Changeset 3930eb for src/builder.cpp

Timestamp:

Dec 19, 2009, 7:31:34 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:

71b20e, bd61b41

Parents:

1cf5df

git-author:

Frederik Heber <heber@…> (12/19/09 19:29:02)

git-committer:

Frederik Heber <heber@…> (12/19/09 19:31:34)

Message:

Smaller fixes.

• analysis_correlation.cpp: Info objects created at start of each function for debugging.
• ParseCommandLineOptions(): case 'I' dissection added, some stuff was unexplained
• molecule::CenterOrigin() - starting at start not next now, which left out first!

Signed-off-by: Frederik Heber <heber@…>

File:

• src/builder.cpp (modified) (9 diffs)

src/builder.cpp

@@ -1410 +1410 @@
             Log() << Verbose(0) << "\t-B xx xy xz yy yz zz\tBound atoms by domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl;
             Log() << Verbose(0) << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl;
-            Log() << Verbose(0) << "\t-C\tPair Correlation analysis." << endl;
+            Log() << Verbose(0) << "\t-C <Z> <output> <bin output>\tPair Correlation analysis." << endl;
             Log() << Verbose(0) << "\t-d x1 x2 x3\tDuplicate cell along each axis by given factor." << endl;
             Log() << Verbose(0) << "\t-D <bond distance>\tDepth-First-Search Analysis of the molecule, giving cycles and tree/back edges." << endl;
@@ -1416 +1416 @@
             Log() << Verbose(0) << "\t-E <id> <Z>\tChange atom <id>'s element to <Z>, <id> begins at 0." << endl;
             Log() << Verbose(0) << "\t-f/F <dist> <order>\tFragments the molecule in BOSSANOVA manner (with/out rings compressed) and stores config files in same dir as config (return code 0 - fragmented, 2 - no fragmentation necessary)." << endl;
+            Log() << Verbose(0) << "\t-F\tFilling Box with water molecules." << endl;
             Log() << Verbose(0) << "\t-g <file>\tParses a bond length table from the given file." << endl;
             Log() << Verbose(0) << "\t-h/-H/-?\tGive this help screen." << endl;
+            Log() << Verbose(0) << "\t-I\t Dissect current system of molecules into a set of disconnected (subgraphs of) molecules." << endl;
             Log() << Verbose(0) << "\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;
             Log() << Verbose(0) << "\t-m <0/1>\tCalculate (0)/ Align in(1) PAS with greatest EV along z axis." << endl;
@@ -1575 +1577 @@
                 else {
                   Log() << Verbose(2) << "File found and parsed." << endl;
-                  // @TODO rather do the dissection afterwards
-//                  mol->SetNameFromFilename(argv[argptr]);
-//                  molecules->ListOfMolecules.remove(mol);
-//                  molecules->DissectMoleculeIntoConnectedSubgraphs(mol,&configuration);
-//                  delete(mol);
-//                  if (molecules->ListOfMolecules.size() != 0) {
-//                    for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
-//                      if ((*ListRunner)->ActiveFlag) {
-//                        mol = *ListRunner;
-//                        break;
-//                      }
-//                  }
                   configPresent = present;
                 }
@@ -1665 +1655 @@
               //argptr+=1;
               break;
+            case 'I':
+              Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl;
+              // @TODO rather do the dissection afterwards
+              molecules->DissectMoleculeIntoConnectedSubgraphs(mol,&configuration);
+              mol = NULL;
+              if (molecules->ListOfMolecules.size() != 0) {
+                for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
+                  if ((*ListRunner)->ActiveFlag) {
+                    mol = *ListRunner;
+                    break;
+                  }
+              }
+              if (mol == NULL) {
+                mol = *(molecules->ListOfMolecules.begin());
+                mol->ActiveFlag = true;
+              }
+              break;
             case 'C':
               if (ExitFlag == 0) ExitFlag = 1;
@@ -1672 +1679 @@
                 performCriticalExit();
               } else {
-                SaveFlag = false;
                 ofstream output(argv[argptr+1]);
                 ofstream binoutput(argv[argptr+2]);
@@ -1692 +1698 @@
                 counter = 0;
                 for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
-                  Actives[counter] = (*BigFinder)->ActiveFlag;
+                  Actives[counter++] = (*BigFinder)->ActiveFlag;
                   (*BigFinder)->ActiveFlag = (*BigFinder == Boundary) ? false : true;
                 }
@@ -1705 +1711 @@
                 binoutput.close();
                 for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++)
-                  (*BigFinder)->ActiveFlag = Actives[counter];
+                  (*BigFinder)->ActiveFlag = Actives[counter++];
                 Free(&Actives);
                 delete(LCList);
@@ -1728 +1734 @@
             case 'F':
               if (ExitFlag == 0) ExitFlag = 1;
-              if (argptr+5 >=argc) {
+              if (argptr+6 >=argc) {
                 ExitFlag = 255;
-                eLog() << Verbose(0) << "Not enough or invalid arguments given for filling box with water: -F <dist_x> <dist_y> <dist_z> <randatom> <randmol> <DoRotate>" << endl;
+                eLog() << Verbose(0) << "Not enough or invalid arguments given for filling box with water: -F <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>" << endl;
                 performCriticalExit();
               } else {
@@ -1740 +1746 @@
                 atom *second = NULL, *third = NULL;
                 first = new atom();
-                first->type = periode->FindElement(1);
-                first->x.Init(0.441, -0.143, 0.);
+                first->type = periode->FindElement(5);
+                first->x.Zero();
                 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);
+//                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(molecules, filler, configuration, distance, atof(argv[argptr+3]), atof(argv[argptr+4]), atoi(argv[argptr+5]));
+                Filling = FillBoxWithMolecule(molecules, filler, configuration, distance, atof(argv[argptr+3]), atof(argv[argptr+4]), atof(argv[argptr+5]), atoi(argv[argptr+6]));
                 if (Filling != NULL) {
+                  Filling->ActiveFlag = false;
                   molecules->insert(Filling);
                 }