Changes in src/molecule_dynamics.cpp [112b09:35b698]

File:

• src/molecule_dynamics.cpp (modified) (6 diffs)

src/molecule_dynamics.cpp

@@ -18 +18 @@
 #include "parser.hpp"
 #include "Plane.hpp"
+#include "ThermoStatContainer.hpp"
 
 /************************************* Functions for class molecule *********************************/
@@ -472 +473 @@
  * \param startstep stating initial configuration in molecule::Trajectories
  * \param endstep stating final configuration in molecule::Trajectories
+ * \param &prefix path and prefix
  * \param &config configuration structure
  * \param MapByIdentity if true we just use the identity to map atoms in start config to end config, if not we find mapping by \sa MinimiseConstrainedPotential()
  * \return true - success in writing step files, false - error writing files or only one step in molecule::Trajectories
  */
-bool molecule::LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity)
+bool molecule::LinearInterpolationBetweenConfiguration(int startstep, int endstep, std::string &prefix, config &configuration, bool MapByIdentity)
 {
   molecule *mol = NULL;
@@ -524 +526 @@
   for (int i=getAtomCount(); i--; )
     SortIndex[i] = i;
-  status = MoleculePerStep->OutputConfigForListOfFragments(&configuration, SortIndex);
+
+  status = MoleculePerStep->OutputConfigForListOfFragments(prefix, SortIndex);
   delete[](SortIndex);
 
@@ -643 +646 @@
 
   // calculate scale configuration
-  ScaleTempFactor = configuration.TargetTemp/ActualTemp;
+  ScaleTempFactor = configuration.Thermostats->TargetTemp/ActualTemp;
 
   // differentating between the various thermostats
@@ -651 +654 @@
       break;
      case Woodcock:
-      if ((configuration.ScaleTempStep > 0) && ((MDSteps-1) % configuration.ScaleTempStep == 0)) {
+      if ((configuration.Thermostats->ScaleTempStep > 0) && ((MDSteps-1) % configuration.Thermostats->ScaleTempStep == 0)) {
         DoLog(2) && (Log() << Verbose(2) <<  "Applying Woodcock thermostat..." << endl);
         ActOnAllAtoms( &atom::Thermostat_Woodcock, sqrt(ScaleTempFactor), MDSteps, &ekin );
@@ -684 +687 @@
       delta_alpha = 0.;
       ActOnAllAtoms( &atom::Thermostat_NoseHoover_init, MDSteps, &delta_alpha );
-      delta_alpha = (delta_alpha - (3.*getAtomCount()+1.) * configuration.TargetTemp)/(configuration.HooverMass*Units2Electronmass);
-      configuration.alpha += delta_alpha*configuration.Deltat;
-      DoLog(3) && (Log() << Verbose(3) << "alpha = " << delta_alpha << " * " << configuration.Deltat << " = " << configuration.alpha << "." << endl);
+      delta_alpha = (delta_alpha - (3.*getAtomCount()+1.) * configuration.Thermostats->TargetTemp)/(configuration.Thermostats->HooverMass*Units2Electronmass);
+      configuration.Thermostats->alpha += delta_alpha*configuration.Deltat;
+      DoLog(3) && (Log() << Verbose(3) << "alpha = " << delta_alpha << " * " << configuration.Deltat << " = " << configuration.Thermostats->alpha << "." << endl);
       // apply updated alpha as additional force
       ActOnAllAtoms( &atom::Thermostat_NoseHoover_scale, MDSteps, &ekin, &configuration );