# set dimer geometry
coor_monomer2 = np.array(coor_monomer1).copy()
coor_monomer2[:, 2] += 4.0
# coor_monomer2[:, 1] -= 5.0
coor_monomer2 = list(coor_monomer2)
symbols_monomer = [
'C', 'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'C', 'C', 'C', 'C', 'C', 'H',
'H', 'H', 'H'
]
coordinates = coor_monomer1 + coor_monomer2
symbols_dimer = symbols_monomer * 2
dimer = Structure(coordinates=coordinates,
symbols=symbols_dimer,
charge=0,
multiplicity=1)
range_f1 = range(len(coor_monomer1))
range_f2 = range(len(coor_monomer1), len(coordinates))
print('Dimer structure')
print(dimer)
# RASCI qchem input
qc_input = QchemInput(
dimer,
unrestricted=False,
jobtype='sp',
exchange='hf',
correlation='rasci',
from pyqchem import Structure
from pyqchem import QchemInput
from pyqchem import get_output_from_qchem
from pyqchem.parsers.basic import basic_parser_qchem
import numpy as np
#Defining molecule
molecule = Structure(coordinates=[[0.0, 0.0, 0.0],
[0.0, 0.0, 0.9],
[0.0, 0.0, -0.9]],
symbols=['O', 'H', 'H'],
charge=0,
multiplicity=1)
#Preparing QCHEM input
qc_input1 = QchemInput(molecule,
jobtype='force',
exchange='hf',
basis='6-31G',
extra_rem_keywords={'multipole_field': 'x 0.001'},
extra_sections=['$multipole_field \n x 0.001 \n $end'])
string = '$multipole_field \n x 0.001 \n$end'
print(string)
exit()
print(type(qc_input1))
inp = qc_input1.get_txt()
qc_input_test =
print(inp)
exit()
from pyqchem import get_output_from_qchem, Structure, QchemInput
from pyqchem.parsers.parser_optimization import basic_optimization
import matplotlib.pyplot as plt
from pyqchem.errors import OutputError
# define molecule
coordinates = [[0.0, 1.0, 0.0], [0.0, 0.0, 1.0], [0.0, 0.0, -1.0]]
symbols = ['O', 'H', 'H']
molecule = Structure(coordinates=coordinates,
symbols=symbols,
charge=0,
multiplicity=1)
print('Initial structure')
print(molecule)
# Optimization constrains definition
constrains = {
'stre': [{
'atoms': [1, 2],
'value': 0.9
}, {
'atoms': [1, 3],
'value': 0.9
}],
'bend': [{
'atoms': [2, 1, 3],
'value': 110.0
}]
[-1.21479, 0.70136, 0.00000],
[-2.15666, 1.24515, 0.00000],
[-1.21479, -0.70136, 0.00000],
[-2.15666, -1.24515, 0.00000],
[0.00000, -1.40272, 0.00000],
[0.00000, -2.49029, 0.00000],
[1.21479, -0.70136, 0.00000],
[2.15666, -1.24515, 0.00000],
[1.21479, 0.70136, 0.00000],
[2.15666, 1.24515, 0.00000]]
symbols = ['C', 'H', 'C', 'H', 'C', 'H', 'C', 'H', 'C', 'H', 'C', 'F']
benzene_coordinates = np.array(benzene_coordinates)
molecule = Structure(coordinates=benzene_coordinates,
symbols=symbols,
charge=0)
parameters = {'jobtype': 'sp', 'exchange': 'hf', 'basis': '6-31G'}
qc_input = create_qchem_input(molecule, **parameters)
_, _, fchk_data = get_output_from_qchem(qc_input,
processors=4,
force_recalculation=True,
read_fchk=True)
from pyqchem.file_io import build_fchk
open('test.fchk', 'w').write(build_fchk(fchk_data))
mo_coeff = _set_zero_to_coefficients(fchk_data['basis'],
def get_symmetry_le(electronic_structure,
data_rasci,
fragment_atoms=(0),
tol=0.1,
group='D2h'):
# This only works for singlets on close shell calculations
types = classify_diabatic_states_of_fragment(
data_rasci['diabatization']['diabatic_states'],
fragment_atoms,
tol=0.1)
functions_range = get_basis_functions_ranges_by_atoms(
electronic_structure['basis'], atoms_range=fragment_atoms)
coordinates_frag = np.array(
electronic_structure['structure'].get_coordinates())[fragment_atoms]
labels_frag = electronic_structure['structure'].get_symbols(
)[fragment_atoms]
inertia_moments, inertia_axis = get_inertia(
Structure(coordinates=coordinates_frag, symbols=labels_frag))
center_frag, normal_frag = get_plane(coordinates_frag)
# print(np.array(inertia_axis))
# print(inertia_moments)
# print(inertia_axis[0])
# print(inertia_axis[1])
# print(inertia_axis[2])
if 'LE' in types:
indices = [i for i, x in enumerate(types) if x == "LE"]
symmetry_labels = []
for index in indices:
print('\nLE state found at diabat {}!'.format(index + 1))
coefficients = electronic_structure['nato_coefficients_multi'][
index + 1]
occupation = electronic_structure['nato_occupancies_multi'][index +
1]
overlap_matrix = np.array(electronic_structure['overlap'])
functions_indices = _indices_from_ranges(functions_range)
overlap_matrix = np.array([
ovm[functions_indices]
for ovm in overlap_matrix[functions_indices]
])
c_alpha = np.array(coefficients['alpha'])
oc_alpha = np.array(occupation['alpha'])
orbitals = []
alpha = 0
beta = 0
coefficients_new = {'alpha': [], 'beta': []}
for i, (va, o) in enumerate(zip(c_alpha, oc_alpha)):
va_frag = va[functions_indices]
frag_dot = np.dot(va_frag, np.dot(overlap_matrix, va_frag))
if np.abs(frag_dot - 0.5) > tol:
if frag_dot > 0.5:
orbitals.append((i, np.round(o)))
orbital = np.zeros(len(c_alpha))
for j, val in zip(functions_indices, va_frag):
orbital[j] = val / np.sqrt(frag_dot)
if np.abs(o - 1) < tol and o < 2 - tol:
if alpha == beta:
alpha += 1
coefficients_new['alpha'].append(list(orbital))
else:
beta += 1
coefficients_new['beta'].append(list(orbital))
else:
pass
if alpha == beta:
multiplicity = 1
else:
multiplicity = 3
n_electrons = alpha + beta
try:
# This only works for singlets
molsym = get_wf_symmetry(electronic_structure['structure'],
electronic_structure['basis'],
coefficients_new,
center=center_frag,
orientation=inertia_axis[0],
orientation2=inertia_axis[1],
group=group)
#molsym.print_alpha_mo_IRD()
#molsym.print_beta_mo_IRD()
molsym.print_wf_mo_IRD()
symmetry_labels.append(molsym.IRLab[np.argmax(molsym.wf_IRd)])
except:
pass
return symmetry_labels
return None
[-3.2670227933, 1.2176289251, -0.0251089819]]
# set dimer geometry
coor_monomer2 = np.array(coor_monomer1).copy()
coor_monomer2[:, 2] += 4.5
coor_monomer2[:, 1] -= 5.0
coor_monomer2 = list(coor_monomer2)
symbols_monomer = ['C', 'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H',
'C', 'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H']
coordinates = coor_monomer1 + coor_monomer2
symbols_dimer = symbols_monomer * 2
dimer = Structure(coordinates=coordinates,
symbols=symbols_dimer,
charge=0,
multiplicity=1)
range_f1 = range(len(coor_monomer1))
range_f2 = range(len(coor_monomer1), len(coordinates))
print('Dimer structure')
print(dimer)
# RASCI qchem input
qc_input = QchemInput(dimer,
unrestricted=False,
jobtype='sp',
exchange='hf',
correlation='rasci',
basis='sto-3g',
else:
angles = [43.22189286, 43.86797247, 103.83908054]
rotmol = R.from_euler('zyx', angles, degrees=True)
#print(optimization_function(res.x))
#rotmol = R.from_euler('zyx', res.x, degrees=True)
#operation = Rotation(label='C3', axis=[0, 0, 1], order=3)
#rotmol = R.from_euler('zyx', [0, 0, 0], degrees=True)
#mode_m, coor_m = operation.get_measure(np.array(coordinates), modes, symbols, orientation=rotmol)
#print('measure', coor_m)
#rotmol = R.from_euler('zyx', [360./3, 0, 0], degrees=True)
#print('---')
print(Structure(coordinates, symbols))
# rotations
rotated_axis = rotmol.apply([0, 0, 1])
operation = rotation(2 * np.pi / 2, rotated_axis)
print('axis', rotated_axis)
# reflection
#rotated_axis_r = rotmol.apply([0, 1, 0])
#operation = reflection(rotated_axis_r)
#print('axis_r', rotated_axis_r)
# C2 rotation
# rotated_axis_i = rotmol.apply([(np.sqrt(8 / 9))/2, 0, (1-1 / 3)/2])
# S4 rotation
import matplotlib.pyplot as plt
import pandas as pd
# define monomer
coor_monomer = [[ 0.6695, 0.0000, 0.0000],
[-0.6695, 0.0000, 0.0000],
[ 1.2321, 0.9289, 0.0000],
[ 1.2321, -0.9289, 0.0000],
[-1.2321, 0.9289, 0.0000],
[-1.2321, -0.9289, 0.0000]]
symbols_monomer = ['C', 'C', 'H', 'H', 'H', 'H']
monomer = Structure(coordinates=coor_monomer,
symbols=symbols_monomer,
charge=0,
multiplicity=1)
# optimization qchem input
qc_input = QchemInput(monomer,
jobtype='opt',
exchange='hf',
basis='sto-3g',
geom_opt_tol_gradient=300,
geom_opt_tol_energy=100,
geom_opt_coords=-1,
geom_opt_tol_displacement=1200)
parsed_data = get_output_from_qchem(qc_input,
processors=4,
parser=basic_optimization)
self._conn.close()
return self._calculation_data
@calculation_data.setter
def calculation_data(self, calculation_data):
self._conn = sqlite3.connect(self._calculation_data_filename)
for key, value in calculation_data.items():
self._conn.execute(
"INSERT or REPLACE into DATA_TABLE (input_hash, parser, qcdata) VALUES (?, ?, ?)",
(key[0], key[1], pickle.dumps(value, protocol=2)))
self._conn.commit()
self._conn.close()
if __name__ == '__main__':
a = SqlCache()
b = SqlCache()
#b.redefine_calculation_data_filename('calculation_data2.db')
from pyqchem import QchemInput, Structure
input = QchemInput(Structure(coordinates=[[0, 0, 0]], symbols=['X']))
b.store_calculation_data(input, 'key1', {'entry1': 454, 'entry2': 2323})
data = b.retrieve_calculation_data(input, 'key1')
print(data)
measures_m0 = []
measures_m1 = []
measures_m2 = []
energies = []
frequencies = []
scan_range = np.arange(-0.2, 0.21, 0.01)
for x_dist in scan_range:
water = [[x_dist, 0.00000000e+00, 2.40297090e-01],
[-1.43261539e+00, -1.75444785e-16, -9.61188362e-01],
[1.43261539e+00, 1.75444785e-16, -9.61188362e-01]]
water = np.array(water) * 0.529177249
molecule_water = Structure(coordinates=water,
symbols=['O', 'H', 'H'],
charge=0,
multiplicity=1)
qc_input = QchemInput(
molecule_water,
jobtype='freq',
exchange='hf',
basis='6-31G',
sym_ignore=True,
)
parsed_data, ee = get_output_from_qchem(qc_input,
parser=basic_frequencies,
read_fchk=True)
molecule_coor = np.array(ee['structure'].get_coordinates())
# Simple single point calculation
from pyqchem import get_output_from_qchem, QchemInput, Structure
from pyqchem.parsers.basic import basic_parser_qchem
from posym import SymmetryFunction, SymmetryBase
import posym.algebra as al
import numpy as np
import matplotlib.pyplot as plt
molecule_cis = Structure(
coordinates=[[-1.07076839, -2.13175980, 0.03234382],
[-0.53741536, -3.05918866, 0.04995793],
[-2.14073783, -2.12969357, 0.04016267],
[-0.39112115, -0.95974916, 0.00012984],
[0.67884827, -0.96181542, -0.00769025],
[-1.15875076, 0.37505495, -0.02522296],
[-0.62213437, 1.30041753, -0.05065831],
[-2.51391203, 0.37767199, -0.01531698],
[-3.04726506, 1.30510083, -0.03293196],
[-3.05052841, -0.54769055, 0.01011971]],
symbols=['C', 'H', 'H', 'C', 'H', 'C', 'H', 'C', 'H', 'H'])
# create qchem input
qc_input = QchemInput(
molecule_cis,
jobtype='sp',
exchange='hf',
basis='sto-3g',
#sym_ignore=True
)
# calculate and parse qchem output
from pyqchem.tools import get_geometry_from_pubchem
import numpy as np
import posym.algebra as al
sh6_coor = [[ 0.16290727, -0.36340852, 0.00000000],
[ 1.47290727, -0.36340852, 0.00000000],
[ 0.16290727, 0.94659148, 0.00000000],
[ 0.16290727, -0.36340852, 1.31000000],
[-1.14709273, -0.36340852, 0.00000000],
[ 0.16290727, -1.67340852, 0.00000000],
[ 0.16290727, -0.36340852, -1.31000000]]
sh6_sym = ['S', 'H', 'H', 'H', 'H', 'H', 'H']
sh6_mol = Structure(coordinates=sh6_coor,
symbols=sh6_sym,
charge=0,
multiplicity=1)
dicloro_coor = [[ 2.1437, 0.1015, -0.0002],
[-2.1439, -0.1011, -0.0002],
[ 0.5135, -0.4232, 0.0002],
[-0.5132, 0.4227, 0.0002],
[ 0.4242, -1.5014, 0.0001],
[-0.4237, 1.5009, 0.0001]]
dcl_symbols = ['Cl', 'Cl', 'C', 'C', 'H', 'H']
# from scipy.spatial.transform import Rotation as R
# angles = [100, 200, 300]
# rotmol = R.from_euler('zyx', angles, degrees=True)
# dicloro_coor = rotmol.apply(dicloro_coor)