import glob
import os
from multiprocessing import Pool
from packaging.version import Version
import dpgen.auto_test.lib.util as util
from dpgen import dlog
from dpgen.auto_test.calculator import make_calculator
from dpgen.auto_test.Elastic import Elastic
from dpgen.auto_test.EOS import EOS
from dpgen.auto_test.Gamma import Gamma
from dpgen.auto_test.Interstitial import Interstitial
from dpgen.auto_test.lib.utils import create_path
from dpgen.auto_test.Surface import Surface
from dpgen.auto_test.Vacancy import Vacancy
from dpgen.dispatcher.Dispatcher import make_submission
from dpgen.remote.decide_machine import convert_mdata
from dpgen.util import sepline
lammps_task_type = ["deepmd", "meam", "eam_fs", "eam_alloy"]
[docs]
def make_property_instance(parameters, inter_param):
"""Make an instance of Property."""
prop_type = parameters["type"]
if prop_type == "eos":
return EOS(parameters, inter_param)
elif prop_type == "elastic":
return Elastic(parameters, inter_param)
elif prop_type == "vacancy":
return Vacancy(parameters, inter_param)
elif prop_type == "interstitial":
return Interstitial(parameters, inter_param)
elif prop_type == "surface":
return Surface(parameters, inter_param)
elif prop_type == "gamma":
return Gamma(parameters, inter_param)
else:
raise RuntimeError(f"unknown property type {prop_type}")
[docs]
def make_property(confs, inter_param, property_list):
# find all POSCARs and their name like mp-xxx
# ...
# conf_dirs = glob.glob(confs)
# conf_dirs.sort()
conf_dirs = []
for conf in confs:
conf_dirs.extend(glob.glob(conf))
conf_dirs.sort()
for ii in conf_dirs:
sepline(ch=ii, screen=True)
for jj in property_list:
if jj.get("skip", False):
continue
if "init_from_suffix" and "output_suffix" in jj:
do_refine = True
suffix = jj["output_suffix"]
elif "reproduce" in jj and jj["reproduce"]:
do_refine = False
suffix = "reprod"
else:
do_refine = False
suffix = "00"
# generate working directory like mp-xxx/eos_00 if jj['type'] == 'eos'
# handel the exception that the working directory exists
# ...
# determine the suffix: from scratch or refine
# ...
property_type = jj["type"]
path_to_equi = os.path.join(ii, "relaxation", "relax_task")
path_to_work = os.path.join(ii, property_type + "_" + suffix)
create_path(path_to_work)
inter_param_prop = inter_param
if "cal_setting" in jj and "overwrite_interaction" in jj["cal_setting"]:
inter_param_prop = jj["cal_setting"]["overwrite_interaction"]
prop = make_property_instance(jj, inter_param_prop)
task_list = prop.make_confs(path_to_work, path_to_equi, do_refine)
for kk in task_list:
poscar = os.path.join(kk, "POSCAR")
inter = make_calculator(inter_param_prop, poscar)
inter.make_potential_files(kk)
dlog.debug(prop.task_type()) ### debug
inter.make_input_file(kk, prop.task_type(), prop.task_param())
prop.post_process(
task_list
) # generate same KPOINTS file for elastic when doing VASP
[docs]
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()
processes = len(property_list)
pool = Pool(processes=processes)
print("Submit job via %d processes" % processes)
conf_dirs = []
for conf in confs:
conf_dirs.extend(glob.glob(conf))
conf_dirs.sort()
task_list = []
work_path_list = []
multiple_ret = []
for ii in conf_dirs:
sepline(ch=ii, screen=True)
for jj in property_list:
# determine the suffix: from scratch or refine
# ...
if jj.get("skip", False):
continue
if "init_from_suffix" and "output_suffix" in jj:
suffix = jj["output_suffix"]
elif "reproduce" in jj and jj["reproduce"]:
suffix = "reprod"
else:
suffix = "00"
property_type = jj["type"]
path_to_work = os.path.abspath(
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)
inter_param_prop = inter_param
if "cal_setting" in jj and "overwrite_interaction" in jj["cal_setting"]:
inter_param_prop = jj["cal_setting"]["overwrite_interaction"]
# dispatch the tasks
# POSCAR here is useless
virtual_calculator = make_calculator(inter_param_prop, "POSCAR")
forward_files = virtual_calculator.forward_files(property_type)
forward_common_files = virtual_calculator.forward_common_files(
property_type
)
backward_files = virtual_calculator.backward_files(property_type)
# backward_files += logs
# ...
inter_type = inter_param_prop["type"]
# vasp
if inter_type in ["vasp", "abacus"]:
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)
work_path = path_to_work
all_task = tmp_task_list
run_tasks = util.collect_task(all_task, inter_type)
if len(run_tasks) == 0:
continue
else:
ret = pool.apply_async(
worker,
(
work_path,
all_task,
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():
print("ERROR:", multiple_ret[ii].get())
raise RuntimeError("Job %d is not successful!" % ii)
print("%d jobs are finished" % len(multiple_ret))
[docs]
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)
api_version = mdata.get("api_version", "1.0")
if Version(api_version) < Version("1.0"):
raise RuntimeError(
"API version %s has been removed. Please upgrade to 1.0." % api_version
)
elif Version(api_version) >= Version("1.0"):
submission = make_submission(
mdata_machine=machine,
mdata_resources=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()
[docs]
def post_property(confs, inter_param, property_list):
# find all POSCARs and their name like mp-xxx
# ...
# task_list = []
# conf_dirs = glob.glob(confs)
# conf_dirs.sort()
conf_dirs = []
for conf in confs:
conf_dirs.extend(glob.glob(conf))
conf_dirs.sort()
for ii in conf_dirs:
for jj in property_list:
# determine the suffix: from scratch or refine
# ...
if jj.get("skip", False):
continue
if "init_from_suffix" and "output_suffix" in jj:
suffix = jj["output_suffix"]
elif "reproduce" in jj and jj["reproduce"]:
suffix = "reprod"
else:
suffix = "00"
inter_param_prop = inter_param
if "cal_setting" in jj and "overwrite_interaction" in jj["cal_setting"]:
inter_param_prop = jj["cal_setting"]["overwrite_interaction"]
property_type = jj["type"]
path_to_work = os.path.join(ii, property_type + "_" + suffix)
prop = make_property_instance(jj, inter_param_prop)
prop.compute(
os.path.join(path_to_work, "result.json"),
os.path.join(path_to_work, "result.out"),
path_to_work,
)