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cwd = os.getcwd()
os.chdir(task_path)
if os.path.isfile('POSCAR') :
os.remove('POSCAR')
os.symlink(os.path.relpath(conf_poscar), 'POSCAR')
os.chdir(cwd)
with open(task_poscar,'r') as fp :
lines = fp.read().split('\n')
ele_list = lines[5].split()
print(task_path)
# make conf.lmp
conf_file = os.path.join(task_path, 'conf.lmp')
lammps.cvt_lammps_conf(task_poscar, os.path.relpath(conf_file))
ptypes = vasp.get_poscar_types(task_poscar)
lammps.apply_type_map(conf_file, type_map, ptypes)
# make lammps.in
ntypes=len(ele_list)
unitcell=get_structure_from_poscar(task_poscar)
if task_type=='deepmd':
fc = lammps.make_lammps_phonon('conf.lmp',
unitcell.masses,
lammps.inter_deepmd,
model_name)
if task_type=='meam':
fc = lammps.make_lammps_phonon('conf.lmp',
unitcell.masses,
lammps.inter_meam,
model_param)
f_lammps_in = os.path.join(task_path, 'lammps.in')
with open(f_lammps_in, 'w') as fp :
fp.write(fc)
os.symlink(os.path.relpath(ii), jj)
share_models = [os.path.join(task_path,ii) for ii in model_name]
for ii in range(n_dfm) :
# make dir
dfm_path = os.path.join(task_path, 'dfm-%03d' % ii)
os.makedirs(dfm_path, exist_ok=True)
os.chdir(dfm_path)
for jj in ['conf.lmp', 'lammps.in'] + model_name :
if os.path.isfile(jj):
os.remove(jj)
# make conf
dfm_ss.deformed_structures[ii].to('POSCAR', 'POSCAR')
lammps.cvt_lammps_conf('POSCAR', 'conf.lmp')
ptypes = vasp.get_poscar_types('POSCAR')
lammps.apply_type_map('conf.lmp', type_map, ptypes)
# record strain
strain = Strain.from_deformation(dfm_ss.deformations[ii])
np.savetxt('strain.out', strain)
# link lammps.in
os.symlink(os.path.relpath(f_lammps_in), 'lammps.in')
# link models
for (ii,jj) in zip(share_models, model_name) :
os.symlink(os.path.relpath(ii), jj)
cwd = os.getcwd()
os.chdir(frame_path)
# clear dir
for jj in ['conf.lmp'] :
if os.path.isfile(jj):
os.remove(jj)
for jj in ['lammps.in'] + model_name :
if os.path.islink(jj):
os.unlink(jj)
# link lammps in
os.symlink(os.path.relpath('../lammps.in'), 'lammps.in')
# make conf
with open('POSCAR', 'w') as fp :
fp.write('\n'.join(xdat_lines[ii*xdat_secsize:(ii+1)*xdat_secsize]))
lammps.cvt_lammps_conf('POSCAR', 'conf.lmp')
ptypes = vasp.get_poscar_types('POSCAR')
lammps.apply_type_map('conf.lmp', type_map, ptypes)
# link models
for (kk,ll) in zip(share_models, model_name) :
os.symlink(os.path.relpath(kk), ll)
os.chdir(ls)
os.chdir(cwd)
os.symlink(os.path.relpath(ii), jj)
share_models = [os.path.join(task_path,ii) for ii in model_name]
for ii in range(len(dss)) :
struct_path = os.path.join(task_path, 'struct-%s-%03d' % (copy_str,ii))
print('# generate %s' % (struct_path))
os.makedirs(struct_path, exist_ok=True)
os.chdir(struct_path)
for jj in ['conf.lmp', 'lammps.in'] + model_name :
if os.path.isfile(jj):
os.remove(jj)
# make conf
dss[ii].to('POSCAR', 'POSCAR')
lammps.cvt_lammps_conf('POSCAR', 'conf.lmp')
ptypes = vasp.get_poscar_types('POSCAR')
lammps.apply_type_map('conf.lmp', type_map, ptypes)
# link lammps.in
os.symlink(os.path.relpath(f_lammps_in), 'lammps.in')
# link models
for (ii,jj) in zip(share_models, model_name) :
os.symlink(os.path.relpath(ii), jj)
# save supercell
np.savetxt('supercell.out', supercell, fmt='%d')
os.chdir(cwd)
slab = all_slabs[ii]
miller_str = "m%d.%d.%dm" % (slab.miller_index[0], slab.miller_index[1], slab.miller_index[2])
# make dir
struct_path = os.path.join(task_path, 'struct-%03d-%s' % (ii, miller_str))
os.makedirs(struct_path, exist_ok=True)
os.chdir(struct_path)
for jj in ['conf.lmp', 'lammps.in'] + model_name :
if os.path.isfile(jj):
os.remove(jj)
print("# %03d generate " % ii, struct_path, " \t %d atoms" % len(slab.sites))
# make conf
slab.to('POSCAR', 'POSCAR')
vasp.regulate_poscar('POSCAR', 'POSCAR')
lammps.cvt_lammps_conf('POSCAR', 'conf.lmp')
ptypes = vasp.get_poscar_types('POSCAR')
lammps.apply_type_map('conf.lmp', type_map, ptypes)
# record miller
np.savetxt('miller.out', slab.miller_index, fmt='%d')
# link lammps.in
os.symlink(os.path.relpath(f_lammps_in), 'lammps.in')
# link models
for (ii,jj) in zip(share_models, model_name) :
os.symlink(os.path.relpath(ii), jj)
cwd = os.getcwd()
to_poscar = os.path.join(equi_path, 'POSCAR')
if os.path.exists(to_poscar) :
assert(filecmp.cmp(from_poscar, to_poscar))
else :
os.chdir(equi_path)
os.symlink(os.path.relpath(from_poscar), 'POSCAR')
os.chdir(cwd)
# lmp path
lmp_path = os.path.join(equi_path, task_type)
os.makedirs(lmp_path, exist_ok = True)
print(lmp_path)
# lmp conf
conf_file = os.path.join(lmp_path, 'conf.lmp')
lammps.cvt_lammps_conf(to_poscar, os.path.relpath(conf_file))
ptypes = vasp.get_poscar_types(to_poscar)
lammps.apply_type_map(conf_file, type_map, ptypes)
# lmp input
if task_type=='deepmd':
fc = lammps.make_lammps_equi(os.path.basename(conf_file),
ntypes,
lammps.inter_deepmd,
model_name)
elif task_type=='meam':
fc = lammps.make_lammps_equi(os.path.basename(conf_file),
ntypes,
lammps.inter_meam,
model_param)
with open(os.path.join(lmp_path, 'lammps.in'), 'w') as fp :
fp.write(fc)
# link models
os.chdir(lmp_path)
for ii in model_name :
# make vols
for vol in np.arange(vol_start, vol_end, vol_step) :
vol_path = os.path.join(task_path, 'vol-%.2f' % vol)
print('# generate %s' % (vol_path))
os.makedirs(vol_path, exist_ok = True)
os.chdir(vol_path)
for ii in ['conf.lmp', 'conf.lmp', 'lammps.in'] + model_name :
if os.path.exists(ii) :
os.remove(ii)
# make conf
scale_ss = ss.copy()
scale_ss.scale_lattice(vol * natoms)
scale_ss.to('POSCAR', 'POSCAR')
lammps.cvt_lammps_conf('POSCAR', 'conf.lmp')
ptypes = vasp.get_poscar_types('POSCAR')
lammps.apply_type_map('conf.lmp', type_map, ptypes)
# link lammps.in
os.symlink(os.path.relpath(f_lammps_in), 'lammps.in')
# link models
for (ii,jj) in zip(share_models,model_name) :
os.symlink(os.path.relpath(ii), jj)
# make lammps input
os.chdir(cwd)