(int)g_iSteps);

3569

else if (ti2 == 0)

3570

fprintf(o->m_pRDF[zr]->m_fDist[0],"%d",(int)g_iSteps);

3571

}

3572

}

3573

3574

if (g_bADF && (o->m_pADF[zr] != NULL))

3575

{

3576

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

3577

o->m_pADF[zr]->m_faData[z3].RemoveAll_KeepSize();

3578

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

3579

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

3580

o->m_pADF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

3581

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

3582

{

3583

if (o->m_bSaveSeparateFiles)

3584

fprintf(o->m_pADF[zr]->m_fAngle[ti2],"%d",(int)g_iSteps);

3585

else if (ti2 == 0)

3586

fprintf(o->m_pADF[zr]->m_fAngle[0],"%d",(int)g_iSteps);

3587

}

3588

}

3589

3590

if (g_bDDF && (o->m_pDDF[zr] != NULL))

3591

{

3592

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

3593

o->m_pDDF[zr]->m_faData[z3].RemoveAll_KeepSize();

3594

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

3595

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

3596

o->m_pDDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

3597

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

3598

{

3599

if (o->m_bSaveSeparateFiles)

3600

fprintf(o->m_pDDF[zr]->m_fAngle[ti2],"%d",(int)g_iSteps);

3601

else if (ti2 == 0)

3602

fprintf(o->m_pDDF[zr]->m_fAngle[0],"%d",(int)g_iSteps);

3603

}

3604

}

3605

3606

if (g_bDipDF && (o->m_pDipDF[zr] != NULL))

3607

{

3608

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

3609

o->m_pDipDF[zr]->m_faData[z3].RemoveAll_KeepSize();

3610

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

3611

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

3612

o->m_pDipDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

3613

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

3614

{

3615

if (o->m_bSaveSeparateFiles)

3616

fprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"%d",(int)g_iSteps);

3617

else if (ti2 == 0)

3618

fprintf(o->m_pDipDF[zr]->m_fDipole[0],"%d",(int)g_iSteps);

3619

}

3620

}

3621

3622

if (g_bVDF && (o->m_pVDF[zr] != NULL))

3623

{

3624

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

3625

o->m_pVDF[zr]->m_faData[z3].RemoveAll_KeepSize();

3626

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

3627

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

3628

o->m_pVDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

3629

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

3630

{

3631

if (o->m_bSaveSeparateFiles)

3632

fprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"%d",(int)g_iSteps);

3633

else if (ti2 == 0)

3634

fprintf(o->m_pVDF[zr]->m_fSpeed[0],"%d",(int)g_iSteps);

3635

}

3636

}

3637

} // END FOR zr

3638

3639

if (g_bSDF)

3640

{

3641

for (z3=0;z3<o->m_iShowMolCount;z3++)

3642

{

3643

o->m_pSDF->m_vaData[z3].RemoveAll_KeepSize();

3644

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

3645

o->m_pSDF->m_baDataEnabled[z3].RemoveAll_KeepSize();

3646

}

3647

}

3648

3649

if (g_bRevSDF)

3650

{

3651

for (z3=0;z3<o->m_iShowMolCount;z3++)

3652

{

3653

o->m_pRevSDF->m_vaData[z3].RemoveAll_KeepSize();

3654

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

3655

o->m_pRevSDF->m_baDataEnabled[z3].RemoveAll_KeepSize();

3656

}

3657

}

3658

3659

if (o->m_bSelf)

3660

{

3661

if (g_bADF)

3662

{

3663

for (zr=0;zr<g_iCDFChannels;zr++)

3664

{

3665

if (o->m_pADF[zr] == NULL)

3666

continue;

3667

o->m_pADF[zr]->BuildAtomList(smfix,NULL,NULL,&templa);

3668

for (z4=0;z4<templa.GetSize();z4+=6)

3669

{

3670

if (o->m_pADF[zr]->m_bOrtho[0])

3671

{

3672

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

3673

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

3674

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

3675

vec1 = CrossP(vec2-vec0,vec3-vec0);

3676

} else

3677

{

3678

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

3679

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

3680

vec1 = vec2-vec0;

3681

}

3682

if (o->m_pADF[zr]->m_bOrtho[1])

3683

{

3684

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

3685

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

3686

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+5]];

3687

vec2 = CrossP(vec3-vec4,vec5-vec4);

3688

} else

3689

{

3690

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

3691

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

3692

vec2 = vec3-vec4;

3693

}

3694

tf = Angle_Deg(vec1,vec2);

3695

if ((tf > 90.0f) && (o->m_pADF[zr]->m_bFoldAngle))

3696

tf = 180.0f-tf;

3697

if (o->m_pADF[zr]->m_bCosine)

3698

tf = cos(tf/180.0*Pi);

3699

3700

if (g_bDeriv)

3701

{

3702

o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6) = tf;

3703

switch(o->m_pADF[zr]->m_iDeriv)

3704

{

3705

case 0:

3706

tf = o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6);

3707

break;

3708

case 1:

3709

tf = (o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6) - o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6)) / (2*g_fTimestepLength);

3710

break;

3711

case 2:

3712

tf = (o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6) + o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6) - 2*o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6)) / (g_fTimestepLength * g_fTimestepLength);

3713

break;

3714

}

3715

}

3716

3717

if (!g_bDeriv || (g_iSteps > 2))

3718

{

3719

if (o->m_bObsCertain && o->m_bDecompDist)

3720

o->m_pADF[zr]->m_pADF->AddToBin_Multi(tic_r,tf);

3721

3722

o->m_pADF[zr]->m_faData[0].Add(tf);

3723

3724

if (o->m_pADF[zr]->m_bACF)

3725

o->m_pADF[zr]->m_pfaACFBuffer[z2*o->m_pADF[zr]->m_iCombinations+z4/6]->Add((float)tf);

3726

3727

/* if (o->m_pADF[zr]->m_bMirror)

3728

{

3729

if (o->m_bObsCertain && o->m_bDecompDist)

3730

o->m_pADF[zr]->m_pADF->AddToBin_Multi(tic_r,180.0-tf);

3731

o->m_pADF[zr]->m_faData[0].Add(180.0-tf);

3732

}*/

3733

3734

if (o->m_bTimeDev && (ti2 != -1))

3735

{

3736

if (o->m_bSaveSeparateFiles)

3737

fprintf(o->m_pADF[zr]->m_fAngle[ti2],"; %8.3f",tf);

3738

else fprintf(o->m_pADF[zr]->m_fAngle[0],"; %8.3f",tf);

3739

if (o->m_bCombinedPlot)

3740

o->m_pADF[zr]->m_pADF->m_pCombinedPlot->AddXYTupel(ti2*o->m_pADF[zr]->m_iCombinations+z4/6,g_iSteps*g_fTimestepLength/1000.0,tf);

3741

}

3742

if (o->m_bTimeDiff)

3743

((CxFloatArray*)o->m_pADF[zr]->m_pADF->m_oaTimeDiffBuf[z2*o->m_pADF[zr]->m_iCombinations+z4/6])->Add((float)tf);

3744

}

3745

} // END FOR z4

3746

} // END FOR zr

3747

} // Ende IF ADF

3748

3749

if (g_bDDF)

3750

{

3751

for (zr=0;zr<g_iCDFChannels;zr++)

3752

{

3753

if (o->m_pDDF[zr] == NULL)

3754

continue;

3755

o->m_pDDF[zr]->BuildAtomList(smfix,smfix,NULL,&templa);

3756

for (z4=0;z4<templa.GetSize();z4+=9)

3757

{

3758

if (o->m_pDDF[zr]->m_bOrtho[0])

3759

{

3760

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

3761

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

3762

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

3763

vec1 = CrossP(vec2-vec0,vec3-vec0);

3764

} else

3765

{

3766

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

3767

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

3768

vec1 = vec2-vec0;

3769

}

3770

if (o->m_pDDF[zr]->m_bOrtho[1])

3771

{

3772

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

3773

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

3774

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+5]];

3775

vec2 = CrossP(vec3-vec4,vec5-vec4);

3776

} else

3777

{

3778

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

3779

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

3780

vec2 = vec3-vec4;

3781

}

3782

if (o->m_pDDF[zr]->m_bOrtho[2])

3783

{

3784

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+6]];

3785

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+7]];

3786

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+8]];

3787

vec3 = CrossP(vec3-vec4,vec5-vec4);

3788

} else

3789

{

3790

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+6]];

3791

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+7]];

3792

vec3 = vec3-vec4;

3793

}

3794

tf = Dihedral(vec1,vec2,vec3,o->m_pDDF[zr]->m_bAbs);

3795

if (o->m_pDDF[zr]->m_bCosine)

3796

tf = cos(tf/180.0*Pi);

3797

if (g_bDeriv)

3798

{

3799

o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9) = tf;

3800

switch(o->m_pDDF[zr]->m_iDeriv)

3801

{

3802

case 0:

3803

tf = o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9);

3804

break;

3805

case 1:

3806

tf = (o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9) - o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9)) / (2*g_fTimestepLength);

3807

break;

3808

case 2:

3809

tf = (o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9) + o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9) - 2*o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9)) / (g_fTimestepLength * g_fTimestepLength);

3810

break;

3811

}

3812

}

3813

if (!g_bDeriv || (g_iSteps > 2))

3814

{

3815

if (o->m_bObsCertain && o->m_bDecompDist)

3816

o->m_pDDF[zr]->m_pDDF->AddToBin_Multi(tic_r,tf);

3817

3818

o->m_pDDF[zr]->m_faData[0].Add(tf);

3819

3820

if (o->m_pDDF[zr]->m_bACF)

3821

o->m_pDDF[zr]->m_pfaACFBuffer[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]->Add((float)tf);

3822

3823

if ((!o->m_pDDF[zr]->m_bAbs) && o->m_pDDF[zr]->m_bSymm)

3824

{

3825

o->m_pDDF[zr]->m_faData[0].Add(-tf);

3826

if (o->m_bObsCertain && o->m_bDecompDist)

3827

o->m_pDDF[zr]->m_pDDF->AddToBin_Multi(tic_r,-tf);

3828

}

3829

3830

if (o->m_bTimeDiff)

3831

((CxFloatArray*)o->m_pDDF[zr]->m_pDDF->m_oaTimeDiffBuf[z2*o->m_pDDF[zr]->m_iCombinations+z4/9])->Add((float)tf);

3832

3833

if (o->m_bTimeDev && (ti2 != -1))

3834

{

3835

if (o->m_pDDF[zr]->m_bRotate)

3836

{

3837

if (g_iSteps > 1)

3838

{

3839

if ((tf - o->m_pDDF[zr]->m_faLastData[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]) > 180.0)

3840

o->m_pDDF[zr]->m_laRotation[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]--;

3841

if ((tf - o->m_pDDF[zr]->m_faLastData[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]) < -180.0)

3842

o->m_pDDF[zr]->m_laRotation[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]++;

3843

}

3844

o->m_pDDF[zr]->m_faLastData[z2*o->m_pDDF[zr]->m_iCombinations+z4/9] = tf;

3845

tf2 = tf + o->m_pDDF[zr]->m_laRotation[z2*o->m_pDDF[zr]->m_iCombinations+z4/9] * 360.0;

3846

} else tf2 = tf;

3847

if (o->m_bSaveSeparateFiles)

3848

fprintf(o->m_pDDF[zr]->m_fAngle[ti2],"; %8.3f",tf2);

3849

else fprintf(o->m_pDDF[zr]->m_fAngle[0],"; %8.3f",tf2);

3850

if (o->m_bCombinedPlot)

3851

o->m_pDDF[zr]->m_pDDF->m_pCombinedPlot->AddXYTupel(ti2*o->m_pDDF[zr]->m_iCombinations+z4/9,g_iSteps*g_fTimestepLength/1000.0,tf);

3852

}

3853

}

3854

}

3855

}

3856

} // END IF DDF

3857

3858

if (g_bVHDF)

3859

{

3860

o->m_pVHDF->BuildAtomList(smfix,smfix,NULL,&templa);

3861

for (z4=0;z4<templa.GetSize();z4+=2)

3862

{

3863

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]] + vecc;

3864

for (z0=0;z0<o->m_pVHDF->m_iDepth/o->m_pVHDF->m_iStride;z0++)

3865

{

3866

g_pT2Timestep = GetTimeStep(z0*o->m_pVHDF->m_iStride);

3867

if (g_pT2Timestep == NULL)

3868

continue;

3869

vec1 = g_pT2Timestep->m_vaCoords[templa[z4+1]];

3870

vec2 = vec0-vec1;

3871

while (vec2[0] > g_fBoxX/2.0) vec2[0] -= g_fBoxX;

3872

while (vec2[0] <= -g_fBoxX/2.0) vec2[0] += g_fBoxX;

3873

while (vec2[1] > g_fBoxY/2.0) vec2[1] -= g_fBoxY;

3874

while (vec2[1] <= -g_fBoxY/2.0) vec2[1] += g_fBoxY;

3875

while (vec2[2] > g_fBoxZ/2.0) vec2[2] -= g_fBoxZ;

3876

while (vec2[2] <= -g_fBoxZ/2.0) vec2[2] += g_fBoxZ;

3877

tf = vec2.GetLength();

3878

o->m_pVHDF->m_pVHDF->AddToBin(tf,z0);

3879

o->m_pVHDF->m_pCount[z0]++;

3880

}

3881

}

3882

} // Ende IF VHDF

3883

3884

if (g_bRDF)

3885

{

3886

for (zr=0;zr<g_iCDFChannels;zr++)

3887

{

3888

if (o->m_pRDF[zr] == NULL)

3889

continue;

3890

o->m_pRDF[zr]->BuildAtomList(smfix,smfix,NULL,&templa);

3891

for (z4=0;z4<templa.GetSize();z4+=2)

3892

{

3893

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

3894

vec1 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

3895

vec2 = vec0-vec1;

3896

tf = vec2.GetLength();

3897

if (g_bDeriv)

3898

{

3899

o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2) = tf;

3900

switch(o->m_pRDF[zr]->m_iDeriv)

3901

{

3902

case 0:

3903

tf = o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2);

3904

break;

3905

case 1:

3906

tf = (o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2) - o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2)) / (2*g_fTimestepLength);

3907

break;

3908

case 2:

3909

tf = (o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2) + o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2) - 2*o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2)) / (g_fTimestepLength * g_fTimestepLength);

3910

break;

3911

}

3912

}

3913

if (!g_bDeriv || (g_iSteps > 2))

3914

{

3915

if (o->m_bObsCertain && o->m_bDecompDist)

3916

o->m_pRDF[zr]->m_pRDF->AddToBin_Multi(tic_r,tf);

3917

3918

if (o->m_bDecompType)

3919

o->m_pRDF[zr]->m_pRDF->AddToBin_Multi(o->m_waDecompTypeRefOffs[templa[z4]]*o->m_waDecompTypeObsOffs.GetSize()+o->m_waDecompTypeObsOffs[templa[z4+1]],tf);

3920

3921

o->m_pRDF[zr]->m_faData[0].Add(tf);

3922

3923

if (o->m_pRDF[zr]->m_bACF)

3924

o->m_pRDF[zr]->m_pfaACFBuffer[z2*o->m_pRDF[zr]->m_iCombinations+z4/2]->Add((float)tf);

3925

3926

if (o->m_bTimeDev && (ti2 != -1))

3927

{

3928

if (o->m_bSaveSeparateFiles)

3929

fprintf(o->m_pRDF[zr]->m_fDist[ti2],"; %10.3f",tf);

3930

else fprintf(o->m_pRDF[zr]->m_fDist[0],"; %10.3f",tf);

3931

if (o->m_bCombinedPlot)

3932

o->m_pRDF[zr]->m_pRDF->m_pCombinedPlot->AddXYTupel(ti2*o->m_pRDF[zr]->m_iCombinations+z4/2,g_iSteps*g_fTimestepLength/1000.0,tf);

3933

}

3934

if (o->m_bTimeDiff)

3935

((CxFloatArray*)o->m_pRDF[zr]->m_pRDF->m_oaTimeDiffBuf[z2*o->m_pRDF[zr]->m_iCombinations+z4/2])->Add((float)tf);

3936

}

3937

}

3938

}

3939

} // Ende IF RDF

3940

3941

if (g_bDipDF)

3942

{

3943

for (zr=0;zr<g_iCDFChannels;zr++)

3944

{

3945

if (o->m_pDipDF[zr] == NULL)

3946

continue;

3947

tf = smfix->m_vDipole.GetLength();

3948

if (g_bDeriv)

3949

{

3950

o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2) = tf;

3951

switch(o->m_pDipDF[zr]->m_iDeriv)

3952

{

3953

case 0:

3954

tf = o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2);

3955

break;

3956

case 1:

3957

tf = (o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2) - o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2)) / (2*g_fTimestepLength);

3958

break;

3959

case 2:

3960

tf = (o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2) + o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2) - 2*o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2)) / (g_fTimestepLength * g_fTimestepLength);

3961

break;

3962

}

3963

}

3964

if (!g_bDeriv || (g_iSteps > 2))

3965

{

3966

if (o->m_bObsCertain && o->m_bDecompDist)

3967

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin_Multi(tic_r,tf);

3968

3969

o->m_pDipDF[zr]->m_faData[0].Add(tf);

3970

3971

if (o->m_pDipDF[zr]->m_bACF)

3972

o->m_pDipDF[zr]->m_pfaACFBuffer[z2]->Add((float)tf);

3973

3974

if (o->m_bTimeDev && (ti2 != -1))

3975

{

3976

if (o->m_bSaveSeparateFiles)

3977

fprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"; %8.3f",tf);

3978

else fprintf(o->m_pDipDF[zr]->m_fDipole[0],"; %8.3f",tf);

3979

if (o->m_bCombinedPlot)

3980

o->m_pDipDF[zr]->m_pDipoleDF->m_pCombinedPlot->AddXYTupel(ti2,g_iSteps*g_fTimestepLength/1000.0,tf);

3981

}

3982

if (o->m_bTimeDiff)

3983

((CxFloatArray*)o->m_pDipDF[zr]->m_pDipoleDF->m_oaTimeDiffBuf[z2])->Add((float)tf);

3984

}

3985

}

3986

} // Ende IF DIPDF

3987

3988

if (g_bVDF)

3989

{

3990

for (zr=0;zr<g_iCDFChannels;zr++)

3991

{

3992

if (o->m_pVDF[zr] == NULL)

3993

continue;

3994

o->m_pVDF[zr]->BuildAtomList(smfix,smfix,NULL,&templa);

3995

for (z4=0;z4<templa.GetSize();z4++)

3996

{

3997

tf = tempvel[templa[z4]].GetLength();

3998

if (g_bDeriv)

3999

{

4000

o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2) = tf;

4001

switch(o->m_pVDF[zr]->m_iDeriv)

4002

{

4003

case 0:

4004

tf = o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2);

4005

break;

4006

case 1:

4007

tf = (o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2) - o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2)) / (2*g_fTimestepLength);

4008

break;

4009

case 2:

4010

tf = (o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2) + o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2) - 2*o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2)) / (g_fTimestepLength * g_fTimestepLength);

4011

break;

4012

}

4013

}

4014

if (!g_bDeriv || (g_iSteps > 2))

4015

{

4016

if (o->m_bObsCertain && o->m_bDecompDist)

4017

o->m_pVDF[zr]->m_pVDF->AddToBin_Multi(tic_r,tf);

4018

4019

o->m_pVDF[zr]->m_faData[0].Add(tf);

4020

4021

if (o->m_pVDF[zr]->m_bACF)

4022

o->m_pVDF[zr]->m_pfaACFBuffer[z2*o->m_pVDF[zr]->m_iCombinations+z4]->Add((float)tf);

4023

4024

if (o->m_bTimeDev && (ti2 != -1))

4025

{

4026

if (o->m_bSaveSeparateFiles)

4027

fprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"; %8.3f",tf);

4028

else fprintf(o->m_pVDF[zr]->m_fSpeed[0],"; %8.3f",tf);

4029

if (o->m_bCombinedPlot)

4030

o->m_pVDF[zr]->m_pVDF->m_pCombinedPlot->AddXYTupel(ti2*o->m_pVDF[zr]->m_iCombinations+z4,g_iSteps*g_fTimestepLength/1000.0,tf);

4031

}

4032

if (o->m_bTimeDiff)

4033

((CxFloatArray*)o->m_pVDF[zr]->m_pVDF->m_oaTimeDiffBuf[z2*o->m_pVDF[zr]->m_iCombinations+z4])->Add((float)tf);

4034

}

4035

}

4036

}

4037

} // Ende IF VDF

4038

4039

if (g_bSDF)

4040

{

4041

o->m_pSDF->BuildAtomList(smfix,smfix,NULL,&templa);

4042

for (z4=0;z4<templa.GetSize();z4++)

4043

{

4044

o->m_pSDF->m_vaData[0].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

4045

4046

if (o->m_pSDF->m_bVdWSpheres)

4047

o->m_pSDF->m_faRadius[0].Add(g_faVdWRadius[templa[z4]]);

4048

}

4049

} // Ende IF SDF

4050

4051

if (g_bRevSDF)

4052

{

4053

o->m_pRevSDF->BuildAtomList(smfix,smfix,NULL,&templa);

4054

for (z4=0;z4<templa.GetSize();z4++)

4055

o->m_pRevSDF->m_vaData[0].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

4056

} // Ende IF RevSDF

4057

4058

} // Ende IF m_bSelf

4059

4060

if (o->m_bOthers)

4061

{

4062

secondmolrun = false;

4063

_secondmolstart:

4064

if (o->m_pConditions != NULL)

4065

{

4066

o->m_pConditions->m_bAnyPassed = false;

4067

o->m_pConditions->ScanNeighborhoodAllOM(g_pTempTimestep,smfix,false);

4068

if (o->m_pConditions->m_bAnyPassed)

4069

o->m_pConditions->m_iRMPassCounter[z2]++;

4070

}

4071

4072

for (z3=0;z3<(secondmolrun?o->m_iShowMol2Count:o->m_iShowMolCount);z3++) // Alle anderen Molekuele durchgehen

4073

{

4074

if (secondmolrun)

4075

{

4076

if ((g_iFixMol == o->m_iShowMol2) && (z3 == z2)) // Wir wollen nicht das Referenzmolekuel mitzaehlen

4077

continue;

4078

if (o->m_bObsCertain)

4079

{

4080

if (!o->m_waObsShow2List.Contains(z3))

4081

continue;

4082

tic_o = o->m_waObsShow2List.GetPosition(z3);

4083

}

4084

} else

4085

{

4086

if ((g_iFixMol == o->m_iShowMol) && (z3 == z2)) // Wir wollen nicht das Referenzmolekuel mitzaehlen

4087

continue;

4088

if (o->m_bObsCertain)

4089

{

4090

if (!o->m_waObsShowList.Contains(z3))

4091

continue;

4092

tic_o = o->m_waObsShowList.GetPosition(z3);

4093

}

4094

}

4095

4096

if (secondmolrun)

4097

{

4098

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_laSingleMolIndex[z3]];

4099

} else

4100

{

4101

ti = o->m_waSaveShowList.GetPosition(z3);

4102

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z3]];

4103

}

4104

4105

if (o->m_bTimeDev && (o->m_pConditions != NULL))

4106

{

4107

if (!o->m_pConditions->Contains(z3) && (!g_bDeriv || (g_iSteps > 2)))

4108

{

4109

for (zr=0;zr<g_iCDFChannels;zr++)

4110

{

4111

if (g_bADF && (o->m_pADF[zr] != NULL))

4112

{

4113

if ((ti2 != -1) && (ti != -1))

4114

{

4115

if (o->m_bSaveSeparateFiles)

4116

fprintf(o->m_pADF[zr]->m_fAngle[ti2],"; - ");

4117

else fprintf(o->m_pADF[zr]->m_fAngle[0],"; - ");

4118

}

4119

}

4120

4121

if (g_bDDF && (o->m_pDDF[zr] != NULL))

4122

{

4123

if ((ti2 != -1) && (ti != -1))

4124

{

4125

if (o->m_bSaveSeparateFiles)

4126

fprintf(o->m_pADF[zr]->m_fAngle[ti2],"; - ");

4127

else fprintf(o->m_pDDF[zr]->m_fAngle[0],"; - ");

4128

}

4129

}

4130

4131

if (g_bDipDF && (o->m_pDipDF[zr] != NULL))

4132

{

4133

if ((ti2 != -1) && (ti != -1))

4134

{

4135

if (o->m_bSaveSeparateFiles)

4136

fprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"; - ");

4137

else fprintf(o->m_pDipDF[zr]->m_fDipole[0],"; - ");

4138

}

4139

}

4140

4141

if (g_bVDF && (o->m_pVDF[zr] != NULL))

4142

{

4143

if ((ti2 != -1) && (ti != -1))

4144

{

4145

if (o->m_bSaveSeparateFiles)

4146

fprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"; - ");

4147

else fprintf(o->m_pVDF[zr]->m_fSpeed[0],"; - ");

4148

}

4149

}

4150

4151

if (g_bRDF && (o->m_pRDF[zr] != NULL))

4152

{

4153

if ((ti2 != -1) && (ti != -1))

4154

{

4155

if (o->m_bSaveSeparateFiles)

4156

fprintf(o->m_pRDF[zr]->m_fDist[ti2],"; - ");

4157

else fprintf(o->m_pRDF[zr]->m_fDist[0],"; - ");

4158

}

4159

}

4160

}

4161

continue;

4162

}

4163

}

4164

4165

if (o->m_pConditions != NULL)

4166

{

4167

if (!o->m_pConditions->Contains(z3))

4168

continue;

4169

4170

if (o->m_bBinOnlyPassedAtoms)

4171

o->m_pConditions->MarkPassedAtoms(z3,true);

4172

4173

if (o->m_bBinOnlyNotPassedAtoms)

4174

o->m_pConditions->MarkPassedAtoms(z3,false);

4175

4176

if (g_bSaveCondSnapshot)

4177

{

4178

g_iSaveCondCount++;

4179

if (g_bSaveCondWholeBox)

4180

{

4181

g_pTempTimestep->WriteTimestep(g_fSaveCondFile);

4182

} else

4183

{

4184

fprintf(g_fSaveCondFile,"%d\nTimestep %lu, RM %d, OM %d\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes - ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laVirtualAtoms.GetSize() + ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_iAtomGes - ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laVirtualAtoms.GetSize(),g_iSteps,z2+1,z3+1);

4185

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z4++)

4186

{

4187

if ((!g_bSaveVirtAtoms) && (((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z4] == g_iVirtAtomType))

4188

continue;

4189

for (z5=0;z5<((CxIntArray*)smfix->m_oaAtomOffset[z4])->GetSize();z5++)

4190

fprintf(g_fSaveCondFile,"%s %f %f %f\n",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z4]])->m_sName,g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[z4])->GetAt(z5)][0]/100.0,g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[z4])->GetAt(z5)][1]/100.0,g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[z4])->GetAt(z5)][2]/100.0);

4191

}

4192

for (z4=0;z4<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex.GetSize();z4++)

4193

{

4194

if ((!g_bSaveVirtAtoms) && (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex[z4] == g_iVirtAtomType))

4195

continue;

4196

for (z5=0;z5<((CxIntArray*)sm->m_oaAtomOffset[z4])->GetSize();z5++)

4197

fprintf(g_fSaveCondFile,"%s %f %f %f\n",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex[z4]])->m_sName,g_pTempTimestep->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z4])->GetAt(z5)][0]/100.0,g_pTempTimestep->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z4])->GetAt(z5)][1]/100.0,g_pTempTimestep->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z4])->GetAt(z5)][2]/100.0);

4198

}

4199

}

4200

}

4201

}

4202

4203

if (g_bVHDF)

4204

{

4205

o->m_pVHDF->BuildAtomList(smfix,sm,NULL,&templa);

4206

for (z4=0;z4<templa.GetSize();z4+=2)

4207

{

4208

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]] + vecc;

4209

for (z0=0;z0<o->m_pVHDF->m_iDepth/o->m_pVHDF->m_iStride;z0++)

4210

{

4211

g_pT2Timestep = GetTimeStep(z0*o->m_pVHDF->m_iStride);

4212

if (g_pT2Timestep == NULL)

4213

continue;

4214

vec1 = g_pT2Timestep->m_vaCoords[templa[z4+1]];

4215

vec2 = vec0-vec1;

4216

while (vec2[0] > g_fBoxX/2.0) vec2[0] -= g_fBoxX;

4217

while (vec2[0] <= -g_fBoxX/2.0) vec2[0] += g_fBoxX;

4218

while (vec2[1] > g_fBoxY/2.0) vec2[1] -= g_fBoxY;

4219

while (vec2[1] <= -g_fBoxY/2.0) vec2[1] += g_fBoxY;

4220

while (vec2[2] > g_fBoxZ/2.0) vec2[2] -= g_fBoxZ;

4221

while (vec2[2] <= -g_fBoxZ/2.0) vec2[2] += g_fBoxZ;

4222

tf = vec2.GetLength();

4223

o->m_pVHDF->m_pVHDF->AddToBin(tf,z0);

4224

o->m_pVHDF->m_pCount[z0]++;

4225

}

4226

}

4227

} // Ende IF VHDF

4228

4229

if (g_bADF)

4230

{

4231

for (zr=0;zr<g_iCDFChannels;zr++)

4232

{

4233

if (o->m_pADF[zr] == NULL)

4234

continue;

4235

if (o->m_bSecondShowMol)

4236

{

4237

if (secondmolrun && (zr == 0))

4238

continue;

4239

if (!secondmolrun && (zr == 1))

4240

continue;

4241

}

4242

o->m_pADF[zr]->BuildAtomList(smfix,sm,NULL,&templa);

4243

for (z4=0;z4<templa.GetSize();z4+=6)

4244

{

4245

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4246

{

4247

tb = true;

4248

if (g_baAtomPassedCondition[templa[z4]] == 0)

4249

tb = false;

4250

if (g_baAtomPassedCondition[templa[z4+1]] == 0)

4251

tb = false;

4252

if (o->m_pADF[zr]->m_bOrtho[0])

4253

if (g_baAtomPassedCondition[templa[z4+2]] == 0)

4254

tb = false;

4255

if (g_baAtomPassedCondition[templa[z4+3]] == 0)

4256

tb = false;

4257

if (g_baAtomPassedCondition[templa[z4+4]] == 0)

4258

tb = false;

4259

if (o->m_pADF[zr]->m_bOrtho[1])

4260

if (g_baAtomPassedCondition[templa[z4+5]] == 0)

4261

tb = false;

4262

if (tb)

4263

{

4264

o->m_pADF[zr]->m_baDataEnabled[z3].Add(1);

4265

} else

4266

{

4267

// mprintf("Nicht bestanden; z2=%d, z3=%d; (%d,%d,%d) (%d,%d,%d).\n",z2,z3,g_baAtomPassedCondition[tempwa[z4]],g_baAtomPassedCondition[tempwa[z4+1]],g_baAtomPassedCondition[tempwa[z4+2]],g_baAtomPassedCondition[tempwa[z4+3]],g_baAtomPassedCondition[tempwa[z4+4]],g_baAtomPassedCondition[tempwa[z4+5]]);

4268

o->m_pADF[zr]->m_baDataEnabled[z3].Add(0);

4269

}

4270

}

4271

if (o->m_pADF[zr]->m_bOrtho[0])

4272

{

4273

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4274

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4275

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

4276

vec1 = CrossP(vec2-vec0,vec3-vec0);

4277

} else

4278

{

4279

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4280

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4281

vec1 = vec2-vec0;

4282

}

4283

if (o->m_pADF[zr]->m_bOrtho[1])

4284

{

4285

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

4286

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

4287

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+5]];

4288

vec2 = CrossP(vec3-vec4,vec5-vec4);

4289

} else

4290

{

4291

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

4292

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

4293

vec2 = vec3-vec4;

4294

}

4295

4296

tf = Angle_Deg(vec1,vec2);

4297

if ((tf > 90.0f) && (o->m_pADF[zr]->m_bFoldAngle))

4298

tf = 180.0f-tf;

4299

if (o->m_pADF[zr]->m_bCosine)

4300

tf = cos(tf/180.0*Pi);

4301

4302

if (g_bDeriv)

4303

{

4304

zi = (z2*o->m_iShowMolCount+z3)*o->m_pADF[zr]->m_iCombinations+z4/6;

4305

o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

4306

switch(o->m_pADF[zr]->m_iDeriv)

4307

{

4308

case 0:

4309

tf = o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

4310

break;

4311

case 1:

4312

tf = (o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

4313

break;

4314

case 2:

4315

tf = (o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi) + o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - 2*o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi)) / (g_fTimestepLength * g_fTimestepLength);

4316

break;

4317

}

4318

}

4319

if (!g_bDeriv || (g_iSteps > 2))

4320

{

4321

if (o->m_bObsCertain && o->m_bDecompDist)

4322

o->m_pADF[zr]->m_pADF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

4323

4324

o->m_pADF[zr]->m_faData[z3].Add(tf);

4325

4326

if (o->m_pADF[zr]->m_bACF)

4327

o->m_pADF[zr]->m_pfaACFBuffer[(z2*o->m_iShowMolCount+z3)*o->m_pADF[zr]->m_iCombinations+z4/6]->Add((float)tf);

4328

4329

/* if (o->m_pADF[zr]->m_bMirror)

4330

{

4331

if (o->m_bObsCertain && o->m_bDecompDist)

4332

o->m_pADF[zr]->m_pADF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,180.0-tf);

4333

o->m_pADF[zr]->m_faData[z3].Add(180.0-tf);

4334

}*/

4335

4336

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

4337

{

4338

// o->m_pAngleStat->AddValue(ti2,ti,tf);

4339

if (o->m_bSaveSeparateFiles)

4340

fprintf(o->m_pADF[zr]->m_fAngle[ti2],"; %8.3f",tf);

4341

else fprintf(o->m_pADF[zr]->m_fAngle[0],"; %8.3f",tf);

4342

if (o->m_bCombinedPlot)

4343

o->m_pADF[zr]->m_pADF->m_pCombinedPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pADF[zr]->m_iCombinations+z4/6,g_iSteps*g_fTimestepLength/1000.0,tf);

4344

}

4345

if (o->m_bTimeDiff)

4346

((CxFloatArray*)o->m_pADF[zr]->m_pADF->m_oaTimeDiffBuf[(z2*o->m_iShowMolCount+z3)*o->m_pADF[zr]->m_iCombinations+z4/6])->Add((float)tf);

4347

}

4348

}

4349

}

4350

} // Ende IF ADF

4351

4352

if (g_bDDF)

4353

{

4354

for (zr=0;zr<g_iCDFChannels;zr++)

4355

{

4356

if (o->m_pDDF[zr] == NULL)

4357

continue;

4358

if (o->m_bSecondShowMol)

4359

{

4360

if (secondmolrun && (zr == 0))

4361

continue;

4362

if (!secondmolrun && (zr == 1))

4363

continue;

4364

}

4365

o->m_pDDF[zr]->BuildAtomList(smfix,sm,NULL,&templa);

4366

for (z4=0;z4<templa.GetSize();z4+=9)

4367

{

4368

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4369

{

4370

tb = true;

4371

for (z5=z4;z5<z4+9;z5++)

4372

if (g_baAtomPassedCondition[templa[z5]] == 0)

4373

tb = false;

4374

if (tb)

4375

o->m_pDDF[zr]->m_baDataEnabled[z3].Add(1);

4376

else o->m_pDDF[zr]->m_baDataEnabled[z3].Add(0);

4377

}

4378

if (o->m_pDDF[zr]->m_bOrtho[0])

4379

{

4380

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4381

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4382

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

4383

vec1 = CrossP(vec2-vec0,vec3-vec0);

4384

} else

4385

{

4386

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4387

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4388

vec1 = vec2-vec0;

4389

}

4390

if (o->m_pDDF[zr]->m_bOrtho[1])

4391

{

4392

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

4393

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

4394

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+5]];

4395

vec2 = CrossP(vec3-vec4,vec5-vec4);

4396

} else

4397

{

4398

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

4399

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

4400

vec2 = vec3-vec4;

4401

}

4402

if (o->m_pDDF[zr]->m_bOrtho[2])

4403

{

4404

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+6]];

4405

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+7]];

4406

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+8]];

4407

vec3 = CrossP(vec3-vec4,vec5-vec4);

4408

} else

4409

{

4410

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+6]];

4411

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+7]];

4412

vec3 = vec3-vec4;

4413

}

4414

tf = Dihedral(vec1,vec2,vec3,o->m_pDDF[zr]->m_bAbs);

4415

if (o->m_pDDF[zr]->m_bCosine)

4416

tf = cos(tf/180.0*Pi);

4417

if (g_bDeriv)

4418

{

4419

zi = (z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9;

4420

o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

4421

switch(o->m_pDDF[zr]->m_iDeriv)

4422

{

4423

case 0:

4424

tf = o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

4425

break;

4426

case 1:

4427

tf = (o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

4428

break;

4429

case 2:

4430

tf = (o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi) + o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - 2*o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi)) / (g_fTimestepLength * g_fTimestepLength);

4431

break;

4432

}

4433

}

4434

if (!g_bDeriv || (g_iSteps > 2))

4435

{

4436

if (o->m_bObsCertain && o->m_bDecompDist)

4437

o->m_pDDF[zr]->m_pDDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

4438

4439

o->m_pDDF[zr]->m_faData[z3].Add(tf);

4440

4441

if (o->m_pDDF[zr]->m_bACF)

4442

o->m_pDDF[zr]->m_pfaACFBuffer[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]->Add((float)tf);

4443

4444

if ((!o->m_pDDF[zr]->m_bAbs) && o->m_pDDF[zr]->m_bSymm)

4445

{

4446

o->m_pDDF[zr]->m_faData[z3].Add(-tf);

4447

if (o->m_bObsCertain && o->m_bDecompDist)

4448

o->m_pDDF[zr]->m_pDDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,-tf);

4449

}

4450

4451

if (o->m_bTimeDiff)

4452

((CxFloatArray*)o->m_pDDF[zr]->m_pDDF->m_oaTimeDiffBuf[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9])->Add((float)tf);

4453

4454

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

4455

{

4456

if (o->m_pDDF[zr]->m_bRotate)

4457

{

4458

if (g_iSteps > 1)

4459

{

4460

if ((tf - o->m_pDDF[zr]->m_faLastData[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]) > 180.0)

4461

o->m_pDDF[zr]->m_laRotation[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]--;

4462

if ((tf - o->m_pDDF[zr]->m_faLastData[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]) < -180.0)

4463

o->m_pDDF[zr]->m_laRotation[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]++;

4464

}

4465

o->m_pDDF[zr]->m_faLastData[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9] = tf;

4466

tf2 = tf + o->m_pDDF[zr]->m_laRotation[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9] * 360.0;

4467

} else tf2 = tf;

4468

if (o->m_bSaveSeparateFiles)

4469

fprintf(o->m_pDDF[zr]->m_fAngle[ti2],"; %8.3f",tf2);

4470

else fprintf(o->m_pDDF[zr]->m_fAngle[0],"; %8.3f",tf2);

4471

if (o->m_bCombinedPlot)

4472

o->m_pDDF[zr]->m_pDDF->m_pCombinedPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pDDF[zr]->m_iCombinations+z4/9,g_iSteps*g_fTimestepLength/1000.0,tf);

4473

}

4474

}

4475

}

4476

}

4477

} // Ende IF DDF

4478

4479

if (g_bDipDF)

4480

{

4481

for (zr=0;zr<g_iCDFChannels;zr++)

4482

{

4483

if (o->m_pDipDF[zr] == NULL)

4484

continue;

4485

if (o->m_bSecondShowMol)

4486

{

4487

if (secondmolrun && (zr == 0))

4488

continue;

4489

if (!secondmolrun && (zr == 1))

4490

continue;

4491

}

4492

if (o->m_pDipDF[zr]->m_iRefOrSec == 0)

4493

tf = smfix->m_vDipole.GetLength();

4494

else tf = sm->m_vDipole.GetLength();

4495

if (g_bDeriv)

4496

{

4497

zi = z2*o->m_iShowMolCount+z3;

4498

o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

4499

switch(o->m_pDipDF[zr]->m_iDeriv)

4500

{

4501

case 0:

4502

tf = o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

4503

break;

4504

case 1:

4505

tf = (o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

4506

break;

4507

case 2:

4508

tf = (o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi) + o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - 2*o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi)) / (g_fTimestepLength * g_fTimestepLength);

4509

break;

4510

}

4511

}

4512

if (!g_bDeriv || (g_iSteps > 2))

4513

{

4514

if (o->m_bObsCertain && o->m_bDecompDist)

4515

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

4516

4517

o->m_pDipDF[zr]->m_faData[z3].Add(tf);

4518

4519

if (o->m_pDipDF[zr]->m_bACF)

4520

o->m_pDipDF[zr]->m_pfaACFBuffer[z2*o->m_iShowMolCount+z3]->Add((float)tf);

4521

4522

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

4523

{

4524

if (o->m_bSaveSeparateFiles)

4525

fprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"; %8.3f",tf);

4526

else fprintf(o->m_pDipDF[zr]->m_fDipole[0],"; %8.3f",tf);

4527

if (o->m_bCombinedPlot)

4528

o->m_pDipDF[zr]->m_pDipoleDF->m_pCombinedPlot->AddXYTupel(ti2*o->m_waSaveShowList.GetSize()+ti,g_iSteps*g_fTimestepLength/1000.0,tf);

4529

}

4530

if (o->m_bTimeDiff)

4531

((CxFloatArray*)o->m_pDipDF[zr]->m_pDipoleDF->m_oaTimeDiffBuf[z2*o->m_iShowMolCount+z3])->Add((float)tf);

4532

}

4533

}

4534

} // Ende IF DIPOLE

4535

4536

if (g_bVDF)

4537

{

4538

for (zr=0;zr<g_iCDFChannels;zr++)

4539

{

4540

if (o->m_pVDF[zr] == NULL)

4541

continue;

4542

if (o->m_bSecondShowMol)

4543

{

4544

if (secondmolrun && (zr == 0))

4545

continue;

4546

if (!secondmolrun && (zr == 1))

4547

continue;

4548

}

4549

o->m_pVDF[zr]->BuildAtomList(smfix,sm,NULL,&templa);

4550

for (z4=0;z4<templa.GetSize();z4++)

4551

{

4552

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4553

{

4554

tb = true;

4555

for (z5=z4;z5<z4+2;z5++)

4556

if (g_baAtomPassedCondition[templa[z5]] == 0)

4557

tb = false;

4558

if (tb)

4559

o->m_pVDF[zr]->m_baDataEnabled[z3].Add(1);

4560

else o->m_pVDF[zr]->m_baDataEnabled[z3].Add(0);

4561

}

4562

tf = tempvel[templa[z4]].GetLength();

4563

if (g_bDeriv)

4564

{

4565

zi = (z2*o->m_iShowMolCount+z3)*o->m_pVDF[zr]->m_iCombinations+z4/2;

4566

o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

4567

switch(o->m_pVDF[zr]->m_iDeriv)

4568

{

4569

case 0:

4570

tf = o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

4571

break;

4572

case 1:

4573

tf = (o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

4574

break;

4575

case 2:

4576

tf = (o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi) + o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - 2*o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi)) / (g_fTimestepLength * g_fTimestepLength);

4577

break;

4578

}

4579

}

4580

if (!g_bDeriv || (g_iSteps > 2))

4581

{

4582

if (o->m_bObsCertain && o->m_bDecompDist)

4583

o->m_pVDF[zr]->m_pVDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

4584

4585

o->m_pVDF[zr]->m_faData[z3].Add(tf);

4586

4587

if (o->m_pVDF[zr]->m_bACF)

4588

o->m_pVDF[zr]->m_pfaACFBuffer[(z2*o->m_iShowMolCount+z3)*o->m_pVDF[zr]->m_iCombinations+z4/2]->Add((float)tf);

4589

4590

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

4591

{

4592

if (o->m_bSaveSeparateFiles)

4593

fprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"; %8.3f",tf);

4594

else fprintf(o->m_pVDF[zr]->m_fSpeed[0],"; %8.3f",tf);

4595

if (o->m_bCombinedPlot)

4596

o->m_pVDF[zr]->m_pVDF->m_pCombinedPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pVDF[zr]->m_iCombinations+z4/2,g_iSteps*g_fTimestepLength/1000.0,tf);

4597

}

4598

if (o->m_bTimeDiff)

4599

((CxFloatArray*)o->m_pVDF[zr]->m_pVDF->m_oaTimeDiffBuf[(z2*o->m_iShowMolCount+z3)*o->m_pVDF[zr]->m_iCombinations+z4/2])->Add((float)tf);

4600

}

4601

}

4602

}

4603

} // Ende IF VDF

4604

4605

if (g_bRDF)

4606

{

4607

for (zr=0;zr<g_iCDFChannels;zr++)

4608

{

4609

if (o->m_pRDF[zr] == NULL)

4610

continue;

4611

if (o->m_bSecondShowMol)

4612

{

4613

if (secondmolrun && (zr == 0))

4614

continue;

4615

if (!secondmolrun && (zr == 1))

4616

continue;

4617

}

4618

o->m_pRDF[zr]->BuildAtomList(smfix,sm,NULL,&templa);

4619

for (z4=0;z4<templa.GetSize();z4+=2)

4620

{

4621

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4622

{

4623

tb = true;

4624

for (z5=z4;z5<z4+2;z5++)

4625

if (g_baAtomPassedCondition[templa[z5]] == 0)

4626

tb = false;

4627

if (tb)

4628

o->m_pRDF[zr]->m_baDataEnabled[z3].Add(1);

4629

else o->m_pRDF[zr]->m_baDataEnabled[z3].Add(0);

4630

}

4631

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4632

vec1 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4633

vec2 = vec0-vec1;

4634

tf = vec2.GetLength();

4635

// mprintf("\n@ z2=%d, z3=%d, z4=%d, templa[z4]=%d, templa[z4+1]=%d, dist=%f ",z2,z3,z4,templa[z4],templa[z4+1],tf);

4636

// mprintf("\n vec0: "); vec0.Dump(); mprintf(", vec1: "); vec1.Dump(); mprintf(", vec2: "); vec2.Dump();

4637

if (g_bDeriv)

4638

{

4639

zi = (z2*o->m_iShowMolCount+z3)*o->m_pRDF[zr]->m_iCombinations+z4/2;

4640

o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

4641

switch(o->m_pRDF[zr]->m_iDeriv)

4642

{

4643

case 0:

4644

tf = o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

4645

break;

4646

case 1:

4647

tf = (o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

4648

break;

4649

case 2:

4650

tf = (o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi) + o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - 2*o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi)) / (g_fTimestepLength * g_fTimestepLength);

4651

break;

4652

}

4653

}

4654

if (!g_bDeriv || (g_iSteps > 2))

4655

{

4656

if (o->m_bObsCertain && o->m_bDecompDist)

4657

o->m_pRDF[zr]->m_pRDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

4658

4659

if (o->m_bDecompType)

4660

o->m_pRDF[zr]->m_pRDF->AddToBin_Multi(o->m_waDecompTypeRefOffs[templa[z4]]*o->m_waDecompTypeObsOffs.GetSize()+o->m_waDecompTypeObsOffs[templa[z4+1]],tf);

4661

4662

o->m_pRDF[zr]->m_faData[z3].Add(tf);

4663

4664

if (o->m_pRDF[zr]->m_bACF)

4665

o->m_pRDF[zr]->m_pfaACFBuffer[(z2*o->m_iShowMolCount+z3)*o->m_pRDF[zr]->m_iCombinations+z4/2]->Add((float)tf);

4666

4667

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

4668

{

4669

if (o->m_bSaveSeparateFiles)

4670

fprintf(o->m_pRDF[zr]->m_fDist[ti2],"; %10.3f",tf);

4671

else fprintf(o->m_pRDF[zr]->m_fDist[0],"; %10.3f",tf);

4672

if (o->m_bCombinedPlot)

4673

o->m_pRDF[zr]->m_pRDF->m_pCombinedPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pRDF[zr]->m_iCombinations+z4/2,g_iSteps*g_fTimestepLength/1000.0,tf);

4674

}

4675

if (o->m_bTimeDiff)

4676

((CxFloatArray*)o->m_pRDF[zr]->m_pRDF->m_oaTimeDiffBuf[(z2*o->m_iShowMolCount+z3)*o->m_pRDF[zr]->m_iCombinations+z4/2])->Add((float)tf);

4677

}

4678

}

4679

}

4680

} // Ende IF RDF

4681

4682

if (g_bSDF)

4683

{

4684

o->m_pSDF->BuildAtomList(smfix,sm,NULL,&templa);

4685

for (z4=0;z4<templa.GetSize();z4++)

4686

{

4687

o->m_pSDF->m_vaData[z3].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

4688

4689

if (o->m_pSDF->m_bVdWSpheres)

4690

o->m_pSDF->m_faRadius[z3].Add(g_faVdWRadius[templa[z4]]);

4691

}

4692

} // Ende IF SDF

4693

4694

if (g_bRevSDF)

4695

{

4696

o->m_pRevSDF->BuildAtomList(smfix,sm,NULL,&templa);

4697

for (z4=0;z4<templa.GetSize();z4++)

4698

o->m_pRevSDF->m_vaData[z3].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

4699

} // Ende IF RevSDF

4700

4701

} // Ende FOR Alle anderen Molekuele durchgehen

4702

if (o->m_bSecondShowMol && (!secondmolrun))

4703

{

4704

secondmolrun = true;

4705

goto _secondmolstart;

4706

}

4707

} // Ende IF m_bOthers

4708

4709

if (g_bSDF)

4710

{

4711

if (o->m_pSDF->m_bSDFMirrorBisect)

4712

{

4713

vec2 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])];

4714

vec3 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])];

4715

vec1 = CrossP(vec2,vec3);

4716

vec2 += vec3;

4717

}

4718

4719

if (o->m_pSDF->m_bCutPlane)

4720

{

4721

o->m_pSDF->m_fAtom2PosX += g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])][0];

4722

o->m_pSDF->m_fAtom3PosX += g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])][0];

4723

o->m_pSDF->m_fAtom3PosY += g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])][1];

4724

o->m_pSDF->m_fPosCounter++;

4725

}

4726

4727

if (o->m_bSelf)

4728

{

4729

for (z5=0;z5<o->m_pSDF->m_vaData[0].GetSize();z5++)

4730

{

4731

vec0 = o->m_pSDF->m_vaData[0][z5];

4732

4733

if (o->m_pSDF->m_bVdWSpheres)

4734

o->m_pSDF->m_pSDF->AddToBin_Sphere(vec0,o->m_pSDF->m_faRadius[0][z5]);

4735

else o->m_pSDF->m_pSDF->AddToBin(vec0);

4736

4737

if (o->m_pSDF->m_bSDFMirrorXY)

4738

{

4739

vec0[2] = -vec0[2];

4740

o->m_pSDF->m_pSDF->AddToBin(vec0);

4741

}

4742

4743

if (o->m_pSDF->m_bSDFMirrorBisect)

4744

{

4745

vec3.PointRoot(vec1,vec2,vec0);

4746

vec3 -= vec0;

4747

vec3 *= 2.0f;

4748

vec0 += vec3;

4749

o->m_pSDF->m_pSDF->AddToBin(vec0);

4750

if (o->m_pSDF->m_bSDFMirrorXY)

4751

{

4752

vec0[2] = -vec0[2];

4753

o->m_pSDF->m_pSDF->AddToBin(vec0);

4754

}

4755

}

4756

}

4757

} else

4758

{

4759

for (z4=0;z4<o->m_iShowMolCount;z4++)

4760

{

4761

for (z5=0;z5<o->m_pSDF->m_vaData[z4].GetSize();z5++)

4762

{

4763

vec0 = o->m_pSDF->m_vaData[z4][z5];

4764

4765

if (o->m_pSDF->m_bVdWSpheres)

4766

o->m_pSDF->m_pSDF->AddToBin_Sphere(vec0,o->m_pSDF->m_faRadius[z4][z5]);

4767

else o->m_pSDF->m_pSDF->AddToBin(vec0);

4768

4769

if (o->m_pSDF->m_bSDFMirrorXY)

4770

{

4771

vec0[2] = -vec0[2];

4772

o->m_pSDF->m_pSDF->AddToBin(vec0);

4773

}

4774

4775

if (o->m_pSDF->m_bSDFMirrorBisect)

4776

{

4777

vec3.PointRoot(vec1,vec2,vec0);

4778

vec3 -= vec0;

4779

vec3 *= 2.0f;

4780

vec0 += vec3;

4781

o->m_pSDF->m_pSDF->AddToBin(vec0);

4782

if (o->m_pSDF->m_bSDFMirrorXY)

4783

{

4784

vec0[2] = -vec0[2];

4785

o->m_pSDF->m_pSDF->AddToBin(vec0);

4786

}

4787

}

4788

}

4789

}

4790

}

4791

}

4792

4793

if (g_bRevSDF)

4794

{

4795

vec2 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])];

4796

tf4 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])].GetLength();

4797

o->m_pRevSDF->m_fSecondAtomPosX += tf4;

4798

o->m_pRevSDF->m_fSecondAtomCount++;

4799

if (o->m_bSelf)

4800

{

4801

for (z5=0;z5<o->m_pRevSDF->m_vaData[0].GetSize();z5++)

4802

{

4803

vec0 = o->m_pRevSDF->m_vaData[0][z5];

4804

tf = fabs(Angle(vec2,vec0));

4805

tf2 = vec0.GetLength();

4806

tf3 = 1.0;

4807

if (o->m_pRevSDF->m_bCorrectAngle)

4808

{

4809

if ((tf < 0.001) || (tf > Pi-0.001))

4810

tf3 /= 0.001;

4811

else tf3 /= sin(tf);

4812

}

4813

if (o->m_pRevSDF->m_bCorrectRadial)

4814

tf3 /= tf2; // Erste Potenz, da 2D-Grid (SDF hat "nullte Potenz" ^^)

4815

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,cos(tf)*tf2,tf3);

4816

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,cos(tf)*tf2,tf3);

4817

if (o->m_pRevSDF->m_bMirrorY)

4818

{

4819

if (o->m_pRevSDF->m_bMirrorBond)

4820

{

4821

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,tf4-cos(tf)*tf2,tf3);

4822

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,tf4-cos(tf)*tf2,tf3);

4823

} else

4824

{

4825

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,-cos(tf)*tf2,tf3);

4826

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,-cos(tf)*tf2,tf3);

4827

}

4828

}

4829

}

4830

} else

4831

{

4832

for (z4=0;z4<o->m_iShowMolCount;z4++)

4833

{

4834

for (z5=0;z5<o->m_pRevSDF->m_vaData[z4].GetSize();z5++)

4835

{

4836

vec0 = o->m_pRevSDF->m_vaData[z4][z5];

4837

tf = fabs(Angle(vec2,vec0));

4838

tf2 = vec0.GetLength();

4839

tf3 = 1.0;

4840

if (o->m_pRevSDF->m_bCorrectAngle)

4841

{

4842

if ((tf < 0.001) || (tf > Pi-0.001))

4843

tf3 /= 0.001;

4844

else tf3 /= sin(tf);

4845

}

4846

if (o->m_pRevSDF->m_bCorrectRadial)

4847

tf3 /= tf2; // Erste Potenz, da 2D-Grid (SDF hat "nullte Potenz" ^^)

4848

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,cos(tf)*tf2,tf3);

4849

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,cos(tf)*tf2,tf3);

4850

if (o->m_pRevSDF->m_bMirrorY)

4851

{

4852

if (o->m_pRevSDF->m_bMirrorBond)

4853

{

4854

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,tf4-cos(tf)*tf2,tf3);

4855

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,tf4-cos(tf)*tf2,tf3);

4856

} else

4857

{

4858

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,-cos(tf)*tf2,tf3);

4859

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,-cos(tf)*tf2,tf3);

4860

}

4861

}

4862

}

4863

}

4864

}

4865

} // END IF REVSDF

4866

4867

if (g_bCDF && (!g_bDeriv || (g_iSteps > 2)))

4868

{

4869

if (o->m_bSecondShowMol)

4870

{

4871

for (zr=0;zr<g_iCDFChannels;zr++)

4872

switch(g_iObsChannel[zr])

4873

{

4874

case 0: apfa[zr] = o->m_pRDF[zr]->m_faData; break;

4875

case 1: apfa[zr] = o->m_pADF[zr]->m_faData; break;

4876

case 2: apfa[zr] = o->m_pDDF[zr]->m_faData; break;

4877

case 3: apfa[zr] = o->m_pDipDF[zr]->m_faData; break;

4878

case 4: apfa[zr] = o->m_pVDF[zr]->m_faData; break;

4879

}

4880

4881

if (g_iCDFChannels == 2)

4882

{

4883

for (z4=0;z4<o->m_iShowMolCount;z4++)

4884

{

4885

for (z5=0;z5<apfa[0][z4].GetSize();z5++)

4886

{

4887

for (z6=0;z6<o->m_iShowMol2Count;z6++)

4888

{

4889

if (o->m_bExclude1eq2 && (z4 == z6))

4890

continue;

4891

for (z7=0;z7<apfa[1][z6].GetSize();z7++)

4892

{

4893

if (o->m_pCDF->m_bDumpDat)

4894

fprintf(o->m_pCDF->m_fDump,"%d; %d; %d; %d; %10.3f; %10.3f\n",g_iSteps,z2+1,z4+1,z5+1,apfa[0][z4][z5],apfa[1][z6][z7]);

4895

o->m_pCDF->m_p2DF->AddToBin(apfa[0][z4][z5],apfa[1][z6][z7]);

4896

}

4897

}

4898

}

4899

}

4900

}

4901

} else // IF NOT SECOND_OM

4902

{

4903

for (zr=0;zr<g_iCDFChannels;zr++)

4904

switch(g_iObsChannel[zr])

4905

{

4906

case 0:

4907

apfa[zr] = o->m_pRDF[zr]->m_faData;

4908

apba[zr] = o->m_pRDF[zr]->m_baDataEnabled;

4909

break;

4910

case 1:

4911

apfa[zr] = o->m_pADF[zr]->m_faData;

4912

apba[zr] = o->m_pADF[zr]->m_baDataEnabled;

4913

break;

4914

case 2:

4915

apfa[zr] = o->m_pDDF[zr]->m_faData;

4916

apba[zr] = o->m_pDDF[zr]->m_baDataEnabled;

4917

break;

4918

case 3:

4919

apfa[zr] = o->m_pDipDF[zr]->m_faData;

4920

apba[zr] = o->m_pDipDF[zr]->m_baDataEnabled;

4921

break;

4922

case 4:

4923

apfa[zr] = o->m_pVDF[zr]->m_faData;

4924

apba[zr] = o->m_pVDF[zr]->m_baDataEnabled;

4925

break;

4926

}

4927

4928

if (g_iCDFChannels == 2)

4929

{

4930

for (z4=0;z4<o->m_iShowMolCount;z4++)

4931

{

4932

ticomb = 0;

4933

for (z5=0;z5<apfa[0][z4].GetSize();z5++)

4934

{

4935

for (z7=0;z7<apfa[1][z4].GetSize();z7++)

4936

{

4937

if (o->m_pCDF->m_pCombineList[z5*o->m_pCDF->m_iCombinations[1]+z7] == 0)

4938

continue;

4939

if (o->m_bBinOnlyPassedAtoms)

4940

{

4941

if ((apba[0][z4][z5] == 0) || (apba[1][z4][z7] == 0))

4942

goto _nocdfbin;

4943

}

4944

if (o->m_bBinOnlyNotPassedAtoms)

4945

{

4946

if ((apba[0][z4][z5] != 0) && (apba[1][z4][z7] != 0))

4947

goto _nocdfbin;

4948

}

4949

o->m_pCDF->m_p2DF->AddToBin(apfa[0][z4][z5],apfa[1][z4][z7]);

4950

_nocdfbin:;

4951

if (o->m_pCDF->m_bDumpDat)

4952

fprintf(o->m_pCDF->m_fDump,"%d; %d; %d; ; %10.3f; %10.3f\n",g_iSteps,z2+1,z4+1,apfa[0][z4][z5],apfa[1][z4][z7]);

4953

if (o->m_bTimeDev)

4954

{

4955

ti = o->m_waSaveShowList.GetPosition(z4);

4956

if ((ti2 != -1) && (ti != -1))

4957

{

4958

if (o->m_bSaveSeparateFiles)

4959

fprintf(o->m_pCDF->m_fTimeDev[ti2],"; %10.3f; %10.3f",apfa[0][z4][z5],apfa[1][z4][z7]);

4960

else fprintf(o->m_pCDF->m_fTimeDev[0],"; %10.3f; %10.3f",apfa[0][z4][z5],apfa[1][z4][z7]);

4961

if (o->m_pCDF->m_bTDAnimation)

4962

o->m_pCDF->m_pTDAPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pCDF->m_iCombinationsEnabled+ticomb,apfa[0][z4][z5],apfa[1][z4][z7]);

4963

}

4964

ticomb++;

4965

}

4966

}

4967

}

4968

}

4969

if (o->m_bTimeDev && (ti2 != -1))

4970

{

4971

if (o->m_bSaveSeparateFiles)

4972

fprintf(o->m_pCDF->m_fTimeDev[ti2],"\n");

4973

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

4974

fprintf(o->m_pCDF->m_fTimeDev[0],"\n");

4975

}

4976

} // END IF CHANNELS == 2

4977

4978

if (g_iCDFChannels == 3)

4979

{

4980

for (z4=0;z4<o->m_iShowMolCount;z4++)

4981

{

4982

ticomb = 0;

4983

for (z5=0;z5<apfa[0][z4].GetSize();z5++)

4984

{

4985

for (z6=0;z6<apfa[1][z4].GetSize();z6++)

4986

{

4987

for (z7=0;z7<apfa[2][z4].GetSize();z7++)

4988

{

4989

if (o->m_pCDF->m_pCombineList[z5*o->m_pCDF->m_iCombinations[1]*o->m_pCDF->m_iCombinations[2]+z6*o->m_pCDF->m_iCombinations[1]+z7] == 0)

4990

continue;

4991

if (o->m_bBinOnlyPassedAtoms)

4992

{

4993

if ((apba[0][z4][z5] == 0) || (apba[1][z4][z6] == 0) || (apba[2][z4][z7] == 0))

4994

goto _3nocdfbin;

4995

}

4996

if (o->m_bBinOnlyNotPassedAtoms)

4997

{

4998

if ((apba[0][z4][z5] != 0) && (apba[1][z4][z6] != 0) && (apba[2][z4][z7] != 0))

4999

goto _3nocdfbin;

5000

}

5001

o->m_pCDF->m_p3DF->AddToBin(apfa[0][z4][z5],apfa[1][z4][z6],apfa[2][z4][z7]);

5002

5003

o->m_pCDF->m_p3DF->m_p2DF[0]->AddToBin(apfa[0][z4][z5],apfa[1][z4][z6]);

5004

o->m_pCDF->m_p3DF->m_p2DF[1]->AddToBin(apfa[0][z4][z5],apfa[2][z4][z7]);

5005

o->m_pCDF->m_p3DF->m_p2DF[2]->AddToBin(apfa[1][z4][z6],apfa[2][z4][z7]);

5006

_3nocdfbin:;

5007

if (o->m_pCDF->m_bDumpDat)

5008

fprintf(o->m_pCDF->m_fDump,"%d; %d; %d; ; %10.3f; %10.3f; %10.3f\n",g_iSteps,z2+1,z4+1,apfa[0][z4][z5],apfa[1][z4][z6],apfa[2][z4][z7]);

5009

}

5010

}

5011

}

5012

}

5013

} // END IF CHANNELS == 3

5014

} // IF NOT SECOND_OM

5015

} // IF CDF

5016

5017

for (zr=0;zr<g_iCDFChannels;zr++)

5018

{

5019

if (g_bRDF && !(o->m_bObsCertain && o->m_bDecompDist) && (!o->m_bDecompType) && (o->m_pRDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

5020

{

5021

if (o->m_bOthers)

5022

{

5023

if (o->m_bSecondShowMol && (zr == 1))

5024

{

5025

for (z4=0;z4<o->m_iShowMol2Count;z4++)

5026

for (z5=0;z5<o->m_pRDF[zr]->m_faData[z4].GetSize();z5++)

5027

o->m_pRDF[zr]->m_pRDF->AddToBin(o->m_pRDF[zr]->m_faData[z4][z5]);

5028

} else

5029

{

5030

for (z4=0;z4<o->m_iShowMolCount;z4++)

5031

for (z5=0;z5<o->m_pRDF[zr]->m_faData[z4].GetSize();z5++)

5032

{

5033

if (o->m_bBinOnlyPassedAtoms)

5034

if (o->m_pRDF[zr]->m_baDataEnabled[z4][z5] == 0)

5035

continue;

5036

if (o->m_bBinOnlyNotPassedAtoms)

5037

if (o->m_pRDF[zr]->m_baDataEnabled[z4][z5] != 0)

5038

continue;

5039

o->m_pRDF[zr]->m_pRDF->AddToBin(o->m_pRDF[zr]->m_faData[z4][z5]);

5040

}

5041

}

5042

} else

5043

{

5044

for (z5=0;z5<o->m_pRDF[zr]->m_faData[0].GetSize();z5++)

5045

o->m_pRDF[zr]->m_pRDF->AddToBin(o->m_pRDF[zr]->m_faData[0][z5]);

5046

}

5047

if (o->m_bTimeDev && (ti2 != -1))

5048

{

5049

if (o->m_bSaveSeparateFiles)

5050

fprintf(o->m_pRDF[zr]->m_fDist[ti2],"\n");

5051

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

5052

fprintf(o->m_pRDF[zr]->m_fDist[0],"\n");

5053

}

5054

}

5055

5056

if (g_bVDF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pVDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

5057

{

5058

if (o->m_bOthers)

5059

{

5060

if (o->m_bSecondShowMol && (zr == 1))

5061

{

5062

for (z4=0;z4<o->m_iShowMol2Count;z4++)

5063

for (z5=0;z5<o->m_pVDF[zr]->m_faData[z4].GetSize();z5++)

5064

o->m_pVDF[zr]->m_pVDF->AddToBin(o->m_pVDF[zr]->m_faData[z4][z5]);

5065

} else

5066

{

5067

for (z4=0;z4<o->m_iShowMolCount;z4++)

5068

for (z5=0;z5<o->m_pVDF[zr]->m_faData[z4].GetSize();z5++)

5069

{

5070

if (o->m_bBinOnlyPassedAtoms)

5071

if (o->m_pVDF[zr]->m_baDataEnabled[z4][z5] == 0)

5072

continue;

5073

if (o->m_bBinOnlyNotPassedAtoms)

5074

if (o->m_pVDF[zr]->m_baDataEnabled[z4][z5] != 0)

5075

continue;

5076

o->m_pVDF[zr]->m_pVDF->AddToBin(o->m_pVDF[zr]->m_faData[z4][z5]);

5077

}

5078

}

5079

} else

5080

{

5081

for (z5=0;z5<o->m_pVDF[zr]->m_faData[0].GetSize();z5++)

5082

o->m_pVDF[zr]->m_pVDF->AddToBin(o->m_pVDF[zr]->m_faData[0][z5]);

5083

}

5084

if (o->m_bTimeDev && (ti2 != -1))

5085

{

5086

if (o->m_bSaveSeparateFiles)

5087

fprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"\n");

5088

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

5089

fprintf(o->m_pVDF[zr]->m_fSpeed[0],"\n");

5090

}

5091

}

5092

5093

if (g_bDipDF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pDipDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

5094

{

5095

if (o->m_bOthers)

5096

{

5097

if (o->m_bSecondShowMol && (zr == 1))

5098

{

5099

for (z4=0;z4<o->m_iShowMol2Count;z4++)

5100

for (z5=0;z5<o->m_pDipDF[zr]->m_faData[z4].GetSize();z5++)

5101

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin(o->m_pDipDF[zr]->m_faData[z4][z5]);

5102

} else

5103

{

5104

for (z4=0;z4<o->m_iShowMolCount;z4++)

5105

for (z5=0;z5<o->m_pDipDF[zr]->m_faData[z4].GetSize();z5++)

5106

{

5107

if (o->m_bBinOnlyPassedAtoms)

5108

if (o->m_pDipDF[zr]->m_baDataEnabled[z4][z5] == 0)

5109

continue;

5110

if (o->m_bBinOnlyNotPassedAtoms)

5111

if (o->m_pDipDF[zr]->m_baDataEnabled[z4][z5] != 0)

5112

continue;

5113

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin(o->m_pDipDF[zr]->m_faData[z4][z5]);

5114

}

5115

}

5116

} else

5117

{

5118

for (z5=0;z5<o->m_pDipDF[zr]->m_faData[0].GetSize();z5++)

5119

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin(o->m_pDipDF[zr]->m_faData[0][z5]);

5120

}

5121

if (o->m_bTimeDev && (ti2 != -1))

5122

{

5123

if (o->m_bSaveSeparateFiles)

5124

fprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"\n");

5125

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

5126

fprintf(o->m_pDipDF[zr]->m_fDipole[0],"\n");

5127

}

5128

}

5129

5130

if (g_bADF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pADF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

5131

{

5132

if (o->m_bOthers)

5133

{

5134

if (o->m_bSecondShowMol && (zr == 1))

5135

{

5136

for (z4=0;z4<o->m_iShowMol2Count;z4++)

5137

for (z5=0;z5<o->m_pADF[zr]->m_faData[z4].GetSize();z5++)

5138

o->m_pADF[zr]->m_pADF->AddToBin(o->m_pADF[zr]->m_faData[z4][z5]);

5139

} else

5140

{

5141

for (z4=0;z4<o->m_iShowMolCount;z4++)

5142

for (z5=0;z5<o->m_pADF[zr]->m_faData[z4].GetSize();z5++)

5143

{

5144

if (o->m_bBinOnlyPassedAtoms)

5145

if (o->m_pADF[zr]->m_baDataEnabled[z4][z5] == 0)

5146

continue;

5147

if (o->m_bBinOnlyNotPassedAtoms)

5148

if (o->m_pADF[zr]->m_baDataEnabled[z4][z5] != 0)

5149

continue;

5150

o->m_pADF[zr]->m_pADF->AddToBin(o->m_pADF[zr]->m_faData[z4][z5]);

5151

}

5152

}

5153

} else

5154

{

5155

for (z5=0;z5<o->m_pADF[zr]->m_faData[0].GetSize();z5++)

5156

o->m_pADF[zr]->m_pADF->AddToBin(o->m_pADF[zr]->m_faData[0][z5]);

5157

}

5158

if (o->m_bTimeDev && (ti2 != -1))

5159

{

5160

if (o->m_bSaveSeparateFiles)

5161

fprintf(o->m_pADF[zr]->m_fAngle[ti2],"\n");

5162

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

5163

fprintf(o->m_pADF[zr]->m_fAngle[0],"\n");

5164

}

5165

}

5166

5167

if (g_bDDF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pDDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

5168

{

5169

if (o->m_bOthers)

5170

{

5171

if (o->m_bSecondShowMol && (zr == 1))

5172

{

5173

for (z4=0;z4<o->m_iShowMol2Count;z4++)

5174

for (z5=0;z5<o->m_pDDF[zr]->m_faData[z4].GetSize();z5++)

5175

o->m_pDDF[zr]->m_pDDF->AddToBin(o->m_pDDF[zr]->m_faData[z4][z5]);

5176

} else

5177

{

5178

for (z4=0;z4<o->m_iShowMolCount;z4++)

5179

for (z5=0;z5<o->m_pDDF[zr]->m_faData[z4].GetSize();z5++)

5180

{

5181

if (o->m_bBinOnlyPassedAtoms)

5182

if (o->m_pDDF[zr]->m_baDataEnabled[z4][z5] == 0)

5183

continue;

5184

if (o->m_bBinOnlyNotPassedAtoms)

5185

if (o->m_pDDF[zr]->m_baDataEnabled[z4][z5] != 0)

5186

continue;

5187

o->m_pDDF[zr]->m_pDDF->AddToBin(o->m_pDDF[zr]->m_faData[z4][z5]);

5188

}

5189

}

5190

} else

5191

{

5192

for (z5=0;z5<o->m_pDDF[zr]->m_faData[0].GetSize();z5++)

5193

o->m_pDDF[zr]->m_pDDF->AddToBin(o->m_pDDF[zr]->m_faData[0][z5]);

5194

}

5195

if (o->m_bTimeDev && (ti2 != -1))

5196

{

5197

if (o->m_bSaveSeparateFiles)

5198

fprintf(o->m_pDDF[zr]->m_fAngle[ti2],"\n");

5199

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

5200

fprintf(o->m_pDDF[zr]->m_fAngle[0],"\n");

5201

}

5202

}

5203

} // FOR CDFChannels

5204

5205

} // Ende FOR g_oaObserv.GetSize

5206

} // Ende IF [blabla]

5207

5208

if (g_bMiddleAvg) // Referenzmolekuel mitteln

5209

{

5210

cc = 0;

5211

ti2 = (g_iSteps-2)*((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()+z2;

5212

// Jeden Atomtyp des Zielmolekuels durchgehen

5213

for (z3=0;z3<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z3++)

5214

{

5215

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z3];z4++)

5216

{

5217

// Atome vertauschen, aber nicht im allerersten Durchgang hier, und nur wenn mehr als 1 Atom dieser Sorte

5218

if ((g_iSwapAtoms) && (ti2 != 0) && (((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z3]>1))

5219

{

5220

vec4 = g_pRefMol[cc];

5221

vec4 /= (float)ti2; // der bisherige Mittelwert des Referenzmolekuels

5222

tf = VecDist(g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])->m_oaAtomOffset[z3])->GetAt(z4)],vec4); // der Abstand dieses Atoms von seinem Aequivalent im Referenzmolekuel

5223

ti3 = -1;

5224

for (z5=z4+1;z5<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z3];z5++) // Alle folgenden Atome dieser Sorte durchgehen

5225

{

5226

tf2 = VecDist(g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])->m_oaAtomOffset[z3])->GetAt(z5)],vec4);

5227

if (tf2 < tf) // Das andere Atom ist naeher am Platz im Referenzmolekuel als das eigentlich vorgesehene

5228

{

5229

ti3 = z5;

5230

tf = tf2;

5231

}

5232

}

5233

if (ti3 != -1) // Ein Anderes ist naeher dran als unseres: Vertausche diese beiden

5234

{

5235

Swap(g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])->m_oaAtomOffset[z3])->GetAt(z4)],g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])->m_oaAtomOffset[z3])->GetAt(ti3)]);

5236

g_pSwapMatrix[cc*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes+(cc-z4+ti3)] += 1;

5237

g_pSwapMatrix[(cc-z4+ti3)*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes+cc] += 1;

5238

}

5239

} // Ende IF SwapAtoms

5240

g_pRefMol[cc] += g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])->m_oaAtomOffset[z3])->GetAt(z4)];

5241

cc++;

5242

} // Ende FOR Atom des Referenzmolekuels

5243

} // Ende FOR Atomtyp des Referenzmolekuels

5244

} // Ende IF Referenzmolekuel mitteln

5245

} // Ende FOR RefMol (z2)

5246

5247

for (z6=0;z6<g_oaObserv.GetSize();z6++)

5248

{

5249

o = (CObservation*)g_oaObserv[z6];

5250

if (o->m_pConditions != NULL)

5251

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z2++)

5252

if (o->m_pConditions->m_iPassCounter[z2] != 0)

5253

o->m_pConditions->m_iOMPassCounter[z2]++;

5254

}

5255

5256

5257

//_end:;

5258

_endstep:

5259

_norefmol:

5260

if ((g_iMaxStep > 0) && ((int)g_iSteps >= g_iMaxStep))

5261

{

5262

mprintf("\n\nMaximum step count of %d reached, stopping.",g_iMaxStep);

5263

break;

5264

}

5265

} // Ende while

5266

5267

/*************************************************************************

5268

*************** Ende Hauptschleife ***************************************

5269

*************************************************************************/

5270

5271

// fclose(fff);

5272

5273

_endmainloop:

5274

if (g_bUseVelocities)

5275

g_iSteps -= 2;

5276

5277

mprintf(WHITE,"\n\n########## Analysis finished ##########\n");

5278

5279

if (g_iStride != 1)

5280

mprintf("\n%d time steps processed (every %dth from %d).\n\n",g_iSteps/g_iStride,g_iStride,g_iSteps);

5281

else mprintf("\n%d time steps processed.\n\n",g_iSteps);

5282

5283

fclose(g_fPos);

5284

if (g_fVel != NULL)

5285

fclose(g_fVel);

5286

if (g_fForce != NULL)

5287

fclose(g_fForce);

5288

if ((g_bNPT) && (g_sNPTFile[0] != 0))

5289

fclose(g_fNPTFile);

5290

5291

if (g_bVoro)

5292

{

5293

g_pVoroWrapper->Finish();

5294

}

5295

5296

if (g_bVoid)

5297

{

5298

g_pVoroAnalysis->Finish();

5299

}

5300

5301

if (g_bReact)

5302

{

5303

if (!ReactSecondRun)

5304

{

5305

g_pReact->Finish();

5306

g_pReact->DumpMolecules();

5307

g_pReact->CreateOutput();

5308

}

5309

if (g_pReact->m_oaReactTrajectories.GetSize() != 0)

5310

{

5311

if (!ReactSecondRun)

5312

{

5313

mprintf(WHITE,"Starting second pass for Reaction Analysis...\n\n");

5314

ReactSecondRun = true;

5315

goto _beginmain;

5316

} else

5317

{

5318

mprintf(WHITE,"Second pass for Reaction Analysis finished.\n\n");

5319

}

5320

}

5321

}

5322

g_bAbortAnalysis = true;

5323

5324

if (g_bSaveCondSnapshot)

5325

{

5326

fclose(g_fSaveCondFile);

5327

mprintf("%d condition snapshots saved as savecondition.xyz\n\n",g_iSaveCondCount);

5328

}

5329

5330

if (g_bMicroHet)

5331

{

5332

mprintf(WHITE,"*** Microheterogeneity Analysis\n\n");

5333

for (z=0;z<g_pMicroHet->m_oaObservations.GetSize();z++)

5334

{

5335

mho = (CMicroHetObservation*)g_pMicroHet->m_oaObservations[z];

5336

mprintf(WHITE," * Observation %d: %s\n",z+1,mho->m_sName);

5337

5338

mprintf(" Creating Microheterogeneity plot...\n");

5339

sprintf(buf,"microhet_df_obs%d%s",z+1,multibuf);

5340

mho->BuildSlices(buf);

5341

5342

mprintf(" Creating entry plot...\n");

5343

sprintf(buf,"microhet_entry_obs%d%s",z+1,multibuf);

5344

mho->BuildZeroPlot(buf,true);

5345

5346

if (mho->m_bCDF)

5347

{

5348

mprintf(" Creating CDF...\n");

5349

mho->BuildCDF();

5350

5351

sprintf(buf,"microhet_cdf_obs%d%s.csv",z+1,multibuf);

5352

mprintf(" Saving CDF as %s ...\n",buf);

5353

mho->m_pCDF->Write("",buf,"");

5354

sprintf(buf,"microhet_cdf_obs%d%s.nb",z+1,multibuf);

5355

mprintf(" Saving CDF Mathematica notebook as %s ...\n",buf);

5356

mho->m_pCDF->WriteMathematicaNb("",buf,"",false);

5357

5358

5359

}

5360

}

5361

mprintf("\n");

5362

}

5363

5364

if (g_bClusterAnalysis)

5365

{

5366

mprintf(WHITE,"*** Cluster Analysis\n\n");

5367

5368

g_pClusterAnalysis->BuildClusterDistribution();

5369

5370

mprintf(WHITE," * Cluster Distance Distribution\n");

5371

// mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",g_pClusterAnalysis->m_pClusterDistanceDF->m_fBinEntries,g_pClusterAnalysis->m_pClusterDistanceDF->m_fSkipEntries,ZeroDivide(g_pClusterAnalysis->m_pClusterDistanceDF->m_fSkipEntries,g_pClusterAnalysis->m_pClusterDistanceDF->m_fBinEntries+g_pClusterAnalysis->m_pClusterDistanceDF->m_fSkipEntries)*100.0);

5372

// g_pClusterAnalysis->m_pClusterDistanceDF->CalcMeanSD();

5373

g_pClusterAnalysis->m_pClusterDistanceDF->MultiplyBin(100.0/g_pClusterAnalysis->m_iCounter);

5374

// mprintf(" Mean value: %.10G pm Standard deviation: %.10G pm\n",g_pClusterAnalysis->m_pClusterDistanceDF->m_fMean,g_pClusterAnalysis->m_pClusterDistanceDF->m_fSD);

5375

// mprintf(" Min. value: %.10G pm Max. value: %.10G pm\n",g_pClusterAnalysis->m_pClusterDistanceDF->m_fMinInput,g_pClusterAnalysis->m_pClusterDistanceDF->m_fMaxInput);

5376

sprintf(buf,"cluster_distance_df%s.csv",multibuf);

5377

mprintf(" Saving Cluster Distance distribution as %s ...\n",buf);

5378

g_pClusterAnalysis->m_pClusterDistanceDF->Write("",buf,"",false);

5379

sprintf(buf,"cluster_distance_df%s.agr",multibuf);

5380

mprintf(" Saving Cluster Distance distribution AGR file as \"%s\"...\n",buf);

5381

g_pClusterAnalysis->m_pClusterDistanceDF->WriteAgr("",buf,"","Cluster Distance distribution",false);

5382

5383

mprintf(WHITE,"\n * Cluster Significance Distribution\n");

5384

sprintf(buf,"cluster_significance_df%s.csv",multibuf);

5385

mprintf(" Saving Cluster Significance distribution as %s ...\n",buf);

5386

g_pClusterAnalysis->m_pClusterDistributionDF->WriteMulti("",buf,"");

5387

sprintf(buf,"cluster_significance_df%s.agr",multibuf);

5388

mprintf(" Saving Cluster Significance distribution AGR file as \"%s\"...\n",buf);

5389

g_pClusterAnalysis->m_pClusterDistributionDF->WriteMultiAgr("",buf,"","Cluster Significance distribution",false);

5390

5391

/* sprintf(buf,"cluster_sizeX_df%s.csv",multibuf);

5392

mprintf(" Saving Cluster size X distribution as %s ...\n",buf);

5393

g_pClusterAnalysis->m_pClusterDistribution2DF->WriteMulti("",buf,"");

5394

sprintf(buf,"cluster_sizeX_df%s.agr",multibuf);

5395

mprintf(" Saving Cluster size X distribution AGR file as \"%s\"...\n",buf);

5396

g_pClusterAnalysis->m_pClusterDistribution2DF->WriteMultiAgr("",buf,"","Cluster size X distribution",false);*/

5397

5398

mprintf(WHITE,"\n * Cluster Size Distribution\n");

5399

sprintf(buf,"cluster_size_df%s.csv",multibuf);

5400

mprintf(" Saving Cluster Size distribution as %s ...\n",buf);

5401

g_pClusterAnalysis->m_pClusterSizeDF->WriteMulti("",buf,"");

5402

sprintf(buf,"cluster_size_df%s.agr",multibuf);

5403

mprintf(" Saving Cluster Size distribution AGR file as \"%s\"...\n",buf);

5404

g_pClusterAnalysis->m_pClusterSizeDF->WriteMultiAgr("",buf,"","Cluster Size distribution",false);

5405

5406

mprintf(WHITE,"\n * Cluster Count Distribution\n");

5407

// mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",g_pClusterAnalysis->m_pClusterCountDF->m_fBinEntries,g_pClusterAnalysis->m_pClusterCountDF->m_fSkipEntries,ZeroDivide(g_pClusterAnalysis->m_pClusterCountDF->m_fSkipEntries,g_pClusterAnalysis->m_pClusterCountDF->m_fBinEntries+g_pClusterAnalysis->m_pClusterCountDF->m_fSkipEntries)*100.0);

5408

// g_pClusterAnalysis->m_pClusterCountDF->CalcMeanSD();

5409

g_pClusterAnalysis->m_pClusterCountDF->MultiplyBin(1.0/g_pClusterAnalysis->m_iCounter);

5410

// mprintf(" Mean value: %.10G pm Standard deviation: %.10G pm\n",g_pClusterAnalysis->m_pClusterCountDF->m_fMean,g_pClusterAnalysis->m_pClusterCountDF->m_fSD);

5411

// mprintf(" Min. value: %.10G pm Max. value: %.10G pm\n",g_pClusterAnalysis->m_pClusterCountDF->m_fMinInput,g_pClusterAnalysis->m_pClusterCountDF->m_fMaxInput);

5412

sprintf(buf,"cluster_count_df%s.csv",multibuf);

5413

mprintf(" Saving Cluster Count distribution as %s ...\n",buf);

5414

g_pClusterAnalysis->m_pClusterCountDF->Write("",buf,"",false);

5415

sprintf(buf,"cluster_count_df%s.agr",multibuf);

5416

mprintf(" Saving Cluster Count distribution AGR file as \"%s\"...\n",buf);

5417

g_pClusterAnalysis->m_pClusterCountDF->WriteAgr("",buf,"","Cluster Count distribution",false);

5418

5419

mprintf(WHITE,"\n * Polymer Distribution\n");

5420

// mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",g_pClusterAnalysis->m_pPolymerDF->m_fBinEntries,g_pClusterAnalysis->m_pPolymerDF->m_fSkipEntries,ZeroDivide(g_pClusterAnalysis->m_pPolymerDF->m_fSkipEntries,g_pClusterAnalysis->m_pPolymerDF->m_fBinEntries+g_pClusterAnalysis->m_pPolymerDF->m_fSkipEntries)*100.0);

5421

// g_pClusterAnalysis->m_pPolymerDF->CalcMeanSD();

5422

g_pClusterAnalysis->m_pPolymerDF->MultiplyBin(1.0/g_pClusterAnalysis->m_iCounter);

5423

// mprintf(" Mean value: %.10G pm Standard deviation: %.10G pm\n",g_pClusterAnalysis->m_pPolymerDF->m_fMean,g_pClusterAnalysis->m_pPolymerDF->m_fSD);

5424

// mprintf(" Min. value: %.10G pm Max. value: %.10G pm\n",g_pClusterAnalysis->m_pPolymerDF->m_fMinInput,g_pClusterAnalysis->m_pPolymerDF->m_fMaxInput);

5425

sprintf(buf,"cluster_polymer_df%s.csv",multibuf);

5426

mprintf(" Saving Polymer distribution as %s ...\n",buf);

5427

g_pClusterAnalysis->m_pPolymerDF->WriteMulti("",buf,"");

5428

sprintf(buf,"cluster_polymer_df_cumulative%s.csv",multibuf);

5429

mprintf(" Saving cumulative Polymer distribution as %s ...\n",buf);

5430

g_pClusterAnalysis->m_pPolymerDF->WriteMulti_Cumulative("",buf,"");

5431

sprintf(buf,"cluster_polymer_df%s.agr",multibuf);

5432

mprintf(" Saving Polymer distribution AGR file as \"%s\"...\n",buf);

5433

g_pClusterAnalysis->m_pPolymerDF->WriteMultiAgr("",buf,"","Polymer distribution",false);

5434

sprintf(buf,"cluster_polymer_df_cumulative%s.agr",multibuf);

5435

mprintf(" Saving cumulative Polymer distribution AGR file as \"%s\"...\n",buf);

5436

g_pClusterAnalysis->m_pPolymerDF->WriteMultiAgr_Cumulative("",buf,"","Cumulative Polymer distribution",false);

5437

5438

if (g_pClusterAnalysis->m_bAnim)

5439

{

5440

mprintf("\n");

5441

a = OpenFileWrite("gracebatch",true);

5442

fprintf(a,"PRINT TO \"output.png\"\n");

5443

fprintf(a,"HARDCOPY DEVICE \"PNG\"\n");

5444

fprintf(a,"PAGE SIZE %d, %d\n",g_pClusterAnalysis->m_iResX,g_pClusterAnalysis->m_iResY);

5445

fprintf(a,"DEVICE \"PNG\" FONT ANTIALIASING on\n");

5446

fprintf(a,"DEVICE \"PNG\" OP \"compression:9\"\n");

5447

fprintf(a,"PRINT\n");

5448

fclose(a);

5449

mprintf(" Saved batch script as \"render_cluster_anim\".\n");

5450

fclose(g_pClusterAnalysis->m_fAnim);

5451

}

5452

mprintf("\n");

5453

}

5454

5455

if (g_bBondACF)

5456

{

5457

mprintf(WHITE,"*** Bond autocorrelation function\n");

5458

if (g_bBondACFDebug)

5459

{

5460

mprintf(" Writing \"bondacf.agr\"...\n");

5461

5462

try { gc = new CGrace(); } catch(...) { gc = NULL; }

5463

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

5464

5465

gc->SetRangeX(0,g_iSteps*g_fTimestepLength/1000.0);

5466

gc->SetRangeY(0,250);

5467

gc->MakeTicks();

5468

gc->SetLabelX("Time [ps]");

5469

gc->SetLabelY("Bond length [pm]");

5470

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

5471

{

5472

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

5473

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

5474

{

5475

bond = (CMolBond*)sm->m_oaBonds[z3];

5476

gc->AddDataset();

5477

for (z4=0;z4<bond->m_faData.GetSize();z4++)

5478

gc->AddXYTupel(z4*g_fTimestepLength/1000.0,bond->m_faData[z4]);

5479

}

5480

}

5481

gc->WriteAgr("bondacf.agr",false);

5482

delete gc;

5483

}

5484

mprintf(" Differentiating bond length developments...\n");

5485

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

5486

{

5487

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

5488

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

5489

{

5490

bond = (CMolBond*)sm->m_oaBonds[z3];

5491

for (z4=0;z4<bond->m_faData.GetSize()-1;z4++)

5492

bond->m_faData[z4] = bond->m_faData[z4+1] - bond->m_faData[z4];

5493

}

5494

}

5495

if (g_bBondACFDebug)

5496

{

5497

mprintf(" Writing \"bondacf_diff.agr\"...\n");

5498

5499

try { gc = new CGrace(); } catch(...) { gc = NULL; }

5500

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

5501

5502

gc->SetRangeX(0,g_iSteps*g_fTimestepLength/1000.0);

5503

gc->SetRangeY(-15,15);

5504

gc->MakeTicks();

5505

gc->SetLabelX("Time [ps]");

5506

gc->SetLabelY("Bond length change rate");

5507

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

5508

{

5509

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

5510

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

5511

{

5512

bond = (CMolBond*)sm->m_oaBonds[z3];

5513

gc->AddDataset();

5514

for (z4=0;z4<bond->m_faData.GetSize();z4++)

5515

gc->AddXYTupel(z4*g_fTimestepLength/1000.0,bond->m_faData[z4]);

5516

}

5517

}

5518

gc->WriteAgr("bondacf_diff.agr",false);

5519

delete gc;

5520

}

5521

mprintf(" Autocorrelating bond length developments...\n");

5522

mprintf(WHITE," [");

5523

tfs = 0;

5524

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

5525

{

5526

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

5527

tfs += sm->m_oaBonds.GetSize();

5528

}

5529

tfs /= 60.0;

5530

ti2 = 0;

5531

/* fft = new CFFT();

5532

fft->PrepareFFT_C2C(g_iSteps*2);

5533

fft2 = new CFFT();

5534

fft2->PrepareInverseFFT_C2C(g_iSteps*2);*/

5535

5536

try { ac = new CAutoCorrelation(); } catch(...) { ac = NULL; }

5537

if (ac == NULL) NewException((double)sizeof(CAutoCorrelation),__FILE__,__LINE__,__PRETTY_FUNCTION__);

5538

5539

ac->Init(g_iSteps,g_iBondACFDepth,g_bACFFFT);

5540

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

5541

{

5542

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

5543

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

5544

{

5545

if (fmod(ti2,tfs) < 1.0)

5546

mprintf(WHITE,"#");

5547

bond = (CMolBond*)sm->m_oaBonds[z3];

5548

ac->AutoCorrelate(&bond->m_faData,&tempfa);

5549

bond->m_faData.CopyFrom(&tempfa);

5550

ti2++;

5551

}

5552

}

5553

delete ac;

5554

mprintf(WHITE,"]\n");

5555

if (g_bBondACFDebug)

5556

{

5557

mprintf(" Writing \"bondacf_autocorr.agr\"...\n");

5558

5559

try { gc = new CGrace(); } catch(...) { gc = NULL; }

5560

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

5561

5562

gc->SetRangeX(0,g_iBondACFDepth*g_fTimestepLength/1000.0);

5563

gc->SetRangeY(-25,25);

5564

gc->MakeTicks();

5565

gc->SetLabelX("Time [ps]");

5566

gc->SetLabelY("ACF(Bond length change rate)");

5567

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

5568

{

5569

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

5570

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

5571

{

5572

bond = (CMolBond*)sm->m_oaBonds[z3];

5573

gc->AddDataset();

5574

for (z4=0;z4<g_iBondACFDepth;z4++)

5575

gc->AddXYTupel(z4*g_fTimestepLength/1000.0,bond->m_faData[z4]);

5576

}

5577

}

5578

gc->WriteAgr("bondacf_autocorr.agr",false);

5579

delete gc;

5580

}

5581

mprintf(" Merging equivalent Bonds...\n");

5582

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

5583

{

5584

m = (CMolecule*)g_oaMolecules[z0];

5585

sm2 = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

5586

for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)

5587

{

5588

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];

5589

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

5590

{

5591

bg = (CMolBondGroup*)sm->m_oaBondGroups[z3];

5592

for (z4=1;z4<bg->m_oaBonds.GetSize();z4++)

5593

{

5594

bond = (CMolBond*)bg->m_oaBonds[z4];

5595

for (z5=0;z5<g_iBondACFDepth;z5++)

5596

((CMolBond*)((CMolBondGroup*)sm2->m_oaBondGroups[z3])->m_oaBonds[0])->m_faData[z5] += bond->m_faData[z5];

5597

}

5598

}

5599

}

5600

}

5601

if (g_bBondACFSymmetrize)

5602

{

5603

mprintf(" Symmetrizing bond ACFs...\n");

5604

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

5605

{

5606

m = (CMolecule*)g_oaMolecules[z0];

5607

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

5608

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

5609

{

5610

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

5611

bond->m_faData.SetSize(2*g_iBondACFDepth);

5612

for (z4=0;z4<g_iBondACFDepth;z4++)

5613

bond->m_faData[z4+g_iBondACFDepth] = bond->m_faData[z4];

5614

for (z4=0;z4<g_iBondACFDepth;z4++)

5615

bond->m_faData[z4] = bond->m_faData[2*g_iBondACFDepth-z4-1];

5616

}

5617

}

5618

g_iBondACFDepth *= 2;

5619

}

5620

if (g_bBondACFWindow)

5621

{

5622

mprintf(" Applying Window Function...\n");

5623

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

5624

{

5625

m = (CMolecule*)g_oaMolecules[z0];

5626

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

5627

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

5628

{

5629

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

5630

for (z4=0;z4<g_iBondACFDepth;z4++)

5631

bond->m_faData[z4] *= (float)pow(sin(z4*Pi/(bond->m_faData.GetSize()-1)),2);

5632

}

5633

}

5634

}

5635

if (g_bBondACFNormalize)

5636

{

5637

mprintf(" Normalizing bond ACFs...\n");

5638

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

5639

{

5640

m = (CMolecule*)g_oaMolecules[z0];

5641

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

5642

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

5643

{

5644

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

5645

tf = 0;

5646

for (z4=0;z4<g_iBondACFDepth;z4++)

5647

if (tf < bond->m_faData[z4])

5648

tf = bond->m_faData[z4];

5649

for (z4=0;z4<g_iBondACFDepth;z4++)

5650

bond->m_faData[z4] /= (float)tf;

5651

}

5652

}

5653

}

5654

mprintf(" Writing \"bondacf_ac_merged.agr\"...\n");

5655

5656

try { gc = new CGrace(); } catch(...) { gc = NULL; }

5657

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

5658

5659

gc->SetRangeX(0,g_iBondACFDepth*g_fTimestepLength/1000.0);

5660

gc->SetRangeY(-200,200);

5661

gc->MakeTicks();

5662

gc->SetLabelX("Time [ps]");

5663

gc->SetLabelY("Sum ACF(Bond length change rate)");

5664

gc->CurrentGraph()->m_bLegend = true;

5665

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

5666

{

5667

m = (CMolecule*)g_oaMolecules[z0];

5668

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

5669

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

5670

{

5671

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

5672

gc->AddDataset();

5673

sprintf(buf,"%s %s%d - %s%d",m->m_sName,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[bond->m_iAtomType[0]]])->m_sName,bond->m_iAtom[0]+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[bond->m_iAtomType[1]]])->m_sName,bond->m_iAtom[1]+1);

5674

gc->SetDatasetName(buf);

5675

((CGraceDataset*)gc->CurrentGraph()->m_oaDatasets[gc->CurrentGraph()->m_oaDatasets.GetSize()-1])->m_faValues.SetMaxSize(g_iBondACFDepth*2);

5676

for (z4=0;z4<g_iBondACFDepth;z4++)

5677

gc->AddXYTupel(z4*g_fTimestepLength/1000.0,bond->m_faData[z4]);

5678

}

5679

}

5680

gc->WriteAgr("bondacf_ac_merged.agr",false);

5681

delete gc;

5682

mprintf(" Applying Fourier Transformation...\n");

5683

5684

try { fft = new CFFT(); } catch(...) { fft = NULL; }

5685

if (fft == NULL) NewException((double)sizeof(CFFT),__FILE__,__LINE__,__PRETTY_FUNCTION__);

5686

5687

fft->PrepareFFT_C2C(g_iBondACFDepth);

5688

tf3 = 0;

5689

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

5690

{

5691

m = (CMolecule*)g_oaMolecules[z0];

5692

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

5693

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

5694

{

5695

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

5696

for (z4=0;z4<g_iBondACFDepth;z4++)

5697

{

5698

fft->m_pInput[z4*2] = bond->m_faData[z4];

5699

fft->m_pInput[z4*2+1] = 0;

5700

}

5701

fft->DoFFT();

5702

for (z4=0;z4<g_iBondACFDepth/2;z4++)

5703

{

5704

bond->m_faData[z4] = (float)(pow(fft->m_pOutput[z4*2],2) + pow(fft->m_pOutput[z4*2+1],2)) / g_iBondACFDepth;

5705

if (bond->m_faData[z4] > tf3)

5706

tf3 = bond->m_faData[z4];

5707

}

5708

}

5709

}

5710

delete fft;

5711

mprintf(" Writing \"bond_spectrum.agr\"...\n");

5712

5713

try { gc = new CGrace(); } catch(...) { gc = NULL; }

5714

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

5715

5716

gc->SetRangeX(0,4000.0);

5717

gc->SetRangeY(0,tf3*1.1);

5718

gc->MakeTicks();

5719

gc->SetLabelX("Wave number [1/cm]");

5720

gc->SetLabelY("Intensity");

5721

gc->CurrentGraph()->m_bInvertXAxis = true;

5722

gc->CurrentGraph()->m_bLegend = true;

5723

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

5724

{

5725

m = (CMolecule*)g_oaMolecules[z0];

5726

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

5727

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

5728

{

5729

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

5730

gc->AddDataset();

5731

sprintf(buf,"%s %s%d - %s%d",m->m_sName,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[bond->m_iAtomType[0]]])->m_sName,bond->m_iAtom[0]+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[bond->m_iAtomType[1]]])->m_sName,bond->m_iAtom[1]+1);

5732

gc->SetDatasetName(buf);

5733

((CGraceDataset*)gc->CurrentGraph()->m_oaDatasets[gc->CurrentGraph()->m_oaDatasets.GetSize()-1])->m_faValues.SetMaxSize(g_iBondACFDepth*2);

5734

for (z4=0;z4<g_iBondACFDepth/2;z4++)

5735

gc->AddXYTupel(z4*2.0/g_iBondACFDepth*1E7f/299.792f/2.0f/g_fTimestepLength/g_iStride,bond->m_faData[z4]);

5736

}

5737

}

5738

gc->WriteAgr("bond_spectrum.agr",false);

5739

delete gc;

5740

for (z5=1;z5<5;z5++)

5741

{

5742

mprintf(" Smoothing spectrum, degree %d...\n",z5);

5743

mprintf(" Writing \"bond_spectrum_s%d.agr\"...\n",z5);

5744

5745

try { gc = new CGrace(); } catch(...) { gc = NULL; }

5746

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

5747

5748

gc->SetRangeX(0,4000.0);

5749

gc->SetRangeY(0,tf3*1.1);

5750

gc->MakeTicks();

5751

gc->SetLabelX("Wave number [1/cm]");

5752

gc->SetLabelY("Intensity");

5753

gc->CurrentGraph()->m_bInvertXAxis = true;

5754

gc->CurrentGraph()->m_bLegend = true;

5755

5756

try { gc2 = new CGrace(); } catch(...) { gc2 = NULL; }

5757

if (gc2 == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

5758

5759

gc2->SetRangeX(0,4000.0);

5760

gc2->SetRangeY(0,tf3*1.1);

5761

gc2->MakeTicks();

5762

gc2->SetLabelX("Wave number [1/cm]");

5763

gc2->SetLabelY("Intensity");

5764

gc2->CurrentGraph()->m_bInvertXAxis = true;

5765

gc2->CurrentGraph()->m_bLegend = true;

5766

5767

tempfa.SetSize(g_iBondACFDepth/2);

5768

tempfa2.SetSize(g_iBondACFDepth/2);

5769

5770

for (z4=0;z4<g_iBondACFDepth/2;z4++)

5771

tempfa2[z4] = 0;

5772

5773

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

5774

{

5775

m = (CMolecule*)g_oaMolecules[z0];

5776

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

5777

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

5778

{

5779

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

5780

5781

for (z4=0;z4<g_iBondACFDepth/2;z4++)

5782

{

5783

tf = 0;

5784

tf2 = 0;

5785

for (z6=-z5;z6<=z5;z6++)

5786

{

5787

if ((z4+z6 < 0) || (z4+z6 >= g_iBondACFDepth/2))

5788

continue;

5789

tf += bond->m_faData[z4+z6] / (pow((double)z6,2)+1.0);

5790

tf2 += 1.0 / (pow((double)z6,2)+1.0);

5791

}

5792

tempfa[z4] = (float)(tf / tf2);

5793

tempfa2[z4] += tempfa[z4];

5794

}

5795

5796

gc->AddDataset();

5797

gc2->AddDataset();

5798

sprintf(buf,"%s %s%d - %s%d",m->m_sName,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[bond->m_iAtomType[0]]])->m_sName,bond->m_iAtom[0]+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[bond->m_iAtomType[1]]])->m_sName,bond->m_iAtom[1]+1);

5799

gc->SetDatasetName(buf);

5800

gc2->SetDatasetName(buf);

5801

((CGraceDataset*)gc->CurrentGraph()->m_oaDatasets[gc->CurrentGraph()->m_oaDatasets.GetSize()-1])->m_faValues.SetMaxSize(g_iBondACFDepth);

5802

((CGraceDataset*)gc2->CurrentGraph()->m_oaDatasets[gc2->CurrentGraph()->m_oaDatasets.GetSize()-1])->m_faValues.SetMaxSize(g_iBondACFDepth);

5803

5804

for (z4=0;z4<g_iBondACFDepth/2;z4++)

5805

gc->AddXYTupel(z4*2.0/g_iBondACFDepth*1E7f/299.792f/2.0f/g_fTimestepLength/g_iStride,tempfa[z4]);

5806

5807

for (z4=0;z4<g_iBondACFDepth/2;z4++)

5808

gc2->AddXYTupel(z4*2.0/g_iBondACFDepth*1E7f/299.792f/2.0f/g_fTimestepLength/g_iStride,tempfa2[z4]);

5809

}

5810

}

5811

5812

sprintf(buf,"bond_spectrum_s%d.agr",z5);

5813

gc->WriteAgr(buf,false);

5814

delete gc;

5815

5816

mprintf(" Writing \"bond_spectrum_cumulative_s%d.agr\"...\n",z5);

5817

sprintf(buf,"bond_spectrum_cumulative_s%d.agr",z5);

5818

gc2->WriteAgr(buf,false);

5819

delete gc2;

5820

}

5821

}

5822

5823

if (g_bSaveRefEnv)

5824

{

5825

fclose(g_fRefEnv);

5826

mprintf("\nTrajectory of reference molecule was saved as %s.\n",g_sRefEnv);

5827

if (g_bTDO)

5828

{

5829

#ifdef TARGET_WINDOWS

5830

sprintf(buf,"tdo_pymol_%s_%d%s.bat",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,multibuf);

5831

#else

5832

sprintf(buf,"tdo_pymol_%s_%d%s.sh",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,multibuf);

5833

#endif

5834

mprintf("Saving TDO PyMol script as %s.\n",buf);

5835

tfi = OpenFileWrite(buf,true);

5836

#ifdef TARGET_WINDOWS

5837

fprintf(tfi,"pymolwin ");

5838

#else

5839

fprintf(tfi,"pymol ");

5840

#endif

5841

for (z=0;z<g_laTDOSteps.GetSize();z++)

5842

fprintf(tfi,"tdo_%s_%d_%06d%s.xyz ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_laTDOSteps[z],multibuf);

5843

fprintf(tfi,"-d \"set sphere_scale,0.25\" ");

5844

fprintf(tfi,"-d \"set stick_radius,0.17\" ");

5845

fprintf(tfi,"-d \"set ray_trace_mode,1\" ");

5846

fprintf(tfi,"-d \"set fog,0\" ");

5847

fprintf(tfi,"-d \"set ray_trace_fog,0\" ");

5848

fprintf(tfi,"-d \"set bg_rgb,(1,1,1)\" ");

5849

fprintf(tfi,"-d \"set ray_shadow,0\" ");

5850

fprintf(tfi,"-d \"set ray_shadows,0\" ");

5851

fprintf(tfi,"-d \"set ray_interior_shadows,0\" ");

5852

fprintf(tfi,"-d \"show sticks; show spheres\" ");

5853

5854

for (z=0;z<g_laTDOSteps.GetSize();z++)

5855

{

5856

for (z2=0;z2<g_oaAtoms.GetSize();z2++)

5857

{

5858

if ((z2 == g_iVirtAtomType) && (!g_bSaveVirtAtoms))

5859

continue;

5860

fprintf(tfi,"-d \"set_color mol_%s_%d, [%d,%d,%d]\" ",((CAtom*)g_oaAtoms[z2])->m_sName,z+1,((CAtom*)g_oaAtoms[z2])->m_pElement->ColorR((float)z/(g_laTDOSteps.GetSize()-1)*g_fTDOBleaching),((CAtom*)g_oaAtoms[z2])->m_pElement->ColorG((float)z/(g_laTDOSteps.GetSize()-1)*g_fTDOBleaching),((CAtom*)g_oaAtoms[z2])->m_pElement->ColorB((float)z/(g_laTDOSteps.GetSize()-1)*g_fTDOBleaching));

5861

}

5862

}

5863

for (z=0;z<g_laTDOSteps.GetSize();z++)

5864

{

5865

for (z2=0;z2<g_oaAtoms.GetSize();z2++)

5866

{

5867

if ((z2 == g_iVirtAtomType) && (!g_bSaveVirtAtoms))

5868

continue;

5869

fprintf(tfi,"-d \"color mol_%s_%d, tdo_%s_%d_%06d and name %s\" ",((CAtom*)g_oaAtoms[z2])->m_sName,z+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_laTDOSteps[z],((CAtom*)g_oaAtoms[z2])->m_sName);

5870

}

5871

}

5872

fprintf(tfi,"\n");

5873

fclose(tfi);

5874

#ifdef TARGET_LINUX

5875

sprintf(buf,"chmod 755 tdo_pymol_%s_%d%s.sh",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,multibuf);

5876

mprintf("Executing \"%s\"...\n",buf);

5877

system(buf);

5878

#endif

5879

}

5880

}

5881

if (g_bCutCluster)

5882

{

5883

fclose(g_fRefEnv);

5884

mprintf("\nCluster trajectory was saved as %s.\n",g_sRefEnv);

5885

}

5886

5887

if (g_bSaveJustTraj)

5888

{

5889

fclose(g_fSaveJustTraj);

5890

/* strcpy(buf,g_sInputTraj);

5891

p = strrchr(buf,'.');

5892

*p = 0;

5893

strcat(buf,multibuf);

5894

strcat(buf,".out.xyz");*/

5895

// mprintf("\nProcessed output trajectory was saved as traj_out.xyz\n",buf);

5896

}

5897

5898

if (g_bVACF && g_bGlobalVACF)

5899

{

5900

mprintf(WHITE,"\n*** Global velocity autocorrelation function\n");

5901

if (g_pGlobalVACF->m_bDerivative)

5902

{

5903

mprintf(" Deriving velocities...\n");

5904

mprintf(WHITE," [");

5905

tfs = g_iGesAtomCount/60.0;

5906

for (z2=0;z2<g_iGesAtomCount;z2++)

5907

{

5908

if (fmod(z2,tfs) < 1)

5909

mprintf(WHITE,"#");

5910

ptfa = (CxFloatArray*)g_pGlobalVACF->m_oaCache[z2];

5911

5912

for (z3=0;z3<(int)g_iSteps*3-3;z3++)

5913

(*ptfa)[z3] = (*ptfa)[z3+3] - (*ptfa)[z3];

5914

}

5915

mprintf(WHITE,"]\n");

5916

}

5917

if (g_bVACFCacheMode)

5918

{

5919

tfs = g_iGesAtomCount/60.0;

5920

/* if (g_bACFFFT)

5921

{*/

5922

mprintf(" Autocorrelating cached vectors...\n");

5923

mprintf(WHITE," [");

5924

/* fft = new CFFT();

5925

fft->PrepareFFT_C2C(2*g_iSteps);

5926

fft2 = new CFFT();

5927

fft2->PrepareInverseFFT_C2C(2*g_iSteps);*/

5928

5929

try { ptfa2 = new CxFloatArray(); } catch(...) { ptfa2 = NULL; }

5930

if (ptfa2 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

5931

5932

ptfa2->SetSize(g_iSteps);

5933

5934

try { ptfa3 = new CxFloatArray(); } catch(...) { ptfa3 = NULL; }

5935

if (ptfa3 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

5936

5937

ptfa3->SetSize(g_iSteps);

5938

5939

try { ac = new CAutoCorrelation(); } catch(...) { ac = NULL; }

5940

if (ac == NULL) NewException((double)sizeof(CAutoCorrelation),__FILE__,__LINE__,__PRETTY_FUNCTION__);

5941

5942

ac->Init(g_iSteps,g_pGlobalVACF->m_iSize,g_bACFFFT);

5943

for (z2=0;z2<g_iGesAtomCount;z2++)

5944

{

5945

if (fmod(z2,tfs) < 1.0)

5946

mprintf(WHITE,"#");

5947

ptfa = (CxFloatArray*)g_pGlobalVACF->m_oaCache[z2];

5948

5949

if (g_pGlobalVACF->m_bMassWeight)

5950

tf = ((CAtom*)g_oaAtoms[g_waAtomRealElement[z2]])->m_pElement->m_fMass;

5951

else tf = 1.0f;

5952

5953

/* X */

5954

for (z3=0;z3<(int)g_iSteps;z3++)

5955

(*ptfa2)[z3] = (*ptfa)[z3*3];

5956

ac->AutoCorrelate(ptfa2,ptfa3);

5957

// mprintf("Global Atom %d X: %f + %f = %f.\n",z2+1,g_pGlobalVACF->m_pData[0],(*ptfa3)[0]*tf,g_pGlobalVACF->m_pData[0]+(*ptfa3)[0]*tf);

5958

for (z3=0;z3<(int)g_pGlobalVACF->m_iSize;z3++)

5959

g_pGlobalVACF->m_pData[z3] += (*ptfa3)[z3] * tf;

5960

5961

/* Y */

5962

for (z3=0;z3<(int)g_iSteps;z3++)

5963

(*ptfa2)[z3] = (*ptfa)[z3*3+1];

5964

ac->AutoCorrelate(ptfa2,ptfa3);

5965

// mprintf("Global Atom %d Y: %f + %f = %f.\n",z2+1,g_pGlobalVACF->m_pData[0],(*ptfa3)[0]*tf,g_pGlobalVACF->m_pData[0]+(*ptfa3)[0]*tf);

5966

for (z3=0;z3<(int)g_pGlobalVACF->m_iSize;z3++)

5967

g_pGlobalVACF->m_pData[z3] += (*ptfa3)[z3] * tf;

5968

5969

/* Z */

5970

for (z3=0;z3<(int)g_iSteps;z3++)

5971

(*ptfa2)[z3] = (*ptfa)[z3*3+2];

5972

ac->AutoCorrelate(ptfa2,ptfa3);

5973

// mprintf("Global Atom %d Z: %f + %f = %f.\n",z2+1,g_pGlobalVACF->m_pData[0],(*ptfa3)[0]*tf,g_pGlobalVACF->m_pData[0]+(*ptfa3)[0]*tf);

5974

for (z3=0;z3<(int)g_pGlobalVACF->m_iSize;z3++)

5975

g_pGlobalVACF->m_pData[z3] += (*ptfa3)[z3] * tf;

5976

}

5977

delete ac;

5978

delete ptfa2;

5979

delete ptfa3;

5980

/* delete fft2;

5981

delete fft;*/

5982

/* } else

5983

{

5984

mprintf(" Autocorrelating cached vectors...\n");

5985

mprintf(WHITE," [");

5986

for (z2=0;z2<g_iGesAtomCount;z2++)

5987

{

5988

if (fmod(z2,tfs) < 1.0)

5989

mprintf(WHITE,"#");

5990

ptfa = (CxFloatArray*)g_pGlobalVACF->m_oaCache[z2];

5991

for (z3=0;z3<g_pGlobalVACF->m_iSize;z3+=g_pGlobalVACF->m_iStride) // Das ist das Tau

5992

{

5993

tf = 0;

5994

for (z4=0;z4<(int)g_iSteps-z3;z4++) // Das ist der Startpunkt

5995

tf += (*ptfa)[z4*3]*(*ptfa)[(z4+z3)*3] + (*ptfa)[z4*3+1]*(*ptfa)[(z4+z3)*3+1] + (*ptfa)[z4*3+2]*(*ptfa)[(z4+z3)*3+2];

5996

g_pGlobalVACF->m_pData[z3/g_pGlobalVACF->m_iStride] += tf/(g_iSteps-z3);

5997

}

5998

}

5999

}*/

6000

mprintf(WHITE,"]\n");

6001

mprintf(" %d atoms and %d frames processed.\n",g_iGesAtomCount,g_pGlobalVACF->m_iSize);

6002

g_pGlobalVACF->MultiplyCached(1.0/g_iGesAtomCount);

6003

} else g_pGlobalVACF->Multiply(1.0/g_iGesAtomCount);

6004

6005

mprintf(" Saving global VACF as acf_global%s.csv ...\n",multibuf);

6006

g_pGlobalVACF->WriteACF("acf_global",multibuf,".csv");

6007

6008

if (g_pGlobalVACF->m_iMirror != 0)

6009

{

6010

mprintf(" Mirroring global VACF...\n");

6011

g_pGlobalVACF->Mirror(g_pGlobalVACF->m_iMirror);

6012

mprintf(" Saving mirrored global VACF as acf_global.m%s.csv ...\n",multibuf);

6013

g_pGlobalVACF->WriteACF("acf_global.m",multibuf,".csv");

6014

}

6015

6016

if (g_pGlobalVACF->m_bWindowFunction)

6017

{

6018

mprintf(" Applying window function...\n");

6019

g_pGlobalVACF->Window();

6020

mprintf(" Saving windowed global VACF as acf_global.w%s.csv ...\n",multibuf);

6021

g_pGlobalVACF->WriteACF("acf_global.w",multibuf,".csv");

6022

}

6023

6024

if (g_pGlobalVACF->m_bSpectrum)

6025

{

6026

mprintf(" Performing Fourier transformation...\n");

6027

6028

try { g_pFFT = new CFFT(); } catch(...) { g_pFFT = NULL; }

6029

if (g_pFFT == NULL) NewException((double)sizeof(CFFT),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6030

6031

g_pFFT->PrepareFFT_C2C(g_pGlobalVACF->m_iSize+g_pGlobalVACF->m_iZeroPadding);

6032

g_pGlobalVACF->Transform(g_pFFT);

6033

delete g_pFFT;

6034

g_pGlobalVACF->m_pSpectrum->SetMaxRWL(1E7f/299.792f/g_fTimestepLength/g_iStride);

6035

if (g_pGlobalVACF->m_bACF_DB)

6036

{

6037

mprintf(" Normalising spectrum to decibel...\n");

6038

g_pGlobalVACF->m_pSpectrum->MakeDB();

6039

}/* else

6040

{

6041

mprintf(" Normalising integral of spectrum...\n");

6042

g_pGlobalVACF->m_pSpectrum->SetIntegral(1000000.0f);

6043

}*/

6044

if (g_pGlobalVACF->m_bWindowFunction)

6045

{

6046

mprintf(" Saving spectrum as power_global_w%s.csv ...\n",multibuf);

6047

g_pGlobalVACF->m_pSpectrum->Write("power_global_w",multibuf,".csv");

6048

} else

6049

{

6050

mprintf(" Saving spectrum as power_global%s.csv ...\n",multibuf);

6051

g_pGlobalVACF->m_pSpectrum->Write("power_global",multibuf,".csv");

6052

}

6053

}

6054

mprintf("\n");

6055

}

6056

6057

if (g_bVFDF)

6058

{

6059

for (z=0;z<g_iVFCorrCount;z++)

6060

fclose(g_fVFCorr[z]);

6061

}

6062

6063

6064

// fclose(ff);

6065

6066

for (z=0;z<g_oaObserv.GetSize();z++)

6067

{

6068

o = (CObservation*)g_oaObserv[z];

6069

mprintf(YELLOW,"\n>>> Observation %d >>>\n",z+1);

6070

6071

if (o->m_pConditions != NULL)

6072

{

6073

o->m_pConditions->PrintData();

6074

if (o->m_pConditions->m_oaConditionSubGroups.GetSize()==2)

6075

o->m_pConditions->PrintTable();

6076

}

6077

6078

if (g_bAggregation)

6079

{

6080

mprintf(WHITE,"* Aggregation Functions\n");

6081

if ((g_iMaxStep > 0) && (((int)g_iSteps*g_iStride) >= g_iMaxStep))

6082

g_pTempTimestep->CopyFrom(GetTimeStep(0)); // Max. Schrittzahl

6083

else g_pTempTimestep->CopyFrom(GetTimeStep(1)); // End Of File

6084

for (zs=0;zs<o->m_pDACF->m_oaSubDACFs.GetSize();zs++)

6085

{

6086

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[zs];

6087

mprintf(WHITE,"\n > Value Set %d: %s\n",zs+1,dacfsub->m_sName);

6088

6089

o->m_pDACF->FinishDACFSub(g_pTempTimestep,dacfsub);

6090

6091

sprintf(buf,"cond_%s.txt",dacfsub->m_sName);

6092

dacfsub->m_pCondition->PrintData(buf);

6093

6094

mprintf(WHITE,"Neighbour Count Distribution\n");

6095

mprintf(" %.0f Bin entries have been made.\n",dacfsub->m_pNDF->m_fBinEntries);

6096

sprintf(buf,"ncd_%s%s.csv",dacfsub->m_sName,multibuf);

6097

mprintf(" Writing Neighbor Count Distribution File \"%s\"...\n",buf);

6098

dacfsub->m_pNDF->Write_Int("",buf,"");

6099

6100

if (g_bDDisp)

6101

{

6102

mprintf(WHITE,"\nDimer Displacement Distribution Function\n");

6103

mprintf(" %.0f Bin entries have been made (%.0f skipped, %.0f total).\n",dacfsub->m_pDDisp->m_fBinEntries,dacfsub->m_pDDisp->m_fSkipEntries,dacfsub->m_pDDisp->m_fBinEntries+dacfsub->m_pDDisp->m_fSkipEntries);

6104

sprintf(buf,"ddisp_%s%s.csv",dacfsub->m_sName,multibuf);

6105

mprintf(" Saving DDisp File as \"%s\"...\n",buf);

6106

dacfsub->m_pDDisp->Write("",buf,"",false);

6107

sprintf(buf,"ddisp_%s%s.agr",dacfsub->m_sName,multibuf);

6108

mprintf(" Saving DDisp Agr File as \"%s\"...\n",buf);

6109

dacfsub->m_pDDisp->WriteAgr("",buf,"","",false);

6110

}

6111

6112

if (g_bDACF)

6113

{

6114

mprintf(WHITE,"\nDimer Existence Autocorrelation Function\n");

6115

mprintf(" %.0f Bin entries have beend made (%.0f skipped, %.0f total).\n",dacfsub->m_pDACF->m_fBinEntries,dacfsub->m_pDACF->m_fSkipEntries,dacfsub->m_pDACF->m_fBinEntries+dacfsub->m_pDACF->m_fSkipEntries);

6116

dacfsub->m_pDACF->MultiplyBin(1.0/dacfsub->m_pDACF->m_pBin[0]);

6117

if (o->m_pDACF->m_bFitDACF)

6118

{

6119

mprintf("\n");

6120

6121

try { dacfsub->m_pDACF->m_pParameters = new double*[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pParameters = NULL; }

6122

if (dacfsub->m_pDACF->m_pParameters == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(double*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6123

6124

try { dacfsub->m_pDACF->m_pFitIntegral = new double[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pFitIntegral = NULL; }

6125

if (dacfsub->m_pDACF->m_pFitIntegral == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6126

6127

try { dacfsub->m_pDACF->m_pCorrCoeff = new double[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pCorrCoeff = NULL; }

6128

if (dacfsub->m_pDACF->m_pCorrCoeff == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6129

6130

try { dacfsub->m_pDACF->m_pAdditionalSets = new double*[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pAdditionalSets = NULL; }

6131

if (dacfsub->m_pDACF->m_pAdditionalSets == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(double*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6132

6133

try { dacfsub->m_pDACF->m_pAdditionalSetLabels = new char*[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pAdditionalSetLabels = NULL; }

6134

if (dacfsub->m_pDACF->m_pAdditionalSetLabels == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(char*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6135

6136

dacfsub->m_pDACF->m_iAdditionalSets = o->m_pDACF->m_iFitDegreeMax+1;

6137

6138

for (z2=0;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

6139

{

6140

dacfsub->m_pDACF->m_pAdditionalSets[z2] = NULL;

6141

dacfsub->m_pDACF->m_pAdditionalSetLabels[z2] = NULL;

6142

}

6143

6144

for (z2=o->m_pDACF->m_iFitDegreeMin;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

6145

dacfsub->m_pDACF->Fit_PolyExp(z2);

6146

6147

if (o->m_pDACF->m_iFitDegreeMin != o->m_pDACF->m_iFitDegreeMax)

6148

{

6149

mprintf(" Fitting overview:\n");

6150

mprintf(" Degree R Integral\n");

6151

for (z2=o->m_pDACF->m_iFitDegreeMin;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

6152

{

6153

if (dacfsub->m_pDACF->m_pFitIntegral[z2] >= 0)

6154

mprintf(" %d %10.8f %.8G\n",z2,dacfsub->m_pDACF->m_pCorrCoeff[z2],dacfsub->m_pDACF->m_pFitIntegral[z2]);

6155

else mprintf(" %d %8.6f -\n",z2,dacfsub->m_pDACF->m_pCorrCoeff[z2]);

6156

}

6157

mprintf("\n");

6158

}

6159

}

6160

sprintf(buf,"dacf_%s%s.csv",dacfsub->m_sName,multibuf);

6161

mprintf(" Saving DACF File as \"%s\"...\n",buf);

6162

dacfsub->m_pDACF->Write("",buf,"",false);

6163

sprintf(buf,"dacf_%s%s.agr",dacfsub->m_sName,multibuf);

6164

mprintf(" Saving DACF Agr File as \"%s\"...\n",buf);

6165

dacfsub->m_pDACF->WriteAgr("",buf,"","",false);

6166

}

6167

6168

if (g_bDLDF)

6169

{

6170

mprintf(WHITE,"\nDimer Lifetime Distribution Function\n");

6171

mprintf(" %.0f Bin entries have been made (%.0f skipped, %.0f total).\n",dacfsub->m_pDLDF->m_fBinEntries,dacfsub->m_pDLDF->m_fSkipEntries,dacfsub->m_pDLDF->m_fBinEntries+dacfsub->m_pDLDF->m_fSkipEntries);

6172

sprintf(buf,"dldf_%s%s.csv",dacfsub->m_sName,multibuf);

6173

mprintf(" Saving DLDF File as \"%s\"...\n",buf);

6174

dacfsub->m_pDLDF->Write("",buf,"",false);

6175

sprintf(buf,"dldf_%s%s.agr",dacfsub->m_sName,multibuf);

6176

mprintf(" Saving DLDF Agr File as \"%s\"...\n",buf);

6177

dacfsub->m_pDLDF->WriteAgr("",buf,"","",false);

6178

}

6179

6180

if (g_bDLDisp)

6181

{

6182

mprintf(WHITE,"\nDimer Lifetime Displacement Distribution Function\n");

6183

mprintf(" %.0f Bin entries have been made (%.0f skipped, %.0f total).\n",dacfsub->m_pDLDisp->m_fBinEntries,dacfsub->m_pDLDisp->m_fSkipEntries,dacfsub->m_pDLDisp->m_fBinEntries+dacfsub->m_pDLDisp->m_fSkipEntries);

6184

mprintf(" Normalizing bin integral to 1000000...\n");

6185

dacfsub->m_pDLDisp->NormalizeBinIntegral(1000000.0);

6186

sprintf(buf,"dldisp_%s%s",dacfsub->m_sName,multibuf);

6187

mprintf(" Saving DLDisp triples as \"%s_triples.csv\"...\n",buf);

6188

dacfsub->m_pDLDisp->Write("",buf,"_triples.csv");

6189

mprintf(" Saving DLDisp matrix as \"%s_matrix.csv\"...\n",buf);

6190

dacfsub->m_pDLDisp->WriteCSV("",buf,"_matrix.csv");

6191

mprintf(" Saving DLDisp Mathematica Notebook \"%s.nb\"...\n",buf);

6192

dacfsub->m_pDLDisp->WriteMathematicaNb("",buf,".nb",false);

6193

}

6194

}

6195

if (o->m_pDACF->m_bDACFGrid && o->m_pDACF->m_bFitDACF)

6196

{

6197

mprintf(WHITE,"\n*** Condition Grid fitting overview:\n\n");

6198

mprintf(" Degree R(min) R(avg) R(max)\n");

6199

o->m_pDACF->CalcGridFitParms();

6200

for (z2=o->m_pDACF->m_iFitDegreeMin;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

6201

mprintf(" %d %10.8f %10.8f %10.8f\n",z2,o->m_pDACF->m_pFitRMin[z2],o->m_pDACF->m_pFitRAvg[z2],o->m_pDACF->m_pFitRMax[z2]);

6202

mprintf("\n");

6203

6204

for (z2=o->m_pDACF->m_iFitDegreeMin;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

6205

{

6206

if ((o->m_pDACF->m_iGridMode == 3) || (o->m_pDACF->m_iGridMode == 5))

6207

{

6208

if (o->m_pDACF->m_bGridCon)

6209

{

6210

try { temp2df = new C2DF(); } catch(...) { temp2df = NULL; }

6211

if (temp2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6212

6213

o->m_pDACF->CreateGridFit2DF(temp2df,z2,false);

6214

sprintf(buf,"dacf_gridint_%s%s_%dexp",o->m_pDACF->m_sName,multibuf,z2);

6215

mprintf(" Saving Grid Integral triples as \"%s_triples.csv\"...\n",buf);

6216

temp2df->Write("",buf,"_triples.csv");

6217

mprintf(" Saving Grid Integral matrix as \"%s_matrix.csv\"...\n",buf);

6218

temp2df->WriteCSV("",buf,"_matrix.csv");

6219

mprintf(" Saving Grid Integral Mathematica Notebook \"%s.nb\"...\n",buf);

6220

temp2df->WriteMathematicaNb("",buf,".nb",false);

6221

delete temp2df;

6222

}

6223

if (o->m_pDACF->m_bGridInt)

6224

{

6225

try { temp2df = new C2DF(); } catch(...) { temp2df = NULL; }

6226

if (temp2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6227

6228

o->m_pDACF->CreateGridFit2DF(temp2df,z2,true);

6229

sprintf(buf,"dacf_gridint_%s%s_%dexp_int%.2f",o->m_pDACF->m_sName,multibuf,z2,o->m_pDACF->m_fGridIntGap);

6230

mprintf(" Saving Grid Integral triples as \"%s_triples.csv\"...\n",buf);

6231

temp2df->Write("",buf,"_triples.csv");

6232

mprintf(" Saving Grid Integral matrix as \"%s_matrix.csv\"...\n",buf);

6233

temp2df->WriteCSV("",buf,"_matrix.csv");

6234

mprintf(" Saving Grid Integral Mathematica Notebook \"%s.nb\"...\n",buf);

6235

temp2df->WriteMathematicaNb("",buf,".nb",false);

6236

delete temp2df;

6237

}

6238

} else

6239

{

6240

if (o->m_pDACF->m_bGridCon)

6241

{

6242

try { tdf = new CDF(); } catch(...) { tdf = NULL; }

6243

if (tdf == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6244

6245

o->m_pDACF->CreateGridFitDF(tdf,z2,false);

6246

delete tdf;

6247

}

6248

}

6249

}

6250

}

6251

}

6252

6253

if (g_bRDyn)

6254

{

6255

mprintf(WHITE,"* Vector Reorientation Dynamics\n");

6256

if (g_bRDynCacheMode)

6257

{

6258

mprintf(" Autocorrelating cached vectors...\n");

6259

mprintf(WHITE," [");

6260

tfs = (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pRDyn->m_iCombinations)/60.0;

6261

/* if (g_bACFFFT)

6262

{*/

6263

/* fft = new CFFT();

6264

fft->PrepareFFT_C2C(2*g_iSteps);

6265

fft2 = new CFFT();

6266

fft2->PrepareInverseFFT_C2C(2*g_iSteps);*/

6267

6268

try { ptfa2 = new CxFloatArray(); } catch(...) { ptfa2 = NULL; }

6269

if (ptfa2 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6270

6271

ptfa2->SetSize(g_iSteps/g_iStride);

6272

6273

try { ptfa3 = new CxFloatArray(); } catch(...) { ptfa3 = NULL; }

6274

if (ptfa3 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6275

6276

ptfa3->SetSize(g_iSteps/g_iStride);

6277

6278

try { ac = new CAutoCorrelation(); } catch(...) { ac = NULL; }

6279

if (ac == NULL) NewException((double)sizeof(CAutoCorrelation),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6280

6281

ac->Init(g_iSteps/g_iStride,o->m_pRDyn->m_iDepth,g_bACFFFT);

6282

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pRDyn->m_iCombinations;z2++)

6283

{

6284

if (fmod(z2,tfs) < 1.0)

6285

mprintf(WHITE,"#");

6286

ptfa = (CxFloatArray*)o->m_pRDyn->m_oaCache[z2];

6287

6288

/* X */

6289

for (z3=0;z3<(int)g_iSteps/g_iStride;z3++)

6290

(*ptfa2)[z3] = (*ptfa)[z3*3];

6291

// (*ptfa2)[z3] = sqrt((*ptfa)[z3*3]*(*ptfa)[z3*3] + (*ptfa)[z3*3+1]*(*ptfa)[z3*3+1] + (*ptfa)[z3*3+2]*(*ptfa)[z3*3+2]);

6292

6293

ac->AutoCorrelate(ptfa2,ptfa3);

6294

for (z3=0;z3<(int)o->m_pRDyn->m_iDepth/o->m_pRDyn->m_iStride;z3++)

6295

o->m_pRDyn->m_pRDyn->AddToBin_Int(z3,(*ptfa3)[z3*o->m_pRDyn->m_iStride]);

6296

6297

/* Y */

6298

for (z3=0;z3<(int)g_iSteps/g_iStride;z3++)

6299

(*ptfa2)[z3] = (*ptfa)[z3*3+1];

6300

ac->AutoCorrelate(ptfa2,ptfa3);

6301

for (z3=0;z3<(int)o->m_pRDyn->m_iDepth/o->m_pRDyn->m_iStride;z3++)

6302

o->m_pRDyn->m_pRDyn->AddToBin_Int(z3,(*ptfa3)[z3*o->m_pRDyn->m_iStride]);

6303

6304

/* Z */

6305

for (z3=0;z3<(int)g_iSteps/g_iStride;z3++)

6306

(*ptfa2)[z3] = (*ptfa)[z3*3+2];

6307

ac->AutoCorrelate(ptfa2,ptfa3);

6308

6309

for (z3=0;z3<(int)o->m_pRDyn->m_iDepth/o->m_pRDyn->m_iStride;z3++)

6310

{

6311

o->m_pRDyn->m_pRDyn->AddToBin_Int(z3,(*ptfa3)[z3*o->m_pRDyn->m_iStride]);

6312

o->m_pRDyn->m_pRDyn->m_fBinEntries += (double)(g_iSteps-z3*o->m_pRDyn->m_iStride) - 3.0;

6313

}

6314

}

6315

delete ac;

6316

delete ptfa2;

6317

delete ptfa3;

6318

/* delete fft2;

6319

delete fft;*/

6320

/* } else

6321

{

6322

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pRDyn->m_iCombinations;z2++)

6323

{

6324

if (fmod(z2,tfs) < 1.0)

6325

mprintf(WHITE,"#");

6326

ptfa = (CxFloatArray*)o->m_pRDyn->m_oaCache[z2];

6327

for (z3=0;z3<o->m_pRDyn->m_iDepth;z3+=o->m_pRDyn->m_iStride) // Das ist das Tau

6328

{

6329

tf = 0;

6330

for (z4=0;z4<(int)g_iSteps-z3;z4++) // Das ist der Startpunkt

6331

tf += (*ptfa)[z4*3]*(*ptfa)[(z4+z3)*3] + (*ptfa)[z4*3+1]*(*ptfa)[(z4+z3)*3+1] + (*ptfa)[z4*3+2]*(*ptfa)[(z4+z3)*3+2];

6332

o->m_pRDyn->m_pRDyn->AddToBin(z3/o->m_pRDyn->m_iStride,tf/(g_iSteps-z3));

6333

o->m_pRDyn->m_pRDyn->m_fBinEntries += g_iSteps-z3-1;

6334

}

6335

}

6336

}*/

6337

mprintf(WHITE,"]\n");

6338

} else

6339

{

6340

for (z2=0;z2<o->m_pRDyn->m_pRDyn->m_iResolution;z2++)

6341

o->m_pRDyn->m_pRDyn->m_pBin[z2] /= o->m_pRDyn->m_pCount[z2];

6342

}

6343

mprintf(" %.0f bin entries.\n",o->m_pRDyn->m_pRDyn->m_fBinEntries);

6344

o->m_pRDyn->m_pRDyn->MultiplyBin(1.0/o->m_pRDyn->m_pRDyn->m_pBin[0]);

6345

sprintf(buf,"rdyn_%s%s.csv",o->m_pRDyn->m_sName,multibuf);

6346

mprintf(" Saving result as %s ...\n",buf);

6347

o->m_pRDyn->m_pRDyn->Write("",buf,"",false);

6348

6349

if (o->m_pRDyn->m_bSpectrum)

6350

{

6351

mprintf("\n Creating reorientation spectrum:\n");

6352

6353

for (z=0;z<o->m_pRDyn->m_iDepth;z++)

6354

o->m_pRDyn->m_pACF->m_pData[z] = o->m_pRDyn->m_pRDyn->m_pBin[z];

6355

6356

if (o->m_pRDyn->m_pACF->m_bDerivative)

6357

{

6358

mprintf(" Deriving ACF...\n");

6359

6360

for (z=0;z<o->m_pRDyn->m_iDepth-2;z++)

6361

o->m_pRDyn->m_pACF->m_pData[z] = -2.0 * o->m_pRDyn->m_pACF->m_pData[z+1] + o->m_pRDyn->m_pACF->m_pData[z+2] + o->m_pRDyn->m_pACF->m_pData[z];

6362

// o->m_pRDyn->m_pACF->m_pData[z] = o->m_pRDyn->m_pACF->m_pData[z+2] - o->m_pRDyn->m_pACF->m_pData[z];

6363

6364

o->m_pRDyn->m_pACF->m_pData[o->m_pRDyn->m_iDepth-2] = 0;

6365

o->m_pRDyn->m_pACF->m_pData[o->m_pRDyn->m_iDepth-1] = 0;

6366

6367

sprintf(buf,"acf_%s%s.d.csv",o->m_pRDyn->m_sName,multibuf);

6368

mprintf(" Saving derived ACF as %s ...\n",buf);

6369

o->m_pRDyn->m_pACF->WriteACF("",buf,"");

6370

}

6371

6372

if (o->m_pRDyn->m_pACF->m_iMirror != 0)

6373

{

6374

mprintf(" Mirroring ACF...\n");

6375

o->m_pRDyn->m_pACF->Mirror(o->m_pRDyn->m_pACF->m_iMirror);

6376

sprintf(buf,"acf_%s%s.m.csv",o->m_pRDyn->m_sName,multibuf);

6377

mprintf(" Saving mirrored ACF as %s ...\n",buf);

6378

o->m_pRDyn->m_pACF->WriteACF("",buf,"");

6379

}

6380

6381

if (o->m_pRDyn->m_pACF->m_bWindowFunction)

6382

{

6383

mprintf(" Applying window function to ACF...\n");

6384

o->m_pRDyn->m_pACF->Window();

6385

sprintf(buf,"acf_%s%s.w.csv",o->m_pRDyn->m_sName,multibuf);

6386

mprintf(" Saving windowed ACF as %s ...\n",buf);

6387

o->m_pRDyn->m_pACF->WriteACF("",buf,"");

6388

}

6389

6390

mprintf(" Performing fourier transformation...\n");

6391

6392

try { g_pFFT = new CFFT(); } catch(...) { g_pFFT = NULL; }

6393

if (g_pFFT == NULL) NewException((double)sizeof(CFFT),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6394

6395

/* if (o->m_pVACF->m_bMirror)

6396

g_pFFT->PrepareFFT_C2C((o->m_pVACF->m_iSize+o->m_pVACF->m_iZeroPadding)*2);

6397

else */g_pFFT->PrepareFFT_C2C(o->m_pRDyn->m_pACF->m_iSize+o->m_pRDyn->m_pACF->m_iZeroPadding);

6398

o->m_pRDyn->m_pACF->Transform(g_pFFT);

6399

delete g_pFFT;

6400

o->m_pRDyn->m_pACF->m_pSpectrum->SetMaxRWL(1E7f/299.792f/g_fTimestepLength/g_iStride);

6401

if (o->m_pRDyn->m_pACF->m_bACF_DB)

6402

{

6403

mprintf(" Normalising spectrum to decibel...\n");

6404

o->m_pRDyn->m_pACF->m_pSpectrum->MakeDB();

6405

}/* else

6406

{

6407

mprintf(" Normalising integral of spectrum...\n");

6408

o->m_pVACF->m_pSpectrum->SetIntegral(1000000.0f);

6409

}*/

6410

/* if (o->m_pVACF->m_bWindowFunction)

6411

{

6412

sprintf(buf,"power_%s_w%s.csv",o->m_pVACF->m_sName,multibuf);

6413

mprintf(" Saving spectrum as %s ...\n",buf);

6414

o->m_pVACF->m_pSpectrum->Write("",buf,"");

6415

} else

6416

{*/

6417

sprintf(buf,"power_%s%s.csv",o->m_pRDyn->m_sName,multibuf);

6418

mprintf(" Saving spectrum as %s ...\n",buf);

6419

o->m_pRDyn->m_pACF->m_pSpectrum->Write("",buf,"");

6420

// }

6421

} // END IF SPECTRUM

6422

}

6423

6424

if (g_bVACF)

6425

{

6426

mprintf(WHITE,"* Velocity Autocorrelation Function\n");

6427

if (o->m_pVACF->m_bDerivative)

6428

{

6429

mprintf(" Deriving velocities...\n");

6430

mprintf(WHITE," [");

6431

tfs = (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes)/60.0;

6432

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes;z2++)

6433

{

6434

if (fmod(z2,tfs) < 1)

6435

mprintf(WHITE,"#");

6436

ptfa = (CxFloatArray*)o->m_pVACF->m_oaCache[z2];

6437

6438

for (z3=0;z3<(int)g_iSteps*3-3;z3++)

6439

(*ptfa)[z3] = (*ptfa)[z3+3] - (*ptfa)[z3];

6440

}

6441

mprintf(WHITE,"]\n");

6442

}

6443

if (g_bVACFCacheMode)

6444

{

6445

mprintf(" Autocorrelating cached vectors...\n");

6446

mprintf(WHITE," [");

6447

tfs = (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes)/60.0;

6448

6449

try { ptfa2 = new CxFloatArray(); } catch(...) { ptfa2 = NULL; }

6450

if (ptfa2 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6451

6452

ptfa2->SetSize(g_iSteps);

6453

6454

try { ptfa3 = new CxFloatArray(); } catch(...) { ptfa3 = NULL; }

6455

if (ptfa3 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6456

6457

ptfa3->SetSize(g_iSteps);

6458

6459

try { ac = new CAutoCorrelation(); } catch(...) { ac = NULL; }

6460

if (ac == NULL) NewException((double)sizeof(CAutoCorrelation),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6461

6462

ac->Init(g_iSteps,o->m_pVACF->m_iSize,g_bACFFFT);

6463

ti = 0;

6464

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z2++)

6465

{

6466

for (z3=0;z3<o->m_pVACF->m_oAtoms.m_baAtomType.GetSize();z3++)

6467

{

6468

if (o->m_pVACF->m_bMassWeight)

6469

tf = ((CAtom*)g_oaAtoms[o->m_pVACF->m_oAtoms.m_baRealAtomType[z3]])->m_pElement->m_fMass;

6470

else tf = 1.0;

6471

for (z4=0;z4<((CxIntArray*)o->m_pVACF->m_oAtoms.m_oaAtoms[z3])->GetSize();z4++)

6472

{

6473

if (fmod(ti,tfs) < 1)

6474

mprintf(WHITE,"#");

6475

ptfa = (CxFloatArray*)o->m_pVACF->m_oaCache[ti];

6476

6477

/* X */

6478

for (z5=0;z5<(int)g_iSteps;z5++)

6479

(*ptfa2)[z5] = (*ptfa)[z5*3];

6480

ac->AutoCorrelate(ptfa2,ptfa3);

6481

// mprintf("Lokal Atom %d X: %f + %f = %f.\n",ti+1,o->m_pVACF->m_pData[0],(*ptfa3)[0]*tf,o->m_pVACF->m_pData[0]+(*ptfa3)[0]*tf);

6482

for (z5=0;z5<(int)o->m_pVACF->m_iSize;z5++)

6483

o->m_pVACF->m_pData[z5] += (*ptfa3)[z5]*tf;

6484

6485

/* Y */

6486

for (z5=0;z5<(int)g_iSteps;z5++)

6487

(*ptfa2)[z5] = (*ptfa)[z5*3+1];

6488

ac->AutoCorrelate(ptfa2,ptfa3);

6489

// mprintf("Lokal Atom %d Y: %f + %f = %f.\n",ti+1,o->m_pVACF->m_pData[0],(*ptfa3)[0]*tf,o->m_pVACF->m_pData[0]+(*ptfa3)[0]*tf);

6490

for (z5=0;z5<(int)o->m_pVACF->m_iSize;z5++)

6491

o->m_pVACF->m_pData[z5] += (*ptfa3)[z5]*tf;

6492

6493

/* Z */

6494

for (z5=0;z5<(int)g_iSteps;z5++)

6495

(*ptfa2)[z5] = (*ptfa)[z5*3+2];

6496

ac->AutoCorrelate(ptfa2,ptfa3);

6497

// mprintf("Lokal Atom %d Z: %f + %f = %f.\n",ti+1,o->m_pVACF->m_pData[0],(*ptfa3)[0]*tf,o->m_pVACF->m_pData[0]+(*ptfa3)[0]*tf);

6498

for (z5=0;z5<(int)o->m_pVACF->m_iSize;z5++)

6499

o->m_pVACF->m_pData[z5] += (*ptfa3)[z5]*tf;

6500

6501

ti++;

6502

}

6503

}

6504

}

6505

delete ac;

6506

delete ptfa2;

6507

delete ptfa3;

6508

6509

/* } else

6510

{

6511

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes;z2++)

6512

{

6513

if (fmod(z2,tfs) < 1)

6514

mprintf(WHITE,"#");

6515

ptfa = (CxFloatArray*)o->m_pVACF->m_oaCache[z2];

6516

for (z3=0;z3<o->m_pVACF->m_iSize;z3+=o->m_pVACF->m_iStride) // Das ist das Tau

6517

{

6518

tf = 0;

6519

for (z4=0;z4<(int)g_iSteps-z3;z4++) // Das ist der Startpunkt

6520

tf += (*ptfa)[z4*3]*(*ptfa)[(z4+z3)*3] + (*ptfa)[z4*3+1]*(*ptfa)[(z4+z3)*3+1] + (*ptfa)[z4*3+2]*(*ptfa)[(z4+z3)*3+2];

6521

o->m_pVACF->m_pData[z3/o->m_pVACF->m_iStride] += tf/(g_iSteps-z3);

6522

}

6523

}

6524

}*/

6525

mprintf(WHITE,"]\n");

6526

mprintf(" %d atoms and %d frames processed.\n",ti,o->m_pVACF->m_iSize);

6527

o->m_pVACF->MultiplyCached(1.0/g_iGesAtomCount);

6528

} else o->m_pVACF->Multiply(1.0/g_iGesAtomCount);

6529

/* sprintf(buf,"acf_%s%s.csv",o->m_pVACF->m_sName,multibuf);

6530

mprintf(" Saving ACF as %s ...\n",buf);

6531

o->m_pVACF->WriteACF("",buf,"");*/

6532

6533

sprintf(buf,"acf_%s%s.csv",o->m_pVACF->m_sName,multibuf);

6534

mprintf(" Saving ACF as %s ...\n",buf);

6535

o->m_pVACF->WriteACF("",buf,"");

6536

6537

if (o->m_pVACF->m_iMirror != 0)

6538

{

6539

mprintf(" Mirroring ACF...\n");

6540

o->m_pVACF->Mirror(o->m_pVACF->m_iMirror);

6541

sprintf(buf,"acf_%s%s.m.csv",o->m_pVACF->m_sName,multibuf);

6542

mprintf(" Saving mirrored ACF as %s ...\n",buf);

6543

o->m_pVACF->WriteACF("",buf,"");

6544

}

6545

6546

if (o->m_pVACF->m_bWindowFunction)

6547

{

6548

mprintf(" Applying window function to ACF...\n");

6549

o->m_pVACF->Window();

6550

sprintf(buf,"acf_%s%s.w.csv",o->m_pVACF->m_sName,multibuf);

6551

mprintf(" Saving windowed ACF as %s ...\n",buf);

6552

o->m_pVACF->WriteACF("",buf,"");

6553

}

6554

6555

if (o->m_pVACF->m_bSpectrum)

6556

{

6557

mprintf(" Performing fourier transformation...\n");

6558

6559

try { g_pFFT = new CFFT(); } catch(...) { g_pFFT = NULL; }

6560

if (g_pFFT == NULL) NewException((double)sizeof(CFFT),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6561

6562

/* if (o->m_pVACF->m_bMirror)

6563

g_pFFT->PrepareFFT_C2C((o->m_pVACF->m_iSize+o->m_pVACF->m_iZeroPadding)*2);

6564

else */g_pFFT->PrepareFFT_C2C(o->m_pVACF->m_iSize+o->m_pVACF->m_iZeroPadding);

6565

o->m_pVACF->Transform(g_pFFT);

6566

delete g_pFFT;

6567

o->m_pVACF->m_pSpectrum->SetMaxRWL(1E7f/299.792f/g_fTimestepLength/g_iStride);

6568

if (o->m_pVACF->m_bACF_DB)

6569

{

6570

mprintf(" Normalising spectrum to decibel...\n");

6571

o->m_pVACF->m_pSpectrum->MakeDB();

6572

}/* else

6573

{

6574

mprintf(" Normalising integral of spectrum...\n");

6575

o->m_pVACF->m_pSpectrum->SetIntegral(1000000.0f);

6576

}*/

6577

/* if (o->m_pVACF->m_bWindowFunction)

6578

{

6579

sprintf(buf,"power_%s_w%s.csv",o->m_pVACF->m_sName,multibuf);

6580

mprintf(" Saving spectrum as %s ...\n",buf);

6581

o->m_pVACF->m_pSpectrum->Write("",buf,"");

6582

} else

6583

{*/

6584

sprintf(buf,"power_%s%s.csv",o->m_pVACF->m_sName,multibuf);

6585

mprintf(" Saving spectrum as %s ...\n",buf);

6586

o->m_pVACF->m_pSpectrum->Write("",buf,"");

6587

// }

6588

}

6589

} // End IF VACF

6590

6591

if (g_bMSD)

6592

{

6593

mprintf(WHITE,"* Mean Square Displacement\n");

6594

if (g_bMSDCacheMode)

6595

{

6596

mprintf(" Autocorrelating cached vectors...\n");

6597

// mprintf(WHITE," [");

6598

// tfs = (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms)/60.0;

6599

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms;z2++)

6600

{

6601

// if (fmod(z2,tfs) < 1.0)

6602

// mprintf(WHITE,"#");

6603

mprintf(" %4d/%d: [",z2+1,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms);

6604

tfs = o->m_pMSD->m_iResolution/50.0;

6605

ptfa = (CxFloatArray*)o->m_pMSD->m_oaCache[z2];

6606

for (z3=0;z3<o->m_pMSD->m_iResolution;z3+=o->m_pMSD->m_iStride) // Das ist das Tau

6607

{

6608

if (fmod(z3,tfs) < 1.0)

6609

mprintf(WHITE,"#");

6610

tf = 0;

6611

6612

for (z4=0;z4<(int)g_iSteps/g_iStride-z3-1;z4+=o->m_pMSD->m_iStride2) // Das ist der Startpunkt

6613

tf += pow((*ptfa)[(z3+z4)*3]-(*ptfa)[z4*3],2) + pow((*ptfa)[(z3+z4)*3+1]-(*ptfa)[z4*3+1],2) + pow((*ptfa)[(z3+z4)*3+2]-(*ptfa)[z4*3+2],2);

6614

6615

o->m_pMSD->m_pMSD->AddToBin_Index(z3/o->m_pMSD->m_iStride,tf/(g_iSteps/g_iStride-z3-1)*o->m_pMSD->m_iStride2);

6616

o->m_pMSD->m_pMSD->m_fBinEntries += (g_iSteps/g_iStride-z3-1)/o->m_pMSD->m_iStride2;

6617

if (o->m_pMSD->m_bSplit)

6618

{

6619

o->m_pMSD->m_pSplitMSD[z2]->AddToBin_Index(z3/o->m_pMSD->m_iStride,tf/(g_iSteps/g_iStride-z3-1)*o->m_pMSD->m_iStride2);

6620

o->m_pMSD->m_pSplitMSD[z2]->m_fBinEntries += (g_iSteps/g_iStride-z3-1)/o->m_pMSD->m_iStride2;

6621

}

6622

}

6623

mprintf("]\n");

6624

}

6625

for (z3=0;z3<o->m_pMSD->m_iResolution;z3+=o->m_pMSD->m_iStride) // Das ist das Tau

6626

o->m_pMSD->m_pMSD->m_pBin[z3/o->m_pMSD->m_iStride] /= ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms;

6627

// mprintf(WHITE,"]\n");

6628

} else

6629

{

6630

o->m_pMSD->m_pMSD->BuildAverage();

6631

}

6632

mprintf(" %.0f bin entries.\n",o->m_pMSD->m_pMSD->m_fBinEntries);

6633

o->m_pMSD->m_pMSD->CalcDeriv(1.0f);

6634

sprintf(buf,"msd_%s%s.csv",o->m_pMSD->m_sName,multibuf);

6635

mprintf(" Saving result as %s ...\n",buf);

6636

if (o->m_pMSD->m_bSplit)

6637

{

6638

o->m_pMSD->WriteSplit(buf);

6639

} else o->m_pMSD->m_pMSD->Write("",buf,"");

6640

mprintf(WHITE,"\n Performing linear regression on interval %.2f - %.2f ps...\n",o->m_pMSD->m_pMSD->m_fMinVal+0.5*(o->m_pMSD->m_pMSD->m_fMaxVal-o->m_pMSD->m_pMSD->m_fMinVal),o->m_pMSD->m_pMSD->m_fMaxVal);

6641

o->m_pMSD->m_pMSD->LinReg(o->m_pMSD->m_pMSD->m_iResolution/2,o->m_pMSD->m_pMSD->m_iResolution-1,&c0,&c1,&r);

6642

mprintf(" MSD(t) = %.6f + %.6f * t (units: [MSD] = pm^2, [t] = ps).\n",c0,c1);

6643

mprintf(" R = %.6f\n",r);

6644

mprintf(" Diffusion coefficient D = %.6f pm^2/ps = %G m^2/s.\n",c1/6.0,c1/6.0e12);

6645

mprintf(" (assuming <x^2> = 6 * D * t)\n\n");

6646

}

6647

6648

if (g_bNbAnalysis)

6649

{

6650

mprintf(WHITE,"* Neighborhood Analysis\n");

6651

mprintf(" %.0f bin entries.\n",o->m_pNbAnalysis->m_fBinEntries);

6652

/* for (z2=0;z2<o->m_pNbAnalysis->m_iMaxNbCount-o->m_pNbAnalysis->m_iMinNbCount;z2++)

6653

mprintf(" - %d: %.0f bin entries, %.0f skipped.\n",z2+1,((CDF*)o->m_pNbAnalysis->m_oaDF[z2])->m_fBinEntries,((CDF*)o->m_pNbAnalysis->m_oaDF[z2])->m_fSkipEntries);

6654

*/

6655

6656

try { pf = new float[o->m_pNbAnalysis->m_iNbCount]; } catch(...) { pf = NULL; }

6657

if (pf == NULL) NewException((double)o->m_pNbAnalysis->m_iNbCount*sizeof(float),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6658

6659

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

6660

pf[z3] = (float)((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->NormBinIntegral();

6661

6662

sprintf(buf,"nbh_ncf_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

6663

mprintf(" Saving neighbor count function as %s ...\n",buf);

6664

a = OpenFileWrite(buf,true);

6665

fprintf(a,"# distance [pm]; ");

6666

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount+1;z3++)

6667

{

6668

fprintf(a,"%d neighbors",z3);

6669

if (z3 < o->m_pNbAnalysis->m_iNbCount)

6670

fprintf(a,"; ");

6671

}

6672

fprintf(a,"\n");

6673

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

6674

{

6675

fprintf(a,"%.4f; ",o->m_pNbAnalysis->m_fMinDist+(z2+0.5)*(o->m_pNbAnalysis->m_fMaxDist-o->m_pNbAnalysis->m_fMinDist)/o->m_pNbAnalysis->m_iResolution);

6676

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount+1;z3++)

6677

{

6678

fprintf(a,"%.6f",((CDF*)o->m_pNbAnalysis->m_oaNPF[z3])->m_pBin[z2]/o->m_pNbAnalysis->m_pNPFCount->m_pBin[z2]*100.0f);

6679

if (z3 < o->m_pNbAnalysis->m_iNbCount)

6680

fprintf(a,"; ");

6681

}

6682

fprintf(a,"\n");

6683

}

6684

fclose(a);

6685

6686

sprintf(buf,"nbh_dist_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

6687

mprintf(" Calculating mean values and standard deviation...\n");

6688

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

6689

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->CalcMeanSD();

6690

mprintf(" Saving neighborhood distribution as %s ...\n",buf);

6691

a = OpenFileWrite(buf,true);

6692

fprintf(a,"# distance [pm]; ");

6693

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

6694

{

6695

fprintf(a,"%d. neighbor",z3+1);

6696

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

6697

fprintf(a,"; ");

6698

}

6699

fprintf(a,"\n");

6700

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

6701

{

6702

fprintf(a,"%.4f; ",o->m_pNbAnalysis->m_fMinDist+(z2+0.5)*(o->m_pNbAnalysis->m_fMaxDist-o->m_pNbAnalysis->m_fMinDist)/o->m_pNbAnalysis->m_iResolution);

6703

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

6704

{

6705

fprintf(a,"%.6f",((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_pBin[z2]);

6706

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

6707

fprintf(a,"; ");

6708

}

6709

fprintf(a,"\n");

6710

}

6711

fclose(a);

6712

6713

sprintf(buf,"nbh_minmaxavgsd_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

6714

mprintf(" Saving neighborhood min/max/avg/sd as %s ...\n",buf);

6715

a = OpenFileWrite(buf,true);

6716

fprintf(a,"# n-th neighbor; min. dist [pm]; max. dist [pm]; avg. dist [pm]; standard deviation [pm]\n");

6717

for (z2=0;z2<o->m_pNbAnalysis->m_iNbCount;z2++)

6718

{

6719

fprintf(a,"%d; %.4f; %.4f; %.4f; %.4f",z2+1,o->m_pNbAnalysis->m_pDistMin[z2],o->m_pNbAnalysis->m_pDistMax[z2],((CDF*)o->m_pNbAnalysis->m_oaDF[z2])->m_fMean,((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_fSD);

6720

fprintf(a,"\n");

6721

}

6722

fclose(a);

6723

6724

sprintf(buf,"nbh_rdf_decomp_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

6725

mprintf(" Saving neighborhood RDF decomposition as %s ...\n",buf);

6726

a = OpenFileWrite(buf,true);

6727

fprintf(a,"# distance [pm]; ");

6728

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

6729

{

6730

fprintf(a,"%d. neighbor",z3+1);

6731

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

6732

fprintf(a,"; ");

6733

}

6734

fprintf(a,"\n");

6735

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

6736

{

6737

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->MultiplyBin(pf[z3]);

6738

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->CorrectRadialDist();

6739

}

6740

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

6741

{

6742

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->MultiplyBin(g_fBoxX*g_fBoxY*g_fBoxZ / (4.0/3.0*Pi) / g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize());

6743

if (g_bDoubleBox)

6744

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->MultiplyBin(g_iDoubleBoxFactor);

6745

}

6746

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

6747

{

6748

fprintf(a,"%.4f; ",o->m_pNbAnalysis->m_fMinDist+(z2+0.5)*(o->m_pNbAnalysis->m_fMaxDist-o->m_pNbAnalysis->m_fMinDist)/o->m_pNbAnalysis->m_iResolution);

6749

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

6750

{

6751

fprintf(a,"%.6f",((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_pBin[z2]);

6752

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

6753

fprintf(a,"; ");

6754

}

6755

fprintf(a,"\n");

6756

}

6757

fclose(a);

6758

6759

sprintf(buf,"nbh_rdf_decomp_cumulative_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

6760

mprintf(" Saving cumulative neighborhood RDF decomposition as %s ...\n",buf);

6761

a = OpenFileWrite(buf,true);

6762

fprintf(a,"# distance [pm]; ");

6763

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

6764

{

6765

fprintf(a,"%d. neighbor",z3+1);

6766

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

6767

fprintf(a,"; ");

6768

}

6769

fprintf(a,"\n");

6770

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

6771

for (z3=1;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

6772

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_pBin[z2] += ((CDF*)o->m_pNbAnalysis->m_oaDF[z3-1])->m_pBin[z2];

6773

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

6774

{

6775

fprintf(a,"%.4f; ",o->m_pNbAnalysis->m_fMinDist+(z2+0.5)*(o->m_pNbAnalysis->m_fMaxDist-o->m_pNbAnalysis->m_fMinDist)/o->m_pNbAnalysis->m_iResolution);

6776

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

6777

{

6778

fprintf(a,"%.6f",((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_pBin[z2]);

6779

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

6780

fprintf(a,"; ");

6781

}

6782

fprintf(a,"\n");

6783

}

6784

fclose(a);

6785

delete[] pf;

6786

}

6787

6788

if (g_bDipDF)

6789

{

6790

for (zr=0;zr<g_iCDFChannels;zr++)

6791

{

6792

if (o->m_pDipDF[zr] == NULL)

6793

continue;

6794

mprintf(WHITE,"* Dipole Distribution Function\n");

6795

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pDipDF[zr]->m_pDipoleDF->m_fBinEntries,o->m_pDipDF[zr]->m_pDipoleDF->m_fSkipEntries,ZeroDivide(o->m_pDipDF[zr]->m_pDipoleDF->m_fSkipEntries,o->m_pDipDF[zr]->m_pDipoleDF->m_fSkipEntries+o->m_pDipDF[zr]->m_pDipoleDF->m_fBinEntries)*100.0);

6796

o->m_pDipDF[zr]->m_pDipoleDF->CalcMeanSD();

6797

mprintf(" Mean value: %.10G Debye Standard deviation: %.10G Debye\n",o->m_pDipDF[zr]->m_pDipoleDF->m_fMean,o->m_pDipDF[zr]->m_pDipoleDF->m_fSD);

6798

mprintf(" Min. value: %.10G Debye Max. value: %.10G Debye\n",o->m_pDipDF[zr]->m_pDipoleDF->m_fMinInput,o->m_pDipDF[zr]->m_pDipoleDF->m_fMaxInput);

6799

o->m_pDipDF[zr]->m_pDipoleDF->NormBinIntegral();

6800

sprintf(buf,"dipole_%s%s.csv",o->m_pDipDF[zr]->m_sName,multibuf);

6801

mprintf(" Saving dipole distribution as %s ...\n",buf);

6802

o->m_pDipDF[zr]->m_pDipoleDF->Write("",buf,"",false);

6803

sprintf(buf,"dipole_%s%s.agr",o->m_pDipDF[zr]->m_sName,multibuf);

6804

mprintf(" Saving dipole distribution AGR file as \"%s\"...\n",buf);

6805

o->m_pDipDF[zr]->m_pDipoleDF->WriteAgr("",buf,"",o->m_pDipDF[zr]->m_sName,false);

6806

if (o->m_pDipDF[zr]->m_iHistogramRes != 0)

6807

{

6808

mprintf(" Calculating Histogram...\n");

6809

o->m_pDipDF[zr]->m_pDipoleDF->CalcHistogram();

6810

sprintf(buf,"his_dipdf_%s%s.csv",o->m_pDipDF[zr]->m_sName,multibuf);

6811

mprintf(" Saving Histogram as \"%s\"...\n",buf);

6812

o->m_pDipDF[zr]->m_pDipoleDF->WriteHistogram("",buf,"");

6813

}

6814

if (o->m_bTimeDev)

6815

{

6816

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

6817

{

6818

fclose(o->m_pDipDF[zr]->m_fDipole[0]);

6819

mprintf(" Saving temporal development as dipole_timedev_%s%s.csv\n",o->m_pDipDF[zr]->m_sName,multibuf);

6820

} else

6821

{

6822

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

6823

{

6824

fclose(o->m_pDipDF[zr]->m_fDipole[z2]);

6825

mprintf(" Saving temporal development as dipole_timedev_%s_ref%d%s.csv\n",o->m_pDipDF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

6826

}

6827

}

6828

if (o->m_bCombinedPlot)

6829

{

6830

sprintf(buf,"combined_%s%s.agr",o->m_pDipDF[zr]->m_sName,multibuf);

6831

mprintf(" Saving combined plot as \"%s\"...\n",buf);

6832

o->m_pDipDF[zr]->m_pDipoleDF->CreateCombinedPlot(false);

6833

o->m_pDipDF[zr]->m_pDipoleDF->m_pCombinedPlot->WriteAgr(buf,false);

6834

}

6835

} // END IF TIMEDEV

6836

6837

if (o->m_bObsCertain && o->m_bDecompDist)

6838

{

6839

sprintf(buf,"dipdf_decomp_%s%s.csv",o->m_pDipDF[zr]->m_sName,multibuf);

6840

mprintf(" Saving DipDF decomposition as \"%s\"...\n",buf);

6841

o->m_pDipDF[zr]->m_pDipoleDF->WriteMulti("",buf,"");

6842

sprintf(buf,"dipdf_decomp_%s%s_cumulative.csv",o->m_pDipDF[zr]->m_sName,multibuf);

6843

mprintf(" Saving cumulative DipoleDF decomposition as \"%s\"...\n",buf);

6844

o->m_pDipDF[zr]->m_pDipoleDF->WriteMulti_Cumulative("",buf,"");

6845

}

6846

6847

if (o->m_bTimeDiff)

6848

o->WriteTimeDiff(o->m_pDipDF[zr]->m_pDipoleDF,"DipDF","dipdf",o->m_pDipDF[zr]->m_sName,multibuf,false);

6849

}

6850

} // END IF DIPOLE

6851

6852

if (g_bVDF)

6853

{

6854

for (zr=0;zr<g_iCDFChannels;zr++)

6855

{

6856

if (o->m_pVDF[zr] == NULL)

6857

continue;

6858

mprintf(WHITE,"* Velocity Distribution Function\n");

6859

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pVDF[zr]->m_pVDF->m_fBinEntries,o->m_pVDF[zr]->m_pVDF->m_fSkipEntries,ZeroDivide(o->m_pVDF[zr]->m_pVDF->m_fSkipEntries,o->m_pVDF[zr]->m_pVDF->m_fBinEntries+o->m_pVDF[zr]->m_pVDF->m_fSkipEntries)*100.0);

6860

o->m_pVDF[zr]->m_pVDF->CalcMeanSD();

6861

mprintf(" Mean value: %.10G pm/ps Standard deviation: %.10G pm/ps\n",o->m_pVDF[zr]->m_pVDF->m_fMean,o->m_pVDF[zr]->m_pVDF->m_fSD);

6862

mprintf(" Min. value: %.10G pm/ps Max. value: %.10G pm/ps\n",o->m_pVDF[zr]->m_pVDF->m_fMinInput,o->m_pVDF[zr]->m_pVDF->m_fMaxInput);

6863

o->m_pVDF[zr]->m_pVDF->NormBinIntegral();

6864

sprintf(buf,"vdf_%s%s.csv",o->m_pVDF[zr]->m_sName,multibuf);

6865

mprintf(" Saving velocity distribution as %s ...\n",buf);

6866

o->m_pVDF[zr]->m_pVDF->Write("",buf,"",false);

6867

sprintf(buf,"vdf_%s%s.agr",o->m_pVDF[zr]->m_sName,multibuf);

6868

mprintf(" Saving velocity distribution AGR file as \"%s\"...\n",buf);

6869

o->m_pVDF[zr]->m_pVDF->WriteAgr("",buf,"",o->m_pVDF[zr]->m_sName,false);

6870

if (o->m_pADF[zr]->m_iHistogramRes != 0)

6871

{

6872

mprintf(" Calculating Histogram...\n");

6873

o->m_pVDF[zr]->m_pVDF->CalcHistogram();

6874

sprintf(buf,"his_vdf_%s%s.agr",o->m_pVDF[zr]->m_sName,multibuf);

6875

mprintf(" Saving Histogram as \"%s\"...\n",buf);

6876

o->m_pVDF[zr]->m_pVDF->WriteHistogram("",buf,"");

6877

}

6878

if (o->m_bTimeDev)

6879

{

6880

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

6881

{

6882

fclose(o->m_pVDF[zr]->m_fSpeed[0]);

6883

mprintf(" Saving temporal development as vdf_timedev_%s%s.csv\n",o->m_pVDF[zr]->m_sName,multibuf);

6884

} else

6885

{

6886

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

6887

{

6888

fclose(o->m_pVDF[zr]->m_fSpeed[z2]);

6889

mprintf(" Saving temporal development as vdf_timedev_%s_ref%d%s.csv\n",o->m_pVDF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

6890

}

6891

}

6892

if (o->m_bCombinedPlot)

6893

{

6894

sprintf(buf,"combined_%s%s.csv",o->m_pVDF[zr]->m_sName,multibuf);

6895

mprintf(" Saving combined plot as \"%s\"...\n",buf);

6896

o->m_pVDF[zr]->m_pVDF->CreateCombinedPlot(false);

6897

o->m_pVDF[zr]->m_pVDF->m_pCombinedPlot->WriteAgr(buf,false);

6898

}

6899

} // END IF TIMEDEV

6900

6901

if (o->m_bObsCertain && o->m_bDecompDist)

6902

{

6903

sprintf(buf,"vdf_decomp_%s%s.csv",o->m_pVDF[zr]->m_sName,multibuf);

6904

mprintf(" Saving VDF decomposition as \"%s\"...\n",buf);

6905

o->m_pVDF[zr]->m_pVDF->WriteMulti("",buf,"");

6906

sprintf(buf,"vdf_decomp_%s%s_cumulative.csv",o->m_pVDF[zr]->m_sName,multibuf);

6907

mprintf(" Saving cumulative VDF decomposition as \"%s\"...\n",buf);

6908

o->m_pVDF[zr]->m_pVDF->WriteMulti_Cumulative("",buf,"");

6909

}

6910

6911

if (o->m_bTimeDiff)

6912

o->WriteTimeDiff(o->m_pVDF[zr]->m_pVDF,"VDF","vdf",o->m_pVDF[zr]->m_sName,multibuf,false);

6913

}

6914

} // END IF VDF

6915

6916

if (g_bADF)

6917

{

6918

for (zr=0;zr<g_iCDFChannels;zr++)

6919

{

6920

if (o->m_pADF[zr] == NULL)

6921

continue;

6922

mprintf(WHITE,"* Angular Distribution Function\n");

6923

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pADF[zr]->m_pADF->m_fBinEntries,o->m_pADF[zr]->m_pADF->m_fSkipEntries,ZeroDivide(o->m_pADF[zr]->m_pADF->m_fSkipEntries,o->m_pADF[zr]->m_pADF->m_fBinEntries+o->m_pADF[zr]->m_pADF->m_fSkipEntries)*100.0);

6924

o->m_pADF[zr]->m_pADF->CalcMeanSD();

6925

if (o->m_pADF[zr]->m_bCosine)

6926

{

6927

mprintf(" Mean value: %.10G Standard deviation: %.10G\n",o->m_pADF[zr]->m_pADF->m_fMean,o->m_pADF[zr]->m_pADF->m_fSD);

6928

mprintf(" Min. value: %.10G Max. value: %.10G\n",o->m_pADF[zr]->m_pADF->m_fMinInput,o->m_pADF[zr]->m_pADF->m_fMaxInput);

6929

} else

6930

{

6931

mprintf(" Mean value: %.10G degree Standard deviation: %.10G degree\n",o->m_pADF[zr]->m_pADF->m_fMean,o->m_pADF[zr]->m_pADF->m_fSD);

6932

mprintf(" Min. value: %.10G degree Max. value: %.10G degree\n",o->m_pADF[zr]->m_pADF->m_fMinInput,o->m_pADF[zr]->m_pADF->m_fMaxInput);

6933

}

6934

if (o->m_pADF[zr]->m_bStat)

6935

{

6936

mprintf(" Applying cone correction...\n");

6937

o->m_pADF[zr]->m_pADF->AngleCorrect();

6938

}

6939

/* if (o->m_pADF[zr]->m_bMirror)

6940

{

6941

mprintf(" Making ADF mirror-symmetric...\n");

6942

if (o->m_pADF[zr]->m_bCosine)

6943

o->m_pADF[zr]->m_pADF->Mirror(0.0f);

6944

else o->m_pADF[zr]->m_pADF->Mirror(90.0f);

6945

}*/

6946

o->m_pADF[zr]->m_pADF->NormBinIntegral();

6947

if (o->m_bTimeDev)

6948

{

6949

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

6950

{

6951

fclose(o->m_pADF[zr]->m_fAngle[0]);

6952

mprintf(" Saving temporal development as adf_timedev_%s%s.csv\n",o->m_pADF[zr]->m_sName,multibuf);

6953

} else

6954

{

6955

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

6956

{

6957

fclose(o->m_pADF[zr]->m_fAngle[z2]);

6958

sprintf(buf,"adf_timedev_%s_ref%d%s.csv",o->m_pADF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

6959

mprintf(" Saving temporal development as %s\n",buf);

6960

}

6961

}

6962

// mprintf(" Speichere Winkel-Statistik als %s_angle_stat.txt\n",o->m_pADF->m_sName);

6963

// FreeFileName("",o->m_pADF->m_sName,"_angle_stat.txt");

6964

// o->m_pADF->m_pAngleStat->Evaluate();

6965

// o->m_pADF->m_pAngleStat->Write("",o->m_pADF->m_sName,"_angle_stat.txt");

6966

// delete o->m_pAngleStat;

6967

delete[] o->m_pADF[zr]->m_fAngle;

6968

o->m_pADF[zr]->m_fAngle = NULL;

6969

if (o->m_bCombinedPlot)

6970

{

6971

sprintf(buf,"combined_%s%s.agr",o->m_pADF[zr]->m_sName,multibuf);

6972

mprintf(" Saving combined plot as \"%s\"...\n",buf);

6973

o->m_pADF[zr]->m_pADF->CreateCombinedPlot(false);

6974

o->m_pADF[zr]->m_pADF->m_pCombinedPlot->WriteAgr(buf,false);

6975

}

6976

} // END IF TIMEDEV

6977

sprintf(buf,"adf_%s%s.csv",o->m_pADF[zr]->m_sName,multibuf);

6978

mprintf(" Saving ADF as %s ...\n",buf);

6979

o->m_pADF[zr]->m_pADF->NormBinIntegral();

6980

o->m_pADF[zr]->m_pADF->Write("",buf,"",false);

6981

sprintf(buf,"adf_%s%s.agr",o->m_pADF[zr]->m_sName,multibuf);

6982

mprintf(" Saving ADF AGR file as \"%s\"...\n",buf);

6983

if (o->m_pADF[zr]->m_bCosine)

6984

o->m_pADF[zr]->m_pADF->WriteAgr("",buf,"",o->m_pADF[zr]->m_sName,false);

6985

else o->m_pADF[zr]->m_pADF->WriteAgr("",buf,"",o->m_pADF[zr]->m_sName,false);

6986

if (o->m_pADF[zr]->m_iHistogramRes != 0)

6987

{

6988

mprintf(" Calculating Histogram...\n");

6989

o->m_pADF[zr]->m_pADF->CalcHistogram();

6990

sprintf(buf,"his_adf_%s%s.csv",o->m_pADF[zr]->m_sName,multibuf);

6991

mprintf(" Saving Histogram as \"%s\"...\n",buf);

6992

o->m_pADF[zr]->m_pADF->WriteHistogram("",buf,"");

6993

}

6994

6995

if (o->m_bObsCertain && o->m_bDecompDist)

6996

{

6997

sprintf(buf,"adf_decomp_%s%s.csv",o->m_pADF[zr]->m_sName,multibuf);

6998

mprintf(" Saving ADF decomposition as \"%s\"...\n",buf);

6999

o->m_pADF[zr]->m_pADF->WriteMulti("",buf,"");

7000

sprintf(buf,"adf_decomp_%s%s_cumulative.csv",o->m_pADF[zr]->m_sName,multibuf);

7001

mprintf(" Saving cumulative ADF decomposition as \"%s\"...\n",buf);

7002

o->m_pADF[zr]->m_pADF->WriteMulti_Cumulative("",buf,"");

7003

}

7004

7005

if (o->m_bTimeDiff)

7006

o->WriteTimeDiff(o->m_pADF[zr]->m_pADF,"ADF","adf",o->m_pADF[zr]->m_sName,multibuf,false);

7007

}

7008

} // END IF ADF

7009

7010

if (g_bDDF)

7011

{

7012

for (zr=0;zr<g_iCDFChannels;zr++)

7013

{

7014

if (o->m_pDDF[zr] == NULL)

7015

continue;

7016

mprintf(WHITE,"* Dihedral Distribution Function\n");

7017

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pDDF[zr]->m_pDDF->m_fBinEntries,o->m_pDDF[zr]->m_pDDF->m_fSkipEntries,ZeroDivide(o->m_pDDF[zr]->m_pDDF->m_fSkipEntries,o->m_pDDF[zr]->m_pDDF->m_fBinEntries+o->m_pDDF[zr]->m_pDDF->m_fSkipEntries)*100.0);

7018

o->m_pDDF[zr]->m_pDDF->CalcMeanSD();

7019

if (o->m_pDDF[zr]->m_bCosine)

7020

{

7021

mprintf(" Mean value: %.10G Standard deviation: %.10G\n",o->m_pDDF[zr]->m_pDDF->m_fMean,o->m_pDDF[zr]->m_pDDF->m_fSD);

7022

mprintf(" Min. value: %.10G Max.value: %.10G\n",o->m_pDDF[zr]->m_pDDF->m_fMinInput,o->m_pDDF[zr]->m_pDDF->m_fMaxInput);

7023

} else

7024

{

7025

mprintf(" Mean value: %.10G degree Standard deviation: %.10G degree\n",o->m_pDDF[zr]->m_pDDF->m_fMean,o->m_pDDF[zr]->m_pDDF->m_fSD);

7026

mprintf(" Min. value: %.10G degree Max.value: %.10G degree\n",o->m_pDDF[zr]->m_pDDF->m_fMinInput,o->m_pDDF[zr]->m_pDDF->m_fMaxInput);

7027

}

7028

if (o->m_bTimeDev)

7029

{

7030

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

7031

{

7032

fclose(o->m_pDDF[zr]->m_fAngle[0]);

7033

mprintf(" Saving temporal development as ddf_timedev_%s%s.csv\n",o->m_pDDF[zr]->m_sName,multibuf);

7034

} else

7035

{

7036

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

7037

{

7038

fclose(o->m_pDDF[zr]->m_fAngle[z2]);

7039

sprintf(buf,"ddf_timedev_%s_ref%d%s.csv",o->m_pDDF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

7040

mprintf(" Saving temporal development as %s\n",buf);

7041

}

7042

}

7043

/* mprintf(" Speichere Winkel-Statistik als %s_angle_stat.txt\n",o->m_sName);

7044

FreeFileName("",o->m_sName,"_angle_stat.txt");

7045

o->m_pAngleStat->Evaluate();

7046

o->m_pAngleStat->Write("",o->m_sName,"_angle_stat.txt");

7047

// delete o->m_pAngleStat;*/

7048

delete[] o->m_pDDF[zr]->m_fAngle;

7049

o->m_pDDF[zr]->m_fAngle = NULL;

7050

if (o->m_bCombinedPlot)

7051

{

7052

sprintf(buf,"combined_%s%s.agr",o->m_pDDF[zr]->m_sName,multibuf);

7053

mprintf(" Saving combined plot as \"%s\"...\n",buf);

7054

o->m_pDDF[zr]->m_pDDF->CreateCombinedPlot(false);

7055

o->m_pDDF[zr]->m_pDDF->m_pCombinedPlot->WriteAgr(buf,false);

7056

}

7057

} // END IF TIMEDEV

7058

/* if (o->m_pDDF->m_iStat != 0)

7059

{

7060

mprintf(" Korrigiere statistische Verteilung...\n");

7061

o->m_pDDF->m_pDDF->AngleCorrect();

7062

}*/

7063

sprintf(buf,"ddf_%s%s.csv",o->m_pDDF[zr]->m_sName,multibuf);

7064

mprintf(" Saving DDF as %s ...\n",buf);

7065

o->m_pDDF[zr]->m_pDDF->NormBinIntegral();

7066

o->m_pDDF[zr]->m_pDDF->Write("",buf,"",false);

7067

sprintf(buf,"ddf_%s%s.agr",o->m_pDDF[zr]->m_sName,multibuf);

7068

mprintf(" Saving DDF AGR file as \"%s\"...\n",buf);

7069

if (o->m_pDDF[zr]->m_bCosine)

7070

o->m_pDDF[zr]->m_pDDF->WriteAgr("",buf,"",o->m_pDDF[zr]->m_sName,false);

7071

else o->m_pDDF[zr]->m_pDDF->WriteAgr("",buf,"",o->m_pDDF[zr]->m_sName,false);

7072

if (o->m_pDDF[zr]->m_iHistogramRes != 0)

7073

{

7074

mprintf(" Calculating Histogram...\n");

7075

o->m_pDDF[zr]->m_pDDF->CalcHistogram();

7076

sprintf(buf,"his_ddf_%s%s.csv",o->m_pDDF[zr]->m_sName,multibuf);

7077

mprintf(" Saving Histogram as \"%s\"...\n",buf);

7078

o->m_pDDF[zr]->m_pDDF->WriteHistogram("",buf,"");

7079

}

7080

7081

if (o->m_bObsCertain && o->m_bDecompDist)

7082

{

7083

sprintf(buf,"ddf_decomp_%s%s.csv",o->m_pDDF[zr]->m_sName,multibuf);

7084

mprintf(" Saving DDF decomposition as \"%s\"...\n",buf);

7085

o->m_pDDF[zr]->m_pDDF->WriteMulti("",buf,"");

7086

sprintf(buf,"ddf_decomp_%s%s_cumulative.csv",o->m_pDDF[zr]->m_sName,multibuf);

7087

mprintf(" Saving cumulative DDF decomposition as \"%s\"...\n",buf);

7088

o->m_pDDF[zr]->m_pDDF->WriteMulti_Cumulative("",buf,"");

7089

}

7090

7091

if (o->m_bTimeDiff)

7092

o->WriteTimeDiff(o->m_pDDF[zr]->m_pDDF,"DDF","ddf",o->m_pDDF[zr]->m_sName,multibuf,true);

7093

}

7094

} // END IF DDF

7095

7096

if (g_bSDF)

7097

{

7098

mprintf(WHITE,"* Spatial Distribution Function\n");

7099

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pSDF->m_pSDF->m_fBinEntries,o->m_pSDF->m_pSDF->m_fSkipEntries,ZeroDivide(o->m_pSDF->m_pSDF->m_fSkipEntries,o->m_pSDF->m_pSDF->m_fBinEntries+o->m_pSDF->m_pSDF->m_fSkipEntries)*100.0);

7100

o->m_pSDF->m_pSDF->CalcMaxEntry();

7101

mprintf(" Raw data range from %.0f to %.0f hits.\n",o->m_pSDF->m_pSDF->m_fMinEntry,o->m_pSDF->m_pSDF->m_fMaxEntry);

7102

mprintf(" The volume of one bin is %.3f pm^3.\n",pow(o->m_pSDF->m_fRadius*2.0/o->m_pSDF->m_iResolution,3));

7103

mprintf(" The uniform particle density of this observation is %.6f nm^-3.\n",o->m_pSDF->m_fParticleDensity);

7104

/* switch(g_iSDFScale)

7105

{

7106

case 0:

7107

mprintf(" Scaling values to ppm...\n");

7108

o->m_pSDF->m_pSDF->MultiplyBin(1000000.0 / (double)g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pSDF->m_iShowAtomGes * (g_bDoubleBox?g_iDoubleBoxFactor:1));

7109

break;

7110

case 1:

7111

mprintf(" Scaling values to pm^-3...\n");

7112

o->m_pSDF->m_pSDF->MultiplyBin(pow(o->m_pSDF->m_iResolution/o->m_pSDF->m_fRadius,3) / (double)g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pSDF->m_iShowAtomGes * (g_bDoubleBox?g_iDoubleBoxFactor:1));

7113

break;

7114

case 2:

7115

mprintf(" Scaling values to nm^-3...\n");*/

7116

/* break;

7117

case 3:

7118

mprintf(" Scaling values relative to average particle density...\n");

7119

o->m_pSDF->m_pSDF->MultiplyBin(pow(o->m_pSDF->m_iResolution/o->m_pSDF->m_fRadius*1000.0,3) / (double)g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pSDF->m_iShowAtomGes / o->m_pSDF->m_fParticleDensity * (g_bDoubleBox?g_iDoubleBoxFactor:1));

7120

break;

7121

}*/

7122

7123

o->m_pSDF->m_pSDF->MultiplyBin(pow(o->m_pSDF->m_iResolution/o->m_pSDF->m_fRadius/2.0*1000.0,3) / (double)g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pSDF->m_iShowAtomGes * (g_bDoubleBox?g_iDoubleBoxFactor:1));

7124

7125

if (g_bSDFUniform)

7126

{

7127

o->m_pSDF->m_pSDF->MultiplyBin(1.0/o->m_pSDF->m_fParticleDensity);

7128

mprintf(WHITE," Bin values are given relative to this uniform particle density.\n");

7129

} else

7130

{

7131

mprintf(WHITE," Bin values are given in nm^-3 (particle density).\n");

7132

}

7133

o->m_pSDF->m_pSDF->CalcMaxEntry();

7134

mprintf(" Data range from %.6f to %.6f%s.\n",o->m_pSDF->m_pSDF->m_fMinEntry,o->m_pSDF->m_pSDF->m_fMaxEntry,g_bSDFUniform?"":" nm^-3");

7135

7136

if (o->m_pSDF->m_bInvert)

7137

{

7138

mprintf(" Inverting SDF...\n");

7139

o->m_pSDF->m_pSDF->Invert();

7140

}

7141

if (o->m_pSDF->m_bCutPlane)

7142

{

7143

mprintf(" Creating Cut Plane...\n");

7144

o->m_pSDF->CreateCutPlane();

7145

sprintf(buf,"sdf_cut_%s%s",o->m_pSDF->m_sName,multibuf);

7146

mprintf(" Saving SDF Cut Plane triples as \"%s_triples.csv\"...\n",buf);

7147

o->m_pSDF->m_pCutPlane->Write("",buf,"_triples.csv");

7148

mprintf(" Saving SDF Cut Plane matrix as \"%s_matrix.csv\"...\n",buf);

7149

o->m_pSDF->m_pCutPlane->WriteCSV("",buf,"_matrix.csv");

7150

mprintf(" Saving CDF Mathematica Notebook as \"%s.nb\"...\n",buf);

7151

o->m_pSDF->m_pCutPlane->WriteMathematicaNb("",buf,".nb",false);

7152

}

7153

for (z2=0;z2<=g_iSDFSmoothGrade;z2++)

7154

{

7155

try { tempSDF = new C3DF(); } catch(...) { tempSDF = NULL; }

7156

if (tempSDF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7157

7158

tempSDF->CopyFrom(o->m_pSDF->m_pSDF);

7159

if (z2 != 0)

7160

{

7161

tempSDF->Smooth(z2);

7162

sprintf(buf,".s%d%s.plt",z2,multibuf);

7163

} else sprintf(buf,"%s.plt",multibuf);

7164

tempSDF->CalcMaxEntry();

7165

mprintf(" Data range from %.6f to %.6f%s.\n",tempSDF->m_fMinEntry,tempSDF->m_fMaxEntry,g_bSDFUniform?"":" nm^-3");

7166

if (o->m_pSDF->m_bClipPlane)

7167

{

7168

mprintf(" Creating Clip Plane in %c direction with value %.3f...\n",(o->m_pSDF->m_iClipDirection==0)?'X':((o->m_pSDF->m_iClipDirection==1)?'Y':'Z'),o->m_pSDF->m_fClipValue);

7169

o->m_pSDF->m_pSDF->ClipPlane(o->m_pSDF->m_iClipDirection,o->m_pSDF->m_fClipValue);

7170

}

7171

mprintf(" Saving SDF as \"sdf_%s%s\"...\n",o->m_pSDF->m_sName,buf);

7172

tempSDF->WritePLT("sdf_",o->m_pSDF->m_sName,buf,true);

7173

7174

if (z2 != 0)

7175

sprintf(buf,".s%d%s.cube",z2,multibuf);

7176

else sprintf(buf,"%s.cube",multibuf);

7177

mprintf(" Saving SDF as \"sdf_%s%s\"...\n",o->m_pSDF->m_sName,buf);

7178

tempSDF->WriteCube("sdf_",o->m_pSDF->m_sName,buf,true);

7179

7180

if (o->m_pSDF->m_iHistogramRes != 0)

7181

{

7182

if (z2 != 0)

7183

sprintf(buf,".s%d%s.csv",z2,multibuf);

7184

else sprintf(buf,"%s.csv",multibuf);

7185

mprintf(" Saving SDF Histogram as \"his_sdf_%s%s\"...\n",o->m_pSDF->m_sName,buf);

7186

tempSDF->CalcHistogram();

7187

tempSDF->WriteHistogram("his_sdf_",o->m_pSDF->m_sName,buf);

7188

}

7189

}

7190

mprintf(YELLOW,"\n Important: ");

7191

mprintf(WHITE,"The PLT/CUBE files only contain the volumetric data.\n");

7192

mprintf(WHITE," The atoms of the reference molecule are saved in the ref_*.xyz file!\n");

7193

mprintf(WHITE," You need to load *both files* into the visualization program (e.g. VMD).\n");

7194

} // END IF SDF

7195

7196

if (g_bRDF)

7197

{

7198

for (zr=0;zr<g_iCDFChannels;zr++)

7199

{

7200

if (o->m_pRDF[zr] == NULL)

7201

continue;

7202

mprintf(WHITE,"* Radial Distribution Function\n");

7203

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pRDF[zr]->m_pRDF->m_fBinEntries,o->m_pRDF[zr]->m_pRDF->m_fSkipEntries,ZeroDivide(o->m_pRDF[zr]->m_pRDF->m_fSkipEntries,o->m_pRDF[zr]->m_pRDF->m_fBinEntries+o->m_pRDF[zr]->m_pRDF->m_fSkipEntries)*100.0);

7204

o->m_pRDF[zr]->m_pRDF->CalcMeanSD();

7205

mprintf(" Mean value: %.10G pm Standard deviation: %.10G pm\n",o->m_pRDF[zr]->m_pRDF->m_fMean,o->m_pRDF[zr]->m_pRDF->m_fSD);

7206

mprintf(" Min. value: %.10G pm Max.value: %.10G pm\n",o->m_pRDF[zr]->m_pRDF->m_fMinInput,o->m_pRDF[zr]->m_pRDF->m_fMaxInput);

7207

if (o->m_pRDF[zr]->m_bAdaptive)

7208

{

7209

// o->m_pRDF[zr]->m_pRDF->WriteHenry("rdf_",o->m_pRDF[zr]->m_sName,".csv");

7210

o->m_pRDF[zr]->m_pRDF->PrepareAdapt();

7211

o->m_pRDF[zr]->m_pRDF->BinTree_RadialDist();

7212

if (o->m_iShowMol == g_iFixMol)

7213

o->m_pRDF[zr]->m_pRDF->BinTree_MultiplyBin(3.0f/4.0f/Pi/g_iSteps*g_fBoxX*g_fBoxY*g_fBoxZ/(((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()-1.0f)/o->m_pRDF[zr]->m_iShowAtomGes/((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()/o->m_pRDF[zr]->m_iRefAtomGes);

7214

else o->m_pRDF[zr]->m_pRDF->BinTree_MultiplyBin(3.0f/4.0f/Pi/g_iSteps*g_fBoxX*g_fBoxY*g_fBoxZ/((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() /o->m_pRDF[zr]->m_iShowAtomGes/((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()/o->m_pRDF[zr]->m_iRefAtomGes);

7215

7216

mprintf(" Saving RDF as \"rdf_%s.csv\"...\n",o->m_pRDF[zr]->m_sName);

7217

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".001.csv",5,10,0.001,true);

7218

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".002.csv",5,10,0.002,true);

7219

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".005.csv",5,10,0.005,true);

7220

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".010.csv",5,10,0.01,true);

7221

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".020.csv",5,10,0.02,true);

7222

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".050.csv",5,10,0.05,true);

7223

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".100.csv",5,10,0.1,true);

7224

7225

/* o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".50.csv",16,0,50,true);

7226

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".100.csv",16,0,100,true);

7227

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".500.csv",16,0,500,true);

7228

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".1000.csv",16,0,1000,true);*/

7229

} else

7230

{

7231

if (o->m_pRDF[zr]->m_bRadialCorrect)

7232

{

7233

mprintf(" Correcting radial distribution...\n");

7234

o->m_pRDF[zr]->m_pRDF->CorrectRadialDist();

7235

}

7236

if (o->m_bOthers && o->m_pRDF[zr]->m_bRadialCorrect)

7237

{

7238

mprintf(" Scaling RDF to uniform density...\n");

7239

if (o->m_bObsCertain)

7240

{

7241

o->m_pRDF[zr]->m_pRDF->Integrate(true,1.0 / g_iSteps / o->m_waObsRefList.GetSize());

7242

o->m_pRDF[zr]->m_pRDF->MultiplyBin(g_fBoxX*g_fBoxY*g_fBoxZ / (4.0/3.0*Pi) / g_iSteps / o->m_waObsRefList.GetSize() / o->m_pRDF[zr]->m_iShowAtomGes / o->m_waObsShowList.GetSize() / o->m_pRDF[zr]->m_iRefAtomGes);

7243

} else

7244

{

7245

o->m_pRDF[zr]->m_pRDF->Integrate(true,1.0 / g_iSteps / (double)((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

7246

o->m_pRDF[zr]->m_pRDF->MultiplyBin(g_fBoxX*g_fBoxY*g_fBoxZ / (4.0/3.0*Pi) / g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pRDF[zr]->m_iShowAtomGes / ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize() / o->m_pRDF[zr]->m_iRefAtomGes);

7247

}

7248

if (g_bDoubleBox)

7249

{

7250

o->m_pRDF[zr]->m_pRDF->MultiplyBin(g_iDoubleBoxFactor);

7251

o->m_pRDF[zr]->m_pRDF->MultiplyIntegral(g_iDoubleBoxFactor);

7252

}

7253

} else

7254

{

7255

mprintf(" Scaling RDF to integral value 1...\n");

7256

o->m_pRDF[zr]->m_pRDF->NormBinIntegral(1.0);

7257

o->m_pRDF[zr]->m_pRDF->Integrate(false,1.0);

7258

}

7259

sprintf(buf,"rdf_%s%s.csv",o->m_pRDF[zr]->m_sName,multibuf);

7260

mprintf(" Saving RDF as \"%s\"...\n",buf);

7261

o->m_pRDF[zr]->m_pRDF->Write("",buf,"",true);

7262

sprintf(buf,"rdf_%s%s.agr",o->m_pRDF[zr]->m_sName,multibuf);

7263

mprintf(" Saving RDF AGR file as \"%s\"...\n",buf);

7264

o->m_pRDF[zr]->m_pRDF->WriteAgr("",buf,"",o->m_pRDF[zr]->m_sName,true);

7265

if (o->m_pRDF[zr]->m_iHistogramRes != 0)

7266

{

7267

mprintf(" Calculating Histogram...\n");

7268

o->m_pRDF[zr]->m_pRDF->CalcHistogram();

7269

sprintf(buf,"his_rdf_%s%s.csv",o->m_pRDF[zr]->m_sName,multibuf);

7270

mprintf(" Saving Histogram as \"%s\"...\n",buf);

7271

o->m_pRDF[zr]->m_pRDF->WriteHistogram("",buf,"");

7272

}

7273

if (o->m_bObsCertain && o->m_bDecompDist)

7274

{

7275

sprintf(buf,"rdf_decomp_mol_%s%s",o->m_pRDF[zr]->m_sName,multibuf);

7276

mprintf(" Saving RDF molecule decomposition as \"%s.csv\"...\n",buf);

7277

o->m_pRDF[zr]->m_pRDF->WriteMulti("",buf,".csv");

7278

mprintf(" Saving RDF molecule decomposition as \"%s.agr\"...\n",buf);

7279

o->m_pRDF[zr]->m_pRDF->WriteMultiAgr("",buf,".agr",buf,true);

7280

7281

sprintf(buf,"rdf_decomp_nb_%s%s_cumulative",o->m_pRDF[zr]->m_sName,multibuf);

7282

mprintf(" Saving cumulative RDF molecule decomposition as \"%s.csv\"...\n",buf);

7283

o->m_pRDF[zr]->m_pRDF->WriteMulti_Cumulative("",buf,".csv");

7284

mprintf(" Saving cumulative RDF molecule decomposition as \"%s.agr\"...\n",buf);

7285

o->m_pRDF[zr]->m_pRDF->WriteMultiAgr_Cumulative("",buf,".agr",buf,true);

7286

}

7287

if (o->m_bDecompType)

7288

{

7289

sprintf(buf,"rdf_decomp_type_%s%s",o->m_pRDF[zr]->m_sName,multibuf);

7290

mprintf(" Saving RDF type decomposition as \"%s.csv\"...\n",buf);

7291

o->m_pRDF[zr]->m_pRDF->WriteMulti("",buf,".csv");

7292

mprintf(" Saving RDF type decomposition as \"%s.agr\"...\n",buf);

7293

o->m_pRDF[zr]->m_pRDF->WriteMultiAgr("",buf,".agr",buf,true);

7294

7295

sprintf(buf,"rdf_decomp_type_%s%s_cumulative",o->m_pRDF[zr]->m_sName,multibuf);

7296

mprintf(" Saving cumulative RDF type decomposition as \"%s.csv\"...\n",buf);

7297

o->m_pRDF[zr]->m_pRDF->WriteMulti_Cumulative("",buf,".csv");

7298

mprintf(" Saving cumulative RDF type decomposition as \"%s.agr\"...\n",buf);

7299

o->m_pRDF[zr]->m_pRDF->WriteMultiAgr_Cumulative("",buf,".agr",buf,true);

7300

}

7301

7302

if (o->m_bTimeDiff)

7303

o->WriteTimeDiff(o->m_pRDF[zr]->m_pRDF,"RDF","rdf",o->m_pRDF[zr]->m_sName,multibuf,false);

7304

7305

if (o->m_pRDF[zr]->m_bACF)

7306

{

7307

o->m_pRDF[zr]->Autocorrelate();

7308

}

7309

}

7310

if (o->m_bTimeDev)

7311

{

7312

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

7313

{

7314

fclose(o->m_pRDF[zr]->m_fDist[0]);

7315

mprintf(" Saving temporal development as \"rdf_timedev_%s%s.csv\"...\n",o->m_pRDF[zr]->m_sName,multibuf);

7316

} else

7317

{

7318

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

7319

{

7320

fclose(o->m_pRDF[zr]->m_fDist[z2]);

7321

sprintf(buf,"rdf_timedev_%s_ref%d%s.csv",o->m_pRDF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

7322

mprintf(" Saving temporal development as \"%s\"...\n",buf);

7323

}

7324

}

7325

delete[] o->m_pRDF[zr]->m_fDist;

7326

o->m_pRDF[zr]->m_fDist = NULL;

7327

if (o->m_bCombinedPlot)

7328

{

7329

sprintf(buf,"combined_%s%s.agr",o->m_pRDF[zr]->m_sName,multibuf);

7330

mprintf(" Saving combined plot as \"%s\"...\n",buf);

7331

o->m_pRDF[zr]->m_pRDF->CreateCombinedPlot(true);

7332

o->m_pRDF[zr]->m_pRDF->m_pCombinedPlot->WriteAgr(buf,false);

7333

}

7334

}

7335

}

7336

} // END IF RDF

7337

7338

if (g_bVHDF)

7339

{

7340

mprintf(WHITE,"* Van Hove Correlation Function\n");

7341

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pVHDF->m_pVHDF->m_fBinEntries,o->m_pVHDF->m_pVHDF->m_fSkipEntries,ZeroDivide(o->m_pVHDF->m_pVHDF->m_fSkipEntries,o->m_pVHDF->m_pVHDF->m_fBinEntries+o->m_pVHDF->m_pVHDF->m_fSkipEntries)*100.0);

7342

o->m_pVHDF->CorrectCount();

7343

if (o->m_pVHDF->m_bRadialCorrect)

7344

{

7345

mprintf(" Correcting radial distribution...\n");

7346

o->m_pVHDF->m_pVHDF->CorrectRadialDist(0);

7347

mprintf(" Normalizing bin to uniform density...\n");

7348

o->m_pVHDF->m_pVHDF->MultiplyBin(3.0f/4.0f/Pi*g_fBoxX*g_fBoxY*g_fBoxZ);

7349

if (g_bDoubleBox)

7350

o->m_pVHDF->m_pVHDF->MultiplyBin(g_iDoubleBoxFactor);

7351

} else

7352

{

7353

mprintf(" Normalizing bin integral to 1000000...\n");

7354

o->m_pVHDF->m_pVHDF->NormalizeBinIntegral(1000000.0);

7355

}

7356

sprintf(buf,"vhcf_%s%s",o->m_pVHDF->m_sName,multibuf);

7357

mprintf(" Saving VHCF triples as \"%s_triples.csv\"...\n",buf);

7358

o->m_pVHDF->m_pVHDF->Write("",buf,"_triples.csv");

7359

mprintf(" Saving VHCF matrix as \"%s_matrix.csv\"...\n",buf);

7360

o->m_pVHDF->m_pVHDF->WriteCSV("",buf,"_matrix.csv");

7361

if (o->m_pVHDF->m_iGraceBunchDist > 0)

7362

{

7363

sprintf(buf,"vhcf_dist_%s%s.agr",o->m_pVHDF->m_sName,multibuf);

7364

mprintf(" Saving VHCF distance Grace Stack as \"%s\"...\n",buf);

7365

o->m_pVHDF->m_pVHDF->WriteGraceBunch(0,o->m_pVHDF->m_iGraceBunchDist,1.0f,"",buf,"");

7366

}

7367

if (o->m_pVHDF->m_iGraceBunchTime > 0)

7368

{

7369

sprintf(buf,"vhcf_time_%s%s.agr",o->m_pVHDF->m_sName,multibuf);

7370

mprintf(" Saving VHCF time Grace Stack as \"%s\"...\n",buf);

7371

o->m_pVHDF->m_pVHDF->WriteGraceBunch(1,o->m_pVHDF->m_iGraceBunchTime,1.0f,"",buf,"");

7372

}

7373

if (o->m_pVHDF->m_bSwapAxes)

7374

{

7375

mprintf(" Swapping time and distance axes...\n");

7376

o->m_pVHDF->m_pVHDF->SwapAxes();

7377

}

7378

sprintf(buf,"vhcf_%s%s.nb",o->m_pVHDF->m_sName,multibuf);

7379

mprintf(" Saving VHCF Mathematica Notebook as \"%s\"...\n",buf);

7380

o->m_pVHDF->m_pVHDF->WriteMathematicaNb("",buf,"",false);

7381

} // END IF VHDF

7382

7383

if (g_bCDF)

7384

{

7385

if (g_iCDFChannels == 2)

7386

{

7387

mprintf(WHITE,"* Combined Distribution Function (2D)\n");

7388

/* if (o->m_pConditions != NULL)

7389

{

7390

mprintf(" Conditions: %.2f percent of the molecules passed.\n",o->m_pConditions->m_fPassed/(o->m_pConditions->m_fPassed+o->m_pConditions->m_fFailed)*100.0);

7391

mprintf(" After conditions: ");

7392

} else mprintf(" ");*/

7393

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pCDF->m_p2DF->m_fBinEntries,o->m_pCDF->m_p2DF->m_fSkipEntries,ZeroDivide(o->m_pCDF->m_p2DF->m_fSkipEntries,o->m_pCDF->m_p2DF->m_fSkipEntries+o->m_pCDF->m_p2DF->m_fBinEntries)*100.0);

7394

if (o->m_pCDF->m_p2DF->m_fBinEntries == 0)

7395

{

7396

eprintf(" There were no bin entries. Check your CDF definition. Skipping this CDF.\n\n");

7397

goto _skipsdf;

7398

}

7399

for (z2=0;z2<2;z2++)

7400

{

7401

if (g_iObsChannel[z2] == 0)

7402

{

7403

if (o->m_pRDF[z2]->m_bRadialCorrect)

7404

{

7405

mprintf(" Correcting radial distribution for CDF channel %d...\n",z2+1);

7406

o->m_pCDF->m_p2DF->CorrectRadialDist(z2);

7407

}

7408

}

7409

if (g_iObsChannel[z2] == 1)

7410

{

7411

if (o->m_pADF[z2]->m_bStat && (!o->m_pADF[z2]->m_bCosine))

7412

{

7413

mprintf(" Correcting angular distribution for CDF channel %d...\n",z2+1);

7414

o->m_pCDF->m_p2DF->CorrectAngle(z2);

7415

}

7416

if (o->m_pADF[z2]->m_bMirror)

7417

{

7418

mprintf(" Making channel %d mirror-symmetric...\n",z2+1);

7419

if (o->m_pADF[z2]->m_bCosine)

7420

o->m_pCDF->m_p2DF->Mirror(0.0f,z2);

7421

else o->m_pCDF->m_p2DF->Mirror(90.0f,z2);

7422

}

7423

}

7424

}

7425

o->m_pCDF->m_fFactor = 1.0;

7426

switch(o->m_pCDF->m_iNormalize)

7427

{

7428

case 2:

7429

mprintf(" Normalizing maximum value to %.2f.\n",o->m_pCDF->m_fNormValue);

7430

o->m_pCDF->m_p2DF->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

7431

break;

7432

case 1:

7433

mprintf(" Normalizing integral value to %.2f.\n",o->m_pCDF->m_fNormValue);

7434

o->m_pCDF->m_fFactor = o->m_pCDF->m_p2DF->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

7435

break;

7436

case 0:

7437

mprintf(" Not normalizing this CDF.\n");

7438

break;

7439

}

7440

mprintf(" Saving CDF triples as \"%s%s_triples.csv\"...\n",o->m_pCDF->m_sName,multibuf);

7441

o->m_pCDF->m_p2DF->Write(o->m_pCDF->m_sName,multibuf,"_triples.csv");

7442

mprintf(" Saving CDF matrix as \"%s%s_matrix.csv\"...\n",o->m_pCDF->m_sName,multibuf);

7443

o->m_pCDF->m_p2DF->WriteCSV(o->m_pCDF->m_sName,multibuf,"_matrix.csv");

7444

mprintf(" Saving CDF Mathematica Notebook as \"%s%s.nb\"...\n",o->m_pCDF->m_sName,multibuf);

7445

o->m_pCDF->m_p2DF->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,".nb",false);

7446

mprintf(" Saving combined plot AGR file as \"%s%s_combined.agr\"...\n",o->m_pCDF->m_sName,multibuf);

7447

o->m_pCDF->m_p2DF->WriteCombinedPlot(o->m_pCDF->m_sName,multibuf,"_combined.agr");

7448

if (o->m_pCDF->m_iHistogramRes != 0)

7449

{

7450

mprintf(" Calculating Histogram...\n");

7451

o->m_pCDF->m_p2DF->CalcHistogram();

7452

sprintf(buf,"his_%s",o->m_pCDF->m_sName);

7453

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf,multibuf);

7454

o->m_pCDF->m_p2DF->WriteHistogram(buf,multibuf,".csv");

7455

}

7456

7457

if (o->m_pCDF->m_bGraceBunch)

7458

{

7459

if (o->m_pCDF->m_iGraceBunchC1 > 0)

7460

{

7461

if ((g_iObsChannel[1] == 0) && (o->m_bOthers))

7462

tf = 1.0 / o->m_pCDF->m_fFactor * 3.0f/4.0f/Pi/g_iSteps*g_fBoxX*g_fBoxY*g_fBoxZ/((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() /o->m_pRDF[1]->m_iShowAtomGes/((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()/o->m_pRDF[1]->m_iRefAtomGes;

7463

else tf = 1;

7464

sprintf(buf,"cdf_c1_%s%s.agr",o->m_pCDF->m_sName,multibuf);

7465

mprintf(" Saving CDF Channel 1 Grace Stack as \"%s\"...\n",buf);

7466

o->m_pCDF->m_p2DF->WriteGraceBunch(0,o->m_pCDF->m_iGraceBunchC1,(float)tf,"",buf,"");

7467

}

7468

if (o->m_pCDF->m_iGraceBunchC2 > 0)

7469

{

7470

if ((g_iObsChannel[0] == 0) && (o->m_bOthers))

7471

tf = 1.0 / o->m_pCDF->m_fFactor * 3.0f/4.0f/Pi/g_iSteps*g_fBoxX*g_fBoxY*g_fBoxZ/((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() /o->m_pRDF[0]->m_iShowAtomGes/((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()/o->m_pRDF[0]->m_iRefAtomGes;

7472

else tf = 1;

7473

sprintf(buf,"cdf_c2_%s%s.agr",o->m_pCDF->m_sName,multibuf);

7474

mprintf(" Saving CDF Channel 2 Grace Stack as \"%s\"...\n",buf);

7475

o->m_pCDF->m_p2DF->WriteGraceBunch(1,o->m_pCDF->m_iGraceBunchC2,(float)tf,"",buf,"");

7476

}

7477

}

7478

7479

if (o->m_pCDF->m_bAxisDivide)

7480

{

7481

mprintf(" Saving CDF X projection as \"%s%s_pX.csv\"...\n",o->m_pCDF->m_sName,multibuf);

7482

o->m_pCDF->m_p2DF->WriteXProjection(o->m_pCDF->m_sName,multibuf,"_pX.csv");

7483

7484

mprintf(" Saving CDF Y projection as \"%s%s_pY.csv\"...\n",o->m_pCDF->m_sName,multibuf);

7485

o->m_pCDF->m_p2DF->WriteYProjection(o->m_pCDF->m_sName,multibuf,"_pY.csv");

7486

7487

mprintf(" Saving X-normalized CDF Mathematica Notebook as \"%s%s_nX.nb\"...\n",o->m_pCDF->m_sName,multibuf);

7488

7489

try { tempc2df = new C2DF(); } catch(...) { tempc2df = NULL; }

7490

if (tempc2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7491

7492

tempc2df->CopyFrom(o->m_pCDF->m_p2DF);

7493

if (g_iObsChannel[0] == 0)

7494

if (o->m_pRDF[0]->m_bRadialCorrect)

7495

tempc2df->UnCorrectRadialDist(0);

7496

if (g_iObsChannel[0] == 1)

7497

if (o->m_pADF[0]->m_bStat && (!o->m_pADF[0]->m_bCosine))

7498

tempc2df->UnCorrectAngle(0);

7499

tempc2df->NormalizeXCount();

7500

switch(o->m_pCDF->m_iNormalize)

7501

{

7502

case 2:

7503

tempc2df->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

7504

break;

7505

case 1:

7506

tempc2df->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

7507

break;

7508

case 0:

7509

break;

7510

}

7511

tempc2df->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_nX.nb",false);

7512

delete tempc2df;

7513

7514

mprintf(" Saving Y-normalized CDF Mathematica Notebook as \"%s%s_nY.nb\"...\n",o->m_pCDF->m_sName,multibuf);

7515

7516

try { tempc2df = new C2DF(); } catch(...) { tempc2df = NULL; }

7517

if (tempc2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7518

7519

tempc2df->CopyFrom(o->m_pCDF->m_p2DF);

7520

if (g_iObsChannel[1] == 0)

7521

if (o->m_pRDF[1]->m_bRadialCorrect)

7522

tempc2df->UnCorrectRadialDist(1);

7523

if (g_iObsChannel[1] == 1)

7524

if (o->m_pADF[1]->m_bStat && (!o->m_pADF[1]->m_bCosine))

7525

tempc2df->UnCorrectAngle(1);

7526

tempc2df->NormalizeYCount();

7527

switch(o->m_pCDF->m_iNormalize)

7528

{

7529

case 2:

7530

tempc2df->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

7531

break;

7532

case 1:

7533

tempc2df->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

7534

break;

7535

case 0:

7536

break;

7537

}

7538

tempc2df->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_nY.nb",false);

7539

delete tempc2df;

7540

7541

mprintf(" Saving XY-normalized CDF Mathematica Notebook as \"%s%s_nXY.nb\"...\n",o->m_pCDF->m_sName,multibuf);

7542

7543

try { tempc2df = new C2DF(); } catch(...) { tempc2df = NULL; }

7544

if (tempc2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7545

7546

tempc2df->CopyFrom(o->m_pCDF->m_p2DF);

7547

for (z2=0;z2<2;z2++)

7548

{

7549

if (g_iObsChannel[z2] == 0)

7550

if (o->m_pRDF[z2]->m_bRadialCorrect)

7551

tempc2df->UnCorrectRadialDist(z2);

7552

if (g_iObsChannel[z2] == 1)

7553

if (o->m_pADF[z2]->m_bStat && (!o->m_pADF[z2]->m_bCosine))

7554

tempc2df->UnCorrectAngle(z2);

7555

}

7556

tempc2df->NormalizeXCount();

7557

tempc2df->NormalizeYCount();

7558

switch(o->m_pCDF->m_iNormalize)

7559

{

7560

case 2:

7561

tempc2df->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

7562

break;

7563

case 1:

7564

tempc2df->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

7565

break;

7566

case 0:

7567

break;

7568

}

7569

tempc2df->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_nXY.nb",false);

7570

delete tempc2df;

7571

7572

mprintf(" Calculating tensor product of CDF projections...\n");

7573

7574

try { o->m_pCDF->m_pTensorProduct = new C2DF(); } catch(...) { o->m_pCDF->m_pTensorProduct = NULL; }

7575

if (o->m_pCDF->m_pTensorProduct == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7576

7577

o->m_pCDF->m_pTensorProduct->CopyFrom(o->m_pCDF->m_p2DF);

7578

o->m_pCDF->m_pTensorProduct->MakeTensorProduct(o->m_pCDF->m_p2DF);

7579

switch(o->m_pCDF->m_iNormalize)

7580

{

7581

case 2:

7582

o->m_pCDF->m_pTensorProduct->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

7583

break;

7584

case 1:

7585

o->m_pCDF->m_pTensorProduct->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

7586

break;

7587

case 0:

7588

break;

7589

}

7590

mprintf(" Saving tensor product as \"%s%s_tensor.dat\"...\n",o->m_pCDF->m_sName,multibuf);

7591

o->m_pCDF->m_pTensorProduct->Write(o->m_pCDF->m_sName,multibuf,"_tensor.dat");

7592

mprintf(" Saving tensor product Mathematica Notebook as \"%s%s_tensor.nb\"...\n",o->m_pCDF->m_sName,multibuf);

7593

o->m_pCDF->m_pTensorProduct->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_tensor.nb",false);

7594

mprintf(" Calculating difference between CDF and tensor product...\n");

7595

o->m_pCDF->m_p2DF->Subtract(o->m_pCDF->m_pTensorProduct);

7596

o->m_pCDF->m_p2DF->CalcMaxEntry();

7597

// o->m_pCDF->m_p2DF->m_fMathematicaColorOffset = max(fabs(o->m_pCDF->m_p2DF->m_fMinEntry),fabs(o->m_pCDF->m_p2DF->m_fMaxEntry)) / 3.0;

7598

// o->m_pCDF->m_p2DF->m_fMathematicaColorScale = o->m_pCDF->m_p2DF->m_fMathematicaColorOffset * 2.0;

7599

mprintf(" Saving tensor difference as \"%s%s_tensordiff.dat\"...\n",o->m_pCDF->m_sName,multibuf);

7600

o->m_pCDF->m_p2DF->Write(o->m_pCDF->m_sName,multibuf,"_tensordiff.dat");

7601

mprintf(" Saving tensor difference Mathematica Notebook as \"%s%s_tensordiff.nb\"...\n",o->m_pCDF->m_sName,multibuf);

7602

o->m_pCDF->m_p2DF->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_tensordiff.nb",false);

7603

} // END IF AXISDIVIDE

7604

if (o->m_pCDF->m_bDumpDat)

7605

{

7606

fclose(o->m_pCDF->m_fDump);

7607

mprintf(" CDF raw data saved as cdfdump_%dd_%s%s.csv.\n",g_iCDFChannels,o->m_pCDF->m_sShortName,multibuf);

7608

}

7609

if (o->m_bTimeDev)

7610

{

7611

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

7612

{

7613

fclose(o->m_pCDF->m_fTimeDev[0]);

7614

// sprintf(buf,"cdf_timedev_%dd_%s_ref%d%s.csv",g_iCDFChannels,o->m_pCDF->m_sShortName,z2+1,multibuf);

7615

mprintf(" Temporal development saved as cdf_timedev_%dd%s%s.csv\n",g_iCDFChannels,o->m_pCDF->m_sShortName,multibuf);

7616

} else

7617

{

7618

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

7619

{

7620

fclose(o->m_pCDF->m_fTimeDev[z2]);

7621

mprintf(" Temporal development saved as cdf_timedev_%dd%s_ref%d%s.csv\n",g_iCDFChannels,o->m_pCDF->m_sShortName,z2+1,multibuf);

7622

}

7623

}

7624

if (o->m_pCDF->m_bTDAnimation)

7625

{

7626

mprintf(WHITE," * Time dependent animation *\n");

7627

sprintf(buf,"animation_complete_%s%s.agr",o->m_pCDF->m_sName,multibuf);

7628

mprintf(" Saving complete Plot as \"%s\"...\n",buf);

7629

for (z2=0;z2<o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled;z2++)

7630

{

7631

o->m_pCDF->m_pTDAPlot->SetSetLineWidth(z2,2.0f);

7632

o->m_pCDF->m_pTDAPlot->SetSetLineColorLong(z2,GraceColor(z2,0.0));

7633

}

7634

o->m_pCDF->m_pTDAPlot->WriteAgr(buf,false);

7635

sprintf(buf,"render_%s%s",o->m_pCDF->m_sName,multibuf);

7636

mprintf(" Saving xmgrace render script for animation as \"%s\"...\n",buf);

7637

a = OpenFileWrite("gracebatch",true);

7638

fprintf(a,"PRINT TO \"output.png\"\n");

7639

fprintf(a,"HARDCOPY DEVICE \"PNG\"\n");

7640

fprintf(a,"PAGE SIZE %d, %d\n",o->m_pCDF->m_iTDAResX,o->m_pCDF->m_iTDAResY);

7641

fprintf(a,"DEVICE \"PNG\" FONT ANTIALIASING on\n");

7642

fprintf(a,"DEVICE \"PNG\" OP \"compression:9\"\n");

7643

fprintf(a,"PRINT\n");

7644

fclose(a);

7645

a = OpenFileWrite(buf,true);

7646

if (o->m_pCDF->m_bTDATrace)

7647

{

7648

for (z2=0;z2<o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled;z2++)

7649

{

7650

o->m_pCDF->m_pTDAPlot->DuplicateSet(z2);

7651

o->m_pCDF->m_pTDAPlot->SetSetLineWidth(z2,2.0f);

7652

o->m_pCDF->m_pTDAPlot->SetSetLineColorLong(z2,GraceColor(z2,0.7));

7653

o->m_pCDF->m_pTDAPlot->SetSetLineWidth(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled+z2,3.0f);

7654

o->m_pCDF->m_pTDAPlot->SetSetLineColorLong(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled+z2,GraceColor(z2,0.0));

7655

}

7656

}

7657

for (z2=0;z2<o->m_pCDF->m_iTDASteps;z2++)

7658

{

7659

if (o->m_pCDF->m_bTDATrace)

7660

{

7661

for (z3=0;z3<o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled;z3++)

7662

{

7663

o->m_pCDF->m_pTDAPlot->SetSetRange(z3+o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled,z2*o->m_pCDF->m_iTDAStride,z2*o->m_pCDF->m_iTDAStride+o->m_pCDF->m_iTDATail);

7664

o->m_pCDF->m_pTDAPlot->SetSetRange(z3,0,z2*o->m_pCDF->m_iTDAStride);

7665

}

7666

} else

7667

{

7668

for (z3=0;z3<o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled;z3++)

7669

o->m_pCDF->m_pTDAPlot->SetSetRange(z3,z2*o->m_pCDF->m_iTDAStride,z2*o->m_pCDF->m_iTDAStride+o->m_pCDF->m_iTDATail);

7670

}

7671

7672

sprintf(buf,"animation_%05d_%s%s.agr",z2+1,o->m_pCDF->m_sName,multibuf);

7673

mprintf(" Saving frame \"%s\"...\n",buf);

7674

o->m_pCDF->m_pTDAPlot->WriteAgr(buf,false);

7675

fprintf(a,"echo 'Printing frame %d of %d'\n",z2+1,o->m_pCDF->m_iTDASteps);

7676

fprintf(a,"xmgrace %s -batch gracebatch -nosafe -hardcopy\n",buf);

7677

fprintf(a,"mv output.png frame%04d.png\n",z2+1);

7678

}

7679

fclose(a);

7680

}

7681

}

7682

} // END IF CHANNELS == 2

7683

7684

if (g_iCDFChannels == 3)

7685

{

7686

mprintf(WHITE,"* Combined Distribution Function (3D)\n");

7687

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pCDF->m_p3DF->m_fBinEntries,o->m_pCDF->m_p3DF->m_fSkipEntries,ZeroDivide(o->m_pCDF->m_p3DF->m_fSkipEntries,o->m_pCDF->m_p3DF->m_fSkipEntries+o->m_pCDF->m_p3DF->m_fBinEntries)*100.0);

7688

if (o->m_pCDF->m_p3DF->m_fBinEntries == 0)

7689

{

7690

eprintf(" There were no bin entries. Check your CDF definition. Skipping this CDF.\n\n");

7691

goto _skipsdf;

7692

}

7693

o->m_pCDF->m_p3DF->CalcMaxEntry();

7694

mprintf(" Data range from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

7695

for (z2=0;z2<g_iCDFChannels;z2++)

7696

{

7697

if (g_iObsChannel[z2] == 0)

7698

{

7699

if (o->m_pRDF[z2]->m_bRadialCorrect)

7700

{

7701

mprintf(" Correcting radial distribution for CDF channel %d...\n",z2+1);

7702

o->m_pCDF->m_p3DF->CorrectRadialDist(z2);

7703

o->m_pCDF->m_p3DF->CalcMaxEntry();

7704

mprintf(" Data range from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

7705

}

7706

}

7707

if (g_iObsChannel[z2] == 1)

7708

{

7709

if (o->m_pADF[z2]->m_bStat && (!o->m_pADF[z2]->m_bCosine))

7710

{

7711

mprintf(" Correcting angular distribution for CDF channel %d...\n",z2+1);

7712

o->m_pCDF->m_p3DF->CorrectAngle(z2);

7713

o->m_pCDF->m_p3DF->CalcMaxEntry();

7714

mprintf(" Data range from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

7715

}

7716

if (o->m_pADF[z2]->m_bMirror)

7717

{

7718

mprintf(" Making channel %d mirror-symmetric...\n",z2+1);

7719

if (o->m_pADF[z2]->m_bCosine)

7720

o->m_pCDF->m_p2DF->Mirror(0.0f,z2);

7721

else o->m_pCDF->m_p2DF->Mirror(90.0f,z2);

7722

o->m_pCDF->m_p3DF->CalcMaxEntry();

7723

mprintf(" Data range from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

7724

}

7725

}

7726

}

7727

// o->m_pCDF->m_p3DF->CalcMaxEntry();

7728

// mprintf(" Data range now from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

7729

o->m_pCDF->m_fFactor = 1.0;

7730

switch(o->m_pCDF->m_iNormalize)

7731

{

7732

case 2:

7733

mprintf(" Normalizing maximum value to %.2f.\n",o->m_pCDF->m_fNormValue);

7734

o->m_pCDF->m_p3DF->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

7735

o->m_pCDF->m_p3DF->CalcMaxEntry();

7736

mprintf(" Data range now from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

7737

break;

7738

case 1:

7739

mprintf(" Normalizing integral value to %.2f.\n",o->m_pCDF->m_fNormValue);

7740

o->m_pCDF->m_fFactor = o->m_pCDF->m_p3DF->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

7741

mprintf(" Factor was %G.\n",o->m_pCDF->m_fFactor);

7742

o->m_pCDF->m_p3DF->CalcMaxEntry();

7743

mprintf(" Data range now from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

7744

break;

7745

case 0:

7746

mprintf(" Not normalizing this CDF.\n");

7747

break;

7748

}

7749

7750

for (z2=0;z2<=g_iSDFSmoothGrade;z2++)

7751

{

7752

try { temp3DF = new C3DF(); } catch(...) { temp3DF = NULL; }

7753

if (temp3DF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7754

7755

temp3DF->CopyFrom(o->m_pCDF->m_p3DF);

7756

if (z2 != 0)

7757

{

7758

temp3DF->Smooth(z2);

7759

sprintf(buf,".s%d%s.plt",z2,multibuf);

7760

} else sprintf(buf,"%s.plt",multibuf);

7761

mprintf(" Saving 3D CDF as \"%s%s\"...\n",o->m_pCDF->m_sName,buf);

7762

temp3DF->WritePLT("",o->m_pCDF->m_sName,buf,false);

7763

7764

if (z2 != 0)

7765

sprintf(buf,".s%d%s.cube",z2,multibuf);

7766

else sprintf(buf,"%s.cube",multibuf);

7767

mprintf(" Saving 3D CDF as \"%s%s\"...\n",o->m_pCDF->m_sName,buf);

7768

temp3DF->WriteCube("",o->m_pCDF->m_sName,buf,false);

7769

if (o->m_pCDF->m_iHistogramRes != 0)

7770

{

7771

mprintf(" Calculating Histogram...\n");

7772

temp3DF->CalcHistogram();

7773

if (z2 != 0)

7774

sprintf(buf,"his_%s.s%d",o->m_pCDF->m_sName,z2);

7775

else sprintf(buf,"his_%s",o->m_pCDF->m_sName);

7776

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf,multibuf);

7777

temp3DF->WriteHistogram(buf,multibuf,".csv");

7778

}

7779

7780

if (o->m_pCDF->m_b3DSlices)

7781

{

7782

for (z3=0;z3<3;z3++)

7783

{

7784

if (o->m_pCDF->m_i3DSliceIntervals[z3] != 0)

7785

{

7786

if (z2 != 0)

7787

mprintf(WHITE," * Creating channel %d smooth grade %d slices...\n",z3+1,z2);

7788

else mprintf(WHITE," * Creating channel %d slices...\n",z3+1);

7789

7790

temp2dfa = new C2DF*[o->m_pCDF->m_i3DSliceIntervals[z3]];

7791

7792

tf = 0;

7793

for (z4=0;z4<o->m_pCDF->m_i3DSliceIntervals[z3];z4++)

7794

{

7795

temp2dfa[z4] = new C2DF();

7796

temp3DF->CreateSlice(z3,(double)z4/o->m_pCDF->m_i3DSliceIntervals[z3]*o->m_pCDF->m_p3DF->m_iRes[z3],(z4+1.0)/o->m_pCDF->m_i3DSliceIntervals[z3]*o->m_pCDF->m_p3DF->m_iRes[z3]-1,temp2dfa[z4]);

7797

mprintf(" - %2d: %9.4f - %9.4f (%3d - %3d), Intensity range %.3f ... %.3f\n",z4+1,o->m_pCDF->m_p3DF->m_fMinVal[z3]+(double)z4/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]),o->m_pCDF->m_p3DF->m_fMinVal[z3]+(z4+1.0)/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]),int((double)z4/o->m_pCDF->m_i3DSliceIntervals[z3]*o->m_pCDF->m_p3DF->m_iRes[z3]),int((z4+1.0)/o->m_pCDF->m_i3DSliceIntervals[z3]*o->m_pCDF->m_p3DF->m_iRes[z3]-1),temp2dfa[z4]->m_fMinEntry,temp2dfa[z4]->m_fMaxEntry);

7798

if (temp2dfa[z4]->m_fMaxEntry > tf)

7799

tf = temp2dfa[z4]->m_fMaxEntry;

7800

}

7801

7802

mprintf(" Setting common intensity range to 0 ... %.3f.\n",tf);

7803

7804

mprintf(" Writing out slice files...\n",z3+1);

7805

7806

for (z4=0;z4<o->m_pCDF->m_i3DSliceIntervals[z3];z4++)

7807

{

7808

temp2dfa[z4]->m_fMinEntry = 0;

7809

temp2dfa[z4]->m_fMaxEntry = tf;

7810

if (z2 != 0)

7811

sprintf(buf,"%s_slice_ch%d_%d_%.3f-%.3f.s%d.nb",o->m_pCDF->m_sName,z3+1,z4+1,o->m_pCDF->m_p3DF->m_fMinVal[z3]+(double)z4/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]),o->m_pCDF->m_p3DF->m_fMinVal[z3]+(z4+1.0)/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]),z2);

7812

else sprintf(buf,"%s_slice_ch%d_%d_%.3f-%.3f.nb",o->m_pCDF->m_sName,z3+1,z4+1,o->m_pCDF->m_p3DF->m_fMinVal[z3]+(double)z4/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]),o->m_pCDF->m_p3DF->m_fMinVal[z3]+(z4+1.0)/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]));

7813

mprintf(" %s ...\n",buf);

7814

temp2dfa[z4]->WriteMathematicaNb("",buf,"",true);

7815

}

7816

7817

for (z4=0;z4<o->m_pCDF->m_i3DSliceIntervals[z3];z4++)

7818

delete temp2dfa[z4];

7819

7820

delete[] temp2dfa;

7821

}

7822

}

7823

}

7824

}

7825

7826

mprintf(" Writing out 2D projections...\n");

7827

for (z3=0;z3<3;z3++)

7828

{

7829

mprintf(WHITE," * CDF 2D projection on channel %d\n",z3+1);

7830

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fBinEntries,o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fSkipEntries,ZeroDivide(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fSkipEntries,o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fSkipEntries+o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fBinEntries)*100.0);

7831

switch(z3)

7832

{

7833

case 0:

7834

tia[0] = 0;

7835

tia[1] = 1;

7836

break;

7837

case 1:

7838

tia[0] = 0;

7839

tia[1] = 2;

7840

break;

7841

case 2:

7842

tia[0] = 1;

7843

tia[1] = 2;

7844

break;

7845

}

7846

for (z2=0;z2<2;z2++)

7847

{

7848

if (g_iObsChannel[tia[z2]] == 0)

7849

{

7850

if (o->m_pRDF[tia[z2]]->m_bRadialCorrect)

7851

{

7852

mprintf(" Correcting radial distribution for CDF channel %d...\n",z2+1);

7853

o->m_pCDF->m_p3DF->m_p2DF[z3]->CorrectRadialDist(z2);

7854

}

7855

}

7856

if (g_iObsChannel[tia[z2]] == 1)

7857

{

7858

if (o->m_pADF[tia[z2]]->m_bStat && (!o->m_pADF[tia[z2]]->m_bCosine))

7859

{

7860

mprintf(" Correcting angular distribution for CDF channel %d...\n",z2+1);

7861

o->m_pCDF->m_p3DF->m_p2DF[z3]->CorrectAngle(z2);

7862

}

7863

/* if (o->m_pADF[z2]->m_bMirror)

7864

{

7865

mprintf(" Making channel %d mirror-symmetric...\n",z2+1);

7866

if (o->m_pADF[z2]->m_bCosine)

7867

o->m_pCDF->m_p2DF->Mirror(0.0f,z2);

7868

else o->m_pCDF->m_p2DF->Mirror(90.0f,z2);

7869

}*/

7870

}

7871

}

7872

o->m_pCDF->m_fFactor = 1.0;

7873

switch(o->m_pCDF->m_iNormalize)

7874

{

7875

case 2:

7876

mprintf(" Normalizing maximum value to %.2f.\n",o->m_pCDF->m_fNormValue);

7877

o->m_pCDF->m_p3DF->m_p2DF[z3]->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

7878

break;

7879

case 1:

7880

mprintf(" Normalizing integral value to %.2f.\n",o->m_pCDF->m_fNormValue);

7881

o->m_pCDF->m_p3DF->m_p2DF[z3]->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

7882

break;

7883

case 0:

7884

mprintf(" Not normalizing this CDF.\n");

7885

break;

7886

}

7887

mprintf(" Saving CDF triples as \"%s%s_triples.csv\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

7888

o->m_pCDF->m_p3DF->m_p2DF[z3]->Write(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,"_triples.csv");

7889

mprintf(" Saving CDF matrix as \"%s%s_matrix.csv\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

7890

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteCSV(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,"_matrix.csv");

7891

mprintf(" Saving CDF Mathematica Notebook as \"%s%s.nb\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

7892

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteMathematicaNb(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,".nb",false);

7893

mprintf(" Saving combined plot AGR file as \"%s%s_combined.agr\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

7894

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteCombinedPlot(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,"_combined.agr");

7895

if (o->m_pCDF->m_iHistogramRes != 0)

7896

{

7897

mprintf(" Calculating Histogram...\n");

7898

o->m_pCDF->m_p3DF->m_p2DF[z3]->CalcHistogram();

7899

sprintf(buf,"his_%s",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName);

7900

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf,multibuf);

7901

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteHistogram(buf,multibuf,".csv");

7902

}

7903

}

7904

} // END IF CHANNELS == 3

7905

_skipsdf:;

7906

} // END IF CDF

7907

7908

if (g_bRevSDF)

7909

{

7910

mprintf(WHITE,"* Pseudo SDF\n");

7911

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pRevSDF->m_p2DF->m_fBinEntries,o->m_pRevSDF->m_p2DF->m_fSkipEntries,ZeroDivide(o->m_pRevSDF->m_p2DF->m_fSkipEntries,o->m_pRevSDF->m_p2DF->m_fSkipEntries+o->m_pRevSDF->m_p2DF->m_fBinEntries)*100.0);

7912

if (o->m_pRevSDF->m_p2DF->m_fBinEntries == 0)

7913

{

7914

eprintf(" There were no bin entries. Check your function definition. Skipping this PseudoSDF.\n\n");

7915

goto _skiprevsdf;

7916

}

7917

mprintf(" Normalizing integral value to %.2f.\n",1000000.0f);

7918

o->m_pRevSDF->m_p2DF->NormalizeBinIntegral(1000000.0f);

7919

if (o->m_pRevSDF->m_bDrawAtoms)

7920

{

7921

mprintf(" Inserting reference atoms into the Pseudo SDF plot...\n");

7922

7923

if (((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_fRadius == 0)

7924

o->m_pRevSDF->m_p2DF->AddCircle(0,0,50.0,0.4,0.4,0.4);

7925

else o->m_pRevSDF->m_p2DF->AddCircle(0,0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_fRadius*0.75,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_iColorR/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_iColorG/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_iColorB/255.0);

7926

7927

if (((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_fRadius == 0)

7928

o->m_pRevSDF->m_p2DF->AddCircle(0,o->m_pRevSDF->m_fSecondAtomPosX/o->m_pRevSDF->m_fSecondAtomCount,50.0,0.4,0.4,0.4);

7929

else o->m_pRevSDF->m_p2DF->AddCircle(0,o->m_pRevSDF->m_fSecondAtomPosX/o->m_pRevSDF->m_fSecondAtomCount,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_fRadius*0.75,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_iColorR/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_iColorG/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_iColorB/255.0);

7930

}

7931

mprintf(" Saving PseudoSDF triples as \"%s%s_triples.csv\"...\n",o->m_pRevSDF->m_sName,multibuf);

7932

o->m_pRevSDF->m_p2DF->Write(o->m_pRevSDF->m_sName,multibuf,"_triples.csv");

7933

mprintf(" Saving PseudoSDF matrix as \"%s%s_matrix.csv\"...\n",o->m_pRevSDF->m_sName,multibuf);

7934

o->m_pRevSDF->m_p2DF->WriteCSV(o->m_pRevSDF->m_sName,multibuf,"_matrix.csv");

7935

mprintf(" Saving PseudoSDF Mathematica Notebook as \"%s%s.nb\"...\n",o->m_pRevSDF->m_sName,multibuf);

7936

o->m_pRevSDF->m_p2DF->WriteMathematicaNb(o->m_pRevSDF->m_sName,multibuf,".nb",false);

7937

if (o->m_pRevSDF->m_iHistogramRes != 0)

7938

{

7939

mprintf(" Calculating Histogram...\n");

7940

o->m_pRevSDF->m_p2DF->CalcHistogram();

7941

sprintf(buf,"his_%s",o->m_pRevSDF->m_sName);

7942

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf,multibuf);

7943

o->m_pRevSDF->m_p2DF->WriteHistogram(buf,multibuf,".csv");

7944

}

7945

if (o->m_pRevSDF->m_bCreateRevSDF)

7946

{

7947

mprintf(" Creating volumetric Revolution SDF...\n");

7948

o->m_pRevSDF->CreateRevSDF();

7949

sprintf(buf,"revsdf_ref_%s.xyz",o->m_pRevSDF->m_sName);

7950

mprintf(" Saving Revolution SDF reference structure as \"%s\"...\n",buf);

7951

a = OpenFileWrite(buf,true);

7952

fprintf(a,"2\n\n%s 0.0 0.0 0.0\n%s 0.0 %f 0.0\n",((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_sName,o->m_pRevSDF->m_fSecondAtomPosX/o->m_pRevSDF->m_fSecondAtomCount/100.0);

7953

fclose(a);

7954

for (z2=0;z2<=g_iSDFSmoothGrade;z2++)

7955

{

7956

try { tempSDF = new C3DF(); } catch(...) { tempSDF = NULL; }

7957

if (tempSDF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7958

7959

tempSDF->CopyFrom(o->m_pRevSDF->m_pRevSDF);

7960

if (z2 != 0)

7961

{

7962

tempSDF->Smooth(z2);

7963

sprintf(buf,".s%d%s.plt",z2,multibuf);

7964

} else sprintf(buf,"%s.plt",multibuf);

7965

mprintf(" Saving Revolution SDF as \"revsdf_%s%s\"...\n",o->m_pRevSDF->m_sName,buf);

7966

tempSDF->WritePLT("revsdf_",o->m_pRevSDF->m_sName,buf,true);

7967

7968

if (z2 != 0)

7969

sprintf(buf,".s%d%s.cube",z2,multibuf);

7970

else sprintf(buf,"%s.cube",multibuf);

7971

mprintf(" Saving Revolution SDF as \"revsdf_%s%s\"...\n",o->m_pRevSDF->m_sName,buf);

7972

tempSDF->WriteCube("revsdf_",o->m_pRevSDF->m_sName,buf,true);

7973

7974

if (z2 != 0)

7975

sprintf(buf,".s%d%s.his",z2,multibuf);

7976

else sprintf(buf,"%s.his",multibuf);

7977

mprintf(" Saving Revolution SDF Histogram as \"revsdf_%s%s\"...\n",o->m_pRevSDF->m_sName,buf);

7978

tempSDF->CalcHistogram();

7979

tempSDF->WriteHistogram("revsdf_",o->m_pRevSDF->m_sName,buf);

7980

if (o->m_pRevSDF->m_iHistogramRes != 0)

7981

{

7982

mprintf(" Calculating Histogram...\n");

7983

tempSDF->CalcHistogram();

7984

sprintf(buf2,"his_revsdf_%s",o->m_pRevSDF->m_sName);

7985

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf2,buf);

7986

tempSDF->WriteHistogram(buf2,buf,".csv");

7987

}

7988

}

7989

}

7990

_skiprevsdf:;

7991

} // END IF REVSDF

7992

}

7993

7994

if (g_bSDF || g_bAvg || g_bVoidSDF)

7995

{

7996

sprintf(buf,"ref_%s_%s%d_%s%d_%s%d%s.xyz",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_sName,g_iFixAtom[1]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_sName,g_iFixAtom[2]+1,multibuf);

7997

strtolower(buf);

7998

mprintf("\n*** Reference molecule ***\n");

7999

FreeFileName(buf);

8000

mprintf("Saving reference molecule as \"%s\"...",buf);

8001

a = OpenFileWrite(buf,true);

8002

if (a == NULL)

8003

{

8004

eprintf("\nError: Could not open %s for writing.\n",buf);

8005

return 0;

8006

}

8007

if (!g_bSaveVirtAtoms)

8008

fprintf(a," %d \n\n",(int)(((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes-((CMolecule*)g_oaMolecules[g_iFixMol])->m_laVirtualAtoms.GetSize()));

8009

else fprintf(a," %d \n\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes);

8010

cc = 0;

8011

for (z=0;z<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z++)

8012

{

8013

if ((!g_bSaveVirtAtoms) && (((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z] == g_iVirtAtomType))

8014

continue;

8015

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z];z2++)

8016

{

8017

if (g_bMiddleAvg)

8018

{

8019

g_pRefMol[cc][0] /= ((float)g_iSteps * ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

8020

g_pRefMol[cc][1] /= ((float)g_iSteps * ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

8021

g_pRefMol[cc][2] /= ((float)g_iSteps * ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

8022

}

8023

if (((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z] == g_iVirtAtomType)

8024

fprintf(a," %s %9.6f %9.6f %9.6f\n",((CVirtualAtom*)g_oaVirtualAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laVirtualAtoms[z2]])->m_sLabel,g_pRefMol[cc][0]/100.0,g_pRefMol[cc][1]/100.0,g_pRefMol[cc][2]/100.0);

8025

else fprintf(a," %s %9.6f %9.6f %9.6f\n",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z]])->m_sName,g_pRefMol[cc][0]/100.0,g_pRefMol[cc][1]/100.0,g_pRefMol[cc][2]/100.0);

8026

cc++;

8027

}

8028

}

8029

fclose(a);

8030

mprintf("Done.\n");

8031

if (g_iSwapAtoms)

8032

{

8033

mprintf("\n*** This is the swap matrix of reference molecule %s:\n (It shows how often the atoms\n have been swapped with each other)\n\n ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);

8034

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z2++)

8035

{

8036

for (z3=0;z3<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z2];z3++)

8037

{

8038

if (((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z2]])->m_sName[1] == 0)

8039

mprintf(" ");

8040

mprintf("%s%d ",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z2]])->m_sName,z3+1);

8041

if (z3 < 10)

8042

mprintf(" ");

8043

}

8044

}

8045

mprintf("\n");

8046

cc = 0;

8047

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z2++)

8048

{

8049

for (z3=0;z3<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z2];z3++)

8050

{

8051

mprintf("%s%d ",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z2]])->m_sName,z3+1);

8052

if (((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z2]])->m_sName[1] == 0)

8053

mprintf(" ");

8054

if (z3 < 9)

8055

mprintf(" ");

8056

cc2 = 0;

8057

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z4++)

8058

{

8059

for (z5=0;z5<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z4];z5++)

8060

{

8061

if ((z2 == z4) && (z3 == z5))

8062

{

8063

mprintf(" *** ");

8064

goto _swm;

8065

}

8066

if (g_pSwapMatrix[cc*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes+cc2] != 0)

8067

mprintf("%3.0f%c ",(double)g_pSwapMatrix[cc*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes+cc2] * 100.0f / g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize(),'%');

8068

else mprintf(" - ");

8069

_swm:

8070

cc2++;

8071

}

8072

}

8073

mprintf("\n");

8074

cc++;

8075

}

8076

}

8077

}

8078

}

8079

_ende:

8080

8081

if (g_bMultiInterval)

8082

{

8083

mprintf("\n");

8084

mprintf(YELLOW,"***********************************************\n");

8085

mprintf(YELLOW,"*** Interval %2d (%6d - %6d) finished. ***\n",multicounter+1,g_laMultiIntervalStart[multicounter]+1,g_laMultiIntervalEnd[multicounter]+1);

8086

mprintf(YELLOW,"***********************************************\n\n");

8087

multicounter++;

8088

if (multicounter < g_laMultiIntervalStart.GetSize())

8089

goto _multiintervalstart;

8090

}

8091

8092

/* if (g_bSDF)

8093

delete g_pSDFBin;

8094

if (g_bRDF)

8095

delete g_pRDFBin;*/

8096

8097

g_iEndTime = time(NULL);

8098

if (((g_iEndTime-g_iStartTime) > 5) && (g_iStartTime != 0))

8099

{

8100

mprintf(WHITE,"\nAnalysis was running for %dh %dm %ds.\n",(g_iEndTime-g_iStartTime)/3600,((g_iEndTime-g_iStartTime)/60)%60,(g_iEndTime-g_iStartTime)%60);

8101

mprintf(WHITE," (%.3f steps per second)\n\n",g_iSteps/g_iStride/((double)g_iEndTime-g_iStartTime));

8102

} else mprintf("\n");

8103

8104

WriteCredits();

8105

8106

if (g_bSMode)

8107

{

8108

PrintSMode();

8109

} else

8110

{

8111

mprintf(WHITE,"*** The End ***\n\n");

8112

}

8113

UninstallSignalHandler();

8114

if (g_fInput != NULL)

8115

fclose(g_fInput);

8116

if (g_pDatabase != NULL)

8117

{

8118

delete g_pDatabase;

8119

g_pDatabase = NULL;

8120

}

8121

if (g_pTempTimestep != NULL)

8122

{

8123

delete g_pTempTimestep;

8124

g_pTempTimestep = NULL;

8125

}

8126

if (apfa != NULL)

8127

{

8128

delete[] apfa;

8129

apfa = NULL;

8130

}

8131

if (tda != NULL)

8132

{

8133

delete[] tda;

8134

tda = NULL;

8135

}

8136

RemoveAllAnalyses();

8137

RemoveAllElements();

8138

RemoveAllAtoms();

8139

RemoveAllMolecules();

8140

RemoveAllObservations();

8141

BTOUT;

8142

return 0;

8143

}