Changes in src/config.cpp [1b2d30:274d45]

File:

• src/config.cpp (modified) (18 diffs)

src/config.cpp

@@ -5 +5 @@
  */
 
+#include "Helpers/MemDebug.hpp"
+
 #include <stdio.h>
 #include <cstring>
 
+#include "World.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
-#include "bondgraph.hpp"
 #include "config.hpp"
-#include "ConfigFileBuffer.hpp"
 #include "element.hpp"
 #include "helpers.hpp"
@@ -22 +23 @@
 #include "molecule.hpp"
 #include "periodentafel.hpp"
-#include "ThermoStatContainer.hpp"
 #include "World.hpp"
 
+/******************************** Functions for class ConfigFileBuffer **********************/
+
+/** Structure containing compare function for Ion_Type sorting.
+ */
+struct IonTypeCompare {
+  bool operator()(const char* s1, const char *s2) const {
+    char number1[8];
+    char number2[8];
+    const char *dummy1, *dummy2;
+    //Log() << Verbose(0) << s1 << "  " << s2 << endl;
+    dummy1 = strchr(s1, '_')+sizeof(char)*5;  // go just after "Ion_Type"
+    dummy2 = strchr(dummy1, '_');
+    strncpy(number1, dummy1, dummy2-dummy1); // copy the number
+    number1[dummy2-dummy1]='\0';
+    dummy1 = strchr(s2, '_')+sizeof(char)*5;  // go just after "Ion_Type"
+    dummy2 = strchr(dummy1, '_');
+    strncpy(number2, dummy1, dummy2-dummy1); // copy the number
+    number2[dummy2-dummy1]='\0';
+    if (atoi(number1) != atoi(number2))
+      return (atoi(number1) < atoi(number2));
+    else {
+      dummy1 = strchr(s1, '_')+sizeof(char);
+      dummy1 = strchr(dummy1, '_')+sizeof(char);
+      dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
+      strncpy(number1, dummy1, dummy2-dummy1); // copy the number
+      number1[dummy2-dummy1]='\0';
+      dummy1 = strchr(s2, '_')+sizeof(char);
+      dummy1 = strchr(dummy1, '_')+sizeof(char);
+      dummy2 = strchr(dummy1, ' ') < strchr(dummy1, '\t') ? strchr(dummy1, ' ') : strchr(dummy1, '\t');
+      strncpy(number2, dummy1, dummy2-dummy1); // copy the number
+      number2[dummy2-dummy1]='\0';
+      return (atoi(number1) < atoi(number2));
+    }
+  }
+};
+
+/** Constructor for ConfigFileBuffer class.
+ */
+ConfigFileBuffer::ConfigFileBuffer() : buffer(NULL), LineMapping(NULL), CurrentLine(0), NoLines(0)
+{
+};
+
+/** Constructor for ConfigFileBuffer class with filename to be parsed.
+ * \param *filename file name
+ */
+ConfigFileBuffer::ConfigFileBuffer(const char * const filename) : buffer(NULL), LineMapping(NULL), CurrentLine(0), NoLines(0)
+{
+  ifstream *file = NULL;
+  char line[MAXSTRINGSIZE];
+
+  // prescan number of lines
+  file= new ifstream(filename);
+  if (file == NULL) {
+    DoeLog(1) && (eLog()<< Verbose(1) << "config file " << filename << " missing!" << endl);
+    return;
+  }
+  NoLines = 0; // we're overcounting by one
+  long file_position = file->tellg(); // mark current position
+  do {
+    file->getline(line, 256);
+    NoLines++;
+  } while (!file->eof());
+  file->clear();
+  file->seekg(file_position, ios::beg);
+  DoLog(1) && (Log() << Verbose(1) << NoLines-1 << " lines were recognized." << endl);
+
+  // allocate buffer's 1st dimension
+  if (buffer != NULL) {
+    DoeLog(1) && (eLog()<< Verbose(1) << "FileBuffer->buffer is not NULL!" << endl);
+    return;
+  } else
+    buffer = new char *[NoLines];
+
+  // scan each line and put into buffer
+  int lines=0;
+  int i;
+  do {
+    buffer[lines] = new char[MAXSTRINGSIZE];
+    file->getline(buffer[lines], MAXSTRINGSIZE-1);
+    i = strlen(buffer[lines]);
+    buffer[lines][i] = '\n';
+    buffer[lines][i+1] = '\0';
+    lines++;
+  } while((!file->eof()) && (lines < NoLines));
+  DoLog(1) && (Log() << Verbose(1) << lines-1 << " lines were read into the buffer." << endl);
+
+  // close and exit
+  file->close();
+  file->clear();
+  delete(file);
+}
+
+/** Destructor for ConfigFileBuffer class.
+ */
+ConfigFileBuffer::~ConfigFileBuffer()
+{
+  for(int i=0;i<NoLines;++i)
+    delete[](buffer[i]);
+  delete[](buffer);
+  delete[](LineMapping);
+}
+
+
+/** Create trivial mapping.
+ */
+void ConfigFileBuffer::InitMapping()
+{
+  LineMapping = new int[NoLines];
+  for (int i=0;i<NoLines;i++)
+    LineMapping[i] = i;
+}
+
+/** Creates a mapping for the \a *FileBuffer's lines containing the Ion_Type keyword such that they are sorted.
+ * \a *map on return contains a list of NoAtom entries such that going through the list, yields indices to the
+ * lines in \a *FileBuffer in a sorted manner of the Ion_Type?_? keywords. We assume that ConfigFileBuffer::CurrentLine
+ * points to first Ion_Type entry.
+ * \param *FileBuffer pointer to buffer structure
+ * \param NoAtoms of subsequent lines to look at
+ */
+void ConfigFileBuffer::MapIonTypesInBuffer(const int NoAtoms)
+{
+  map<const char *, int, IonTypeCompare> IonTypeLineMap;
+  if (LineMapping == NULL) {
+    DoeLog(0) && (eLog()<< Verbose(0) << "map pointer is NULL: " << LineMapping << endl);
+    performCriticalExit();
+    return;
+  }
+
+  // put all into hashed map
+  for (int i=0; i<NoAtoms; ++i) {
+    IonTypeLineMap.insert(pair<const char *, int> (buffer[CurrentLine+i], CurrentLine+i));
+  }
+
+  // fill map
+  int nr=0;
+  for (map<const char *, int, IonTypeCompare>::iterator runner = IonTypeLineMap.begin(); runner != IonTypeLineMap.end(); ++runner) {
+    if (CurrentLine+nr < NoLines)
+      LineMapping[CurrentLine+(nr++)] = runner->second;
+    else {
+      DoeLog(0) && (eLog()<< Verbose(0) << "config::MapIonTypesInBuffer - NoAtoms is wrong: We are past the end of the file!" << endl);
+      performCriticalExit();
+    }
+  }
+}
+
 /************************************* Functions for class config ***************************/
 
 /** Constructor for config file class.
  */
-config::config() : BG(NULL), Thermostats(0), PsiType(0), MaxPsiDouble(0), PsiMaxNoUp(0), PsiMaxNoDown(0), MaxMinStopStep(1), InitMaxMinStopStep(1), ProcPEGamma(8), ProcPEPsi(1), configpath(NULL),
-    configname(NULL), FastParsing(false), Deltat(0.01), basis(""), databasepath(NULL), DoConstrainedMD(0), MaxOuterStep(0), mainname(NULL), defaultpath(NULL), pseudopotpath(NULL),
+config::config() : BG(NULL), PsiType(0), MaxPsiDouble(0), PsiMaxNoUp(0), PsiMaxNoDown(0), MaxMinStopStep(1), InitMaxMinStopStep(1), ProcPEGamma(8), ProcPEPsi(1), configpath(NULL),
+    configname(NULL), FastParsing(false), Deltat(0.01), basis(""), databasepath(NULL), DoConstrainedMD(0), MaxOuterStep(0), Thermostat(4), ThermostatImplemented(NULL),
+    ThermostatNames(NULL), TempFrequency(2.5), alpha(0.), HooverMass(0.), TargetTemp(0.00095004455), ScaleTempStep(25),  mainname(NULL), defaultpath(NULL), pseudopotpath(NULL),
     DoOutVis(0), DoOutMes(1), DoOutNICS(0), DoOutOrbitals(0), DoOutCurrent(0), DoFullCurrent(0), DoPerturbation(0), DoWannier(0), CommonWannier(0), SawtoothStart(0.01),
     VectorPlane(0), VectorCut(0.), UseAddGramSch(1), Seed(1), OutVisStep(10), OutSrcStep(5), MaxPsiStep(0), EpsWannier(1e-7), MaxMinStep(100), RelEpsTotalEnergy(1e-7),
@@ -42 +188 @@
   configpath = new char[MAXSTRINGSIZE];
   configname = new char[MAXSTRINGSIZE];
-  Thermostats = new ThermoStatContainer();
   strcpy(mainname,"pcp");
   strcpy(defaultpath,"not specified");
@@ -49 +194 @@
   configname[0]='\0';
   basis = "3-21G";
+
+  InitThermostats();
 };
 
@@ -61 +208 @@
   delete[](configpath);
   delete[](configname);
-  if (Thermostats != NULL)
-    delete(Thermostats);
+  delete[](ThermostatImplemented);
+  for (int j=0;j<MaxThermostats;j++)
+    delete[](ThermostatNames[j]);
+  delete[](ThermostatNames);
 
   if (BG != NULL)
     delete(BG);
 };
+
+/** Initialises variables in class config for Thermostats.
+ */
+void config::InitThermostats()
+{
+  ThermostatImplemented = new int[MaxThermostats];
+  ThermostatNames = new char *[MaxThermostats];
+  for (int j=0;j<MaxThermostats;j++)
+    ThermostatNames[j] = new char[12];
+
+  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;
+};
+
+/** Readin 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, ThermostatNames[0]) == 0) { // None
+      if (ThermostatImplemented[0] == 1) {
+        Thermostat = None;
+      } else {
+        DoLog(1) && (Log() << 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,fb,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read scaling frequency
+      } else {
+        DoLog(1) && (Log() << 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,fb,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read collision rate
+      } else {
+        DoLog(1) && (Log() << 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,fb,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read gamma
+        if (ParseForParameter(verbose,fb,"Thermostat", 0, 3, 1, double_type, &alpha, 1, optional)) {
+          DoLog(2) && (Log() << Verbose(2) << "Extended Stochastic Thermostat detected with interpolation coefficient " << alpha << "." << endl);
+        } else {
+          alpha = 1.;
+        }
+      } else {
+        DoLog(1) && (Log() << 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,fb,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read \tau_T
+      } else {
+        DoLog(1) && (Log() << 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,fb,"Thermostat", 0, 2, 1, double_type, &HooverMass, 1, critical); // read Hoovermass
+        alpha = 0.;
+      } else {
+        DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
+        Thermostat = None;
+      }
+    } else {
+      DoLog(1) && (Log() << Verbose(1) << " Warning: thermostat name was not understood!" << endl);
+      Thermostat = None;
+    }
+  } else {
+    if ((MaxOuterStep > 0) && (TargetTemp != 0)) 
+      DoLog(2) && (Log() << Verbose(2) <<  "No thermostat chosen despite finite temperature MD, falling back to None." << endl);
+    Thermostat = None;
+  }
+  delete[](thermo);
+};
+
 
 /** Displays menu for editing each entry of the config file.
@@ -408 +656 @@
 };
 
+/** Initializes ConfigFileBuffer from a file.
+ * \param *file input file stream being the opened config file
+ * \param *FileBuffer pointer to FileBuffer on return, should point to NULL
+ */
+void PrepareFileBuffer(const char * const filename, struct ConfigFileBuffer *&FileBuffer)
+{
+  if (FileBuffer != NULL) {
+    DoeLog(2) && (eLog()<< Verbose(2) << "deleting present FileBuffer in PrepareFileBuffer()." << endl);
+    delete(FileBuffer);
+  }
+  FileBuffer = new ConfigFileBuffer(filename);
+
+  FileBuffer->InitMapping();
+};
+
 /** Loads a molecule from a ConfigFileBuffer.
  * \param *mol molecule to load
@@ -604 +867 @@
 
   // ParseParameterFile
-  class ConfigFileBuffer *FileBuffer = new ConfigFileBuffer(filename);
+  struct ConfigFileBuffer *FileBuffer = NULL;
+  PrepareFileBuffer(filename,FileBuffer);
 
   /* Oeffne Hauptparameterdatei */
@@ -613 +877 @@
   int verbose = 0;
   
-  //TODO: This is actually sensible?: if (MaxOuterStep > 0)
   ParseThermostats(FileBuffer);
   
@@ -678 +941 @@
   ParseForParameter(verbose,FileBuffer,"OutVisStep", 0, 1, 1, int_type, &(config::OutVisStep), 1, optional);
   ParseForParameter(verbose,FileBuffer,"OutSrcStep", 0, 1, 1, int_type, &(config::OutSrcStep), 1, optional);
-  ParseForParameter(verbose,FileBuffer,"TargetTemp", 0, 1, 1, double_type, &(Thermostats->TargetTemp), 1, optional);
+  ParseForParameter(verbose,FileBuffer,"TargetTemp", 0, 1, 1, double_type, &(config::TargetTemp), 1, optional);
   //ParseForParameter(verbose,FileBuffer,"Thermostat", 0, 1, 1, int_type, &(config::ScaleTempStep), 1, optional);
   if (!ParseForParameter(verbose,FileBuffer,"EpsWannier", 0, 1, 1, double_type, &(config::EpsWannier), 1, optional))
@@ -887 +1150 @@
   ParseForParameter(verbose,file,"VisOuterStep", 0, 1, 1, int_type, &(config::OutVisStep), 1, optional);
   ParseForParameter(verbose,file,"VisSrcOuterStep", 0, 1, 1, int_type, &(config::OutSrcStep), 1, optional);
-  ParseForParameter(verbose,file,"TargetTemp", 0, 1, 1, double_type, &(Thermostats->TargetTemp), 1, optional);
-  ParseForParameter(verbose,file,"ScaleTempStep", 0, 1, 1, int_type, &(Thermostats->ScaleTempStep), 1, optional);
+  ParseForParameter(verbose,file,"TargetTemp", 0, 1, 1, double_type, &(config::TargetTemp), 1, optional);
+  ParseForParameter(verbose,file,"ScaleTempStep", 0, 1, 1, int_type, &(config::ScaleTempStep), 1, optional);
   config::EpsWannier = 1e-8;
 
@@ -1076 +1339 @@
     *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" << Thermostats->ThermostatNames[Thermostats->Thermostat] << "\t";
-    switch(Thermostats->Thermostat) {
+    *output << "Thermostat\t" << ThermostatNames[Thermostat] << "\t";
+    switch(Thermostat) {
       default:
       case None:
         break;
       case Woodcock:
-        *output << Thermostats->ScaleTempStep;
+        *output << ScaleTempStep;
         break;
       case Gaussian:
-        *output << Thermostats->ScaleTempStep;
+        *output << ScaleTempStep;
         break;
       case Langevin:
-        *output << Thermostats->TempFrequency << "\t" << Thermostats->alpha;
+        *output << TempFrequency << "\t" << alpha;
         break;
       case Berendsen:
-        *output << Thermostats->TempFrequency;
+        *output << TempFrequency;
         break;
       case NoseHoover:
-        *output << Thermostats->HooverMass;
+        *output << HooverMass;
         break;
     };
@@ -1109 +1372 @@
     *output << "OutVisStep\t" << config::OutVisStep << "\t# Output visual data every ...th step" << endl;
     *output << "OutSrcStep\t" << config::OutSrcStep << "\t# Output \"restart\" data every ..th step" << endl;
-    *output << "TargetTemp\t" << Thermostats->TargetTemp << "\t# Target temperature" << endl;
+    *output << "TargetTemp\t" << config::TargetTemp << "\t# Target temperature" << endl;
     *output << "MaxPsiStep\t" << config::MaxPsiStep << "\t# number of Minimisation steps per state (0 - default)" << endl;
     *output << "EpsWannier\t" << config::EpsWannier << "\t# tolerance value for spread minimisation of orbitals" << endl;
@@ -1220 +1483 @@
     // output of atoms
     AtomNo = 0;
-    mol->ActOnAllAtoms( &atom::OutputMPQCLine, (ostream * const) output, (const Vector *)center, &AtomNo );
+    mol->ActOnAllAtoms( &atom::OutputMPQCLine, output, (const Vector *)center, &AtomNo );
     delete(center);
     *output << "\t}" << endl;
@@ -1262 +1525 @@
     // output of atoms
     AtomNo = 0;
-    mol->ActOnAllAtoms( &atom::OutputMPQCLine, (ostream * const) output, (const Vector *)center, &AtomNo );
+    mol->ActOnAllAtoms( &atom::OutputMPQCLine, output, (const Vector *)center, &AtomNo );
     delete(center);
     *output << "\t}" << endl;
@@ -1521 +1784 @@
   char filename[MAXSTRINGSIZE];
   ofstream output;
-  molecule *mol = World::getInstance().createMolecule();
-  mol->SetNameFromFilename(ConfigFileName);
+  molecule *mol = NULL;
 
   if (!strcmp(configpath, GetDefaultPath())) {
@@ -1553 +1815 @@
   // translate each to its center and merge all molecules in MoleculeListClass into this molecule
   int N = molecules->ListOfMolecules.size();
-  int *src = new int[N];
-  N=0;
-  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
-    src[N++] = (*ListRunner)->IndexNr;
-    (*ListRunner)->Translate(&(*ListRunner)->Center);
-  }
-  molecules->SimpleMultiAdd(mol, src, N);
-  delete[](src);
-
-  // ... and translate back
-  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
-    (*ListRunner)->Center.Scale(-1.);
-    (*ListRunner)->Translate(&(*ListRunner)->Center);
-    (*ListRunner)->Center.Scale(-1.);
+  if (N != 1) { // don't do anything in case of only one molecule (shifts mol ids otherwise)
+    int *src = new int[N];
+    N=0;
+    for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
+      src[N++] = (*ListRunner)->IndexNr;
+      (*ListRunner)->Translate(&(*ListRunner)->Center);
+    }
+    mol = World::getInstance().createMolecule();
+    mol->SetNameFromFilename(ConfigFileName);
+    molecules->SimpleMultiMerge(mol, src, N);
+    mol->doCountAtoms();
+    mol->CountElements();
+    mol->CalculateOrbitals(*this);
+    delete[](src);
+  } else {
+    if (!molecules->ListOfMolecules.empty()) {
+      mol = *(molecules->ListOfMolecules.begin());
+      mol->doCountAtoms();
+      mol->CalculateOrbitals(*this);
+    } else {
+      DoeLog(1) && (eLog() << Verbose(1) << "There are no molecules to save!" << endl);
+    }
   }
 
   Log() << Verbose(0) << "Storing configuration ... " << endl;
   // get correct valence orbitals
-  mol->CalculateOrbitals(*this);
-  InitMaxMinStopStep = MaxMinStopStep = MaxPsiDouble;
   if (ConfigFileName != NULL) { // test the file name
     strcpy(filename, ConfigFileName);
@@ -1632 +1900 @@
   }
 
-  World::getInstance().destroyMolecule(mol);
+  // don't destroy molecule as it contains all our atoms
+  //World::getInstance().destroyMolecule(mol);
 };
 
@@ -2077 +2346 @@
   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);
-};
-