Merge devel to master #795
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Merge master into devel
* add amber model_devi_engine and amber/corr fp_style (and make the code more like a 💩 hill) * fix show error * use new dpdispatcher * update new dpdispatcher * update for new dpdispatcher * support dpdispatcher * fix bug when using new dpdispatcher * update for new dpdispatcher init_bulk * update examples for new dpdispatcher * fix install * fix typo use LooseVersion Co-authored-by: Jinzhe Zeng <[email protected]> * update LooseVersion * update dependency dpdispatcher min version * kk * support hybrid descriptor (fix deepmodeling#458) (deepmodeling#459) * support multiple param7 files * hdf5 & other improvements * disable sort * kk * migrate parameters into parm file * fix the issue to detect the list in the yaml * append ref to sander command * bugfix * skip the first "active learning" line * bugfix * separate low level and high level mdin * add quote to dpamber command * Revert "skip the first "active learning" line" This reverts commit 3ac4026. * only skip first active line if not restarting * generate sub models * fix the bug of sys_counter * set the seed of type_embedding network * sync with devel * sync with devel * make symlink symlink * fix * fix merge issue * rewrite simplify; support hdf5 as initial training data * bugfix * fix typo * revert changes to simplify; going to submit in another PR * revert training * revert changes * fix bug * add comments * add comments * add tests * fix typo * add an example * add netCDF4 to require * raise RuntimeError when model_devi_engine is unknown Co-authored-by: Yuan Fengbo <[email protected]> Co-authored-by: felix5572 <[email protected]> Co-authored-by: Yuan Fengbo (袁奉博) <[email protected]>
* Create Performing the Run process.md Description of the output files in DP-GEN run process. * Create Specify the Run process.md Description of an example of param.json. * Update and rename Specify the Run process.md to example-of-param.md * Update and rename Performing the Run process.md to Overview-of-the-run-process.md * Update and rename Overview-of-the-run-process.md to overview-of-the-run-process.md Specify the format of the code * Update example-of-param.md Specify the format of code * Update example-of-param.md * Update example-of-param.md * Create example-of-machine * Rename example-of-machine to example-of-machine.md * add param.rst param.rst generated by dargs * Update param.rst * updata dpgen run param parameters * Update param.rst * Update param.rst * Update example-of-param.md * Update overview-of-the-run-process.md * Update example-of-machine.md * Update example-of-machine.md * Update overview-of-the-run-process.md * Create run-process.rst * Update index.rst * Update param.rst * Update param.rst * Update index.rst
* refactor simplify 1. Used `dp model-devi` to calculate model deviation, instead of local calculation. Supported by deepmodeling/deepmd-kit#1618, released in v2.1.1. So the version earlier than 2.1.1 is not supported any more. 2. Assumed all systems are MultiSystems. 3. Removed energy model deviation support * expand path when getting multisystems * let `make_train` and `run_train` expand paths * load numpy array instead * use dpdata to get nframes * fix tests * update README
* supports non-list mdata The mdata of a task is a list of a single dict. This "list" looks useless and not clear enough. So this commit supports using the dict without a list. Note that old parameters are still supported, so no breaking changes are made. The "list" is just removed from all examples. Both list and non-list parameters are in the unittest. * fix typo
* upgrade all tasks to dpdispatcher This commit upgrades init_reaction and init_surf to use dpdispatcher * fix method args * fix typo * change the variable name from `work_dir` to `work_path`
…/EOS.py (deepmodeling#741) * update: add a new option of absolute volume in ./dpgen/auto_test/EOS.py * update: add doc in /dpgen/doc/toymodels/ * update: change the description for eos, change the doc in /dpgen/doc/toymodels/ * update: change the notice of absolute volume from print into dlog.info
Co-authored-by: LiuRenxi <[email protected]>
* generate machine parameter page for simplify and init * switching to new dargs directive
* add auto cli docs * fix typo * fix package name... * forgot to return parser * add the blank line
* fix ‘post_fp_cp2k’, add param rfailed * Update run.py
* add init-reaction docs and args The commit includes: - add docs - add detailed arguments - add strict argument checking - strict check the init-reaction example * init-reaction -> init_reaction * fix links * add the example to doc * add Geom=PrintInputOrient to keywords
* generate run arg doc from scripts This commit generates run argument documentations from scripts at runtime, so we can work on the script to improve the docs. * remove `init_multi_systems` see deepmodeling#730 * set repeat=True for model_devi_jobs * switch to dargs directive * switch for mdata * add extension * the current model_devi_args is indeed lammps arguments * fix error * fix error
* Update simplify.py * Update simplify.py Co-authored-by: Han Wang <[email protected]>
* Update simplify.py for sys_entire, set labeled=False * get labeled from jdata * Update simplify.py
The way to organize fp style argument is incorrect before.
* add simplify jdata docs; fix and check example Fix deepmodeling#779. * `use_ele_temp` should be optional * `sys_format` should be optional * `sys_configs` should be list * `labeled` should be optional * `use_clusters` and `cluster_cutoff` are optional * fix keyword option * add to toc
…vi_job (deepmodeling#786) * adapt different trust level for different sys_configs * fix deepmodeling#746; add iter dependent trust level * add document for deepmodeling#786 * some fix accroding to review * fix unexpected 0 bug * fix document not supporting typing bug * change value for trust level in unittest
* Change mv to cp when downloading softlinks. * Add explanations relevant to POTCAR's examples. * Fix CH4's vasp-md INCAR example. * Fix bug in make_submission of Auto-test * Add ase, custodian, GromacsWrapper in conda packages. * Fix bug of fp_task_min * Add gromacswrapper to conda recipe * Revert "Fix bug of fp_task_min" This reverts commit 8d7f8a7. * Add numkit recipe * Add `convert_mdata` definition to fix simplify bug. * Add netCDF4's dependency to conda recipe * Delete gromacswrapper and numkit dependency
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