docs: remove set_prefix (#1537)

See: - deepmodeling/deepmd-kit#3477 - deepmodeling/deepmd-kit#3753  ## Summary by CodeRabbit - **Refactor** - Removed the `"set_prefix": "set"` attribute across various JSON and YAML configuration files, streamlining data handling and batch processing setups.  --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Han Wang <[email protected]>
deepmodeling · May 7, 2024 · d5dd205 · d5dd205
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diff --git a/doc/simplify/simplify.md b/doc/simplify/simplify.md
@@ -84,7 +84,6 @@ Here is an example of `param.json` for QM7 dataset:
  "limit_pref_pf": 0
  },
  "training": {
- "set_prefix": "set",
  "numb_steps": 10000,
  "disp_file": "lcurve.out",
  "disp_freq": 1000,

diff --git a/examples/run/ch4/param.json b/examples/run/ch4/param.json
@@ -92,7 +92,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json b/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json
@@ -140,9 +140,7 @@
  "time_training": true,
  "profiling": false,
  "profiling_file": "timeline.json",
- "training_data": {
- "set_prefix": "set"
- }
+ "training_data": {}
  }
  },
  "model_devi_engine": "gromacs",

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
@@ -85,7 +85,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.yaml b/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.yaml
@@ -43,7 +43,6 @@ default_training_param:
  coord_norm: true
  type_fitting_net: false
  systems: []
- set_prefix: set
  stop_batch: 40000
  batch_size: 1
  start_lr: 0.001

diff --git a/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json
@@ -88,7 +88,6 @@
  "systems": [
  "./00.data/"
  ],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

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
@@ -85,7 +85,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.yaml b/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.yaml
@@ -42,7 +42,6 @@ default_training_param:
  coord_norm: true
  type_fitting_net: false
  systems: []
- set_prefix: set
  stop_batch: 40000
  batch_size: 1
  start_lr: 0.001

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
@@ -178,7 +178,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.yaml b/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.yaml
@@ -91,7 +91,6 @@ default_training_param:
  coord_norm: true
  type_fitting_net: false
  systems: []
- set_prefix: set
  stop_batch: 400000
  batch_size: 1
  start_lr: 0.001

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
@@ -86,7 +86,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.yaml b/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.yaml
@@ -43,7 +43,6 @@ default_training_param:
  coord_norm: true
  type_fitting_net: false
  systems: []
- set_prefix: set
  stop_batch: 2000
  batch_size: 1
  start_lr: 0.001

diff --git a/examples/run/deprecated/param-h2oscan-vasp.json b/examples/run/deprecated/param-h2oscan-vasp.json
@@ -386,7 +386,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/deprecated/param-mg-vasp-ucloud.json b/examples/run/deprecated/param-mg-vasp-ucloud.json
@@ -214,7 +214,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/deprecated/param-mg-vasp.json b/examples/run/deprecated/param-mg-vasp.json
@@ -214,7 +214,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/deprecated/param-pyridine-pwscf.json b/examples/run/deprecated/param-pyridine-pwscf.json
@@ -114,7 +114,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/dp-calypso-vasp/param.json b/examples/run/dp-calypso-vasp/param.json
@@ -89,8 +89,7 @@
  "disp_training": true,
  "time_training": true,
  "profiling": false,
- "profiling_file": "timeline.json",
- "set_prefix": "set"
+ "profiling_file": "timeline.json"
  }
  },
  "sys_configs": "",

diff --git a/examples/run/dp-lammps-enhance_sampling/param.json b/examples/run/dp-lammps-enhance_sampling/param.json
@@ -97,7 +97,6 @@
  "profiling_file": "timeline.json",
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

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
@@ -94,7 +94,6 @@
  "profiling_file": "timeline.json",
  "_comment4": "that's all",
  "training_data": {
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json b/examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json
@@ -94,7 +94,6 @@
  "profiling_file": "timeline.json",
  "_comment4": "that's all",
  "training_data": {
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json b/examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json
@@ -88,7 +88,6 @@
  "profiling_file": "timeline.json",
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

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
@@ -68,7 +68,6 @@
  "limit_pref_v": 0.0
  },
  "training": {
- "_set_prefix": "set",
  "stop_batch": 40000,
  "_batch_size": 1,
  "disp_file": "lcurve.out",

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
@@ -81,7 +81,6 @@
  "limit_pref_v": 0.0
  },
  "training": {
- "_set_prefix": "set",
  "stop_batch": 20000,
  "_batch_size": 1,
  "disp_file": "lcurve.out",

diff --git a/examples/run/dp2.x-lammps-pwscf/Al/param_al_all_gpu-deepmd-kit-2.x.json b/examples/run/dp2.x-lammps-pwscf/Al/param_al_all_gpu-deepmd-kit-2.x.json
@@ -158,7 +158,6 @@
  "_comment6": "that's all",
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/dp2.x-lammps-pwscf/CH4/param_CH4_deepmd-kit-2.x.json b/examples/run/dp2.x-lammps-pwscf/CH4/param_CH4_deepmd-kit-2.x.json
@@ -81,7 +81,6 @@
  "profiling_file": "timeline.json",
  "_comment2": "that's all",
  "training_data": {
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/dp2.x-lammps-pwscf/param_CH4_deepmd-kit-2.0.1.json b/examples/run/dp2.x-lammps-pwscf/param_CH4_deepmd-kit-2.0.1.json
@@ -69,7 +69,6 @@
  "limit_pref_v": 0.0
  },
  "training": {
- "set_prefix": "set",
  "numb_steps": 2000,
  "batch_size": 1,
  "disp_file": "lcurve.out",

diff --git a/examples/run/dp2.x-lammps-vasp-et/param_elet.json b/examples/run/dp2.x-lammps-vasp-et/param_elet.json
@@ -83,7 +83,6 @@
  "profiling_file": "timeline.json",
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  },

diff --git a/examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-2.x.json b/examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-2.x.json
@@ -158,7 +158,6 @@
  "_comment6": "that's all",
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json b/examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json
@@ -81,7 +81,6 @@
  "profiling_file": "timeline.json",
  "_comment2": "that's all",
  "training_data": {
- "set_prefix": "set",
  "batch_size": 1
  }
  }

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
@@ -69,7 +69,6 @@
  "limit_pref_v": 0.0
  },
  "training": {
- "set_prefix": "set",
  "numb_steps": 2000,
  "batch_size": 1,
  "disp_file": "lcurve.out",

diff --git a/examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json b/examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json
@@ -75,9 +75,7 @@
  "time_training": true,
  "profiling": false,
  "profiling_file": "timeline.json",
- "training_data": {
- "set_prefix": "set"
- }
+ "training_data": {}
  }
  },
  "use_clusters": true,

diff --git a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json
@@ -114,7 +114,6 @@
  "profiling": false,
  "profiling_file": "timeline.json",
  "training_data": {
- "set_prefix": "set",
  "batch_size": "auto"
  }
  }

diff --git a/examples/simplify/qm7.json b/examples/simplify/qm7.json
@@ -84,9 +84,7 @@
  "time_training": true,
  "profiling": false,
  "profiling_file": "timeline.json",
- "training_data": {
- "set_prefix": "set"
- }
+ "training_data": {}
  },
  "_comment1": "that's all"
  },

diff --git a/tests/generator/param-custom-fp.json b/tests/generator/param-custom-fp.json
@@ -114,7 +114,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/tests/generator/param-methane-abacus-diy.json b/tests/generator/param-methane-abacus-diy.json
@@ -96,7 +96,6 @@
  "profiling_file": "timeline.json",
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/tests/generator/param-methane-abacus.json b/tests/generator/param-methane-abacus.json
@@ -96,7 +96,6 @@
  "profiling_file": "timeline.json",
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/tests/generator/param-mg-pimd-vasp.json b/tests/generator/param-mg-pimd-vasp.json
@@ -84,7 +84,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/tests/generator/param-mg-vasp-diy.json b/tests/generator/param-mg-vasp-diy.json
@@ -84,7 +84,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/tests/generator/param-mg-vasp-multi-trust.json b/tests/generator/param-mg-vasp-multi-trust.json
@@ -85,7 +85,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/tests/generator/param-mg-vasp-old.json b/tests/generator/param-mg-vasp-old.json
@@ -84,7 +84,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/tests/generator/param-mg-vasp-v1-et.json b/tests/generator/param-mg-vasp-v1-et.json
@@ -87,7 +87,6 @@
  "profiling_file": "timeline.json",
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/tests/generator/param-mg-vasp-v1.json b/tests/generator/param-mg-vasp-v1.json
@@ -73,7 +73,6 @@
  },
  "training": {
  "systems": [],
- "set_prefix": "set",
  "stop_batch": 1000,
  "batch_size": 1,
  "seed": 1,

diff --git a/tests/generator/param-mg-vasp.json b/tests/generator/param-mg-vasp.json
@@ -84,7 +84,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/tests/generator/param-mg-vasp_merge_traj.json b/tests/generator/param-mg-vasp_merge_traj.json
@@ -84,7 +84,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/tests/generator/param-mgo-cp2k-exinput.json b/tests/generator/param-mgo-cp2k-exinput.json
@@ -114,7 +114,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/tests/generator/param-pyridine-cp2k.json b/tests/generator/param-pyridine-cp2k.json
@@ -114,7 +114,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/tests/generator/param-pyridine-gaussian.json b/tests/generator/param-pyridine-gaussian.json
@@ -114,7 +114,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }

diff --git a/tests/generator/param-pyridine-pwmat.json b/tests/generator/param-pyridine-pwmat.json
@@ -114,7 +114,6 @@
  "profiling": false,
  "training_data": {
  "systems": [],
- "set_prefix": "set",
  "batch_size": 1
  }
  }