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Viewing changes to src/timestep.cpp

Committer: Package Import Robot
Author(s): Daniel Leidert
Date: 2013-12-13 23:35:55 UTC
mfrom: (1.1.7)
Revision ID: package-import@ubuntu.com-20131213233555-4o11bd1ybycqh0l7

Tags: 131115-1

* New upstream release.
* debian/control (Standards-Version): Bumped to 3.9.5.

Show diffs side-by-side

added added

removed removed

src/timestep.cpp

CVirtualAtom *v;

CSingleMolecule *sm;

tv = 0;

// mprintf("** CalcCenters **");

if (m_vaCoords.GetSize() < g_iGesVirtAtomCount)

534

536

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

535

537

{

536

538

ta[z] = 0;

537

g_laAtomSMIndex[z] = 0;

539

g_laAtomSMIndex[z] = -1;

538

540

}

539

541

g_iBondBlackListUsed = 0;

540

542

g_oaSingleMolecules.RemoveAll();

1862

1864

}

1863

1865

1864

1866

1865

void CTimeStep::WriteTimestepNb(FILE *a, CNbSet *nbs)

1867

void CTimeStep::WriteTimestepNb(FILE *a, CNbSet *nbs, int singlemol)

1866

1868

{

1867

1869

BTIN;

1868

int z, z2, z3, z4, z0, n;

1870

int z, z2, z3, z4, z0, n, ti;

1869

1871

CMolecule *m;

1870

1872

CSingleMolecule *sm;

1873

CConditionGroup *cg;

1874

CConditionSubGroup *cs;

1875

CNbSearch *nb;

1871

1876

1872

1877

n = 0;

1878

1873

1879

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

1874

1880

{

1875

1881

if (nbs->m_oaConditionGroups[z] == NULL)

1887

1893

}

1888

1894

1889

1895

mfprintf(a," %d\n",n);

1890

if (m_pComment != NULL)

1891

mfprintf(a,"%s\n",m_pComment);

1892

else mfprintf(a,"\n");

1896

1897

mfprintf(a,"# Step %d",((int)g_iSteps));

1898

1899

if (singlemol >= 0)

1900

{

1901

sm = (CSingleMolecule*)g_oaSingleMolecules[singlemol];

1902

m = (CMolecule*)g_oaMolecules[sm->m_iMolType];

1903

if (!g_bSaveVirtAtoms)

1904

{

1905

if (g_bWriteAtomwise)

1906

mfprintf(a,", RM=%s[%d]",m->m_sName,sm->m_iMolSMIndex+1);

1907

else mfprintf(a,", RM=%s[%d] (%d atoms)",m->m_sName,sm->m_iMolSMIndex+1,m->m_iAtomGes-m->m_laVirtualAtoms.GetSize());

1908

} else

1909

{

1910

if (g_bWriteAtomwise)

1911

mfprintf(a,", RM=%s[%d]",m->m_sName,sm->m_iMolSMIndex+1);

1912

else mfprintf(a,", RM=%s[%d] (%d atoms)",m->m_sName,sm->m_iMolSMIndex+1,m->m_iAtomGes);

1913

}

1914

}

1915

1916

if (g_bEnvWriteDetailedInfo)

1917

{

1918

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

1919

{

1920

if (nbs->m_oaConditionGroups[z] == NULL)

1921

continue;

1922

m = (CMolecule*)g_oaMolecules[z];

1923

1924

cg = (CConditionGroup*)nbs->m_oaConditionGroups[z];

1925

1926

if (g_bEnvSortNb)

1927

{

1928

nb = NULL;

1929

if (cg->m_oaConditionSubGroups.GetSize() == 1)

1930

{

1931

cs = (CConditionSubGroup*)cg->m_oaConditionSubGroups[0];

1932

if (cs->m_oaConditions.GetSize() == 1)

1933

nb = (CNbSearch*)cs->m_oaConditions[0];

1934

}

1935

if (nb == NULL)

1936

goto _nosortinfo;

1937

1938

if (nb->m_iNbCountMin <= -1)

1939

goto _nosortinfo;

1940

1941

for (z2=nb->m_iNbCountMin;z2<=nb->m_iNbCountMax;z2++)

1942

{

1943

ti = nb->m_pNbSort[z2].m_iOM;

1944

if (!g_bSaveVirtAtoms)

1945

{

1946

if (m->m_laSingleMolIndex[ti] != singlemol)

1947

{

1948

if (g_bWriteAtomwise)

1949

mfprintf(a,", %s[%d] d=%.3fpm",m->m_sName,z2+1,nb->m_pNbSort[z2].m_fMinDist);

1950

else mfprintf(a,", %s[%d] d=%.3fpm (%d atoms)",m->m_sName,ti+1,nb->m_pNbSort[z2].m_fMinDist,m->m_iAtomGes-m->m_laVirtualAtoms.GetSize());

1951

}

1952

} else

1953

{

1954

if (m->m_laSingleMolIndex[ti] != singlemol)

1955

{

1956

if (g_bWriteAtomwise)

1957

mfprintf(a,", %s[%d] d=%.3fpm",m->m_sName,z2+1,nb->m_pNbSort[z2].m_fMinDist);

1958

else mfprintf(a,", %s[%d] d=%.3fpm (%d atoms)",m->m_sName,ti+1,nb->m_pNbSort[z2].m_fMinDist,m->m_iAtomGes);

1959

}

1960

}

1961

}

1962

} else

1963

{

1964

_nosortinfo:

1965

for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)

1966

{

1967

if (cg->Contains(z2))

1968

{

1969

if (!g_bSaveVirtAtoms)

1970

{

1971

if (m->m_laSingleMolIndex[z2] != singlemol)

1972

{

1973

if (g_bWriteAtomwise)

1974

mfprintf(a,", %s[%d]",m->m_sName,z2+1);

1975

else mfprintf(a,", %s[%d] (%d atoms)",m->m_sName,z2+1,m->m_iAtomGes-m->m_laVirtualAtoms.GetSize());

1976

}

1977

} else

1978

{

1979

if (m->m_laSingleMolIndex[z2] != singlemol)

1980

{

1981

if (g_bWriteAtomwise)

1982

mfprintf(a,", %s[%d]",m->m_sName,z2+1);

1983

else mfprintf(a,", %s[%d] (%d atoms)",m->m_sName,z2+1,m->m_iAtomGes);

1984

}

1985

}

1986

}

1987

}

1988

}

1989

}

1990

}

1991

1992

mfprintf(a,"\n");

1893

1993

1894

1994

if (g_bWriteAtomwise)

1895

1995

{

1920

2020

}

1921

2021

} else

1922

2022

{

2023

if (singlemol >= 0)

2024

{

2025

sm = (CSingleMolecule*)g_oaSingleMolecules[singlemol];

2026

m = (CMolecule*)g_oaMolecules[sm->m_iMolType];

2027

for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)

2028

{

2029

if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))

2030

continue;

2031

for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)

2032

mfprintf(a," %s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]/100.0f);

2033

}

2034

}

2035

1923

2036

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

1924

2037

{

1925

2038

if (nbs->m_oaConditionGroups[z] == NULL)

1926

2039

continue;

1927

2040

m = (CMolecule*)g_oaMolecules[z];

1928

for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)

2041

cg = (CConditionGroup*)nbs->m_oaConditionGroups[z];

2042

2043

if (g_bEnvSortNb)

1929

2044

{

1930

if (((CConditionGroup*)nbs->m_oaConditionGroups[z])->Contains(z2))

1931

{

1932

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];

2045

nb = NULL;

2046

if (cg->m_oaConditionSubGroups.GetSize() == 1)

2047

{

2048

cs = (CConditionSubGroup*)cg->m_oaConditionSubGroups[0];

2049

if (cs->m_oaConditions.GetSize() == 1)

2050

nb = (CNbSearch*)cs->m_oaConditions[0];

2051

}

2052

if (nb == NULL)

2053

goto _nosort;

2054

2055

if (nb->m_iNbCountMin <= -1)

2056

goto _nosort;

2057

2058

for (z2=nb->m_iNbCountMin;z2<=nb->m_iNbCountMax;z2++)

2059

{

2060

ti = nb->m_pNbSort[z2].m_iOM;

2061

2062

if (m->m_laSingleMolIndex[ti] == singlemol)

2063

continue;

2064

2065

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

1933

2066

for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)

1934

2067

{

1935

2068

if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))

1938

2071

1939

2072

}

1940

2073

}

2074

} else

2075

{

2076

_nosort:

2077

for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)

2078

{

2079

if (((CConditionGroup*)nbs->m_oaConditionGroups[z])->Contains(z2))

2080

{

2081

if (m->m_laSingleMolIndex[z2] == singlemol)

2082

continue;

2083

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];

2084

for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)

2085

{

2086

if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))

2087

continue;

2088

for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)

2089

2090

}

2091

}

2092

}

1941

2093

}

1942

2094

}

1943

2095

}

3407

3559

m_faCharge[z] = (float)atof(q);

3408

3560

} else if (needinfo && (z==0))

3409

3561

{

3562

if (*p == 0)

3563

goto _no4;

3410

3564

q = p+1;

3565

if (*q == 0)

3566

goto _no4;

3411

3567

while (strchr(separators,*q) != NULL)

3412

3568

q++;

3413

3569

p = q;

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