def main():
parser = argparse.ArgumentParser()
parser.add_argument('-s',
'--structure',
dest='structure',
help='POSCAR file of the structure.')
args = parser.parse_args()
struc = Structure.from_file(args.structure)
working_path = os.getcwd()
import random
import string
rd_suffix = ''.join(
random.choices(string.ascii_uppercase + string.digits, k=4))
vasp_path = os.path.join(working_path, 'vasp_tmp_{0:}'.format(rd_suffix))
if not os.path.exists(vasp_path):
os.makedirs(vasp_path)
else:
shutil.rmtree(vasp_path)
os.makedirs(vasp_path)
relaxset = MPRelaxSet(struc,
force_gamma=True,
user_incar_settings={
"ISMEAR": 1,
"SIGMA": 0.2
})
relaxset.write_input(vasp_path)
os.chdir(vasp_path)
subprocess.call("mpirun -np 10 vasp5.2-openmpi", shell=True)
contcar = os.path.join(vasp_path, 'CONTCAR')
dst = os.path.join(working_path, 'POSCAR_optimized')
shutil.copyfile(contcar, dst)
def make_atom_mp_relax_set():
for element, potcar in PotcarSet.mp_relax_set.potcar_dict().items():
if potcar is None:
continue
if is_target_element(element) is False:
continue
structure = Structure(Lattice.cubic(10),
coords=[[0.5] * 3],
species=[element])
mp_set = MPRelaxSet(structure,
user_kpoints_settings=Kpoints(kpts=((1, 1, 1), )),
user_incar_settings={
"ALGO": "D",
"ISIF": 2,
"ISMEAR": 0,
"MAGMOM": {
"H": 1.0
},
"NELM": 300
})
Path(element).mkdir()
mp_set.write_input(element)
def disorder(self,apecies,spacegroup="C2"):
from pymatgen import Structure, Lattice
from pymatgen.io.vasp.sets import MPRelaxSet
import numpy as np
import os
cod=[]
for i in apecies:
cod.append(np.random.rand(3).tolist())
# print(cod)
custom_settings = {"NELMIN": 5}
specie = apecies
cuau = Structure.from_spacegroup(sg=spacegroup, lattice=Lattice.cubic(10), species=apecies, coords=cod)
relax = MPRelaxSet(cuau, user_incar_settings=custom_settings)
os.chdir(self.dire)
print (os.getcwd())
gge=[]
for n in specie:
for key,value in n.items():
gge.append(key)
jji=[]
for j in gge:
jji.append(str(j)[:-2])
str1 = "-".join(jji)
print (str1)
relax.write_input(str(str1))
def write_vasp_files(self):
"""
Writes:
a folder that includes vasp input file for a single structure, this is for relaxation
"""
mpset = MPRelaxSet(self.out_struc, user_incar_settings={'EDIFF': 1e-5, 'EDIFFG': 0.001, 'ALGO': 'F', 'ISMEAR': 0, 'ISIF': 2, 'IBRION': 2, 'NSW': 500}, \
user_kpoints_settings={'reciprocal_density': 1})
mpset.write_input(self.wd)
def Phonopy (self,mpid,supcell):
from pymatgen.io.vasp.outputs import Poscar
from pymatgen.io.vasp.inputs import Kpoints, Poscar
from pymatgen.io.vasp.outputs import Potcar
from pymatgen.io.vasp.sets import MPNMRSet
from pymatgen.io.phonopy import get_displaced_structures
from pymatgen.symmetry.bandstructure import HighSymmKpath
import shutil
import os
import subprocess
from pymatgen import Structure
from pymatgen.io.vasp.sets import MPRelaxSet
from pymatgen.ext.matproj import MPRester
import shutil
from shutil import copyfile
import sys
os.chdir(self.dire)
print (os.getcwd())
# isExists=os.path.exists(mpid+"isotope")
# if not isExists:
# os.mkdir( mpid+"isotope" )
# print ("Directory created")
# else:
# print (' directory already exists')
# pat = os.path.join(self.dire, mpid+"isotope")
# diree = os.chdir(pat)
# print (os.getcwd())
# print ("Directory entered ")
mpr = MPRester()
mp_id = mpid
structure = mpr.get_structure_by_material_id(mp_id)
relax = MPRelaxSet(structure)
relax.write_input(mp_id+"isotope")
print ("Input created")
pat = os.path.join(self.dire, mpid+"isotope")
os.chdir(pat)
print (os.getcwd())
print ("Directory entered ")
eb=str("phonopy -d --dim="+supcell)
with open('command.bat', 'w') as file_object:
file_object.write(eb )
subprocess.Popen("command.bat")
for filenames in os.walk(pat):
print (filenames)
def run_task(self, fw_spec):
struct = self.get("structure") or fw_spec["structure"]
s = Structure.from_dict(struct.as_dict())
user_incar_settings = fw_spec.get("user_incar_settings", {})
vasp_input_set = MPRelaxSet(s, user_incar_settings=user_incar_settings)
dec = MontyDecoder()
vis = dec.process_decoded(vasp_input_set.as_dict())
output_dir = os.getcwd()
vis.write_input(output_dir=output_dir)
return FWAction()
def write_vasp_files_relax(self, incar_path):
"""
should relax the structure again in tight criteria before running dfpt calculation
pymatgen inputset may not work very well, so just copy incar from a source
"""
mpset = MPRelaxSet(self.struc, user_kpoints_settings={'reciprocal_density': 250}, force_gamma=True)
mpset.write_input(os.path.join(self.wd, 'relax'))
p = subprocess.Popen(['cp', incar_path, 'INCAR'], cwd=os.path.join(self.wd, 'relax'))
p.wait()
def wf_bandstructure2D(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
vdw_kernel = c.get("VDW_KERNEL_DIR", VDW_KERNEL_DIR)
incar = _read_user_incar('Relax2D.txt')
print(incar)
mpr2d = MPRelaxSet(structure, force_gamma=True, user_incar_settings=incar)
mpr2dstatic = MPRelaxSet(structure,
force_gamma=True,
user_incar_settings={
"NEDOS": "3001",
"EMIN": "-15.0",
"EMAX": "15.0"
})
#fws = [OptimizeFW2D(structure=structure, vasp_input_set=mpr2d, vasp_cmd=vasp_cmd, db_file=db_file, vdw_kernel_dir=vdw_kernel)]
fws = [
OptimizeFW2D(structure=structure,
vasp_input_set=mpr2d,
vasp_cmd=vasp_cmd,
vdw_kernel_dir=vdw_kernel)
]
fws.append(StaticFW2D(parents=fws[0], vasp_input_set=mpr2dstatic))
#fws.append(NonSCFFW2D(parents=fws[1], mode='uniform'))
fws.append(NonSCFFW2D(parents=fws[1], mode='line'))
wf = Workflow(fws)
'''check bandstructure.yaml'''
'''
wf = get_wf(structure, "bandstructure.yaml", vis=MPScanRelaxSet2D(structure, force_gamma=True,), \
params=[{'vasp_input_set': mpr2d},{},{},{}], common_params={"vasp_cmd": vasp_cmd, "db_file": db_file,}) #"vdw_kernel_dir": vdw_kernel})
'''
wf = add_common_powerups(wf, c)
if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
wf = add_small_gap_multiply(wf, 0.5, 5, "static")
wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf,
fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
wf.name = "{}:{}".format(structure.composition.reduced_formula,
"bandStructure")
'''
fws = wf.fws
fws[0] = new_firework
print(fws)
'''
return wf
def download_structure(file_timestamp, download_option, data):
if not file_timestamp:
raise PreventUpdate
structure = self.from_data(data)
if isinstance(structure, StructureGraph):
structure = structure.structure
file_prefix = structure.composition.reduced_formula
if "VASP" not in download_option:
extension = self.download_options["Structure"][
download_option]["fmt"]
options = self.download_options["Structure"][download_option]
try:
contents = structure.to(**options)
except Exception as exc:
# don't fail silently, tell user what went wrong
contents = exc
base64 = b64encode(contents.encode("utf-8")).decode("ascii")
download_data = {
"content": base64,
"base64": True,
"type": "text/plain",
"filename": f"{file_prefix}.{extension}",
}
else:
if "Relax" in download_option:
vis = MPRelaxSet(structure)
expected_filename = "MPRelaxSet.zip"
else:
raise ValueError(
"No other VASP input sets currently supported.")
with TemporaryDirectory() as tmpdir:
vis.write_input(tmpdir, potcar_spec=True, zip_output=True)
path = Path(tmpdir) / expected_filename
bytes = b64encode(path.read_bytes()).decode("ascii")
download_data = {
"content": bytes,
"base64": True,
"type": "application/zip",
"filename": f"{file_prefix} {expected_filename}",
}
return download_data
def phase_sol(self, EB_K_2, judge='', appendage=""):
import os
from pymatgen import Structure
from pymatgen.io.vasp.sets import MPRelaxSet
from pymatgen import Structure, Lattice, MPRester, Molecule
import shutil
ass = self.cif_route
print(ass)
# os.chdir(r"D:\Desktop\VASP practical\Input")
# print (os.getcwd())
# Note that you must provide your own API Key, which can
# be accessed via the Dashboard at materialsproject.org
#mpr = MPRester()#密钥
molecule = Molecule.from_file(ass)
structure = molecule.get_boxed_structure(self.a, self.b, self.c)
print(structure)
os.chdir(r"D:\Desktop\VASP practical\Input")
print(os.getcwd())
custom_settings = {"NELMIN": 5} # user custom incar settings
relax = MPRelaxSet(structure, user_incar_settings=custom_settings)
os.chdir(r"D:\Desktop\VASP practical\Input")
print(os.getcwd())
relax.write_input(ass + '---' + "sol" + str(EB_K_2) + 'phase')
os.chdir("./" + ass + '---' + "sol" + str(EB_K_2) + 'phase')
#定义一个更改当前目录的变量
dire2 = './vaspstd_sub'
#确立脚本名称
shutil.copy(r"C:\Users\41958\.spyder-py3\vaspstd_sub", dire2)
eb = str(EB_K_2) #将介电常数参数作为字符串
ls = str('TURE') #加入开启溶剂参数
with open('INCAR', 'a') as file_object:
file_object.write('LSOL = ' + ls + '\n' + 'EB_K = ' + eb)
#将两个参数写入INCAR
eb = appendage #储存WAVECAR
with open('INCAR', 'r') as f1:
lines = f1.readlines()
with open('INCAR', 'w') as f2:
for line in lines:
if judge in line:
continue
f2.write(line)
with open('INCAR', 'a') as f3:
f3.write(eb)
os.chdir(r"D:\Desktop\VASP practical\workdir")
print(os.getcwd())
def phase(self, judge='', appendage=""):
import os
import re
from pymatgen import Structure
from pymatgen.io.vasp.sets import MPRelaxSet
from pymatgen.io.cif import CifParser
import shutil
ass = self.cif_route
print(ass)
# os.chdir(r"E:\VASP practical\Input")
# print (os.getcwd())
# Note that you must provide your own API Key, which can
# be accessed via the Dashboard at materialsproject.org
#mpr = MPRester()#密钥
struct = CifParser(ass)
structure = struct.get_structures()[0]
print(structure)
os.chdir(r"E:\VASP practical\Input")
print(os.getcwd())
structure.make_supercell(self.supercell)
custom_settings = {"NPAR": 4} # user custom incar settings
relax = MPRelaxSet(structure, user_incar_settings=custom_settings)
os.chdir(r"E:\VASP practical\Input")
print(os.getcwd())
relax.write_input(ass + '---' + 'phase')
os.chdir("./" + ass + '---' + 'phase')
#定义一个更改当前目录的变量
dire2 = './vaspstd_sub'
#确立脚本名称
shutil.copy(r"C:\Users\41958\.spyder-py3\vaspstd_sub", dire2)
eb = appendage #储存WAVECAR
with open('INCAR', 'r') as f1:
lines = f1.readlines()
with open('INCAR', 'w') as f2:
for line in lines:
if judge in line:
continue
f2.write(line)
with open('INCAR', 'a') as f3:
f3.write(eb)
#将两个参数写入INCAR
os.chdir(r"D:\Desktop\VASP practical\workdir")
print(os.getcwd())
def test_setup(self):
try:
vi = MPRelaxSet(self.struct_si, force_gamma=True)
vi.write_input(".")
except ValueError:
import traceback
traceback.print_exc()
help_str = "This system is not set up to run VASP jobs. See further error tracebacks " \
"for help. Try making sure your PMG_VASP_PSP_DIR has the proper subdirs as " \
"outlined in PotcarSingle class of pymatgen, e.g. POT_GGA_PAW_PBE subdir."
raise ValueError(help_str)
self._verify_files()
def wf_thermal_expansion(structure, c=None):
"""
Thermal expansion coefficient workflow from the given structure and config dict.
Args:
structure (Structure): input structure
c (dict): workflow config dict
Returns:
Workflow
"""
c = c or {}
eos = c.get("EOS", "vinet")
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
pressure = c.get("PRESSURE", 0.0)
user_kpoints_settings = {"grid_density": 7000}
# 10 deformations
deformations = [(np.identity(3) * (1 + x)).tolist() for x in np.linspace(-0.1, 0.1, 10)]
tag = "thermal_expansion group: >>{}<<".format(str(uuid4()))
# input set for structure optimization
vis_relax = MPRelaxSet(structure, force_gamma=True)
v = vis_relax.as_dict()
v.update({"user_kpoints_settings": user_kpoints_settings})
vis_relax = vis_relax.__class__.from_dict(v)
# optimization only workflow
wf = get_wf(structure, "optimize_only.yaml",
params=[{"vasp_cmd": vasp_cmd, "db_file": db_file,
"name": "{} structure optimization".format(tag)}],
vis=vis_relax)
wf_thermal = get_wf_thermal_expansion(structure, user_kpoints_settings=user_kpoints_settings,
deformations=deformations, vasp_cmd=vasp_cmd, db_file=db_file,
eos=eos, pressure=pressure, tag=tag)
# chain it
wf.append_wf(wf_thermal, wf.leaf_fw_ids)
wf = add_modify_incar(wf, modify_incar_params={"incar_update": {"ENCUT": 600, "EDIFF": 1e-6}})
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def __init__(self, mp_id, incar_settings: dict):
self.mp_id = str(mp_id)
self.structure = mpr.get_structure_by_material_id(self.mp_id)
self.primitive_structure = self.structure.get_primitive_structure()
self.kpath = HighSymmKpath(self.primitive_structure)
# self.new_kpoints = self.add_kpoints(self.kpath)
self.add_kpoints(self.kpath) # Add inverse kpoints intp kpath.__dict__['kpoints ']
self.relaxed_structure = MPRelaxSet(self.structure,
user_incar_settings=incar_settings)
self.relaxed_structure.potcar_functional = 'PW91' # Vasp functional set as potpaw_GGA
def test_setup(self):
try:
vi = MPRelaxSet(self.struct_si, force_gamma=True)
vi.write_input(".")
except ValueError:
import traceback
traceback.print_exc()
help_str = "This system is not set up to run VASP jobs. See further error tracebacks " \
"for help. Try making sure your PMG_VASP_PSP_DIR has the proper subdirs as " \
"outlined in PotcarSingle class of pymatgen, e.g. POT_GGA_PAW_PBE subdir."
raise ValueError(help_str)
self._verify_files()
def __init__(self,
structure,
name="structure optimization",
vasp_input_set=None,
vasp_cmd=VASP_CMD,
override_default_vasp_params=None,
ediffg=None,
db_file=DB_FILE,
force_gamma=True,
job_type="double_relaxation_run",
max_force_threshold=RELAX_MAX_FORCE,
auto_npar=">>auto_npar<<",
half_kpts_first_relax=HALF_KPOINTS_FIRST_RELAX,
parents=None,
**kwargs):
"""
Optimize the given structure.
Args:
structure (Structure): Input structure.
name (str): Name for the Firework.
vasp_input_set (VaspInputSet): input set to use. Defaults to MPRelaxSet() if None.
override_default_vasp_params (dict): If this is not None, these params are passed to
the default vasp_input_set, i.e., MPRelaxSet. This allows one to easily override
some settings, e.g., user_incar_settings, etc.
vasp_cmd (str): Command to run vasp.
ediffg (float): Shortcut to set ediffg in certain jobs
db_file (str): Path to file specifying db credentials to place output parsing.
force_gamma (bool): Force gamma centered kpoint generation
job_type (str): custodian job type (default "double_relaxation_run")
max_force_threshold (float): max force on a site allowed at end; otherwise, reject job
auto_npar (bool or str): whether to set auto_npar. defaults to env_chk: ">>auto_npar<<"
half_kpts_first_relax (bool): whether to use half the kpoints for the first relaxation
parents ([Firework]): Parents of this particular Firework.
\*\*kwargs: Other kwargs that are passed to Firework.__init__.
"""
override_default_vasp_params = override_default_vasp_params or {}
vasp_input_set = vasp_input_set or MPRelaxSet(
structure, force_gamma=force_gamma, **override_default_vasp_params)
t = []
t.append(
WriteVaspFromIOSet(structure=structure,
vasp_input_set=vasp_input_set))
t.append(
RunVaspCustodian(vasp_cmd=vasp_cmd,
job_type=job_type,
max_force_threshold=max_force_threshold,
ediffg=ediffg,
auto_npar=auto_npar,
half_kpts_first_relax=half_kpts_first_relax))
t.append(PassCalcLocs(name=name))
t.append(
VaspToDb(db_file=db_file, additional_fields={"task_label": name}))
super(OptimizeFW,
self).__init__(t,
parents=parents,
name="{}-{}".format(
structure.composition.reduced_formula, name),
**kwargs)
def wf_bandstructure_plus_boltztrap(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
params = []
for x in range(4): # everything but BoltzTrap task
params.append({"vasp_cmd": vasp_cmd, "db_file": db_file})
params.append({"db_file": db_file})
wf = get_wf(
structure,
"bandstructure_boltztrap.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
params=params,
)
wf = add_common_powerups(wf, c)
if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
wf = add_small_gap_multiply(wf, 0.5, 5, "static")
wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf,
fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def Write_Vasp_POTCAR(cal_loc, structure_filename, workflow):
"""
Write POTCAR in folder cal_loc as follows:
If POTCAR is missing, write POTCAR using pymatgen.io.vasp.sets.MPRelaxSet
Input arguments:
cal_loc (str): the absolute path
structure_filename (str): the file from which the structure is read using pymatgen.Structure.from_file
workflow
"""
firework = get_current_firework_from_cal_loc(cal_loc, workflow)
log_txt_loc, firework_name = os.path.split(cal_loc)
log_txt = os.path.join(log_txt_loc, "log.txt")
if not os.path.isfile(os.path.join(cal_loc, "POTCAR")):
structure = Structure.from_file(
os.path.join(cal_loc, structure_filename))
vis = MPRelaxSet(structure=structure)
vis.potcar.write_file(filename=os.path.join(cal_loc, "POTCAR"))
write_INCAR = True
with open(log_txt, "a") as f:
f.write("{} INFO: no POTCAR in {}\n".format(
get_time_str(), firework_name))
f.write(
"\t\t\tuse pymatgen.io.vasp.sets.MPRelaxSet to write POTCAR\n")
def test_ioset_explicit(self):
ft = WriteVaspFromIOSet(
dict(structure=self.struct_si,
vasp_input_set=MPRelaxSet(self.struct_si, force_gamma=True)))
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files()
def test_bandgap_check_Vasp(self):
# add the workflow
structure = self.struct_si
# instructs to use db_file set by FWorker, see env_chk
my_wf = get_wf(structure,
"bandstructure.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
common_params={
"vasp_cmd": VASP_CMD,
"db_file": ">>db_file<<"
})
if not VASP_CMD:
my_wf = use_fake_vasp(my_wf, ref_dirs_si)
else:
my_wf = use_custodian(my_wf)
my_wf = add_namefile(my_wf) # add a slug of fw-name to output files
my_wf = add_bandgap_check(my_wf,
check_bandgap_params={"max_gap": 0.1},
fw_name_constraint="structure optimization")
self.lp.add_wf(my_wf)
# run the workflow
# set the db_file variable
rapidfire(self.lp, fworker=_fworker)
# structure optimization should be completed
self.assertEqual(
self.lp.fireworks.find_one({"name": "Si-structure optimization"},
{"state": 1})["state"], "COMPLETED")
self.assertEqual(
self.lp.fireworks.find_one({"name": "Si-static"},
{"state": 1})["state"], "DEFUSED")
def test_trackers(self):
# add the workflow
structure = self.struct_si
my_wf = get_wf(structure,
"optimize_only.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
common_params={"vasp_cmd": VASP_CMD})
if not VASP_CMD:
my_wf = use_fake_vasp(my_wf, ref_dirs_si)
else:
my_wf = use_custodian(my_wf)
my_wf = add_trackers(my_wf)
self.lp.add_wf(my_wf)
# run the workflow
rapidfire(self.lp, fworker=_fworker)
for x in self.lp.get_tracker_data(1):
for t in x["trackers"]:
self.assertGreater(len(t.content.split("\n")), 20)
wf = self.lp.get_wf_by_fw_id(1)
self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
def wf_bandstructure(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
wf = get_wf(structure,
"bandstructure.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
common_params={
"vasp_cmd": vasp_cmd,
"db_file": db_file
})
wf = add_common_powerups(wf, c)
if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
wf = add_small_gap_multiply(wf, 0.5, 5, "static")
wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")
if c.get("STABILITY_CHECK", STABILITY_CHECK):
wf = add_stability_check(wf,
fw_name_constraint="structure optimization")
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def test_single_Vasp_dbinsertion(self):
# add the workflow
structure = self.struct_si
# instructs to use db_file set by FWorker, see env_chk
my_wf = get_wf(structure,
"optimize_only.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
common_params={
"vasp_cmd": VASP_CMD,
"db_file": ">>db_file<<"
})
if not VASP_CMD:
my_wf = use_fake_vasp(my_wf, ref_dirs_si)
else:
my_wf = use_custodian(my_wf)
# add an msonable object to additional fields
my_wf.fws[0].tasks[-1]['additional_fields'].update(
{"test_additional_field": self.struct_si})
self.lp.add_wf(my_wf)
# run the workflow
rapidfire(self.lp, fworker=_fworker)
d = self.get_task_collection().find_one()
self._check_run(d, mode="structure optimization")
self._check_run(d, mode="additional field")
wf = self.lp.get_wf_by_fw_id(1)
self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
def wf_structure_optimization(structure, c=None):
c = c or {}
vasp_cmd = c.get("VASP_CMD", VASP_CMD)
db_file = c.get("DB_FILE", DB_FILE)
user_incar_settings = c.get("USER_INCAR_SETTINGS")
wf = get_wf(
structure,
"optimize_only.yaml",
vis=MPRelaxSet(structure,
force_gamma=True,
user_incar_settings=user_incar_settings),
common_params={
"vasp_cmd": vasp_cmd,
"db_file": db_file
},
)
wf = add_common_powerups(wf, c)
if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
wf = add_wf_metadata(wf, structure)
return wf
def run_task(self, fw_spec):
chgcar_start = False
# read the VaspInput from the previous run
poscar = Poscar.from_file(zpath('POSCAR'))
incar = Incar.from_file(zpath('INCAR'))
# figure out what GGA+U values to use and override them
# LDAU values to use
mpvis = MPRelaxSet(poscar.structure)
ggau_incar = mpvis.incar.as_dict()
incar_updates = {
k: ggau_incar[k]
for k in ggau_incar.keys() if 'LDAU' in k
}
for k in ggau_incar:
# update any parameters not set explicitly in previous INCAR
if k not in incar and k in ggau_incar:
incar_updates[k] = ggau_incar[k]
incar.update(incar_updates) # override the +U keys
# start from the CHGCAR of previous run
if os.path.exists('CHGCAR'):
incar['ICHARG'] = 1
chgcar_start = True
# write back the new INCAR to the current directory
incar.write_file('INCAR')
return FWAction(stored_data={'chgcar_start': chgcar_start})
def test_single_Vasp_dbinsertion(self):
# add the workflow
structure = self.struct_si
# instructs to use db_file set by FWorker, see env_chk
my_wf = get_wf(structure,
"optimize_only.yaml",
vis=MPRelaxSet(structure, force_gamma=True),
common_params={
"vasp_cmd": VASP_CMD,
"db_file": ">>db_file<<"
})
if not VASP_CMD:
my_wf = use_fake_vasp(my_wf, ref_dirs_si)
else:
my_wf = use_custodian(my_wf)
self.lp.add_wf(my_wf)
# run the workflow
# set the db_file variable
rapidfire(
self.lp,
fworker=FWorker(env={"db_file": os.path.join(db_dir, "db.json")}))
d = self.get_task_collection().find_one()
self._check_run(d, mode="structure optimization")
wf = self.lp.get_wf_by_fw_id(1)
self.assertTrue(all([s == 'COMPLETED' for s in wf.fw_states.values()]))
def PBEsol_relaxation(self,output_dir='./'):
path = os.path.join(output_dir,self.name)
inputs = MPRelaxSet(self.stru).all_input
incar = inputs['INCAR']
if self.is_spin_polarized:
incar['ISPIN']=2
else:
incar['ISPIN']=1
enmax = round(max([i.PSCTR['ENMAX'] for i in inputs['POTCAR']])*1.3)
incar['ENCUT'] = int(enmax)
incar["SYSTEM"]=self.name + "_PBEsol_Relax"
incar["ALGO"] = "Normal"
incar["EDIFF"] = 0.0001
incar["EDIFFG"] = 0.001
incar["ISMEAR"] = 0
incar["GGA"] = "PS"
incar["NSW"] = 99
profile = {'source':self.mpid,'calculation':'PBEsol_relaxation'}
os.mkdir(path)
f=open(os.path.join(path,'profile.json'),'w')
f.write(json.dumps(jsanitize(profile)))
inputs['KPOINTS'].write_file(path+"/KPOINTS")
inputs['POSCAR'].write_file(path+"/POSCAR")
inputs['POTCAR'].write_file(path+"/POTCAR")
incar.write_file(path+"/INCAR")
def _snl_to_spec(snl, enforce_gga=False, parameters=None):
parameters = parameters if parameters else {}
parameters.setdefault('boltztrap', True) # by default run boltztrap
parameters.setdefault('force_gamma', False) # by default not force gamma
parameters.setdefault('exact_structure', True)
spec = {'parameters': parameters}
incar_enforce = {'NCORE': 8}
if parameters['exact_structure']:
structure = snl.structure
else:
structure = snl.structure.get_primitive_structure()
if enforce_gga:
incar_enforce.update({"LDAU": False})
mpvis = MPRelaxSet(structure,
user_incar_settings=incar_enforce,
force_gamma=parameters['force_gamma'])
incar = mpvis.incar
poscar = mpvis.poscar
kpoints = mpvis.kpoints
potcar = mpvis.potcar
spec['vasp'] = {}
spec['vasp']['incar'] = incar.as_dict()
spec['vasp']['poscar'] = poscar.as_dict()
spec['vasp']['kpoints'] = kpoints.as_dict()
spec['vasp']['potcar'] = potcar.as_dict()
# Add run tags of pseudopotential
spec['run_tags'] = spec.get('run_tags', [potcar.functional])
spec['run_tags'].extend(potcar.symbols)
# Add run tags of +U
u_tags = [
'%s=%s' % t
for t in zip(poscar.site_symbols,
incar.get('LDAUU', [0] * len(poscar.site_symbols)))
]
spec['run_tags'].extend(u_tags)
# add user run tags
if 'run_tags' in parameters:
spec['run_tags'].extend(parameters['run_tags'])
del spec['parameters']['run_tags']
# add exact structure run tag automatically if we have a unique situation
if 'exact_structure' in parameters and parameters['exact_structure'] and \
structure != snl.structure.get_primitive_structure():
spec['run_tags'].extend('exact_structure')
spec['_dupefinder'] = DupeFinderVasp().to_dict()
spec['vaspinputset_name'] = mpvis.__class__.__name__
spec['task_type'] = 'GGA+U optimize structure (2x)' if spec['vasp'][
'incar'].get('LDAU', False) else 'GGA optimize structure (2x)'
return spec
def make_atom_mp_relax_set():
for element, potcar in PotcarSet.mp_relax_set.potcar_dict().items():
if potcar is None:
continue
Path(element).mkdir()
structure = Structure(Lattice.cubic(10),
coords=[[0.5] * 3],
species=[element])
mp_set = MPRelaxSet(structure,
user_kpoints_settings=Kpoints(kpts=((1, 1, 1), )),
user_incar_settings={
"ISIF": 2,
"ISMEAR": 0,
"NUPDOWN": nupdown[element],
"NELM": 300
})
mp_set.write_input(element)
def test_pmgobjects(self):
mpvis = MPRelaxSet(self.struct_si, force_gamma=True)
ft = WriteVaspFromPMGObjects({"incar": mpvis.incar,
"poscar": mpvis.poscar,
"kpoints": mpvis.kpoints,
"potcar": mpvis.potcar})
ft = load_object(ft.to_dict()) # simulate database insertion
ft.run_task({})
self._verify_files()
def setUpClass(cls):
struct_si = PymatgenTest.get_structure("Si")
vis = MPRelaxSet(struct_si, force_gamma=True)
cls.bs_wf = get_wf(struct_si,
"bandstructure.yaml",
vis=vis, common_params={"vasp_cmd": "test_VASP"})
cls.bsboltz_wf = get_wf(struct_si,
"bandstructure_boltztrap.yaml",
vis=vis)
def __init__(self, structures, unset_encut=False, **kwargs):
if len(structures) < 3:
raise ValueError("You need at least 3 structures for an NEB.")
kwargs["sort_structure"] = False
MPRelaxSet.__init__(self, structures[0], **kwargs)
self.structures = self._process_structures(structures)
self.unset_encut = False
if unset_encut:
self.config_dict["INCAR"].pop("ENCUT", None)
if "EDIFF" not in self.config_dict["INCAR"]:
self.config_dict["INCAR"]["EDIFF"] = self.config_dict[
"INCAR"].pop("EDIFF_PER_ATOM")
# NEB specific defaults
defaults = {'IMAGES': len(structures) - 2, 'IBRION': 1, 'ISYM': 0,
'LCHARG': False, "LDAU": False}
self.config_dict["INCAR"].update(defaults)