Merge branch 'master' into pmg4

materialsproject · Jun 19, 2016 · ee6afcf · ee6afcf
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diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,6 +1,13 @@
 Change log
 ==========
 
+v3.7.0
+------
+* Last version before pymatgen 4.0, where deprecated modules will be removed!
+* Massive update to LAMMPS (Kiran Matthews).
+* New input sets with a different interface that replaces old input sets.
+* Massive update to elastic properties.
+
 v3.6.1
 ------
 * Massive cleanup to Boltztrap interface (Anubhav Jain)

diff --git a/README.rst b/README.rst
@@ -1,6 +1,6 @@
 **Official docs:** http://www.pymatgen.org
 
-.. image:: https://coveralls.io/repos/github/materialsproject/pymatgen/badge.svg?branch=master :target: https://coveralls.io/github/materialsproject/pymatgen?branch=master
+.. image:: https://coveralls.io/repos/github/materialsproject/pymatgen/badge.svg?branch=master
 
 Pymatgen (Python Materials Genomics) is a robust, open-source Python library
 for materials analysis. These are some of the main features:

diff --git a/docs/change_log.rst b/docs/change_log.rst
@@ -1,6 +1,13 @@
 Change log
 ==========
 
+v3.7.0
+------
+* Last version before pymatgen 4.0, where deprecated modules will be removed!
+* Massive update to LAMMPS (Kiran Matthews).
+* New input sets with a different interface that replaces old input sets.
+* Massive update to elastic properties.
+
 v3.6.1
 ------
 * Massive cleanup to Boltztrap interface (Anubhav Jain)

diff --git a/docs/index.rst b/docs/index.rst
@@ -6,6 +6,8 @@
 Introduction
 ============
 
+.. image:: https://coveralls.io/repos/github/materialsproject/pymatgen/badge.svg?branch=master
+
 Pymatgen (Python Materials Genomics) is a robust, open-source Python library
 for materials analysis. These are some of the main features:
 

diff --git a/docs/latest_changes.rst b/docs/latest_changes.rst
@@ -1,8 +1,9 @@
 Change log
 ==========
 
-v3.6.1
+v3.7.0
 ------
-* Massive cleanup to Boltztrap interface (Anubhav Jain)
-* Refactor of piezoelectric analysis to use tensor base class (Joey)
-* More robust CIF parsing.
+* Last version before pymatgen 4.0, where deprecated modules will be removed!
+* Massive update to LAMMPS (Kiran Matthews).
+* New input sets with a different interface that replaces old input sets.
+* Massive update to elastic properties.
diff --git a/docs/pymatgen.io.vasp.rst b/docs/pymatgen.io.vasp.rst
@@ -42,6 +42,14 @@ pymatgen.io.vasp.sets module
     :undoc-members:
     :show-inheritance:
 
+pymatgen.io.vasp.sets_deprecated module
+---------------------------------------
+
+.. automodule:: pymatgen.io.vasp.sets_deprecated
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

diff --git a/pymatgen/__init__.py b/pymatgen/__init__.py
@@ -4,8 +4,8 @@
 __email__ ="pymatgen@googlegroups.com"
 __maintainer__ = "Shyue Ping Ong"
 __maintainer_email__ ="shyuep@gmail.com"
-__date__ = "May 25 2016"
-__version__ = "3.6.1"
+__date__ = "Jun 19 2016"
+__version__ = "3.7.0"
 
 
 # Useful aliases for commonly used objects and modules.

diff --git a/pymatgen/analysis/defects/tests/test_dilute_solution_model.py b/pymatgen/analysis/defects/tests/test_dilute_solution_model.py
@@ -10,6 +10,7 @@
 
 from monty.json import MontyDecoder
 from pymatgen.analysis.defects.dilute_solution_model import *
+import random
 
 try:
     import sympy
@@ -31,92 +32,94 @@
 # monstrously slow. It takes more than 10 mins to get through this test alone.
 
 
-# @unittest.skipIf(not sympy, "sympy not present.")
-# class DiluteSolutionModelTest(unittest.TestCase):
-#     def setUp(self):
-#         """
-#         Setup mandatory inputs for dilute_solution_model
-#         """
-#         self.e0 = raw_energy_dict['bulk_energy']
-#         self.asites = raw_energy_dict['antisites']
-#         self.vac = raw_energy_dict['vacancies']
-#         self.struct = raw_energy_dict['structure']
-#         self.T = 600
-#         self.trial_mu = formation_energy_dict[str(self.T)]['chemical_potential']
-#
-#     def test_formation_energies_without_chem_pot(self):
-#         """
-#         Should generate formation energies without input chempot
-#         """
-#         energies, chem_pot = dilute_solution_model(
-#             self.struct, self.e0, self.vac, self.asites, self.T,
-#             generate='energy')
-#         self.assertIsNotNone(energies)
-#         self.assertIsNotNone(chem_pot)
-#
-#     def test_formation_energies_with_chem_pot(self):
-#         energies, chem_pot = dilute_solution_model(
-#             self.struct, self.e0, self.vac, self.asites, self.T,
-#             trial_chem_pot=self.trial_mu, generate='energy')
-#         self.assertIsNotNone(energies)
-#         self.assertIsNotNone(chem_pot)
-#
-#     def test_plot_data_without_chem_pot(self):
-#         conc_data, en_data, mu_data = dilute_solution_model(
-#             self.struct, self.e0, self.vac, self.asites, self.T,
-#             generate='plot')
-#         self.assertIsNotNone(conc_data)
-#         self.assertIsNotNone(en_data)
-#         self.assertIsNotNone(mu_data)
-#         for key, value in conc_data.items():
-#             self.assertIsNotNone(value)
-#         for key, value in mu_data.items():
-#             self.assertIsNotNone(value)
-#         for key, value in en_data.items():
-#             self.assertIsNotNone(value)
-#
-#     def test_plot_data_with_chem_pot(self):
-#         conc_data, en_data, mu_data = dilute_solution_model(
-#             self.struct, self.e0, self.vac, self.asites, self.T,
-#             trial_chem_pot=self.trial_mu, generate='plot')
-#         self.assertIsNotNone(conc_data)
-#         self.assertIsNotNone(en_data)
-#         self.assertIsNotNone(mu_data)
-#         for key, value in conc_data.items():
-#             self.assertIsNotNone(value)
-#         for key, value in mu_data.items():
-#             self.assertIsNotNone(value)
-#         for key, value in en_data.items():
-#             self.assertIsNotNone(value)
-#             # print(plot_data['y'])
-#
-#
-# @unittest.skipIf(not sympy, "sympy not present.")
-# class SoluteSiteFinderTest(unittest.TestCase):
-#     def setUp(self):
-#         """
-#         Setup mandatory inputs for dilute_solution_model
-#         """
-#         self.e0 = mp1487_raw_energy_dict['bulk_energy']
-#         self.asites = mp1487_raw_energy_dict['antisites']
-#         self.vac = mp1487_raw_energy_dict['vacancies']
-#         self.solutes = mp1487_raw_energy_dict['solutes']
-#         self.struct = mp1487_raw_energy_dict['structure']
-#         self.T = 1000
-#
-#     def test_plot_data_without_chem_pot(self):
-#         plot_data = solute_site_preference_finder(
-#             self.struct, self.e0, self.T, self.vac, self.asites, self.solutes,
-#             solute_concen=0.01)
-#         self.assertIsNotNone(plot_data)
-#
-#     def still_wait_plot_data_with_chem_pot(self):
-#         plot_data = dilute_solution_model(
-#             self.struct, self.e0, self.vac, self.asites, self.T,
-#             trial_chem_pot=self.trial_mu, generate='plot')
-#         self.assertIsNotNone(plot_data)
-#         for key, value in plot_data.items():
-#             self.assertIsNotNone(value)
+@unittest.skipIf((not sympy) or random.randint(0, 10) % 10 != 0,
+                 "sympy not present or random skip.")
+class DiluteSolutionModelTest(unittest.TestCase):
+    def setUp(self):
+        """
+        Setup mandatory inputs for dilute_solution_model
+        """
+        self.e0 = raw_energy_dict['bulk_energy']
+        self.asites = raw_energy_dict['antisites']
+        self.vac = raw_energy_dict['vacancies']
+        self.struct = raw_energy_dict['structure']
+        self.T = 600
+        self.trial_mu = formation_energy_dict[str(self.T)]['chemical_potential']
+
+    def test_formation_energies_without_chem_pot(self):
+        """
+        Should generate formation energies without input chempot
+        """
+        energies, chem_pot = dilute_solution_model(
+            self.struct, self.e0, self.vac, self.asites, self.T,
+            generate='energy')
+        self.assertIsNotNone(energies)
+        self.assertIsNotNone(chem_pot)
+
+    def test_formation_energies_with_chem_pot(self):
+        energies, chem_pot = dilute_solution_model(
+            self.struct, self.e0, self.vac, self.asites, self.T,
+            trial_chem_pot=self.trial_mu, generate='energy')
+        self.assertIsNotNone(energies)
+        self.assertIsNotNone(chem_pot)
+
+    def test_plot_data_without_chem_pot(self):
+        conc_data, en_data, mu_data = dilute_solution_model(
+            self.struct, self.e0, self.vac, self.asites, self.T,
+            generate='plot')
+        self.assertIsNotNone(conc_data)
+        self.assertIsNotNone(en_data)
+        self.assertIsNotNone(mu_data)
+        for key, value in conc_data.items():
+            self.assertIsNotNone(value)
+        for key, value in mu_data.items():
+            self.assertIsNotNone(value)
+        for key, value in en_data.items():
+            self.assertIsNotNone(value)
+
+    def test_plot_data_with_chem_pot(self):
+        conc_data, en_data, mu_data = dilute_solution_model(
+            self.struct, self.e0, self.vac, self.asites, self.T,
+            trial_chem_pot=self.trial_mu, generate='plot')
+        self.assertIsNotNone(conc_data)
+        self.assertIsNotNone(en_data)
+        self.assertIsNotNone(mu_data)
+        for key, value in conc_data.items():
+            self.assertIsNotNone(value)
+        for key, value in mu_data.items():
+            self.assertIsNotNone(value)
+        for key, value in en_data.items():
+            self.assertIsNotNone(value)
+            # print(plot_data['y'])
+
+
+@unittest.skipIf((not sympy) or random.randint(0, 10) % 10 != 0,
+                 "sympy not present or random skip.")
+class SoluteSiteFinderTest(unittest.TestCase):
+    def setUp(self):
+        """
+        Setup mandatory inputs for dilute_solution_model
+        """
+        self.e0 = mp1487_raw_energy_dict['bulk_energy']
+        self.asites = mp1487_raw_energy_dict['antisites']
+        self.vac = mp1487_raw_energy_dict['vacancies']
+        self.solutes = mp1487_raw_energy_dict['solutes']
+        self.struct = mp1487_raw_energy_dict['structure']
+        self.T = 1000
+
+    def test_plot_data_without_chem_pot(self):
+        plot_data = solute_site_preference_finder(
+            self.struct, self.e0, self.T, self.vac, self.asites, self.solutes,
+            solute_concen=0.01)
+        self.assertIsNotNone(plot_data)
+
+    def still_wait_plot_data_with_chem_pot(self):
+        plot_data = dilute_solution_model(
+            self.struct, self.e0, self.vac, self.asites, self.T,
+            trial_chem_pot=self.trial_mu, generate='plot')
+        self.assertIsNotNone(plot_data)
+        for key, value in plot_data.items():
+            self.assertIsNotNone(value)
 
 
 if __name__ == "__main__":

diff --git a/pymatgen/core/lattice.py b/pymatgen/core/lattice.py
@@ -519,9 +519,9 @@ def find_all_mappings(self, other_lattice, ltol=1e-5, atol=1,
                                                   max(lengths) * (1 + ltol),
                                                   zip_results=False)
         cart = self.get_cartesian_coords(frac)
-
         # this can't be broadcast because they're different lengths
-        inds = [np.abs(dist - l) / l <= ltol for l in lengths]
+        inds = [np.logical_and(dist / l < 1 + ltol,
+                               dist / l > 1 / (1 + ltol)) for l in lengths]
         c_a, c_b, c_c = (cart[i] for i in inds)
         f_a, f_b, f_c = (frac[i] for i in inds)
         l_a, l_b, l_c = (np.sum(c ** 2, axis=-1) ** 0.5 for c in (c_a, c_b, c_c))
@@ -955,15 +955,21 @@ def get_points_in_sphere(self, frac_points, center, r, zip_results=True):
 
         shifted_coords = fcoords[:, None, None, None, :] + \
             images[None, :, :, :, :]
-        coords = self.get_cartesian_coords(shifted_coords)
-        dists = np.sqrt(np.sum((coords - center[None, None, None, None, :]) ** 2,
-                               axis=4))
-        within_r = np.where(dists <= r)
+
+        cart_coords = self.get_cartesian_coords(fcoords)
+        cart_images = self.get_cartesian_coords(images)
+        coords = cart_coords[:, None, None, None, :] + \
+            cart_images[None, :, :, :, :]
+        coords -= center[None, None, None, None, :]
+        coords **= 2
+        d_2 = np.sum(coords, axis=4)
+
+        within_r = np.where(d_2 <= r ** 2)
         if zip_results:
-            return list(zip(shifted_coords[within_r], dists[within_r],
+            return list(zip(shifted_coords[within_r], np.sqrt(d_2[within_r]),
                             indices[within_r[0]]))
         else:
-            return shifted_coords[within_r], dists[within_r], \
+            return shifted_coords[within_r], np.sqrt(d_2[within_r]), \
                 indices[within_r[0]]
 
     def get_all_distances(self, fcoords1, fcoords2):

diff --git a/pymatgen/core/tests/test_lattice.py b/pymatgen/core/tests/test_lattice.py
@@ -268,6 +268,15 @@ def test_find_all_mappings(self):
         for l, _, _ in latt.find_all_mappings(latt, ltol=0.05, atol=11):
             self.assertTrue(isinstance(l, Lattice))
 
+    def test_mapping_symmetry(self):
+        l = Lattice.cubic(1)
+        l2 = Lattice.orthorhombic(1.1001, 1, 1)
+        self.assertEqual(l.find_mapping(l2, ltol=0.1), None)
+        self.assertEqual(l2.find_mapping(l, ltol=0.1), None)
+        l2 = Lattice.orthorhombic(1.0999, 1, 1)
+        self.assertNotEqual(l2.find_mapping(l, ltol=0.1), None)
+        self.assertNotEqual(l.find_mapping(l2, ltol=0.1), None)
+
     def test_to_from_dict(self):
         d = self.tetragonal.as_dict()
         t = Lattice.from_dict(d)