fix examples; adapt readme a bit

nanotech-empa · Feb 5, 2025 · 527ce85 · 527ce85
1 parent 4d68a5f
commit 527ce85
Show file tree

Hide file tree

Showing 11 changed files with 24 additions and 17 deletions.
diff --git a/README.md b/README.md
@@ -14,18 +14,20 @@ Features include:
 
 ### Installation
 
-The package requires an MPI implementation to be available on your system for `mpi4py`. You can install it:
+The package requires an MPI implementation to be available on your system for `mpi4py`. One option is `mpich`, which you can install with:
 
 - On Linux: through your package manager (e.g., `apt install mpich` or `yum install mpich`)
 - On macOS: through Homebrew (`brew install mpich`)
-- On Windows: through conda (`conda install -c conda-forge mpich`)
+- Or via conda, but then it's recommended to install it together with `mpi4py`: `conda install -c conda-forge mpi4py mpich`
 
 Then install the package with pip:
+
 ```bash
 pip install cp2k-spm-tools
 ```
 
 Or, for development:
+
 ```bash
 git clone https://github.com/nanotech-empa/cp2k-spm-tools.git
 cd cp2k-spm-tools
@@ -64,11 +66,15 @@ cgo.load_restart_wfn_file("./PROJ-RESTART.wfn", n_occ=2, n_virt=2)
 
 ### Evaluate the orbitals in the specific region ###
 cgo.calc_morbs_in_region(
-    dr_guess = 0.15,                          # grid spacing
+    dr_guess = 0.15,                          # grid spacing, can change very slightly
     x_eval_region = None,                     # take whole cell in x
     y_eval_region = [0.0, cgo.cell_ang[1]/2], # half cell in y
     z_eval_region = [19.0, 24.0],             # around the molecule in z
 )
 
 cgo.write_cube("./homo.cube", orbital_nr=0)
 ```
+
+Here's the resulting cube file, illustrating the constrained region of evaluation:
+
+<img src="examples/example.png" width="500">
diff --git a/examples/benzene_cube_from_wfn/run.sh b/examples/benzene_cube_from_wfn/run.sh
@@ -5,7 +5,7 @@ BASIS_PATH="../data/BASIS_MOLOPT"
 
 mkdir cubes
 
-../../cube_from_wfn.py \
+cp2k-cube-from-wfn \
   --cp2k_input_file $DATA_PATH/cp2k.inp \
   --basis_set_file $BASIS_PATH \
   --xyz_file $DATA_PATH/geom.xyz \

diff --git a/examples/benzene_overlap/run.sh b/examples/benzene_overlap/run.sh
@@ -7,7 +7,7 @@ BASIS_PATH="../data/BASIS_MOLOPT"
 
 mkdir out
 
-mpirun -n 2  python3 ../../overlap_from_wfns.py \
+mpirun -n 2  cp2k-overlap-from-wfns \
   --cp2k_input_file1 "$SLAB_FOLDER"/cp2k.inp \
   --basis_set_file1 $BASIS_PATH \
   --xyz_file1 "$SLAB_FOLDER"/geom.xyz \

diff --git a/examples/benzene_stm/run.sh b/examples/benzene_stm/run.sh
@@ -5,7 +5,7 @@ BASIS_PATH="../data/BASIS_MOLOPT"
 
 mkdir out
 
-mpirun -n 2 python3 ../../stm_sts_from_wfn.py \
+mpirun -n 2 cp2k-stm-sts-wfn \
   --cp2k_input_file "$FOLDER"/cp2k.inp \
   --basis_set_file $BASIS_PATH \
   --xyz_file "$FOLDER"/geom.xyz \
@@ -32,5 +32,5 @@ mpirun -n 2 python3 ../../stm_sts_from_wfn.py \
   --fwhms 0.5 \
 
 cd out 
-../../../stm_sts_plotter.py --orb_npz orb.npz --stm_npz stm.npz
+cp2k-stm-sts-plot --orb_npz orb.npz --stm_npz stm.npz
 
diff --git a/examples/c2h2_bader_bond_order/run.sh b/examples/c2h2_bader_bond_order/run.sh
@@ -7,7 +7,7 @@ mkdir out
 
 echo "### 1: calculate charge density cube ###"
 
-mpirun -n 2 python3 ../../cube_from_wfn.py \
+mpirun -n 2 cp2k-cube-from-wfn \
   --cp2k_input_file "$FOLDER"/cp2k.inp \
   --basis_set_file $BASIS_PATH \
   --xyz_file "$FOLDER"/geom.xyz \
@@ -43,7 +43,7 @@ cd ..
 
 echo "### 3: calculate bond order based on the Bader basins ###"
 
-mpirun -n 2 python3 ../../bader_bond_order.py \
+mpirun -n 2 cp2k-bader-bond-order \
   --cp2k_input_file "$FOLDER"/cp2k.inp \
   --basis_set_file $BASIS_PATH \
   --xyz_file "$FOLDER"/geom.xyz \

diff --git a/examples/c2h2_bader_charge_wfn/run.sh b/examples/c2h2_bader_charge_wfn/run.sh
@@ -5,7 +5,7 @@ BASIS_PATH="../data/BASIS_MOLOPT"
 
 mkdir out
 
-mpirun -n 2 python3 ../../cube_from_wfn.py \
+mpirun -n 2 cp2k-cube-from-wfn \
   --cp2k_input_file "$FOLDER"/cp2k.inp \
   --basis_set_file $BASIS_PATH \
   --xyz_file "$FOLDER"/geom.xyz \

diff --git a/examples/o2_cube_from_wfn/run.sh b/examples/o2_cube_from_wfn/run.sh
@@ -5,7 +5,7 @@ BASIS_PATH="../data/BASIS_MOLOPT"
 
 mkdir cubes
 
-../../cube_from_wfn.py \
+cp2k-cube-from-wfn \
   --cp2k_input_file $DIR/inp \
   --basis_set_file $BASIS_PATH \
   --xyz_file $DIR/aiida.coords.xyz \

diff --git a/examples/o2_overlap/run.sh b/examples/o2_overlap/run.sh
@@ -6,7 +6,7 @@ BASIS_PATH="../data/BASIS_MOLOPT"
 
 mkdir out
 
-mpirun -n 2  python3 ../../overlap_from_wfns.py \
+mpirun -n 2  cp2k-overlap-from-wfns \
   --cp2k_input_file1 "$SLAB_FOLDER"/inp \
   --basis_set_file1 $BASIS_PATH \
   --xyz_file1 "$SLAB_FOLDER"/aiida.coords.xyz \

diff --git a/examples/run_all_examples.sh b/examples/run_all_examples.sh
@@ -3,9 +3,10 @@
 # Loop through all subdirectories
 for dir in */ ; do
   if [ -f "$dir/run.sh" ]; then
-    echo "####"
-    echo "#### Running example in $dir"
-    echo "####"
+    echo ""
+    echo "# ----"
+    echo "# Running example in $dir"
+    echo "# ----"
     (cd "$dir" && ./run.sh)
   fi
 done
diff --git a/examples/tbau2_cube_from_wfn/run.sh b/examples/tbau2_cube_from_wfn/run.sh
@@ -5,7 +5,7 @@ BASIS_PATH="../data/BASIS_MOLOPT"
 
 mkdir cubes
 
-../../cube_from_wfn.py \
+cp2k-cube-from-wfn \
   --cp2k_input_file $DIR/inp \
   --basis_set_file $BASIS_PATH \
   --xyz_file $DIR/aiida.coords.xyz \

diff --git a/pyproject.toml b/pyproject.toml
@@ -38,7 +38,7 @@ cp2k-cube-operations = "cp2k_spm_tools.cli.cube_operations:main"
 cp2k-cube-single-column = "cp2k_spm_tools.cli.cube_single_column:main"
 cp2k-cube-split = "cp2k_spm_tools.cli.cube_split:main"
 cp2k-hrstm-from-wfn = "cp2k_spm_tools.cli.hrstm_from_wfn:main"
-cp2k-overlap-from-wfn = "cp2k_spm_tools.cli.overlap_from_wfns:main"
+cp2k-overlap-from-wfns = "cp2k_spm_tools.cli.overlap_from_wfns:main"
 cp2k-stm-sts-wfn = "cp2k_spm_tools.cli.stm_sts_from_wfn:main"
 cp2k-stm-sts-plot = "cp2k_spm_tools.cli.stm_sts_plotter:main"