Changeset 631dcb for src/builder.cpp

Timestamp:

Jul 23, 2009, 11:23:59 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:

71e7c7

Parents:

b38b64 (diff), fcbfc8 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'Thermostat'

Conflicts:

.gitignore
Makefile.am
molecuilder/src/analyzer.cpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/molecules.cpp
molecuilder/src/molecules.hpp

• config::SaveMPQC() has different call parameters
• analyzer and joiner had conflicts due to Chi and ChiPAS values
• molecule::VerletForceIntegration() is slightly different too, but Thermostat supposedly is old version

File:

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

src/builder.cpp

@@ -822 +822 @@
             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-t x1 x2 x3\tTranslate all atoms by this vector (x1,x2,x3)." << endl;
@@ -1065 +1066 @@
               }
               break;
+            case 'L':
+              ExitFlag = 1;
+              SaveFlag = true;
+              cout << Verbose(1) << "Linear interpolation between configuration " << argv[argptr] << " and " << argv[argptr+1] << "." << endl;
+              if (!mol->LinearInterpolationBetweenConfiguration((ofstream *)&cout, atoi(argv[argptr]), atoi(argv[argptr+1]), argv[argptr+2], configuration))
+                cout << Verbose(2) << "Could not store " << argv[argptr+2] << " files." << endl;
+              else
+                cout << Verbose(2) << "Steps created and " << argv[argptr+2] << " files stored." << endl;
+              argptr+=3;
+              break;
             case 'P':
               ExitFlag = 1;
@@ -1073 +1084 @@
                 SaveFlag = true;
                 cout << Verbose(1) << "Parsing forces file and Verlet integrating." << endl;
-                if (!mol->VerletForceIntegration(argv[argptr], configuration.Deltat, configuration.GetIsAngstroem()))
+                if (!mol->VerletForceIntegration((ofstream *)&cout, argv[argptr], configuration))
                   cout << Verbose(2) << "File not found." << endl;
                 else