Changeset cee0b57 for src/molecule.hpp

Timestamp:

Oct 5, 2009, 10:10:53 PM (15 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:

ebcade

Parents:

d09ff7

Message:

class molecule implementation split up into six separate parts.

• dynamics: Verlet integration and constraint potential
• fragmentation: BOSSANOVA scheme
• geometry: all operations acting on the Vector's inside the atom's
• graph: supplementary functions for fragmentation, treating molecule as a bonding graph
• pointcloud: implementations of virtual functions for pointcloud class, needed for Tesselation

File:

• src/molecule.hpp (modified) (7 diffs)

src/molecule.hpp

@@ -1 @@
-/** \file molecules.hpp
+/** \file molecule.hpp
  *
  * Class definitions of atom and molecule, element and periodentafel
@@ -133 +133 @@
 
   // templates for allowing global manipulation of all vectors
+  template <typename res> void ActOnAllVectors( res (Vector::*f)() );
   template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t );
   template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u );
   template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v);
+
+  // templates for allowing global manipulation of all atoms
+  template <typename res> void ActOnAllAtoms( res (molecule::*f)(atom *) );
+  template <typename res> void ActOnAllAtoms( res (atom::*f)() );
+  template <typename res, typename T> void ActOnAllAtoms( res (atom::*f)(T), T t );
+  template <typename res, typename T, typename U> void ActOnAllAtoms( res (atom::*f)(T, U), T t, U u );
+  template <typename res, typename T, typename U, typename V> void ActOnAllAtoms( res (atom::*f)(T, U, V), T t, U u, V v);
 
   /// remove atoms from molecule.
@@ -147 +155 @@
   bool AddXYZFile(string filename);
   bool AddHydrogenReplacementAtom(ofstream *out, bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bond **BondList, int NumBond, bool IsAngstroem);
-  bond * AddBond(atom *first, atom *second, int degree);
+  bond * AddBond(atom *first, atom *second, int degree = 1);
   bool RemoveBond(bond *pointer);
   bool RemoveBonds(atom *BondPartner);
@@ -255 +263 @@
 
 
+template <typename res> void molecule::ActOnAllVectors( res (Vector::*f)() ) {
+  atom *Walker = start;
+  while (Walker->next != end) {
+    Walker = Walker->next;
+    ((Walker->node)->*f)();
+  }
+};
 template <typename res, typename T> void molecule::ActOnAllVectors( res (Vector::*f)(T), T t )
 {
@@ -260 +275 @@
   while (Walker->next != end) {
     Walker = Walker->next;
-    ((*Walker->node)->*f)(t);
-  }
-};
-
+    ((Walker->node)->*f)(t);
+  }
+};
 template <typename res, typename T, typename U> void molecule::ActOnAllVectors( res (Vector::*f)(T, U), T t, U u )
 {
@@ -269 +283 @@
   while (Walker->next != end) {
     Walker = Walker->next;
-    ((*Walker->node)->*f)(t, u);
-  }
-};
-
+    ((Walker->node)->*f)(t, u);
+  }
+};
 template <typename res, typename T, typename U, typename V> void molecule::ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v)
 {
@@ -278 +291 @@
   while (Walker->next != end) {
     Walker = Walker->next;
-    ((*Walker->node)->*f)(t, u, v);
+    ((Walker->node)->*f)(t, u, v);
+  }
+};
+
+template <typename res> void molecule::ActOnAllAtoms( res (molecule::*f)(atom *)) {
+  atom *Walker = start;
+  while (Walker->next != end) {
+    Walker = Walker->next;
+    (*f)(Walker);
+  }
+};
+
+template <typename res> void molecule::ActOnAllAtoms( res (atom::*f)()) {
+  atom *Walker = start;
+  while (Walker->next != end) {
+    Walker = Walker->next;
+    (Walker->*f)();
+  }
+};
+template <typename res, typename T> void molecule::ActOnAllAtoms( res (atom::*f)(T), T t )
+{
+  atom *Walker = start;
+  while (Walker->next != end) {
+    Walker = Walker->next;
+    (Walker->*f)(t);
+  }
+};
+template <typename res, typename T, typename U> void molecule::ActOnAllAtoms( res (atom::*f)(T, U), T t, U u )
+{
+  atom *Walker = start;
+  while (Walker->next != end) {
+    Walker = Walker->next;
+    (Walker->*f)(t, u);
+  }
+};
+template <typename res, typename T, typename U, typename V> void molecule::ActOnAllAtoms( res (atom::*f)(T, U, V), T t, U u, V v)
+{
+  atom *Walker = start;
+  while (Walker->next != end) {
+    Walker = Walker->next;
+    (Walker->*f)(t, u, v);
   }
 };