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Searched refs:nSites (Results 1 – 25 of 46) sorted by relevance

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/dports/science/pcmsolver/pcmsolver-1.3.0/src/mmfq/
H A DFQOhno.cpp40 PCMSolverIndex nSites = nFragments * nSitesPerFragment; in buildSystemMatrix_impl() local
41 PCMSolverIndex fq_dim = nSites + nFragments; in buildSystemMatrix_impl()
45 for (PCMSolverIndex i = 0; i < nSites; ++i) { in buildSystemMatrix_impl()
46 for (PCMSolverIndex j = 0; j < nSites; ++j) { in buildSystemMatrix_impl()
58 Dlambda_(i + nSites, j + i * nSitesPerFragment) = 1.0; in buildSystemMatrix_impl()
59 Dlambda_(j + i * nSitesPerFragment, i + nSites) = 1.0; in buildSystemMatrix_impl()
/dports/science/jdftx/jdftx-1.6.0/fluid1D/fluid/
H A DIdealGasPsiAlpha.cpp28 for(int i=0; i<molecule->nSites; i++) in countIndep()
40 siteToIndep.assign(molecule->nSites, -1); in IdealGasPsiAlpha()
45 for(int i=0; i<molecule->nSites; i++) in IdealGasPsiAlpha()
69 for(int i=0; i<molecule->nSites; i++) in initState()
95 for(int i=0; i<molecule->nSites; i++) in getDensities()
100 for(int i=0; i<molecule->nSites; i++) in getDensities()
142 for(int i=0; i<molecule->nSites; i++) in convertGradients()
146 for(int i=0; i<molecule->nSites; i++) in convertGradients()
152 for(int i=0; i<molecule->nSites; i++) in convertGradients()
H A DMolecule.cpp53 for(int i=0; i<nSites; i++) in get_charge()
63 for(int i=0; i<nSites; i++) in get_dipole()
77 for(int i=0; i<nSites; i++) in getBonds()
80 { for(int j=i+1; j<nSites; j++) in getBonds()
H A DIdealGasPomega.cpp43 for(int i=0; i<molecule->nSites; i++) in initState()
72 for(int i=0; i<molecule->nSites; i++) in getDensities()
117 for(int i=0; i<molecule->nSites; i++) in convertGradients()
H A DMolecule.h69 const int nSites; //!< total number of sites (including multiplicities) equal to site.size() member
81 : name(name), site(make_site(args...)), nSites(site.size()), nIndices(site.back().index+1) in Molecule()
H A DIdealGasMuEps.cpp44 for(int i=0; i<molecule->nSites; i++) in initState()
79 for(int i=0; i<molecule->nSites; i++) in getDensities()
125 for(int i=0; i<molecule->nSites; i++) in convertGradients()
H A DIdealGasMonoatomic.cpp24 { assert(molecule->nSites==1); //IdealGasMonoatomic must be used only with single site molecules. in IdealGasMonoatomic()
H A DFluidMixture.cpp42 { for(int j=0; j<c->molecule->nSites; j++) in setPressure()
215 for(int i=0; i<comp.molecule->nSites; i++) in addComponent()
499 for(int i=0; i<c.molecule->nSites; i++) in operator ()()
502 if((i+1!=c.molecule->nSites) in operator ()()
596 for(int j=0; j<c.molecule->nSites; j++) in computeUniformEx()
671 for(int j=0; j<c.molecule->nSites; j++) in computeUniformEx()
/dports/biology/bio-mocha/bcftools-1.14/test/
H A Dguess-ploidy.PL.out1 # [1]SEX [2]Sample [3]Predicted sex [4]log P(Haploid)/nSites [5]log P(Diploid)/nSites [6]nSites [7]…
H A Dguess-ploidy.GL.out1 # [1]SEX [2]Sample [3]Predicted sex [4]log P(Haploid)/nSites [5]log P(Diploid)/nSites [6]nSites [7]…
/dports/biology/bcftools/bcftools-1.14/test/
H A Dguess-ploidy.GL.out1 # [1]SEX [2]Sample [3]Predicted sex [4]log P(Haploid)/nSites [5]log P(Diploid)/nSites [6]nSites [7]…
H A Dguess-ploidy.PL.out1 # [1]SEX [2]Sample [3]Predicted sex [4]log P(Haploid)/nSites [5]log P(Diploid)/nSites [6]nSites [7]…
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/locusiterator/
H A DPerSampleReadStateManager.java40 private int nSites = 0; field in PerSampleReadStateManager
146 nSites++; in captureDownsamplingStats()
155 if ( downsampling || nSites % 10000 == 0 ) { in captureDownsamplingStats()
157 … message, loc, size(), downsamplingTarget, (1.0 * nSitesNeedingDownsampling / nSites))); in captureDownsamplingStats()
/dports/news/inn-current/inn-2.7-20211226/innd/
H A Dnewsfeeds.c794 for (j = 0; j < ngp->nSites; j++) in SITEparseone()
799 if (j == ngp->nSites) in SITEparseone()
800 ngp->Sites[ngp->nSites++] = isp; in SITEparseone()
844 for (length = 0, i = nSites, sp = Sites; --i >= 0; sp++) in SITEfunnelpatch()
849 for (result = true, i = nSites, sp = Sites; --i >= 0; sp++) { in SITEfunnelpatch()
898 for (i = nSites, sp = Sites; --i >= 0; sp++) { in SITEparsefile()
907 for (strings = SITEreadfile(false), nSites = 0; strings[nSites]; nSites++) in SITEparsefile()
909 Sites = xcalloc(nSites, sizeof(SITE)); in SITEparsefile()
919 for (sp = Sites, errors = 0, setuperrors = 0, i = 0; i < nSites; i++) { in SITEparsefile()
962 nSites = sp - Sites; in SITEparsefile()
H A Dcc.c387 for (i = nSites, sp = Sites; --i >= 0; sp++) in CCbegin()
391 nSites++; in CCbegin()
392 Sites = xrealloc(Sites, nSites * sizeof(SITE)); in CCbegin()
393 sp = &Sites[nSites - 1]; in CCbegin()
396 ngp->Sites = xrealloc(ngp->Sites, nSites * sizeof(int)); in CCbegin()
397 ngp->Poison = xrealloc(ngp->Poison, nSites * sizeof(int)); in CCbegin()
577 for (j = ngp->nSites, ip = ngp->Sites; --j >= 0; ip++) in CCdrop()
608 for (i = nSites, sp = Sites; --i >= 0; sp++) in CCfeedinfo()
667 for (sp = Sites, i = nSites; --i >= 0; sp++) in CCflush()
699 for (sp = Sites, i = nSites; --i >= 0; sp++) { in CCflushlogs()
H A Dsite.c452 for (spx = Sites, i = nSites; --i >= 0; spx++) in SITEwritefromflags()
783 for (i = nSites, sp = Sites; --i >= 0; sp++) in SITEchanclose()
910 for (i = nSites, sp = Sites; --i >= 0; sp++) in SITEflushall()
991 for (i = nSites, sp = Sites; --i >= 0; sp++) in SITEfind()
1006 for (sp++, end = &Sites[nSites]; sp < end; sp++) in SITEfindnext()
1087 for (new = NOSITE, s = Sites, i = nSites; --i >= 0; s++) in SITEfree()
/dports/news/inn/inn-2.6.4/innd/
H A Dnewsfeeds.c767 for (j = 0; j < ngp->nSites; j++) in SITEparseone()
772 if (j == ngp->nSites) in SITEparseone()
773 ngp->Sites[ngp->nSites++] = isp; in SITEparseone()
817 for (length = 0, i = nSites, sp = Sites; --i >= 0; sp++) in SITEfunnelpatch()
822 for (result = true, i = nSites, sp = Sites; --i >= 0; sp++) { in SITEfunnelpatch()
871 for (i = nSites, sp = Sites; --i >= 0; sp++) { in SITEparsefile()
880 for (strings = SITEreadfile(false), nSites = 0; strings[nSites]; nSites++) in SITEparsefile()
882 Sites = xcalloc(nSites, sizeof(SITE)); in SITEparsefile()
892 for (sp = Sites, errors = 0, setuperrors = 0, i = 0; i < nSites; i++) { in SITEparsefile()
933 nSites = sp - Sites; in SITEparsefile()
H A Dcc.c386 for (i = nSites, sp = Sites; --i >= 0; sp++) in CCbegin()
390 nSites++; in CCbegin()
391 Sites = xrealloc(Sites, nSites * sizeof(SITE)); in CCbegin()
392 sp = &Sites[nSites - 1]; in CCbegin()
395 ngp->Sites = xrealloc(ngp->Sites, nSites * sizeof(int)); in CCbegin()
396 ngp->Poison = xrealloc(ngp->Poison, nSites * sizeof(int)); in CCbegin()
575 for (j = ngp->nSites, ip = ngp->Sites; --j >= 0; ip++) in CCdrop()
607 for (i = nSites, sp = Sites; --i >= 0; sp++) in CCfeedinfo()
666 for (sp = Sites, i = nSites; --i >= 0; sp++) in CCflush()
699 for (sp = Sites, i = nSites; --i >= 0; sp++) { in CCflushlogs()
H A Dsite.c458 for (spx = Sites, i = nSites; --i >= 0; spx++) in SITEwritefromflags()
775 for (i = nSites, sp = Sites; --i >= 0; sp++) in SITEchanclose()
904 for (i = nSites, sp = Sites; --i >= 0; sp++) in SITEflushall()
985 for (i = nSites, sp = Sites; --i >= 0; sp++) in SITEfind()
1000 for (sp++, end = &Sites[nSites]; sp < end; sp++) in SITEfindnext()
1081 for (new = NOSITE, s = Sites, i = nSites; --i >= 0; s++) in SITEfree()
/dports/sysutils/shlock/inn-2.6.4/innd/
H A Dnewsfeeds.c767 for (j = 0; j < ngp->nSites; j++) in SITEparseone()
772 if (j == ngp->nSites) in SITEparseone()
773 ngp->Sites[ngp->nSites++] = isp; in SITEparseone()
817 for (length = 0, i = nSites, sp = Sites; --i >= 0; sp++) in SITEfunnelpatch()
822 for (result = true, i = nSites, sp = Sites; --i >= 0; sp++) { in SITEfunnelpatch()
871 for (i = nSites, sp = Sites; --i >= 0; sp++) { in SITEparsefile()
880 for (strings = SITEreadfile(false), nSites = 0; strings[nSites]; nSites++) in SITEparsefile()
882 Sites = xcalloc(nSites, sizeof(SITE)); in SITEparsefile()
892 for (sp = Sites, errors = 0, setuperrors = 0, i = 0; i < nSites; i++) { in SITEparsefile()
933 nSites = sp - Sites; in SITEparsefile()
H A Dcc.c386 for (i = nSites, sp = Sites; --i >= 0; sp++) in CCbegin()
390 nSites++; in CCbegin()
391 Sites = xrealloc(Sites, nSites * sizeof(SITE)); in CCbegin()
392 sp = &Sites[nSites - 1]; in CCbegin()
395 ngp->Sites = xrealloc(ngp->Sites, nSites * sizeof(int)); in CCbegin()
396 ngp->Poison = xrealloc(ngp->Poison, nSites * sizeof(int)); in CCbegin()
575 for (j = ngp->nSites, ip = ngp->Sites; --j >= 0; ip++) in CCdrop()
607 for (i = nSites, sp = Sites; --i >= 0; sp++) in CCfeedinfo()
666 for (sp = Sites, i = nSites; --i >= 0; sp++) in CCflush()
699 for (sp = Sites, i = nSites; --i >= 0; sp++) { in CCflushlogs()
H A Dsite.c458 for (spx = Sites, i = nSites; --i >= 0; spx++) in SITEwritefromflags()
775 for (i = nSites, sp = Sites; --i >= 0; sp++) in SITEchanclose()
904 for (i = nSites, sp = Sites; --i >= 0; sp++) in SITEflushall()
985 for (i = nSites, sp = Sites; --i >= 0; sp++) in SITEfind()
1000 for (sp++, end = &Sites[nSites]; sp < end; sp++) in SITEfindnext()
1081 for (new = NOSITE, s = Sites, i = nSites; --i >= 0; s++) in SITEfree()
/dports/science/thermofun/thermofun-0.3.8/ThermoFun/Common/
H A Dformulaparser.cpp322 nSites = 0; in parse()
326 { case PSUR_L_PLUS: nSites++; in parse()
341 moit_.push_back( MOITERM(moiName.c_str(), nSites, nj )); in parse()
349 moit_.push_back( MOITERM("Va", nSites, nj )); in parse()
357 return nSites; in parse()
/dports/biology/iqtree/IQ-TREE-2.0.6/model/
H A Drategammainvar.cpp226 size_t nSites = phylo_tree->aln->getNSite(); in optimizeWithEM() local
243 double newPInvar = ppInvar / nSites; in optimizeWithEM()
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/
H A DUpperBound.bf48 "\nSites : ",filteredData.sites,

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