Changeset 0a4f7f for src/molecule_dynamics.cpp

Timestamp:

Apr 7, 2010, 3:45:38 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

72e7fa

Parents:

f9352d

Message:

Made data internal data-structure of vector class private

• Replaced occurences of access to internals with operator
• moved Vector-class into LinAlg-Module
• Reworked Vector to allow clean modularization
• Added Plane class to describe arbitrary planes in 3d space

File:

• src/molecule_dynamics.cpp (modified) (5 diffs)

src/molecule_dynamics.cpp

@@ -14 +14 @@
 #include "molecule.hpp"
 #include "parser.hpp"
+#include "Plane.hpp"
 
 /************************************* Functions for class molecule *********************************/
@@ -79 +80 @@
   //        Log() << Verbose(0) << trajectory2 << endl;
       // determine normal vector for both
-      normal.MakeNormalVector(&trajectory1, &trajectory2);
+      normal = Plane(trajectory1, trajectory2,0).getNormal();
       // print all vectors for debugging
   //        Log() << Verbose(0) << "Normal vector in between: ";
@@ -85 +86 @@
       // setup matrix
       for (int i=NDIM;i--;) {
-        gsl_matrix_set(A, 0, i, trajectory1.x[i]);
-        gsl_matrix_set(A, 1, i, trajectory2.x[i]);
-        gsl_matrix_set(A, 2, i, normal.x[i]);
-        gsl_vector_set(x,i, (Walker->Trajectory.R.at(Params.startstep).x[i] - Runner->Trajectory.R.at(Params.startstep).x[i]));
+        gsl_matrix_set(A, 0, i, trajectory1[i]);
+        gsl_matrix_set(A, 1, i, trajectory2[i]);
+        gsl_matrix_set(A, 2, i, normal[i]);
+        gsl_vector_set(x,i, (Walker->Trajectory.R.at(Params.startstep)[i] - Runner->Trajectory.R.at(Params.startstep)[i]));
       }
       // solve the linear system by Householder transformations
@@ -514 +515 @@
       Sprinter = mol->AddCopyAtom(Walker);
       for (int n=NDIM;n--;) {
-        Sprinter->x.x[n] = Walker->Trajectory.R.at(startstep).x[n] + (PermutationMap[Walker->nr]->Trajectory.R.at(endstep).x[n] - Walker->Trajectory.R.at(startstep).x[n])*((double)step/(double)MaxSteps);
+        Sprinter->x[n] = Walker->Trajectory.R.at(startstep)[n] + (PermutationMap[Walker->nr]->Trajectory.R.at(endstep)[n] - Walker->Trajectory.R.at(startstep)[n])*((double)step/(double)MaxSteps);
         // add to Trajectories
         //Log() << Verbose(3) << step << ">=" << MDSteps-1 << endl;
         if (step < MaxSteps) {
-          Walker->Trajectory.R.at(step).x[n] = Walker->Trajectory.R.at(startstep).x[n] + (PermutationMap[Walker->nr]->Trajectory.R.at(endstep).x[n] - Walker->Trajectory.R.at(startstep).x[n])*((double)step/(double)MaxSteps);
-          Walker->Trajectory.U.at(step).x[n] = 0.;
-          Walker->Trajectory.F.at(step).x[n] = 0.;
+          Walker->Trajectory.R.at(step)[n] = Walker->Trajectory.R.at(startstep)[n] + (PermutationMap[Walker->nr]->Trajectory.R.at(endstep)[n] - Walker->Trajectory.R.at(startstep)[n])*((double)step/(double)MaxSteps);
+          Walker->Trajectory.U.at(step)[n] = 0.;
+          Walker->Trajectory.F.at(step)[n] = 0.;
         }
       }
@@ -582 +583 @@
     for(int i=0;i<AtomCount;i++)
       for(int d=0;d<NDIM;d++) {
-        Velocity.x[d] += Force.Matrix[0][i][d+5];
+        Velocity[d] += Force.Matrix[0][i][d+5];
       }
     for(int i=0;i<AtomCount;i++)
       for(int d=0;d<NDIM;d++) {
-        Force.Matrix[0][i][d+5] -= Velocity.x[d]/(double)AtomCount;
+        Force.Matrix[0][i][d+5] -= Velocity[d]/(double)AtomCount;
       }
     // solve a constrained potential if we are meant to