Changeset 14c57a for src/Parser

Timestamp:

Aug 25, 2010, 12:04:11 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

51c3e4

Parents:

8d1dd4

Message:

Made all parts of the programm use the new thermostat structure

File:

• src/Parser/PcpParser.cpp (modified) (2 diffs)

src/Parser/PcpParser.cpp

@@ -402 +402 @@
     *file << "DoConstrainedMD\t" << Switches.DoConstrainedMD << "\t# Do perform a constrained (>0, relating to current MD step) instead of unconstrained (0) MD" << endl;
     ASSERT(Thermostats != NULL, "PcpParser::save() - Thermostats not initialized!");
-    ASSERT(Thermostats->ThermostatNames != NULL, "PcpParser::save() - Thermostats not initialized!");
-    *file << "Thermostat\t" << Thermostats->ThermostatNames[Thermostats->Thermostat] << "\t";
-    switch(Thermostats->Thermostat) {
-      default:
-      case None:
-        break;
-      case Woodcock:
-        *file << Thermostats->ScaleTempStep;
-        break;
-      case Gaussian:
-        *file << Thermostats->ScaleTempStep;
-        break;
-      case Langevin:
-        *file << Thermostats->TempFrequency << "\t" << Thermostats->alpha;
-        break;
-      case Berendsen:
-        *file << Thermostats->TempFrequency;
-        break;
-      case NoseHoover:
-        *file << Thermostats->HooverMass;
-        break;
-    };
+    *file << "Thermostat\t" << Thermostats->activeThermostat->name() << "\t";
+    *file << Thermostats->activeThermostat->writeParams();
     *file << "\t# Which Thermostat and its parameters to use in MD case." << endl;
     *file << "CommonWannier\t" << LocalizedOrbitals.CommonWannier << "\t# Put virtual centers at indivual orbits, all common, merged by variance, to grid point, to cell center" << endl;
@@ -588 +568 @@
   // read desired Thermostat from file along with needed additional parameters
   if (ParseForParameter(verbose,fb,"Thermostat", 0, 1, 1, string_type, thermo, 1, optional)) {
-    if (strcmp(thermo, Thermostats->ThermostatNames[0]) == 0) { // None
-      if (Thermostats->ThermostatImplemented[0] == 1) {
-        Thermostats->Thermostat = None;
-      } else {
-        DoLog(1) && (Log() << Verbose(1) << "Warning: " << Thermostats->ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
-        Thermostats->Thermostat = None;
-      }
-    } else if (strcmp(thermo, Thermostats->ThermostatNames[1]) == 0) { // Woodcock
-      if (Thermostats->ThermostatImplemented[1] == 1) {
-        Thermostats->Thermostat = Woodcock;
-        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &Thermostats->ScaleTempStep, 1, critical); // read scaling frequency
-      } else {
-        DoLog(1) && (Log() << Verbose(1) << "Warning: " << Thermostats->ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
-        Thermostats->Thermostat = None;
-      }
-    } else if (strcmp(thermo, Thermostats->ThermostatNames[2]) == 0) { // Gaussian
-      if (Thermostats->ThermostatImplemented[2] == 1) {
-        Thermostats->Thermostat = Gaussian;
-        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &Thermostats->ScaleTempStep, 1, critical); // read collision rate
-      } else {
-        DoLog(1) && (Log() << Verbose(1) << "Warning: " << Thermostats->ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
-        Thermostats->Thermostat = None;
-      }
-    } else if (strcmp(thermo, Thermostats->ThermostatNames[3]) == 0) { // Langevin
-      if (Thermostats->ThermostatImplemented[3] == 1) {
-        Thermostats->Thermostat = Langevin;
-        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &Thermostats->TempFrequency, 1, critical); // read gamma
-        if (ParseForParameter(verbose,fb,"Thermostat", 0, 3, 1, double_type, &Thermostats->alpha, 1, optional)) {
-          DoLog(2) && (Log() << Verbose(2) << "Extended Stochastic Thermostat detected with interpolation coefficient " << Thermostats->alpha << "." << endl);
-        } else {
-          Thermostats->alpha = 1.;
-        }
-      } else {
-        DoLog(1) && (Log() << Verbose(1) << "Warning: " << Thermostats->ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
-        Thermostats->Thermostat = None;
-      }
-    } else if (strcmp(thermo, Thermostats->ThermostatNames[4]) == 0) { // Berendsen
-      if (Thermostats->ThermostatImplemented[4] == 1) {
-        Thermostats->Thermostat = Berendsen;
-        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &Thermostats->TempFrequency, 1, critical); // read \tau_T
-      } else {
-        DoLog(1) && (Log() << Verbose(1) << "Warning: " << Thermostats->ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
-        Thermostats->Thermostat = None;
-      }
-    } else if (strcmp(thermo, Thermostats->ThermostatNames[5]) == 0) { // Nose-Hoover
-      if (Thermostats->ThermostatImplemented[5] == 1) {
-        Thermostats->Thermostat = NoseHoover;
-        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &Thermostats->HooverMass, 1, critical); // read Hoovermass
-        Thermostats->alpha = 0.;
-      } else {
-        DoLog(1) && (Log() << Verbose(1) << "Warning: " << Thermostats->ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
-        Thermostats->Thermostat = None;
-      }
-    } else {
-      DoLog(1) && (Log() << Verbose(1) << " Warning: thermostat name was not understood!" << endl);
-      Thermostats->Thermostat = None;
-    }
+    Thermostats->makeActive(thermo,fb);
   } else {
     if ((Thermostats->TargetTemp != 0))
       DoLog(2) && (Log() << Verbose(2) <<  "No thermostat chosen despite finite temperature MD, falling back to None." << endl);
-    Thermostats->Thermostat = None;
+    Thermostats->chooseNone();
   }
   delete[](thermo);