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 testB1BondGenMol(self):
ini_mono_type_list = [S, S, S, G, S]
sg_ratio = 1.0
max_monos = 12
random_num = 55
initial_monomers = [
Monomer(mono_type, i)
for i, mono_type in enumerate(ini_mono_type_list)
]
initial_events = create_initial_events(initial_monomers, DEF_RXN_RATES)
initial_events.append(Event(GROW, [], rate=1e4))
initial_state = create_initial_state(initial_events, initial_monomers)
result = run_kmc(DEF_RXN_RATES,
initial_state,
initial_events,
n_max=max_monos,
t_max=2,
random_seed=random_num,
sg_ratio=sg_ratio)
nodes = result[MONO_LIST]
adj = result[ADJ_MATRIX]
# generate_mol(adj, nodes)
with capture_stderr(generate_mol, adj, nodes) as output:
self.assertFalse(output)
mol = MolFromMolBlock(generate_mol(adj, nodes))
mols = GetMolFrags(mol)
analysis = analyze_adj_matrix(adj)
frag_sizes = analysis[CHAIN_LEN]
# Make sure there are the same number of separate fragments calculated by RDKIT
# as we get from just separating the alternate B1
self.assertEqual(np.sum(list(frag_sizes.values())), len(mols))
def testMissingTpl(self):
test_input = ["-f", LOG_FILE, "-c"]
# main(test_input)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("No template file" in output)
def testMissingJobTpl(self):
test_input = [ETHYLRAD, "-c", MISSING_JOB_TPL_INI]
# main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue(
"For job 'stable', could not find a template file 'stable.tpl"
in output)
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 testSortByEnthalpy(self):
test_input = ["-l", LOG_LIST, '-n']
good_output = ''.join([HEADER, LME2_TS3, LME2_25_T]) + '\n'
with capture_stdout(main, test_input) as output:
self.assertTrue(good_output in output)
with capture_stderr(main, test_input) as output:
self.assertTrue('Check convergence' in output)
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 testNoScanInfo(self):
no_scan_log = os.path.join(SUB_DATA_DIR, 'me2propprpnt_7.log')
test_input = ["-f", no_scan_log, "--scan", "test.png"]
# main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue(
"Did not find expected parameter scan info" in output)
def testNonIntLastStepNum(self):
test_input = ["-t", "ghost"]
# main(test_input)
# if logger.isEnabledFor(logging.DEBUG):
# main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("integer must be provided" in output)
def testNoArgs(self):
test_input = []
# main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("required" in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testNoSuchFile(self):
test_input = ["ghost.log"]
# main(test_input)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Could not find" in output)
def testMissingValue(self):
test_input = [TEST_LOG1, "-c"]
# main(test_input)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("expected one argument" in output)
def testNoSMI(self):
test_input = ['-t', GAU_TPL]
# main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("SMILES " in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testNoLastStepNum(self):
test_input = ["-t"]
# main(test_input)
# if logger.isEnabledFor(logging.DEBUG):
# main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("expected one argument" in output)
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 testNoArgs(self):
with capture_stderr(main, []) as output:
self.assertTrue(
"WARNING: Problems reading file: Could not read file" in
output)
with capture_stdout(main, []) as output:
self.assertTrue("optional arguments" in output)
def testFewerMaxThanIniMonos(self):
test_input = ["-r", "10", "-i", "6", "-m", "4"]
# main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue('is less than' in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("Lignin KMC created 6 monomers" in output)
def testCP(self):
test_input = [TEST_LOG5, "--cpu"]
# main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Could not find frequency" in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("0 days 0 hrs 27 mins 11 secs" in output)
def testHelp(self):
test_input = ['-h']
# main(test_input)
with capture_stderr(main, test_input) as output:
self.assertFalse(output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testMissingListIni(self):
test_input = [ETHYLRAD, "-c", MISSING_TPL_INI]
# main(test_input)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("not find the submit template" in output)
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 testMissingFile(self):
test_input = ["-t", TPL_FILE, "-f", "ghost.txt"]
# main(test_input)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Problems reading file" in output)
def testNoFilesToProcess(self):
test_input = ["-t", TPL_FILE]
main(test_input)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("No files have been specified to be read" in output)
def testNotIni(self):
# gracefully fail if give the wrong file to the -c option
test_input = ["-c", GOOD_PDB_OUT]
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue(
"WARNING: File contains no section headers" in output)
def testHelp(self):
test_input = ['-h']
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertFalse(output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testUnknownArg(self):
test_input = ['--ghost']
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("unrecognized arguments" in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testCheckForValenceError(self):
random_seed = 1
test_input = ["-i", "5", "-m", "200", "-a", "1", "-sg", "1, 3, 5, 10", "-n", "3", "-r", str(random_seed)]
# main(test_input)
with capture_stderr(main, test_input) as output:
if output:
print("Encountered error:\n", output)
self.assertFalse(output)
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 testNoneFloatVib(self):
test_input = ["-l", TPA_LIST, "-d", SUB_DATA_DIR, "-t", "-v", "ghost"]
# main(test_input)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("not convert string" in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
def testBadConfigFile(self):
test_input = ["-c", "ghost.ini"]
# main(test_input)
if logger.isEnabledFor(logging.DEBUG):
main(test_input)
with capture_stderr(main, test_input) as output:
self.assertTrue("Could not find specified configuration file" in output)
with capture_stdout(main, test_input) as output:
self.assertTrue("optional arguments" in output)
