Commit 8ab0c666 authored by Berk Onat's avatar Berk Onat

Corrected a typo in x_amber metainfo

parent 08d245f5
......@@ -326,7 +326,7 @@ class AMBERParser(AmberC.AMBERParserBase):
# self.superP.addValue('interaction_kind', bondFunctional) # functional form of the interaction
# this points to the relative section_atom_type
self.superP.addArrayValues('x_lammps_interaction_atom_to_atom_type_ref',
self.superP.addArrayValues('x_amber_interaction_atom_to_atom_type_ref',
np.asarray(interTypeDict[elm]))
# interaction parameters for the functional
#self.superP.addValue('interaction_parameters', bondParameters)
......@@ -502,6 +502,7 @@ class AMBERParser(AmberC.AMBERParserBase):
updateDict = {
'startSection' : [
['section_topology']],
'muteSections' : [['section_sampling_method']],
#'muteSections' : [['section_method']],
'dictionary' : section_topology_Dict
}
......@@ -545,7 +546,8 @@ class AMBERParser(AmberC.AMBERParserBase):
self.trajRefSingleConfigurationCalculation = gIndex
SloppyBackend.addArrayValues('atom_positions', np.transpose(np.asarray(self.atompositions[0])))
if self.topology is not None:
#SloppyBackend.addArrayValues('atom_labels', np.asarray(atom_labels))
atom_labels = self.topologyDict["element"]
SloppyBackend.addArrayValues('atom_labels', np.asarray(atom_labels))
pass
# Read the next step at trajectory in advance
......@@ -604,7 +606,7 @@ class AMBERParser(AmberC.AMBERParserBase):
updateFrameDict = {
'startSection' : [
['section_frame_sequence']],
'muteSections' : [['section_method']],
'muteSections' : [['section_sampling_method']],
'dictionary' : section_frameseq_Dict
}
self.metaStorage.update(updateFrameDict)
......@@ -612,6 +614,7 @@ class AMBERParser(AmberC.AMBERParserBase):
updateDictVDW = {
'startSection' : [
['section_energy_van_der_Waals']],
'muteSections' : [['section_sampling_method']],
#'muteSections' : [['section_method']],
'dictionary' : section_singlevdw_Dict
}
......@@ -625,6 +628,7 @@ class AMBERParser(AmberC.AMBERParserBase):
updateDict = {
'startSection' : [
['section_single_configuration_calculation']],
'muteSections' : [['section_sampling_method']],
#'muteSections' : [['section_method']],
'dictionary' : section_singlecalc_Dict
}
......
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