def run_short_ci(model_input, cuda_device_index, long_check=True):
start_dir = os.getcwd()
model, xml_path = prepare.prepare(model_input, force_overwrite=False)
model_dir = os.path.dirname(xml_path)
model.anchor_rootdir = os.path.abspath(model_dir)
check.check_pre_simulation_all(model)
run.run(model,
"any",
min_b_surface_simulation_length=1000,
num_rev_launches=10,
cuda_device_index=cuda_device_index,
save_state_file=True)
data_sample_list = converge.converge(model, k_on_state=0)
rmsd_convergence_results = common_converge.calc_RMSD_conv_amount(
model, data_sample_list)
transition_minima, transition_details, transition_times \
= common_converge.calc_transition_steps(
model, data_sample_list[-1])
converge.print_convergence_results(
model,
rmsd_convergence_results,
cutoff=0.1,
transition_results=transition_details,
transition_time_results=transition_times,
minimum_anchor_transitions=10,
bd_transition_counts=data_sample_list[-1].bd_transition_counts)
check.check_post_simulation_all(model, long_check=long_check)
analysis = analyze.analyze(model)
analysis.print_results()
os.chdir(start_dir)
return
def toy_elber_model_persistent(toy_elber_model_input_persistent):
"""
Create a model object that is persistent across the tests in this file.
"""
os.chdir(TEST_DIRECTORY)
toy_elber_model_obj, model_xml_path \
= prepare.prepare(toy_elber_model_input_persistent,
force_overwrite=False)
model_dir = os.path.dirname(model_xml_path)
toy_elber_model_obj.anchor_rootdir = os.path.abspath(model_dir)
return toy_elber_model_obj
def rmsd_mmvt_model_persistent(rmsd_mmvt_model_input_persistent):
"""
Create a model object that is persistent across the tests in this file.
"""
os.chdir(TEST_DIRECTORY)
rmsd_mmvt_model_obj, model_xml_path \
= prepare.prepare(rmsd_mmvt_model_input_persistent,
force_overwrite=False)
model_dir = os.path.dirname(model_xml_path)
rmsd_mmvt_model_obj.anchor_rootdir = os.path.abspath(model_dir)
rmsd_mmvt_model_obj.openmm_settings.cuda_platform_settings = None
rmsd_mmvt_model_obj.openmm_settings.reference_platform = True
return rmsd_mmvt_model_obj
def host_guest_mmvt_model_persistent_forcefield(
host_guest_mmvt_model_input_persistent_forcefield):
"""
Create a model object that is persistent across the tests in this file.
Uses an OpenMM forcefield input.
"""
os.chdir(TEST_DIRECTORY)
host_guest_mmvt_model_obj, model_xml_path \
= prepare.prepare(host_guest_mmvt_model_input_persistent_forcefield,
force_overwrite=False)
model_dir = os.path.dirname(model_xml_path)
host_guest_mmvt_model_obj.anchor_rootdir = os.path.abspath(model_dir)
return host_guest_mmvt_model_obj
def toy_multi_model_persistent(toy_multi_model_input_persistent):
"""
Create a model object that is persistent across the tests in this file.
"""
os.chdir(TEST_DIRECTORY)
toy_multi_model_obj, model_xml_path \
= prepare.prepare(toy_multi_model_input_persistent,
force_overwrite=False)
model_dir = os.path.dirname(model_xml_path)
toy_multi_model_obj.anchor_rootdir = os.path.abspath(model_dir)
toy_multi_model_obj.anchors[0].starting_positions = np.array(
[[[-0.7, -0.7, 0.0]]])
return toy_multi_model_obj
def host_guest_mmvt_model_persistent_npt(
tmpdir_factory, host_guest_mmvt_model_input_persistent):
"""
Create a model object that is persistent across the tests in this file.
It uses the NAMD engine.
"""
os.chdir(TEST_DIRECTORY)
host_guest_mmvt_model_input_persistent.ensemble = "npt"
rootdir = tmpdir_factory.mktemp("hostguest_mmvt_npt")
host_guest_mmvt_model_input_persistent.root_directory = rootdir
host_guest_mmvt_model_input_persistent.browndye_settings_input = None
host_guest_mmvt_model_obj, model_xml_path \
= prepare.prepare(host_guest_mmvt_model_input_persistent,
force_overwrite=False)
model_dir = os.path.dirname(model_xml_path)
host_guest_mmvt_model_obj.anchor_rootdir = os.path.abspath(model_dir)
return host_guest_mmvt_model_obj
def host_guest_mmvt_model_persistent_namd(
tmpdir_factory, host_guest_mmvt_model_input_persistent):
"""
Create a model object that is persistent across the tests in this file.
It uses the NAMD engine.
"""
os.chdir(TEST_DIRECTORY)
host_guest_mmvt_model_input_persistent.md_program = "namd"
host_guest_mmvt_model_input_persistent.waterModel = "tip3p"
rootdir = tmpdir_factory.mktemp("hostguest_mmvt_namd")
host_guest_mmvt_model_input_persistent.root_directory = rootdir
host_guest_mmvt_model_input_persistent.browndye_settings_input = None
host_guest_mmvt_model_obj, model_xml_path \
= prepare.prepare(host_guest_mmvt_model_input_persistent,
force_overwrite=False)
model_dir = os.path.dirname(model_xml_path)
host_guest_mmvt_model_obj.anchor_rootdir = os.path.abspath(model_dir)
host_guest_mmvt_model_obj.namd_settings.PMEGridSpacing = None
return host_guest_mmvt_model_obj