#!/usr/bin/env python3
import argparse
import glob
import json
import os
import shutil
import sys
sys.path.insert(0, os.path.join(os.path.dirname(os.path.realpath(__file__)), ".."))
import dpdata
from dpgen.generator.lib.pwscf import make_pwscf_input
from dpgen.generator.lib.siesta import make_siesta_input
from dpgen.generator.run import update_mass_map
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def get_lmp_info(input_file):
with open(input_file) as fp:
lines = [line.rstrip("\n") for line in fp]
for ii in lines:
words = ii.split()
if len(words) >= 4 and words[0] == "variable":
if words[1] == "TEMP":
temp = float(words[3])
elif words[1] == "PRES":
pres = float(words[3])
if len(words) >= 4 and words[0] == "fix":
if words[3] == "nvt":
ens = "nvt"
elif words[3] == "npt":
ens = "npt"
return ens, temp, pres
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def link_pp_files(tdir, fp_pp_path, fp_pp_files):
cwd = os.getcwd()
os.chdir(tdir)
for ii in fp_pp_files:
if os.path.lexists(ii):
os.remove(ii)
os.symlink(os.path.join(fp_pp_path, ii), ii)
os.chdir(cwd)
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def copy_pp_files(tdir, fp_pp_path, fp_pp_files):
cwd = os.getcwd()
os.chdir(tdir)
for ii in fp_pp_files:
if os.path.lexists(ii):
os.remove(ii)
if os.path.exists(ii):
os.remove(ii)
shutil.copyfile(os.path.join(fp_pp_path, ii), ii)
os.chdir(cwd)
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def make_vasp(tdir, fp_params):
cwd = os.getcwd()
os.chdir(tdir)
incar = make_vasp_incar(fp_params)
with open("INCAR", "w") as fp:
fp.write(incar)
os.chdir(cwd)
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def make_vasp_incar(tdir, fp_incar):
cwd = os.getcwd()
os.chdir(tdir)
shutil.copyfile(fp_incar, "INCAR")
os.chdir(cwd)
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def make_pwscf(tdir, fp_params, mass_map, fp_pp_path, fp_pp_files, user_input):
cwd = os.getcwd()
os.chdir(tdir)
sys_data = dpdata.System("POSCAR").data
sys_data["atom_masses"] = mass_map
ret = make_pwscf_input(sys_data, fp_pp_files, fp_params)
open("input", "w").write(ret)
os.chdir(cwd)
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def make_siesta(tdir, fp_params, fp_pp_path, fp_pp_files):
cwd = os.getcwd()
os.chdir(tdir)
sys_data = dpdata.System("POSCAR").data
ret = make_siesta_input(sys_data, fp_pp_files, fp_params)
open("input", "w").write(ret)
os.chdir(cwd)
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def create_init_tasks(target_folder, param_file, output, fp_json, verbose=True):
target_folder = os.path.abspath(target_folder)
output = os.path.abspath(output)
tool_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "..", "template"
)
jdata = json.load(open(os.path.join(target_folder, param_file)))
update_mass_map(jdata)
fp_jdata = json.load(open(fp_json))
# fp settings
mass_map = jdata["mass_map"]
type_map = jdata["type_map"]
fp_style = fp_jdata["fp_style"]
fp_pp_path = fp_jdata["fp_pp_path"]
fp_pp_files = fp_jdata["fp_pp_files"]
cwd_ = os.getcwd()
os.chdir(target_folder)
fp_pp_path = os.path.abspath(fp_pp_path)
os.chdir(cwd_)
# init data sys
init_data_prefix = jdata["init_data_prefix"]
init_data_sys = jdata["init_data_sys"]
for idx, ii in enumerate(init_data_sys):
sys = dpdata.LabeledSystem(
os.path.join(init_data_prefix, ii), fmt="deepmd/npy", type_map=type_map
)
nframes = sys.get_nframes()
sys_dir = os.path.join(output, "init_system.%03d" % idx)
os.makedirs(sys_dir, exist_ok=True)
if verbose:
print("# working on " + sys_dir)
with open(os.path.join(sys_dir, "record"), "w") as fp:
fp.write(os.path.join(init_data_prefix, ii) + "\n")
for ff in range(nframes):
task_dir = os.path.join(sys_dir, "task.%06d" % ff)
os.makedirs(task_dir, exist_ok=True)
sys.to_vasp_poscar(os.path.join(task_dir, "POSCAR"), frame_idx=ff)
# make fp
cwd_ = os.getcwd()
os.chdir(task_dir)
for pp in fp_pp_files:
if os.path.lexists(pp):
os.remove(pp)
os.symlink(os.path.relpath(os.path.join(output, pp)), pp)
if fp_style == "vasp":
if os.path.lexists("INCAR"):
os.remove("INCAR")
os.symlink(os.path.relpath(os.path.join(output, "INCAR")), "INCAR")
elif fp_style == "pwscf":
try:
fp_params = fp_jdata["user_fp_params"]
user_input = True
except Exception:
fp_params = fp_jdata["fp_params"]
user_input = False
make_pwscf(
".", fp_params, mass_map, fp_pp_files, fp_pp_files, user_input
)
elif fp_style == "siesta":
make_siesta(".", fp_params, fp_pp_files, fp_pp_files)
os.chdir(cwd_)
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def create_tasks(
target_folder, param_file, output, fp_json, verbose=True, numb_iter=-1
):
target_folder = os.path.abspath(target_folder)
output = os.path.abspath(output)
tool_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), "..", "template"
)
jdata = json.load(open(os.path.join(target_folder, param_file)))
update_mass_map(jdata)
fp_jdata = json.load(open(fp_json))
# goto input
cwd = os.getcwd()
os.chdir(target_folder)
sys = jdata["sys_configs"]
# fp settings
mass_map = jdata["mass_map"]
fp_style = fp_jdata["fp_style"]
fp_pp_path = fp_jdata["fp_pp_path"]
fp_pp_files = fp_jdata["fp_pp_files"]
cwd_ = os.getcwd()
os.chdir(target_folder)
fp_pp_path = os.path.abspath(fp_pp_path)
os.chdir(cwd_)
fp_params = fp_jdata["fp_params"]
# collect tasks from iter dirs
sys_tasks = [[] for ii in sys]
sys_tasks_record = [[] for ii in sys]
sys_tasks_cc = [0 for ii in sys]
numb_sys = len(sys)
iters = glob.glob("iter.[0-9]*[0-9]")
iters.sort()
# iters = iters[:2]
for ii in iters[:numb_iter]:
iter_tasks = glob.glob(
os.path.join(ii, "02.fp", "task.[0-9]*[0-9].[0-9]*[0-9]")
)
iter_tasks.sort()
if verbose:
print("# check iter " + ii + " with %6d tasks" % len(iter_tasks))
for jj in iter_tasks:
sys_idx = int(os.path.basename(jj).split(".")[-2])
sys_tasks[sys_idx].append(jj)
if os.path.islink(os.path.join(jj, "conf.lmp")):
linked_file = os.path.realpath(os.path.join(jj, "conf.lmp"))
elif os.path.islink(os.path.join(jj, "conf.dump")):
linked_file = os.path.realpath(os.path.join(jj, "conf.dump"))
else:
raise RuntimeError("cannot file linked conf file")
linked_keys = linked_file.split("/")
task_record = (
linked_keys[-5]
+ "."
+ linked_keys[-3]
+ "."
+ linked_keys[-1].split(".")[0]
)
task_record_keys = task_record.split(".")
ens, temp, pres = get_lmp_info(
os.path.join(ii, "01.model_devi", linked_keys[-3], "input.lammps")
)
human_record = (
"iter: %s system: %s model_devi_task: %s frame: %6d fp_task: %s ens: %s temp: %10.2f pres: %10.2f"
% (
task_record_keys[1],
task_record_keys[3],
linked_keys[-3],
int(task_record_keys[-1]),
os.path.basename(jj),
ens,
temp,
pres,
)
)
# print(human_record)
sys_tasks_record[sys_idx].append(human_record)
# for ii in range(numb_sys) :
# for jj in range(len(sys_tasks[ii])) :
# print(sys_tasks[ii][jj], sys_tasks_record[ii][jj])
# mk output
os.makedirs(output, exist_ok=True)
if fp_style == "vasp":
copy_pp_files(output, fp_pp_path, fp_pp_files)
make_vasp_incar(fp_params, output)
if fp_style == "pwscf":
copy_pp_files(output, fp_pp_path, fp_pp_files)
if fp_style == "siesta":
copy_pp_files(output, fp_pp_path, fp_pp_files)
for si in range(numb_sys):
sys_dir = os.path.join(output, "system.%03d" % si)
if verbose:
print("# working on " + sys_dir)
for tt, rr in zip(sys_tasks[si], sys_tasks_record[si]):
# copy poscar
source_path = os.path.join(("iter.%s/02.fp" % rr.split()[1]), rr.split()[9])
source_file = os.path.join(source_path, "POSCAR")
target_path = os.path.join(sys_dir, "task.%06d" % sys_tasks_cc[si])
sys_tasks_cc[si] += 1
os.makedirs(target_path, exist_ok=True)
target_file = os.path.join(target_path, "POSCAR")
target_recd = os.path.join(target_path, "record")
if os.path.exists(target_file):
os.remove(target_file)
if os.path.exists(target_recd):
os.remove(target_recd)
shutil.copyfile(source_file, target_file)
with open(target_recd, "w") as fp:
fp.write("\n".join([target_folder, rr, ""]))
# make fp
cwd_ = os.getcwd()
os.chdir(target_path)
for pp in fp_pp_files:
if os.path.lexists(pp):
os.remove(pp)
os.symlink(os.path.relpath(os.path.join(output, pp)), pp)
if fp_style == "vasp":
if os.path.lexists("INCAR"):
os.remove("INCAR")
os.symlink(os.path.relpath(os.path.join(output, "INCAR")), "INCAR")
elif fp_style == "pwscf":
try:
fp_params = fp_jdata["user_fp_params"]
user_input = True
except Exception:
fp_params = fp_jdata["fp_params"]
user_input = False
make_pwscf(
".", fp_params, mass_map, fp_pp_files, fp_pp_files, user_input
)
elif fp_style == "siesta":
make_siesta(".", fp_params, mass_map, fp_pp_files, fp_pp_files)
os.chdir(cwd_)
os.chdir(cwd)
def _main():
parser = argparse.ArgumentParser(
description="Create tasks for relabeling from a DP-GEN job"
)
parser.add_argument("JOB_DIR", type=str, help="the directory of the DP-GEN job")
parser.add_argument(
"PARAM", type=str, default="fp.json", help="the json file defines vasp tasks"
)
parser.add_argument(
"OUTPUT", type=str, help="the output directory of relabel tasks"
)
parser.add_argument(
"-p",
"--parameter",
type=str,
default="param.json",
help="the json file provides DP-GEN paramters, should be located in JOB_DIR",
)
parser.add_argument(
"-n",
"--numb-iter",
type=int,
default=-1,
help="number of iterations to relabel",
)
parser.add_argument("-v", "--verbose", action="store_true", help="being loud")
args = parser.parse_args()
create_tasks(
args.JOB_DIR,
args.parameter,
args.OUTPUT,
args.PARAM,
numb_iter=args.numb_iter,
verbose=args.verbose,
)
create_init_tasks(
args.JOB_DIR, args.parameter, args.OUTPUT, args.PARAM, verbose=args.verbose
)
if __name__ == "__main__":
_main()