Changeset f7f7a4 for src/molecules.cpp

Timestamp:

Sep 28, 2009, 6:41:52 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, Candidate_v1.7.0, 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:

d52e70c

Parents:

8cd903

git-author:

Frederik Heber <heber@…> (09/28/09 18:39:28)

git-committer:

Frederik Heber <heber@…> (09/28/09 18:41:52)

Message:

Implemenation of embedding merge, untested. LinearInterpolation now has switch for using identity map.

• embed merge in MoleculeListClass determines the non-convex envelope and tries to fill the domain with the filler molecule everywhere outside of this domain
• is added to MergeMolecule in builder.cpp, case 'e'
• in molecule::LinearInterpolationBetweenConfiguration() now has additional parameter to tell whether we have to look for a mapping or use the identity.

File:

• src/molecules.cpp (modified) (3 diffs)

src/molecules.cpp

@@ -662 +662 @@
 {
   int length = 0;
-  char *molname = strrchr(filename, '/')+sizeof(char);  // search for filename without dirs
+  const char *molname = strrchr(filename, '/');
+  if (molname != NULL)
+    molname += sizeof(char);  // search for filename without dirs
+  else
+    molname = filename; // contains no slashes
   char *endname = strchr(molname, '.');
   if ((endname == NULL) || (endname < molname))
@@ -1562 +1566 @@
  * \param endstep stating final configuration in molecule::Trajectories
  * \param &config configuration structure
+ * \param MapByIdentity if true we just use the identity to map atoms in start config to end config, if not we find mapping by \sa MinimiseConstrainedPotential()
  * \return true - success in writing step files, false - error writing files or only one step in molecule::Trajectories
  */
-bool molecule::LinearInterpolationBetweenConfiguration(ofstream *out, int startstep, int endstep, const char *prefix, config &configuration) 
+bool molecule::LinearInterpolationBetweenConfiguration(ofstream *out, int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity)
 {
   molecule *mol = NULL;
@@ -1573 +1578 @@
   atom **PermutationMap = NULL;
   atom *Walker = NULL, *Sprinter = NULL;
-  MinimiseConstrainedPotential(out, PermutationMap, startstep, endstep, configuration.GetIsAngstroem());
+  if (!MapByIdentity)
+    MinimiseConstrainedPotential(out, PermutationMap, startstep, endstep, configuration.GetIsAngstroem());
+  else {
+    PermutationMap = (atom **) Malloc(AtomCount*sizeof(atom *), "molecule::LinearInterpolationBetweenConfiguration: **PermutationMap");
+    Walker = start;
+    while (Walker->next != end) {
+      Walker = Walker->next;
+      PermutationMap[Walker->nr] = Walker;   // always pick target with the smallest distance
+    }
+  }
 
   // check whether we have sufficient space in Trajectories for each atom