Try to fix tests due to allowing charge to be float.

pymatgen/analysis/path_finder.py

@@ -15,6 +15,7 @@
 import scipy.stats
 from scipy.interpolate import interp1d
 import math
+import logging
 
 from abc import ABCMeta
 
@@ -29,6 +30,8 @@
 __status__ = "Development"
 __date__ = "March 17, 2015"
 
+logger = logging.getLogger(__name__)
+
 
 class NEBPathfinder:
     def __init__(self, start_struct, end_struct, relax_sites, v, n_images=20):
@@ -61,7 +64,7 @@ def interpolate(self):
         in relax_sites, the path is relaxed by the elastic band method within
         the static potential V.
         """
-        images = self.__s1.interpolate(self.__s2, images=self.__n_images,
+        images = self.__s1.interpolate(self.__s2, nimages=self.__n_images,
                                        interpolate_lattices=False)
         for site_i in self.__relax_sites:
             start_f = images[0].sites[site_i].frac_coords
@@ -145,7 +148,7 @@ def string_relax(start, end, V, n_images=25, dr=None, h=3.0, k=0.17,
         # (http://www.cims.nyu.edu/~eve2/main.htm)
         #
 
-        # print("Getting path from {} to {} (coords wrt V grid)".format(start, end))
+        # logger.debug("Getting path from {} to {} (coords wrt V grid)".format(start, end))
 
         # Set parameters
         if not dr:
@@ -195,7 +198,7 @@ def string_relax(start, end, V, n_images=25, dr=None, h=3.0, k=0.17,
                              dV[2][int(pt[0]) % d[0]][int(pt[1]) % d[1]][
                                  int(pt[2]) % d[2]] / dr[0]] for pt in s])
             # if(step % 100 == 0):
-            #    print(edV)
+            #    logger.debug(edV)
 
             # Update according to force due to potential and string elasticity
             ds_plus = s - np.roll(s, 1, axis=0)
@@ -229,11 +232,11 @@ def string_relax(start, end, V, n_images=25, dr=None, h=3.0, k=0.17,
                     "avoid divergence.")
 
             if step > min_iter and tol < max_tol:
-                print("Converged at step {}".format(step))
+                logger.debug("Converged at step {}".format(step))
                 break
 
             if step % 100 == 0:
-                print("Step {} - ds = {}".format(step, tol))
+                logger.debug("Step {} - ds = {}".format(step, tol))
         return s
 
     @staticmethod
@@ -299,8 +302,8 @@ def rescale_field(self, new_dim):
             np.ndindex(v_dim[0] + 1, v_dim[1] + 1, v_dim[2] + 1))])
         v_ogrid = padded_v.reshape(
             ((v_dim[0] + 1) * (v_dim[1] + 1) * (v_dim[2] + 1), -1))
-        ngrid_a, ngrid_b, ngrid_c = np.mgrid[0: v_dim[0]: v_dim[0] / new_dim[0], 0: v_dim[1]: v_dim[1] / new_dim[1],
-                                             0: v_dim[2]: v_dim[2] / new_dim[2]]
+        ngrid_a, ngrid_b, ngrid_c = (np.mgrid[0: v_dim[0]: v_dim[0] / new_dim[0], 0: v_dim[1]: v_dim[1] / new_dim[1],
+                                     0: v_dim[2]: v_dim[2] / new_dim[2]])
 
         v_ngrid = scipy.interpolate.griddata(ogrid_list, v_ogrid,
                                              (ngrid_a, ngrid_b, ngrid_c),
@@ -412,7 +415,7 @@ def __add_gaussians(s, dim, r=1.5):
                         [a_d / dim[0], b_d / dim[1], c_d / dim[2]])
                     d_f = sorted(s.get_sites_in_sphere(coords_f, s.lattice.a),
                                  key=lambda x: x[1])[0][1]
-                    # print(d_f)
+                    # logger.debug(d_f)
                     gauss_dist[int(a_d)][int(b_d)][int(c_d)] = d_f / r
         v = scipy.stats.norm.pdf(gauss_dist)
         return v

pymatgen/io/babel.py

@@ -70,7 +70,7 @@ def __init__(self, mol):
             obmol.ConnectTheDots()
             obmol.PerceiveBondOrders()
             obmol.SetTotalSpinMultiplicity(mol.spin_multiplicity)
-            obmol.SetTotalCharge(mol.charge)
+            obmol.SetTotalCharge(int(mol.charge))
             obmol.Center()
             obmol.Kekulize()
             obmol.EndModify()

pymatgen/io/gaussian.py

@@ -435,7 +435,7 @@ def para_dict_to_string(para, joiner=" "):
         output.append("")
         output.append(self.title)
         output.append("")
-        output.append("{} {}".format(self.charge, self.spin_multiplicity))
+        output.append("%d %d" % (self.charge, self.spin_multiplicity))
         if isinstance(self._mol, Molecule):
             if cart_coords is True:
                 output.append(self.get_cart_coords())

pymatgen/io/nwchem.py

@@ -181,7 +181,7 @@ def __str__(self):
 """)
 
         output = t.substitute(
-            title=self.title, charge=self.charge,
+            title=self.title, charge=int(self.charge),
             spinmult=self.spin_multiplicity,
             basis_set_option=self.basis_set_option,
             bset_spec="\n".join(bset_spec),

pymatgen/io/tests/test_gaussian.py

@@ -8,20 +8,18 @@
 from pymatgen import Molecule
 from pymatgen.io.gaussian import GaussianInput, GaussianOutput
 from pymatgen.electronic_structure.core import Spin
+
 """
 Created on Apr 17, 2012
 """
 
-
 __author__ = "Shyue Ping Ong"
 __copyright__ = "Copyright 2012, The Materials Project"
 __version__ = "0.1"
 __maintainer__ = "Shyue Ping Ong"
 __email__ = "shyuep@gmail.com"
 __date__ = "Apr 17, 2012"
 
-
-
 test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
                         'test_files', "molecules")
 
@@ -230,7 +228,7 @@ def test_props(self):
         self.assertEqual(d["input"]["functional"], "hf")
         self.assertAlmostEqual(d["output"]["final_energy"], -39.9768775602)
         self.assertEqual(len(gau.cart_forces), 3)
-        self.assertEqual(gau.cart_forces[0][5],  0.009791094)
+        self.assertEqual(gau.cart_forces[0][5], 0.009791094)
         self.assertEqual(gau.cart_forces[0][-1], -0.003263698)
         self.assertEqual(gau.cart_forces[2][-1], -0.000000032)
         self.assertEqual(gau.eigenvalues[Spin.up][-1], 1.95586)
@@ -262,7 +260,7 @@ def test_props(self):
         self.assertEqual(h2o.frequencies[0][1]["symmetry"], "A'")
         self.assertEqual(h2o.hessian[0, 0], 0.356872)
         self.assertEqual(h2o.hessian.shape, (9, 9))
-        self.assertEqual(h2o.hessian[8, :].tolist(), [-0.143692e-01,  0.780136e-01,
+        self.assertEqual(h2o.hessian[8, :].tolist(), [-0.143692e-01, 0.780136e-01,
                                                       -0.362637e-01, -0.176193e-01,
                                                       0.277304e-01, -0.583237e-02,
                                                       0.319885e-01, -0.105744e+00,
@@ -273,12 +271,12 @@ def test_pop(self):
         self.assertEqual(gau.num_basis_func, 13)
         self.assertEqual(gau.electrons, (5, 5))
         self.assertEqual(gau.is_spin, True)
-        self.assertListEqual(gau.eigenvalues[Spin.down], [-20.55343,  -1.35264,
-                                                          -0.72655,  -0.54824,
-                                                          -0.49831,   0.20705,
-                                                          0.30297,   1.10569,
-                                                          1.16144,   1.16717,
-                                                          1.20460,   1.38903,
+        self.assertListEqual(gau.eigenvalues[Spin.down], [-20.55343, -1.35264,
+                                                          -0.72655, -0.54824,
+                                                          -0.49831, 0.20705,
+                                                          0.30297, 1.10569,
+                                                          1.16144, 1.16717,
+                                                          1.20460, 1.38903,
                                                           1.67608])
         mo = gau.molecular_orbital
         self.assertEqual(len(mo), 2)  # la 6
@@ -310,7 +308,6 @@ def test_pop(self):
         self.assertEqual(gau.bond_orders[(0, 1)], 0.7582)
         self.assertEqual(gau.bond_orders[(1, 2)], 0.0002)
 
-
     def test_scan(self):
         gau = GaussianOutput(os.path.join(test_dir, "so2_scan.log"))
         d = gau.read_scan()