Changeset 99b0dc for src/Fragmentation

Timestamp:

Oct 26, 2011, 3:02:46 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:

07a47e

Parents:

babcc1

git-author:

Frederik Heber <heber@…> (10/25/11 12:31:39)

git-committer:

Frederik Heber <heber@…> (10/26/11 15:02:46)

Message:

FragmentAction now has instead of path a types parameter.

• new output-types parameter, is a vector<string> for giving a list of desired output types similar to SetOutputFormatAction.
• TESTFIX: as vector<string> cannot have default value, we had to adapt the two regression tests Fragmentation/FragmentMolecule.. and the fragmentation tests.

Location:

src/Fragmentation

Files:

• Fragmentation.cpp (modified) (5 diffs)
• Fragmentation.hpp (modified) (3 diffs)

src/Fragmentation/Fragmentation.cpp

@@ -39 +39 @@
 #include "MoleculeLeafClass.hpp"
 #include "MoleculeListClass.hpp"
-#include "Parser/ParserTypes.hpp"
+#include "Parser/FormatParserStorage.hpp"
 #include "World.hpp"
 
@@ -59 +59 @@
 /** Performs a many-body bond order analysis for a given bond order.
  * -# parses adjacency, keysets and orderatsite files
- * -# performs DFS to find connected subgraphs (to leave this in was a design decision: might be useful later)
  * -# RootStack is created for every subgraph (here, later we implement the "update 10 sites with highest energ
 y contribution", and that's why this consciously not done in the following loop)
@@ -71 +70 @@
  * subgraph in the MoleculeListClass.
  * \param Order up to how many neighbouring bonds a fragment contains in BondOrderScheme::BottumUp scheme
- * \param &prefix path and prefix of the bond order configs to be written
+ * \param prefix prefix string for every fragment file name (may include path)
  * \param &DFS contains bond structure analysis data
  * \return 1 - continue, 2 - stop (no fragmentation occured)
  */
-int Fragmentation::FragmentMolecule(int Order, std::string &prefix, DepthFirstSearchAnalysis &DFS)
+int Fragmentation::FragmentMolecule(int Order, std::string prefix, DepthFirstSearchAnalysis &DFS)
 {
   MoleculeListClass *BondFragments = NULL;
@@ -216 +215 @@
 
     DoLog(1) && (Log() << Verbose(1) << "Writing " << BondFragments->ListOfMolecules.size() << " possible bond fragmentation configs" << endl);
-    if ((BondFragments->OutputConfigForListOfFragments(prefix, SortIndex, xyz))
-        && (BondFragments->OutputConfigForListOfFragments(prefix, SortIndex, mpqc))
-        && (BondFragments->OutputConfigForListOfFragments(prefix, SortIndex, pcp)))
+    bool write_status = true;
+    for (std::vector<std::string>::const_iterator iter = typelist.begin();
+        iter != typelist.end();
+        ++iter) {
+      LOG(2, "INFO: Writing bond fragments for type " << (*iter) << ".");
+      write_status = write_status
+      && BondFragments->OutputConfigForListOfFragments(
+          prefix,
+          SortIndex,
+          FormatParserStorage::getInstance().getTypeFromName(*iter));
+    }
+    if (write_status)
       DoLog(1) && (Log() << Verbose(1) << "All configs written." << endl);
     else
@@ -715 +723 @@
 };
 
+/** Sets the desired output types of the fragment configurations.
+ *
+ * @param types vector of desired types.
+ */
+void Fragmentation::setOutputTypes(const std::vector<std::string> &types)
+{
+  typelist = types;
+}

src/Fragmentation/Fragmentation.hpp

@@ -20 +20 @@
 #include "Fragmentation/fragmentation_helpers.hpp"
 
+#include <string>
+#include <vector>
+
 class atom;
 class Graph;
@@ -31 +34 @@
   ~Fragmentation();
 
-  int FragmentMolecule(int Order, std::string &prefix, DepthFirstSearchAnalysis &DFS);
+  int FragmentMolecule(int Order, std::string prefix, DepthFirstSearchAnalysis &DFS);
+
+  void setOutputTypes(const std::vector<std::string> &types);
 
 private:
@@ -51 +56 @@
 
 private:
+  //!> pointer to molecule that is fragmented
   molecule *mol;
+  //!> list of parser types for which a configuration file per fragment is stored
+  std::vector<std::string> typelist;
 };