def compare_fchkfiles(expected, computed, digits, label):
# """Function to compare two FCHK files.
# an older format description can be found here
# http://wild.life.nctu.edu.tw/~jsyu/compchem/g09/g09ur/f_formchk.htm
# It lists more fields (logical, character) that are not included in this
# test function. They should be covered by the string comparison.
# This function is only meant to work with PSI4's FCHK files.
#
# :param expected: reference FCHK file name
# :param computed: computed FCHK file name
# :param digits: tolerance for high accuracy fields -- 1.e-8 or 1.e-9 suitable
# :param label: string labelling the test
# """
fchk_ref = fchkfile_to_string(expected).splitlines()
fchk_calc = fchkfile_to_string(computed).splitlines()
high_accuracy = digits
low_accuracy = 3
# Those listed below need super high scf convergence (d_conv 1e-12) and might
# show machine dependence. They will be tested with low_accuracy.
sensitive = ['Current cartesian coordinates', 'MO coefficients']
if len(fchk_ref) != len(fchk_calc):
raise ValidationError('The two FCHK files to compare have a different file length! \n')
index = 0
max_length = len(fchk_calc)
tests = []
for start in range(max_length):
if index >= max_length:
break
line = fchk_calc[index]
if "N=" in line:
offset, calc = _consume_fchk_section(fchk_calc, index)
_, ref = _consume_fchk_section(fchk_ref, index)
if any(x in line for x in sensitive):
test = compare_arrays(ref, calc, low_accuracy, f" matrix section: {line}")
else:
test = compare_arrays(ref, calc, high_accuracy, f" matrix section: {line}")
index += offset
elif " R " in line and not "N=" in line:
calc = line.split()[-1]
ref = fchk_ref[index].split()[-1]
test = compare_values(ref, calc, high_accuracy, f" float value: {line}")
index += 1
elif " I " in line and not "N=" in line:
calc = line.split()[-1]
ref = fchk_ref[index].split()[-1]
test = compare_integers(ref, calc, f" int value: {line}")
index += 1
else:
test = compare_strings(line, fchk_ref[index], f"FCK text line {index+1}.")
index += 1
tests.append(test)
return compare_integers(True, all(tests), label)
def compare_fcidumps(expected: str, computed: str, label: str):
"""Comparison function for FCIDUMP files.
Compares the first six below, then computes energies from MO integrals and compares the last four.
- 'norb' : number of basis functions
- 'nelec' : number of electrons
- 'ms2' : spin polarization of the system
- 'isym' : symmetry of state (if present in FCIDUMP)
- 'orbsym' : list of symmetry labels of each orbital
- 'uhf' : whether restricted or unrestricted
- 'ONE-ELECTRON ENERGY' : SCF one-electron energy
- 'TWO-ELECTRON ENERGY' : SCF two-electron energy
- 'SCF TOTAL ENERGY' : SCF total energy
- 'MP2 CORRELATION ENERGY' : MP2 correlation energy
:param expected: Reference FCIDUMP file against which `computed` is compared.
:param computed: Input FCIDUMP file to compare against `expected`.
:param label: string labeling the test
"""
# Grab expected header and integrals
ref_intdump = fcidump_from_file(expected)
intdump = fcidump_from_file(computed)
# Compare headers
compare_recursive(ref_intdump,
intdump,
'FCIDUMP header',
forgive=['enuc', 'hcore', 'eri', 'epsilon'])
ref_energies = energies_from_fcidump(ref_intdump)
energies = energies_from_fcidump(intdump)
pass_1el = compare_values(ref_energies['ONE-ELECTRON ENERGY'],
energies['ONE-ELECTRON ENERGY'], 7,
label + '. 1-electron energy')
pass_2el = compare_values(ref_energies['TWO-ELECTRON ENERGY'],
energies['TWO-ELECTRON ENERGY'], 7,
label + '. 2-electron energy')
pass_scf = compare_values(ref_energies['SCF TOTAL ENERGY'],
energies['SCF TOTAL ENERGY'], 10,
label + '. SCF total energy')
pass_mp2 = compare_values(ref_energies['MP2 CORRELATION ENERGY'],
energies['MP2 CORRELATION ENERGY'], 10,
label + '. MP2 correlation energy')
compare_integers(True, (pass_1el and pass_2el and pass_scf and pass_mp2),
label)
def compare_fcidumps(expected, computed, label):
"""Function to compare two FCIDUMP files. 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.
:returns: a dictionary of energies computed from the MO integrals.
The key-value pairs are:
- 'NUCLEAR REPULSION ENERGY' : nuclear repulsion plus frozen core energy
- 'ONE-ELECTRON ENERGY' : SCF one-electron energy
- 'TWO-ELECTRON ENERGY' : SCF two-electron energy
- 'SCF TOTAL ENERGY' : SCF total energy
- 'MP2 CORRELATION ENERGY' : MP2 correlation energy
:param expected: reference FCIDUMP file
:param computed: computed FCIDUMP file
:param label: string labelling the test
"""
# Grab expected header and integrals
ref_intdump = fcidump_from_file(expected)
intdump = fcidump_from_file(computed)
# Compare headers
compare_recursive(ref_intdump,
intdump,
'FCIDUMP header',
forgive=['enuc', 'hcore', 'eri', 'epsilon'])
ref_energies = energies_from_fcidump(ref_intdump)
energies = energies_from_fcidump(intdump)
pass_1el = compare_values(ref_energies['ONE-ELECTRON ENERGY'],
energies['ONE-ELECTRON ENERGY'], 7,
label + '. 1-electron energy')
pass_2el = compare_values(ref_energies['TWO-ELECTRON ENERGY'],
energies['TWO-ELECTRON ENERGY'], 7,
label + '. 2-electron energy')
pass_scf = compare_values(ref_energies['SCF TOTAL ENERGY'],
energies['SCF TOTAL ENERGY'], 10,
label + '. SCF total energy')
pass_mp2 = compare_values(ref_energies['MP2 CORRELATION ENERGY'],
energies['MP2 CORRELATION ENERGY'], 10,
label + '. MP2 correlation energy')
compare_integers(True, (pass_1el and pass_2el and pass_scf and pass_mp2),
label)
def compare_fcidumps(expected, computed, label):
"""Function to compare two FCIDUMP files. 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.
:returns: a dictionary of energies computed from the MO integrals.
The key-value pairs are:
- 'NUCLEAR REPULSION ENERGY' : nuclear repulsion plus frozen core energy
- 'ONE-ELECTRON ENERGY' : SCF one-electron energy
- 'TWO-ELECTRON ENERGY' : SCF two-electron energy
- 'SCF TOTAL ENERGY' : SCF total energy
- 'MP2 CORRELATION ENERGY' : MP2 correlation energy
:param expected: reference FCIDUMP file
:param computed: computed FCIDUMP file
:param label: string labelling the test
"""
# Grab expected header and integrals
ref_intdump = fcidump_from_file(expected)
intdump = fcidump_from_file(computed)
# Compare headers
compare_recursive(
ref_intdump,
intdump,
'FCIDUMP header',
forgive=['enuc', 'hcore', 'eri', 'epsilon'])
ref_energies = energies_from_fcidump(ref_intdump)
energies = energies_from_fcidump(intdump)
pass_1el = compare_values(ref_energies['ONE-ELECTRON ENERGY'], energies['ONE-ELECTRON ENERGY'], 7,
label + '. 1-electron energy')
pass_2el = compare_values(ref_energies['TWO-ELECTRON ENERGY'], energies['TWO-ELECTRON ENERGY'], 7,
label + '. 2-electron energy')
pass_scf = compare_values(ref_energies['SCF TOTAL ENERGY'], energies['SCF TOTAL ENERGY'], 10,
label + '. SCF total energy')
pass_mp2 = compare_values(ref_energies['MP2 CORRELATION ENERGY'], energies['MP2 CORRELATION ENERGY'], 10,
label + '. MP2 correlation energy')
compare_integers(True, (pass_1el and pass_2el and pass_scf and pass_mp2), label)
def compare_moldenfiles(expected, computed, digits=7, label='Compare Molden'):
ref = moldenfile_to_string(expected).splitlines()
calc = moldenfile_to_string(computed).splitlines()
if len(ref) != len(calc):
raise ValidationError(
f"These two molden files have different lengths...\n")
high_accuracy = digits
index = 0
max_len = len(calc)
tests = []
section = 0
geom_re = re.compile(
r'^\s*(\w*)\s+(\d+)\s+(\d+)\s+(-?\d+.\d+)\s+(-?\d+.\d+)\s+(-?\d+.\d+)\s*$'
)
basis_header_re = re.compile(r'^\s*([s,p,d,f,g])\s*(\d*)\s*(\d*.\d*)\s*$')
s1_re = re.compile(r'^\s*(\d+.?\d*)\s+(\d+.?\d*)$')
s2_re = re.compile(r'^\s*(\d+)\s+(-?\d+.\d+[e,E][\+,-]\d+)\s*$')
sym_re = re.compile(r'^\s*Sym\s*=\s*(\w*)\s*$')
energy_re = re.compile(r'^\s*Ene\s*=\s*(-?\d*.?\d*[e,E]?\+?-?\d*)\s*$')
spin_re = re.compile(r'^\s*Spin\s*=\s*(\w*)\s*$')
occ_re = re.compile(r'^\s*Occup\s*=\s*(-?\d*.\d*[e,E]?-?\+?\d*)\s*$')
for i in range(max_len):
line = calc[i]
if geom_re.match(line):
c1, c2, c3, c4, c5, c6 = geom_re.match(line).groups()
r1, r2, r3, r4, r5, r6 = geom_re.match(line).groups()
test = compare_strings(r1, c1) and compare_integers(
r2, c2) and compare_integers(r3, c3) and compare_values(
r4, c4, high_accuracy) and compare_values(
r5, c5, high_accuracy) and compare_values(
r6, c6, high_accuracy)
elif basis_header_re.match(line):
c1, c2, c3 = basis_header_re.match(line).groups()
r1, r2, r3 = basis_header_re.match(ref[i]).groups()
test = compare_strings(r1, c1) and compare_integers(
r2, c2) and compare_values(r3, c3, 3)
elif s1_re.match(line):
c1, c2 = s1_re.match(line).groups()
r1, r2 = s1_re.match(ref[i]).groups()
test = compare_values(r1, c1, high_accuracy) and compare_values(
r2, c2, high_accuracy)
elif sym_re.match(line):
c = sym_re.match(line).group(1)
r = sym_re.match(ref[i]).group(1)
test = compare_strings(r, c, f'text line: {line}')
elif energy_re.match(line):
c = energy_re.match(line).group(1)
r = energy_re.match(ref[i]).group(1)
test = compare_values(r, c, high_accuracy, f'float value: {line}')
elif spin_re.match(line):
c = spin_re.match(line).group(1)
r = spin_re.match(ref[i]).group(1)
test = compare_strings(r, c, f'text line: {line}')
elif occ_re.match(line):
c = occ_re.match(line).group(1)
r = occ_re.match(ref[i]).group(1)
test = compare_values(r, c, high_accuracy, f'float value: {line}')
elif s2_re.match(line):
c1, c2 = s2_re.match(line).groups()
r1, r2 = s2_re.match(line).groups()
test = compare_integers(
r1, c1, f'int value: {line}') and compare_values(
r2, c2, high_accuracy, f'float value: {line}')
else:
test = compare_strings(line, ref[i])
tests.append(test)
return compare_integers(True, all(tests), label)
def compare_fchkfiles(expected, computed, atol_exponent, label):
"""Comparison function for output data in FCHK (formatted checkpoint) file format.
Compares many fields including number of electrons, highest angular momentum, basis
set exponents, densities, final gradient.
Note only Psi4-style signature (``(expected, computed, atol_exponent, label)``) available.
An older format description can be found here
http://wild.life.nctu.edu.tw/~jsyu/compchem/g09/g09ur/f_formchk.htm
It lists more fields (logical, character) that are not included in this
test function. They should be covered by the string comparison.
This function is only meant to work with PSI4's FCHK files.
Parameters
----------
expected : file
Reference FCHK file against which `computed` is compared.
computed : file
Input FCHK file to compare against `expected`.
atol_exponent : int or float
Absolute tolerance for high accuracy fields -- 1.e-8 or 1.e-9 is suitable.
Values less than one are taken literally; one or greater taken as decimal digits for comparison.
So `1` means `atol=0.1` and `2` means `atol=0.01` but `0.04` means `atol=0.04`
Note that the largest expressable processed atol will be `~0.99`.
label : str
Label for passed and error messages.
"""
fchk_ref = fchkfile_to_string(expected).splitlines()
fchk_calc = fchkfile_to_string(computed).splitlines()
high_accuracy = atol_exponent
low_accuracy = 3
# Those listed below need super high scf convergence (d_conv 1e-12) and might
# show machine dependence. They will be tested with low_accuracy.
sensitive = ['Current cartesian coordinates', 'MO coefficients']
if len(fchk_ref) != len(fchk_calc):
raise ValidationError(
'The two FCHK files to compare have a different file length! \n')
index = 0
max_length = len(fchk_calc)
tests = []
for start in range(max_length):
if index >= max_length:
break
line = fchk_calc[index]
if "N=" in line:
offset, calc = _consume_fchk_section(fchk_calc, index)
_, ref = _consume_fchk_section(fchk_ref, index)
if any(x in line for x in sensitive):
test = compare_arrays(ref, calc, low_accuracy,
f" matrix section: {line}")
else:
test = compare_arrays(ref, calc, high_accuracy,
f" matrix section: {line}")
index += offset
elif " R " in line and "N=" not in line:
calc = line.split()[-1]
ref = fchk_ref[index].split()[-1]
test = compare_values(ref, calc, high_accuracy,
f" float value: {line}")
index += 1
elif " I " in line and "N=" not in line:
calc = line.split()[-1]
ref = fchk_ref[index].split()[-1]
test = compare_integers(ref, calc, f" int value: {line}")
index += 1
else:
test = compare_strings(line, fchk_ref[index],
f"FCK text line {index+1}.")
index += 1
tests.append(test)
return compare_integers(True, all(tests), label)
def compare_moldenfiles(expected,
computed,
atol_exponent=7,
label="Compare Molden"):
"""Comparison function for output data in Molden file format.
Compares many fields including geometry, basis set, occupations, symmetries, energies.
Note only Psi4-style signature (``(expected, computed, atol_exponent, label)``) available.
A format description is found https://www3.cmbi.umcn.nl/molden/molden_format.html
Parameters
----------
expected : file
Reference Molden file against which `computed` is compared.
computed : file
Input Molden file to compare against `expected`.
atol_exponent : int or float
Absolute tolerance for high accuracy fields -- 1.e-8 or 1.e-9 is suitable.
Values less than one are taken literally; one or greater taken as decimal digits for comparison.
So `1` means `atol=0.1` and `2` means `atol=0.01` but `0.04` means `atol=0.04`
Note that the largest expressable processed atol will be `~0.99`.
label : str
Label for passed and error messages.
"""
def moldenfile_to_string(fname):
with open(fname, 'r') as fn:
molden_string = fn.read()
return molden_string
ref = moldenfile_to_string(expected).splitlines()
calc = moldenfile_to_string(computed).splitlines()
if len(ref) != len(calc):
raise ValidationError(
f"These two molden files have different lengths...\n")
high_accuracy = atol_exponent
index = 0
max_len = len(calc)
tests = []
section = 0
geom_re = re.compile(
r'^\s*(\w*)\s+(\d+)\s+(\d+)\s+(-?\d+.\d+)\s+(-?\d+.\d+)\s+(-?\d+.\d+)\s*$'
)
basis_header_re = re.compile(r'^\s*([s,p,d,f,g])\s*(\d*)\s*(\d*.\d*)\s*$')
s1_re = re.compile(r'^\s*(\d+.?\d*)\s+(\d+.?\d*)$')
s2_re = re.compile(r'^\s*(\d+)\s+(-?\d+.\d+[e,E][\+,-]\d+)\s*$')
sym_re = re.compile(r'^\s*Sym\s*=\s*(\w*)\s*$')
energy_re = re.compile(r'^\s*Ene\s*=\s*(-?\d*.?\d*[e,E]?\+?-?\d*)\s*$')
spin_re = re.compile(r'^\s*Spin\s*=\s*(\w*)\s*$')
occ_re = re.compile(r'^\s*Occup\s*=\s*(-?\d*.\d*[e,E]?-?\+?\d*)\s*$')
for i in range(max_len):
line = calc[i]
if geom_re.match(line):
c1, c2, c3, c4, c5, c6 = geom_re.match(line).groups()
r1, r2, r3, r4, r5, r6 = geom_re.match(line).groups()
test = compare_strings(r1, c1) and compare_integers(
r2, c2) and compare_integers(r3, c3) and compare_values(
r4, c4, high_accuracy) and compare_values(
r5, c5, high_accuracy) and compare_values(
r6, c6, high_accuracy)
elif basis_header_re.match(line):
c1, c2, c3 = basis_header_re.match(line).groups()
r1, r2, r3 = basis_header_re.match(ref[i]).groups()
test = compare_strings(r1, c1) and compare_integers(
r2, c2) and compare_values(r3, c3, 3)
elif s1_re.match(line):
c1, c2 = s1_re.match(line).groups()
r1, r2 = s1_re.match(ref[i]).groups()
test = compare_values(r1, c1, high_accuracy) and compare_values(
r2, c2, high_accuracy)
elif sym_re.match(line):
c = sym_re.match(line).group(1)
r = sym_re.match(ref[i]).group(1)
test = compare_strings(r, c, f'text line: {line}')
elif energy_re.match(line):
c = energy_re.match(line).group(1)
r = energy_re.match(ref[i]).group(1)
test = compare_values(r, c, high_accuracy, f'float value: {line}')
elif spin_re.match(line):
c = spin_re.match(line).group(1)
r = spin_re.match(ref[i]).group(1)
test = compare_strings(r, c, f'text line: {line}')
elif occ_re.match(line):
c = occ_re.match(line).group(1)
r = occ_re.match(ref[i]).group(1)
test = compare_values(r, c, high_accuracy, f'float value: {line}')
elif s2_re.match(line):
c1, c2 = s2_re.match(line).groups()
r1, r2 = s2_re.match(line).groups()
test = compare_integers(
r1, c1, f'int value: {line}') and compare_values(
r2, c2, high_accuracy, f'float value: {line}')
else:
test = compare_strings(line, ref[i])
tests.append(test)
return compare_integers(True, all(tests), label)