Skip to content

Commit

Permalink
Merge branch 'devel' of ssh://115.27.161.2:/data1/anguse/yingze/dpgen…
Browse files Browse the repository at this point in the history 
… into devel
  • Loading branch information
@Ericwang6
Ericwang6 committed Aug 13, 2021
2 parents 06e5959 + cbdb486 commit 1e7e516
Show file tree
Hide file tree
Showing 4 changed files with 230 additions and 1 deletion.
2 changes: 1 addition & 1 deletion dpgen/generator/run.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1253,7 +1253,7 @@ def run_model_devi (iter_index,
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 += "&& dp model-devi -m ../graph.000.pb ../graph.001.pb ../graph.002.pb ../graph.003.pb -s traj_deepmd -o model_devi.out"
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" ]
Expand Down
0 ...les/run/dp1.x-gromacs-gaussian/param.json → ...recated/dp1.x-gromacs-gaussian/param.json
View file
File renamed without changes.
69 changes: 69 additions & 0 deletions examples/run/dp2.x-gromacs-gaussian/machine.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,69 @@
{
"deepmd_version" : "2.0",
"train": [
{
"machine": {
"batch": "slurm",
"work_path": "/work/path"
},
"resources": {
"numb_node": 1,
"numb_gpu": 1,
"partition": "all",
"time_limit": "120:0:0",
"task_per_node": 8,
"exclude_list": [],
"module_list": [],
"source_list": ["/path/to/dp-2.0.env"]
},
"command": "dp"
}
],
"model_devi": [
{
"machine": {
"batch": "slurm",
"work_path": "/work/path"
},
"resources": {
"numb_node": 1,
"numb_gpu": 1,
"partition": "all",
"time_limit": "120:0:0",
"task_per_node": 8,
"source_list": [
"/path/to/gromacs-dp/env"
],
"module_list": [],
"exclude_list": [],
"envs": {
"GMX_DEEPMD_INPUT_JSON": "input.json"
}
},
"command": "gmx_mpi",
"group_size": 1
}
],
"fp": [
{
"machine": {
"batch": "slurm",
"work_path": "/work/path"
},
"resources": {
"numb_node": 1,
"numb_gpu": 0,
"time_limit": "120:0:0",
"task_per_node": 28,
"partition": "cpu",
"exclude_list": [],
"source_list": [
"/path/to/gaussian/bashrc"
],
"module_list": []
},
"command": "g16 < input",
"group_size": 20
}
]
}
160 changes: 160 additions & 0 deletions examples/run/dp2.x-gromacs-gaussian/param.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,160 @@
{
"type_map": ["H", "C", "N", "O", "F", "S", "Cl"],
"mass_map": [2, 12, 14, 16, 17, 32, 35],
"init_data_prefix": "/path/to/init/data",
"init_data_sys": ["data.init"],
"init_multi_systems": true,
"sys_configs_prefix": "/path/to/model/devi/data",
"sys_configs": [
["model_devi/CHEMBL3402749_500"],
["model_devi/CHEMBL3402741_400"],
["model_devi/CHEMBL3402748_5300"],
["model_devi/CHEMBL3402743_42"],
["model_devi/CHEMBL3402761_1"],
["model_devi/CHEMBL3402756_2.7"],
["model_devi/CHEMBL3402750_400"],
["model_devi/CHEMBL3402764_90"],
["model_devi/CHEMBL3402758_10"],
["model_devi/CHEMBL3402754_40"],
["model_devi/CHEMBL3402747_3400"],
["model_devi/CHEMBL3402762_1"],
["model_devi/CHEMBL3402744_300"],
["model_devi/CHEMBL3402752_30000"],
["model_devi/CHEMBL3402742_23"],
["model_devi/CHEMBL3402759_5.7"],
["model_devi/CHEMBL3402745_200"],
["model_devi/CHEMBL3402757_6.5"],
["model_devi/CHEMBL3402755_4200"],
["model_devi/CHEMBL3402751_2100"],
["model_devi/CHEMBL3402753_200"],
["model_devi/CHEMBL3402763_90"],
["model_devi/CHEMBL3402765_11-charged-pKa-8.1"],
["model_devi/CHEMBL3402760_1"]
],
"sys_charges": [
0,
1,
0,
1,
0,
1,
0,
1,
1,
0,
0,
1,
0,
0,
1,
1,
0,
1,
0,
0,
0,
1,
1,
1
],
"sys_format": "gromacs/gro",
"numb_models": 4,
"training_reuse_iter": 1,
"training_reuse_old_ratio": 0.3,
"training_reuse_start_lr": 0.0001,
"training_reuse_decay_steps": 500,
"training_reuse_numb_steps": 200000,
"training_reuse_start_pref_e": 1,
"training_reuse_start_pref_f": 100,
"train_param": "input.json",
"default_training_param": {
"model": {
"type_map": ["H", "C", "N", "O", "F", "S", "Cl"],
"descriptor": {
"type": "se_e2_a",
"sel": [40, 48, 48, 48, 48, 48, 48],
"rcut_smth": 0.50,
"rcut": 6.00,
"neuron": [25, 50, 100],
"resnet_dt": false,
"axis_neuron": 16,
"type_one_side": true
},
"fitting_net": {
"neuron": [240, 240, 240],
"resnet_dt": true,
"type": "ener"
}
},
"learning_rate": {
"type": "exp",
"start_lr": 0.001,
"decay_steps": 5000
},
"loss": {
"start_pref_e": 0.02,
"limit_pref_e": 8,
"start_pref_f": 1000,
"limit_pref_f": 1,
"start_pref_v": 0,
"limit_pref_v": 0
},
"training": {
"numb_steps": 1000000,
"disp_file": "lcurve.out",
"disp_freq": 1000,
"numb_test": 1,
"save_freq": 1000,
"save_ckpt": "model.ckpt"
}
},
"model_devi_engine": "gromacs",
"gromacs_settings": {
"mdp_filename": "md.mdp",
"topol_filename": "processed.top",
"conf_filename": "npt.gro",
"index_filename": "index.raw",
"ref_filename": "em.tpr",
"model_devi_script": "model_devi.py",
"traj_filename": "deepmd_traj.gro",
"group_name": "Other"
},
"model_devi_dt": 0.001,
"model_devi_f_trust_lo": 0.20,
"model_devi_f_trust_hi": 0.60,
"model_devi_e_trust_lo": 1e10,
"model_devi_e_trust_hi": 1e10,
"model_devi_clean_traj": false,
"model_devi_skip": 0,
"model_devi_nopbc": true,
"model_devi_activation_func": [
["tanh", "tanh"],
["tanh", "tanh"],
["tanh", "tanh"],
["tanh", "tanh"]
],
"model_devi_jobs": [
{
"_idx": 0,
"ensemble": "nvt",
"nsteps": 100,
"press": [],
"sys_idx": [ 0, 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23],
"temps": [],
"trj_freq": 1
}
],
"fp_style": "gaussian",
"shuffle_poscar": false,
"fp_task_max": 50,
"fp_task_min": 1,
"fp_pp_path": "./",
"fp_pp_files": [],
"fp_params": {
"keywords": "force m062x/6-31** nosymm",
"nproc": 28,
"multiplicity": 1
}
}

0 comments on commit 1e7e516

Please sign in to comment.