#
# @BEGIN LICENSE
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# Psi4: an open-source quantum chemistry software package
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# Copyright (c) 2007-2024 The Psi4 Developers.
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# The copyrights for code used from other parties are included in
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# Psi4 is free software; you can redistribute it and/or modify
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"""Module with utility functions for use in input files."""
__all__ = [
"copy_file_to_scratch",
"copy_file_from_scratch",
"cubeprop",
"get_memory",
"libint2_configuration",
"libint2_print_out",
"oeprop",
"set_memory",
]
import os
import re
from typing import Dict, List, Union
from psi4 import core
from .exceptions import ValidationError
from .prop_util import *
[docs]
def oeprop(wfn: core.Wavefunction, *args: List[str], **kwargs):
"""Evaluate one-electron properties.
:returns: None
:param wfn: set of molecule, basis, orbitals from which to compute properties
:param args:
Arbitrary-number of properties to be computed from *wfn*.
See :ref:`Available One-Electron Properties <table:oe_features>`.
: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.upper())
# 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: core.Wavefunction, **kwargs):
"""Evaluate properties on a grid and generate cube files.
.. versionadded:: 0.5
*wfn* parameter passed explicitly
:returns: None
: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:
"""Reset the total memory allocation.
Parameters
----------
inputval
Memory value. An Integer or float is taken literally as bytes to be set.
A string is taken as a unit-containing value (e.g., 30 mb), which is
case-insensitive.
execute
When False, interpret *inputval* without setting in Psi4 core.
quiet
When True, do not print to the output file.
Returns
-------
int
Number of bytes of memory set.
Raises
------
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() -> int:
"""Return the total memory allocation in bytes."""
return core.get_memory()
[docs]
def copy_file_to_scratch(filename: str, prefix: str, namespace: str, unit: int, move: bool = False):
"""Move a file into scratch following the naming convention.
Parameters
----------
filename
Full path to file.
prefix
Computation prefix, usually 'psi'.
namespace
Context namespace, usually molecule name.
unit
Unit number, e.g. 32.
move
Whether to copy (default) or move?
Examples
--------
>>> # Assume PID is 12345 and SCRATCH is /scratch/parrish/
>>> copy_file_to_scratch('temp', 'psi', 'h2o', 32):
Out[1]: -cp ./temp /scratch/parrish/psi.12345.h2o.32
>>> copy_file_to_scratch('/tmp/temp', 'psi', 'h2o', 32):
Out[2]: -cp /tmp/temp /scratch/parrish/psi.12345.h2o.32
>>> copy_file_to_scratch('/tmp/temp', 'psi', '', 32):
Out[3]: -cp /tmp/temp /scratch/parrish/psi.12345.32
>>> copy_file_to_scratch('/tmp/temp', 'psi', '', 32, True):
Out[4]: -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)
[docs]
def copy_file_from_scratch(filename: str, prefix: str, namespace: str, unit: int, move: bool = False):
"""Move a file out of scratch following the naming convention.
Parameters
----------
filename
Full path to target file.
prefix
Computation prefix, usually 'psi'.
namespace
Context namespace, usually molecule name.
unit
Unit number, e.g. 32
move
Whether to copy (default) or move?
Examples
--------
>>> # Assume PID is 12345 and SCRATCH is /scratch/parrish/
>>> copy_file_to_scratch('temp', 'psi', 'h2o', 32):
Out[1]: -cp /scratch/parrish/psi.12345.h2o.32 .temp
>>> copy_file_to_scratch('/tmp/temp', 'psi', 'h2o', 32):
Out[2]: -cp /scratch/parrish/psi.12345.h2o.32 /tmp/temp
>>> copy_file_to_scratch('/tmp/temp', 'psi', '', 32):
Out[3]: -cp /scratch/parrish/psi.12345.32 /tmp/temp
>>> copy_file_to_scratch('/tmp/temp', 'psi', '', 32, True):
Out[4]: -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)
[docs]
def libint2_configuration() -> Dict[str, List[int]]:
"""Returns information on integral classes, derivatives, and AM from currently linked Libint2.
Returns
-------
Dictionary of integrals classes with values an array of max angular momentum per derivative level.
Usual configuration returns:
`{'eri': [5, 4, 3], 'eri2': [6, 5, 4], 'eri3': [6, 5, 4], 'onebody': [6, 5, 4]}`
"""
if "eri_c4_d0_l2" in core._libint2_configuration():
return _l2_config_style_eri_c4()
elif "eri_dddd_d0" in core._libint2_configuration():
return _l2_config_style_eri_llll()
def _l2_config_style_eri_llll():
skel = {"onebody_": [], "eri_c4_": [], "eri_c3_": [], "eri_c2_": []}
skel_re = {"onebody_": r"onebody_\w_d\d", "eri_c4_": r"eri_\w..._d\d", "eri_c3_": r"eri_\w.._d\d", "eri_c2_": r"eri_\w._d\d"}
amstr = "SPDFGHIKLMNOQRTUVWXYZ"
libint2_configuration = core._libint2_configuration()
for k, v in skel_re.items():
t = re.findall(v, libint2_configuration)
skel[k] = t
for cat in list(skel.keys()):
der_max_store = []
for der in ["d0", "d1", "d2"]:
lmax = -1
for itm2 in skel[cat]:
if itm2.endswith(der):
lmax = max(amstr.index(itm2[-4].upper()), lmax)
der_max_store.append(None if lmax == -1 else lmax)
skel[cat] = der_max_store
# rename keys from components
skel["onebody"] = skel.pop("onebody_")
skel["eri"] = skel.pop("eri_c4_")
skel["eri3"] = skel.pop("eri_c3_")
skel["eri2"] = skel.pop("eri_c2_")
return skel
def _l2_config_style_eri_c4():
skel = {"onebody_": [], "eri_c4_": [], "eri_c3_": [], "eri_c2_": []}
for itm in core._libint2_configuration().split(";"):
for cat in list(skel.keys()):
if itm.startswith(cat):
skel[cat].append(itm[len(cat):])
for cat in list(skel.keys()):
der_max_store = []
for der in ["d0_l", "d1_l", "d2_l"]:
lmax = -1
for itm2 in skel[cat]:
if itm2.startswith(der):
lmax = max(int(itm2[len(der):]), lmax)
der_max_store.append(None if lmax == -1 else lmax)
skel[cat] = der_max_store
# rename keys from components
skel["onebody"] = skel.pop("onebody_")
skel["eri"] = skel.pop("eri_c4_")
skel["eri3"] = skel.pop("eri_c3_")
skel["eri2"] = skel.pop("eri_c2_")
return skel
[docs]
def libint2_print_out() -> None:
ams = libint2_configuration()
core.print_out(" => Libint2 <=\n\n");
# when L2 is pure cmake core.print_out(core.libint2_citation());
core.print_out(f" Primary basis highest AM E, G, H: {', '.join(('-' if d is None else str(d)) for d in ams['eri'])}\n")
core.print_out(f" Auxiliary basis highest AM E, G, H: {', '.join(('-' if d is None else str(d)) for d in ams['eri3'])}\n")
core.print_out(f" Onebody basis highest AM E, G, H: {', '.join(('-' if d is None else str(d)) for d in ams['onebody'])}\n")
# excluding sph_emultipole
core.print_out(f" Solid Harmonics ordering: {core.libint2_solid_harmonics_ordering()}\n")
