Changeset 5e0d1f for src/config.cpp

Timestamp:

Aug 6, 2008, 12:00:18 PM (17 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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

9e5a04d

Parents:

e9b8bb

Message:

config::Save() and config::Load() parse MD steps into and out of molecule::Trajectories. Tested.

File:

• src/config.cpp (modified) (4 diffs)

src/config.cpp

@@ -461 +461 @@
   int Z, No[MAX_ELEMENTS];
   int verbose = 0;
+  int MinSteps = -1;
   
   /* Namen einlesen */
@@ -652 +653 @@
         while (ParseForParameter(verbose,file, keyword, 0, 1, 1, double_type, &neues->x.x[0], repetition, (repetition == 1) ? critical : optional) &&
           ParseForParameter(verbose,file, keyword, 0, 2, 1, double_type, &neues->x.x[1], repetition, (repetition == 1) ? critical : optional) &&
-          ParseForParameter(verbose,file, keyword, 0, 3, 1, double_type, &neues->x.x[2], repetition, (repetition == 1) ? critical : optional))
+          ParseForParameter(verbose,file, keyword, 0, 3, 1, double_type, &neues->x.x[2], repetition, (repetition == 1) ? critical : optional)) {
+          // check size of vectors
+          if (mol->Trajectories[neues].R.size() <= (unsigned int)(repetition-1)) {
+            cout << "Increasing size for trajectory array of " << keyword << " to " << (repetition+10) << "." << endl;
+            mol->Trajectories[neues].R.resize(repetition+10);
+            mol->Trajectories[neues].U.resize(repetition+10);
+            mol->Trajectories[neues].F.resize(repetition+10);
+          }
+            
+          // put into trajectories list
+          for (int d=0;d<NDIM;d++)
+            mol->Trajectories[neues].R.at(repetition-1).x[d] = neues->x.x[d];
+          
+          // parse velocities if present
+          if(!ParseForParameter(verbose,file, keyword, 0, 5, 1, double_type, &neues->v.x[0], repetition,optional))
+            neues->v.x[0] = 0.;
+          if(!ParseForParameter(verbose,file, keyword, 0, 6, 1, double_type, &neues->v.x[1], repetition,optional))
+            neues->v.x[1] = 0.;
+          if(!ParseForParameter(verbose,file, keyword, 0, 7, 1, double_type, &neues->v.x[2], repetition,optional))
+            neues->v.x[2] = 0.;
+          for (int d=0;d<NDIM;d++)
+            mol->Trajectories[neues].U[repetition-1].x[d] = neues->v.x[d];
+          
+          // parse forces if present
+          if(!ParseForParameter(verbose,file, keyword, 0, 8, 1, double_type, &neues->v.x[0], repetition,optional))
+            neues->v.x[0] = 0.;
+          if(!ParseForParameter(verbose,file, keyword, 0, 9, 1, double_type, &neues->v.x[1], repetition,optional))
+            neues->v.x[1] = 0.;
+          if(!ParseForParameter(verbose,file, keyword, 0, 10, 1, double_type, &neues->v.x[2], repetition,optional))
+            neues->v.x[2] = 0.;
+          for (int d=0;d<NDIM;d++)
+            mol->Trajectories[neues].F[repetition-1].x[d] = neues->v.x[d];
+          
+          cout << "Parsed position of step " << (repetition-1) << " "; 
+          for (int d=0;d<NDIM;d++)
+            cout << mol->Trajectories[neues].R.at(repetition-1).x[d] << "  ";          // next step
+          cout << endl;
+          
           repetition++;
+        }
         repetition--;
-        //cout << "Found " << repetition << " times of the keyword " << keyword << "." << endl;
+        cout << "Found " << repetition << " times of the keyword " << keyword << "." << endl;
       }
+      if ((repetition < MinSteps) || (MinSteps == -1))
+        MinSteps = repetition;
       ParseForParameter(verbose,file, keyword, 0, 1, 1, double_type, &neues->x.x[0], repetition,critical);
       ParseForParameter(verbose,file, keyword, 0, 2, 1, double_type, &neues->x.x[1], repetition,critical);
@@ -667 +708 @@
       if(!ParseForParameter(verbose,file, keyword, (int)FastParsing, 7, 1, double_type, &neues->v.x[2], repetition,optional))
         neues->v.x[2] = 0.;
+      // here we don't care if forces are present (last in trajectories is always equal to current position)
       neues->type = elementhash[i]; // find element type
       mol->AddAtom(neues);
     }
   }
+  mol->MDSteps = MinSteps;    // set equal to smallest number of parsed steps
   file->close();
   delete(file);
@@ -972 +1015 @@
     *output << endl;
     result = result && mol->Checkout(output);
-    result = result && mol->Output(output);
+    result = result && mol->OutputTrajectories(output);
     return result;
   } else