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 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)
def testSetupSubmit(self):
test_input = [ETHYLRAD, "-s", "-c", SETUP_SUBMIT_INI, "-n"]
try:
main(test_input)
self.assertFalse(diff_lines(SPAWN0_INI, GOOD_SETUP_INI_OUT))
self.assertFalse(diff_lines(SPAWN0_SLURM, GOOD_SETUP_SLURM_OUT))
finally:
for fname in [SPAWN0_INI, SPAWN0_SLURM]:
silent_remove(fname, disable=DISABLE_REMOVE)
pass
def testSetupOneJobIni(self):
test_input = [ETHYLRAD, "-c", ONE_JOB_INI, "-t", "-s"]
try:
main(test_input)
self.assertFalse(diff_lines(ONE_INI_OUT, GOOD_ONE_INI_OUT))
self.assertFalse(diff_lines(ONE_SLM_OUT, GOOD_ONE_SLM_OUT))
finally:
silent_remove(ONE_INI_OUT, disable=DISABLE_REMOVE)
silent_remove(ONE_SLM_OUT, disable=DISABLE_REMOVE)
pass
def testFromListCase(self):
test_input = ["-t", TPL_FILE, "-l", LIST_FILE, "-c"]
try:
main(test_input)
self.assertFalse(diff_lines(COM_OUT_FILE, GOOD_COM_OUT_FILE))
self.assertFalse(diff_lines(COM_OUT_FILE2, GOOD_COM_OUT_FILE2))
finally:
silent_remove(COM_OUT_FILE, disable=DISABLE_REMOVE)
silent_remove(COM_OUT_FILE2, disable=DISABLE_REMOVE)
pass
def testMultIni(self):
test_input = ["-c", MULT_INI]
try:
main(test_input)
self.assertFalse(diff_lines(PDB_OUT, GOOD_PDB_LAST_OUT))
self.assertFalse(diff_lines(PDB2_OUT, GOOD_PDB2_LAST_OUT))
finally:
silent_remove(PDB_OUT, disable=DISABLE_REMOVE)
silent_remove(PDB2_OUT, disable=DISABLE_REMOVE)
pass
def testNTripleBond(self):
test_input = ["-c", N_TRIPLE_BOND_INI]
try:
main(test_input)
self.assertFalse(diff_lines(CP_N_OUT, GOOD_CP_N_OUT))
self.assertFalse(diff_lines(F2_N_OUT, GOOD_F2_N_OUT))
finally:
silent_remove(CP_N_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_N_OUT, disable=DISABLE_REMOVE)
pass
def testCPTpl(self):
test_input = ["-t", CP_COM_TPL, "-l", LOG_LIST, "-c"]
try:
main(test_input)
self.assertFalse(diff_lines(COM1_OUT, GOOD_COM1_OUT))
self.assertFalse(diff_lines(COM2_OUT, GOOD_COM2_OUT))
finally:
silent_remove(COM1_OUT, disable=DISABLE_REMOVE)
silent_remove(COM2_OUT, disable=DISABLE_REMOVE)
pass
def testDefIni(self):
test_input = ["-c", DEF_INI]
try:
main(test_input)
self.assertFalse(diff_lines(GAU_OUT1, GOOD_GAU_OUT1))
self.assertFalse(diff_lines(GAU_OUT2, GOOD_GAU_OUT2))
self.assertFalse(diff_lines(GAU_OUT3, GOOD_GAU_OUT3))
finally:
silent_remove(GAU_OUT1, disable=DISABLE_REMOVE)
silent_remove(GAU_OUT2, disable=DISABLE_REMOVE)
silent_remove(GAU_OUT3, disable=DISABLE_REMOVE)
def testRemoveH(self):
test_input = ["-c", REMOVE_H_INI]
try:
main(test_input)
self.assertFalse(diff_lines(REMOVE_H_OUT1, GOOD_REMOVE_H_OUT1))
self.assertFalse(diff_lines(REMOVE_H_OUT2, GOOD_REMOVE_H_OUT2))
self.assertFalse(diff_lines(REMOVE_H_OUT3, GOOD_REMOVE_H_OUT3))
finally:
silent_remove(REMOVE_H_OUT1, disable=DISABLE_REMOVE)
silent_remove(REMOVE_H_OUT2, disable=DISABLE_REMOVE)
silent_remove(REMOVE_H_OUT3, disable=DISABLE_REMOVE)
def testSepMolecules(self):
# to help when there is a reactant or product complex that is two different molecules; ignores the
# larger distance between the atoms belonging to two different molecules
test_input = ["-c", IGNORE_MAX_INI]
try:
main(test_input)
self.assertFalse(diff_lines(CP_TPA_OUT, GOOD_CP_TPA_OUT))
self.assertFalse(diff_lines(F2_TPA_OUT, GOOD_F2_TPA_OUT))
finally:
silent_remove(CP_TPA_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_TPA_OUT, disable=DISABLE_REMOVE)
pass
def testCommandLineOptions(self):
test_input = ["-t", "tests/test_data/pdbs2gausscoms/gau.tpl",
"-l", "tests/test_data/pdbs2gausscoms/pdb_list.txt"]
try:
main(test_input)
self.assertFalse(diff_lines(GAU_OUT1, GOOD_GAU_OUT1))
self.assertFalse(diff_lines(GAU_OUT2, GOOD_GAU_OUT2))
self.assertFalse(diff_lines(GAU_OUT3, GOOD_GAU_OUT3))
finally:
silent_remove(GAU_OUT1, disable=DISABLE_REMOVE)
silent_remove(GAU_OUT2, disable=DISABLE_REMOVE)
silent_remove(GAU_OUT3, disable=DISABLE_REMOVE)
def testMetalBond(self):
# Uses a longer bond cut-off when one of the atoms is a metal
test_input = ["-c", METAL_BOND_INI]
try:
main(test_input)
self.assertFalse(diff_lines(CP_METAL_OUT, GOOD_CP_METAL_OUT))
self.assertFalse(diff_lines(F1_METAL_OUT, GOOD_F1_METAL_OUT))
self.assertFalse(diff_lines(F2_METAL_OUT, GOOD_F2_METAL_OUT))
finally:
silent_remove(CP_METAL_OUT, disable=DISABLE_REMOVE)
silent_remove(F1_METAL_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_METAL_OUT, disable=DISABLE_REMOVE)
pass
def testNTripleBondSubDir(self):
# Test that output files were created in subdir
test_input = ["-c", N_TRIPLE_BOND_SUB_DIR_INI]
try:
silent_remove(TEMP_DIR, dir_with_files=True)
main(test_input)
self.assertFalse(diff_lines(CP_N_OUT_SUB_DIR, GOOD_CP_N_OUT))
self.assertFalse(diff_lines(F2_N_OUT_SUB_DIR, GOOD_F2_N_OUT))
finally:
silent_remove(TEMP_DIR,
disable=DISABLE_REMOVE,
dir_with_files=True)
pass
def testDefIni(self):
test_input = [ETHYLRAD, "-c", DEF_INI, "-t"]
try:
main(test_input)
self.assertFalse(diff_lines(DEF_SH_OUT, GOOD_SH_OUT))
self.assertFalse(diff_lines(OPT_SH_OUT, GOOD_OPT_SH_OUT))
self.assertFalse(
diff_lines(OPT_STABLE_SH_OUT, GOOD_OPT_STABLE_SH_OUT))
finally:
for file in [
DEF_SH_OUT, DEF_LOG_OUT, OPT_SH_OUT, OPT_STABLE_SH_OUT
]:
silent_remove(file, disable=DISABLE_REMOVE)
pass
def testDubO(self):
test_input = ["-c", DIMER_INI]
try:
main(test_input)
self.assertFalse(diff_lines(CP_DI_18_24_OUT, GOOD_CP_DI_18_24_OUT))
self.assertFalse(diff_lines(F2_DI_18_24_OUT, GOOD_F2_DI_18_24_OUT))
self.assertFalse(diff_lines(CP_DI_18_16_OUT, GOOD_CP_DI_18_16_OUT))
self.assertFalse(diff_lines(F1_DI_18_16_OUT, GOOD_F1_DI_18_16_OUT))
self.assertFalse(diff_lines(F2_DI_18_16_OUT, GOOD_F2_DI_18_16_OUT))
finally:
silent_remove(CP_DI_18_24_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_DI_18_24_OUT, disable=DISABLE_REMOVE)
silent_remove(CP_DI_18_16_OUT, disable=DISABLE_REMOVE)
silent_remove(F1_DI_18_16_OUT, disable=DISABLE_REMOVE)
silent_remove(F2_DI_18_16_OUT, disable=DISABLE_REMOVE)
pass
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 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 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 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 testFindNodeProc(self):
test_input = [ETHYLRAD, "-c", SETUP_GET_PROCS_INI, "-t"]
try:
# main(test_input)
with capture_stdout(main, test_input) as output:
# each assert from a different print command
self.assertTrue("the whole node will" in output)
self.assertFalse("Will allocate up to 63124196 kB" in output)
self.assertTrue("0-35" in output)
self.assertTrue("user may override these" in output)
self.assertFalse(diff_lines(DEF_SH_OUT, GOOD_PROC_SH_OUT))
self.assertFalse(diff_lines(OPT_SH_OUT, GOOD_PROC_OPT_SH_OUT))
finally:
for fname in [DEF_SH_OUT, OPT_SH_OUT]:
silent_remove(fname, 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 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 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 testSpecify2SetsCommandLine(self):
# As ALT_INI, but command-line only
# make sure old files are cleaned up before starting
for fname in [REMOVE_H_OUT1, REMOVE_H_OUT2, REMOVE_H_OUT3]:
silent_remove(fname)
test_input = ["-t", 'tests/test_data/pdbs2gausscoms/gau.tpl',
'-f', 'tests/test_data/pdbs2gausscoms/pet_mono_f1hs.pdb', "-r", "-n", "2"]
try:
main(test_input)
self.assertFalse(diff_lines(REMOVE_H_OUT1, GOOD_REMOVE_H_OUT1))
self.assertFalse(diff_lines(REMOVE_H_OUT2, GOOD_REMOVE_H_OUT2))
self.assertFalse(os.path.isfile(REMOVE_H_OUT3))
finally:
silent_remove(REMOVE_H_OUT1, disable=DISABLE_REMOVE)
silent_remove(REMOVE_H_OUT2, 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 testLink0Ini(self):
test_input = ["-c", LINK0_INI]
try:
main(test_input)
self.assertFalse(diff_lines(PDB_LINK0_OUT, GOOD_PDB_OUT))
finally:
silent_remove(PDB_LINK0_OUT, 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 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 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