Merge recent devel into master #613
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for INCAR param of VASP, NSW = 0 and 1 both lead to the output of 1 converged SCF, thus 1 valid frame of labeled data. NSW = 0 (actually single-point calculation) was not supported to be used as the "md_incar". Though, the previous limitation might be reasonable in semantics, this update just support the practical branching in VASP settings and eliminates the annoying exception for users.
…eepmodeling#530) pert_numb = jdata['pert_numb'] stages 2 pert makes 000000+pert_numb structures (dirs), pert_numb + 1 in total stages 3 was copying those in range(pert_numb), the first pert_numb structures(dir), lost the last one.
* Add type.raw for gromacs engine * Add restarting from .cpt in gmx calculation * Remove catch UnboundLocalError * Resolve conflicts
The bare `pair_coeff` is not supported in the latest version of LAMMPS. `pair_coeff * *` should be used instead. Fix deepmodeling/deepmd-kit#1201.
* Change mv to cp when downloading softlinks. * Add explanations relevant to POTCAR's examples. * Fix CH4's vasp-md INCAR example.
* fix typo in github actions release to conda * Get from_poscar_path only when from_poscar is true (deepmodeling#537) Change-Id: I17774bee345634e4e72bd783e8112eefaaf9f0d3 Co-authored-by: Zhengju Sha <jenny@bytedance.com> * fix dispatcher bugs in autotest run Change-Id: I0e48ec74d0a0d0d6c26988c6e8c28428a362b5d9 Co-authored-by: Han Wang <amcadmus@gmail.com> Co-authored-by: felix5572 <felix5572@github.com> Co-authored-by: Zhengju Sha <jenny@bytedance.com>
Change-Id: I4430b2c2e20da6cb28640dbc6139e62bed5357a2 Co-authored-by: Zhengju Sha <jenny@bytedance.com>
Change-Id: I9ef3f65729cc2e2f553ea7ac038e77d219ad4712 Co-authored-by: Zhengju Sha <jenny@bytedance.com>
…pmodeling#572) Change-Id: Ia138ee7c31b6c41d9f41f5943affa9ebf8803c46 Co-authored-by: Zhengju Sha <jenny@bytedance.com>
* Fix bug in make_submission of Auto-test
* update abacus_scf * add new parameters in test cases * add assertion info
* Add ase, custodian, GromacsWrapper in conda packages.
* add lebesgue ch4 example * fix readme nad machine file * fix machine.json
Change-Id: I26e8f7120703f131ffb005e4c0c927c108821ae0 Co-authored-by: Zhengju Sha <jenny@bytedance.com>
* model_devi_clean_traj support buffer * fix clean index * update readme
* fix bug issue:597 * fix energies mismatch bug for dpdata cp2k unittest * fix issue 597
* bump dpdata version to 0.2.4 * fix AssertionErrors in TestPostGaussian (#5) * fix bug issue:597 (deepmodeling#598) (#6) * fix bug issue:597 * fix energies mismatch bug for dpdata cp2k unittest * fix issue 597 Co-authored-by: Yongbin Zhuang <38876805+robinzyb@users.noreply.github.com> Co-authored-by: Han Wang <wang_han@iapcm.ac.cn> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: Han Wang <amcadmus@gmail.com> Co-authored-by: Yongbin Zhuang <38876805+robinzyb@users.noreply.github.com>
Change-Id: I12cc467e5956a5deb29ac4bd43719db1c0ef8942 Co-authored-by: Zhengju Sha <jenny@bytedance.com>
Set `dp_compress` to `true` in parameters will enable model compression.
* fix typo in github actions release to conda * Get from_poscar_path only when from_poscar is true (deepmodeling#537) Change-Id: I17774bee345634e4e72bd783e8112eefaaf9f0d3 Co-authored-by: Zhengju Sha <jenny@bytedance.com> * adapt different trust level for different sys_configs Co-authored-by: Han Wang <amcadmus@gmail.com> Co-authored-by: felix5572 <felix5572@github.com> Co-authored-by: shazj99 <shazj99@gmail.com> Co-authored-by: Zhengju Sha <jenny@bytedance.com>
currently, only count the #atoms of the first element when evaluating E-per-atom;
if kspacing is provided in json, will in fact use KSPACING=1 (default) to cal
…odeling#610) * model_devi | sort models in default&support user-defined order current behavior: 1）the list of models written in input.lammps for model_devi is created by "glob" without "sort" --> may give different (random) orders in different machine environments --> would randomly alter the model being used to sample configurations (always use the first model written in imput.lammps) ---> could lead to unexpected performance, such as, when using together with "model_devi_activation_func" that allows four models to be nonequivalent. 2）when preparing input.lammps from iuser-provided template, the line begin with "pair_style deepmd" will be overwritten by dpgen, thus overwrites the user defined order of models ---> could lead to unexpected performance, such as, when using together with "model_devi_activation_func" that allows four models to be nonequivalent and users indeed expected a specific order of models. changes: 1）sorted the list of models in default, thus always use graph.000.pb to sample configurations; 2）check weather user writes the full line of begin with "pair_style deepmd" (by checking the length), if yes, leave it be; if not, overwrites with the default settings (use graph.000.pb to sample); besides, the original error trigger is retained if key words "pair_style deepmd" are not provided in the template. * adjust space/tab * adjust annotation
Codecov Report
@@ Coverage Diff @@
## master #613 +/- ##
==========================================
+ Coverage 33.03% 33.16% +0.13%
==========================================
Files 86 86
Lines 14730 14837 +107
==========================================
+ Hits 4866 4921 +55
- Misses 9864 9916 +52
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