Changeset 9f97c5 for src

Timestamp:

Aug 4, 2009, 1:55:11 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:

1953f9

Parents:

ef0e6d

Message:

FillWithMolecule() for testing built into ParseCommandLine()

File:

• src/builder.cpp (modified) (5 diffs)

src/builder.cpp

@@ -584 +584 @@
         LinkedCell LCList(mol, 10.);
         class Tesselation *TesselStruct = NULL;
-        Find_convex_border((ofstream *)&cout, mol, TesselStruct, &LCList, NULL);
+        Find_convex_border((ofstream *)&cout, mol, &LCList, NULL);
         double clustervolume = VolumeOfConvexEnvelope((ofstream *)&cout, TesselStruct, configuration);
         cout << Verbose(0) << "The tesselated surface area is " << clustervolume << "." << endl;
@@ -1562 +1562 @@
               }
               break;
+            case 'F':
+              ExitFlag = 1;
+              if (argptr+5 >=argc) {
+                ExitFlag = 255;
+                cerr << "Not enough or invalid arguments given for filling box with water: -F <dist_x> <dist_y> <dist_z> <randatom> <randmol> <DoRotate>" << endl;
+              } else {
+                SaveFlag = true;
+                cout << Verbose(1) << "Filling Box with water molecules." << endl;
+                // construct water molecule
+                molecule *filler = new molecule(periode);;
+                molecule *Filling = NULL;
+                atom *second = NULL, *third = NULL;
+                first = new atom();
+                first->type = periode->FindElement(1);
+                first->x.Init(0.441, -0.143, 0.);
+                filler->AddAtom(first);
+                second = new atom();
+                second->type = periode->FindElement(1);
+                second->x.Init(-0.464, 1.137, 0.0);
+                filler->AddAtom(second);
+                third = new atom();
+                third->type = periode->FindElement(8);
+                third->x.Init(-0.464, 0.177, 0.);
+                filler->AddAtom(third);
+                filler->AddBond(first, third, 1);
+                filler->AddBond(second, third, 1);
+                // call routine
+                double distance[NDIM];
+                for (int i=0;i<NDIM;i++)
+                  distance[i] = atof(argv[argptr+i]);
+                Filling = FillBoxWithMolecule((ofstream *)&cout, molecules, filler, configuration, distance, atof(argv[argptr+3]), atof(argv[argptr+4]), atoi(argv[argptr+5]));
+                if (Filling != NULL) {
+                  molecules->insert(Filling);
+                }
+                delete(filler);
+                argptr+=6;
+              }
+              break;
             case 'A':
               ExitFlag = 1;
@@ -1587 +1625 @@
                 cout << Verbose(1) << "Using rolling ball of radius " << atof(argv[argptr]) << " and storing tecplot data in " << argv[argptr+1] << "." << endl;
                 LinkedCell LCList(mol, atof(argv[argptr])*2.);
-                Find_non_convex_border((ofstream *)&cout, mol, &T, &LCList, argv[argptr+1], atof(argv[argptr]));
+                Find_non_convex_border((ofstream *)&cout, mol, &LCList, argv[argptr+1], atof(argv[argptr]));
                 //FindDistributionOfEllipsoids((ofstream *)&cout, &T, &LCList, N, number, filename.c_str());
                 argptr+=2;
@@ -1770 +1808 @@
               cout << Verbose(1) << "Converting config file from supposed old to new syntax." << endl;
               break;
-            case 'F':
             case 'f':
               ExitFlag = 1;
@@ -1814 +1851 @@
                 LinkedCell LCList(mol, 10.);
                 class Tesselation *TesselStruct = NULL;
-                Find_convex_border((ofstream *)&cout, mol, TesselStruct, &LCList, argv[argptr]);
+                Find_convex_border((ofstream *)&cout, mol, &LCList, argv[argptr]);
                 double clustervolume = VolumeOfConvexEnvelope((ofstream *)&cout, TesselStruct, &configuration);
                 cout << Verbose(0) << "The tesselated surface area is " << clustervolume << "." << endl;