Changeset 43dad6 for src/config.cpp

Timestamp:

Jun 12, 2010, 3:54:26 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, Candidate_v1.7.0, 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:

1b2d30

Parents:

a3fded

Message:

Introducing (but not yet incorporated) FormatParser specializations for MPQC and PCP config files.

• new modules MpqcParser.[ch]pp and PcpParser.[ch]pp.
• class MpqcParser:
  • just a skeleton so far
• class PcpParser:
  • load and save basically adapted from config::Load and config::Save.
  • new functions OutputAtoms() and OutputElements() from molecule::Output() and molecule::CheckOut().
  • ne function ParseThermostats() - as the parsing is specific to the format it should be handled by the FormatParser, not bz ThermoStatContainer.
  • most of the variables from config placed into struct to put them into groups (for later splitting up load&save into subfunctions).
• new overload ConfigFileBuffer::InitFileBuffer() accepting streams (FormatParser works on streams, config still with filenames).
• World: new member Thermostats which contains all thermostat parameters with getter function.
• ThermoStatContainer::ParseThermostats() moved over to PcpParser and re-introduced in config.
• atom::OutputArrayIndexed() now works on ostream, not ofstream.
• molecule::Output() adapted to ostream change.

File:

• src/config.cpp (modified) (2 diffs)

src/config.cpp

@@ -614 +614 @@
   
   //TODO: This is actually sensible?: if (MaxOuterStep > 0)
-  Thermostats->ParseThermostats(FileBuffer);
+  ParseThermostats(FileBuffer);
   
   /* Namen einlesen */
@@ -2077 +2077 @@
   return (found); // true if found, false if not
 }
+
+/** Reading of Thermostat related values from parameter file.
+ * \param *fb file buffer containing the config file
+ */
+void config::ParseThermostats(class ConfigFileBuffer * const fb)
+{
+  char * const thermo = new char[12];
+  const int verbose = 0;
+
+  // 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;
+    }
+  } 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;
+  }
+  delete[](thermo);
+};
+