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"]
backward_files = ["OUTCAR","CONTCAR"]
forward_common_files = []
if 'cvasp' in mdata['fp_resources']:
if mdata['fp_resources']['cvasp']:
forward_common_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]
dispatcher = make_dispatcher(mdata['fp_machine'], mdata['fp_resources'], work_dir, run_tasks, fp_group_size)
#dlog.info(run_tasks)
dispatcher.run_jobs(fp_resources,
[fp_command],
work_dir,
run_tasks,
fp_group_size,
forward_common_files,
forward_files,
backward_files)
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_model_devi(iter_index, jdata, mdata):
"""submit dp test tasks"""
iter_name = make_iter_name(iter_index)
work_path = os.path.join(iter_name, model_devi_name)
# generate command
commands = []
tasks = glob.glob(os.path.join(work_path, "task.*"))
run_tasks = [os.path.basename(ii) for ii in tasks]
# get models
models = glob.glob(os.path.join(work_path, "graph*pb"))
model_names = [os.path.basename(ii) for ii in models]
task_model_list = []
for ii in model_names:
task_model_list.append(os.path.join('..', ii))
# get max data size
data_size = max([
len(dpdata.System(os.path.join(task, rest_data_name),
fmt="deepmd/npy")) for task in tasks
])
# models
commands = []
detail_file_names = []
for ii, mm in enumerate(task_model_list):
detail_file_name = "{prefix}.{ii}".format(
prefix=detail_file_name_prefix,
ii=ii,
)
# TODO: support 0.x?
command = "{python} -m deepmd test -m {model} -s {system} -n {numb_test} -d {detail_file}".format(
python=mdata['python_test_path'],
model=mm,
system=rest_data_name,
numb_test=data_size,
detail_file=detail_file_name,
)
commands.append(command)
detail_file_names.append(detail_file_name)
# submit
try:
model_devi_group_size = mdata['model_devi_group_size']
except:
model_devi_group_size = 1
forward_files = [rest_data_name]
backward_files = sum([[pf + ".e.out", pf + ".f.out", pf + ".v.out"]
for pf in detail_file_names], [])
dispatcher = make_dispatcher(mdata['model_devi_machine'],
mdata['model_devi_resources'], work_path,
run_tasks, model_devi_group_size)
dispatcher.run_jobs(mdata['model_devi_resources'],
commands,
work_path,
run_tasks,
model_devi_group_size,
model_names,
forward_files,
backward_files,
outlog='model_devi.log',
errlog='model_devi.log')
def gen_init_reaction(args):
try:
import ruamel
from monty.serialization import loadfn, dumpfn
warnings.simplefilter('ignore',
ruamel.yaml.error.MantissaNoDotYAML1_1Warning)
jdata = loadfn(args.PARAM)
if args.MACHINE is not None:
mdata = loadfn(args.MACHINE)
except:
with open(args.PARAM, 'r') as fp:
jdata = json.load(fp)
if args.MACHINE is not None:
with open(args.MACHINE, "r") as fp:
mdata = json.load(fp)
record = "record.reaction"
iter_rec = -1
numb_task = 7
if os.path.isfile(record):
with open(record) as frec:
for line in frec:
iter_rec = int(line.strip())
dlog.info("continue from task %02d" % iter_rec)
for ii in range(numb_task):
sepline(str(ii), '-')
if ii <= iter_rec:
continue
elif ii == 0:
link_reaxff(jdata)
elif ii == 1:
dispatcher = make_dispatcher(mdata["reaxff_machine"])
run_reaxff(jdata, mdata, dispatcher)
elif ii == 2:
link_trj(jdata)
elif ii == 3:
dispatcher = make_dispatcher(mdata["build_machine"])
run_build_dataset(jdata, mdata, dispatcher)
elif ii == 4:
link_fp_input()
elif ii == 5:
dispatcher = make_dispatcher(mdata["fp_machine"])
run_fp(jdata, mdata, dispatcher)
elif ii == 6:
convert_data(jdata)
with open(record, "a") as frec:
frec.write(str(ii) + '\n')
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_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 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_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"]
backward_files = ["OUTCAR"]
forward_common_files = []
if 'cvasp' in mdata['fp_resources']:
if mdata['fp_resources']['cvasp']:
forward_common_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)
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)
def gen_init_surf(args):
try:
import ruamel
from monty.serialization import loadfn, dumpfn
warnings.simplefilter('ignore',
ruamel.yaml.error.MantissaNoDotYAML1_1Warning)
jdata = loadfn(args.PARAM)
if args.MACHINE is not None:
mdata = loadfn(args.MACHINE)
except:
with open(args.PARAM, 'r') as fp:
jdata = json.load(fp)
if args.MACHINE is not None:
with open(args.MACHINE, "r") as fp:
mdata = json.load(fp)
out_dir = out_dir_name(jdata)
jdata['out_dir'] = out_dir
dlog.info("# working dir %s" % out_dir)
if args.MACHINE is not None:
# Decide a proper machine
mdata = decide_fp_machine(mdata)
disp = make_dispatcher(mdata["fp_machine"])
#stage = args.STAGE
stage_list = [int(i) for i in jdata['stages']]
for stage in stage_list:
if stage == 1:
create_path(out_dir)
make_super_cell_pymatgen(jdata)
place_element(jdata)
make_vasp_relax(jdata)
if args.MACHINE is not None:
run_vasp_relax(jdata, mdata, disp)
elif stage == 2:
make_scale(jdata)
pert_scaled(jdata)
else:
raise RuntimeError("unknown stage %d" % stage)
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_iter(param_file, machine_file):
""" init (iter 0): init_pick
tasks (iter > 0):
00 make_train (same as generator)
01 run_train (same as generator)
02 post_train (same as generator)
03 make_model_devi
04 run_model_devi
05 post_model_devi
06 make_fp
07 run_fp (same as generator)
08 post_fp (same as generator)
"""
# TODO: function of handling input json should be combined as one function
try:
import ruamel
from monty.serialization import loadfn, dumpfn
warnings.simplefilter('ignore',
ruamel.yaml.error.MantissaNoDotYAML1_1Warning)
jdata = loadfn(param_file)
mdata = loadfn(machine_file)
except:
with open(param_file, 'r') as fp:
jdata = json.load(fp)
with open(machine_file, 'r') as fp:
mdata = json.load(fp)
if jdata.get('pretty_print', False):
fparam = SHORT_CMD+'_' + \
param_file.split('.')[0]+'.'+jdata.get('pretty_format', 'json')
dumpfn(jdata, fparam, indent=4)
fmachine = SHORT_CMD+'_' + \
machine_file.split('.')[0]+'.'+jdata.get('pretty_format', 'json')
dumpfn(mdata, fmachine, indent=4)
if mdata.get('handlers', None):
if mdata['handlers'].get('smtp', None):
que = queue.Queue(-1)
queue_handler = logging.handlers.QueueHandler(que)
smtp_handler = logging.handlers.SMTPHandler(
**mdata['handlers']['smtp'])
listener = logging.handlers.QueueListener(que, smtp_handler)
dlog.addHandler(queue_handler)
listener.start()
max_tasks = 10000
numb_task = 9
record = "record.dpgen"
iter_rec = [0, -1]
if os.path.isfile(record):
with open(record) as frec:
for line in frec:
iter_rec = [int(x) for x in line.split()]
dlog.info("continue from iter %03d task %02d" %
(iter_rec[0], iter_rec[1]))
cont = True
ii = -1
while cont:
ii += 1
iter_name = make_iter_name(ii)
sepline(iter_name, '=')
for jj in range(numb_task):
if ii * max_tasks + jj <= iter_rec[0] * max_tasks + iter_rec[1]:
continue
task_name = "task %02d" % jj
sepline("{} {}".format(iter_name, task_name), '-')
jdata['model_devi_jobs'] = [{} for _ in range(ii + 1)]
if ii == 0 and jj < 6:
if jj == 0:
log_iter("init_pick", ii, jj)
init_pick(ii, jdata, mdata)
dlog.info("first iter, skip step 1-5")
elif jj == 0:
log_iter("make_train", ii, jj)
make_train(ii, jdata, mdata)
elif jj == 1:
log_iter("run_train", ii, jj)
mdata = decide_train_machine(mdata)
disp = make_dispatcher(mdata['train_machine'])
run_train(ii, jdata, mdata)
elif jj == 2:
log_iter("post_train", ii, jj)
post_train(ii, jdata, mdata)
elif jj == 3:
log_iter("make_model_devi", ii, jj)
cont = make_model_devi(ii, jdata, mdata)
if not cont or ii >= jdata.get("stop_iter", ii + 1):
break
elif jj == 4:
log_iter("run_model_devi", ii, jj)
mdata = decide_model_devi_machine(mdata)
disp = make_dispatcher(mdata['model_devi_machine'])
run_model_devi(ii, jdata, mdata, disp)
elif jj == 5:
log_iter("post_model_devi", ii, jj)
post_model_devi(ii, jdata, mdata)
elif jj == 6:
log_iter("make_fp", ii, jj)
make_fp(ii, jdata, mdata)
elif jj == 7:
log_iter("run_fp", ii, jj)
if jdata.get("labeled", False):
dlog.info("already have labeled data, skip run_fp")
else:
mdata = decide_fp_machine(mdata)
disp = make_dispatcher(mdata['fp_machine'])
run_fp(ii, jdata, mdata)
elif jj == 8:
log_iter("post_fp", ii, jj)
if jdata.get("labeled", False):
dlog.info("already have labeled data, skip post_fp")
else:
post_fp(ii, jdata)
else:
raise RuntimeError("unknown task %d, something wrong" % jj)
record_iter(record, ii, jj)
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')
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')
backward_files = ['OUTCAR','vasprun.xml','CONTCAR']
forward_common_files=[]
mark_failure =False
log_file='runlog'
err_file='errlog'
mdata=loadfn('machine.json')
mdata = decide_fp_machine(mdata)
#dumpfn(mdata,'new.json',indent=4)
fp_command = mdata['fp_command']
fp_group_size = mdata['fp_group_size']
#---------------------------------------------------
dispatcher = make_dispatcher(mdata['fp_machine'],
mdata_resource=mdata['fp_resources'],
work_path=work_path,
run_tasks=run_tasks,
group_size=fp_group_size)
dispatcher.run_jobs(mdata['fp_resources'],
[fp_command],
work_path,
run_tasks,
fp_group_size,
forward_common_files,
forward_files,
backward_files,
mark_failure=mark_failure,
outlog = log_file,
errlog = err_file)
def gen_init_bulk(args) :
try:
import ruamel
from monty.serialization import loadfn,dumpfn
warnings.simplefilter('ignore', ruamel.yaml.error.MantissaNoDotYAML1_1Warning)
jdata=loadfn(args.PARAM)
if args.MACHINE is not None:
mdata=loadfn(args.MACHINE)
except:
with open (args.PARAM, 'r') as fp :
jdata = json.load (fp)
if args.MACHINE is not None:
with open (args.MACHINE, "r") as fp:
mdata = json.load(fp)
if args.MACHINE is not None:
# Selecting a proper machine
mdata = decide_fp_machine(mdata)
disp = make_dispatcher(mdata["fp_machine"])
# Decide work path
out_dir = out_dir_name(jdata)
jdata['out_dir'] = out_dir
dlog.info ("# working dir %s" % out_dir)
# Decide whether to use a given poscar
from_poscar = False
if 'from_poscar' in jdata :
from_poscar = jdata['from_poscar']
# Verify md_nstep
md_nstep_jdata = jdata["md_nstep"]
try:
md_incar = jdata['md_incar']
if os.path.isfile(md_incar):
with open(md_incar , "r") as fr:
md_incar_lines = fr.readlines()
nsw_flag = False
for incar_line in md_incar_lines:
line = incar_line.split()
if "NSW" in line:
nsw_flag = True
nsw_steps = int(incar_line.split()[-1])
break
#dlog.info("nsw_steps is", nsw_steps)
#dlog.info("md_nstep_jdata is", md_nstep_jdata)
if nsw_flag:
if (nsw_steps != md_nstep_jdata):
dlog.info("WARNING: your set-up for MD steps in PARAM and md_incar are not consistent!")
dlog.info("MD steps in PARAM is %d"%(md_nstep_jdata))
dlog.info("MD steps in md_incar is %d"%(nsw_steps))
dlog.info("DP-GEN will use settings in md_incar!")
jdata['md_nstep'] = nsw_steps
except:
pass
## correct element name
temp_elements = []
for ele in jdata['elements']:
temp_elements.append(ele[0].upper() + ele[1:])
jdata['elements'] = temp_elements
dlog.info("Elements are %s"% ' '.join(jdata['elements']))
## Iteration
stage_list = [int(i) for i in jdata['stages']]
for stage in stage_list:
if stage == 1 :
dlog.info("Current stage is 1, relax")
create_path(out_dir)
shutil.copy2(args.PARAM, os.path.join(out_dir, 'param.json'))
if from_poscar :
make_super_cell_poscar(jdata)
else :
make_unit_cell(jdata)
make_super_cell(jdata)
place_element(jdata)
if args.MACHINE is not None:
make_vasp_relax(jdata, mdata)
run_vasp_relax(jdata, mdata, disp)
else:
make_vasp_relax(jdata, {"fp_resources":{}})
elif stage == 2 :
dlog.info("Current stage is 2, perturb and scale")
make_scale(jdata)
pert_scaled(jdata)
elif stage == 3 :
dlog.info("Current stage is 3, run a short md")
make_vasp_md(jdata)
if args.MACHINE is not None:
run_vasp_md(jdata, mdata, disp)
elif stage == 4 :
dlog.info("Current stage is 4, collect data")
coll_vasp_md(jdata)
else :
raise RuntimeError("unknown stage %d" % stage)
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()
