def run_phonon(task_type, jdata, mdata):
user = ('user_incar' in jdata.keys())
work_path = util.make_work_path(jdata, '06.phonon', False, False, user)
all_task = glob.glob(os.path.join(work_path, '.'))
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
machine, machine_type, ssh_sess, resources, command, group_size = util.get_machine_info(
mdata, task_type)
run_tasks = util.collect_task(all_task, task_type)
forward_files = ['INCAR', 'POTCAR', 'KPOINTS']
backward_files = ['OUTCAR', 'OSZICAR', 'vasprun.xml']
common_files = ['POSCAR']
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files,
backward_files)
#lammps
elif task_type in lammps_task_type:
None
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
def run_phonon(task_type,jdata,mdata):
user= ('user_incar' in jdata.keys())
work_path=util.make_work_path(jdata,'06.phonon',False,False,user)
all_task = glob.glob(os.path.join(work_path,'.'))
#vasp
if task_type == "vasp":
mdata=decide_fp_machine(mdata)
machine,resources,command,group_size=util.get_machine_info(mdata,task_type)
run_tasks = util.collect_task(all_task,task_type)
forward_files = ['INCAR', 'POTCAR','KPOINTS','KPOINTS']
backward_files = ['OUTCAR', task_type+'.out' , 'OSZICAR','vasprun.xml']
common_files=['POSCAR']
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
mdata['fp_resources']['cvasp'] = True
forward_files.append('cvasp.py')
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
#lammps
elif task_type in lammps_task_type:
None
else:
raise RuntimeError ("unknown task %s, something wrong" % task_type)
def run_equi(task_type,jdata,mdata):
#rmprint("This module has been run !")
work_path=util.make_work_path(jdata,'00.equi',False,False,False)
all_task = glob.glob(os.path.join(work_path,'.'))
#vasp
if task_type=="vasp":
mdata=decide_fp_machine(mdata)
forward_files = ['INCAR', 'POTCAR', 'KPOINTS']
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
mdata['fp_resources']['cvasp'] = True
forward_files.append('cvasp.py')
backward_files = ['OUTCAR', task_type+'.out' , 'CONTCAR','OSZICAR']
common_files=['POSCAR']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
forward_files = ['conf.lmp', 'lammps.in']
backward_files = ['dump.relax','log.lammps', task_type+'.out']
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name =fp_params['model_name']
if not model_name :
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir,ii) for ii in model_name]
common_files = model_name
if len(model_name)>1 and task_type == 'deepmd':
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError ("unknow task %s, something wrong" % task_type)
run_tasks = util.collect_task(all_task,task_type)
if len(run_tasks)==0: return
machine,resources,command,group_size=util.get_machine_info(mdata,task_type)
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
#debug#
#print(' '.join(common_files))
#print(' '.join(forward_files))
#print(' '.join(backward_files))
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
def run_surf(task_type,jdata,mdata):
static=jdata['static-opt']
work_path=util.make_work_path(jdata,'05.surf',False,static,False)
all_task = glob.glob(os.path.join(work_path,'struct-*'))
#vasp
if task_type == "vasp":
mdata=decide_fp_machine(mdata)
forward_files = ['INCAR', 'POSCAR','POTCAR','KPOINTS']
backward_files = ['OUTCAR', task_type+'.out' , 'OSZICAR']
common_files=['INCAR','POTCAR']
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
mdata['fp_resources']['cvasp'] = True
forward_files.append('cvasp.py')
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name =fp_params['model_name']
if not model_name :
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir,ii) for ii in model_name]
forward_files = ['conf.lmp', 'lammps.in']+model_name
backward_files = ['log.lammps',task_type+'.out']
common_files=['lammps.in']+model_name
if len(model_name)>1 and task_type == 'deepmd':
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError ("unknow task %s, something wrong" % task_type)
run_tasks = util.collect_task(all_task,task_type)
if len(run_tasks)==0: return
else:
run_tasks = [os.path.basename(ii) for ii in all_task]
machine,resources,command,group_size=util.get_machine_info(mdata,task_type)
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
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 = decide_fp_machine(mdata)
elif inter_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
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:
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))
disp.run_jobs(resources,
command,
work_path,
[run_tasks[ii]],
group_size,
forward_common_files,
forward_files,
backward_files,
outlog='outlog',
errlog='errlog')
def run_vacancy(task_type,jdata,mdata):
work_path=util.make_work_path(jdata,'03.vacancy',False,False,False)
all_task = glob.glob(os.path.join(work_path,'struct-*'))
#vasp
if task_type == "vasp":
mdata=decide_fp_machine(mdata)
forward_files = ['INCAR', 'POSCAR','POTCAR']
backward_files = ['OUTCAR', 'autotest.out' , 'OSZICAR']
common_files=['INCAR','POTCAR']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name =fp_params['model_name']
if not model_name :
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir,ii) for ii in model_name]
common_files = model_name
forward_files = ['conf.lmp', 'lammps.in']+model_name
backward_files = ['log.lammps','autotest.out']
common_files=['lammps.in']+model_name
if len(model_name)>1 and task_type == 'deepmd':
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError ("unknow task %s, something wrong" % task_type)
run_tasks = util.collect_task(all_task,task_type)
if len(run_tasks)==0: return
machine,machine_type,ssh_sess,resources,command,group_size=util.get_machine_info(mdata,task_type)
disp = make_dispatcher(machine)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog='autotest.out',
errlog='autotest.err')
def run_equi(confs, inter_param, mdata):
# find all POSCARs and their name like mp-xxx
# ...
conf_dirs = glob.glob(confs)
conf_dirs.sort()
# generate a list of task names like mp-xxx/relaxation
# ...
work_path_list = []
for ii in conf_dirs:
work_path_list.append(os.path.join(ii, 'relaxation'))
all_task = []
for ii in work_path_list:
all_task.append(os.path.join(ii, '.'))
inter_type = inter_param['type']
# vasp
if inter_type == "vasp":
mdata = decide_fp_machine(mdata)
elif inter_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
else:
raise RuntimeError("unknown task %s, something wrong" % task_type)
# dispatch the tasks
forward_files, forward_common_files, backward_files = make_task_trans_files(
inter_param)
# backward_files += logs
# ...
run_tasks = util.collect_task(all_task, inter_type)
if len(run_tasks) == 0:
return
else:
run_tasks = [os.path.basename(ii) for ii in all_task]
machine, resources, command, group_size = util.get_machine_info(
mdata, inter_type)
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)
disp.run_jobs(resources,
command,
work_path,
run_tasks[ii],
group_size,
forward_common_files,
forward_files,
backward_files,
outlog=inter_type + '.out',
errlog=inter_type + '.err')
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)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
forward_common_files,
forward_files,
backward_files,
outlog='outlog',
errlog='errlog')
def run_equi(task_type, jdata, mdata):
#rmprint("This module has been run !")
work_path = util.make_work_path(jdata, '00.equi', False, False, False)
all_task = glob.glob(os.path.join(work_path, '.'))
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
forward_files = ['INCAR', 'POTCAR']
backward_files = ['OUTCAR', 'CONTCAR', 'OSZICAR']
common_files = ['POSCAR']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
forward_files = ['conf.lmp', 'lammps.in']
backward_files = ['dump.relax', 'log.lammps', 'model_devi.log']
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name = fp_params['model_name']
if not model_name:
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir, ii) for ii in model_name]
common_files = model_name
if len(model_name) > 1 and task_type == 'deepmd':
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
run_tasks = util.collect_task(all_task, task_type)
machine, machine_type, ssh_sess, resources, command, group_size = util.get_machine_info(
mdata, task_type)
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files, backward_files)
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_interstitial(task_type,jdata,mdata):
reprod_opt=jdata['reprod-opt']
work_path=util.make_work_path(jdata,'04.interstitial',reprod_opt,False,False)
all_task = glob.glob(os.path.join(work_path,'struct-*'))
#vasp
if task_type == "vasp":
mdata=decide_fp_machine(mdata)
forward_files = ['INCAR', 'POSCAR','POTCAR',"KPOINTS"]
backward_files = ['OUTCAR', task_type+'.out' , 'XDATCAR','OSZICAR']
common_files=['INCAR']
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
mdata['fp_resources']['cvasp'] = True
forward_files.append('cvasp.py')
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
if reprod_opt:
all_frame=[]
for ii in all_task:
all_frame+=(glob.glob(os.path.join(ii,'frame.*')))
work_path = all_task
all_task = all_frame
run_tasks_ = []
for ii in all_task:
# fres = os.path.join(ii, 'log.lammps')
# if os.path.isfile(fres) :
# if not lammps.check_finished(fres):
# run_tasks_.append(ii)
# else :
# run_tasks_.append(ii)
run_tasks_.append(ii)
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name =fp_params['model_name']
if not model_name :
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir,ii) for ii in model_name]
forward_files = ['conf.lmp', 'lammps.in']+model_name
backward_files = ['log.lammps', task_type+'.out']
common_files=['lammps.in']+model_name
if len(model_name)>1 and task_type == 'deepmd':
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError ("unknow task %s, something wrong" % task_type)
machine,resources,command,group_size=util.get_machine_info(mdata,task_type)
if reprod_opt:
for ii in work_path:
run_tasks=[]
for jj in run_tasks_:
if ii in jj:
run_tasks.append(os.path.basename(jj))
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
ii,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
else:
run_tasks = util.collect_task(all_task,task_type)
if len(run_tasks)==0: return
else:
run_tasks = [os.path.basename(ii) for ii in all_task]
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
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()
processes = len(conf_dirs)
pool = Pool(processes=processes)
print("Submit job via %d processes" % processes)
# 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:
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))
multiple_ret = []
for ii in range(len(work_path_list)):
work_path = work_path_list[ii]
ret = pool.apply_async(worker, (
work_path,
run_tasks[ii],
forward_common_files,
forward_files,
backward_files,
mdata,
inter_type,
))
multiple_ret.append(ret)
pool.close()
pool.join()
for ii in range(len(multiple_ret)):
if not multiple_ret[ii].successful():
raise RuntimeError(
"Task %d is not successful! work_path: %s " %
(ii, work_path_list[ii]))
print('finished')
def run_property(confs, inter_param, property_list, mdata):
# find all POSCARs and their name like mp-xxx
# ...
conf_dirs = glob.glob(confs)
conf_dirs.sort()
task_list = []
work_path_list = []
for ii in conf_dirs:
for jj in property_list:
# determine the suffix: from scratch or refine
# ...
if 'init_from_suffix' and 'output_suffix' in jj:
suffix = jj['output_suffix']
else:
suffix = 0
property_type = jj['type']
path_to_work = os.path.join(ii, property_type + '_' + suffix)
work_path_list.append(path_to_work)
tmp_task_list = glob.glob(
os.path.join(path_to_work, 'task.[0-9]*[0-9]'))
tmp_task_list.sort()
task_list.append(tmp_task_list)
# dispatch the tasks
forward_files, forward_common_files, backward_files = make_task_trans_files(
inter_param)
# backward_files += logs
# ...
task_type = inter_param['type']
# vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
else:
raise RuntimeError("unknown task %s, something wrong" % task_type)
for ii in range(len(work_path_list)):
work_path = work_path_list[ii]
all_task = task_list[ii]
run_tasks = util.collect_task(all_task, task_type)
if len(run_tasks) == 0:
return
else:
run_tasks = [os.path.basename(ii) for ii in all_task]
machine, resources, command, group_size = util.get_machine_info(
mdata, task_type)
disp = make_dispatcher(machine, resources, work_path, run_tasks,
group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
forward_common_files,
forward_files,
backward_files,
outlog=task_type + '.out',
errlog=task_type + '.err')
