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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/qchem/
H A Doutputs.py189 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 …]
/dports/science/py-ase/ase-3.22.0/ase/io/nwchem/
H A Dnwreader.py139 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 …]
/dports/science/py-ase/ase-3.22.0/ase/io/
H A Dcfg.py105 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 …]
H A Dwannier90.py14 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]))
H A Dproteindatabank.py32 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 …]
/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/topology/
H A DPSFParser.py167 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 …]
H A DLAMMPSParser.py195 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 …]
H A DHoomdXMLParser.py113 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))
/dports/devel/py-cclib/cclib-1.7.1/cclib/parser/
H A Dorcaparser.py262 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 …]
H A Dgaussianparser.py725 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 …]
H A Dgamessparser.py569 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 …]
H A Djaguarparser.py113 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 …]
H A Dgamessukparser.py139 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 …]
/dports/science/py-ase/ase-3.22.0/ase/io/vasp_parsers/
H A Dvasp_outcar_parsers.py259 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 …]
/dports/misc/py-orange3-network/orange3-network-ec534c9/orangecontrib/network/network/
H A Dreadwrite.py31 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 …]
/dports/math/qposases/qpOASES-3.2.1/interfaces/python/tests/
H A Dtest_examples.py246 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 …]
/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/ML/
H A Dfiles.py32 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)
/dports/science/py-molmod/molmod-1.4.8/molmod/io/
H A Dcube.py51 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 …]
H A Dgamess.py120 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 …]
H A Dsdf.py84 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)
/dports/cad/sumo/sumo-1.2.0/tools/contributed/sumopy/coremodules/simulation/
H A Dresults.py159 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 …]
/dports/science/qmcpack/qmcpack-3.11.0/nexus/bin/
H A Deshdf78 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('[]')
/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/phylo/
H A Dphast.py6 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()]
/dports/science/qmcpack/qmcpack-3.11.0/utils/afqmctools/afqmctools/wavefunction/
H A Dconverter.py17 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 …]
/dports/science/spglib/spglib-1.16.2/python/spglib/
H A Dspglib.py269 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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