Changeset 41a467 for src/Parser

Timestamp:

Nov 3, 2011, 7:44:01 PM (13 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

ab26c3

Parents:

47d041

git-author:

Frederik Heber <heber@…> (10/27/11 15:08:36)

git-committer:

Frederik Heber <heber@…> (11/03/11 19:44:01)

Message:

LARGE: config class is now just a tiny container.

• this was loooooobg overdue. Config.cpp contained remnants from parsing pcp files and much else. Also fragmentation depended on it. Since refactoring of MoleculeListClass and the fragmentation, we don't need it anymore.
• helper functions ParseForParameters(), LoadMolecule() extracted into new module PcpParser_helper.
• config class now just contains 4 variables that are generally required (especially IsAngstroem) and they should probably remain with the world.
• removed some places where config.hpp was no unnecessarily included.
• Moved ConfigFileBuffer.* over to subfolder src/Parser/ where it rather belongs (associated with PcpParser).

Location:

src/Parser

Files:

• ConfigFileBuffer.cpp (moved) (moved from src/ConfigFileBuffer.cpp )
• ConfigFileBuffer.hpp (moved) (moved from src/ConfigFileBuffer.hpp )
• Makefile.am (modified) (4 diffs)
• MpqcParser.cpp (modified) (1 diff)
• PcpParser.cpp (modified) (1 diff)
• PcpParser_helper.cpp (added)
• PcpParser_helper.hpp (added)
• Psi3Parser.cpp (modified) (3 diffs)

src/Parser/Makefile.am ¶

@@ -5 +5 @@
 PARSERSOURCE = \
   Parser/ChangeTracker.cpp \
+  Parser/ConfigFileBuffer.cpp \
   Parser/FormatParser_common.cpp \
   Parser/FormatParser_Parameters.cpp \
@@ -13 +14 @@
   Parser/ParserTypes.cpp \
   Parser/PcpParser.cpp \
+  Parser/PcpParser_helper.cpp \
   Parser/PdbAtomInfoContainer.cpp \
   Parser/PdbParser.cpp \
@@ -23 +25 @@
 PARSERHEADER = \
   Parser/ChangeTracker.hpp \
+  Parser/ConfigFileBuffer.hpp \
   Parser/FormatParser.hpp \
   Parser/FormatParser_specializations_header.hpp \
@@ -37 +40 @@
   Parser/ParserTypes.undef \
   Parser/PcpParser.hpp \
+  Parser/PcpParser_helper.hpp \
   Parser/PdbAtomInfoContainer.hpp \
   Parser/PdbKey.hpp \

src/Parser/MpqcParser.cpp ¶

@@ -28 +28 @@
 
 #include "atom.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/toString.hpp"
 #include "config.hpp"
 #include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "molecule.hpp"
 #include "MoleculeListClass.hpp"
-#include "CodePatterns/Log.hpp"
-#include "CodePatterns/toString.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "LinearAlgebra/Vector.hpp"
-#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/Parser/PcpParser.cpp ¶

@@ -23 +23 @@
 #include <iomanip>
 
-//#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
 #include "atom.hpp"
-#include "config.hpp"
-#include "ConfigFileBuffer.hpp"
-#include "Element/element.hpp"
+#include "Box.hpp"
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "molecule.hpp"
 #include "MoleculeListClass.hpp"
 #include "PcpParser.hpp"
-#include "Element/periodentafel.hpp"
+#include "Parser/ConfigFileBuffer.hpp"
+#include "Parser/PcpParser_helper.hpp"
 #include "ThermoStatContainer.hpp"
 #include "World.hpp"
-#include "Box.hpp"
 
 

src/Parser/Psi3Parser.cpp ¶

@@ -28 +28 @@
 
 #include "atom.hpp"
-#include "config.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/toString.hpp"
 #include "Element/element.hpp"
 #include "Element/periodentafel.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "molecule.hpp"
 #include "MoleculeListClass.hpp"
-#include "CodePatterns/Log.hpp"
-#include "CodePatterns/toString.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"
 
@@ -60 +58 @@
 {}
 
-/** Load an MPQC config file into the World.
+/** Load an PSI3 config file into the World.
  * \param *file input stream
  */
@@ -155 +153 @@
 }
 
-/** Saves all atoms and data into a MPQC config file.
+/** Saves all atoms and data into a PSI3 config file.
  * \param *file output stream
  * \param atoms atoms to store