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VASP_OPs.py
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from dflow import config, s3_config
config["host"] = "xxx"
s3_config["endpoint"] = "xxx"
config["k8s_api_server"] = "xxx"
config["token"] = "xxx"
from typing import List
from dflow import (
Workflow,
Step,
argo_range,
SlurmRemoteExecutor,
upload_artifact,
download_artifact,
InputArtifact,
OutputArtifact,
ShellOPTemplate
)
from dflow.python import (
PythonOPTemplate,
OP,
OPIO,
OPIOSign,
Artifact,
Slices,
upload_packages
)
import time
import subprocess, os, shutil, glob,dpdata,pathlib
from pathlib import Path
from typing import List
from monty.serialization import loadfn
from dflow.plugins.bohrium import BohriumContext, BohriumExecutor
from dpdata.periodic_table import Element
from monty.serialization import loadfn
from dflow.python import upload_packages
upload_packages.append(__file__)
class PhononMakeVASP(OP):
"""
class for making calculation tasks
"""
def __init__(self):
pass
@classmethod
def get_input_sign(cls):
return OPIOSign({
'input': Artifact(Path)
})
@classmethod
def get_output_sign(cls):
return OPIOSign({
'output' : Artifact(Path),
'njobs':int,
'jobs': Artifact(List[Path])
})
@OP.exec_sign_check
def execute(
self,
op_in: OPIO,
) -> OPIO:
cwd = os.getcwd()
os.chdir(op_in["input"])
work_d = os.getcwd()
parameter = loadfn("param.json")["properties"]
inter_param_prop = loadfn("param.json")["interaction"]
parameter['primitive'] = parameter.get('primitive', False)
parameter['approach'] =parameter.get('approach', "linear")
band_path = parameter['band_path']
supercell_matrix = parameter['supercell_matrix']
primitive = parameter['primitive']
approach = parameter['approach']
if primitive:
subprocess.call('phonopy --symmetry',shell=True)
subprocess.call('cp PPOSCAR POSCAR',shell=True)
shutil.copyfile("PPOSCAR","POSCAR-unitcell")
else:
shutil.copyfile("POSCAR","POSCAR-unitcell")
with open("POSCAR","r") as fp:
lines = fp.read().split('\n')
ele_list = lines[5].split()
cmd = "phonopy -d --dim='%d %d %d' -c POSCAR"%(int(supercell_matrix[0]),int(supercell_matrix[1]),int(supercell_matrix[2]))
subprocess.call(cmd,shell=True)
task_list = []
if(approach == "linear"):
output_task = os.path.join(work_d,'task.000000')
os.makedirs(output_task,exist_ok = True)
os.chdir(output_task)
for jj in ['INCAR', 'POTCAR', 'POSCAR', 'conf.lmp', 'in.lammps','POSCAR-unitcell','SPOSCAR']:
if os.path.exists(jj):
os.remove(jj)
task_list.append(output_task)
os.symlink(os.path.join(work_d,"SPOSCAR"),"POSCAR")
os.symlink(os.path.join(work_d,"POSCAR-unitcell"),"POSCAR-unitcell")
os.symlink(os.path.join(work_d,"INCAR"),"INCAR")
os.symlink(os.path.join(work_d,"POTCAR"),"POTCAR")
os.symlink(os.path.join(work_d,"param.json"),"param.json")
with open('band.conf','w') as fp:
fp.write('ATOM_NAME = ')
for ii in ele_list:
fp.write(ii)
fp.write(' ')
fp.write('\n')
fp.write('DIM = %s %s %s\n'%(supercell_matrix[0],supercell_matrix[1],supercell_matrix[2]))
fp.write('BAND = %s\n'%band_path)
fp.write('FORCE_CONSTANTS=READ\n')
elif(approach == "displacement"):
poscar_list = glob.glob("POSCAR-0*")
n_task = len(poscar_list)
for ii in range(n_task):
output_task = os.path.join(work_d,'task.%06d' % ii)
os.makedirs(output_task,exist_ok=True)
os.chdir(output_task)
for jj in ['INCAR', 'POTCAR', 'POSCAR', 'conf.lmp', 'in.lammps','POSCAR-unitcell','SPOSCAR']:
if os.path.exists(jj):
os.remove(jj)
task_list.append(output_task)
os.symlink(os.path.join(work_d,poscar_list[ii]), 'POSCAR')
os.symlink(os.path.join(work_d,"PPOSCAR"),"POSCAR-unitcell")
os.symlink(os.path.join(work_d,"INCAR"),"INCAR")
os.symlink(os.path.join(work_d,"POTCAR"),"POTCAR")
os.symlink(os.path.join(work_d,"param.json"),"param.json")
os.chdir("../")
with open('band.conf','w') as fp:
fp.write('ATOM_NAME = ')
for ii in ele_list:
fp.write(ii)
fp.write(' ')
fp.write('\n')
fp.write('DIM = %s %s %s\n'%(supercell_matrix[0],supercell_matrix[1],supercell_matrix[2]))
fp.write('BAND = %s\n'%band_path)
shutil.copyfile("band.conf","task.000000/band.conf")
shutil.copyfile("phonopy_disp.yaml","task.000000/phonopy_disp.yaml")
jobss = glob.glob(os.path.join(work_d,"task*"))
njobs = len(jobss)
jobs = []
for job in jobss:
jobs.append(pathlib.Path(job))
os.chdir(cwd)
op_out = OPIO({
"output" : op_in["input"],
"njobs": njobs,
"jobs": jobs
})
return op_out
class VASP(OP):
"""
class for VASP calculation
"""
def __init__(self,infomode=1):
self.infomode = infomode
@classmethod
def get_input_sign(cls):
return OPIOSign({
'input_dfpt': Artifact(Path),
})
@classmethod
def get_output_sign(cls):
return OPIOSign({
'output_dfpt': Artifact(Path)
})
@OP.exec_sign_check
def execute(self, op_in: OPIO) -> OPIO:
cwd = os.getcwd()
os.chdir(op_in["input_dfpt"])
cmd = "bash -c \"source /opt/intel/oneapi/setvars.sh && ulimit -s unlimited && mpirun -n 64 /opt/vasp.5.4.4/bin/vasp_std \""
subprocess.call(cmd, shell=True)
os.chdir(cwd)
op_out = OPIO({
"output_dfpt": op_in["input_dfpt"]
})
return op_out
class PhononPostVASP(OP):
"""
class for analyse calculation results
"""
def __init__(self):
pass
@classmethod
def get_input_sign(cls):
return OPIOSign({
'input_post': Artifact(Path)
})
@classmethod
def get_output_sign(cls):
return OPIOSign({
'output_post': Artifact(Path)
})
@OP.exec_sign_check
def execute(self, op_in: OPIO) -> OPIO:
os.chdir(op_in["input_post"])
cwdd = os.getcwd()
try:
os.chdir(os.path.join(cwdd,"work_dir"))
shutil.copyfile("task.000000/band.conf","band.conf")
shutil.copyfile("task.000000/param.json","param.json")
shutil.copyfile("task.000000/POSCAR-unitcell","POSCAR-unitcell")
except:
pass
parameter = loadfn("param.json")["properties"]
inter_param_prop = loadfn("param.json")["interaction"]
parameter['primitive'] = parameter.get('primitive', False)
parameter['approach'] =parameter.get('approach', "linear")
band_path = parameter['band_path']
supercell_matrix = parameter['supercell_matrix']
primitive = parameter['primitive']
approach = parameter['approach']
if(approach == "linear"):
if os.path.isfile('vasprun.xml'):
os.system('phonopy --fc vasprun.xml')
if os.path.isfile('FORCE_CONSTANTS'):
os.system('phonopy --dim="%s %s %s" -c POSCAR-unitcell band.conf'%(supercell_matrix[0],supercell_matrix[1],supercell_matrix[2]))
os.system('phonopy-bandplot --gnuplot band.yaml > band.dat')
print('band.dat is created')
shutil.copyfile("band.dat","../band.dat")
else:
print('FORCE_CONSTANTS No such file')
else:
print('vasprun.xml No such file')
elif(approach == "displacement"):
try:
os.chdir(os.path.join(cwdd,"work_dir"))
shutil.copyfile("task.000000/band.conf","band.conf")
shutil.copyfile("task.000000/phonopy_disp.yaml","phonopy_disp.yaml")
os.system('phonopy -f task.0*/vasprun.xml')
except:
os.system('phonopy -f vasprun.xml')
if os.path.exists("FORCE_SETS"):
print('FORCE_SETS is created')
else:
print('FORCE_SETS can not be created')
os.system('phonopy --dim="%s %s %s" -c POSCAR-unitcell band.conf'%(supercell_matrix[0],supercell_matrix[1],supercell_matrix[2]))
os.system('phonopy-bandplot --gnuplot band.yaml > band.dat')
try:
shutil.copyfile("band.dat","task.000000/band.dat")
except:
pass
op_out = OPIO({
"output_post": op_in["input_post"]
})
return op_out