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‎.github/workflows/mirror_gitee.yml‎

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jobs:
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git-mirror:
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runs-on: ubuntu-latest
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if: github.repository_owner == 'deepmodeling'
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steps:
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- uses: wearerequired/git-mirror-action@v1
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env:

‎.github/workflows/test.yml‎

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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.7, 3.8]
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PYMATGEN_VERSION: [2019.1.13, 2019.7.30]
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python-version: [3.8, 3.9]
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PYMATGEN_VERSION: [2022.7.19]
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steps:
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- uses: actions/checkout@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: pip install coverage codecov pymatgen==${{ matrix.PYMATGEN_VERSION }} .
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run: pip install coverage pymatgen==${{ matrix.PYMATGEN_VERSION }} -e .
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- name: Test
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run: coverage run --source=./dpgen -m unittest -v && coverage report
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- run: codecov
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- uses: codecov/codecov-action@v3
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pass:
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needs: [build]
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runs-on: ubuntu-latest
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steps:
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- run: echo "All jobs passed"

‎.gitignore‎

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_build
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tests/generator/calypso_test_path
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doc/api/
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‎.readthedocs.yaml‎

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# .readthedocs.yaml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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# Set the version of Python and other tools you might need
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build:
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os: ubuntu-22.04
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tools:
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python: "3.10"
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: doc/conf.py
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# If using Sphinx, optionally build your docs in additional formats such as PDF
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formats: all
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# Optionally declare the Python requirements required to build your docs
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python:
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install:
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- requirements: doc/requirements.txt

‎README.md‎

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‎doc/CONTRIBUTING.md‎

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‎doc/README.md‎

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‎doc/autotest/Auto-test.md‎

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## Autotest Overview: Autotest for Deep Generator
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Suppose that we have a potential (can be DFT, DP, MEAM ...), `autotest` helps us automatically calculate M properties on N configurations. The folder where the `autotest` runs is called the working directory of `autotest`. Different potentials should be tested in different working directories.
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A property is tested in three steps: `make`, `run` and `post`. `make` prepares all computational tasks that are needed to calculate the property. For example to calculate EOS, `make` prepares a series of tasks, each of which has a scaled configuration with certain volume, and all necessary input files necessary for starting a VASP, ABACUS, or LAMMPS calculations. `run` sends all the computational tasks to remote computational resources defined in a machine configuration file like `machine.json`, and automatically collects the results when remote calculations finish. `post` calculates the desired property from the collected results.
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### Relaxation
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The relaxation of a structure should be carried out before calculating all other properties:
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```bash
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dpgen autotest make relax.json
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dpgen autotest run relax.json machine.json
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dpgen autotest post relax.json
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```
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If, for some reasons, the main program terminated at stage `run`, one can easily restart with the same command.
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`relax.json` is the parameter file. An example for `deepmd` relaxation is given as:
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```json
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{
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"structures": "confs/mp-*",
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"interaction": {
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"type": "deepmd",
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"model": "frozen_model.pb",
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"type_map": {"Al": 0, "Mg": 1}
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},
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"relaxation": {}
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}
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```
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where the key `structures` provides the structures to relax. `interaction` is provided with `deepmd`, and other options are `vasp`, `abacus`, `meam`...
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### Task type
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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:
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**VASP**:
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The default of `potcar_prefix` is "".
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```json
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"interaction": {
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"type": "vasp",
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"incar": "vasp_input/INCAR",
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"potcar_prefix":"vasp_input",
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"potcars": {"Al": "POTCAR.al", "Mg": "POTCAR.mg"}
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}
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```
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**ABACUS**:
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The default of `potcar_prefix` is "". The path of potcars/orb_files/deepks_desc is `potcar_prefix` + `potcars`/`orb_files`/`deepks_desc`.
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```json
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"interaction": {
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"type": "abacus",
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"incar": "abacus_input/INPUT",
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"potcar_prefix":"abacus_input",
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"potcars": {"Al": "pseudo_potential.al", "Mg": "pseudo_potential.mg"},
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"orb_files": {"Al": "numerical_orb.al", "Mg": "numerical_orb.mg"},
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"atom_masses": {"Al": 26.9815, "Mg":24.305},
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"deepks_desc": "jle.orb"
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}
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```
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**deepmd**:
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**Only 1** model can be used in autotest in one working directory.
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```json
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"interaction": {
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"type": "deepmd",
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"model": "frozen_model.pb",
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"type_map": {"Al": 0, "Mg": 1}
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}
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```
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**meam**:
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Please make sure the [USER-MEAMC package](https://lammps.sandia.gov/doc/Packages_details.html#pkg-user-meamc) has already been installed in LAMMPS.
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```json
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"interaction": {
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"type": "meam",
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"model": ["meam.lib","AlMg.meam"],
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"type_map": {"Al": 1, "Mg": 2}
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}
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```
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**eam_fs & eam_alloy**:
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Please make sure the [MANYBODY package](https://lammps.sandia.gov/doc/Packages_details.html#pkg-manybody) has already been installed in LAMMPS
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```json
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"interaction": {
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"type": "eam_fs (eam_alloy)",
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"model": "AlMg.eam.fs (AlMg.eam.alloy)",
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"type_map": {"Al": 1, "Mg": 2}
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}
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```
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### Property type
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Now the supported property types are `eos`, `elastic`, `vacancy`, `interstitial`, `surface`, and `gamma`. Before property tests, `relaxation` should be done first or the relaxation results should be present in the corresponding directory `confs/mp-*/relaxation/relax_task`. A file named `task.json` in json format containing the property parameter will be written in the directory of each task after `make` step. Multiple property tests can be performed simultaneously.
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## Make run and post
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There are three operations in auto test package, namely `make`, `run`, and `post`. Here we take `eos` property as an example for property type.
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### Make
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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:
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```bash
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dpgen autotest make relaxation.json
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```
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### Run
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The jobs would be dispatched according to the parameter in `machine.json` file and the calculation results would be sent back. Example:
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```bash
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dpgen autotest run relaxation.json machine.json
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```
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### Post
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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:
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```bash
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dpgen autotest post relaxation.json
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```

‎doc/autotest/index.rst‎

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==========================
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Auto test
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==========================
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.. _Guidelines::
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.. toctree::
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:maxdepth: 2
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:caption: Guidelines
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Auto-test
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.. _Main-components::
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.. toctree::
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:maxdepth: 2
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:caption: Main components
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Task-type
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Property-type
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Make-run-and-post
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.. _Structure-relaxation::
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.. toctree::
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:maxdepth: 2
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:caption: Structure relaxation
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relaxation/index.rst
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.. _Property::
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.. toctree::
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:maxdepth: 2
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:caption: Property
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property/index.rst
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.. _Refine::
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.. toctree::
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:maxdepth: 2
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:caption: Refine
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refine/index.rst
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.. _Reproduce::
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.. toctree::
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:maxdepth: 2
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:caption: Reproduce
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reproduce/index.rst

‎doc/autotest/property/Property-get-started-and-input-examples.md‎

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## Property get started and input examples
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Here we take deepmd for example and the input file for other task types is similar.
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```json
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{
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"structures": ["confs/std-*"],
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"interaction": {
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"type": "deepmd",
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"model": "frozen_model.pb",
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"type_map": {"Al": 0}
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},
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"properties": [
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{
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"type": "eos",
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"vol_start": 0.9,
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"vol_end": 1.1,
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"vol_step": 0.01
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},
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{
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"type": "elastic",
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"norm_deform": 1e-2,
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"shear_deform": 1e-2
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},
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{
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"type": "vacancy",
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"supercell": [3, 3, 3],
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"start_confs_path": "../vasp/confs"
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},
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{
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"type": "interstitial",
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"supercell": [3, 3, 3],
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"insert_ele": ["Al"],
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"conf_filters":{"min_dist": 1.5},
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"cal_setting": {"input_prop": "lammps_input/lammps_high"}
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},
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{
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"type": "surface",
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"min_slab_size": 10,
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"min_vacuum_size":11,
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"max_miller": 2,
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"cal_type": "static"
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},
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{
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"type": "gamma",
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"lattice_type": "fcc",
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"miller_index": [1, 1, 1],
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"displace_direction": [1, 1, 0],
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"supercell_size": [1, 1, 10],
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"min_vacuum_size": 10,
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"add_fix": ["true", "true", "false"],
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"n_steps": 20
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}
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]
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}
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```
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Universal key words for properties
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Key words | data structure | example | description
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---|---|---|---
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**type** | String | "eos" | property type
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skip | Boolean | true | whether to skip current property or not
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start_confs_path | String | "../vasp/confs" | start from the equilibrium configuration in other path only for the current property type
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cal_setting["input_prop"] | String | "lammps_input/lammps_high" |input commands file
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cal_setting["overwrite_interaction"] | Dict | | overwrite the interaction in the `interaction` part only for the current property type
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other parameters in `cal_setting` and `cal_type` in `relaxation` also apply in `property`.
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Key words for **EOS**
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Key words | data structure | example | description
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---|---|---|---
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**vol_start** | Float | 0.9 | the starting volume related to the equilibrium structure
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**vol_end** | Float | 1.1 | the biggest volume related to the equilibrium structure
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**vol_step** | Float | 0.01 | the volume increment related to the equilibrium structure
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vol_abs | Boolean | false | whether to treat vol_start, vol_end and vol_step as absolute volume or not (as relative volume), default = false
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Key words for **Elastic**
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Key words | data structure | example | description
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---|---|---|---
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norm_deform | Float | 1e-2 | deformation in xx, yy, zz, default = 1e-2
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shear_deform | Float | 1e-2 | deformation in other directions, default = 1e-2
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Key words for **Vacancy**
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Key words | data structure | example | description
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---|---|---|---
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supercell | List of Int | [3,3,3] | the supercell to be constructed, default = [1,1,1]
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Key words for **Interstitial**
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Key words | data structure | example | description
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---|---|---|---
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**insert_ele** | List of String | ["Al"] | the element to be inserted
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supercell | List of Int | [3,3,3] | the supercell to be constructed, default = [1,1,1]
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conf_filters | Dict | "min_dist": 1.5 | filter out the undesirable configuration
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bcc_self | Boolean | false | whether to do the self-interstitial calculations for bcc structures, default = false
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Key words for **Surface**
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Key words | data structure | example | description
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---|---|---|---
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**min_slab_size** | Int | 10 | minimum size of slab thickness
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**min_vacuum_size** | Int | 11 | minimum size of vacuum width
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pert_xz | Float | 0.01 | perturbation through xz direction used to compute surface energy, default = 0.01
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max_miller | Int | 2 | the maximum miller index, default = 2
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Key words for **Gamma**
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Key words | data structure | example | description
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---|---|---|---
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**lattice_type** | String | "fcc" | "bcc" or "fcc" at this stage
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**miller_index** | List of Int | [1,1,1] | slip plane for gamma-line calculation
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**displace_direction** | List of Int | [1,1,0] | slip direction for gamma-line calculation
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supercell_size | List of Int | [1,1,10] | the supercell to be constructed, default = [1,1,5]
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min_vacuum_size | Int or Float | 10 | minimum size of vacuum width, default = 20
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add_fix | List of String | ['true','true','false'] | whether to fix atoms in the direction, default = ['true','true','false'] (standard method)
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n_steps | Int | 20 | Number of points for gamma-line calculation, default = 10

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