def run_vasp_relax(jdata, mdata):
fp_command = mdata['fp_command']
fp_group_size = mdata['fp_group_size']
fp_resources = mdata['fp_resources']
#machine_type = mdata['fp_machine']['machine_type']
work_dir = os.path.join(jdata['out_dir'], global_dirname_02)
forward_files = ["POSCAR", "INCAR", "POTCAR"]
user_forward_files = mdata.get("fp" + "_user_forward_files", [])
forward_files += [os.path.basename(file) for file in user_forward_files]
backward_files = ["OUTCAR","CONTCAR"]
backward_files += mdata.get("fp" + "_user_backward_files", [])
forward_common_files = []
if 'cvasp' in mdata['fp_resources']:
if mdata['fp_resources']['cvasp']:
forward_files +=['cvasp.py']
relax_tasks = glob.glob(os.path.join(work_dir, "sys-*"))
relax_tasks.sort()
#dlog.info("work_dir",work_dir)
#dlog.info("relax_tasks",relax_tasks)
if len(relax_tasks) == 0:
return
relax_run_tasks = relax_tasks
#for ii in relax_tasks :
# if not _vasp_check_fin(ii):
# relax_run_tasks.append(ii)
run_tasks = [os.path.basename(ii) for ii in relax_run_tasks]
api_version = mdata.get('api_version', '0.9')
if LooseVersion(api_version) < LooseVersion('1.0'):
warnings.warn(f"the dpdispatcher will be updated to new version."
f"And the interface may be changed. Please check the documents for more details")
dispatcher = make_dispatcher(mdata['fp_machine'], mdata['fp_resources'], work_dir, run_tasks, fp_group_size)
dispatcher.run_jobs(fp_resources,
[fp_command],
work_dir,
run_tasks,
fp_group_size,
forward_common_files,
forward_files,
backward_files)
elif LooseVersion(api_version) >= LooseVersion('1.0'):
submission = make_submission(
mdata['fp_machine'],
mdata['fp_resources'],
commands=[fp_command],
work_path=work_dir,
run_tasks=run_tasks,
group_size=fp_group_size,
forward_common_files=forward_common_files,
forward_files=forward_files,
backward_files=backward_files,
outlog = 'fp.log',
errlog = 'fp.log')
submission.run_submission()
def worker(work_path,
all_task,
forward_common_files,
forward_files,
backward_files,
mdata,
inter_type):
run_tasks = [os.path.basename(ii) for ii in all_task]
machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
api_version = mdata.get('api_version', '0.9')
if LooseVersion(api_version) < LooseVersion('1.0'):
warnings.warn(f"the dpdispatcher will be updated to new version."
f"And the interface may be changed. Please check the documents for more details")
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
forward_common_files,
forward_files,
backward_files,
outlog='outlog',
errlog='errlog')
elif LooseVersion(api_version) >= LooseVersion('1.0'):
submission = make_submission(
mdata_machine=machine,
mdata_resource=resources,
commands=[command],
work_path=work_path,
run_tasks=run_tasks,
group_size=group_size,
forward_common_files=forward_common_files,
forward_files=forward_files,
backward_files=backward_files,
outlog = 'outlog',
errlog = 'errlog'
)
submission.run_submission()
def run_equi(confs, inter_param, mdata):
# find all POSCARs and their name like mp-xxx
# ...
conf_dirs = []
for conf in confs:
conf_dirs.extend(glob.glob(conf))
conf_dirs.sort()
# generate a list of task names like mp-xxx/relaxation/relax_task
# ...
work_path_list = []
for ii in conf_dirs:
work_path_list.append(os.path.abspath(os.path.join(ii, 'relaxation')))
all_task = []
for ii in work_path_list:
all_task.append(os.path.join(ii, 'relax_task'))
inter_type = inter_param['type']
# vasp
if inter_type == "vasp":
mdata = convert_mdata(mdata, ["fp"])
elif inter_type in lammps_task_type:
mdata = convert_mdata(mdata, ["model_devi"])
else:
raise RuntimeError("unknown task %s, something wrong" % inter_type)
# dispatch the tasks
# POSCAR here is useless
virtual_calculator = make_calculator(inter_param, "POSCAR")
forward_files = virtual_calculator.forward_files()
forward_common_files = virtual_calculator.forward_common_files()
backward_files = virtual_calculator.backward_files()
# backward_files += logs
# ...
run_tasks = util.collect_task(all_task, inter_type)
if len(run_tasks) == 0:
return
else:
# if LooseVersion()
run_tasks = [os.path.basename(ii) for ii in all_task]
machine, resources, command, group_size = util.get_machine_info(
mdata, inter_type)
print('%d tasks will be submited ' % len(run_tasks))
for ii in range(len(work_path_list)):
work_path = work_path_list[ii]
disp = make_dispatcher(machine, resources, work_path,
[run_tasks[ii]], group_size)
print("%s --> Runing... " % (work_path))
api_version = mdata.get('api_version', '0.9')
if LooseVersion(api_version) < LooseVersion('1.0'):
warnings.warn(
f"the dpdispatcher will be updated to new version."
f"And the interface may be changed. Please check the documents for more details"
)
disp.run_jobs(resources,
command,
work_path, [run_tasks[ii]],
group_size,
forward_common_files,
forward_files,
backward_files,
outlog='outlog',
errlog='errlog')
elif LooseVersion(api_version) >= LooseVersion('1.0'):
submission = make_submission(
mdata_machine=machine,
mdata_resource=resources,
commands=[command],
work_path=work_path,
run_tasks=run_tasks,
group_size=group_size,
forward_common_files=forward_common_files,
forward_files=forward_files,
backward_files=backward_files,
outlog='outlog',
errlog='errlog')
submission.run_submission()
def run_vasp_md(jdata, mdata):
fp_command = mdata['fp_command']
fp_group_size = mdata['fp_group_size']
fp_resources = mdata['fp_resources']
#machine_type = mdata['fp_machine']['machine_type']
work_dir = os.path.join(jdata['out_dir'], global_dirname_04)
scale = jdata['scale']
pert_numb = jdata['pert_numb']
md_nstep = jdata['md_nstep']
forward_files = ["POSCAR", "INCAR", "POTCAR"]
user_forward_files = mdata.get("fp" + "_user_forward_files", [])
forward_files += [os.path.basename(file) for file in user_forward_files]
backward_files = ["OUTCAR"]
backward_files += mdata.get("fp" + "_user_backward_files", [])
forward_common_files = []
if 'cvasp' in mdata['fp_resources']:
if mdata['fp_resources']['cvasp']:
forward_files +=['cvasp.py']
path_md = work_dir
path_md = os.path.abspath(path_md)
cwd = os.getcwd()
assert(os.path.isdir(path_md)), "md path should exists"
md_tasks = glob.glob(os.path.join(work_dir, 'sys-*/scale*/00*'))
md_tasks.sort()
if len(md_tasks) == 0:
return
md_run_tasks = md_tasks
#for ii in md_tasks :
# if not _vasp_check_fin(ii):
# md_run_tasks.append(ii)
run_tasks = [ii.replace(work_dir+"/", "") for ii in md_run_tasks]
#dlog.info("md_work_dir", work_dir)
#dlog.info("run_tasks",run_tasks)
api_version = mdata.get('api_version', '0.9')
if LooseVersion(api_version) < LooseVersion('1.0'):
warnings.warn(f"the dpdispatcher will be updated to new version."
f"And the interface may be changed. Please check the documents for more details")
dispatcher = make_dispatcher(mdata['fp_machine'], mdata['fp_resources'], work_dir, run_tasks, fp_group_size)
dispatcher.run_jobs(fp_resources,
[fp_command],
work_dir,
run_tasks,
fp_group_size,
forward_common_files,
forward_files,
backward_files)
elif LooseVersion(api_version) >= LooseVersion('1.0'):
submission = make_submission(
mdata['fp_machine'],
mdata['fp_resources'],
commands=[fp_command],
work_path=work_dir,
run_tasks=run_tasks,
group_size=fp_group_size,
forward_common_files=forward_common_files,
forward_files=forward_files,
backward_files=backward_files,
outlog = 'fp.log',
errlog = 'fp.log')
submission.run_submission()