ValueError: 'S' is not in list

[phyoung123]

Dear all,
I have successfully tested the CH4 example provided in the dpGEN's Github, but an error occurs when i turn the focus to Si and Al, the error infos are 'ValueError: 'S' is not in list' for Si, and 'ValueError: 'A' is not in list' for Al. I cannot figure out what parameter is improper in my input files, any advices provided here are appreciated.

here is the param.json

{
"type_map": [
"Si"
],
"mass_map": [
28
],
"init_data_prefix": "./",
"init_data_sys": [
"POSCAR.02x02x02/02.md/sys-0016/deepmd"
],
"sys_configs_prefix": "./",
"sys_configs": [
[
"POSCAR.02x02x02/01.scale_pert/sys-0016/scale-1.000/00000*/POSCAR"
],
[
"POSCAR.02x02x02/01.scale_pert/sys-0016/scale-1.000/00001*/POSCAR"
]
],
"_comment": " that's all ",
"numb_models": 4,
"default_training_param": {
"model": {
"type_map": [
"Si"
],
"descriptor": {
"type": "se_a",
"sel": [
30
],
"rcut_smth": 0.5,
"rcut": 5.0,
"neuron": [
25,
50,
100
],
"resnet_dt": false,
"axis_neuron": 12,
"seed": 1
},
"fitting_net": {
"neuron": [
120,
120,
120
],
"resnet_dt": true,
"seed": 1
}
},
"learning_rate": {
"type": "exp",
"start_lr": 0.001,
"decay_steps": 100,
"decay_rate":0.95
},
"loss": {
"start_pref_e": 0.02,
"limit_pref_e": 1,
"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": 100,
"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"
],
"fp_incar": "./INCAR_fp"
}

the train.log as follow

WARNING:tensorflow:From /apps/users/caep-lzg/package/anaconda/envs/deepmd/lib/python3.9/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
WARNING:root:Environment variable KMP_BLOCKTIME is empty. Use the default value 0
WARNING:root:Environment variable KMP_AFFINITY is empty. Use the default value granularity=fine,verbose,compact,1,0
/apps/users/caep-lzg/package/anaconda/envs/deepmd/lib/python3.9/importlib/init.py:169: UserWarning: The NumPy module was reloaded (imported a second time). This can in some cases result in small but subtle issues and is discouraged.
_bootstrap.exec(spec, module)
/apps/users/caep-lzg/package/anaconda/envs/deepmd/lib/python3.9/site-packages/deepmd/utils/compat.py:316: UserWarning: It seems that you are using a deepmd-kit input of version 1.x.x, which is deprecated. we have converted the input to >2.0.0 compatible, and output it to file input_v2_compat.json
warnings.warn(msg)
Traceback (most recent call last):
File "/apps/users/caep-lzg/package/anaconda/envs/deepmd/bin/dp", line 10, in
sys.exit(main())
File "/apps/users/caep-lzg/package/anaconda/envs/deepmd/lib/python3.9/site-packages/deepmd/entrypoints/main.py", line 437, in main
train_dp(**dict_args)
File "/apps/users/caep-lzg/package/anaconda/envs/deepmd/lib/python3.9/site-packages/deepmd/entrypoints/train.py", line 91, in train
jdata = update_sel(jdata)
File "/apps/users/caep-lzg/package/anaconda/envs/deepmd/lib/python3.9/site-packages/deepmd/entrypoints/train.py", line 341, in update_sel
descrpt_data = update_one_sel(jdata, descrpt_data)
File "/apps/users/caep-lzg/package/anaconda/envs/deepmd/lib/python3.9/site-packages/deepmd/entrypoints/train.py", line 317, in update_one_sel
tmp_sel = get_sel(jdata, rcut)
File "/apps/users/caep-lzg/package/anaconda/envs/deepmd/lib/python3.9/site-packages/deepmd/entrypoints/train.py", line 280, in get_sel
, max_nbor_size = get_nbor_stat(jdata, rcut)
File "/apps/users/caep-lzg/package/anaconda/envs/deepmd/lib/python3.9/site-packages/deepmd/entrypoints/train.py", line 255, in get_nbor_stat
train_data = get_data(jdata["training"]["training_data"], max_rcut, type_map, None)
File "/apps/users/caep-lzg/package/anaconda/envs/deepmd/lib/python3.9/site-packages/deepmd/entrypoints/train.py", line 199, in get_data
data = DeepmdDataSystem(
File "/apps/users/caep-lzg/package/anaconda/envs/deepmd/lib/python3.9/site-packages/deepmd/utils/data_system.py", line 79, in init
DeepmdData(
File "/apps/users/caep-lzg/package/anaconda/envs/deepmd/lib/python3.9/site-packages/deepmd/utils/data.py", line 62, in init
atom_type = [type_map.index(self.type_map[ii]) for ii in self.atom_type]
File "/apps/users/caep-lzg/package/anaconda/envs/deepmd/lib/python3.9/site-packages/deepmd/utils/data.py", line 62, in
atom_type = [type_map.index(self.type_map[ii]) for ii in self.atom_type]
ValueError: 'S' is not in list

Thanks in advance.

caep-feiyang

[njzjz]

This should have been fixed in deepmodeling/deepmd-kit#1196.

[phyoung123]

Thanks, now it works