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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Descriptors/
H A DAUTOCORR2D.cpp61 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()
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H A DMolData3Ddescriptors.cpp14 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
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H A DAUTOCORR3D.cpp61 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()
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H A DWHIM.cpp151 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
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H A DGETAWAY.cpp264 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()
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H A DEEM.cpp208 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()
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/tests/
H A Dupdategroupscog.cpp82 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()
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H A Dleapfrogtestrunners_gpu.cpp77 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()
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H A Dshake.cpp150 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
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H A Dconstrtestrunners.cu75 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()
H A Dsettletestrunners.cu86 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()
H A Dconstrtestdata.cpp81 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()
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H A Dleapfrogtestdata.cpp70 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()
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/core/
H A Davospglib.cpp50 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()
/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/core/
H A Davospglib.cpp50 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()
/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/io/
H A Dxyzformat.cpp57 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()
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/io/
H A Dxyzformat.cpp57 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()
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/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/java/
H A DFragment.java4 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()
/dports/science/nwchem-data/nwchem-7.0.2-release/src/java/
H A DFragment.java4 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()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/trajectoryanalysis/tests/
H A Dtopologyinformation.cpp116 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()
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/dports/science/gabedit/GabeditSrc251_300720/src/Display/
H A DRingsOrb.c871 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()
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/contrib/iapbs/modules/NAMD/
H A DGlobalMasterAPBS.C459 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FMCS/Wrap/
H A DtestFMCS.py218 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)
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/dports/science/cdk/cdk-cdk-2.3/tool/sdg/src/main/java/org/openscience/cdk/layout/
H A DMacroCycleLayout.java118 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()
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/dports/science/py-spglib/spglib-1.16.2/ruby/
H A Dposcar.rb243 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|
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