def testTCLTruncateSegname(self):
# Tests providing a chain_id that is longer than one character
try:
# easier to run_kmc to create monomer_list than recreate it here (adj easier) so doing so
# minimize random calls by providing set list of monomer types
initial_mono_type_list = [S, S, G, S, S, S, G, S]
num_monos = len(initial_mono_type_list)
initial_monomers = [
Monomer(mono_type, i)
for i, mono_type in enumerate(initial_mono_type_list)
]
initial_events = create_initial_events(initial_monomers,
DEF_RXN_RATES)
initial_state = create_initial_state(initial_events,
initial_monomers)
# since GROW is not added to event_dict, no additional monomers will be added
result = run_kmc(DEF_RXN_RATES,
initial_state,
sorted(initial_events),
t_max=2,
random_seed=8)
# quick tests to make sure run_kmc gives expected results (not what we want to test here)
# self.assertAlmostEqual(result[TIME][-1], 0.000766574526703574)
self.assertTrue(len(result[MONO_LIST]) == num_monos)
# the function we want to test here is below
with capture_stderr(gen_tcl,
result[ADJ_MATRIX],
result[MONO_LIST],
chain_id="lignin",
out_dir=SUB_DATA_DIR) as output:
self.assertTrue("should be one character" in output)
self.assertFalse(diff_lines(TCL_FILE_LOC, GOOD_TCL_SHORT))
finally:
silent_remove(TCL_FILE_LOC, disable=DISABLE_REMOVE)
pass
def testBadAtomIni(self):
test_input = ["-c", BAD_ATOM_INI]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Atom types do not match" in output)
silent_remove(PDB_OUT, disable=DISABLE_REMOVE)
def testNoTplIni(self):
test_input = ["-c", NO_TPL_INI]
try:
main(test_input)
self.assertFalse(diff_lines(PDB_OUT, GOOD_NO_TPL_OUT))
finally:
silent_remove(PDB_OUT, disable=DISABLE_REMOVE)
def testDyn4(self):
# also has multiple sg_ratio
expected_files = [BOND_V_STEP_PNG, MONO_V_STEP_PNG]
try:
for fname in expected_files:
silent_remove(fname)
test_input = [
"-r", "10", "-i", "3", "-m", "20", "-dy", "-a", "1e6", "-n",
"4", "-x"
]
# main(test_input)
with capture_stdout(main, test_input) as output:
self.assertTrue(
"BO4: 2 BB: 7 B5: 2 B1: 0 5O4: 2 AO4: 0 "
" 55: 0" in output)
self.assertTrue(
"BO4: 6 BB: 3 B5: 4 B1: 0 5O4: 4 AO4: 0 "
" 55: 0" in output)
self.assertTrue(
"BO4: 5 BB: 2 B5: 6 B1: 0 5O4: 2 AO4: 0 "
" 55: 1" in output)
self.assertTrue(
"BO4: 7 BB: 5 B5: 2 B1: 0 5O4: 5 AO4: 0 "
" 55: 0" in output)
for fname in expected_files:
self.assertTrue(os.path.isfile(fname))
finally:
for fname in expected_files:
silent_remove(fname, disable=DISABLE_REMOVE)
pass
def testWrongDir(self):
test_input = ["-d", "ghost"]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Could not find" in output)
silent_remove(FOR_HARTREE_DIR, disable=DISABLE_REMOVE)
def testLastIni(self):
test_input = ["-c", LAST_INI]
try:
main(test_input)
self.assertFalse(diff_lines(PDB_OUT, GOOD_PDB_LAST_OUT))
finally:
silent_remove(PDB_OUT, disable=DISABLE_REMOVE)
def testProduction(self):
# new_out_dir = os.path.join(DATA_DIR, 'new_plots')
plot_input = [
"-x",
"-p",
# next line: testing
"-i",
"5",
"-m",
"100",
"-a",
"1",
"-sg",
"1, 10",
"-n",
"3",
"-d",
TEMP_DIR,
# # alt lines: production
# "-i", "2", "-m", "500", "-l", "1e5", "-a", "1e8, 1e6, 1e4, 1e2, 1",
# "-sg", "0.1, 0.2, 0.25, 0.33, 0.5, 1, 2, 3, 4, 5, 10", "-n", "100", "-d", new_out_dir,
]
try:
with capture_stderr(main, plot_input) as output:
self.assertFalse(output)
finally:
silent_remove(TEMP_DIR,
dir_with_files=True,
disable=DISABLE_REMOVE)
pass
def testSubmitMultIni(self):
# Create and submit more than one ini
temp_file_list = [
'ethylrad.com', 'ircr.tpl', 'ircf.tpl', 'opt.tpl', 'ethylrad.chk'
]
for fname in temp_file_list:
with open(fname, 'w') as f:
f.write("# for test only\n")
test_input = ['ethylrad', "-c", SETUP_IRCS_INI, "-s", "-n"]
try:
main(test_input)
self.assertFalse(
diff_lines(SETUP_IRCR_INI_OUT, GOOD_SETUP_IRCR_INI_OUT))
self.assertFalse(
diff_lines(SETUP_IRCR_SLM_OUT, GOOD_SETUP_IRCR_SLM_OUT))
self.assertFalse(
diff_lines(SETUP_IRCF_INI_OUT, GOOD_SETUP_IRCF_INI_OUT))
self.assertFalse(
diff_lines(SETUP_IRCF_SLM_OUT, GOOD_SETUP_IRCF_SLM_OUT))
finally:
for fname in temp_file_list + [
SETUP_IRCR_INI_OUT, SETUP_IRCR_SLM_OUT, SETUP_IRCF_INI_OUT,
SETUP_IRCF_SLM_OUT
]:
silent_remove(fname, disable=DISABLE_REMOVE)
pass
def testNoGrowth(self):
# Here, all the monomers are available at the beginning of the simulation
try:
# minimize random calls by providing set list of monomer types
mono_type_list = [
S, S, S, S, G, S, S, S, S, S, S, G, S, S, S, S, S, S, S, S, S,
S, S, S
]
random_num = 24
initial_monomers = [
Monomer(mono_type, i)
for i, mono_type in enumerate(mono_type_list)
]
initial_events = create_initial_events(initial_monomers,
DEF_RXN_RATES)
initial_state = create_initial_state(initial_events,
initial_monomers)
# since GROW is not added to event_dict, no additional monomers will be added
result = run_kmc(DEF_RXN_RATES,
initial_state,
sorted(initial_events),
t_max=0.0001,
random_seed=random_num)
gen_tcl(result[ADJ_MATRIX],
result[MONO_LIST],
tcl_fname=TCL_FNAME,
chain_id="L",
out_dir=SUB_DATA_DIR)
self.assertFalse(diff_lines(TCL_FILE_LOC, GOOD_TCL_NO_GROW_OUT))
finally:
silent_remove(TCL_FILE_LOC, disable=DISABLE_REMOVE)
pass
def testTCLGenEmptySegname(self):
# tcl_fname="psfgen.tcl", psf_fname='lignin', chain_id="L", toppar_dir="toppar/"
# Here, all the monomers are available at the beginning of the simulation
# Increases coverage of gen_tcl
try:
# easier to run_kmc to create monomer_list than recreate it here (adj easier) so doing so
# minimize random calls by providing set list of monomer types
initial_mono_type_list = [S, S, G, S, S, S, G, S]
num_monos = len(initial_mono_type_list)
initial_monomers = [Monomer(mono_type, i) for i, mono_type in enumerate(initial_mono_type_list)]
initial_events = create_initial_events(initial_monomers, DEF_RXN_RATES)
initial_state = create_initial_state(initial_events, initial_monomers)
# since GROW is not added to event_dict, no additional monomers will be added
result = run_kmc(DEF_RXN_RATES, initial_state, sorted(initial_events), t_max=2, random_seed=8)
# quick tests to make sure run_kmc gives expected results (not what we want to test here)
self.assertAlmostEqual(result[TIME][-1], 0.00015059250794459398)
self.assertTrue(len(result[MONO_LIST]) == num_monos)
# the function we want to test here is below
with capture_stderr(gen_tcl, result[ADJ_MATRIX], result[MONO_LIST], chain_id=" ",
out_dir=SUB_DATA_DIR) as output:
self.assertTrue("should be one character" in output)
self.assertFalse(diff_lines(TCL_FILE_LOC, GOOD_TCL_SHORT))
finally:
silent_remove(TCL_FILE_LOC, disable=DISABLE_REMOVE)
pass
def testRouteNoChargeTpl(self):
test_input = ["-t", ROUTE_NO_CHARGE_TPL, "-f", CP_COM_IN, "-c"]
try:
main(test_input)
self.assertFalse(diff_lines(CP_COM_OUT, GOOD_ROUTE_ONLY_COM_OUT))
finally:
silent_remove(CP_COM_OUT, disable=DISABLE_REMOVE)
pass
def testFromFileCase(self):
test_input = ["-t", TPL_FILE, "-f", COM_IN_NO_CHARGE_FILE]
try:
main(test_input)
self.assertFalse(diff_lines(MISSING_MULT_COM_OUT_FILE, GOOD_COM_OUT_FILE))
finally:
silent_remove(MISSING_MULT_COM_OUT_FILE, disable=DISABLE_REMOVE)
pass
def testFileCPTpl(self):
test_input = ["-t", CP_COM_TPL, "-f", CP_COM_IN]
try:
main(test_input)
self.assertFalse(diff_lines(CP_COM_OUT, GOOD_CP_COM_OUT))
finally:
silent_remove(CP_COM_OUT, disable=DISABLE_REMOVE)
pass
def testPinnedTpl(self):
test_input = ["-t", PINNED_TPL_FILE, "-f", COM_IN_FILE]
try:
main(test_input)
self.assertFalse(diff_lines(COM_OUT_FILE, GOOD_PINNED_OUT_FILE))
finally:
silent_remove(COM_OUT_FILE, disable=DISABLE_REMOVE)
pass
def testConflictingOptions(self):
test_input = ["-s", "-z"]
# main(test_input)
# if logger.isEnabledFor(logging.DEBUG):
# main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Choose either" in output)
silent_remove(FOR_HARTREE_DIR, disable=DISABLE_REMOVE)
def testMultPDB(self):
test_input = ["-c", MULT_PDB_INI]
try:
main(test_input)
self.assertFalse(diff_lines(MULT_PDB_OUT, GOOD_MULT_PDB_OUT))
finally:
silent_remove(MULT_PDB_OUT, disable=DISABLE_REMOVE)
pass
def testFragments(self):
test_input = ["-t", LOW_E_TPL, "-f", FRAG_LOG_FILE]
try:
main(test_input)
self.assertFalse(diff_lines(FRAG_COM_OUT, GOOD_FRAG_COM_OUT))
finally:
silent_remove(FRAG_COM_OUT, disable=DISABLE_REMOVE)
pass
def testTemplateTypeMatching(self):
test_input = ["-t", TYPE_MATCH_TPL, "-f", TYPE_MATCH_LOG, "-e"]
try:
main(test_input)
self.assertFalse(diff_lines(TYPE_MATCH_OUT, GOOD_TYPE_MATCH_OUT))
finally:
silent_remove(TYPE_MATCH_OUT, disable=DISABLE_REMOVE)
pass
def testLowEn(self):
test_input = ["-t", LOW_E_TPL, "-f", LOG_LOW_E_FILE, "-e"]
try:
main(test_input)
self.assertFalse(diff_lines(COM_LOW_E_OUT, GOOD_COM_LOW_E_FILE))
finally:
silent_remove(COM_LOW_E_OUT, disable=DISABLE_REMOVE)
pass
def testSingle(self):
test_input = ["-c", SINGLE_INI]
try:
main(test_input)
self.assertFalse(diff_lines(SINGLE_OUT, GOOD_SINGLE_OUT))
finally:
silent_remove(SINGLE_OUT, disable=DISABLE_REMOVE)
pass
def testMultipleHeaderLinesIni(self):
test_input = ["-c", MORE_HEADER_LINES_INI]
try:
main(test_input)
self.assertFalse(diff_lines(PDB_MULT_HEADER_OUT, GOOD_PDB_OUT))
finally:
silent_remove(PDB_MULT_HEADER_OUT, disable=DISABLE_REMOVE)
pass
def testComb2Ini(self):
test_input = ["-c", COMB2_INI, "-o", "pet_mono_test_comb.pdb"]
try:
main(test_input)
self.assertFalse(diff_lines(COMB_PDB_OUT, GOOD_COMB_PDB_OUT))
finally:
silent_remove(COMB_PDB_OUT, disable=DISABLE_REMOVE)
pass
def testAltIni(self):
test_input = ["-c", ALT_INI]
try:
main(test_input)
self.assertFalse(diff_lines(ALT_OUT, GOOD_ALT_OUT))
finally:
silent_remove(ALT_OUT, disable=DISABLE_REMOVE)
pass
def testFromPinnedAtomFileCase(self):
test_input = ["-t", TPL_FILE, "-f", PINNED_ATOM_IN]
try:
main(test_input)
self.assertFalse(diff_lines(PINNED_ATOM_OUT, GOOD_COM_OUT_FILE))
finally:
silent_remove(PINNED_ATOM_OUT, disable=DISABLE_REMOVE)
pass
def testFirstIni(self):
test_input = ["-c", DEF_INI, "-a", "-o", 'pet_mono_f1hs_0.pdb']
try:
main(test_input)
self.assertFalse(diff_lines(ALT_PDB_OUT, GOOD_PDB_FIRST_OUT))
finally:
silent_remove(ALT_PDB_OUT, disable=DISABLE_REMOVE)
pass
def testSaveSmi(self):
try:
test_input = ["-r", "10", "-o", TEST_SMI_BASENAME, "-d", SUB_DATA_DIR, "-a", "1.0"]
main(test_input)
self.assertFalse(diff_lines(TEST_SMI_OUT, GOOD_TEST_SMI_OUT))
finally:
silent_remove(TEST_SMI_OUT, disable=DISABLE_REMOVE)
pass
def testTCLGenOptions(self):
try:
test_input = ["-r", "8", "-i", "4", "-m", "4", "-f", "tcl", "-d", SUB_DATA_DIR,
"--chain_id", "1", "--psf_fname", "birch", "--toppar_dir", "", "-a", "1.0", "-x"]
main(test_input)
self.assertFalse(diff_lines(DEF_TCL_OUT, GOOD_TCL_OPTIONS_OUT))
finally:
silent_remove(DEF_TCL_OUT, disable=DISABLE_REMOVE)
pass
def testDirInBasename(self):
# This should ignore the temp_dir; will throw error if it doesn't
try:
test_input = ["-r", "10", "-o", TEST_SMI_OUT, "-d", TEMP_DIR, "-a", "1.0"]
main(test_input)
self.assertFalse(diff_lines(TEST_SMI_OUT, GOOD_TEST_SMI_OUT))
finally:
silent_remove(TEST_SMI_OUT, disable=DISABLE_REMOVE)
pass
def testMixMatchTheory(self):
test_input = [UNI_REACT, UNI_TS]
try:
# main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Different basis sets" in output)
finally:
silent_remove(GOODVIBES_CSV, disable=DISABLE_REMOVE)
pass
def testFirstOnly(self):
test_input = ["-c", MULTI_FIRST_ONLY_INI]
try:
main(test_input)
self.assertFalse(diff_lines(REMOVE_H_OUT1, GOOD_KEEP_H_OUT1))
self.assertFalse(diff_lines(GAU_OUT1, GOOD_GAU_OUT1))
finally:
silent_remove(REMOVE_H_OUT1, disable=DISABLE_REMOVE)
silent_remove(GAU_OUT1, disable=DISABLE_REMOVE)
