Merge pull request #76 from amcadmus/devel

fix the bug of energy file with comments, warning when ibrav is nor supported

Author: amcadmus

dpdata/qe/traj.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python3 
 
 import numpy as np
-import dpdata
+import dpdata,warnings
 
 ry2ev = 13.605693009
 hartree2ev = 27.211386018
@@ -36,8 +36,10 @@ def convert_celldm(ibrav, celldm) :
         return celldm[0] * 0.5 * np.array([[1,1,1], [-1,1,1], [-1,-1,1]])
     elif ibrav == -3 :
         return celldm[0] * 0.5 * np.array([[-1,1,1], [1,-1,1], [1,1,-1]])
-    else :
-        raise RuntimeError('unsupported ibrav ' + str(ibrav))    
+    else :        
+        warnings.warn('unsupported ibrav ' + str(ibrav) + ' if no .cel file, the cell convertion may be wrong. ')
+        return np.eye(3)
+        #raise RuntimeError('unsupported ibrav ' + str(ibrav))
 
 def load_cell_parameters(lines) :
     blk = load_block(lines, 'CELL_PARAMETERS', 3)
@@ -152,11 +154,13 @@ def load_energy(fname, begin = 0, step = 1) :
     for ii in data[begin::step,0]:
         steps.append('%d'%ii)
     with open(fname) as fp:
-        line = fp.readline()
-        if line :
-            nw = len(line.split())
-        else :
-            return None
+        while True:
+            line = fp.readline()
+            if not line :
+                return None
+            if line.split()[0][0] != '#':
+                nw = len(line.split())
+                break
     data = np.reshape(data, [-1, nw])
     return energy_convert * data[begin::step,5], steps
 

tests/qe.traj/traj6.evp

@@ -1,3 +1,4 @@
+# comments here
     195  9.433649E-03  1.290500E-05  0.000000E+00  1.057182E-02      -1100.03076389      -1100.03076389      -1100.03075434      -1100.03073209  1.300606E+04      -3.31610
     200  9.675537E-03  7.090171E-05  0.000000E+00  1.257319E+00      -1100.03189493      -1100.03189493      -1100.03076015      -1100.03068120  1.300606E+04      -3.31683
     201  9.675537E-03  7.090171E-05  0.000000E+00  2.257319E+00      -1100.03189493      -1100.03189493      -1100.03076015      -1100.03068120  1.300606E+04      -3.31683

tests/test_qe_cp_traj.py

@@ -4,7 +4,7 @@
 from context import dpdata
 
 
-class TestPWSCFProps :
+class TestCPTRAJProps :
     def test_atom_names(self) :
         self.assertEqual(self.system.data['atom_names'], ['O','H'])
 
@@ -44,18 +44,25 @@ def test_coord(self) :
                 self.assertAlmostEqual(self.system['coords'][-1][ii][jj], coords[ii][jj])
 
 
-class TestPWSCFTraj(unittest.TestCase, TestPWSCFProps):    
+class TestCPTRAJTraj(unittest.TestCase, TestCPTRAJProps):    
 
     def setUp(self): 
         self.system = dpdata.System('qe.traj/oh-md', fmt = 'qe/cp/traj')
 
 
-class TestPWSCFLabeledTraj(unittest.TestCase, TestPWSCFProps):    
+class TestCPTRAJLabeledTraj(unittest.TestCase, TestCPTRAJProps):    
 
     def setUp(self): 
         self.system = dpdata.LabeledSystem('qe.traj/oh-md', fmt = 'qe/cp/traj')
 
 
+class TestConverCellDim(unittest.TestCase):    
+    def test_case_null(self):
+        cell = dpdata.qe.traj.convert_celldm(8, [1, 1, 1])
+        ref = np.eye(3)
+        for ii in range(3):
+            for jj in range(3):
+                self.assertAlmostEqual(cell[ii][jj], ref[ii][jj])
 
 
 if __name__ == '__main__':