Changes in src/molecule_dynamics.cpp [112b09:a3fded]

File:

• src/molecule_dynamics.cpp (modified) (5 diffs)

src/molecule_dynamics.cpp

@@ -5 +5 @@
  *      Author: heber
  */
-
-#include "Helpers/MemDebug.hpp"
 
 #include "World.hpp"
@@ -18 +16 @@
 #include "parser.hpp"
 #include "Plane.hpp"
+#include "ThermoStatContainer.hpp"
 
 /************************************* Functions for class molecule *********************************/
@@ -643 +642 @@
 
   // calculate scale configuration
-  ScaleTempFactor = configuration.TargetTemp/ActualTemp;
+  ScaleTempFactor = configuration.Thermostats->TargetTemp/ActualTemp;
 
   // differentating between the various thermostats
@@ -651 +650 @@
       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 +683 @@
       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 );