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# PSI4: an ab initio quantum chemistry software package
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"""Module with utility functions for use in input files."""
import psi4
import sys
import os
import math
from psiexceptions import *
[docs]def oeprop(*args, **kwargs):
oe = psi4.OEProp()
if 'title' in kwargs:
oe.set_title(kwargs['title'])
for prop in args:
oe.add(prop)
oe.compute()
[docs]def set_memory(bytes):
"""Function to reset the total memory allocation."""
psi4.set_memory(bytes)
[docs]def get_memory():
"""Function to return the total memory allocation."""
return psi4.get_memory()
[docs]def set_num_threads(nthread):
"""Function to reset the number of threads to parallelize across."""
psi4.set_nthread(nthread)
[docs]def get_num_threads():
"""Function to return the number of threads to parallelize across."""
return psi4.nthread()
[docs]def success(label):
"""Function to print a '*label*...PASSED' line to screen.
Used by :py:func:`util.compare_values` family when functions pass.
"""
print('\t{0:.<66}PASSED'.format(label))
sys.stdout.flush()
# Test functions
[docs]def compare_values(expected, computed, digits, label):
"""Function to compare two values. Prints :py:func:`util.success`
when value *computed* matches value *expected* to number of *digits*.
Performs a system exit on failure. Used in input files in the test suite.
"""
if (abs(expected - computed) > 10 ** (-digits)):
print(("\t%s: computed value (%." + str(digits+1) + "f) does not match (%." + str(digits+1) + "f) to %d decimal places.") % (label, computed, expected, digits))
sys.exit(1)
if ( math.isnan(computed) ):
print("\t%s: computed value (%f) does not match (%f) to %d decimal places.\n" % (label, computed, expected, digits))
print("\tprobably because the computed value is nan.")
sys.exit(1)
success(label)
[docs]def compare_integers(expected, computed, label):
"""Function to compare two integers. Prints :py:func:`util.success`
when value *computed* matches value *expected*.
Performs a system exit on failure. Used in input files in the test suite.
"""
if (expected != computed):
print("\t%s: computed value (%d) does not match (%d)." % (label, computed, expected))
sys.exit(1)
success(label)
[docs]def compare_strings(expected, computed, label):
"""Function to compare two strings. Prints :py:func:`util.success`
when string *computed* exactly matches string *expected*.
Performs a system exit on failure. Used in input files in the test suite.
"""
if(expected != computed):
print("\t%s: computed value (%s) does not match (%s)." % (label, computed, expected))
sys.exit(1)
success(label)
[docs]def compare_matrices(expected, computed, digits, label):
"""Function to compare two matrices. Prints :py:func:`util.success`
when elements of matrix *computed* match elements of matrix *expected* to
number of *digits*. Performs a system exit on failure to match symmetry
structure, dimensions, or element values. Used in input files in the test suite.
"""
if (expected.nirrep() != computed.nirrep()):
print("\t%s has %d irreps, but %s has %d\n." % (expected.name(), expected.nirrep(), computed.name(), computed.nirrep()))
sys.exit(1)
if (expected.symmetry() != computed.symmetry()):
print("\t%s has %d symmetry, but %s has %d\n." % (expected.name(), expected.symmetry(), computed.name(), computed.symmetry()))
sys.exit(1)
nirreps = expected.nirrep()
symmetry = expected.symmetry()
for irrep in range(nirreps):
if(expected.rows(irrep) != computed.rows(irrep)):
print("\t%s has %d rows in irrep %d, but %s has %d\n." % (expected.name(), expected.rows(irrep), irrep, computed.name(), computed.rows(irrep)))
sys.exit(1)
if(expected.cols(irrep ^ symmetry) != computed.cols(irrep ^ symmetry)):
print("\t%s has %d columns in irrep, but %s has %d\n." % (expected.name(), expected.cols(irrep), irrep, computed.name(), computed.cols(irrep)))
sys.exit(1)
rows = expected.rows(irrep)
cols = expected.cols(irrep ^ symmetry)
failed = 0
for row in range(rows):
for col in range(cols):
if(abs(expected.get(irrep, row, col) - computed.get(irrep, row, col)) > 10 ** (-digits)):
print("\t%s: computed value (%s) does not match (%s)." % (label, expected.get(irrep, row, col), computed.get(irrep, row, col)))
failed = 1
break
if(failed):
print("Check your output file for reporting of the matrices.")
psi4.print_out("The Failed Test Matrices\n")
psi4.print_out("Computed Matrix (2nd matrix passed in)\n")
computed.print_out()
psi4.print_out("Expected Matrix (1st matrix passed in)\n")
expected.print_out()
sys.exit(1)
success(label)
[docs]def compare_vectors(expected, computed, digits, label):
"""Function to compare two vectors. Prints :py:func:`util.success`
when elements of vector *computed* match elements of vector *expected* to
number of *digits*. Performs a system exit on failure to match symmetry
structure, dimension, or element values. Used in input files in the test suite.
"""
if (expected.nirrep() != computed.nirrep()):
print("\t%s has %d irreps, but %s has %d\n." % (expected.name(), expected.nirrep(), computed.name(), computed.nirrep()))
sys.exit(1)
nirreps = expected.nirrep()
for irrep in range(nirreps):
if(expected.dim(irrep) != computed.dim(irrep)):
print("\tThe reference has %d entries in irrep %d, but the computed vector has %d\n." % (expected.dim(irrep), irrep, computed.dim(irrep)))
sys.exit(1)
dim = expected.dim(irrep)
failed = 0
for entry in range(dim):
if(abs(expected.get(irrep, entry) - computed.get(irrep, entry)) > 10 ** (-digits)):
print("\t%s: computed value (%s) does not match (%s)." % (label, computed.get(irrep, entry), expected.get(irrep, entry)))
failed = 1
break
if(failed):
psi4.print_out("The computed vector\n")
computed.print_out()
psi4.print_out("The reference vector\n")
expected.print_out()
sys.exit(1)
success(label)
[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 = psi4.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 = psi4.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)
#print command