Changes in src/World.cpp [387b36:84c494]

File:

• src/World.cpp (modified) (12 diffs)

src/World.cpp

@@ -6 +6 @@
  */
 
+#include "Helpers/MemDebug.hpp"
+
 #include "World.hpp"
 
@@ -12 +14 @@
 #include "molecule.hpp"
 #include "periodentafel.hpp"
+#include "ThermoStatContainer.hpp"
 #include "Descriptors/AtomDescriptor.hpp"
 #include "Descriptors/AtomDescriptor_impl.hpp"
@@ -18 +21 @@
 #include "Descriptors/SelectiveIterator_impl.hpp"
 #include "Actions/ManipulateAtomsProcess.hpp"
+#include "Helpers/Assert.hpp"
+#include "Box.hpp"
+#include "Matrix.hpp"
 
 #include "Patterns/Singleton_impl.hpp"
@@ -70 +76 @@
 // system
 
-double * World::getDomain() {
-  return cell_size;
+Box& World::getDomain() {
+  return *cell_size;
+}
+
+void World::setDomain(const Matrix &mat){
+  *cell_size = mat;
 }
 
 void World::setDomain(double * matrix)
 {
-
+  Matrix M = ReturnFullMatrixforSymmetric(matrix);
+  cell_size->setM(M);
 }
 
@@ -87 +98 @@
   defaultName = name;
 };
+
+class ThermoStatContainer * World::getThermostats()
+{
+  return Thermostats;
+}
+
 
 int World::getExitFlag() {
@@ -103 +120 @@
   molecule *mol = NULL;
   mol = NewMolecule();
-  assert(!molecules.count(currMoleculeId));
+  ASSERT(!molecules.count(currMoleculeId),"currMoleculeId did not specify an unused ID");
   mol->setId(currMoleculeId++);
   // store the molecule by ID
@@ -119 +136 @@
   OBSERVE;
   molecule *mol = molecules[id];
-  assert(mol);
+  ASSERT(mol,"Molecule id that was meant to be destroyed did not exist");
   DeleteMolecule(mol);
   molecules.erase(id);
 }
-
-double *World::cell_size = NULL;
 
 atom *World::createAtom(){
@@ -155 +170 @@
   OBSERVE;
   atom *atom = atoms[id];
-  assert(atom);
+  ASSERT(atom,"Atom ID that was meant to be destroyed did not exist");
   DeleteAtom(atom);
   atoms.erase(id);
@@ -167 +182 @@
   if(!target){
     target = atoms[oldId];
-    assert(target && "Atom with that ID not found");
+    ASSERT(target,"Atom with that ID not found");
     return target->changeId(newId);
   }
@@ -276 +291 @@
 
 World::World() :
+    Observable("World"),
     periode(new periodentafel),
     configuration(new config),
+    Thermostats(new ThermoStatContainer),
     ExitFlag(0),
     atoms(),
@@ -285 +302 @@
     molecules_deprecated(new MoleculeListClass(this))
 {
-  cell_size = new double[6];
-  cell_size[0] = 20.;
-  cell_size[1] = 0.;
-  cell_size[2] = 20.;
-  cell_size[3] = 0.;
-  cell_size[4] = 0.;
-  cell_size[5] = 20.;
+  cell_size = new Box;
+  Matrix domain;
+  domain.at(0,0) = 20;
+  domain.at(1,1) = 20;
+  domain.at(2,2) = 20;
+  cell_size->setM(domain);
   defaultName = "none";
   molecules_deprecated->signOn(this);
@@ -299 +315 @@
 {
   molecules_deprecated->signOff(this);
-  delete[] cell_size;
+  delete cell_size;
   delete molecules_deprecated;
   delete periode;
   delete configuration;
+  delete Thermostats;
   MoleculeSet::iterator molIter;
   for(molIter=molecules.begin();molIter!=molecules.end();++molIter){