Changeset c3a303 for molecuilder/src/config.cpp

Timestamp:

Jul 24, 2009, 10:38:32 AM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

53d153

Parents:

a048fa (diff), 47548d (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.

git-author:

Frederik Heber <heber@…> (07/23/09 14:23:32)

git-committer:

Frederik Heber <heber@…> (07/24/09 10:38:32)

Message:

Merge branch 'master' into ConcaveHull

Conflicts:

molecuilder/src/analyzer.cpp
molecuilder/src/bond.cpp
molecuilder/src/boundary.cpp
molecuilder/src/boundary.hpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/datacreator.cpp
molecuilder/src/datacreator.hpp
molecuilder/src/defs.hpp
molecuilder/src/ellipsoid.cpp
molecuilder/src/joiner.cpp
molecuilder/src/molecules.cpp
molecuilder/src/molecules.hpp
molecuilder/src/parser.cpp
molecuilder/src/parser.hpp

merges:

• analyzer.cpp: all from master, due to Hessian; only Chi(PAS)Fragments from HEAD
• bond.cpp: bond::GetOtherAtom gives cerr output if neither atom matches from master
• boundary.cpp: all from HEAD, is tesselation stuff
• boundary.hpp: all from HEAD, is tesselation stuff
• builder.cpp: Center...(), RemoveAtoms(), SaveConfig() from master, is MultipleMolecules, rest from HEAD (Translation and ...)
• config.cpp: FileBuffer stuff from HEAD, only some taken over from HEAD
• datacreator.cpp: all from master, is Hessian
• datacreator.hpp: all from master, is Hessian
• defs.hpp: all from master, is Thermostat
• ellipsoid.cpp: all from HEAD, created during tesselation
• joiner.cpp: all from master, is Hessian
• molecules.cpp: molecule::molecule(), ConstrainedPotential() stuff, Thermostats(), RemoveAtom(),CreateAdjacencyList(), FragmentMolecule() from master, CenterInBox(), CenterEdge(), CenterOrigin(), CenterPeriodic() (instead of CenterAtVector()), TranslatePeriodically(), DeterminePeriodicCenter(), Output...(), ReturnFullForSymmnetricMatrix() from HEAD
• molecules.hpp: see above, ConfigfileBuffer struct from HEAD, class config joined
• parser.cpp: all from master, is Hessian
• parser.hpp: all from master, is Hessian

compilation fixes:

• molecules.cpp: PrincipalAxisSystem() - CenterGravity() -> CenterOrigin(), DetermineCenter() -> DeterminePeriodicCenter
• datacreator.cpp: all char * to const char *
• builder.cpp: ParseCommandLineOptions() - case 'c': had argptr++ and argptr+=3; case 'O' - x was not zero'd

File:

• molecuilder/src/config.cpp (modified) (10 diffs)

molecuilder/src/config.cpp

@@ -169 +169 @@
   configpath = (char *) MallocString(sizeof(char)*MAXSTRINGSIZE,"config constructor: configpath");
   configname = (char *) MallocString(sizeof(char)*MAXSTRINGSIZE,"config constructor: configname");
+  ThermostatImplemented = (int *) Malloc((MaxThermostats)*(sizeof(int)), "config constructor: *ThermostatImplemented");
+  ThermostatNames = (char **) Malloc((MaxThermostats)*(sizeof(char *)), "config constructor: *ThermostatNames");
+  for (int j=0;j<MaxThermostats;j++)
+    ThermostatNames[j] = (char *) MallocString(12*(sizeof(char)), "config constructor: ThermostatNames[]");
+  Thermostat = 4;
+  alpha = 0.;
+  ScaleTempStep = 25;
+  TempFrequency = 2.5;
   strcpy(mainname,"pcp");
   strcpy(defaultpath,"not specified");
@@ -175 +183 @@
   configname[0]='\0';
   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;
@@ -187 +208 @@
   DoFullCurrent=0;
   DoWannier=0;
+  DoConstrainedMD=0;
   CommonWannier=0;
   SawtoothStart=0.01;
@@ -195 +217 @@
 
   MaxOuterStep=0;
-  Deltat=1;
+  Deltat=0.01;
   OutVisStep=10;
   OutSrcStep=5;
@@ -247 +269 @@
   Free((void **)&configpath, "config::~config: *configpath");
   Free((void **)&configname, "config::~config: *configname");
+  Free((void **)&ThermostatImplemented, "config::~config: *ThermostatImplemented");
+  for (int j=0;j<MaxThermostats;j++)
+    Free((void **)&ThermostatNames[j], "config::~config: *ThermostatNames[]");
+  Free((void **)&ThermostatNames, "config::~config: **ThermostatNames");
 };
+
+/** 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.
@@ -597 +699 @@
 void config::Load(char *filename, periodentafel *periode, molecule *mol)
 {
+  ifstream *file = new ifstream(filename);
+  if (file == NULL) {
+    cerr << "ERROR: config file " << filename << " missing!" << endl;
+    return;
+  }
   RetrieveConfigPathAndName(filename);
 
@@ -614 +721 @@
   int verbose = 0;
   double value[3];
-
+  
+  InitThermostats(file);
+  
   /* Namen einlesen */
 
@@ -667 +776 @@
     if (config::SawtoothStart > 1.) config::SawtoothStart = 1.;
   }
-
+  
+  if (ParseForParameter(verbose,FileBuffer,"DoConstrainedMD", 0, 1, 1, int_type, &(config::DoConstrainedMD), 1, optional))
+    if (config::DoConstrainedMD < 0) 
+      config::DoConstrainedMD = 0;
   ParseForParameter(verbose,FileBuffer,"MaxOuterStep", 0, 1, 1, int_type, &(config::MaxOuterStep), 1, critical);
   if (!ParseForParameter(verbose,FileBuffer,"Deltat", 0, 1, 1, double_type, &(config::Deltat), 1, optional))
@@ -1168 +1280 @@
     *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;
@@ -1305 +1440 @@
   *output << ")" << endl;
   *output << "basis<GaussianBasisSet>: (" << endl;
-  *output << "\tname = \""<< basis << "\"" << endl;
+  *output << "\tname = \"" << basis << "\"" << endl;
   *output << "\tmolecule = $:molecule" << endl;
   *output << ")" << endl;