Changeset c5805a for src

Timestamp:

Mar 3, 2010, 9:31:24 AM (15 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:

b34306

Parents:

cb85c2e

Message:

FIX: allowing empty config files, and filling can deal with no molecules being present.

FillBoxWithMolecule():

• Additional checks whether AtomCount>0
• FIX: CopyAtoms was not initialised to NULL, hence wrong atoms might get "bonded".
• if TesselStruct or LCList are NULL, these refer to empty molecules not to an error
• breaking when atom would be placed was wrong, just continue to next atom of filler molecule.

config::LoadMolecule()

• we do not performCriticalExit() when MaxTypes==0, indicating present config file with no atoms.

Location:

src

Files:

• boundary.cpp (modified) (5 diffs)
• config.cpp (modified) (1 diff)

src/boundary.cpp

@@ -819 +819 @@
   map<molecule *, LinkedCell *> LCList;
 
-  for (MoleculeList::iterator ListRunner = List->ListOfMolecules.begin(); ListRunner != List->ListOfMolecules.end(); ListRunner++) {
-    Log() << Verbose(1) << "Pre-creating linked cell lists for molecule " << *ListRunner << "." << endl;
-    LCList[(*ListRunner)] = new LinkedCell((*ListRunner), 10.); // get linked cell list
-    Log() << Verbose(1) << "Pre-creating tesselation for molecule " << *ListRunner << "." << endl;
-    TesselStruct[(*ListRunner)] = NULL;
-    FindNonConvexBorder((*ListRunner), TesselStruct[(*ListRunner)], (const LinkedCell *&)LCList[(*ListRunner)], 5., NULL);
-  }
+  for (MoleculeList::iterator ListRunner = List->ListOfMolecules.begin(); ListRunner != List->ListOfMolecules.end(); ListRunner++)
+    if ((*ListRunner)->AtomCount > 0) {
+      Log() << Verbose(1) << "Pre-creating linked cell lists for molecule " << *ListRunner << "." << endl;
+      LCList[(*ListRunner)] = new LinkedCell((*ListRunner), 10.); // get linked cell list
+      Log() << Verbose(1) << "Pre-creating tesselation for molecule " << *ListRunner << "." << endl;
+      TesselStruct[(*ListRunner)] = NULL;
+      FindNonConvexBorder((*ListRunner), TesselStruct[(*ListRunner)], (const LinkedCell *&)LCList[(*ListRunner)], 5., NULL);
+    }
 
   // Center filler at origin
-  filler->CenterOrigin();
+  filler->CenterEdge(&Inserter);
   filler->Center.Zero();
 
@@ -845 +846 @@
 
   // go over [0,1]^3 filler grid
-  for (n[0] = 0; n[0] <= N[0]; n[0]++)
-    for (n[1] = 0; n[1] <= N[1]; n[1]++)
-      for (n[2] = 0; n[2] <= N[2]; n[2]++) {
+  for (n[0] = 0; n[0] < N[0]; n[0]++)
+    for (n[1] = 0; n[1] < N[1]; n[1]++)
+      for (n[2] = 0; n[2] < N[2]; n[2]++) {
         // calculate position of current grid vector in untransformed box
         CurrentPosition.Init((double)n[0]/(double)N[0], (double)n[1]/(double)N[1], (double)n[2]/(double)N[2]);
@@ -857 +858 @@
 
         // go through all atoms
+        for (int i=0;i<filler->AtomCount;i++)
+          CopyAtoms[i] = NULL;
         Walker = filler->start;
         while (Walker->next != filler->end) {
@@ -900 +903 @@
           for (MoleculeList::iterator ListRunner = List->ListOfMolecules.begin(); ListRunner != List->ListOfMolecules.end(); ListRunner++) {
             // get linked cell list
-            if (TesselStruct[(*ListRunner)] == NULL) {
-              eLog() << Verbose(0) << "TesselStruct of " << (*ListRunner) << " is NULL. Didn't we pre-create it?" << endl;
-              FillIt = false;
-            } else {
+            if (TesselStruct[(*ListRunner)] != NULL) {
               const double distance = (TesselStruct[(*ListRunner)]->GetDistanceToSurface(Inserter, LCList[(*ListRunner)]));
               FillIt = FillIt && (distance > boundary) && ((MaxDistance < 0) || (MaxDistance > distance));
@@ -919 +919 @@
             Log() << Verbose(1) << "INFO: Position at " << Inserter << " is inner point, within boundary or outside of MaxDistance." << endl;
             CopyAtoms[Walker->nr] = NULL;
-            break;
+            continue;
           }
 

src/config.cpp

@@ -689 +689 @@
   ParseForParameter(verbose,FileBuffer,"MaxTypes", 0, 1, 1, int_type, &(MaxTypes), 1, critical);
   if (MaxTypes == 0) {
-    eLog() << Verbose(0) << "There are no atoms according to MaxTypes in this config file." << endl;
-    performCriticalExit();
+    eLog() << Verbose(1) << "There are no atoms according to MaxTypes in this config file." << endl;
+    //performCriticalExit();
   } else {
     // prescan number of ions per type