def test_psi4api_ammonia():
"""Main test of the psi4api mode with the ammonia crystal."""
with pytest.raises(SystemExit):
crystalatte.main(cif_input="crystalatte/data/Carbon_Dioxide.cif",
cif_output="crystalatte/data/Carbon_Dioxide.xyz",
cif_a=3,
cif_b=3,
cif_c=3,
nmers_up_to=2,
r_cut_monomer=8.2,
cle_run_type=["test"])
def test_less_than_dimers():
"""Checks that the program prints an error message when an invalid
input with an 'nmers_up_to' keyword that is less than 2 is
provided."""
with pytest.raises(SystemExit):
crystalatte.main(cif_input="crystalatte/data/cif/Carbon_Dioxide.cif",
nmers_up_to=1,
cle_run_type=["test"])
# Clean-up generated test files
subprocess.call(["rm", "sc.xyz"])
def test_makefp_benzene():
"""
."""
# At the moment this test only checks that makefp mode ends.
with pytest.raises(SystemExit):
crystalatte.main(cif_input="crystalatte/data/Benzene.cif",
cif_a=3,
cif_b=3,
cif_c=3,
nmers_up_to=2,
r_cut_monomer=2.0,
cle_run_type=["makefp"],
verbose=2)
def test_psi4api_ammonia():
"""Checks that the program prints an error message when an invalid
monomer cutoff, that is loger than half the smallest dimension of
the supercell has been chosen."""
with pytest.raises(SystemExit):
crystalatte.main(cif_input="crystalatte/data/cif/Carbon_Dioxide.cif",
cif_a=3,
cif_b=3,
cif_c=3,
nmers_up_to=2,
r_cut_monomer=8.2,
cle_run_type=["test"])
# Clean-up generated test files
subprocess.call(["rm", "sc.xyz"])
def test_makefp_benzene():
"""Checks that the program exits normally after producing a makefp
input for GAMESS."""
# At the moment this test only checks that makefp mode ends.
with pytest.raises(SystemExit):
crystalatte.main(cif_input="crystalatte/data/cif/Benzene.cif",
cif_a=3,
cif_b=3,
cif_c=3,
nmers_up_to=2,
r_cut_monomer=2.0,
cle_run_type=["makefp"],
verbose=2)
# Clean-up generated test files
subprocess.call(["rm", "-r", "sc/"])
subprocess.call(["rm", "sc.xyz"])
def test_timings_ammonia():
"""Checks the timings mode with the ammonia crystal."""
# Execute the main function of crystalatte and retrieve the N-mers dictionary.
nmers, cle = crystalatte.main(
cif_input="crystalatte/data/cif/Ammonia.cif",
cif_output="crystalatte/data/cif/Ammonia.xyz",
cif_a=3,
cif_b=3,
cif_c=3,
nmers_up_to=5,
r_cut_com=6.5,
r_cut_monomer=3.5,
r_cut_dimer=2.6,
r_cut_trimer=3.7,
r_cut_tetramer=3.7,
r_cut_pentamer=6.1,
cle_run_type=["test", "timings"],
psi4_method="HF/STO-3G",
psi4_bsse="nocp",
psi4_memory="500 MB",
verbose=2)
# For debugging.
#import pprint
#pprint.pprint(nmers)
# Test the number of N-mers.
number_mono = len([k for k in nmers.keys() if k.startswith("1mer-")])
number_di = len([k for k in nmers.keys() if k.startswith("2mer-")])
number_tri = len([k for k in nmers.keys() if k.startswith("3mer-")])
number_tetra = len([k for k in nmers.keys() if k.startswith("4mer-")])
number_penta = len([k for k in nmers.keys() if k.startswith("5mer-")])
assert compare(7, number_mono, "Number of Monomers: ")
assert compare(1, number_di, "Number of Monomers: ")
assert compare(2, number_tri, "Number of Monomers: ")
assert compare(1, number_tetra, "Number of Monomers: ")
assert compare(1, number_penta, "Number of Monomers: ")
# Test the number of atoms per monomer in each N-mer.
for k, v in nmers.items():
n = int(k[0])
ref = [4] * n
if n != 1:
assert compare(ref, v["atoms_per_monomer"])
# Test replicas for each N-mer.
assert compare_values(6, nmers["2mer-0+1"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(3, nmers["3mer-0+1+2"]["replicas"],
"3mer-0+1+2 Replicas: ")
assert compare_values(3, nmers["3mer-0+1+5"]["replicas"],
"3mer-0+1+5 Replicas: ")
assert compare_values(1, nmers["4mer-0+1+2+3"]["replicas"],
"4mer-0+1+2+3 Replicas: ")
assert compare_values(3, nmers["5mer-0+1+2+3+4"]["replicas"],
"5mer-0+1+2+3+4 Replicas: ")
# Test the nuclear repulsion energies for each N-mer.
assert compare_values(38.18102741857883,
nmers["2mer-0+1"]["nre"],
atol=1.e-8)
assert compare_values(79.5638545934053,
nmers["3mer-0+1+2"]["nre"],
atol=1.e-8)
assert compare_values(77.87320866497402,
nmers["3mer-0+1+5"]["nre"],
atol=1.e-8)
assert compare_values(136.3717727214002,
nmers["4mer-0+1+2+3"]["nre"],
atol=1.e-8)
assert compare_values(194.64346937372983,
nmers["5mer-0+1+2+3+4"]["nre"],
atol=1.e-8)
# Test the COM-based priority for each N-mer.
assert compare_values(0.0025317103172576337,
nmers["2mer-0+1"]["priority_com"],
atol=1.e-5)
assert compare_values(2.3782189167926454e-08,
nmers["3mer-0+1+2"]["priority_com"],
atol=1.e-10)
assert compare_values(1.6227141916361213e-08,
nmers["3mer-0+1+5"]["priority_com"],
atol=1.e-10)
assert compare_values(8.289215938603657e-16,
nmers["4mer-0+1+2+3"]["priority_com"],
atol=1.e-18)
assert compare_values(3.2435020503790996e-27,
nmers["5mer-0+1+2+3+4"]["priority_com"],
atol=1.e-29)
# Test the N-mer-separation-based priority for each N-mer.
assert compare_values(0.008552208792327147,
nmers["2mer-0+1"]["priority_min"],
atol=1.e-5)
assert compare_values(7.570854620127571e-07,
nmers["3mer-0+1+2"]["priority_min"],
atol=1.e-9)
assert compare_values(6.255109048743461e-07,
nmers["3mer-0+1+5"]["priority_min"],
atol=1.e-9)
assert compare_values(6.937449498781642e-13,
nmers["4mer-0+1+2+3"]["priority_min"],
atol=1.e-15)
assert compare_values(1.441820074805934e-22,
nmers["5mer-0+1+2+3+4"]["priority_min"],
atol=1.e-24)
# Test the N-mer-cutoff-based priority for each N-mer.
assert compare_values(1.7489244e-03,
nmers["2mer-0+1"]["priority_cutoff"],
atol=1.e-10)
assert compare_values(6.2551090e-07,
nmers["3mer-0+1+2"]["priority_cutoff"],
atol=1.e-14)
assert compare_values(6.2551090e-07,
nmers["3mer-0+1+5"]["priority_cutoff"],
atol=1.e-14)
assert compare_values(9.3558713e-12,
nmers["4mer-0+1+2+3"]["priority_cutoff"],
atol=1.e-19)
assert compare_values(4.0052011e-25,
nmers["5mer-0+1+2+3+4"]["priority_cutoff"],
atol=1.e-32)
# Test the N-mer cutoffs for each N-mer.
assert compare_values(4.889981712498321,
min(nmers["2mer-0+1"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(4.588498152619043,
min(nmers["3mer-0+1+2"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(4.889981712498321,
min(nmers["3mer-0+1+5"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(
4.588498152619042,
min(nmers["4mer-0+1+2+3"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(
4.588498152619042,
min(nmers["5mer-0+1+2+3+4"]["min_monomer_separations"]),
atol=1.e-8)
# Test the COM cutoffs for each N-mer.
assert compare_values(7.337171371615357,
min(nmers["2mer-0+1"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(6.459398295191971,
min(nmers["3mer-0+1+2"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(7.337171371615357,
min(nmers["3mer-0+1+5"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(
6.459398295191971,
min(nmers["4mer-0+1+2+3"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(
6.459398295191971,
min(nmers["5mer-0+1+2+3+4"]["com_monomer_separations"]),
atol=1.e-8)
# Test the crystal lattice energy.
assert compare_values(0.0, cle, atol=1.e-8)
# Clean-up generated test files.
subprocess.call(["rm", "crystalatte/data/cif/Ammonia.xyz"])
def test_supercell_triazine():
"""Checks that the program prints a warning message indicating that
the supercell contains duplicate coordinates and that they will be
skipped. Then, it should state the new number of unique coordinates
in the supercell."""
# Execute the main function of crystalatte and retrieve the N-mers dictionary.
nmers, cle = crystalatte.main(
cif_input="crystalatte/data/cif/Triazine.cif",
cif_a=3,
cif_b=3,
cif_c=3,
nmers_up_to=2,
r_cut_monomer=8.0,
r_cut_dimer=2.9,
cle_run_type=["test"],
verbose=2)
# For debug.
#import pprint
#pprint.pprint(nmers)
# Test the number of N-mers.
number_mono = len([k for k in nmers.keys() if k.startswith("1mer-")])
number_di = len([k for k in nmers.keys() if k.startswith("2mer-")])
assert compare(39, number_mono, "Number of Monomers: ")
assert compare(3, number_di, "Number of Monomers: ")
# Test the number of atoms per monomer in each N-mer.
for k, v in nmers.items():
n = int(k[0])
ref = [9] * n
if n != 1:
assert compare(ref, v["atoms_per_monomer"])
# Test replicas for each N-mer.
assert compare_values(4, nmers["2mer-0+1"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(1, nmers["2mer-0+8"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(1, nmers["2mer-0+10"]["replicas"],
"2mer-0+1 Replicas: ")
# Test the nuclear repulsion energies for each N-mer.
assert compare_values(603.1478166922, nmers["2mer-0+1"]["nre"], atol=1.e-8)
assert compare_values(603.1478268883, nmers["2mer-0+8"]["nre"], atol=1.e-8)
assert compare_values(603.1478008660,
nmers["2mer-0+10"]["nre"],
atol=1.e-8)
# Test the COM-based priority for each N-mer.
assert compare_values(0.0008000115,
nmers["2mer-0+1"]["priority_com"],
atol=1.e-8)
assert compare_values(0.0008000115,
nmers["2mer-0+8"]["priority_com"],
atol=1.e-8)
assert compare_values(0.0008000115,
nmers["2mer-0+10"]["priority_com"],
atol=1.e-8)
# Test the N-mer-separation-based priority for each N-mer.
assert compare_values(0.0067549722,
nmers["2mer-0+1"]["priority_min"],
atol=1.e-8)
assert compare_values(0.0067549681,
nmers["2mer-0+8"]["priority_min"],
atol=1.e-8)
assert compare_values(0.0067549700,
nmers["2mer-0+10"]["priority_min"],
atol=1.e-8)
# Test the N-mer-cutoff-based priority for each N-mer.
assert compare_values(0.0012769231,
nmers["2mer-0+1"]["priority_cutoff"],
atol=1.e-8)
assert compare_values(0.0012769220,
nmers["2mer-0+8"]["priority_cutoff"],
atol=1.e-8)
assert compare_values(0.0012769225,
nmers["2mer-0+10"]["priority_cutoff"],
atol=1.e-8)
# Test the N-mer cutoffs for each N-mer.
assert compare_values(5.2900382498,
min(nmers["2mer-0+1"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(5.2900393127,
min(nmers["2mer-0+8"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(5.2900388235,
min(nmers["2mer-0+10"]["min_monomer_separations"]),
atol=1.e-8)
## Test the COM cutoffs for each N-mer.
assert compare_values(10.7721217992,
min(nmers["2mer-0+1"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(10.7721212935,
min(nmers["2mer-0+8"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(10.7721220245,
min(nmers["2mer-0+10"]["com_monomer_separations"]),
atol=1.e-8)
# Test the crystal lattice energy.
assert compare_values(0.0, cle, atol=1.e-8)
# Clean-up generated test files
subprocess.call(["rm", "sc.xyz"])
def test_testmode_benzene():
"""Checks that the program is able to reproduce the generation of
the structures communicated in A. L. Ringer and C. D. Sherrill,
Chem. Eur. J., 2008, 14, pp 2542–2547, using the chemical space
eigenvalues filter in test mode."""
# Execute the main function of crystalatte and retrieve the N-mers dictionary.
nmers, cle = crystalatte.main(cif_input="crystalatte/data/cif/Benzene.cif",
cif_a=5,
cif_b=5,
cif_c=5,
nmers_up_to=2,
r_cut_com=9.5,
r_cut_monomer=11.4,
r_cut_dimer=11.4,
cle_run_type=["test"],
verbose=2)
# For debug.
#import pprint
#pprint.pprint(nmers)
# Test the number of N-mers.
number_mono = len([k for k in nmers.keys() if k.startswith("1mer-")])
number_di = len([k for k in nmers.keys() if k.startswith("2mer-")])
assert compare(84, number_mono, "Number of Monomers: ")
assert compare(10, number_di, "Number of Monomers: ")
# Test the number of atoms per monomer in each N-mer.
for k, v in nmers.items():
n = int(k[0])
ref = [12] * n
if n != 1:
assert compare(ref, v["atoms_per_monomer"])
# Test replicas for each N-mer.
assert compare_values(4, nmers["2mer-0+1"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(4, nmers["2mer-0+2"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(4, nmers["2mer-0+6"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(2, nmers["2mer-0+16"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(2, nmers["2mer-0+5"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(2, nmers["2mer-0+21"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(4, nmers["2mer-0+12"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(4, nmers["2mer-0+14"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(4, nmers["2mer-0+15"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(4, nmers["2mer-0+27"]["replicas"],
"2mer-0+1 Replicas: ")
# Test the non-additive many-body energies.
assert compare_values(0.0, nmers["2mer-0+1"]["nambe"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+2"]["nambe"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+6"]["nambe"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+16"]["nambe"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+5"]["nambe"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+21"]["nambe"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+12"]["nambe"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+14"]["nambe"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+15"]["nambe"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+27"]["nambe"], atol=1.e-8)
# Test contributions for each N-mer.
assert compare_values(0.0, nmers["2mer-0+1"]["contrib"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+2"]["contrib"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+6"]["contrib"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+16"]["contrib"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+5"]["contrib"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+21"]["contrib"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+12"]["contrib"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+14"]["contrib"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+15"]["contrib"], atol=1.e-8)
assert compare_values(0.0, nmers["2mer-0+27"]["contrib"], atol=1.e-8)
# Test the nuclear repulsion energies for each N-mer.
assert compare_values(564.7978818358, nmers["2mer-0+1"]["nre"], atol=1.e-8)
assert compare_values(569.6323170325, nmers["2mer-0+2"]["nre"], atol=1.e-8)
assert compare_values(588.8876674569, nmers["2mer-0+6"]["nre"], atol=1.e-8)
assert compare_values(542.3197525768,
nmers["2mer-0+16"]["nre"],
atol=1.e-8)
assert compare_values(507.4201406916, nmers["2mer-0+5"]["nre"], atol=1.e-8)
assert compare_values(532.0439341175,
nmers["2mer-0+21"]["nre"],
atol=1.e-8)
assert compare_values(507.4677080555,
nmers["2mer-0+12"]["nre"],
atol=1.e-8)
assert compare_values(510.6225302261,
nmers["2mer-0+14"]["nre"],
atol=1.e-8)
assert compare_values(509.3453310551,
nmers["2mer-0+15"]["nre"],
atol=1.e-8)
assert compare_values(505.1441258078,
nmers["2mer-0+27"]["nre"],
atol=1.e-8)
# Test the COM-based priority for each N-mer.
assert compare_values(0.0006907226,
nmers["2mer-0+1"]["priority_com"],
atol=1.e-8)
assert compare_values(0.0007548316,
nmers["2mer-0+2"]["priority_com"],
atol=1.e-8)
assert compare_values(0.0011681199,
nmers["2mer-0+6"]["priority_com"],
atol=1.e-8)
assert compare_values(0.0004692044,
nmers["2mer-0+16"]["priority_com"],
atol=1.e-8)
assert compare_values(0.0001772763,
nmers["2mer-0+5"]["priority_com"],
atol=1.e-8)
assert compare_values(0.0003671724,
nmers["2mer-0+21"]["priority_com"],
atol=1.e-8)
assert compare_values(0.0001783188,
nmers["2mer-0+12"]["priority_com"],
atol=1.e-8)
assert compare_values(0.0001987883,
nmers["2mer-0+14"]["priority_com"],
atol=1.e-8)
assert compare_values(0.0001987883,
nmers["2mer-0+15"]["priority_com"],
atol=1.e-8)
assert compare_values(0.0001783188,
nmers["2mer-0+27"]["priority_com"],
atol=1.e-8)
# Test the N-mer-separation-based priority for each N-mer.
assert compare_values(0.0090014493,
nmers["2mer-0+1"]["priority_min"],
atol=1.e-8)
assert compare_values(0.0081275168,
nmers["2mer-0+2"]["priority_min"],
atol=1.e-8)
assert compare_values(0.0077024945,
nmers["2mer-0+6"]["priority_min"],
atol=1.e-8)
assert compare_values(0.0014125011,
nmers["2mer-0+16"]["priority_min"],
atol=1.e-8)
assert compare_values(0.0012169745,
nmers["2mer-0+5"]["priority_min"],
atol=1.e-8)
assert compare_values(0.0011442584,
nmers["2mer-0+21"]["priority_min"],
atol=1.e-8)
assert compare_values(0.0010809527,
nmers["2mer-0+12"]["priority_min"],
atol=1.e-8)
assert compare_values(0.0009506992,
nmers["2mer-0+14"]["priority_min"],
atol=1.e-8)
assert compare_values(0.0006261051,
nmers["2mer-0+15"]["priority_min"],
atol=1.e-8)
assert compare_values(0.0003528237,
nmers["2mer-0+27"]["priority_min"],
atol=1.e-8)
# Test the N-mer-cutoff-based priority for each N-mer.
assert compare_values(0.0018724774,
nmers["2mer-0+1"]["priority_cutoff"],
atol=1.e-8)
assert compare_values(0.0016340945,
nmers["2mer-0+2"]["priority_cutoff"],
atol=1.e-8)
assert compare_values(0.0015211610,
nmers["2mer-0+6"]["priority_cutoff"],
atol=1.e-8)
assert compare_values(0.0001584838,
nmers["2mer-0+16"]["priority_cutoff"],
atol=1.e-8)
assert compare_values(0.0001299297,
nmers["2mer-0+5"]["priority_cutoff"],
atol=1.e-8)
assert compare_values(0.0001196829,
nmers["2mer-0+21"]["priority_cutoff"],
atol=1.e-8)
assert compare_values(0.0001109367,
nmers["2mer-0+12"]["priority_cutoff"],
atol=1.e-8)
assert compare_values(0.0000934811,
nmers["2mer-0+14"]["priority_cutoff"],
atol=1.e-8)
assert compare_values(0.0000535627,
nmers["2mer-0+15"]["priority_cutoff"],
atol=1.e-8)
assert compare_values(0.0000249312,
nmers["2mer-0+27"]["priority_cutoff"],
atol=1.e-8)
# Test the N-mer cutoffs for each N-mer.
assert compare_values(4.8072405390,
min(nmers["2mer-0+1"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(4.9737128407,
min(nmers["2mer-0+2"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(5.0635628061,
min(nmers["2mer-0+6"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(8.9125861155,
min(nmers["2mer-0+16"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(9.3664029960,
min(nmers["2mer-0+5"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(9.5607501286,
min(nmers["2mer-0+21"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(9.7438615012,
min(nmers["2mer-0+12"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(10.1699533857,
min(nmers["2mer-0+14"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(11.6891856781,
min(nmers["2mer-0+15"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(14.1518785972,
min(nmers["2mer-0+27"]["min_monomer_separations"]),
atol=1.e-8)
# Test the COM cutoffs for each N-mer.
assert compare_values(11.3126785806,
min(nmers["2mer-0+1"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(10.9828900652,
min(nmers["2mer-0+2"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(9.4952015406,
min(nmers["2mer-0+6"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(12.8690349144,
min(nmers["2mer-0+16"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(17.8012201018,
min(nmers["2mer-0+5"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(13.9650760671,
min(nmers["2mer-0+21"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(17.7664634564,
min(nmers["2mer-0+12"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(17.1344318930,
min(nmers["2mer-0+14"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(17.1344318930,
min(nmers["2mer-0+15"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(17.7664634564,
min(nmers["2mer-0+27"]["com_monomer_separations"]),
atol=1.e-8)
# Test the crystal lattice energy.
assert compare_values(0.0, cle, atol=1.e-8)
# Clean-up generated test files
subprocess.call(["rm", "sc.xyz"])
def test_supercell_triazine():
"""Test to reproduce the structures of A. L. Ringer and C. D.
Sherrill, Chem. Eur. J., 2008, 14, pp 2542–2547."""
# Execute the main function of crystalatte and retrieve the N-mers dictionary.
nmers, cle = crystalatte.main(cif_input="crystalatte/data/Triazine.cif",
cif_output="crystalatte/data/Triazine.xyz",
cif_a=3,
cif_b=3,
cif_c=3,
nmers_up_to=2,
r_cut_com=8.0,
r_cut_monomer=8.0,
r_cut_dimer=2.9,
r_cut_trimer=2.9,
r_cut_tetramer=2.9,
r_cut_pentamer=2.9,
cle_run_type=["test"],
psi4_method="HF/STO-3G",
psi4_bsse="nocp",
psi4_memory="500 MB",
verbose=2)
# For debug.
#import pprint
#pprint.pprint(nmers)
# Test the number of N-mers.
number_mono = len([k for k in nmers.keys() if k.startswith("1mer-")])
number_di = len([k for k in nmers.keys() if k.startswith("2mer-")])
assert compare(39, number_mono, "Number of Monomers: ")
assert compare(3, number_di, "Number of Monomers: ")
# Test the number of atoms per monomer in each N-mer.
for k, v in nmers.items():
n = int(k[0])
ref = [9] * n
if n != 1:
assert compare(ref, v["atoms_per_monomer"])
# Test replicas for each N-mer.
assert compare_values(4, nmers["2mer-0+1"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(1, nmers["2mer-0+8"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(1, nmers["2mer-0+10"]["replicas"],
"2mer-0+1 Replicas: ")
# Test the nuclear repulsion energies for each N-mer.
assert compare_values(603.1478166922, nmers["2mer-0+1"]["nre"], atol=1.e-8)
assert compare_values(603.1478268883, nmers["2mer-0+8"]["nre"], atol=1.e-8)
assert compare_values(603.1478008660,
nmers["2mer-0+10"]["nre"],
atol=1.e-8)
# Test the COM-based priority for each N-mer.
assert compare_values(0.0008000115,
nmers["2mer-0+1"]["priority_com"],
atol=1.e-8)
assert compare_values(0.0008000115,
nmers["2mer-0+8"]["priority_com"],
atol=1.e-8)
assert compare_values(0.0008000115,
nmers["2mer-0+10"]["priority_com"],
atol=1.e-8)
# Test the N-mer-cutoff-based priority for each N-mer.
assert compare_values(0.0067549722,
nmers["2mer-0+1"]["priority_min"],
atol=1.e-8)
assert compare_values(0.0067549681,
nmers["2mer-0+8"]["priority_min"],
atol=1.e-8)
assert compare_values(0.0067549700,
nmers["2mer-0+10"]["priority_min"],
atol=1.e-8)
# Test the N-mer cutoffs for each N-mer.
assert compare_values(5.2900382498,
min(nmers["2mer-0+1"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(5.2900393127,
min(nmers["2mer-0+8"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(5.2900388235,
min(nmers["2mer-0+10"]["min_monomer_separations"]),
atol=1.e-8)
## Test the COM cutoffs for each N-mer.
assert compare_values(10.7721217992,
min(nmers["2mer-0+1"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(10.7721212935,
min(nmers["2mer-0+8"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(10.7721220245,
min(nmers["2mer-0+10"]["com_monomer_separations"]),
atol=1.e-8)
# Test the crystal lattice energy.
assert compare_values(0.0, cle, atol=1.e-8)
def test_psi4api_ammonia():
"""Main test of the psi4api mode with the ammonia crystal."""
# Execute the main function of crystalatte and retrieve the N-mers dictionary.
nmers, cle = crystalatte.main(cif_input="crystalatte/data/Ammonia.cif",
cif_output="crystalatte/data/Ammonia.xyz",
cif_a=3,
cif_b=3,
cif_c=3,
nmers_up_to=5,
r_cut_com=6.5,
r_cut_monomer=3.5,
r_cut_dimer=2.6,
r_cut_trimer=3.7,
r_cut_tetramer=3.7,
r_cut_pentamer=6.1,
cle_run_type=["psi4api"],
psi4_method="HF/STO-3G",
psi4_bsse="nocp",
psi4_memory="500 MB",
verbose=2)
# For debugging.
#import pprint
#pprint.pprint(nmers)
# Test the number of N-mers.
number_mono = len([k for k in nmers.keys() if k.startswith("1mer-")])
number_di = len([k for k in nmers.keys() if k.startswith("2mer-")])
number_tri = len([k for k in nmers.keys() if k.startswith("3mer-")])
number_tetra = len([k for k in nmers.keys() if k.startswith("4mer-")])
number_penta = len([k for k in nmers.keys() if k.startswith("5mer-")])
assert compare(7, number_mono, "Number of Monomers: ")
assert compare(1, number_di, "Number of Monomers: ")
assert compare(2, number_tri, "Number of Monomers: ")
assert compare(1, number_tetra, "Number of Monomers: ")
assert compare(1, number_penta, "Number of Monomers: ")
# Test the number of atoms per monomer in each N-mer.
for k, v in nmers.items():
n = int(k[0])
ref = [4] * n
if n != 1:
assert compare(ref, v["atoms_per_monomer"])
# Test replicas for each N-mer.
assert compare_values(6, nmers["2mer-0+1"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(3, nmers["3mer-0+1+2"]["replicas"],
"3mer-0+1+2 Replicas: ")
assert compare_values(3, nmers["3mer-0+1+5"]["replicas"],
"3mer-0+1+5 Replicas: ")
assert compare_values(1, nmers["4mer-0+1+2+3"]["replicas"],
"4mer-0+1+2+3 Replicas: ")
assert compare_values(3, nmers["5mer-0+1+2+3+4"]["replicas"],
"5mer-0+1+2+3+4 Replicas: ")
# Test the non-additive many-body energies.
assert compare_values(0.00033410465863426,
nmers["2mer-0+1"]["nambe"],
atol=1.e-8)
assert compare_values(1.3679718790626794e-05,
nmers["3mer-0+1+2"]["nambe"],
atol=1.e-8)
assert compare_values(-4.049166795994097e-05,
nmers["3mer-0+1+5"]["nambe"],
atol=1.e-8)
assert compare_values(2.4491332624165807e-06,
nmers["4mer-0+1+2+3"]["nambe"],
atol=1.e-8)
assert compare_values(-3.28520798120735e-07,
nmers["5mer-0+1+2+3+4"]["nambe"],
atol=1.e-8)
# Test contributions for each N-mer.
assert compare_values(0.0010023139755617194,
nmers["2mer-0+1"]["contrib"],
atol=1.e-8)
assert compare_values(1.3679718705361665e-05,
nmers["3mer-0+1+2"]["contrib"],
atol=1.e-8)
assert compare_values(-4.049166741992849e-05,
nmers["3mer-0+1+5"]["contrib"],
atol=1.e-8)
assert compare_values(6.122833582367093e-07,
nmers["4mer-0+1+2+3"]["contrib"],
atol=1.e-8)
assert compare_values(-1.9695794435392598e-07,
nmers["5mer-0+1+2+3+4"]["contrib"],
atol=1.e-8)
# Test the nuclear repulsion energies for each N-mer.
assert compare_values(38.18102741857883,
nmers["2mer-0+1"]["nre"],
atol=1.e-8)
assert compare_values(79.5638545934053,
nmers["3mer-0+1+2"]["nre"],
atol=1.e-8)
assert compare_values(77.87320866497402,
nmers["3mer-0+1+5"]["nre"],
atol=1.e-8)
assert compare_values(136.3717727214002,
nmers["4mer-0+1+2+3"]["nre"],
atol=1.e-8)
assert compare_values(194.64346937372983,
nmers["5mer-0+1+2+3+4"]["nre"],
atol=1.e-8)
# Test the COM-based priority for each N-mer.
assert compare_values(0.0025317103172576337,
nmers["2mer-0+1"]["priority_com"],
atol=1.e-5)
assert compare_values(2.3782189167926454e-08,
nmers["3mer-0+1+2"]["priority_com"],
atol=1.e-10)
assert compare_values(1.6227141916361213e-08,
nmers["3mer-0+1+5"]["priority_com"],
atol=1.e-10)
assert compare_values(8.289215938603657e-16,
nmers["4mer-0+1+2+3"]["priority_com"],
atol=1.e-18)
assert compare_values(3.2435020503790996e-27,
nmers["5mer-0+1+2+3+4"]["priority_com"],
atol=1.e-29)
# Test the N-mer-cutoff-based priority for each N-mer.
assert compare_values(0.008552208792327147,
nmers["2mer-0+1"]["priority_min"],
atol=1.e-5)
assert compare_values(7.570854620127571e-07,
nmers["3mer-0+1+2"]["priority_min"],
atol=1.e-9)
assert compare_values(6.255109048743461e-07,
nmers["3mer-0+1+5"]["priority_min"],
atol=1.e-9)
assert compare_values(6.937449498781642e-13,
nmers["4mer-0+1+2+3"]["priority_min"],
atol=1.e-15)
assert compare_values(1.441820074805934e-22,
nmers["5mer-0+1+2+3+4"]["priority_min"],
atol=1.e-24)
# Test the N-mer cutoffs for each N-mer.
assert compare_values(4.889981712498321,
min(nmers["2mer-0+1"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(4.588498152619043,
min(nmers["3mer-0+1+2"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(4.889981712498321,
min(nmers["3mer-0+1+5"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(
4.588498152619042,
min(nmers["4mer-0+1+2+3"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(
4.588498152619042,
min(nmers["5mer-0+1+2+3+4"]["min_monomer_separations"]),
atol=1.e-8)
# Test the COM cutoffs for each N-mer.
assert compare_values(7.337171371615357,
min(nmers["2mer-0+1"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(6.459398295191971,
min(nmers["3mer-0+1+2"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(7.337171371615357,
min(nmers["3mer-0+1+5"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(
6.459398295191971,
min(nmers["4mer-0+1+2+3"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(
6.459398295191971,
min(nmers["5mer-0+1+2+3+4"]["com_monomer_separations"]),
atol=1.e-8)
# Test the crystal lattice energy.
assert compare_values(0.00097592, cle, atol=1.e-8)
def test_psi4api_ammonia():
"""Checks the psi4api mode with the ammonia crystal."""
# Execute the main function of crystalatte and retrieve the N-mers dictionary.
nmers, cle = crystalatte.main(
cif_input="crystalatte/data/cif/Ammonia.cif",
cif_output="crystalatte/data/cif/Ammonia.xyz",
cif_a=3,
cif_b=3,
cif_c=3,
nmers_up_to=5,
r_cut_com=6.5,
r_cut_monomer=3.5,
r_cut_dimer=2.6,
r_cut_trimer=3.7,
r_cut_tetramer=3.7,
r_cut_pentamer=6.1,
cle_run_type=["psi4api"],
psi4_method="HF/STO-3G",
psi4_bsse="nocp",
psi4_memory="500 MB",
verbose=2)
# For debugging.
#import pprint
#pprint.pprint(nmers)
# Test the number of N-mers.
number_mono = len([k for k in nmers.keys() if k.startswith("1mer-")])
number_di = len([k for k in nmers.keys() if k.startswith("2mer-")])
number_tri = len([k for k in nmers.keys() if k.startswith("3mer-")])
number_tetra = len([k for k in nmers.keys() if k.startswith("4mer-")])
number_penta = len([k for k in nmers.keys() if k.startswith("5mer-")])
assert compare(7, number_mono, "Number of Monomers: ")
assert compare(1, number_di, "Number of Monomers: ")
assert compare(2, number_tri, "Number of Monomers: ")
assert compare(1, number_tetra, "Number of Monomers: ")
assert compare(1, number_penta, "Number of Monomers: ")
# Test the number of atoms per monomer in each N-mer.
for k, v in nmers.items():
n = int(k[0])
ref = [4] * n
if n != 1:
assert compare(ref, v["atoms_per_monomer"])
# Test replicas for each N-mer.
assert compare_values(6, nmers["2mer-0+1"]["replicas"],
"2mer-0+1 Replicas: ")
assert compare_values(3, nmers["3mer-0+1+2"]["replicas"],
"3mer-0+1+2 Replicas: ")
assert compare_values(3, nmers["3mer-0+1+5"]["replicas"],
"3mer-0+1+5 Replicas: ")
assert compare_values(1, nmers["4mer-0+1+2+3"]["replicas"],
"4mer-0+1+2+3 Replicas: ")
assert compare_values(3, nmers["5mer-0+1+2+3+4"]["replicas"],
"5mer-0+1+2+3+4 Replicas: ")
# Test the non-additive many-body energies.
assert compare_values(0.00033410465863426,
nmers["2mer-0+1"]["nambe"],
atol=1.e-8)
assert compare_values(1.3679718790626794e-05,
nmers["3mer-0+1+2"]["nambe"],
atol=1.e-8)
assert compare_values(-4.049166795994097e-05,
nmers["3mer-0+1+5"]["nambe"],
atol=1.e-8)
assert compare_values(2.4491332624165807e-06,
nmers["4mer-0+1+2+3"]["nambe"],
atol=1.e-8)
assert compare_values(-3.28520798120735e-07,
nmers["5mer-0+1+2+3+4"]["nambe"],
atol=1.e-8)
# Test contributions for each N-mer.
assert compare_values(0.0010023139755617194,
nmers["2mer-0+1"]["contrib"],
atol=1.e-8)
assert compare_values(1.3679718705361665e-05,
nmers["3mer-0+1+2"]["contrib"],
atol=1.e-8)
assert compare_values(-4.049166741992849e-05,
nmers["3mer-0+1+5"]["contrib"],
atol=1.e-8)
assert compare_values(6.122833582367093e-07,
nmers["4mer-0+1+2+3"]["contrib"],
atol=1.e-8)
assert compare_values(-1.9695794435392598e-07,
nmers["5mer-0+1+2+3+4"]["contrib"],
atol=1.e-8)
# Test the nuclear repulsion energies for each N-mer.
assert compare_values(38.18102741857883,
nmers["2mer-0+1"]["nre"],
atol=1.e-8)
assert compare_values(79.5638545934053,
nmers["3mer-0+1+2"]["nre"],
atol=1.e-8)
assert compare_values(77.87320866497402,
nmers["3mer-0+1+5"]["nre"],
atol=1.e-8)
assert compare_values(136.3717727214002,
nmers["4mer-0+1+2+3"]["nre"],
atol=1.e-8)
assert compare_values(194.64346937372983,
nmers["5mer-0+1+2+3+4"]["nre"],
atol=1.e-8)
# Test the COM-based priority for each N-mer.
assert compare_values(0.0025317103172576337,
nmers["2mer-0+1"]["priority_com"],
atol=1.e-5)
assert compare_values(2.3782189167926454e-08,
nmers["3mer-0+1+2"]["priority_com"],
atol=1.e-10)
assert compare_values(1.6227141916361213e-08,
nmers["3mer-0+1+5"]["priority_com"],
atol=1.e-10)
assert compare_values(8.289215938603657e-16,
nmers["4mer-0+1+2+3"]["priority_com"],
atol=1.e-18)
assert compare_values(3.2435020503790996e-27,
nmers["5mer-0+1+2+3+4"]["priority_com"],
atol=1.e-29)
# Test the N-mer-separation-based priority for each N-mer.
assert compare_values(0.008552208792327147,
nmers["2mer-0+1"]["priority_min"],
atol=1.e-5)
assert compare_values(7.570854620127571e-07,
nmers["3mer-0+1+2"]["priority_min"],
atol=1.e-9)
assert compare_values(6.255109048743461e-07,
nmers["3mer-0+1+5"]["priority_min"],
atol=1.e-9)
assert compare_values(6.937449498781642e-13,
nmers["4mer-0+1+2+3"]["priority_min"],
atol=1.e-15)
assert compare_values(1.441820074805934e-22,
nmers["5mer-0+1+2+3+4"]["priority_min"],
atol=1.e-24)
# Test the N-mer-cutoff-based priority for each N-mer.
assert compare_values(1.7489244e-03,
nmers["2mer-0+1"]["priority_cutoff"],
atol=1.e-10)
assert compare_values(6.2551090e-07,
nmers["3mer-0+1+2"]["priority_cutoff"],
atol=1.e-14)
assert compare_values(6.2551090e-07,
nmers["3mer-0+1+5"]["priority_cutoff"],
atol=1.e-14)
assert compare_values(9.3558713e-12,
nmers["4mer-0+1+2+3"]["priority_cutoff"],
atol=1.e-19)
assert compare_values(4.0052011e-25,
nmers["5mer-0+1+2+3+4"]["priority_cutoff"],
atol=1.e-32)
# Test the N-mer cutoffs for each N-mer.
assert compare_values(4.889981712498321,
min(nmers["2mer-0+1"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(4.588498152619043,
min(nmers["3mer-0+1+2"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(4.889981712498321,
min(nmers["3mer-0+1+5"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(
4.588498152619042,
min(nmers["4mer-0+1+2+3"]["min_monomer_separations"]),
atol=1.e-8)
assert compare_values(
4.588498152619042,
min(nmers["5mer-0+1+2+3+4"]["min_monomer_separations"]),
atol=1.e-8)
# Test the COM cutoffs for each N-mer.
assert compare_values(7.337171371615357,
min(nmers["2mer-0+1"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(6.459398295191971,
min(nmers["3mer-0+1+2"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(7.337171371615357,
min(nmers["3mer-0+1+5"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(
6.459398295191971,
min(nmers["4mer-0+1+2+3"]["com_monomer_separations"]),
atol=1.e-8)
assert compare_values(
6.459398295191971,
min(nmers["5mer-0+1+2+3+4"]["com_monomer_separations"]),
atol=1.e-8)
# Test the fist eight eigenvalues of the chemical similarity matrix for each N-mer
ref_eigenvalues = {
"2mer-0+1": [
61.0577465, 47.27888919, 0.47526893, 0.24647406, 0.19289154,
0.17243445, 0.15959053, 0.1341196
],
"3mer-0+1+2": [
68.7489044, 47.64038823, 46.16025, 0.54602448, 0.27553, 0.24654741,
0.19155801, 0.18623255
],
"3mer-0+1+5": [
67.98553018, 47.27916218, 47.27916218, 0.56261868, 0.24797375,
0.24797375, 0.21507249, 0.17507582
],
"4mer-0+1+2+3": [
76.65031347, 47.80875755, 46.16191286, 46.16191286, 0.59866536,
0.27665228, 0.27665228, 0.25452003
],
"5mer-0+1+2+3+4": [
81.63568805, 50.70144021, 47.31855835, 46.16210417, 45.17840185,
0.64552605, 0.33151774, 0.28139148
],
}
assert compare_values(ref_eigenvalues["2mer-0+1"],
nmers["2mer-0+1"]["chsev"][:8],
atol=1e-7)
assert compare_values(ref_eigenvalues["3mer-0+1+2"],
nmers["3mer-0+1+2"]["chsev"][:8],
atol=1e-7)
assert compare_values(ref_eigenvalues["3mer-0+1+5"],
nmers["3mer-0+1+5"]["chsev"][:8],
atol=1e-7)
assert compare_values(ref_eigenvalues["4mer-0+1+2+3"],
nmers["4mer-0+1+2+3"]["chsev"][:8],
atol=1e-7)
assert compare_values(ref_eigenvalues["5mer-0+1+2+3+4"],
nmers["5mer-0+1+2+3+4"]["chsev"][:8],
atol=1e-7)
# Test the crystal lattice energy.
assert compare_values(0.00097592, cle, atol=1.e-8)
# Clean-up generated test files.
subprocess.call(["rm", "-r", "crystalatte/data/cif/Ammonia"])
subprocess.call(["rm", "crystalatte/data/cif/Ammonia.xyz"])
