Small tweaks

Author: ifilot

.gitignore

@@ -152,4 +152,7 @@ anaconda-upload/*
 
 # managlyph .abo files
 *.abo
-.vscode
+.vscode
+
+*.jpg
+*.png

examples/blender_render.py

@@ -30,7 +30,7 @@ def build_orbitals_co():
     res = HF().rhf(mol, 'sto3g')
     resfb = FosterBoys(res).run()
 
-    build(molname, res, resfb, nrows=2, npts=151)
+    build(molname, res, resfb, nrows=2, npts=100)
 
 def build_orbitals_h2o():
     """

examples/ethylene_symap.py

@@ -84,18 +84,24 @@ def main():
 
     overlap = P @ overlap @ P.T
 
-    fig, ax = plt.subplots(1,1, dpi=144, figsize=(7,7))
+    fig, ax = plt.subplots(1,1, dpi=300, figsize=(5,5))
     plot_matrix(ax, P @ B, basislabels, symlabels)
+    plt.tight_layout()
+    plt.savefig('ethylene_symbasis.png')
     plt.show()
 
     # construct new basis
+    integrator = PyQInt()
     B = P @ B
     cgfs_symad = [CGF() for i in range(len(B))]
     for i in range(len(B)): # loop over new basis functions
         for j in range(len(cgfs)): # loop over old basis functions
             if abs(B[i,j]) > 0.01:  # verify non-negligble contribution
                 for g in cgfs[j].gtos:
                     cgfs_symad[i].gtos.append(GTO(g.c*B[i,j], g.p, g.alpha, g.l, g.m, g.n))
+        S = integrator.overlap(cgfs_symad[i], cgfs_symad[i])
+        for g in cgfs_symad[i].gtos:
+            g.c /= np.sqrt(S)
 
     # re-perform Hartree-Fock calculation using the symmetry adapted basis
     res = HF().rhf(mol, cgfs_symad, verbose=True)
@@ -111,7 +117,8 @@ def plot_matrix(ax, mat, xlabels, ylabels, xlabelrot = 0):
     """
     Produce plot of matrix
     """
-    mv = np.max(np.abs(mat))
+    #mv = np.max(np.abs(mat))
+    mv = 1
     ax.imshow(mat, vmin=-mv, vmax=mv, cmap='PiYG')
     for i in range(mat.shape[0]):
         for j in range(mat.shape[1]):

pyqint/blender/blender_render_molecule.py

@@ -17,7 +17,7 @@
 def main():
     # set the scene
     settings = {
-        'resolution': 1024,
+        'resolution': 512,
         'camera_location': (-10,0,0),
         'camera_rotation': (np.pi/2,0,-np.pi/2),
         'camera_scale' : 10
@@ -142,7 +142,7 @@ def set_environment(settings):
     bpy.context.scene.render.resolution_x = settings['resolution']
     bpy.context.scene.render.resolution_y = settings['resolution']
     print('Setting resolution to: ', settings['resolution'])
-    bpy.context.scene.cycles.samples = 2048
+    bpy.context.scene.cycles.samples = 1024
     bpy.context.scene.cycles.tile_size = 2048
 
     # remove cube

pyqint/blenderrender.py

@@ -26,7 +26,7 @@ def __init__(self):
     def render_molecular_orbitals(self, molecule, cgfs, orbc, outpath,
                                   mo_indices=None, sz=5, isovalue=0.03,
                                   prefix='MO', npts=100,
-                                  negcol='8f0153', poscol='276419'):
+                                  negcol='276419', poscol='8f0153'):
         if mo_indices is None: # render all orbitals
             mo_indices = np.arange(0, len(orbc))