Changeset bae8b0 for src

Timestamp:

Oct 10, 2011, 4:58:24 PM (13 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:

d7d022

Parents:

f08ae7

git-author:

Frederik Heber <heber@…> (09/09/11 12:00:41)

git-committer:

Frederik Heber <heber@…> (10/10/11 16:58:24)

Message:

FIX: some smaller changes to class element.

• removed those nonsense ref getter for symbol and name. Now, getter only return const ref.
• NDIM -> 3 and removed inclusion of defs.hpp.
• int -> size_t as we desire an array size.
• initializing now some forgotten values in default cstor.

Location:

src

Files:

• element.cpp (modified) (6 diffs)
• element.hpp (modified) (3 diffs)
• periodentafel.cpp (modified) (1 diff)

src/element.cpp

@@ -35 +35 @@
   mass(0),
   CovalentRadius(0),
+  Electronegativity(0.),
   VanDerWaalsRadius(0),
-        Z(-1),
+        Z(0),
+        period(""),
+        group(""),
+        block(""),
         Valence(0),
-        NoValenceOrbitals(0)
-{
+        NoValenceOrbitals(0),
+        name(""),
+        symbol("")
+{
+  for (size_t i =0; i<3;++i)
+    color[i] = (unsigned char)0;
+  for (size_t i =0; i<3;++i)
+    HBondDistance[i] = 0.;
+  for (size_t i =0; i<3;++i)
+    HBondAngle[i] = 0.;
 };
 
@@ -45 +57 @@
   mass(src.mass),
   CovalentRadius(src.CovalentRadius),
+  Electronegativity(src.Electronegativity),
   VanDerWaalsRadius(src.VanDerWaalsRadius),
   Z(src.Z),
+  period(src.period),
+  group(src.group),
+  block(src.block),
   Valence(src.Valence),
   NoValenceOrbitals(src.NoValenceOrbitals),
@@ -52 +68 @@
   symbol(src.symbol)
 {
-  period = src.period;
-  group = src.group;
-  block = src.block;
   for (size_t i =0; i<3;++i)
     color[i] = src.color[i];
+  for (size_t i =0; i<3;++i)
+    HBondDistance[i] = src.HBondDistance[i];
+  for (size_t i =0; i<3;++i)
+    HBondAngle[i] = src.HBondAngle[i];
 }
 
@@ -67 +84 @@
     mass=src.mass;
     CovalentRadius=src.CovalentRadius;
+    Electronegativity=src.Electronegativity;
     VanDerWaalsRadius=src.VanDerWaalsRadius;
     Z=src.Z;
-    Valence=src.Valence;
-    NoValenceOrbitals=src.NoValenceOrbitals;
-    name=src.name;
-    symbol=src.symbol;
-    for (size_t i =0; i<3;++i)
-      color[i] = src.color[i];
     period = src.period;
     group = src.group;
     block = src.block;
+    Valence=src.Valence;
+    NoValenceOrbitals=src.NoValenceOrbitals;
+    for (size_t i =0; i<3;++i)
+      color[i] = src.color[i];
+    for (size_t i =0; i<3;++i)
+      HBondDistance[i] = src.HBondDistance[i];
+    for (size_t i =0; i<3;++i)
+      HBondAngle[i] = src.HBondAngle[i];
+    name=src.name;
+    symbol=src.symbol;
   }
   return *this;
@@ -153 +175 @@
 }
 
-double element::getHBondDistance(const int i) const
-{
-  ASSERT((i>=0) && (i<3), "Access to element::HBondDistance out of bounds.");
+double element::getHBondDistance(const size_t i) const
+{
+  ASSERT((i<3), "Access to element::HBondDistance out of bounds.");
   return HBondDistance[i];
 }
 
-double element::getHBondAngle(const int i) const
-{
-  ASSERT((i>=0) && (i<3), "Access to element::HBondAngle out of bounds.");
+double element::getHBondAngle(const size_t i) const
+{
+  ASSERT((i<3), "Access to element::HBondAngle out of bounds.");
   return HBondAngle[i];
-}
-
-string &element::getSymbol(){
-  return symbol;
 }
 
@@ -176 +194 @@
 {
   symbol = temp;
-}
-
-std::string &element::getName(){
-  return name;
 }
 

src/element.hpp

@@ -19 +19 @@
 #include <string>
 
-#include "LinearAlgebra/defs.hpp"
 #include "types.hpp"
+
+#include "boost/serialization/array.hpp"
+#include "boost/serialization/string.hpp"
 
 class periodentafel;
@@ -48 +50 @@
     double getValence() const;
     int getNoValenceOrbitals() const;
-    double getHBondDistance(const int i) const;
-    double getHBondAngle(const int i) const;
+    double getHBondDistance(const size_t i) const;
+    double getHBondAngle(const size_t i) const;
 
-    std::string &getSymbol();
     const std::string &getSymbol() const;
     void setSymbol(const std::string &temp);
 
-    std::string &getName();
     const std::string &getName() const;
     void setName(const std::string &temp);
@@ -74 +74 @@
     double Valence;   //!< number of valence electrons for this element
     int NoValenceOrbitals;  //!< number of valence orbitals, used for determining bond degree in molecule::CreateConnectmatrix()
-    double HBondDistance[NDIM]; //!< distance in Angstrom of this element to hydrogen  (for single, double and triple bonds)
-    double HBondAngle[NDIM];     //!< typical angle for one, two, three bonded hydrogen (in degrees)
+    double HBondDistance[3]; //!< distance in Angstrom of this element to hydrogen  (for single, double and triple bonds)
+    double HBondAngle[3];     //!< typical angle for one, two, three bonded hydrogen (in degrees)
     unsigned char color[3];   //!< typical color for this element (from Jmol)
 

src/periodentafel.cpp

@@ -207 +207 @@
     cin >> tmp->mass;
     DoLog(0) && (Log() << Verbose(0) << "Name [max 64 chars]: " << endl);
-    cin >> tmp->getName();
+    cin >> tmp->name;
     DoLog(0) && (Log() << Verbose(0) << "Short form [max 3 chars]: " << endl);
-    cin >> tmp->getSymbol();
+    cin >> tmp->symbol;
     AddElement(tmp);
     return tmp;