Merge devel to master (#1161)

deepmodeling · Mar 21, 2023 · 4be4f6d · 4be4f6d
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diff --git a/.github/ISSUE_TEMPLATE/request-for-help.md b/.github/ISSUE_TEMPLATE/request-for-help.md
@@ -13,7 +13,7 @@ Before asking questions, you can
 search the previous issues or discussions
 check [Manual](https://github.com/deepmodeling/dpgen).
 
-Please **do not** post requests for help (e.g. with installing or using dpgen) here. 
+Please **do not** post requests for help (e.g. with installing or using dpgen) here.
 Instead go to [discussions](https://github.com/deepmodeling/dpgen/discussions).
 
 This issue tracker is for tracking dpgen development related issues only.

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -10,7 +10,6 @@ jobs:
     strategy:
       matrix:
         python-version: [3.8, 3.9]
-        PYMATGEN_VERSION: [2022.7.19]
 
     steps:
     - uses: actions/checkout@v2
@@ -19,12 +18,16 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
-      run: pip install coverage pymatgen==${{ matrix.PYMATGEN_VERSION }} -e .
+      run: pip install coverage git+https://github.com/materialsproject/pymatgen@b56698019098247ff54f50997a67c562b4375fc3 -e .
     - name: Test
       run: coverage run --source=./dpgen -m unittest -v && coverage report
     - uses: codecov/codecov-action@v3
   pass:
     needs: [build]
     runs-on: ubuntu-latest
+    if: always()
     steps:
-      - run: echo "All jobs passed"
+    - name: Decide whether the needed jobs succeeded or failed
+      uses: re-actors/alls-green@release/v1
+      with:
+        jobs: ${{ toJSON(needs) }}
diff --git a/.gitignore b/.gitignore
@@ -42,4 +42,3 @@ dbconfig.json
 _build
 tests/generator/calypso_test_path
 doc/api/
-
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,38 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    # there are many log files in tests
+    # TODO: seperate py files and log files
+    -   id: trailing-whitespace
+        exclude: "^tests/.*$"
+    -   id: end-of-file-fixer
+        exclude: "^tests/.*$"
+    -   id: check-yaml
+        exclude: "^conda/.*$"
+    #-   id: check-json
+    -   id: check-added-large-files
+    -   id: check-merge-conflict
+    -   id: check-symlinks
+        exclude: "^tests/tools/run_report_test_output/.*$"
+    -   id: check-toml
+# Python
+-   repo: https://github.com/psf/black
+    rev: 22.12.0
+    hooks:
+    -   id: black-jupyter
+-   repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.253
+    hooks:
+    - id: ruff
+      args: ["--fix"]
+# numpydoc
+-   repo: https://github.com/Carreau/velin
+    rev: 0.0.12
+    hooks:
+    - id: velin
+      args: ["--write"]
+ci:
+  autoupdate_branch: devel
diff --git a/README.md b/README.md
@@ -1,8 +1,12 @@
+![logo](./doc/logo.svg)
+
+--------------------------------------------------------------------------------
+
 # DP-GEN: A concurrent learning platform for the generation of reliable deep learning based potential energy models
 
 [![GitHub release](https://img.shields.io/github/release/deepmodeling/dpgen.svg?maxAge=86400)](https://github.com/deepmodeling/dpgen/releases/)
 [![doi:10.1016/j.cpc.2020.107206](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2020.107206-blue)](https://doi.org/10.1016/j.cpc.2020.107206)
-![Citations](https://citations.njzjz.win/10.1016/j.cpc.2020.107206)
+[![Citations](https://citations.njzjz.win/10.1016/j.cpc.2020.107206)](https://badge.dimensions.ai/details/doi/10.1016/j.cpc.2020.107206)
 [![conda install](https://img.shields.io/conda/dn/conda-forge/dpgen?label=conda%20install)](https://anaconda.org/conda-forge/dpgen)
 [![pip install](https://img.shields.io/pypi/dm/dpgen?label=pip%20install)](https://pypi.org/project/dpgen)
 

diff --git a/codecov.yml b/codecov.yml
@@ -0,0 +1,10 @@
+ignore:
+  - "tests"
+coverage:
+  status:
+    project:
+      default:
+        threshold: 100%
+    patch:
+      default:
+        threshold: 100%
diff --git a/conda/conda_build_config.yaml b/conda/conda_build_config.yaml
@@ -1,5 +1,5 @@
-channel_sources: 
+channel_sources:
   - defaults
   - conda-forge
-channel_targets: 
+channel_targets:
   - deepmodeling
diff --git a/conda/construct.yaml b/conda/construct.yaml
@@ -11,7 +11,7 @@ channels:
 specs:
   - python 3.8
   - pip
-  - dpgen {{ version }} 
+  - dpgen {{ version }}
 
 ignore_duplicate_files: True
 

diff --git a/doc/autotest/Auto-test.md b/doc/autotest/Auto-test.md
@@ -15,7 +15,7 @@ If, for some reasons, the main program terminated at stage `run`, one can easily
 `relax.json` is the parameter file. An example for `deepmd` relaxation is given as:
 ```json
 {
-        "structures":   "confs/mp-*",
+        "structures":   ["confs/mp-*"],
         "interaction": {
                 "type":         "deepmd",
                 "model":        "frozen_model.pb",
@@ -30,8 +30,8 @@ where the key `structures` provides the structures to relax. `interaction` is pr
 ### Task type
 There are now six task types implemented in the package: `vasp`, `abacus`, `deepmd`, `meam`, `eam_fs`, and `eam_alloy`. An `inter.json` file in json format containing the interaction parameters will be written in the directory of each task after `make`. We give input examples of the `interaction` part for each type below:
 
-**VASP**: 
-    
+**VASP**:
+
 The default of `potcar_prefix` is "".
 ```json
 	"interaction": {
@@ -41,8 +41,8 @@ The default of `potcar_prefix` is "".
 		"potcars":	{"Al": "POTCAR.al", "Mg": "POTCAR.mg"}
 	}
 ```
-**ABACUS**: 
-    
+**ABACUS**:
+
 The default of `potcar_prefix` is "". The path of potcars/orb_files/deepks_desc is `potcar_prefix` + `potcars`/`orb_files`/`deepks_desc`.
 ```json
 	"interaction": {
@@ -62,7 +62,7 @@ The default of `potcar_prefix` is "". The path of potcars/orb_files/deepks_desc
 ```json
 	"interaction": {
 		"type":		 "deepmd",
-		"model":	 "frozen_model.pb", 
+		"model":	 "frozen_model.pb",
 		"type_map":      {"Al": 0, "Mg": 1}
 	}
 ```
@@ -81,8 +81,8 @@ Please make sure the [USER-MEAMC package](https://lammps.sandia.gov/doc/Packages
 Please make sure the [MANYBODY package](https://lammps.sandia.gov/doc/Packages_details.html#pkg-manybody) has already been installed in LAMMPS
 ```json
 	"interaction": {
-		"type":		 "eam_fs (eam_alloy)", 
-		"model":	 "AlMg.eam.fs (AlMg.eam.alloy)", 
+		"type":		 "eam_fs (eam_alloy)",
+		"model":	 "AlMg.eam.fs (AlMg.eam.alloy)",
 		"type_map":      {"Al": 1, "Mg": 2}
 	}
 ```
@@ -96,9 +96,9 @@ Now the supported property types are `eos`, `elastic`, `vacancy`, `interstitial`
 There are three operations in auto test package, namely `make`, `run`, and `post`. Here we take `eos` property as an example for property type.
 
 ### Make
-The `INCAR`, `POSCAR`, `POTCAR` input files for VASP or `in.lammps`, `conf.lmp`, and the interatomic potential files for LAMMPS will be generated in the directory `confs/mp-*/relaxation/relax_task` for relaxation or `confs/mp-*/eos_00/task.[0-9]*[0-9]` for EOS. The `machine.json` file is not needed for `make`. Example: 
+The `INCAR`, `POSCAR`, `POTCAR` input files for VASP or `in.lammps`, `conf.lmp`, and the interatomic potential files for LAMMPS will be generated in the directory `confs/mp-*/relaxation/relax_task` for relaxation or `confs/mp-*/eos_00/task.[0-9]*[0-9]` for EOS. The `machine.json` file is not needed for `make`. Example:
 ```bash
-dpgen autotest make relaxation.json 
+dpgen autotest make relaxation.json
 ```
 
 ### Run
@@ -110,5 +110,5 @@ dpgen autotest run relaxation.json machine.json
 ### Post
 The post process of calculation results would be performed. `result.json` in json format will be generated in `confs/mp-*/relaxation/relax_task` for relaxation and `result.json` in json format and `result.out` in txt format in `confs/mp-*/eos_00` for EOS. The `machine.json` file is also not needed for `post`. Example:
 ```bash
-dpgen autotest post relaxation.json 
+dpgen autotest post relaxation.json
 ```
diff --git a/doc/autotest/index.rst b/doc/autotest/index.rst
@@ -9,13 +9,13 @@ Auto test
    :caption: Guidelines
 
    Auto-test
-  
+
 .. _Main-components::
 
 .. toctree::
    :maxdepth: 2
    :caption: Main components
-   
+
    Task-type
    Property-type
    Make-run-and-post
@@ -25,7 +25,7 @@ Auto test
 .. toctree::
    :maxdepth: 2
    :caption: Structure relaxation
-   
+
    relaxation/index.rst
 
 .. _Property::
@@ -41,13 +41,13 @@ Auto test
 .. toctree::
    :maxdepth: 2
    :caption: Refine
-   
+
    refine/index.rst
 
 .. _Reproduce::
 
 .. toctree::
    :maxdepth: 2
    :caption: Reproduce
-   
+
    reproduce/index.rst
diff --git a/doc/autotest/property/Property-get-started-and-input-examples.md b/doc/autotest/property/Property-get-started-and-input-examples.md
@@ -61,7 +61,7 @@ Key words | data structure | example | description
 **type** | String | "eos" | property type
 skip | Boolean | true | whether to skip current property or not
 start_confs_path | String | "../vasp/confs" | start from the equilibrium configuration in other path only for the current property type
-cal_setting["input_prop"] | String | "lammps_input/lammps_high" |input commands file 
+cal_setting["input_prop"] | String | "lammps_input/lammps_high" |input commands file
 cal_setting["overwrite_interaction"] | Dict | | overwrite the interaction in the `interaction` part only for the current property type
 
 other parameters in `cal_setting` and `cal_type` in `relaxation` also apply in `property`.
@@ -116,4 +116,4 @@ Key words | data structure | example | description
 supercell_size | List of Int | [1,1,10] | the supercell to be constructed, default = [1,1,5]
 min_vacuum_size | Int or Float | 10 | minimum size of vacuum width, default = 20
 add_fix | List of String | ['true','true','false'] | whether to fix atoms in the direction, default = ['true','true','false'] (standard method)
-n_steps | Int | 20 | Number of points for gamma-line calculation, default = 10
+n_steps | Int | 20 | Number of points for gamma-line calculation, default = 10
diff --git a/doc/autotest/property/Property-post.md b/doc/autotest/property/Property-post.md
@@ -4,4 +4,4 @@ Use command
 ```bash
 dpgen autotest post property.json
 ```
-to post results as `result.json` and `result.out` in each property's path.
+to post results as `result.json` and `result.out` in each property's path.
diff --git a/doc/autotest/property/index.rst b/doc/autotest/property/index.rst
@@ -9,4 +9,4 @@ Property
    Property-make
    Property-run
    Property-post
-   properties/index.rst
+   properties/index.rst
diff --git a/doc/autotest/property/properties/EOS-make.md b/doc/autotest/property/properties/EOS-make.md
@@ -1,10 +1,10 @@
 ## EOS make
 
-**Step 1.** Before `make` in EOS, the equilibrium configuration `CONTCAR` must be present in `confs/mp-*/relaxation`. 
+**Step 1.** Before `make` in EOS, the equilibrium configuration `CONTCAR` must be present in `confs/mp-*/relaxation`.
 
-**Step 2.** For the input example in the previous section, when we do `make`, 40 tasks would be generated as `confs/mp-*/eos_00/task.000000, confs/mp-*/eos_00/task.000001, ... , confs/mp-*/eos_00/task.000039`. The suffix `00` is used  for possible `refine` later. 
+**Step 2.** For the input example in the previous section, when we do `make`, 40 tasks would be generated as `confs/mp-*/eos_00/task.000000, confs/mp-*/eos_00/task.000001, ... , confs/mp-*/eos_00/task.000039`. The suffix `00` is used  for possible `refine` later.
 
-**Step 3.** If the task directory, for example `confs/mp-*/eos_00/task.000000` is not empty, the old input files in it including `INCAR`, `POSCAR`, `POTCAR`, `conf.lmp`, `in.lammps` would be deleted. 
+**Step 3.** If the task directory, for example `confs/mp-*/eos_00/task.000000` is not empty, the old input files in it including `INCAR`, `POSCAR`, `POTCAR`, `conf.lmp`, `in.lammps` would be deleted.
 
 **Step 4.** In each task directory, `POSCAR.orig` would link to `confs/mp-*/relaxation/CONTCAR`. Then the `scale` parameter can be calculated as:
 
@@ -14,4 +14,4 @@ scale = (vol_current / vol_equi) ** (1. / 3.)
 
 `vol_current` is the corresponding volume per atom of the current task and `vol_equi` is the volume per atom of the equilibrium configuration. Then the `poscar_scale` function in `dpgen.auto_test.lib.vasp` module would help to generate `POSCAR` file with `vol_current` in `confs/mp-*/eos_00/task.[0-9]*[0-9]`.
 
-**Step 5.** According to the task type, the input file including `INCAR`, `POTCAR` or `conf.lmp`, `in.lammps` would be written in every `confs/mp-*/eos_00/task.[0-9]*[0-9]`. 
+**Step 5.** According to the task type, the input file including `INCAR`, `POTCAR` or `conf.lmp`, `in.lammps` would be written in every `confs/mp-*/eos_00/task.[0-9]*[0-9]`.
diff --git a/doc/autotest/property/properties/EOS-post.md b/doc/autotest/property/properties/EOS-post.md
@@ -31,5 +31,3 @@ onf_dir: /root/auto_test_example/deepmd/confs/std-fcc/eos_00
    ...      ...
  17.935   -3.7088
 ```
-
-
diff --git a/doc/autotest/property/properties/Interstitial-make.md b/doc/autotest/property/properties/Interstitial-make.md
@@ -4,4 +4,4 @@
 
 **Step 2.** If `refine` is `True`, we do [refine process](../../refine/Refine-get-started-and-input-examples). If `reprod-opt` is `True` (the default is **False**), we do [reproduce process](../../reproduce/Reproduce-get-started-and-input-examples). Else, the vacancy structure (`POSCAR`) and supercell information (`supercell.out`) are written in the task directory, for example, in `confs/mp-*/interstitial_00/task.000000` with the check and possible removing of the old input files like before.
 
-**Step 3.** In `interstitial` by VASP, `ISIF = 3`. In `interstitial` by LAMMPS, the same `in.lammps` as that in [EOS (change_box is True)](./EOS-make) would be generated with `scale` set to one. 
+**Step 3.** In `interstitial` by VASP, `ISIF = 3`. In `interstitial` by LAMMPS, the same `in.lammps` as that in [EOS (change_box is True)](./EOS-make) would be generated with `scale` set to one.
diff --git a/doc/autotest/property/properties/Interstitial-post.md b/doc/autotest/property/properties/Interstitial-post.md
@@ -1,6 +1,6 @@
 ## Interstitial post
 
-For `Interstitial`, we need to calculate the energy difference between a crystal structure with and without atom added in. 
+For `Interstitial`, we need to calculate the energy difference between a crystal structure with and without atom added in.
 The examples of the output files `result.json` in json format and `result.out` in txt format are given below.
 
 #### result.json

diff --git a/doc/autotest/property/properties/Surface-get-started-and-input-examples.md b/doc/autotest/property/properties/Surface-get-started-and-input-examples.md
@@ -1,6 +1,6 @@
 ## Surface get started and input examples
 
-`Surface` calculates the surface energy. We need to give the information of `min_slab_size`, `min_vacuum_size`, `max_miller` (default value is 2), and `pert_xz` which means perturbations in xz and will help work around vasp bug. 
+`Surface` calculates the surface energy. We need to give the information of `min_slab_size`, `min_vacuum_size`, `max_miller` (default value is 2), and `pert_xz` which means perturbations in xz and will help work around vasp bug.
 
 #### An example of the input file for Surface by deepmd:
 
@@ -18,7 +18,7 @@
                 "min_slab_size":  10,
                 "min_vacuum_size":11,
                 "max_miller":     2,
-                "cal_type":       "static" 
+                "cal_type":       "static"
 	    }
         ]
 }

diff --git a/doc/autotest/property/properties/Surface-make.md b/doc/autotest/property/properties/Surface-make.md
@@ -1,5 +1,5 @@
 ## Surface make
 
-**Step 1.** Based on the equilibrium configuration, `generate_all_slabs` module in [pymatgen.core.surface](https://pymatgen.org/pymatgen.core.surface.html) would help to generate surface structure list with using `max_miller`, `min_slab_size`, and `min_vacuum_size` parameters. 
+**Step 1.** Based on the equilibrium configuration, `generate_all_slabs` module in [pymatgen.core.surface](https://pymatgen.org/pymatgen.core.surface.html) would help to generate surface structure list with using `max_miller`, `min_slab_size`, and `min_vacuum_size` parameters.
 
 **Step 2.** If `refine` is True, we do [refine process](../../refine/Refine-get-started-and-input-examples). If `reprod-opt` is True (the default is False), we do [reproduce process](../../reproduce/Reproduce-get-started-and-input-examples). Otherwise, the surface structure (`POSCAR`) with perturbations in xz and miller index information (`miller.out`) are written in the task directory, for example, in `confs/mp-*/interstitial_00/task.000000` with the check and possible removing of the old input files like before.
diff --git a/doc/autotest/property/properties/Vacancy-make.md b/doc/autotest/property/properties/Vacancy-make.md
@@ -1,7 +1,7 @@
 ## Vacancy make
 
-**Step 1.** The `VacancyGenerator` module in [pymatgen.analysis.defects.generators](https://pymatgen.org/pymatgen.analysis.defects.generators.html) is used to generate a set of structures with vacancy. 
+**Step 1.** The `VacancyGenerator` module in [pymatgen.analysis.defects.generators](https://pymatgen.org/pymatgen.analysis.defects.generators.html) is used to generate a set of structures with vacancy.
 
 **Step 2.** If there are `init_from_suffix` and `output_suffix` parameter in the `properties` part, the [refine process](../../refine/Refine-get-started-and-input-examples) follows. If reproduce is evoked, the [reproduce process](../../reproduce/Reproduce-get-started-and-input-examples) follows. Otherwise, the vacancy structure (`POSCAR`) and supercell information (`supercell.out`) are written in the task directory, for example, in `confs/mp-*/vacancy_00/task.000000` with the check and possible removing of the old input files like before.
 
-**Step 3.** When doing `vacancy` by VASP, `ISIF = 3`. When doing `vacancy` by LAMMPS, the same `in.lammps` as that in [EOS (change_box is True)](./EOS-make) would be generated with `scale` set to one. 
+**Step 3.** When doing `vacancy` by VASP, `ISIF = 3`. When doing `vacancy` by LAMMPS, the same `in.lammps` as that in [EOS (change_box is True)](./EOS-make) would be generated with `scale` set to one.
diff --git a/doc/autotest/property/properties/Vacancy-post.md b/doc/autotest/property/properties/Vacancy-post.md
@@ -1,6 +1,6 @@
 ## Vacancy post
 
-For `Vacancy`, we need to calculate the energy difference between a crystal structure with and without a vacancy. 
+For `Vacancy`, we need to calculate the energy difference between a crystal structure with and without a vacancy.
 The examples of the output files `result.json` in json format and `result.out` in txt format are given below.
 
 #### result.json

diff --git a/doc/autotest/property/properties/index.rst b/doc/autotest/property/properties/index.rst
@@ -24,4 +24,4 @@ Properties
    Surface-get-started-and-input-examples
    Surface-make
    Surface-run
-   Surface-post
+   Surface-post
diff --git a/doc/autotest/refine/Refine-get-started-and-input-examples.md b/doc/autotest/refine/Refine-get-started-and-input-examples.md
@@ -1,6 +1,6 @@
 ## Refine get started and input examples
 
-Sometimes we want to refine the calculation of a property from previous results. For example, when higher convergence criteria `EDIFF` and `EDIFFG` are necessary in VASP, the new VASP calculation is desired to start from the previous output configuration, rather than starting from scratch. 
+Sometimes we want to refine the calculation of a property from previous results. For example, when higher convergence criteria `EDIFF` and `EDIFFG` are necessary in VASP, the new VASP calculation is desired to start from the previous output configuration, rather than starting from scratch.
 
 
 An example of the input file `refine.json` is given below:

diff --git a/doc/autotest/refine/index.rst b/doc/autotest/refine/index.rst
@@ -4,8 +4,8 @@ Refine
 
 .. toctree::
    :maxdepth: 2
-   
+
    Refine-get-started-and-input-examples
    Refine-make
    Refine-run
-   Refine-post
+   Refine-post
diff --git a/doc/autotest/relaxation/Relaxation-get-started-and-input-examples.md b/doc/autotest/relaxation/Relaxation-get-started-and-input-examples.md
@@ -1,8 +1,8 @@
 ## Relaxation get started and input examples
 
-The relaxation of a structure should be carried out before calculating all other properties. 
+The relaxation of a structure should be carried out before calculating all other properties.
 
-First, we need input parameter file and we name it `relax.json` here. All the relaxation calculations should be taken either by `VASP`, `ABACUS`, or `LAMMPS`. Here are two input examples for `VASP` and `LAMMPS` respectively. 
+First, we need input parameter file and we name it `relax.json` here. All the relaxation calculations should be taken either by `VASP`, `ABACUS`, or `LAMMPS`. Here are two input examples for `VASP` and `LAMMPS` respectively.
 
 An example of the input file for relaxation by VASP:
 
@@ -81,5 +81,3 @@ maxiter | Int | 5000 | max iterations of minimizer
 maxeval | Int | 500000 | max number of force/energy evaluations
 
 For LAMMPS relaxation and all the property calculations, **package will help to generate `in.lammps` file for user automatically** according to the property type. We can also make the final changes in the `minimize` setting (`minimize etol ftol maxiter maxeval`) in `in.lammps`. In addition, users can apply the input file for lammps commands in the `interaction` part. For further information of the LAMMPS relaxation, we refer users to [minimize command](https://lammps.sandia.gov/doc/minimize.html).
-
-
diff --git a/doc/autotest/relaxation/Relaxation-make.md b/doc/autotest/relaxation/Relaxation-make.md
@@ -96,7 +96,3 @@ print "Final Stress (xx yy zz xy xz yz) = ${Pxx} ${Pyy} ${Pzz} ${Pxy} ${Pxz} ${P
 If user provides lammps input command file `in.lammps`, the `thermo_style` and `dump` commands should be the same as the above file.
 
 **interatomic potential model**: the `frozen_model.pb` in `confs/mp-*/relaxation` would link to the `frozen_model.pb` file given in the input.
-
-
-
-