/dports/science/pcmsolver/pcmsolver-1.3.0/src/mmfq/ |
H A D | FQOhno.cpp | 40 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()
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/dports/science/jdftx/jdftx-1.6.0/fluid1D/fluid/ |
H A D | IdealGasPsiAlpha.cpp | 28 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()
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H A D | Molecule.cpp | 53 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()
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H A D | IdealGasPomega.cpp | 43 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()
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H A D | Molecule.h | 69 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()
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H A D | IdealGasMuEps.cpp | 44 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()
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H A D | IdealGasMonoatomic.cpp | 24 { assert(molecule->nSites==1); //IdealGasMonoatomic must be used only with single site molecules. in IdealGasMonoatomic()
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H A D | FluidMixture.cpp | 42 { 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()
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/dports/biology/bio-mocha/bcftools-1.14/test/ |
H A D | guess-ploidy.PL.out | 1 # [1]SEX [2]Sample [3]Predicted sex [4]log P(Haploid)/nSites [5]log P(Diploid)/nSites [6]nSites [7]…
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H A D | guess-ploidy.GL.out | 1 # [1]SEX [2]Sample [3]Predicted sex [4]log P(Haploid)/nSites [5]log P(Diploid)/nSites [6]nSites [7]…
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/dports/biology/bcftools/bcftools-1.14/test/ |
H A D | guess-ploidy.GL.out | 1 # [1]SEX [2]Sample [3]Predicted sex [4]log P(Haploid)/nSites [5]log P(Diploid)/nSites [6]nSites [7]…
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H A D | guess-ploidy.PL.out | 1 # [1]SEX [2]Sample [3]Predicted sex [4]log P(Haploid)/nSites [5]log P(Diploid)/nSites [6]nSites [7]…
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/locusiterator/ |
H A D | PerSampleReadStateManager.java | 40 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()
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/dports/news/inn-current/inn-2.7-20211226/innd/ |
H A D | newsfeeds.c | 794 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()
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H A D | cc.c | 387 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()
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H A D | site.c | 452 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()
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/dports/news/inn/inn-2.6.4/innd/ |
H A D | newsfeeds.c | 767 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()
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H A D | cc.c | 386 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()
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H A D | site.c | 458 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()
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/dports/sysutils/shlock/inn-2.6.4/innd/ |
H A D | newsfeeds.c | 767 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()
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H A D | cc.c | 386 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()
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H A D | site.c | 458 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()
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/dports/science/thermofun/thermofun-0.3.8/ThermoFun/Common/ |
H A D | formulaparser.cpp | 322 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()
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/dports/biology/iqtree/IQ-TREE-2.0.6/model/ |
H A D | rategammainvar.cpp | 226 size_t nSites = phylo_tree->aln->getNSite(); in optimizeWithEM() local 243 double newPInvar = ppInvar / nSites; in optimizeWithEM()
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/ |
H A D | UpperBound.bf | 48 "\nSites : ",filteredData.sites,
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