Changeset 48ab70a

Timestamp:

Jun 8, 2010, 12:13:11 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:

e4b5de

Parents:

f2a1d3

Message:

Case 'u' is now handled by CommandLineUI.

Location:

src

Files:

• Actions/MapOfActions.cpp (modified) (3 diffs)
• builder.cpp (modified) (1 diff)

src/Actions/MapOfActions.cpp

@@ -159 +159 @@
   ShortFormMap["set-basis"] = "M";
   ShortFormMap["subspace-dissect"] = "I";
-  ShortFormMap["suspend-in-water"] = "U";
+  ShortFormMap["suspend-in-water"] = "u";
   ShortFormMap["translate-mol"] = "t";
   ShortFormMap["verbose"] = "v";
@@ -198 +198 @@
   TypeMap["set-basis"] = String;
   TypeMap["start-mol"] = Molecule;
-  TypeMap["suspend-in-water"] = Molecule;
+  TypeMap["suspend-in-water"] = Double;
   TypeMap["translate-mol"] = Vector;
   TypeMap["verlet-integrate"] = String;
@@ -261 +261 @@
 //  generic.insert("set-basis");
 //      generic.insert("subspace-dissect");
-//  generic.insert("suspend-in-water");
+  generic.insert("suspend-in-water");
 //  generic.insert("translate-mol");
         generic.insert("verbose");

src/builder.cpp

@@ -2312 +2312 @@
                   performCriticalExit();
               } else {
-                double density;
-                SaveFlag = true;
-                DoLog(0) && (Log() << Verbose(0) << "Evaluating necessary cell volume for a cluster suspended in water.");
-                density = atof(argv[argptr++]);
-                if (density < 1.0) {
-                  DoeLog(1) && (eLog()<< Verbose(1) << "Density must be greater than 1.0g/cm^3 !" << endl);
-                  density = 1.3;
-                }
-//                for(int i=0;i<NDIM;i++) {
-//                  repetition[i] = atoi(argv[argptr++]);
-//                  if (repetition[i] < 1)
-//                    DoeLog(1) && (eLog()<< Verbose(1) << "repetition value must be greater 1!" << endl);
-//                  repetition[i] = 1;
-//                }
-                PrepareClustersinWater(&configuration, mol, volume, density);  // if volume == 0, will calculate from ConvexEnvelope
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                argptr+=1;
               }
               break;