Changeset 4882d5 for src/Actions/MoleculeAction

Timestamp:

Dec 14, 2012, 5:39:30 PM (12 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:

5251af

Parents:

8b886f

git-author:

Frederik Heber <heber@…> (10/05/12 07:59:22)

git-committer:

Frederik Heber <heber@…> (12/14/12 17:39:30)

Message:

Rewrote VerletIntegrationAction to diminish dependence on ForceMatrix.

• atom::VelocityVerletUpdate() now works on the forces stored in AtomicForces.
• ThermoStatContainer::getActive() getter for the currently active thermostat.
• VerletForceIntegration::operator() split up into several smaller functions.

Location:

src/Actions/MoleculeAction

Files:

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

src/Actions/MoleculeAction/VerletIntegrationAction.cpp

@@ -57 +57 @@
 /** =========== define the function ====================== */
 Action::state_ptr MoleculeVerletIntegrationAction::performCall() {
-  LOG(1, "Parsing forces file and Verlet integrating.");
   // TODO: sollte besser stream nutzen, nicht filename direkt (es sei denn, ist prefix), besser fuer unit test
-  char outputname[MAXSTRINGSIZE];
-  strcpy(outputname, params.forcesfile.get().string().c_str());
   AtomSetMixin<std::vector<atom *> > set(World::getInstance().getSelectedAtoms());
   for (unsigned int step = 0; step < params.MDSteps.get(); ++step) {
-    VerletForceIntegration<std::vector<atom *> > Verlet(set, params.Deltat.get(), step, false);
-    if (!Verlet(outputname, 1, 0, params.FixedCenterOfMass.get()))
+    VerletForceIntegration<std::vector<atom *> > Verlet(set, params.Deltat.get(), false);
+    // parse forces into next step
+    if (!params.forcesfile.get().string().empty()) {
+      LOG(1, "Parsing forces file.");
+      if (!Verlet.parseForcesFile(params.forcesfile.get().string().c_str(), step))
+        LOG(2, "File " << params.forcesfile.get() << " not found.");
+      else
+        LOG(2, "File " << params.forcesfile.get() << " found and parsed.");
+    }
+    // perform velocity verlet update
+    LOG(1, "Verlet integrating.");
+    if (!Verlet(step+1, 1, 0, params.FixedCenterOfMass.get()))
       LOG(2, "File " << params.forcesfile.get() << " not found.");
     else

src/Actions/MoleculeAction/VerletIntegrationAction.def

@@ -11 +11 @@
 #include "Parameters/Validators/DummyValidator.hpp"
 #include "Parameters/Validators/GenericValidators.hpp"
+#include "Parameters/Validators/Ops_Validator.hpp"
 #include "Parameters/Validators/Specific/FilePresentValidator.hpp"
 
@@ -17 +18 @@
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)(double)(unsigned 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 paramtokens ("forces-file")("deltat")("MDSteps")("keep-fixed-CenterOfMass")
+#define paramdescriptions ("file containing")("time step width")("number of MDSteps to integrate")("whether forces and velocities shall be corrected such that center of mass remains at rest")
+#define paramdefaults (PARAM_DEFAULT(""))(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)
 #define paramreferences (forcesfile)(Deltat)(MDSteps)(FixedCenterOfMass)
 #define paramvalids \
-(FilePresentValidator()) \
+(DummyValidator< boost::filesystem::path >()) \
 (PositiveValidator< double >()) \
 (NotZeroValidator< unsigned int >()) \