Changeset 8009ce for src

Timestamp:

Mar 1, 2011, 1:17:09 PM (14 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, 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:

fe6f20

Parents:

20943b

git-author:

Frederik Heber <heber@…> (02/25/11 09:57:50)

git-committer:

Frederik Heber <heber@…> (03/01/11 13:17:09)

Message:

Rewrote OutputTemperature into a functor in Dynamics/

• formerly called molecule::OutputTemperatureFromTrajectories().
• removed shortform of SaveTemperatureAction.

Location:

src

Files:

• Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) (3 diffs)
• Actions/MoleculeAction/SaveTemperatureAction.def (modified) (1 diff)
• AtomSet.hpp (modified) (3 diffs)
• Dynamics/OutputTemperature.hpp (added)
• Makefile.am (modified) (1 diff)
• molecule.cpp (modified) (1 diff)
• molecule.hpp (modified) (1 diff)

src/Actions/MoleculeAction/SaveTemperatureAction.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include "atom.hpp"
+#include "AtomSet.hpp"
 #include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
+#include "Dynamics/OutputTemperature.hpp"
 #include "molecule.hpp"
-#include "CodePatterns/Verbose.hpp"
 #include "World.hpp"
 
@@ -28 +31 @@
 #include <fstream>
 #include <string>
+#include <vector>
 
 using namespace std;
@@ -38 +42 @@
 /** =========== define the function ====================== */
 Action::state_ptr MoleculeSaveTemperatureAction::performCall() {
-  molecule *mol = NULL;
-
   // obtain information
   getParametersfromValueStorage();
 
-  for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
-    mol = iter->second;
-    DoLog(1) && (Log() << Verbose(1) << "Storing temperatures in " << params.temperaturefile << "." << endl);
-    ofstream output;
-    output.open(params.temperaturefile.string().c_str(), ios::trunc);
-    if (output.fail() || !mol->OutputTemperatureFromTrajectories((ofstream * const) &output, 0, mol->MDSteps))
-      DoLog(2) && (Log() << Verbose(2) << "File could not be written." << endl);
-    else
-      DoLog(2) && (Log() << Verbose(2) << "File stored." << endl);
-    output.close();
-  }
+  DoLog(1) && (Log() << Verbose(1) << "Storing temperatures in " << params.temperaturefile << "." << endl);
+  ofstream output;
+  output.open(params.temperaturefile.string().c_str(), ios::trunc);
+  AtomSetMixin<std::vector<atom *> > set(World::getInstance().getSelectedAtoms());
+  const size_t MDSteps = set.getMaxTrajectorySize();
+  OutputTemperature<std::vector<atom *> > writer(set);
+  if (output.fail() || !writer((ofstream * const) &output, 0, MDSteps))
+    DoLog(2) && (Log() << Verbose(2) << "File could not be written." << endl);
+  else
+    DoLog(2) && (Log() << Verbose(2) << "File stored." << endl);
+  output.close();
   return Action::success;
 }

src/Actions/MoleculeAction/SaveTemperatureAction.def

@@ -31 +31 @@
 // finally the information stored in the ActionTrait specialization
 #define DESCRIPTION "save the temperature per time step to file"
-#define SHORTFORM "S"
+#undef SHORTFORM

src/AtomSet.hpp

@@ -72 +72 @@
   Vector totalMomentumAtStep(unsigned int step) const;
 
+  size_t getMaxTrajectorySize() const;
+
 private:
   template<class Function>
@@ -90 +92 @@
     T operator+(AtomInfo *atom){
       return value + (atom->*f)();
+    }
+    T operator=(T _value){
+      value = _value;
+      return value;
+    }
+    T (AtomInfo::*f)() const;
+    T value;
+  };
+
+  template<class T>
+  struct valueMax {
+    valueMax(T (AtomInfo::*_f)() const,T startValue) :
+      f(_f),
+      value(startValue)
+    {}
+    T operator+(AtomInfo *atom){
+      const T temp = (atom->*f)();
+      return value < temp ? temp : value;
     }
     T operator=(T _value){
@@ -157 +177 @@
           class iterator_type,
           class const_iterator_type>
+inline size_t AtomSetMixin<container_type,iterator_type,const_iterator_type>::getMaxTrajectorySize() const
+{
+  return accumulate(this->begin(),this->end(),valueMax<size_t>(&AtomInfo::getTrajectorySize,(size_t)1)).value;
+}
+
+template <class container_type,
+          class iterator_type,
+          class const_iterator_type>
 inline double AtomSetMixin<container_type,iterator_type,const_iterator_type>::totalTemperatureAtStep(unsigned int step) const{
   return accumulate(this->begin(),this->end(),stepValueSum<double>(step,&AtomInfo::getKineticEnergy,0)).value;

src/Makefile.am

@@ -124 +124 @@
 DYNAMICSHEADER = \
         Dynamics/LinearInterpolationBetweenSteps.hpp \
-        Dynamics/MinimiseConstrainedPotential.hpp
+        Dynamics/MinimiseConstrainedPotential.hpp \
+        Dynamics/OutputTemperature.hpp
 
 GRAPHSOURCE = \

src/molecule.cpp

@@ -1076 +1076 @@
 };
 
-/** Stores the temperature evaluated from velocities in molecule::Trajectories.
- * We simply use the formula equivaleting temperature and kinetic energy:
- * \f$k_B T = \sum_i m_i v_i^2\f$
- * \param *output output stream of temperature file
- * \param startstep first MD step in molecule::Trajectories
- * \param endstep last plus one MD step in molecule::Trajectories
- * \return file written (true), failure on writing file (false)
- */
-bool molecule::OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep)
-{
-  double temperature;
-  // test stream
-  if (output == NULL)
-    return false;
-  else
-    *output << "# Step Temperature [K] Temperature [a.u.]" << endl;
-  for (int step=startstep;step < endstep; step++) { // loop over all time steps
-    temperature = atoms.totalTemperatureAtStep(step);
-    *output << step << "\t" << temperature*AtomicEnergyToKelvin << "\t" << temperature << endl;
-  }
-  return true;
-};
 
 void molecule::flipActiveFlag(){

src/molecule.hpp

@@ -237 +237 @@
   bool OutputTrajectoriesXYZ(ofstream * const output);
   bool Checkout(ofstream * const output) const;
-  bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
 
   // Manipulation routines