def test_mmvt_sim_namd_amber(tmp_path):
mymodel = make_test_model.make_test_model(tmp_path, engine="namd")
myanchor = mymodel.anchors[1]
output_file = os.path.join(tmp_path, "output.txt")
my_sim_openmm = mmvt_sim_namd.create_sim_namd(mymodel, myanchor,
output_file)
return
def test_mmvt_sim_namd_amber(tmp_path, host_guest_mmvt_model_namd):
myanchor = host_guest_mmvt_model_namd.anchors[1]
output_file = os.path.join(tmp_path, "output.txt")
my_sim_openmm = mmvt_sim_namd.create_sim_namd(host_guest_mmvt_model_namd,
myanchor, output_file)
assert my_sim_openmm.colvars_config is not None
assert my_sim_openmm.seekr_namd_settings is not None
return
def run_namd(model, anchor_index, restart, total_simulation_length,
cuda_device_index=False, force_overwrite=False,
save_state_file=False, save_state_boundaries=False,
namd_command="namd2", namd_arguments="",
load_state_file=None):
"""Run a NAMD simulation."""
import seekr2.modules.runner_namd as runner_namd
import seekr2.modules.mmvt_sim_namd as mmvt_sim_namd
assert anchor_index >= 0, "only positive indices allowed."
try:
myanchor = model.anchors[anchor_index]
except IndexError:
print("Invalid anchor index provided.")
exit()
if cuda_device_index is not None:
assert model.openmm_settings.cuda_platform_settings is not None
model.openmm_settings.cuda_platform_settings.cuda_device_index = \
cuda_device_index
if total_simulation_length is not None:
old_num_production_steps = \
model.calculation_settings.num_production_steps
model.calculation_settings.num_production_steps = \
total_simulation_length
if model.calculation_settings.num_production_steps \
< model.calculation_settings.restart_checkpoint_interval:
model.calculation_settings.restart_checkpoint_interval \
= model.calculation_settings.num_production_steps
runner = runner_namd.Runner_namd(model, myanchor, namd_command,
namd_arguments)
default_output_file, output_basename, state_file_prefix, restart_index \
= runner.prepare(restart, save_state_file, save_state_boundaries,
force_overwrite)
if model.get_type() == "mmvt":
sim_namd_obj = mmvt_sim_namd.create_sim_namd(
model, myanchor, output_basename)
else:
raise Exception("Method not implemented for NAMD:", model.get_type())
sim_namd_obj.seekr_namd_settings.save_state = save_state_file
sim_namd_obj.seekr_namd_settings.save_one_state_for_all_boundaries\
= runner.save_one_state_for_all_boundaries
sim_namd_obj.seekr_namd_settings.check_state_interval\
= runner.check_state_interval
runner.run(sim_namd_obj, default_output_file, restart, load_state_file,
restart_index)
model.calculation_settings.num_production_steps = old_num_production_steps
def test_Runner_namd_default(host_guest_mmvt_model):
host_guest_mmvt_model.calculation_settings.num_production_steps = 10
host_guest_mmvt_model.namd_settings = base.Namd_settings()
myanchor = host_guest_mmvt_model.anchors[1]
namd_command = "namd2"
namd_arguments = ""
runner = runner_namd.Runner_namd(host_guest_mmvt_model, myanchor,
namd_command, namd_arguments)
default_output_file, output_basename, state_file_prefix, restart_index = \
runner.prepare()
mmvt_output_filename = os.path.join(
host_guest_mmvt_model.anchor_rootdir, myanchor.directory, "prod",
"%s%d" % (mmvt_base.NAMDMMVT_BASENAME, 1))
my_sim_namd = mmvt_sim_namd.create_sim_namd(host_guest_mmvt_model,
myanchor, mmvt_output_filename)
my_sim_namd.namd_root.periodic_boundary_conditions.PMEGridSpacing = None
runner.run(my_sim_namd, mmvt_output_filename + ".out")
myglob = mmvt_output_filename + ".out*"
outfiles = glob.glob(myglob)
outfile = outfiles[0]
assert os.path.exists(outfile)
return
assert anchor_index >= 0, "only positive indices allowed."
try:
myanchor = model.anchors[anchor_index]
except IndexError:
print("Invalid anchor index provided.")
exit()
if total_simulation_length is not None:
model.namd_settings.total_simulation_length = \
total_simulation_length
runner = Runner_namd(model, myanchor, namd_command, namd_arguments)
default_output_file, output_basename, state_file_prefix, restart_index \
= runner.prepare(restart, save_state_file, force_overwrite)
if output_file is None:
output_file = default_output_file
if model.get_type() == "mmvt":
sim_namd_obj = mmvt_sim_namd.create_sim_namd(model, myanchor,
output_basename)
else:
raise Exception("Calculation type not supported for NAMD: {1}".format(
model.get_type()))
sim_namd_obj.seekr_namd_settings.save_state = save_state_file
sim_namd_obj.seekr_namd_settings.save_one_state_for_all_boundaries\
= runner.save_one_state_for_all_boundaries
sim_namd_obj.seekr_namd_settings.check_state_interval\
= runner.check_state_interval
runner.run(sim_namd_obj, output_file, restart, load_state_file,
restart_index)
def test_Runner_namd_default(tmp_path):
if not os.path.exists(tmp_path):
os.mkdir(tmp_path)
mymodel = make_test_model.make_test_model(tmp_path, engine="namd")
#sim_namd_factory = sim_namd.Sim_namd_factory()
myanchor = mymodel.anchors[1]
mmvt_output_filename = os.path.join(
tmp_path, myanchor.name, "prod",
"%s%d" % (mmvt_base.NAMDMMVT_BASENAME, 1))
namd_command = "namd2"
namd_arguments = ""
runner = runner_namd.Runner_namd(mymodel, myanchor, namd_command,
namd_arguments)
default_output_file, output_basename, state_file_prefix, restart_index = \
runner.prepare()
#sim_namd_factory = sim_namd.Sim_namd_factory()
my_sim_namd = mmvt_sim_namd.create_sim_namd(mymodel, myanchor,
mmvt_output_filename)
my_sim_namd.namd_root.periodic_boundary_conditions.PMEGridSpacing = None
print("PME turned off")
runner.run(my_sim_namd, mmvt_output_filename+".out")
myglob = mmvt_output_filename+".out*"
outfiles = glob.glob(myglob)
outfile = outfiles[0]
assert os.path.exists(outfile)
has_correct_line1 = False
has_correct_line2 = False
with open(outfile,"r") as f:
for line in f:
if re.search("^WallClock", line):
has_correct_line1 = True
if re.search("^WRITING", line):
has_correct_line2 = True
assert has_correct_line1 == True
assert has_correct_line2 == True
"""
namd_arguments = "+wtf"
runner = runner_namd.Runner_namd(mymodel, myanchor, namd_command,
namd_arguments)
default_output_file, output_basename, state_file_prefix, restart_index = \
runner.prepare(force_overwrite=True)
#sim_namd_factory = sim_namd.Sim_namd_factory()
my_sim_namd = mmvt_sim_namd.create_sim_namd(mymodel, myanchor,
mmvt_output_filename)
runner.run(my_sim_namd, mmvt_output_filename+".out")
myglob = mmvt_output_filename+".out*"
outfiles = glob.glob(myglob)
outfile = outfiles[0]
assert os.path.exists(outfile)
has_correct_line1 = False
has_correct_line2 = False
with open(outfile,"r") as f:
for line in f:
print("line:", line)
if re.search("^WallClock", line):
has_correct_line1 = True
if re.search("^WRITING", line):
has_correct_line2 = True
with pytest.raises(Exception):
assert has_correct_line1 == True
with pytest.raises(Exception):
assert has_correct_line2 == True
"""
return