Changeset aa5702 for src

Timestamp:

Sep 28, 2008, 5:55:04 PM (16 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:

ba4432

Parents:

62f793

Message:

corrected molecule::VerletForceIntegration() and analyzer creates data and plot file for shielding values

Location:

src

Files:

• analyzer.cpp (modified) (3 diffs)
• config.cpp (modified) (1 diff)
• molecules.cpp (modified) (4 diffs)

src/analyzer.cpp

@@ -116 +116 @@
   if (!ForceFragments.ParseFragmentMatrix(argv[1], dir, ForceFragmentSuffix,0,0)) return 1;
   if (periode != NULL) { // also look for PAS values
-    if (!ShieldingFragments.ParseFragmentMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
-    if (!ShieldingPASFragments.ParseFragmentMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
+    if (!ShieldingFragments.ParseFragmentMatrix(argv[1], dir, ShieldingFragmentSuffix, 1, 0)) return 1;
+    if (!ShieldingPASFragments.ParseFragmentMatrix(argv[1], dir, ShieldingPASFragmentSuffix, 1, 0)) return 1;
   }
 
@@ -211 +211 @@
   output2.close();
 
-
+  // +++++++++++++++++++++++++++++++++++++++ Plotting shieldings
+  if (periode != NULL) { // also look for PAS values
+    if (!OpenOutputFile(output, argv[3], "ShieldingPAS-Atom.dat" )) return false;
+    output << "#" << ShieldingPAS.Header << endl;
+    for(int j=0;j<ShieldingPAS.RowCounter[ShieldingPAS.MatrixCounter];j++) {
+      for(int k=0;k<ShieldingPAS.ColumnCounter;k++)
+        output << scientific << ShieldingPAS.Matrix[ ShieldingPAS.MatrixCounter ][j][k]*(((k>1) && (k<6))? 1.e6 : 1.) << "\t";
+      output << endl;
+    }
+    output << endl << endl; // another two newlines to partition the data
+    for(int j=0;j<ShieldingPASFragments.RowCounter[ShieldingPASFragments.MatrixCounter];j++) {
+      for(int k=0;k<ShieldingPASFragments.ColumnCounter;k++)
+        output << scientific << ShieldingPASFragments.Matrix[ ShieldingPASFragments.MatrixCounter ][j][k]*(((k>1) && (k<6))? 1.e6 : 1.) << "\t";
+      output << endl;
+    }
+    output << endl;
+  }
+  output.close();
+
+  
   // +++++++++++++++++++++++++++++++++++++++ Plotting deviation in energy to full QM
   if (!CreateDataDeltaEnergyOrder(Energy, EnergyFragments, KeySet, argv[3], "DeltaEnergies-Order", "Plot of error between approximated and full energies energies versus the Bond Order", datum)) return 1;
@@ -359 +378 @@
   if (!CreatePlotOrder(ForceFragments, KeySet, argv[3], "MaxForces-FragmentOrder", 5, "below", "y", "set boxwidth 0.2", 1, 1, "bond order", "maximum of approximated forces [Ht/a.u.]", Orderxrange.str().c_str(), yrange.str().c_str(), "1" , "with boxes fillcolor", BoxesForcePlotLine)) return 1;
  
+  // +++++++++++++++++++++++++++++++=Ploting approximated and true shielding for each atom
+  if (periode != NULL) { // also look for PAS values
+    if(!OpenOutputFile(output, argv[3], "ShieldingPAS-Atom.pyx")) return 1;
+    CreatePlotHeader(output, "ShieldingPAS-Atom", 1, "top right", NULL, NULL,  1, 5, "nuclei index", "chemical shielding value [ppm]");
+    output << "plot \\" << endl;  
+    output << "'ShieldingPAS-Atom.dat' index 0 title 'DFT' using 2:6 with linespoints, \\" << endl;
+    output << "'ShieldingPAS-Atom.dat' index 1 title 'BOSSANOVA' using 2:6 with linespoints" << endl;
+    output.close();  
+  }
+
   // create Makefile
   if(!OpenOutputFile(output, argv[3], "Makefile")) return 1;

src/config.cpp

@@ -63 +63 @@
   UseAddGramSch=1;
   Seed=1;
-  
   MaxOuterStep=0;
-  Deltat=1;
+  Deltat=0.01;
   OutVisStep=10;
   OutSrcStep=5;

src/molecules.cpp

@@ -1493 +1493 @@
   string token;
   stringstream item;
-  double a, IonMass, Vector[NDIM], ConstrainedPotentialEnergy, ActualTemp = 0.;
+  double a, IonMass, Vector[NDIM], ConstrainedPotentialEnergy, ActualTemp;
   ForceMatrix Force;
 
@@ -1535 +1535 @@
     while (walker->next != end) { // go through every atom of this element
       walker = walker->next;
-      a = configuration.Deltat*0.5/walker->type->mass;        // (F+F_old)/2m = a and thus: v = (F+F_old)/2m * t = (F + F_old) * a
+      //a = configuration.Deltat*0.5/walker->type->mass;        // (F+F_old)/2m = a and thus: v = (F+F_old)/2m * t = (F + F_old) * a
       // check size of vectors
       if (Trajectories[walker].R.size() <= (unsigned int)(MDSteps)) {
@@ -1546 +1546 @@
       // Update R (and F)
       for (int d=0; d<NDIM; d++) {
-        Trajectories[walker].F.at(MDSteps).x[d] = -Force.Matrix[0][AtomNo][d+5]*(configuration.GetIsAngstroem() ? AtomicLengthToAngstroem : 1.);
+        Trajectories[walker].F.at(MDSteps).x[d] = -Force.Matrix[0][walker->nr][d+5]*(configuration.GetIsAngstroem() ? AtomicLengthToAngstroem : 1.);
         Trajectories[walker].R.at(MDSteps).x[d] = Trajectories[walker].R.at(MDSteps-1).x[d];
-        Trajectories[walker].R.at(MDSteps).x[d] += configuration.Deltat*(Trajectories[walker].U.at(MDSteps-1).x[d]);
-        Trajectories[walker].R.at(MDSteps).x[d] += configuration.Deltat*a*(Trajectories[walker].F.at(MDSteps).x[d]);     // F = m * a and s = 0.5 * F/m * t^2 = F * a * t
+        Trajectories[walker].R.at(MDSteps).x[d] += configuration.Deltat*(Trajectories[walker].U.at(MDSteps-1).x[d]);     // s(t) = s(0) + v * deltat + 1/2 a * deltat^2 
+        Trajectories[walker].R.at(MDSteps).x[d] += 0.5*configuration.Deltat*configuration.Deltat*(Trajectories[walker].F.at(MDSteps).x[d]/walker->type->mass);     // F = m * a and s = 0.5 * F/m * t^2 = F * a * t
       }
       // Update U
       for (int d=0; d<NDIM; d++) {
         Trajectories[walker].U.at(MDSteps).x[d] = Trajectories[walker].U.at(MDSteps-1).x[d]; 
-        Trajectories[walker].U.at(MDSteps).x[d] += a * (Trajectories[walker].F.at(MDSteps).x[d]+Trajectories[walker].F.at(MDSteps-1).x[d]);
+        Trajectories[walker].U.at(MDSteps).x[d] += configuration.Deltat * (Trajectories[walker].F.at(MDSteps).x[d]+Trajectories[walker].F.at(MDSteps-1).x[d]/walker->type->mass); // v = F/m * t
       }
 //      out << "Integrated position&velocity of step " << (MDSteps) << ": ("; 
@@ -1578 +1578 @@
     }
   }
+  for(int d=0;d<NDIM;d++)
+    Vector[d] /= IonMass;
+  ActualTemp = 0.;
   walker = start;
   while (walker->next != end) { // go through every atom of this element
     walker = walker->next;
     for(int d=0;d<NDIM;d++) {
-      Trajectories[walker].U.at(MDSteps).x[d] -= Vector[d]*walker->type->mass/IonMass;
+      Trajectories[walker].U.at(MDSteps).x[d] -= Vector[d];
       ActualTemp += 0.5 * walker->type->mass * Trajectories[walker].U.at(MDSteps).x[d] * Trajectories[walker].U.at(MDSteps).x[d];
     }