Changeset a9099d for src/Actions/PotentialAction

Timestamp:

May 7, 2016, 7:05:19 AM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, 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_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:

9ff818

Parents:

666e9e

git-author:

Frederik Heber <heber@…> (03/03/16 10:25:34)

git-committer:

Frederik Heber <heber@…> (05/07/16 07:05:19)

Message:

FitPartialChargesAction enforces net charge neutrality on default now.

• also particle prints charge with higher precision.
• this is required if we use charge as implicit charge for long-range calculations where a neutral charge in the order of 1e-10 is desired.

Location:

src/Actions/PotentialAction

Files:

• FitPartialChargesAction.cpp (modified) (2 diffs)
• FitPartialChargesAction.def (modified) (1 diff)

src/Actions/PotentialAction/FitPartialChargesAction.cpp

@@ -44 +44 @@
 #include "World.hpp"
 
+#include <boost/bind.hpp>
 #include <boost/filesystem.hpp>
 #include <boost/foreach.hpp>
@@ -184 +185 @@
   );
 
+  // make sum of charges zero if desired
+  if (params.enforceZeroCharge.get()) {
+    double charge_sum = 0.;
+    charge_sum = std::accumulate(averaged_charges.begin(), averaged_charges.end(), charge_sum);
+    if (fabs(charge_sum) > MYEPSILON) {
+      std::transform(
+          averaged_charges.begin(), averaged_charges.end(),
+          averaged_charges.begin(),
+          boost::bind(std::minus<double>(), _1, charge_sum/averaged_charges.size()));
+    }
+    charge_sum = 0.;
+    charge_sum = std::accumulate(averaged_charges.begin(), averaged_charges.end(), charge_sum);
+    ASSERT( fabs(charge_sum) < MYEPSILON,
+        "PotentialFitPartialChargesAction::performCall() - enforcing neutral net charge failed, "
+        +toString(charge_sum)+" is the remaining net charge.");
+  }
+
   // place all fitted charges into ParticleRegistry
   const ParticleFactory &factory =

src/Actions/PotentialAction/FitPartialChargesAction.def

@@ -19 +19 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (std::vector<const element *>)(double)
-#define paramtokens ("fragment-charges")("radius")
-#define paramdescriptions ("charges specifying the fragment")("radius of sphere around nuclei where potential does not need to match")
-#define paramdefaults (NOPARAM_DEFAULT)(PARAM_DEFAULT(0))
-#define paramreferences (fragment)(radius)
+#define paramtypes (std::vector<const element *>)(double)(bool)
+#define paramtokens ("fragment-charges")("radius")("enforce-net-zero-charge")
+#define paramdescriptions ("charges specifying the fragment")("radius of sphere around nuclei where potential does not need to match")("whether to make the sum of fitted charged become zero")
+#define paramdefaults (NOPARAM_DEFAULT)(PARAM_DEFAULT(0))(PARAM_DEFAULT(1))
+#define paramreferences (fragment)(radius)(enforceZeroCharge)
 #define paramvalids \
 (STLVectorValidator< std::vector<const element *> >(1,99, ElementValidator())) \
-(NonNegativeValidator<double>())
+(NonNegativeValidator<double>()) \
+(DummyValidator<bool>())
 
 #undef statetypes