Added initial functionality for opening cube files.

parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py

@@ -54,6 +54,7 @@ class CP2KCommonParser(CommonParser):
         self.cache_service.add("map_kind_to_basis", single=False, update=False)
         self.cache_service.add("map_index_to_kind", single=False, update=False)
         self.cache_service.add("map_kind_number_to_basis_ref", single=False, update=False)
+        self.cache_service.add("electron_density_filename", single=False, update=True)
 
     #===========================================================================
     # SimpleMatchers
@@ -191,6 +192,15 @@ class CP2KCommonParser(CommonParser):
                 SM( r"  \*\*\* SCF run NOT converged \*\*\*",
                     adHoc=self.adHoc_single_point_not_converged
                 ),
+                SM( r" The electron density is written in cube file format to the file:",
+                    subMatchers=[
+                        SM(""),
+                        SM(
+                            "\s+(.+\.cube)",
+                            startReAction=self.startReAction_save_cube_filename,
+                        ),
+                    ]
+                ),
                 SM( r"  Electronic kinetic energy:\s+(?P<x_cp2k_electronic_kinetic_energy__hartree>{})".format(self.regexs.float)),
                 SM( r" **************************** NUMERICAL STRESS ********************************".replace("*", "\*"),
                     # endReStr=" **************************** NUMERICAL STRESS END *****************************".replace("*", "\*"),
@@ -556,6 +566,10 @@ class CP2KCommonParser(CommonParser):
         # Cell dependent basis mapping
         self.cache_service.addValue("mapping_section_basis_set_cell_dependent")
 
+        # If a cube file was found, open it and store values.
+        filename = self.cache_service["electron_density_filename"]
+        absolute_filepath = self.parser_context.file_service.get_absolute_path_to_file(filename)
+
         backend.closeSection("section_basis_set", scc_basis_id)
 
     #===========================================================================
@@ -736,3 +750,9 @@ class CP2KCommonParser(CommonParser):
         def wrapper(parser, groups):
             print(msg)
         return wrapper
+
+    #=======================================================================
+    # StarReActions
+    def startReAction_save_cube_filename(self, backend, groups):
+        filename = groups[0]
+        self.cache_service["electron_density_filename"] = filename

regtests/cp2k_2.6.2/cube/single_point_default_name/si_bulk8.inp

+&GLOBAL
+  PROJECT Si_bulk8
+  RUN_TYPE ENERGY_FORCE
+  PRINT_LEVEL MEDIUM
+&END GLOBAL
+&FORCE_EVAL
+  METHOD Quickstep
+  STRESS_TENSOR ANALYTICAL
+  &SUBSYS
+    &KIND Si
+      ELEMENT   Si
+      BASIS_SET DZVP-GTH-PADE
+      POTENTIAL GTH-PADE-q4
+    &END KIND
+    &CELL
+      A     5.430697500    0.000000000    0.000000000
+      B     0.000000000    5.430697500    0.000000000
+      C     0.000000000    0.000000000    5.430697500
+    &END CELL
+    &COORD
+      Si    0.000000000    0.000000000    0.000000000
+      Si    0.000000000    2.715348700    2.715348700
+      Si    2.715348700    2.715348700    0.000000000
+      Si    2.715348700    0.000000000    2.715348700
+      Si    4.073023100    1.357674400    4.073023100
+      Si    1.357674400    1.357674400    1.357674400
+      Si    1.357674400    4.073023100    4.073023100
+      Si    4.073023100    4.073023100    1.357674400
+    &END COORD
+  &END SUBSYS
+  &DFT
+    BASIS_SET_FILE_NAME  ../../BASIS_SET
+    POTENTIAL_FILE_NAME  ../../GTH_POTENTIALS
+    &QS
+      EPS_DEFAULT 1.0E-10
+    &END QS
+    &MGRID
+      NGRIDS 4
+      CUTOFF 300
+      REL_CUTOFF 60
+    &END MGRID
+    &XC
+      &XC_FUNCTIONAL PADE
+      &END XC_FUNCTIONAL
+    &END XC
+    &SCF
+      SCF_GUESS ATOMIC
+      EPS_SCF 1.0E-7
+      MAX_SCF 300
+      &DIAGONALIZATION  ON
+        ALGORITHM STANDARD
+      &END DIAGONALIZATION
+      &MIXING  T
+        METHOD BROYDEN_MIXING
+        ALPHA 0.4
+        NBROYDEN 8
+      &END MIXING
+    &END SCF
+    &PRINT
+      &E_DENSITY_CUBE MEDIUM
+        ADD_LAST  NUMERIC
+        STRIDE  3 3 3
+      &END E_DENSITY_CUBE
+    &END PRINT
+  &END DFT
+  &PRINT
+    &FORCES ON
+    &END FORCES
+  &END PRINT
+&END FORCE_EVAL

regtests/regtests.py

@@ -1326,6 +1326,13 @@ class TestElectronicStructureMethod(unittest.TestCase):
         self.assertEqual(result, "RPA")
 
 
+class TestCubeFiles(unittest.TestCase):
+    """Tests that different methods are recognized correctly.
+    """
+    def test_electron_density(self):
+        results = get_result("cube/single_point_default_name")
+
+
 if __name__ == '__main__':
 
     logger = logging.getLogger("cp2kparser")
@@ -1335,28 +1342,29 @@ if __name__ == '__main__':
 
     for VERSION in VERSIONS:
         suites = []
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestErrors))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestUnknownInput))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeometryInfo))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestStressTensorMethods))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSelfInteractionCorrectionMethod))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestConfigurationPeriodicDimensions))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSCFConvergence))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestForceFiles))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestPreprocessor))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOpt))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajFormats))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptOptimizers))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajectory))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestRestart))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMD))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDPrintSettings))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDEnsembles))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDEnsembles))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestVDWMethod))
-        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestElectronicStructureMethod))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestErrors))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestUnknownInput))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeometryInfo))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestStressTensorMethods))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSelfInteractionCorrectionMethod))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestConfigurationPeriodicDimensions))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSCFConvergence))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestForceFiles))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestPreprocessor))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOpt))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajFormats))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptOptimizers))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajectory))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestRestart))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMD))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDPrintSettings))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDEnsembles))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDEnsembles))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestVDWMethod))
+        # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestElectronicStructureMethod))
+        suites.append(unittest.TestLoader().loadTestsFromTestCase(TestCubeFiles))
 
         alltests = unittest.TestSuite(suites)
         result = unittest.TextTestRunner(verbosity=0).run(alltests)