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, 'r') 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
def make_property(confs, inter_param, property_list):
# find all POSCARs and their name like mp-xxx
# ...
# conf_dirs = glob.glob(confs)
# conf_dirs.sort()
conf_dirs = []
for conf in confs:
conf_dirs.extend(glob.glob(conf))
conf_dirs.sort()
for ii in conf_dirs:
sepline(ch=ii, screen=True)
for jj in property_list:
if jj.get("skip", False):
continue
if 'init_from_suffix' and 'output_suffix' in jj:
do_refine = True
suffix = jj['output_suffix']
elif 'reproduce' in jj and jj['reproduce']:
do_refine = False
suffix = 'reprod'
else:
do_refine = False
suffix = '00'
# generate working directory like mp-xxx/eos_00 if jj['type'] == 'eos'
# handel the exception that the working directory exists
# ...
# determine the suffix: from scratch or refine
# ...
property_type = jj['type']
path_to_equi = os.path.join(ii, 'relaxation', 'relax_task')
path_to_work = os.path.join(ii, property_type + '_' + suffix)
if os.path.exists(path_to_work):
dlog.warning('%s already exists' % path_to_work)
else:
os.makedirs(path_to_work)
prop = make_property_instance(jj)
task_list = prop.make_confs(path_to_work, path_to_equi, do_refine)
inter_param_prop = inter_param
if 'cal_setting' in jj and 'overwrite_interaction' in jj[
'cal_setting']:
inter_param_prop = jj['cal_setting']['overwrite_interaction']
for kk in task_list:
poscar = os.path.join(kk, 'POSCAR')
inter = make_calculator(inter_param_prop, poscar)
inter.make_potential_files(kk)
dlog.debug(prop.task_type()) ### debug
inter.make_input_file(kk, prop.task_type(), prop.task_param())
prop.post_process(
task_list
) # generate same KPOINTS file for elastic when doing VASP
def exec_command(self, cmd, retry = 0):
"""Calling self.ssh.exec_command but has an exception check."""
try:
return self.ssh.exec_command(cmd)
except paramiko.ssh_exception.SSHException:
# SSH session not active
# retry for up to 3 times
if retry < 3:
dlog.warning("SSH session not active in calling %s, retry the command..." % cmd)
# ensure alive
self.ensure_alive()
return self.exec_command(cmd, retry = retry+1)
raise RuntimeError("SSH session not active")
def block_checkcall(self,
cmd,
retry=0) :
self.ssh_session.ensure_alive()
stdin, stdout, stderr = self.ssh_session.exec_command(('cd %s ;' % self.remote_root) + cmd)
exit_status = stdout.channel.recv_exit_status()
if exit_status != 0:
if retry<3:
# sleep 60 s
dlog.warning("Get error code %d in calling %s through ssh with job: %s . message: %s" %
(exit_status, cmd, self.job_uuid, stderr.read().decode('utf-8')))
dlog.warning("Sleep 60 s and retry the command...")
time.sleep(60)
return self.block_checkcall(cmd, retry=retry+1)
raise RuntimeError("Get error code %d in calling %s through ssh with job: %s . message: %s" %
(exit_status, cmd, self.job_uuid, stderr.read().decode('utf-8')))
return stdin, stdout, stderr
def make_confs(self, path_to_work, path_to_equi, refine=False):
path_to_work = os.path.abspath(path_to_work)
if os.path.exists(path_to_work):
dlog.warning('%s already exists' % path_to_work)
else:
os.makedirs(path_to_work)
path_to_equi = os.path.abspath(path_to_equi)
if 'start_confs_path' in self.parameter and os.path.exists(
self.parameter['start_confs_path']):
init_path_list = glob.glob(
os.path.join(self.parameter['start_confs_path'], '*'))
struct_init_name_list = []
for ii in init_path_list:
struct_init_name_list.append(ii.split('/')[-1])
struct_output_name = path_to_work.split('/')[-2]
assert struct_output_name in struct_init_name_list
path_to_equi = os.path.abspath(
os.path.join(self.parameter['start_confs_path'],
struct_output_name, 'relaxation', 'relax_task'))
task_list = []
cwd = os.getcwd()
equi_contcar = os.path.join(path_to_equi, 'CONTCAR')
os.chdir(path_to_work)
if os.path.isfile('POSCAR'):
os.remove('POSCAR')
if os.path.islink('POSCAR'):
os.remove('POSCAR')
os.symlink(os.path.relpath(equi_contcar), 'POSCAR')
# task_poscar = os.path.join(output, 'POSCAR')
# stress, deal with unsupported stress in dpdata
#with open(os.path.join(path_to_equi, 'result.json')) as fin:
# equi_result = json.load(fin)
#equi_stress = np.array(equi_result['stress']['data'])[-1]
equi_result = loadfn(os.path.join(path_to_equi, 'result.json'))
equi_stress = equi_result['stress'][-1]
dumpfn(equi_stress, 'equi.stress.json', indent=4)
os.chdir(cwd)
if refine:
print('elastic refine starts')
task_list = make_refine(self.parameter['init_from_suffix'],
self.parameter['output_suffix'],
path_to_work)
# record strain
# df = Strain.from_deformation(dfm_ss.deformations[idid])
# dumpfn(df.as_dict(), 'strain.json', indent=4)
init_from_path = re.sub(self.parameter['output_suffix'][::-1],
self.parameter['init_from_suffix'][::-1],
path_to_work[::-1],
count=1)[::-1]
task_list_basename = list(map(os.path.basename, task_list))
for ii in task_list_basename:
init_from_task = os.path.join(init_from_path, ii)
output_task = os.path.join(path_to_work, ii)
os.chdir(output_task)
if os.path.isfile('strain.json'):
os.remove('strain.json')
copyfile(os.path.join(init_from_task, 'strain.json'),
'strain.json')
#os.symlink(os.path.relpath(
# os.path.join((re.sub(self.parameter['output_suffix'], self.parameter['init_from_suffix'], ii)),
# 'strain.json')),
# 'strain.json')
os.chdir(cwd)
else:
norm_def = self.norm_deform
shear_def = self.shear_deform
norm_strains = [
-norm_def, -0.5 * norm_def, 0.5 * norm_def, norm_def
]
shear_strains = [
-shear_def, -0.5 * shear_def, 0.5 * shear_def, shear_def
]
if not os.path.exists(equi_contcar):
raise RuntimeError("please do relaxation first")
ss = Structure.from_file(equi_contcar)
dfm_ss = DeformedStructureSet(ss,
symmetry=False,
norm_strains=norm_strains,
shear_strains=shear_strains)
n_dfm = len(dfm_ss)
print('gen with norm ' + str(norm_strains))
print('gen with shear ' + str(shear_strains))
for ii in range(n_dfm):
output_task = os.path.join(path_to_work, 'task.%06d' % ii)
os.makedirs(output_task, exist_ok=True)
os.chdir(output_task)
for jj in [
'INCAR', 'POTCAR', 'POSCAR', 'conf.lmp', 'in.lammps'
]:
if os.path.exists(jj):
os.remove(jj)
task_list.append(output_task)
dfm_ss.deformed_structures[ii].to('POSCAR', 'POSCAR')
# record strain
df = Strain.from_deformation(dfm_ss.deformations[ii])
dumpfn(df.as_dict(), 'strain.json', indent=4)
os.chdir(cwd)
return task_list
def make_confs(self, path_to_work, path_to_equi, refine=False):
path_to_work = os.path.abspath(path_to_work)
if os.path.exists(path_to_work):
dlog.warning('%s already exists' % path_to_work)
else:
os.makedirs(path_to_work)
path_to_equi = os.path.abspath(path_to_equi)
if 'start_confs_path' in self.parameter and os.path.exists(
self.parameter['start_confs_path']):
init_path_list = glob.glob(
os.path.join(self.parameter['start_confs_path'], '*'))
struct_init_name_list = []
for ii in init_path_list:
struct_init_name_list.append(ii.split('/')[-1])
struct_output_name = path_to_work.split('/')[-2]
assert struct_output_name in struct_init_name_list
path_to_equi = os.path.abspath(
os.path.join(self.parameter['start_confs_path'],
struct_output_name, 'relaxation', 'relax_task'))
cwd = os.getcwd()
task_list = []
if self.reprod:
print('eos reproduce starts')
if 'init_data_path' not in self.parameter:
raise RuntimeError(
"please provide the initial data path to reproduce")
init_data_path = os.path.abspath(self.parameter['init_data_path'])
task_list = make_repro(
init_data_path, self.init_from_suffix, path_to_work,
self.parameter.get('reprod_last_frame', True))
os.chdir(cwd)
else:
if refine:
print('eos refine starts')
task_list = make_refine(self.parameter['init_from_suffix'],
self.parameter['output_suffix'],
path_to_work)
os.chdir(cwd)
init_from_path = re.sub(
self.parameter['output_suffix'][::-1],
self.parameter['init_from_suffix'][::-1],
path_to_work[::-1],
count=1)[::-1]
task_list_basename = list(map(os.path.basename, task_list))
for ii in task_list_basename:
init_from_task = os.path.join(init_from_path, ii)
output_task = os.path.join(path_to_work, ii)
os.chdir(output_task)
if os.path.isfile('eos.json'):
os.remove('eos.json')
if os.path.islink('eos.json'):
os.remove('eos.json')
os.symlink(
os.path.relpath(
os.path.join(init_from_task, 'eos.json')),
'eos.json')
os.chdir(cwd)
else:
print('gen eos from ' + str(self.vol_start) + ' to ' +
str(self.vol_end) + ' by every ' + str(self.vol_step))
equi_contcar = os.path.join(path_to_equi, 'CONTCAR')
if not os.path.exists(equi_contcar):
raise RuntimeError("please do relaxation first")
vol_to_poscar = vasp.poscar_vol(
equi_contcar) / vasp.poscar_natoms(equi_contcar)
self.parameter['scale2equi'] = []
task_num = 0
while self.vol_start + self.vol_step * task_num < self.vol_end:
# for vol in np.arange(int(self.vol_start * 100), int(self.vol_end * 100), int(self.vol_step * 100)):
# vol = vol / 100.0
vol = self.vol_start + task_num * self.vol_step
#task_num = int((vol - self.vol_start) / self.vol_step)
output_task = os.path.join(path_to_work,
'task.%06d' % task_num)
os.makedirs(output_task, exist_ok=True)
os.chdir(output_task)
for ii in [
'INCAR', 'POTCAR', 'POSCAR.orig', 'POSCAR',
'conf.lmp', 'in.lammps'
]:
if os.path.exists(ii):
os.remove(ii)
task_list.append(output_task)
os.symlink(os.path.relpath(equi_contcar), 'POSCAR.orig')
# scale = (vol / vol_to_poscar) ** (1. / 3.)
scale = vol**(1. / 3.)
eos_params = {
'volume': vol * vol_to_poscar,
'scale': scale
}
dumpfn(eos_params, 'eos.json', indent=4)
self.parameter['scale2equi'].append(scale) # 06/22
vasp.poscar_scale('POSCAR.orig', 'POSCAR', scale)
task_num += 1
os.chdir(cwd)
return task_list
def make_equi(confs, inter_param, relax_param):
# find all POSCARs and their name like mp-xxx
# ...
dlog.debug('debug info make equi')
if 'type_map' in inter_param:
ele_list = [key for key in inter_param['type_map'].keys()]
else:
ele_list = [key for key in inter_param['potcars'].keys()]
# ele_list = inter_param['type_map']
dlog.debug("ele_list %s" % ':'.join(ele_list))
conf_dirs = []
for conf in confs:
conf_dirs.extend(glob.glob(conf))
conf_dirs.sort()
# generate a list of task names like mp-xxx/relaxation/relax_task
# ...
cwd = os.getcwd()
# generate poscar for single element crystal
if len(ele_list) == 1:
for ii in conf_dirs:
os.chdir(ii)
crys_type = ii.split('/')[-1]
dlog.debug('crys_type: %s' % crys_type)
dlog.debug('pwd: %s' % os.getcwd())
if crys_type == 'std-fcc':
if not os.path.exists('POSCAR'):
crys.fcc1(ele_list[0]).to('POSCAR', 'POSCAR')
elif crys_type == 'std-hcp':
if not os.path.exists('POSCAR'):
crys.hcp(ele_list[0]).to('POSCAR', 'POSCAR')
elif crys_type == 'std-dhcp':
if not os.path.exists('POSCAR'):
crys.dhcp(ele_list[0]).to('POSCAR', 'POSCAR')
elif crys_type == 'std-bcc':
if not os.path.exists('POSCAR'):
crys.bcc(ele_list[0]).to('POSCAR', 'POSCAR')
elif crys_type == 'std-diamond':
if not os.path.exists('POSCAR'):
crys.diamond(ele_list[0]).to('POSCAR', 'POSCAR')
elif crys_type == 'std-sc':
if not os.path.exists('POSCAR'):
crys.sc(ele_list[0]).to('POSCAR', 'POSCAR')
os.chdir(cwd)
task_dirs = []
# make task directories like mp-xxx/relaxation/relax_task
# if mp-xxx/exists then print a warning and exit.
# ...
for ii in conf_dirs:
crys_type = ii.split('/')[-1]
dlog.debug('crys_type: %s' % crys_type)
if 'mp-' in crys_type and not os.path.exists(os.path.join(
ii, 'POSCAR')):
get_structure(crys_type).to('POSCAR', os.path.join(ii, 'POSCAR'))
poscar = os.path.abspath(os.path.join(ii, 'POSCAR'))
if not os.path.exists(poscar):
raise FileNotFoundError('no configuration for autotest')
relax_dirs = os.path.abspath(
os.path.join(ii, 'relaxation', 'relax_task')
) # to be consistent with property in make dispatcher
if os.path.exists(relax_dirs):
dlog.warning('%s already exists' % relax_dirs)
else:
os.makedirs(relax_dirs)
task_dirs.append(relax_dirs)
os.chdir(relax_dirs)
# copy POSCARs to mp-xxx/relaxation/relax_task
# ...
if os.path.isfile('POSCAR'):
os.remove('POSCAR')
os.symlink(os.path.relpath(poscar), 'POSCAR')
os.chdir(cwd)
task_dirs.sort()
# generate task files
relax_param['cal_type'] = 'relaxation'
if 'cal_setting' not in relax_param:
relax_param['cal_setting'] = {
"relax_pos": True,
"relax_shape": True,
"relax_vol": True
}
elif "relax_pos" not in relax_param['cal_setting']:
relax_param['cal_setting']['relax_pos'] = True
elif "relax_shape" not in relax_param['cal_setting']:
relax_param['cal_setting']['relax_shape'] = True
elif "relax_vol" not in relax_param['cal_setting']:
relax_param['cal_setting']['relax_vol'] = True
for ii in task_dirs:
poscar = os.path.join(ii, 'POSCAR')
dlog.debug('task_dir %s' % ii)
inter = make_calculator(inter_param, poscar)
inter.make_potential_files(ii)
inter.make_input_file(ii, 'relaxation', relax_param)
def make_confs(self,
path_to_work,
path_to_equi,
refine=False):
path_to_work = os.path.abspath(path_to_work)
if os.path.exists(path_to_work):
dlog.warning('%s already exists' % path_to_work)
else:
os.makedirs(path_to_work)
path_to_equi = os.path.abspath(path_to_equi)
if 'start_confs_path' in self.parameter and os.path.exists(self.parameter['start_confs_path']):
init_path_list = glob.glob(os.path.join(self.parameter['start_confs_path'], '*'))
struct_init_name_list = []
for ii in init_path_list:
struct_init_name_list.append(ii.split('/')[-1])
struct_output_name = path_to_work.split('/')[-2]
assert struct_output_name in struct_init_name_list
path_to_equi = os.path.abspath(os.path.join(self.parameter['start_confs_path'],
struct_output_name, 'relaxation', 'relax_task'))
task_list = []
cwd = os.getcwd()
if self.reprod:
print('surface reproduce starts')
if 'init_data_path' not in self.parameter:
raise RuntimeError("please provide the initial data path to reproduce")
init_data_path = os.path.abspath(self.parameter['init_data_path'])
task_list = make_repro(init_data_path, self.init_from_suffix,
path_to_work, self.parameter.get('reprod_last_frame', True))
os.chdir(cwd)
else:
if refine:
print('surface refine starts')
task_list = make_refine(self.parameter['init_from_suffix'],
self.parameter['output_suffix'],
path_to_work)
os.chdir(cwd)
# record miller
init_from_path = re.sub(self.parameter['output_suffix'][::-1],
self.parameter['init_from_suffix'][::-1],
path_to_work[::-1], count=1)[::-1]
task_list_basename = list(map(os.path.basename, task_list))
for ii in task_list_basename:
init_from_task = os.path.join(init_from_path, ii)
output_task = os.path.join(path_to_work, ii)
os.chdir(output_task)
if os.path.isfile('miller.json'):
os.remove('miller.json')
if os.path.islink('miller.json'):
os.remove('miller.json')
os.symlink(os.path.relpath(os.path.join(init_from_task, 'miller.json')), 'miller.json')
os.chdir(cwd)
else:
equi_contcar = os.path.join(path_to_equi, 'CONTCAR')
if not os.path.exists(equi_contcar):
raise RuntimeError("please do relaxation first")
ptypes = vasp.get_poscar_types(equi_contcar)
# gen structure
ss = Structure.from_file(equi_contcar)
# gen slabs
all_slabs = generate_all_slabs(ss, self.miller, self.min_slab_size, self.min_vacuum_size)
os.chdir(path_to_work)
if os.path.isfile('POSCAR'):
os.remove('POSCAR')
if os.path.islink('POSCAR'):
os.remove('POSCAR')
os.symlink(os.path.relpath(equi_contcar), 'POSCAR')
# task_poscar = os.path.join(output, 'POSCAR')
for ii in range(len(all_slabs)):
output_task = os.path.join(path_to_work, 'task.%06d' % ii)
os.makedirs(output_task, exist_ok=True)
os.chdir(output_task)
for jj in ['INCAR', 'POTCAR', 'POSCAR', 'conf.lmp', 'in.lammps']:
if os.path.exists(jj):
os.remove(jj)
task_list.append(output_task)
print("# %03d generate " % ii, output_task, " \t %d atoms" % len(all_slabs[ii].sites))
# make confs
all_slabs[ii].to('POSCAR', 'POSCAR.tmp')
vasp.regulate_poscar('POSCAR.tmp', 'POSCAR')
vasp.sort_poscar('POSCAR', 'POSCAR', ptypes)
vasp.perturb_xz('POSCAR', 'POSCAR', self.pert_xz)
# record miller
dumpfn(all_slabs[ii].miller_index, 'miller.json')
os.chdir(cwd)
return task_list
def make_confs(self, path_to_work, path_to_equi, refine=False):
path_to_work = os.path.abspath(path_to_work)
if os.path.exists(path_to_work):
dlog.warning('%s already exists' % path_to_work)
else:
os.makedirs(path_to_work)
path_to_equi = os.path.abspath(path_to_equi)
if 'start_confs_path' in self.parameter and os.path.exists(
self.parameter['start_confs_path']):
init_path_list = glob.glob(
os.path.join(self.parameter['start_confs_path'], '*'))
struct_init_name_list = []
for ii in init_path_list:
struct_init_name_list.append(ii.split('/')[-1])
struct_output_name = path_to_work.split('/')[-2]
assert struct_output_name in struct_init_name_list
path_to_equi = os.path.abspath(
os.path.join(self.parameter['start_confs_path'],
struct_output_name, 'relaxation', 'relax_task'))
task_list = []
cwd = os.getcwd()
if self.reprod:
print('vacancy reproduce starts')
if 'init_data_path' not in self.parameter:
raise RuntimeError(
"please provide the initial data path to reproduce")
init_data_path = os.path.abspath(self.parameter['init_data_path'])
task_list = make_repro(
init_data_path, self.init_from_suffix, path_to_work,
self.parameter.get('reprod_last_frame', False))
os.chdir(cwd)
else:
if refine:
print('vacancy refine starts')
task_list = make_refine(self.parameter['init_from_suffix'],
self.parameter['output_suffix'],
path_to_work)
init_from_path = re.sub(
self.parameter['output_suffix'][::-1],
self.parameter['init_from_suffix'][::-1],
path_to_work[::-1],
count=1)[::-1]
task_list_basename = list(map(os.path.basename, task_list))
for ii in task_list_basename:
init_from_task = os.path.join(init_from_path, ii)
output_task = os.path.join(path_to_work, ii)
os.chdir(output_task)
if os.path.isfile('supercell.json'):
os.remove('supercell.json')
if os.path.islink('supercell.json'):
os.remove('supercell.json')
os.symlink(
os.path.relpath(
os.path.join(init_from_task, 'supercell.json')),
'supercell.json')
os.chdir(cwd)
else:
equi_contcar = os.path.join(path_to_equi, 'CONTCAR')
if not os.path.exists(equi_contcar):
raise RuntimeError("please do relaxation first")
ss = Structure.from_file(equi_contcar)
vds = VacancyGenerator(ss)
dss = []
for jj in vds:
dss.append(jj.generate_defect_structure(self.supercell))
print('gen vacancy with supercell ' + str(self.supercell))
os.chdir(path_to_work)
if os.path.isfile('POSCAR'):
os.remove('POSCAR')
if os.path.islink('POSCAR'):
os.remove('POSCAR')
os.symlink(os.path.relpath(equi_contcar), 'POSCAR')
# task_poscar = os.path.join(output, 'POSCAR')
for ii in range(len(dss)):
output_task = os.path.join(path_to_work, 'task.%06d' % ii)
os.makedirs(output_task, exist_ok=True)
os.chdir(output_task)
for jj in [
'INCAR', 'POTCAR', 'POSCAR', 'conf.lmp',
'in.lammps'
]:
if os.path.exists(jj):
os.remove(jj)
task_list.append(output_task)
dss[ii].to('POSCAR', 'POSCAR')
# np.savetxt('supercell.out', self.supercell, fmt='%d')
dumpfn(self.supercell, 'supercell.json')
os.chdir(cwd)
return task_list