Changeset 62f793 for src/config.cpp

Timestamp:

Sep 25, 2008, 5:57:19 PM (17 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, Candidate_v1.7.1, 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:

aa5702

Parents:

16a52b

Message:

thermostats enumerator, necessary variables included in class config, molecule::Thermostats() and ..::Constrained
Potential()

Thermostat header definitions implemented. Can be parsed from the ESPACK config file into class config
ConstrainedPotential() calculates the transformation between two given configurations my minimsing a penalty func
tional of the distance to travel per atom. This was implemented due to Michael Griebel's talk during the MultiMat

Closing meeting in order to produce some visuals. It basically mimics a "Bain Transformation". But it is not yet
perfectly implemented.

Also, MD was corrected in VerletIntegration(). However, forces are still wrong with mpqc, as the kinetic energy increases dramatically during the MD simulation.

File:

• src/config.cpp (modified) (5 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");
@@ -23 +31 @@
   configpath[0]='\0';
   configname[0]='\0';
-  
+
+  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;
@@ -96 +117 @@
   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 +562 @@
   double value[3];
   
+  InitThermostats(file);
+  
   /* Namen einlesen */
 
@@ -1001 +1100 @@
     *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;