Changeset d40189 for src/Actions

Timestamp:

Apr 23, 2021, 8:31:23 PM (5 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, Candidate_v1.7.1, stable

Children:

61cc0f

Parents:

cbbb6a

git-author:

Frederik Heber <frederik.heber@…> (04/28/19 22:01:20)

git-committer:

Frederik Heber <frederik.heber@…> (04/23/21 20:31:23)

Message:

OutputTemperature -> OutputEnergies, SaveTemperature -> SaveEnergies.

• added force and momentum calculation.
• TESTS: adapted test.ekin test file and integration/MolecularDynamics tests.
• DOCU: Adapted userguide for changed action.

Location:

src/Actions

Files:

• GlobalListOfActions.hpp (modified) (1 diff)
• Makefile.am (modified) (3 diffs)
• MoleculeAction/SaveEnergiesAction.cpp (moved) (moved from src/Actions/MoleculeAction/SaveTemperatureAction.cpp ) (6 diffs)
• MoleculeAction/SaveEnergiesAction.def (moved) (moved from src/Actions/MoleculeAction/SaveTemperatureAction.def ) (3 diffs)
• MoleculeAction/SaveEnergiesAction.hpp (moved) (moved from src/Actions/MoleculeAction/SaveTemperatureAction.hpp ) (2 diffs)

src/Actions/GlobalListOfActions.hpp

@@ -96 +96 @@
   (MoleculeSaveBonds) \
   (MoleculeSaveSelectedMolecules) \
-  (MoleculeSaveTemperature) \
+  (MoleculeSaveEnergies) \
   (MoleculeStretchBond) \
   (MoleculeTranslate) \

src/Actions/Makefile.am

@@ -351 +351 @@
   Actions/MoleculeAction/SaveAdjacencyAction.cpp \
   Actions/MoleculeAction/SaveBondsAction.cpp \
-  Actions/MoleculeAction/SaveTemperatureAction.cpp \
+  Actions/MoleculeAction/SaveEnergiesAction.cpp \
   Actions/MoleculeAction/StretchBondAction.cpp \
   Actions/MoleculeAction/TranslateAction.cpp \
@@ -370 +370 @@
   Actions/MoleculeAction/SaveAdjacencyAction.hpp \
   Actions/MoleculeAction/SaveBondsAction.hpp \
-  Actions/MoleculeAction/SaveTemperatureAction.hpp \
+  Actions/MoleculeAction/SaveEnergiesAction.hpp \
   Actions/MoleculeAction/StretchBondAction.hpp \
   Actions/MoleculeAction/TranslateAction.hpp \
@@ -389 +389 @@
   Actions/MoleculeAction/SaveAdjacencyAction.def \
   Actions/MoleculeAction/SaveBondsAction.def \
-  Actions/MoleculeAction/SaveTemperatureAction.def \
+  Actions/MoleculeAction/SaveEnergiesAction.def \
   Actions/MoleculeAction/StretchBondAction.def \
   Actions/MoleculeAction/TranslateAction.def \

src/Actions/MoleculeAction/SaveEnergiesAction.cpp

@@ -3 +3 @@
  * Description: creates and alters molecular systems
  * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
+ * Copyright (C) 2019  Frederik Heber
  * 
  *
@@ -22 +23 @@
 
 /*
- * SaveTemperatureAction.cpp
+ * SaveEnergiesAction.cpp
  *
  *  Created on: May 10, 2010
@@ -39 +40 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
-#include "Dynamics/OutputTemperature.hpp"
+#include "Dynamics/OutputEnergies.hpp"
 #include "molecule.hpp"
 #include "World.hpp"
@@ -48 +49 @@
 #include <vector>
 
-#include "Actions/MoleculeAction/SaveTemperatureAction.hpp"
+#include "Actions/MoleculeAction/SaveEnergiesAction.hpp"
 
 using namespace MoleCuilder;
 
 // and construct the stuff
-#include "SaveTemperatureAction.def"
+#include "SaveEnergiesAction.def"
 #include "Action_impl_pre.hpp"
 /** =========== define the function ====================== */
-ActionState::ptr MoleculeSaveTemperatureAction::performCall() {
-  LOG(1, "Storing temperatures in " << params.temperaturefile.get() << ".");
+ActionState::ptr MoleculeSaveEnergiesAction::performCall() {
+  LOG(1, "Storing temperatures in " << params.energiesfile.get() << ".");
   ofstream output;
-  output.open(params.temperaturefile.get().string().c_str(), ios::trunc);
+  output.open(params.energiesfile.get().string().c_str(), ios::trunc);
   AtomSetMixin<std::vector<const atom *> > set =
       const_cast<const World &>(World::getInstance()).getSelectedAtoms();
   const size_t MDSteps = set.getMaxTrajectorySize();
-  OutputTemperature<std::vector<const atom *> > writer(set);
+  OutputEnergies<std::vector<const atom *> > writer(set);
   if (output.fail() || !writer((ofstream * const) &output, 0, MDSteps)) {
     STATUS("File could not be written.");
@@ -73 +74 @@
 }
 
-ActionState::ptr MoleculeSaveTemperatureAction::performUndo(ActionState::ptr _state) {
-//  MoleculeSaveTemperatureState *state = assert_cast<MoleculeSaveTemperatureState*>(_state.get());
+ActionState::ptr MoleculeSaveEnergiesAction::performUndo(ActionState::ptr _state) {
+//  MoleculeSaveEnergiesState *state = assert_cast<MoleculeSaveEnergiesState*>(_state.get());
 
 //  string newName = state->mol->getName();
@@ -82 +83 @@
 }
 
-ActionState::ptr MoleculeSaveTemperatureAction::performRedo(ActionState::ptr _state){
+ActionState::ptr MoleculeSaveEnergiesAction::performRedo(ActionState::ptr _state){
   // Undo and redo have to do the same for this action
   return performUndo(_state);
 }
 
-bool MoleculeSaveTemperatureAction::canUndo() {
+bool MoleculeSaveEnergiesAction::canUndo() {
   return false;
 }
 
-bool MoleculeSaveTemperatureAction::shouldUndo() {
+bool MoleculeSaveEnergiesAction::shouldUndo() {
   return false;
 }

src/Actions/MoleculeAction/SaveEnergiesAction.def

@@ -1 +1 @@
 /*
- * SaveTemperatureAction.def
+ * SaveEnergiesAction.def
  *
  *  Created on: Aug 26, 2010
@@ -14 +14 @@
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
 #define paramtypes (boost::filesystem::path)
-#define paramtokens ("save-temperature")
-#define paramdescriptions ("name of the temperature file to write to")
+#define paramtokens ("save-energies")
+#define paramdescriptions ("name of the energies file to write to")
 #undef paramdefaults
-#define paramreferences (temperaturefile)
+#define paramreferences (energiesfile)
 #define paramvalids \
 (!FilePresentValidator())
@@ -28 +28 @@
 #define MENUNAME "molecule"
 #define MENUPOSITION 12
-#define ACTIONNAME SaveTemperature
-#define TOKEN "save-temperature"
+#define ACTIONNAME SaveEnergies
+#define TOKEN "save-energies"
 
 
 // finally the information stored in the ActionTrait specialization
-#define DESCRIPTION "save the temperature per time step to file"
+#define DESCRIPTION "save several energies (kinetic, momentum, mean force) per time step to file"
 #undef SHORTFORM

src/Actions/MoleculeAction/SaveEnergiesAction.hpp

@@ -1 +1 @@
 /*
- * SaveTemperatureAction.hpp
+ * SaveEnergiesAction.hpp
  *
  *  Created on: May 10, 2010
@@ -17 +17 @@
 #include "Actions/Action.hpp"
 
-#include "SaveTemperatureAction.def"
+#include "SaveEnergiesAction.def"
 #include "Action_impl_header.hpp"