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_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 test_algorithm_equilibrium_path_sampling_prod_not_accepted(self):
"""Tests algorithm with job_type = 'equilibrium_path_sampling' and thread.current_type = ['prod', 'prod'] for a
move that isn't accepted"""
settings = config_equilibrium_path_sampling()
settings.min_dt = -1
settings.max_dt = -1 # set these to the same value to guarantee which frame is chosen
settings.eps_dynamic_seed = 0
allthreads = main.init_threads(settings)
allthreads[0].current_type = ['prod', 'prod']
allthreads[0].history.prod_results = [[-34.12, -35.1,
-36], [12, 13, 11]
] # accepted then not accepted
allthreads[0].history.prod_trajs = [['test.nc', 'test.nc'],
[
'not_a_real_file.nc',
'not_a_real_file.nc'
]]
allthreads[0].history.init_coords = [[
'../test_data/test_velocities.rst7',
'../test_data/test_velocities.rst7'
]]
allthreads[0].suffix = 1
allthreads[0].history.last_accepted = 0
shutil.copy('../test_data/test.nc', 'test.nc')
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
def test_get_batch_file_equilibrium_path_sampling_broken(self):
"""Tests thread.get_batch_template with job_type = 'equilibrium_path_sampling' and invalid type = 'fwdd'"""
settings = config_equilibrium_path_sampling()
settings.job_type = 'equilibrium_path_sampling'
allthreads = main.init_threads(settings)
with pytest.raises(ValueError):
allthreads[0].get_batch_template('fwdd', settings)
def test_get_next_step_equilibrium_path_sampling_init(self):
"""Tests get_next_step with job_type = 'equilibrium_path_sampling' and current_type = ['init']"""
settings = config_equilibrium_path_sampling()
allthreads = main.init_threads(settings)
allthreads[0].current_type = ['init']
assert allthreads[0].get_next_step(settings) == (['prod', 'prod'],
['fwd', 'bwd'])
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_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_check_termination_equilibrium_path_sampling_thread(self):
"""Tests check_termination thread criterion with job_type = 'equilibrium_path_sampling'"""
settings = config_equilibrium_path_sampling()
settings.initial_coordinates = [
'../test_data/test_velocities.rst7',
'../test_data/test_velocities.rst7'
]
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.prod_lens = [[2, 2]]
allthreads[0].history.init_coords = [[
'../test_data/test_velocities.rst7',
'../test_data/test_velocities.rst7'
]]
jobtype = factory.jobtype_factory(settings.job_type)
jobtype.update_results(allthreads[0], allthreads, settings)
settings.samples_per_window = 1
jobtype = factory.jobtype_factory(settings.job_type)
assert jobtype.check_termination(
allthreads[0], allthreads,
settings) == False # global termination False
assert allthreads[0].terminated == True # thread termination True
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_gatekeep_equilibrium_path_sampling(self):
"""Tests gatekeep with job_type = 'committor_analysis'"""
settings = config_equilibrium_path_sampling()
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_get_batch_file_equilibrium_path_sampling_amber(self):
"""Tests thread.get_batch_template with job_type = 'equilibrium_path_sampling' and md_engine = 'amber'"""
settings = config_equilibrium_path_sampling()
settings.job_type = 'equilibrium_path_sampling'
settings.md_engine = 'amber'
allthreads = main.init_threads(settings)
assert allthreads[0].get_batch_template(
'init', settings) == 'amber_' + settings.batch_system + '.tpl'
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_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_update_history_equilibrium_path_sampling_init(self):
"""Tests update_history with job_type = 'equilibrium_path_sampling' with current_type = ['init']"""
settings = config_equilibrium_path_sampling()
allthreads = main.init_threads(settings)
allthreads[0].current_type = ['init']
these_kwargs = {'rst': 'fakey_mcfakename.rst7'}
jobtype = factory.jobtype_factory(settings.job_type)
jobtype.update_history(allthreads[0], settings, **these_kwargs)
assert allthreads[0].history.init_coords == [['fakey_mcfakename.rst7']]
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_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_equilibrium_path_sampling_global(self):
"""Tests check_termination global criterion with job_type = 'equilibrium_path_sampling'"""
settings = config_equilibrium_path_sampling()
settings.samples_per_window = -1
allthreads = main.init_threads(settings)
allthreads[0].current_type = ['prod', 'prod']
jobtype = factory.jobtype_factory(settings.job_type)
assert jobtype.check_termination(allthreads[0], allthreads,
settings) == False
assert allthreads[0].terminated == False
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_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_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_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_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_get_inpcrd_equilibrium_path_sampling(self):
"""Tests get_inpcrd with job_type = 'equilibrium_path_sampling'"""
settings = config_equilibrium_path_sampling()
allthreads = main.init_threads(settings)
allthreads[0].current_type = ['prod', 'prod']
allthreads[0].history.init_coords = [[
'not_a_real_file_at_all_init.rst7'
]]
jobtype = factory.jobtype_factory(settings.job_type)
assert jobtype.get_inpcrd(
allthreads[0]) == ['not_a_real_file_at_all_init.rst7']
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']
def test_init_threads_new(self):
"""Tests successful initialization of new threads"""
settings = configure('../../data/atesa.config')
settings.initial_coordinates = [
'../test_data/test.rst7', '../test_data/test_two_init.rst7'
]
settings.degeneracy = 1
allthreads = main.init_threads(settings)
assert len(allthreads) == 2
assert allthreads[0].history.init_inpcrd == ['test.rst7']
assert allthreads[1].history.init_inpcrd == ['test_two_init.rst7']
assert allthreads[0].topology == 'test.prmtop'
assert allthreads[1].topology == 'test.prmtop'
