Patch v1.4.3 (#79)

* Adding failing unit test

* Fixing issue #78

* Fixing issue #76 and tuning test for MacOS

* Fixing bug in symmetry example

* Updating function header comments

* Updating example

* Updating documentation

* Simplifying CGF normalization

* Fixing naming in gallery

Author: ifilot

docs/gallery.rst

@@ -3,44 +3,44 @@
 Gallery
 =======
 
-.. figure:: _static/img/gallery/MO_ch4_can.jpg
+.. figure:: _static/img/gallery/MO_ch4_CAN.jpg
 
     Isosurface visualization of all canonical molecular orbitals of
     methane computed at the Hartree-Fock level using a STO-3G basis set.
     The orbitals are shown as constant-value isosurfaces of the molecular
     wavefunction, illustrating the highly delocalized nature of the canonical
     eigenstates imposed by molecular symmetry.
 
-.. figure:: _static/img/gallery/MO_ch4_fb.jpg
+.. figure:: _static/img/gallery/MO_ch4_FB.jpg
 
     Isosurface visualization of Foster-Boys localized molecular orbitals of
     methane computed at the Hartree-Fock/STO-3G level. Orbital
     localization transforms the delocalized canonical states into chemically
     intuitive orbitals. For methane, this results in a quadruple degenerate
     set of state corresponding to the equivalent C-H bonds.
 
-.. figure:: _static/img/gallery/MO_co_can.jpg
+.. figure:: _static/img/gallery/MO_co_CAN.jpg
 
     Isosurface visualization of all canonical molecular orbitals of
     carbon monoxide computed at the Hartree-Fock level using a STO-3G basis set.
 
-.. figure:: _static/img/gallery/MO_co_fb.jpg
+.. figure:: _static/img/gallery/MO_co_FB.jpg
 
     Isosurface visualization of Foster-Boys localized molecular orbitals of
     carbon monoxide computed at the Hartree-Fock/STO-3G level. Orbital
     localization transforms the delocalized canonical states into chemically
     intuitive orbitals. For carbon monoxide, we see a threefold degenerate set
     of states correspond to the C-O triple bond.
 
-.. figure:: _static/img/gallery/MO_dodecahedrane_can.jpg
+.. figure:: _static/img/gallery/MO_dodecahedrane_CAN.jpg
 
     Isosurface visualization of all canonical molecular orbitals of
     dodecahedrane computed at the Hartree-Fock level using a STO-3G basis set.
     The orbitals are shown as constant-value isosurfaces of the molecular
     wavefunction, illustrating the highly delocalized nature of the canonical
     eigenstates imposed by molecular symmetry.
 
-.. figure:: _static/img/gallery/MO_dodecahedrane_fb.jpg
+.. figure:: _static/img/gallery/MO_dodecahedrane_FB.jpg
 
     Isosurface visualization of Foster-Boys localized molecular orbitals of
     dodecahedrane computed at the Hartree-Fock/STO-3G level. Orbital

docs/orbital_visualization.rst

@@ -133,11 +133,11 @@ using three atoms and an explicit *up direction*. The three atoms uniquely
 define the plane, while the up direction removes the sign ambiguity of the plane
 normal.
 
-The plane specification is given as a list:
+The plane specification is given as a **tuple**:
 
 .. math::
 
-    [i, j, k, \vec{u}]
+    (i, j, k, \vec{u})
 
 where:
 
@@ -159,7 +159,7 @@ the up direction:
     ContourPlotter.build_contourplot(
         res,
         'ch4_contour.png',
-        plane=[0, 1, 2, up],
+        plane=(0, 1, 2, up), # note: this needs to be a tuple
         sz=3.0,
         npts=101,
         nrows=3,

examples/ch4_contour.py

@@ -4,4 +4,4 @@
 res = HF(mol, 'sto3g').rhf(verbose=True)
 
 up = [0,0,1]
-ContourPlotter.build_contourplot(res, 'ch4.png', [0,1,2,up], 3, 101, 3, 3)
+ContourPlotter.build_contourplot(res, 'ch4.png', (0,1,2,up), 3, 101, 3, 3)

examples/ethylene_symap.py

@@ -104,7 +104,7 @@ def main():
             g.c /= np.sqrt(S)
 
     # re-perform Hartree-Fock calculation using the symmetry adapted basis
-    res = HF().rhf(mol, cgfs_symad, verbose=True)
+    res = HF(mol, cgfs_symad).rhf(verbose=True)
     fig, ax = plt.subplots(1,1, dpi=144, figsize=(7,7))
     plot_matrix(ax, res['overlap'], symlabels, symlabels)
     plt.show()

pyproject.toml

@@ -43,7 +43,7 @@ module-path = "src"
 # ---------------------------------------------------------------------------
 [project]
 name = "pyqint"
-version = "1.4.2"
+version = "1.4.3"
 description = "Python package for evaluating integrals of Gaussian type orbitals"
 readme = "README.md"
 license = { text = "GPL-3.0-only" }