Skip to content

Commit 1e7e516

Browse files
Ericwang6Ericwang6
committed
Merge branch 'devel' of ssh://115.27.161.2:/data1/anguse/yingze/dpgen into devel
2 parents 06e5959 + cbdb486 commit 1e7e516

File tree

4 files changed

+230
-1
lines changed

4 files changed

+230
-1
lines changed

‎dpgen/generator/run.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1253,7 +1253,7 @@ def run_model_devi (iter_index,
12531253
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)
12541254
command += "&& if [ ! -d traj ]; then \n mkdir traj; fi\n"
12551255
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')\""
1256-
command += "&& dp model-devi -m ../graph.000.pb ../graph.001.pb ../graph.002.pb ../graph.003.pb -s traj_deepmd -o model_devi.out"
1256+
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}"
12571257
commands = [command]
12581258

12591259
forward_files = [mdp_filename, topol_filename, conf_filename, index_filename, ref_filename, "input.json", "job.json" ]

examples/run/dp1.x-gromacs-gaussian/param.json renamed to examples/run/deprecated/dp1.x-gromacs-gaussian/param.json

File renamed without changes.

‎examples/run/dp2.x-gromacs-gaussian/machine.json‎

Lines changed: 69 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,69 @@
1+
{
2+
"deepmd_version" : "2.0",
3+
"train": [
4+
{
5+
"machine": {
6+
"batch": "slurm",
7+
"work_path": "/work/path"
8+
},
9+
"resources": {
10+
"numb_node": 1,
11+
"numb_gpu": 1,
12+
"partition": "all",
13+
"time_limit": "120:0:0",
14+
"task_per_node": 8,
15+
"exclude_list": [],
16+
"module_list": [],
17+
"source_list": ["/path/to/dp-2.0.env"]
18+
},
19+
"command": "dp"
20+
}
21+
],
22+
"model_devi": [
23+
{
24+
"machine": {
25+
"batch": "slurm",
26+
"work_path": "/work/path"
27+
},
28+
"resources": {
29+
"numb_node": 1,
30+
"numb_gpu": 1,
31+
"partition": "all",
32+
"time_limit": "120:0:0",
33+
"task_per_node": 8,
34+
"source_list": [
35+
"/path/to/gromacs-dp/env"
36+
],
37+
"module_list": [],
38+
"exclude_list": [],
39+
"envs": {
40+
"GMX_DEEPMD_INPUT_JSON": "input.json"
41+
}
42+
},
43+
"command": "gmx_mpi",
44+
"group_size": 1
45+
}
46+
],
47+
"fp": [
48+
{
49+
"machine": {
50+
"batch": "slurm",
51+
"work_path": "/work/path"
52+
},
53+
"resources": {
54+
"numb_node": 1,
55+
"numb_gpu": 0,
56+
"time_limit": "120:0:0",
57+
"task_per_node": 28,
58+
"partition": "cpu",
59+
"exclude_list": [],
60+
"source_list": [
61+
"/path/to/gaussian/bashrc"
62+
],
63+
"module_list": []
64+
},
65+
"command": "g16 < input",
66+
"group_size": 20
67+
}
68+
]
69+
}

‎examples/run/dp2.x-gromacs-gaussian/param.json‎

Lines changed: 160 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,160 @@
1+
{
2+
"type_map": ["H", "C", "N", "O", "F", "S", "Cl"],
3+
"mass_map": [2, 12, 14, 16, 17, 32, 35],
4+
"init_data_prefix": "/path/to/init/data",
5+
"init_data_sys": ["data.init"],
6+
"init_multi_systems": true,
7+
"sys_configs_prefix": "/path/to/model/devi/data",
8+
"sys_configs": [
9+
["model_devi/CHEMBL3402749_500"],
10+
["model_devi/CHEMBL3402741_400"],
11+
["model_devi/CHEMBL3402748_5300"],
12+
["model_devi/CHEMBL3402743_42"],
13+
["model_devi/CHEMBL3402761_1"],
14+
["model_devi/CHEMBL3402756_2.7"],
15+
["model_devi/CHEMBL3402750_400"],
16+
["model_devi/CHEMBL3402764_90"],
17+
["model_devi/CHEMBL3402758_10"],
18+
["model_devi/CHEMBL3402754_40"],
19+
["model_devi/CHEMBL3402747_3400"],
20+
["model_devi/CHEMBL3402762_1"],
21+
["model_devi/CHEMBL3402744_300"],
22+
["model_devi/CHEMBL3402752_30000"],
23+
["model_devi/CHEMBL3402742_23"],
24+
["model_devi/CHEMBL3402759_5.7"],
25+
["model_devi/CHEMBL3402745_200"],
26+
["model_devi/CHEMBL3402757_6.5"],
27+
["model_devi/CHEMBL3402755_4200"],
28+
["model_devi/CHEMBL3402751_2100"],
29+
["model_devi/CHEMBL3402753_200"],
30+
["model_devi/CHEMBL3402763_90"],
31+
["model_devi/CHEMBL3402765_11-charged-pKa-8.1"],
32+
["model_devi/CHEMBL3402760_1"]
33+
],
34+
"sys_charges": [
35+
0,
36+
1,
37+
0,
38+
1,
39+
0,
40+
1,
41+
0,
42+
1,
43+
1,
44+
0,
45+
0,
46+
1,
47+
0,
48+
0,
49+
1,
50+
1,
51+
0,
52+
1,
53+
0,
54+
0,
55+
0,
56+
1,
57+
1,
58+
1
59+
],
60+
"sys_format": "gromacs/gro",
61+
"numb_models": 4,
62+
"training_reuse_iter": 1,
63+
"training_reuse_old_ratio": 0.3,
64+
"training_reuse_start_lr": 0.0001,
65+
"training_reuse_decay_steps": 500,
66+
"training_reuse_numb_steps": 200000,
67+
"training_reuse_start_pref_e": 1,
68+
"training_reuse_start_pref_f": 100,
69+
"train_param": "input.json",
70+
"default_training_param": {
71+
"model": {
72+
"type_map": ["H", "C", "N", "O", "F", "S", "Cl"],
73+
"descriptor": {
74+
"type": "se_e2_a",
75+
"sel": [40, 48, 48, 48, 48, 48, 48],
76+
"rcut_smth": 0.50,
77+
"rcut": 6.00,
78+
"neuron": [25, 50, 100],
79+
"resnet_dt": false,
80+
"axis_neuron": 16,
81+
"type_one_side": true
82+
},
83+
"fitting_net": {
84+
"neuron": [240, 240, 240],
85+
"resnet_dt": true,
86+
"type": "ener"
87+
}
88+
},
89+
"learning_rate": {
90+
"type": "exp",
91+
"start_lr": 0.001,
92+
"decay_steps": 5000
93+
},
94+
"loss": {
95+
"start_pref_e": 0.02,
96+
"limit_pref_e": 8,
97+
"start_pref_f": 1000,
98+
"limit_pref_f": 1,
99+
"start_pref_v": 0,
100+
"limit_pref_v": 0
101+
},
102+
"training": {
103+
"numb_steps": 1000000,
104+
"disp_file": "lcurve.out",
105+
"disp_freq": 1000,
106+
"numb_test": 1,
107+
"save_freq": 1000,
108+
"save_ckpt": "model.ckpt"
109+
}
110+
},
111+
"model_devi_engine": "gromacs",
112+
"gromacs_settings": {
113+
"mdp_filename": "md.mdp",
114+
"topol_filename": "processed.top",
115+
"conf_filename": "npt.gro",
116+
"index_filename": "index.raw",
117+
"ref_filename": "em.tpr",
118+
"model_devi_script": "model_devi.py",
119+
"traj_filename": "deepmd_traj.gro",
120+
"group_name": "Other"
121+
},
122+
"model_devi_dt": 0.001,
123+
"model_devi_f_trust_lo": 0.20,
124+
"model_devi_f_trust_hi": 0.60,
125+
"model_devi_e_trust_lo": 1e10,
126+
"model_devi_e_trust_hi": 1e10,
127+
"model_devi_clean_traj": false,
128+
"model_devi_skip": 0,
129+
"model_devi_nopbc": true,
130+
"model_devi_activation_func": [
131+
["tanh", "tanh"],
132+
["tanh", "tanh"],
133+
["tanh", "tanh"],
134+
["tanh", "tanh"]
135+
],
136+
"model_devi_jobs": [
137+
{
138+
"_idx": 0,
139+
"ensemble": "nvt",
140+
"nsteps": 100,
141+
"press": [],
142+
"sys_idx": [ 0, 1, 2, 3, 4, 5, 6, 7,
143+
8, 9, 10, 11, 12, 13, 14, 15,
144+
16, 17, 18, 19, 20, 21, 22, 23],
145+
"temps": [],
146+
"trj_freq": 1
147+
}
148+
],
149+
"fp_style": "gaussian",
150+
"shuffle_poscar": false,
151+
"fp_task_max": 50,
152+
"fp_task_min": 1,
153+
"fp_pp_path": "./",
154+
"fp_pp_files": [],
155+
"fp_params": {
156+
"keywords": "force m062x/6-31** nosymm",
157+
"nproc": 28,
158+
"multiplicity": 1
159+
}
160+
}

0 commit comments

Comments
 (0)