def test_init_threads_restart(self):
"""Tests successful initialization of restarted threads"""
settings = configure('../../data/atesa.config')
# First, make restart.pkl
settings.degeneracy = 1
settings.initial_coordinates = [
'../test_data/test.rst7', '../test_data/test_two_init.rst7'
]
settings.rc_definition = '1.00 + 2.34*CV0 - 5.67*CV1'
settings.rc_reduced_cvs = False
settings.cvs = [
'pytraj.distance(traj, \'@1 @2\')[0]',
'pytraj.angle(traj, \'@2 @3 @4\')[0]'
]
settings.include_qdot = False
settings.topology = '../test_data/test.prmtop'
allthreads = main.init_threads(settings)
allthreads[0].history.init_coords = [
[
'../test_data/test_velocities_init.rst7',
'../test_data/test_velocities_init_bwd.rst7'
],
[
'../test_data/test_two_init.rst7',
'../test_data/test_two_init_bwd.rst7'
]
]
allthreads[0].history.prod_results = [['fwd', 'bwd'], ['bwd', 'bwd']]
allthreads[1].history.init_coords = [
[
'../test_data/test_velocities_init.rst7',
'../test_data/test_velocities_init_bwd.rst7'
],
[
'../test_data/test_two_init.rst7',
'../test_data/test_two_init_bwd.rst7'
]
]
allthreads[1].history.prod_results = [['bwd', 'bwd'], ['fwd', 'bwd']]
allthreads[0].history.timestamps = [1, 3]
allthreads[1].history.timestamps = [2, 4]
pickle.dump(allthreads, open('restart.pkl', 'wb'), protocol=2)
# Then, reset settings, set restart = True, and try again
settings = configure('../../data/atesa.config')
settings.restart = True
settings.degeneracy = 1
allthreads = main.init_threads(settings)
assert len(allthreads) == 2
assert allthreads[0].history.prod_results == [['fwd', 'bwd'],
['bwd', 'bwd']]
assert allthreads[1].history.prod_results == [['bwd', 'bwd'],
['fwd', 'bwd']]
assert allthreads[0].topology == 'test.prmtop'
assert allthreads[1].topology == 'test.prmtop'
def test_main(self):
"""Tests information_error.main using sham shooting points in test_data"""
settings = configure('../../data/atesa.config')
settings.topology = '../test_data/test.prmtop'
settings.cvs = ['pytraj.distance(traj, \'@1 @2\')[0]', 'pytraj.angle(traj, \'@2 @3 @4\')[0]']
settings.include_qdot = False
settings.DEBUG = True # to skip resampling and substitute our own as_decorr.out file
shutil.copy('../test_data/test_velocities_init.rst7', '../test_temp')
shutil.copy('../test_data/test_two_init.rst7', '../test_temp')
shutil.copy('../test_data/as.out', '../test_temp')
shutil.copy('../test_data/as_big.out', 'as_decorr_6054.out')
# First test without extant settings.pkl file
with pytest.raises(FileNotFoundError):
information_error.main()
settings.__dict__.pop('env') # env attribute is not picklable
pickle.dump(settings, open('settings.pkl', 'wb'), protocol=2) # main will look for this file to load in settings
shutil.copy('../test_data/as_big.out', 'as_decorr_6054.out')
information_error.main()
assert os.path.exists('info_err.out')
assert float(open('info_err.out', 'r').readlines()[0].split(' ')[0]) == 6054
assert float('%.2f' % float(open('info_err.out', 'r').readlines()[0].split(' ')[1])) == pytest.approx(0.16, 1E-2)
def test_algorithm_aimless_shooting_prod_always_new_not_accepted(self):
"""Tests algorithm with job_type = 'aimless_shooting', always_new = True and thread.current_type =
['prod', 'prod'] for a move that isn't accepted"""
settings = configure('../../data/atesa.config')
settings.job_type = 'aimless_shooting'
settings.topology = '../test_data/test.prmtop'
settings.always_new = True
settings.initial_coordinates = ['../test_data/test_velocities.rst7']
settings.min_dt = -1
settings.max_dt = -1 # set these to the same value to guarantee which frame is chosen
allthreads = main.init_threads(settings)
allthreads[0].current_type = ['prod', 'prod']
allthreads[0].history.prod_results = [['bwd', 'fwd'], ['fwd', 'fwd']
] # accepted then not accepted
allthreads[0].history.prod_trajs = [[
'../test_data/test.nc', '../test_data/test.nc'
], ['../test_data/test.nc', '../test_data/test.nc']]
allthreads[0].suffix = 1
allthreads[0].history.last_accepted = 0
jobtype = factory.jobtype_factory(settings.job_type)
jobtype.algorithm(allthreads[0], allthreads, allthreads, settings)
assert filecmp.cmp(
allthreads[0].history.init_inpcrd[1],
'../test_data/test.rst7') # test.rst7 is last frame of test.nc
os.remove(
'../test_data/test.nc_frame_-1.rst7'
) # have to do this manually because aimless shooting's mdengine getframe method keeps the '../test_data/' in front of the file name
def config_equilibrium_path_sampling():
"""Sets up configuration settings for equilibrium path sampling tests, to be overwritten as needed"""
shutil.copy('../../data/atesa.config', 'eps.config')
with open('eps.config',
'a') as f: # need to set these things before calling configure()
f.write('\njob_type = \'equilibrium_path_sampling\'')
f.write('\neps_rc_min = -50'
) # crazy wide range so everything gets included
f.write('\neps_rc_max = 50')
f.write('\neps_rc_step = 1')
f.write('\neps_rc_overlap = 0.1')
f.write('\neps_n_steps = 6')
f.write('\neps_out_freq = 1')
f.write('\neps_dynamic_seed = 3')
f.write('\nsamples_per_window = -1')
f.close()
settings = configure('eps.config')
settings.DEBUG = True
settings.job_type = 'equilibrium_path_sampling'
settings.topology = '../test_data/test.prmtop'
settings.rc_reduced_cvs = False
settings.include_qdot = False
settings.cvs = [
'pytraj.distance(traj, \'@1 @2\')[0]',
'pytraj.angle(traj, \'@2 @3 @4\')[0]'
]
settings.rc_definition = '1.00 + 2.34*CV1 - 0.67*CV2'
settings.initial_coordinates = ['../test_data/test.rst7']
return settings
def test_update_results_aimless_shooting_prod(self):
"""Tests update_results with job_type = 'aimless_shooting' and thread.current_type = ['prod', 'prod']"""
settings = configure('../../data/atesa.config')
settings.job_type = 'aimless_shooting'
settings.initial_coordinates = [
'../test_data/test_velocities.rst7',
'../test_data/test_velocities.rst7'
]
settings.topology = '../test_data/test.prmtop'
settings.commit_fwd = [[1, 2], [3, 4], [1.5, 2.0], ['lt', 'gt']]
settings.commit_bwd = [[1, 2], [3, 4], [2.0, 1.5], ['gt', 'lt']]
allthreads = main.init_threads(settings)
allthreads[0].current_type = ['prod', 'prod']
allthreads[0].history.prod_trajs = [[
'../test_data/test.nc', '../test_data/test.nc'
]]
allthreads[0].history.init_coords = [[
'test_velocities.rst7_0_init.rst7'
]]
shutil.copy(
'../test_data/test_velocities.rst7',
'test_velocities.rst7_0_init.rst7') # create the needed file
jobtype = factory.jobtype_factory(settings.job_type)
jobtype.update_results(allthreads[0], allthreads, settings)
assert os.path.exists('restart.pkl')
assert os.path.exists('status.txt')
assert allthreads[0].history.prod_results == [['', '']]
def test_interpret_cv(self):
"""Test interpret_cv for a distance, angle, dihedral, and difference of distances for both pytraj and mdtraj"""
settings = configure('../../data/atesa.config')
settings.cvs = [
'pytraj.distance(traj, \'@1 @2\')[0]',
'pytraj.angle(traj, \'@1 @2 @3\')[0]',
'pytraj.dihedral(traj, \'@1 @2 @3 @4\')[0]',
'pytraj.distance(traj, \'@1 @2\')[0] - pytraj.distance(traj, \'@3 @4\')[0]',
'mdtraj.compute_distances(mtraj, numpy.array([[83, 84]]))[0][0] * 10',
'mdtraj.compute_angles(mtraj, numpy.array([[83, 85, 86]]))[0][0] * 180 / numpy.pi',
'mdtraj.compute_dihedrals(mtraj, numpy.array([[84, 83, 85, 86]]))[0][0] * 180 / numpy.pi',
'(mdtraj.compute_distances(mtraj, numpy.array([[101, 103]]))[0][0] * 10) - (mdtraj.compute_distances(mtraj, numpy.array([[101, 104]]))[0][0] * 10)'
]
assert utilities.interpret_cv(1, settings) == (['1',
'2'], 'distance', 2)
assert utilities.interpret_cv(2, settings) == (['1', '2',
'3'], 'angle', 3)
assert utilities.interpret_cv(3, settings) == (['1', '2', '3',
'4'], 'dihedral', 4)
assert utilities.interpret_cv(4,
settings) == (['1', '2', '3',
'4'], 'diffdistance', 4)
assert utilities.interpret_cv(5, settings) == (['84',
'85'], 'distance', 2)
assert utilities.interpret_cv(6, settings) == (['84', '86',
'87'], 'angle', 3)
assert utilities.interpret_cv(7,
settings) == (['85', '84', '86',
'87'], 'dihedral', 4)
assert utilities.interpret_cv(
8, settings) == (['102', '104', '102', '105'], 'diffdistance', 4)
def test_algorithm_aimless_shooting_init(self):
"""Tests algorithm with job_type = 'aimless_shooting' and thread.current_type = ['init']"""
settings = configure('../../data/atesa.config')
settings.job_type = 'aimless_shooting'
settings.degeneracy = 1
settings.initial_coordinates = ['../test_data/test_velocities.rst7']
allthreads = main.init_threads(settings)
allthreads[0].current_type = ['init']
allthreads[0].history.init_coords = [[
'test_velocities.rst7_0_init.rst7'
]]
jobtype = factory.jobtype_factory(settings.job_type)
jobtype.algorithm(allthreads[0], allthreads, allthreads, settings)
assert allthreads[0].current_type == [
] # result for missing .rst7 file (haven't copied it yet)
allthreads[0].current_type = ['init'] # reset last result
shutil.copy(
'../test_data/test_velocities.rst7',
'test_velocities.rst7_0_init.rst7') # create the needed file
jobtype.algorithm(allthreads[0], allthreads, allthreads, settings)
assert allthreads[0].current_type == ['init'
] # results for .rst7 was found
assert allthreads[0].history.init_coords == [[
'test_velocities.rst7_0_init.rst7',
'test_velocities.rst7_0_init_bwd.rst7'
]]
def test_update_history_equilibrium_path_sampling_out_of_bounds(self):
"""Tests update_history with job_type = 'equilibrium_path_sampling' with an initially out-of-bounds RC value"""
shutil.copy('../../data/atesa.config', 'eps.config')
with open(
'eps.config', 'a'
) as f: # need to set these things before calling configure()
f.write('\njob_type = \'equilibrium_path_sampling\'')
f.write('\neps_rc_min = -0.1'
) # crazy wide range so everything gets included
f.write('\neps_rc_max = 0.1')
f.write('\neps_rc_step = 0.1')
f.write('\neps_overlap = 0.01')
f.write('\neps_dynamic_seed = 3')
f.close()
settings = configure('eps.config')
settings.DEBUG = True
settings.job_type = 'equilibrium_path_sampling'
settings.topology = '../test_data/test.prmtop'
settings.rc_reduced_cvs = False
settings.include_qdot = False
settings.cvs = [
'pytraj.distance(traj, \'@1 @2\')[0]',
'pytraj.angle(traj, \'@2 @3 @4\')[0]'
]
settings.rc_definition = '1.00 + 2.34*CV1 - 0.67*CV2'
settings.initial_coordinates = ['../test_data/test.rst7']
with pytest.raises(RuntimeError):
allthreads = main.init_threads(settings)
def test_check_commit_none(self):
"""Tests check_commit using a dummy coordinate file and commitments defined to get result ''"""
settings = configure('../../data/atesa.config')
settings.topology = '../test_data/test.prmtop'
settings.commit_fwd = [[1, 2], [3, 4], [1.0, 1.5], ['gt', 'lt']]
settings.commit_bwd = [[1, 2], [3, 4], [0.5, 2.0], ['lt', 'gt']]
assert utilities.check_commit('../test_data/test.rst7', settings) == ''
def test_check_commit_traj(self):
"""Tests check_commit using a dummy trajectory file and commitments defined to get result 'fwd'"""
settings = configure('../../data/atesa.config')
settings.topology = '../test_data/test.prmtop'
settings.commit_fwd = [[1, 2], [3, 4], [1.0, 1.7], ['gt', 'lt']]
settings.commit_bwd = [[1, 2], [3, 4], [0.5, 2.0], ['lt', 'gt']]
assert utilities.check_commit('../test_data/test.nc',
settings) == 'fwd'
def test_get_batch_file_aimless_shooting_broken(self):
"""Tests thread.get_batch_template with job_type = 'aimless_shooting' and invalid type = 'fwdd'"""
settings = configure('../../data/atesa.config')
settings.job_type = 'aimless_shooting'
settings.degeneracy = 1
allthreads = main.init_threads(settings)
with pytest.raises(ValueError):
allthreads[0].get_batch_template('fwdd', settings)
def test_get_next_step_aimless_shooting_prod(self):
"""Tests thread.get_next_step with job_type = 'aimless_shooting' and type = ['fwd','bwd']"""
settings = configure('../../data/atesa.config')
settings.degeneracy = 1
settings.job_type = 'aimless_shooting'
allthreads = main.init_threads(settings)
allthreads[0].current_type = ['prod', 'prod']
assert allthreads[0].get_next_step(settings) == (['init'], ['init'])
def test_check_for_successful_step_committor_analysis(self):
"""Tests check_for_successful_step with job_type = 'committor_analysis'"""
settings = configure('../../data/atesa.config')
settings.job_type = 'committor_analysis'
settings.committor_analysis_use_rc_out = False
allthreads = main.init_threads(settings)
jobtype = factory.jobtype_factory(settings.job_type)
assert jobtype.check_for_successful_step(allthreads[0],
settings) == True
def test_process_to_be_terminated(self):
"""Tests process.py for a thread with terminated = True"""
settings = configure('../../data/atesa.config')
settings.degeneracy = 1
allthreads = main.init_threads(settings)
allthreads[0].terminated = True
running = [allthreads[0]]
process(allthreads[0], running, settings)
assert running == []
def test_get_batch_file_aimless_shooting_amber(self):
"""Tests thread.get_batch_template with job_type = 'aimless_shooting' and md_engine = 'amber'"""
settings = configure('../../data/atesa.config')
settings.job_type = 'aimless_shooting'
settings.degeneracy = 1
settings.md_engine = 'amber'
allthreads = main.init_threads(settings)
assert allthreads[0].get_batch_template(
'init', settings) == 'amber_' + settings.batch_system + '.tpl'
def test_gatekeep_committor_analysis(self):
"""Tests gatekeep with job_type = 'committor_analysis'"""
settings = configure('../../data/atesa.config')
settings.job_type = 'committor_analysis'
settings.DEBUG = True
settings.committor_analysis_use_rc_out = False
allthreads = main.init_threads(settings)
allthreads[0].jobids = ['123456']
jobtype = factory.jobtype_factory(settings.job_type)
assert jobtype.gatekeeper(allthreads[0], settings) == True
def test_update_results_aimless_shooting_init(self):
"""Tests update_results with job_type = 'aimless_shooting' and thread.current_type = ['init']"""
settings = configure('../../data/atesa.config')
settings.job_type = 'aimless_shooting'
settings.degeneracy = 1
allthreads = main.init_threads(settings)
allthreads[0].current_type = ['init']
jobtype = factory.jobtype_factory(settings.job_type)
jobtype.update_results(allthreads[0], allthreads, settings)
assert os.path.exists('restart.pkl')
def test_main(self):
"""Tests main.main with DEBUG = True to skip actual job submission/monitoring"""
settings = configure('../../data/atesa.config')
settings.initial_coordinates = ['../test_data/test.rst7']
settings.topology = '../test_data/test.prmtop'
settings.degeneracy = 2
settings.overwrite = True
settings.resample = False
settings.DEBUG = True
assert main.main(settings) == 'ATESA run exiting normally'
def test_gatekeep_aimless_shooting(self):
"""Tests gatekeep with job_type = 'aimless_shooting'"""
settings = configure('../../data/atesa.config')
settings.job_type = 'aimless_shooting'
settings.degeneracy = 1
settings.DEBUG = True
allthreads = main.init_threads(settings)
allthreads[0].jobids = ['123456']
jobtype = factory.jobtype_factory(settings.job_type)
assert jobtype.gatekeeper(allthreads[0], settings) == True
def test_check_termination_aimless_shooting_init(self):
"""Tests check_termination with job_type = 'aimless_shooting' and thread.current_type = ['init']"""
settings = configure('../../data/atesa.config')
settings.job_type = 'aimless_shooting'
settings.degeneracy = 1
allthreads = main.init_threads(settings)
allthreads[0].current_type = ['init']
jobtype = factory.jobtype_factory(settings.job_type)
assert jobtype.check_termination(
allthreads[0], allthreads,
settings) == False # never terminate after an 'init' step
def test_get_cvs_with_qdot_broken(self):
"""Tests get_cvs with a dummy coordinate file, include_qdot = True, and a coordinate file without velocities"""
settings = configure('../../data/atesa.config')
settings.include_qdot = True
settings.topology = '../test_data/test.prmtop'
settings.cvs = [
'pytraj.distance(traj, \'@1 @3\')[0]',
'pytraj.distance(traj, \'@2 @4\')[0]'
]
with pytest.raises(IndexError):
result = utilities.get_cvs('../test_data/test.rst7', settings)
def test_check_termination_committor_analysis(self):
"""Tests check_termination with job_type = 'committor_analysis'"""
settings = configure('../../data/atesa.config')
settings.job_type = 'committor_analysis'
settings.committor_analysis_use_rc_out = False
allthreads = main.init_threads(settings)
allthreads[0].current_type = ['prod', 'prod', 'prod']
jobtype = factory.jobtype_factory(settings.job_type)
assert jobtype.check_termination(allthreads[0], allthreads,
settings) == False
assert allthreads[0].terminated == True
def test_get_initial_coordinates_committor_analysis_rc_out_does_not_exist(
self):
"""Tests get_initial_coordinates with job_type = 'committor_analysis' using an RC out file that does not exist"""
settings = configure('../../data/atesa.config')
settings.job_type = 'committor_analysis'
settings.committor_analysis_use_rc_out = True
settings.path_to_rc_out = '../test_data/rc_eval_FAKE.out'
settings.rc_threshold = 0.002
jobtype = factory.jobtype_factory(settings.job_type)
with pytest.raises(FileNotFoundError):
allthreads = main.init_threads(settings)
def test_get_next_step_committor_analysis(self):
"""Tests get_next_step with job_type = 'committor_analysis'"""
settings = configure('../../data/atesa.config')
settings.job_type = 'committor_analysis'
settings.committor_analysis_use_rc_out = False
settings.committor_analysis_n = 3
allthreads = main.init_threads(settings)
jobtype = factory.jobtype_factory(settings.job_type)
this_types, this_names = jobtype.get_next_step(allthreads[0], settings)
assert this_types == ['prod', 'prod', 'prod']
assert this_names == ['0', '1', '2']
def test_configure_directory(self):
"""Tests configure.py behavior in correcting an improperly formatted directory"""
shutil.copy(
'../../data/atesa.config', 'atesa.config'
) # todo: make a dedicated 'test' copy of atesa.config for tests to use.
config_lines = open('atesa.config', 'r').readlines()
for line in config_lines:
if 'working_directory' in line:
line = 'working_directory = \'/foo/bar/\'\n'
open('atesa_temp.config', 'a').write(line)
settings = configure('atesa_temp.config')
assert settings.working_directory == '/foo/bar'
def test_check_commit_value_errors(self):
"""Tests check_commit using a dummy coordinate file and commitments defined to get ValueErrors"""
settings = configure('../../data/atesa.config')
settings.topology = '../test_data/test.prmtop'
settings.commit_fwd = [[1, 2], [3, 4], [1.0, 1.5], ['t', 'lt']]
settings.commit_bwd = [[1, 2], [3, 4], [0.5, 2.0], ['lt', 'gt']]
with pytest.raises(ValueError):
utilities.check_commit('../test_data/test.rst7', settings)
settings.commit_fwd = [[1, 2], [3, 4], [1.0, 1.5], ['gt', 'lt']]
settings.commit_bwd = [[1, 2], [3, 4], [1.0, 1.5], ['t', 'lt']]
with pytest.raises(ValueError):
utilities.check_commit('../test_data/test.rst7', settings)
def test_get_initial_coordinates_committor_analysis_rc_out(self):
"""Tests get_initial_coordinates with job_type = 'committor_analysis' using an RC out file"""
settings = configure('../../data/atesa.config')
settings.job_type = 'committor_analysis'
settings.committor_analysis_use_rc_out = True
settings.path_to_rc_out = '../test_data/rc_eval.out'
settings.rc_threshold = 0.002
jobtype = factory.jobtype_factory(settings.job_type)
assert jobtype.get_initial_coordinates(settings) == [
'1.1_1.2_2.2_2.6.rst7_2_10_init_fwd.rst_2_1_2.rst7_5_init_fwd.rst',
'1.1_1.2_2.2_2.6.rst7_2_10_init_fwd.rst_4_58_3.rst7_4_init_fwd.rst'
]
def test_get_initial_coordinates_committor_analysis_rc_out_no_shooting_points(
self):
"""Tests get_initial_coordinates with job_type = 'committor_analysis' using an RC out file containing no
shooting points within the threshold"""
settings = configure('../../data/atesa.config')
settings.job_type = 'committor_analysis'
settings.committor_analysis_use_rc_out = True
settings.path_to_rc_out = '../test_data/rc_eval.out'
settings.rc_threshold = 0.0002
jobtype = factory.jobtype_factory(settings.job_type)
with pytest.raises(RuntimeError):
allthreads = main.init_threads(settings)
def test_get_batch_template_committor_analysis(self):
"""Tests get_batch_template with job_type = 'committor_analysis'"""
settings = configure('../../data/atesa.config')
settings.job_type = 'committor_analysis'
settings.md_engine = 'amber'
settings.batch_system = 'slurm'
settings.committor_analysis_use_rc_out = False
settings.path_to_templates = sys.path[0] + '/atesa/data/templates'
allthreads = main.init_threads(settings)
jobtype = factory.jobtype_factory(settings.job_type)
assert jobtype.get_batch_template(allthreads[0], 'prod',
settings) == 'amber_slurm.tpl'
def test_get_inpcrd_aimless_shooting_init(self):
"""Tests get_inpcrd with job_type = 'aimless_shooting' and thread.current_type = ['init']"""
settings = configure('../../data/atesa.config')
settings.job_type = 'aimless_shooting'
settings.degeneracy = 1
settings.initial_coordinates = ['../test_data/test_velocities.rst7']
allthreads = main.init_threads(settings)
allthreads[0].current_type = ['init']
jobtype = factory.jobtype_factory(settings.job_type)
assert jobtype.get_inpcrd(
allthreads[0]) == allthreads[0].history.init_inpcrd
assert allthreads[0].history.init_inpcrd == ['test_velocities.rst7']
