def delete_machine(self):
request = DeleteInstancesRequest()
request.set_accept_format('json')
if len(self.instance_list) <= 100:
request.set_InstanceIds(self.instance_list)
request.set_Force(True)
response = self.client.do_action_with_exception(request)
else:
iteration = len(self.instance_list) // 100
for i in range(iteration):
request.set_InstanceIds(self.instance_list[i * 100:(i + 1) *
100])
request.set_Force(True)
response = self.client.do_action_with_exception(request)
if len(self.instance_list) - iteration * 100 != 0:
request.set_InstanceIds(self.instance_list[iteration * 100:])
request.set_Force(True)
response = self.client.do_action_with_exception(request)
self.instance_list = []
self.ip_list = []
os.remove('machine_record.json')
dlog.debug("Successfully free the machine!")
def AWS_check_status(cls, job_id=""):
"""
to aviod query jobStatus too often, set a time interval
query_dict example:
{job_id: JobStatus}
{'40fb24b2-d0ca-4443-8e3a-c0906ea03622': <JobStatus.running: 3>,
'41bda50c-0a23-4372-806c-87d16a680d85': <JobStatus.waiting: 2>}
"""
query_dict = {}
if datetime.now().timestamp() > cls._query_next_allow_time:
cls.batch_client = boto3.client('batch')
cls._query_next_allow_time = datetime.now().timestamp(
) + cls._query_time_interval
for status in [
'SUBMITTED', 'PENDING', 'RUNNABLE', 'STARTING', 'RUNNING',
'SUCCEEDED', 'FAILED'
]:
status_response = cls.batch_client.list_jobs(
jobQueue=cls._jobQueue,
jobStatus=status,
maxResults=cls._query_max_results)
status_list = status_response.get('jobSummaryList', [])
for job_dict in status_list:
cls._job_id_map_status.update({
job_dict['jobId']:
cls.map_aws_status_to_dpgen_status(job_dict['status'])
})
# for job in cls._job_id_map_status:
# cls._job_id_map_status[job]=query_dict.get(job, JobStatus.unknown)
dlog.debug('20000:_map: %s' % (cls._job_id_map_status))
dlog.debug('62000:job_id:%s, _query: %s, _map: %s' %
(job_id, query_dict, cls._job_id_map_status))
if job_id:
return cls._job_id_map_status.get(job_id, JobStatus.unknown)
return cls._job_id_map_status
def do_submit(self,
job_dirs,
cmd,
args=None,
res=None,
outlog='log',
errlog='err'):
res = self.default_resources(res)
dlog.debug("2000, params=(%s, %s, %s, %s, %s, %s, )" %
(job_dirs, cmd, args, res, outlog, errlog))
dlog.debug(
'2200, self.context.remote_root: %s , self.context.local_root: %s'
% (self.context.remote_root, self.context.local_root))
# concreate_command =
script_str = self.sub_script(job_dirs,
cmd,
args=args,
res=res,
outlog=outlog,
errlog=errlog)
dlog.debug('2300, script_str: %s, self.sub_script_name: %s' %
(script_str, self.sub_script_name))
"""
jobName example:
home-ec2-user-Ag_init-run_gen-iter_000000-01_model_devi-task_000_000048
"""
jobName = os.path.join(self.context.remote_root,
job_dirs.pop())[1:].replace('/', '-').replace(
'.', '_')
jobName += ("_" + str(self.context.job_uuid))
response = self.__class__.batch_client.submit_job(
jobName=jobName,
jobQueue=res['jobQueue'],
jobDefinition=res['jobDefinition'],
parameters={'task_command': script_str},
containerOverrides={
'vcpus': res['cpu_num'],
'memory': res['memory_size']
})
dlog.debug('4000, response:%s' % response)
self.job_id = (response, res['jobQueue'])
def all_finished(self, job_handler):
task_chunks = job_handler['task_chunks']
task_chunks_str = ['+'.join(ii) for ii in task_chunks]
task_hashes = [
sha1(ii.encode('utf-8')).hexdigest() for ii in task_chunks_str
]
job_list = job_handler['job_list']
job_record = job_handler['job_record']
command = job_handler['command']
resources = job_handler['resources']
outlog = job_handler['outlog']
errlog = job_handler['errlog']
backward_task_files = job_handler['backward_task_files']
dlog.debug('checking jobs')
nchunks = len(task_chunks)
for idx in range(nchunks):
cur_hash = task_hashes[idx]
rjob = job_list[idx]
if not job_record.check_finished(cur_hash):
# chunk not finished according to record
status = rjob['batch'].check_status()
job_uuid = rjob['context'].job_uuid
dlog.debug('checked job %s' % job_uuid)
if status == JobStatus.terminated:
job_record.increase_nfail(cur_hash)
if job_record.check_nfail(cur_hash) > 3:
raise RuntimeError(
'Job %s failed for more than 3 times' % job_uuid)
dlog.info('job %s terminated, submit again' % job_uuid)
dlog.debug('try %s times for %s' %
(job_record.check_nfail(cur_hash), job_uuid))
rjob['batch'].submit(task_chunks[idx],
command,
res=resources,
outlog=outlog,
errlog=errlog,
restart=True)
elif status == JobStatus.finished:
dlog.info('job %s finished' % job_uuid)
rjob['context'].download(task_chunks[idx],
backward_task_files)
rjob['context'].clean()
job_record.record_finish(cur_hash)
job_record.dump()
job_record.dump()
return job_record.check_all_finished()
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 submit(self, job_dirs, cmd, args=None, resources=None, restart=False):
dlog.debug(restart)
if restart:
status = self.check_status()
if status in [
JobStatus.unsubmitted, JobStatus.unknown,
JobStatus.terminated
]:
dlog.debug('task restart point !!!')
self._submit(job_dirs, cmd, args, resources)
elif status == JobStatus.waiting:
dlog.debug('task is waiting')
elif status == JobStatus.running:
dlog.debug('task is running')
else:
dlog.debug('task is finished')
#except:
#dlog.debug('no job_id file')
#dlog.debug('task restart point !!!')
#self._submit(job_dirs, cmd, args, resources)
else:
dlog.debug('new task!!!')
self._submit(job_dirs, cmd, args, resources)
def submit(self, job_dirs, cmd, args=None, resources=None, restart=False):
def _submit():
script_name = self._make_script(job_dirs, cmd, args, res=resources)
stdin, stdout, stderr = self.block_checkcall(
('cd %s; sbatch %s' % (self.remote_root, script_name)))
subret = (stdout.readlines())
job_id = subret[0].split()[-1]
sftp = self.ssh.open_sftp()
with sftp.open(os.path.join(self.remote_root, 'job_id'),
'w') as fp:
fp.write(job_id)
sftp.close()
dlog.debug(restart)
if restart:
try:
status = self.check_status()
dlog.debug(status)
if status in [
JobStatus.unsubmitted, JobStatus.unknown,
JobStatus.terminated
]:
dlog.debug('task restart point !!!')
_submit()
elif status == JobStatus.waiting:
dlog.debug('task is waiting')
elif status == JobStatus.running:
dlog.debug('task is running')
else:
dlog.debug('task is finished')
except:
dlog.debug('no job_id file')
dlog.debug('task restart point !!!')
_submit()
else:
dlog.debug('new task!!!')
_submit()
def submit(self,
job_dirs,
cmd,
args=None,
res=None,
restart=False,
outlog='log',
errlog='err'):
if restart:
dlog.debug('restart task')
status = self.check_status()
if status in [
JobStatus.unsubmitted, JobStatus.unknown,
JobStatus.terminated
]:
dlog.debug('task restart point !!!')
self.do_submit(job_dirs,
cmd,
args,
res,
outlog=outlog,
errlog=errlog)
elif status == JobStatus.waiting:
dlog.debug('task is waiting')
elif status == JobStatus.running:
dlog.debug('task is running')
elif status == JobStatus.finished:
dlog.debug('task is finished')
else:
raise RuntimeError('unknow job status, must be wrong')
else:
dlog.debug('new task')
self.do_submit(job_dirs,
cmd,
args,
res,
outlog=outlog,
errlog=errlog)
if res is None:
sleep = 0
else:
sleep = res.get('submit_wait_time', 0)
time.sleep(
sleep) # For preventing the crash of the tasks while submitting
def run_jobs(self,
resources,
command,
work_path,
tasks,
group_size,
forward_common_files,
forward_task_files,
backward_task_files,
forward_task_deference=True,
outlog='log',
errlog='err'):
# task_chunks = [
# [os.path.basename(j) for j in tasks[i:i + group_size]] \
# for i in range(0, len(tasks), group_size)
# ]
task_chunks = _split_tasks(tasks, group_size)
_pmap = PMap(work_path)
path_map = _pmap.load()
_fr = FinRecord(work_path, len(task_chunks))
job_list = []
task_chunks_ = ['+'.join(ii) for ii in task_chunks]
job_fin = _fr.get_record()
assert (len(job_fin) == len(task_chunks))
for ii, chunk in enumerate(task_chunks):
if not job_fin[ii]:
# map chunk info. to uniq id
chunk_sha1 = sha1(task_chunks_[ii].encode('utf-8')).hexdigest()
# if hash in map, recover job, else start a new job
if chunk_sha1 in path_map:
# job_uuid = path_map[chunk_sha1][1].split('/')[-1]
job_uuid = path_map[chunk_sha1][2]
dlog.debug("load uuid %s for chunk %s" %
(job_uuid, task_chunks_[ii]))
else:
job_uuid = None
# communication context, bach system
context = self.context(work_path, self.session, job_uuid)
batch = self.batch(context, uuid_names=self.uuid_names)
rjob = {'context': context, 'batch': batch}
# upload files
if not rjob['context'].check_file_exists('tag_upload'):
rjob['context'].upload('.', forward_common_files)
rjob['context'].upload(chunk,
forward_task_files,
dereference=forward_task_deference)
rjob['context'].write_file('tag_upload', '')
dlog.debug('uploaded files for %s' % task_chunks_[ii])
# submit new or recover old submission
if job_uuid is None:
rjob['batch'].submit(chunk,
command,
res=resources,
outlog=outlog,
errlog=errlog)
job_uuid = rjob['context'].job_uuid
dlog.debug('assigned uudi %s for %s ' %
(job_uuid, task_chunks_[ii]))
dlog.info('new submission of %s' % job_uuid)
else:
rjob['batch'].submit(chunk,
command,
res=resources,
outlog=outlog,
errlog=errlog,
restart=True)
dlog.info('restart from old submission %s ' % job_uuid)
# record job and its hash
job_list.append(rjob)
path_map[chunk_sha1] = [
context.local_root, context.remote_root, job_uuid
]
else:
# finished job, append a None to list
job_list.append(None)
_pmap.dump(path_map)
assert (len(job_list) == len(task_chunks))
fcount = [0] * len(job_list)
while not all(job_fin):
dlog.debug('checking jobs')
for idx, rjob in enumerate(job_list):
if not job_fin[idx]:
status = rjob['batch'].check_status()
job_uuid = rjob['context'].job_uuid
if status == JobStatus.terminated:
fcount[idx] += 1
if fcount[idx] > 3:
raise RuntimeError(
'Job %s failed for more than 3 times' %
job_uuid)
dlog.info('job %s terminated, submit again' % job_uuid)
dlog.debug('try %s times for %s' %
(fcount[idx], job_uuid))
rjob['batch'].submit(task_chunks[idx],
command,
res=resources,
outlog=outlog,
errlog=errlog,
restart=True)
elif status == JobStatus.finished:
dlog.info('job %s finished' % job_uuid)
rjob['context'].download(task_chunks[idx],
backward_task_files)
rjob['context'].clean()
job_fin[idx] = True
_fr.write_record(job_fin)
time.sleep(10)
# delete path map file when job finish
_pmap.delete()
def group_slurm_jobs(ssh_sess,
resources,
command,
work_path,
tasks,
group_size,
forward_common_files,
forward_task_files,
backward_task_files,
remote_job=SlurmJob,
forward_task_deference=True):
task_chunks = [
[os.path.basename(j) for j in tasks[i:i + group_size]] \
for i in range(0, len(tasks), group_size)
]
cwd = os.getcwd()
_pmap = PMap(cwd)
path_map = _pmap.load()
dlog.debug("work_path: %s" % work_path)
dlog.debug("curr_path: %s" % cwd)
job_list = []
task_chunks_ = ['+'.join(ii) for ii in task_chunks]
for ii in task_chunks_:
dlog.debug("task_chunk %s" % ii)
#dlog.debug(path_map)
for ii, chunk in enumerate(task_chunks):
# map chunk info. to uniq id
chunk_uni = task_chunks_[ii].encode('utf-8')
chunk_sha1 = sha1(chunk_uni).hexdigest()
if chunk_sha1 in path_map:
job_uuid = path_map[chunk_sha1][1].split('/')[-1]
dlog.debug("load uuid %s" % job_uuid)
else:
job_uuid = None
rjob = remote_job(ssh_sess, work_path, job_uuid)
dlog.debug('uuid %s' % job_uuid)
rjob.upload('.', forward_common_files)
rjob.upload(chunk,
forward_task_files,
dereference=forward_task_deference)
if job_uuid:
rjob.submit(chunk, command, resources=resources, restart=True)
else:
rjob.submit(chunk, command, resources=resources)
job_list.append(rjob)
path_map[chunk_sha1] = [rjob.local_root, rjob.remote_root]
_pmap.dump(path_map)
job_fin = [False for ii in job_list]
lcount = [0] * len(job_list)
count_fail = 0
while not all(job_fin):
for idx, rjob in enumerate(job_list):
if not job_fin[idx]:
try:
status = rjob.check_status()
except:
ssh_sess = SSHSession(ssh_sess.remote_profile)
for _idx, _rjob in enumerate(job_list):
job_list[_idx] = SlurmJob(ssh_sess, work_path,
_rjob.job_uuid)
count_fail = count_fail + 1
dlog.info("ssh_sess failed for %d times" % count_fail)
break
if status == JobStatus.terminated:
lcount[idx] += 1
_job_uuid = rjob.remote_root.split('/')[-1]
dlog.info('Job at %s terminated, submit again' %
_job_uuid)
dlog.debug('try %s times for %s' %
(lcount[idx], _job_uuid))
rjob.submit(task_chunks[idx],
command,
resources=resources,
restart=True)
if lcount[idx] > 3:
dlog.info('Too many errors for ! %s ' % _job_uuid)
rjob.download(task_chunks[idx],
backward_task_files,
back_error=True)
rjob.clean()
job_fin[idx] = True
elif status == JobStatus.finished:
rjob.download(task_chunks[idx], backward_task_files)
rjob.clean()
job_fin[idx] = True
time.sleep(10)
dlog.debug('error count')
dlog.debug(lcount)
# delete path map file when job finish
_pmap.delete()
def submit(self, job_dirs, cmd, args=None, resources=None, restart=False):
dlog.debug(restart)
if restart:
status = self.check_status()
if status in [
JobStatus.unsubmitted, JobStatus.unknown,
JobStatus.terminated
]:
dlog.debug('task restart point !!!')
if 'task_max' in resources and resources['task_max'] > 0:
while self.check_limit(task_max=resources['task_max']):
time.sleep(60)
self._submit(job_dirs, cmd, args, resources)
elif status == JobStatus.waiting:
dlog.debug('task is waiting')
elif status == JobStatus.running:
dlog.debug('task is running')
else:
dlog.debug('task is finished')
#except:
#dlog.debug('no job_id file')
#dlog.debug('task restart point !!!')
#self._submit(job_dirs, cmd, args, resources)
else:
dlog.debug('new task!!!')
if 'task_max' in resources and resources['task_max'] > 0:
while self.check_limit(task_max=resources['task_max']):
time.sleep(60)
self._submit(job_dirs, cmd, args, resources)
time.sleep(
20) # For preventing the crash of the tasks while submitting.
def submit_jobs(self,
resources,
command,
work_path,
tasks,
group_size,
forward_common_files,
forward_task_files,
backward_task_files,
forward_task_deference=True,
outlog='log',
errlog='err'):
self.backward_task_files = backward_task_files
# task_chunks = [
# [os.path.basename(j) for j in tasks[i:i + group_size]] \
# for i in range(0, len(tasks), group_size)
# ]
task_chunks = _split_tasks(tasks, group_size)
task_chunks_str = ['+'.join(ii) for ii in task_chunks]
task_hashes = [
sha1(ii.encode('utf-8')).hexdigest() for ii in task_chunks_str
]
job_record = JobRecord(work_path, task_chunks, fname=self.jrname)
job_record.dump()
nchunks = len(task_chunks)
job_list = []
for ii in range(nchunks):
cur_chunk = task_chunks[ii]
cur_hash = task_hashes[ii]
if not job_record.check_finished(cur_hash):
# chunk is not finished
# check if chunk is submitted
submitted = job_record.check_submitted(cur_hash)
if not submitted:
job_uuid = None
else:
job_uuid = job_record.get_uuid(cur_hash)
dlog.debug("load uuid %s for chunk %s" %
(job_uuid, cur_hash))
# communication context, bach system
context = self.context(work_path, self.session, job_uuid)
batch = self.batch(context, uuid_names=self.uuid_names)
rjob = {'context': context, 'batch': batch}
# upload files
if not rjob['context'].check_file_exists(
rjob['batch'].upload_tag_name):
rjob['context'].upload('.', forward_common_files)
rjob['context'].upload(cur_chunk,
forward_task_files,
dereference=forward_task_deference)
rjob['context'].write_file(rjob['batch'].upload_tag_name,
'')
dlog.debug('uploaded files for %s' % task_chunks_str[ii])
# submit new or recover old submission
if not submitted:
rjob['batch'].submit(cur_chunk,
command,
res=resources,
outlog=outlog,
errlog=errlog)
job_uuid = rjob['context'].job_uuid
dlog.debug('assigned uuid %s for %s ' %
(job_uuid, task_chunks_str[ii]))
dlog.info('new submission of %s for chunk %s' %
(job_uuid, cur_hash))
else:
rjob['batch'].submit(cur_chunk,
command,
res=resources,
outlog=outlog,
errlog=errlog,
restart=True)
dlog.info('restart from old submission %s for chunk %s' %
(job_uuid, cur_hash))
# record job and its remote context
job_list.append(rjob)
ip = None
instance_id = None
if 'cloud_resources' in self.remote_profile:
ip = self.remote_profile['hostname']
instance_id = self.remote_profile['instance_id']
job_record.record_remote_context(cur_hash, context.local_root,
context.remote_root, job_uuid,
ip, instance_id)
job_record.dump()
else:
# finished job, append a None to list
job_list.append(None)
assert (len(job_list) == nchunks)
job_handler = {
'task_chunks': task_chunks,
'job_list': job_list,
'job_record': job_record,
'command': command,
'resources': resources,
'outlog': outlog,
'errlog': errlog,
'backward_task_files': backward_task_files
}
return job_handler
def compute(self,
output_dir):
log_lammps = os.path.join(output_dir, 'log.lammps')
dump_lammps = os.path.join(output_dir, 'dump.relax')
if not os.path.isfile(log_lammps):
warnings.warn("cannot find log.lammps in " + output_dir + " skip")
return None
if not os.path.isfile(dump_lammps):
warnings.warn("cannot find dump.relax in " + output_dir + " skip")
return None
else:
box = []
coord = []
vol = []
energy = []
force = []
virial = []
stress = []
with open(dump_lammps, 'r') as fin:
dump = fin.read().split('\n')
dumptime = []
for idx, ii in enumerate(dump):
if ii == 'ITEM: TIMESTEP':
box.append([])
coord.append([])
force.append([])
dumptime.append(int(dump[idx + 1]))
natom = int(dump[idx + 3])
xlo_bound = float(dump[idx + 5].split()[0])
xhi_bound = float(dump[idx + 5].split()[1])
xy = float(dump[idx + 5].split()[2])
ylo_bound = float(dump[idx + 6].split()[0])
yhi_bound = float(dump[idx + 6].split()[1])
xz = float(dump[idx + 6].split()[2])
zlo = float(dump[idx + 7].split()[0])
zhi = float(dump[idx + 7].split()[1])
yz = float(dump[idx + 7].split()[2])
xx = xhi_bound - max([0, xy, xz, xy + xz]) - (xlo_bound - min([0, xy, xz, xy + xz]))
yy = yhi_bound - max([0, yz]) - (ylo_bound - min([0, yz]))
zz = zhi - zlo
box[-1].append([xx, 0.0, 0.0])
box[-1].append([xy, yy, 0.0])
box[-1].append([xz, yz, zz])
vol.append(xx * yy * zz)
type_list = []
for jj in range(natom):
type_list.append(int(dump[idx + 9 + jj].split()[1]) - 1)
if 'xs ys zs' in dump[idx + 8]:
a_x = float(dump[idx + 9 + jj].split()[2]) * xx + float(
dump[idx + 9 + jj].split()[3]) * xy \
+ float(dump[idx + 9 + jj].split()[4]) * xz
a_y = float(dump[idx + 9 + jj].split()[3]) * yy + float(
dump[idx + 9 + jj].split()[4]) * yz
a_z = float(dump[idx + 9 + jj].split()[4]) * zz
else:
a_x = float(dump[idx + 9 + jj].split()[2])
a_y = float(dump[idx + 9 + jj].split()[3])
a_z = float(dump[idx + 9 + jj].split()[4])
coord[-1].append([a_x, a_y, a_z])
fx = float(dump[idx + 9 + jj].split()[5])
fy = float(dump[idx + 9 + jj].split()[6])
fz = float(dump[idx + 9 + jj].split()[7])
force[-1].append([fx, fy, fz])
with open(log_lammps, 'r') as fp:
if 'Total wall time:' not in fp.read():
warnings.warn("lammps not finished " + log_lammps + " skip")
return None
else:
fp.seek(0)
lines = fp.read().split('\n')
idid = -1
for ii in dumptime:
idid += 1
for jj in lines:
line = jj.split()
if len(line) and str(ii) == line[0]:
try:
[float(kk) for kk in line]
except:
continue
stress.append([])
virial.append([])
energy.append(float(line[1]))
# virials = stress * vol * 1e5 *1e-30 * 1e19/1.6021766208
stress[-1].append([float(line[2]) / 1000.0, float(line[5]) / 1000.0, float(line[6]) / 1000.0])
stress[-1].append([float(line[5]) / 1000.0, float(line[3]) / 1000.0, float(line[7]) / 1000.0])
stress[-1].append([float(line[6]) / 1000.0, float(line[7]) / 1000.0, float(line[4]) / 1000.0])
stress_to_virial = vol[idid] * 1e5 * 1e-30 * 1e19 / 1.6021766208
virial[-1].append([float(line[2]) * stress_to_virial, float(line[5]) * stress_to_virial,
float(line[6]) * stress_to_virial])
virial[-1].append([float(line[5]) * stress_to_virial, float(line[3]) * stress_to_virial,
float(line[7]) * stress_to_virial])
virial[-1].append([float(line[6]) * stress_to_virial, float(line[7]) * stress_to_virial,
float(line[4]) * stress_to_virial])
break
_tmp = self.type_map
dlog.debug(_tmp)
type_map_list = lammps.element_list(self.type_map)
type_map_idx = list(range(len(type_map_list)))
atom_numbs = []
for ii in type_map_idx:
count = 0
for jj in type_list:
if jj == ii:
count += 1
atom_numbs.append(count)
# d_dump = dpdata.System(dump_lammps, fmt='lammps/dump', type_map=type_map_list)
# d_dump.to('vasp/poscar', contcar, frame_idx=-1)
result_dict = {"@module": "dpdata.system", "@class": "LabeledSystem", "data": {"atom_numbs": atom_numbs,
"atom_names": type_map_list,
"atom_types": {
"@module": "numpy",
"@class": "array",
"dtype": "int64",
"data": type_list},
"orig": {"@module": "numpy",
"@class": "array",
"dtype": "int64",
"data": [0, 0, 0]},
"cells": {"@module": "numpy",
"@class": "array",
"dtype": "float64",
"data": box},
"coords": {
"@module": "numpy",
"@class": "array",
"dtype": "float64",
"data": coord},
"energies": {
"@module": "numpy",
"@class": "array",
"dtype": "float64",
"data": energy},
"forces": {
"@module": "numpy",
"@class": "array",
"dtype": "float64",
"data": force},
"virials": {
"@module": "numpy",
"@class": "array",
"dtype": "float64",
"data": virial},
"stress": {
"@module": "numpy",
"@class": "array",
"dtype": "float64",
"data": stress}}}
contcar = os.path.join(output_dir, 'CONTCAR')
dumpfn(result_dict, contcar, indent=4)
d_dump = loadfn(contcar)
d_dump.to('vasp/poscar', contcar, frame_idx=-1)
return result_dict
