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import os
import re
import numpy as np
from ase.units import Hartree, Bohr
from ase.io.orca import write_orca
from ase.calculators.calculator import FileIOCalculator, Parameters, ReadError
class ORCA(FileIOCalculator):
implemented_properties = ['energy', 'forces']
if 'ORCA_COMMAND' in os.environ:
command = os.environ['ORCA_COMMAND'] + ' PREFIX.inp > PREFIX.out'
else:
command = 'orca PREFIX.inp > PREFIX.out'
default_parameters = dict(
charge=0, mult=1,
task='gradient',
orcasimpleinput='tightscf PBE def2-SVP',
orcablocks='%scf maxiter 200 end')
def __init__(self, restart=None,
ignore_bad_restart_file=FileIOCalculator._deprecated,
label='orca', atoms=None, **kwargs):
""" ASE interface to ORCA 4
by Ragnar Bjornsson, Based on NWchem interface but simplified.
Only supports energies and gradients (no dipole moments,
orbital energies etc.) for now.
For more ORCA-keyword flexibility, method/xc/basis etc.
keywords are not used. Instead, two keywords:
orcasimpleinput: str
What you'd put after the "!" in an orca input file.
orcablock: str
What you'd put in the "% ... end"-blocks.
are used to define the ORCA simple-inputline and the ORCA-block input.
This allows for more flexible use of any ORCA method or keyword
available in ORCA instead of hardcoding stuff.
Point Charge IO functionality added by A. Dohn.
"""
FileIOCalculator.__init__(self, restart, ignore_bad_restart_file,
label, atoms, **kwargs)
self.pcpot = None
def set(self, **kwargs):
changed_parameters = FileIOCalculator.set(self, **kwargs)
if changed_parameters:
self.reset()
def write_input(self, atoms, properties=None, system_changes=None):
FileIOCalculator.write_input(self, atoms, properties, system_changes)
p = self.parameters
p.write(self.label + '.ase')
p['label'] = self.label
if self.pcpot: # also write point charge file and add things to input
p['pcpot'] = self.pcpot
write_orca(atoms, **p)
def read(self, label):
FileIOCalculator.read(self, label)
if not os.path.isfile(self.label + '.out'):
raise ReadError
with open(self.label + '.inp') as fd:
for line in fd:
if line.startswith('geometry'):
break
symbols = []
positions = []
for line in fd:
if line.startswith('end'):
break
words = line.split()
symbols.append(words[0])
positions.append([float(word) for word in words[1:]])
self.parameters = Parameters.read(self.label + '.ase')
self.read_results()
def read_results(self):
self.read_energy()
if self.parameters.task.find('gradient') > -1:
self.read_forces()
def read_energy(self):
"""Read Energy from ORCA output file."""
with open(self.label + '.out', mode='r', encoding='utf-8') as fd:
text = fd.read()
# Energy:
re_energy = re.compile(r"FINAL SINGLE POINT ENERGY.*\n")
re_not_converged = re.compile(r"Wavefunction not fully converged")
found_line = re_energy.search(text)
if found_line and not re_not_converged.search(found_line.group()):
self.results['energy'] = float(found_line.group().split()[-1]) * Hartree
def read_forces(self):
"""Read Forces from ORCA output file."""
with open(f'{self.label}.engrad', 'r') as fd:
lines = fd.readlines()
getgrad = False
gradients = []
tempgrad = []
for i, line in enumerate(lines):
if line.find('# The current gradient') >= 0:
getgrad = True
gradients = []
tempgrad = []
continue
if getgrad and "#" not in line:
grad = line.split()[-1]
tempgrad.append(float(grad))
if len(tempgrad) == 3:
gradients.append(tempgrad)
tempgrad = []
if '# The at' in line:
getgrad = False
self.results['forces'] = -np.array(gradients) * Hartree / Bohr
def embed(self, mmcharges=None, **parameters):
"""Embed atoms in point-charges (mmcharges)
"""
self.pcpot = PointChargePotential(mmcharges, label=self.label)
return self.pcpot
class PointChargePotential:
def __init__(self, mmcharges, label=None, positions=None, directory=None):
""" Point Charge Potential Interface to ORCA """
if positions is not None:
self.set_positions(positions)
if directory is None:
directory = os.getcwd()
self.directory = directory + os.sep
self.mmcharges = mmcharges
self.label = label
def set_positions(self, positions):
self.positions = positions
def set_charges(self, mmcharges):
self.q_p = mmcharges
def write_mmcharges(self, filename='orca_mm'):
pc_file = open(os.path.join(self.directory,
filename + '.pc'), 'w')
pc_file.write('{0:d}\n'.format(len(self.mmcharges)))
for [pos, pc] in zip(self.positions, self.mmcharges):
[x, y, z] = pos
pc_file.write('{0:12.6f} {1:12.6f} {2:12.6f} {3:12.6f}\n'
.format(pc, x, y, z))
pc_file.close()
def get_forces(self, calc):
''' reads forces on point charges from .pcgrad file '''
with open(os.path.join(self.directory, self.label + '.pcgrad'),
'r', encoding='utf-8') as f:
lines = f.readlines()
numpc = int(lines[0])
forces = np.zeros((numpc, 3))
for i in range(numpc):
[fx, fy, fz] = [float(f) for f in lines[i + 1].split()]
forces[i, :] = fx, fy, fz
return -forces * Hartree / Bohr
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