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Remove the outlier frames that satisfy
$$
\frac{\left \| E - \bar{E} \right \|}{\sigma(E)} \geq \text{threshold}
$$
---------
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/psf/black: 22.12.0 → 23.1.0](psf/black@22.12.0...23.1.0) <!--pre-commit.ci end--> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
From QE v7.2, pw.x prints each contributions to forces acting on atoms (i.e. non-local, ionic, local, core correction, etc...), right after original 'Forces acting on atoms' without blank line. Thus, it make 'list index out of range' error, from ret.append(...) in get_force. This changes make length of list blk in get_forces same as total number of atoms, avoiding out of range error. --------- Signed-off-by: pee8379 <pee8379@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/psf/black: 23.1.0 → 23.3.0](psf/black@23.1.0...23.3.0) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
modification: 1. float precision from float32 to float 64 2. comparison between pos.xyz and log file is too strict!. just approximately checking is sufficient. math.isclose(log_info_dict["energies"], xyz_info_dict["energies"], abs_tol=1.0e-6), --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
In ABACUS version >= v3.1.4, the format of file "MD_dump" is different. The lattice constant line is added by the unit "Angstrom" at the end, and the position is the real cartesian coordinate. MD_dump is changed from ``` MDSTEP: 0 LATTICE_CONSTANT: 23.453780000000 LATTICE_VECTORS 1.000000000000 0.000000000000 0.000000000000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 0.000000000000 1.000000000000 VIRIAL (KBAR) 36.689617311102 0.000000000001 -0.000000000000 0.000000000001 36.689617311104 -0.000000000001 -0.000000000000 -0.000000000001 36.689617311147 INDEX LABEL POSITIONS FORCE (eV/Angstrom) 0 Sn 0.000000000000 0.000000000000 0.000000000000 -0.000000000000 0.000000000000 -0.000000000000 1 Sn 0.000000000000 0.250000000000 0.250000000000 -0.000186795145 -0.000453823732 -0.000453823732 ``` to ``` MDSTEP: 0 LATTICE_CONSTANT: 12.411200939060 Angstrom LATTICE_VECTORS 1.000000000000 0.000000000000 0.000000000000 0.000000000000 1.000000000000 0.000000000000 0.000000000000 0.000000000000 1.000000000000 VIRIAL (kbar) 36.689617311101 0.000000000003 -0.000000000000 0.000000000003 36.689617311089 -0.000000000001 -0.000000000000 -0.000000000001 36.689617311135 INDEX LABEL POSITION (Angstrom) FORCE (eV/Angstrom) VELOCITY (Angstrom/fs) 0 Sn 0.000000000000 0.000000000000 0.000000000000 -0.000000000000 -0.000000000001 -0.000000000001 0.001244557166 -0.000346684288 0.000768457739 1 Sn 0.000000000000 3.102800034079 3.102800034079 -0.000186795145 -0.000453823768 -0.000453823768 0.000550996187 -0.000886442775 0.001579501983 ``` --------- Signed-off-by: pxlxingliang <91927439+pxlxingliang@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
<!--pre-commit.ci start--> updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.243 → v0.0.262](astral-sh/ruff-pre-commit@v0.0.243...v0.0.262) <!--pre-commit.ci end--> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Split a MultiSystems into training and test sub sets --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/charliermarsh/ruff-pre-commit: v0.0.262 → v0.0.263](astral-sh/ruff-pre-commit@v0.0.262...v0.0.263) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #464 +/- ##
==========================================
+ Coverage 82.51% 82.76% +0.25%
==========================================
Files 68 70 +2
Lines 6198 6313 +115
==========================================
+ Hits 5114 5225 +111
- Misses 1084 1088 +4
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