Changeset 51c910 for src/builder.cpp

Timestamp:

Jul 23, 2009, 2:04:47 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:

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

File:

• src/builder.cpp (modified) (5 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;