diff --git a/docs/tutorial.rst b/docs/tutorial.rst index f92b4da..2d8608d 100644 --- a/docs/tutorial.rst +++ b/docs/tutorial.rst @@ -114,7 +114,7 @@ The package comes with functions to visualize meshes. The function :func:`plot_m >>> mesh = dft.Grids(mol) >>> mesh.level = 0 >>> mesh.build() - >>> plot_mesh_3d(mesh=mesh, weight=True) + >>> plot_mesh_3d(mesh, weight=True) .. figure:: _images/plot_mesh_3d.png :align: center @@ -125,7 +125,7 @@ The grid can be projected to a given plane, and the grid points can be scaled by .. code-block:: python >>> from var_mesh import plot_mesh_2d - >>> plot_mesh_2d(mesh=mesh, weight=5, plane='xz') + >>> plot_mesh_2d(mesh, weight=5, plane='xz') .. figure:: _images/plot_mesh_2d.png :align: center @@ -170,7 +170,7 @@ The script for this example can be downloaded :download:`here >> var_mesh(mesh, precise=True, mode='erkale') mode=ERKALE: - WARN: The precise option will have no effect when using gamess mode + WARN: The precise parameter has no effect when using 'gamess' mode. ERKALE grid: DFTGrid 60 -302 -Also, only the largest atom grid will be used in an optimization step. Thus, the atom grids will differ from the default ``pyscf`` mode and will be the same for every atom type. +Also, only the largest atom grid will be used in an optimization step. Thus, the atom grids will differ from the default ``'pyscf'`` mode and will be the same for every atom type. .. code-block:: python diff --git a/examples/03_helper_functions/03_helper_functions.py b/examples/03_helper_functions/03_helper_functions.py index 94bb731..ad1bf25 100644 --- a/examples/03_helper_functions/03_helper_functions.py +++ b/examples/03_helper_functions/03_helper_functions.py @@ -12,5 +12,5 @@ mesh.build() # Plot the mesh with helper functions -plot_mesh_3d(mesh=mesh, weight=True) -plot_mesh_2d(mesh=mesh, weight=5, plane='xz') +plot_mesh_3d(mesh, weight=True) +plot_mesh_2d(mesh, weight=5, plane='xz') diff --git a/examples/README.md b/examples/README.md index 7167d21..f5431e2 100644 --- a/examples/README.md +++ b/examples/README.md @@ -4,6 +4,7 @@ | 02_custom_grids | Custom grids, verbosity level, and grid parameters | | 03_helper_functions | Plot grids | | 04_precise_option | Show impact of the precise option | -| 05_mesh_time | Time the mesh generation for different thresholds | -| 06_calculation_time | Mesh generation time vs SCF calculation time | -| 07_pyflosic_usage | Usage with PyFLOSIC (needs extra packages) | +| 05_mode_option | Show the functionality of the mode option | +| 06_mesh_time | Time the mesh generation for different thresholds | +| 07_calculation_time | Mesh generation time vs SCF calculation time | +| 08_pyflosic_usage | Usage with PyFLOSIC (needs extra packages) | diff --git a/var_mesh/gen_mesh.py b/var_mesh/gen_mesh.py index 53b45df..9779667 100644 --- a/var_mesh/gen_mesh.py +++ b/var_mesh/gen_mesh.py @@ -60,7 +60,7 @@ def var_mesh(mesh, thres=1e-6, precise=True, mode='pyscf'): log.error('The mode parameter has to be one of \'%s\'.', '\', \''.join(supported)) if mode != 'pyscf' and precise: - log.warn('The precise parameter has no effect when using %s mode.', + log.warn('The precise parameter has no effect when using \'%s\' mode.', mode) # Create calculator to generate the initial density