updated readme

Reviewed-on: #6

README.md

@@ -26,9 +26,13 @@ time, msd = md.correlation.shifted_correlation(
 
 ## Installation
 
+=== DEPRECATED: 2025-08-19 === 
 The package requires the Python package [pygmx](https://github.com/mdevaluate/pygmx),
 which handles reading of Gromacs file formats.
 Installation of pygmx is described in its own repository.
+=== DEPRECATED: 2025-08-19 === 
+
+The package requires the Python package [pygmx](https://github.com/mdevaluate/pygmx),
 
 The mdevaluate package itself is plain Python code and, hence, can be imported from its directory directly, 
 or may be installed via setuptools to the local Python environment by running

create_mdevaluate_module.sh

@@ -0,0 +1,71 @@
+#!/bin/bash
+
+CONDA_VERSION=2024.10
+PYTHON_VERSION=3.12
+
+if [ -z "$1" ]; then
+    echo "No argument supplied, version to create expected"
+    exit 1
+fi
+
+
+if [ ! -w "/nfsopt/mdevaluate"]; then
+	echo "Please remount /nfsopt writable"
+	exit 2
+fi
+
+MD_VERSION=$1
+
+# purge evtl. loaded modules
+module purge
+
+
+echo "Create mdevaluate Python environemnt using conda"
+echo "Using conda version: $CONDA_VERSION"
+echo "Using Python version: $PYTHON_VERSION"
+
+module load anaconda3/$CONDA_VERSION
+conda create -y --prefix /nfsopt/mdevaluate/mdevaluate-${MD_VERSION} \
+             python=$PYTHON_VERSION
+module purge
+
+echo "Create modulefile for mdevaluate/$MD_VERSION"
+cat > /nfsopt/modulefiles/mdevaluate/$MD_VERSION <<EOF
+#%Module1.0#####################################################################
+##
+## dot modulefile
+##
+## modulefiles/dot.  Generated from dot.in by configure.
+##
+
+module-whatis	"Enables the mdevaluate Python environment."
+
+set version	${MD_VERSION}
+set module_path /nfsopt/mdevaluate/mdevaluate-\$version/bin
+
+prepend-path PATH \$module_path
+
+EOF
+
+echo "Loading mdevaluate environment and install packages"
+module load mdevaluate/${MD_VERSION}
+pip install jupyter \
+spyder \
+mdanalysis \
+pathos \
+pandas \
+dask \
+sqlalchemy \
+psycopg2-binary \
+trimesh \
+pyvista \
+seaborn \
+black \
+black[jupyter] \
+tables \
+pyedr \
+pytest
+
+pip install git+https://gitea.pkm.physik.tu-darmstadt.de/IPKM/mdevaluate.git
+pip install git+https://gitea.pkm.physik.tu-darmstadt.de/IPKM/python-store.git
+pip install git+https://gitea.pkm.physik.tu-darmstadt.de/IPKM/python-tudplot.git

src/mdevaluate/distribution.py

@@ -182,10 +182,10 @@ def tetrahedral_order(
     )
 
     # Connection vectors
-    neighbors_1 -= atoms
+    neighbors_1 = pbc_diff(neighbors_1, atoms, box=atoms.box)
-    neighbors_2 -= atoms
+    neighbors_2 = pbc_diff(neighbors_2, atoms, box=atoms.box)
-    neighbors_3 -= atoms
+    neighbors_3 = pbc_diff(neighbors_3, atoms, box=atoms.box)
-    neighbors_4 -= atoms
+    neighbors_4 = pbc_diff(neighbors_4, atoms, box=atoms.box)
 
     # Normed Connection vectors
     neighbors_1 /= np.linalg.norm(neighbors_1, axis=-1).reshape(-1, 1)

src/mdevaluate/pbc.py

@@ -149,32 +149,21 @@ def nojump(frame: CoordinateFrame, usecache: bool = True) -> CoordinateFrame:
             i0 = 0
             delta = 0
 
-        delta = (
+        delta = (delta
-            delta
+            + np.vstack(
-            + np.array(
+                [m[i0 : abstep + 1].sum(axis=0) for m in reader.nojump_matrices]
-                np.vstack(
+            ).T)
-                    [m[i0 : abstep + 1].sum(axis=0) for m in reader.nojump_matrices]
-                ).T
-            )
-            @ frame.box
-        )
 
         reader._nojump_cache[abstep] = delta
         while len(reader._nojump_cache) > NOJUMP_CACHESIZE:
             reader._nojump_cache.popitem(last=False)
-        delta = delta[selection, :]
     else:
-        delta = (
+        delta = np.vstack(
-            np.array(
+                [m[: frame.step + 1, selection].sum(axis=0) for m in reader.nojump_matrices]
-                np.vstack(
-                    [
-                        m[: frame.step + 1, selection].sum(axis=0)
-                        for m in reader.nojump_matrices
-                    ]
                 ).T
-            )
+    
-            @ frame.box
+    delta = delta[selection, :]
-        )
+    delta = np.array(delta @ frame.box)
     return frame - delta