Changeset 2746be for src

Timestamp:

Feb 9, 2009, 11:17:38 PM (16 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:

b77416

Parents:

5bc4d0

Message:

Basis for MPQC can now be specified via command line switch

• -B is ParseCommandLineOptions added
• configuration::basis added, set to 3-21G in constructor
• used in configuration::SaveMPQC()

Location:

src

Files:

• builder.cpp (modified) (3 diffs)
• config.cpp (modified) (2 diffs)
• moleculelist.cpp (modified) (2 diffs)
• molecules.hpp (modified) (1 diff)

src/builder.cpp

@@ -697 +697 @@
   char filename[MAXSTRINGSIZE];
   ofstream output;
+  string basis("3-21G");
 
   cout << Verbose(0) << "Storing configuration ... " << endl;
@@ -806 +807 @@
             cout << "\t-A <source>\tCreate adjacency list from bonds parsed from 'dbond'-style file." <<endl;
             cout << "\t-b x1 x2 x3\tCenter atoms in domain with given edge lengths of (x1,x2,x3)." << endl;
+            cout << "\t-B <basis>\tgive gaussian basis for MPQC output." << 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 <bond distance>\tDepth-First-Search Analysis of the molecule, giving cycles and tree/back edges." << endl;
@@ -961 +963 @@
         if (config_present == present) {
           switch(argv[argptr-1][1]) {
+            case 'B':
+              if ((argptr >= argc) || (!IsValidNumber(argv[argptr])) || (argv[argptr][0] == '-')) {
+                ExitFlag = 255;
+                cerr << "Not enough or invalid arguments given for giving gaussian basis: -B <basis>" << endl;
+              } else {
+                cout << Verbose(1) << "Setting gaussian basis to " << argv[argptr] << "." << endl;
+                configuration.basis.copy(argv[argptr],strlen(argv[argptr]));
+                argptr+=1;
+              }
+              break;
             case 'D':
               ExitFlag = 1;

src/config.cpp

@@ -23 +23 @@
   configpath[0]='\0';
   configname[0]='\0';
+  basis="3-21G";
   
   FastParsing = false;
@@ -1131 +1132 @@
   *output << ")" << endl;
   *output << "basis<GaussianBasisSet>: (" << endl;
-  *output << "\tname = \"3-21G\"" << endl;
+  *output << "\tname = \"" << basis << "\"" << endl;
   *output << "\tmolecule = $:molecule" << endl;
   *output << ")" << endl;

src/moleculelist.cpp

@@ -393 +393 @@
   int FragmentCounter = 0;
   ofstream output;
+  string basis("3-21G");
   
   // store the fragments as config and as xyz
@@ -404 +405 @@
 
     // correct periodic
-    ListOfMolecules[i]->ScanForPeriodicCorrection(out);
+    //ListOfMolecules[i]->ScanForPeriodicCorrection(out);
 
     // output xyz file

src/molecules.hpp

@@ -387 +387 @@
     bool FastParsing;
     double Deltat;
+    string basis;
 
     private: