Code cleanup

moldesign/_tests/helpers.py

@@ -243,6 +243,6 @@ def generate_grid(g, g2=None):
     ranges = np.ones((3, 2))*5.0*width
     ranges[:, 0] *= -1
     ranges += ((g.center + g2.center)/2.0)[:, None]
-    grid = mathutils.VolumetricGrid(*ranges, 64)
+    grid = mathutils.VolumetricGrid(*ranges, npoints=64)
     allpoints = grid.allpoints()
     return allpoints, grid

moldesign/_tests/test_gaussian_math.py

@@ -128,7 +128,7 @@ def _make_rando_linear_combination(withunits=True):
                 moldesign.orbitals.CartesianGaussian(
                         center=center,
                         powers=pwr,
-                        alpha=10.0 * random.random()/(length**2),
+                        alpha=(10.0 * (random.random()+3))/(length**2),
                         coeff=1/(np.sqrt(3.0))))
     lc = moldesign.orbitals.PrimitiveSum(gaussians)
     lc.ndims = 3  # so it works with the test suite

moldesign/mathutils/grids.py

@@ -32,21 +32,22 @@ class VolumetricGrid(object):
         xrange (Tuple[len=2]): (min,max) in x direction
         yrange (Tuple[len=2]): (min,max) in y direction
         zrange (Tuple[len=2]): (min,max) in z direction
-        xpoints (int): number of grid lines in x direction (default: 25)
-        ypoints (int): number of grid lines in y direction (default: xpoints)
-        zpoints (int): number of grid lines in z direction (default: xpoints)
+        npoints (int): default number of grid lines in each direction (default: 32)
+        xpoints (int): number of grid lines in x direction (default: npoints)
+        ypoints (int): number of grid lines in y direction (default: npoints)
+        zpoints (int): number of grid lines in z direction (default: npoints)
     """
     dx, dy, dz = (utils.IndexView('deltas', i) for i in range(3))
     xr, yr, zr = (utils.IndexView('ranges', i) for i in range(3))
     xpoints, ypoints, zpoints = (utils.IndexView('points', i) for i in range(3))
     xspace, yspace, zspace = (utils.IndexView('spaces', i) for i in range(3))
 
     def __init__(self, xrange, yrange, zrange,
-                 xpoints=32, ypoints=None, zpoints=None):
+                 npoints=32, xpoints=None, ypoints=None, zpoints=None):
 
-        self.points = np.array([xpoints,
-                                ypoints if ypoints is not None else xpoints,
-                                zpoints if zpoints is not None else xpoints],
+        self.points = np.array([xpoints if xpoints is not None else npoints,
+                                ypoints if ypoints is not None else npoints,
+                                zpoints if zpoints is not None else npoints],
                                dtype='int')
 
         self.ranges = u.array([xrange, yrange, zrange])

moldesign/models/pyscf.py

@@ -452,7 +452,6 @@ def _get_ao_basis_functions(self):
                     assert l == angular
                     # Note: this is for metadata only, should not be used in any calculations
                     n = int(''.join(x for x in label[2] if x.isdigit()))
-
                     primitives = [orbitals.SphericalGaussian(atom.position.copy(),
                                                              exp, l, m,
                                                              coeff=coeff[ictr],

moldesign/orbitals/cartesian.py

@@ -79,7 +79,7 @@ def __init__(self, center, alpha, powers, coeff=None, normalized=True):
     def __repr__(self):
         return ("<{ndim}-D cartesian gaussian (norm: {norm:4.2f}, "
                 "cartesian powers: {powers}, "
-                "width: {exp:4.2f}, "
+                "alpha: {exp:4.2f}, "
                 "center: {center}>").format(
                 ndim=self.ndim,
                 center=self.center, exp=self.alpha,

moldesign/orbitals/spherical.py

@@ -64,8 +64,8 @@ def __init__(self, center, alpha, l, m, coeff=None, normalized=True):
 
     def __repr__(self):
         return ("<3D Gaussian (Spherical) (coeff: {coeff:4.2f}, "
-                "width: {alpha:4.2f}, "
-                "(l,m) = {qnums}").format(
+                "alpha: {alpha:4.2f}, "
+                "(l,m) = {qnums}>").format(
                 center=self.center, alpha=self.alpha, coeff=self.coeff,
                 qnums=(self.l, self.m))
 

moldesign/orbitals/wfn.py

@@ -109,7 +109,9 @@ def align_orbital_phases(self, other, assert_same=True):
         """
         for orbtype in self.orbitals:
             if orbtype not in other.orbitals:
-                if assert_same: assert False, '%s has orbital type %s, but %s does not.' % (self, orbtype, other)
+                if assert_same:
+                    assert False, '%s has orbital type %s, but %s does not.' % (
+                        self, orbtype, other)
                 else: continue
             self.orbitals[orbtype].align_phases(other.orbitals[orbtype])