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Update CP2K new example and slurm-lsf-mix machine (#456)
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‎examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json‎

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{
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"train": [
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{
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"machine": {
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"machine_type": "slurm",
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"hostname": "210.34.15.205",
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"port": 22,
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"username": "ybzhuang",
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"work_path": "/home/ybzhuang/workdir"
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},
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"resources": {
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"numb_gpu": 1,
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"numb_node": 1,
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"task_per_node": 1,
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"partition": "gpu",
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"job_name": "train",
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"qos":"emergency",
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"exclude_list": [],
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"source_list": [
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],
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"module_list": [
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"deepmd/1.2"
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],
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"time_limit": "96:0:0",
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"submit_wait_time": 60
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},
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"python_path": "/share/apps/deepmd/compress/bin/python3.8"
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}
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],
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"model_devi": [
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{
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"machine": {
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"machine_type": "slurm",
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"hostname": "210.34.15.205",
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"port": 22,
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"username": "ybzhuang",
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"work_path": "/home/ybzhuang/workdir"
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},
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"resources": {
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"numb_gpu": 1,
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"numb_node": 1,
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"task_per_node": 1,
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"partition": "gpu",
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"job_name": "md",
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"qos":"emergency",
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"exclude_list": [],
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"source_list": [
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],
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"module_list": [
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"deepmd/1.2"
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],
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"time_limit": "96:0:0",
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"submit_wait_time": 60
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},
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"command": "lmp_mpi",
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"group_size": 5
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}
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],
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"fp": [
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{
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"machine": {
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"machine_type": "lsf",
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"hostname": "localhost",
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"port": 6666,
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"username": "ybzhuang",
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"work_path": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/workpath"
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},
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"resources": {
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"cvasp": false,
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"task_per_node": 32,
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"numb_node": 1,
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"node_cpu": 32,
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"exclude_list": [],
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"with_mpi": true,
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"source_list": [
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],
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"module_list": [
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"intel/17.5.239",
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"mpi/intel/2017.5.239",
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"gcc/5.5.0",
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"cp2k/7.1"
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],
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"time_limit": "12:00:00",
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"partition": "53-medium",
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"_comment": "that's Bel"
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},
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"command": "cp2k.popt -i input.inp",
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"group_size": 50
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}
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]
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}

‎examples/run/dp1.x-lammps-cp2k/methane/param-ch4.json‎

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{
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"type_map": [
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"H",
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"C"
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],
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"mass_map": [
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1,
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12
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],
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"init_data_prefix": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/data",
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"init_data_sys": [
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"deepmd"
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],
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"init_batch_size": [
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8
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],
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"sys_configs": [
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["/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR"],
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["/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR"]
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],
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"sys_batch_size": [
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8,
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8,
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8,
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8
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],
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"_comment": " that's all ",
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"numb_models": 4,
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"train_param": "input.json",
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"default_training_param": {
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"model": {
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"descriptor": {
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"type": "se_a",
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"sel": [
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16,
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4
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],
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"rcut_smth": 0.5,
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"rcut": 5.0,
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"_comment": "modify according your system",
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"neuron": [
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10,
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20,
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40
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],
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"resnet_dt": false,
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"axis_neuron": 12,
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"seed": 1
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},
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"fitting_net": {
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"n_neuron": [
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120,
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120,
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120
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],
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"resnet_dt": true,
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"seed": 1
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}},
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"learning_rate": {
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"type": "exp",
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"start_lr": 0.001,
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"decay_steps": 100,
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"_comment": "nope",
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"decay_rate": 0.95
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},
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"loss": {
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"start_pref_e": 0.02,
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"limit_pref_e": 2,
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"start_pref_f": 1000,
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"limit_pref_f": 1,
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"start_pref_v": 0.0,
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"limit_pref_v": 0.0
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},
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"training": {
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"systems": [ ],
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"set_prefix": "set",
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"stop_batch": 2000,
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"batch_size": 1,
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"seed": 1,
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"disp_file": "lcurve.out",
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"disp_freq": 1000,
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"numb_test": 4,
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"save_freq": 1000,
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"save_ckpt": "model.ckpt",
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"load_ckpt": "model.ckpt",
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"disp_training": true,
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"time_training": true,
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"profiling": false,
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"profiling_file": "timeline.json"
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}
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},
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"model_devi_dt": 0.002,
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"model_devi_skip": 0,
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"model_devi_f_trust_lo": 0.05,
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"model_devi_f_trust_hi": 0.15,
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"model_devi_clean_traj": true,
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"model_devi_jobs": [
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{
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"sys_idx": [
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0
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],
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"temps": [
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100
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],
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"press": [
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1
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],
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"trj_freq": 10,
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"nsteps": 300,
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"ensemble": "nvt",
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"_idx": "00"
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},
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{
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"sys_idx": [
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1
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],
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"temps": [
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100
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],
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"press": [
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1
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],
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"trj_freq": 10,
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"nsteps": 3000,
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"ensemble": "nvt",
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"_idx": "01"
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}
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],
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"fp_style": "cp2k",
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"shuffle_poscar": false,
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"fp_task_max": 20,
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"fp_task_min": 5,
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"fp_pp_path": ".",
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"fp_pp_files": [],
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"external_input_path": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/cp2k_dpgen/template.inp"
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}

‎examples/run/dp1.x-lammps-cp2k/methane/template.inp‎

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#Basis setting
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@SET SCALE_FACTOR 1.000
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@SET NREPA 1
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@SET NREPB 1
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@SET NREPC 1
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@SET CELL_A 10
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@SET CELL_B 10
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@SET CELL_C 10
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@SET ANGLE_A 90.0
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@SET ANGLE_B 90.0
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@SET ANGLE_C 90.0
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@SET COORDFILE coord.xyz
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@SET CUTOFF 400
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@SET JOBNAME DPGEN
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&FORCE_EVAL
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METHOD QS
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STRESS_TENSOR ANALYTICAL
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&PRINT
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&FORCES ON
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&END FORCES
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&STRESS_TENSOR ON
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&END STRESS_TENSOR
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&END PRINT
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&DFT
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BASIS_SET_FILE_NAME BASIS_MOLOPT
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POTENTIAL_FILE_NAME GTH_POTENTIALS
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&MGRID
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CUTOFF ${CUTOFF}
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REL_CUTOFF 60
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&END MGRID
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&QS
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EPS_DEFAULT 1.0E-13
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&END QS
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&SCF
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SCF_GUESS RESTART
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EPS_SCF 3.0E-7
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MAX_SCF 50
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&OUTER_SCF
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EPS_SCF 3.0E-7
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MAX_SCF 15
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&END OUTER_SCF
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&OT
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MINIMIZER DIIS
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PRECONDITIONER FULL_SINGLE_INVERSE
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&END OT
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&END SCF
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&XC
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########## This part is PBE ##########
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&XC_FUNCTIONAL PBE
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&END XC_FUNCTIONAL
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########## This part is PBE ##########
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&END XC
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########## This part controls the print information ##########
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&END DFT
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&SUBSYS
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&CELL
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ABC [angstrom] ${CELL_A}*${SCALE_FACTOR} ${CELL_B}*${SCALE_FACTOR} ${CELL_C}*${SCALE_FACTOR}
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ALPHA_BETA_GAMMA ${ANGLE_A} ${ANGLE_B} ${ANGLE_C}
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MULTIPLE_UNIT_CELL ${NREPA} ${NREPB} ${NREPC}
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&END CELL
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&TOPOLOGY
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MULTIPLE_UNIT_CELL ${NREPA} ${NREPB} ${NREPC}
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&END TOPOLOGY
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&COORD
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@include ${COORDFILE}
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&END COORD
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&KIND H
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BASIS_SET DZVP-MOLOPT-SR-GTH
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POTENTIAL GTH-PBE-q1
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&END KIND
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&KIND C
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BASIS_SET DZVP-MOLOPT-SR-GTH
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POTENTIAL GTH-PBE-q4
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&END KIND
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&END SUBSYS
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&END FORCE_EVAL
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&GLOBAL
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PROJECT ${JOBNAME}
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&END GLOBAL

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