merge devel to master for v0.2.18 #628
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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>
See https://astral.sh/blog/the-ruff-formatter. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Per https://pypi.org/project/dpdata/0.2.17/#files, these files are too large.
…eling#568) Fix deepmodeling#512. --------- 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>
The length conversion in Psi4 is not fixed to Bohr. Instead, the output unit follows the input unit and is written in the output file. --------- 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>
support qe output files which do not contain stress --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Fix deepmodeling#212. --------- 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>
Fix deepmodeling#480. deepmodeling#250 doesn't handle this situation. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Dear developers, I added a new format key, `openmx` to read output files from OpenMX. I wrote the codes with reference to the `qe/cp/traj` format ones. Thank you in advance. --------- Co-authored-by: yaotang.zhang <yaotang.zhang@OSXITsinicxkomunoMacBook-Air.local> Co-authored-by: Zhang Yaotang <60209970+chouyoudou@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Han Wang <wang_han@iapcm.ac.cn> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
PWmat adds `nonperiodic_Position` block to MOVEMENT file, used to output the atomic positions without non periodic boundary conditions. Due to the fact that dpdata previously locates the number of atoms based on the keyword `Position`, when MOVEMENT contains `nonperiodic_Position`, it will cause the number of atoms to double, resulting in a bug. --------- Co-authored-by: Uper <41718895+Hyliu-BUAA@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Added support for ORCA single point energy files --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Based on deepmodeling#603 --------- Co-authored-by: robinzyb <38876805+robinzyb@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.3 → v0.2.0](astral-sh/ruff-pre-commit@v0.1.3...v0.2.0) <!--pre-commit.ci end--> --------- 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: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.2.0 → v0.2.1](astral-sh/ruff-pre-commit@v0.2.0...v0.2.1) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](astral-sh/ruff-pre-commit@v0.2.1...v0.2.2) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.2 → v0.3.3](astral-sh/ruff-pre-commit@v0.3.2...v0.3.3) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Dear developers, I would like to make some improvements on the format for OpenMX. 1. Change the format name from `openmx/out` to `openmx/md` 2. Add the if statement to read geometry optimization trajectories 3. Add the if statement to check if the SCF calculation has converged Thank you in advance.
See njzjz-bot/njzjz-bot#2. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.3.4](astral-sh/ruff-pre-commit@v0.3.3...v0.3.4) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.3.5](astral-sh/ruff-pre-commit@v0.3.4...v0.3.5) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
`sys.exit` is a lousy implementation when one wants to catch the error. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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