def comput_vasp_nev(jdata, conf_dir, write_stable=False):
kspacing = jdata['vasp_params']['kspacing']
conf_path = re.sub('confs', global_equi_name, conf_dir)
conf_path = os.path.abspath(conf_path)
poscar = os.path.join(conf_path, 'POSCAR')
if write_stable:
ele_types = vasp.get_poscar_types(poscar)
if len(ele_types) > 1:
raise RuntimeError(
'stable energy and volume only for one element, current you have %s from POSCAR'
% str(ele_types))
ener_shift = comput_e_shift(poscar, 'vasp-k%.2f' % kspacing)
vasp_path = os.path.join(conf_path, 'vasp-k%.2f' % kspacing)
outcar = os.path.join(vasp_path, 'OUTCAR')
# tag_fin = os.path.join(vasp_path, 'tag_finished')
if not os.path.isfile(outcar):
warnings.warn("cannot find OUTCAR in " + vasp_path + " skip")
elif not vasp.check_finished(outcar):
warnings.warn("incomplete job " + vasp_path + " use the last frame")
if os.path.isfile(outcar):
natoms, epa, vpa = vasp.get_nev(outcar)
epa = (epa * natoms - ener_shift) / natoms
if write_stable:
stable_dir = 'stables'
os.makedirs(stable_dir, exist_ok=True)
name_prefix = os.path.join(
stable_dir, '%s.vasp-k%.2f' % (ele_types[0], kspacing))
open(name_prefix + '.e', 'w').write('%.16f\n' % (epa))
open(name_prefix + '.v', 'w').write('%.16f\n' % (vpa))
return natoms, epa, vpa
else:
return None, None, None
def run_phonon(task_type, jdata, mdata, ssh_sess):
conf_dir = jdata['conf_dir']
fp_params = jdata['vasp_params']
kspacing = fp_params['kspacing']
conf_path = os.path.abspath(conf_dir)
task_path = re.sub('confs', '06.phonon', conf_path)
if task_type == "vasp":
work_path = os.path.join(task_path, 'vasp-k%.2f' % kspacing)
elif task_type in lammps_task_type:
work_path = os.path.join(task_path, task_type)
assert (os.path.isdir(work_path))
all_task = glob.glob(os.path.join(work_path, '.'))
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
vasp_exec = mdata['fp_command']
group_size = mdata['fp_group_size']
resources = mdata['fp_resources']
machine = mdata['fp_machine']
machine_type = mdata['fp_machine']['machine_type']
command = vasp_exec
command = cmd_append_log(command, "log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'OUTCAR')
if os.path.isfile(fres):
if not vasp.check_finished(fres):
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
run_tasks = [os.path.basename(ii) for ii in run_tasks_]
forward_files = ['INCAR', 'POTCAR', 'KPOINTS']
backward_files = ['OUTCAR', 'OSZICAR', 'vasprun.xml']
common_files = ['POSCAR']
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files,
backward_files)
#lammps
elif task_type in lammps_task_type:
None
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
def run_phonon(task_type, jdata, mdata, ssh_sess):
user = ('user_incar' in jdata.keys())
work_path = make_work_path(jdata, '06.phonon', False, False, user)
all_task = glob.glob(os.path.join(work_path, '.'))
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
vasp_exec = mdata['fp_command']
group_size = mdata['fp_group_size']
resources = mdata['fp_resources']
machine = mdata['fp_machine']
machine_type = mdata['fp_machine']['machine_type']
command = vasp_exec
command = cmd_append_log(command, "log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'OUTCAR')
if os.path.isfile(fres):
if not vasp.check_finished(fres):
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
run_tasks = [os.path.basename(ii) for ii in run_tasks_]
forward_files = ['INCAR', 'POTCAR', 'KPOINTS']
backward_files = ['OUTCAR', 'OSZICAR', 'vasprun.xml']
common_files = ['POSCAR']
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files,
backward_files)
#lammps
elif task_type in lammps_task_type:
None
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
def comput_vasp_nev(jdata, conf_dir, write_shift=False):
conf_path = re.sub('confs', global_equi_name, conf_dir)
conf_path = os.path.abspath(conf_path)
poscar = os.path.join(conf_path, 'POSCAR')
ele_types = vasp.get_poscar_types(poscar)
if 'relax_incar' in jdata.keys():
vasp_str = 'vasp-relax_incar'
else:
kspacing = jdata['vasp_params']['kspacing']
vasp_str = 'vasp-k%.2f' % kspacing
vasp_path = os.path.join(conf_path, vasp_str)
outcar = os.path.join(vasp_path, 'OUTCAR')
# tag_fin = os.path.join(vasp_path, 'tag_finished')
if not os.path.isfile(outcar):
warnings.warn("cannot find OUTCAR in " + vasp_path + " skip")
elif not vasp.check_finished(outcar):
warnings.warn("incomplete job " + vasp_path + " use the last frame")
if os.path.isfile(outcar):
natoms, epa, vpa = vasp.get_nev(outcar)
if write_shift and len(ele_types) > 1:
ener_shift = comput_e_shift(poscar, vasp_str)
shift = (epa * natoms - ener_shift) / natoms
return natoms, epa, vpa, shift
if len(ele_types) == 1:
stable_dir = 'stables'
os.makedirs(stable_dir, exist_ok=True)
name_prefix = os.path.join(stable_dir,
'%s.' % (ele_types[0]) + vasp_str)
open(name_prefix + '.e', 'w').write('%.16f\n' % (epa))
open(name_prefix + '.v', 'w').write('%.16f\n' % (vpa))
return natoms, epa, vpa, None
else:
return None, None, None, None
def run_surf(task_type, jdata, mdata, ssh_sess):
static = jdata['static-opt']
work_path = make_work_path(jdata, '05.surf', False, static, False)
all_task = glob.glob(os.path.join(work_path, 'struct-*'))
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
vasp_exec = mdata['fp_command']
group_size = mdata['fp_group_size']
resources = mdata['fp_resources']
machine = mdata['fp_machine']
machine_type = mdata['fp_machine']['machine_type']
command = vasp_exec
command = cmd_append_log(command, "log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'OUTCAR')
if os.path.isfile(fres):
if not vasp.check_finished(fres):
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
forward_files = ['INCAR', 'POSCAR', 'POTCAR']
backward_files = ['OUTCAR', 'OSZICAR']
common_files = ['INCAR', 'POTCAR']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
lmp_exec = mdata['lmp_command']
group_size = mdata['model_devi_group_size']
resources = mdata['model_devi_resources']
machine = mdata['model_devi_machine']
machine_type = mdata['model_devi_machine']['machine_type']
command = lmp_exec + " -i lammps.in"
command = cmd_append_log(command, "model_devi.log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'log.lammps')
if os.path.isfile(fres):
with open(fres, 'r') as fp:
lines = fp.read().split('\n')
flag = False
for jj in lines:
if ("Final energy per atoms"
in jj) and (not 'print' in jj):
flag = True
if not flag:
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name = fp_params['model_name']
if not model_name:
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir, ii) for ii in model_name]
forward_files = ['conf.lmp', 'lammps.in'] + model_name
backward_files = ['log.lammps', 'model_devi.log']
common_files = ['lammps.in'] + model_name
if len(model_name) > 1 and task_type == 'deepmd':
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
run_tasks = [os.path.basename(ii) for ii in run_tasks_]
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files, backward_files)
def run_interstitial(task_type, jdata, mdata, ssh_sess):
conf_dir = jdata['conf_dir']
fp_params = jdata['vasp_params']
kspacing = fp_params['kspacing']
reprod_opt = jdata['reprod-opt']
conf_path = os.path.abspath(conf_dir)
task_path = re.sub('confs', '04.interstitial', conf_path)
if task_type == "vasp":
work_path = os.path.join(task_path, 'vasp-k%.2f' % kspacing)
elif task_type in lammps_task_type:
work_path = os.path.join(task_path, task_type)
if reprod_opt:
work_path = os.path.join(task_path,
'%s-reprod-k%.2f' % (task_type, kspacing))
assert (os.path.isdir(work_path))
all_task = glob.glob(os.path.join(work_path, 'struct-*'))
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
vasp_exec = mdata['fp_command']
group_size = mdata['fp_group_size']
resources = mdata['fp_resources']
machine = mdata['fp_machine']
machine_type = mdata['fp_machine']['machine_type']
command = vasp_exec
command = cmd_append_log(command, "log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'OUTCAR')
if os.path.isfile(fres):
if not vasp.check_finished(fres):
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
forward_files = ['INCAR', 'POSCAR', 'POTCAR']
backward_files = ['OUTCAR', 'XDATCAR', 'OSZICAR']
common_files = ['INCAR']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
lmp_exec = mdata['lmp_command']
group_size = mdata['model_devi_group_size']
resources = mdata['model_devi_resources']
machine = mdata['model_devi_machine']
machine_type = mdata['model_devi_machine']['machine_type']
command = lmp_exec + " -i lammps.in"
command = cmd_append_log(command, "model_devi.log")
if reprod_opt:
all_frame = []
for ii in all_task:
all_frame += (glob.glob(os.path.join(ii, 'frame.*')))
work_path = all_task
all_task = all_frame
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'log.lammps')
if os.path.isfile(fres):
with open(fres, 'r') as fp:
lines = fp.read().split('\n')
flag = False
for jj in lines:
if ("Final energy per atoms"
in jj) and (not 'print' in jj):
flag = True
if not flag:
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name = fp_params['model_name']
if not model_name:
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir, ii) for ii in model_name]
forward_files = ['conf.lmp', 'lammps.in'] + model_name
backward_files = ['log.lammps', 'model_devi.log']
common_files = ['lammps.in'] + model_name
if len(model_name) > 1:
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
if reprod_opt:
for ii in work_path:
run_tasks = []
for jj in run_tasks_:
if ii in jj:
run_tasks.append(os.path.basename(jj))
_run(machine, machine_type, ssh_sess, resources, command, ii,
run_tasks, group_size, common_files, forward_files,
backward_files)
else:
run_tasks = [os.path.basename(ii) for ii in run_tasks_]
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files,
backward_files)
def run_elastic(task_type, jdata, mdata, ssh_sess):
conf_dir = jdata['conf_dir']
fp_params = jdata['vasp_params']
kspacing = fp_params['kspacing']
conf_path = os.path.abspath(conf_dir)
task_path = re.sub('confs', '02.elastic', conf_path)
if task_type == "vasp":
work_path = os.path.join(task_path, 'vasp-k%.2f' % kspacing)
elif task_type in lammps_task_type:
work_path = os.path.join(task_path, task_type)
assert (os.path.isdir(work_path))
print(work_path)
all_task = glob.glob(os.path.join(work_path, "dfm-*"))
all_task.sort()
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
vasp_exec = mdata['fp_command']
group_size = mdata['fp_group_size']
resources = mdata['fp_resources']
machine = mdata['fp_machine']
machine_type = mdata['fp_machine']['machine_type']
command = vasp_exec
command = cmd_append_log(command, "log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'OUTCAR')
if os.path.isfile(fres):
if not vasp.check_finished(fres):
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
forward_files = ['INCAR', 'POSCAR', 'POTCAR', 'KPOINTS']
backward_files = ['OUTCAR', 'CONTCAR', 'OSZICAR']
common_files = ['INCAR', 'POTCAR', 'KPOINTS']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
lmp_exec = mdata['lmp_command']
group_size = mdata['model_devi_group_size']
resources = mdata['model_devi_resources']
machine = mdata['model_devi_machine']
machine_type = mdata['model_devi_machine']['machine_type']
command = lmp_exec + " -i lammps.in"
command = cmd_append_log(command, "model_devi.log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'log.lammps')
if os.path.isfile(fres):
with open(fres, 'r') as fp:
lines = fp.read().split('\n')
flag = False
for jj in lines:
if ('Final Stress' in jj) and (not 'print' in jj):
flag = True
if not flag:
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
model_dir = os.path.abspath(model_dir)
model_name = fp_params['model_name']
if not model_name:
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir, ii) for ii in model_name]
forward_files = ['conf.lmp', 'lammps.in', 'strain.out'] + model_name
backward_files = ['log.lammps', 'model_devi.log']
common_files = ['lammps.in'] + model_name
if len(model_name) > 1:
backward_files = backward_files + ['model_devi.out']
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
run_tasks = [os.path.basename(ii) for ii in run_tasks_]
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files, backward_files)
def run_surf(task_type, jdata, mdata, ssh_sess):
conf_dir = jdata['conf_dir']
fp_params = jdata['vasp_params']
kspacing = fp_params['kspacing']
deepmd_model_dir = jdata['deepmd_model_dir']
deepmd_model_dir = os.path.abspath(deepmd_model_dir)
conf_path = os.path.abspath(conf_dir)
task_path = re.sub('confs', '05.surf', conf_path)
if task_type == "vasp":
work_path = os.path.join(task_path, 'vasp-k%.2f' % kspacing)
elif task_type == "deepmd":
work_path = os.path.join(task_path, 'deepmd')
elif task_type == "meam":
work_path = os.path.join(task_path, 'meam')
assert (os.path.isdir(work_path))
all_task = glob.glob(os.path.join(work_path, 'struct-*'))
#vasp
if task_type == "vasp":
vasp_exec = mdata['fp_command']
group_size = mdata['fp_group_size']
resources = mdata['fp_resources']
machine = mdata['fp_machine']
machine_type = mdata['fp_machine']['machine_type']
command = vasp_exec
command = cmd_append_log(command, "log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'OUTCAR')
if os.path.isfile(fres):
if not vasp.check_finished(fres):
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
run_tasks = [os.path.basename(ii) for ii in run_tasks_]
forward_files = ['INCAR', 'POSCAR', 'POTCAR']
backward_files = ['OUTCAR']
common_files = ['INCAR', 'POTCAR']
#lammps
elif task_type == "deepmd" or task_type == "meam":
lmp_exec = mdata['lmp_command']
group_size = mdata['model_devi_group_size']
resources = mdata['model_devi_resources']
machine = mdata['model_devi_machine']
machine_type = mdata['model_devi_machine']['machine_type']
command = lmp_exec + " -i lammps.in"
command = cmd_append_log(command, "model_devi.log")
run_tasks_ = []
for ii in all_task:
fres = os.path.join(ii, 'log.lammps')
if os.path.isfile(fres):
with open(fres, 'r') as fp:
lines = fp.read().split('\n')
flag = False
for jj in lines:
if ("Final energy per atoms"
in jj) and (not 'print' in jj):
flag = True
if not flag:
run_tasks_.append(ii)
else:
run_tasks_.append(ii)
run_tasks = [os.path.basename(ii) for ii in run_tasks_]
all_models = glob.glob(os.path.join(deepmd_model_dir, '*.pb'))
model_names = [os.path.basename(ii) for ii in all_models]
forward_files = ['conf.lmp', 'lammps.in'] + model_names
backward_files = ['log.lammps', 'model_devi.out', 'model_devi.log']
common_files = ['lammps.in'] + model_names
else:
raise RuntimeError("unknow task %s, something wrong" % task_type)
_run(machine, machine_type, ssh_sess, resources, command, work_path,
run_tasks, group_size, common_files, forward_files, backward_files)
