Merge pull request #111 from amcadmus/devel

fix bug of append systems with different formula

Author: amcadmus

dpdata/system.py

@@ -331,7 +331,8 @@ def append(self, system) :
             # this system is non-converged but the system to append is converged
             self.data = system.data
             return False
-        assert(system.formula == self.formula)
+        if system.uniq_formula != self.uniq_formula:
+            raise RuntimeError('systems with inconsistent formula could not be append: %s v.s. %s' % (self.uniq_formula, system.uniq_formula))
         if system.data['atom_names'] != self.data['atom_names']:
             # allow to append a system with different atom_names order
             system.sort_atom_names()
@@ -418,6 +419,16 @@ def formula(self):
         return ''.join(["{}{}".format(symbol,numb) for symbol,numb in 
             zip(self.data['atom_names'], self.data['atom_numbs'])])
 
+    @property
+    def uniq_formula(self):
+        """
+        Return the uniq_formula of this system. 
+        The uniq_formula sort the elements in formula by names.
+        Systems with the same uniq_formula can be append together.
+        """
+        return ''.join(["{}{}".format(symbol,numb) for symbol,numb in sorted(
+            zip(self.data['atom_names'], self.data['atom_numbs']))])
+
 
     def extend(self, systems):
         """

tests/poscars/POSCAR.h4o3

@@ -0,0 +1,15 @@
+POSCAR file written by OVITO
+1
+10 0.0 0.0
+-0.011409 10 0.0
+0.1411083 -0.0595569 10
+ H O
+ 4 3
+d
+.428    .424    .520
+.428    .424    .520
+.230    .628    .113
+.458    .352    .458
+.389    .384    .603
+.137    .626    .150
+.231    .589    .021

tests/test_system_append.py

@@ -6,6 +6,16 @@
 from comp_sys import CompLabeledSys
 from comp_sys import IsPBC, IsNoPBC
 
+
+class TestFailedAppend(unittest.TestCase):
+    def test_failed_append(self):
+        sys1 = dpdata.System('poscars/POSCAR.h2o.md', fmt='vasp/poscar')
+        sys2 = dpdata.System('poscars/POSCAR.h4o3', fmt='vasp/poscar')
+        with self.assertRaises(Exception) as c:
+            sys1.append(sys2)
+        self.assertTrue("systems with inconsistent formula could not be append" in str(c.exception))
+
+
 class TestVaspXmlAppend(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp (self) :
         self.places = 6