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Viewing changes to src/lib/chemistry/molecule/molecule.cc

Committer: Bazaar Package Importer
Author(s): Michael Banck
Date: 2006-09-10 22:32:33 UTC
mfrom: (1.1.3 upstream) (3.1.1 etch)
Revision ID: james.westby@ubuntu.com-20060910223233-5dza8qes8de6qbdk

Tags: 2.3.1-1

http://bugs.debian.org/320604

* New upstream release.
  + Includes updated libtool; closes: #320604.
* debian/control.in (libsc7-dev): Remove superfluous Depends on
  libc6-dev.
* debian/control.in (libsc7): Remove conflicts with older versions of
  libsc.
* debian/rules (SO_NAME): Override to 7.

files added:
src/bin/mpqc/validate/ckpt/ckpt_0clkskmlyp.in

src/bin/mpqc/validate/ckpt/ckpt_0clkskmlyp.qci

src/bin/mpqc/validate/ckpt/ckpt_1clkskmlyp.in

src/bin/mpqc/validate/ckpt/ckpt_1clkskmlyp.qci

src/bin/mpqc/validate/ckpt/ckpt_clkskmlyp.in

src/bin/mpqc/validate/ckpt/ckpt_clkskmlyp.qci

src/bin/mpqc/validate/methods/clks_kmlyp.in

src/bin/mpqc/validate/methods/clks_kmlyp.qci

src/bin/mpqc/validate/methods/hsosks_kmlyp.in

src/bin/mpqc/validate/methods/hsosks_kmlyp.qci

src/bin/mpqc/validate/methods/uks_kmlyp.in

src/bin/mpqc/validate/methods/uks_kmlyp.qci

src/bin/mpqc/validate/ref/ckpt_0clkskmlyp.in

src/bin/mpqc/validate/ref/ckpt_0clkskmlyp.out

src/bin/mpqc/validate/ref/ckpt_0clkskmlyp.qci

src/bin/mpqc/validate/ref/ckpt_1clkskmlyp.in

src/bin/mpqc/validate/ref/ckpt_1clkskmlyp.out

src/bin/mpqc/validate/ref/ckpt_1clkskmlyp.qci

src/bin/mpqc/validate/ref/ckpt_clkskmlyp.in

src/bin/mpqc/validate/ref/ckpt_clkskmlyp.out

src/bin/mpqc/validate/ref/ckpt_clkskmlyp.qci

src/bin/mpqc/validate/ref/clscf_h2okmlyp6311gssc1.in

src/bin/mpqc/validate/ref/clscf_h2okmlyp6311gssc1.out

src/bin/mpqc/validate/ref/clscf_h2okmlyp6311gssc1.qci

src/bin/mpqc/validate/ref/clscf_h2okmlyp6311gssc2v.in

src/bin/mpqc/validate/ref/clscf_h2okmlyp6311gssc2v.out

src/bin/mpqc/validate/ref/clscf_h2okmlyp6311gssc2v.qci

src/bin/mpqc/validate/ref/clscf_h2okmlypsto3gc1.in

src/bin/mpqc/validate/ref/clscf_h2okmlypsto3gc1.out

src/bin/mpqc/validate/ref/clscf_h2okmlypsto3gc1.qci

src/bin/mpqc/validate/ref/clscf_h2okmlypsto3gc2v.in

src/bin/mpqc/validate/ref/clscf_h2okmlypsto3gc2v.out

src/bin/mpqc/validate/ref/clscf_h2okmlypsto3gc2v.qci

src/bin/mpqc/validate/ref/hsosscf_ch2hsoskmlyp6311gssc2v.in

src/bin/mpqc/validate/ref/hsosscf_ch2hsoskmlyp6311gssc2v.out

src/bin/mpqc/validate/ref/hsosscf_ch2hsoskmlyp6311gssc2v.qci

src/bin/mpqc/validate/ref/hsosscf_ch2hsoskmlypsto3gc2v.in

src/bin/mpqc/validate/ref/hsosscf_ch2hsoskmlypsto3gc2v.out

src/bin/mpqc/validate/ref/hsosscf_ch2hsoskmlypsto3gc2v.qci

src/bin/mpqc/validate/ref/hsosscf_h2ohsoskmlyp6311gssc2v.in

src/bin/mpqc/validate/ref/hsosscf_h2ohsoskmlyp6311gssc2v.out

src/bin/mpqc/validate/ref/hsosscf_h2ohsoskmlyp6311gssc2v.qci

src/bin/mpqc/validate/ref/hsosscf_h2ohsoskmlypsto3gc2v.in

src/bin/mpqc/validate/ref/hsosscf_h2ohsoskmlypsto3gc2v.out

src/bin/mpqc/validate/ref/hsosscf_h2ohsoskmlypsto3gc2v.qci

src/bin/mpqc/validate/ref/methods_clks_kmlyp.in

src/bin/mpqc/validate/ref/methods_clks_kmlyp.out

src/bin/mpqc/validate/ref/methods_clks_kmlyp.qci

src/bin/mpqc/validate/ref/methods_hsosks_kmlyp.in

src/bin/mpqc/validate/ref/methods_hsosks_kmlyp.out

src/bin/mpqc/validate/ref/methods_hsosks_kmlyp.qci

src/bin/mpqc/validate/ref/methods_uks_kmlyp.in

src/bin/mpqc/validate/ref/methods_uks_kmlyp.out

src/bin/mpqc/validate/ref/methods_uks_kmlyp.qci

src/bin/mpqc/validate/ref/uscf_ch2ukmlyp6311gssc2v.in

src/bin/mpqc/validate/ref/uscf_ch2ukmlyp6311gssc2v.out

src/bin/mpqc/validate/ref/uscf_ch2ukmlyp6311gssc2v.qci

src/bin/mpqc/validate/ref/uscf_ch2ukmlypsto3gc2v.in

src/bin/mpqc/validate/ref/uscf_ch2ukmlypsto3gc2v.out

src/bin/mpqc/validate/ref/uscf_ch2ukmlypsto3gc2v.qci

src/bin/mpqc/validate/ref/uscf_dh2ukmlyp6311gssd2h.in

src/bin/mpqc/validate/ref/uscf_dh2ukmlyp6311gssd2h.out

src/bin/mpqc/validate/ref/uscf_dh2ukmlyp6311gssd2h.qci

src/bin/mpqc/validate/ref/uscf_dh2ukmlypsto3gd2h.in

src/bin/mpqc/validate/ref/uscf_dh2ukmlypsto3gd2h.out

src/bin/mpqc/validate/ref/uscf_dh2ukmlypsto3gd2h.qci

src/bin/mpqc/validate/ref/uscf_h2oukmlyp6311gssc2v.in

src/bin/mpqc/validate/ref/uscf_h2oukmlyp6311gssc2v.out

src/bin/mpqc/validate/ref/uscf_h2oukmlyp6311gssc2v.qci

src/bin/mpqc/validate/ref/uscf_h2oukmlypsto3gc2v.in

src/bin/mpqc/validate/ref/uscf_h2oukmlypsto3gc2v.out

src/bin/mpqc/validate/ref/uscf_h2oukmlypsto3gc2v.qci

src/lib/math/optimize/lbfgs.f

src/lib/math/optimize/mcsearch.cc

src/lib/math/optimize/mcsearch.h

files modified:
CHANGES

CITATION

bin/config.guess

bin/config.sub

bin/install-sh

bin/ltmain.sh

configure

configure.in

debian/changelog

debian/control

debian/control.in

debian/rules

lib/autoconf/libtool.m4

lib/perl/QCParse.pm

src/bin/mpqc/validate/Makefile

src/bin/mpqc/validate/clscf.qci

src/bin/mpqc/validate/hsosscf.qci

src/bin/mpqc/validate/uscf.qci

src/lib/chemistry/molecule/atominfo.h

src/lib/chemistry/molecule/energy.h

src/lib/chemistry/molecule/fdhess.h

src/lib/chemistry/molecule/hess.cc

src/lib/chemistry/molecule/hess.h

src/lib/chemistry/molecule/molecule.cc

src/lib/chemistry/molecule/molecule.h

src/lib/chemistry/qc/dft/functional.cc

src/lib/chemistry/qc/dft/functional.h

src/lib/chemistry/qc/scf/scf.h

src/lib/chemistry/qc/scf/scfvector.cc

src/lib/chemistry/qc/wfn/linkage.h

src/lib/math/optimize/Makefile

src/lib/math/optimize/diis.cc

src/lib/math/optimize/diis.h

src/lib/math/optimize/linkage.h

src/lib/math/optimize/opt.h

src/lib/math/optimize/qnewton.cc

src/lib/util/misc/unittest.cc

Show diffs side-by-side

added added

removed removed

src/lib/chemistry/molecule/molecule.cc

107

107

clear_symmetry_info();

108

108

}

109

109

110

void

111

Molecule::throw_if_atom_duplicated(int begin, double tol)

112

{

113

for (int i=begin; i<natoms_; i++) {

114

SCVector3 ri(r_[i]);

115

for (int j=0; j<i; j++) {

116

SCVector3 rj(r_[j]);

117

if (ri.dist(rj) < tol) {

118

throw InputError("duplicated atom coordinate",

119

__FILE__, __LINE__, 0, 0, class_desc());

120

}

121

}

122

}

123

}

124

110

125

Molecule::Molecule(const Ref<KeyVal>&input):

111

126

natoms_(0), r_(0), Z_(0), charges_(0), mass_(0), labels_(0)

112

127

{

362

377

}

363

378

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natoms_++;

380

381

throw_if_atom_duplicated(natoms_-1);

365

382

}

366

383

367

384

void

1148

1165

// evals: principal moments of inertia

1149

1166

// evecs: principal axes (optional argument)

1150

1167

1151

const double au_to_angs = 0.2800283608302436; // for moments of inertia

1168

Ref<Units> units = new Units("angstroms * angstroms");

1169

double au_to_angs = units->from_atomic_units();

1152

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double *inert[3]; // inertia tensor

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1172

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