Merge pull request #52 from amcadmus/devel

Devel

Author: amcadmus

dpdata/qe/scf.py

@@ -5,7 +5,7 @@
 
 ry2ev = 13.605693009
 bohr2ang = 0.52917721067
-kbar2evperang3 = 1./1602
+kbar2evperang3 = 1e3 / 1.602176621e6
 
 def get_block (lines, keyword, skip = 0) :
     ret = []

dpdata/qe/traj.py

@@ -6,7 +6,7 @@
 ry2ev = 13.605693009
 hartree2ev = 27.211386018
 bohr2ang = 0.52917721067
-kbar2evperang3 = 1./1602
+kbar2evperang3 = 1e3 / 1.602176621e6
 
 length_convert = bohr2ang
 energy_convert = hartree2ev

dpdata/system.py

@@ -519,22 +519,17 @@ def from_siesta_output(self, fname):
         self.data['atom_types'], \
         self.data['cells'], \
         self.data['coords'], \
-        self.data['energies'], \
-        self.data['forces'], \
-        self.data['virials'] \
+        _e, _f, _v \
             = dpdata.siesta.output.obtain_frame(fname)
         # self.rot_lower_triangular()
 
-
     def from_siesta_aiMD_output(self, fname):
         self.data['atom_names'], \
         self.data['atom_numbs'], \
         self.data['atom_types'], \
         self.data['cells'], \
         self.data['coords'], \
-        self.data['energies'], \
-        self.data['forces'], \
-        self.data['virials'] \
+        _e, _f, _v \
             = dpdata.siesta.aiMD_output.get_aiMD_frame(fname)
 
     def affine_map(self, trans, f_idx = 0) :

tests/test_qe_pw_scf.py

@@ -28,7 +28,7 @@ def test_cell(self) :
         cell = 10 * np.eye(3)
         for ii in range(cell.shape[0]) :
             for jj in range(cell.shape[1]) :
-                self.assertEqual(self.system_ch4.data['cells'][0][ii][jj], cell[ii][jj])
+                self.assertAlmostEqual(self.system_ch4.data['cells'][0][ii][jj], cell[ii][jj])
 
         fp = open('qe.scf/h2o_cell')
         cell = []
@@ -37,7 +37,7 @@ def test_cell(self) :
         cell = np.array(cell)
         for ii in range(cell.shape[0]) :
             for jj in range(cell.shape[1]) :
-                self.assertEqual(self.system_h2o.data['cells'][0][ii][jj], cell[ii][jj])
+                self.assertAlmostEqual(self.system_h2o.data['cells'][0][ii][jj], cell[ii][jj])
 
 
     def test_coord(self) :
@@ -48,7 +48,7 @@ def test_coord(self) :
         coord = np.array(coord)
         for ii in range(coord.shape[0]) :
             for jj in range(coord.shape[1]) :
-                self.assertEqual(self.system_ch4.data['coords'][0][ii][jj], coord[ii][jj])
+                self.assertAlmostEqual(self.system_ch4.data['coords'][0][ii][jj], coord[ii][jj])
         fp.close()
 
         fp = open('qe.scf/h2o_coord')
@@ -58,7 +58,7 @@ def test_coord(self) :
         coord = np.array(coord)
         for ii in range(coord.shape[0]) :
             for jj in range(coord.shape[1]) :
-                self.assertEqual(self.system_h2o.data['coords'][0][ii][jj], coord[ii][jj])
+                self.assertAlmostEqual(self.system_h2o.data['coords'][0][ii][jj], coord[ii][jj])
         fp.close()
 
     def test_force(self) :
@@ -69,7 +69,7 @@ def test_force(self) :
         force = np.array(force)
         for ii in range(force.shape[0]) :
             for jj in range(force.shape[1]) :
-                self.assertEqual(self.system_ch4.data['forces'][0][ii][jj], force[ii][jj])
+                self.assertAlmostEqual(self.system_ch4.data['forces'][0][ii][jj], force[ii][jj])
         fp.close()
 
         fp = open('qe.scf/h2o_force')
@@ -79,7 +79,7 @@ def test_force(self) :
         force = np.array(force)
         for ii in range(force.shape[0]) :
             for jj in range(force.shape[1]) :
-                self.assertEqual(self.system_h2o.data['forces'][0][ii][jj], force[ii][jj])
+                self.assertAlmostEqual(self.system_h2o.data['forces'][0][ii][jj], force[ii][jj])
         fp.close()
 
     def test_virial(self) :
@@ -90,7 +90,7 @@ def test_virial(self) :
         virial = np.array(virial)
         for ii in range(virial.shape[0]) :
             for jj in range(virial.shape[1]) :
-                self.assertEqual(self.system_ch4.data['virials'][0][ii][jj], virial[ii][jj])
+                self.assertAlmostEqual(self.system_ch4.data['virials'][0][ii][jj], virial[ii][jj], places = 3)
         fp.close()
 
         fp = open('qe.scf/h2o_virial')
@@ -100,14 +100,14 @@ def test_virial(self) :
         virial = np.array(virial)
         for ii in range(virial.shape[0]) :
             for jj in range(virial.shape[1]) :
-                self.assertEqual(self.system_h2o.data['virials'][0][ii][jj], virial[ii][jj])
+                self.assertAlmostEqual(self.system_h2o.data['virials'][0][ii][jj], virial[ii][jj], places = 2)
         fp.close()
 
     def test_energy(self) :
         ref_energy = -219.74425946528794
-        self.assertEqual(self.system_ch4.data['energies'][0], ref_energy)
+        self.assertAlmostEqual(self.system_ch4.data['energies'][0], ref_energy)
         ref_energy = -30007.651851226798
-        self.assertEqual(self.system_h2o.data['energies'][0], ref_energy)
+        self.assertAlmostEqual(self.system_h2o.data['energies'][0], ref_energy)