def run(job, runner=None, path=None, folder=None, **kwargs):
"""
Pickup a runner and initialize it.
:params job: computation to run
:type job: Promise Object
:param runner: Type of runner to use
:type runner: String
"""
plams.init(path=path, folder=folder)
plams.config.log.stdout = 0
if runner is None:
ret = call_default(job, kwargs.get('n_processes', 1))
else:
raise "Don't know runner: {}".format(runner)
plams.finish()
return ret
def main():
"""
Main interface that reads the file and retrieve all useful geoms etc.
Then rewrite geometries in a usable formatter_class
Prep all NBO computations
Run ADF on each computation
"""
# Retrieve command line values
args = get_input_arguments()
input_file = args['input_file']
output_file = args['output_file']
# Init PLAMS, Setting up a plams.$PID directory in the working dir
init()
# Retrieve settings from input file
settings = get_settings(args)
geometries = IRC_coordinates_from_t21(input_file)
natoms = number_of_atoms(input_file)
# Prep a bunch of NBO computations
NBO_jobs = [prepare_NBO_computation(geom, settings) for geom in geometries]
# Run each job in parallel as managed by plams
for job in NBO_jobs:
job.run()
# NBO_values is a list of list of charges
NBO_values = [
extract_NBO_charges(job._filenames.get('out'), natoms)
for job in NBO_jobs
]
# Write NBO data
print_NBO_charges_to_file(NBO_values, output_file)
# Close plams session
finish()
def init_plams(self):
"""Init PLAMS."""
plams.init()
plams.config.log.stdout = -1
plams.config.erase_workdir = True
def restart_init(path: Union[str, 'os.PathLike[str]'],
folder: Union[str, 'os.PathLike[str]'],
hashing: str = 'input') -> None:
"""Wrapper around the plams.init_ function; used for importing one or more previous jobs.
All pickled .dill files in **path**/**folder**/ will be loaded into the
:class:`GenJobManager` instance initiated by :func:`init()<scm.plams.core.functions.init>`.
.. _plams.init: https://www.scm.com/doc/plams/components/functions.html#scm.plams.core.functions.init
Note
----
Previous jobs are stored in a more generator-esque manner in :attr:`GenJobManager.hashes` and
:class:`Job` instances are thus created on demand rather than
permanently storing them in memory.
Paramaters
----------
path : str
The path to the PLAMS workdir.
folder : str
The name of the PLAMS workdir.
hashing : str
Optional: The type of hashing used by the PLAMS :class:`JobManager`.
Accepted values are: ``"input"``, ``"runscript"``, ``"input+runscript"`` and ``None``.
""" # noqa
# Create a job manager
settings = Settings({'counter_len': 3, 'hashing': hashing, 'remove_empty_directories': True})
manager = GenJobManager(settings, path, folder, hashing)
# Change the default job manager
with open(os.devnull, 'w') as f_, redirect_stdout(f_):
init()
rmtree(config.default_jobmanager.workdir)
config.default_jobmanager = manager
config.log.file = 3
config.log.stdout = 0
workdir = manager.workdir
if not isdir(workdir): # workdir does not exist, dont bother trying to load previous jobs
os.mkdir(workdir)
return None
# Update the default job manager with previous Jobs
for f in os.listdir(workdir):
job_dir = join(workdir, f)
if not isdir(job_dir): # Not a directory; move along
continue
hash_file = join(job_dir, f + '.hash')
if isfile(hash_file): # Update JobManager.hashes
manager.load_job(hash_file)
# Grab the job name
try:
name, _num = f.rsplit('.', 1)
num = int(_num)
except ValueError: # Jobname is not appended with a number
name = f
num = 1
# Update JobManager.names
try:
manager.names[name] = max(manager.names[name], num)
except KeyError:
manager.names[name] = num
return None
def run(self):
"""Run the calculation
Raises:
ValueError: [description]
Returns:
np.ndarray -- molecular orbital matrix
"""
wd = ''.join(self.atoms) + '_' + self.basis_name
t21_name = wd + '.t21'
plams_wd = './plams_workdir'
t21_path = os.path.join(plams_wd, os.path.join(wd, t21_name))
if os.path.isfile(t21_name):
print('Reusing previous calculation from ', t21_name)
kf = plams.KFFile(t21_name)
e = kf.read('Total Energy', 'Total energy')
else:
# init PLAMS
plams.init()
plams.config.log.stdout = -1
plams.config.erase_workdir = True
# create the molecule
mol = plams.Molecule()
for at, xyz in zip(self.atoms, self.atom_coords):
mol.add_atom(plams.Atom(symbol=at, coords=tuple(xyz)))
# settings in PLAMS
sett = plams.Settings()
sett.input.basis.type = self.basis_name.upper()
sett.input.basis.core = 'None'
sett.input.symmetry = 'nosym'
sett.input.XC.HartreeFock = ''
# correct unit
if self.units == 'angs':
sett.input.units.length = 'Angstrom'
elif self.units == 'bohr':
sett.input.units.length = 'Bohr'
# total energy
sett.input.totalenergy = True
# run the ADF job
job = plams.ADFJob(molecule=mol, settings=sett, name=wd)
job.run()
# read the energy from the t21 file
e = job.results.readkf('Total Energy', 'Total energy')
# make a copy of the t21 file
shutil.copyfile(t21_path, t21_name)
shutil.rmtree(plams_wd)
# print energy
print('== SCF Energy : ', e)
self.out_file = t21_name
# Default imports
from qmflows import Settings, templates, run, molkit
from qmflows.draw_workflow import draw_workflow
from noodles import gather
# User Defined imports
from qmflows.packages.SCM import dftb
from qmflows.packages.SCM import dftb as adf # This is for testing purposes
from qmflows.components import Distance, PES, select_max
from scm import plams
# ========== =============
plams.init()
config.log.stdout = -1000 # noqa
hartree2kcal = 627.5095
# List of reactions, defined by name, reactants and products (as smiles strings)
reactions = [
["et01", "C=C", "[CH]#[N+][CH2-]", "C1C=NCC1"],
["et02", "C=C", "[CH]#[N+][NH-]", "C1C=NNC1"],
["et03", "C=C", "[CH]#[N+][O-]", "C1C=NOC1"],
["et04", "C=C", "[N]#[N+][CH2-]", "C1N=NCC1"],
["et05", "C=C", "[N]#[N+][NH-]", "C1N=NNC1"],
["et06", "C=C", "[N]#[N+][O-]", "C1N=NOC1"],
["et07", "C=C", "[CH2]=[NH+][CH2-]", "C1CNCC1"],
["et08", "C=C", "[CH2]=[NH+][NH-]", "C1CNNC1"],
["et09", "C=C", "[CH2]=[NH+][O-]", "C1CNOC1"],
["et10", "C=C", "[NH]=[NH+][NH-]", "C1NNNC1"],
["et11", "C=C", "[NH]=[NH+][O-]", "C1NNOC1"],
# mol_dirs = os.listdir(dataset_dir)
# mol_names = [d + '_' + p.strip('.xyz') for d in mol_dirs for p in os.listdir(dataset_dir + '/' + d)]
# mol_paths = [dataset_dir + '/' + d + '/' + p for d in mol_dirs for p in os.listdir(dataset_dir + '/' + d)]
# print(f'Starting singlepoint DFT and DFTB vibration calculations for {len(mol_names)} molecules from the {dataset_name} dataset:')
# print('Molecules:')
# [print('\t'+i+1,n) for i,n in enumerate(mol_names)]
# for n, p in zip(mol_names, mol_paths):
# kf_DFT = jobs.DFTJob(p, job_name=f'{n}_DFT', geo_opt=True).run(init=False)
# shutil.copy2(kf_DFT, f'{kf_dir}/{n}_DFT.t21')
# kf_DFTB = jobs.DFTBJob(p, job_name=f'{n}_DFTB', geo_opt=True).run(init=False)
# shutil.copy2(kf_DFTB, f'{kf_dir}/{n}_DFTB.rkf')
plams.init(path=os.getcwd() + r'/RUNS',
folder=time.strftime("[%H-%M](%d-%m-%Y)", time.localtime()))
kf_dir = os.getcwd(
) + f'/RUNS/#KFFiles/{time.strftime("[%H-%M](%d-%m-%Y)", time.localtime())}'
try:
os.mkdir(kf_dir)
except:
pass
dataset_name = 'second_set'
dataset_dir = os.getcwd() + f'/structures/{dataset_name}'
mol_dirs = os.listdir(dataset_dir)
mol_names = [
d + '_' + p.strip('.xyz') for d in mol_dirs
for p in os.listdir(dataset_dir + '/' + d)
]
mol_paths = [
def get_lig_charge(ligand: Molecule,
desired_charge: float,
ligand_idx: Union[None, int, Iterable[int], slice] = None,
invert_idx: bool = False,
settings: Optional[Settings] = None,
path: Union[None, str, PathLike] = None,
folder: Union[None, str, PathLike] = None) -> pd.Series:
"""Calculate and rescale the **ligand** charges using MATCH_.
The atomic charges in **ligand_idx** wil be altered such that the molecular
charge of **ligand** is equal to **desired_charge**.
.. _MATCH: http://brooks.chem.lsa.umich.edu/index.php?page=match&subdir=articles/resources/software
Examples
--------
.. code:: python
>>> import pandas as pd
>>> from scm.plams import Molecule
>>> from CAT.recipes import get_lig_charge
>>> ligand = Molecule(...)
>>> desired_charge = 0.66
>>> ligand_idx = 0, 1, 2, 3, 4
>>> charge_series: pd.Series = get_lig_charge(
... ligand, desired_charge, ligand_idx
... )
>>> charge_series.sum() == desired_charge
True
Parameters
----------
ligand : :class:`~scm.plams.core.mol.molecule.Molecule`
The input ligand.
desired_charge : :class:`float`
The desired molecular charge of the ligand.
ligand_idx : :class:`int` or :class:`~collections.abc.Iterable` [:class:`int`], optional
An integer or iterable of integers representing atomic indices.
The charges of these atoms will be rescaled;
all others will be frozen with respect to the MATCH output.
Setting this value to ``None`` means that *all* atomic charges are considered variable.
Indices should be 0-based.
invert_idx : :class:`bool`
If ``True`` invert **ligand_idx**, *i.e.* all atoms specified therein are
now threated as constants and the rest as variables,
rather than the other way around.
settings : :class:`~scm.plams.core.settings.Settings`, optional
The input settings for :class:`~nanoCAT.ff.match_job.MatchJob`.
Will default to the ``"top_all36_cgenff_new"`` forcefield if not specified.
path : :class:`str` or :class:`~os.PathLike`, optional
The path to the PLAMS workdir as passed to :func:`~scm.plams.core.functions.init`.
Will default to the current working directory if ``None``.
folder : :class:`str` or :class:`~os.PathLike`, optional
The name of the to-be created to the PLAMS working directory
as passed to :func:`~scm.plams.core.functions.init`.
Will default to ``"plams_workdir"`` if ``None``.
Returns
-------
:class:`pd.Series` [:class:`str`, :class:`float`]
A Series with the atom types of **ligand** as keys and atomic charges as values.
See Also
--------
:class:`MatchJob`
A :class:`~scm.plams.core.basejob.Job` subclass for interfacing with MATCH_:
Multipurpose Atom-Typer for CHARMM.
""" # noqa
if settings is None:
settings = Settings()
settings.input.forcefield = 'top_all36_cgenff_new'
# Run the MATCH Job
init(path, folder)
ligand = ligand.copy()
run_match_job(ligand, settings, action='raise')
finish()
# Extract the charges and new atom types
count = len(ligand)
charge = np.fromiter((at.properties.charge_float for at in ligand), count=count, dtype=float)
symbol = np.fromiter((at.properties.symbol for at in ligand), count=count, dtype='<U4')
# Identify the atom subset
idx = _parse_ligand_idx(ligand_idx)
if invert_idx:
idx = _invert_idx(idx, count)
try:
idx_len = len(idx) # type: ignore
except TypeError: # idx is a slice object
idx_len = len(charge[idx])
# Correct the charges and return
charge[idx] -= (charge.sum() - desired_charge) / idx_len
return pd.Series(charge, index=symbol, name='charge')