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/dports/science/gabedit/GabeditSrc251_300720/src/SemiEmpirical/
H A DMoleculeSE.c47 molecule.nAtoms = 0; in newMoleculeSE()
88 molecule->nAtoms = 0; in freeMoleculeSE()
117 gint nAtoms = molecule->nAtoms; in createBondedMatrix() local
121 if(nAtoms<1) in createBondedMatrix()
125 for(i=0;i<nAtoms;i++) in createBondedMatrix()
140 gint nAtoms = molecule->nAtoms; in freeBondedMatrix() local
574 molecule.nAtoms = m->nAtoms; in copyMoleculeSE()
646 int nAtoms; in saveMoleculeSEHIN() local
651 nAtoms = mol->nAtoms; in saveMoleculeSEHIN()
953 if(mol->nAtoms>0) in readGeometryFromGenericOutputFile()
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/dports/science/gabedit/GabeditSrc251_300720/src/Geometry/
H A DPreviewGeom.c74 gint nAtoms; member
208 nAtoms = prevData->nAtoms; in setMultipleBonds()
291 gint nAtoms; in set_connections() local
296 nAtoms = prevData->nAtoms; in set_connections()
396 gint nAtoms; in define_good_factor() local
403 nAtoms = prevData->nAtoms; in define_good_factor()
467 gint nAtoms; in getXiYi() local
474 nAtoms = prevData->nAtoms; in getXiYi()
525 nAtoms = prevData->nAtoms; in define_coord_ecran()
1081 gint nAtoms; in get_atom_to_select() local
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H A DTreeMolecule.c51 for(i=0;i<treeMolecule->nAtoms;i++) in freeConnections()
57 treeMolecule->nAtoms = 0; in freeConnections()
64 if(treeMolecule->nAtoms<1) return; in disconnect()
93 if(treeMolecule->nAtoms<1) return; in initConnections()
95 for(i=0;i<treeMolecule->nAtoms;i++) in initConnections()
100 for(i=0;i<treeMolecule->nAtoms;i++) in initConnections()
102 for(j=0;j<treeMolecule->nAtoms;j++) in initConnections()
120 treeMolecule->nAtoms = NAtoms; in initTreeMolecule()
176 for(i=0;i<treeMolecule->nAtoms;i++) in getRingTreeMolecule()
338 for(i=0;i<treeMolecule.nAtoms;i++) in getListGroupe()
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/dports/science/gabedit/GabeditSrc251_300720/src/Crystallography/
H A DGabeditSPG.c123 int nAtoms = 0; in crystalloGetDataSet() local
129 nAtoms = 0; in crystalloGetDataSet()
134 nAtoms++; in crystalloGetDataSet()
164 int nAtoms = 0; in crystalloGetGroupName() local
170 nAtoms = 0; in crystalloGetGroupName()
175 nAtoms++; in crystalloGetGroupName()
210 int nAtoms = 0; in crystalloPrimitiveSPG() local
218 nAtoms = 0; in crystalloPrimitiveSPG()
223 nAtoms++; in crystalloPrimitiveSPG()
287 nAtoms = 0; in crystalloStandardizeCellSPG()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/cn3d/
H A Datom_set.cpp66 unsigned int nAtoms = coords.GetNumber_of_points(); in BEGIN_SCOPE() local
67 TRACEMSG("model has " << nAtoms << " atomic coords"); in BEGIN_SCOPE()
74 if (coords.GetAtoms().GetMolecule_ids().size()!=nAtoms || in BEGIN_SCOPE()
75 coords.GetAtoms().GetResidue_ids().size()!=nAtoms || in BEGIN_SCOPE()
76 coords.GetAtoms().GetAtom_ids().size()!=nAtoms || in BEGIN_SCOPE()
77 coords.GetSites().GetX().size()!=nAtoms || in BEGIN_SCOPE()
78 coords.GetSites().GetY().size()!=nAtoms || in BEGIN_SCOPE()
79 coords.GetSites().GetZ().size()!=nAtoms || in BEGIN_SCOPE()
90 (haveOccup && coords.GetOccupancies().GetO().size()!=nAtoms) || in BEGIN_SCOPE()
91 (haveAlt && coords.GetAlternate_conf_ids().Get().size()!=nAtoms)) in BEGIN_SCOPE()
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/dports/science/siesta/siesta-4.1.5/Src/
H A Dzmatrix.F286 nAtoms = 0
379 nAtoms = nAtoms + 1
601 species(1:nAtoms) = nspecies(1:nAtoms)
612 do i = 1,3*nAtoms
635 do i=1,nAtoms
645 do i=1,nAtoms
683 nAtoms = nZmolAtoms(m)
698 if (nAtoms.gt.1) then
710 if (nAtoms.gt.2) then
806 nAtoms = nZmolAtoms(m)
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/dports/science/gabedit/GabeditSrc251_300720/src/MolecularMechanics/
H A DMolecule.c43 molecule.nAtoms = 0; in newMolecule()
91 molecule->nAtoms = 0; in freeMolecule()
125 gint nAtoms = molecule->nAtoms; in createBondedMatrix() local
129 if(nAtoms<1) in createBondedMatrix()
133 for(i=0;i<nAtoms;i++) in createBondedMatrix()
136 for(i=0;i<nAtoms;i++) in createBondedMatrix()
138 for(j=0;j<nAtoms;j++) in createBondedMatrix()
148 gint nAtoms = molecule->nAtoms; in freeBondedMatrix() local
153 for(i=0;i<nAtoms;i++) in freeBondedMatrix()
201 k = molecule->nAtoms; in set2Connections()
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/dports/x11/libX11/libX11-1.7.2/src/xkb/
H A DXKBNames.c385 nAtoms++; in XkbSetNames()
387 nAtoms++; in XkbSetNames()
389 nAtoms++; in XkbSetNames()
391 nAtoms++; in XkbSetNames()
393 nAtoms++; in XkbSetNames()
395 nAtoms++; in XkbSetNames()
632 nAtoms++; in XkbChangeNames()
634 nAtoms++; in XkbChangeNames()
636 nAtoms++; in XkbChangeNames()
638 nAtoms++; in XkbChangeNames()
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/dports/science/jdftx/jdftx-1.6.0/jdftx/electronic/
H A DSpeciesInfo.cu34 if(n<nbasis) Vnl_calc<l,m>(n, atomStride, nAtoms, k, iGarr, G, pos, VnlRadial, V); in Vnl_kernel()
169 SG[i] = invVol * getSG_calc(iG, nAtoms, atpos); in getSG_kernel()
174 getSG_kernel<<<glc.nBlocks,glc.nPerBlock>>>(zBlock, S, nAtoms, atpos, invVol, SG); in getSG_gpu()
182 int nAtoms, const vector3<>* atpos, double invVol, const RadialFunctionG VlocRadial, in updateLocal_kernel() argument
188 nCore, tauCore, nAtoms, atpos, invVol, VlocRadial, in updateLocal_kernel()
193 int nAtoms, const vector3<>* atpos, double invVol, const RadialFunctionG& VlocRadial, in updateLocal_gpu() argument
199 nCore, tauCore, nAtoms, atpos, invVol, VlocRadial, in updateLocal_gpu()
254 int nAtoms, const vector3<>* atpos, const RadialFunctionG VlocRadial, double Z, in gradLocalToStress_kernel() argument
260 ccgrad_nCore, ccgrad_tauCore, grad_RRT, nAtoms, atpos, VlocRadial, Z, in gradLocalToStress_kernel()
266 int nAtoms, const vector3<>* atpos, const RadialFunctionG& VlocRadial, double Z, in gradLocalToStress_gpu() argument
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H A DSpeciesInfo_internal.cpp128 int nAtoms, const vector3<>* atpos, double invVol, complex* SG) in getSG_sub() argument
129 { THREAD_halfGspaceLoop( SG[i] = invVol * getSG_calc(iG, nAtoms, atpos); ) in getSG_sub()
132 { threadLaunch(getSG_sub, S[0]*S[1]*(S[2]/2+1), S, nAtoms, atpos, invVol, SG); in getSG()
138 int nAtoms, const vector3<>* atpos, double invVol, const RadialFunctionG& VlocRadial, in updateLocal_sub() argument
144 nAtoms, atpos, invVol, VlocRadial, in updateLocal_sub()
149 int nAtoms, const vector3<>* atpos, double invVol, const RadialFunctionG& VlocRadial, in updateLocal() argument
154 nAtoms, atpos, invVol, VlocRadial, in updateLocal()
197 int nAtoms, const vector3<>* atpos, const RadialFunctionG& VlocRadial, double Z, in gradLocalToStress_sub() argument
203 ccgrad_nCore, ccgrad_tauCore, grad_RRT, nAtoms, atpos, VlocRadial, in gradLocalToStress_sub()
209 int nAtoms, const vector3<>* atpos, const RadialFunctionG& VlocRadial, double Z, in gradLocalToStress() argument
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/dports/math/mlpack/mlpack-3.4.2/src/mlpack/tests/
H A Dsparse_coding_test.cpp55 uword nAtoms = 25; variable
67 SparseCoding sc(nAtoms, lambda1);
85 uword nAtoms = 25; variable
95 SparseCoding sc(nAtoms, lambda1, lambda2);
105 (trans(D) * D + lambda2 * eye(nAtoms, nAtoms)) * Z.unsafe_col(i)
117 uword nAtoms = 25; variable
127 SparseCoding sc(nAtoms, lambda1, 0.0, 0, 0.01, tol);
143 size_t nAtoms = 25; variable
145 SparseCoding sc(nAtoms, 0.05, 0.1);
202 uword nAtoms = 25; variable
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H A Dlocal_coordinate_coding_test.cpp56 uword nAtoms = 10; in BOOST_AUTO_TEST_CASE() local
69 LocalCoordinateCoding lcc(X, nAtoms, lambda1, 10); in BOOST_AUTO_TEST_CASE()
76 vec sqDists = vec(nAtoms); in BOOST_AUTO_TEST_CASE()
77 for (uword j = 0; j < nAtoms; ++j) in BOOST_AUTO_TEST_CASE()
94 uword nAtoms = 10; in BOOST_AUTO_TEST_CASE() local
107 LocalCoordinateCoding lcc(X, nAtoms, lambda, 10); in BOOST_AUTO_TEST_CASE()
117 grad += (D - repmat(X.unsafe_col(i), 1, nAtoms)) * in BOOST_AUTO_TEST_CASE()
128 size_t nAtoms = 10; in BOOST_AUTO_TEST_CASE() local
130 LocalCoordinateCoding lcc(nAtoms, 0.05, 2 /* don't care about quality */); in BOOST_AUTO_TEST_CASE()
175 uword nAtoms = 10; in BOOST_AUTO_TEST_CASE() local
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/dports/science/mmdb2/mmdb2-2.0.20/mmdb2/
H A Dmmdb_atom.cpp1054 nAtoms = res[i]->nAtoms; in GetChainCalphas()
1066 nAtoms = res[i]->nAtoms; in GetChainCalphas()
1096 nAtoms = residue->nAtoms; in GetChainCalphas()
2275 nAtoms = 0; in MakeFactoryFunctions()
2566 nAtoms = 0; in FreeMemory()
2592 nAtoms++; in _AddAtom()
2634 nAtoms++; in AddAtom()
2683 nAtoms++; in InsertAtom()
2730 nAtoms--; in _ExcludeAtom()
2816 nAtoms = res->nAtoms; in _copy()
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H A Dmmdb_root.cpp71 nAtoms = 0; in InitMMDBRoot()
124 nAtoms = 0; in FreeCoordMemory()
1006 nAtoms = k; in PDBCleanup()
1096 nAtoms = k; in PDBCleanup()
1111 nAtoms = k; in PDBCleanup()
1359 nAtoms = n; in FinishStructEdit()
1915 nAtoms++; in CheckInAtom()
1920 if (kndex>nAtoms) nAtoms = kndex; in CheckInAtom()
1994 nAtoms = IMax(nAtoms,kndex); in CheckInAtoms()
2248 nAtoms = IMax(nAtoms,index); in AllocateAtom()
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/dports/science/v_sim/v_sim-3.8.0/lib/plug-ins/abinit/
H A Dm_ab7_symmetry.F9039 integer :: nAtoms component
436 integer, intent(in) :: nAtoms local
447 do i = 1, nAtoms, 1
459 token%data%nAtoms = nAtoms
484 integer, intent(in) :: nAtoms local
493 do i = 1, nAtoms, 1
504 if (token%data%nAtoms /= nAtoms) then
529 integer, intent(in) :: nAtoms local
538 do i = 1, nAtoms, 1
549 if (token%data%nAtoms /= nAtoms) then
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/fileio/
H A Dtngio.cpp915 GMX_UNUSED_VALUE(nAtoms); in gmx_fwrite_tng()
1054 if ((!index.empty()) && nAtoms > 0) in gmx_prepare_tng_writing()
1062 if (nAtoms >= 0) in gmx_prepare_tng_writing()
1071 GMX_UNUSED_VALUE(nAtoms); in gmx_prepare_tng_writing()
1140 for (i = 0; i < nAtoms; i++) in convert_array_to_real_array()
1214 tng_num_particles_get(tng, &nAtoms); in gmx_tng_setup_atom_subgroup()
1216 if (nAtoms == ind.ssize()) in gmx_tng_setup_atom_subgroup()
1226 if (nAtoms == ind.ssize()) in gmx_tng_setup_atom_subgroup()
1580 atomCharges.resize(nAtoms); in gmx_print_tng_molecule_system()
1599 atomMasses.resize(nAtoms); in gmx_print_tng_molecule_system()
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/dports/science/gabedit/GabeditSrc251_300720/src/VibrationalCorrections/
H A DGabeditGaussianInput.c494 for(i=0;i<nAtoms;i++) in showVibCorrections()
512 for(i=0;i<nAtoms;i++) in showVibCorrections()
684 for(i=0;i<nAtoms;i++) in printVibCorrections()
980 for(i=0;i<nAtoms;i++) in readLastShieldingTensors()
1114 gint nBlock = nAtoms/5; in readLastSpinSpins()
1115 gint rest = nAtoms%5; in readLastSpinSpins()
1135 nl = nAtoms-ib*5; in readLastSpinSpins()
1175 for(i=0;i<nAtoms;i++) spinspins0[i]=g_malloc(nAtoms*sizeof(gdouble)); in readSpinSpins()
1177 for(i=0;i<nAtoms;i++) spinspinsP[i]=g_malloc(nAtoms*sizeof(gdouble)); in readSpinSpins()
1179 for(i=0;i<nAtoms;i++) spinspinsM[i]=g_malloc(nAtoms*sizeof(gdouble)); in readSpinSpins()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/minimize/
H A DMMConstraint.java18 public int nAtoms; field in MMConstraint
27 nAtoms = Math.abs(indexes[0]); in set()
28 type = nAtoms - 2; in set()
29 for (int j = 1; j <= nAtoms; j++) { in set()
31 indexes[0] = -nAtoms; // disable in set()
/dports/science/pcmsolver/pcmsolver-1.3.0/tests/
H A DTestingMolecules.hpp127 int nAtoms = 4; in NH3() local
134 Eigen::MatrixXd geom(3, nAtoms); in NH3()
168 int nAtoms = 3; in H3() local
174 Eigen::MatrixXd geom(3, nAtoms); in H3()
215 int nAtoms = 2; in H2() local
220 Eigen::MatrixXd geom(3, nAtoms); in H2()
244 int nAtoms = 3; in CO2() local
316 int nAtoms = 4; in CH3() local
357 int nAtoms = 6; in C2H4() local
408 int nAtoms = 12; in C6H6() local
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/dports/science/gabedit/GabeditSrc251_300720/src/IsotopeDistribution/
H A DIsotopeDistributionCalculator.c83 e.nAtoms = 1; in get_element_data()
103 if(!nAtoms) return elements; in get_elements()
109 elements[i].nAtoms = nAtoms[i]; in get_elements()
268 for(j = 0; j<elements[i].nAtoms; j++) in compute_peaks()
329 elements = get_elements(nElements, nAtoms, symbols); in compute_isotope_distribution()
343 gint* nAtoms = NULL; in parse_formula() local
452 nAtoms = g_malloc(nElements*sizeof(gint)); in parse_formula()
455 nAtoms[i] = atoi(nA[i]); in parse_formula()
456 if(nAtoms[i]<1) nAtoms[i] = 1; in parse_formula()
461 *nAtomsP = nAtoms; in parse_formula()
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/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/EMT_Asap__MD_128315414717_004/
H A DKimAtoms.cpp53 int nAtoms, in ReInit() argument
59 this->nAtoms = nAtoms; in ReInit()
60 positions.resize(nAtoms); in ReInit()
61 numbers.resize(nAtoms); in ReInit()
63 for (int i = 0; i < nAtoms; i++) in ReInit()
82 for (int i = 0; i < nAtoms; i++) in GetListOfElements()
124 int n = nAtoms; in GetPositions()
135 int n = nAtoms; in GetScaledPositions()
H A Dasap_kim_api.cpp187 int nAtoms = 0; in Compute() local
203 nAtoms = *nAtoms_p; in Compute()
204 assert(nAtoms >= 0); in Compute()
260 atoms->ReInit(modelComputeArguments, nAtoms, coords, particleSpecies, particleContributing); in Compute()
273 atoms->ReInit(modelComputeArguments, nAtoms, coords, particleSpecies, particleContributing); in Compute()
282 assert(energies_v.size() == nAtoms); in Compute()
283 for (int i = 0; i < nAtoms; i++) in Compute()
291 assert(virials.size() == nAtoms); in Compute()
293 for (int i = 0; i < 6*(nAtoms); i++) in Compute()
305 assert(forces_v.size() == nAtoms); in Compute()
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/dports/science/nwchem-data/nwchem-7.0.2-release/src/dimqm/
H A Ddimqm_energy.F1 subroutine dimqm_energy(nAtoms, muind, eqme, eqmn) argument
10 integer nAtoms
11 double precision muind(3,nAtoms)
12 double precision eqme(3, nAtoms)
13 double precision eqmn(3, nAtoms)
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/dimqm/
H A Ddimqm_energy.F1 subroutine dimqm_energy(nAtoms, muind, eqme, eqmn) argument
10 integer nAtoms
11 double precision muind(3,nAtoms)
12 double precision eqme(3, nAtoms)
13 double precision eqmn(3, nAtoms)
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Fingerprints/
H A DMorganFingerprints.cpp106 unsigned int nAtoms = lmol->getNumAtoms(); in calcFingerprint() local
114 std::vector<uint32_t> invariantCpy(nAtoms); in calcFingerprint()
118 for (unsigned int i = 0; i < nAtoms; ++i) { in calcFingerprint()
130 boost::dynamic_bitset<> chiralAtoms(nAtoms); in calcFingerprint()
138 boost::dynamic_bitset<> deadAtoms(nAtoms); in calcFingerprint()
140 boost::dynamic_bitset<> includeAtoms(nAtoms); in calcFingerprint()
149 std::vector<unsigned int> atomOrder(nAtoms); in calcFingerprint()
152 for (unsigned int i = 0; i < nAtoms; ++i) { in calcFingerprint()
160 for (unsigned int i = 0; i < nAtoms; ++i) { in calcFingerprint()
164 for (unsigned int i = 0; i < nAtoms; ++i) { in calcFingerprint()
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