Changeset c7a473

Timestamp:

May 30, 2010, 4:09:06 PM (15 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:

9b7db1

Parents:

f8f14d

Message:

Added cased '-P' (force integration) to testsuite.

• this is currently not working at all with los of memory corruption, hence testsuite checks for this failure only.

Files:

• src/atom_trajectoryparticle.cpp (modified) (2 diffs)
• src/molecule_dynamics.cpp (modified) (3 diffs)
• tests/regression/Molecules/5/pre/test.conf (added)
• tests/regression/Molecules/5/pre/test.forces (added)
• tests/regression/testsuite.at (modified) (1 diff)

src/atom_trajectoryparticle.cpp

@@ -10 +10 @@
 #include "config.hpp"
 #include "element.hpp"
+#include "info.hpp"
 #include "log.hpp"
 #include "parser.hpp"
@@ -71 +72 @@
 void TrajectoryParticle::ResizeTrajectory(int MaxSteps)
 {
+  Info FunctionInfo(__func__);
   if (Trajectory.R.size() <= (unsigned int)(MaxSteps)) {
-    //Log() << Verbose(0) << "Increasing size for trajectory array of " << keyword << " to " << (MaxSteps+1) << "." << endl;
+    DoLog(0) && (Log() << Verbose(0) << "Increasing size for trajectory array of " << nr << " from " << Trajectory.R.size() << " to " << (MaxSteps+1) << "." << endl);
     Trajectory.R.resize(MaxSteps+1);
     Trajectory.U.resize(MaxSteps+1);

src/molecule_dynamics.cpp

@@ -10 +10 @@
 #include "config.hpp"
 #include "element.hpp"
+#include "info.hpp"
 #include "log.hpp"
 #include "memoryallocator.hpp"
@@ -548 +549 @@
 bool molecule::VerletForceIntegration(char *file, config &configuration)
 {
+  Info FunctionInfo(__func__);
   ifstream input(file);
   string token;
@@ -593 +595 @@
     // and perform Verlet integration for each atom with position, velocity and force vector
     // check size of vectors
-    ActOnAllAtoms( &atom::ResizeTrajectory, MDSteps+10 );
-
-    ActOnAllAtoms( &atom::VelocityVerletUpdate, MDSteps, &configuration, &Force);
+    //ActOnAllAtoms( &atom::ResizeTrajectory, MDSteps+10 );
+
+    ActOnAllAtoms( &atom::VelocityVerletUpdate, MDSteps+1, &configuration, &Force);
   }
   // correct velocities (rather momenta) so that center of mass remains motionless
   Velocity.Zero();
   IonMass = 0.;
-  ActOnAllAtoms ( &atom::SumUpKineticEnergy, MDSteps, &IonMass, &Velocity );
+  ActOnAllAtoms ( &atom::SumUpKineticEnergy, MDSteps+1, &IonMass, &Velocity );
 
   // correct velocities (rather momenta) so that center of mass remains motionless
   Velocity.Scale(1./IonMass);
   ActualTemp = 0.;
-  ActOnAllAtoms ( &atom::CorrectVelocity, &ActualTemp, MDSteps, &Velocity );
+  ActOnAllAtoms ( &atom::CorrectVelocity, &ActualTemp, MDSteps+1, &Velocity );
   Thermostats(configuration, ActualTemp, Berendsen);
   MDSteps++;

tests/regression/testsuite.at

@@ -243 +243 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/4/pre/test.conf .], 0)
 AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -L 0 1 teststep 1], 0, [stdout], [stderr])
+AT_CLEANUP
+
+# 5. Verlet force integration
+AT_SETUP([Graph - Verlet force integration])
+AT_KEYWORDS([Molecules])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/5/pre/test.* .], 0)
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -P test.forces], 134, [stdout], [stderr])
+#AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/5/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP