pymdkit 1.7.1__tar.gz → 1.7.2__tar.gz

{pymdkit-1.7.1 → pymdkit-1.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.7.1
+Version: 1.7.2
 Summary: A Python command-line toolkit for high-throughput atomistic workflows in AI-driven materials design.
 Author-email: Yueda Wang <ydwang0608@ustc.edu.cn>
 License-Expression: GPL-3.0-or-later
@@ -86,7 +86,7 @@ installed.
 On a machine with Internet access, run:
 
 ```bash
-python -m pip download pymdkit==1.7.1 -d pymdkit-offline
+python -m pip download pymdkit==1.7.2 -d pymdkit-offline
 ```
 
 This downloads `pymdkit` and the dependencies resolved by pip into the
@@ -94,14 +94,14 @@ This downloads `pymdkit` and the dependencies resolved by pip into the
 system. Then, inside the target pymdkit Python or conda environment, run:
 
 ```bash
-python -m pip install --no-index --find-links=pymdkit-offline pymdkit==1.7.1
+python -m pip install --no-index --find-links=pymdkit-offline pymdkit==1.7.2
 ```
 
 For optional GPU use, prepare the bundle on a networked machine compatible with
 the target HPC platform and Python environment:
 
 ```bash
-python -m pip download "pymdkit[gpu-cuda12]==1.7.1" -d pymdkit-offline
+python -m pip download "pymdkit[gpu-cuda12]==1.7.2" -d pymdkit-offline
 ```
 
 Transfer the whole `pymdkit-offline` directory, then install from it on the
@@ -109,7 +109,7 @@ target system:
 
 ```bash
 python -m pip install --no-index --find-links=pymdkit-offline \
-    "pymdkit[gpu-cuda12]==1.7.1"
+    "pymdkit[gpu-cuda12]==1.7.2"
 ```
 
 This GPU bundle includes the optional `cupy-cuda12x` package. Its wheels must also
@@ -558,6 +558,32 @@ standalone `substitute` command is removed.
 - Standalone `gpumd-group` tagging and `gpumd-trjcat` are removed without
   replacement. `gpumd-job -group` remains available during job creation.
 
+### Generated VASP structures
+
+New `.vasp` files written by `convert`, standalone `supercell`, and
+`dope -output-format vasp` automatically group atoms by species using
+pymatgen's POSCAR ordering. For example, a 64-atom LiI supercell has a single
+`Li I` species line and a `32 32` count line. Site order changes to group
+species; the lattice, species-resolved positions, and selective-dynamics
+flags remain associated with their sites.
+
+Direct (fractional) coordinates are the default. Both `convert` and
+`supercell` accept mutually exclusive `-direct` and `-cartesian` flags for
+`.vasp` output. These flags also apply in folder mode and when `convert`
+creates a supercell. They have no effect on CIF, XYZ, extxyz, or other output
+formats. VASP job input sets and collected CONTCAR files retain their existing
+behavior.
+
+```bash
+pmk convert -i LiI.cif -o LiI.vasp -direct
+pmk convert -i LiI.cif -o LiI-cart.vasp -cartesian
+pmk convert -if structures -of vasp-direct -oe vasp
+pmk convert -i LiI.cif -o LiI-222.vasp -supercell-matrix 2x2x2 -cartesian
+pmk supercell -i LiI.vasp -o LiI-222.vasp -matrix 2x2x2 -direct
+pmk supercell -i LiI.vasp -o LiI-222-cart.vasp -matrix 2x2x2 -cartesian
+pmk supercell -if vasp-direct -of vasp-cart -matrix 2x2x2 -cartesian
+```
+
 ### Other behavior
 
 `convert -d2o` first symmetrizes the disordered structure so each distinct