Changeset 708ec1

Timestamp:

May 7, 2016, 7:03:56 AM (9 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_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:

276e2f

Parents:

2082637

git-author:

Frederik Heber <heber@…> (02/29/16 17:15:34)

git-committer:

Frederik Heber <heber@…> (05/07/16 07:03:56)

Message:

Modified FitPartialChargesAction to register fitted particles with ParticleRegistry.

• removed unused parameter "potential-file", superceded by save/parse-particle- parameters.
• extended fit-partial-charges regression test to use save-particle-parameters.

Files:

• src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) (2 diffs)
• src/Actions/PotentialAction/FitPartialChargesAction.def (modified) (1 diff)
• tests/Python/AllActions/options.dat (modified) (1 diff)
• tests/regression/Potential/FitPartialCharges/post/water.particles (added)
• tests/regression/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at (modified) (2 diffs)

src/Actions/PotentialAction/FitPartialChargesAction.cpp

@@ -62 +62 @@
 #include "FunctionApproximation/Extractors.hpp"
 #include "Potentials/PartialNucleiChargeFitter.hpp"
+#include "Potentials/Particles/ParticleFactory.hpp"
+#include "Potentials/Particles/ParticleRegistry.hpp"
 #include "Potentials/SerializablePotential.hpp"
 #include "World.hpp"
@@ -182 +184 @@
   );
 
+  // place all fitted charges into ParticleRegistry
+  const ParticleFactory &factory =
+      const_cast<const ParticleFactory&>(ParticleFactory::getInstance());
+  const periodentafel &periode = *World::getInstance().getPeriode();
+  ASSERT(averaged_charges.size() == fragmentnumbers.size(),
+      "PotentialFitPartialChargesAction::performCall() - charges and elements length mismatch.");
+  for (size_t i=0;i<averaged_charges.size(); ++i) {
+    const std::string name = Particle::findFreeName(periode, fragmentnumbers[i]);
+    LOG(2, "INFO: Adding particle " << name << " for element "
+        << fragmentnumbers[i] << ", charge " << averaged_charges[i]);
+    factory.createInstance(name, fragmentnumbers[i], averaged_charges[i]);
+  }
 
   // output fitted charges

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 (boost::filesystem::path)(std::vector<const element *>)(double)
-#define paramtokens ("potential-file")("fragment-charges")("radius")
-#define paramdescriptions ("potential file specifying multiple potentials to fit")("charges specifying the fragment")("radius of sphere around nuclei where potential does not need to match")
-#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(0))
-#define paramreferences (potential_file)(fragment)(radius)
+#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 paramvalids \
-(DummyValidator<boost::filesystem::path>()) \
 (STLVectorValidator< std::vector<const element *> >(1,99, ElementValidator())) \
 (NonNegativeValidator<double>())

tests/Python/AllActions/options.dat

@@ -146 +146 @@
 position        "9.78 2.64 2.64"
 potential-charges       "1 1"
-potential-file  "test.potentials"
 potential-type  "morse"
 radius  "20."

tests/regression/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at

@@ -22 +22 @@
 
 AT_SETUP([Potential - Fit partial charges to water])
-AT_KEYWORDS([potential parse-homologies fit-partial-charges])
+AT_KEYWORDS([potential parse-homologies fit-partial-charges save-particle-parameters])
 AT_SKIP_IF([../../molecuilder --help fit-partial-charges; if test $? -eq 5; then /bin/true; else /bin/false; fi])
 
@@ -30 +30 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPartialCharges/pre/$file $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder --parse-homologies $file --fit-partial-charges --fragment-charges 8 1 1 --radius 1.5], 0, [stdout], [ignore])
+AT_CHECK([../../molecuilder --parse-homologies $file --fit-partial-charges --fragment-charges 8 1 1 --radius 1.5 --save-particle-parameters water.particles], 0, [stdout], [ignore])
 # check that L_2 error is below 1e-6
 AT_CHECK([grep "L2-Norm" stdout | awk '{if ($6 > 1e1) exit 1}'], 0, [ignore], [ignore])
 AT_CHECK([grep "L1-Norm" stdout | awk '{if ($6 > 1e0) exit 1}'], 0, [ignore], [ignore])
 AT_CHECK([grep "We have fitted the following charges ( -0.73.*; 0.36.*; 0.36.*; )." stdout], 0, [ignore], [ignore])
+AT_CHECK([diff water.particles ${abs_top_srcdir}/tests/regression/Potential/FitPartialCharges/post/water.particles], 0)
 
 AT_CLEANUP