/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Descriptors/ |
H A D | AUTOCORR2D.cpp | 61 w[0 * numAtoms + i] = wm[i]; in get2DautocorrelationDesc() 62 w[1 * numAtoms + i] = wv[i]; in get2DautocorrelationDesc() 63 w[2 * numAtoms + i] = we[i]; in get2DautocorrelationDesc() 64 w[3 * numAtoms + i] = wp[i]; in get2DautocorrelationDesc() 65 w[4 * numAtoms + i] = wi[i]; in get2DautocorrelationDesc() 66 w[5 * numAtoms + i] = ws[i]; in get2DautocorrelationDesc() 71 wmean[t] += w[t * numAtoms + i] / (double)numAtoms; in get2DautocorrelationDesc() 79 (w[t * numAtoms + i] - wmean[t]) * (w[t * numAtoms + i] - wmean[t]); in get2DautocorrelationDesc() 97 TDBmatG[t * 8 + k] += (w[t * numAtoms + i] - w[t * numAtoms + j]) * in get2DautocorrelationDesc() 98 (w[t * numAtoms + i] - w[t * numAtoms + j]); in get2DautocorrelationDesc() [all …]
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H A D | MolData3Ddescriptors.cpp | 14 std::vector<double> u(numAtoms, 1.0); in GetUn() 22 int numAtoms = mol.getNumAtoms(); in GetRelativeMW() local 25 for (int i = 0; i < numAtoms; ++i) { in GetRelativeMW() 33 int numAtoms = mol.getNumAtoms(); in GetRelativePol() local 37 for (int i = 0; i < numAtoms; ++i) { in GetRelativePol() 45 int numAtoms = mol.getNumAtoms(); in GetRelativeVdW() local 57 int numAtoms = mol.getNumAtoms(); in GetRelativeRcov() local 69 int numAtoms = mol.getNumAtoms(); in GetRelativeENeg() local 81 int numAtoms = mol.getNumAtoms(); in GetRelativeIonPol() local 93 int numAtoms = mol.getNumAtoms(); in GetCustomAtomProp() local [all …]
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H A D | AUTOCORR3D.cpp | 61 int sizeArray = numAtoms * numAtoms; in GetGeodesicMatrix() 81 Map<MatrixXd> dm(dist3D, numAtoms, numAtoms); in get3DautocorrelationDesc() 82 Map<MatrixXd> di(topologicaldistance, numAtoms, numAtoms); in get3DautocorrelationDesc() 99 std::vector<double> wu = moldata3D.GetUn(numAtoms); in get3DautocorrelationDesc() 115 Map<MatrixXd> Bi(Bimat, numAtoms, numAtoms); in get3DautocorrelationDesc() 181 std::round(1000 * TDBmat[j][i] / (numAtoms * (numAtoms - 1))) / 1000; in get3DautocorrelationDesc() 190 Map<MatrixXd> dm(dist3D, numAtoms, numAtoms); in get3DautocorrelationDescCustom() 191 Map<MatrixXd> di(topologicaldistance, numAtoms, numAtoms); in get3DautocorrelationDescCustom() 204 Map<MatrixXd> Bi(Bimat, numAtoms, numAtoms); in get3DautocorrelationDescCustom() 217 res[i] = std::round(1000 * TDBmat[i] / (numAtoms * (numAtoms - 1))) / 1000; in get3DautocorrelationDescCustom() [all …]
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H A D | WHIM.cpp | 151 auto nAT = (double)numAtoms; in getWhimD() 155 for (int j = 0; j < numAtoms; j++) { in getWhimD() 167 for (int j = 0; j < numAtoms; j++) { in getWhimD() 180 Symmetric[j + numAtoms] = 2.0; in getWhimD() 182 Symmetric[k + numAtoms] = 2.0; in getWhimD() 229 int numAtoms = conf.getNumAtoms(); in GetWHIMs() local 286 int numAtoms = conf.getNumAtoms(); in GetWHIMsCustom() local 305 int numAtoms = mol.getNumAtoms(); in getWHIM() local 309 for (int i = 0; i < numAtoms; ++i) { in getWHIM() 354 int numAtoms = mol.getNumAtoms(); in getWHIMone() local [all …]
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H A D | GETAWAY.cpp | 264 int sizeArray = numAtoms * numAtoms; in GetGeodesicMatrix() 309 MatrixXd R = MatrixXd::Zero(numAtoms, numAtoms); in GetRmatrix() 323 HeavyList.reserve(numAtoms); in GetHeavyList() 453 Map<MatrixXd> D2(dist, numAtoms, numAtoms); in getGETAWAYDescCustom() 485 Map<MatrixXd> Bj(Bimat.data(), numAtoms, numAtoms); in getGETAWAYDescCustom() 707 Map<MatrixXd> D2(dist, numAtoms, numAtoms); in getGETAWAYDesc() 790 Map<MatrixXd> Bj(Bimat.data(), numAtoms, numAtoms); in getGETAWAYDesc() 1175 Map<MatrixXd> ADJ(AdjMat, numAtoms, numAtoms); in GetGETAWAYone() 1177 Map<MatrixXd> DM(dist3D, numAtoms, numAtoms); in GetGETAWAYone() 1204 Map<MatrixXd> ADJ(AdjMat, numAtoms, numAtoms); in GetGETAWAY() [all …]
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H A D | EEM.cpp | 208 MatrixXd AM = Map<MatrixXd>(A.get(), numAtoms + 1, numAtoms + 1); in calculate_charges() 209 VectorXd bv = Map<VectorXd>(b.get(), numAtoms + 1); in calculate_charges() 210 VectorXd Res(numAtoms + 1); in calculate_charges() 215 for (unsigned int aix = 0; aix < numAtoms; aix++) { in calculate_charges() 222 unsigned int numAtoms, int confId) { in getEEMs() argument 225 EEM_arrays EEMatoms(mol, numAtoms); in getEEMs() 228 result.resize(numAtoms); in getEEMs() 229 calculate_charges(mol, dist3D, numAtoms, EEMatoms, result); in getEEMs() 236 unsigned int numAtoms = mol.getNumAtoms(); in EEM() 239 res.resize(numAtoms); in EEM() [all …]
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/tests/ |
H A D | updategroupscog.cpp | 82 const int numAtoms = sizeof(positions) / sizeof(positions[0]); in TEST() local 83 const int numMolecules = gmx::exactDiv(numAtoms, atomsPerSettle); in TEST() 100 mtop.natoms = numAtoms; in TEST() 115 UpdateGroupsCog updateGroupsCog(mtop, updateGroups, temperature, numAtoms); in TEST() 119 std::vector<int> globalAtomIndices(numAtoms); in TEST() 120 for (int i = 0; i < numAtoms; i++) in TEST() 126 for (int i = 0; i < numAtoms; i++) in TEST() 128 int a1 = std::rand() % numAtoms; in TEST() 129 int a2 = std::rand() % numAtoms; in TEST() 141 std::vector<gmx::RVec> cogPerAtom(numAtoms); in TEST() [all …]
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H A D | leapfrogtestrunners_gpu.cpp | 77 int numAtoms = testData->numAtoms_; in integrate() local 88 allocateDeviceBuffer(&d_x, numAtoms, deviceContext); in integrate() 89 allocateDeviceBuffer(&d_xp, numAtoms, deviceContext); in integrate() 90 allocateDeviceBuffer(&d_v, numAtoms, deviceContext); in integrate() 91 allocateDeviceBuffer(&d_f, numAtoms, deviceContext); in integrate() 93 copyToDeviceBuffer(&d_x, h_x, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr); in integrate() 94 copyToDeviceBuffer(&d_xp, h_xp, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr); in integrate() 95 copyToDeviceBuffer(&d_v, h_v, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr); in integrate() 96 copyToDeviceBuffer(&d_f, h_f, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr); in integrate() 115 copyFromDeviceBuffer(h_xp, &d_x, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullptr); in integrate() [all …]
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H A D | shake.cpp | 150 static void runTest(size_t gmx_unused numAtoms, in runTest() argument 160 assert(numAtoms == inverseMasses.size()); in runTest() 161 assert(numAtoms == positions.size()); in runTest() 243 int numAtoms = 2; in TEST_F() local 255 inverseMassesDatabase_.begin() + numAtoms); in TEST_F() 263 int numAtoms = 4; in TEST_F() local 280 inverseMassesDatabase_.begin() + numAtoms); in TEST_F() 288 int numAtoms = 3; in TEST_F() local 305 inverseMassesDatabase_.begin() + numAtoms); in TEST_F() 313 int numAtoms = 4; in TEST_F() local [all …]
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H A D | constrtestrunners.cu | 75 int numAtoms = testData->numAtoms_; in applyConstraints() local 82 allocateDeviceBuffer(&d_x, numAtoms, deviceContext); in applyConstraints() 83 allocateDeviceBuffer(&d_xp, numAtoms, deviceContext); in applyConstraints() 84 allocateDeviceBuffer(&d_v, numAtoms, deviceContext); in applyConstraints() 86 copyToDeviceBuffer(&d_x, (float3*)(testData->x_.data()), 0, numAtoms, deviceStream, in applyConstraints() 88 copyToDeviceBuffer(&d_xp, (float3*)(testData->xPrime_.data()), 0, numAtoms, deviceStream, in applyConstraints() 92 copyToDeviceBuffer(&d_v, (float3*)(testData->v_.data()), 0, numAtoms, deviceStream, in applyConstraints() 98 copyFromDeviceBuffer((float3*)(testData->xPrime_.data()), &d_xp, 0, numAtoms, deviceStream, in applyConstraints() 102 copyFromDeviceBuffer((float3*)(testData->v_.data()), &d_v, 0, numAtoms, deviceStream, in applyConstraints()
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H A D | settletestrunners.cu | 86 int numAtoms = testData->numAtoms_; in applySettle() local 94 allocateDeviceBuffer(&d_x, numAtoms, deviceContext); in applySettle() 95 allocateDeviceBuffer(&d_xp, numAtoms, deviceContext); in applySettle() 96 allocateDeviceBuffer(&d_v, numAtoms, deviceContext); in applySettle() 98 …copyToDeviceBuffer(&d_x, (float3*)h_x, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullpt… in applySettle() 99 …copyToDeviceBuffer(&d_xp, (float3*)h_xp, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, null… in applySettle() 102 …copyToDeviceBuffer(&d_v, (float3*)h_v, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nullpt… in applySettle() 107 …copyFromDeviceBuffer((float3*)h_xp, &d_xp, 0, numAtoms, deviceStream, GpuApiCallBehavior::Sync, nu… in applySettle() 110 copyFromDeviceBuffer((float3*)h_v, &d_v, 0, numAtoms, deviceStream, in applySettle()
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H A D | constrtestdata.cpp | 81 numAtoms_ = numAtoms; // Number of atoms in ConstraintsTestData() 85 invmass_.resize(numAtoms); // Vector of inverse masses in ConstraintsTestData() 87 for (int i = 0; i < numAtoms; i++) in ConstraintsTestData() 163 molType.atoms.nr = numAtoms; in ConstraintsTestData() 173 mtop_.natoms = numAtoms; in ConstraintsTestData() 177 x_.resizeWithPadding(numAtoms); in ConstraintsTestData() 178 xPrime_.resizeWithPadding(numAtoms); in ConstraintsTestData() 179 xPrime0_.resizeWithPadding(numAtoms); in ConstraintsTestData() 180 xPrime2_.resizeWithPadding(numAtoms); in ConstraintsTestData() 182 v_.resizeWithPadding(numAtoms); in ConstraintsTestData() [all …]
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H A D | leapfrogtestdata.cpp | 70 LeapFrogTestData::LeapFrogTestData(int numAtoms, in LeapFrogTestData() argument 76 numAtoms_(numAtoms), in LeapFrogTestData() 78 x0_(numAtoms), in LeapFrogTestData() 79 x_(numAtoms), in LeapFrogTestData() 80 xPrime_(numAtoms), in LeapFrogTestData() 81 v0_(numAtoms), in LeapFrogTestData() 82 v_(numAtoms), in LeapFrogTestData() 83 f_(numAtoms), in LeapFrogTestData() 84 inverseMasses_(numAtoms), in LeapFrogTestData() 85 inverseMassesPerDim_(numAtoms), in LeapFrogTestData() [all …]
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/core/ |
H A D | avospglib.cpp | 50 Index numAtoms = mol.atomCount(); in getHallNumber() local 51 double(*positions)[3] = new double[numAtoms][3]; in getHallNumber() 52 int* types = new int[numAtoms]; in getHallNumber() 58 for (Index i = 0; i < numAtoms; ++i) { in getHallNumber() 67 spg_get_dataset(lattice, positions, types, numAtoms, cartTol); in getHallNumber() 119 Index numAtoms = mol.atomCount(); in standardizeCell() local 126 double(*positions)[3] = new double[numAtoms * numAtomsMultiplier][3]; in standardizeCell() 127 int* types = new int[numAtoms * numAtomsMultiplier]; in standardizeCell() 133 for (Index i = 0; i < numAtoms; ++i) { in standardizeCell() 142 Index newNumAtoms = spg_standardize_cell(lattice, positions, types, numAtoms, in standardizeCell()
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/core/ |
H A D | avospglib.cpp | 50 Index numAtoms = mol.atomCount(); in getHallNumber() local 51 double(*positions)[3] = new double[numAtoms][3]; in getHallNumber() 52 int* types = new int[numAtoms]; in getHallNumber() 58 for (Index i = 0; i < numAtoms; ++i) { in getHallNumber() 67 spg_get_dataset(lattice, positions, types, numAtoms, cartTol); in getHallNumber() 119 Index numAtoms = mol.atomCount(); in standardizeCell() local 126 double(*positions)[3] = new double[numAtoms * numAtomsMultiplier][3]; in standardizeCell() 127 int* types = new int[numAtoms * numAtomsMultiplier]; in standardizeCell() 133 for (Index i = 0; i < numAtoms; ++i) { in standardizeCell() 142 Index newNumAtoms = spg_standardize_cell(lattice, positions, types, numAtoms, in standardizeCell()
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/io/ |
H A D | xyzformat.cpp | 57 size_t numAtoms = 0; in read() local 58 if (!(inStream >> numAtoms)) { in read() 95 for (size_t i = 0; i < numAtoms; ++i) { in read() 118 if (mol.atomCount() != numAtoms) { in read() 130 numAtoms == numAtoms2) { in read() 134 while (numAtoms == numAtoms2) { in read() 136 positions.reserve(numAtoms); in read() 155 if (numAtoms == numAtoms2) in read() 173 size_t numAtoms = mol.atomCount(); in write() local 175 outStream << numAtoms << std::endl; in write() [all …]
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/io/ |
H A D | xyzformat.cpp | 57 size_t numAtoms = 0; in read() local 58 if (!(inStream >> numAtoms)) { in read() 95 for (size_t i = 0; i < numAtoms; ++i) { in read() 118 if (mol.atomCount() != numAtoms) { in read() 130 numAtoms == numAtoms2) { in read() 134 while (numAtoms == numAtoms2) { in read() 136 positions.reserve(numAtoms); in read() 155 if (numAtoms == numAtoms2) in read() 173 size_t numAtoms = mol.atomCount(); in write() local 175 outStream << numAtoms << std::endl; in write() [all …]
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/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/java/ |
H A D | Fragment.java | 4 public int numAtoms, numBonds, numZmatrix; field in Fragment 20 numAtoms=Integer.parseInt(card.substring(0,5).trim()); in read() 21 int maxBonds=10*numAtoms; in read() 22 int maxZmatrix=10*numAtoms; in read() 26 atom = new AtomDefinition[numAtoms]; in read() 29 for(int i=0; i<numAtoms; i++){ in read()
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/dports/science/nwchem-data/nwchem-7.0.2-release/src/java/ |
H A D | Fragment.java | 4 public int numAtoms, numBonds, numZmatrix; field in Fragment 20 numAtoms=Integer.parseInt(card.substring(0,5).trim()); in read() 21 int maxBonds=10*numAtoms; in read() 22 int maxZmatrix=10*numAtoms; in read() 26 atom = new AtomDefinition[numAtoms]; in read() 29 for(int i=0; i<numAtoms; i++){ in read()
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/trajectoryanalysis/tests/ |
H A D | topologyinformation.cpp | 116 EXPECT_EQ(numAtoms, topInfo.x().size()); in runCommonTests() 117 EXPECT_EQ(numAtoms, topInfo.v().size()); in runCommonTests() 134 const int numAtoms = 156; in TEST() local 138 runCommonTests(topInfo, numAtoms); in TEST() 143 ASSERT_EQ(numAtoms, atoms->nr); in TEST() 166 const int numAtoms = 156; in TEST() local 170 runCommonTests(topInfo, numAtoms); in TEST() 176 ASSERT_EQ(numAtoms, atoms->nr); in TEST() 218 const int numAtoms = 156; in TEST() local 222 runCommonTests(topInfo, numAtoms); in TEST() [all …]
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/dports/science/gabedit/GabeditSrc251_300720/src/Display/ |
H A D | RingsOrb.c | 871 gint ki=numAtoms[i]; in addListRMSRing6() 893 gint k = numAtoms[i]; in addListRMSRing6() 1044 for(i=nAtoms-1;i>=1;i--) numAtoms[i]=numAtoms[i-1]; in permutationRight() 1045 numAtoms[0] = zero; in permutationRight() 1062 gint t = numAtoms[i]; in permutationInvers() 1063 numAtoms[i]=numAtoms[nAtoms-i]; in permutationInvers() 1090 k = numAtoms[i]; in permutationSugar() 1162 numAtoms[i] = k; in computeConformerTypeRing6() 1271 numAtoms[i] = k; in computeConformerTypeRing6MinInfo() 1584 numAtoms[i] = k; in computeConformerTypeRing5() [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/contrib/iapbs/modules/NAMD/ |
H A D | GlobalMasterAPBS.C | 459 numAtoms = mol->numAtoms; in GlobalMasterAPBS() 460 charges = new double[numAtoms]; in GlobalMasterAPBS() 461 radii = new double[numAtoms]; in GlobalMasterAPBS() 462 positionx = new double[numAtoms]; in GlobalMasterAPBS() 463 positiony = new double[numAtoms]; in GlobalMasterAPBS() 464 positionz = new double[numAtoms]; in GlobalMasterAPBS() 491 for (int i=0; i<numAtoms; i++) { in GlobalMasterAPBS() 543 for (int i=0; i<numAtoms; i++) { in calculate() 610 for (int i=0; i<numAtoms; i++) { in call_apbs() 720 &numAtoms, in call_apbs() [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FMCS/Wrap/ |
H A D | testFMCS.py | 218 self.assertEqual(mcs.numAtoms, 21) 309 self.assertEqual(mcs.numAtoms, 2) 320 self.assertEqual(mcs.numAtoms, 3) 337 self.assertEqual(mcs.numAtoms, 5) 347 self.assertEqual(mcs.numAtoms, 3) 360 self.assertEqual(mcs.numAtoms, 3) 373 self.assertEqual(mcs.numAtoms, 3) 384 self.assertEqual(mcs.numAtoms, 2) 567 self.assertEqual(r.numAtoms, 4) 578 self.assertEqual(r.numAtoms, 4) [all …]
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/dports/science/cdk/cdk-cdk-2.3/tool/sdg/src/main/java/org/openscience/cdk/layout/ |
H A D | MacroCycleLayout.java | 118 final int numAtoms = macrocycle.getAtomCount(); in bestScore() local 124 for (int i = 0; i < numAtoms; i++) { in bestScore() 151 r1 = (ringAttach.get(0) + i) % numAtoms; in bestScore() 152 r2 = (ringAttach.get(1) + i) % numAtoms; in bestScore() 161 r1 = (ringAttach.get(0) + i) % numAtoms; in bestScore() 162 r2 = (ringAttach.get(1) + i) % numAtoms; in bestScore() 163 r3 = (ringAttach.get(2) + i) % numAtoms; in bestScore() 174 r1 = (ringAttach.get(0) + i) % numAtoms; in bestScore() 175 r2 = (ringAttach.get(1) + i) % numAtoms; in bestScore() 176 r3 = (ringAttach.get(2) + i) % numAtoms; in bestScore() [all …]
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/dports/science/py-spglib/spglib-1.16.2/ruby/ |
H A D | poscar.rb | 243 def namePoscar(numAtoms, potcarName) argument 249 numAtoms.size.times.collect {|i| atomName[i]} 254 numAtoms.size.times do |i| 255 numAtoms[i].times {|j| name << "#{atomName[i]}"} 272 numAtoms = numAtomsPoscar.collect {|x| x.to_i} 274 numAtoms = numAtomsAry.collect {|x| x.to_i} 275 names = namePoscar(numAtoms, potcarName) 293 @atoms = positionPoscar(numAtoms, names) # line 9(8): [Atom, ...] 298 def positionPoscar(numAtoms, names) argument 300 numAtoms.size.times do |i| [all …]
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