Changeset 51c910

Timestamp:

Jul 23, 2009, 2:04:47 PM (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:

36ec71

Parents:

d067d45 (diff), 375b458 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'AtomRemoval'

Conflicts:

molecuilder/src/builder.cpp
molecuilder/src/molecules.cpp

merges:

• builder.cpp: case 'R' in ParseCommandLineOptions from AtomRemoval, also bugfix in RemoveAtoms(), rest from HEAD
• molecules.cpp: Basically all from HEAD because of MultipleMolecules and ConstrainedMD

Location:

src

Files:

• builder.cpp (modified) (5 diffs)
• molecules.cpp (modified) (7 diffs)

src/builder.cpp

@@ -463 +463 @@
       cin >> tmp1;
       first = mol->start;
-      while(first->next != mol->end) {
-        first = first->next;
+      second = first->next;
+      while(second != mol->end) {
+        first = second;
+        second = first->next;
         if (first->x.DistanceSquared((const Vector *)&second->x) > tmp1*tmp1) // distance to first above radius ...
           mol->RemoveAtom(first);
@@ -472 +474 @@
       cout << Verbose(0) << "Which axis is it: ";
       cin >> axis;
-      cout << Verbose(0) << "Left inward boundary: ";
+      cout << Verbose(0) << "Lower boundary: ";
       cin >> tmp1;
-      cout << Verbose(0) << "Right inward boundary: ";
+      cout << Verbose(0) << "Upper boundary: ";
       cin >> tmp2;
       first = mol->start;
-      while(first->next != mol->end) {
-        first = first->next;
-        if ((first->x.x[axis] > tmp2) || (first->x.x[axis] < tmp1)) // out of boundary ...
+      second = first->next;
+      while(second != mol->end) {
+        first = second;
+        second = first->next;
+        if ((first->x.x[axis] < tmp1) || (first->x.x[axis] > tmp2)) {// out of boundary ...
+          //cout << "Atom " << *first << " with " << first->x.x[axis] << " on axis " << axis << " is out of bounds [" << tmp1 << "," << tmp2 << "]." << endl;
           mol->RemoveAtom(first);
+        }
       }
       break;
@@ -1349 +1355 @@
             cout << "\t-m <0/1>\tCalculate (0)/ Align in(1) PAS with greatest EV along z axis." << endl;
             cout << "\t-n\tFast parsing (i.e. no trajectories are looked for)." << endl;
-            cout << "\t-N\tGet non-convex-envelope." << endl;
+            cout << "\t-N <radius> <file>\tGet non-convex-envelope." << endl;
             cout << "\t-o <out>\tGet volume of the convex envelope (and store to tecplot file)." << endl;
             cout << "\t-p <file>\tParse given xyz file and create raw config file from it." << endl;
@@ -1355 +1361 @@
             cout << "\t-L <step0> <step1> <prefix>\tStore a linear interpolation between two configurations <step0> and <step1> into single config files with prefix <prefix> and as Trajectories into the current config file." << endl; 
             cout << "\t-r\t\tConvert file from an old pcp syntax." << endl;
+            cout << "\t-R\t\tRemove all atoms out of sphere around a given one." << endl;
             cout << "\t-t x1 x2 x3\tTranslate all atoms by this vector (x1,x2,x3)." << endl;
             cout << "\t-T <file> Store temperatures from the config file in <file>." << endl;
@@ -1621 +1628 @@
                   cout << Verbose(2) << "File found and parsed." << endl;
                 argptr+=1;
+              }
+              break;
+            case 'R':
+              ExitFlag = 1;
+              if ((argptr+1 >= argc) || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1])))  {
+                ExitFlag = 255;
+                cerr << "Not enough or invalid arguments given for removing atoms: -R <id> <distance>" << endl;
+              } else {
+                SaveFlag = true;
+                cout << Verbose(1) << "Removing atoms around " << argv[argptr] << " with radius " << argv[argptr+1] << "." << endl;
+                double tmp1 = atof(argv[argptr+1]);
+                atom *third = mol->FindAtom(atoi(argv[argptr]));
+                atom *first = mol->start;
+                if ((third != NULL) && (first != mol->end)) {
+                  atom *second = first->next;
+                  while(second != mol->end) {
+                    first = second;
+                    second = first->next;
+                    if (first->x.DistanceSquared((const Vector *)&third->x) > tmp1*tmp1) // distance to first above radius ...
+                      mol->RemoveAtom(first);
+                  }
+                } else {
+                  cerr << "Removal failed due to missing atoms on molecule or wrong id." << endl;
+                }
+                argptr+=2;
               }
               break;

src/molecules.cpp

@@ -1860 +1860 @@
 bool molecule::RemoveAtom(atom *pointer)
 {
-  if (ElementsInMolecule[pointer->type->Z] != 0)  // this would indicate an error
+  if (ElementsInMolecule[pointer->type->Z] != 0)  { // this would indicate an error
     ElementsInMolecule[pointer->type->Z]--;  // decrease number of atom of this element
-  else
+    AtomCount--;
+  } else
     cerr << "ERROR: Atom " << pointer->Name << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl;
   if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
@@ -2845 +2846 @@
     ColorList[i] = white;
   }
-  
+
   *out << Verbose(1) << "Back edge list - ";
   BackEdgeStack->Output(out);
@@ -3852 +3853 @@
         OtherAtom = ListOfBondsPerAtom[Walker->nr][i]->GetOtherAtom(Walker);
         if (OtherAtom == ListOfLocalAtoms[Binder->rightatom->nr]) { // found the bond
-            LocalStack->Push(ListOfBondsPerAtom[Walker->nr][i]);
-                *out << Verbose(3) << "Found local edge " << *(ListOfBondsPerAtom[Walker->nr][i]) << "." << endl;
+          LocalStack->Push(ListOfBondsPerAtom[Walker->nr][i]);
+          *out << Verbose(3) << "Found local edge " << *(ListOfBondsPerAtom[Walker->nr][i]) << "." << endl;
           break;
         }
@@ -3861 +3862 @@
     ReferenceStack->Push(Binder);
   } while (FirstBond != Binder);
-  
+
   return status;
 };
@@ -4006 +4007 @@
   Walker = start;
   while (Walker->next != end) {
-    Walker = Walker->next; 
+    Walker = Walker->next;
     *out << Verbose(4) << "Atom " << Walker->Name << "/" << Walker->nr << " with " << NumberOfBondsPerAtom[Walker->nr] << " bonds: ";
     TotalDegree = 0;
@@ -4365 +4366 @@
 #ifdef ADDHYDROGEN
    && (Walker->type->Z == 1)
-#endif
-                        ) { // search for first non-hydrogen atom
-    *out << Verbose(4) << "Current Root candidate is " << Walker->Name << "." << endl;
-    Walker = Walker->next;
-  }
-  if (Walker != end)
-    RootStack->Push(Walker);
-  else
-    *out << Verbose(0) << "ERROR: Could not find an appropriate Root atom!" << endl;
-  *out << Verbose(3) << "Root " << Walker->Name << " is on AtomStack, beginning loop through all vertices ..." << endl;
-
-  ///// OUTER LOOP ////////////
-  while (!RootStack->IsEmpty()) {
-    // get new root vertex from atom stack
-    Root = RootStack->PopFirst();
-    ShortestPathList[Root->nr] = 0;
-    if (Labels[Root->nr] == -1)
-      Labels[Root->nr] = RunningIndex++; // prevent it from getting again on AtomStack
-    PredecessorList[Root->nr] = Root;
-    TouchedStack->Push(Root);
-    *out << Verbose(0) << "Root for this loop is: " << Root->Name << ".\n";
-
-    // clear snake stack
-    SnakeStack->ClearStack();
-    //SnakeStack->TestImplementation(out, start->next);
-
-    ///// INNER LOOP ////////////
-    // Problems:
-    // - what about cyclic bonds?
-    Walker = Root;
-    do {
-      *out << Verbose(1) << "Current Walker is: " << Walker->Name;
-      // initial setting of the new Walker: label, color, shortest path and put on stacks
-      if (Labels[Walker->nr] == -1)  {  // give atom a unique, monotonely increasing number
-        Labels[Walker->nr] = RunningIndex++;
-        RootStack->Push(Walker);
-      }
-      *out << ", has label " << Labels[Walker->nr];
-      if ((ColorVertexList[Walker->nr] == white) || ((Binder != NULL) && (ColorEdgeList[Binder->nr] == white))) {  // color it if newly discovered and push on stacks (and if within reach!)
-        if ((Binder != NULL) && (ColorEdgeList[Binder->nr] == white)) {
-          // Binder ought to be set still from last neighbour search
-          *out << ", coloring bond " << *Binder << " black";
-          ColorEdgeList[Binder->nr] = black; // mark this bond as used
-        }
-        if (ShortestPathList[Walker->nr] == -1) {
-          ShortestPathList[Walker->nr] = ShortestPathList[PredecessorList[Walker->nr]->nr]+1;
-          TouchedStack->Push(Walker); // mark every atom for lists cleanup later, whose shortest path has been changed
-        }
-        if ((ShortestPathList[Walker->nr] < Order) && (ColorVertexList[Walker->nr] != darkgray)) {  // if not already on snake stack
-          SnakeStack->Push(Walker);
-          ColorVertexList[Walker->nr] = darkgray; // mark as dark gray of on snake stack
         }
       }
@@ -4452 +4402 @@
             } else { // otherwise check its colour and element
               if (
-#ifdef ADDHYDROGEN
               (OtherAtom->type->Z != 1) &&
 #endif