Source code for psi4.driver.p4util.util

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# Psi4: an open-source quantum chemistry software package
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"""Module with utility functions for use in input files."""

import os
import re
import sys
import warnings
from typing import Union

from psi4 import core
from psi4.driver.procrouting import *
from .exceptions import ValidationError
from .prop_util import *

[docs]def oeprop(wfn: core.Wavefunction, *args, **kwargs): """Evaluate one-electron properties. :returns: None :param wfn: set of molecule, basis, orbitals from which to compute properties How to specify args, which are actually the most important :type title: str :param title: label prepended to all psivars computed :examples: >>> # [1] Moments with specific label >>> E, wfn = energy('hf', return_wfn=True) >>> oeprop(wfn, 'DIPOLE', 'QUADRUPOLE', title='H3O+ SCF') """ oe = core.OEProp(wfn) if 'title' in kwargs: oe.set_title(kwargs['title']) for prop in args: oe.add(prop) # If we're doing MBIS, we want the free-atom volumes # in order to compute volume ratios, # but only if we're calling oeprop as the whole molecule free_atom = kwargs.get('free_atom',False) if "MBIS_VOLUME_RATIOS" in prop.upper() and not free_atom: core.print_out(" Computing free-atom volumes\n") free_atom_volumes(wfn) oe.compute()
[docs]def cubeprop(wfn, **kwargs): """Evaluate properties on a grid and generate cube files. .. versionadded:: 0.5 *wfn* parameter passed explicitly :returns: None :type wfn: :py:class:`~psi4.core.Wavefunction` :param wfn: set of molecule, basis, orbitals from which to generate cube files :examples: >>> # [1] Cube files for all orbitals >>> E, wfn = energy('b3lyp', return_wfn=True) >>> cubeprop(wfn) >>> # [2] Cube files for density (alpha, beta, total, spin) and four orbitals >>> # (two alpha, two beta) >>> set cubeprop_tasks ['orbitals', 'density'] >>> set cubeprop_orbitals [5, 6, -5, -6] >>> E, wfn = energy('scf', return_wfn=True) >>> cubeprop(wfn) """ # By default compute the orbitals if not core.has_global_option_changed('CUBEPROP_TASKS'): core.set_global_option('CUBEPROP_TASKS', ['ORBITALS']) if ((core.get_global_option('INTEGRAL_PACKAGE') == 'ERD') and ('ESP' in core.get_global_option('CUBEPROP_TASKS'))): raise ValidationError('INTEGRAL_PACKAGE ERD does not play nicely with electrostatic potential, so stopping.') cp = core.CubeProperties(wfn) cp.compute_properties()
[docs]def set_memory(inputval: Union[str, int, float], execute: bool = True, quiet: bool = False) -> int: """Function to reset the total memory allocation. Takes memory value *inputval* as type int, float, or str; int and float are taken literally as bytes to be set, string taken as a unit-containing value (e.g., 30 mb) which is case-insensitive. Set *execute* to False to interpret *inputval* without setting in Psi4 core. :returns: *memory_amount* Number of bytes of memory set :raises: :py:class:`psi4.ValidationError` when <500MiB or disallowed type or misformatted :examples: >>> # [1] Passing absolute number of bytes >>> psi4.set_memory(600000000) >>> psi4.get_memory() Out[1]: 600000000L >>> # [2] Passing memory value as string with units >>> psi4.set_memory('30 GB') >>> psi4.get_memory() Out[2]: 30000000000L >>> # Good examples >>> psi4.set_memory(800000000) # 800000000 >>> psi4.set_memory(2004088624.9) # 2004088624 >>> psi4.set_memory(1.0e9) # 1000000000 >>> psi4.set_memory('600 mb') # 600000000 >>> psi4.set_memory('600.0 MiB') # 629145600 >>> psi4.set_memory('.6 Gb') # 600000000 >>> psi4.set_memory(' 100000000kB ') # 100000000000 >>> psi4.set_memory('2 eb') # 2000000000000000000 >>> # Bad examples >>> psi4.set_memory({}) # odd type >>> psi4.set_memory('') # no info >>> psi4.set_memory("8 dimms") # unacceptable units >>> psi4.set_memory("1e5 gb") # string w/ exponent >>> psi4.set_memory("5e5") # string w/o units >>> psi4.set_memory(2000) # mem too small >>> psi4.set_memory(-5e5) # negative (and too small) """ # Handle memory given in bytes directly (int or float) if isinstance(inputval, (int, float)): val = inputval units = '' # Handle memory given as a string elif isinstance(inputval, str): memory_string = re.compile(r'^\s*(\d*\.?\d+)\s*([KMGTPBE]i?B)\s*$', re.IGNORECASE) matchobj = re.search(memory_string, inputval) if matchobj: val = float(matchobj.group(1)) units = matchobj.group(2) else: raise ValidationError("""Invalid memory specification: {}. Try 5e9 or '5 gb'.""".format(repr(inputval))) else: raise ValidationError("""Invalid type {} in memory specification: {}. Try 5e9 or '5 gb'.""".format( type(inputval), repr(inputval))) # Units decimal or binary? multiplier = 1000 if "i" in units.lower(): multiplier = 1024 units = units.lower().replace("i", "").upper() # Build conversion factor, convert units unit_list = ["", "KB", "MB", "GB", "TB", "PB", "EB"] mult = 1 for unit in unit_list: if units.upper() == unit: break mult *= multiplier memory_amount = int(val * mult) # Check minimum memory requirement min_mem_allowed = 262144000 if memory_amount < min_mem_allowed: raise ValidationError( """set_memory(): Requested {:.3} MiB ({:.3} MB); minimum 250 MiB (263 MB). Please, sir, I want some more.""" .format(memory_amount / 1024**2, memory_amount / 1000**2)) if execute: core.set_memory_bytes(memory_amount, quiet) return memory_amount
[docs]def get_memory(): """Function to return the total memory allocation.""" return core.get_memory()
[docs]def copy_file_to_scratch(filename, prefix, namespace, unit, move=False): """Function to move file into scratch with correct naming convention. Arguments: @arg filename full path to file @arg prefix computation prefix, usually 'psi' @arg namespace context namespace, usually molecule name @arg unit unit number, e.g. 32 @arg move copy or move? (default copy) Example: Assume PID is 12345 and SCRATCH is /scratch/parrish/ copy_file_to_scratch('temp', 'psi', 'h2o', 32): -cp ./temp /scratch/parrish/psi.12345.h2o.32 copy_file_to_scratch('/tmp/temp', 'psi', 'h2o', 32): -cp /tmp/temp /scratch/parrish/psi.12345.h2o.32 copy_file_to_scratch('/tmp/temp', 'psi', '', 32): -cp /tmp/temp /scratch/parrish/psi.12345.32 copy_file_to_scratch('/tmp/temp', 'psi', '', 32, True): -mv /tmp/temp /scratch/parrish/psi.12345.32 """ pid = str(os.getpid()) scratch = core.IOManager.shared_object().get_file_path(int(unit)) cp = '/bin/cp' if move: cp = '/bin/mv' unit = str(unit) target = '' target += prefix target += '.' target += pid if len(namespace): target += '.' target += namespace target += '.' target += unit command = ('%s %s %s/%s' % (cp, filename, scratch, target)) os.system(command)
#print command
[docs]def copy_file_from_scratch(filename, prefix, namespace, unit, move=False): """Function to move file out of scratch with correct naming convention. Arguments: @arg filename full path to target file @arg prefix computation prefix, usually 'psi' @arg namespace context namespace, usually molecule name @arg unit unit number, e.g. 32 @arg move copy or move? (default copy) Example: Assume PID is 12345 and SCRATCH is /scratch/parrish/ copy_file_to_scratch('temp', 'psi', 'h2o', 32): -cp /scratch/parrish/psi.12345.h2o.32 .temp copy_file_to_scratch('/tmp/temp', 'psi', 'h2o', 32): -cp /scratch/parrish/psi.12345.h2o.32 /tmp/temp copy_file_to_scratch('/tmp/temp', 'psi', '', 32): -cp /scratch/parrish/psi.12345.32 /tmp/temp copy_file_to_scratch('/tmp/temp', 'psi', '', 32, True): -mv /scratch/parrish/psi.12345.32 /tmp/temp """ pid = str(os.getpid()) scratch = core.IOManager.shared_object().get_file_path(int(unit)) cp = '/bin/cp' if move: cp = '/bin/mv' unit = str(unit) target = '' target += prefix target += '.' target += pid if len(namespace): target += '.' target += namespace target += '.' target += unit command = ('%s %s/%s %s' % (cp, scratch, target, filename)) os.system(command)