Patch 0.14.0.0

examples/.gitignore

@@ -1,3 +1,5 @@
 *.npy
 *.jpg
 *.ply
+*.png
+*.txt

examples/blender_render.py

@@ -0,0 +1,133 @@
+from pyqint import Molecule, PyQInt, FosterBoys, GeometryOptimization, HF
+from pyqint import MoleculeBuilder, BlenderRender
+import pyqint
+import numpy as np
+import matplotlib.pyplot as plt
+import os
+import subprocess
+
+#
+# Plot the isosurfaces for a number of molecules, prior and after
+# orbital localization. Note that this script has been designed to be executed
+# in a Linux Ubuntu 22.04 LTS (WSL) container.
+#
+
+outpath = os.path.dirname(__file__)
+
+def main():
+    build_orbitals_co()
+    build_orbitals_ch4()
+    build_orbitals_ethylene()
+
+def build_orbitals_co():
+    """
+    Build a montage image of the canonical and localized molecular orbitals
+    of CO
+    """
+    molname = 'CO'
+    mol = Molecule('CO')
+    mol.add_atom('C', 0, 0, -1.08232106)
+    mol.add_atom('O', 0, 0, 1.08232106)
+    res = HF().rhf(mol, 'sto3g')
+    resfb = FosterBoys(res).run()
+
+    build(molname, res, resfb, nrows=2)
+
+def build_orbitals_ch4():
+    """
+    Build a montage image of the canonical and localized molecular orbitals
+    of CH4
+    """
+    molname = 'CH4'
+    mol = MoleculeBuilder().from_name('ch4')
+    res = GeometryOptimization().run(mol, 'sto3g')['data']
+    resfb = FosterBoys(res).run()
+
+    build(molname, res, resfb, nrows=3)
+
+def build_orbitals_ethylene():
+    """
+    Build a montage image of the canonical and localized molecular orbitals
+    of CH4
+    """
+    molname = 'ethylene'
+    mol = MoleculeBuilder().from_name('ethylene')
+    res = GeometryOptimization().run(mol, 'sto3g')['data']
+    resfb = FosterBoys(res).run()
+
+    build(molname, res, resfb, nrows=2)
+
+def build(molname, res, resfb, nrows=2):
+    """
+    Build isosurfaces, montage and print energies to a file
+
+    :param      molname:  Name of the molecule
+    :type       molname:  string
+    :param      res:      Results of a Hartree-Fock calculation
+    :type       res:      dictionary
+    :param      resfb:    Results of a Foster-Boys localization
+    :type       resfb:    dictionary
+    :param      nrows:    Number of rows in the montage
+    :type       nrows:    int
+    """
+    build_isosurfaces(molname, res, resfb)
+    montage(molname, nrows)
+    store_energies(os.path.join(os.path.dirname(__file__), 'MO_%s_energies.txt' % molname), res['orbe'], resfb['orbe'])
+
+def build_isosurfaces(molname, res, resfb):
+    """
+    Builds isosurfaces.
+
+    :param      molname:  Name of the molecule
+    :type       molname:  string
+    :param      res:      Result of a Hartree-Fock calculation
+    :type       res:      dictionary
+    :param      resfb:    Result of a Foster-Boys localization
+    :type       resfb:    dictionary
+    """
+    br = BlenderRender()
+    br.render_molecular_orbitals(res['mol'], res['cgfs'], res['orbc'], outpath,
+        prefix='MO_CAN_%s' % molname)
+
+    br.render_molecular_orbitals(resfb['mol'], res['cgfs'], resfb['orbc'], outpath,
+        prefix='MO_FB_%s' % molname)
+
+def montage(molname, nrows=2):
+    """
+    Produce a montage of the images
+
+    :param      molname:  Name of the molecule
+    :type       molname:  string
+    :param      nrows:    Number of rows in the montage
+    :type       nrows:    int
+    """
+    out = subprocess.check_output(
+        ['montage', 'MO_CAN_%s_????.png' % molname, '-tile', 'x%i' % nrows, '-geometry', '128x128+2+2', 'MO_%s_CAN.png' % molname],
+        cwd=os.path.dirname(__file__)
+    )
+
+    out = subprocess.check_output(
+        ['montage', 'MO_FB_%s_????.png' % molname, '-tile', 'x%i' % nrows, '-geometry', '128x128+2+2', 'MO_%s_FB.png' % molname],
+        cwd=os.path.dirname(__file__)
+    )
+
+def store_energies(filename, orbe, orbe_fb):
+    """
+    Stores energies.
+
+    :param      filename:  Name of the molecule
+    :type       filename:  string
+    :param      orbe:      Array of the canonical molecular orbital energies
+    :type       orbe:      list or numpy array
+    :param      orbe_fb:   Array of the localized molecular orbital energies
+    :type       orbe_fb:   list or numpy array
+    """
+    f = open(filename, 'w')
+    f.write('id    localized    canonical\n')
+    f.write('----------------------------\n')
+    for i in range(len(orbe)):
+        f.write("%02i %12.4f %12.4f\n" % (i+1, orbe[i], orbe_fb[i]))
+    f.close()
+
+if __name__ == '__main__':
+    main()

examples/foster_boys.py

@@ -40,6 +40,8 @@ def optimize_co():
 
     res = GeometryOptimization().run(mol, 'sto3g')
 
+    print(res['data']['nuclei'])
+
     return res['data']
 
 def build_contourplot(cgfs, coeff, sz=2, npts=50, plane='xy'):

meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: "pyqint"
-  version: "0.13.1.0"
+  version: "0.14.0.0"
 
 source:
   path: .

pyqint/_version.py

@@ -1,2 +1,2 @@
-__version__ = "0.13.1.0"
+__version__ = "0.14.0.0"
 

pyqint/blender/blender_render_molecule.py

@@ -121,10 +121,13 @@ def set_environment(settings):
     Specify canvas size, remove default objects, reset positions of
     camera and light, define film and set background
     """
+    print('Set render engine to: CYCLES')
     bpy.context.scene.render.engine = 'CYCLES'
+    print('Set rendering device to GPU')
     bpy.context.scene.cycles.device = 'GPU'
     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 = 1024
     bpy.context.scene.cycles.tile_size = 2048