Source code for dpgen.auto_test.VASP
import os
from dpdata import LabeledSystem
from monty.serialization import dumpfn
from pymatgen.core.structure import Structure
from pymatgen.io.vasp import Incar, Kpoints
import dpgen.auto_test.lib.vasp as vasp
from dpgen import dlog
from dpgen.auto_test.Task import Task
from dpgen.generator.lib.vasp import incar_upper
from dpgen.util import sepline
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class VASP(Task):
def __init__(self, inter_parameter, path_to_poscar):
self.inter = inter_parameter
self.inter_type = inter_parameter["type"]
self.incar = inter_parameter["incar"]
self.potcar_prefix = inter_parameter.get("potcar_prefix", "")
self.potcars = inter_parameter["potcars"]
self.path_to_poscar = path_to_poscar
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def make_potential_files(self, output_dir):
potcar_not_link_list = ["vacancy", "interstitial"]
task_type = output_dir.split("/")[-2].split("_")[0]
ele_pot_list = [key for key in self.potcars.keys()]
poscar = os.path.abspath(os.path.join(output_dir, "POSCAR"))
pos_str = Structure.from_file(poscar)
ele_pos_list_tmp = list(ii.as_dict()["element"] for ii in pos_str.species)
ele_pos_list = [ele_pos_list_tmp[0]]
for ii in range(1, len(ele_pos_list_tmp)):
if not ele_pos_list_tmp[ii] == ele_pos_list_tmp[ii - 1]:
ele_pos_list.append(ele_pos_list_tmp[ii])
if task_type in potcar_not_link_list:
with open(os.path.join(output_dir, "POTCAR"), "w") as fp:
for ii in ele_pos_list:
for jj in ele_pot_list:
if ii == jj:
with open(
os.path.join(self.potcar_prefix, self.potcars[jj])
) as fin:
for line in fin:
print(line.strip("\n"), file=fp)
else:
if not os.path.isfile(os.path.join(output_dir, "../POTCAR")):
with open(os.path.join(output_dir, "../POTCAR"), "w") as fp:
for ii in ele_pos_list:
for jj in ele_pot_list:
if ii == jj:
with open(
os.path.join(self.potcar_prefix, self.potcars[jj]),
) as fin:
for line in fin:
print(line.strip("\n"), file=fp)
cwd = os.getcwd()
os.chdir(output_dir)
if not os.path.islink("POTCAR"):
os.symlink("../POTCAR", "POTCAR")
elif not "../POTCAR" == os.readlink("POTCAR"):
os.remove("POTCAR")
os.symlink("../POTCAR", "POTCAR")
os.chdir(cwd)
dumpfn(self.inter, os.path.join(output_dir, "inter.json"), indent=4)
[docs]
def make_input_file(self, output_dir, task_type, task_param):
sepline(ch=output_dir)
dumpfn(task_param, os.path.join(output_dir, "task.json"), indent=4)
assert os.path.exists(self.incar), "no INCAR file for relaxation"
relax_incar_path = os.path.abspath(self.incar)
incar_relax = incar_upper(Incar.from_file(relax_incar_path))
# deal with relaxation
cal_type = task_param["cal_type"]
cal_setting = task_param["cal_setting"]
# user input INCAR for property calculation
if "input_prop" in cal_setting and os.path.isfile(cal_setting["input_prop"]):
incar_prop = os.path.abspath(cal_setting["input_prop"])
incar = incar_upper(Incar.from_file(incar_prop))
# revise INCAR based on the INCAR provided in the "interaction"
else:
incar = incar_relax
if cal_type == "relaxation":
relax_pos = cal_setting["relax_pos"]
relax_shape = cal_setting["relax_shape"]
relax_vol = cal_setting["relax_vol"]
if [relax_pos, relax_shape, relax_vol] == [True, False, False]:
isif = 2
elif [relax_pos, relax_shape, relax_vol] == [True, True, True]:
isif = 3
elif [relax_pos, relax_shape, relax_vol] == [True, True, False]:
isif = 4
elif [relax_pos, relax_shape, relax_vol] == [False, True, False]:
isif = 5
elif [relax_pos, relax_shape, relax_vol] == [False, True, True]:
isif = 6
elif [relax_pos, relax_shape, relax_vol] == [False, False, True]:
isif = 7
elif [relax_pos, relax_shape, relax_vol] == [False, False, False]:
nsw = 0
isif = 2
if not ("NSW" in incar and incar.get("NSW") == nsw):
dlog.info(
"%s setting NSW to %d"
% (self.make_input_file.__name__, nsw)
)
incar["NSW"] = nsw
else:
raise RuntimeError("not supported calculation setting for VASP")
if not ("ISIF" in incar and incar.get("ISIF") == isif):
dlog.info(
"%s setting ISIF to %d" % (self.make_input_file.__name__, isif)
)
incar["ISIF"] = isif
elif cal_type == "static":
nsw = 0
if not ("NSW" in incar and incar.get("NSW") == nsw):
dlog.info(
"%s setting NSW to %d" % (self.make_input_file.__name__, nsw)
)
incar["NSW"] = nsw
else:
raise RuntimeError("not supported calculation type for VASP")
if "ediff" in cal_setting:
dlog.info(
"{} setting EDIFF to {}".format(
self.make_input_file.__name__, cal_setting["ediff"]
)
)
incar["EDIFF"] = cal_setting["ediff"]
if "ediffg" in cal_setting:
dlog.info(
"{} setting EDIFFG to {}".format(
self.make_input_file.__name__, cal_setting["ediffg"]
)
)
incar["EDIFFG"] = cal_setting["ediffg"]
if "encut" in cal_setting:
dlog.info(
"{} setting ENCUT to {}".format(
self.make_input_file.__name__, cal_setting["encut"]
)
)
incar["ENCUT"] = cal_setting["encut"]
if "kspacing" in cal_setting:
dlog.info(
"{} setting KSPACING to {}".format(
self.make_input_file.__name__, cal_setting["kspacing"]
)
)
incar["KSPACING"] = cal_setting["kspacing"]
if "kgamma" in cal_setting:
dlog.info(
"{} setting KGAMMA to {}".format(
self.make_input_file.__name__, cal_setting["kgamma"]
)
)
incar["KGAMMA"] = cal_setting["kgamma"]
try:
kspacing = incar.get("KSPACING")
except KeyError:
raise RuntimeError("KSPACING must be given in INCAR")
if "KGAMMA" in incar:
kgamma = incar.get("KGAMMA")
else:
kgamma = False
incar.write_file(os.path.join(output_dir, "../INCAR"))
cwd = os.getcwd()
os.chdir(output_dir)
if not os.path.islink("INCAR"):
os.symlink("../INCAR", "INCAR")
elif not "../INCAR" == os.readlink("INCAR"):
os.remove("INCAR")
os.symlink("../INCAR", "INCAR")
os.chdir(cwd)
ret = vasp.make_kspacing_kpoints(self.path_to_poscar, kspacing, kgamma)
try:
kp = Kpoints.from_string(ret)
except AttributeError:
kp = Kpoints.from_str(ret)
kp.write_file(os.path.join(output_dir, "KPOINTS"))
[docs]
def compute(self, output_dir):
outcar = os.path.join(output_dir, "OUTCAR")
if not os.path.isfile(outcar):
dlog.warning("cannot find OUTCAR in " + output_dir + " skip")
return None
else:
ls = LabeledSystem(outcar)
stress = []
with open(outcar) as fin:
lines = fin.read().split("\n")
for line in lines:
if "in kB" in line:
stress_xx = float(line.split()[2])
stress_yy = float(line.split()[3])
stress_zz = float(line.split()[4])
stress_xy = float(line.split()[5])
stress_yz = float(line.split()[6])
stress_zx = float(line.split()[7])
stress.append([])
stress[-1].append([stress_xx, stress_xy, stress_zx])
stress[-1].append([stress_xy, stress_yy, stress_yz])
stress[-1].append([stress_zx, stress_yz, stress_zz])
outcar_dict = ls.as_dict()
outcar_dict["data"]["stress"] = {
"@module": "numpy",
"@class": "array",
"dtype": "float64",
"data": stress,
}
return outcar_dict
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def forward_files(self, property_type="relaxation"):
return ["INCAR", "POSCAR", "KPOINTS", "POTCAR"]
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def forward_common_files(self, property_type="relaxation"):
potcar_not_link_list = ["vacancy", "interstitial"]
if property_type == "elastic":
return ["INCAR", "KPOINTS", "POTCAR"]
elif property_type in potcar_not_link_list:
return ["INCAR"]
else:
return ["INCAR", "POTCAR"]
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def backward_files(self, property_type="relaxation"):
return ["OUTCAR", "outlog", "CONTCAR", "OSZICAR", "XDATCAR"]