From 2a25606a790824ea8f4136bb942066f2fe25d062 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Mon, 28 Aug 2023 06:15:06 -0400 Subject: [PATCH] update deepmd input to v2; format JSON files (#1315) This PR updates all JSON files: - convert `default_training_param` to v2 format - format JSON files - update `_comment` to `_commentN` to avoid duplicated keys - enable `check-json` and `pretty-format-json` hooks ```py import json from glob import glob from deepmd.utils.compat import update_deepmd_input, convert_input_v1_v2 for ii in glob("**/*.json", recursive=True): with open(ii) as f: content = f.read() count = 1 while True: if r'"_comment"' not in content: break content = content.replace('"_comment"', '"_comment%d"' % count, 1) count += 1 try: jdata = json.loads(content) except Exception as e: print(ii, e) continue if "default_training_param" in jdata: jdata["default_training_param"] = update_deepmd_input( jdata["default_training_param"], warning=False) if "decay_rate" in jdata["default_training_param"]["learning_rate"]: jdata["default_training_param"] = convert_input_v1_v2( jdata["default_training_param"], warning=False) if "load_ckpt" in jdata["default_training_param"]["training"]: del jdata["default_training_param"]["training"]["load_ckpt"] content = json.dumps(jdata, indent=2) with open(ii, "w") as f: f.write(content) ``` --------- Signed-off-by: Jinzhe Zeng Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 10 +- doc/simplify/simplify.md | 5 +- dpgen/data/jsons/al.diamond.111.json | 54 +- dpgen/data/jsons/al.diamond.222.json | 54 +- dpgen/data/jsons/al.fcc.111.json | 54 +- dpgen/data/jsons/al.fcc.222.json | 54 +- dpgen/data/jsons/al.hcp.111.json | 54 +- dpgen/data/jsons/al.hcp.222.json | 54 +- dpgen/data/jsons/al.hcp.332.json | 54 +- dpgen/data/jsons/al.sc.222.json | 54 +- dpgen/data/jsons/almg.diamond.111.json | 57 +- dpgen/data/jsons/almg.diamond.222.json | 57 +- dpgen/data/jsons/almg.fcc.111.json | 57 +- dpgen/data/jsons/almg.fcc.222.json | 57 +- dpgen/data/jsons/almg.hcp.111.json | 57 +- dpgen/data/jsons/almg.hcp.222.json | 57 +- dpgen/data/jsons/almg.hcp.332.json | 57 +- dpgen/data/jsons/almg.sc.222.json | 57 +- dpgen/data/jsons/almg.sc.333.json | 57 +- dpgen/data/jsons/mg.diamond.111.json | 54 +- dpgen/data/jsons/mg.diamond.222.json | 54 +- dpgen/data/jsons/mg.fcc.111.json | 54 +- dpgen/data/jsons/mg.fcc.222.json | 54 +- dpgen/data/jsons/mg.hcp.111.json | 54 +- dpgen/data/jsons/mg.hcp.222.json | 50 +- dpgen/data/jsons/mg.hcp.332.json | 50 +- dpgen/data/jsons/mg.sc.222.json | 54 +- dpgen/data/jsons/param.json | 58 +- dpgen/data/jsons/si.diamond.111.json | 54 +- dpgen/data/jsons/si.diamond.222.json | 54 +- dpgen/data/jsons/si.fcc.111.json | 54 +- dpgen/data/jsons/si.fcc.222.json | 54 +- dpgen/data/jsons/si.hcp.111.json | 54 +- dpgen/data/jsons/si.hcp.222.json | 54 +- dpgen/data/jsons/si.sc.222.json | 54 +- dpgen/data/jsons/surf.al.fcc.json | 62 +- dpgen/data/jsons/surf.al.hcp.json | 62 +- dpgen/data/jsons/surf.almg.fcc.json | 65 +- dpgen/data/jsons/surf.almg.hcp.json | 65 +- dpgen/data/jsons/surf.mg.fcc.json | 62 +- dpgen/data/jsons/surf.mg.hcp.json | 62 +- dpgen/data/jsons/surf.si.diamond.json | 82 +- dpgen/data/jsons/w.bcc.111.json | 58 +- dpgen/data/jsons/w.bcc.222.json | 58 +- dpgen/data/jsons/w.diamond.111.json | 58 +- dpgen/data/jsons/w.fcc.111.json | 58 +- dpgen/data/jsons/w.hcp.111.json | 58 +- dpgen/data/jsons/water.111.json | 62 +- .../CH4-refact-dpdispatcher/INCAR_methane | 2 +- .../machine-ali-ehpc.json | 163 ++-- .../machine-dpcloudserver.json | 225 +++-- .../param_CH4_deepmd-kit-1.1.0.json | 1 - .../param_CH4_deepmd-kit-2.x.json | 1 + examples/database/param_Ti.json | 115 ++- examples/init/abacus/CuW/CuW.json | 27 +- examples/init/abacus/fcc-Al-lcao/init.json | 61 +- examples/init/abacus/fcc-Al-lcao/machine.json | 201 ++-- examples/init/abacus/fcc-Al-pw/init.json | 55 +- examples/init/abacus/fcc-Al-pw/machine.json | 201 ++-- examples/init/al.json | 2 +- examples/init/ch4.json | 51 +- examples/init/cu.surf.hcp.111.json | 107 ++- examples/init/surf.json | 104 +- .../DeePMD-kit-1.0/machine-local-4GPU.json | 26 +- .../machine/DeePMD-kit-1.x/machine-local.json | 10 +- .../DeePMD-kit-1.x/machine-slurm-qe.json | 26 +- .../DeePMD-kit-2.x/lebesgue_v2_machine.json | 191 ++-- examples/run/ch4/machine.json | 134 +-- examples/run/ch4/param.json | 297 +++--- .../dp0.12-lammps-cp2k/CH4/param_CH4.json | 136 --- .../machine-slurm-pwmat-single.json | 80 -- .../dp0.12-lammps-pwmat/param_CH4.json | 97 -- .../dp-lammps-siesta/CH4/param_CH4.json | 134 --- .../Al/param_al_all_gpu.json | 393 -------- .../dp0.12-lammps-vasp/CH4/param_CH4.json | 98 -- .../dp1.x-gromacs-gaussian/param.json | 176 ---- .../dp2.x-gromacs-gaussian/param.json | 209 ++++ .../dp2.x-lammps-cp2k/CH4/param_CH4.json | 156 +++ .../CH4/param_CH4.yaml | 1 - .../machine-slurm-pwmat-single.json | 80 ++ .../dp2.x-lammps-pwmat/param_CH4.json | 147 +++ .../dp-lammps-siesta/CH4/param_CH4.json | 148 +++ .../dp-lammps-siesta/CH4/param_CH4.yaml | 1 - .../Al/param_al_all_gpu.json | 450 +++++++++ .../Al/param_al_all_gpu.yaml | 1 - .../dp2.x-lammps-vasp/CH4/param_CH4.json | 146 +++ .../CH4/param_CH4.yaml | 1 - .../run/deprecated/param-h2oscan-vasp.json | 891 ++++++++++++++---- .../run/deprecated/param-mg-vasp-ucloud.json | 602 +++++++++--- examples/run/deprecated/param-mg-vasp.json | 615 +++++++++--- .../run/deprecated/param-pyridine-pwscf.json | 427 ++++++--- examples/run/dp-calypso-vasp/machine.json | 148 +-- examples/run/dp-calypso-vasp/param.json | 465 +++++++-- .../run/dp-lammps-enhance_sampling/param.json | 335 ++++--- .../methane/machine.json | 75 -- .../methane/param.json | 150 --- .../methane/machine.json | 75 -- .../dp1.x-lammps-ABACUS-pw/methane/param.json | 144 --- .../dp1.x-lammps-cp2k/methane/param-ch4.json | 134 --- .../run/dp1.x-lammps-vasp-et/param_elet.json | 99 -- .../Al/param_al_all_gpu-deepmd-kit-1.1.0.json | 371 -------- .../dodecane/dodecane.json | 84 -- .../run/dp2.x-gromacs-gaussian/param.json | 428 ++++++--- .../methane/machine.json | 85 ++ .../methane/param.json | 171 ++++ .../fcc-al/machine.json | 186 ++-- .../fcc-al/run_param.json | 85 +- .../fcc-al/machine.json | 186 ++-- .../fcc-al/run_param.json | 9 +- .../methane/machine.json | 85 ++ .../dp2.x-lammps-ABACUS-pw/methane/param.json | 162 ++++ .../dp2.x-lammps-cp2k/methane/param-ch4.json | 138 +++ .../methane/template.inp | 0 .../param_CH4_deepmd-kit-2.0.1.json | 33 +- .../run/dp2.x-lammps-gaussian/machine.json | 198 ++-- .../param_C4H16N4_deepmd-kit-2.0.1.json | 34 +- .../run/dp2.x-lammps-vasp-et/param_elet.json | 131 +++ .../Al/param_al_all_gpu-deepmd-kit-2.x.json | 430 +++++++++ .../CH4/INCAR_methane | 0 .../CH4/POT_C | 0 .../CH4/POT_H | 0 .../CH4/param_CH4_deepmd-kit-2.x.json} | 16 +- .../param_CH4_deepmd-kit-2.0.1.json | 5 +- .../dodecane/dodecane.json | 152 +++ .../simplify_example/machine.json | 194 ++-- .../simplify_example/simplify.json | 231 +++-- examples/simplify/qm7.json | 31 +- examples/test/deepmd_param.json | 29 +- examples/test/meam_param.json | 29 +- examples/test/vasp_param.json | 105 +-- examples/test/vasp_param_from_incar.json | 26 +- tests/auto_test/equi/abacus/cell-relax.json | 2 +- tests/auto_test/equi/vasp/Al-fcc.json | 2 +- tests/auto_test/equi/vasp/outcar.json | 2 +- .../output/gamma_00/task.000000/inter.json | 2 +- .../output/gamma_00/task.000000/miller.json | 6 +- .../gamma_00/task.000000/result_task.json | 2 +- .../output/gamma_00/task.000000/task.json | 2 +- .../output/gamma_00/task.000001/inter.json | 2 +- .../output/gamma_00/task.000001/miller.json | 6 +- .../gamma_00/task.000001/result_task.json | 2 +- .../output/gamma_00/task.000001/task.json | 2 +- .../output/gamma_00/task.000002/inter.json | 2 +- .../output/gamma_00/task.000002/miller.json | 6 +- .../gamma_00/task.000002/result_task.json | 2 +- .../output/gamma_00/task.000002/task.json | 2 +- .../output/relaxation/relax_task/result.json | 2 +- tests/data/CuW.json | 21 +- tests/data/al.json | 47 +- tests/data/alloy.json | 46 +- tests/data/ch4.json | 62 +- tests/data/surf.json | 88 +- tests/data/surf_poscar.json | 85 +- tests/database/param_Al.json | 115 ++- .../gromacs/model_devi_case/input.json | 2 +- tests/generator/machine-local-v1.json | 63 +- tests/generator/machine-local.json | 101 +- .../02.fp/task.000.000000/job.json | 4 +- .../02.fp/task.000.000001/job.json | 4 +- .../02.fp/task.001.000000/job.json | 4 +- .../02.fp/task.001.000001/job.json | 4 +- tests/generator/param-amber.json | 22 +- tests/generator/param-custom-fp.json | 418 ++++++-- tests/generator/param-methane-abacus-diy.json | 290 +++--- tests/generator/param-methane-abacus.json | 332 ++++--- tests/generator/param-mg-vasp-diy.json | 210 +++-- .../generator/param-mg-vasp-multi-trust.json | 260 ++--- tests/generator/param-mg-vasp-old.json | 240 +++-- tests/generator/param-mg-vasp-v1-et.json | 220 +++-- tests/generator/param-mg-vasp-v1.json | 218 +++-- tests/generator/param-mg-vasp.json | 248 +++-- tests/generator/param-mg-vasp_merge_traj.json | 246 +++-- tests/generator/param-mgo-cp2k-exinput.json | 408 ++++++-- tests/generator/param-pyridine-cp2k.json | 443 ++++++--- tests/generator/param-pyridine-gaussian.json | 414 ++++++-- tests/generator/param-pyridine-pwmat.json | 447 ++++++--- tests/generator/param-pyridine-pwscf-old.json | 428 ++++++--- tests/generator/param-pyridine-pwscf.json | 454 ++++++--- tests/generator/param-pyridine-siesta.json | 424 +++++++-- tests/sample.json | 4 +- tests/test_check_examples.py | 28 +- tests/tools/machine_fp_single.json | 28 +- tests/tools/machine_fp_single2.json | 25 +- tests/tools/run_report_test_output/param.json | 207 ++-- 184 files changed, 13612 insertions(+), 7972 deletions(-) delete mode 120000 examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-1.1.0.json create mode 120000 examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-2.x.json delete mode 100644 examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.json delete mode 100644 examples/run/deprecated/dp0.12-lammps-pwmat/machine-slurm-pwmat-single.json delete mode 100644 examples/run/deprecated/dp0.12-lammps-pwmat/param_CH4.json delete mode 100644 examples/run/deprecated/dp0.12-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json delete mode 100644 examples/run/deprecated/dp0.12-lammps-vasp/Al/param_al_all_gpu.json delete mode 100644 examples/run/deprecated/dp0.12-lammps-vasp/CH4/param_CH4.json delete mode 100644 examples/run/deprecated/dp1.x-gromacs-gaussian/param.json create mode 100644 examples/run/deprecated/dp2.x-gromacs-gaussian/param.json create mode 100644 examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json rename examples/run/deprecated/{dp0.12-lammps-cp2k => dp2.x-lammps-cp2k}/CH4/param_CH4.yaml (98%) create mode 100644 examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json create mode 100644 examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json create mode 100644 examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json rename examples/run/deprecated/{dp0.12-lammps-siesta => dp2.x-lammps-siesta}/dp-lammps-siesta/CH4/param_CH4.yaml (98%) create mode 100644 examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.json rename examples/run/deprecated/{dp0.12-lammps-vasp => dp2.x-lammps-vasp}/Al/param_al_all_gpu.yaml (99%) create mode 100644 examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.json rename examples/run/deprecated/{dp0.12-lammps-vasp => dp2.x-lammps-vasp}/CH4/param_CH4.yaml (98%) delete mode 100644 examples/run/dp1.x-lammps-ABACUS-lcao-dpks/methane/machine.json delete mode 100644 examples/run/dp1.x-lammps-ABACUS-lcao-dpks/methane/param.json delete mode 100644 examples/run/dp1.x-lammps-ABACUS-pw/methane/machine.json delete mode 100644 examples/run/dp1.x-lammps-ABACUS-pw/methane/param.json delete mode 100644 examples/run/dp1.x-lammps-cp2k/methane/param-ch4.json delete mode 100644 examples/run/dp1.x-lammps-vasp-et/param_elet.json delete mode 100644 examples/run/dp1.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json delete mode 100644 examples/run/dp1.x_lammps_gaussian/dodecane/dodecane.json create mode 100644 examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/machine.json create mode 100644 examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/param.json create mode 100644 examples/run/dp2.x-lammps-ABACUS-pw/methane/machine.json create mode 100644 examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json create mode 100644 examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json rename examples/run/{dp1.x-lammps-cp2k => dp2.x-lammps-cp2k}/methane/template.inp (100%) create mode 100644 examples/run/dp2.x-lammps-vasp-et/param_elet.json create mode 100644 examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-2.x.json rename examples/run/{dp1.x-lammps-vasp => dp2.x-lammps-vasp}/CH4/INCAR_methane (100%) rename examples/run/{dp1.x-lammps-vasp => dp2.x-lammps-vasp}/CH4/POT_C (100%) rename examples/run/{dp1.x-lammps-vasp => dp2.x-lammps-vasp}/CH4/POT_H (100%) rename examples/run/{dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json => dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json} (89%) create mode 100644 examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 078492395..904018833 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,12 +12,20 @@ repos: exclude: "^tests/.*$" - id: check-yaml exclude: "^conda/.*$" - #- id: check-json + - id: check-json + exclude: "^examples/CH4-lebesgue/.*$" - id: check-added-large-files - id: check-merge-conflict - id: check-symlinks exclude: "^tests/tools/run_report_test_output/.*$" - id: check-toml + - id: pretty-format-json + args: + - "--autofix" + - "--no-sort-keys" + - "--indent=4" + exclude: "^examples/CH4-lebesgue/.*$" + # Python - repo: https://github.com/psf/black rev: 23.7.0 diff --git a/doc/simplify/simplify.md b/doc/simplify/simplify.md index c462c85df..8a1fa6dec 100644 --- a/doc/simplify/simplify.md +++ b/doc/simplify/simplify.md @@ -70,7 +70,7 @@ Here is an example of `param.json` for QM7 dataset: "learning_rate": { "type": "exp", "start_lr": 0.001, - "decay_steps": 10, + "stop_lr": 5e-8, "decay_rate": 0.99 }, "loss": { @@ -85,12 +85,11 @@ Here is an example of `param.json` for QM7 dataset: }, "training": { "set_prefix": "set", - "stop_batch": 10000, + "numb_steps": 10000, "disp_file": "lcurve.out", "disp_freq": 1000, "numb_test": 1, "save_freq": 1000, - "save_ckpt": "model.ckpt", "disp_training": true, "time_training": true, "profiling": false, diff --git a/dpgen/data/jsons/al.diamond.111.json b/dpgen/data/jsons/al.diamond.111.json index ff015329f..8fe91110c 100644 --- a/dpgen/data/jsons/al.diamond.111.json +++ b/dpgen/data/jsons/al.diamond.111.json @@ -1,22 +1,36 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [1, 1, 1], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.diamond.222.json b/dpgen/data/jsons/al.diamond.222.json index 693390f4c..ef9ff78c7 100644 --- a/dpgen/data/jsons/al.diamond.222.json +++ b/dpgen/data/jsons/al.diamond.222.json @@ -1,22 +1,36 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [2, 2, 2], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.fcc.111.json b/dpgen/data/jsons/al.fcc.111.json index 4b0649d03..64ec32688 100644 --- a/dpgen/data/jsons/al.fcc.111.json +++ b/dpgen/data/jsons/al.fcc.111.json @@ -1,22 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [1, 1, 1], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.fcc.222.json b/dpgen/data/jsons/al.fcc.222.json index c23f6ebe6..901a43156 100644 --- a/dpgen/data/jsons/al.fcc.222.json +++ b/dpgen/data/jsons/al.fcc.222.json @@ -1,22 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [2, 2, 2], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.hcp.111.json b/dpgen/data/jsons/al.hcp.111.json index 493fed54e..b9aa495f8 100644 --- a/dpgen/data/jsons/al.hcp.111.json +++ b/dpgen/data/jsons/al.hcp.111.json @@ -1,22 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [1, 1, 1], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.hcp.222.json b/dpgen/data/jsons/al.hcp.222.json index ce057c5ef..85ecc8b9d 100644 --- a/dpgen/data/jsons/al.hcp.222.json +++ b/dpgen/data/jsons/al.hcp.222.json @@ -1,22 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [2, 2, 2], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.hcp.332.json b/dpgen/data/jsons/al.hcp.332.json index d16c2f1cc..990e13e4e 100644 --- a/dpgen/data/jsons/al.hcp.332.json +++ b/dpgen/data/jsons/al.hcp.332.json @@ -1,22 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [3, 3, 2], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 3, + 3, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.sc.222.json b/dpgen/data/jsons/al.sc.222.json index 6ab46dd98..9b7d0ee1e 100644 --- a/dpgen/data/jsons/al.sc.222.json +++ b/dpgen/data/jsons/al.sc.222.json @@ -1,22 +1,36 @@ { - "cell_type": "sc", - "latt": 2.5, - "super_cell": [2, 2, 2], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "sc", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.diamond.111.json b/dpgen/data/jsons/almg.diamond.111.json index c41b905be..d6800a15e 100644 --- a/dpgen/data/jsons/almg.diamond.111.json +++ b/dpgen/data/jsons/almg.diamond.111.json @@ -1,23 +1,38 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [1, 1, 1], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.diamond.222.json b/dpgen/data/jsons/almg.diamond.222.json index b94c24b06..968f7a781 100644 --- a/dpgen/data/jsons/almg.diamond.222.json +++ b/dpgen/data/jsons/almg.diamond.222.json @@ -1,23 +1,38 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [2, 2, 2], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.fcc.111.json b/dpgen/data/jsons/almg.fcc.111.json index e6fb8d951..7a81d8f7a 100644 --- a/dpgen/data/jsons/almg.fcc.111.json +++ b/dpgen/data/jsons/almg.fcc.111.json @@ -1,23 +1,38 @@ { - "cell_type": "fcc", - "latt": 4.3, - "super_cell": [1, 1, 1], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "fcc", + "latt": 4.3, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.fcc.222.json b/dpgen/data/jsons/almg.fcc.222.json index dab0caf8f..526296e14 100644 --- a/dpgen/data/jsons/almg.fcc.222.json +++ b/dpgen/data/jsons/almg.fcc.222.json @@ -1,23 +1,38 @@ { - "cell_type": "fcc", - "latt": 4.3, - "super_cell": [2, 2, 2], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "fcc", + "latt": 4.3, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.hcp.111.json b/dpgen/data/jsons/almg.hcp.111.json index 9ef72bd4c..c3e6f959b 100644 --- a/dpgen/data/jsons/almg.hcp.111.json +++ b/dpgen/data/jsons/almg.hcp.111.json @@ -1,23 +1,38 @@ { - "cell_type": "hcp", - "latt": 4.3, - "super_cell": [1, 1, 1], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.3, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.hcp.222.json b/dpgen/data/jsons/almg.hcp.222.json index 1abe49cc5..bd294960e 100644 --- a/dpgen/data/jsons/almg.hcp.222.json +++ b/dpgen/data/jsons/almg.hcp.222.json @@ -1,23 +1,38 @@ { - "cell_type": "hcp", - "latt": 4.3, - "super_cell": [2, 2, 2], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.3, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.hcp.332.json b/dpgen/data/jsons/almg.hcp.332.json index 024c1eb21..a42c819d2 100644 --- a/dpgen/data/jsons/almg.hcp.332.json +++ b/dpgen/data/jsons/almg.hcp.332.json @@ -1,23 +1,38 @@ { - "cell_type": "hcp", - "latt": 4.3, - "super_cell": [3, 3, 2], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.3, + "super_cell": [ + 3, + 3, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.sc.222.json b/dpgen/data/jsons/almg.sc.222.json index c27f9fd82..f13f31309 100644 --- a/dpgen/data/jsons/almg.sc.222.json +++ b/dpgen/data/jsons/almg.sc.222.json @@ -1,23 +1,38 @@ { - "cell_type": "sc", - "latt": 2.5, - "super_cell": [2, 2, 2], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "sc", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.sc.333.json b/dpgen/data/jsons/almg.sc.333.json index 31bf2e42c..48434e6e9 100644 --- a/dpgen/data/jsons/almg.sc.333.json +++ b/dpgen/data/jsons/almg.sc.333.json @@ -1,23 +1,38 @@ { - "cell_type": "sc", - "latt": 2.5, - "super_cell": [3, 3, 3], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "sc", + "latt": 2.5, + "super_cell": [ + 3, + 3, + 3 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.diamond.111.json b/dpgen/data/jsons/mg.diamond.111.json index 27e9cf944..9cf5929cd 100644 --- a/dpgen/data/jsons/mg.diamond.111.json +++ b/dpgen/data/jsons/mg.diamond.111.json @@ -1,22 +1,36 @@ { - "cell_type": "diamond", - "latt": 3.3, - "super_cell": [1, 1, 1], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "diamond", + "latt": 3.3, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.diamond.222.json b/dpgen/data/jsons/mg.diamond.222.json index 91e371b20..3e57d89fb 100644 --- a/dpgen/data/jsons/mg.diamond.222.json +++ b/dpgen/data/jsons/mg.diamond.222.json @@ -1,22 +1,36 @@ { - "cell_type": "diamond", - "latt": 3.3, - "super_cell": [2, 2, 2], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "diamond", + "latt": 3.3, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.fcc.111.json b/dpgen/data/jsons/mg.fcc.111.json index aee62759b..4b410025d 100644 --- a/dpgen/data/jsons/mg.fcc.111.json +++ b/dpgen/data/jsons/mg.fcc.111.json @@ -1,22 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.48, - "super_cell": [1, 1, 1], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "fcc", + "latt": 4.48, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.fcc.222.json b/dpgen/data/jsons/mg.fcc.222.json index dd42387a1..1c336433a 100644 --- a/dpgen/data/jsons/mg.fcc.222.json +++ b/dpgen/data/jsons/mg.fcc.222.json @@ -1,22 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.48, - "super_cell": [2, 2, 2], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "fcc", + "latt": 4.48, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.hcp.111.json b/dpgen/data/jsons/mg.hcp.111.json index cc36f847f..de791a650 100644 --- a/dpgen/data/jsons/mg.hcp.111.json +++ b/dpgen/data/jsons/mg.hcp.111.json @@ -1,22 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.48, - "super_cell": [1, 1, 1], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.48, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.hcp.222.json b/dpgen/data/jsons/mg.hcp.222.json index 54b06974a..228085b5e 100644 --- a/dpgen/data/jsons/mg.hcp.222.json +++ b/dpgen/data/jsons/mg.hcp.222.json @@ -1,20 +1,34 @@ { - "cell_type": "hcp", - "latt": 4.48, - "super_cell": [2, 2, 2], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.48, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.hcp.332.json b/dpgen/data/jsons/mg.hcp.332.json index d81ce2bfe..c072c16e3 100644 --- a/dpgen/data/jsons/mg.hcp.332.json +++ b/dpgen/data/jsons/mg.hcp.332.json @@ -1,20 +1,34 @@ { - "cell_type": "hcp", - "latt": 4.48, - "super_cell": [3, 3, 2], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.48, + "super_cell": [ + 3, + 3, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.sc.222.json b/dpgen/data/jsons/mg.sc.222.json index 137b39104..b05669cc3 100644 --- a/dpgen/data/jsons/mg.sc.222.json +++ b/dpgen/data/jsons/mg.sc.222.json @@ -1,22 +1,36 @@ { - "cell_type": "sc", - "latt": 2.7, - "super_cell": [2, 2, 2], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "sc", + "latt": 2.7, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/param.json b/dpgen/data/jsons/param.json index 70eb96ea1..5527819e0 100644 --- a/dpgen/data/jsons/param.json +++ b/dpgen/data/jsons/param.json @@ -1,22 +1,40 @@ { - "cell_type": "hcp", - "latt": 4.03, - "super_cell": [2, 1, 1], - "elements": ["Al", "Mg"], - "potcars": ["/gpfs/share/home/1600017784/start/data/POTCAR/Al/POTCAR", - "/gpfs/share/home/1600017784/start/data/POTCAR/Mg/POTCAR" - ], - "encut": 600, - "kspacing": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": true, - "relax_incar": "INCAR", - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 20, - "_comment": "that's all", - "stages":[1,2] + "cell_type": "hcp", + "latt": 4.03, + "super_cell": [ + 2, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/gpfs/share/home/1600017784/start/data/POTCAR/Al/POTCAR", + "/gpfs/share/home/1600017784/start/data/POTCAR/Mg/POTCAR" + ], + "encut": 600, + "kspacing": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "relax_incar": "INCAR", + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 20, + "_comment1": "that's all", + "stages": [ + 1, + 2 + ] } diff --git a/dpgen/data/jsons/si.diamond.111.json b/dpgen/data/jsons/si.diamond.111.json index b9c63547c..153435fec 100644 --- a/dpgen/data/jsons/si.diamond.111.json +++ b/dpgen/data/jsons/si.diamond.111.json @@ -1,22 +1,36 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [1, 1, 1], - "elements": ["Si"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/si.diamond.222.json b/dpgen/data/jsons/si.diamond.222.json index a7dc5a8c6..8d648cad7 100644 --- a/dpgen/data/jsons/si.diamond.222.json +++ b/dpgen/data/jsons/si.diamond.222.json @@ -1,22 +1,36 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [2, 2, 2], - "elements": ["Si"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/si.fcc.111.json b/dpgen/data/jsons/si.fcc.111.json index 2f13eda55..a63cbcc37 100644 --- a/dpgen/data/jsons/si.fcc.111.json +++ b/dpgen/data/jsons/si.fcc.111.json @@ -1,22 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [1, 1, 1], - "elements": ["Si"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/si.fcc.222.json b/dpgen/data/jsons/si.fcc.222.json index f0c1a620e..4c1a48548 100644 --- a/dpgen/data/jsons/si.fcc.222.json +++ b/dpgen/data/jsons/si.fcc.222.json @@ -1,22 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [2, 2, 2], - "elements": ["Si"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/si.hcp.111.json b/dpgen/data/jsons/si.hcp.111.json index fd65bd6e3..b3a66a6cd 100644 --- a/dpgen/data/jsons/si.hcp.111.json +++ b/dpgen/data/jsons/si.hcp.111.json @@ -1,22 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [1, 1, 1], - "elements": ["Si"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/si.hcp.222.json b/dpgen/data/jsons/si.hcp.222.json index b7dcd70d3..a6f7e2157 100644 --- a/dpgen/data/jsons/si.hcp.222.json +++ b/dpgen/data/jsons/si.hcp.222.json @@ -1,22 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [2, 2, 2], - "elements": ["Si"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/si.sc.222.json b/dpgen/data/jsons/si.sc.222.json index c1d015060..a136c51f8 100644 --- a/dpgen/data/jsons/si.sc.222.json +++ b/dpgen/data/jsons/si.sc.222.json @@ -1,22 +1,36 @@ { - "cell_type": "sc", - "latt": 2.5, - "super_cell": [2, 2, 2], - "elements": ["Si"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "sc", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.al.fcc.json b/dpgen/data/jsons/surf.al.fcc.json index 17787a5bc..30efd029a 100644 --- a/dpgen/data/jsons/surf.al.fcc.json +++ b/dpgen/data/jsons/surf.al.fcc.json @@ -1,26 +1,40 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [1, 1, 1], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.al.hcp.json b/dpgen/data/jsons/surf.al.hcp.json index 9bc1971ea..4c28934e7 100644 --- a/dpgen/data/jsons/surf.al.hcp.json +++ b/dpgen/data/jsons/surf.al.hcp.json @@ -1,26 +1,40 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [1, 1, 1], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.almg.fcc.json b/dpgen/data/jsons/surf.almg.fcc.json index c1cc480cb..cda94f5ae 100644 --- a/dpgen/data/jsons/surf.almg.fcc.json +++ b/dpgen/data/jsons/surf.almg.fcc.json @@ -1,27 +1,42 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [1, 1, 1], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.almg.hcp.json b/dpgen/data/jsons/surf.almg.hcp.json index bb83686a5..59fba4af5 100644 --- a/dpgen/data/jsons/surf.almg.hcp.json +++ b/dpgen/data/jsons/surf.almg.hcp.json @@ -1,27 +1,42 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [1, 1, 1], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.mg.fcc.json b/dpgen/data/jsons/surf.mg.fcc.json index d6353e3e0..43a55b0af 100644 --- a/dpgen/data/jsons/surf.mg.fcc.json +++ b/dpgen/data/jsons/surf.mg.fcc.json @@ -1,26 +1,40 @@ { - "cell_type": "fcc", - "latt": 4.48, - "super_cell": [1, 1, 1], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "fcc", + "latt": 4.48, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.mg.hcp.json b/dpgen/data/jsons/surf.mg.hcp.json index b18e8c365..c7c91d2df 100644 --- a/dpgen/data/jsons/surf.mg.hcp.json +++ b/dpgen/data/jsons/surf.mg.hcp.json @@ -1,26 +1,40 @@ { - "cell_type": "hcp", - "latt": 4.48, - "super_cell": [1, 1, 1], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.48, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.si.diamond.json b/dpgen/data/jsons/surf.si.diamond.json index fc374346d..725a9b90f 100644 --- a/dpgen/data/jsons/surf.si.diamond.json +++ b/dpgen/data/jsons/surf.si.diamond.json @@ -1,28 +1,58 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [1, 1, 1], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "pymatgen_surf": true, - "millers": [[0,0,1], [1,1,0], [1,1,1]], - "elements": ["Si"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "pymatgen_surf": true, + "millers": [ + [ + 0, + 0, + 1 + ], + [ + 1, + 1, + 0 + ], + [ + 1, + 1, + 1 + ] + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/w.bcc.111.json b/dpgen/data/jsons/w.bcc.111.json index 7d18285bd..210514e6c 100644 --- a/dpgen/data/jsons/w.bcc.111.json +++ b/dpgen/data/jsons/w.bcc.111.json @@ -1,24 +1,38 @@ { - "cell_type": "bcc", - "latt": 3.2, - "super_cell": [1, 1, 1], - "elements": ["W"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 30, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "bcc", + "latt": 3.2, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 30, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/w.bcc.222.json b/dpgen/data/jsons/w.bcc.222.json index 6a3b223e1..0fa54012e 100644 --- a/dpgen/data/jsons/w.bcc.222.json +++ b/dpgen/data/jsons/w.bcc.222.json @@ -1,24 +1,38 @@ { - "cell_type": "bcc", - "latt": 3.173, - "super_cell": [2, 2, 2], - "elements": ["W"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "bcc", + "latt": 3.173, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/w.diamond.111.json b/dpgen/data/jsons/w.diamond.111.json index a0d04fc83..89ce0e8af 100644 --- a/dpgen/data/jsons/w.diamond.111.json +++ b/dpgen/data/jsons/w.diamond.111.json @@ -1,24 +1,38 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [1, 1, 1], - "elements": ["W"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 30, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 30, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/w.fcc.111.json b/dpgen/data/jsons/w.fcc.111.json index e94ecaa56..705181620 100644 --- a/dpgen/data/jsons/w.fcc.111.json +++ b/dpgen/data/jsons/w.fcc.111.json @@ -1,24 +1,38 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [1, 1, 1], - "elements": ["W"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 30, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 30, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/w.hcp.111.json b/dpgen/data/jsons/w.hcp.111.json index 033bd13b6..dc8093a63 100644 --- a/dpgen/data/jsons/w.hcp.111.json +++ b/dpgen/data/jsons/w.hcp.111.json @@ -1,24 +1,38 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [1, 1, 1], - "elements": ["W"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 30, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 30, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/water.111.json b/dpgen/data/jsons/water.111.json index 4f5733a90..6cd01b135 100644 --- a/dpgen/data/jsons/water.111.json +++ b/dpgen/data/jsons/water.111.json @@ -1,29 +1,37 @@ { - "_comment": "init poscars form a crystal structure", - "cell_type": "diamond", - "latt": 2.5, - "elements": ["Si"], - "_comment": "if set from poscar, the options above will be ignored", - "from_poscar": true, - "from_poscar_path": "ice6.POSCAR", - - "_comment": "", - "super_cell": [1, 1, 1], - "potcars": [ "/home/wanghan/Soft/vasp/potcar.52/potpaw_PBE.52/O/POTCAR", - "/home/wanghan/Soft/vasp/potcar.52/potpaw_PBE.52/H/POTCAR" - ], - "encut": 900, - "kspacing_relax": 0.75, - "kspacing_md": 0.75, - "kgamma": false, - "scale": [1.0], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "_comment1": "init poscars form a crystal structure", + "cell_type": "diamond", + "latt": 2.5, + "elements": [ + "Si" + ], + "_comment2": "if set from poscar, the options above will be ignored", + "from_poscar": true, + "from_poscar_path": "ice6.POSCAR", + "_comment3": "", + "super_cell": [ + 1, + 1, + 1 + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.52/potpaw_PBE.52/O/POTCAR", + "/home/wanghan/Soft/vasp/potcar.52/potpaw_PBE.52/H/POTCAR" + ], + "encut": 900, + "kspacing_relax": 0.75, + "kspacing_md": 0.75, + "kgamma": false, + "scale": [ + 1.0 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment4": "that's all" } diff --git a/examples/CH4-refact-dpdispatcher/INCAR_methane b/examples/CH4-refact-dpdispatcher/INCAR_methane index b946fb7e5..4d1d7d039 120000 --- a/examples/CH4-refact-dpdispatcher/INCAR_methane +++ b/examples/CH4-refact-dpdispatcher/INCAR_methane @@ -1 +1 @@ -../run/dp1.x-lammps-vasp/CH4/INCAR_methane \ No newline at end of file +../run/dp2.x-lammps-vasp/CH4/INCAR_methane \ No newline at end of file diff --git a/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json b/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json index 40bf56abe..372545587 100644 --- a/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json +++ b/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json @@ -1,83 +1,92 @@ { - "api_version": "1.0", - "train": - { - "command": "dp", - "machine": { - "batch_type": "PBS", - "context_type": "SSHContext", - "local_root": "./", - "remote_root": "/home/fengbo/work_path_dpdispatcher_test", - "remote_profile": { - "hostname": "39.xxx.xx.xx", - "username": "fengbo" + "api_version": "1.0", + "train": { + "command": "dp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/fengbo/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "fengbo" + } + }, + "resources": { + "batch_type": "PBS", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 1, + "custom_flags": [ + "#SBATCH --mem=32G" + ], + "strategy": { + "if_cuda_multi_devices": true + }, + "para_deg": 3, + "source_list": [ + "/home/fengbo/deepmd.1.2.4.env" + ] } - }, - "resources": { - "batch_type": "PBS", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "T4_4_15", - "group_size": 1, - "custom_flags":["#SBATCH --mem=32G"], - "strategy": {"if_cuda_multi_devices": true}, - "para_deg": 3, - "source_list": ["/home/fengbo/deepmd.1.2.4.env"] - } }, - "model_devi": - { - "command": "lmp", - "machine":{ - "batch_type": "PBS", - "context_type": "SSHContext", - "local_root": "./", - "remote_root": "/home/fengbo/work_path_dpdispatcher_test", - "remote_profile": { - "hostname": "39.xxx.xx.xx", - "username": "fengbo" - } - }, - "resources": { - "batch_type": "PBS", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "T4_4_15", - "group_size": 5, - "source_list": ["/home/fengbo/deepmd.1.2.4.env"] - }, - "_comments" : "In user_forward_files, define input files to be uploaded.", - "user_forward_files" : [], - "_comments" : "In user_backward_files, define output files to be collected.", - "user_backward_files" : ["HILLS"] + "model_devi": { + "command": "lmp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/fengbo/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "fengbo" + } + }, + "resources": { + "batch_type": "PBS", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 5, + "source_list": [ + "/home/fengbo/deepmd.1.2.4.env" + ] + }, + "_comments": "In user_backward_files, define output files to be collected.", + "user_forward_files": [], + "user_backward_files": [ + "HILLS" + ] }, - "fp": - { - "command": "vasp_std", - "machine":{ - "batch_type": "PBS", - "context_type": "SSHContext", - "local_root": "./", - "remote_root": "/home/fengbo/work_path_dpdispatcher_test", - "remote_profile": { - "hostname": "39.xxx.xx.xx", - "username": "fengbo" - } - }, - "resources": { - "batch_type": "PBS", - "number_node": 1, - "cpu_per_node": 32, - "gpu_per_node": 0, - "queue_name": "G_32_128", - "group_size": 1, - "source_list": ["~/vasp.env"] - }, - "_comments" : "In user_forward_files, define input files to be uploaded.", - "user_forward_files" : ["vdw_kernel.bindat"], - "_comments" : "In user_backward_files, define output files to be collected.", - "user_backward_files" : [] + "fp": { + "command": "vasp_std", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/fengbo/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "fengbo" + } + }, + "resources": { + "batch_type": "PBS", + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "G_32_128", + "group_size": 1, + "source_list": [ + "~/vasp.env" + ] + }, + "_comments": "In user_backward_files, define output files to be collected.", + "user_forward_files": [ + "vdw_kernel.bindat" + ], + "user_backward_files": [] } } diff --git a/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json b/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json index b13293fe1..d3a1c9db1 100644 --- a/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json +++ b/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json @@ -1,131 +1,128 @@ { - "api_version": "1.0", - "train" : - { - "command": "dp", - "machine": { - "batch_type": "DpCloudServer", - "context_type": "DpCloudServerContext", - "local_root" : "./", - "remote_profile":{ - "email": "yfb222333", - "password": "", - "program_id": 0, - "input_data":{ - "job_type": "indicate", - "log_file": "dp_cloud_server.log", - "command": null, - "backward_files": [], - "job_name": "dpgen_20210630_job", - "machine": { - "platform": "ali", - "resources": { - "gpu_type": "1 * NVIDIA P100", - "cpu_num": 4, - "mem_limit": 30, - "disk_size": 100, - "region": "cn-beijing", - "time_limit": "2:00:00", - "image_name": "yfb-deepmd-kit-1.2.4-cuda10" + "api_version": "1.0", + "train": { + "command": "dp", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "yfb222333", + "password": "", + "program_id": 0, + "input_data": { + "job_type": "indicate", + "log_file": "dp_cloud_server.log", + "command": null, + "backward_files": [], + "job_name": "dpgen_20210630_job", + "machine": { + "platform": "ali", + "resources": { + "gpu_type": "1 * NVIDIA P100", + "cpu_num": 4, + "mem_limit": 30, + "disk_size": 100, + "region": "cn-beijing", + "time_limit": "2:00:00", + "image_name": "yfb-deepmd-kit-1.2.4-cuda10" } }, - "job_resources": null + "job_resources": null + } } + }, + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "GPU", + "group_size": 1 } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "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": "yfb222333", - "password": "", - "program_id": 0, - "input_data":{ - "job_type": "indicate", - "log_file": "dp_cloud_server.log", - "command": null, - "backward_files": [], - "job_name": "dpgen_20210630_job", - "machine": { - "platform": "ali", - "resources": { - "gpu_type": "1 * NVIDIA P100", - "cpu_num": 4, - "mem_limit": 30, - "disk_size": 100, - "region": "cn-beijing", - "time_limit": "2:00:00", - "image_name": "yfb-deepmd-kit-1.2.4-cuda10" + "model_devi": { + "command": "lmp -i input.lammps -v restart 0", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "yfb222333", + "password": "", + "program_id": 0, + "input_data": { + "job_type": "indicate", + "log_file": "dp_cloud_server.log", + "command": null, + "backward_files": [], + "job_name": "dpgen_20210630_job", + "machine": { + "platform": "ali", + "resources": { + "gpu_type": "1 * NVIDIA P100", + "cpu_num": 4, + "mem_limit": 30, + "disk_size": 100, + "region": "cn-beijing", + "time_limit": "2:00:00", + "image_name": "yfb-deepmd-kit-1.2.4-cuda10" } }, - "job_resources": null + "job_resources": null + } } + }, + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "GPU", + "group_size": 5 } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "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": "yfb222333", - "password": "", - "program_id": 0, - "input_data":{ - "job_type": "indicate", - "log_file": "dp_cloud_server.log", - "command": null, - "backward_files": [], - "job_name": "dpgen_20210630_job", - "machine": { - "platform": "ali", - "resources": { - "cpu_num": 32, - "mem_limit": 64, - "disk_size": 200, - "region": "cn-beijing", - "time_limit": "2:00:00", - "image_name": "deepmd-vasp-cloudserver-v8" + "fp": { + "command": "mpirun -n 16 vasp_std", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "yfb222333", + "password": "", + "program_id": 0, + "input_data": { + "job_type": "indicate", + "log_file": "dp_cloud_server.log", + "command": null, + "backward_files": [], + "job_name": "dpgen_20210630_job", + "machine": { + "platform": "ali", + "resources": { + "cpu_num": 32, + "mem_limit": 64, + "disk_size": 200, + "region": "cn-beijing", + "time_limit": "2:00:00", + "image_name": "deepmd-vasp-cloudserver-v8" } }, - "job_resources": null + "job_resources": null + } } + }, + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "CPU", + "group_size": 5, + "source_list": [ + "/opt/intel/oneapi/setvars.sh" + ] } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 32, - "gpu_per_node": 0, - "queue_name": "CPU", - "group_size": 5, - "source_list": [ - "/opt/intel/oneapi/setvars.sh" - ] - } } } diff --git a/examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-1.1.0.json b/examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-1.1.0.json deleted file mode 120000 index 2916f7885..000000000 --- a/examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-1.1.0.json +++ /dev/null @@ -1 +0,0 @@ -../run/dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json \ No newline at end of file diff --git a/examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-2.x.json b/examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-2.x.json new file mode 120000 index 000000000..3f11d42a7 --- /dev/null +++ b/examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-2.x.json @@ -0,0 +1 @@ +../run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json \ No newline at end of file diff --git a/examples/database/param_Ti.json b/examples/database/param_Ti.json index be78af113..ed2e6b556 100644 --- a/examples/database/param_Ti.json +++ b/examples/database/param_Ti.json @@ -1,19 +1,100 @@ { - "path" : "/path/to/Ti", - "calculator" : "vasp", - "_comment" : "Current only support VASP", - "output" : "./db_Ti.json", - "id_prefix" : "", - "config_info_dict" : { - "fcc-bulk" : [0,1,2,3,4,5,6,7], - "hcp-bulk" : [8,9,10,11,12,13,14,15], - "bcc-bulk" : [16,17,18,19,20,21,22,23], - "fcc-surf-100" : [24,25,26,27,28,29,30,31], - "fcc-surf-111" : [32,33,34,35,36,37,38,39], - "fcc-surf-110" : [40,41,42,43,44,45,46,47], - "hcp-surf-001" : [48,49,50,51,52,53,54,55], - "hcp-surf-100" : [56,57,58,59,60,61,62,63], - "hcp-surf-110" : [64,65,66,67,68,69,70,71] - }, - "skip_init" : true + "path": "/path/to/Ti", + "calculator": "vasp", + "_comment1": "Current only support VASP", + "output": "./db_Ti.json", + "id_prefix": "", + "config_info_dict": { + "fcc-bulk": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7 + ], + "hcp-bulk": [ + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15 + ], + "bcc-bulk": [ + 16, + 17, + 18, + 19, + 20, + 21, + 22, + 23 + ], + "fcc-surf-100": [ + 24, + 25, + 26, + 27, + 28, + 29, + 30, + 31 + ], + "fcc-surf-111": [ + 32, + 33, + 34, + 35, + 36, + 37, + 38, + 39 + ], + "fcc-surf-110": [ + 40, + 41, + 42, + 43, + 44, + 45, + 46, + 47 + ], + "hcp-surf-001": [ + 48, + 49, + 50, + 51, + 52, + 53, + 54, + 55 + ], + "hcp-surf-100": [ + 56, + 57, + 58, + 59, + 60, + 61, + 62, + 63 + ], + "hcp-surf-110": [ + 64, + 65, + 66, + 67, + 68, + 69, + 70, + 71 + ] + }, + "skip_init": true } diff --git a/examples/init/abacus/CuW/CuW.json b/examples/init/abacus/CuW/CuW.json index 9abd406ce..0703bfb21 100644 --- a/examples/init/abacus/CuW/CuW.json +++ b/examples/init/abacus/CuW/CuW.json @@ -1,6 +1,11 @@ { - "init_fp_style": "ABACUS", - "stages": [1, 2, 3, 4], + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], "cell_type": "fcc", "latt": 3.76, "super_cell": [ @@ -9,14 +14,18 @@ 1 ], "elements": [ - "Cu", "W" + "Cu", + "W" + ], + "atom_masses": [ + 63.55, + 183.8 ], - "atom_masses": [63.55, 183.8], "potcars": [ "Cu_ONCV_PBE-1.0.upf", - "W_ONCV_PBE-1.0.upf" + "W_ONCV_PBE-1.0.upf" ], - "orb_files":[ + "orb_files": [ "Cu_gga_9au_60Ry_4s2p2d1f.orb", "W_gga_10au_60Ry_4s2p2d2f.orb" ], @@ -24,8 +33,8 @@ "relax_kpt": "KPT", "md_kpt": "KPT", "md_incar": "INPUT.md", - "dpks_descriptor": "jle.orb", - "dpks_model": "model.ptg", + "dpks_descriptor": "jle.orb", + "dpks_model": "model.ptg", "scale": [ 0.99 ], @@ -39,5 +48,5 @@ "Cu", "W" ], - "_comment": "that's all" + "_comment1": "that's all" } diff --git a/examples/init/abacus/fcc-Al-lcao/init.json b/examples/init/abacus/fcc-Al-lcao/init.json index fccb79da7..1095fa54b 100644 --- a/examples/init/abacus/fcc-Al-lcao/init.json +++ b/examples/init/abacus/fcc-Al-lcao/init.json @@ -1,24 +1,41 @@ { - "init_fp_style": "ABACUS", - "stages": [1,2,3,4], - "cell_type": "diamond", - "super_cell": [2, 1, 1], - "elements": ["Al"], - "from_poscar": true, - "from_poscar_path": "./Al.STRU", - "potcars": ["Al_ONCV_PBE-1.0.upf"], - "orb_files": ["Al_gga_9au_100Ry_4s4p1d.orb"], - "relax_incar": "./INPUT.rlx", - "md_incar" : "./INPUT.md", - "relax_kpt": "./KPT.rlx", - "md_kpt": "./KPT.md", - "md_nstep": 3, - "scale": [1.00], - "skip_relax": false, - "pert_numb": 2, - "pert_box": 0.03, - "pert_atom": 0.01, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], + "cell_type": "diamond", + "super_cell": [ + 2, + 1, + 1 + ], + "elements": [ + "Al" + ], + "from_poscar": true, + "from_poscar_path": "./Al.STRU", + "potcars": [ + "Al_ONCV_PBE-1.0.upf" + ], + "orb_files": [ + "Al_gga_9au_100Ry_4s4p1d.orb" + ], + "relax_incar": "./INPUT.rlx", + "md_incar": "./INPUT.md", + "relax_kpt": "./KPT.rlx", + "md_kpt": "./KPT.md", + "md_nstep": 3, + "scale": [ + 1.0 + ], + "skip_relax": false, + "pert_numb": 2, + "pert_box": 0.03, + "pert_atom": 0.01, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/examples/init/abacus/fcc-Al-lcao/machine.json b/examples/init/abacus/fcc-Al-lcao/machine.json index ba74f0297..1a35c7107 100644 --- a/examples/init/abacus/fcc-Al-lcao/machine.json +++ b/examples/init/abacus/fcc-Al-lcao/machine.json @@ -1,106 +1,111 @@ { - "api_version": "1.0", - "deepmd_version": "2.0.1", - "train" :[ - { - "command": "dp", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": , - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "00*/train.log", - "grouped":true, - "job_name": "dpgen_train_job", - "disk_size": 200, - "scass_type":"", - "checkpoint_files":["00*/checkpoint","00*/model.ckpt*"], - "checkpoint_time":30, - "platform": "", - "region":"", - "image_name":"", - "on_demand":0, - "job_type":"" + "api_version": "1.0", + "deepmd_version": "2.0.1", + "train": [ + { + "command": "dp", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "00*/train.log", + "grouped": true, + "job_name": "dpgen_train_job", + "disk_size": 200, + "scass_type": "", + "checkpoint_files": [ + "00*/checkpoint", + "00*/model.ckpt*" + ], + "checkpoint_time": 30, + "platform": "", + "region": "", + "image_name": "", + "on_demand": 0 + } + } + }, + "resources": { + "local_root": "./", + "group_size": 1 } } - }, - "resources": { - "local_root":"./", - "group_size": 1 - } - }], - "model_devi": - [{ - "command": "lmp -i input.lammps -v restart 0", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": , - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "*/model_devi.log", - "grouped":true, - "job_name": "dpgen_model_devi_job", - "disk_size": 200, - "scass_type":"", - "platform": "", - "region":"", - "image_name":"", - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "on_demand":0, - "job_type":"" + ], + "model_devi": [ + { + "command": "lmp -i input.lammps -v restart 0", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "*/model_devi.log", + "grouped": true, + "job_name": "dpgen_model_devi_job", + "disk_size": 200, + "scass_type": "", + "platform": "", + "region": "", + "image_name": "", + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "on_demand": 0 + } + } + }, + "resources": { + "local_root": "./", + "group_size": 50 } } - }, - "resources": { - "local_root":"./", - "group_size": 50 - } - }], - "fp": - [{ - "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": , - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "task*/fp.log", - "grouped":true, - "job_name": "dpgen_fp_job", - "disk_size": 100, - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "scass_type":"", - "platform": "", - "image_name":"", - "on_demand":0 + ], + "fp": [ + { + "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "task*/fp.log", + "grouped": true, + "job_name": "dpgen_fp_job", + "disk_size": 100, + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "scass_type": "", + "platform": "", + "image_name": "", + "on_demand": 0 + } + } + }, + "resources": { + "group_size": 50, + "local_root": "./", + "source_list": [ + "" + ] } } - }, - "resources": { - "group_size": 50, - "local_root":"./", - "source_list": [""] - } - } - ] + ] } diff --git a/examples/init/abacus/fcc-Al-pw/init.json b/examples/init/abacus/fcc-Al-pw/init.json index 0874040e4..d90cef3bd 100644 --- a/examples/init/abacus/fcc-Al-pw/init.json +++ b/examples/init/abacus/fcc-Al-pw/init.json @@ -1,23 +1,38 @@ { "init_fp_style": "ABACUS", - "stages": [1,2,3,4], - "cell_type": "fcc", - "super_cell": [2, 1, 1], - "elements": ["Al"], - "from_poscar": true, - "from_poscar_path": "./Al.STRU", - "potcars": ["Al_ONCV_PBE-1.0.upf"], - "relax_incar": "INPUT.rlx", - "relax_kpt": "KPT", - "md_incar" : "INPUT.md", - "md_kpt" : "KPT", - "skip_relax": false, - "scale": [1.00], - "pert_numb": 10, - "md_nstep" : 10, - "pert_box": 0.01, - "pert_atom": 0.01, - "deepgen_templ": "../generator/template/", - "coll_ndata": 10, - "_comment": "that's all" + "stages": [ + 1, + 2, + 3, + 4 + ], + "cell_type": "fcc", + "super_cell": [ + 2, + 1, + 1 + ], + "elements": [ + "Al" + ], + "from_poscar": true, + "from_poscar_path": "./Al.STRU", + "potcars": [ + "Al_ONCV_PBE-1.0.upf" + ], + "relax_incar": "INPUT.rlx", + "relax_kpt": "KPT", + "md_incar": "INPUT.md", + "md_kpt": "KPT", + "skip_relax": false, + "scale": [ + 1.0 + ], + "pert_numb": 10, + "md_nstep": 10, + "pert_box": 0.01, + "pert_atom": 0.01, + "deepgen_templ": "../generator/template/", + "coll_ndata": 10, + "_comment1": "that's all" } diff --git a/examples/init/abacus/fcc-Al-pw/machine.json b/examples/init/abacus/fcc-Al-pw/machine.json index ba74f0297..1a35c7107 100644 --- a/examples/init/abacus/fcc-Al-pw/machine.json +++ b/examples/init/abacus/fcc-Al-pw/machine.json @@ -1,106 +1,111 @@ { - "api_version": "1.0", - "deepmd_version": "2.0.1", - "train" :[ - { - "command": "dp", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": , - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "00*/train.log", - "grouped":true, - "job_name": "dpgen_train_job", - "disk_size": 200, - "scass_type":"", - "checkpoint_files":["00*/checkpoint","00*/model.ckpt*"], - "checkpoint_time":30, - "platform": "", - "region":"", - "image_name":"", - "on_demand":0, - "job_type":"" + "api_version": "1.0", + "deepmd_version": "2.0.1", + "train": [ + { + "command": "dp", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "00*/train.log", + "grouped": true, + "job_name": "dpgen_train_job", + "disk_size": 200, + "scass_type": "", + "checkpoint_files": [ + "00*/checkpoint", + "00*/model.ckpt*" + ], + "checkpoint_time": 30, + "platform": "", + "region": "", + "image_name": "", + "on_demand": 0 + } + } + }, + "resources": { + "local_root": "./", + "group_size": 1 } } - }, - "resources": { - "local_root":"./", - "group_size": 1 - } - }], - "model_devi": - [{ - "command": "lmp -i input.lammps -v restart 0", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": , - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "*/model_devi.log", - "grouped":true, - "job_name": "dpgen_model_devi_job", - "disk_size": 200, - "scass_type":"", - "platform": "", - "region":"", - "image_name":"", - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "on_demand":0, - "job_type":"" + ], + "model_devi": [ + { + "command": "lmp -i input.lammps -v restart 0", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "*/model_devi.log", + "grouped": true, + "job_name": "dpgen_model_devi_job", + "disk_size": 200, + "scass_type": "", + "platform": "", + "region": "", + "image_name": "", + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "on_demand": 0 + } + } + }, + "resources": { + "local_root": "./", + "group_size": 50 } } - }, - "resources": { - "local_root":"./", - "group_size": 50 - } - }], - "fp": - [{ - "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": , - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "task*/fp.log", - "grouped":true, - "job_name": "dpgen_fp_job", - "disk_size": 100, - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "scass_type":"", - "platform": "", - "image_name":"", - "on_demand":0 + ], + "fp": [ + { + "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "task*/fp.log", + "grouped": true, + "job_name": "dpgen_fp_job", + "disk_size": 100, + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "scass_type": "", + "platform": "", + "image_name": "", + "on_demand": 0 + } + } + }, + "resources": { + "group_size": 50, + "local_root": "./", + "source_list": [ + "" + ] } } - }, - "resources": { - "group_size": 50, - "local_root":"./", - "source_list": [""] - } - } - ] + ] } diff --git a/examples/init/al.json b/examples/init/al.json index 41e365cad..6f1fbb2ab 100644 --- a/examples/init/al.json +++ b/examples/init/al.json @@ -28,5 +28,5 @@ "Mg", "Al" ], - "_comment": "that's all" + "_comment1": "that's all" } diff --git a/examples/init/ch4.json b/examples/init/ch4.json index 3902c24da..622b74b5f 100644 --- a/examples/init/ch4.json +++ b/examples/init/ch4.json @@ -1,19 +1,36 @@ { - "stages": [1,2,3,4], - "cell_type": "diamond", - "super_cell": [1, 1, 1], - "elements": ["H","C"], - "from_poscar": true, - "from_poscar_path": "./CH4.POSCAR", - "potcars": ["./POTCAR_H", "./POTCAR_C"], - "relax_incar": "./INCAR_methane.rlx", - "md_incar" : "./INCAR_methane.md", - "scale": [1.00], - "skip_relax": false, - "pert_numb": 30, - "md_nstep" : 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 5000, - "_comment": "that's all" + "stages": [ + 1, + 2, + 3, + 4 + ], + "cell_type": "diamond", + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "H", + "C" + ], + "from_poscar": true, + "from_poscar_path": "./CH4.POSCAR", + "potcars": [ + "./POTCAR_H", + "./POTCAR_C" + ], + "relax_incar": "./INCAR_methane.rlx", + "md_incar": "./INCAR_methane.md", + "scale": [ + 1.0 + ], + "skip_relax": false, + "pert_numb": 30, + "md_nstep": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/examples/init/cu.surf.hcp.111.json b/examples/init/cu.surf.hcp.111.json index 00816e09d..7ed24507f 100644 --- a/examples/init/cu.surf.hcp.111.json +++ b/examples/init/cu.surf.hcp.111.json @@ -1,56 +1,59 @@ { - "_comments": "This is an example to generate Cu-hcp surface configurations.", - "_comments": "This example is used in Computer Physics Communications, 2020, 107206.", - "_comments" : "Last modified on 2019.8.27 by Yuzhi Zhang.", - "stages": [ - 1, - 2 - ], - "cell_type": "hcp", - "latt": 3.63, - "super_cell": [ - 1, - 1, - 1 - ], - "z_min": 10, - "vacuum_max": 10, - "vacuum_resol": [ - 0.5, - 1 - ], - "mid_point": 4.0, - "millers": [ - [ - 1, - 0, - 0 + "_comments": "Last modified on 2019.8.27 by Yuzhi Zhang.", + "stages": [ + 1, + 2 ], - [ - 1, - 1, - 0 + "cell_type": "hcp", + "latt": 3.63, + "super_cell": [ + 1, + 1, + 1 ], - [ - 0, - 0, - 1 - ] - ], - "elements": [ - "Cu" - ], - "potcars": [ - "PATH/POTCAR" - ], - "relax_incar" : "PATH/INCAR_surf_rlx", - "scale": [ - 0.96,0.98, 1.0,1.02, 1.04, 1.06 - ], - "skip_relax": false, - "pert_numb": 20, - "pert_box": 0.03, - "pert_atom": 0.01, - "lmp_cmd" : "PATH/lmp_serial", - "_comment": "that's all" + "z_min": 10, + "vacuum_max": 10, + "vacuum_resol": [ + 0.5, + 1 + ], + "mid_point": 4.0, + "millers": [ + [ + 1, + 0, + 0 + ], + [ + 1, + 1, + 0 + ], + [ + 0, + 0, + 1 + ] + ], + "elements": [ + "Cu" + ], + "potcars": [ + "PATH/POTCAR" + ], + "relax_incar": "PATH/INCAR_surf_rlx", + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 20, + "pert_box": 0.03, + "pert_atom": 0.01, + "lmp_cmd": "PATH/lmp_serial", + "_comment1": "that's all" } diff --git a/examples/init/surf.json b/examples/init/surf.json index 902fc8d0b..08ec0f05a 100644 --- a/examples/init/surf.json +++ b/examples/init/surf.json @@ -1,56 +1,56 @@ { - "stages": [ - 1, - 2 - ], - "cell_type": "fcc", - "latt": 4.1, - "super_cell": [ - 1, - 1, - 1 - ], - "z_min": 9, - "vacuum_max": 9.0, - "vacuum_resol": [ - 0.5, - 1 - ], - "mid_point": 4.0, - "head_ratio": 0.6, - "vacuum_numb": 20, - "millers": [ - [ - 1, - 0, - 0 + "stages": [ + 1, + 2 ], - [ - 1, - 1, - 0 + "cell_type": "fcc", + "latt": 4.1, + "super_cell": [ + 1, + 1, + 1 ], - [ - 1, - 1, - 1 - ] - ], - "elements": [ - "Al" - ], - "potcars": [ - "./POTCAR" - ], - "relax_incar" : "INCAR_metal_rlx_low", - "scale": [ - 0.98, - 1.0 - ], - "skip_relax": true, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 5000, - "_comment": "that's all" + "z_min": 9, + "vacuum_max": 9.0, + "vacuum_resol": [ + 0.5, + 1 + ], + "mid_point": 4.0, + "head_ratio": 0.6, + "vacuum_numb": 20, + "millers": [ + [ + 1, + 0, + 0 + ], + [ + 1, + 1, + 0 + ], + [ + 1, + 1, + 1 + ] + ], + "elements": [ + "Al" + ], + "potcars": [ + "./POTCAR" + ], + "relax_incar": "INCAR_metal_rlx_low", + "scale": [ + 0.98, + 1.0 + ], + "skip_relax": true, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json b/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json index e0e6bfca0..854ee01ba 100644 --- a/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json +++ b/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json @@ -1,12 +1,12 @@ { - "_comment" : "This is an example of DP-GEN on Local device running with 4 GPUs", - "_comment": "Last updated on 2021.5.9 for DP-GEN 0.9.2 by Ke XU", + "_comment1": "This is an example of DP-GEN on Local device running with 4 GPUs", + "_comment2": "Last updated on 2021.5.9 for DP-GEN 0.9.2 by Ke XU", "train": { - "_comment" : "Specify the installed path of DeePMD-kit", + "_comment3": "Specify the installed path of DeePMD-kit", "command": "/home/user/anaconda3/bin/dp", - "_comment" : "Specify machine settings", + "_comment4": "Specify machine settings", "machine": { - "_comment": "Supported batches include slurm, pbs, shell, lsf.", + "_comment5": "Supported batches include slurm, pbs, shell, lsf.", "batch_type": "shell", "context_type": "local", "remote_root": "/tmp/dpwork", @@ -14,22 +14,22 @@ }, "resources": { "module_list": [], - "_comment": "Environment to be activated. This will generate source xxx/psxevars.sh in scripts. ", + "_comment6": "Environment to be activated. This will generate source xxx/psxevars.sh in scripts. ", "source_list": [ "/opt/intel/parallel_studio_xe_2020/psxevars.sh" ], "batch_type": "shell", - "_comment": "DP-GEN will put 4 tasks together in one submitting script.", + "_comment7": "DP-GEN will put 4 tasks together in one submitting script.", "group_size": 4, - "_comment" : "The number of nodes.", + "_comment8": "The number of nodes.", "number_node": 1, - "_comment" : "The number of CPUs.", + "_comment9": "The number of CPUs.", "cpu_per_node": 4, - "_comment" : "If you choose to run with multiple GPUs simultaneously, just ignore numb_gpu.", + "_comment10": "If you choose to run with multiple GPUs simultaneously, just ignore numb_gpu.", "gpu_per_node": 0, "kwargs": {}, "strategy": { - "_comment" : "Allow the multi-GPU task running.", + "_comment11": "Allow the multi-GPU task running.", "if_cuda_multi_devices": true }, "para_deg": 4, @@ -68,11 +68,11 @@ "local_root": "./" }, "resources": { - "_comment" : "Load the intel compiler.", + "_comment12": "Load the intel compiler.", "source_list": [ "/opt/intel/parallel_studio_xe_2020/psxevars.sh" ], - "_comment": "This will generate export PATH=/home/user/Soft/VASP/vasp.5.4.4-allbak/bin:$PATH in scripts;", + "_comment13": "This will generate export PATH=/home/user/Soft/VASP/vasp.5.4.4-allbak/bin:$PATH in scripts;", "envs": { "PATH": "/home/user/Soft/VASP/vasp.5.4.4-allbak/bin:$PATH" }, diff --git a/examples/machine/DeePMD-kit-1.x/machine-local.json b/examples/machine/DeePMD-kit-1.x/machine-local.json index 2eb999743..eaac4cb5d 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-local.json +++ b/examples/machine/DeePMD-kit-1.x/machine-local.json @@ -1,7 +1,7 @@ { "api_version": "1.0", "train": { - "_comment": "training on localhost", + "_comment1": "training on localhost", "machine": { "batch_type": "shell", "context_type": "local", @@ -21,9 +21,9 @@ "command": "/home/wanghan/local/deepmd/1.*/dp" }, "model_devi": { - "_comment": "model devi on localhost", + "_comment2": "model devi on localhost", "machine": { - "_comment": "If lazy_local, calculations are done directly in current folders.", + "_comment3": "If lazy_local, calculations are done directly in current folders.", "batch_type": "shell", "context_type": "lazylocal", "local_root": "./" @@ -40,7 +40,7 @@ "command": "/home/wanghan/local/bin/lmp_mpi_010" }, "fp": { - "_comment": "fp on localhost", + "_comment4": "fp on localhost", "machine": { "batch_type": "shell", "context_type": "local", @@ -51,7 +51,7 @@ "module_list": [ "mpi" ], - "_comment": "that's all", + "_comment5": "that's all", "batch_type": "shell", "group_size": 2, "cpu_per_node": 4, diff --git a/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json b/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json index 6f96d397d..40ed09746 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json +++ b/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json @@ -1,39 +1,39 @@ { - "_comment": "Last updated on 2021.4.30 for DP-GEN 0.9.2 by Yuzhi Zhang", + "_comment1": "Last updated on 2021.4.30 for DP-GEN 0.9.2 by Yuzhi Zhang", "train": { - "_comment" : "Specify the installed path of DeePMD-kit", + "_comment2": "Specify the installed path of DeePMD-kit", "command": "PATH_TO_DEEPMD/dp", - "_comment" : "Specify machine settings", + "_comment3": "Specify machine settings", "machine": { "batch_type": "slurm", "context_type": "ssh", "remote_profile": { "hostname": "localhost", - "_comment" : "The port for connection, most common settings is 22", + "_comment4": "The port for connection, most common settings is 22", "port": 22, - "_comment" : "Specify your username.", + "_comment5": "Specify your username.", "username": "USERNAME" }, - "_comment" : "You should alwasy make sure that directory of work_path exits. ", + "_comment6": "You should alwasy make sure that directory of work_path exits. ", "remote_root": "PATH_TO_WORK", "local_root": "./" }, "resources": { - "_comment" : "Environment to be activated. This will generate source PATH/train_new.env . ", + "_comment7": "Environment to be activated. This will generate source PATH/train_new.env . ", "source_list": [ "PATH/train_new.env" ], - "_comment" : " Module is a common tools on HPC clustes to manage softwares for multiple users.", - "_comment" : "Modules to be loaded. This will generate module load intel", + "_comment8": " Module is a common tools on HPC clustes to manage softwares for multiple users.", + "_comment9": "Modules to be loaded. This will generate module load intel", "module_list": [ "intel" ], "batch_type": "slurm", - "_comment" : "The number of nodes. This will generate #SBATCH -N 1 in your script. ", + "_comment10": "The number of nodes. This will generate #SBATCH -N 1 in your script. ", "number_node": 1, - "_comment" : "The number of CPUs. #SBATCH -n 4", + "_comment11": "The number of CPUs. #SBATCH -n 4", "cpu_per_node": 4, - "_comment" : "The number of GPU cards. #SBATCH --gres=gpu:1", + "_comment12": "The number of GPU cards. #SBATCH --gres=gpu:1", "gpu_per_node": 1, "queue_name": "all", "custom_flags": [ @@ -63,7 +63,7 @@ ], "module_list": [], "batch_type": "slurm", - "_comment": "DP-GEN will put 5 tasks together in one submitting script.", + "_comment13": "DP-GEN will put 5 tasks together in one submitting script.", "group_size": 5, "number_node": 1, "cpu_per_node": 4, diff --git a/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json b/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json index ae6ac31ab..8fdd1db35 100644 --- a/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json +++ b/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json @@ -1,107 +1,106 @@ { - "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 + "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": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "GPU", + "group_size": 1 } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "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 + "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": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "GPU", + "group_size": 5 } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "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 + "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": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "CPU", + "group_size": 5, + "source_list": [ + "/opt/intel/oneapi/setvars.sh" + ] } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 32, - "gpu_per_node": 0, - "queue_name": "CPU", - "group_size": 5, - "source_list": ["/opt/intel/oneapi/setvars.sh"] - } } } diff --git a/examples/run/ch4/machine.json b/examples/run/ch4/machine.json index 653f613d6..70b8ee67a 100644 --- a/examples/run/ch4/machine.json +++ b/examples/run/ch4/machine.json @@ -1,75 +1,77 @@ { - "deepmd_path": "/sharedext4/local/deepmd-kit-0.12.4/", - "train_machine": { - "machine_type": "slurm", - "hostname" : "localhost", - "port" : 22, - "username": "root", - "work_path" : "/sharedext4/generator/example/deep.gen/generator/ch4/", - "_comment" : "that's all" + "deepmd_path": "/sharedext4/local/deepmd-kit-0.12.4/", + "train_machine": { + "machine_type": "slurm", + "hostname": "localhost", + "port": 22, + "username": "root", + "work_path": "/sharedext4/generator/example/deep.gen/generator/ch4/", + "_comment1": "that's all" }, - "train_resources": { - "numb_node": 1, - "numb_gpu": 1, - "task_per_node":8, - "partition" : "GPU-H", - "exclude_list" : [], - "source_list": [ "/sharedext4/local/deepmd-kit-0.12.4/bin/activate" ], - "module_list": [ ], - "time_limit": "23:0:0", - "mem_limit": 32, - "_comment": "that's all" + "train_resources": { + "numb_node": 1, + "numb_gpu": 1, + "task_per_node": 8, + "partition": "GPU-H", + "exclude_list": [], + "source_list": [ + "/sharedext4/local/deepmd-kit-0.12.4/bin/activate" + ], + "module_list": [], + "time_limit": "23:0:0", + "mem_limit": 32, + "_comment2": "that's all" }, - - "model_devi_command": "/sharedext4/softwares/lammps/bin/lmp_serial", - "model_devi_group_size": 1, - "_comment": "model_devi on localhost", - "model_devi_machine": { - "machine_type": "slurm", - "hostname" : "localhost", - "port" : 22, - "username": "root", - "work_path" : "/sharedext4/generator/example/deep.gen/generator/ch4/", - "_comment" : "that's all" + "model_devi_command": "/sharedext4/softwares/lammps/bin/lmp_serial", + "model_devi_group_size": 1, + "_comment3": "model_devi on localhost", + "model_devi_machine": { + "machine_type": "slurm", + "hostname": "localhost", + "port": 22, + "username": "root", + "work_path": "/sharedext4/generator/example/deep.gen/generator/ch4/", + "_comment4": "that's all" }, - "_comment": " if use GPU, numb_nodes(nn) should always be 1 ", - "_comment": " if numb_nodes(nn) = 1 multi-threading rather than mpi is assumed", - "model_devi_resources": { - "numb_node": 1, - "numb_gpu": 0, - "task_per_node":1, - "source_list": ["/sharedext4/local/deepmd-kit-0.12.4/bin/lammps.activate" ], - "module_list": [ ], - "time_limit": "19:0:0", - "mem_limit": 32, - "partition" : "GPU-All", - "_comment": "that's all" + "_comment5": " if use GPU, numb_nodes(nn) should always be 1 ", + "_comment6": " if numb_nodes(nn) = 1 multi-threading rather than mpi is assumed", + "model_devi_resources": { + "numb_node": 1, + "numb_gpu": 0, + "task_per_node": 1, + "source_list": [ + "/sharedext4/local/deepmd-kit-0.12.4/bin/lammps.activate" + ], + "module_list": [], + "time_limit": "19:0:0", + "mem_limit": 32, + "partition": "GPU-All", + "_comment7": "that's all" }, - - "_comment": "fp on localhost ", - "fp_command": "/sharedext4/vasp/vasp.5.4.4/bin/vasp_std", - "fp_group_size": 1, - "fp_machine": { + "_comment8": "fp on localhost ", + "fp_command": "/sharedext4/vasp/vasp.5.4.4/bin/vasp_std", + "fp_group_size": 1, + "fp_machine": { "machine_type": "slurm", - "hostname" : "localhost", - "port" : 22, - "username": "root", - "work_path" : "/sharedext4/generator/example/deep.gen/generator/ch4/", - "_comment" : "that's all" + "hostname": "localhost", + "port": 22, + "username": "root", + "work_path": "/sharedext4/generator/example/deep.gen/generator/ch4/", + "_comment9": "that's all" }, - "fp_resources": { - "numb_node": 1, - "task_per_node":1, - "numb_gpu": 0, - "exclude_list" : [], - "source_list": ["/sharedext4/softwares/source/vasp_cpu.activate" ], - "module_list": [], - "with_mpi" : 1, - "time_limit": "1:0:0", - "partition" : "GPU-All", - "_comment": "that's all" + "fp_resources": { + "numb_node": 1, + "task_per_node": 1, + "numb_gpu": 0, + "exclude_list": [], + "source_list": [ + "/sharedext4/softwares/source/vasp_cpu.activate" + ], + "module_list": [], + "with_mpi": 1, + "time_limit": "1:0:0", + "partition": "GPU-All", + "_comment10": "that's all" }, - - - "_comment": " that's all " + "_comment11": " that's all " } diff --git a/examples/run/ch4/param.json b/examples/run/ch4/param.json index 2a996e5fe..9983473b8 100644 --- a/examples/run/ch4/param.json +++ b/examples/run/ch4/param.json @@ -1,114 +1,193 @@ { - "type_map": ["H","C"], - "mass_map": [1, 12], - - "init_data_prefix": "/sharedext4/generator/example/deep.gen/data/", - - "init_data_sys": [ - "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" - ], - "init_batch_size": [ - 8 - ], - "sys_configs": [ - ["/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000[0-4]/POSCAR"], - ["/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000[5-9]/POSCAR"], - ["/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR"], - ["/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00002*/POSCAR"] - ], - "_comment": "0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25", - "sys_batch_size": [ - 8, 8, 8, 8 + "type_map": [ + "H", + "C" ], - - - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "_comment": " model parameters", - "use_smooth": true, - "sel_a": [16,4], - "rcut_smth": 0.50, - "rcut": 5, - "filter_neuron": [10, 20, 40], - "filter_resnet_dt": false, - "n_axis_neuron": 12, - "n_neuron": [120,120,120], - "resnet_dt": true, - "coord_norm": true, - "type_fitting_net": false, - - "_comment": " traing controls", - "systems": [], - "set_prefix": "set", - "stop_batch": 30000, - "batch_size": 1, - "start_lr": 0.001, - "decay_steps": 150, - "decay_rate": 0.95, - "seed": 0, - - "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, - - "_comment": " display and restart", - "_comment": " frequencies counted in batch", - "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" + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/sharedext4/generator/example/deep.gen/data/", + "init_data_sys": [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" + ], + "init_batch_size": [ + 8 + ], + "sys_configs": [ + [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000[0-4]/POSCAR" + ], + [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000[5-9]/POSCAR" + ], + [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" + ], + [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00002*/POSCAR" + ] + ], + "_comment1": "0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25", + "sys_batch_size": [ + 8, + 8, + 8, + 8 + ], + "_comment2": " 00.train ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut": 5, + "rcut_smth": 0.5, + "neuron": [ + 10, + 20, + 40 + ], + "axis_neuron": 12, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "decay_steps": 150, + "start_lr": 0.001, + "stop_lr": 3.505266624882874e-08 + }, + "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": { + "seed": 0, + "stop_batch": 30000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + } }, - - "_comment": " 01.model_devi ", - "_comment": "model_devi_skip: the first x of the recorded frames", - "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_clean_traj": true, - "model_devi_jobs": [ - {"sys_idx": [0], - "temps": [ 100], "press": [1.0], "trj_freq": 10, "nsteps": 300, "ensemble": "npt", "_idx": "00"}, - {"sys_idx": [1], - "temps": [ 100], "press": [1.0], "trj_freq": 10, "nsteps": 1000, "ensemble": "npt", "_idx": "01"}, - {"sys_idx": [2], - "temps": [ 100], "press": [1.0], "trj_freq": 10, "nsteps": 3000, "ensemble": "npt", "_idx": "02"}, - {"sys_idx": [3], - "temps": [ 100], "press": [1.0], "trj_freq": 10, "nsteps": 3000, "ensemble": "npt", "_idx": "03"} - ], - - - "_comment": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 30, - "fp_task_min": 5, - "fp_pp_path": "/sharedext4/generator/example/deep.gen/data/ch4/", - "fp_pp_files": ["POTCAR"], - "fp_params": { - "_comment": "given in unit depending on the fp method", - "ecut": 400, - "ediff": 1e-6, - "kspacing": 2, - "_comment": "gauss, mp:N(methfessel-paxton:order by default order=1), fd(Fermi-Dirac)", - "smearing": "gauss", - "sigma": 0.05, - "_comment": "only for vasp, can be NONE, SCAN, TPSS, RTPSS, M06L or MBJ", - "metagga": "NONE", - "npar": 4, - "kpar": 1, - "_comment": " that's all " + "_comment8": " 01.model_devi ", + "_comment9": "model_devi_skip: the first x of the recorded frames", + "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_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 300, + "ensemble": "npt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 1000, + "ensemble": "npt", + "_idx": "01" + }, + { + "sys_idx": [ + 2 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "npt", + "_idx": "02" + }, + { + "sys_idx": [ + 3 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "npt", + "_idx": "03" + } + ], + "_comment10": " 02.fp ", + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 30, + "fp_task_min": 5, + "fp_pp_path": "/sharedext4/generator/example/deep.gen/data/ch4/", + "fp_pp_files": [ + "POTCAR" + ], + "fp_params": { + "_comment11": "given in unit depending on the fp method", + "ecut": 400, + "ediff": 1e-06, + "kspacing": 2, + "_comment12": "gauss, mp:N(methfessel-paxton:order by default order=1), fd(Fermi-Dirac)", + "smearing": "gauss", + "sigma": 0.05, + "_comment13": "only for vasp, can be NONE, SCAN, TPSS, RTPSS, M06L or MBJ", + "metagga": "NONE", + "npar": 4, + "kpar": 1, + "_comment14": " that's all " }, - "_comment": " that's all " + "_comment15": " that's all " } diff --git a/examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.json b/examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.json deleted file mode 100644 index b8163e785..000000000 --- a/examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.json +++ /dev/null @@ -1,136 +0,0 @@ -{ - "type_map": [ - "H", - "C" - ], - "mass_map": [ - 1, - 12 - ], - "init_data_prefix": "/public/data/deepmd-tutorial/data/", - "init_data_sys": [ - "deepmd" - ], - "init_batch_size": [ - 8 - ], - "sys_configs": [ - [ - "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR" - ], - [ - "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" - ] - ], - "sys_batch_size": [ - 8, - 8, - 8, - 8 - ], - "_comment": " that's all ", - "numb_models": 4, - "default_training_param": { - "_comment": "that's all", - "use_smooth": true, - "sel_a": [ - 16, - 4 - ], - "rcut_smth": 0.5, - "rcut": 5, - "filter_neuron": [ - 10, - 20, - 40 - ], - "filter_resnet_dt": false, - "n_axis_neuron": 12, - "n_neuron": [ - 120, - 120, - 120 - ], - "resnet_dt": true, - "coord_norm": true, - "type_fitting_net": false, - "systems": [ ], - "set_prefix": "set", - "stop_batch": 40000, - "batch_size": 1, - "start_lr": 0.001, - "decay_steps": 200, - "decay_rate": 0.95, - "seed": 0, - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 4, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "load_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json" - }, - "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_clean_traj": true, - "model_devi_jobs": [ - { - "sys_idx": [ - 0 - ], - "temps": [ - 100 - ], - "press": [ - 1 - ], - "trj_freq": 10, - "nsteps": 1000, - "ensemble": "nvt", - "_idx": "00" - }, - { - "sys_idx": [ - 1 - ], - "temps": [ - 100 - ], - "press": [ - 1 - ], - "trj_freq": 10, - "nsteps": 5000, - "ensemble": "nvt", - "_idx": "01" - } - ], - "fp_style": "cp2k", - "shuffle_poscar": false, - "fp_task_max": 20, - "fp_task_min": 5, - "fp_params": { - "cutoff": "400", - "rel_cutoff": "50", - "functional": "PBE", - "pair_potential_path": "dftd3.dat", - "pair_ref_functional": "PBE", - "basis_path": "BASIS_MOLOPT", - "pp_path": "GTH_POTENTIALS", - "element_list": ["H", "C"], - "basis_list": ["DZVP-MOLOPT-GTH", "DZVP-MOLOPT-GTH"], - "_comment": "elment_list, basis_list, pp_list should be one to one correspondance", - "pp_list": ["GTH-PBE-q1", "GTH-PBE-q4"] - } -} diff --git a/examples/run/deprecated/dp0.12-lammps-pwmat/machine-slurm-pwmat-single.json b/examples/run/deprecated/dp0.12-lammps-pwmat/machine-slurm-pwmat-single.json deleted file mode 100644 index 9138f0cbf..000000000 --- a/examples/run/deprecated/dp0.12-lammps-pwmat/machine-slurm-pwmat-single.json +++ /dev/null @@ -1,80 +0,0 @@ -{ - "train": [ - { - "machine": { - "machine_type": "slurm", - "hostname": "mstation", - "port": 22, - "username": "test", - "password": "PWmat2019", - "work_path": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/work_train" - }, - "resources": { - "numb_node": 1, - "numb_gpu": 4, - "task_per_node": 4, - "partition": "control", - "exclude_list": [], - "source_list": [ - "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/train.env" - ], - "module_list": [], - "time_limit": "23:0:0" - }, - "deepmd_path" : "/home/test/anaconda2/envs/python3/" - } - ], - "model_devi": [ - { - "machine": { - "machine_type": "slurm", - "hostname": "mstation", - "port": 22, - "username": "test", - "password": "PWmat2019", - "work_path": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/work_model" - }, - "resources": { - "numb_node": 1, - "numb_gpu": 4, - "task_per_node": 4, - "partition": "control", - "exclude_list": [], - "source_list": [ - "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/train.env" - ], - "module_list": [], - "time_limit": "23:0:0" - }, - "command": "srun --mpi=pmi2 lmp_mpi", - "group_size": 10 - } - ], - "fp": [ - { - "machine": { - "machine_type": "slurm", - "hostname": "mstation", - "port": 22, - "username": "test", - "password": "PWmat2019", - "work_path": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/work_fp" - }, - "resources": { - "task_per_node": 4, - "numb_gpu": 4, - "exclude_list": [], - "with_mpi": false, - "source_list": [], - "module_list": [ - "cuda/8.0" - ], - "time_limit": "120:0:0", - "partition": "control", - "_comment": "that's All" - }, - "command": "mpirun -np 4 PWmat", - "group_size": 5 - } - ] -} diff --git a/examples/run/deprecated/dp0.12-lammps-pwmat/param_CH4.json b/examples/run/deprecated/dp0.12-lammps-pwmat/param_CH4.json deleted file mode 100644 index b1b3756ad..000000000 --- a/examples/run/deprecated/dp0.12-lammps-pwmat/param_CH4.json +++ /dev/null @@ -1,97 +0,0 @@ -{ - "type_map": ["H","C"], - "mass_map": [1, 12], - - "init_data_prefix": 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"temps": [ 100], "press": [1.0], "trj_freq": 10, "nsteps": 3000, "ensemble": "nvt", "_idx": "01"} - ], - - "_comment": " 02.fp ", - "cvasp": false, - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 20, - "fp_task_min": 5, - "fp_pp_path": "/gpfs/share/home/1600017784/yuzhi/methane/", - "fp_pp_files": ["POT_H","POT_C"], -"fp_incar" : "/gpfs/share/home/1600017784/yuzhi/methane/INCAR_methane", - "_comment": " that's all " -} diff --git a/examples/run/deprecated/dp1.x-gromacs-gaussian/param.json b/examples/run/deprecated/dp1.x-gromacs-gaussian/param.json deleted file mode 100644 index 29065b3e4..000000000 --- a/examples/run/deprecated/dp1.x-gromacs-gaussian/param.json +++ /dev/null @@ -1,176 +0,0 @@ -{ - "type_map": [ - "H", - "C", - "N", - "O", - "Cl" - ], - "mass_map": [ - 2, - 12, - 14, - 16, - 35 - ], - "init_data_prefix": "somplace/tyk2-dpgen", - "init_data_sys": ["init_data", "mdtraj_data"], - "sys_configs_prefix": "somplace/tyk2-dpgen", - "sys_configs": [ - ["model_devi/lig_ejm_31"], - ["model_devi/lig_ejm_42"], - ["model_devi/lig_ejm_43"], - ["model_devi/lig_ejm_44"], - ["model_devi/lig_ejm_45"], - ["model_devi/lig_ejm_46"], - ["model_devi/lig_ejm_47"], - ["model_devi/lig_ejm_48"], - ["model_devi/lig_ejm_49"], - ["model_devi/lig_ejm_50"], - ["model_devi/lig_ejm_54"], - ["model_devi/lig_ejm_55"], - ["model_devi/lig_jmc_27"], - ["model_devi/lig_jmc_28"], - ["model_devi/lig_jmc_30"] - ], - "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_stop_batch": 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", - "Cl" - ], - "descriptor": { - "type": "se_a", - "sel": [ - 40, - 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": [ - 60, - 60, - 60 - ], - "resnet_dt": true - } - }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 2000, - "decay_rate": 0.95 - }, - "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, - "start_pref_pf": 0, - "limit_pref_pf": 0 - }, - "training": { - "set_prefix": "set", - "stop_batch": 1000000, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 1, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "load_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json" - } - }, - "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" - }, - "model_devi_dt": 0.001, - "model_devi_f_trust_lo": 0.20, - "model_devi_f_trust_hi": 0.40, - "model_devi_clean_traj": false, - "model_devi_skip": 0, - "model_devi_nopbc": true, - "model_devi_activation_func": [ - "tanh", - "tanh", - "gelu", - "gelu" - ], - "model_devi_jobs": [ - { - "_idx": 0, - "ensemble": "nvt", - "nsteps": 5000, - "press": [], - "sys_idx": [ - 0, - 1, - 2, - 3, - 4, - 5, - 6, - 7, - 8, - 9, - 10, - 11, - 12, - 13, - 14 - ], - "temps": [], - "trj_freq": 10, - "_comment": "trj_freq should be consistent with nstxout in mdp" - } - ], - "fp_style": "gaussian", - "shuffle_poscar": false, - "fp_task_max": 20, - "fp_task_min": 1, - "fp_pp_path": "./", - "fp_pp_files": [], - "fp_params": { - "keywords": "force m062x/6-31g(d) nosymm", - "nproc": 16, - "multiplicity": "auto" - } -} diff --git a/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json b/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json new file mode 100644 index 000000000..99842df95 --- /dev/null +++ b/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json @@ -0,0 +1,209 @@ +{ + "type_map": [ + "H", + "C", + "N", + "O", + "Cl" + ], + "mass_map": [ + 2, + 12, + 14, + 16, + 35 + ], + "init_data_prefix": "somplace/tyk2-dpgen", + "init_data_sys": [ + "init_data", + "mdtraj_data" + ], + "sys_configs_prefix": "somplace/tyk2-dpgen", + "sys_configs": [ + [ + "model_devi/lig_ejm_31" + ], + [ + "model_devi/lig_ejm_42" + ], + [ + "model_devi/lig_ejm_43" + ], + [ + "model_devi/lig_ejm_44" + ], + [ + "model_devi/lig_ejm_45" + ], + [ + "model_devi/lig_ejm_46" + ], + [ + "model_devi/lig_ejm_47" + ], + [ + "model_devi/lig_ejm_48" + ], + [ + "model_devi/lig_ejm_49" + ], + [ + "model_devi/lig_ejm_50" + ], + [ + "model_devi/lig_ejm_54" + ], + [ + "model_devi/lig_ejm_55" + ], + [ + "model_devi/lig_jmc_27" + ], + [ + "model_devi/lig_jmc_28" + ], + [ + "model_devi/lig_jmc_30" + ] + ], + "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_stop_batch": 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", + "Cl" + ], + "descriptor": { + "type": "se_a", + "sel": [ + 40, + 48, + 48, + 48, + 48 + ], + "rcut_smth": 0.5, + "rcut": 6.0, + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "axis_neuron": 16, + "type_one_side": true + }, + "fitting_net": { + "neuron": [ + 60, + 60, + 60 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 2000, + "stop_lr": 7.274491561439049e-15 + }, + "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, + "start_pref_pf": 0, + "limit_pref_pf": 0 + }, + "training": { + "stop_batch": 1000000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "set_prefix": "set" + } + } + }, + "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" + }, + "model_devi_dt": 0.001, + "model_devi_f_trust_lo": 0.2, + "model_devi_f_trust_hi": 0.4, + "model_devi_clean_traj": false, + "model_devi_skip": 0, + "model_devi_nopbc": true, + "model_devi_activation_func": [ + "tanh", + "tanh", + "gelu", + "gelu" + ], + "model_devi_jobs": [ + { + "_idx": 0, + "ensemble": "nvt", + "nsteps": 5000, + "press": [], + "sys_idx": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11, + 12, + 13, + 14 + ], + "temps": [], + "trj_freq": 10, + "_comment1": "trj_freq should be consistent with nstxout in mdp" + } + ], + "fp_style": "gaussian", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 1, + "fp_pp_path": "./", + "fp_pp_files": [], + "fp_params": { + "keywords": "force m062x/6-31g(d) nosymm", + "nproc": 16, + "multiplicity": "auto" + } +} diff --git a/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json new file mode 100644 index 000000000..bc07d204a --- /dev/null +++ b/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json @@ -0,0 +1,156 @@ +{ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/public/data/deepmd-tutorial/data/", + "init_data_sys": [ + "deepmd" + ], + "init_batch_size": [ + 8 + ], + "sys_configs": [ + [ + "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR" + ], + [ + "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" + ] + ], + "sys_batch_size": [ + 8, + 8, + 8, + 8 + ], + "_comment1": " that's all ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut": 5, + "rcut_smth": 0.5, + "neuron": [ + 10, + 20, + 40 + ], + "axis_neuron": 12, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "decay_steps": 200, + "start_lr": 0.001, + "stop_lr": 3.505266624882874e-08 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "training": { + "seed": 0, + "stop_batch": 40000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "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_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 1000, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 5000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "fp_style": "cp2k", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 5, + "fp_params": { + "cutoff": "400", + "rel_cutoff": "50", + "functional": "PBE", + "pair_potential_path": "dftd3.dat", + "pair_ref_functional": "PBE", + "basis_path": "BASIS_MOLOPT", + "pp_path": "GTH_POTENTIALS", + "element_list": [ + "H", + "C" + ], + "basis_list": [ + "DZVP-MOLOPT-GTH", + "DZVP-MOLOPT-GTH" + ], + "_comment3": "elment_list, basis_list, pp_list should be one to one correspondance", + "pp_list": [ + "GTH-PBE-q1", + "GTH-PBE-q4" + ] + } +} diff --git a/examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.yaml b/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.yaml similarity index 98% rename from examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.yaml rename to examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.yaml index 8a7b83baf..358648077 100644 --- a/examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.yaml +++ b/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.yaml @@ -61,7 +61,6 @@ default_training_param: numb_test: 4 save_freq: 1000 save_ckpt: model.ckpt - load_ckpt: model.ckpt disp_training: true time_training: true profiling: false diff --git a/examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json b/examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json new file mode 100644 index 000000000..be8a6b027 --- /dev/null +++ b/examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json @@ -0,0 +1,80 @@ +{ + "train": [ + { + "machine": { + "machine_type": "slurm", + "hostname": "mstation", + "port": 22, + "username": "test", + "password": "PWmat2019", + "work_path": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/work_train" + }, + "resources": { + "numb_node": 1, + "numb_gpu": 4, + "task_per_node": 4, + "partition": "control", + "exclude_list": [], + "source_list": [ + "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/train.env" + ], + "module_list": [], + "time_limit": "23:0:0" + }, + "deepmd_path": "/home/test/anaconda2/envs/python3/" + } + ], + "model_devi": [ + { + "machine": { + "machine_type": "slurm", + "hostname": "mstation", + "port": 22, + "username": "test", + "password": "PWmat2019", + "work_path": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/work_model" + }, + "resources": { + "numb_node": 1, + "numb_gpu": 4, + "task_per_node": 4, + "partition": "control", + "exclude_list": [], + "source_list": [ + "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/train.env" + ], + "module_list": [], + "time_limit": "23:0:0" + }, + "command": "srun --mpi=pmi2 lmp_mpi", + "group_size": 10 + } + ], + "fp": [ + { + "machine": { + "machine_type": "slurm", + "hostname": "mstation", + "port": 22, + "username": "test", + "password": "PWmat2019", + "work_path": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/work_fp" + }, + "resources": { + "task_per_node": 4, + "numb_gpu": 4, + "exclude_list": [], + "with_mpi": false, + "source_list": [], + "module_list": [ + "cuda/8.0" + ], + "time_limit": "120:0:0", + "partition": "control", + "_comment1": "that's All" + }, + "command": "mpirun -np 4 PWmat", + "group_size": 5 + } + ] +} diff --git a/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json new file mode 100644 index 000000000..3c2ebfdef --- /dev/null +++ b/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json @@ -0,0 +1,147 @@ +{ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/", + "init_data_sys": [ + "ch4/00.data" + ], + "init_batch_size": [ + 8 + ], + "sys_configs_prefix": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/", + "sys_configs": [ + [ + "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/scale-1.000/00000*/POSCAR" + ], + [ + "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/scale-1.000/00001*/POSCAR" + ] + ], + "sys_batch_size": [ + 8, + 8, + 8, + 8 + ], + "_comment1": " 00.train ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut": 5, + "rcut_smth": 0.5, + "neuron": [ + 10, + 20, + 40 + ], + "axis_neuron": 12, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "decay_steps": 100, + "start_lr": 0.001, + "stop_lr": 0.0003584859224085419 + }, + "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": { + "seed": 0, + "stop_batch": 2000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "training_data": { + "systems": [ + "./00.data/" + ], + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "_comment7": " 01.model_devi ", + "_comment8": "model_devi_skip: the first x of the recorded frames", + "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_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 300 + ], + "press": [ + 0.0 + ], + "trj_freq": 10, + "nsteps": 300, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 300 + ], + "press": [ + 0.0 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "_comment9": " 02.fp ", + "fp_style": "pwmat", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 8, + "fp_pp_path": ".", + "fp_pp_files": [ + "C.SG15.PBE.UPF", + "H.SG15.PBE.UPF" + ], + "fp_incar": "etot.input", + "_comment10": " that's all " +} diff --git a/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json new file mode 100644 index 000000000..56555f0fd --- /dev/null +++ b/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json @@ -0,0 +1,148 @@ +{ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/public/data/deepmd-tutorial/data/", + "init_data_sys": [ + "deepmd" + ], + "init_batch_size": [ + 8 + ], + "sys_configs": [ + [ + "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR" + ], + [ + "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" + ] + ], + "sys_batch_size": [ + 8, + 8, + 8, + 8 + ], + "_comment1": " that's all ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut": 5, + "rcut_smth": 0.5, + "neuron": [ + 10, + 20, + 40 + ], + "axis_neuron": 12, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "decay_steps": 200, + "start_lr": 0.001, + "stop_lr": 3.505266624882874e-08 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "training": { + "seed": 0, + "stop_batch": 40000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "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_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 1000, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + 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+60,6 @@ default_training_param: numb_test: 4 save_freq: 1000 save_ckpt: model.ckpt - load_ckpt: model.ckpt disp_training: true time_training: true profiling: false diff --git a/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.json b/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.json new file mode 100644 index 000000000..e3383a2e1 --- /dev/null +++ b/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.json @@ -0,0 +1,450 @@ +{ + "type_map": [ + "Al" + ], + "mass_map": [ + 27 + ], + "init_data_prefix": "/gpfs/share/home/1600017784/generator/Al/init/", + "init_data_sys": [ + "al.fcc.02x02x02/02.md/sys-0032/deepmd", + "al.hcp.02x02x02/02.md/sys-0016/deepmd", + "al.bcc.02x02x02/02.md/sys-0016/deepmd" + ], + "init_batch_size": [ + 1, + 2, + 2 + ], + "sys_configs": [ + [ + "/gpfs/share/home/1600017784/generator/Al/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR" + ], + [ + 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50, + 132.0, + 198.0, + 264.0 + ], + "trj_freq": 10 + }, + { + "_idx": 8, + "ensemble": "npt", + "nsteps": 1000, + "press": [ + 1.0, + 10.0, + 100.0, + 1000.0, + 5000.0, + 10000.0, + 20000.0, + 50000.0 + ], + "sys_idx": [ + 0, + 8, + 16 + ], + "temps": [ + 330.0, + 396.0, + 462.0, + 528.0, + 594.0 + ], + "trj_freq": 10 + } + ], + "_comment9": " 02.fp ", + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 300, + "fp_task_min": 5, + "fp_pp_path": "/gpfs/share/home/1600017784/start/data/POTCAR/Al/", + "fp_pp_files": [ + "POTCAR" + ], + "fp_incar": "/gpfs/share/home/1600017784/start/pku_input_set/INCAR_metal_scf_gpu", + "_comment10": " that's all " +} diff --git a/examples/run/deprecated/dp0.12-lammps-vasp/Al/param_al_all_gpu.yaml b/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.yaml similarity index 99% rename from examples/run/deprecated/dp0.12-lammps-vasp/Al/param_al_all_gpu.yaml rename to examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.yaml index 37409d69a..0a8d362fb 100644 --- a/examples/run/deprecated/dp0.12-lammps-vasp/Al/param_al_all_gpu.yaml +++ b/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.yaml @@ -109,7 +109,6 @@ default_training_param: numb_test: 4 save_freq: 2000 save_ckpt: model.ckpt - load_ckpt: model.ckpt disp_training: true time_training: true profiling: false diff --git a/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.json new file mode 100644 index 000000000..8ff640f7e --- /dev/null +++ b/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.json @@ -0,0 +1,146 @@ +{ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/gpfs/share/home/1600017784/yuzhi/methane/init/", + "init_data_sys": [ + "CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" + ], + "init_batch_size": [ + 8 + ], + "sys_configs_prefix": "/gpfs/share/home/1600017784/yuzhi/methane/init/", + "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" + ] + ], + "sys_batch_size": [ + 8, + 8, + 8, + 8 + ], + "_comment1": " 00.train ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut": 5, + "rcut_smth": 0.5, + "neuron": [ + 10, + 20, + 40 + ], + "axis_neuron": 12, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "decay_steps": 100, + "start_lr": 0.001, + "stop_lr": 0.0003584859224085419 + }, + "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": { + "seed": 0, + "stop_batch": 2000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "_comment7": " 01.model_devi ", + "_comment8": "model_devi_skip: the first x of the recorded frames", + "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_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" + } + ], + "_comment9": " 02.fp ", + "cvasp": false, + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 5, + "fp_pp_path": "/gpfs/share/home/1600017784/yuzhi/methane/", + "fp_pp_files": [ + "POT_H", + "POT_C" + ], + "fp_incar": "/gpfs/share/home/1600017784/yuzhi/methane/INCAR_methane", + "_comment10": " that's all " +} diff --git a/examples/run/deprecated/dp0.12-lammps-vasp/CH4/param_CH4.yaml b/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.yaml similarity index 98% rename from examples/run/deprecated/dp0.12-lammps-vasp/CH4/param_CH4.yaml rename to examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.yaml index 2a77eddef..7a34e9ef9 100644 --- a/examples/run/deprecated/dp0.12-lammps-vasp/CH4/param_CH4.yaml +++ b/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.yaml @@ -61,7 +61,6 @@ default_training_param: numb_test: 4 save_freq: 1000 save_ckpt: model.ckpt - load_ckpt: model.ckpt disp_training: true time_training: true profiling: false diff --git a/examples/run/deprecated/param-h2oscan-vasp.json b/examples/run/deprecated/param-h2oscan-vasp.json index 1ccc592b7..84e7dbb3c 100644 --- a/examples/run/deprecated/param-h2oscan-vasp.json +++ 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"_comment11": " 02.fp ", + "fp_style": "pwscf", + "shuffle_poscar": false, + "fp_task_max": 100, + "fp_task_min": 10, + "fp_pp_path": "/home/linfengz/SCR/wanghan/deepgen.pyridine/pwscf/", + "fp_pp_files": [ + "C_HSCV_PBE-1.0.UPF", + "H_HSCV_PBE-1.0.UPF", + "N_HSCV_PBE-1.0.UPF" ], - - "_comment": " 02.fp ", - "fp_style": "pwscf", - "shuffle_poscar": false, - "fp_task_max": 100, - "fp_task_min": 10, - "fp_pp_path": "/home/linfengz/SCR/wanghan/deepgen.pyridine/pwscf/", - "fp_pp_files": ["C_HSCV_PBE-1.0.UPF", "H_HSCV_PBE-1.0.UPF", "N_HSCV_PBE-1.0.UPF"], - "fp_params": { - "_comment": "given in unit depending on the fp method", - "ecut": 110.0, - "ediff": 1e-8, - "kspacing": 0.6, - "npar": 1, - "kpar": 1, - "_comment": " that's all " + "fp_params": { + "_comment12": "given in unit depending on the fp method", + "ecut": 110.0, + "ediff": 1e-08, + "kspacing": 0.6, + "npar": 1, + "kpar": 1, + "_comment13": " that's all " }, - - "_comment": " that's all " + "_comment14": " that's all " } diff --git a/examples/run/dp-calypso-vasp/machine.json b/examples/run/dp-calypso-vasp/machine.json index f07f2dd87..b563d27c4 100644 --- a/examples/run/dp-calypso-vasp/machine.json +++ b/examples/run/dp-calypso-vasp/machine.json @@ -1,70 +1,82 @@ { - "api_version": "1.0", - "deepmd_version": "2.0.1", - "train" :[ - { - "command": "dp", - "machine": { - "batch_type": "pbs", - "context_type": "lazylocal", - "local_root" : "./" - }, - "resources": { - "envs": {"LD_LIBRARY_PATH": "/opt/software/cuda/10.1/lib64:$LD_LIBRARY_PATH"}, - "custom_flags":["#PBS -l walltime=48:0:0"], - "number_node": 1, - "local_root":"./", - "cpu_per_node": 16, - "gpu_per_node": 1, - "queue_name": "T4_16_62", - "group_size": 1 - } - }], - "model_devi": - [{ - "calypso_path":"/home/zhenyu/workplace/dpgen/AA-2400/debug/calypso_input", - "deepmdkit_python":"/home/zhenyu/soft/deepmd-kit/envs/debug/bin/python", - "_deepmdkit_python":"this python will be used to optimize structures generated by CALYPSO with ase", - "_deepmdkit_python":"and also will be used to calculate model deviation in iter.000001/01.model_devi/model_devi_results", - "_deepmdkit_python":"with calypso_run_model_devi.py script", - "command": "", - "machine": { - "_batch_type": "pbs", - "batch_type": "shell", - "context_type": "lazylocal", - "remote_root": "/home/zhenyu/workplace/dpgen/AA-2400/debug/temp", - "local_root" : "./" - }, - "resources": { - "envs": {"LD_LIBRARY_PATH": "/opt/software/cuda/10.1/lib64:$LD_LIBRARY_PATH"}, - "custom_flags":["#PBS -l walltime=48:0:0"], - "number_node": 1, - "local_root":"./", - "cpu_per_node": 16, - "gpu_per_node": 1, - "queue_name": "T4_16_62", - "group_size": 50 - } - }], - "fp": - [{ - "command": "mpirun -n 32 /opt/vasp/vasp_std", - "machine": { - "batch_type": "shell", - "context_type": "lazylocal", - "local_root" : "./", - "remote_root": "/home/zhenyu/workplace/dpgen/AA-2400/debug/temp" - }, - "resources": { - "number_node": 1, - "cpu_per_node": 12, - "gpu_per_node": 0, - "queue_name": "C_32_64", - "group_size": 10, - "local_root":"./", - "custom_flags":["#PBS -l walltime=200:0:0"], - "source_list": ["/opt/intel/oneapi/setvars.sh"] - } - } - ] + "api_version": "1.0", + "deepmd_version": "2.0.1", + "train": [ + { + "command": "dp", + "machine": { + "batch_type": "pbs", + "context_type": "lazylocal", + "local_root": "./" + }, + "resources": { + "envs": { + "LD_LIBRARY_PATH": "/opt/software/cuda/10.1/lib64:$LD_LIBRARY_PATH" + }, + "custom_flags": [ + "#PBS -l walltime=48:0:0" + ], + "number_node": 1, + "local_root": "./", + "cpu_per_node": 16, + "gpu_per_node": 1, + "queue_name": "T4_16_62", + "group_size": 1 + } + } + ], + "model_devi": [ + { + "calypso_path": "/home/zhenyu/workplace/dpgen/AA-2400/debug/calypso_input", + "deepmdkit_python": "/home/zhenyu/soft/deepmd-kit/envs/debug/bin/python", + "_deepmdkit_python": "with calypso_run_model_devi.py script", + "command": "", + "machine": { + "_batch_type": "pbs", + "batch_type": "shell", + "context_type": "lazylocal", + "remote_root": "/home/zhenyu/workplace/dpgen/AA-2400/debug/temp", + "local_root": "./" + }, + "resources": { + "envs": { + "LD_LIBRARY_PATH": "/opt/software/cuda/10.1/lib64:$LD_LIBRARY_PATH" + }, + "custom_flags": [ + "#PBS -l walltime=48:0:0" + ], + "number_node": 1, + "local_root": "./", + "cpu_per_node": 16, + "gpu_per_node": 1, + "queue_name": "T4_16_62", + "group_size": 50 + } + } + ], + "fp": [ + { + "command": "mpirun -n 32 /opt/vasp/vasp_std", + "machine": { + "batch_type": "shell", + "context_type": "lazylocal", + "local_root": "./", + "remote_root": "/home/zhenyu/workplace/dpgen/AA-2400/debug/temp" + }, + "resources": { + "number_node": 1, + "cpu_per_node": 12, + "gpu_per_node": 0, + "queue_name": "C_32_64", + "group_size": 10, + "local_root": "./", + "custom_flags": [ + "#PBS -l walltime=200:0:0" + ], + "source_list": [ + "/opt/intel/oneapi/setvars.sh" + ] + } + } + ] } diff --git a/examples/run/dp-calypso-vasp/param.json b/examples/run/dp-calypso-vasp/param.json index 96f566938..401216b89 100644 --- a/examples/run/dp-calypso-vasp/param.json +++ b/examples/run/dp-calypso-vasp/param.json @@ -1,103 +1,99 @@ { - "model_devi_engine":"calypso", - "_calypso_path":"/home/zhenyu/workplace/dpgen/AA-2400/debug", - "_calypso_input_path":"/home/zhenyu/workplace/dpgen/AA-2400/debug/calypso_input", - "_model_devi_max_iter": 50, - "vsc":false, - + "model_devi_engine": "calypso", + "_calypso_path": "/home/zhenyu/workplace/dpgen/AA-2400/debug", + "_calypso_input_path": "/home/zhenyu/workplace/dpgen/AA-2400/debug/calypso_input", + "_model_devi_max_iter": 50, + "vsc": false, "type_map": [ - "Mg", + "Mg", "Al", "Cu" ], "mass_map": [ - 24, + 24, 27, 64 ], - "init_data_prefix":"/home/zhenyu/workplace/dpgen/AA-2400/data/", + "init_data_prefix": "/home/zhenyu/workplace/dpgen/AA-2400/data/", "init_data_sys": [ - "data.init/data.init/AlCuMg/init.000" + "data.init/data.init/AlCuMg/init.000" ], - "_comment": " that's all ", - + "_comment1": " that's all ", "training_init_model": false, "training_iter0_model_path": "/home/zhenyu/workplace/dpgen/AA-2400/pb/00[0-3]", - "training_reuse_iter": 0, - "training_reuse_old_ratio": 0.9, - "training_reuse_start_lr": 1e-4, - "training_reuse_stop_batch": 1000000, - "training_reuse_start_pref_e": 0.2, - "training_reuse_start_pref_f": 100, - + "training_reuse_iter": 0, + "training_reuse_old_ratio": 0.9, + "training_reuse_start_lr": 0.0001, + "training_reuse_stop_batch": 1000000, + "training_reuse_start_pref_e": 0.2, + "training_reuse_start_pref_f": 100, "numb_models": 4, "default_training_param": { - "model": { - "descriptor": { - "type": "se_e2_a", - "sel": [ - 500, - 700, - 1100 - ], - "rcut_smth": 2.0, - "rcut": 12.0, - "neuron": [ - 25, - 50, - 100 - ], - "resnet_dt": false, - "axis_neuron": 12, - "type_one_side": true, - "seed": 1801819940, - "_activation_function": "tanh" + "model": { + "descriptor": { + "type": "se_e2_a", + "sel": [ + 500, + 700, + 1100 + ], + "rcut_smth": 2.0, + "rcut": 12.0, + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "axis_neuron": 12, + "type_one_side": true, + "seed": 1801819940, + "_activation_function": "tanh" + }, + "fitting_net": { + "neuron": [ + 240, + 240, + 240 + ], + "resnet_dt": true, + "seed": 2375417769 + }, + "type_map": [ + "Mg", + "Al", + "Cu" + ] }, - "fitting_net": { - "neuron": [ - 240, - 240, - 240 - ], - "resnet_dt": true, - "seed": 2375417769 + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 5000 }, - "type_map": [ - "Mg", - "Al", - "Cu" - ] - }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 5000 - }, - "loss": { - "start_pref_e": 0.2, - "limit_pref_e": 2, - "start_pref_f": 100, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0 + "loss": { + "start_pref_e": 0.2, + "limit_pref_e": 2, + "start_pref_f": 100, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "training": { + "stop_batch": 6000, + "seed": 3982377700, + "_comment2": "that's all", + "disp_file": "lcurve.out", + "disp_freq": 2000, + "save_freq": 2000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "set_prefix": "set" + } }, - "training": { - "stop_batch": 6000, - "seed": 3982377700, - "_comment": "that's all", - "disp_file": "lcurve.out", - "disp_freq": 2000, - "numb_test": 4, - "save_freq": 2000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - "set_prefix": "set" - } - }, - "sys_configs":"", + "sys_configs": "", "model_devi_dt": 0.002, "model_devi_skip": 0, "model_devi_f_trust_lo": 0.05, @@ -106,22 +102,311 @@ "model_devi_e_trust_hi": 10000000000.0, "model_devi_clean_traj": true, "model_devi_jobs": [ 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"fmax": 0.01 + } ], - "fp_style": "vasp", "shuffle_poscar": false, "fp_task_max": 10, "fp_task_min": 1, "fp_pp_path": "/home/zhenyu/workplace/dpgen/AA-2400/vasp_input", "fp_pp_files": [ - "POTCAR.Mg", + "POTCAR.Mg", "POTCAR.Al", "POTCAR.Cu" ], - "fp_incar":"/home/zhenyu/workplace/dpgen/AA-2400/vasp_input/INCAR" + "fp_incar": "/home/zhenyu/workplace/dpgen/AA-2400/vasp_input/INCAR" } diff --git a/examples/run/dp-lammps-enhance_sampling/param.json b/examples/run/dp-lammps-enhance_sampling/param.json index f63d04985..6bfb043a1 100644 --- a/examples/run/dp-lammps-enhance_sampling/param.json +++ b/examples/run/dp-lammps-enhance_sampling/param.json @@ -1,126 +1,223 @@ { - "type_map": ["C", "H"], - "mass_map": [12.0, 1.0], - - "_comment": "initial data set for Training and the number of frames in each training batch", - "init_data_prefix": "someplace/tutorial-dpgen-enhance", - "init_data_sys": [ - "raw_file" - ], - "init_batch_size": [ - 4 - ], - - "_comment": "configurations for starting MD 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a/examples/run/dp1.x-lammps-cp2k/methane/param-ch4.json b/examples/run/dp1.x-lammps-cp2k/methane/param-ch4.json deleted file mode 100644 index bab722abf..000000000 --- a/examples/run/dp1.x-lammps-cp2k/methane/param-ch4.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "type_map": [ - "H", - "C" - ], - "mass_map": [ - 1, - 12 - ], - "init_data_prefix": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/data", - "init_data_sys": [ - "deepmd" - ], - "init_batch_size": [ - 8 - ], - "sys_configs": [ - ["/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"], - ["/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"] - ], - "sys_batch_size": [ - 8, - 8, - 8, - 8 - ], - "_comment": " that's all ", - "numb_models": 4, - "default_training_param": { - "model": { - 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[27, 24], - "use_ele_temp": 2, - - "init_data_prefix": "/home/wanghan/study/deep.md/data/almgop.20/init//", - - "init_data_sys": [ - "al.fcc.01x01x01/02.md/sys-0004/deepmd", - "mg.fcc.01x01x01/02.md/sys-0004/deepmd" - ], - "sys_configs": [ - ["/home/wanghan/study/deep.md/data/almgop.20/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR"], - ["/home/wanghan/study/deep.md/data/almgop.20/init/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR"] - ], - - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "_comment": " model parameters", - "model" : { - "descriptor": { - "type": "se_a", - "sel": [90, 90], - "rcut_smth": 1.80, - "rcut": 6.00, - "neuron": [10, 20, 40], - "resnet_dt": false, - "axis_neuron": 4, - "seed": 1 - }, - "fitting_net" : { - "neuron": [120, 120, 120], - "resnet_dt": true, - "numb_fparam": 10, - "seed": 1 - } - }, - - "loss" : { - "start_pref_e": 0.02, - "limit_pref_e": 1, - "start_pref_f": 1000, - 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"nsteps": 50, "press": [1.0,2.0], "sys_idx": [0, 1], "temps": [50,100], "trj_freq": 10 } - ], - "_comment": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 8, - "fp_task_min": 2, - "fp_pp_path": "/home/wanghan/study/deep.md/dpgen/almg/vasp", - "fp_pp_files": ["POTCAR.Al", "POTCAR.Mg"], - "fp_incar": "/home/wanghan/study/deep.md/dpgen/almg/vasp/INCAR", - "_comment": " that's all " -} diff --git a/examples/run/dp1.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json b/examples/run/dp1.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json deleted file mode 100644 index 4b4d92ba2..000000000 --- a/examples/run/dp1.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json +++ /dev/null @@ -1,371 +0,0 @@ -{ - "type_map": ["Al"], - "mass_map": [27], - - "init_data_prefix": "/data1/yfb222333/2_dpgen_gpu_multi/init/", - - "init_data_sys": [ - "al.fcc.02x02x02/02.md/sys-0032/deepmd", - "al.hcp.02x02x02/02.md/sys-0016/deepmd", - 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recorded frames", - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.20, - "model_devi_clean_traj": false, - "model_devi_jobs": -[ - { - "_idx": 0, - "ensemble": "npt", - "nsteps": 1000, - "press": [ - 1.0, - 10.0, - 100.0, - 1000.0, - 5000.0, - 10000.0, - 20000.0, - 50000.0 - ], - "sys_idx": [ - 0, - 8, - 16 - ], - "temps": [ - 50, - 132.0, - 198.0, - 264.0 - ], - "trj_freq": 10 - }, - { - "_idx": 1, - "ensemble": "npt", - "nsteps": 1000, - "press": [ - 1.0, - 10.0, - 100.0, - 1000.0, - 5000.0, - 10000.0, - 20000.0, - 50000.0 - ], - "sys_idx": [ - 1, - 9, - 17 - ], - "temps": [ - 50, - 132.0, - 198.0, - 264.0 - ], - "trj_freq": 10 - }, - { - "_idx": 2, - "ensemble": "npt", - "nsteps": 3000, - "press": [ - 1.0, - 10.0, - 100.0, - 1000.0, - 5000.0, - 10000.0, - 20000.0, - 50000.0 - ], - "sys_idx": [ - 2, - 10, - 18 - ], - "temps": [ - 50, - 132.0, - 198.0, - 264.0 - ], - "trj_freq": 10 - }, - { - "_idx": 3, - "ensemble": 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100644 index b6f80d142..000000000 --- a/examples/run/dp1.x_lammps_gaussian/dodecane/dodecane.json +++ /dev/null @@ -1,84 +0,0 @@ -{ - "type_map": ["C", "H"], - "mass_map": [12.011, 1.008], - "init_data_prefix": "/home/jzzeng/0719dodecane/gen/", - "init_data_sys": ["init_data"], - "sys_configs": [ - ["/home/jzzeng/0719dodecane/gen/data.dodecane.atomic"] - ], - "sys_format":"lammps/lmp", - "numb_models": 4, - "default_training_param" : { - "model":{ - "type_map": ["C","H"], - "descriptor":{ - "type":"se_a", - "sel": [40, 80], - "rcut_smth": 1.00, - "rcut": 6.00, - "neuron": [25, 50, 100], - "resnet_dt": false, - "axis_neuron": 12 - }, - "fitting_net":{ - "neuron": [240, 240, 240], - "resnet_dt": true - } - }, - "learning_rate":{ - "type": "exp", - "start_lr": 0.001, - "decay_steps": 400, - "decay_rate": 0.99 - }, - "loss":{ - "start_pref_e": 0.02, - "limit_pref_e": 1, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0, - "start_pref_pf": 0, - "limit_pref_pf": 0 - }, - "training":{ - "set_prefix": "set", - "stop_batch": 400000, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 1, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "load_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json" - } - }, - "use_clusters": true, - "cluster_cutoff": 3.5, - "cluster_minify": true, - "use_relative": true, - "epsilon": 1.0, - "model_devi_dt": 0.0001, - "model_devi_skip": 100, - "model_devi_f_trust_lo": 0.20, - "model_devi_f_trust_hi": 0.45, - "model_devi_clean_traj": false, - "model_devi_jobs": [ - {"sys_idx": [0], "temps": [ 3000], "trj_freq": 10, "nsteps": 2000, "ensemble": "nvt", "_idx": "00"}, - {"sys_idx": [0], "temps": [ 3000], "trj_freq": 10, "nsteps": 4000, "ensemble": "nvt", "_idx": "01"}, - {"sys_idx": [0], "temps": [ 3000], "trj_freq": 10, "nsteps": 8000, "ensemble": "nvt", "_idx": "02"}, - {"sys_idx": [0], "temps": [ 3000], "trj_freq": 10, "nsteps": 16000, "ensemble": "nvt", "_idx": "03"} - ], - "fp_style": "gaussian", - "shuffle_poscar": false, - "fp_task_max": 1000, - "fp_task_min": 10, - "fp_params": { - "keywords": "force mn15/6-31g**", - "nproc": 4, - "multiplicity": "auto" - } -} diff --git a/examples/run/dp2.x-gromacs-gaussian/param.json b/examples/run/dp2.x-gromacs-gaussian/param.json index 86561e34a..3371cda38 100644 --- a/examples/run/dp2.x-gromacs-gaussian/param.json +++ b/examples/run/dp2.x-gromacs-gaussian/param.json @@ -1,157 +1,281 @@ { - "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"], - "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"], - 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"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 } - ], - "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 - } } diff --git a/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/machine.json b/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/machine.json new file mode 100644 index 000000000..0ff483640 --- /dev/null +++ b/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/machine.json @@ -0,0 +1,85 @@ +{ + "api_version": "1.0", + "train": [ + { + "command": "dp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } + }, + "resources": { + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 1, + "custom_flags": [ + "#SBATCH --mem=32G" + ], + "strategy": { + "if_cuda_multi_devices": true + }, + "para_deg": 3, + "source_list": [ + "/home/user1234/deepmd.1.2.4.env" + ] + } + } + ], + "model_devi": [ + { + "command": "lmp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } + }, + "resources": { + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 5, + "source_list": [ + "/home/user1234/deepmd.1.2.4.env" + ] + } + } + ], + "fp": [ + { + "command": "ABACUS.mpi", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } + }, + "resources": { + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "G_32_128", + "group_size": 1, + "source_list": [ + "~/abacus.env" + ] + } + } + ] +} diff --git a/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/param.json b/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/param.json new file mode 100644 index 000000000..6f99f4ae2 --- /dev/null +++ b/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/param.json @@ -0,0 +1,171 @@ +{ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1.0, + 12.0 + ], + "_comment1": "initial data set for Training and the number of frames in each training batch", + "init_data_prefix": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run_abacus/", + "init_data_sys": [ + "abacus_init_data" + ], + "init_batch_size": [ + 8 + ], + "_comment2": "configurations for starting MD in Exploration and batch sizes when traning snapshots derived from these configs (if they were selected)", + "sys_configs_prefix": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run", + "sys_configs": [ + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/000000/POSCAR", + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/000001/POSCAR", + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000[2-9]/POSCAR" + ], + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" + ] + ], + "sys_batch_size": [ + 8, + 8 + ], + "_comment3": " 00.train ", + "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": [ + 10, + 20, + 40 + ], + "resnet_dt": false, + "axis_neuron": 12, + "seed": 0 + }, + "fitting_net": { + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true, + "coord_norm": true, + "type_fitting_net": false, + "seed": 0 + } + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 180, + "stop_lr": 0.0005655675757628467 + }, + "training": { + "numb_steps": 2000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "_comment4": "that's all", + "training_data": { + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "_comment5": " 01.model_devi ", + "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_clean_traj": false, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 150 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 9000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "_comment6": " 02.fp ", + "fp_style": "abacus", + "shuffle_poscar": false, + "fp_task_max": 50, + "fp_task_min": 8, + "fp_pp_path": "./", + "fp_pp_files": [ + "H_ONCV_PBE-1.0.upf", + "C_ONCV_PBE-1.0.upf" + ], + "fp_orb_files": [ + "H_gga_8au_60Ry_2s1p.orb", + "C_gga_8au_60Ry_2s2p1d.orb" + ], + "fp_dpks_descriptor": "jle.orb", + "user_fp_params": { + "ntype": 2, + "cal_force": 1, + "cal_stress": 1, + "deepks_model": "model.ptg", + "deepks_out_labels": 1, + "basis_type": "lcao", + "gamma_only": 1, + "ecutwfc": 80, + "mixing_type": "pulay", + "mixing_beta": 0.4, + "symmetry": 1, + "nbands": 5, + "nspin": 1, + "smearing_method": "fixed" + } +} diff --git a/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/machine.json b/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/machine.json index 21d234673..92e6fba99 100644 --- a/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/machine.json +++ b/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/machine.json @@ -1,103 +1,105 @@ { - "api_version": "1.0", - "deepmd_version": "2.0.1", - "train" : - { - "command": "dp", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "00*/train.log", - "grouped":true, - "job_name": "dpgen_train_job", - "disk_size": 200, - "scass_type":"", - "checkpoint_files":["00*/checkpoint","00*/model.ckpt*"], - "checkpoint_time":30, - "platform": "", - "region":"", - "image_name":"", - "on_demand":0 + "api_version": "1.0", + "deepmd_version": "2.0.1", + "train": { + "command": "dp", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "00*/train.log", + "grouped": true, + "job_name": "dpgen_train_job", + "disk_size": 200, + "scass_type": "", + "checkpoint_files": [ + "00*/checkpoint", + "00*/model.ckpt*" + ], + "checkpoint_time": 30, + "platform": "", + "region": "", + "image_name": "", + "on_demand": 0 + } } + }, + "resources": { + "batch_type": "Lebesgue", + "group_size": 1 } - }, - "resources": { - "batch_type": "Lebesgue", - "group_size": 1 - } }, - "model_devi": - { - "command": "lmp -i input.lammps -v restart 0", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "*/model_devi.log", - "grouped":true, - "job_name": "dpgen_model_devi_job", - "disk_size": 200, - "scass_type":"", - "platform": "", - "region":"", - "image_name":"", - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "on_demand":0 + "model_devi": { + "command": "lmp -i input.lammps -v restart 0", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "*/model_devi.log", + "grouped": true, + "job_name": "dpgen_model_devi_job", + "disk_size": 200, + "scass_type": "", + "platform": "", + "region": "", + "image_name": "", + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "on_demand": 0 + } } + }, + "resources": { + "batch_type": "Lebesgue", + "group_size": 50 } - }, - "resources": { - "batch_type": "Lebesgue", - "group_size": 50 - } }, - "fp": - { - "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "task*/fp.log", - "grouped":true, - "job_name": "dpgen_fp_job", - "disk_size": 100, - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "scass_type":"", - "platform": "", - "image_name":"", - "on_demand":0 + "fp": { + "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "task*/fp.log", + "grouped": true, + "job_name": "dpgen_fp_job", + "disk_size": 100, + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "scass_type": "", + "platform": "", + "image_name": "", + "on_demand": 0 + } } + }, + "resources": { + "batch_type": "Lebesgue", + "group_size": 50, + "source_list": [ + "" + ] } - }, - "resources": { - "batch_type": "Lebesgue", - "group_size": 50, - "source_list": [""] - } } } diff --git a/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/run_param.json b/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/run_param.json index cdfc177a7..59b0f22c9 100644 --- a/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/run_param.json +++ b/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/run_param.json @@ -9,14 +9,14 @@ "init_data_sys": [ "Al.STRU.02x01x01/02.md/sys-0008/deepmd" ], - "sys_format":"abacus/stru", + "sys_format": "abacus/stru", "sys_configs_prefix": "./", "sys_configs": [ [ "Al.STRU.02x01x01/01.scale_pert/sys-0008/scale*/00000*/STRU" ] ], - "_comment": " that's all ", + "_comment1": " that's all ", "numb_models": 4, "default_training_param": { "model": { @@ -66,14 +66,13 @@ "stop_batch": 20000, "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" + "_comment2": "that's all" } }, "model_devi_dt": 0.002, @@ -82,29 +81,69 @@ "model_devi_f_trust_hi": 0.15, "model_devi_clean_traj": false, "model_devi_jobs": [ - { "sys_idx": [0], "temps": [100], "press": [1.0], "trj_freq": 10,"nsteps": 300, "ensemble": "nvt", "_idx": "00"}, - { "sys_idx": [0], "temps": [100, 300], "press": [1.0, 100.0], "trj_freq": 10,"nsteps": 300, "ensemble": "nvt", "_idx": "01"} - + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 300, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 0 + ], + "temps": [ + 100, + 300 + ], + "press": [ + 1.0, + 100.0 + ], + "trj_freq": 10, + "nsteps": 300, + "ensemble": "nvt", + "_idx": "01" + } ], "fp_style": "abacus", "shuffle_poscar": false, "fp_task_max": 20, "fp_task_min": 5, "fp_pp_path": "./", - "fp_pp_files": ["Al_ONCV_PBE-1.0.upf"], - "fp_orb_files": ["Al_gga_9au_100Ry_4s4p1d.orb"], - "k_points": [1,1,1,0,0,0], - "user_fp_params":{ - "ntype": 1, - "symmetry": 0, - "basis_type": "lcao", - "ecutwfc": 100, - "scf_thr": 1e-8, - "scf_nmax": 100, - "smearing_method": "gauss", - "smearing_sigma": 0.002, - "mixing_type": "pulay", - "mixing_beta": 0.3, - "cal_force": 1 - } + "fp_pp_files": [ + "Al_ONCV_PBE-1.0.upf" + ], + "fp_orb_files": [ + "Al_gga_9au_100Ry_4s4p1d.orb" + ], + "k_points": [ + 1, + 1, + 1, + 0, + 0, + 0 + ], + "user_fp_params": { + "ntype": 1, + "symmetry": 0, + "basis_type": "lcao", + "ecutwfc": 100, + "scf_thr": 1e-08, + "scf_nmax": 100, + "smearing_method": "gauss", + "smearing_sigma": 0.002, + "mixing_type": "pulay", + "mixing_beta": 0.3, + "cal_force": 1 + } } diff --git a/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/machine.json b/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/machine.json index 21d234673..92e6fba99 100644 --- a/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/machine.json +++ b/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/machine.json @@ -1,103 +1,105 @@ { - "api_version": "1.0", - "deepmd_version": "2.0.1", - "train" : - { - "command": "dp", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "00*/train.log", - "grouped":true, - "job_name": "dpgen_train_job", - "disk_size": 200, - "scass_type":"", - "checkpoint_files":["00*/checkpoint","00*/model.ckpt*"], - "checkpoint_time":30, - "platform": "", - "region":"", - "image_name":"", - "on_demand":0 + "api_version": "1.0", + "deepmd_version": "2.0.1", + "train": { + "command": "dp", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "00*/train.log", + "grouped": true, + "job_name": "dpgen_train_job", + "disk_size": 200, + "scass_type": "", + "checkpoint_files": [ + "00*/checkpoint", + "00*/model.ckpt*" + ], + "checkpoint_time": 30, + "platform": "", + "region": "", + "image_name": "", + "on_demand": 0 + } } + }, + "resources": { + "batch_type": "Lebesgue", + "group_size": 1 } - }, - "resources": { - "batch_type": "Lebesgue", - "group_size": 1 - } }, - "model_devi": - { - "command": "lmp -i input.lammps -v restart 0", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "*/model_devi.log", - "grouped":true, - "job_name": "dpgen_model_devi_job", - "disk_size": 200, - "scass_type":"", - "platform": "", - "region":"", - "image_name":"", - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "on_demand":0 + "model_devi": { + "command": "lmp -i input.lammps -v restart 0", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "*/model_devi.log", + "grouped": true, + "job_name": "dpgen_model_devi_job", + "disk_size": 200, + "scass_type": "", + "platform": "", + "region": "", + "image_name": "", + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "on_demand": 0 + } } + }, + "resources": { + "batch_type": "Lebesgue", + "group_size": 50 } - }, - "resources": { - "batch_type": "Lebesgue", - "group_size": 50 - } }, - "fp": - { - "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "task*/fp.log", - "grouped":true, - "job_name": "dpgen_fp_job", - "disk_size": 100, - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "scass_type":"", - "platform": "", - "image_name":"", - "on_demand":0 + "fp": { + "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "task*/fp.log", + "grouped": true, + "job_name": "dpgen_fp_job", + "disk_size": 100, + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "scass_type": "", + "platform": "", + "image_name": "", + "on_demand": 0 + } } + }, + "resources": { + "batch_type": "Lebesgue", + "group_size": 50, + "source_list": [ + "" + ] } - }, - "resources": { - "batch_type": "Lebesgue", - "group_size": 50, - "source_list": [""] - } } } diff --git a/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/run_param.json b/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/run_param.json index 1c492b309..e295f1db0 100644 --- a/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/run_param.json +++ b/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/run_param.json @@ -9,7 +9,7 @@ "init_data_sys": [ "Al.STRU.02x01x01/02.md/sys-0008/deepmd" ], - "sys_format":"abacus/stru", + "sys_format": "abacus/stru", "sys_configs_prefix": "./", "sys_configs": [ [ @@ -19,7 +19,7 @@ "Al.STRU.02x01x01/01.scale_pert/sys-0008/scale*/000010/STRU" ] ], - "_comment": " 00.train ", + "_comment1": " 00.train ", "numb_models": 4, "default_training_param": { "model": { @@ -69,17 +69,16 @@ "stop_batch": 20000, "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" + "_comment2": "that's all" } }, - "_comment": "01.model_devi ", + "_comment3": "01.model_devi ", "model_devi_dt": 0.002, "model_devi_skip": 0, "model_devi_f_trust_lo": 0.05, diff --git a/examples/run/dp2.x-lammps-ABACUS-pw/methane/machine.json b/examples/run/dp2.x-lammps-ABACUS-pw/methane/machine.json new file mode 100644 index 000000000..0ff483640 --- /dev/null +++ b/examples/run/dp2.x-lammps-ABACUS-pw/methane/machine.json @@ -0,0 +1,85 @@ +{ + "api_version": "1.0", + "train": [ + { + "command": "dp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } + }, + "resources": { + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 1, + "custom_flags": [ + "#SBATCH --mem=32G" + ], + "strategy": { + "if_cuda_multi_devices": true + }, + "para_deg": 3, + "source_list": [ + "/home/user1234/deepmd.1.2.4.env" + ] + } + } + ], + "model_devi": [ + { + "command": "lmp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } + }, + "resources": { + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 5, + "source_list": [ + "/home/user1234/deepmd.1.2.4.env" + ] + } + } + ], + "fp": [ + { + "command": "ABACUS.mpi", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } + }, + "resources": { + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "G_32_128", + "group_size": 1, + "source_list": [ + "~/abacus.env" + ] + } + } + ] +} diff --git a/examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json b/examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json new file mode 100644 index 000000000..d0ebc40a0 --- /dev/null +++ b/examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json @@ -0,0 +1,162 @@ +{ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1.0, + 12.0 + ], + "_comment1": "initial data set for Training and the number of frames in each training batch", + "init_data_prefix": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run_abacus/", + "init_data_sys": [ + "abacus_init_data" + ], + "init_batch_size": [ + 8 + ], + "_comment2": "configurations for starting MD in Exploration and batch sizes when traning snapshots derived from these configs (if they were selected)", + "sys_configs_prefix": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run", + "sys_configs": [ + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/000000/POSCAR", + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/000001/POSCAR", + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000[2-9]/POSCAR" + ], + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" + ] + ], + "sys_batch_size": [ + 8, + 8 + ], + "_comment3": " 00.train ", + "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": [ + 10, + 20, + 40 + ], + "resnet_dt": false, + "axis_neuron": 12, + "seed": 0 + }, + "fitting_net": { + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true, + "coord_norm": true, + "type_fitting_net": false, + "seed": 0 + } + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 180, + "stop_lr": 0.0005655675757628467 + }, + "training": { + "numb_steps": 2000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "_comment4": "that's all", + "training_data": { + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "_comment5": " 01.model_devi ", + "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_clean_traj": false, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 50 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 1000, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 50 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "_comment6": " 02.fp ", + "fp_style": "abacus", + "shuffle_poscar": false, + "fp_task_max": 30, + "fp_task_min": 8, + "fp_pp_path": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/SG15_ONCV_v1.0_upf", + "fp_pp_files": [ + "H_ONCV_PBE-1.0.upf", + "C_ONCV_PBE-1.0.upf" + ], + "user_fp_params": { + "ntype": 2, + "ecutwfc": 80, + "mixing_type": "pulay", + "mixing_beta": 0.4, + "symmetry": 1, + "nbands": 5, + "nspin": 1, + "ks_solver": "cg", + "smearing": "fixed", + "sigma": 0.001 + } +} diff --git a/examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json b/examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json new file mode 100644 index 000000000..9f998fb46 --- /dev/null +++ b/examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json @@ -0,0 +1,138 @@ +{ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/data", + "init_data_sys": [ + "deepmd" + ], + "init_batch_size": [ + 8 + ], + "sys_configs": [ + [ + "/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" + ], + [ + "/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" + ] + ], + "sys_batch_size": [ + 8, + 8, + 8, + 8 + ], + "_comment1": " that's all ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut_smth": 0.5, + "rcut": 5.0, + "_comment2": "modify according your system", + "neuron": [ + 10, + 20, + 40 + ], + "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, + "_comment3": "nope", + "stop_lr": 0.0003584859224085419 + }, + "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": { + "stop_batch": 2000, + "seed": 1, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "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_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 300, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "fp_style": "cp2k", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 5, + "external_input_path": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/cp2k_dpgen/template.inp" +} diff --git a/examples/run/dp1.x-lammps-cp2k/methane/template.inp b/examples/run/dp2.x-lammps-cp2k/methane/template.inp similarity index 100% rename from examples/run/dp1.x-lammps-cp2k/methane/template.inp rename to examples/run/dp2.x-lammps-cp2k/methane/template.inp diff --git a/examples/run/dp2.x-lammps-cp2k/param_CH4_deepmd-kit-2.0.1.json b/examples/run/dp2.x-lammps-cp2k/param_CH4_deepmd-kit-2.0.1.json index df596a6d1..7c7f5acbb 100644 --- a/examples/run/dp2.x-lammps-cp2k/param_CH4_deepmd-kit-2.0.1.json +++ b/examples/run/dp2.x-lammps-cp2k/param_CH4_deepmd-kit-2.0.1.json @@ -19,7 +19,7 @@ "./data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" ] ], - "_comment": " that's all ", + "_comment1": " that's all ", "numb_models": 4, "default_training_param": { "model": { @@ -73,14 +73,13 @@ "_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" + "_comment2": "that's all" } }, "model_devi_dt": 0.002, @@ -119,24 +118,32 @@ "ensemble": "nvt", "_idx": "01" } - ], - "ratio_failed": 0.20, + "ratio_failed": 0.2, "fp_style": "cp2k", "shuffle_poscar": false, "fp_task_max": 30, "fp_task_min": 1, - "user_fp_params": { - "FORCE_EVAL":{ - "DFT":{ + "user_fp_params": { + "FORCE_EVAL": { + "DFT": { "BASIS_SET_FILE_NAME": "BASIS_MOLOPT", "POTENTIAL_FILE_NAME": "GTH_POTENTIALS" }, - "SUBSYS":{ - "KIND":{ - "_": ["C","H"], - "POTENTIAL": ["GTH-PBE-q4", "GTH-PBE-q1"], - "BASIS_SET": ["DZVP-MOLOPT-GTH","DZVP-MOLOPT-GTH"] + "SUBSYS": { + "KIND": { + "_": [ + "C", + "H" + ], + "POTENTIAL": [ + "GTH-PBE-q4", + "GTH-PBE-q1" + ], + "BASIS_SET": [ + "DZVP-MOLOPT-GTH", + "DZVP-MOLOPT-GTH" + ] } } } diff --git a/examples/run/dp2.x-lammps-gaussian/machine.json b/examples/run/dp2.x-lammps-gaussian/machine.json index f9f19c37a..450baa944 100644 --- a/examples/run/dp2.x-lammps-gaussian/machine.json +++ b/examples/run/dp2.x-lammps-gaussian/machine.json @@ -1,109 +1,111 @@ { - "api_version": "1.0", - "deepmd_version": "2.1.0", - "train" : - { - "command": "dp", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "xxx", - "password": "xxx", - "program_id": 123, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "00*/train.log", - "grouped":true, - "job_name": "dpgen_train_job", - "disk_size": 100, - "scass_type":"c4_m15_1 * NVIDIA T4", - "checkpoint_files":["00*/checkpoint","00*/model.ckpt*"], - "checkpoint_time":30, - "platform": "ali", - "image_name":"LBG_DeePMD-kit_2.1.0_v1", - "on_demand":0 + "api_version": "1.0", + "deepmd_version": "2.1.0", + "train": { + "command": "dp", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "xxx", + "password": "xxx", + "program_id": 123, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "00*/train.log", + "grouped": true, + "job_name": "dpgen_train_job", + "disk_size": 100, + "scass_type": "c4_m15_1 * NVIDIA T4", + "checkpoint_files": [ + "00*/checkpoint", + "00*/model.ckpt*" + ], + "checkpoint_time": 30, + "platform": "ali", + "image_name": "LBG_DeePMD-kit_2.1.0_v1", + "on_demand": 0 + } } + }, + "resources": { + "batch_type": "Lebesgue", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 1 } - }, - "resources": { - "batch_type": "Lebesgue", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "T4_4_15", - "group_size": 1 - } }, - "model_devi": - { - "command": "lmp", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "xxx", - "password": "xxx", - "program_id": 123, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "*/model_devi.log", - "grouped":true, - "job_name": "dpgen_model_devi_job", - "disk_size": 200, - "scass_type":"c4_m15_1 * NVIDIA T4", - "platform": "ali", - "image_name":"LBG_DeePMD-kit_2.1.0_v1", - "on_demand":0 + "model_devi": { + "command": "lmp", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "xxx", + "password": "xxx", + "program_id": 123, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "*/model_devi.log", + "grouped": true, + "job_name": "dpgen_model_devi_job", + "disk_size": 200, + "scass_type": "c4_m15_1 * NVIDIA T4", + "platform": "ali", + "image_name": "LBG_DeePMD-kit_2.1.0_v1", + "on_demand": 0 + } } + }, + "resources": { + "batch_type": "Lebesgue", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 50 } - }, - "resources": { - "batch_type": "Lebesgue", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "T4_4_15", - "group_size": 50 - } }, - "fp": - { - "command": "g09 < input > output ||:", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "xxx", - "password": "xxx", - "program_id": 123, - "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":"c16_m32_cpu", - "platform": "ali", - "image_name":"LBG_Gaussian_09_v2", - "on_demand":0 + "fp": { + "command": "g09 < input > output ||:", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "xxx", + "password": "xxx", + "program_id": 123, + "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": "c16_m32_cpu", + "platform": "ali", + "image_name": "LBG_Gaussian_09_v2", + "on_demand": 0 + } } + }, + "resources": { + "batch_type": "Lebesgue", + "source_list": [ + "/root/g09.sh" + ], + "number_node": 1, + "cpu_per_node": 16, + "gpu_per_node": 0, + "queue_name": "CPU", + "group_size": 10 } - }, - "resources": { - "batch_type": "Lebesgue", - "source_list": ["/root/g09.sh"], - "number_node": 1, - "cpu_per_node": 16, - "gpu_per_node": 0, - "queue_name": "CPU", - "group_size": 10 - } } } diff --git a/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json b/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json index 4f422fe73..5dac25455 100644 --- a/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json +++ b/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json @@ -11,17 +11,29 @@ ], "init_data_prefix": "./data/deepmd/", "init_data_sys": [ - "data.000","data.001","data.002","data.003","data.004","data.005" + "data.000", + "data.001", + "data.002", + "data.003", + "data.004", + "data.005" + ], + "init_batch_size": [ + "auto", + "auto", + "auto", + "auto", + "auto", + "auto" ], - "init_batch_size": ["auto","auto","auto","auto","auto","auto"], "sys_configs": [ [ "./data/md_sys/data.ch4n2" ] ], - "_comment": " that's all ", + "_comment1": " that's all ", "numb_models": 4, - "sys_format":"lammps/lmp", + "sys_format": "lammps/lmp", "default_training_param": { "model": { "type_map": [ @@ -74,14 +86,13 @@ "_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" + "_comment2": "that's all" } }, "model_devi_dt": 0.002, @@ -120,21 +131,20 @@ "ensemble": "nvt", "_idx": "01" } - ], "use_clusters": true, "cluster_cutoff": 5.0, "cluster_minify": true, "use_relative": true, "epsilon": 1.0, - "ratio_failed": 0.20, + "ratio_failed": 0.2, "fp_style": "gaussian", "shuffle_poscar": false, "fp_task_max": 20, "fp_task_min": 5, - "fp_params":{ - "keywords": "force B3LYP 6-31g(d,p) nosymm", - "nproc":2 , - "multiplicity": "auto" + "fp_params": { + "keywords": "force B3LYP 6-31g(d,p) nosymm", + "nproc": 2, + "multiplicity": "auto" } } diff --git a/examples/run/dp2.x-lammps-vasp-et/param_elet.json b/examples/run/dp2.x-lammps-vasp-et/param_elet.json new file mode 100644 index 000000000..92c34262a --- /dev/null +++ b/examples/run/dp2.x-lammps-vasp-et/param_elet.json @@ -0,0 +1,131 @@ +{ + "type_map": [ + "Al", + "Mg" + ], + "mass_map": [ + 27, + 24 + ], + "use_ele_temp": 2, + "init_data_prefix": "/home/wanghan/study/deep.md/data/almgop.20/init//", + "init_data_sys": [ + "al.fcc.01x01x01/02.md/sys-0004/deepmd", + "mg.fcc.01x01x01/02.md/sys-0004/deepmd" + ], + "sys_configs": [ + [ + "/home/wanghan/study/deep.md/data/almgop.20/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR" + ], + [ + "/home/wanghan/study/deep.md/data/almgop.20/init/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR" + ] + ], + "_comment1": " 00.train ", + "numb_models": 4, + "default_training_param": { + "_comment2": " model parameters", + "model": { + "descriptor": { + "type": "se_a", + "sel": [ + 90, + 90 + ], + "rcut_smth": 1.8, + "rcut": 6.0, + "neuron": [ + 10, + 20, + 40 + ], + "resnet_dt": false, + "axis_neuron": 4, + "seed": 1 + }, + "fitting_net": { + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true, + "numb_fparam": 10, + "seed": 1 + } + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 1, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "learning_rate": { + "start_lr": 0.001, + "decay_steps": 5000, + "stop_lr": 0.0009897937816869885 + }, + "_comment3": " traing controls", + "training": { + "stop_batch": 1000, + "seed": 1, + "_comment4": " display and restart", + "_comment5": " frequencies counted in batch", + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + }, + "_comment6": "that's all" + }, + "_comment7": " 01.model_devi ", + "_comment8": "model_devi_skip: the first x of the recorded frames", + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.2, + "model_devi_clean_traj": false, + "model_devi_jobs": [ + { + "_idx": 0, + "ensemble": "npt", + "nsteps": 50, + "press": [ + 1.0, + 2.0 + ], + "sys_idx": [ + 0, + 1 + ], + "temps": [ + 50, + 100 + ], + "trj_freq": 10 + } + ], + "_comment9": " 02.fp ", + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 8, + "fp_task_min": 2, + "fp_pp_path": "/home/wanghan/study/deep.md/dpgen/almg/vasp", + "fp_pp_files": [ + "POTCAR.Al", + "POTCAR.Mg" + ], + "fp_incar": "/home/wanghan/study/deep.md/dpgen/almg/vasp/INCAR", + "_comment10": " that's all " +} diff --git a/examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-2.x.json 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"type_fitting_net": false, + "_comment3": " traing controls", + "stop_batch": 20000, + "seed": 0, + "_comment4": " display and restart", + "_comment5": " frequencies counted in batch", + "disp_file": "lcurve.out", + "disp_freq": 2000, + "save_freq": 2000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "_comment6": "that's all", + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "_comment7": " 01.model_devi ", + "_comment8": "model_devi_skip: the first x of the recorded frames", + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.2, + "model_devi_clean_traj": false, + "model_devi_jobs": [ + { + "_idx": 0, + "ensemble": "npt", + "nsteps": 1000, + "press": [ + 1.0, + 10.0, + 100.0, + 1000.0, + 5000.0, + 10000.0, + 20000.0, + 50000.0 + ], + "sys_idx": [ + 0, + 8, + 16 + ], + "temps": [ + 50, + 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+ 20 + ], + "temps": [ + 50, + 132.0, + 198.0, + 264.0 + ], + "trj_freq": 10 + }, + { + "_idx": 5, + "ensemble": "npt", + "nsteps": 3000, + "press": [ + 1.0, + 10.0, + 100.0, + 1000.0, + 5000.0, + 10000.0, + 20000.0, + 50000.0 + ], + "sys_idx": [ + 5, + 13, + 21 + ], + "temps": [ + 50, + 132.0, + 198.0, + 264.0 + ], + "trj_freq": 10 + }, + { + "_idx": 6, + "ensemble": "npt", + "nsteps": 3000, + "press": [ + 1.0, + 10.0, + 100.0, + 1000.0, + 5000.0, + 10000.0, + 20000.0, + 50000.0 + ], + "sys_idx": [ + 6, + 14, + 22 + ], + "temps": [ + 50, + 132.0, + 198.0, + 264.0 + ], + "trj_freq": 10 + }, + { + "_idx": 7, + "ensemble": "npt", + "nsteps": 3000, + "press": [ + 1.0, + 10.0, + 100.0, + 1000.0, + 5000.0, + 10000.0, + 20000.0, + 50000.0 + ], + "sys_idx": [ + 7, + 15, + 23 + ], + "temps": [ + 50, + 132.0, + 198.0, + 264.0 + ], + "trj_freq": 10 + }, + { + "_idx": 8, + "ensemble": "npt", + "nsteps": 1000, + "press": [ + 1.0, + 10.0, + 100.0, + 1000.0, + 5000.0, + 10000.0, + 20000.0, + 50000.0 + ], + "sys_idx": [ + 0, + 8, + 16 + ], + "temps": [ + 330.0, + 396.0, + 462.0, + 528.0, + 594.0 + ], + "trj_freq": 10 + } + ], + "_comment9": " 02.fp ", + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 300, + "fp_task_min": 5, + "fp_pp_path": "/data1/yfb222333/2_dpgen_gpu_multi/POTCAR-Al", + "fp_pp_files": [ + "POTCAR" + ], + "fp_incar": "/data1/yfb222333/2_dpgen_gpu_multi/INCAR_metal_scf_gpu", + "_comment10": " that's all " +} diff --git a/examples/run/dp1.x-lammps-vasp/CH4/INCAR_methane b/examples/run/dp2.x-lammps-vasp/CH4/INCAR_methane similarity index 100% rename from examples/run/dp1.x-lammps-vasp/CH4/INCAR_methane rename to examples/run/dp2.x-lammps-vasp/CH4/INCAR_methane diff --git a/examples/run/dp1.x-lammps-vasp/CH4/POT_C b/examples/run/dp2.x-lammps-vasp/CH4/POT_C similarity index 100% rename from examples/run/dp1.x-lammps-vasp/CH4/POT_C rename to examples/run/dp2.x-lammps-vasp/CH4/POT_C diff --git a/examples/run/dp1.x-lammps-vasp/CH4/POT_H b/examples/run/dp2.x-lammps-vasp/CH4/POT_H similarity index 100% rename from examples/run/dp1.x-lammps-vasp/CH4/POT_H rename to examples/run/dp2.x-lammps-vasp/CH4/POT_H diff --git a/examples/run/dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json b/examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json similarity index 89% rename from examples/run/dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json rename to examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json index 7925ce3ee..5c094f0fb 100644 --- a/examples/run/dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json +++ b/examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json @@ -20,7 +20,7 @@ "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" ] ], - "_comment": " that's all ", + "_comment1": " that's all ", "numb_models": 4, "default_training_param": { "model": { @@ -59,7 +59,7 @@ "type": "exp", "start_lr": 0.001, "decay_steps": 100, - "decay_rate": 0.95 + "stop_lr": 0.0003584859224085419 }, "loss": { "start_pref_e": 0.02, @@ -70,20 +70,20 @@ "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", - "load_ckpt": "model.ckpt", "disp_training": true, "time_training": true, "profiling": false, "profiling_file": "timeline.json", - "_comment": "that's all" + "_comment2": "that's all", + "training_data": { + "set_prefix": "set", + "batch_size": 1 + } } }, "model_devi_dt": 0.002, @@ -132,6 +132,6 @@ "POTCAR_H", "POTCAR_C" ], - "_comments" : "We can only provide empty files in public, you should provide valid POTCARS yourself when running DP-GEN", + "_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 index b732f34e9..a59f44f9f 100644 --- 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 @@ -20,7 +20,7 @@ "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" ] ], - "_comment": " that's all ", + "_comment1": " that's all ", "numb_models": 4, "default_training_param": { "model": { @@ -74,14 +74,13 @@ "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" + "_comment2": "that's all" } }, "model_devi_dt": 0.002, diff --git a/examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json b/examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json new file mode 100644 index 000000000..e28574bb9 --- /dev/null +++ b/examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json @@ -0,0 +1,152 @@ +{ + "type_map": [ + "C", + "H" + ], + "mass_map": [ + 12.011, + 1.008 + ], + "init_data_prefix": "/home/jzzeng/0719dodecane/gen/", + "init_data_sys": [ + "init_data" + ], + "sys_configs": [ + [ + "/home/jzzeng/0719dodecane/gen/data.dodecane.atomic" + ] + ], + "sys_format": "lammps/lmp", + "numb_models": 4, + "default_training_param": { + "model": { + "type_map": [ + "C", + "H" + ], + "descriptor": { + "type": "se_a", + "sel": [ + 40, + 80 + ], + "rcut_smth": 1.0, + "rcut": 6.0, + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "axis_neuron": 12 + }, + "fitting_net": { + "neuron": [ + 240, + 240, + 240 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 400, + "stop_lr": 4.317124741065782e-08 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 1, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0, + "start_pref_pf": 0, + "limit_pref_pf": 0 + }, + "training": { + "stop_batch": 400000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "set_prefix": "set" + } + } + }, + "use_clusters": true, + "cluster_cutoff": 3.5, + "cluster_minify": true, + "use_relative": true, + "epsilon": 1.0, + "model_devi_dt": 0.0001, + "model_devi_skip": 100, + "model_devi_f_trust_lo": 0.2, + "model_devi_f_trust_hi": 0.45, + "model_devi_clean_traj": false, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 3000 + ], + "trj_freq": 10, + "nsteps": 2000, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 0 + ], + "temps": [ + 3000 + ], + "trj_freq": 10, + "nsteps": 4000, + "ensemble": "nvt", + "_idx": "01" + }, + { + "sys_idx": [ + 0 + ], + "temps": [ + 3000 + ], + "trj_freq": 10, + "nsteps": 8000, + "ensemble": "nvt", + "_idx": "02" + }, + { + "sys_idx": [ + 0 + ], + "temps": [ + 3000 + ], + "trj_freq": 10, + "nsteps": 16000, + "ensemble": "nvt", + "_idx": "03" + } + ], + "fp_style": "gaussian", + "shuffle_poscar": false, + "fp_task_max": 1000, + "fp_task_min": 10, + "fp_params": { + "keywords": "force mn15/6-31g**", + "nproc": 4, + "multiplicity": "auto" + } +} diff --git a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/machine.json b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/machine.json index ae25aa061..967735fb5 100644 --- a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/machine.json +++ b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/machine.json @@ -1,113 +1,115 @@ { "api_version": "1.0", - "_comment": "dependent on dpdispatcher 0.4.15", - "train" : - { + "_comment1": "dependent on dpdispatcher 0.4.15", + "train": { "command": "dp", "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "input_data":{ - "api_version":2, - "job_type": "indicate", - "log_file": "00*/lcurve.out", - "grouped": true, - "job_name": "simplify_MAPbI3-scan_train_job", - "disk_size": 100, - "scass_type":"c8_m32_1 * NVIDIA V100", - "platform": "ali", - "checkpoint_files": ["00*/model.ckpt*", "00*/checkpoint"], - "checkpoint_time": 15, - "image_name":"LBG_DeePMD-kit_2.1.1_v1.1", - "on_demand":0 - } - } + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "input_data": { + "api_version": 2, + "job_type": "indicate", + "log_file": "00*/lcurve.out", + "grouped": true, + "job_name": "simplify_MAPbI3-scan_train_job", + "disk_size": 100, + "scass_type": "c8_m32_1 * NVIDIA V100", + "platform": "ali", + "checkpoint_files": [ + "00*/model.ckpt*", + "00*/checkpoint" + ], + "checkpoint_time": 15, + "image_name": "LBG_DeePMD-kit_2.1.1_v1.1", + "on_demand": 0 + } + } }, "resources": { - "batch_type": "Lebesgue", - "number_node": 15, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "V100_8_32", - "group_size": 1 + "batch_type": "Lebesgue", + "number_node": 15, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "V100_8_32", + "group_size": 1 } - }, - "model_devi": - { + }, + "model_devi": { "command": "dp", "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "input_data":{ - "api_version":2, - "job_type": "indicate", - "log_file": "cubic-*/*/md.log", - "grouped": true, - "job_name": "MAPbI3-scan_md_job", - "disk_size": 100, - "scass_type":"c8_m32_1 * NVIDIA V100", - "platform": "ali", - "checkpoint_files": "sync_files", - "checkpoint_time": 15, - "image_name":"LBG_DeePMD-kit_2.1.1_v1.1", - "on_demand":0 - } - } + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "input_data": { + "api_version": 2, + "job_type": "indicate", + "log_file": "cubic-*/*/md.log", + "grouped": true, + "job_name": "MAPbI3-scan_md_job", + "disk_size": 100, + "scass_type": "c8_m32_1 * NVIDIA V100", + "platform": "ali", + "checkpoint_files": "sync_files", + "checkpoint_time": 15, + "image_name": "LBG_DeePMD-kit_2.1.1_v1.1", + "on_demand": 0 + } + } }, "resources": { - "batch_type": "Lebesgue", - "number_node": 15, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "V100_8_32", - "group_size": 10 + "batch_type": "Lebesgue", + "number_node": 15, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "V100_8_32", + "group_size": 10 } - }, - "fp": - { + }, + "fp": { "command": "ulimit -m unlimited; ulimit -s unlimited; mpirun -n 32 vasp_std", "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "input_data":{ - "api_version":2, - "job_type": "indicate", - "log_file": "**/fp.log", - "grouped": true, - "job_name": "simplify_MAPbI3-scan_fp_job", - "disk_size": 100, - "scass_type":"c32_m64_cpu", - "platform": "ali", - "checkpoint_files": "sync_files", - "checkpoint_time": 15, - "image_name":"LBG_vasp-5-4-4_v1", - "on_demand":0 - } - } + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "input_data": { + "api_version": 2, + "job_type": "indicate", + "log_file": "**/fp.log", + "grouped": true, + "job_name": "simplify_MAPbI3-scan_fp_job", + "disk_size": 100, + "scass_type": "c32_m64_cpu", + "platform": "ali", + "checkpoint_files": "sync_files", + "checkpoint_time": 15, + "image_name": "LBG_vasp-5-4-4_v1", + "on_demand": 0 + } + } }, "resources": { - "batch_type": "Lebesgue", - "number_node": 15, - "cpu_per_node": 32, - "gpu_per_node": 0, - "queue_name": "CPU", - "group_size": 10, - "source_list": ["/opt/intel/oneapi/setvars.sh"] + "batch_type": "Lebesgue", + "number_node": 15, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "CPU", + "group_size": 10, + "source_list": [ + "/opt/intel/oneapi/setvars.sh" + ] } - } - } + } +} diff --git a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json index cb5420910..23d0f8083 100644 --- a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json +++ b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json @@ -1,94 +1,147 @@ { - "type_map": ["I","Pb","C","N","H"], - "mass_map": [126.90447, 207.2, 12.0108, 14.0067, 1.00795], - - "pick_data": "../data", - "init_data_prefix": "", - "init_data_sys": [], - "sys_configs": [null], - "sys_batch_size": [1], - - "_comment": " 00.train ", - "numb_models": 4, - "model_devi_activation_func":[["tanh","tanh"],["tanh","gelu"],["gelu","gelu"],["gelu","tanh"]], - - "default_training_param": { - "model": { - "type_map": ["I","Pb","C","N","H"], - "descriptor": { - "type": "se_e2_a", - "sel": + "type_map": [ + "I", + "Pb", + "C", + "N", + "H" + ], + "mass_map": [ + 126.90447, + 207.2, + 12.0108, + 14.0067, + 1.00795 + ], + "pick_data": "../data", + "init_data_prefix": "", + "init_data_sys": [], + "sys_configs": [ + null + ], + "sys_batch_size": [ + 1 + ], + "_comment1": " 00.train ", + "numb_models": 4, + "model_devi_activation_func": [ [ - 20, - 8, - 8, - 8, - 48 + "tanh", + "tanh" ], - "rcut_smth": 2.00, - "rcut": 6.00, - "neuron": [25, 50, 100], - "resnet_dt": false, - "type_one_side": true, - "trainable": true, - "axis_neuron": 12, - "seed": 0 - }, - "fitting_net": { - "neuron": [240, 240, 240], - "resnet_dt": true, - "trainable": [true, true, true, true], - "seed": 0 - } - }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 2, - "start_pref_v": 0.01, - "limit_pref_v": 1 - }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 25, - "decay_rate": 0.95 + [ + "tanh", + "gelu" + ], + [ + "gelu", + "gelu" + ], + [ + "gelu", + "tanh" + ] + ], + "default_training_param": { + "model": { + "type_map": [ + "I", + "Pb", + "C", + "N", + "H" + ], + "descriptor": { + "type": "se_e2_a", + "sel": [ + 20, + 8, + 8, + 8, + 48 + ], + "rcut_smth": 2.0, + "rcut": 6.0, + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "type_one_side": true, + "trainable": true, + "axis_neuron": 12, + "seed": 0 + }, + "fitting_net": { + "neuron": [ + 240, + 240, + 240 + ], + "resnet_dt": true, + "trainable": [ + true, + true, + true, + true + ], + "seed": 0 + } + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 2, + "start_pref_v": 0.01, + "limit_pref_v": 1 + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 25, + "stop_lr": 3.505266624882874e-08 + }, + "training": { + "stop_batch": 5000, + "seed": 1, + "_comment2": "frequencies counted in batch", + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 10000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "set_prefix": "set", + "batch_size": "auto" + } + } }, - "training": { - "set_prefix": "set", - "stop_batch": 5000, - "batch_size": "auto", - "seed": 1, - "_comment": "frequencies counted in batch", - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 4, - "save_freq": 10000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json" - } - }, - - "_comment": "02.fp", - "fp_style": "vasp", - "fp_skip_bad_box": "length_ratio:5;height_ratio:5", - "fp_accurate_threshold": 0.10, - "fp_accurate_soft_threshold": 0.00, - "fp_task_max": 20, - "fp_task_min": 5, - "ratio_failed": 0.30, - "fp_pp_path": "../vasp_inputs/", - "fp_pp_files": ["POTCAR_I","POTCAR_Pb_d","POTCAR_C","POTCAR_N","POTCAR_H"], - "fp_incar": "INCAR", - - "labeled": false, - "init_pick_number":5, - "iter_pick_number":5, - "model_devi_f_trust_lo":0.30, - "model_devi_f_trust_hi":100.00, - "cvasp": false + "_comment3": "02.fp", + "fp_style": "vasp", + "fp_skip_bad_box": "length_ratio:5;height_ratio:5", + "fp_accurate_threshold": 0.1, + "fp_accurate_soft_threshold": 0.0, + "fp_task_max": 20, + "fp_task_min": 5, + "ratio_failed": 0.3, + "fp_pp_path": "../vasp_inputs/", + "fp_pp_files": [ + "POTCAR_I", + "POTCAR_Pb_d", + "POTCAR_C", + "POTCAR_N", + "POTCAR_H" + ], + "fp_incar": "INCAR", + "labeled": false, + "init_pick_number": 5, + "iter_pick_number": 5, + "model_devi_f_trust_lo": 0.3, + "model_devi_f_trust_hi": 100.0, + "cvasp": false } diff --git a/examples/simplify/qm7.json b/examples/simplify/qm7.json index 38ba048c2..bee5a1536 100644 --- a/examples/simplify/qm7.json +++ b/examples/simplify/qm7.json @@ -16,7 +16,9 @@ "pick_data": "/scratch/jz748/simplify/qm7", "init_data_prefix": "", "init_data_sys": [], - "sys_configs": [null], + "sys_configs": [ + null + ], "sys_batch_size": [ "auto" ], @@ -39,8 +41,8 @@ 3, 1 ], - "rcut_smth": 1.00, - "rcut": 6.00, + "rcut_smth": 1.0, + "rcut": 6.0, "neuron": [ 25, 50, @@ -62,7 +64,7 @@ "type": "exp", "start_lr": 0.001, "decay_steps": 10, - "decay_rate": 0.99 + "stop_lr": 4.317124741065782e-08 }, "loss": { "start_pref_e": 0.02, @@ -75,19 +77,20 @@ "limit_pref_pf": 0 }, "training": { - "set_prefix": "set", "stop_batch": 10000, "disp_file": "lcurve.out", "disp_freq": 1000, - "numb_test": 1, "save_freq": 1000, "save_ckpt": "model.ckpt", "disp_training": true, "time_training": true, "profiling": false, - "profiling_file": "timeline.json" + "profiling_file": "timeline.json", + "training_data": { + "set_prefix": "set" + } }, - "_comment": "that's all" + "_comment1": "that's all" }, "use_clusters": true, "fp_style": "gaussian", @@ -97,11 +100,11 @@ "keywords": "mn15/6-31g** force nosymm scf(maxcyc=512)", "nproc": 28, "multiplicity": 1, - "_comment": " that's all " + "_comment2": " that's all " }, - "init_pick_number":100, - "iter_pick_number":100, - "model_devi_f_trust_lo":0.10, - "model_devi_f_trust_hi":0.30, - "_comment": " that's all " + "init_pick_number": 100, + "iter_pick_number": 100, + "model_devi_f_trust_lo": 0.1, + "model_devi_f_trust_hi": 0.3, + "_comment3": " that's all " } diff --git a/examples/test/deepmd_param.json b/examples/test/deepmd_param.json index ae920184d..5d04afc66 100644 --- a/examples/test/deepmd_param.json +++ b/examples/test/deepmd_param.json @@ -1,5 +1,5 @@ { - "_comment": "models", + "_comment1": "models", "potcar_map": { "Al": "/somewhere/example/POTCAR" }, @@ -7,15 +7,14 @@ "key_id": "key id of Material project", "task_type": "deepmd", "task": "all", - "vasp_params": { "ecut": 650, - "ediff": 1e-6, + "ediff": 1e-06, "kspacing": 0.1, "kgamma": false, "npar": 1, "kpar": 1, - "_comment": " that's all " + "_comment2": " that's all " }, "lammps_params": { "model_dir": "somewhere/example/Al_model", @@ -25,39 +24,39 @@ "model_name": false, "model_param_type": false }, - "_comment": "00.equi", + "_comment3": "00.equi", "alloy_shift": false, - "_comment": "01.eos", + "_comment4": "01.eos", "vol_start": 12, "vol_end": 22, "vol_step": 0.5, - "_comment": "02.elastic", - "norm_deform": 2e-2, - "shear_deform": 5e-2, - "_comment": "03.vacancy", + "_comment5": "02.elastic", + "norm_deform": 0.02, + "shear_deform": 0.05, + "_comment6": "03.vacancy", "supercell": [ 3, 3, 3 ], - "_comment": "04.interstitial", + "_comment7": "04.interstitial", "insert_ele": [ "Al" ], "reprod-opt": false, - "_comment": "05.surface", + "_comment8": "05.surface", "min_slab_size": 10, "min_vacuum_size": 11, - "_comment": "pert xz to work around vasp bug...", + "_comment9": "pert xz to work around vasp bug...", "pert_xz": 0.01, "max_miller": 2, "relax_box": false, - "_comment": "06.phonon", + "_comment10": "06.phonon", "supercell_matrix": [ 2, 2, 2 ], "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", - "_comment": "that's all" + "_comment11": "that's all" } diff --git a/examples/test/meam_param.json b/examples/test/meam_param.json index 1790bb2a9..7eeec66d2 100644 --- a/examples/test/meam_param.json +++ b/examples/test/meam_param.json @@ -1,5 +1,5 @@ { - "_comment": "models", + "_comment1": "models", "potcar_map": { "Al": "/somewhere/example/POTCAR" }, @@ -7,15 +7,14 @@ "key_id": "key id of Material project", "task_type": "meam", "task": "all", - "vasp_params": { "ecut": 650, - "ediff": 1e-6, + "ediff": 1e-06, "kspacing": 0.1, "kgamma": false, "npar": 1, "kpar": 1, - "_comment": " that's all " + "_comment2": " that's all " }, "lammps_params": { "model_dir": "somewhere/example/meam", @@ -38,39 +37,39 @@ "FeS" ] }, - "_comment": "00.equi", + "_comment3": "00.equi", "alloy_shift": false, - "_comment": "01.eos", + "_comment4": "01.eos", "vol_start": 12, "vol_end": 22, "vol_step": 0.5, - "_comment": "02.elastic", - "norm_deform": 2e-2, - "shear_deform": 5e-2, - "_comment": "03.vacancy", + "_comment5": "02.elastic", + "norm_deform": 0.02, + "shear_deform": 0.05, + "_comment6": "03.vacancy", "supercell": [ 3, 3, 3 ], - "_comment": "04.interstitial", + "_comment7": "04.interstitial", "insert_ele": [ "Al" ], "reprod-opt": false, - "_comment": "05.surface", + "_comment8": "05.surface", "min_slab_size": 10, "min_vacuum_size": 11, - "_comment": "pert xz to work around vasp bug...", + "_comment9": "pert xz to work around vasp bug...", "pert_xz": 0.01, "max_miller": 2, "relax_box": false, - "_comment": "06.phonon", + "_comment10": "06.phonon", "supercell_matrix": [ 2, 2, 2 ], "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", - "_comment": "that's all" + "_comment11": "that's all" } diff --git a/examples/test/vasp_param.json b/examples/test/vasp_param.json index d1dfb9a1d..981b78f02 100644 --- a/examples/test/vasp_param.json +++ b/examples/test/vasp_param.json @@ -1,55 +1,54 @@ { - "_comment": "models", - "potcar_map": { - "Al": "/somewhere/example/POTCAR" - }, - "conf_dir": "confs/Al/std-fcc", - "key_id": "key id of Material project", - "task_type": "vasp", - "task": "all", - - "vasp_params": { - "ecut": 650, - "ediff": 1e-6, - "kspacing": 0.1, - "kgamma": false, - "npar": 1, - "kpar": 1, - "_comment": " that's all " - }, - "_comment": "00.equi", - "alloy_shift": false, - "_comment": "01.eos", - "vol_start": 12, - "vol_end": 22, - "vol_step": 0.5, - "_comment": "02.elastic", - "norm_deform": 2e-2, - "shear_deform": 5e-2, - "_comment": "03.vacancy", - "supercell": [ - 3, - 3, - 3 - ], - "_comment": "04.interstitial", - "insert_ele": [ - "Al" - ], - "reprod-opt": false, - "_comment": "05.surface", - "min_slab_size": 10, - "min_vacuum_size": 11, - "_comment": "pert xz to work around vasp bug...", - "pert_xz": 0.01, - "max_miller": 2, - "relax_box": false, - "_comment": "06.phonon", - "supercell_matrix": [ - 2, - 2, - 2 - ], - "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", - "_comment": "that's all" + "_comment1": "models", + "potcar_map": { + "Al": "/somewhere/example/POTCAR" + }, + "conf_dir": "confs/Al/std-fcc", + "key_id": "key id of Material project", + "task_type": "vasp", + "task": "all", + "vasp_params": { + "ecut": 650, + "ediff": 1e-06, + "kspacing": 0.1, + "kgamma": false, + "npar": 1, + "kpar": 1, + "_comment2": " that's all " + }, + "_comment3": "00.equi", + "alloy_shift": false, + "_comment4": "01.eos", + "vol_start": 12, + "vol_end": 22, + "vol_step": 0.5, + "_comment5": "02.elastic", + "norm_deform": 0.02, + "shear_deform": 0.05, + "_comment6": "03.vacancy", + "supercell": [ + 3, + 3, + 3 + ], + "_comment7": "04.interstitial", + "insert_ele": [ + "Al" + ], + "reprod-opt": false, + "_comment8": "05.surface", + "min_slab_size": 10, + "min_vacuum_size": 11, + "_comment9": "pert xz to work around vasp bug...", + "pert_xz": 0.01, + "max_miller": 2, + "relax_box": false, + "_comment10": "06.phonon", + "supercell_matrix": [ + 2, + 2, + 2 + ], + "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", + "_comment11": "that's all" } diff --git a/examples/test/vasp_param_from_incar.json b/examples/test/vasp_param_from_incar.json index c5cf91ba4..9acf0928e 100644 --- a/examples/test/vasp_param_from_incar.json +++ b/examples/test/vasp_param_from_incar.json @@ -1,5 +1,5 @@ { - "_comment": "models", + "_comment1": "models", "potcar_map": { "Al": "/somewhere/example/POTCAR" }, @@ -7,43 +7,41 @@ "key_id": "key id of Material project", "task_type": "vasp", "task": "all", - "relax_incar": "somewhere/relax_incar", "scf_incar": "somewhere/scf_incar", - - "_comment": "00.equi", + "_comment2": "00.equi", "alloy_shift": false, - "_comment": "01.eos", + "_comment3": "01.eos", "vol_start": 12, "vol_end": 22, "vol_step": 0.5, - "_comment": "02.elastic", - "norm_deform": 2e-2, - "shear_deform": 5e-2, - "_comment": "03.vacancy", + "_comment4": "02.elastic", + "norm_deform": 0.02, + "shear_deform": 0.05, + "_comment5": "03.vacancy", "supercell": [ 3, 3, 3 ], - "_comment": "04.interstitial", + "_comment6": "04.interstitial", "insert_ele": [ "Al" ], "reprod-opt": false, - "_comment": "05.surface", + "_comment7": "05.surface", "min_slab_size": 10, "min_vacuum_size": 11, - "_comment": "pert xz to work around vasp bug...", + "_comment8": "pert xz to work around vasp bug...", "pert_xz": 0.01, "max_miller": 2, "relax_box": false, - "_comment": "06.phonon", + "_comment9": "06.phonon", "supercell_matrix": [ 2, 2, 2 ], "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", - "_comment": "that's all" + "_comment10": "that's all" } diff --git a/tests/auto_test/equi/abacus/cell-relax.json b/tests/auto_test/equi/abacus/cell-relax.json index 03d7fcb71..f394f46db 100644 --- a/tests/auto_test/equi/abacus/cell-relax.json +++ b/tests/auto_test/equi/abacus/cell-relax.json @@ -4776,4 +4776,4 @@ ] } } -} \ No newline at end of file +} diff --git a/tests/auto_test/equi/vasp/Al-fcc.json b/tests/auto_test/equi/vasp/Al-fcc.json index ad921e693..e0d30e9ab 100644 --- a/tests/auto_test/equi/vasp/Al-fcc.json +++ b/tests/auto_test/equi/vasp/Al-fcc.json @@ -267,4 +267,4 @@ ] } } -} \ No newline at end of file +} diff --git a/tests/auto_test/equi/vasp/outcar.json b/tests/auto_test/equi/vasp/outcar.json index 9866ee2d3..48ff14c96 100644 --- a/tests/auto_test/equi/vasp/outcar.json +++ b/tests/auto_test/equi/vasp/outcar.json @@ -4668,4 +4668,4 @@ ] } } -} \ No newline at end of file +} diff --git a/tests/auto_test/output/gamma_00/task.000000/inter.json b/tests/auto_test/output/gamma_00/task.000000/inter.json index 052167468..3f046499f 100644 --- a/tests/auto_test/output/gamma_00/task.000000/inter.json +++ b/tests/auto_test/output/gamma_00/task.000000/inter.json @@ -5,4 +5,4 @@ "type_map": { "Mo": 0 } -} \ No newline at end of file +} diff --git a/tests/auto_test/output/gamma_00/task.000000/miller.json b/tests/auto_test/output/gamma_00/task.000000/miller.json index 0a6e1ab11..35084a204 100644 --- a/tests/auto_test/output/gamma_00/task.000000/miller.json +++ b/tests/auto_test/output/gamma_00/task.000000/miller.json @@ -1 +1,5 @@ -[1, 1, 0] \ No newline at end of file +[ + 1, + 1, + 0 +] diff --git a/tests/auto_test/output/gamma_00/task.000000/result_task.json b/tests/auto_test/output/gamma_00/task.000000/result_task.json index 591103fc6..bcc319404 100644 --- a/tests/auto_test/output/gamma_00/task.000000/result_task.json +++ b/tests/auto_test/output/gamma_00/task.000000/result_task.json @@ -10680,4 +10680,4 @@ ] } } -} \ No newline at end of file +} diff --git a/tests/auto_test/output/gamma_00/task.000000/task.json b/tests/auto_test/output/gamma_00/task.000000/task.json index dfe1db76b..b757d2c2f 100644 --- a/tests/auto_test/output/gamma_00/task.000000/task.json +++ b/tests/auto_test/output/gamma_00/task.000000/task.json @@ -31,4 +31,4 @@ "relax_shape": false, "relax_vol": false } -} \ No newline at end of file +} diff --git a/tests/auto_test/output/gamma_00/task.000001/inter.json b/tests/auto_test/output/gamma_00/task.000001/inter.json index 052167468..3f046499f 100644 --- a/tests/auto_test/output/gamma_00/task.000001/inter.json +++ b/tests/auto_test/output/gamma_00/task.000001/inter.json @@ -5,4 +5,4 @@ "type_map": { "Mo": 0 } -} \ No newline at end of file +} diff --git a/tests/auto_test/output/gamma_00/task.000001/miller.json b/tests/auto_test/output/gamma_00/task.000001/miller.json index 0a6e1ab11..35084a204 100644 --- a/tests/auto_test/output/gamma_00/task.000001/miller.json +++ b/tests/auto_test/output/gamma_00/task.000001/miller.json @@ -1 +1,5 @@ -[1, 1, 0] \ No newline at end of file +[ + 1, + 1, + 0 +] diff --git a/tests/auto_test/output/gamma_00/task.000001/result_task.json b/tests/auto_test/output/gamma_00/task.000001/result_task.json index 50f35afdf..7be63eddc 100644 --- a/tests/auto_test/output/gamma_00/task.000001/result_task.json +++ b/tests/auto_test/output/gamma_00/task.000001/result_task.json @@ -10680,4 +10680,4 @@ ] } } -} \ No newline at end of file +} diff --git a/tests/auto_test/output/gamma_00/task.000001/task.json b/tests/auto_test/output/gamma_00/task.000001/task.json index dfe1db76b..b757d2c2f 100644 --- a/tests/auto_test/output/gamma_00/task.000001/task.json +++ b/tests/auto_test/output/gamma_00/task.000001/task.json @@ -31,4 +31,4 @@ "relax_shape": false, "relax_vol": false } -} \ No newline at end of file +} diff --git a/tests/auto_test/output/gamma_00/task.000002/inter.json b/tests/auto_test/output/gamma_00/task.000002/inter.json index 052167468..3f046499f 100644 --- a/tests/auto_test/output/gamma_00/task.000002/inter.json +++ b/tests/auto_test/output/gamma_00/task.000002/inter.json @@ -5,4 +5,4 @@ "type_map": { "Mo": 0 } -} \ No newline at end of file +} diff --git a/tests/auto_test/output/gamma_00/task.000002/miller.json b/tests/auto_test/output/gamma_00/task.000002/miller.json index 0a6e1ab11..35084a204 100644 --- a/tests/auto_test/output/gamma_00/task.000002/miller.json +++ b/tests/auto_test/output/gamma_00/task.000002/miller.json @@ -1 +1,5 @@ -[1, 1, 0] \ No newline at end of file +[ + 1, + 1, + 0 +] diff --git a/tests/auto_test/output/gamma_00/task.000002/result_task.json b/tests/auto_test/output/gamma_00/task.000002/result_task.json index cb2da59ad..6d11eb0c0 100644 --- a/tests/auto_test/output/gamma_00/task.000002/result_task.json +++ b/tests/auto_test/output/gamma_00/task.000002/result_task.json @@ -10680,4 +10680,4 @@ ] } } -} \ No newline at end of file +} diff --git a/tests/auto_test/output/gamma_00/task.000002/task.json b/tests/auto_test/output/gamma_00/task.000002/task.json index dfe1db76b..b757d2c2f 100644 --- a/tests/auto_test/output/gamma_00/task.000002/task.json +++ b/tests/auto_test/output/gamma_00/task.000002/task.json @@ -31,4 +31,4 @@ "relax_shape": false, "relax_vol": false } -} \ No newline at end of file +} diff --git a/tests/auto_test/output/relaxation/relax_task/result.json b/tests/auto_test/output/relaxation/relax_task/result.json index 051fe8cf2..cc38cd7fd 100644 --- a/tests/auto_test/output/relaxation/relax_task/result.json +++ b/tests/auto_test/output/relaxation/relax_task/result.json @@ -374,4 +374,4 @@ ] } } -} \ No newline at end of file +} diff --git a/tests/data/CuW.json b/tests/data/CuW.json index d60dfb187..9ad025de7 100644 --- a/tests/data/CuW.json +++ b/tests/data/CuW.json @@ -1,6 +1,11 @@ { - "init_fp_style": "ABACUS", - "stages": [1, 2, 3, 4], + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], "cell_type": "fcc", "latt": 3.76, "super_cell": [ @@ -9,12 +14,16 @@ 2 ], "elements": [ - "Cu", "W" + "Cu", + "W" + ], + "atom_masses": [ + 63.55, + 183.8 ], - "atom_masses": [63.55, 183.8], "potcars": [ "abacus.in/Cu_ONCV_PBE-1.0.upf", - "abacus.in/W_ONCV_PBE-1.0.upf" + "abacus.in/W_ONCV_PBE-1.0.upf" ], "relax_incar": "abacus.in/INPUT", "relax_kpt": "abacus.in/KPT", @@ -33,5 +42,5 @@ "Cu", "W" ], - "_comment": "that's all" + "_comment1": "that's all" } diff --git a/tests/data/al.json b/tests/data/al.json index b19e7c884..3c96c484f 100644 --- a/tests/data/al.json +++ b/tests/data/al.json @@ -1,19 +1,32 @@ { - "cell_type": "fcc", - "super_cell": [1, 1, 1], - "elements": ["Al"], - "from_poscar": false, - "from_poscar_path": "example/POSCAR", - "potcars": ["example/POTCAR"], - "relax_incar": "example/INCAR.rlx", - "md_incar" : "example/INCAR.md", - "scale": [1.00], - "skip_relax": false, - "pert_numb": 2, - "md_nstep" : 1, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 10, - "type_map" : ["Mg", "Al"], - "_comment": "that's all" + "cell_type": "fcc", + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "from_poscar": false, + "from_poscar_path": "example/POSCAR", + "potcars": [ + "example/POTCAR" + ], + "relax_incar": "example/INCAR.rlx", + "md_incar": "example/INCAR.md", + "scale": [ + 1.0 + ], + "skip_relax": false, + "pert_numb": 2, + "md_nstep": 1, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 10, + "type_map": [ + "Mg", + "Al" + ], + "_comment1": "that's all" } diff --git a/tests/data/alloy.json b/tests/data/alloy.json index 78cfa5e61..dd42d585c 100644 --- a/tests/data/alloy.json +++ b/tests/data/alloy.json @@ -1,19 +1,31 @@ { - "cell_type": "fcc", - "latt": 2.4, - "super_cell": [1, 1, 1], - "elements": ["Al","Mg"], - "from_poscar": false, - "from_poscar_path": "example/POSCAR", - "potcars": ["./POTCAR","./POTCAR"], - "relax_incar": "./INCAR_metal_rlx_low", - "md_incar" : "example/INCAR.md", - "scale": [1.00], - "skip_relax": true, - "pert_numb": 3, - "md_nstep" : 1, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 3, - "_comment": "that's all" + "cell_type": "fcc", + "latt": 2.4, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "from_poscar": false, + "from_poscar_path": "example/POSCAR", + "potcars": [ + "./POTCAR", + "./POTCAR" + ], + "relax_incar": "./INCAR_metal_rlx_low", + "md_incar": "example/INCAR.md", + "scale": [ + 1.0 + ], + "skip_relax": true, + "pert_numb": 3, + "md_nstep": 1, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 3, + "_comment1": "that's all" } diff --git a/tests/data/ch4.json b/tests/data/ch4.json index 7f3a74933..ce67eeb1f 100644 --- a/tests/data/ch4.json +++ b/tests/data/ch4.json @@ -1,26 +1,46 @@ { - "init_fp_style": "ABACUS", - "stages": [1, 2, 3, 4], - "super_cell": [1, 1, 1], - "_comment": "if from_poscar = true, the cell_type and super_cell keys are actually useless", + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], + "super_cell": [ + 1, + 1, + 1 + ], + "_comment1": "if from_poscar = true, the cell_type and super_cell keys are actually useless", "cell_type": "fcc", - "elements": ["H","C"], - "atom_masses": [1, 12], - "_comment": "if from_poscar = false, you have to set atom_masse.", - "out_dir": "./", - "from_poscar": true, - "from_poscar_path": "./STRU", - "potcars": ["./H_ONCV_PBE-1.0.upf", "./C_ONCV_PBE-1.0.upf"], - "relax_incar": "./INPUT", + "elements": [ + "H", + "C" + ], + "atom_masses": [ + 1, + 12 + ], + "_comment2": "if from_poscar = false, you have to set atom_masse.", + "out_dir": "./", + "from_poscar": true, + "from_poscar_path": "./STRU", + "potcars": [ + "./H_ONCV_PBE-1.0.upf", + "./C_ONCV_PBE-1.0.upf" + ], + "relax_incar": "./INPUT", "relax_kspacing": 10, - "md_incar" : "./INPUT.md", + "md_incar": "./INPUT.md", "md_kspacing": 10, - "scale": [0.95], - "skip_relax": false, - "pert_numb": 2, - "md_nstep" : 3, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 10, - "_comment": "that's all" + "scale": [ + 0.95 + ], + "skip_relax": false, + "pert_numb": 2, + "md_nstep": 3, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 10, + "_comment3": "that's all" } diff --git a/tests/data/surf.json b/tests/data/surf.json index f0bcc45b1..d3f5afee4 100644 --- a/tests/data/surf.json +++ b/tests/data/surf.json @@ -1,46 +1,46 @@ { - "stages": [ - 1, - 2 - ], - "cell_type": "fcc", - "latt": 4.1, - "super_cell": [ - 1, - 1, - 1 - ], - "layer_numb": 3, - "vacuum_max": 9.0, - "vacuum_resol": [ - 0.5, - 1 - ], - "mid_point": 4.0, - "head_ratio": 0.6, - "vacuum_numb": 20, - "millers": [ - [ - 1, - 0, - 0 - ] - ], - "elements": [ - "Al" - ], - "potcars": [ - "./POTCAR" - ], - "relax_incar" : "INCAR_metal_rlx_low", - "scale": [ - 0.98, - 1.0 - ], - "skip_relax": true, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 5000, - "_comment": "that's all" + "stages": [ + 1, + 2 + ], + "cell_type": "fcc", + "latt": 4.1, + "super_cell": [ + 1, + 1, + 1 + ], + "layer_numb": 3, + "vacuum_max": 9.0, + "vacuum_resol": [ + 0.5, + 1 + ], + "mid_point": 4.0, + "head_ratio": 0.6, + "vacuum_numb": 20, + "millers": [ + [ + 1, + 0, + 0 + ] + ], + "elements": [ + "Al" + ], + "potcars": [ + "./POTCAR" + ], + "relax_incar": "INCAR_metal_rlx_low", + "scale": [ + 0.98, + 1.0 + ], + "skip_relax": true, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/tests/data/surf_poscar.json b/tests/data/surf_poscar.json index 3399b920f..2cfbc27a4 100644 --- a/tests/data/surf_poscar.json +++ b/tests/data/surf_poscar.json @@ -1,43 +1,46 @@ { - "stages": [ - 1, - 2 - ], - "cell_type": "fcc", - "from_poscar": true, - "from_poscar_path": "POSCAR", - "super_cell": [ - 1, - 1, - 1 - ], - "layer_numb": 3, - "vacuum_max": 5, - "vacuum_resol": [0.5,2], - "mid_point": 2.0, - "_head_ratio": 0.6, - "_vacuum_numb": 20, - "millers": [ - [ - 1, - 0, - 0 - ] - ], - "elements": [ - "Al" - ], - "potcars": [ - "./POTCAR" - ], - "relax_incar" : "INCAR_metal_rlx_low", - "scale": [ - 1.0 - ], - "skip_relax": true, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 5000, - "_comment": "that's all" + "stages": [ + 1, + 2 + ], + "cell_type": "fcc", + "from_poscar": true, + "from_poscar_path": "POSCAR", + "super_cell": [ + 1, + 1, + 1 + ], + "layer_numb": 3, + "vacuum_max": 5, + "vacuum_resol": [ + 0.5, + 2 + ], + "mid_point": 2.0, + "_head_ratio": 0.6, + "_vacuum_numb": 20, + "millers": [ + [ + 1, + 0, + 0 + ] + ], + "elements": [ + "Al" + ], + "potcars": [ + "./POTCAR" + ], + "relax_incar": "INCAR_metal_rlx_low", + "scale": [ + 1.0 + ], + "skip_relax": true, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/tests/database/param_Al.json b/tests/database/param_Al.json index 3295d8ce8..48f767d30 100644 --- a/tests/database/param_Al.json +++ b/tests/database/param_Al.json @@ -1,19 +1,100 @@ { - "path" : "./", - "calculator" : "vasp", - "_comment" : "vasp/pwscf/gaussian", - "output" : "dpgen_db.json", - "id_prefix" : "", - "config_info_dict" : { - "fcc-bulk" : [0,1,2,3,4,5,6,7], - "hcp-bulk" : [8,9,10,11,12,13,14,15], - "bcc-bulk" : [16,17,18,19,20,21,22,23], - "fcc-surf-100" : [24,25,26,27,28,29,30,31], - "fcc-surf-111" : [32,33,34,35,36,37,38,39], - "fcc-surf-110" : [40,41,42,43,44,45,46,47], - "hcp-surf-001" : [48,49,50,51,52,53,54,55], - "hcp-surf-100" : [56,57,58,59,60,61,62,63], - "hcp-surf-110" : [64,65,66,67,68,69,70,71] - }, - "skip_init" : true + "path": "./", + "calculator": "vasp", + "_comment1": "vasp/pwscf/gaussian", + "output": "dpgen_db.json", + "id_prefix": "", + "config_info_dict": { + "fcc-bulk": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7 + ], + "hcp-bulk": [ + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15 + ], + "bcc-bulk": [ + 16, + 17, + 18, + 19, + 20, + 21, + 22, + 23 + ], + "fcc-surf-100": [ + 24, + 25, + 26, + 27, + 28, + 29, + 30, + 31 + ], + "fcc-surf-111": [ + 32, + 33, + 34, + 35, + 36, + 37, + 38, + 39 + ], + "fcc-surf-110": [ + 40, + 41, + 42, + 43, + 44, + 45, + 46, + 47 + ], + "hcp-surf-001": [ + 48, + 49, + 50, + 51, + 52, + 53, + 54, + 55 + ], + "hcp-surf-100": [ + 56, + 57, + 58, + 59, + 60, + 61, + 62, + 63 + ], + "hcp-surf-110": [ + 64, + 65, + 66, + 67, + 68, + 69, + 70, + 71 + ] + }, + "skip_init": true } diff --git a/tests/generator/gromacs/model_devi_case/input.json b/tests/generator/gromacs/model_devi_case/input.json index 99449ec0d..bd68970d2 100644 --- a/tests/generator/gromacs/model_devi_case/input.json +++ b/tests/generator/gromacs/model_devi_case/input.json @@ -4,4 +4,4 @@ "type_file": "/data1/anguse/yuzhi/fep/DP_FF/tyk2/init_data/lig_ejm_31/type.raw", "index_file": "index.raw", "lambda": 1.0 -} \ No newline at end of file +} diff --git a/tests/generator/machine-local-v1.json b/tests/generator/machine-local-v1.json index 2218884f2..6ffac93a7 100644 --- a/tests/generator/machine-local-v1.json +++ b/tests/generator/machine-local-v1.json @@ -1,48 +1,51 @@ { "train_machine": { - "machine_type": "shell", - "lazy_local": true + "machine_type": "shell", + "lazy_local": true }, "train_resources": { - "numb_node": 1, - "numb_gpu": 0, - "task_per_node": 4, - "exclude_list": [], - "source_list": ["/home/wanghan/study/deep.md/venvs/py3.6-tf1.8/bin/active"], - "envs" : { - }, - "_comment": "that's All" + "numb_node": 1, + "numb_gpu": 0, + "task_per_node": 4, + "exclude_list": [], + "source_list": [ + "/home/wanghan/study/deep.md/venvs/py3.6-tf1.8/bin/active" + ], + "envs": {}, + "_comment1": "that's All" }, "python_path": "/home/wanghan/study/deep.md/venvs/py3.6-tf1.8/bin/python", - "model_devi_machine": { - "machine_type": "shell", - "work_path": "/home/wanghan/study/deep.md/dpgen/almg/tmp" + "machine_type": "shell", + "work_path": "/home/wanghan/study/deep.md/dpgen/almg/tmp" }, "model_devi_resources": { - "numb_node": 1, - "task_per_node": 4, - "with_mpi": true, - "module_list" : ["mpi"], - "exclude_list": [], - "source_list": [], - "_comment": "that's All" + "numb_node": 1, + "task_per_node": 4, + "with_mpi": true, + "module_list": [ + "mpi" + ], + "exclude_list": [], + "source_list": [], + "_comment2": "that's All" }, "model_devi_command": "/home/wanghan/local/bin/lmp_mpi_1_1_0", "model_devi_group_size": 10, - "fp_machine": { - "machine_type": "shell", - "work_path": "/home/wanghan/study/deep.md/dpgen/almg/tmp" + "machine_type": "shell", + "work_path": "/home/wanghan/study/deep.md/dpgen/almg/tmp" }, "fp_resources": { - "cvasp": false, - "task_per_node": 4, - "exclude_list": [], - "with_mpi": true, - "module_list" : ["mpi"], - "source_list": [], - "_comment": "that's All" + "cvasp": false, + "task_per_node": 4, + "exclude_list": [], + "with_mpi": true, + "module_list": [ + "mpi" + ], + "source_list": [], + "_comment3": "that's All" }, "fp_command": "/home/wanghan/local/bin/vasp_std", "fp_group_size": 5 diff --git a/tests/generator/machine-local.json b/tests/generator/machine-local.json index a4743c964..fb2d47073 100644 --- a/tests/generator/machine-local.json +++ b/tests/generator/machine-local.json @@ -1,54 +1,55 @@ { - "_comment": "training on localhost ", - "deepmd_path": "/home/wanghan/local/deepmd/0.10.1/", - "train_machine": { - "machine_type": "local", - "hostname" : "127.0.0.1", - "port" : 22, - "username": "wanghan", - "work_path" : "/home/wanghan/tmp/subs/", - "_comment" : "that's all" - }, - "train_resources": { - "envs": { - "PYTHONPATH" : "/home/wanghan/local/tensorflow/1.8.py/lib/python3.6/site-packages/" - }, - "_comment": "that's all" - }, - - - "_comment": "model_devi on localhost ", - "model_devi_command": "/home/wanghan/local/bin/lmp_mpi_010", + "_comment1": "training on localhost ", + "deepmd_path": "/home/wanghan/local/deepmd/0.10.1/", + "train_machine": { + "machine_type": "local", + "hostname": "127.0.0.1", + "port": 22, + "username": "wanghan", + "work_path": "/home/wanghan/tmp/subs/", + "_comment2": "that's all" + }, + "train_resources": { + "envs": { + "PYTHONPATH": "/home/wanghan/local/tensorflow/1.8.py/lib/python3.6/site-packages/" + }, + "_comment3": "that's all" + }, + "_comment4": "model_devi on localhost ", + "model_devi_command": "/home/wanghan/local/bin/lmp_mpi_010", "model_devi_group_size": 5, - "model_devi_machine": { - "machine_type": "local", - "hostname" : "127.0.0.1", - "port" : 22, - "username": "wanghan", - "work_path" : "/home/wanghan/tmp/subs/", - "_comment" : "that's all" - }, - "model_devi_resources": { - "_comment": "that's all" - }, - - "_comment": "fp on localhost ", - "fp_command": "/home/wanghan/local/bin/vasp_std", - "fp_group_size": 2, - "fp_machine": { - "machine_type": "local", - "hostname" : "127.0.0.1", - "port" : 22, - "username": "wanghan", - "work_path" : "/home/wanghan/tmp/subs/", - "_comment" : "that's all" - }, - "fp_resources": { - "module_list": ["mpi"], - "task_per_node":4, - "with_mpi": true, - "_comment": "that's all" + "model_devi_machine": { + "machine_type": "local", + "hostname": "127.0.0.1", + "port": 22, + "username": "wanghan", + "work_path": "/home/wanghan/tmp/subs/", + "_comment5": "that's all" + }, + "model_devi_resources": { + "_comment6": "that's all" + }, + "_comment7": "fp on localhost ", + "fp_command": "/home/wanghan/local/bin/vasp_std", + "fp_group_size": 2, + "fp_machine": { + "machine_type": "local", + "hostname": "127.0.0.1", + "port": 22, + "username": "wanghan", + "work_path": "/home/wanghan/tmp/subs/", + "_comment8": "that's all" + }, + "fp_resources": { + "module_list": [ + "mpi" + ], + "task_per_node": 4, + "with_mpi": true, + "_comment9": "that's all" }, - "fp_user_forward_files" : ["vdw_kernel.bindat"], - "_comment": " that's all " + "fp_user_forward_files": [ + "vdw_kernel.bindat" + ], + "_comment10": " that's all " } diff --git a/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000000/job.json b/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000000/job.json index e2f74b65b..660b8b34d 100644 --- a/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000000/job.json +++ b/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000000/job.json @@ -1 +1,3 @@ -{ "ele_temp": 0 } +{ + "ele_temp": 0 +} diff --git a/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000001/job.json b/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000001/job.json index ec49f8a06..4d97f09db 100644 --- a/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000001/job.json +++ b/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000001/job.json @@ -1 +1,3 @@ -{ "ele_temp": 1 } +{ + "ele_temp": 1 +} diff --git a/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000000/job.json b/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000000/job.json index c4924f0bd..75362c521 100644 --- a/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000000/job.json +++ b/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000000/job.json @@ -1 +1,3 @@ -{ "ele_temp": 100000 } +{ + "ele_temp": 100000 +} diff --git a/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000001/job.json b/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000001/job.json index a393fb733..ce0542325 100644 --- a/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000001/job.json +++ b/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000001/job.json @@ -1 +1,3 @@ -{ "ele_temp": 110000 } +{ + "ele_temp": 110000 +} diff --git a/tests/generator/param-amber.json b/tests/generator/param-amber.json index 69df44ed3..6dc97aee9 100644 --- a/tests/generator/param-amber.json +++ b/tests/generator/param-amber.json @@ -1,7 +1,9 @@ { "model_devi_jobs": [ { - "sys_idx": [0] + "sys_idx": [ + 0 + ] } ], "use_multi_systems": true, @@ -33,22 +35,32 @@ 0 ], "r": [ - [-1.20] + [ + -1.2 + ] ], "nsteps": [ 1000 ], - "type_map": ["C", "H", "O", "N", "P", "HW", "OW"], + "type_map": [ + "C", + "H", + "O", + "N", + "P", + "HW", + "OW" + ], "shuffle_poscar": false, "low_level": "DFTB2", "high_level": "PBE0", "cutoff": 6.0, "fp_task_max": 1000, "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.10, + "model_devi_f_trust_lo": 0.1, "model_devi_f_trust_hi": 0.25, "fp_params": { "low_level_mdin": "ml.mdin", "high_level_mdin": "ml.mdin" } -} \ No newline at end of file +} diff --git a/tests/generator/param-custom-fp.json b/tests/generator/param-custom-fp.json index f66cad71f..f62a48816 100644 --- a/tests/generator/param-custom-fp.json +++ b/tests/generator/param-custom-fp.json @@ -1,107 +1,321 @@ -{ - "type_map": ["C", "H", "N"], - "mass_map": [16, 2, 14], - - "init_data_prefix": "/home/linfengz/SCR/wanghan/deepgen.pyridine/init", - "init_data_sys": ["Pyridine-I", - "Pyridine-II" - ], - "init_batch_size": [1, 1], - "sys_configs": [ - ["/home/linfengz/SCR/wanghan/data/pyridine/pyI.POSCAR.01x01x01/01.scale_pert/sys-0080-0080-0016/scale-1.000/00009?/POSCAR"], - ["/home/linfengz/SCR/wanghan/data/pyridine/pyI.POSCAR.01x01x01/01.scale_pert/sys-0080-0080-0016/scale-1.000/0000[7-8]?/POSCAR"], - ["/home/linfengz/SCR/wanghan/data/pyridine/pyI.POSCAR.01x01x01/01.scale_pert/sys-0080-0080-0016/scale-1.000/0000[5-6]?/POSCAR"], - ["/home/linfengz/SCR/wanghan/data/pyridine/pyI.POSCAR.01x01x01/01.scale_pert/sys-0080-0080-0016/scale-1.000/0000[0-4]?/POSCAR"], - ["/home/linfengz/SCR/wanghan/data/pyridine/pyII.POSCAR.01x01x01/01.scale_pert/sys-0080-0080-0016/scale-1.000/00009?/POSCAR"], - ["/home/linfengz/SCR/wanghan/data/pyridine/pyII.POSCAR.01x01x01/01.scale_pert/sys-0080-0080-0016/scale-1.000/0000[7-8]?/POSCAR"], - ["/home/linfengz/SCR/wanghan/data/pyridine/pyII.POSCAR.01x01x01/01.scale_pert/sys-0080-0080-0016/scale-1.000/0000[5-6]?/POSCAR"], - ["/home/linfengz/SCR/wanghan/data/pyridine/pyII.POSCAR.01x01x01/01.scale_pert/sys-0080-0080-0016/scale-1.000/0000[0-4]?/POSCAR"] +{ + "type_map": [ + "C", + "H", + "N" ], - "_comment": "0 1 2 3", - "_comment": "4 5 6 7", - "sys_batch_size": [1, 1, 1, 1, - 1, 1, 1, 1 - ], - - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "_comment": " model parameters", - "use_smooth": true, - "sel_a": [81, 81, 20], - "rcut_smth": 0.50, - "rcut": 6.50, - "filter_neuron": [25, 50, 100], - "filter_resnet_dt": false, - "n_axis_neuron": 12, - "n_neuron": [240, 240, 240], - "resnet_dt": true, - "coord_norm": true, - "type_fitting_net": false, - - "_comment": " traing controls", - "systems": [], - "set_prefix": "set", - "stop_batch": 400000, - "batch_size": 1, - "start_lr": 0.002, - "decay_steps": 2000, - "decay_rate": 0.95, - "seed": 0, - - "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, - - "_comment": " display and restart", - "_comment": " frequencies counted in batch", - "disp_file": "lcurve.out", - "disp_freq": 2000, - "numb_test": 10, - "save_freq": 20000, - "save_ckpt": "model.ckpt", - "load_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - - "_comment": "that's all" + "mass_map": [ + 16, + 2, + 14 + ], + "init_data_prefix": "/home/linfengz/SCR/wanghan/deepgen.pyridine/init", + "init_data_sys": [ + "Pyridine-I", + "Pyridine-II" + ], + "init_batch_size": [ + 1, + 1 + ], + "sys_configs": [ + [ + "/home/linfengz/SCR/wanghan/data/pyridine/pyI.POSCAR.01x01x01/01.scale_pert/sys-0080-0080-0016/scale-1.000/00009?/POSCAR" + ], + [ + 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"type_map": ["Mg", "Al"], - "mass_map": [24, 27], - - "init_data_prefix": "data", - "init_data_sys": ["deepmd" - ], - "init_batch_size": [16], - "sys_configs": [ - ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000010/POSCAR"], - ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/00000[8-9]/POSCAR"] + "type_map": [ + "Mg", + "Al" ], - "_comment": "0 1 2 3", - "_comment": "4 5 6 7", - "sys_batch_size": [1, 1 - ], - - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "_comment": " model parameters", - "use_smooth": true, - "sel_a": [90], - "rcut_smth": 2.00, - "rcut": 6.00, - "filter_neuron": [25, 50, 100], - "filter_resnet_dt": false, - "n_axis_neuron": 12, - "n_neuron": [240, 240, 240], - "resnet_dt": true, - "coord_norm": true, - "type_fitting_net": false, - - "_comment": " traing controls", - "systems": [], - "set_prefix": "set", - "stop_batch": 400000, - "batch_size": 1, - "start_lr": 0.002, - "decay_steps": 2000, - "decay_rate": 0.95, - "seed": 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["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000001/POSCAR"] +{ + "type_map": [ + "Mg", + "Al" ], - "_comment": "0 1 2 3", - "_comment": "4 5 6 7", - "sys_batch_size": [1, 1 - ], - - "_comment": " 00.train ", - "numb_models": 4, - "train_param": "input.json", - "default_training_param" : { - "_comment": " model parameters", - "use_smooth": true, - "sel_a": [90], - "rcut_smth": 2.00, - "rcut": 6.00, - "filter_neuron": [25, 50, 100], - "filter_resnet_dt": false, - "n_axis_neuron": 12, - "n_neuron": [240, 240, 240], - "resnet_dt": true, - "coord_norm": true, - "type_fitting_net": false, - - "_comment": " traing controls", - "systems": [], - "set_prefix": "set", - "stop_batch": 400000, - "batch_size": 1, - "start_lr": 0.002, - "decay_steps": 2000, - "decay_rate": 0.95, - "seed": 0, - - "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, - - "_comment": " display and restart", - "_comment": " 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01.model_devi ", - "_comment": "model_devi_skip: the first x of the recorded frames", - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": [0.000, 0.050], - "model_devi_f_trust_hi": {"1": 0.100, "0": 0.150}, - "model_devi_e_trust_lo": 1e10, - "model_devi_e_trust_hi": 1e10, - "model_devi_clean_traj": false, - "model_devi_jobs": [ - {"sys_idx": [0, 1], "temps": [50,100], "press": [1.0,2.0], "trj_freq": 10, "nsteps": 1000, "ensemble": "npt", "_idx": "00"} + "model_devi_e_trust_lo": 10000000000.0, + "model_devi_e_trust_hi": 10000000000.0, + "model_devi_clean_traj": false, + "model_devi_jobs": [ + { + "sys_idx": [ + 0, + 1 + ], + "temps": [ + 50, + 100 + ], + "press": [ + 1.0, + 2.0 + ], + "trj_freq": 10, + "nsteps": 1000, + "ensemble": "npt", + "_idx": "00" + } + ], + "_comment11": " 02.fp ", + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 100, + "fp_task_min": 10, + "fp_pp_path": ".", + "fp_pp_files": [ + "vasp/potcars/POTCAR.mg", + "vasp/potcars/POTCAR.al" ], - - "_comment": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 100, - "fp_task_min": 10, - "fp_pp_path": ".", - "fp_pp_files": ["vasp/potcars/POTCAR.mg", "vasp/potcars/POTCAR.al"], - "_comment": " user provided vasp script ", + "_comment12": " user provided vasp script ", "user_fp_params": { - "PREC": "A", - "ENCUT": 600, - "ISYM": 0, - "ALGO": "fast", - "EDIFF": 1e-05, - "LREAL": "A", - "NPAR": 1, - "KPAR": 1, - "NELMIN": 4, - "ISIF": 2, - "ISMEAR": 1, - "SIGMA": 0.25, - "IBRION": -1, - "NSW": 0, - "LWAVE": false, - "LCHARG": false, - "PSTRESS": 0, - "KSPACING": 0.16, - "KGAMMA": false + "PREC": "A", + "ENCUT": 600, + "ISYM": 0, + "ALGO": "fast", + "EDIFF": 1e-05, + "LREAL": "A", + "NPAR": 1, + "KPAR": 1, + "NELMIN": 4, + "ISIF": 2, + "ISMEAR": 1, + "SIGMA": 0.25, + "IBRION": -1, + "NSW": 0, + "LWAVE": false, + "LCHARG": false, + "PSTRESS": 0, + "KSPACING": 0.16, + "KGAMMA": false }, - "_comment": " that's all " + "_comment13": " that's all " } diff --git a/tests/generator/param-mg-vasp-old.json b/tests/generator/param-mg-vasp-old.json index 3926876c2..83a86a439 100644 --- a/tests/generator/param-mg-vasp-old.json +++ b/tests/generator/param-mg-vasp-old.json @@ -1,103 +1,147 @@ -{ - "type_map": ["Mg", "Al"], - "mass_map": [24, 27], - - "init_data_prefix": "data", - "init_data_sys": ["deepmd" - ], - "init_batch_size": [16], - "sys_configs": [ - ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000010/POSCAR"], - ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/00000[8-9]/POSCAR"] +{ + "type_map": [ + "Mg", + "Al" ], - "_comment": "0 1 2 3", - "_comment": "4 5 6 7", - "sys_batch_size": [1, 1 - ], - - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "_comment": " model parameters", - "use_smooth": true, - "sel_a": [90], - "rcut_smth": 2.00, - "rcut": 6.00, - "filter_neuron": [25, 50, 100], - "filter_resnet_dt": false, - "n_axis_neuron": 12, - "n_neuron": [240, 240, 240], - 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"trj_freq": 10, + "nsteps": 1000, + "ensemble": "npt", + "_idx": "00" + } + ], + "_comment11": " 02.fp ", + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 100, + "fp_task_min": 10, + "fp_pp_path": ".", + "fp_pp_files": [ + "vasp/potcars/POTCAR.mg", + "vasp/potcars/POTCAR.al" ], - - "_comment": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 100, - "fp_task_min": 10, - "fp_pp_path": ".", - "fp_pp_files": ["vasp/potcars/POTCAR.mg", "vasp/potcars/POTCAR.al"], - "fp_params": { - "_comment": "given in unit depending on the fp method", - "ecut": 600, - "ediff": 1e-6, - "kspacing": 0.16, - "_comment": "gauss, mp:N(methfessel-paxton:order by default order=1), fd(Fermi-Dirac)", - "smearing": "mp", - "sigma": 0.25, - "_comment": "only for vasp, can be NONE, SCAN, TPSS, RTPSS, M06L or MBJ", - "metagga": "NONE", - "npar": 1, - "kpar": 1, - "user_vasp_params": { - "EDIFF" : 1e-5 - }, - "_comment": " that's all " + "fp_params": { + "_comment12": "given in unit depending on the fp method", + "ecut": 600, + "ediff": 1e-06, + "kspacing": 0.16, + "_comment13": "gauss, mp:N(methfessel-paxton:order by default order=1), fd(Fermi-Dirac)", + "smearing": "mp", + "sigma": 0.25, + "_comment14": "only for vasp, can be NONE, SCAN, TPSS, RTPSS, M06L or MBJ", + "metagga": "NONE", + "npar": 1, + "kpar": 1, + "user_vasp_params": { + "EDIFF": 1e-05 + }, + "_comment15": " that's all " }, - "_comment": " that's all " + "_comment16": " that's all " } diff --git a/tests/generator/param-mg-vasp-v1-et.json b/tests/generator/param-mg-vasp-v1-et.json index cfa8071d1..80c088102 100644 --- a/tests/generator/param-mg-vasp-v1-et.json +++ b/tests/generator/param-mg-vasp-v1-et.json @@ -1,96 +1,134 @@ { - "type_map": ["Al", "Mg"], - "mass_map": [27, 24], - "use_ele_temp": 2, - - "init_data_prefix": "data", - "init_data_sys": ["deepmd" - ], - "init_batch_size": [16], - "sys_configs": [ - ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000010/POSCAR"], - ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/00000[8-9]/POSCAR"] + "type_map": [ + "Al", + "Mg" ], - "sys_batch_size": [1,1], - - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "model" : { - "descriptor": { - "type": "se_a", - "sel": [90, 90], - "rcut_smth": 1.80, - "rcut": 6.00, - "neuron": [10, 20, 40], - "resnet_dt": false, - "axis_neuron": 4, - "seed": 1 - }, - "fitting_net" : { - "neuron": [120, 120, 120], - "resnet_dt": true, - "numb_fparam": 10, - "seed": 1 - } - }, - - "loss" : { - "start_pref_e": 0.02, - "limit_pref_e": 1, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0 - }, - - "learning_rate" : { - "start_lr": 0.001, - "decay_steps": 5000, - "decay_rate": 0.95 - }, - - "training" : { - "systems": [], - "set_prefix": "set", - "stop_batch": 1000, - "batch_size": 1, - - "seed": 1, - - "_comment": " display and restart", - "_comment": " frequencies counted in batch", - "disp_file": "lcurve.out", - 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"npt", "nsteps": 50, "press": [1.0,2.0], "sys_idx": [0, 1], "temps": [50,100], "trj_freq": 10 } + "_comment4": " 01.model_devi ", + "_comment5": "model_devi_skip: the first x of the recorded frames", + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.2, + "model_devi_clean_traj": false, + "model_devi_jobs": [ + { + "_idx": 0, + "ensemble": "npt", + "nsteps": 50, + "press": [ + 1.0, + 2.0 + ], + "sys_idx": [ + 0, + 1 + ], + "temps": [ + 50, + 100 + ], + "trj_freq": 10 + } + ], + "_comment6": " 02.fp ", + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 8, + "fp_task_min": 2, + "fp_pp_path": "/home/wanghan/study/deep.md/dpgen/almg/vasp", + "fp_pp_files": [ + "POTCAR.Al", + "POTCAR.Mg" ], - "_comment": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 8, - "fp_task_min": 2, - "fp_pp_path": "/home/wanghan/study/deep.md/dpgen/almg/vasp", - "fp_pp_files": ["POTCAR.Al", "POTCAR.Mg"], - 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"deepmd" + ], + "init_batch_size": [ + 16 + ], + "sys_configs": [ + [ + "data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000010/POSCAR" + ], + [ + "data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/00000[8-9]/POSCAR" + ] + ], + "sys_batch_size": [ + 1, + 1 + ], + "_comment1": " 00.train ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "type": "se_a", + "sel": [ + 90, + 90 + ], + "rcut_smth": 1.8, + "rcut": 6.0, + "neuron": [ + 10, + 20, + 40 + ], + "resnet_dt": false, + "axis_neuron": 4, + "seed": 1 + }, + "fitting_net": { + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true, + "seed": 1 + } + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 1, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "learning_rate": { + "start_lr": 0.001, + "decay_steps": 5000, + "decay_rate": 0.95 + }, + "training": { + "systems": [], + "set_prefix": "set", + "stop_batch": 1000, + "batch_size": 1, + "seed": 1, 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a/tests/generator/param-mg-vasp.json +++ b/tests/generator/param-mg-vasp.json @@ -1,108 +1,152 @@ -{ - "type_map": ["Mg", "Al"], - "mass_map": [24, 27], - - "init_data_prefix": "data", - "init_data_sys": ["deepmd" - ], - "init_batch_size": [16], - "sys_configs": [ - ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000000/POSCAR"], - ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000001/POSCAR"] +{ + "type_map": [ + "Mg", + "Al" ], - "_comment": "0 1 2 3", - "_comment": "4 5 6 7", - "sys_batch_size": [1, 1 - ], - - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "_comment": " model parameters", - "use_smooth": true, - "sel_a": [90], - "rcut_smth": 2.00, - "rcut": 6.00, - "filter_neuron": [25, 50, 100], - "filter_resnet_dt": false, - "n_axis_neuron": 12, - "n_neuron": [240, 240, 240], - "resnet_dt": true, - "coord_norm": true, - "type_fitting_net": false, - - "_comment": " traing controls", - "systems": [], - "set_prefix": "set", - "stop_batch": 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"ensemble": "npt", + "_idx": "06" + }, + { + "sys_idx": [ + 1, + 5 + ], + "temps": [ + 100 + ], + "press": [ + 1.0, + 10.0, + 100.0, + 1000.0, + 10000.0, + 20000.0, + 40000.0 + ], + "trj_freq": 10, + "nsteps": 1000, + "ensemble": "npt", + "_idx": "07" + } ], - - "_comment": " 02.fp ", - "fp_style": "cp2k", - "shuffle_poscar": false, - "fp_task_max": 100, - "fp_task_min": 10, - "fp_pp_path": ".", - "fp_pp_files": [], - "user_fp_params": { - "FORCE_EVAL":{ - "DFT":{ + "_comment11": " 02.fp ", + "fp_style": "cp2k", + "shuffle_poscar": false, + "fp_task_max": 100, + "fp_task_min": 10, + "fp_pp_path": ".", + "fp_pp_files": [], + "user_fp_params": { + "FORCE_EVAL": { + "DFT": { "SCF": { "OT": { "MINIMIZER": "DIIS", @@ -107,15 +321,26 @@ } } }, - "SUBSYS":{ - "KIND":{ - "_": ["N","C","H"], - "POTENTIAL": ["GTH-PBE-q5","GTH-PBE-q4", "GTH-PBE-q1"], - "BASIS_SET": ["DZVP-MOLOPT-GTH","DZVP-MOLOPT-GTH","DZVP-MOLOPT-GTH"] - } - } - } - + "SUBSYS": { + "KIND": { + "_": [ + "N", + "C", + "H" + ], + "POTENTIAL": [ + "GTH-PBE-q5", + "GTH-PBE-q4", + "GTH-PBE-q1" + ], + "BASIS_SET": [ + "DZVP-MOLOPT-GTH", + "DZVP-MOLOPT-GTH", + "DZVP-MOLOPT-GTH" + ] + } + } + } }, - "_comment": " that's all " + "_comment12": " that's all " } diff --git a/tests/generator/param-pyridine-gaussian.json b/tests/generator/param-pyridine-gaussian.json index a92f6ee6f..a456b26fb 100644 --- a/tests/generator/param-pyridine-gaussian.json +++ b/tests/generator/param-pyridine-gaussian.json @@ -1,105 +1,319 @@ -{ - "type_map": ["C", "H", "N"], - "mass_map": [16, 2, 14], - - "init_data_prefix": "/home/linfengz/SCR/wanghan/deepgen.pyridine/init", - "init_data_sys": ["Pyridine-I", - "Pyridine-II" - ], - "init_batch_size": [1, 1], - "sys_configs": [ - ["/home/linfengz/SCR/wanghan/data/pyridine/pyI.POSCAR.01x01x01/01.scale_pert/sys-0080-0080-0016/scale-1.000/00009?/POSCAR"], - ["/home/linfengz/SCR/wanghan/data/pyridine/pyI.POSCAR.01x01x01/01.scale_pert/sys-0080-0080-0016/scale-1.000/0000[7-8]?/POSCAR"], - 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- "scf_iter0_2": "94 4 3 1.0000 0.025 2", - "xcfunctional": "PBE", - "convergence": "EASY", - "kspacing": 0.1 - + "user_fp_params": { + "node1": 4, + "node2": 1, + "job": "SCF", + "in.atom": "atom.config", + "in.psp1": "C.SG15.PBE.UPF", + "in.psp2": "H.SG15.PBE.UPF", + "in.psp3": "N.SG15.PBE.UPF", + "ecut": 50, + "flag_symm": 2, + "e_error": 0.0001, + "rho_error": 0.0001, + "scf_iter0_1": "6 4 3 0.0000 0.025 2", + "scf_iter0_2": "94 4 3 1.0000 0.025 2", + "xcfunctional": "PBE", + "convergence": "EASY", + "kspacing": 0.1 }, - "_comment": " that's all " + "_comment12": " that's all " } diff --git a/tests/generator/param-pyridine-pwscf-old.json b/tests/generator/param-pyridine-pwscf-old.json index 145d9aadf..11a419f9e 100644 --- a/tests/generator/param-pyridine-pwscf-old.json +++ b/tests/generator/param-pyridine-pwscf-old.json @@ -1,110 +1,328 @@ -{ - "type_map": ["C", "H", "N"], - "mass_map": [16, 2, 14], - - "init_data_prefix": "/home/linfengz/SCR/wanghan/deepgen.pyridine/init", - 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"electrons": { - "conv_thr": 1e-8 - }, - "kspacing": 0.6 + "user_fp_params": { + "_comment12": "pseudo_dir will be added automatically", + "control": { + "calculation": "scf", + "restart_mode": "from_scratch", + "outdir": "./OUT", + "tprnfor": true, + "tstress": true, + "disk_io": "none" + }, + "_comment13": "ibrav, nat and ntyp will be added automatically", + "system": { + "vdw_corr": "TS", + "ecutwfc": 110, + "ts_vdw_econv_thr": 1e-08, + "nosym": true + }, + "electrons": { + "conv_thr": 1e-08 + }, + "kspacing": 0.6 }, - "_comment": " that's all " + "_comment14": " that's all " } diff --git a/tests/generator/param-pyridine-siesta.json b/tests/generator/param-pyridine-siesta.json index d718d52ed..3667402fa 100644 --- a/tests/generator/param-pyridine-siesta.json +++ b/tests/generator/param-pyridine-siesta.json @@ -1,108 +1,326 @@ -{ - "type_map": ["C", "H", "N"], - "mass_map": [16, 2, 14], - - "init_data_prefix": "/home/linfengz/SCR/wanghan/deepgen.pyridine/init", - "init_data_sys": 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"ensemble": "npt", + "_idx": "06" + }, + { + "sys_idx": [ + 1, + 5 + ], + "temps": [ + 100 + ], + "press": [ + 1.0, + 10.0, + 100.0, + 1000.0, + 10000.0, + 20000.0, + 40000.0 + ], + "trj_freq": 10, + "nsteps": 1000, + "ensemble": "npt", + "_idx": "07" + } + ], + "_comment11": " 02.fp ", + "fp_style": "siesta", + "shuffle_poscar": false, + "fp_task_max": 100, + "fp_task_min": 10, + "fp_pp_path": ".", + "fp_pp_files": [ + "C.psf", + "H.psf", + "N.psf" ], - - "_comment": " 02.fp ", - "fp_style": "siesta", - "shuffle_poscar": false, - "fp_task_max": 100, - "fp_task_min": 10, - "fp_pp_path": ".", - "fp_pp_files": ["C.psf", "H.psf", "N.psf"], - "fp_params":{ - "ecut": 300, - "ediff": 1.0e-4, - "mixingWeight": 0.05, - "NumberPulay":5, - "kspacing": 0.5 + "fp_params": { + "ecut": 300, + "ediff": 0.0001, + "mixingWeight": 0.05, + "NumberPulay": 5, + "kspacing": 0.5 }, - "_comment": " that's all " + "_comment12": " that's all " } diff --git a/tests/sample.json b/tests/sample.json index c068f91ac..603a4ea06 100644 --- a/tests/sample.json +++ b/tests/sample.json @@ -1 +1,3 @@ -{"aa": "bb"} \ No newline at end of file +{ + "aa": "bb" +} diff --git a/tests/test_check_examples.py b/tests/test_check_examples.py index 976980b15..8522e8568 100644 --- a/tests/test_check_examples.py +++ b/tests/test_check_examples.py @@ -54,19 +54,19 @@ run_jdata, p_examples / "run" - / "dp1.x-lammps-vasp" + / "dp2.x-lammps-vasp" / "CH4" - / "param_CH4_deepmd-kit-1.1.0.json", + / "param_CH4_deepmd-kit-2.x.json", ), ( run_jdata, p_examples / "run" - / "dp1.x-lammps-vasp" + / "dp2.x-lammps-vasp" / "Al" - / "param_al_all_gpu-deepmd-kit-1.1.0.json", + / "param_al_all_gpu-deepmd-kit-2.x.json", ), - (run_jdata, p_examples / "run" / "dp1.x-lammps-vasp-et" / "param_elet.json"), + (run_jdata, p_examples / "run" / "dp2.x-lammps-vasp-et" / "param_elet.json"), ( run_jdata, p_examples / "run" / "dp2.x-lammps-ABACUS-lcao" / "fcc-al" / "run_param.json", @@ -77,19 +77,19 @@ ), ( run_jdata, - p_examples / "run" / "dp1.x-lammps-cp2k" / "methane" / "param-ch4.json", + p_examples / "run" / "dp2.x-lammps-cp2k" / "methane" / "param-ch4.json", ), ( run_jdata, - p_examples / "run" / "dp1.x-lammps-ABACUS-pw" / "methane" / "param.json", + p_examples / "run" / "dp2.x-lammps-ABACUS-pw" / "methane" / "param.json", ), ( run_jdata, - p_examples / "run" / "dp1.x-lammps-ABACUS-lcao-dpks" / "methane" / "param.json", + p_examples / "run" / "dp2.x-lammps-ABACUS-lcao-dpks" / "methane" / "param.json", ), ( run_jdata, - p_examples / "run" / "dp1.x_lammps_gaussian" / "dodecane" / "dodecane.json", + p_examples / "run" / "dp2.x_lammps_gaussian" / "dodecane" / "dodecane.json", ), (run_jdata, p_examples / "run" / "dp-lammps-enhance_sampling" / "param.json"), # (run_jdata, p_examples / "run" / "deprecated" / "param-mg-vasp.json"), @@ -101,17 +101,17 @@ p_examples / "run" / "deprecated" - / "dp0.12-lammps-cp2k" + / "dp2.x-lammps-cp2k" / "CH4" / "param_CH4.json", ), - # (run_jdata, p_examples / "run" / "deprecated" / "dp0.12-lammps-pwmat" / "param_CH4.json"), + # (run_jdata, p_examples / "run" / "deprecated" / "dp2.x-lammps-pwmat" / "param_CH4.json"), ( run_jdata, p_examples / "run" / "deprecated" - / "dp0.12-lammps-siesta" + / "dp2.x-lammps-siesta" / "dp-lammps-siesta" / "CH4" / "param_CH4.json", @@ -121,7 +121,7 @@ p_examples / "run" / "deprecated" - / "dp0.12-lammps-vasp" + / "dp2.x-lammps-vasp" / "Al" / "param_al_all_gpu.json", ), @@ -130,7 +130,7 @@ p_examples / "run" / "deprecated" - / "dp0.12-lammps-vasp" + / "dp2.x-lammps-vasp" / "CH4" / "param_CH4.json", ), diff --git a/tests/tools/machine_fp_single.json b/tests/tools/machine_fp_single.json index f998388eb..bb828fc32 100644 --- a/tests/tools/machine_fp_single.json +++ b/tests/tools/machine_fp_single.json @@ -1,15 +1,17 @@ { - "fp":[ - { - "command": "vasp_std", - "machine":{ - "batch_type": "PBS" - }, - "resources": { - "group_size" : 8 - }, - "_comments" : "In user_forward_files, define input files to be uploaded.", - "user_forward_files" : ["vdw_kernel.bindat"] - } + "fp": [ + { + "command": "vasp_std", + "machine": { + "batch_type": "PBS" + }, + "resources": { + "group_size": 8 + }, + "_comments": "In user_forward_files, define input files to be uploaded.", + "user_forward_files": [ + "vdw_kernel.bindat" + ] + } ] -} \ No newline at end of file +} diff --git a/tests/tools/machine_fp_single2.json b/tests/tools/machine_fp_single2.json index 8c2212927..772f655ca 100644 --- a/tests/tools/machine_fp_single2.json +++ b/tests/tools/machine_fp_single2.json @@ -1,14 +1,15 @@ { - "fp": - { - "command": "vasp_std", - "machine":{ - "batch_type": "PBS" - }, - "resources": { - "group_size" : 8 - }, - "_comments" : "In user_forward_files, define input files to be uploaded.", - "user_forward_files" : ["vdw_kernel.bindat"] + "fp": { + "command": "vasp_std", + "machine": { + "batch_type": "PBS" + }, + "resources": { + "group_size": 8 + }, + "_comments": "In user_forward_files, define input files to be uploaded.", + "user_forward_files": [ + "vdw_kernel.bindat" + ] } -} \ No newline at end of file +} diff --git a/tests/tools/run_report_test_output/param.json b/tests/tools/run_report_test_output/param.json index e8d11b9a8..397a785df 100644 --- a/tests/tools/run_report_test_output/param.json +++ b/tests/tools/run_report_test_output/param.json @@ -1,87 +1,132 @@ { - "type_map": ["Al", "Mg"], - "mass_map": [27, 24], - - "init_data_prefix": "/home/wanghan/study/deep.md/data/almgop.20/init//", - - "init_data_sys": [ - "al.fcc.01x01x01/02.md/sys-0004/deepmd", - "mg.fcc.01x01x01/02.md/sys-0004/deepmd" + "type_map": [ + "Al", + "Mg" ], - "init_batch_size": [1,1], - "sys_configs": [ - ["/home/wanghan/study/deep.md/data/almgop.20/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR"], - ["/home/wanghan/study/deep.md/data/almgop.20/init/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR"] + "mass_map": [ + 27, + 24 ], - "sys_batch_size": [1,1], - - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "_comment": " model parameters", - "use_smooth": true, - "sel_a": [90, 90], - "rcut_smth": 2.00, - "rcut": 6.00, - "filter_neuron": [10, 20, 40], - "filter_resnet_dt": false, - "n_axis_neuron": 4, - "n_neuron": [120, 120, 120], - "resnet_dt": true, - "coord_norm": true, - "type_fitting_net": false, - - "_comment": " traing controls", - "systems": [], - "set_prefix": "set", - "stop_batch": 1000, - "batch_size": 1, - "start_lr": 0.001, - "decay_steps": 2000, - "decay_rate": 0.95, - "seed": 0, - - "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, - - "_comment": " display and restart", - "_comment": " frequencies counted in batch", - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 1, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "load_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - - "_comment": "that's all" + "init_data_prefix": "/home/wanghan/study/deep.md/data/almgop.20/init//", + "init_data_sys": [ + "al.fcc.01x01x01/02.md/sys-0004/deepmd", + "mg.fcc.01x01x01/02.md/sys-0004/deepmd" + ], + "init_batch_size": [ + 1, + 1 + ], + "sys_configs": [ + [ + "/home/wanghan/study/deep.md/data/almgop.20/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR" + ], + [ + "/home/wanghan/study/deep.md/data/almgop.20/init/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR" + ] + ], + "sys_batch_size": [ + 1, + 1 + ], + "_comment1": " 00.train ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 90, + 90 + ], + "rcut": 6.0, + "rcut_smth": 2.0, + "neuron": [ + 10, + 20, + 40 + ], + "axis_neuron": 4, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "decay_steps": 2000, + "start_lr": 0.001, + "stop_lr": 0.0009746794344808964 + }, + "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": { + "seed": 0, + "stop_batch": 1000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + } }, - - "_comment": " 01.model_devi ", - "_comment": "model_devi_skip: the first x of the recorded frames", - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.20, - "model_devi_clean_traj": false, - "model_devi_jobs": [ - { "_idx": 0, "ensemble": "npt", "nsteps": 50, "press": [1.0,2.0], "sys_idx": [0, 1], "temps": [50,100], "trj_freq": 10 } + "_comment7": " 01.model_devi ", + "_comment8": "model_devi_skip: the first x of the recorded frames", + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.2, + "model_devi_clean_traj": false, + "model_devi_jobs": [ + { + "_idx": 0, + "ensemble": "npt", + "nsteps": 50, + "press": [ + 1.0, + 2.0 + ], + "sys_idx": [ + 0, + 1 + ], + "temps": [ + 50, + 100 + ], + "trj_freq": 10 + } + ], + "_comment9": " 02.fp ", + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 8, + "fp_task_min": 2, + "fp_pp_path": "/home/wanghan/study/deep.md/dpgen/almg/vasp", + "fp_pp_files": [ + "POTCAR.Al", + "POTCAR.Mg" ], - "_comment": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 8, - "fp_task_min": 2, - "fp_pp_path": "/home/wanghan/study/deep.md/dpgen/almg/vasp", - "fp_pp_files": ["POTCAR.Al", "POTCAR.Mg"], - "fp_incar": "/home/wanghan/study/deep.md/dpgen/almg/vasp/INCAR", - "_comment": " that's all " + "fp_incar": "/home/wanghan/study/deep.md/dpgen/almg/vasp/INCAR", + "_comment10": " that's all " } -