Changeset 435065 for src/Actions/MoleculeAction

Timestamp:

Mar 2, 2011, 9:48:20 PM (14 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:

341f22

Parents:

eb33c4

Message:

Rewrote VerletForceIntegration into a functor in Dynamics/.

• we now have the regression test working with checking against an integrated file which has not been checked though (just by eye and logged output to make sense, not against other code).

Location:

src/Actions/MoleculeAction

Files:

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

src/Actions/MoleculeAction/VerletIntegrationAction.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include "atom.hpp"
+#include "AtomSet.hpp"
 #include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
+#include "Dynamics/VerletForceIntegration.hpp"
 #include "molecule.hpp"
-#include "CodePatterns/Verbose.hpp"
 #include "World.hpp"
 
+#include <vector>
 #include <iostream>
 #include <fstream>
@@ -38 +42 @@
 /** =========== define the function ====================== */
 Action::state_ptr MoleculeVerletIntegrationAction::performCall() {
-  molecule *mol = NULL;
-
   // obtain information
   getParametersfromValueStorage();
 
-  for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
-    mol = iter->second;
-    DoLog(1) && (Log() << Verbose(1) << "Parsing forces file and Verlet integrating." << endl);
-    // TODO: sollte besser stream nutzen, nicht filename direkt (es sei denn, ist prefix), besser fuer unit test
-    char outputname[MAXSTRINGSIZE];
-    strcpy(outputname, params.forcesfile.string().c_str());
-    if (!mol->VerletForceIntegration(outputname, *(World::getInstance().getConfig()), 0))
+
+  DoLog(1) && (Log() << Verbose(1) << "Parsing forces file and Verlet integrating." << endl);
+  // TODO: sollte besser stream nutzen, nicht filename direkt (es sei denn, ist prefix), besser fuer unit test
+  char outputname[MAXSTRINGSIZE];
+  strcpy(outputname, params.forcesfile.string().c_str());
+  AtomSetMixin<std::vector<atom *> > set(World::getInstance().getSelectedAtoms());
+  for (int step = 0; step < params.MDSteps; ++step) {
+    VerletForceIntegration<std::vector<atom *> > Verlet(set, params.Deltat, step, false);
+    if (!Verlet(outputname, 1, 0, params.FixedCenterOfMass))
       DoLog(2) && (Log() << Verbose(2) << "File " << params.forcesfile << " not found." << endl);
     else
       DoLog(2) && (Log() << Verbose(2) << "File " << params.forcesfile << " found and parsed." << endl);
   }
+
   return Action::success;
 }

src/Actions/MoleculeAction/VerletIntegrationAction.def

@@ -12 +12 @@
 // 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 (boost::filesystem::path)
-#define paramtokens ("verlet-integration")
-#define paramdescriptions ("perform verlet integration of a given force file")
+#define paramtypes (boost::filesystem::path)(double)(int)(bool)
+#define paramtokens ("verlet-integration")("deltat")("MDSteps")("keep-fixed-CenterOfMass")
+#define paramdescriptions ("perform verlet integration of a given force file")("time step width")("number of MDSteps to integrate")("whether forces and velocities shall be corrected such that center of mass remains at rest")
 #undef paramdefaults
-#define paramreferences (forcesfile)
+#define paramreferences (forcesfile)(Deltat)(MDSteps)(FixedCenterOfMass)
 
 #undef statetypes