Changeset 631dcb for src/config.cpp

Timestamp:

Jul 23, 2009, 11:23:59 AM (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:

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/config.cpp (modified) (8 diffs)

src/config.cpp

@@ -18 +18 @@
   configpath = (char *) MallocString(sizeof(char)*MAXSTRINGSIZE,"config constructor: mainname");
   configname = (char *) MallocString(sizeof(char)*MAXSTRINGSIZE,"config constructor: mainname");
+  ThermostatImplemented = (int *) Malloc((MaxThermostats)*(sizeof(int)), "IonsInitRead: *ThermostatImplemented");
+  ThermostatNames = (char **) Malloc((MaxThermostats)*(sizeof(char *)), "IonsInitRead: *ThermostatNames");
+  for (int j=0;j<MaxThermostats;j++)
+    ThermostatNames[j] = (char *) MallocString(12*(sizeof(char)), "IonsInitRead: ThermostatNames[]");
+  Thermostat = 4;
+  alpha = 0.;
+  ScaleTempStep = 25;
+  TempFrequency = 2.5;
   strcpy(mainname,"pcp");
   strcpy(defaultpath,"not specified");
@@ -25 +33 @@
   basis="3-21G";
   
+
+  strcpy(ThermostatNames[0],"None");
+  ThermostatImplemented[0] = 1;
+  strcpy(ThermostatNames[1],"Woodcock"); 
+  ThermostatImplemented[1] = 1;
+  strcpy(ThermostatNames[2],"Gaussian"); 
+  ThermostatImplemented[2] = 1;
+  strcpy(ThermostatNames[3],"Langevin"); 
+  ThermostatImplemented[3] = 1;
+  strcpy(ThermostatNames[4],"Berendsen"); 
+  ThermostatImplemented[4] = 1;
+  strcpy(ThermostatNames[5],"NoseHoover"); 
+  ThermostatImplemented[5] = 1;
+
   FastParsing = false;
   ProcPEGamma=8;
@@ -36 +58 @@
   DoFullCurrent=0;
   DoWannier=0;
+  DoConstrainedMD=0;
   CommonWannier=0;
   SawtoothStart=0.01;
@@ -42 +65 @@
   UseAddGramSch=1;
   Seed=1;
-  
   MaxOuterStep=0;
-  Deltat=1;
+  Deltat=0.01;
   OutVisStep=10;
   OutSrcStep=5;
@@ -96 +118 @@
   Free((void **)&configname, "config::~config: *configname");
 };
+
+/** Readin of Thermostat related values from parameter file.
+ * \param *source parameter file
+ */
+void config::InitThermostats(ifstream *source)
+{
+  char *thermo = MallocString(12, "IonsInitRead: thermo");
+  int verbose = 0;
+
+  // read desired Thermostat from file along with needed additional parameters
+  if (ParseForParameter(verbose,source,"Thermostat", 0, 1, 1, string_type, thermo, 1, optional)) {
+    if (strcmp(thermo, ThermostatNames[0]) == 0) { // None
+      if (ThermostatImplemented[0] == 1) {
+        Thermostat = None;
+      } else {
+        cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
+        Thermostat = None;
+      }
+    } else if (strcmp(thermo, ThermostatNames[1]) == 0) { // Woodcock
+      if (ThermostatImplemented[1] == 1) {
+        Thermostat = Woodcock;
+        ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read scaling frequency
+      } else {
+        cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
+        Thermostat = None;
+      }
+    } else if (strcmp(thermo, ThermostatNames[2]) == 0) { // Gaussian
+      if (ThermostatImplemented[2] == 1) {
+        Thermostat = Gaussian;
+        ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read collision rate
+      } else {
+        cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
+        Thermostat = None;
+      }
+    } else if (strcmp(thermo, ThermostatNames[3]) == 0) { // Langevin
+      if (ThermostatImplemented[3] == 1) {
+        Thermostat = Langevin;
+        ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read gamma
+        if (ParseForParameter(verbose,source,"Thermostat", 0, 3, 1, double_type, &alpha, 1, optional)) {
+          cout << Verbose(2) << "Extended Stochastic Thermostat detected with interpolation coefficient " << alpha << "." << endl;
+        } else {
+          alpha = 1.;
+        }
+      } else {
+        cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
+        Thermostat = None;
+      }
+    } else if (strcmp(thermo, ThermostatNames[4]) == 0) { // Berendsen
+      if (ThermostatImplemented[4] == 1) {
+        Thermostat = Berendsen;
+        ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read \tau_T
+      } else {
+        cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
+        Thermostat = None;
+      }
+    } else if (strcmp(thermo, ThermostatNames[5]) == 0) { // Nose-Hoover
+      if (ThermostatImplemented[5] == 1) {
+        Thermostat = NoseHoover;
+        ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, double_type, &HooverMass, 1, critical); // read Hoovermass
+        alpha = 0.;
+      } else {
+        cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
+        Thermostat = None;
+      }
+    } else {
+      cout << Verbose(1) << " Warning: thermostat name was not understood!" << endl;
+      Thermostat = None;
+    }
+  } else {
+    if ((MaxOuterStep > 0) && (TargetTemp != 0)) 
+      cout << Verbose(2) <<  "No thermostat chosen despite finite temperature MD, falling back to None." << endl;
+    Thermostat = None;
+  }
+  Free((void **)&thermo, "InitThermostats: thermo");
+};
+
 
 /** Displays menu for editing each entry of the config file.
@@ -465 +563 @@
   double value[3];
   
+  InitThermostats(file);
+  
   /* Namen einlesen */
 
@@ -518 +618 @@
   }
   
+  if (ParseForParameter(verbose,file,"DoConstrainedMD", 0, 1, 1, int_type, &(config::DoConstrainedMD), 1, optional))
+    if (config::DoConstrainedMD < 0) 
+      config::DoConstrainedMD = 0;
   ParseForParameter(verbose,file,"MaxOuterStep", 0, 1, 1, int_type, &(config::MaxOuterStep), 1, critical);
   if (!ParseForParameter(verbose,file,"Deltat", 0, 1, 1, double_type, &(config::Deltat), 1, optional))
@@ -999 +1102 @@
     *output << "DoPerturbation\t" << config::DoPerturbation << "\t# Do perturbation calculate and determine susceptibility and shielding" << endl;
     *output << "DoFullCurrent\t" << config::DoFullCurrent << "\t# Do full perturbation" << endl;
+    *output << "DoConstrainedMD\t" << config::DoConstrainedMD << "\t# Do perform a constrained (>0, relating to current MD step) instead of unconstrained (0) MD" << endl;
+    *output << "Thermostat\t" << ThermostatNames[Thermostat] << "\t";
+    switch(Thermostat) {
+      default:
+      case None:
+        break;
+      case Woodcock:
+        *output << ScaleTempStep;
+        break;
+      case Gaussian:
+        *output << ScaleTempStep;
+        break;
+      case Langevin:
+        *output << TempFrequency << "\t" << alpha;
+        break;
+      case Berendsen:
+        *output << TempFrequency;
+        break;
+      case NoseHoover:
+        *output << HooverMass;
+        break;
+    };
+    *output << "\t# Which Thermostat and its parameters to use in MD case." << endl;
     *output << "CommonWannier\t" << config::CommonWannier << "\t# Put virtual centers at indivual orbits, all common, merged by variance, to grid point, to cell center" << endl;
     *output << "SawtoothStart\t" << config::SawtoothStart << "\t# Absolute value for smooth transition at cell border " << endl;