def run_phonon(task_type,jdata,mdata):
user= ('user_incar' in jdata.keys())
work_path=util.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)
machine,resources,command,group_size=util.get_machine_info(mdata,task_type)
run_tasks = util.collect_task(all_task,task_type)
forward_files = ['INCAR', 'POTCAR','KPOINTS','KPOINTS']
backward_files = ['OUTCAR', task_type+'.out' , 'OSZICAR','vasprun.xml']
common_files=['POSCAR']
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
mdata['fp_resources']['cvasp'] = True
forward_files.append('cvasp.py')
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
#lammps
elif task_type in lammps_task_type:
None
else:
raise RuntimeError ("unknown task %s, something wrong" % task_type)
def run_phonon(task_type, jdata, mdata):
user = ('user_incar' in jdata.keys())
work_path = util.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)
machine, machine_type, ssh_sess, resources, command, group_size = util.get_machine_info(
mdata, task_type)
run_tasks = util.collect_task(all_task, task_type)
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_equi(task_type,jdata,mdata):
#rmprint("This module has been run !")
work_path=util.make_work_path(jdata,'00.equi',False,False,False)
all_task = glob.glob(os.path.join(work_path,'.'))
#vasp
if task_type=="vasp":
mdata=decide_fp_machine(mdata)
forward_files = ['INCAR', 'POTCAR', 'KPOINTS']
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
mdata['fp_resources']['cvasp'] = True
forward_files.append('cvasp.py')
backward_files = ['OUTCAR', task_type+'.out' , 'CONTCAR','OSZICAR']
common_files=['POSCAR']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
forward_files = ['conf.lmp', 'lammps.in']
backward_files = ['dump.relax','log.lammps', task_type+'.out']
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]
common_files = 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 = util.collect_task(all_task,task_type)
if len(run_tasks)==0: return
machine,resources,command,group_size=util.get_machine_info(mdata,task_type)
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
#debug#
#print(' '.join(common_files))
#print(' '.join(forward_files))
#print(' '.join(backward_files))
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
def run_surf(task_type,jdata,mdata):
static=jdata['static-opt']
work_path=util.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)
forward_files = ['INCAR', 'POSCAR','POTCAR','KPOINTS']
backward_files = ['OUTCAR', task_type+'.out' , 'OSZICAR']
common_files=['INCAR','POTCAR']
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
mdata['fp_resources']['cvasp'] = True
forward_files.append('cvasp.py')
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
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',task_type+'.out']
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 = util.collect_task(all_task,task_type)
if len(run_tasks)==0: return
else:
run_tasks = [os.path.basename(ii) for ii in all_task]
machine,resources,command,group_size=util.get_machine_info(mdata,task_type)
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
def run_vacancy(task_type,jdata,mdata):
work_path=util.make_work_path(jdata,'03.vacancy',False,False,False)
all_task = glob.glob(os.path.join(work_path,'struct-*'))
#vasp
if task_type == "vasp":
mdata=decide_fp_machine(mdata)
forward_files = ['INCAR', 'POSCAR','POTCAR']
backward_files = ['OUTCAR', 'autotest.out' , 'OSZICAR']
common_files=['INCAR','POTCAR']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
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]
common_files = model_name
forward_files = ['conf.lmp', 'lammps.in']+model_name
backward_files = ['log.lammps','autotest.out']
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 = util.collect_task(all_task,task_type)
if len(run_tasks)==0: return
machine,machine_type,ssh_sess,resources,command,group_size=util.get_machine_info(mdata,task_type)
disp = make_dispatcher(machine)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog='autotest.out',
errlog='autotest.err')
def run_equi(task_type, jdata, mdata):
#rmprint("This module has been run !")
work_path = util.make_work_path(jdata, '00.equi', False, False, False)
all_task = glob.glob(os.path.join(work_path, '.'))
#vasp
if task_type == "vasp":
mdata = decide_fp_machine(mdata)
forward_files = ['INCAR', 'POTCAR']
backward_files = ['OUTCAR', 'CONTCAR', 'OSZICAR']
common_files = ['POSCAR']
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
forward_files = ['conf.lmp', 'lammps.in']
backward_files = ['dump.relax', 'log.lammps', 'model_devi.log']
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]
common_files = 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 = util.collect_task(all_task, task_type)
machine, machine_type, ssh_sess, resources, command, group_size = util.get_machine_info(
mdata, task_type)
_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):
reprod_opt=jdata['reprod-opt']
work_path=util.make_work_path(jdata,'04.interstitial',reprod_opt,False,False)
all_task = glob.glob(os.path.join(work_path,'struct-*'))
#vasp
if task_type == "vasp":
mdata=decide_fp_machine(mdata)
forward_files = ['INCAR', 'POSCAR','POTCAR',"KPOINTS"]
backward_files = ['OUTCAR', task_type+'.out' , 'XDATCAR','OSZICAR']
common_files=['INCAR']
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
mdata['fp_resources']['cvasp'] = True
forward_files.append('cvasp.py')
#lammps
elif task_type in lammps_task_type:
mdata = decide_model_devi_machine(mdata)
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) :
# if not lammps.check_finished(fres):
# run_tasks_.append(ii)
# else :
# run_tasks_.append(ii)
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', task_type+'.out']
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)
machine,resources,command,group_size=util.get_machine_info(mdata,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))
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
ii,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
else:
run_tasks = util.collect_task(all_task,task_type)
if len(run_tasks)==0: return
else:
run_tasks = [os.path.basename(ii) for ii in all_task]
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
common_files,
forward_files,
backward_files,
outlog=task_type+'.out',
errlog=task_type+'.err')
