| /dports/science/gromacs/gromacs-2021.4/src/gromacs/hardware/ |
| H A D | printhardware.cpp | 83 static void check_use_of_rdtscp_on_this_cpu(const gmx::MDLogger& mdlog, const gmx::CpuInfo& cpuInfo) in check_use_of_rdtscp_on_this_cpu()
140 s = gmx::formatString("\n"); in detected_hardware_string()
164 s += gmx::formatString("\n"); in detected_hardware_string()
183 s += gmx::formatString("\n"); in detected_hardware_string()
237 s += gmx::formatString(" %s", gmx::CpuInfo::featureString(f).c_str()); in detected_hardware_string()
239 s += gmx::formatString("\n"); in detected_hardware_string()
264 case gmx::HardwareTopology::SupportLevel::None: s += gmx::formatString("None\n"); break; in detected_hardware_string()
268 case gmx::HardwareTopology::SupportLevel::Basic: s += gmx::formatString("Basic\n"); break; in detected_hardware_string()
269 case gmx::HardwareTopology::SupportLevel::Full: s += gmx::formatString("Full\n"); break; in detected_hardware_string()
389 gmx::simdCheck(static_cast<gmx::SimdType>(hwinfo->simd_suggest_min), fplog, warnToStdErr); in gmx_print_detected_hardware()
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| /dports/science/gromacs/gromacs-2021.4/src/programs/view/ |
| H A D | view.cpp | 82 done_dlgs(gmx); in done_gmx()
111 pd = gmx->pd; in HandleClient()
132 write_sto_conf(gmx->confout, *gmx->man->top.name, &(gmx->man->top.atoms), gmx->man->x, in HandleClient()
150 case IDDOFILTER: do_filter(x11, gmx->man, gmx->filter); break; in HandleClient()
188 t_gmx* gmx; in MainCallBack() local
239 t_gmx* gmx; in init_gmx() local
249 snew(gmx, 1); in init_gmx()
261 InitWin(gmx->wd, 0, 0, w0, h0, 3, gmx::bromacs().c_str()); in init_gmx()
262 … gmx->wd->self = XCreateSimpleWindow(x11->disp, x11->root, gmx->wd->x, gmx->wd->y, gmx->wd->width, in init_gmx()
279 gmx->logo = init_logo(x11, gmx->wd->self, false); in init_gmx()
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| H A D | dialogs.cpp | 121 if (gmx->which_mb >= 0 && gmx->which_mb < emNR) in hide_mb()
123 HideDlg(gmx->mboxes[gmx->which_mb]); in hide_mb()
130 t_gmx* gmx; in MBCallback() local
135 hide_mb(gmx); in MBCallback()
146 return MessageBox(x11, gmx->wd->self, gmx->wd->text, asize(lines), lines, in about_mb()
152 t_gmx* gmx; in QuitCB() local
155 hide_mb(gmx); in QuitCB()
201 t_gmx* gmx; in ExportCB() local
260 t_gmx* gmx; in BondsCB() local
399 gmx->dlgs[edFilter] = select_filter(x11, gmx); in init_dlgs()
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/options/tests/ |
| H A D | treesupport.cpp | 79 gmx::Options options; in TEST()
85 gmx::KeyValueTreeBuilder builder; in TEST()
110 gmx::Options options; in TEST()
115 gmx::KeyValueTreeBuilder builder; in TEST()
141 gmx::Options options; in TEST()
145 gmx::KeyValueTreeBuilder builder; in TEST()
150 …EXPECT_THROW_GMX(gmx::assignOptionsFromKeyValueTree(&options, tree, nullptr), gmx::InvalidInputErr… in TEST()
170 gmx::Options options_;
171 gmx::KeyValueTreeBuilder builder_;
240 gmx::Options options_;
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| H A D | optionsassigner.cpp | 76 gmx::Options options; in TEST()
86 gmx::Options options; in TEST()
146 gmx::Options options; in TEST()
167 gmx::Options options; in TEST()
219 gmx::Options options; in TEST()
255 gmx::Options options; in TEST()
288 gmx::Options options; in TEST()
306 gmx::Options options; in TEST()
323 gmx::Options options; in TEST()
341 gmx::Options options; in TEST()
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/math/tests/ |
| H A D | functions.cpp | 59 gmx::test::TestReferenceData data; in TEST()
88 result.push_back(gmx::log2I(i)); in TEST()
290 EXPECT_EQ(4, gmx::square(2)); in TEST()
291 EXPECT_EQ(8, gmx::power3(2)); in TEST()
292 EXPECT_EQ(16, gmx::power4(2)); in TEST()
293 EXPECT_EQ(32, gmx::power5(2)); in TEST()
294 EXPECT_EQ(64, gmx::power6(2)); in TEST()
295 EXPECT_EQ(4096, gmx::power12(2)); in TEST()
297 EXPECT_EQ(6.25, gmx::square(2.5)); in TEST()
344 EXPECT_FLOAT_EQ_TOL(r, std::erf(gmx::erfinv(r)), gmx::test::ulpTolerance(10)); in TEST()
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/utility/tests/ |
| H A D | stringutil.cpp | 63 namespace gmx namespace
244 gmx::formatAndJoin(gmx::ArrayRef<const char* const>(words), ".", in TEST()
249 … gmx::formatAndJoin(gmx::ArrayRef<const int>(values), ",", gmx::StringFormatter("%d"))); in TEST()
331 gmx::TextLineWrapper wrapper; in TEST_F()
345 gmx::TextLineWrapper wrapper; in TEST_F()
357 gmx::TextLineWrapper wrapper; in TEST_F()
395 gmx::TextLineWrapper wrapper; in TEST_F()
410 gmx::TextLineWrapper wrapper; in TEST_F()
421 gmx::TextLineWrapper wrapper; in TEST_F()
431 gmx::TextLineWrapper wrapper; in TEST_F()
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| H A D | keyvaluetreetransform.cpp | 60 …void testTransform(const gmx::KeyValueTreeObject& input, const gmx::KeyValueTreeTransformer& trans… in testTransform()
76 …static void checkMappedPath(gmx::test::TestReferenceChecker* checker, const gmx::KeyValueTreePath&… in checkMappedPath()
112 gmx::KeyValueTreeBuilder builder; in TEST_F()
119 &gmx::fromStdString<int>); in TEST_F()
121 &gmx::fromStdString<int>); in TEST_F()
128 gmx::KeyValueTreeBuilder builder; in TEST_F()
145 gmx::KeyValueTreeBuilder builder; in TEST_F()
162 gmx::KeyValueTreeBuilder builder; in TEST_F()
179 gmx::KeyValueTreeBuilder builder; in TEST_F()
199 gmx::KeyValueTreeBuilder builder; in TEST_F()
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| H A D | logger.cpp | 55 gmx::MDLogger logger; in TEST_F()
65 gmx::StringOutputStream stream; in TEST_F()
66 gmx::LoggerBuilder builder; in TEST_F()
85 gmx::LoggerBuilder builder; in TEST_F()
102 gmx::StringOutputStream stream; in TEST_F()
103 gmx::LoggerBuilder builder; in TEST_F()
118 gmx::StringOutputStream stream1; in TEST_F()
119 gmx::StringOutputStream stream2; in TEST_F()
120 gmx::StringOutputStream stream3; in TEST_F()
121 gmx::StringOutputStream stream4; in TEST_F()
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| /dports/science/plumed/plumed2-2.7.2/src/molfile/ |
| H A D | gromacsplugin.cpp | 114 gmxdata *gmx; in open_gro_read() local
134 gmx->mf = mf; in open_gro_read()
140 return gmx; in open_gro_read()
210 delete gmx; in close_gro_read()
235 return gmx; in open_gro_write()
272 fprintf(gmx->mf->f, "%d\n", gmx->natoms); in write_gro_timestep()
298 delete gmx; in close_gro_write()
464 delete gmx; in close_g96_read()
506 return gmx; in open_trr_read()
549 delete gmx; in close_trr_read()
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| /dports/science/py-pymol/pymol-open-source-2.4.0/contrib/uiuc/plugins/molfile_plugin/src/ |
| H A D | gromacsplugin.cpp | 79 gmxdata *gmx; in open_gro_read() local
99 gmx->mf = mf; in open_gro_read()
105 return gmx; in open_gro_read()
175 delete gmx; in close_gro_read()
200 return gmx; in open_gro_write()
237 fprintf(gmx->mf->f, "%d\n", gmx->natoms); in write_gro_timestep()
263 delete gmx; in close_gro_write()
429 delete gmx; in close_g96_read()
471 return gmx; in open_trr_read()
514 delete gmx; in close_trr_read()
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/random/tests/ |
| H A D | tabulatednormaldistribution.cpp | 52 namespace gmx namespace
60 gmx::test::TestReferenceData data; in TEST()
63 gmx::ThreeFry2x64<2> rng(123456, gmx::RandomDomain::Other); in TEST()
77 gmx::test::TestReferenceData data; in TEST()
80 gmx::ThreeFry2x64<2> rng(123456, gmx::RandomDomain::Other); in TEST()
94 gmx::test::TestReferenceData data; in TEST()
97 gmx::ThreeFry2x64<2> rng(123456, gmx::RandomDomain::Other); in TEST()
111 gmx::ThreeFry2x64<2> rng(123456, gmx::RandomDomain::Other); in TEST()
125 gmx::ThreeFry2x64<2> rng(123456, gmx::RandomDomain::Other); in TEST()
143 gmx::ThreeFry2x64<2> rngA(123456, gmx::RandomDomain::Other); in TEST()
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| H A D | threefry.cpp | 52 namespace gmx namespace
146 gmx::ThreeFry2x64<10> rngA(123456, gmx::RandomDomain::Other); in TEST_F()
147 gmx::ThreeFry2x64<10> rngB(123456, gmx::RandomDomain::Other); in TEST_F()
148 gmx::ThreeFry2x64<10> rngC(123456, gmx::RandomDomain::Other); in TEST_F()
168 gmx::ThreeFry2x64<66> rngA(123456, gmx::RandomDomain::Other); in TEST_F()
179 gmx::ThreeFry2x64<64> rngB(123456, gmx::RandomDomain::Other); in TEST_F()
195 gmx::ThreeFry2x64<10> rngA(123456, gmx::RandomDomain::Other); in TEST_F()
208 gmx::ThreeFry2x64<10> rngA(123456, gmx::RandomDomain::Other); in TEST_F()
209 gmx::ThreeFry2x64<10> rngB(123456, gmx::RandomDomain::Other); in TEST_F()
222 gmx::ThreeFry2x64<10> rngA(123456, gmx::RandomDomain::Other); in TEST_F()
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| H A D | uniformrealdistribution.cpp | 52 namespace gmx namespace
60 gmx::test::TestReferenceData data; in TEST()
63 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
76 gmx::test::TestReferenceData data; in TEST()
79 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
80 gmx::UniformRealDistribution<real> dist(1.0, 10.0); in TEST()
93 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
94 gmx::UniformRealDistribution<real> distA(2.0, 5.0); in TEST()
107 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
127 gmx::ThreeFry2x64<8> rngA(123456, gmx::RandomDomain::Other); in TEST()
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| H A D | exponentialdistribution.cpp | 52 namespace gmx namespace
60 gmx::test::TestReferenceData data; in TEST()
63 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
64 gmx::ExponentialDistribution<real> dist(5.0); in TEST()
85 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
86 gmx::ExponentialDistribution<real> distA(2.0); in TEST()
87 gmx::ExponentialDistribution<real> distB(2.0); in TEST()
88 gmx::ExponentialDistribution<real> distC(3.0); in TEST()
97 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
115 gmx::ThreeFry2x64<8> rngA(123456, gmx::RandomDomain::Other); in TEST()
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| H A D | normaldistribution.cpp | 52 namespace gmx namespace
60 gmx::test::TestReferenceData data; in TEST()
63 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
64 gmx::NormalDistribution<real> dist(2.0, 5.0); in TEST()
78 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
79 gmx::NormalDistribution<real> distA(2.0, 5.0); in TEST()
80 gmx::NormalDistribution<real> distB(2.0, 5.0); in TEST()
81 gmx::NormalDistribution<real> distC(3.0, 5.0); in TEST()
92 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
113 gmx::ThreeFry2x64<8> rngA(123456, gmx::RandomDomain::Other); in TEST()
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| H A D | gammadistribution.cpp | 52 namespace gmx namespace
60 gmx::test::TestReferenceData data; in TEST()
63 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
64 gmx::GammaDistribution<real> distA(0.1, 5.0); in TEST()
65 gmx::GammaDistribution<real> distB(1.0, 5.0); in TEST()
66 gmx::GammaDistribution<real> distC(2.0, 5.0); in TEST()
88 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
89 gmx::GammaDistribution<real> distA(2.0, 5.0); in TEST()
102 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
120 gmx::ThreeFry2x64<8> rngA(123456, gmx::RandomDomain::Other); in TEST()
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| H A D | uniformintdistribution.cpp | 52 namespace gmx namespace
60 gmx::test::TestReferenceData data; in TEST()
63 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
78 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
79 gmx::UniformIntDistribution<int> distA(2, 5); in TEST()
80 gmx::UniformIntDistribution<int> distB(2, 5); in TEST()
81 gmx::UniformIntDistribution<int> distC(3, 5); in TEST()
82 gmx::UniformIntDistribution<int> distD(2, 4); in TEST()
92 gmx::ThreeFry2x64<8> rng(123456, gmx::RandomDomain::Other); in TEST()
110 gmx::ThreeFry2x64<8> rngA(123456, gmx::RandomDomain::Other); in TEST()
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/selection/tests/ |
| H A D | selectionoption.cpp | 110 gmx::Selection sel; in TEST_F()
128 gmx::Selection sel; in TEST_F()
144 gmx::Selection sel; in TEST_F()
163 gmx::Selection sel; in TEST_F()
182 gmx::Selection sel; in TEST_F()
200 gmx::Selection sel; in TEST_F()
218 gmx::Selection sel; in TEST_F()
251 gmx::Selection sel; in TEST_F()
287 gmx::Selection sel; in TEST_F()
341 gmx::Selection sel; in TEST_F()
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/nbnxm/ |
| H A D | nbnxm.h | 144 namespace gmx
243 gmx::ArrayRef<const int> getLocalAtomOrder() const;
249 gmx::ArrayRef<const int> getGridIndices() const;
269 void setAtomProperties(gmx::ArrayRef<const int> atomTypes,
281 …void convertCoordinates(gmx::AtomLocality locality, bool fillLocal, gmx::ArrayRef<const gmx::RVec>…
294 DeviceBuffer<gmx::RVec> d_x,
343 void atomdata_add_nbat_f_to_f(gmx::AtomLocality locality, gmx::ArrayRef<gmx::RVec> force);
366 int getNumAtoms(gmx::AtomLocality locality);
387 … void setupGpuShortRangeWork(const gmx::GpuBonded* gpuBonded, gmx::InteractionLocality iLocality);
462 gmx::ArrayRef<const gmx::RVec> x,
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| H A D | grid.h | 70 namespace gmx
341 gmx::RVec lowerCorner,
342 gmx::RVec upperCorner,
355 gmx::ArrayRef<const gmx::RVec> x,
363 gmx::ArrayRef<const gmx::RVec> x,
381 gmx::ArrayRef<const gmx::RVec> x,
388 gmx::ArrayRef<const gmx::RVec> x,
397 gmx::ArrayRef<const gmx::RVec> x,
424 gmx::HostVector<int> cxy_na_;
428 gmx::HostVector<int> cxy_ind_;
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| H A D | atomdata.h | 59 namespace gmx
126 gmx::HostVector<real> f;
128 gmx::HostVector<real> fshift;
130 gmx::HostVector<real> Vvdw;
132 gmx::HostVector<real> Vc;
188 gmx::HostVector<real> nbfp;
196 gmx::HostVector<int> type;
200 gmx::HostVector<real> q;
206 gmx::HostVector<int> energrp;
270 gmx::HostVector<gmx::RVec> shift_vec;
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| /dports/graphics/ossim/ossim-OrchidIsland-2.11.1/src/matrix/ |
| H A D | newmat5.cpp | 63 GeneralMatrix* gmx = new RowVector; MatrixErrorNoSpace(gmx); in UpperTriangularMatrix()
64 gmx->nrows = 1; gmx->ncols = gmx->storage = storage; in UpperTriangularMatrix()
72 gmx->ncols = 1; gmx->nrows = gmx->storage = storage; in DiagonalMatrix()
88 tDelete(); gmx->ReleaseAndDelete(); return gmx; in SquareMatrix()
164 gmx->ReleaseAndDelete(); gmx->Multiply(gm,f); in ~GeneralMatrix()
195 gmx->ReleaseAndDelete(); gmx->Negate(gm); in ~CroutMatrix()
226 gmx->ReverseElements(gm); gmx->ReleaseAndDelete();
245 gmx->nrows = 1; gmx->ncols = gmx->storage = gm->storage;
253 gmx->ncols = 1; gmx->nrows = gmx->storage = gm->storage; in ReSize()
261 gmx->nrows = gmx->ncols = gmx->storage = gm->storage; in ReSize()
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/analysisdata/tests/ |
| H A D | histogram.cpp | 60 using gmx::test::AnalysisDataTestInput;
75 gmx::AnalysisHistogramSettings settings(gmx::histogramFromBins(1.0, 5, 0.5)); in TEST()
85 gmx::AnalysisHistogramSettings settings(gmx::histogramFromBins(1.0, 5, 0.5).integerBins()); in TEST()
95 gmx::AnalysisHistogramSettings settings(gmx::histogramFromRange(1.0, 4.0).binCount(6)); in TEST()
105 gmx::AnalysisHistogramSettings settings(gmx::histogramFromRange(1.0, 4.0).binWidth(0.5)); in TEST()
115 …gmx::AnalysisHistogramSettings settings(gmx::histogramFromRange(1.0, 4.0).binCount(7).integerBins(… in TEST()
194 … new gmx::AnalysisDataSimpleHistogramModule(gmx::histogramFromRange(1.0, 3.0).binCount(4))); in TEST_F()
212 gmx::AnalysisDataSimpleHistogramModulePointer module(new gmx::AnalysisDataSimpleHistogramModule( in TEST_F()
378 new gmx::AnalysisDataBinAverageModule(gmx::histogramFromRange(1.0, 3.0).binCount(4))); in TEST_F()
394 gmx::AnalysisDataBinAverageModulePointer module(new gmx::AnalysisDataBinAverageModule( in TEST_F()
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| /dports/science/gromacs/gromacs-2021.4/src/programs/ |
| H A D | legacymodules.cpp | 177 manager, gmx::DumpInfo::name, gmx::DumpInfo::shortDescription, &gmx::DumpInfo::create); in registerLegacyModules()
179 gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::ConvertTprInfo::name, in registerLegacyModules()
186 manager, &gmx::gmx_mdrun, "mdrun", in registerLegacyModules()
191 gmx::NonbondedBenchmarkInfo::shortDescription, &gmx::NonbondedBenchmarkInfo::create); in registerLegacyModules()
193 gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::InsertMoleculesInfo::name(), in registerLegacyModules()
197 gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::ReportMethodsInfo::name, in registerLegacyModules()
201 gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::pdb2gmxInfo::name, in registerLegacyModules()
332 gmx::CommandLineModuleGroup group = in registerLegacyModules()
398 gmx::CommandLineModuleGroup group = in registerLegacyModules()
406 gmx::CommandLineModuleGroup group = in registerLegacyModules()
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