diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py
index 17ef33ffea0638e57a4f8acd667fb61dcca3cc57..e2e2b145768f5967517fc093fd1ed2b2bb318a85 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py
@@ -47,7 +47,7 @@ class CommonMatcher(object):
#=======================================================================
# Globally cached values
- self.cache_service.add("simulation_cell", single=False, update=True)
+ self.cache_service.add("simulation_cell", single=False, update=False)
self.cache_service.add("number_of_scf_iterations", 0)
self.cache_service.add("atom_positions", single=False, update=True)
self.cache_service.add("atom_labels", single=False, update=False)
@@ -313,6 +313,12 @@ class CommonMatcher(object):
if number_of_atoms is not None:
self.cache_service["number_of_atoms"] = number_of_atoms
+ # def onClose_x_cp2k_section_quickstep_calculation(self, backend, gIndex, section):
+ # print "quickstep CLOSED"
+
+ # def onClose_x_cp2k_section_geometry_optimization_step(self, backend, gIndex, section):
+ # print "Optimisation step CLOSED"
+
def onClose_section_method(self, backend, gIndex, section):
"""When all the functional definitions have been gathered, matches them
with the nomad correspondents and combines into one single string which
@@ -591,10 +597,10 @@ class CommonMatcher(object):
self.test_electronic_structure_method = "RPA"
return wrapper
- def debug(self):
- def wrapper(parser):
- print("FOUND")
- return wrapper
+ # def debug(self):
+ # def wrapper(parser):
+ # print("FOUND")
+ # return wrapper
#===========================================================================
# MISC functions
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
index 49c3a7c298db7391324a8feed52489b8b3c7e229..f1a9c007bd36da9a411bb8d1d8b93e0eeb13fab9 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
@@ -19,6 +19,7 @@ class CP2KGeoOptParser(MainHierarchicalParser):
super(CP2KGeoOptParser, self).__init__(file_path, parser_context)
self.setup_common_matcher(CommonMatcher(parser_context))
self.traj_iterator = None
+ self.energy_reeval_quickstep = None
#=======================================================================
# Globally cached values
@@ -30,11 +31,10 @@ class CP2KGeoOptParser(MainHierarchicalParser):
#=======================================================================
# Cache levels
self.caching_level_for_metaname.update({
- 'x_cp2k_optimization_energy': CachingLevel.ForwardAndCache,
'x_cp2k_section_geometry_optimization_step': CachingLevel.ForwardAndCache,
'x_cp2k_section_quickstep_calculation': CachingLevel.ForwardAndCache,
'x_cp2k_section_geometry_optimization': CachingLevel.ForwardAndCache,
- 'x_cp2k_section_geometry_optimization_energy_reevaluation': CachingLevel.ForwardAndCache,
+ # 'x_cp2k_section_geometry_optimization_energy_reevaluation': CachingLevel.ForwardAndCache,
})
#=======================================================================
@@ -73,7 +73,6 @@ class CP2KGeoOptParser(MainHierarchicalParser):
endReStr=" Conv. in RMS gradients =",
name="geooptstep",
repeats=True,
- # sections=["section_single_configuration_calculation", "section_system"],
subMatchers=[
SM( "",
forwardMatch=True,
@@ -140,12 +139,19 @@ class CP2KGeoOptParser(MainHierarchicalParser):
otherMetaInfo=["geometry_optimization_converged"]
),
SM( " Reevaluating energy at the minimum",
- sections=["x_cp2k_section_geometry_optimization_energy_reevaluation"],
+ # sections=["x_cp2k_section_geometry_optimization_energy_reevaluation"],
subMatchers=[
self.cm.quickstep_calculation(),
+ # SM("",
+ # adHoc=self.adHoc_save_energy_reeval_quickstep()
+ # )
],
- # adHoc=self.adHoc_step()
+ # adHoc=self.adHoc_save_energy_reeval_quickstep()
),
+ # SM( "",
+ # forwardMatch=True,
+ # adHoc=self.adHoc_save_energy_reeval_quickstep()
+ # )
],
)
@@ -173,13 +179,11 @@ class CP2KGeoOptParser(MainHierarchicalParser):
def onClose_x_cp2k_section_geometry_optimization(self, backend, gIndex, section):
# Get the re-evaluated energy and add it to frame_sequence_potential_energy
- energy = section.get_latest_value([
- "x_cp2k_section_geometry_optimization_energy_reevaluation",
- "x_cp2k_section_quickstep_calculation",
- "x_cp2k_energy_total"]
- )
- if energy is not None:
- self.cache_service["frame_sequence_potential_energy"].append(energy)
+ reeval_quickstep = self.energy_reeval_quickstep
+ if reeval_quickstep is not None:
+ energy = reeval_quickstep.get_latest_value("x_cp2k_energy_total")
+ if energy is not None:
+ self.cache_service["frame_sequence_potential_energy"].append(energy)
# Push values from cache
self.cache_service.push_array_values("frame_sequence_potential_energy")
@@ -231,6 +235,9 @@ class CP2KGeoOptParser(MainHierarchicalParser):
def onClose_section_sampling_method(self, backend, gIndex, section):
self.backend.addValue("sampling_method", "geometry_optimization")
+ def onClose_x_cp2k_section_quickstep_calculation(self, backend, gIndex, section):
+ self.energy_reeval_quickstep = section
+
def onClose_x_cp2k_section_geometry_optimization_step(self, backend, gIndex, section):
energy = section["x_cp2k_optimization_energy"]
if energy is not None:
@@ -283,11 +290,18 @@ class CP2KGeoOptParser(MainHierarchicalParser):
self.cache_service["geometry_optimization_method"] = "bfgs"
return wrapper
- # def adHoc_step(self):
- # """Called when all the step information has been retrieved from the
- # output file. Here further information is gathered from external files.
- # """
+ # def adHoc_save_energy_reeval_quickstep(self):
# def wrapper(parser):
- # self.cache_service["number_of_frames_in_sequence"] += 1
-
+ # section_managers = parser.backend.sectionManagers
+ # section_run_manager = section_managers["section_run"]
+ # section_run = section_run_manager.openSections[0]
+ # print section_run.subSectionValues
+ # # quickstep = section_run.get_latest_value("x_cp2k_section_quickstep_calculation")
+ # # print quickstep
+ # # self.energy_reeval_quickstep = quickstep
# return wrapper
+
+ def debug(self):
+ def wrapper(parser):
+ print "DEBUG"
+ return wrapper
diff --git a/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py b/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
index 049912584df585a5957dca293b32d87b03de2d38..cca527c2ce983e8da71ab8befeaae1545ee99ee4 100644
--- a/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
+++ b/parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
@@ -31,6 +31,7 @@ class CP2KMDParser(MainHierarchicalParser):
self.velo_freq = None
self.energy_freq = None
self.cell_freq = None
+ self.md_quicksteps = []
#=======================================================================
# Globally cached values
@@ -88,10 +89,12 @@ class CP2KMDParser(MainHierarchicalParser):
SM( " INITIAL CELL LNTHS\[bohr\] =\s+(?P<x_cp2k_md_cell_length_a_instantaneous__bohr>{0})\s+(?P<x_cp2k_md_cell_length_b_instantaneous__bohr>{0})\s+(?P<x_cp2k_md_cell_length_c_instantaneous__bohr>{0})".format(self.cm.regex_f)),
SM( " INITIAL CELL ANGLS\[deg\] =\s+(?P<x_cp2k_md_cell_angle_a_instantaneous__deg>{0})\s+(?P<x_cp2k_md_cell_angle_b_instantaneous__deg>{0})\s+(?P<x_cp2k_md_cell_angle_c_instantaneous__deg>{0})".format(self.cm.regex_f)),
],
+ adHoc=self.adHoc_save_md_quickstep()
),
SM( " SCF WAVEFUNCTION OPTIMIZATION",
endReStr=" TEMPERATURE \[K\] =",
name="md_step",
+ forwardMatch=True,
repeats=True,
sections=["x_cp2k_section_md_step"],
subMatchers=[
@@ -113,6 +116,7 @@ class CP2KMDParser(MainHierarchicalParser):
SM( " CELL ANGLS\[deg\] =\s+(?P<x_cp2k_md_cell_angle_a_instantaneous__deg>{0})\s+(?P<x_cp2k_md_cell_angle_b_instantaneous__deg>{0})\s+(?P<x_cp2k_md_cell_angle_c_instantaneous__deg>{0})".format(self.cm.regex_f)),
SM( " AVE. CELL ANGLS\[deg\] =\s+(?P<x_cp2k_md_cell_angle_a_average__deg>{0})\s+(?P<x_cp2k_md_cell_angle_b_average__deg>{0})\s+(?P<x_cp2k_md_cell_angle_c_average__deg>{0})".format(self.cm.regex_f)),
],
+ adHoc=self.adHoc_save_md_quickstep()
),
]
)
@@ -321,7 +325,7 @@ class CP2KMDParser(MainHierarchicalParser):
if md_steps:
if (i_step + 1) % freqs["output"][0] == 0:
md_step = md_steps[i_md_step]
- quickstep = md_step.get_latest_value("x_cp2k_section_quickstep_calculation")
+ quickstep = self.md_quicksteps[i_md_step]
if quickstep is not None:
quickstep.add_latest_value("x_cp2k_atom_forces", "atom_forces")
quickstep.add_latest_value("x_cp2k_stress_tensor", "stress_tensor")
@@ -388,3 +392,14 @@ class CP2KMDParser(MainHierarchicalParser):
mean_pressure = frame_sequence_pressure.mean()
std_pressure = frame_sequence_pressure.std()
backend.addArrayValues("frame_sequence_pressure_stats", np.array([mean_pressure, std_pressure]))
+
+ #===========================================================================
+ # adHoc functions
+ def adHoc_save_md_quickstep(self):
+ def wrapper(parser):
+ section_managers = parser.backend.sectionManagers
+ section_run_manager = section_managers["section_run"]
+ section_run = section_run_manager.openSections[0]
+ quickstep = section_run.get_latest_value("x_cp2k_section_quickstep_calculation")
+ self.md_quicksteps.append(quickstep)
+ return wrapper
diff --git a/test/unittests/cp2k_2.6.2/run_tests.py b/test/unittests/cp2k_2.6.2/run_tests.py
index e55d6e22dcb68b9bda7565481285bfebf693d978..f7850e378e714324ba14c0321a7173d7d9ac4a8c 100644
--- a/test/unittests/cp2k_2.6.2/run_tests.py
+++ b/test/unittests/cp2k_2.6.2/run_tests.py
@@ -1022,14 +1022,14 @@ if __name__ == '__main__':
logger.setLevel(logging.ERROR)
suites = []
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestErrors))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
- # suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce))
- # 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(TestErrors))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce))
+ 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))