diff --git a/README.md b/README.md
index 52d608313..897cd1cf0 100644
--- a/README.md
+++ b/README.md
@@ -22,6 +22,7 @@
[](https://github.com/deepmodeling/dpgen/releases/)
[](https://doi.org/10.1016/j.cpc.2020.107206)
+
[](https://anaconda.org/conda-forge/dpgen)
[](https://pypi.org/project/dpgen)
@@ -544,20 +545,21 @@ The bold notation of key (such aas **type_map**) means that it's a necessary key
| training_iter0_model_path | list of string | ["/path/to/model0_ckpt/", ...] | The model used to init the first iter training. Number of element should be equal to `numb_models` |
| training_init_model | bool | False | Iteration > 0, the model parameters will be initilized from the model trained at the previous iteration. Iteration == 0, the model parameters will be initialized from `training_iter0_model_path`. |
| **default_training_param** | Dict | | Training parameters for `deepmd-kit` in `00.train`.
You can find instructions from here: (https://github.com/deepmodeling/deepmd-kit)..
|
+| dp_compress | bool | false | Use `dp compress` to compress the model. Default is false. |
| *#Exploration*
| **model_devi_dt** | Float | 0.002 (recommend) | Timestep for MD |
| **model_devi_skip** | Integer | 0 | Number of structures skipped for fp in each MD
-| **model_devi_f_trust_lo** | Float | 0.05 | Lower bound of forces for the selection.
- | **model_devi_f_trust_hi** | Float | 0.15 | Upper bound of forces for the selection
-| **model_devi_v_trust_lo** | Float | 1e10 | Lower bound of virial for the selection. Should be used with DeePMD-kit v2.x |
-| **model_devi_v_trust_hi** | Float | 1e10 | Upper bound of virial for the selection. Should be used with DeePMD-kit v2.x |
+| **model_devi_f_trust_lo** | Float or List of float | 0.05 | Lower bound of forces for the selection. If List, should be set for each index in `sys_configs`, respectively. |
+| **model_devi_f_trust_hi** | Float or List of float | 0.15 | Upper bound of forces for the selection. If List, should be set for each index in `sys_configs`, respectively. |
+| **model_devi_v_trust_lo** | Float or List of float | 1e10 | Lower bound of virial for the selection. If List, should be set for each index in `sys_configs`, respectively. Should be used with DeePMD-kit v2.x. |
+| **model_devi_v_trust_hi** | Float or List of float | 1e10 | Upper bound of virial for the selection. If List, should be set for each index in `sys_configs`, respectively. Should be used with DeePMD-kit v2.x. |
| model_devi_adapt_trust_lo | Boolean | False | Adaptively determines the lower trust levels of force and virial. This option should be used together with `model_devi_numb_candi_f`, `model_devi_numb_candi_v` and optionally with `model_devi_perc_candi_f` and `model_devi_perc_candi_v`. `dpgen` will make two sets: 1. From the frames with force model deviation lower than `model_devi_f_trust_hi`, select `max(model_devi_numb_candi_f, model_devi_perc_candi_f*n_frames)` frames with largest force model deviation. 2. From the frames with virial model deviation lower than `model_devi_v_trust_hi`, select `max(model_devi_numb_candi_v, model_devi_perc_candi_v*n_frames)` frames with largest virial model deviation. The union of the two sets is made as candidate dataset|
| model_devi_numb_candi_f | Int | 10 | See `model_devi_adapt_trust_lo`.|
| model_devi_numb_candi_v | Int | 0 | See `model_devi_adapt_trust_lo`.|
| model_devi_perc_candi_f | Float | 0.0 | See `model_devi_adapt_trust_lo`.|
| model_devi_perc_candi_v | Float | 0.0 | See `model_devi_adapt_trust_lo`.|
| model_devi_f_avg_relative | Boolean | False | Normalized the force model deviations by the RMS force magnitude along the trajectory. This key should not be used with `use_relative`. |
-| **model_devi_clean_traj** | Boolean | true | Deciding whether to clean traj folders in MD since they are too large. |
+| **model_devi_clean_traj** | Boolean or Int | true | If type of model_devi_clean_traj is boolean type then it denote whether to clean traj folders in MD since they are too large. If it is Int type, then the most recent n iterations of traj folders will be retained, others will be removed. |
| **model_devi_nopbc** | Boolean | False | Assume open boundary condition in MD simulations. |
| model_devi_activation_func | List of list of string | [["tanh","tanh"],["tanh","gelu"],["gelu","tanh"],["gelu","gelu"]] | Set activation functions for models, length of the List should be the same as `numb_models`, and two elements in the list of string respectively assign activation functions to the embedding and fitting nets within each model. *Backward compatibility*: the orginal "List of String" format is still supported, where embedding and fitting nets of one model use the same activation function, and the length of the List should be the same as `numb_models`|
| **model_devi_jobs** | [
{
"sys_idx": [0],
"temps":
[100],
"press":
[1],
"trj_freq":
10,
"nsteps":
1000,
"ensembles":
"nvt"
},
...
] | List of dict | Settings for exploration in `01.model_devi`. Each dict in the list corresponds to one iteration. The index of `model_devi_jobs` exactly accord with index of iterations |
diff --git a/conda/meta.yaml b/conda/meta.yaml
index c599c642f..e5480ba7a 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -25,6 +25,9 @@ requirements:
- requests
- dpdata
- dpdispatcher
+ - ase
+ - GromacsWrapper
+ - custodian
run:
- python >=3.6
@@ -34,6 +37,9 @@ requirements:
- dpdata
- dpdispatcher
- pymatgen
+ - ase
+ - GromacsWrapper
+ - custodian
test:
imports:
diff --git a/dpgen/auto_test/EOS.py b/dpgen/auto_test/EOS.py
index b69db6e1c..83a7482ab 100644
--- a/dpgen/auto_test/EOS.py
+++ b/dpgen/auto_test/EOS.py
@@ -169,8 +169,8 @@ def _compute_lower(self,
# vol = self.vol_start + ii * self.vol_step
vol = loadfn(os.path.join(all_tasks[ii], 'eos.json'))['volume']
task_result = loadfn(all_res[ii])
- res_data[vol] = task_result['energies'][-1] / task_result['atom_numbs'][0]
- ptr_data += '%7.3f %8.4f \n' % (vol, task_result['energies'][-1] / task_result['atom_numbs'][0])
+ res_data[vol] = task_result['energies'][-1] / task_result['atom_numbs'].sum()
+ ptr_data += '%7.3f %8.4f \n' % (vol, task_result['energies'][-1] / task_result['atom_numbs'].sum())
# res_data[vol] = all_res[ii]['energy'] / len(all_res[ii]['force'])
# ptr_data += '%7.3f %8.4f \n' % (vol, all_res[ii]['energy'] / len(all_res[ii]['force']))
diff --git a/dpgen/auto_test/VASP.py b/dpgen/auto_test/VASP.py
index 410bde02c..61cbeb931 100644
--- a/dpgen/auto_test/VASP.py
+++ b/dpgen/auto_test/VASP.py
@@ -140,8 +140,8 @@ def make_input_file(self,
incar['ENCUT'] = cal_setting['encut']
if 'kspacing' in cal_setting:
- dlog.info("%s setting KSAPCING to %s" % (self.make_input_file.__name__, cal_setting['kspacing']))
- incar['KSAPCING'] = cal_setting['kspacing']
+ dlog.info("%s setting KSPACING to %s" % (self.make_input_file.__name__, cal_setting['kspacing']))
+ incar['KSPACING'] = cal_setting['kspacing']
if 'kgamma' in cal_setting:
dlog.info("%s setting KGAMMA to %s" % (self.make_input_file.__name__, cal_setting['kgamma']))
diff --git a/dpgen/auto_test/common_equi.py b/dpgen/auto_test/common_equi.py
index 103e16dcc..ce5df94e8 100644
--- a/dpgen/auto_test/common_equi.py
+++ b/dpgen/auto_test/common_equi.py
@@ -2,6 +2,7 @@
import os
import warnings
from monty.serialization import dumpfn
+from multiprocessing import Pool
import dpgen.auto_test.lib.crys as crys
import dpgen.auto_test.lib.util as util
@@ -12,6 +13,8 @@
from distutils.version import LooseVersion
from dpgen.dispatcher.Dispatcher import make_submission
from dpgen.remote.decide_machine import convert_mdata
+from dpgen.auto_test.lib.utils import create_path
+
lammps_task_type = ['deepmd', 'meam', 'eam_fs', 'eam_alloy']
@@ -76,11 +79,11 @@ def make_equi(confs,
poscar = os.path.abspath(os.path.join(ii, 'POSCAR'))
if not os.path.exists(poscar):
raise FileNotFoundError('no configuration for autotest')
+ if os.path.exists(os.path.join(ii, 'relaxation', 'jr.json')):
+ os.remove(os.path.join(ii, 'relaxation', 'jr.json'))
+
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)
+ create_path(relax_dirs)
task_dirs.append(relax_dirs)
os.chdir(relax_dirs)
# copy POSCARs to mp-xxx/relaxation/relax_task
@@ -111,6 +114,47 @@ def make_equi(confs,
inter.make_input_file(ii, 'relaxation', relax_param)
+def worker(work_path,
+ run_task,
+ forward_common_files,
+ forward_files,
+ backward_files,
+ mdata,
+ inter_type):
+ machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
+ disp = make_dispatcher(machine, resources, work_path, [run_task], group_size)
+ print("%s --> Runing... " % (work_path))
+
+ api_version = mdata.get('api_version', '0.9')
+ if LooseVersion(api_version) < LooseVersion('1.0'):
+ warnings.warn(f"the dpdispatcher will be updated to new version."
+ f"And the interface may be changed. Please check the documents for more details")
+ disp.run_jobs(resources,
+ command,
+ work_path,
+ [run_task],
+ group_size,
+ forward_common_files,
+ forward_files,
+ backward_files,
+ outlog='outlog',
+ errlog='errlog')
+ elif LooseVersion(api_version) >= LooseVersion('1.0'):
+ submission = make_submission(
+ mdata_machine=machine,
+ mdata_resources=resources,
+ commands=[command],
+ work_path=work_path,
+ run_tasks=run_task,
+ group_size=group_size,
+ forward_common_files=forward_common_files,
+ forward_files=forward_files,
+ backward_files=backward_files,
+ outlog='outlog',
+ errlog='errlog'
+ )
+ submission.run_submission()
+
def run_equi(confs,
inter_param,
mdata):
@@ -120,6 +164,11 @@ def run_equi(confs,
for conf in confs:
conf_dirs.extend(glob.glob(conf))
conf_dirs.sort()
+
+ processes = len(conf_dirs)
+ pool = Pool(processes=processes)
+ print("Submit job via %d processes" % processes)
+
# generate a list of task names like mp-xxx/relaxation/relax_task
# ...
work_path_list = []
@@ -150,45 +199,28 @@ def run_equi(confs,
if len(run_tasks) == 0:
return
else:
- # if LooseVersion()
run_tasks = [os.path.basename(ii) for ii in all_task]
machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
print('%d tasks will be submited '%len(run_tasks))
+ multiple_ret = []
for ii in range(len(work_path_list)):
work_path = work_path_list[ii]
- disp = make_dispatcher(machine, resources, work_path, [run_tasks[ii]], group_size)
- print("%s --> Runing... "%(work_path))
-
- api_version = mdata.get('api_version', '0.9')
- if LooseVersion(api_version) < LooseVersion('1.0'):
- warnings.warn(f"the dpdispatcher will be updated to new version."
- f"And the interface may be changed. Please check the documents for more details")
- disp.run_jobs(resources,
- command,
- work_path,
- [run_tasks[ii]],
- group_size,
- forward_common_files,
- forward_files,
- backward_files,
- outlog='outlog',
- errlog='errlog')
- elif LooseVersion(api_version) >= LooseVersion('1.0'):
- submission = make_submission(
- mdata_machine=machine,
- mdata_resource=resources,
- commands=[command],
- work_path=work_path,
- run_tasks=run_tasks,
- group_size=group_size,
- forward_common_files=forward_common_files,
- forward_files=forward_files,
- backward_files=backward_files,
- outlog = 'outlog',
- errlog = 'errlog'
- )
- submission.run_submission()
+ ret = pool.apply_async(worker, (work_path,
+ run_tasks[ii],
+ forward_common_files,
+ forward_files,
+ backward_files,
+ mdata,
+ inter_type,
+ ))
+ multiple_ret.append(ret)
+ pool.close()
+ pool.join()
+ for ii in range(len(multiple_ret)):
+ if not multiple_ret[ii].successful():
+ raise RuntimeError("Task %d is not successful! work_path: %s " % (ii, work_path_list[ii]))
+ print('finished')
def post_equi(confs, inter_param):
# find all POSCARs and their name like mp-xxx
diff --git a/dpgen/auto_test/common_prop.py b/dpgen/auto_test/common_prop.py
index 00f439d37..bda655cf3 100644
--- a/dpgen/auto_test/common_prop.py
+++ b/dpgen/auto_test/common_prop.py
@@ -15,6 +15,7 @@
from dpgen.dispatcher.Dispatcher import make_dispatcher
from dpgen.dispatcher.Dispatcher import make_submission
from dpgen.remote.decide_machine import convert_mdata
+from dpgen.auto_test.lib.utils import create_path
lammps_task_type = ['deepmd', 'meam', 'eam_fs', 'eam_alloy']
@@ -73,10 +74,7 @@ def make_property(confs,
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)
+ create_path(path_to_work)
prop = make_property_instance(jj)
task_list = prop.make_confs(path_to_work, path_to_equi, do_refine)
@@ -112,6 +110,7 @@ def run_property(confs,
conf_dirs.sort()
task_list = []
work_path_list = []
+ multiple_ret = []
for ii in conf_dirs:
sepline(ch=ii, screen=True)
for jj in property_list:
@@ -159,7 +158,7 @@ def run_property(confs,
all_task = tmp_task_list
run_tasks = util.collect_task(all_task, inter_type)
if len(run_tasks) == 0:
- return
+ continue
else:
ret = pool.apply_async(worker, (work_path,
all_task,
@@ -169,23 +168,13 @@ def run_property(confs,
mdata,
inter_type,
))
- # run_tasks = [os.path.basename(ii) for ii in all_task]
- # machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
- # disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
- # disp.run_jobs(resources,
- # command,
- # work_path,
- # run_tasks,
- # group_size,
- # forward_common_files,
- # forward_files,
- # backward_files,
- # outlog='outlog',
- # errlog='errlog')
+ multiple_ret.append(ret)
pool.close()
pool.join()
- if ret.successful():
- print('finished')
+ for ii in range(len(multiple_ret)):
+ if not multiple_ret[ii].successful():
+ raise RuntimeError("Job %d is not successful!" % ii)
+ print('%d jobs are finished' % len(multiple_ret))
def worker(work_path,
@@ -215,7 +204,7 @@ def worker(work_path,
elif LooseVersion(api_version) >= LooseVersion('1.0'):
submission = make_submission(
mdata_machine=machine,
- mdata_resource=resources,
+ mdata_resources=resources,
commands=[command],
work_path=work_path,
run_tasks=run_tasks,
diff --git a/dpgen/data/gen.py b/dpgen/data/gen.py
index fa718455a..842752b88 100644
--- a/dpgen/data/gen.py
+++ b/dpgen/data/gen.py
@@ -464,7 +464,7 @@ def make_vasp_md(jdata, mdata) :
for ii in sys_ps :
for jj in scale :
- for kk in range(pert_numb) :
+ for kk in range(pert_numb+1) :
path_work = path_md
path_work = os.path.join(path_work, ii)
path_work = os.path.join(path_work, "scale-%.3f" % jj)
@@ -534,6 +534,8 @@ def coll_vasp_md(jdata) :
#dlog.info("md_nstep", md_nstep)
if nforce == md_nstep :
valid_outcars.append(outcar)
+ elif md_nstep == 0 and nforce == 1 :
+ valid_outcars.append(outcar)
else:
dlog.info("WARNING : in directory %s nforce in OUTCAR is not equal to settings in INCAR"%(os.getcwd()))
arg_cvt = " "
@@ -767,13 +769,14 @@ def gen_init_bulk(args) :
dlog.info("Current stage is 1, relax")
create_path(out_dir)
shutil.copy2(args.PARAM, os.path.join(out_dir, 'param.json'))
+ skip_relax = jdata['skip_relax']
if from_poscar :
make_super_cell_poscar(jdata)
else :
make_unit_cell(jdata)
make_super_cell(jdata)
place_element(jdata)
- if args.MACHINE is not None:
+ if args.MACHINE is not None and not skip_relax:
make_vasp_relax(jdata, mdata)
run_vasp_relax(jdata, mdata)
else:
diff --git a/dpgen/dispatcher/Dispatcher.py b/dpgen/dispatcher/Dispatcher.py
index 655761816..239654b26 100644
--- a/dpgen/dispatcher/Dispatcher.py
+++ b/dpgen/dispatcher/Dispatcher.py
@@ -346,11 +346,17 @@ def make_dispatcher(mdata, mdata_resource=None, work_path=None, run_tasks=None,
def make_submission(mdata_machine, mdata_resources, commands, work_path, run_tasks, group_size,
forward_common_files, forward_files, backward_files, outlog, errlog):
- machine = Machine.load_from_dict(mdata_machine)
- resources = Resources.load_from_dict(mdata_resources)
-
if mdata_machine['local_root'] != './':
raise RuntimeError(f"local_root must be './' in dpgen's machine.json.")
+
+ abs_local_root = os.path.abspath('./')
+
+ abs_mdata_machine = mdata_machine.copy()
+ abs_mdata_machine['local_root'] = abs_local_root
+
+ machine = Machine.load_from_dict(abs_mdata_machine)
+ resources = Resources.load_from_dict(mdata_resources)
+
command = "&&".join(commands)
diff --git a/dpgen/dispatcher/LocalContext.py b/dpgen/dispatcher/LocalContext.py
index 4c341f7aa..136dea4b0 100644
--- a/dpgen/dispatcher/LocalContext.py
+++ b/dpgen/dispatcher/LocalContext.py
@@ -117,7 +117,13 @@ def download(self,
pass
elif (os.path.exists(rfile)) and (not os.path.exists(lfile)) :
# trivial case, download happily
- shutil.move(rfile, lfile)
+ # If the file to be downloaded is a softlink, `cp` should be performed instead of `mv`.
+ # Otherwise, `lfile` is still a file linked to some original file,
+ # and when this file's removed, `lfile` will be invalid.
+ if os.path.islink(rfile):
+ shutil.copyfile(rfile,lfile)
+ else:
+ shutil.move(rfile, lfile)
elif (os.path.exists(rfile)) and (os.path.exists(lfile)) :
# both exists, replace!
dlog.info('find existing %s, replacing by %s' % (lfile, rfile))
diff --git a/dpgen/dispatcher/SSHContext.py b/dpgen/dispatcher/SSHContext.py
index 1ce2e5520..35a7e5997 100644
--- a/dpgen/dispatcher/SSHContext.py
+++ b/dpgen/dispatcher/SSHContext.py
@@ -280,7 +280,7 @@ def _put_files(self,
os.chdir(self.local_root)
if os.path.isfile(of) :
os.remove(of)
- with tarfile.open(of, "w:gz", dereference = dereference) as tar:
+ with tarfile.open(of, "w:gz", dereference = dereference, compresslevel=6) as tar:
for ii in files :
tar.add(ii)
os.chdir(cwd)
@@ -307,18 +307,18 @@ def _get_files(self,
per_nfile = 100
ntar = len(files) // per_nfile + 1
if ntar <= 1:
- self.block_checkcall('tar czf %s %s' % (of, " ".join(files)))
+ self.block_checkcall('tar czfh %s %s' % (of, " ".join(files)))
else:
of_tar = self.job_uuid + '.tar'
for ii in range(ntar):
ff = files[per_nfile * ii : per_nfile * (ii+1)]
if ii == 0:
# tar cf for the first time
- self.block_checkcall('tar cf %s %s' % (of_tar, " ".join(ff)))
+ self.block_checkcall('tar cfh %s %s' % (of_tar, " ".join(ff)))
else:
# append using tar rf
# -r, --append append files to the end of an archive
- self.block_checkcall('tar rf %s %s' % (of_tar, " ".join(ff)))
+ self.block_checkcall('tar rfh %s %s' % (of_tar, " ".join(ff)))
# compress the tar file using gzip, and will get a tar.gz file
# overwrite considering dpgen may stop and restart
# -f, --force force overwrite of output file and compress links
diff --git a/dpgen/generator/lib/abacus_pw_scf.py b/dpgen/generator/lib/abacus_pw_scf.py
deleted file mode 100644
index 5db58cc10..000000000
--- a/dpgen/generator/lib/abacus_pw_scf.py
+++ /dev/null
@@ -1,95 +0,0 @@
-import numpy as np
-bohr2ang = 0.52917721067
-def make_abacus_pw_scf_kpt(fp_params):
- # Make KPT file for abacus pw scf calculation.
- # KPT file is the file containing k points infomation in ABACUS scf calculation.
- k_points = [1, 1, 1, 0, 0, 0]
- if "k_points" in fp_params:
- k_points = fp_params["k_points"]
- if len(k_points) != 6:
- raise RuntimeError("k_points has to be a list containig 6 integers specifying MP k points generation.")
- ret = "K_POINTS\n0\nGamma\n"
- for i in range(6):
- ret += str(k_points[i]) + " "
- return ret
-
-def make_abacus_pw_scf_input(fp_params):
- # Make INPUT file for abacus pw scf calculation.
- ret = "INPUT_PARAMETERS\n"
- assert(fp_params['ntype'] >= 0 and type(fp_params["ntype"]) == int)
- ret += "ntype %d\n" % fp_params['ntype']
- ret += "pseudo_dir ./\n"
- if "ecutwfc" in fp_params:
- assert(fp_params["ecutwfc"] >= 0)
- ret += "ecutwfc %f\n" % fp_params["ecutwfc"]
- if "mixing_type" in fp_params:
- assert(fp_params["mixing_type"] in ["plain", "kerker", "pulay", "pulay-kerker", "broyden"])
- ret += "mixing_type %s\n" % fp_params["mixing_type"]
- if "mixing_beta" in fp_params:
- assert(fp_params["mixing_beta"] >= 0 and fp_params["mixing_beta"] < 1)
- ret += "mixing_beta %f\n" % fp_params["mixing_beta"]
- if "symmetry" in fp_params:
- assert(fp_params["symmetry"] == 0 or fp_params["symmetry"] == 1)
- ret += "symmetry %d\n" % fp_params["symmetry"]
- if "nbands" in fp_params:
- assert(fp_params["nbands"] > 0 and type(fp_params["nbands"]) == int)
- ret += "nbands %f\n" % fp_params["nbands"]
- if "nspin" in fp_params:
- assert(fp_params["nspin"] == 1 or fp_params["nspin"] == 2 or fp_params["nspin"] == 4)
- ret += "nspin %d\n" % fp_params["nspin"]
- if "ks_solver" in fp_params:
- assert(fp_params["ks_solver"] in ["cg", "dav", "lapack", "genelpa", "hpseps", "scalapack_gvx"])
- ret += "ks_solver %s\n" % fp_params["ks_solver"]
- if "smearing" in fp_params:
- assert(fp_params["smearing"] in ["gauss", "fd", "fixed", "mp", "mp2", "mv"])
- ret += "smearing %s\n" % fp_params["smearing"]
- if "sigma" in fp_params:
- assert(fp_params["sigma"] >= 0)
- ret += "sigma %f\n" % fp_params["sigma"]
- ret += "force 1\nstress 1\n"
- return ret
-
-def make_abacus_pw_scf_stru(sys_data, fp_pp_files):
- atom_names = sys_data['atom_names']
- atom_numbs = sys_data['atom_numbs']
- assert(len(atom_names) == len(fp_pp_files))
- assert(len(atom_names) == len(atom_numbs))
- cell = sys_data["cells"][0].reshape([3, 3])
- coord = sys_data['coords'][0]
- #volume = np.linalg.det(cell)
- #lattice_const = np.power(volume, 1/3)
- lattice_const = 1/bohr2ang # in Bohr, in this way coord and cell are in Angstrom
-
- ret = "ATOMIC_SPECIES\n"
- for iatom in range(len(atom_names)):
- ret += atom_names[iatom] + " 1.00 " + fp_pp_files[iatom] + "\n"
-
- ret += "\nLATTICE_CONSTANT\n"
- ret += str(lattice_const) + "\n\n"
-
- ret += "LATTICE_VECTORS\n"
- for ix in range(3):
- for iy in range(3):
- ret += str(cell[ix][iy]) + " "
- ret += "\n"
- ret += "\n"
-
- ret += "ATOMIC_POSITIONS\n"
- ret += "Cartesian # Cartesian(Unit is LATTICE_CONSTANT)\n"
- natom_tot = 0
- for iele in range(len(atom_names)):
- ret += atom_names[iele] + "\n"
- ret += "0.0\n"
- ret += str(atom_numbs[iele]) + "\n"
- for iatom in range(atom_numbs[iele]):
- ret += "%.12f %.12f %.12f %d %d %d\n" % (coord[natom_tot, 0], coord[natom_tot, 1], coord[natom_tot, 2], 0, 0, 0)
- natom_tot += 1
- assert(natom_tot == sum(atom_numbs))
-
- return ret
-
-
-if __name__ == "__main__":
- fp_params = {"k_points": [1, 1, 1, 0, 0, 0]}
- ret = make_abacus_pw_scf_kpt(fp_params)
- print(ret)
\ No newline at end of file
diff --git a/dpgen/generator/lib/abacus_scf.py b/dpgen/generator/lib/abacus_scf.py
new file mode 100644
index 000000000..8e68f91aa
--- /dev/null
+++ b/dpgen/generator/lib/abacus_scf.py
@@ -0,0 +1,141 @@
+import numpy as np
+bohr2ang = 0.52917721067
+def make_abacus_scf_kpt(fp_params):
+ # Make KPT file for abacus pw scf calculation.
+ # KPT file is the file containing k points infomation in ABACUS scf calculation.
+ k_points = [1, 1, 1, 0, 0, 0]
+ if "k_points" in fp_params:
+ k_points = fp_params["k_points"]
+ if len(k_points) != 6:
+ raise RuntimeError("k_points has to be a list containig 6 integers specifying MP k points generation.")
+ ret = "K_POINTS\n0\nGamma\n"
+ for i in range(6):
+ ret += str(k_points[i]) + " "
+ return ret
+
+def make_abacus_scf_input(fp_params):
+ # Make INPUT file for abacus pw scf calculation.
+ ret = "INPUT_PARAMETERS\n"
+ ret += "calculation scf\n"
+ assert(fp_params['ntype'] >= 0 and type(fp_params["ntype"]) == int), "'ntype' should be a positive integer."
+ ret += "ntype %d\n" % fp_params['ntype']
+ #ret += "pseudo_dir ./\n"
+ if "ecutwfc" in fp_params:
+ assert(fp_params["ecutwfc"] >= 0) , "'ntype' should be non-negative."
+ ret += "ecutwfc %f\n" % fp_params["ecutwfc"]
+ if "dr2" in fp_params:
+ ret += "dr2 %e\n" % fp_params["dr2"]
+ if "niter" in fp_params:
+ assert(fp_params['niter'] >= 0 and type(fp_params["niter"])== int), "'niter' should be a positive integer."
+ ret += "niter %d\n" % fp_params["niter"]
+ if "basis_type" in fp_params:
+ assert(fp_params["basis_type"] in ["pw", "lcao", "lcao_in_pw"]) , "'basis_type' must in 'pw', 'lcao' or 'lcao_in_pw'."
+ ret+= "basis_type %s\n" % fp_params["basis_type"]
+ if "dft_functional" in fp_params:
+ ret += "dft_functional %s\n" % fp_params["dft_functional"]
+ if "gamma_only" in fp_params:
+ assert(fp_params["gamma_only"] ==1 ) , "'gamma_only' should be 1. Multi-k algorithm will be supported after the KPT generator is completed."
+ ret+= "gamma_only %d\n" % fp_params["gamma_only"]
+ if "mixing_type" in fp_params:
+ assert(fp_params["mixing_type"] in ["plain", "kerker", "pulay", "pulay-kerker", "broyden"])
+ ret += "mixing_type %s\n" % fp_params["mixing_type"]
+ if "mixing_beta" in fp_params:
+ assert(fp_params["mixing_beta"] >= 0 and fp_params["mixing_beta"] < 1), "'mixing_beta' should between 0 and 1."
+ ret += "mixing_beta %f\n" % fp_params["mixing_beta"]
+ if "symmetry" in fp_params:
+ assert(fp_params["symmetry"] == 0 or fp_params["symmetry"] == 1), "'symmetry' should be either 0 or 1."
+ ret += "symmetry %d\n" % fp_params["symmetry"]
+ if "nbands" in fp_params:
+ assert(fp_params["nbands"] > 0 and type(fp_params["nbands"]) == int), "'nbands' should be a positive integer."
+ ret += "nbands %d\n" % fp_params["nbands"]
+ if "nspin" in fp_params:
+ assert(fp_params["nspin"] == 1 or fp_params["nspin"] == 2 or fp_params["nspin"] == 4), "'nspin' can anly take 1, 2 or 4"
+ ret += "nspin %d\n" % fp_params["nspin"]
+ if "ks_solver" in fp_params:
+ assert(fp_params["ks_solver"] in ["cg", "dav", "lapack", "genelpa", "hpseps", "scalapack_gvx"]), "'ks_sover' should in 'cgx', 'dav', 'lapack', 'genelpa', 'hpseps', 'scalapack_gvx'."
+ ret += "ks_solver %s\n" % fp_params["ks_solver"]
+ if "smearing" in fp_params:
+ assert(fp_params["smearing"] in ["gaussian", "fd", "fixed", "mp", "mp2", "mv"]), "'smearing' should in 'gaussian', 'fd', 'fixed', 'mp', 'mp2', 'mv'. "
+ ret += "smearing %s\n" % fp_params["smearing"]
+ if "sigma" in fp_params:
+ assert(fp_params["sigma"] >= 0), "'sigma' should be non-negative."
+ ret += "sigma %f\n" % fp_params["sigma"]
+ if "force" in fp_params:
+ assert(fp_params["force"] == 0 or fp_params["force"] == 1), "'force' should be either 0 or 1."
+ ret += "force %d\n" % fp_params["force"]
+ if "stress" in fp_params:
+ assert(fp_params["stress"] == 0 or fp_params["stress"] == 1), "'stress' should be either 0 or 1."
+ ret += "stress %d\n" % fp_params["stress"]
+ #paras for deepks
+ if "out_descriptor" in fp_params:
+ assert(fp_params["out_descriptor"] == 0 or fp_params["out_descriptor"] == 1), "'out_descriptor' should be either 0 or 1."
+ ret += "out_descriptor %d\n" % fp_params["out_descriptor"]
+ if "lmax_descriptor" in fp_params:
+ assert(fp_params["lmax_descriptor"] >= 0), "'lmax_descriptor' should be a positive integer."
+ ret += "lmax_descriptor %d\n" % fp_params["lmax_descriptor"]
+ if "deepks_scf" in fp_params:
+ assert(fp_params["deepks_scf"] == 0 or fp_params["deepks_scf"] == 1), "'deepks_scf' should be either 0 or 1."
+ ret += "deepks_scf %d\n" % fp_params["deepks_scf"]
+ if "model_file" in fp_params:
+ ret += "model_file %s\n" % fp_params["model_file"]
+ return ret
+
+def make_abacus_scf_stru(sys_data, fp_pp_files, fp_params):
+ atom_names = sys_data['atom_names']
+ atom_numbs = sys_data['atom_numbs']
+ assert(len(atom_names) == len(fp_pp_files)), "the number of pp_files must be equal to the number of atom types. "
+ assert(len(atom_names) == len(atom_numbs)), "Please check the name of atoms. "
+ cell = sys_data["cells"][0].reshape([3, 3])
+ coord = sys_data['coords'][0]
+ #volume = np.linalg.det(cell)
+ #lattice_const = np.power(volume, 1/3)
+
+ ret = "ATOMIC_SPECIES\n"
+ for iatom in range(len(atom_names)):
+ ret += atom_names[iatom] + " 1.00 " + fp_pp_files[iatom] + "\n"
+ ret += "\n"
+
+ if "lattice_constant" in fp_params:
+ ret += "\nLATTICE_CONSTANT\n"
+ ret += str(fp_params["lattice_constant"]) + "\n\n" # in Bohr, in this way coord and cell are in Angstrom
+ else:
+ ret += "\nLATTICE_CONSTANT\n"
+ ret += str(1/bohr2ang) + "\n\n"
+
+ ret += "LATTICE_VECTORS\n"
+ for ix in range(3):
+ for iy in range(3):
+ ret += str(cell[ix][iy]) + " "
+ ret += "\n"
+ ret += "\n"
+
+ ret += "ATOMIC_POSITIONS\n"
+ ret += "Cartesian # Cartesian(Unit is LATTICE_CONSTANT)\n"
+ ret += "\n"
+ natom_tot = 0
+ for iele in range(len(atom_names)):
+ ret += atom_names[iele] + "\n"
+ ret += "0.0\n"
+ ret += str(atom_numbs[iele]) + "\n"
+ for iatom in range(atom_numbs[iele]):
+ ret += "%.12f %.12f %.12f %d %d %d\n" % (coord[natom_tot, 0], coord[natom_tot, 1], coord[natom_tot, 2], 0, 0, 0)
+ natom_tot += 1
+ assert(natom_tot == sum(atom_numbs))
+
+ if "basis_type" in fp_params and fp_params["basis_type"]=="lcao":
+ ret +="\nNUMERICAL_ORBITAL\n"
+ assert(len(fp_params["orb_files"])==len(atom_names))
+ for iatom in range(len(atom_names)):
+ ret += fp_params["orb_files"][iatom] +"\n"
+
+ if "deepks_scf" in fp_params and fp_params["out_descriptor"]==1:
+ ret +="\nNUMERICAL_DESCRIPTOR\n"
+ ret +=fp_params["proj_file"][0]+"\n"
+
+ return ret
+
+
+if __name__ == "__main__":
+ fp_params = {"k_points": [1, 1, 1, 0, 0, 0]}
+ ret = make_abacus_scf_kpt(fp_params)
+ print(ret)
\ No newline at end of file
diff --git a/dpgen/generator/lib/lammps.py b/dpgen/generator/lib/lammps.py
index 3190d9f01..3b80b8d10 100644
--- a/dpgen/generator/lib/lammps.py
+++ b/dpgen/generator/lib/lammps.py
@@ -85,7 +85,7 @@ def make_lammps_input(ensemble,
if ele_temp_a is not None:
keywords += "aparam ${ELE_TEMP}"
ret+= "pair_style deepmd %s out_freq ${THERMO_FREQ} out_file model_devi.out %s\n" % (graph_list, keywords)
- ret+= "pair_coeff \n"
+ ret+= "pair_coeff * *\n"
ret+= "\n"
ret+= "thermo_style custom step temp pe ke etotal press vol lx ly lz xy xz yz\n"
ret+= "thermo ${THERMO_FREQ}\n"
diff --git a/dpgen/generator/run.py b/dpgen/generator/run.py
index ab77da8f9..1c4733037 100644
--- a/dpgen/generator/run.py
+++ b/dpgen/generator/run.py
@@ -45,7 +45,7 @@
from dpgen.generator.lib.vasp import make_vasp_incar_user_dict
from dpgen.generator.lib.vasp import incar_upper
from dpgen.generator.lib.pwscf import make_pwscf_input
-from dpgen.generator.lib.abacus_pw_scf import make_abacus_pw_scf_stru, make_abacus_pw_scf_input, make_abacus_pw_scf_kpt
+from dpgen.generator.lib.abacus_scf import make_abacus_scf_stru, make_abacus_scf_input, make_abacus_scf_kpt
#from dpgen.generator.lib.pwscf import cvt_1frame
from dpgen.generator.lib.pwmat import make_pwmat_input_dict
from dpgen.generator.lib.pwmat import write_input_dict
@@ -514,6 +514,8 @@ def run_train (iter_index,
commands.append(command)
command = '%s freeze' % train_command
commands.append(command)
+ if jdata.get("dp_compress", False):
+ commands.append("%s compress" % train_command)
else:
raise RuntimeError("DP-GEN currently only supports for DeePMD-kit 1.x or 2.x version!" )
@@ -536,6 +538,8 @@ def run_train (iter_index,
]
backward_files = ['frozen_model.pb', 'lcurve.out', 'train.log']
backward_files+= ['model.ckpt.meta', 'model.ckpt.index', 'model.ckpt.data-00000-of-00001', 'checkpoint']
+ if jdata.get("dp_compress", False):
+ backward_files.append('frozen_model_compressed.pb')
init_data_sys_ = jdata['init_data_sys']
init_data_sys = []
for ii in init_data_sys_ :
@@ -621,7 +625,11 @@ def post_train (iter_index,
return
# symlink models
for ii in range(numb_models) :
- task_file = os.path.join(train_task_fmt % ii, 'frozen_model.pb')
+ if not jdata.get("dp_compress", False):
+ model_name = 'frozen_model.pb'
+ else:
+ model_name = 'frozen_model_compressed.pb'
+ task_file = os.path.join(train_task_fmt % ii, model_name)
ofile = os.path.join(work_path, 'graph.%03d.pb' % ii)
if os.path.isfile(ofile) :
os.remove(ofile)
@@ -796,7 +804,7 @@ def make_model_devi (iter_index,
iter_name = make_iter_name(iter_index)
train_path = os.path.join(iter_name, train_name)
train_path = os.path.abspath(train_path)
- models = glob.glob(os.path.join(train_path, "graph*pb"))
+ models = sorted(glob.glob(os.path.join(train_path, "graph*pb")))
work_path = os.path.join(iter_name, model_devi_name)
create_path(work_path)
for mm in models :
@@ -882,7 +890,7 @@ def _make_model_devi_revmat(iter_index, jdata, mdata, conf_systems):
iter_name = make_iter_name(iter_index)
train_path = os.path.join(iter_name, train_name)
train_path = os.path.abspath(train_path)
- models = glob.glob(os.path.join(train_path, "graph*pb"))
+ models = sorted(glob.glob(os.path.join(train_path, "graph*pb")))
task_model_list = []
for ii in models:
task_model_list.append(os.path.join('..', os.path.basename(ii)))
@@ -939,7 +947,23 @@ def _make_model_devi_revmat(iter_index, jdata, mdata, conf_systems):
# revise input of lammps
with open('input.lammps') as fp:
lmp_lines = fp.readlines()
- lmp_lines = revise_lmp_input_model(lmp_lines, task_model_list, trj_freq, deepmd_version = deepmd_version)
+ # only revise the line "pair_style deepmd" if the user has not written the full line (checked by then length of the line)
+ template_has_pair_deepmd=1
+ for line_idx,line_context in enumerate(lmp_lines):
+ if (line_context[0] != "#") and ("pair_style" in line_context) and ("deepmd" in line_context):
+ template_has_pair_deepmd=0
+ template_pair_deepmd_idx=line_idx
+ if template_has_pair_deepmd == 0:
+ if LooseVersion(deepmd_version) < LooseVersion('1'):
+ if len(lmp_lines[template_pair_deepmd_idx].split()) != (len(models) + len(["pair_style","deepmd","10", "model_devi.out"])):
+ lmp_lines = revise_lmp_input_model(lmp_lines, task_model_list, trj_freq, deepmd_version = deepmd_version)
+ else:
+ if len(lmp_lines[template_pair_deepmd_idx].split()) != (len(models) + len(["pair_style","deepmd","out_freq", "10", "out_file", "model_devi.out"])):
+ lmp_lines = revise_lmp_input_model(lmp_lines, task_model_list, trj_freq, deepmd_version = deepmd_version)
+ #use revise_lmp_input_model to raise error message if "part_style" or "deepmd" not found
+ else:
+ lmp_lines = revise_lmp_input_model(lmp_lines, task_model_list, trj_freq, deepmd_version = deepmd_version)
+
lmp_lines = revise_lmp_input_dump(lmp_lines, trj_freq)
lmp_lines = revise_by_keys(
lmp_lines, total_rev_keys[:total_num_lmp], total_rev_item[:total_num_lmp]
@@ -1140,7 +1164,7 @@ def _make_model_devi_native_gromacs(iter_index, jdata, mdata, conf_systems):
create_path(task_path)
gromacs_settings = jdata.get("gromacs_settings" , "")
for key,file in gromacs_settings.items():
- if key != "traj_filename" and key != "mdp_filename" and key != "group_name":
+ if key != "traj_filename" and key != "mdp_filename" and key != "group_name" and key != "maxwarn":
os.symlink(os.path.join(cc,file), os.path.join(task_path, file))
# input.json for DP-Gromacs
with open(os.path.join(cc, "input.json")) as f:
@@ -1160,6 +1184,8 @@ def _make_model_devi_native_gromacs(iter_index, jdata, mdata, conf_systems):
mdp['nstenergy'] = trj_freq
# dt
mdp['dt'] = model_devi_dt
+ # nsteps
+ mdp['nsteps'] = nsteps
# temps
if "ref_t" in list(mdp.keys()):
mdp["ref_t"] = tt
@@ -1238,6 +1264,8 @@ def run_model_devi (iter_index,
topol_filename = gromacs_settings.get("topol_filename", "processed.top")
conf_filename = gromacs_settings.get("conf_filename", "conf.gro")
index_filename = gromacs_settings.get("index_filename", "index.raw")
+ type_filename = gromacs_settings.get("type_filename", "type.raw")
+ ndx_filename = gromacs_settings.get("ndx_filename", "")
# Initial reference to process pbc condition.
# Default is em.tpr
ref_filename = gromacs_settings.get("ref_filename", "em.tpr")
@@ -1245,18 +1273,21 @@ def run_model_devi (iter_index,
maxwarn = gromacs_settings.get("maxwarn", 1)
traj_filename = gromacs_settings.get("traj_filename", "deepmd_traj.gro")
grp_name = gromacs_settings.get("group_name", "Other")
- nsteps = cur_job["nsteps"]
trj_freq = cur_job.get("trj_freq", 10)
command = "%s grompp -f %s -p %s -c %s -o %s -maxwarn %d" % (model_devi_exec, mdp_filename, topol_filename, conf_filename, deffnm, maxwarn)
- command += "&& %s mdrun -deffnm %s -nsteps %d" %(model_devi_exec, deffnm, nsteps)
- command += "&& echo -e \"%s\n%s\n\" | %s trjconv -s %s -f %s.trr -o %s -pbc mol -ur compact -center" % (grp_name, grp_name, model_devi_exec, ref_filename, deffnm, traj_filename)
+ command += "&& %s mdrun -deffnm %s -cpi" %(model_devi_exec, deffnm)
+ if ndx_filename:
+ command += f"&& echo -e \"{grp_name}\\n{grp_name}\\n\" | {model_devi_exec} trjconv -s {ref_filename} -f {deffnm}.trr -n {ndx_filename} -o {traj_filename} -pbc mol -ur compact -center"
+ else:
+ command += "&& echo -e \"%s\\n%s\\n\" | %s trjconv -s %s -f %s.trr -o %s -pbc mol -ur compact -center" % (grp_name, grp_name, model_devi_exec, ref_filename, deffnm, traj_filename)
command += "&& if [ ! -d traj ]; then \n mkdir traj; fi\n"
command += f"python -c \"import dpdata;system = dpdata.System('{traj_filename}', fmt='gromacs/gro'); [system.to_gromacs_gro('traj/%d.gromacstrj' % (i * {trj_freq}), frame_idx=i) for i in range(system.get_nframes())]; system.to_deepmd_npy('traj_deepmd')\""
command += f"&& dp model-devi -m ../graph.000.pb ../graph.001.pb ../graph.002.pb ../graph.003.pb -s traj_deepmd -o model_devi.out -f {trj_freq}"
commands = [command]
- forward_files = [mdp_filename, topol_filename, conf_filename, index_filename, ref_filename, "input.json", "job.json" ]
+ forward_files = [mdp_filename, topol_filename, conf_filename, index_filename, ref_filename, type_filename, "input.json", "job.json" ]
+ if ndx_filename: forward_files.append(ndx_filename)
backward_files = ["%s.tpr" % deffnm, "%s.log" %deffnm , traj_filename, 'model_devi.out', "traj", "traj_deepmd" ]
@@ -1578,18 +1609,32 @@ def _make_fp_vasp_inner (modd_path,
skip_bad_box = jdata.get('fp_skip_bad_box')
# skip discrete structure in cluster
fp_cluster_vacuum = jdata.get('fp_cluster_vacuum',None)
- for ss in system_index :
+
+ def _trust_limitation_check(sys_idx, lim):
+ if isinstance(lim, list):
+ sys_lim = lim[sys_idx]
+ else:
+ sys_lim = lim
+ return sys_lim
+
+ for ss in system_index:
modd_system_glob = os.path.join(modd_path, 'task.' + ss + '.*')
modd_system_task = glob.glob(modd_system_glob)
modd_system_task.sort()
+ # convert global trust limitations to local ones
+ f_trust_lo_sys = _trust_limitation_check(ss, f_trust_lo)
+ f_trust_hi_sys = _trust_limitation_check(ss, f_trust_hi)
+ v_trust_lo_sys = _trust_limitation_check(ss, v_trust_lo)
+ v_trust_hi_sys = _trust_limitation_check(ss, v_trust_hi)
+
# assumed e -> v
if not model_devi_adapt_trust_lo:
fp_rest_accurate, fp_candidate, fp_rest_failed, counter \
= _select_by_model_devi_standard(
modd_system_task,
- f_trust_lo, f_trust_hi,
- v_trust_lo, v_trust_hi,
+ f_trust_lo_sys, f_trust_hi_sys,
+ v_trust_lo_sys, v_trust_hi_sys,
cluster_cutoff,
model_devi_skip,
model_devi_f_avg_relative = model_devi_f_avg_relative,
@@ -1603,8 +1648,8 @@ def _make_fp_vasp_inner (modd_path,
fp_rest_accurate, fp_candidate, fp_rest_failed, counter, f_trust_lo_ad, v_trust_lo_ad \
= _select_by_model_devi_adaptive_trust_low(
modd_system_task,
- f_trust_hi, numb_candi_f, perc_candi_f,
- v_trust_hi, numb_candi_v, perc_candi_v,
+ f_trust_hi_sys, numb_candi_f, perc_candi_f,
+ v_trust_hi_sys, numb_candi_v, perc_candi_v,
model_devi_skip = model_devi_skip,
model_devi_f_avg_relative = model_devi_f_avg_relative,
)
@@ -2056,7 +2101,7 @@ def make_fp_pwscf(iter_index,
# link pp files
_link_fp_vasp_pp(iter_index, jdata)
-def make_fp_abacus_pw_scf(iter_index,
+def make_fp_abacus_scf(iter_index,
jdata) :
# make config
fp_tasks = _make_fp_vasp_configs(iter_index, jdata)
@@ -2077,13 +2122,13 @@ def make_fp_abacus_pw_scf(iter_index,
sys_data = dpdata.System('POSCAR').data
if 'mass_map' in jdata:
sys_data['atom_masses'] = jdata['mass_map']
- ret_input = make_abacus_pw_scf_input(fp_params)
+ ret_input = make_abacus_scf_input(fp_params)
with open('INPUT', 'w') as fp:
fp.write(ret_input)
- ret_kpt = make_abacus_pw_scf_kpt(fp_params)
+ ret_kpt = make_abacus_scf_kpt(fp_params)
with open("KPT", "w") as fp:
fp.write(ret_kpt)
- ret_stru = make_abacus_pw_scf_stru(sys_data, fp_pp_files)
+ ret_stru = make_abacus_scf_stru(sys_data, fp_pp_files, fp_params)
with open("STRU", "w") as fp:
fp.write(ret_stru)
@@ -2217,7 +2262,7 @@ def make_fp (iter_index,
elif fp_style == "pwscf" :
make_fp_pwscf(iter_index, jdata)
elif fp_style == "abacus/scf" :
- make_fp_abacus_pw_scf(iter_index, jdata)
+ make_fp_abacus_scf(iter_index, jdata)
elif fp_style == "siesta" :
make_fp_siesta(iter_index, jdata)
elif fp_style == "gaussian" :
@@ -2255,7 +2300,7 @@ def _qe_check_fin(ii) :
return False
return True
-def _abacus_pw_scf_check_fin(ii) :
+def _abacus_scf_check_fin(ii) :
if os.path.isfile(os.path.join(ii, 'OUT.ABACUS/running_scf.log')) :
with open(os.path.join(ii, 'OUT.ABACUS/running_scf.log'), 'r') as fp :
content = fp.read()
@@ -2400,7 +2445,7 @@ def run_fp (iter_index,
elif fp_style == "abacus/scf":
forward_files = ["INPUT", "STRU", "KPT"] + fp_pp_files
backward_files = ["output", "OUT.ABACUS"]
- run_fp_inner(iter_index, jdata, mdata, forward_files, backward_files, _abacus_pw_scf_check_fin, log_file = 'output')
+ run_fp_inner(iter_index, jdata, mdata, forward_files, backward_files, _abacus_scf_check_fin, log_file = 'output')
elif fp_style == "siesta":
forward_files = ['input'] + fp_pp_files
backward_files = ['output']
@@ -2575,7 +2620,7 @@ def post_fp_pwscf (iter_index,
all_sys.to_deepmd_raw(sys_data_path)
all_sys.to_deepmd_npy(sys_data_path, set_size = len(sys_output))
-def post_fp_abacus_pw_scf (iter_index,
+def post_fp_abacus_scf (iter_index,
jdata):
model_devi_jobs = jdata['model_devi_jobs']
assert (iter_index < len(model_devi_jobs))
@@ -2693,7 +2738,6 @@ def post_fp_gaussian (iter_index,
sys_output = glob.glob(os.path.join(work_path, "task.%s.*/output"%ss))
sys_output.sort()
for idx,oo in enumerate(sys_output) :
- # TODO : UnboundLocalError sometimes occurs when parsing gaussian log
sys = dpdata.LabeledSystem(oo, fmt = 'gaussian/log')
if len(sys) > 0:
sys.check_type_map(type_map = jdata['type_map'])
@@ -2822,7 +2866,7 @@ def post_fp (iter_index,
elif fp_style == "pwscf" :
post_fp_pwscf(iter_index, jdata)
elif fp_style == "abacus/scf":
- post_fp_abacus_pw_scf(iter_index, jdata)
+ post_fp_abacus_scf(iter_index, jdata)
elif fp_style == "siesta":
post_fp_siesta(iter_index, jdata)
elif fp_style == 'gaussian' :
@@ -2834,15 +2878,24 @@ def post_fp (iter_index,
else :
raise RuntimeError ("unsupported fp style")
# clean traj
- iter_name = make_iter_name(iter_index)
clean_traj = True
if 'model_devi_clean_traj' in jdata :
clean_traj = jdata['model_devi_clean_traj']
- if clean_traj:
- modd_path = os.path.join(iter_name, model_devi_name)
+ modd_path = None
+ if isinstance(clean_traj, bool):
+ iter_name = make_iter_name(iter_index)
+ if clean_traj:
+ modd_path = os.path.join(iter_name, model_devi_name)
+ elif isinstance(clean_traj, int):
+ clean_index = iter_index - clean_traj
+ if clean_index >= 0:
+ modd_path = os.path.join(make_iter_name(clean_index), model_devi_name)
+ if modd_path is not None:
md_trajs = glob.glob(os.path.join(modd_path, 'task*/traj'))
- for ii in md_trajs :
+ for ii in md_trajs:
shutil.rmtree(ii)
+
+
def set_version(mdata):
diff --git a/examples/CH4-lebesgue/CH4.POSCAR b/examples/CH4-lebesgue/CH4.POSCAR
new file mode 100644
index 000000000..2f9def780
--- /dev/null
+++ b/examples/CH4-lebesgue/CH4.POSCAR
@@ -0,0 +1 @@
+../init/CH4.POSCAR
\ No newline at end of file
diff --git a/examples/CH4-lebesgue/INCAR_methane b/examples/CH4-lebesgue/INCAR_methane
new file mode 100644
index 000000000..b946fb7e5
--- /dev/null
+++ b/examples/CH4-lebesgue/INCAR_methane
@@ -0,0 +1 @@
+../run/dp1.x-lammps-vasp/CH4/INCAR_methane
\ No newline at end of file
diff --git a/examples/CH4-lebesgue/INCAR_methane.md b/examples/CH4-lebesgue/INCAR_methane.md
new file mode 100644
index 000000000..4c48cdd86
--- /dev/null
+++ b/examples/CH4-lebesgue/INCAR_methane.md
@@ -0,0 +1 @@
+../init/INCAR_methane.md
\ No newline at end of file
diff --git a/examples/CH4-lebesgue/INCAR_methane.rlx b/examples/CH4-lebesgue/INCAR_methane.rlx
new file mode 100644
index 000000000..e44202f43
--- /dev/null
+++ b/examples/CH4-lebesgue/INCAR_methane.rlx
@@ -0,0 +1 @@
+../init/INCAR_methane.rlx
\ No newline at end of file
diff --git a/examples/CH4-lebesgue/README.md b/examples/CH4-lebesgue/README.md
new file mode 100644
index 000000000..d550d16f0
--- /dev/null
+++ b/examples/CH4-lebesgue/README.md
@@ -0,0 +1 @@
+../machine/DeePMD-kit-2.x/lebesgue_v2_machine_README.md
\ No newline at end of file
diff --git a/examples/CH4-lebesgue/init.json b/examples/CH4-lebesgue/init.json
new file mode 100644
index 000000000..72cc77ef5
--- /dev/null
+++ b/examples/CH4-lebesgue/init.json
@@ -0,0 +1 @@
+../init/ch4.json
\ No newline at end of file
diff --git a/examples/CH4-lebesgue/lebesgue_v2_machine.json b/examples/CH4-lebesgue/lebesgue_v2_machine.json
new file mode 100644
index 000000000..02f838b49
--- /dev/null
+++ b/examples/CH4-lebesgue/lebesgue_v2_machine.json
@@ -0,0 +1 @@
+../machine/DeePMD-kit-2.x/lebesgue_v2_machine.json
\ No newline at end of file
diff --git a/examples/CH4-lebesgue/param_CH4_deepmd-kit-2.0.1.json b/examples/CH4-lebesgue/param_CH4_deepmd-kit-2.0.1.json
new file mode 100644
index 000000000..1b19d3d66
--- /dev/null
+++ b/examples/CH4-lebesgue/param_CH4_deepmd-kit-2.0.1.json
@@ -0,0 +1 @@
+../run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json
\ No newline at end of file
diff --git a/examples/init/INCAR_methane.md b/examples/init/INCAR_methane.md
index 9831387aa..a0e3ca29b 100644
--- a/examples/init/INCAR_methane.md
+++ b/examples/init/INCAR_methane.md
@@ -1,33 +1,21 @@
PREC=A
-ENCUT=400.000000
+ENCUT=400
ISYM=0
-ALGO=fast
-EDIFF=1E-6
-LREAL=F
+ALGO=Fast
+EDIFF=1.000000e-06
+LREAL=False
NPAR=4
KPAR=1
-
-NELM=200
-ISTART=0
-ICHARG=2
+NELM=120
+NELMIN=4
ISIF=2
ISMEAR=0
-SIGMA=0.200000
+SIGMA=0.20000
IBRION=0
-MAXMIX=50
-NBLOCK=1
-KBLOCK=100
-
-SMASS=0
-POTIM=2g
-TEBEG=50
-TEEND=50
-
+POTIM=0.5
NSW=10
-
LWAVE=F
LCHARG=F
PSTRESS=0
-
KSPACING=0.500000
-KGAMMA=F
+KGAMMA=.FALSE.
diff --git a/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json b/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json
new file mode 100644
index 000000000..6b9ead467
--- /dev/null
+++ b/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json
@@ -0,0 +1,108 @@
+{
+ "api_version": "1.0",
+ "deepmd_version": "2.0.1",
+ "train" :[
+ {
+ "command": "dp",
+ "machine": {
+ "batch_type": "DpCloudServer",
+ "context_type": "DpCloudServerContext",
+ "local_root" : "./",
+ "remote_profile":{
+ "email": "your lebesgue register email",
+ "password": "your lebesgue password",
+ "program_id": 0,
+ "input_data":{
+ "api_version":2,
+ "job_type": "indicate",
+ "log_file": "00*/train.log",
+ "grouped":true,
+ "job_name": "dpgen_train_job",
+ "disk_size": 100,
+ "scass_type":"c8_m60_1 * NVIDIA P100",
+ "platform": "ali",
+ "image_name":"deepmd-kit:2.0.1",
+ "on_demand":0
+ }
+ }
+ },
+ "resources": {
+ "number_node": 1,
+ "local_root":"./",
+ "cpu_per_node": 4,
+ "gpu_per_node": 1,
+ "queue_name": "GPU",
+ "group_size": 1
+ }
+ }],
+ "model_devi":
+ [{
+ "command": "lmp -i input.lammps -v restart 0",
+ "machine": {
+ "batch_type": "DpCloudServer",
+ "context_type": "DpCloudServerContext",
+ "local_root" : "./",
+ "remote_profile":{
+ "email": "your lebesgue register email",
+ "password": "your lebesgue password",
+ "program_id": 0,
+ "input_data":{
+ "api_version":2,
+ "job_type": "indicate",
+ "log_file": "*/model_devi.log",
+ "grouped":true,
+ "job_name": "dpgen_model_devi_job",
+ "disk_size": 200,
+ "scass_type":"c8_m60_1 * NVIDIA P100",
+ "platform": "ali",
+ "image_name":"deepmd-kit:2.0.1",
+ "on_demand":0
+ }
+ }
+ },
+ "resources": {
+ "number_node": 1,
+ "local_root":"./",
+ "cpu_per_node": 4,
+ "gpu_per_node": 1,
+ "queue_name": "GPU",
+ "group_size": 5
+ }
+ }],
+ "fp":
+ [{
+ "command": "mpirun -n 16 vasp_std",
+ "machine": {
+ "batch_type": "DpCloudServer",
+ "context_type": "DpCloudServerContext",
+ "local_root" : "./",
+ "remote_profile":{
+ "email": "your lebesgue register email",
+ "password": "your lebesgue password",
+ "program_id": 0,
+ "input_data":{
+ "api_version":2,
+ "job_type": "indicate",
+ "log_file": "task*/fp.log",
+ "grouped":true,
+ "job_name": "dpgen_fp_job",
+ "disk_size": 100,
+ "scass_type":"c8_m8_cpu",
+ "platform": "ali",
+ "image_name":"vasp:5.4.4",
+ "on_demand":0
+ }
+ }
+ },
+ "resources": {
+ "number_node": 1,
+ "cpu_per_node": 32,
+ "gpu_per_node": 0,
+ "queue_name": "CPU",
+ "group_size": 5,
+ "local_root":"./",
+ "source_list": ["/opt/intel/oneapi/setvars.sh"]
+ }
+ }
+ ]
+}
diff --git a/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine_README.md b/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine_README.md
new file mode 100644
index 000000000..3c81f5d04
--- /dev/null
+++ b/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine_README.md
@@ -0,0 +1,24 @@
+# Config machine.json file in order to submit task to lebesgue platform.
+
+You can login to lebesgue official website http://lebesgue.dp.tech/ . Then click [Function]-[DPGEN]-[manual]\(On the top left corner of the function panel\) from left navigator bar http://lebesgue.dp.tech/#/jobs/dpgen.
+
+Below is the description of each json fields, please visit official documentation for more information and update.
+
+| field | optional | type | description |
+| --- | --- | --- | --- |
+| email | false | string | your lebesgue login email |
+| password | false | string | your lebesgue login password (note this is not your remote machine login password) |
+| program_id | false | int | your program id(int) you can find it in [Lebesgue Official website]-[Programs]-[Program ID] to view your program id |
+| api_version | true | int| (default 1) the api_version inside input_data is different from the outside one, which is used to decide which api version will be called to lebesgue. lebesgue currently support version 1 and 2, and version 1 will be deprecate in the future. |
+| job_group_id | true | int | config this to specific job_group so submitted jobs can be view as a whole group in the webpage.
+| rerun | true | int | if the submitted job terminate unsuccessfully, does it need to be rerun.
+| job_type | false | string | job type, should be indicate |
+| log_file | true | string | the location of log file, where you can view the log in webpage |
+| job_name | false | string | job group name |
+| on_demand | true | int | default:0, 0:use spot machine 1:use ondemand machine |
+| image_name | true/false | int | image name, necessary when platform is ali or aws, optional when platform is sugon |
+| disk_size | true/false | int | disk size (GB), necessary when platform is ali or aws, optional when platform is sugon |
+| scass_type | false | string | machine configuration, about scass_type, you can find them on [lebesgue official website] - [Finance]-[Price calculator] to select disire machine configuration. invalid when instance_group_id is present |
+| instance_group_id | true | int | group of scass type |
+| platform | false | string | avaliable platform: "aws" "ali" "sugon" |
+| grouped | false | bool | weather group same task in to one job group. |
\ No newline at end of file
diff --git a/examples/run/dp1.x-lammps-vasp/CH4/POT_C b/examples/run/dp1.x-lammps-vasp/CH4/POT_C
index 8b1378917..4c6399dc0 100644
--- a/examples/run/dp1.x-lammps-vasp/CH4/POT_C
+++ b/examples/run/dp1.x-lammps-vasp/CH4/POT_C
@@ -1 +1 @@
-
+# We can only provide empty files in public, you should provide valid POTCARS yourself when running DP-GEN.
diff --git a/examples/run/dp1.x-lammps-vasp/CH4/POT_H b/examples/run/dp1.x-lammps-vasp/CH4/POT_H
index 8b1378917..81ae32edd 100644
--- a/examples/run/dp1.x-lammps-vasp/CH4/POT_H
+++ b/examples/run/dp1.x-lammps-vasp/CH4/POT_H
@@ -1 +1 @@
-
+# We can only provide empty files in public, you should provide valid POTCARS yourself when running DP-GEN.
\ No newline at end of file
diff --git a/examples/run/dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json b/examples/run/dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json
index b80946710..e63c6236b 100644
--- a/examples/run/dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json
+++ b/examples/run/dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json
@@ -134,5 +134,6 @@
"POTCAR_H",
"POTCAR_C"
],
+ "_comments" : "We can only provide empty files in public, you should provide valid POTCARS yourself when running DP-GEN",
"fp_incar": "/data1/yfb222333/2_dpgen_gpu_multi/INCAR_methane"
}
diff --git a/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json b/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json
new file mode 100644
index 000000000..15f682cdc
--- /dev/null
+++ b/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json
@@ -0,0 +1,136 @@
+{
+ "type_map": [
+ "H",
+ "C"
+ ],
+ "mass_map": [
+ 1,
+ 12
+ ],
+ "init_data_prefix": "./",
+ "init_data_sys": [
+ "CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd"
+ ],
+ "sys_configs_prefix": "./",
+ "sys_configs": [
+ [
+ "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000*/POSCAR"
+ ],
+ [
+ "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR"
+ ]
+ ],
+ "_comment": " that's all ",
+ "numb_models": 4,
+ "default_training_param": {
+ "model": {
+ "type_map": [
+ "H",
+ "C"
+ ],
+ "descriptor": {
+ "type": "se_a",
+ "sel": [
+ 16,
+ 4
+ ],
+ "rcut_smth": 0.5,
+ "rcut": 5.0,
+ "neuron": [
+ 120,
+ 120,
+ 120
+ ],
+ "resnet_dt": true,
+ "axis_neuron": 12,
+ "seed": 1
+ },
+ "fitting_net": {
+ "neuron": [
+ 25,
+ 50,
+ 100
+ ],
+ "resnet_dt": false,
+ "seed": 1
+ }
+ },
+ "learning_rate": {
+ "type": "exp",
+ "start_lr": 0.001,
+ "decay_steps": 100
+ },
+ "loss": {
+ "start_pref_e": 0.02,
+ "limit_pref_e": 2,
+ "start_pref_f": 1000,
+ "limit_pref_f": 1,
+ "start_pref_v": 0.0,
+ "limit_pref_v": 0.0
+ },
+ "training": {
+ "set_prefix": "set",
+ "stop_batch": 2000,
+ "batch_size": 1,
+ "disp_file": "lcurve.out",
+ "disp_freq": 1000,
+ "numb_test": 4,
+ "save_freq": 1000,
+ "save_ckpt": "model.ckpt",
+ "disp_training": true,
+ "time_training": true,
+ "profiling": false,
+ "profiling_file": "timeline.json",
+ "_comment": "that's all"
+ }
+ },
+ "model_devi_dt": 0.002,
+ "model_devi_skip": 0,
+ "model_devi_f_trust_lo": 0.05,
+ "model_devi_f_trust_hi": 0.15,
+ "model_devi_e_trust_lo": 10000000000.0,
+ "model_devi_e_trust_hi": 10000000000.0,
+ "model_devi_clean_traj": true,
+ "model_devi_jobs": [
+ {
+ "sys_idx": [
+ 0
+ ],
+ "temps": [
+ 100
+ ],
+ "press": [
+ 1.0
+ ],
+ "trj_freq": 10,
+ "nsteps": 300,
+ "ensemble": "nvt",
+ "_idx": "00"
+ },
+ {
+ "sys_idx": [
+ 1
+ ],
+ "temps": [
+ 100
+ ],
+ "press": [
+ 1.0
+ ],
+ "trj_freq": 10,
+ "nsteps": 3000,
+ "ensemble": "nvt",
+ "_idx": "01"
+ }
+ ],
+ "fp_style": "vasp",
+ "shuffle_poscar": false,
+ "fp_task_max": 20,
+ "fp_task_min": 5,
+ "fp_pp_path": "./",
+ "fp_pp_files": [
+ "POTCAR_H",
+ "POTCAR_C"
+ ],
+ "fp_incar": "./INCAR_methane"
+}
diff --git a/setup.py b/setup.py
index f86886544..e051389bf 100755
--- a/setup.py
+++ b/setup.py
@@ -17,7 +17,7 @@
with open(path.join('dpgen', '_date.py'), 'w') as fp :
fp.write('date = \'%s\'' % today)
-install_requires=['numpy>=1.14.3', 'dpdata>=0.1.14', 'pymatgen>=2019.1.13', 'ase', 'monty>2.0.0', 'paramiko', 'custodian','GromacsWrapper>=0.8.0', 'dpdispatcher>=0.3.11']
+install_requires=['numpy>=1.14.3', 'dpdata>=0.2.4', 'pymatgen>=2019.1.13', 'ase', 'monty>2.0.0', 'paramiko', 'custodian','GromacsWrapper>=0.8.0', 'dpdispatcher>=0.3.11']
setuptools.setup(
name=NAME,
diff --git a/tests/generator/out_data_post_fp_cp2k/02.fp/task.000.000000/output b/tests/generator/out_data_post_fp_cp2k/02.fp/task.000.000000/output
index 03543b509..9a5bdd19e 100644
--- a/tests/generator/out_data_post_fp_cp2k/02.fp/task.000.000000/output
+++ b/tests/generator/out_data_post_fp_cp2k/02.fp/task.000.000000/output
@@ -877,7 +877,7 @@
Total energy: -31.04389446913810
- *** WARNING in qs_scf.F:542 :: SCF run NOT converged ***
+ *** SCF run converged in 29 steps ***
!-----------------------------------------------------------------------------!
diff --git a/tests/generator/out_data_post_fp_cp2k/orig/energy.raw b/tests/generator/out_data_post_fp_cp2k/orig/energy.raw
index 48fcacaef..362e9a65e 100644
--- a/tests/generator/out_data_post_fp_cp2k/orig/energy.raw
+++ b/tests/generator/out_data_post_fp_cp2k/orig/energy.raw
@@ -1 +1 @@
--8.447581865210245269e+02
+-8.447582606992446017e+02
diff --git a/tests/generator/out_data_post_fp_cp2k/orig/force.raw b/tests/generator/out_data_post_fp_cp2k/orig/force.raw
index 6fa5a5550..0ad41126e 100644
--- a/tests/generator/out_data_post_fp_cp2k/orig/force.raw
+++ b/tests/generator/out_data_post_fp_cp2k/orig/force.raw
@@ -1 +1 @@
-6.917655894184945309e-01 7.553510274301609151e-01 2.274964525840567742e+00 -3.209682908751355646e-01 2.775192185863639693e-01 9.094058723076186013e-01 -6.332575659257858036e-02 -6.449617417274867703e-01 -8.145295946268114040e-01 -1.756150875299649639e-01 -3.121818029385921012e-01 -2.260577661002467487e+00 1.112470571386751095e+00 1.688658903147764123e+00 -1.721519658405964881e+00 -1.208800036573186576e+00 -1.778025306758221902e+00 1.601097413955125504e+00
+6.917656471387700901e-01 7.553510904559461725e-01 2.274964715661485837e+00 -3.209683176564304130e-01 2.775192417423087421e-01 9.094059481875964579e-01 -6.332576187642065257e-02 -6.449617955424929994e-01 -8.145296625904011600e-01 -1.756151021831240944e-01 -3.121818289867506202e-01 -2.260577849622959601e+00 1.112470664210258198e+00 1.688659044047888358e+00 -1.721519802047959624e+00 -1.208800137434334454e+00 -1.778025455114995435e+00 1.601097547549200639e+00
diff --git a/tests/generator/out_data_post_fp_cp2k/orig/type_map.raw b/tests/generator/out_data_post_fp_cp2k/orig/type_map.raw
index dc4df7f2f..101da0cbf 100644
--- a/tests/generator/out_data_post_fp_cp2k/orig/type_map.raw
+++ b/tests/generator/out_data_post_fp_cp2k/orig/type_map.raw
@@ -1 +1,3 @@
-C H N
+C
+H
+N
diff --git a/tests/generator/out_data_post_fp_gaussian/orig/energy.raw b/tests/generator/out_data_post_fp_gaussian/orig/energy.raw
index fd4a649a7..a0dea2026 100644
--- a/tests/generator/out_data_post_fp_gaussian/orig/energy.raw
+++ b/tests/generator/out_data_post_fp_gaussian/orig/energy.raw
@@ -1 +1 @@
--1102.7145808882785
+-1102.7145898692427
diff --git a/tests/generator/out_data_post_fp_gaussian/orig/nopbc b/tests/generator/out_data_post_fp_gaussian/orig/nopbc
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/generator/param-methane-abacus.json b/tests/generator/param-methane-abacus.json
index 2fca7d924..ab8c4d34e 100644
--- a/tests/generator/param-methane-abacus.json
+++ b/tests/generator/param-methane-abacus.json
@@ -131,17 +131,29 @@
"fp_task_max": 30,
"fp_task_min": 8,
"fp_pp_path": ".",
- "fp_pp_files": [ "H_HSCV_PBE-1.0.UPF","C_HSCV_PBE-1.0.UPF"],
+ "fp_pp_files": [ "./H_HSCV_PBE-1.0.UPF","./C_HSCV_PBE-1.0.UPF"],
"user_fp_params":{
+ "lattice_constant":1,
"ntype": 2,
"ecutwfc": 80,
- "mixing_type": "pulay",
+ "dr2": 1e-7,
+ "niter": 50,
+ "basis_type": "pw",
+ "gamma_only": true,
+ "dft_functional": "pbe",
+ "mixing_type": "pulay",
"mixing_beta": 0.4,
"symmetry": 1,
"nbands": 5,
"nspin": 1,
"ks_solver": "cg",
"smearing": "fixed",
- "sigma": 0.001
+ "sigma": 0.001,
+ "force":1,
+ "stress":1,
+ "out_descriptor":0,
+ "lmax_descriptor":0,
+ "deepks_scf":0,
+ "model_file":"model.ptg"
}
}
diff --git a/tests/generator/test_make_fp.py b/tests/generator/test_make_fp.py
index 914c9b149..1687b695d 100644
--- a/tests/generator/test_make_fp.py
+++ b/tests/generator/test_make_fp.py
@@ -150,19 +150,28 @@
IN.PSP3 = N.SG15.PBE.UPF\n";
abacus_input_ref = "INPUT_PARAMETERS\n\
+calculation scf\n\
ntype 2\n\
-pseudo_dir ./\n\
ecutwfc 80.000000\n\
+dr2 1.000000e-07\n\
+niter 50\n\
+basis_type pw\n\
+dft_functional pbe\n\
+gamma_only 1\n\
mixing_type pulay\n\
mixing_beta 0.400000\n\
symmetry 1\n\
-nbands 5.000000\n\
+nbands 5\n\
nspin 1\n\
ks_solver cg\n\
smearing fixed\n\
sigma 0.001000\n\
force 1\n\
-stress 1\n"
+stress 1\n\
+out_descriptor 0\n\
+lmax_descriptor 0\n\
+deepks_scf 0\n\
+model_file model.ptg\n"
abacus_kpt_ref = "K_POINTS\n\
0\n\
diff --git a/tests/generator/test_post_fp.py b/tests/generator/test_post_fp.py
index 8c14889f6..f0028db92 100644
--- a/tests/generator/test_post_fp.py
+++ b/tests/generator/test_post_fp.py
@@ -7,7 +7,7 @@
__package__ = 'generator'
from .context import post_fp
from .context import post_fp_pwscf
-from .context import post_fp_abacus_pw_scf
+from .context import post_fp_abacus_scf
from .context import post_fp_siesta
from .context import post_fp_vasp
from .context import post_fp_gaussian