Changeset 86381b for src

Timestamp:

Aug 17, 2009, 10:29:03 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:

16d866

Parents:

7e19c35

Message:

Sorted the menu list in ParseCommandLineParamaters() and print volume instead of surface for case 'o'

File:

• src/builder.cpp (modified) (3 diffs)

src/builder.cpp

@@ -1350 +1350 @@
             cout << "\t-B xx xy xz yy yz zz\tBound atoms by domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl;
             cout << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl;
+            cout << "\t-d x1 x2 x3\tDuplicate cell along each axis by given factor." << endl;
             cout << "\t-D <bond distance>\tDepth-First-Search Analysis of the molecule, giving cycles and tree/back edges." << endl;
-            cout << "\t-O\tCenter atoms in origin." << endl;
-            cout << "\t-d x1 x2 x3\tDuplicate cell along each axis by given factor." << endl;
             cout << "\t-e <file>\tSets the databases path to be parsed (default: ./)." << endl;
             cout << "\t-E <id> <Z>\tChange atom <id>'s element to <Z>, <id> begins at 0." << endl;
             cout << "\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;
             cout << "\t-h/-H/-?\tGive this help screen." << endl;
+            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-m <0/1>\tCalculate (0)/ Align in(1) PAS with greatest EV along z axis." << endl;
             cout << "\t-M <basis>\tSetting basis to store to MPQC config files." << endl;
@@ -1362 +1362 @@
             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-O\tCenter atoms in origin." << endl;
             cout << "\t-p <file>\tParse given xyz file and create raw config file from it." << endl;
             cout << "\t-P <file>\tParse given forces file and append as an MD step to config file via Verlet." << endl;
-            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-s x1 x2 x3\tScale all atom coordinates by this vector (x1,x2,x3)." << endl;
+            cout << "\t-S <file> Store temperatures from the config file in <file>." << endl;
             cout << "\t-t x1 x2 x3\tTranslate all atoms by this vector (x1,x2,x3)." << endl;
             cout << "\t-T x1 x2 x3\tTranslate periodically all atoms by this vector (x1,x2,x3)." << endl;
-            cout << "\t-S <file> Store temperatures from the config file in <file>." << endl;
-            cout << "\t-s x1 x2 x3\tScale all atom coordinates by this vector (x1,x2,x3)." << endl;
             cout << "\t-u rho\tsuspend in water solution and output necessary cell lengths, average density rho and repetition." << endl;
             cout << "\t-v/-V\t\tGives version information." << endl;
@@ -1874 +1874 @@
                 Find_non_convex_border((ofstream *)&cout, mol, &LCList, argv[argptr], 10.);
 
-                double volumedifference = ConvexizeNonconvexEnvelope((ofstream *)&cout, mol->TesselStruct);
+                double volumedifference = ConvexizeNonconvexEnvelope((ofstream *)&cout, mol->TesselStruct, mol, argv[argptr]);
                 double clustervolume = VolumeOfConvexEnvelope((ofstream *)&cout, mol->TesselStruct, &configuration);
-                cout << Verbose(0) << "The tesselated surface area is " << clustervolume << " " << (configuration.GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3." << endl;
-                cout << Verbose(0) << "The non-convex tesselated surface area is " << clustervolume-volumedifference << " " << (configuration.GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3." << endl;
+                cout << Verbose(0) << "The tesselated volume area is " << clustervolume << " " << (configuration.GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3." << endl;
+                cout << Verbose(0) << "The non-convex tesselated volume area is " << clustervolume-volumedifference << " " << (configuration.GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3." << endl;
                 argptr+=1;
               }