Changeset 34e0592 for src/builder.cpp

Timestamp:

Aug 20, 2009, 7:48:07 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:

78b73c, 9ba9ee

Parents:

1d9b7aa (diff), 7c14ec (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.

git-author:

Frederik Heber <heber@…> (08/19/09 14:40:33)

git-committer:

Frederik Heber <heber@…> (08/20/09 07:48:07)

Message:

Merge branch 'ConcaveHull' of ​ssh://stud64d-02/home/metzler/workspace/espack into Ticket14

Conflicts:

molecuilder/src/boundary.cpp
molecuilder/src/tesselation.cpp

• in boundary.cpp: FindConvexBorder() - overlay due to PickFarthestofTwoBaselines()
• in tesselation.cpp: CheckConvexityCriterion() - overlay due to verbosity change on return, getAngle() -> GetAngle()

File:

• src/builder.cpp (modified) (12 diffs)

src/builder.cpp

@@ -584 +584 @@
         LinkedCell LCList(mol, 10.);
         class Tesselation *TesselStruct = NULL;
-        Find_convex_border((ofstream *)&cout, mol, &LCList, NULL);
+        FindConvexBorder((ofstream *)&cout, mol, &LCList, NULL);
         double clustervolume = VolumeOfConvexEnvelope((ofstream *)&cout, TesselStruct, configuration);
         cout << Verbose(0) << "The tesselated surface area is " << clustervolume << "." << endl;
@@ -644 +644 @@
   Vector x,y,z,n; // coordinates for absolute point in cell volume
   double *factor; // unit factor if desired
-  double bond, min_bond;
+  double bond, minBond;
   char choice;  // menu choice char
   bool valid;
@@ -683 +683 @@
         first = mol->AskAtom("Enter first (fixed) atom: ");
         second = mol->AskAtom("Enter second (shifting) atom: ");
-        min_bond = 0.;
+        minBond = 0.;
         for (int i=NDIM;i--;)
-          min_bond += (first->x.x[i]-second->x.x[i])*(first->x.x[i] - second->x.x[i]);
-        min_bond = sqrt(min_bond);
-        cout << Verbose(0) << "Current Bond length between " << first->type->name << " Atom " << first->nr << " and " << second->type->name << " Atom " << second->nr << ": " << min_bond << " a.u." << endl;
+          minBond += (first->x.x[i]-second->x.x[i])*(first->x.x[i] - second->x.x[i]);
+        minBond = sqrt(minBond);
+        cout << Verbose(0) << "Current Bond length between " << first->type->name << " Atom " << first->nr << " and " << second->type->name << " Atom " << second->nr << ": " << minBond << " a.u." << endl;
         cout << Verbose(0) << "Enter new bond length [a.u.]: ";
         cin >> bond;
         for (int i=NDIM;i--;) {
-          second->x.x[i] -= (second->x.x[i]-first->x.x[i])/min_bond*(min_bond-bond);
+          second->x.x[i] -= (second->x.x[i]-first->x.x[i])/minBond*(minBond-bond);
         }
         //cout << Verbose(0) << "New coordinates of Atom " << second->nr << " are: ";
@@ -1325 +1325 @@
   int j;
   double volume = 0.;
-  enum ConfigStatus config_present = absent;
+  enum ConfigStatus configPresent = absent;
   clock_t start,end;
   int argptr;
@@ -1425 +1425 @@
         if (output == NULL) {
           cout << Verbose(1) << "Specified config file " << argv[1] << " not found." << endl;
-          config_present = absent;
+          configPresent = absent;
         } else {
           cout << "Empty configuration file." << endl;
           ConfigFileName = argv[1];
-          config_present = empty;
+          configPresent = empty;
           output.close();
         }
@@ -1440 +1440 @@
             cout << "new syntax." << endl;
             configuration.Load(ConfigFileName, periode, mol);
-            config_present = present;
+            configPresent = present;
             break;
           case 0:
             cout << "old syntax." << endl;
             configuration.LoadOld(ConfigFileName, periode, mol);
-            config_present = present;
+            configPresent = present;
             break;
           default:
             cout << "Unknown syntax or empty, yet present file." << endl;
-            config_present = empty;
+            configPresent = empty;
        }
       }
     } else
-      config_present = absent;
+      configPresent = absent;
     // 4. parse again through options, now for those depending on elements db and config presence
     argptr = 1;
@@ -1460 +1460 @@
       if (argv[argptr][0] == '-') {
         argptr++;
-        if ((config_present == present) || (config_present == empty)) {
+        if ((configPresent == present) || (configPresent == empty)) {
           switch(argv[argptr-1][1]) {
             case 'p':
@@ -1474 +1474 @@
                 else {
                   cout << Verbose(2) << "File found and parsed." << endl;
-                  config_present = present;
+                  configPresent = present;
                 }
               }
@@ -1494 +1494 @@
                 if (first->type != NULL) {
                   mol->AddAtom(first);  // add to molecule
-                  if ((config_present == empty) && (mol->AtomCount != 0))
-                    config_present = present;
+                  if ((configPresent == empty) && (mol->AtomCount != 0))
+                    configPresent = present;
                 } else
                   cerr << Verbose(1) << "Could not find the specified element." << endl;
@@ -1505 +1505 @@
           }
         }
-        if (config_present == present) {
+        if (configPresent == present) {
           switch(argv[argptr-1][1]) {
             case 'M':
@@ -1627 +1627 @@
                 start = clock();
                 LinkedCell LCList(mol, atof(argv[argptr])*2.);
-                Find_non_convex_border((ofstream *)&cout, mol, &LCList, argv[argptr+1], atof(argv[argptr]));
+                FindNonConvexBorder((ofstream *)&cout, mol, &LCList, argv[argptr+1], atof(argv[argptr]));
                 //FindDistributionOfEllipsoids((ofstream *)&cout, &T, &LCList, N, number, filename.c_str());
                 end = clock();
@@ -1871 +1871 @@
                 cout << Verbose(1) << "Storing tecplot data in " << argv[argptr] << "." << endl;
                 LinkedCell LCList(mol, 10.);
-                //Find_convex_border((ofstream *)&cout, mol, &LCList, argv[argptr]);
-                Find_non_convex_border((ofstream *)&cout, mol, &LCList, argv[argptr], 10.);
+                //FindConvexBorder((ofstream *)&cout, mol, &LCList, argv[argptr]);
+                FindNonConvexBorder((ofstream *)&cout, mol, &LCList, argv[argptr], 10.);
 
                 double volumedifference = ConvexizeNonconvexEnvelope((ofstream *)&cout, mol->TesselStruct, mol, argv[argptr]);