| /dports/science/py-pyscf/pyscf-2.0.1/pyscf/fci/ |
| H A D | direct_ep.py | 49 def make_shape(nsite, nelec, nphonon): argument
55 def contract_1e(h1e, fcivec, nsite, nelec, nphonon): argument
122 def slices_for(psite_id, nsite, nphonon): argument
126 def slices_for_cre(psite_id, nsite, nphonon): argument
128 def slices_for_des(psite_id, nsite, nphonon): argument
133 def contract_ep(g, fcivec, nsite, nelec, nphonon): argument
234 def kernel(t, u, g, hpp, nsite, nelec, nphonon, argument
254 def make_rdm1e(fcivec, nsite, nelec): argument
274 def make_rdm12e(fcivec, nsite, nelec): argument
305 def make_rdm1p(fcivec, nsite, nelec, nphonon): argument
[all …]
|
| /dports/science/tinker/tinker/source/ |
| H A D | lights.f | 35 subroutine lights (cutoff,nsite,xsort,ysort,zsort,unique) argument
43 integer nsite local
|
| /dports/biology/iqtree/IQ-TREE-2.0.6/whtest/ |
| H A D | whtest_wrapper.cpp | 55 int nsite = tree.aln->getNSite(); in WHTest() local
|
| H A D | whtest.c | 141 void WHT_setAlignmentSize(int ntax, int nsite) { in WHT_setAlignmentSize()
|
| /dports/biology/iqtree/IQ-TREE-2.0.6/alignment/ |
| H A D | alignment.cpp | 881 int nsite = getNSite(); in printSiteInfo() local
1702 int nseq = 0, nsite = 0; in readPhylip() local
1778 int nseq = 0, nsite = 0; in readPhylipSequential() local
2988 int nsite = aln->getNSite(); in convertToCodonOrAA() local
3078 int nsite = getNSite(); in convertCodonToAA() local
3124 int nsite = getNSite(); in convertCodonToDNA() local
3523 int nsite = aln.getNSite(); in buildFromPatternFreq() local
4641 int nsite = getNSite(); in doSymTest() local
4812 int nsite = getNSite(), i; in computeUnconstrainedLogL() local
4825 int nsite = getNSite(); in printSiteGaps() local
[all …]
|
| H A D | maalignment.cpp | 169 int nsite = aln->getNSite(); in generateExpectedAlignment() local
|
| H A D | superalignment.cpp | 152 int site, seq, nsite = partitions.size(); in init() local
185 int site, seq, nsite = partitions.size(); in buildPattern() local
1038 int nsite = pattern_index.size(); in getSitePatternIndex() local
1579 int site, seq, nsite = ids.size(); in concatenateAlignments() local
|
| /dports/biology/treepuzzle/tree-puzzle-5.2/src/ |
| H A D | puzzle2.c | 86 char readnextcharacter(FILE *ifp, int notu, int nsite) in readnextcharacter()
111 int nsite) /* sequence position - for error msg. */ in skiprestofline()
136 int nsite) /* sequence position - for error msg. */ in skipcntrl()
175 int notu, nsite, endofline, linelength, i; in getseqs() local
740 int notu, nsite; in guessdatatype() local
|
| /dports/biology/iqtree/IQ-TREE-2.0.6/tree/ |
| H A D | phylokernelsitemodel.cpp | 182 int nsite = aln->getNSite(); in computeSitemodelPartialLikelihoodEigen() local
331 int nsite = aln->getNSite(); in computeSitemodelPartialLikelihoodEigen() local
416 int nsite = aln->getNSite(); in computeSitemodelPartialLikelihoodEigen() local
|
| H A D | phylokernelsitemodel.h | 247 int nsite = aln->getNSite(); in computeSitemodelPartialLikelihoodEigenSIMD() local
348 int nsite = aln->getNSite(); in computeSitemodelPartialLikelihoodEigenSIMD() local
|
| H A D | upperbounds.cpp | 658 int nsite = tree->aln->getNSite(); in getBestNNIForBranUB() local
|
| H A D | phylosupertreeplen.cpp | 91 size_t nsite = 0; in normalizePartRate() local
|
| H A D | phylotree.cpp | 1706 int nsite = getAlnNSite(); in computeLogLVariance() local
1734 int nsite = getAlnNSite(); in computeLogLDiffVariance() local
5563 int nsite = aln->getNSite(); in writeSiteRates() local
|
| H A D | iqtree.cpp | 538 int nsite = (aln->seq_type == SEQ_CODON) ? getAlnNSite()*3 : getAlnNSite(); in createPLLPartition() local
|
| /dports/science/qmcpack/qmcpack-3.11.0/src/QMCHamiltonians/ |
| H A D | LatticeDeviationEstimator.cpp | 108 int nsite(0); // site index in evaluate() local
|
| /dports/biology/iqtree/IQ-TREE-2.0.6/model/ |
| H A D | partitionmodelplen.cpp | 248 size_t nsite = 0; in optimizeGeneRate() local
|
| /dports/biology/bcftools/bcftools-1.14/plugins/ |
| H A D | ad-bias.c | 60 uint64_t nsite,ncmp; member
|
| H A D | fixref.c | 116 uint32_t nsite,nok,nflip,nunresolved,nswap,nflip_swap,nonSNP,nonACGT,nonbiallelic; member
|
| /dports/biology/bio-mocha/bcftools-1.14/plugins/ |
| H A D | ad-bias.c | 60 uint64_t nsite,ncmp; member
|
| H A D | fixref.c | 116 uint32_t nsite,nok,nflip,nunresolved,nswap,nflip_swap,nonSNP,nonACGT,nonbiallelic; member
|
| /dports/biology/iqtree/IQ-TREE-2.0.6/main/ |
| H A D | treetesting.cpp | 340 size_t site, nsite = (*it)->aln->getNSite(); in printSiteProbCategory() local
352 int nsite = tree->getAlnNSite(); in printSiteProbCategory() local
|
| H A D | phylotesting.cpp | 699 size_t nsite = 0; in transferModelFinderParameters() local
|
| /dports/biology/mafft/mafft-7.267-without-extensions/core/ |
| H A D | io.c | 2005 int nsite = 0; in getnumlen_casepreserve() local
2049 int nsite = 0; in getnumlen_nogap() local
2094 int nsite = 0; in getnumlen_nogap_outallreg() local
2182 int nsite = 0; in getnumlen_nogap_outallreg_web() local
2313 int nsite = 0; in getnumlen() local
|
| /dports/biology/iqtree/IQ-TREE-2.0.6/obsolete/ |
| H A D | guidedbootstrap.cpp | 375 int ntrees, nsite, nptn, scale; in readPatternLh() local
|