Fixed issue with missing references from scc to method.

parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/run_tests.py

@@ -258,6 +258,12 @@ class TestGeoOpt(unittest.TestCase):
         result = self.results["number_of_frames_in_sequence"]
         self.assertEqual(result, 5)
 
+    def test_single_configuration_calculation_to_system_ref(self):
+        result = self.results["section_single_configuration_calculation"]
+        for i_scc, scc in enumerate(result.values()):
+            self.assertEqual(scc["single_configuration_to_calculation_method_ref"], 0)
+            self.assertEqual(scc["single_configuration_calculation_to_system_ref"], i_scc)
+
     def test_geometry_optimization_threshold_force(self):
         result = self.results["geometry_optimization_threshold_force"]
         expected_result = convert_unit(1.000000E-04, "bohr^-1*hartree")
@@ -487,6 +493,12 @@ class TestMD(unittest.TestCase):
         result = self.results["frame_sequence_temperature"]
         self.assertTrue(np.array_equal(result, self.temp))
 
+    def test_single_configuration_calculation_to_system_ref(self):
+        result = self.results["section_single_configuration_calculation"]
+        for i_scc, scc in enumerate(result.values()):
+            self.assertEqual(scc["single_configuration_to_calculation_method_ref"], 0)
+            self.assertEqual(scc["single_configuration_calculation_to_system_ref"], i_scc)
+
     def test_frame_sequence_time(self):
         result = self.results["frame_sequence_time"]
         expected_result = convert_unit(

parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py

@@ -35,6 +35,9 @@ class CPMDCommonParser(CommonParser):
         self.cache_service.add("print_freq", 1)
         self.cache_service.add("configuration_periodic_dimensions", single=False, update=False)
 
+        self.cache_service.add("single_configuration_calculation_to_system_ref", single=False, update=True)
+        self.cache_service.add("single_configuration_to_calculation_method_ref", single=False, update=False)
+
     #===========================================================================
     # Common SimpleMatchers
     def header(self):
@@ -209,12 +212,24 @@ class CPMDCommonParser(CommonParser):
             ]
         )
 
+    #===========================================================================
+    # onOpen triggers
+    def onOpen_section_method(self, backend, gIndex, section):
+        self.cache_service["single_configuration_to_calculation_method_ref"] = gIndex
+
+    def onOpen_section_system(self, backend, gIndex, section):
+        self.cache_service["single_configuration_calculation_to_system_ref"] = gIndex
+
     #===========================================================================
     # onClose triggers
     def onClose_section_run(self, backend, gIndex, section):
         backend.addValue("program_name", "CPMD")
         backend.addValue("program_basis_set_type", "plane waves")
 
+    def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
+        self.cache_service.addValue("single_configuration_calculation_to_system_ref")
+        self.cache_service.addValue("single_configuration_to_calculation_method_ref")
+
     def onClose_section_system(self, backend, gIndex, section):
         self.cache_service.addArrayValues("configuration_periodic_dimensions")
 

parser/parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py

@@ -108,9 +108,6 @@ class CPMDGeoOptParser(MainHierarchicalParser):
         self.n_frames += 1
 
     def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
-        # For single point calculations there is only one method and system.
-        backend.addValue("single_configuration_calculation_to_system_ref", 0)
-        backend.addValue("single_configuration_to_calculation_method_ref", 0)
         self.frame_refs.append(gIndex)
 
     def onClose_section_frame_sequence(self, backend, gIndex, section):

parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py

@@ -84,7 +84,7 @@ class CPMDMDParser(MainHierarchicalParser):
             ]
         )
 
-    #=======================================================================
+    #===========================================================================
     # onClose triggers
     def onClose_section_sampling_method(self, backend, gIndex, section):
         self.sampling_method_gid = gIndex
@@ -108,7 +108,7 @@ class CPMDMDParser(MainHierarchicalParser):
         if pot_mean is not None and pot_std is not None:
             backend.addArrayValues("frame_sequence_potential_energy_stats", np.array([pot_mean, pot_std]), unit="hartree")
 
-    #=======================================================================
+    #===========================================================================
     # adHoc
     def parse_md(self):
         """Parses all the md step information.
@@ -239,9 +239,6 @@ class CPMDMDParser(MainHierarchicalParser):
                     self.backend.addRealValue("energy_total", potential_energy, unit="hartree")
                     self.backend.addValue("time_calculation", tcpu)
 
-            # Add reference to system
-            self.backend.addValue("single_configuration_calculation_to_system_ref", sys_id)
-
             # Close sections
             self.backend.closeSection("section_single_configuration_calculation", scc_id)
             self.backend.closeSection("section_system", sys_id)

parser/parser-cpmd/cpmdparser/versions/cpmd41/singlepointparser.py

@@ -77,11 +77,6 @@ class CPMDSinglePointParser(MainHierarchicalParser):
     def onClose_x_cpmd_section_scf(self, backend, gIndex, section):
         backend.addValue("number_of_scf_iterations", self.n_scf_iterations)
 
-    def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
-        # For single point calculations there is only one method and system.
-        backend.addValue("single_configuration_calculation_to_system_ref", 0)
-        backend.addValue("single_configuration_to_calculation_method_ref", 0)
-
     def onClose_section_system(self, backend, gIndex, section):
         self.cache_service.addArrayValues("atom_positions", "initial_positions", unit="bohr")
         self.cache_service.addArrayValues("atom_labels")