from tcutility.job.generic import Job
from tcutility import spell_check
import os
from typing import Union
j = os.path.join
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class XTBJob(Job):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.xtb_path = 'xtb'
self._options = ['coords.xyz']
self._scan = {}
def _setup_job(self):
os.makedirs(self.workdir, exist_ok=True)
self._molecule.write(j(self.workdir, 'coords.xyz'))
if self._scan:
with open(j(self.workdir, 'scan.inp'), 'w+') as scaninp:
for key, value in self._scan.items():
scaninp.write(f'${key}\n')
for line in value:
scaninp.write(f' {line}\n')
scaninp.write('$end\n')
options = ' '.join(self._options)
with open(self.runfile_path, 'w+') as runf:
runf.write('#!/bin/sh\n\n') # the shebang is not written by default by ADF
runf.write('\n'.join(self._preambles) + '\n\n')
runf.write(f'{self.xtb_path} {options}\n')
runf.write('\n'.join(self._postambles))
return True
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def model(self, method: Union[str, int]):
'''
Set the method used by XTB. This includes GFN0-xTB, GFN1-xTB, GFN2-xTB and GFNFF.
Args:
method: the method to use. Can be specified by its full name, e.g. 'GFN2-xTB', is the same as 'GFN2' or simply 2.
'''
if isinstance(method, int):
if not 0 >= method >= 2:
raise ValueError(f'GFN{method}-xTB does not exist. Please choose one of GFN[0, 1, 2]-xTB.')
self._options.append(f'--gfn {method}')
return
if method.lower() in ['gfn0', 'gfn0-xtb']:
self._options.append('--gfn 0')
return
if method.lower() in ['gfn1', 'gfn1-xtb']:
self._options.append('--gfn 1')
return
if method.lower() in ['gfn2', 'gfn2-xtb']:
self._options.append('--gfn 2')
return
if method.lower() in ['gfnff', 'ff']:
self._options.append('--gfnff')
return
raise ValueError(f'Did not recognize the method {method} for XTB.')
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def solvent(self, name: str = None, model: str = 'alpb'):
'''
Model solvation using the ALPB or GBSA model.
Args:
name: the name of the solvent you want to use. Must be ``None``, ``Acetone``, ``Acetonitrile``, ``CHCl3``, ``CS2``, ``DMSO``, ``Ether``, ``H2O``, ``Methanol``, ``THF`` or ``Toluene``.
grid_size: the size of the grid used to construct the solvent accessible surface. Must be ``230``, ``974``, ``2030`` or ``5810``.
'''
spell_check.check(model, ['alpb', 'gbsa'], ignore_case=True)
self._options.append(f'--{model} {name}')
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def spin_polarization(self, val: int):
'''
Set the spin-polarization of the system.
'''
self._options.append(f'-u {val}')
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def multiplicity(self, val: int):
'''
Set the multiplicity of the system. If the value is not one the calculation will also be unrestricted.
We use the following values:
1) singlet
2) doublet
3) triplet
4) ...
The multiplicity is equal to 2*S+1 for spin-polarization of S.
'''
self._options.append(f'-u {(val - 1)//2}')
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def charge(self, val: int):
'''
Set the charge of the system.
'''
self._options.append(f'-c {val}')
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def vibrations(self, enable: bool = True):
self._options.append('--hess')
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def optimization(self, quality: str = 'Normal', calculate_hess: bool = True):
'''
Do a geometry optimization and calculate the normal modes of the input structure.
Args:
quality: the convergence criteria of the optimization.
See https://xtb-docs.readthedocs.io/en/latest/optimization.html#optimization-levels.
calculate_hess: whether to calculate the Hessian and do a normal mode analysis after optimization.
'''
spell_check.check(quality, ['crude', 'sloppy', 'loose', 'lax', 'normal', 'tight', 'vtight', 'extreme'], ignore_case=True)
if calculate_hess:
self._options.append(f'--ohess {quality}')
else:
self._options.append(f'--opt {quality}')
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def PESScan(self, distances: list = [], angles: list = [], dihedrals: list = [], npoints: int = 20, quality: str = 'Normal', mode: str = 'concerted'):
'''
Set the task of the job to potential energy surface scan (PESScan).
Args:
distances: sequence of tuples or lists containing ``[atom_index1, atom_index2, start, end]``.
Atom indices start at 1. Distances are given in |angstrom|.
angles: sequence of tuples or lists containing ``[atom_index1, atom_index2, atom_index3, start, end]``.
Atom indices start at 1. Angles are given in degrees
dihedrals: sequence of tuples or lists containing ``[atom_index1, atom_index2, atom_index3, atom_index4, start, end]``.
Atom indices start at 1. Angles are given in degrees
npoints: the number of PES points to optimize.
.. note::
Currently we only support generating settings for 1-dimensional PESScans.
We will add support for N-dimensional PESScans later.
'''
self.optimization(quality=quality, calculate_hess=False)
self._options.append('--input scan.inp')
self._scan.setdefault('scan', [f'mode={mode}'])
# self._scan.setdefault('opt', [f'maxcycles=50'])
for i, d in enumerate(distances):
self._scan['scan'].append(f'distance: {d[0]},{d[1]},{d[2]}; {d[2]}, {d[3]}, {npoints}')
for i, a in enumerate(angles, start=i):
self._scan['scan'].append(f'angle: {a[0]},{a[1]},{a[2]},{a[3]}; {a[3]}, {a[4]}, {npoints}')
for i, a in enumerate(dihedrals, start=i):
self._scan['scan'].append(f'dihedral: {a[0]},{a[1]},{a[2]},{a[3]},{a[4]}; {a[4]}, {a[5]}, {npoints}')
@property
def output_mol_path(self):
return f'{self.workdir}/xtbopt.xyz'
TCutility