Changeset 6625c3 for src/atom.cpp

Timestamp:

Feb 24, 2011, 5:46:46 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, Candidate_v1.7.0, 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:

056e70

Parents:

54b42e

git-author:

Frederik Heber <heber@…> (02/24/11 11:18:59)

git-committer:

Frederik Heber <heber@…> (02/24/11 17:46:46)

Message:

Removed atom_trajectoryparticle*, replaced by AtomInfo class now having std::vector<> for trajectories.

AtomInfo:

• AtomInfo stores position, velocity, and force in vectors.
• getter and setter implemented for velocity and force.
• all functions from TrajectoryParticle put into AtomInfo.
• Direct access to velocity and force exchanged by getter/setter everywhere.
• FIX: molecule::LinearInterpolationBetweenConfiguration() extends trajectory to MaxSteps+1 (for endstep).

Other changes:

• gsl_rng_gaussian() exchanged by boost::random specific type.

File:

• src/atom.cpp (modified) (8 diffs)

src/atom.cpp

@@ -55 +55 @@
   setPosition(pointer->getPosition()); // copy coordination
   setAtomicVelocity(pointer->getAtomicVelocity()); // copy velocity
-  FixedIon = pointer->FixedIon;
+  setFixedIon(pointer->getFixedIon());
 };
 
@@ -152 +152 @@
     *out << "Ion_Type" << ElementNo << "_" << AtomNo << "\t"  << fixed << setprecision(9) << showpoint;
     *out << at(0) << "\t" << at(1) << "\t" << at(2);
-    *out << "\t" << FixedIon;
+    *out << "\t" << (int)(getFixedIon());
     if (getAtomicVelocity().Norm() > MYEPSILON)
       *out << "\t" << scientific << setprecision(6) << getAtomicVelocity()[0] << "\t" << getAtomicVelocity()[1] << "\t" << getAtomicVelocity()[2] << "\t";
@@ -179 +179 @@
     *out << "Ion_Type" << elementLookup.there.find(elemental)->second << "_" << AtomNo[elemental->getAtomicNumber()] << "\t"  << fixed << setprecision(9) << showpoint;
     *out << at(0) << "\t" << at(1) << "\t" << at(2);
-    *out << "\t" << FixedIon;
+    *out << "\t" << getFixedIon();
     if (getAtomicVelocity().Norm() > MYEPSILON)
       *out << "\t" << scientific << setprecision(6) << getAtomicVelocity()[0] << "\t" << getAtomicVelocity()[1] << "\t" << getAtomicVelocity()[2] << "\t";
@@ -191 +191 @@
 };
 
-/** Output of a single atom as one lin in xyz file.
+/** Output of a single atom as one line in xyz file.
  * \param *out stream to output to
   * \return true - \a *out present, false - \a *out is NULL
@@ -204 +204 @@
 };
 
-/** Output of a single atom as one lin in xyz file.
+/** Output of a single atom as one line in xyz file.
  * \param *out stream to output to
  * \param *ElementNo array with ion type number in the config file this atom's element shall have
@@ -218 +218 @@
     ASSERT(elementLookup.there.find(elemental)!=elementLookup.there.end(),"Type of this atom was not in the formula upon enumeration");
     *out << "Ion_Type" << elementLookup.there.find(elemental)->second << "_" << AtomNo[getType()->getAtomicNumber()] << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << Trajectory.R.at(step)[0] << "\t" << Trajectory.R.at(step)[1] << "\t" << Trajectory.R.at(step)[2];
-    *out << "\t" << FixedIon;
-    if (Trajectory.U.at(step).Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << Trajectory.U.at(step)[0] << "\t" << Trajectory.U.at(step)[1] << "\t" << Trajectory.U.at(step)[2] << "\t";
-    if (Trajectory.F.at(step).Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << Trajectory.F.at(step)[0] << "\t" << Trajectory.F.at(step)[1] << "\t" << Trajectory.F.at(step)[2] << "\t";
+    *out << getPosition(step)[0] << "\t" << getPosition(step)[1] << "\t" << getPosition(step)[2];
+    *out << "\t" << (int)(getFixedIon());
+    if (getAtomicVelocity(step).Norm() > MYEPSILON)
+      *out << "\t" << scientific << setprecision(6) << getAtomicVelocity(step)[0] << "\t" << getAtomicVelocity(step)[1] << "\t" << getAtomicVelocity(step)[2] << "\t";
+    if (getAtomicForce(step).Norm() > MYEPSILON)
+      *out << "\t" << scientific << setprecision(6) << getAtomicForce(step)[0] << "\t" << getAtomicForce(step)[1] << "\t" << getAtomicForce(step)[2] << "\t";
     *out << "\t# Number in molecule " << nr << endl;
     return true;
@@ -239 +239 @@
   if (out != NULL) {
     *out << getType()->getSymbol() << "\t";
-    *out << Trajectory.R.at(step)[0] << "\t";
-    *out << Trajectory.R.at(step)[1] << "\t";
-    *out << Trajectory.R.at(step)[2] << endl;
+    *out << getPosition(step)[0] << "\t";
+    *out << getPosition(step)[1] << "\t";
+    *out << getPosition(step)[2] << endl;
     return true;
   } else
@@ -383 +383 @@
 }
 
-double atom::getMass() const{
-  return getType()->getMass();
-}
-
 int atom::getNr() const{
   return nr;