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parser-cp2k
Commit 2b827c50 authored by Lauri Himanen's avatar Lauri Himanen
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Added initial functionality for opening cube files.

parent 39930754
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Showing with 2532 additions and 22 deletions
parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py
View file @ 2b827c50
......@@ -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-ELECTRON_DENSITY-1_0.cube 0 → 100644
View file @ 2b827c50
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regtests/cp2k_2.6.2/cube/single_point_default_name/si_bulk8.inp 0 → 100644
View file @ 2b827c50
&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
View file @ 2b827c50
......@@ -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)
......
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