#!/usr/bin/env python3
import os
import re
import sys
import argparse
import glob
import json
import random
import logging
import warnings
import shutil
import time
import dpdata
import numpy as np
from dpgen import dlog
import subprocess as sp
import dpgen.data.tools.hcp as hcp
import dpgen.data.tools.fcc as fcc
import dpgen.data.tools.bcc as bcc
import dpgen.data.tools.diamond as diamond
import dpgen.data.tools.sc as sc
from distutils.version import LooseVersion
from dpgen.generator.lib.vasp import incar_upper
from dpgen.generator.lib.utils import symlink_user_forward_files
from dpgen.generator.lib.abacus_scf import get_abacus_input_parameters, get_abacus_STRU, make_supercell_abacus, make_abacus_scf_stru\
, make_kspacing_kpoints_stru, make_abacus_scf_kpt
from pymatgen.core import Structure
from pymatgen.io.vasp import Incar
from dpgen.remote.decide_machine import convert_mdata
from dpgen import ROOT_PATH
from dpgen.dispatcher.Dispatcher import Dispatcher, make_dispatcher, make_submission
[docs]def create_path (path,back=False) :
if path[-1] != "/":
path += '/'
if os.path.isdir(path) :
if back:
dirname = os.path.dirname(path)
counter = 0
while True :
bk_dirname = dirname + ".bk%03d" % counter
if not os.path.isdir(bk_dirname) :
shutil.move (dirname, bk_dirname)
break
counter += 1
os.makedirs (path)
return path
else:
return path
os.makedirs (path)
return path
[docs]def replace (file_name, pattern, subst) :
file_handel = open (file_name, 'r')
file_string = file_handel.read ()
file_handel.close ()
file_string = ( re.sub (pattern, subst, file_string) )
file_handel = open (file_name, 'w')
file_handel.write (file_string)
file_handel.close ()
"""
0, make unit cell
1, copy
2, place element
3, relax
4, perturb
"""
global_dirname_02 = '00.place_ele'
global_dirname_03 = '01.scale_pert'
global_dirname_04 = '02.md'
[docs]def out_dir_name(jdata) :
elements = jdata['elements']
super_cell = jdata['super_cell']
from_poscar = jdata.get('from_poscar', False)
if from_poscar:
from_poscar_path = jdata['from_poscar_path']
poscar_name = os.path.basename(from_poscar_path)
cell_str = "%02d" % (super_cell[0])
for ii in range(1,len(super_cell)) :
cell_str = cell_str + ("x%02d" % super_cell[ii])
return poscar_name + '.' + cell_str
else :
cell_type = jdata['cell_type']
ele_str = ""
for ii in elements:
ele_str = ele_str + ii.lower()
cell_str = "%02d" % (super_cell[0])
for ii in range(1,len(super_cell)) :
cell_str = cell_str + ("x%02d" % super_cell[ii])
return ele_str + '.' + cell_type + '.' + cell_str
[docs]def class_cell_type(jdata) :
ct = jdata['cell_type']
if ct == "hcp" :
cell_type = hcp
elif ct == "fcc" :
cell_type = fcc
elif ct == "diamond" :
cell_type = diamond
elif ct == "sc" :
cell_type = sc
elif ct == "bcc" :
cell_type = bcc
else :
raise RuntimeError("unknown cell type %s" % ct)
return cell_type
[docs]def poscar_ele(poscar_in, poscar_out, eles, natoms) :
ele_line = ""
natom_line = ""
for ii in eles :
ele_line += str(ii) + " "
for ii in natoms :
natom_line += str(ii) + " "
with open(poscar_in, 'r') as fin :
lines = list(fin)
lines[5] = ele_line + "\n"
lines[6] = natom_line + "\n"
with open(poscar_out, 'w') as fout :
fout.write("".join(lines))
[docs]def stru_ele(supercell_stru, stru_out, eles, natoms, jdata, path_work):
supercell_stru["types"] = []
supercell_stru["atom_numbs"] = list(natoms)
for iele in range(len(natoms)):
for iatom in range(natoms[iele]):
supercell_stru["types"].append(iele)
pp_file_names = [os.path.basename(a) for a in jdata['potcars']]
orb_file_names = None
dpks_descriptor_name = None
if 'orb_files' in jdata:
orb_file_names = [os.path.basename(a) for a in jdata['orb_files']]
if 'dpks_descriptor' in jdata:
dpks_descriptor_name = os.path.basename(jdata['dpks_descriptor'])
supercell_stru["atom_masses"] = jdata["atom_masses"]
supercell_stru["atom_names"] = eles
stru_text = make_abacus_scf_stru(supercell_stru, pp_file_names, orb_file_names, dpks_descriptor_name)
with open(stru_out, "w") as f:
f.write(stru_text)
absolute_pp_file_path = [os.path.abspath(a) for a in jdata["potcars"]]
if 'orb_files' in jdata:
absolute_orb_file_path = [os.path.abspath(a) for a in jdata['orb_files']]
if 'dpks_descriptor' in jdata:
absolute_dpks_descriptor_path = os.path.abspath(jdata['dpks_descriptor'])
for ipp, pp_file in enumerate(absolute_pp_file_path):
os.symlink(pp_file, os.path.join(path_work, pp_file_names[ipp]))
if 'orb_files' in jdata:
os.symlink(absolute_orb_file_path[ipp], os.path.join(path_work, orb_file_names[ipp]))
if 'dpks_descriptor' in jdata:
os.symlink(absolute_dpks_descriptor_path, os.path.join(path_work, dpks_descriptor_name))
[docs]def poscar_natoms(lines) :
numb_atoms = 0
for ii in lines[6].split() :
numb_atoms += int(ii)
return numb_atoms
[docs]def poscar_shuffle(poscar_in, poscar_out) :
with open(poscar_in, 'r') as fin :
lines = list(fin)
numb_atoms = poscar_natoms(lines)
idx = np.arange(8, 8+numb_atoms)
np.random.shuffle(idx)
out_lines = lines[0:8]
for ii in range(numb_atoms) :
out_lines.append(lines[idx[ii]])
with open(poscar_out, 'w') as fout:
fout.write("".join(out_lines))
[docs]def shuffle_stru_data(supercell_stru):
atom_numb = sum(supercell_stru["atom_numbs"])
assert(np.shape(supercell_stru["coords"]) == (atom_numb, 3))
new_coord = np.zeros([atom_numb, 3])
order = np.arange(0, atom_numb)
np.random.shuffle(order)
for idx in range(atom_numb):
new_coord[idx] = supercell_stru["coords"][order[idx]]
supercell_stru['coords'] = new_coord
return supercell_stru
[docs]def poscar_scale_direct (str_in, scale) :
lines = str_in.copy()
numb_atoms = poscar_natoms(lines)
pscale = float(lines[1])
pscale = pscale * scale
lines[1] = str(pscale) + "\n"
return lines
[docs]def poscar_scale_cartesian (str_in, scale) :
lines = str_in.copy()
numb_atoms = poscar_natoms(lines)
# scale box
for ii in range(2,5) :
boxl = lines[ii].split()
boxv = [float(ii) for ii in boxl]
boxv = np.array(boxv) * scale
lines[ii] = "%.16e %.16e %.16e\n" % (boxv[0], boxv[1], boxv[2])
# scale coord
for ii in range(8, 8+numb_atoms) :
cl = lines[ii].split()
cv = [float(ii) for ii in cl]
cv = np.array(cv) * scale
lines[ii] = "%.16e %.16e %.16e\n" % (cv[0], cv[1], cv[2])
return lines
[docs]def poscar_scale (poscar_in, poscar_out, scale) :
with open(poscar_in, 'r') as fin :
lines = list(fin)
if 'D' == lines[7][0] or 'd' == lines[7][0]:
lines = poscar_scale_direct(lines, scale)
elif 'C' == lines[7][0] or 'c' == lines[7][0] :
lines = poscar_scale_cartesian(lines, scale)
else :
raise RuntimeError("Unknow poscar style at line 7: %s" % lines[7])
with open(poscar_out, 'w') as fout:
fout.write("".join(lines))
[docs]def poscar_scale_abacus(poscar_in, poscar_out, scale, jdata):
stru = get_abacus_STRU(poscar_in, n_ele=len(jdata["elements"]))
stru["cells"] *= scale
stru["coords"] *= scale
pp_files = [os.path.basename(a) for a in jdata['potcars']]
orb_file_names = None
dpks_descriptor_name = None
if 'orb_files' in jdata:
orb_file_names = [os.path.basename(a) for a in jdata['orb_files']]
if 'dpks_descriptor' in jdata:
dpks_descriptor_name = os.path.basename(jdata['dpks_descriptor'])
ret = make_abacus_scf_stru(stru, pp_files, orb_file_names, dpks_descriptor_name)
#ret = make_abacus_scf_stru(stru, pp_files)
with open(poscar_out, "w") as fp:
fp.write(ret)
[docs]def make_unit_cell (jdata) :
latt = jdata['latt']
out_dir = jdata['out_dir']
path_uc = os.path.join(out_dir, global_dirname_02)
cell_type = class_cell_type(jdata)
cwd = os.getcwd()
# for ii in scale :
# path_work = create_path(os.path.join(path_uc, '%.3f' % ii))
path_work = create_path(path_uc)
os.chdir(path_work)
with open('POSCAR.unit', 'w') as fp:
fp.write (cell_type.poscar_unit(latt))
os.chdir(cwd)
[docs]def make_unit_cell_ABACUS (jdata) :
latt = jdata['latt']
out_dir = jdata['out_dir']
path_uc = os.path.join(out_dir, global_dirname_02)
cell_type = class_cell_type(jdata)
cwd = os.getcwd()
path_work = create_path(path_uc)
os.chdir(path_work)
with open('POSCAR.unit', 'w') as fp:
fp.write (cell_type.poscar_unit(latt))
stru_data = dpdata.System("POSCAR.unit", fmt = 'vasp/poscar').data
os.chdir(cwd)
stru_data['coords'] = np.squeeze(stru_data['coords'])
stru_data['cells'] = np.squeeze(stru_data['cells'])
del stru_data["atom_names"]
return stru_data
[docs]def make_super_cell (jdata) :
out_dir = jdata['out_dir']
super_cell = jdata['super_cell']
path_uc = os.path.join(out_dir, global_dirname_02)
path_sc = os.path.join(out_dir, global_dirname_02)
assert(os.path.isdir(path_uc)), "path %s should exists" % path_uc
assert(os.path.isdir(path_sc)), "path %s should exists" % path_sc
# for ii in scale :
from_path = path_uc
from_file = os.path.join(from_path, 'POSCAR.unit')
to_path = path_sc
to_file = os.path.join(to_path, 'POSCAR')
#minor bug for element symbol behind the coordinates
from_struct=Structure.from_file(from_file)
from_struct.make_supercell(super_cell)
from_struct.to('poscar',to_file)
[docs]def make_super_cell_ABACUS (jdata, stru_data) :
out_dir = jdata['out_dir']
super_cell = jdata['super_cell']
path_uc = os.path.join(out_dir, global_dirname_02)
path_sc = os.path.join(out_dir, global_dirname_02)
assert(os.path.isdir(path_uc)), "path %s should exists" % path_uc
assert(os.path.isdir(path_sc)), "path %s should exists" % path_sc
# for ii in scale :
#from_path = path_uc
#from_file = os.path.join(from_path, 'POSCAR.unit')
#to_path = path_sc
#to_file = os.path.join(to_path, 'POSCAR')
#minor bug for element symbol behind the coordinates
#from_struct=Structure.from_file(from_file)
#from_struct.make_supercell(super_cell)
#from_struct.to('poscar',to_file)
supercell_stru = make_supercell_abacus(stru_data, super_cell)
return supercell_stru
[docs]def make_super_cell_poscar(jdata) :
out_dir = jdata['out_dir']
super_cell = jdata['super_cell']
path_sc = os.path.join(out_dir, global_dirname_02)
create_path(path_sc)
from_poscar_path = jdata['from_poscar_path']
assert(os.path.isfile(from_poscar_path)), "file %s should exists" % from_poscar_path
from_file = os.path.join(path_sc, 'POSCAR.copied')
shutil.copy2(from_poscar_path, from_file)
to_path = path_sc
to_file = os.path.join(to_path, 'POSCAR')
#minor bug for element symbol behind the coordinates
from_struct=Structure.from_file(from_file)
from_struct.make_supercell(super_cell)
from_struct.to('poscar',to_file)
# make system dir (copy)
lines = open(to_file, 'r').read().split('\n')
natoms_str = lines[6]
natoms_list = [int(ii) for ii in natoms_str.split()]
dlog.info(natoms_list)
comb_name = "sys-"
for idx,ii in enumerate(natoms_list) :
comb_name += "%04d" % ii
if idx != len(natoms_list)-1 :
comb_name += "-"
path_work = os.path.join(path_sc, comb_name)
create_path(path_work)
cwd = os.getcwd()
to_file = os.path.abspath(to_file)
os.chdir(path_work)
try:
os.symlink(os.path.relpath(to_file), 'POSCAR')
except FileExistsError:
pass
os.chdir(cwd)
[docs]def make_super_cell_STRU(jdata) :
out_dir = jdata['out_dir']
super_cell = jdata['super_cell']
path_sc = os.path.join(out_dir, global_dirname_02)
create_path(path_sc)
from_poscar_path = jdata['from_poscar_path']
assert(os.path.isfile(from_poscar_path)), "file %s should exists" % from_poscar_path
from_file = os.path.join(path_sc, 'STRU.copied')
shutil.copy2(from_poscar_path, from_file)
to_path = path_sc
to_file = os.path.join(to_path, 'STRU')
from_struct=get_abacus_STRU(from_file, n_ele=len(jdata["elements"]))
from_struct = make_supercell_abacus(from_struct, super_cell)
pp_file_names = [os.path.basename(a) for a in jdata['potcars']]
orb_file_names = None
dpks_descriptor_name = None
if 'orb_files' in jdata:
orb_file_names = [os.path.basename(a) for a in jdata['orb_files']]
if 'dpks_descriptor' in jdata:
dpks_descriptor_name = os.path.basename(jdata['dpks_descriptor'])
stru_text = make_abacus_scf_stru(from_struct, pp_file_names, orb_file_names, dpks_descriptor_name)
with open(to_file, "w") as fp:
fp.write(stru_text)
# make system dir (copy)
natoms_list = from_struct['atom_numbs']
dlog.info(natoms_list)
comb_name = "sys-"
for idx,ii in enumerate(natoms_list) :
comb_name += "%04d" % ii
if idx != len(natoms_list)-1 :
comb_name += "-"
path_work = os.path.join(path_sc, comb_name)
create_path(path_work)
cwd = os.getcwd()
absolute_pp_file_path = [os.path.abspath(a) for a in jdata['potcars']]
if 'orb_files' in jdata:
absolute_orb_file_path = [os.path.abspath(a) for a in jdata['orb_files']]
if 'dpks_descriptor' in jdata:
absolute_dpks_descriptor_path = os.path.abspath(jdata['dpks_descriptor'])
to_file = os.path.abspath(to_file)
os.chdir(path_work)
try:
os.symlink(os.path.relpath(to_file), 'STRU')
for ipp, pp_file in enumerate(absolute_pp_file_path):
os.symlink(pp_file, pp_file_names[ipp]) # create pseudo-potential files
if 'orb_files' in jdata:
os.symlink(absolute_orb_file_path[ipp], orb_file_names[ipp])
if 'dpks_descriptor' in jdata:
os.symlink(absolute_dpks_descriptor_path, dpks_descriptor_name)
except FileExistsError:
pass
os.chdir(cwd)
[docs]def make_combines (dim, natoms) :
if dim == 1 :
return [[natoms]]
else :
res = []
for ii in range(natoms+1) :
rest = natoms - ii
tmp_combines = make_combines(dim-1, rest)
for jj in tmp_combines :
jj.append(ii)
if len(res) == 0 :
res = tmp_combines
else :
res += tmp_combines
return res
[docs]def place_element (jdata) :
out_dir = jdata['out_dir']
super_cell = jdata['super_cell']
cell_type = class_cell_type(jdata)
natoms = np.cumprod(super_cell)[-1] * cell_type.numb_atoms()
elements = jdata['elements']
path_sc = os.path.join(out_dir, global_dirname_02)
path_pe = os.path.join(out_dir, global_dirname_02)
combines = np.array(make_combines(len(elements), natoms), dtype = int)
assert(os.path.isdir(path_pe))
cwd = os.getcwd()
for ii in combines :
if any(ii == 0) :
continue
comb_name = "sys-"
for idx,jj in enumerate(ii) :
comb_name += "%04d" % jj
if idx != len(ii)-1 :
comb_name += "-"
path_pos_in = path_sc
path_work = os.path.join(path_pe, comb_name)
create_path(path_work)
pos_in = os.path.join(path_pos_in, 'POSCAR')
pos_out = os.path.join(path_work, 'POSCAR')
poscar_ele(pos_in, pos_out, elements, ii)
poscar_shuffle(pos_out, pos_out)
[docs]def place_element_ABACUS(jdata, supercell_stru):
out_dir = jdata['out_dir']
super_cell = jdata['super_cell']
cell_type = class_cell_type(jdata)
natoms = sum(supercell_stru['atom_numbs'])
elements = jdata['elements']
#path_sc = os.path.join(out_dir, global_dirname_02)
path_pe = os.path.join(out_dir, global_dirname_02)
combines = np.array(make_combines(len(elements), natoms), dtype = int)
assert(os.path.isdir(path_pe))
cwd = os.getcwd()
for ii in combines :
if any(ii == 0) :
continue
comb_name = "sys-"
for idx,jj in enumerate(ii) :
comb_name += "%04d" % jj
if idx != len(ii)-1 :
comb_name += "-"
#path_pos_in = path_sc
path_work = os.path.join(path_pe, comb_name)
create_path(path_work)
#pos_in = os.path.join(path_pos_in, 'POSCAR')
pos_out = os.path.join(path_work, 'STRU')
supercell_stru = shuffle_stru_data(supercell_stru)
stru_ele(supercell_stru, pos_out, elements, ii, jdata, path_work)
[docs]def make_vasp_relax (jdata, mdata) :
out_dir = jdata['out_dir']
potcars = jdata['potcars']
cwd = os.getcwd()
work_dir = os.path.join(out_dir, global_dirname_02)
assert (os.path.isdir(work_dir))
work_dir = os.path.abspath(work_dir)
if os.path.isfile(os.path.join(work_dir, 'INCAR' )) :
os.remove(os.path.join(work_dir, 'INCAR' ))
if os.path.isfile(os.path.join(work_dir, 'POTCAR')) :
os.remove(os.path.join(work_dir, 'POTCAR'))
shutil.copy2( jdata['relax_incar'],
os.path.join(work_dir, 'INCAR'))
out_potcar = os.path.join(work_dir, 'POTCAR')
with open(out_potcar, 'w') as outfile:
for fname in potcars:
with open(fname) as infile:
outfile.write(infile.read())
os.chdir(work_dir)
sys_list = glob.glob('sys-*')
for ss in sys_list:
os.chdir(ss)
ln_src = os.path.relpath(os.path.join(work_dir,'INCAR'))
try:
os.symlink(ln_src, 'INCAR')
except FileExistsError:
pass
ln_src = os.path.relpath(os.path.join(work_dir,'POTCAR'))
try:
os.symlink(ln_src, 'POTCAR')
except FileExistsError:
pass
is_cvasp = False
if 'cvasp' in mdata['fp_resources'].keys():
is_cvasp = mdata['fp_resources']['cvasp']
if is_cvasp:
cvasp_file = os.path.join(ROOT_PATH, 'generator/lib/cvasp.py')
shutil.copyfile(cvasp_file, 'cvasp.py')
os.chdir(work_dir)
os.chdir(cwd)
symlink_user_forward_files(mdata=mdata, task_type="fp",
work_path=os.path.join(os.path.basename(out_dir),global_dirname_02),
task_format= {"fp" : "sys-*"})
[docs]def make_abacus_relax (jdata, mdata) :
relax_incar = jdata['relax_incar']
standard_incar = get_abacus_input_parameters(relax_incar) # a dictionary in which all of the values are strings
if "kspacing" not in standard_incar:
if "gamma_only" in standard_incar:
if type(standard_incar["gamma_only"])==str:
standard_incar["gamma_only"] = int(eval(standard_incar["gamma_only"]))
if standard_incar["gamma_only"] == 0:
if "relax_kpt" not in jdata:
raise RuntimeError("Cannot find any k-points information.")
else:
md_kpt_path = jdata['relax_kpt']
assert(os.path.isfile(relax_kpt_path)), "file %s should exists" % relax_kpt_path
else:
gamma_param = {"k_points":[1,1,1,0,0,0]}
ret_kpt = make_abacus_scf_kpt(gamma_param)
else:
if "relax_kpt" not in jdata:
raise RuntimeError("Cannot find any k-points information.")
else:
relax_kpt_path = jdata['relax_kpt']
assert(os.path.isfile(relax_kpt_path)), "file %s should exists" % relax_kpt_path
out_dir = jdata['out_dir']
cwd = os.getcwd()
work_dir = os.path.join(out_dir, global_dirname_02)
assert (os.path.isdir(work_dir))
work_dir = os.path.abspath(work_dir)
if os.path.isfile(os.path.join(work_dir, 'INPUT' )) :
os.remove(os.path.join(work_dir, 'INPUT' ))
shutil.copy2( jdata['relax_incar'],
os.path.join(work_dir, 'INPUT'))
if "kspacing" not in standard_incar:
if os.path.isfile(os.path.join(work_dir, 'KPT' )) :
os.remove(os.path.join(work_dir, 'KPT' ))
if "gamma_only" in standard_incar and standard_incar["gamma_only"]==1:
with open(os.path.join(work_dir,'KPT'),"w") as fp:
fp.write(ret_kpt)
else:
jdata['relax_kpt'] = os.path.relpath(jdata['relax_kpt'])
shutil.copy2(jdata['relax_kpt'],os.path.join(work_dir, 'KPT'))
if "dpks_model" in jdata:
dpks_model_absolute_path = os.path.abspath(jdata["dpks_model"])
assert(os.path.isfile(dpks_model_absolute_path))
dpks_model_name = os.path.basename(jdata["dpks_model"])
shutil.copy2( dpks_model_absolute_path,
os.path.join(work_dir, dpks_model_name))
os.chdir(work_dir)
sys_list = glob.glob('sys-*')
for ss in sys_list:
os.chdir(ss)
ln_src = os.path.relpath(os.path.join(work_dir,'INPUT'))
if "kspacing" not in standard_incar:
kpt_src = os.path.relpath(os.path.join(work_dir,'KPT'))
if "dpks_model" in jdata:
ksmd_src = os.path.relpath(os.path.join(work_dir,dpks_model_name))
try:
os.symlink(ln_src, 'INPUT')
if "kspacing" not in standard_incar:
os.symlink(kpt_src, 'KPT')
if "dpks_model" in jdata:
os.symlink(ksmd_src, dpks_model_name)
except FileExistsError:
pass
os.chdir(work_dir)
os.chdir(cwd)
symlink_user_forward_files(mdata=mdata, task_type="fp",
work_path=os.path.join(os.path.basename(out_dir),global_dirname_02),
task_format= {"fp" : "sys-*"})
[docs]def make_scale(jdata):
out_dir = jdata['out_dir']
scale = jdata['scale']
skip_relax = jdata['skip_relax']
cwd = os.getcwd()
init_path = os.path.join(out_dir, global_dirname_02)
init_path = os.path.abspath(init_path)
work_path = os.path.join(out_dir, global_dirname_03)
os.chdir(init_path)
init_sys = glob.glob("sys-*")
init_sys.sort()
os.chdir(cwd)
create_path(work_path)
for ii in init_sys :
for jj in scale :
if skip_relax :
pos_src = os.path.join(os.path.join(init_path, ii), 'POSCAR')
assert(os.path.isfile(pos_src))
else :
try:
pos_src = os.path.join(os.path.join(init_path, ii), 'CONTCAR')
assert(os.path.isfile(pos_src))
except Exception:
raise RuntimeError("not file %s, vasp relaxation should be run before scale poscar")
scale_path = os.path.join(work_path, ii)
scale_path = os.path.join(scale_path, "scale-%.3f" % jj)
create_path(scale_path)
os.chdir(scale_path)
poscar_scale(pos_src, 'POSCAR', jj)
os.chdir(cwd)
[docs]def make_scale_ABACUS(jdata):
out_dir = jdata['out_dir']
scale = jdata['scale']
skip_relax = jdata['skip_relax']
cwd = os.getcwd()
init_path = os.path.join(out_dir, global_dirname_02)
init_path = os.path.abspath(init_path)
work_path = os.path.join(out_dir, global_dirname_03)
os.chdir(init_path)
init_sys = glob.glob("sys-*")
init_sys.sort()
os.chdir(cwd)
create_path(work_path)
for ii in init_sys :
for jj in scale :
if skip_relax :
pos_src = os.path.join(os.path.join(init_path, ii), 'STRU')
assert(os.path.isfile(pos_src))
else :
try:
pos_src = os.path.join(os.path.join(init_path, ii), 'OUT.ABACUS/STRU_ION_D')
assert(os.path.isfile(pos_src))
except Exception:
raise RuntimeError("not file %s, vasp relaxation should be run before scale poscar")
scale_path = os.path.join(work_path, ii)
scale_path = os.path.join(scale_path, "scale-%.3f" % jj)
create_path(scale_path)
os.chdir(scale_path)
poscar_scale_abacus(pos_src, 'STRU', jj, jdata)
os.chdir(cwd)
[docs]def pert_scaled(jdata) :
if "init_fp_style" not in jdata:
jdata["init_fp_style"] = "VASP"
out_dir = jdata['out_dir']
scale = jdata['scale']
pert_box = jdata['pert_box']
pert_atom = jdata['pert_atom']
pert_numb = jdata['pert_numb']
pp_file = [os.path.basename(a) for a in jdata['potcars']]
orb_file_names = None
dpks_descriptor_name = None
if 'orb_files' in jdata:
orb_file_names = [os.path.basename(a) for a in jdata['orb_files']]
if 'dpks_descriptor' in jdata:
dpks_descriptor_name = os.path.basename(jdata['dpks_descriptor'])
from_poscar = False
if 'from_poscar' in jdata :
from_poscar = jdata['from_poscar']
cwd = os.getcwd()
path_sp = os.path.join(out_dir, global_dirname_03)
assert(os.path.isdir(path_sp))
os.chdir(path_sp)
sys_pe = glob.glob('sys-*')
sys_pe.sort()
os.chdir(cwd)
pert_cmd = os.path.dirname(__file__)
pert_cmd = os.path.join(pert_cmd, 'tools')
pert_cmd = os.path.join(pert_cmd, 'create_random_disturb.py')
fp_style = "vasp"
poscar_name = "POSCAR"
if jdata['init_fp_style'] == "ABACUS":
fp_style = "abacus"
poscar_name = "STRU"
pert_cmd = 'python3 ' + pert_cmd + ' -etmax %f -ofmt %s %s %d %f > /dev/null' %(pert_box, fp_style, poscar_name, pert_numb, pert_atom)
for ii in sys_pe :
for jj in scale :
path_work = path_sp
path_work = os.path.join(path_work, ii)
path_work = os.path.join(path_work, 'scale-%.3f' % jj)
assert(os.path.isdir(path_work))
os.chdir(path_work)
sp.check_call(pert_cmd, shell = True)
for kk in range(pert_numb) :
if fp_style == "vasp":
pos_in = 'POSCAR%d.vasp' % (kk+1)
elif fp_style == "abacus":
pos_in = 'STRU%d.abacus' % (kk+1)
dir_out = '%06d' % (kk+1)
create_path(dir_out)
if fp_style == "vasp":
pos_out = os.path.join(dir_out, 'POSCAR')
elif fp_style == "abacus":
pos_out = os.path.join(dir_out, 'STRU')
if not from_poscar:
if fp_style == "vasp":
poscar_shuffle(pos_in, pos_out)
elif fp_style == "abacus":
stru_in = get_abacus_STRU(pos_in)
stru_out = shuffle_stru_data(stru_in)
with open(pos_out, "w") as fp:
fp.write(make_abacus_scf_stru(stru_out, pp_file, orb_file_names, dpks_descriptor_name))
else :
shutil.copy2(pos_in, pos_out)
os.remove(pos_in)
kk = -1
if fp_style == "vasp":
pos_in = 'POSCAR'
elif fp_style == "abacus":
pos_in = 'STRU'
dir_out = '%06d' % (kk+1)
create_path(dir_out)
if fp_style == "vasp":
pos_out = os.path.join(dir_out, 'POSCAR')
elif fp_style == "abacus":
pos_out = os.path.join(dir_out, 'STRU')
if not from_poscar:
if fp_style == "vasp":
poscar_shuffle(pos_in, pos_out)
elif fp_style == "abacus":
stru_in = get_abacus_STRU(pos_in)
stru_out = shuffle_stru_data(stru_in)
with open(pos_out, "w") as fp:
fp.write(make_abacus_scf_stru(stru_out, pp_file, orb_file_names, dpks_descriptor_name))
else :
shutil.copy2(pos_in, pos_out)
os.chdir(cwd)
[docs]def make_vasp_md(jdata, mdata) :
out_dir = jdata['out_dir']
potcars = jdata['potcars']
scale = jdata['scale']
pert_numb = jdata['pert_numb']
md_nstep = jdata['md_nstep']
cwd = os.getcwd()
path_ps = os.path.join(out_dir, global_dirname_03)
path_ps = os.path.abspath(path_ps)
assert(os.path.isdir(path_ps))
os.chdir(path_ps)
sys_ps = glob.glob('sys-*')
sys_ps.sort()
os.chdir(cwd)
path_md = os.path.join(out_dir, global_dirname_04)
path_md = os.path.abspath(path_md)
create_path(path_md)
shutil.copy2(jdata['md_incar'],
os.path.join(path_md, 'INCAR'))
out_potcar = os.path.join(path_md, 'POTCAR')
with open(out_potcar, 'w') as outfile:
for fname in potcars:
with open(fname) as infile:
outfile.write(infile.read())
os.chdir(path_md)
os.chdir(cwd)
for ii in sys_ps :
for jj in scale :
for kk in range(pert_numb+1) :
path_work = path_md
path_work = os.path.join(path_work, ii)
path_work = os.path.join(path_work, "scale-%.3f" % jj)
path_work = os.path.join(path_work, "%06d" % kk)
create_path(path_work)
os.chdir(path_work)
path_pos = path_ps
path_pos = os.path.join(path_pos, ii)
path_pos = os.path.join(path_pos, "scale-%.3f" % jj)
path_pos = os.path.join(path_pos, "%06d" % kk)
init_pos = os.path.join(path_pos, 'POSCAR')
shutil.copy2 (init_pos, 'POSCAR')
file_incar = os.path.join(path_md, 'INCAR')
file_potcar = os.path.join(path_md, 'POTCAR')
try:
os.symlink(os.path.relpath(file_incar), 'INCAR')
except FileExistsError:
pass
try:
os.symlink(os.path.relpath(file_potcar), 'POTCAR')
except FileExistsError:
pass
is_cvasp = False
if 'cvasp' in mdata['fp_resources'].keys():
is_cvasp = mdata['fp_resources']['cvasp']
if is_cvasp:
cvasp_file = os.path.join(ROOT_PATH, 'generator/lib/cvasp.py')
shutil.copyfile(cvasp_file, 'cvasp.py')
os.chdir(cwd)
symlink_user_forward_files(mdata=mdata, task_type="fp",
work_path=os.path.join(os.path.basename(out_dir),global_dirname_04),
task_format= {"fp" :"sys-*/scale*/00*"})
[docs]def make_abacus_md(jdata, mdata) :
md_incar = jdata['md_incar']
standard_incar = get_abacus_input_parameters(md_incar) # a dictionary in which all of the values are strings
#assert("md_kpt" in jdata or "kspacing" in standard_incar or "gamma_only" in standard_incar) \
# "Cannot find any k-points information."
if "kspacing" not in standard_incar:
if "gamma_only" in standard_incar:
if type(standard_incar["gamma_only"])==str:
standard_incar["gamma_only"] = int(eval(standard_incar["gamma_only"]))
if standard_incar["gamma_only"] == 0:
if "md_kpt" not in jdata:
raise RuntimeError("Cannot find any k-points information.")
else:
md_kpt_path = jdata['md_kpt']
assert(os.path.isfile(md_kpt_path)), "file %s should exists" % md_kpt_path
else:
ret_kpt = make_abacus_scf_kpt({"k_points":[1,1,1,0,0,0]})
else:
if "md_kpt" not in jdata:
raise RuntimeError("Cannot find any k-points information.")
else:
md_kpt_path = jdata['md_kpt']
assert(os.path.isfile(md_kpt_path)), "file %s should exists" % md_kpt_path
out_dir = jdata['out_dir']
potcars = jdata['potcars']
scale = jdata['scale']
pert_numb = jdata['pert_numb']
md_nstep = jdata['md_nstep']
cwd = os.getcwd()
path_ps = os.path.join(out_dir, global_dirname_03)
path_ps = os.path.abspath(path_ps)
assert(os.path.isdir(path_ps))
os.chdir(path_ps)
sys_ps = glob.glob('sys-*')
sys_ps.sort()
os.chdir(cwd)
path_md = os.path.join(out_dir, global_dirname_04)
path_md = os.path.abspath(path_md)
create_path(path_md)
shutil.copy2(jdata['md_incar'],
os.path.join(path_md, 'INPUT'))
if "kspacing" not in standard_incar:
if "gamma_only" in standard_incar and standard_incar["gamma_only"]==1:
with open(os.path.join(path_md,"KPT"),"w") as fp:
fp.write(ret_kpt)
else:
shutil.copy2(jdata['md_kpt'],os.path.join(path_md, 'KPT'))
orb_file_names = None
orb_file_abspath = None
dpks_descriptor_name = None
dpks_descriptor_abspath = None
dpks_model_name = None
dpks_model_abspath = None
if 'orb_files' in jdata:
orb_file_names = [os.path.basename(a) for a in jdata['orb_files']]
orb_file_abspath = [os.path.abspath(a) for a in jdata['orb_files']]
for iorb, orb_file in enumerate(orb_file_names):
shutil.copy2(orb_file_abspath[iorb],
os.path.join(path_md, orb_file))
if 'dpks_descriptor' in jdata:
dpks_descriptor_name = os.path.basename(jdata['dpks_descriptor'])
dpks_descriptor_abspath = os.path.abspath(jdata['dpks_descriptor'])
shutil.copy2(dpks_descriptor_abspath,
os.path.join(path_md, dpks_descriptor_name))
if 'dpks_model' in jdata:
dpks_model_name = os.path.basename(jdata['dpks_model'])
dpks_model_abspath = os.path.abspath(jdata['dpks_model'])
shutil.copy2(dpks_model_abspath,
os.path.join(path_md, dpks_model_name))
for pp_file in jdata['potcars']:
shutil.copy2(pp_file,
os.path.join(path_md, os.path.basename(pp_file)))
os.chdir(path_md)
os.chdir(cwd)
for ii in sys_ps :
for jj in scale :
for kk in range(pert_numb+1) :
path_work = path_md
path_work = os.path.join(path_work, ii)
path_work = os.path.join(path_work, "scale-%.3f" % jj)
path_work = os.path.join(path_work, "%06d" % kk)
create_path(path_work)
os.chdir(path_work)
path_pos = path_ps
path_pos = os.path.join(path_pos, ii)
path_pos = os.path.join(path_pos, "scale-%.3f" % jj)
path_pos = os.path.join(path_pos, "%06d" % kk)
init_pos = os.path.join(path_pos, 'STRU')
if "kspacing" not in standard_incar:
file_kpt = os.path.join(path_md, 'KPT')
shutil.copy2 (init_pos, 'STRU')
file_incar = os.path.join(path_md, 'INPUT')
try:
os.symlink(os.path.relpath(file_incar), 'INPUT')
if "kspacing" not in standard_incar:
os.symlink(os.path.relpath(file_kpt), 'KPT')
except FileExistsError:
pass
try:
for pp_file in [os.path.basename(a) for a in jdata['potcars']]:
os.symlink(os.path.relpath(os.path.join(path_md, pp_file)), pp_file)
if 'orb_files' in jdata:
for orb_file in orb_file_names:
os.symlink(os.path.relpath(os.path.join(path_md, orb_file)), orb_file)
if 'dpks_model' in jdata:
os.symlink(os.path.relpath(os.path.join(path_md, dpks_model_name)), dpks_model_name)
if 'dpks_descriptor' in jdata:
os.symlink(os.path.relpath(os.path.join(path_md, dpks_descriptor_name)), dpks_descriptor_name)
except FileExistsError:
pass
os.chdir(cwd)
symlink_user_forward_files(mdata=mdata, task_type="fp",
work_path=os.path.join(os.path.basename(out_dir),global_dirname_04),
task_format= {"fp" :"sys-*/scale*/00*"})
[docs]def coll_vasp_md(jdata) :
out_dir = jdata['out_dir']
md_nstep = jdata['md_nstep']
scale = jdata['scale']
pert_numb = jdata['pert_numb']
coll_ndata = jdata['coll_ndata']
cwd = os.getcwd()
path_md = os.path.join(out_dir, global_dirname_04)
path_md = os.path.abspath(path_md)
assert(os.path.isdir(path_md)), "md path should exists"
os.chdir(path_md)
sys_md = glob.glob('sys-*')
sys_md.sort()
for ii in sys_md :
os.chdir(ii)
# convert outcars
valid_outcars = []
for jj in scale :
for kk in range(pert_numb) :
path_work = os.path.join("scale-%.3f" % jj, "%06d" % kk)
outcar = os.path.join(path_work, 'OUTCAR')
#dlog.info("OUTCAR",outcar)
if os.path.isfile(outcar) :
#dlog.info("*"*40)
with open(outcar, 'r') as fin:
nforce = fin.read().count('TOTAL-FORCE')
#dlog.info("nforce is", nforce)
#dlog.info("md_nstep", md_nstep)
if nforce == md_nstep :
valid_outcars.append(outcar)
elif md_nstep == 0 and nforce == 1 :
valid_outcars.append(outcar)
else:
dlog.info("WARNING : in directory %s nforce in OUTCAR is not equal to settings in INCAR"%(os.getcwd()))
arg_cvt = " "
if len(valid_outcars) == 0:
raise RuntimeError("MD dir: %s: find no valid outcar in sys %s, "
"check if your vasp md simulation is correctly done"
% (path_md, ii))
flag=True
if ("type_map" in jdata) and isinstance(jdata["type_map"], list):
type_map = jdata["type_map"]
else:
type_map = None
for oo in valid_outcars :
if flag:
_sys = dpdata.LabeledSystem(oo, type_map= type_map)
if len(_sys)>0:
all_sys=_sys
flag=False
else:
pass
else:
_sys = dpdata.LabeledSystem(oo, type_map= type_map)
if len(_sys)>0:
all_sys.append(_sys)
# create deepmd data
if all_sys.get_nframes() >= coll_ndata :
all_sys = all_sys.sub_system(np.arange(coll_ndata))
all_sys.to_deepmd_raw('deepmd')
all_sys.to_deepmd_npy('deepmd', set_size = all_sys.get_nframes())
os.chdir(path_md)
os.chdir(cwd)
def _vasp_check_fin (ii) :
if os.path.isfile(os.path.join(ii, 'OUTCAR')) :
with open(os.path.join(ii, 'OUTCAR'), 'r') as fp :
content = fp.read()
count = content.count('Elapse')
if count != 1 :
return False
else :
return False
return True
[docs]def run_vasp_relax(jdata, mdata):
fp_command = mdata['fp_command']
fp_group_size = mdata['fp_group_size']
fp_resources = mdata['fp_resources']
#machine_type = mdata['fp_machine']['machine_type']
work_dir = os.path.join(jdata['out_dir'], global_dirname_02)
forward_files = ["POSCAR", "INCAR", "POTCAR"]
user_forward_files = mdata.get("fp" + "_user_forward_files", [])
forward_files += [os.path.basename(file) for file in user_forward_files]
backward_files = ["OUTCAR","CONTCAR"]
backward_files += mdata.get("fp" + "_user_backward_files", [])
forward_common_files = []
if 'cvasp' in mdata['fp_resources']:
if mdata['fp_resources']['cvasp']:
forward_files +=['cvasp.py']
relax_tasks = glob.glob(os.path.join(work_dir, "sys-*"))
relax_tasks.sort()
#dlog.info("work_dir",work_dir)
#dlog.info("relax_tasks",relax_tasks)
if len(relax_tasks) == 0:
return
relax_run_tasks = relax_tasks
#for ii in relax_tasks :
# if not _vasp_check_fin(ii):
# relax_run_tasks.append(ii)
run_tasks = [os.path.basename(ii) for ii in relax_run_tasks]
api_version = mdata.get('api_version', '0.9')
if LooseVersion(api_version) < LooseVersion('1.0'):
warnings.warn(f"the dpdispatcher will be updated to new version."
f"And the interface may be changed. Please check the documents for more details")
dispatcher = make_dispatcher(mdata['fp_machine'], mdata['fp_resources'], work_dir, run_tasks, fp_group_size)
dispatcher.run_jobs(fp_resources,
[fp_command],
work_dir,
run_tasks,
fp_group_size,
forward_common_files,
forward_files,
backward_files)
elif LooseVersion(api_version) >= LooseVersion('1.0'):
submission = make_submission(
mdata['fp_machine'],
mdata['fp_resources'],
commands=[fp_command],
work_path=work_dir,
run_tasks=run_tasks,
group_size=fp_group_size,
forward_common_files=forward_common_files,
forward_files=forward_files,
backward_files=backward_files,
outlog = 'fp.log',
errlog = 'fp.log')
submission.run_submission()
[docs]def coll_abacus_md(jdata) :
out_dir = jdata['out_dir']
md_nstep = jdata['md_nstep']
scale = jdata['scale']
pert_numb = jdata['pert_numb']
coll_ndata = jdata['coll_ndata']
cwd = os.getcwd()
path_md = os.path.join(out_dir, global_dirname_04)
path_md = os.path.abspath(path_md)
assert(os.path.isdir(path_md)), "md path should exists"
os.chdir(path_md)
sys_md = glob.glob('sys-*')
sys_md.sort()
for ii in sys_md :
os.chdir(ii)
# convert outcars
valid_outcars = []
for jj in scale :
for kk in range(pert_numb+1) :
path_work = os.path.join("scale-%.3f" % jj, "%06d" % kk)
print("path_work = %s" %path_work)
#outcar = os.path.join(path_work, 'OUT.ABACUS/')
outcar = path_work
#dlog.info("OUTCAR",outcar)
if os.path.exists(os.path.join(outcar, "OUT.ABACUS/running_md.log")) :
with open(os.path.join(outcar, "OUT.ABACUS/running_md.log")) as fp:
if "!FINAL_ETOT_IS" in fp.read():
valid_outcars.append(outcar)
print(outcar)
else:
dlog.info("WARNING : file %s does not have !FINAL_ETOT_IS note. MD simulation is not completed normally."%os.path.join(outcar, "OUT.ABACUS/running_md.log"))
else:
dlog.info("WARNING : in directory %s NO running_md.log file found."%(os.getcwd()))
arg_cvt = " "
if len(valid_outcars) == 0:
raise RuntimeError("MD dir: %s: find no valid OUT.ABACUS in sys %s, "
"check if your abacus md simulation is correctly done."
% (path_md, ii))
flag=True
if ("type_map" in jdata) and isinstance(jdata["type_map"], list):
type_map = jdata["type_map"]
else:
type_map = None
for oo in valid_outcars :
if flag:
_sys = dpdata.LabeledSystem(oo, type_map= type_map, fmt='abacus/md')
if len(_sys)>0:
all_sys=_sys
flag=False
else:
pass
else:
_sys = dpdata.LabeledSystem(oo, type_map= type_map, fmt='abacus/md')
if len(_sys)>0:
all_sys.append(_sys)
# create deepmd data
if all_sys.get_nframes() >= coll_ndata :
all_sys = all_sys.sub_system(np.arange(coll_ndata))
print(all_sys.get_nframes())
all_sys.to_deepmd_raw('deepmd')
all_sys.to_deepmd_npy('deepmd', set_size = all_sys.get_nframes())
os.chdir(path_md)
os.chdir(cwd)
[docs]def run_abacus_relax(jdata, mdata):
fp_command = mdata['fp_command']
fp_group_size = mdata['fp_group_size']
fp_resources = mdata['fp_resources']
#machine_type = mdata['fp_machine']['machine_type']
work_dir = os.path.join(jdata['out_dir'], global_dirname_02)
pp_files = [os.path.basename(a) for a in jdata["potcars"]]
orb_file_names = []
dpks_descriptor_name = []
dpks_model_name = []
if 'orb_files' in jdata:
orb_file_names = [os.path.basename(a) for a in jdata['orb_files']]
if 'dpks_descriptor' in jdata:
dpks_descriptor_name = [os.path.basename(jdata['dpks_descriptor'])]
if 'dpks_model' in jdata:
dpks_model_name = [os.path.basename(jdata['dpks_model'])]
relax_incar = jdata['relax_incar']
standard_incar = get_abacus_input_parameters(relax_incar) # a dictionary in which all of the values are strings
forward_files = ["STRU", "INPUT"]
if "kspacing" not in standard_incar:
forward_files = ["STRU", "INPUT", "KPT"]
forward_files += pp_files + orb_file_names + dpks_descriptor_name + dpks_model_name
user_forward_files = mdata.get("fp" + "_user_forward_files", [])
forward_files += [os.path.basename(file) for file in user_forward_files]
backward_files = ["OUT.ABACUS"]
backward_files += mdata.get("fp" + "_user_backward_files", [])
forward_common_files = []
relax_tasks = glob.glob(os.path.join(work_dir, "sys-*"))
relax_tasks.sort()
#dlog.info("work_dir",work_dir)
#dlog.info("relax_tasks",relax_tasks)
if len(relax_tasks) == 0:
return
relax_run_tasks = relax_tasks
#for ii in relax_tasks :
# if not _vasp_check_fin(ii):
# relax_run_tasks.append(ii)
run_tasks = [os.path.basename(ii) for ii in relax_run_tasks]
api_version = mdata.get('api_version', '0.9')
if LooseVersion(api_version) < LooseVersion('1.0'):
warnings.warn(f"the dpdispatcher will be updated to new version."
f"And the interface may be changed. Please check the documents for more details")
dispatcher = make_dispatcher(mdata['fp_machine'], mdata['fp_resources'], work_dir, run_tasks, fp_group_size)
dispatcher.run_jobs(fp_resources,
[fp_command],
work_dir,
run_tasks,
fp_group_size,
forward_common_files,
forward_files,
backward_files)
elif LooseVersion(api_version) >= LooseVersion('1.0'):
submission = make_submission(
mdata['fp_machine'],
mdata['fp_resources'],
commands=[fp_command],
work_path=work_dir,
run_tasks=run_tasks,
group_size=fp_group_size,
forward_common_files=forward_common_files,
forward_files=forward_files,
backward_files=backward_files,
outlog = 'fp.log',
errlog = 'fp.log')
submission.run_submission()
[docs]def run_vasp_md(jdata, mdata):
fp_command = mdata['fp_command']
fp_group_size = mdata['fp_group_size']
fp_resources = mdata['fp_resources']
#machine_type = mdata['fp_machine']['machine_type']
work_dir = os.path.join(jdata['out_dir'], global_dirname_04)
scale = jdata['scale']
pert_numb = jdata['pert_numb']
md_nstep = jdata['md_nstep']
forward_files = ["POSCAR", "INCAR", "POTCAR"]
user_forward_files = mdata.get("fp" + "_user_forward_files", [])
forward_files += [os.path.basename(file) for file in user_forward_files]
backward_files = ["OUTCAR"]
backward_files += mdata.get("fp" + "_user_backward_files", [])
forward_common_files = []
if 'cvasp' in mdata['fp_resources']:
if mdata['fp_resources']['cvasp']:
forward_files +=['cvasp.py']
path_md = work_dir
path_md = os.path.abspath(path_md)
cwd = os.getcwd()
assert(os.path.isdir(path_md)), "md path should exists"
md_tasks = glob.glob(os.path.join(work_dir, 'sys-*/scale*/00*'))
md_tasks.sort()
if len(md_tasks) == 0:
return
md_run_tasks = md_tasks
#for ii in md_tasks :
# if not _vasp_check_fin(ii):
# md_run_tasks.append(ii)
run_tasks = [ii.replace(work_dir+"/", "") for ii in md_run_tasks]
#dlog.info("md_work_dir", work_dir)
#dlog.info("run_tasks",run_tasks)
api_version = mdata.get('api_version', '0.9')
if LooseVersion(api_version) < LooseVersion('1.0'):
warnings.warn(f"the dpdispatcher will be updated to new version."
f"And the interface may be changed. Please check the documents for more details")
dispatcher = make_dispatcher(mdata['fp_machine'], mdata['fp_resources'], work_dir, run_tasks, fp_group_size)
dispatcher.run_jobs(fp_resources,
[fp_command],
work_dir,
run_tasks,
fp_group_size,
forward_common_files,
forward_files,
backward_files)
elif LooseVersion(api_version) >= LooseVersion('1.0'):
submission = make_submission(
mdata['fp_machine'],
mdata['fp_resources'],
commands=[fp_command],
work_path=work_dir,
run_tasks=run_tasks,
group_size=fp_group_size,
forward_common_files=forward_common_files,
forward_files=forward_files,
backward_files=backward_files,
outlog = 'fp.log',
errlog = 'fp.log')
submission.run_submission()
[docs]def run_abacus_md(jdata, mdata):
fp_command = mdata['fp_command']
fp_group_size = mdata['fp_group_size']
fp_resources = mdata['fp_resources']
#machine_type = mdata['fp_machine']['machine_type']
work_dir = os.path.join(jdata['out_dir'], global_dirname_04)
scale = jdata['scale']
pert_numb = jdata['pert_numb']
md_nstep = jdata['md_nstep']
orb_file_names = []
dpks_descriptor_name = []
dpks_model_name = []
if 'orb_files' in jdata:
orb_file_names = [os.path.basename(a) for a in jdata['orb_files']]
if 'dpks_descriptor' in jdata:
dpks_descriptor_name = [os.path.basename(jdata['dpks_descriptor'])]
if 'dpks_model' in jdata:
dpks_model_name = [os.path.basename(jdata['dpks_model'])]
md_incar = jdata['md_incar']
standard_incar = get_abacus_input_parameters(md_incar) # a dictionary in which all of the values are strings
forward_files = ["STRU", "INPUT"]
if "kspacing" not in standard_incar:
forward_files = ["STRU", "INPUT", "KPT"]
forward_files += orb_file_names + dpks_descriptor_name + dpks_model_name
for pp_file in [os.path.basename(a) for a in jdata['potcars']]:
forward_files.append(pp_file)
user_forward_files = mdata.get("fp" + "_user_forward_files", [])
forward_files += [os.path.basename(file) for file in user_forward_files]
backward_files = ["OUT.ABACUS"]
backward_files += mdata.get("fp" + "_user_backward_files", [])
forward_common_files = []
path_md = work_dir
path_md = os.path.abspath(path_md)
cwd = os.getcwd()
assert(os.path.isdir(path_md)), "md path should exists"
md_tasks = glob.glob(os.path.join(work_dir, 'sys-*/scale*/00*'))
md_tasks.sort()
if len(md_tasks) == 0:
return
md_run_tasks = md_tasks
#for ii in md_tasks :
# if not _vasp_check_fin(ii):
# md_run_tasks.append(ii)
run_tasks = [ii.replace(work_dir+"/", "") for ii in md_run_tasks]
#dlog.info("md_work_dir", work_dir)
#dlog.info("run_tasks",run_tasks)
api_version = mdata.get('api_version', '0.9')
if LooseVersion(api_version) < LooseVersion('1.0'):
warnings.warn(f"the dpdispatcher will be updated to new version."
f"And the interface may be changed. Please check the documents for more details")
dispatcher = make_dispatcher(mdata['fp_machine'], mdata['fp_resources'], work_dir, run_tasks, fp_group_size)
dispatcher.run_jobs(fp_resources,
[fp_command],
work_dir,
run_tasks,
fp_group_size,
forward_common_files,
forward_files,
backward_files)
elif LooseVersion(api_version) >= LooseVersion('1.0'):
submission = make_submission(
mdata['fp_machine'],
mdata['fp_resources'],
commands=[fp_command],
work_path=work_dir,
run_tasks=run_tasks,
group_size=fp_group_size,
forward_common_files=forward_common_files,
forward_files=forward_files,
backward_files=backward_files,
outlog = 'fp.log',
errlog = 'fp.log')
submission.run_submission()
[docs]def gen_init_bulk(args) :
try:
import ruamel
from monty.serialization import loadfn,dumpfn
warnings.simplefilter('ignore', ruamel.yaml.error.MantissaNoDotYAML1_1Warning)
jdata=loadfn(args.PARAM)
if args.MACHINE is not None:
mdata=loadfn(args.MACHINE)
except Exception:
with open (args.PARAM, 'r') as fp :
jdata = json.load (fp)
if args.MACHINE is not None:
with open (args.MACHINE, "r") as fp:
mdata = json.load(fp)
if args.MACHINE is not None:
# Selecting a proper machine
mdata = convert_mdata(mdata, ["fp"])
#disp = make_dispatcher(mdata["fp_machine"])
# Decide work path
out_dir = out_dir_name(jdata)
jdata['out_dir'] = out_dir
dlog.info ("# working dir %s" % out_dir)
# Decide whether to use a given poscar
from_poscar = jdata.get('from_poscar', False)
# Verify md_nstep
md_nstep_jdata = jdata["md_nstep"]
if 'init_fp_style' not in jdata:
jdata['init_fp_style'] = "VASP"
try:
md_incar = jdata['md_incar']
if os.path.isfile(md_incar):
if jdata['init_fp_style'] == "VASP":
standard_incar = incar_upper(Incar.from_file(md_incar))
nsw_flag = False
if "NSW" in standard_incar:
nsw_flag = True
nsw_steps = standard_incar['NSW']
#dlog.info("nsw_steps is", nsw_steps)
#dlog.info("md_nstep_jdata is", md_nstep_jdata)
elif jdata['init_fp_style'] == "ABACUS":
standard_incar = get_abacus_input_parameters(md_incar) # a dictionary in which all of the values are strings
nsw_flag = False
if "md_nstep" in standard_incar:
nsw_flag = True
nsw_steps = int(standard_incar['md_nstep'])
if nsw_flag:
if (nsw_steps != md_nstep_jdata):
dlog.info("WARNING: your set-up for MD steps in PARAM and md_incar are not consistent!")
dlog.info("MD steps in PARAM is %d"%(md_nstep_jdata))
dlog.info("MD steps in md_incar is %d"%(nsw_steps))
dlog.info("DP-GEN will use settings in md_incar!")
jdata['md_nstep'] = nsw_steps
except KeyError:
pass
## correct element name
temp_elements = []
for ele in jdata['elements']:
temp_elements.append(ele[0].upper() + ele[1:])
jdata['elements'] = temp_elements
dlog.info("Elements are %s"% ' '.join(jdata['elements']))
## Iteration
stage_list = [int(i) for i in jdata['stages']]
for stage in stage_list:
if stage == 1 :
dlog.info("Current stage is 1, relax")
create_path(out_dir)
shutil.copy2(args.PARAM, os.path.join(out_dir, 'param.json'))
if from_poscar :
if jdata['init_fp_style'] == "VASP":
make_super_cell_poscar(jdata)
elif jdata['init_fp_style'] == "ABACUS":
make_super_cell_STRU(jdata)
else :
if jdata['init_fp_style'] == "VASP":
make_unit_cell(jdata)
make_super_cell(jdata)
place_element(jdata)
elif jdata['init_fp_style'] == "ABACUS":
stru_data = make_unit_cell_ABACUS(jdata)
supercell_stru = make_super_cell_ABACUS(jdata, stru_data)
place_element_ABACUS(jdata, supercell_stru)
if args.MACHINE is not None:
if jdata['init_fp_style'] == "VASP":
make_vasp_relax(jdata, mdata)
run_vasp_relax(jdata, mdata)
elif jdata['init_fp_style'] == "ABACUS":
make_abacus_relax(jdata, mdata)
run_abacus_relax(jdata, mdata)
else:
if jdata['init_fp_style'] == "VASP":
make_vasp_relax(jdata, {"fp_resources":{}})
elif jdata['init_fp_style'] == "ABACUS":
make_abacus_relax(jdata, {"fp_resources":{}})
elif stage == 2 :
dlog.info("Current stage is 2, perturb and scale")
if jdata['init_fp_style'] == "VASP":
make_scale(jdata)
pert_scaled(jdata)
elif jdata['init_fp_style'] == "ABACUS":
make_scale_ABACUS(jdata)
pert_scaled(jdata)
elif stage == 3 :
dlog.info("Current stage is 3, run a short md")
if args.MACHINE is not None:
if jdata['init_fp_style'] == "VASP":
make_vasp_md(jdata, mdata)
run_vasp_md(jdata, mdata)
elif jdata['init_fp_style'] == "ABACUS":
make_abacus_md(jdata, mdata)
run_abacus_md(jdata, mdata)
else:
if jdata['init_fp_style'] == "VASP":
make_vasp_md(jdata, {"fp_resources":{}})
elif jdata['init_fp_style'] == "ABACUS":
make_abacus_md(jdata, {"fp_resources":{}})
elif stage == 4 :
dlog.info("Current stage is 4, collect data")
if jdata['init_fp_style'] == "VASP":
coll_vasp_md(jdata)
elif jdata['init_fp_style'] == "ABACUS":
coll_abacus_md(jdata)
else :
raise RuntimeError("unknown stage %d" % stage)
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description="Generating initial data for bulk systems.")
parser.add_argument('PARAM', type=str,
help="parameter file, json/yaml format")
parser.add_argument('MACHINE', type=str,default=None,nargs="?",
help="machine file, json/yaml format")
args = parser.parse_args()
gen_init_bulk(args)