/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/qchem/ |
H A D | outputs.py | 189 real_d3 = np.zeros(len(temp_d3)) 210 real_S2 = np.zeros(len(temp_S2)) 390 geometry = np.zeros(shape=(len(temp_geom), 3), dtype=float) 462 temp = np.zeros(shape=(len(one_scf), 2)) 537 temp = np.zeros(len(one_mulliken)) 554 temp = np.zeros(len(one_entry)) 1458 if header in line.strip(): 1489 return line[1:7].strip() 1791 entry["perturbation energy"] = float(line[50:62].strip()) 1792 entry["energy difference"] = float(line[62:70].strip()) [all …]
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/dports/science/py-ase/ase-3.22.0/ase/io/nwchem/ |
H A D | nwreader.py | 139 pos = np.zeros((natoms, 3)) 141 line = line.strip().split() 148 cell = np.zeros((3, 3)) 150 line = line.strip().split() 225 pos = np.zeros((natoms, 3)) 226 forces = np.zeros((natoms, 3)) 228 line = line.strip().split() 294 quadrupole = np.zeros(9) 437 forces = np.zeros((natoms, 3)) 482 stress = np.zeros((3, 3)) [all …]
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/dports/science/py-ase/ase-3.22.0/ase/io/ |
H A D | cfg.py | 105 color = np.zeros([len(atoms), 3], dtype=float) 110 radius = np.zeros(len(atoms), dtype=float) 130 cell = np.zeros([3, 3]) 132 eta = np.zeros([3, 3]) 140 L = L.strip() 149 key = key.strip() 150 value = [x.strip() for x in value.split()] 153 spos = np.zeros([nat, 3]) 154 masses = np.zeros(nat) 156 vels = np.zeros([nat, 3]) [all …]
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H A D | wannier90.py | 14 if line.strip().lower().startswith('lattice vectors (ang)'): 19 cell = [[float(x) for x in line.split()[-3:]] 35 positions.append([float(x) for x in words[-4:-1]]) 43 if lines[n].strip().lower().startswith('final state'): 48 'centers': np.zeros((0, 3)), 49 'spreads': np.zeros((0,))} 55 line = lines[n].strip() 57 centers.append([float(x) 60 spreads.append(float(line.split()[-1]))
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H A D | proteindatabank.py | 32 name = line[12:16].strip() 43 coord = np.array([float(line[30:38]), 44 float(line[38:46]), 51 occupancy = float(line[54:60]) 59 bfactor = float(line[60:66]) 65 symbol = line[76:78].strip().upper() 78 trans = np.zeros(3) 116 cellpar = [float(line[6:15]), # a 126 orig[c] = [float(line[10:20]), 129 trans[c] = float(line[45:55]) [all …]
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/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/topology/ |
H A D | PSFParser.py | 167 while header.strip() == "": 171 num = float(header[0]) 172 sect_type = header[1].strip('!:') 239 l[19:23].strip(), l[24:28].strip(), 244 l[29:37].strip(), l[38:46].strip(), 252 x[4], x[5], float(x[6]), float(x[7])) 266 atomids = np.zeros(numlines, dtype=np.int32) 267 segids = np.zeros(numlines, dtype=object) 268 resids = np.zeros(numlines, dtype=np.int32) 269 resnames = np.zeros(numlines, dtype=object) [all …]
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H A D | LAMMPSParser.py | 195 line = line.partition('#')[0].strip() 548 masses[line[0]] = float(line[1]) 727 line = l.strip() 736 headers[keyword] = (float(values[0]), float(values[1])) 750 line = l.strip() 759 fields = file_iter.next().strip().split() 768 fields = file_iter.next().strip().split() 775 fields = file_iter.next().strip().split() 781 … positions[index] = np.array([float(fields[4]), float(fields[5]), float(fields[6])]) 787 fields = file_iter.next().strip().split() [all …]
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H A D | HoomdXMLParser.py | 113 atypes = atype.text.strip().split('\n') 119 ('diameter', Radii, lambda x: float(x) / 2., np.float32), 120 ('mass', Masses, float, np.float64), 121 ('charge', Charges, float, np.float32), 125 vals = [mapper(el) for el in val.text.strip().split()] 140 for line in val.text.strip().split('\n') 141 if line.strip()] 149 attrs['masses'] = Masses(np.zeros(natoms)) 151 attrs['charges'] = Charges(np.zeros(natoms, dtype=np.float32))
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/dports/devel/py-cclib/cclib-1.7.1/cclib/parser/ |
H A D | orcaparser.py | 262 current_params.append(float(line.split(':')[-1].strip())) 507 current_params.append(float(line.split(':')[-1].strip())) 861 mocoeffs = [numpy.zeros((self.nbasis, self.nbasis), "d")] 1345 tensor = numpy.zeros((3, 3)) 1375 vibfreqs = numpy.zeros(3 * self.natom) 1436 all_vibirs = numpy.zeros((3 * self.natom,), "d") 1462 all_vibramans = numpy.zeros(3 * self.natom) 1764 density = numpy.zeros((num_orbs, num_orbs)) 1782 spin_density = numpy.zeros((num_orbs, num_orbs)) 1811 energy = float(next(inputfile).strip()) [all …]
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H A D | gaussianparser.py | 725 scftargets.append(utils.float(line.strip().split('=')[1][:-1])) 729 scftargets.append(utils.float(line.strip().split('=')[1][:-1])) 1627 self.aooverlaps = numpy.zeros((self.nbasis, self.nbasis), "d") 1665 self.mocoeffs.append(numpy.zeros((self.nmo, self.nbasis), "d")) 1670 mocoeffs = [numpy.zeros((self.nmo, self.nbasis), "d")] 1738 coeffs = numpy.zeros((self.nmo, self.nbasis), "d") 1823 self.vibanharms = numpy.zeros((Nvibs, Nvibs), "d") 1870 self.coreelectrons = numpy.zeros(self.natom, "i") 2077 polarizability = numpy.zeros(shape=(3, 3)) 2091 polarizability = numpy.zeros(shape=(3, 3)) [all …]
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H A D | gamessparser.py | 569 while line.strip(): 686 while line.strip(): 717 while line.strip(): 874 self.vibrmasses.extend(list(map(float, line.strip().split()[2:]))) 879 irIntensity = map(float, line.strip().split()[2:]) 1030 self.mocoeffs = [numpy.zeros((self.nmo, self.nbasis), "d")] 1171 self.mocoeffs.append(numpy.zeros((self.nmo, self.nbasis), "d")) 1220 self.nocoeffs = numpy.zeros((self.nmo, self.nbasis), "d") 1317 self.aooverlaps = numpy.zeros((self.nbasis, self.nbasis), "d") 1393 while line.strip(): [all …]
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H A D | jaguarparser.py | 113 while line.strip(): 196 while line.strip(): 212 while line.strip(): 257 self.homos = numpy.array([float(line.strip().split()[-1])-1], "i") 406 mocoeffs = numpy.zeros((len(self.moenergies[s]), self.nbasis), "d") 500 self.aooverlaps = numpy.zeros((self.nbasis, self.nbasis), "d") 546 self.geotargets = numpy.zeros(5, "d") 559 while blank.strip(): 583 while line.strip(): 611 if not line.strip(): [all …]
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H A D | gamessukparser.py | 139 while line.strip(): 141 if line.strip()[1:10].strip() and list(set(line.strip())) != ['*']: 225 self.aooverlaps = numpy.zeros((self.nbasis, self.nbasis), "d") 245 self.coreelectrons = numpy.zeros(self.natom, 'i') 369 while line.strip(): 479 temp = line[25:30].strip() 511 mocoeffs = numpy.zeros((self.nmo, self.nbasis), "d") 556 while not line.strip(): 624 if not line.strip(): 673 while line.strip(): [all …]
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/dports/science/py-ase/ase-3.22.0/ase/io/vasp_parsers/ |
H A D | vasp_outcar_parsers.py | 259 line = line.strip() 262 ibzkpts = np.zeros((nkpts, 3)) 263 kpt_weights = np.zeros(nkpts) 302 cell = np.zeros((3, 3)) 318 positions = np.zeros((natoms, 3)) 319 forces = np.zeros((natoms, 3)) 349 magmom = float(magmom_lst[0]) 370 magmoms = np.zeros(natoms) 385 efermi = float(parts[2]) 447 eigenvalues = np.zeros(nbands) [all …]
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/dports/misc/py-orange3-network/orange3-network-ec534c9/orangecontrib/network/network/ |
H A D | readwrite.py | 31 coordinates = np.zeros((len(lines), 2)) 41 x, y = float(x), float(y) 45 label = line.strip().split(maxsplit=1)[1] 72 indptr = np.zeros(nvertices + 1, dtype=int) 90 lines = [line.strip() for line in f] 110 network_name = part_args.strip() 125 name=part_args.strip() or part_type[1:])) 131 name=part_args.strip() or part_type[1:])) 190 coords = np.zeros((n_nodes, 0), dtype=float) 193 modes = np.ones((n_nodes, 1), dtype=float) [all …]
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/dports/math/qposases/qpOASES-3.2.1/interfaces/python/tests/ |
H A D | test_examples.py | 246 maxViol = np.zeros(1) 247 maxStat = np.zeros(1) 248 maxFeas = np.zeros(1) 249 maxCmpl = np.zeros(1) 275 maxViol = np.zeros(1) 276 maxStat = np.zeros(1) 277 maxFeas = np.zeros(1) 278 maxCmpl = np.zeros(1) 291 Var = np.zeros(5*5) 314 expected = match.group('VAR').strip().split("\n") [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/ML/ |
H A D | files.py | 32 result = self.regExp.split(inLine)[0].strip() 44 result = self.regExp.split(line)[0].strip() 63 def ReadDataFile(fileName, comment=r'#', depVarCol=0, dataType=numpy.float): 88 if dataType in [numpy.float, numpy.float32, numpy.float64]: 89 _convfunc = float 94 indVarMat = numpy.zeros((nPts, nIndVars), dataType) 95 depVarVect = numpy.zeros(nPts, dataType)
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/dports/science/py-molmod/molmod-1.4.8/molmod/io/ |
H A D | cube.py | 51 points = np.zeros((nrep[0], nrep[1], nrep[2], 3), float) 61 title = f.readline().strip() 62 subtitle = f.readline().strip() 69 np.array([float(words[1]), float(words[2]), float(words[3])], float) 86 int(words[0]), float(words[1]), 87 np.array([float(words[2]), float(words[3]), float(words[4])], float) 91 numbers = np.zeros(natom, int) 92 nuclear_charges = np.zeros(natom, float) 93 coordinates = np.zeros((natom, 3), float) 179 data = np.zeros(tuple(nrep), float) [all …]
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H A D | gamess.py | 120 data["title"] = f.readline().strip() 148 numbers = np.zeros(N, int) 152 coordinates = np.zeros((N,3), float) 156 numbers[i] = int(float(words[1])) 176 gradient = np.zeros((N,3), float) 180 gradient[i,0] = float(words[2]) 181 gradient[i,1] = float(words[3]) 182 gradient[i,2] = float(words[4]) 212 hessian = np.zeros((3*N, 3*N), float) 236 masses = np.zeros(N, float) [all …]
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H A D | sdf.py | 84 title = title.strip() 96 numbers = np.zeros(num_atoms, int) 97 coordinates = np.zeros((num_atoms, 3), float) 103 coordinates[i, 0] = float(words[0]) 104 coordinates[i, 1] = float(words[1]) 105 coordinates[i, 2] = float(words[2]) 115 orders = np.zeros(num_bonds, int) 126 formal_charges = np.zeros(len(numbers), int)
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/dports/cad/sumo/sumo-1.2.0/tools/contributed/sumopy/coremodules/simulation/ |
H A D | results.py | 159 ids = np.zeros(n, dtype=np.int32) 173 values_attr = np.zeros(n, int) 179 values_attr = np.zeros(n, dtype=np.bool) 351 ids = np.zeros(n, dtype=np.int32) 371 values_attr = np.zeros(n, int) 374 values_attr = np.zeros(n, float) 377 values_attr = np.zeros(n, obj) 596 if a.strip() != '': 617 if a.strip() != '': 705 if a.strip() != '': [all …]
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/dports/science/qmcpack/qmcpack-3.11.0/nexus/bin/ |
H A D | eshdf | 78 from numpy import array,pi,dot,sqrt,abs,zeros 103 nelec_k = zeros((ns,),dtype=float) 199 print('\n'+parser.format_help().strip()+'\n') 219 opt.E_fermi = float(opt.E_fermi) 231 nspin = np.zeros((nspins,),dtype=int) 232 kspin = np.zeros((nspins,),dtype=float) 233 normspin = np.zeros((nspins,),dtype=float) 252 ksorb = np.array(ksorb,dtype=float) 253 esorb = np.array(esorb,dtype=float) 274 return '{}'.format(a).strip().strip('[]')
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/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/phylo/ |
H A D | phast.py | 6 from numpy import zeros 32 tm.background = tuple(map(float, line.split()[1:])) 34 tm.tree = line[6:].strip() 36 matrix = zeros((tm.radix, tm.radix), float) 38 matrix[i] = [float(_) for _ in next(input).split()]
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/dports/science/qmcpack/qmcpack-3.11.0/utils/afqmctools/afqmctools/wavefunction/ |
H A D | converter.py | 17 line = f.readline().strip().split('=') 19 if line[0].strip() == 'NCI': 21 elif line[0].strip() == 'TYPE': 22 wfn_type = line[1].strip() 23 elif line[0].strip() == 'UHF': 190 assert cf.dtype == numpy.dtype(float) or cf.dtype == numpy.dtype(complex) 199 cfx = numpy.ascontiguousarray(numpy.zeros((2*nb*no,), 200 dtype=float, 229 cfx = numpy.ascontiguousarray(numpy.zeros((4*nb*no,), 230 dtype=float, [all …]
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/dports/science/spglib/spglib-1.16.2/python/spglib/ |
H A D | spglib.py | 269 dataset['international'] = dataset['international'].strip() 270 dataset['hall'] = dataset['hall'].strip() 271 dataset['choice'] = dataset['choice'].strip() 282 s.strip() for s in dataset['site_symmetry_symbols']] 301 dataset['pointgroup'] = dataset['pointgroup'].strip() 364 spg_type[key] = spg_type[key].strip() 740 _is_shift = np.zeros(3, dtype='intc') 796 _is_shift = np.zeros(3, dtype='intc') 859 _is_shift = np.zeros(3, dtype='intc') 903 result = spg.delaunay_reduce(delaunay_lattice, float(eps)) [all …]
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