fix two bugs that implemented in #168

dpdata/format.py

@@ -106,11 +106,11 @@ def from_multi_systems(self, directory, **kwargs):
             list of filenames
         """
         if self.MultiMode == self.MultiModes.Directory:
-            return [name for name in os.listdir(directory) if os.path.isdir(os.path.join(directory, name))]
+            return [os.path.join(directory, name) for name in os.listdir(directory) if os.path.isdir(os.path.join(directory, name))]
         raise NotImplementedError("%s doesn't support MultiSystems.from" %(self.__class__.__name__))
 
     def to_multi_systems(self, formulas, directory, **kwargs):
         if self.MultiMode == self.MultiModes.Directory:
             return [os.path.join(directory, ff) for ff in formulas]
         raise NotImplementedError("%s doesn't support MultiSystems.to" %(self.__class__.__name__))
-
+

dpdata/plugins/deepmd.py

@@ -15,7 +15,7 @@ def to_system(self, data, file_name, **kwargs):
         """
         dpdata.deepmd.raw.dump(file_name, data)
 
-    def from_labeled_system(self, file_name, type_map, **kwargs):
+    def from_labeled_system(self, file_name, type_map=None, **kwargs):
         return dpdata.deepmd.raw.to_system_data(file_name, type_map=type_map, labels=True)
 
     MultiMode = Format.MultiModes.Directory
@@ -50,7 +50,7 @@ def to_system(self, data, file_name, set_size=5000, prec=np.float32, **kwargs):
         dpdata.deepmd.comp.dump(
             file_name, data, set_size=set_size, comp_prec=prec)
 
-    def from_labeled_system(self, file_name, type_map, **kwargs):
+    def from_labeled_system(self, file_name, type_map=None, **kwargs):
         return dpdata.deepmd.comp.to_system_data(file_name, type_map=type_map, labels=True)
 
     MultiMode = Format.MultiModes.Directory

tests/test_multisystems.py

@@ -30,6 +30,15 @@ def setUp(self):
         self.system_sizes = {'C1H4':2, 'C1H3':1}
         self.atom_names = ['C', 'H']
 
+    def test_len(self):
+        self.assertEqual(len(self.systems), 2)
+
+    def test_get_nframes(self):
+        self.assertEqual(self.systems.get_nframes(), 3)
+
+    def test_str(self):
+        self.assertEqual(str(self.systems), "MultiSystems (2 systems containing 3 frames)")
+
 
 class TestMultiSystemsAdd(unittest.TestCase, CompLabeledSys, MultiSystems, IsNoPBC):
     def setUp(self):
@@ -117,5 +126,18 @@ def test_type_map(self):
             self.assertEqual(type_map, systems.atom_names)
 
 
+class TestMultiSystemsTo(unittest.TestCase, MultiSystems):
+    def setUp(self):
+        # CH4 and O2
+        system_1 = dpdata.LabeledSystem('gaussian/methane.gaussianlog', fmt='gaussian/log')
+        system_2 = dpdata.LabeledSystem('gaussian/oxygen.gaussianlog', fmt='gaussian/log')
+        systems1 = dpdata.MultiSystems(system_1, system_2)
+        systems1.to_deepmd_npy("tmp.multi.to")
+        self.systems = dpdata.MultiSystems().from_deepmd_npy("tmp.multi.to")
+
+        self.system_names = ['C1H4O0', 'C0H0O2']
+        self.system_sizes = {'C1H4O0':1, 'C0H0O2':1}
+        self.atom_names = ['C', 'H', 'O']
+
 if __name__ == '__main__':
     unittest.main()