Changeset 943d02

Timestamp:

Apr 23, 2008, 5:33:51 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, 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:

d3a46d

Parents:

14de469

Message:

molecuilder reads and stored ion velocities

Class atom has new variables velocity vector v and integer FixedIon. These are parse during config:load(), and stored via atom:Output() (but only if norm of v is above MYEPSILON), values are copied to son atoms/nodes in AddCopyAtom and AddHydrogenAtom (there: no fancy splitting of the vector as done with the InBondVector)

Location:

src

Files:

• atom.cpp (modified) (2 diffs)
• config.cpp (modified) (1 diff)
• molecules.cpp (modified) (4 diffs)
• molecules.hpp (modified) (2 diffs)

src/atom.cpp

@@ -20 +20 @@
   type = NULL;
   sort = NULL;
+  FixedIon = 0;
   nr = -1;
   GraphNr = -1;
@@ -59 +60 @@
   if (out != NULL) {
     *out << "Ion_Type" << ElementNo << "_" << AtomNo << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2] << "\t";
-    *out << "\t" << "0\t# Number in molecule " << nr << endl;
+    *out << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2];
+    *out << "\t" << FixedIon;
+    if (v.Norm() > MYEPSILON)
+      *out << "\t" << scientific << setprecision(6) << v.x[0] << "\t" << v.x[1] << "\t" << v.x[2] << "\t";
+    *out << " # Number in molecule " << nr << endl;
     return true;
   } else

src/config.cpp

@@ -604 +604 @@
       ParseForParameter(verbose,file, keyword, 0, 2, 1, double_type, &neues->x.x[1], repetition,critical);
       ParseForParameter(verbose,file, keyword, 0, 3, 1, double_type, &neues->x.x[2], repetition,critical);
+      ParseForParameter(verbose,file, keyword, 0, 4, 1, int_type, &neues->FixedIon, repetition,critical);
+      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.;
       neues->type = elementhash[i]; // find element type
       mol->AddAtom(neues);

src/molecules.cpp

@@ -120 +120 @@
         walker->type = pointer->type;   // copy element of atom
         walker->x.CopyVector(&pointer->x); // copy coordination
+    walker->v.CopyVector(&pointer->v); // copy velocity
+    walker->FixedIon = pointer->FixedIon;
     walker->sort = &walker->nr; 
     walker->nr = last_atom++;  // increase number within molecule
@@ -231 +233 @@
       FirstOtherAtom = new atom();    // new atom
       FirstOtherAtom->type = elemente->FindElement(1);  // element is Hydrogen
+      FirstOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
+      FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
       if (TopReplacement->type->Z == 1) { // neither rescale nor replace if it's already hydrogen
         FirstOtherAtom->father = TopReplacement;
@@ -288 +292 @@
       FirstOtherAtom->type = elemente->FindElement(1);
       SecondOtherAtom->type = elemente->FindElement(1);
+      FirstOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
+      FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
+      SecondOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
+      SecondOtherAtom->FixedIon = TopReplacement->FixedIon;
       FirstOtherAtom->father = NULL;  // we are just an added hydrogen with no father
       SecondOtherAtom->father = NULL;  //  we are just an added hydrogen with no father
@@ -340 +348 @@
       SecondOtherAtom->type = elemente->FindElement(1);
       ThirdOtherAtom->type = elemente->FindElement(1);
+      FirstOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
+      FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
+      SecondOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
+      SecondOtherAtom->FixedIon = TopReplacement->FixedIon;
+      ThirdOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
+      ThirdOtherAtom->FixedIon = TopReplacement->FixedIon;
       FirstOtherAtom->father = NULL;  //  we are just an added hydrogen with no father
       SecondOtherAtom->father = NULL;  //  we are just an added hydrogen with no father

src/molecules.hpp

@@ -345 +345 @@
 class atom {
   public:
-    vector x;    //!< coordinate array of atom, giving position within cell
+    vector x;       //!< coordinate array of atom, giving position within cell
+    vector v;       //!< velocity array of atom
     element *type;  //!< pointing to element
     atom *previous; //!< previous atom in molecule list
@@ -352 +353 @@
     atom *Ancestor; //!< "Father" in Depth-First-Search
     char *Name;                 //!< unique name used during many-body bond-order fragmentation
+    int FixedIon;   //!< config variable that states whether forces act on the ion or not
     int *sort;      //!< sort criteria
     int nr;         //!< continuous, unique number