Changeset 99b0dc for src/Actions/FragmentationAction

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/Actions/FragmentationAction

Files:

• FragmentationAction.cpp (modified) (2 diffs)
• FragmentationAction.def (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAction.cpp ¶

@@ -50 +50 @@
   getParametersfromValueStorage();
 
+  LOG(0, "STATUS: Fragmenting molecular system with current connection matrix maximum bond distance "
+      << params.distance << " up to "
+      << params.order << " order. Fragment files begin with "
+      << params.prefix << " and are stored as: "
+      << params.types << "." << std::endl);
+
   DepthFirstSearchAnalysis DFS;
   for (World::MoleculeSelectionConstIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
@@ -58 +64 @@
     if (mol->hasBondStructure()) {
       Fragmentation Fragmenter(mol);
-      LOG(1, "STAUS: Fragmenting molecule with current connection matrix ...");
-      ExitFlag = Fragmenter.FragmentMolecule(params.order, params.path, DFS);
+      Fragmenter.setOutputTypes(params.types);
+      ExitFlag = Fragmenter.FragmentMolecule(params.order, params.prefix, DFS);
     }
     World::getInstance().setExitFlag(ExitFlag);

src/Actions/FragmentationAction/FragmentationAction.def ¶

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
-
+#include <string>
+#include <vector>
 
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
-#define paramtypes (std::string)(double)(int)
-#define paramtokens ("fragment-molecule")("distance")("order")
-#define paramdescriptions ("path to where the fragment configurations shall be stored")("distance in space")("order of a discretization, dissection, ...")
-#undef paramdefaults
-#define paramreferences (path)(distance)(order)
+#define paramtypes (std::string)(double)(int)(std::vector<std::string>)
+#define paramtokens ("fragment-molecule")("distance")("order")("output-types")
+#define paramdescriptions ("prefix of each fragment file")("distance in space")("order of a discretization, dissection, ...")("type(s) of parsers that output fragment config files")
+#define paramdefaults (NODEFAULT)(NODEFAULT)(NODEFAULT)("pcp tremolo xyz")
+#define paramreferences (prefix)(distance)(order)(types)
 
 #undef statetypes