Changeset 666e9e

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:

a9099d

Parents:

0ba27c9

git-author:

Frederik Heber <heber@…> (02/17/16 18:24:55)

git-committer:

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

Message:

VMGFragmentController and FragmentationAutomationAction accept UseImplicitCharge.

• this causes nuclei charges for the full solution to be taken from the ParticleRegistry that contains partial charges table and not the elementary charges.

Files:

• src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) (5 diffs)
• src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) (1 diff)
• src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (2 diffs)
• src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) (2 diffs)
• src/Fragmentation/Automation/VMGFragmentController.cpp (modified) (4 diffs)
• src/Fragmentation/Automation/VMGFragmentController.hpp (modified) (2 diffs)
• tests/Python/AllActions/options.dat (modified) (1 diff)

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

@@ -62 +62 @@
 
 #include "Descriptors/AtomIdDescriptor.hpp"
+#include "Atom/atom.hpp"
+#include "Element/element.hpp"
 #include "Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp"
 #include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
@@ -86 +88 @@
 #endif
 #include "Helpers/defs.hpp"
+#include "Potentials/Particles/ParticleRegistry.hpp"
 #include "World.hpp"
 
@@ -672 +675 @@
 
     // Final phase: sum up and print result
+    IndexedVectors::indices_t implicit_indices;
+    if (params.UseImplicitCharges.get()) {
+      // place all in implicit charges that are not selected but contained in ParticleRegistry
+      const World &world = const_cast<const World &>(World::getInstance());
+      const ParticleRegistry &registry = const_cast<const ParticleRegistry &>(ParticleRegistry::getInstance());
+      const World::ConstAtomComposite &atoms = world.getAllAtoms();
+      for (World::ConstAtomComposite::const_iterator iter = atoms.begin();
+          iter != atoms.end(); ++iter) {
+        const atomId_t atomid = (*iter)->getId();
+        if (!world.isAtomSelected(atomid)) {
+          const std::string &symbol = (*iter)->getElement().getSymbol();
+          if (registry.isPresentByName(symbol))
+            implicit_indices.push_back(atomid);
+        }
+      }
+      LOG(2, "INFO: We added " << implicit_indices.size() << " indices due to implicit charges.");
+    }
+
     FragmentationLongRangeResults longrangeresults(
         shortrangedata,longrangeData,keysets, forcekeysets);
@@ -678 +699 @@
         longrangeData,
         fullsolutionData,
-        full_sample);
+        full_sample,
+        implicit_indices);
     printReceivedFullResults(longrangeresults);
 
@@ -698 +720 @@
     std::map<JobId_t, VMGData> longrangeData;
     FragmentationLongRangeResults longrangeresults(
-        shortrangedata,longrangeData,keysets, forcekeysets);
+        shortrangedata, longrangeData, keysets, forcekeysets);
     appendToHomologies(shortrangeresults, longrangeresults, false);
   }

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def

@@ -15 +15 @@
 // 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)(bool)(std::string)
-#define paramtokens ("fragment-resultfile")("store-grids")("fragment-prefix")
-#define paramdescriptions ("parse fragment results from the given file")("whether to store sampled grids in homology files")("prefix of each fragment file")
-#define paramdefaults (NOPARAM_DEFAULT)(PARAM_DEFAULT("0"))(PARAM_DEFAULT("BondFragment"))
-#define paramreferences (resultsfile)(DoStoreGrids)(prefix)
+#define paramtypes (boost::filesystem::path)(bool)(std::string)(bool)
+#define paramtokens ("fragment-resultfile")("store-grids")("fragment-prefix")("UseImplicitCharges")
+#define paramdescriptions ("parse fragment results from the given file")("whether to store sampled grids in homology files")("prefix of each fragment file")("whether to model any non-selected atoms by partial charges implicitly")
+#define paramdefaults (NOPARAM_DEFAULT)(PARAM_DEFAULT("0"))(PARAM_DEFAULT("BondFragment"))(PARAM_DEFAULT("0"))
+#define paramreferences (resultsfile)(DoStoreGrids)(prefix)(UseImplicitCharges)
 #define paramvalids \
 (DummyValidator< boost::filesystem::path >()) \
 (DummyValidator< bool >()) \
-(DummyValidator< std::string >())
+(DummyValidator< std::string >()) \
+(DummyValidator< bool >())
 
 #undef statetypes

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -261 +261 @@
         params.DoPrintDebug.get(),
         OpenBoundaryConditions,
-        params.DoSmearCharges.get())) {
+        params.DoSmearCharges.get(),
+        false)) {
       STATUS("Could not create long-range jobs for electronic charge distribution.");
       return Action::failure;
@@ -292 +293 @@
           params.DoPrintDebug.get(),
           OpenBoundaryConditions,
-          params.DoSmearCharges.get())) {
+          params.DoSmearCharges.get(),
+          params.UseImplicitCharges.get())) {
         STATUS("Could not create long-range jobs for nuclei charge distribution.");
         return Action::failure;

src/Actions/FragmentationAction/FragmentationAutomationAction.def

@@ -18 +18 @@
 // 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::string)(std::string)(boost::filesystem::path)(unsigned int)(unsigned int)(unsigned int)(bool)(boost::filesystem::path)(bool)(bool)(bool)
-#define paramtokens ("server-address")("server-port")("fragment-executable")("grid-level")("near-field-cells")("interpolation-degree")("DoLongrange")("fragment-resultfile")("DoValenceOnly")("DoPrintDebug")("DoSmearElectronicCharges")
-#define paramdescriptions ("hostname of server")("controller port of server")("executable to launch on clients")("resolution of multigrid")("number of cells used in smearing out core charge")("interpolation degree for getting the nuclei potential from the grid")("whether to calculate long-range contributions")("parse fragment results from the given file")("whether the sampling uses only the valence electron and nuclei charge")("whether to print grids for debug visualization")("whether to smear out electronic charge distributions with bsplines or not") 
-#define paramdefaults (PARAM_DEFAULT("127.0.0.1"))(NOPARAM_DEFAULT)(PARAM_DEFAULT("mpqc"))(PARAM_DEFAULT(5))(PARAM_DEFAULT(3))(PARAM_DEFAULT(3))(PARAM_DEFAULT("0"))(PARAM_DEFAULT(""))(PARAM_DEFAULT("0"))(PARAM_DEFAULT("0"))(PARAM_DEFAULT("0"))
-#define paramreferences (host)(port)(executable)(level)(near_field_cells)(interpolation_degree)(DoLongrange)(resultsfile)(DoValenceOnly)(DoPrintDebug)(DoSmearCharges)
+#define paramtypes (std::string)(std::string)(boost::filesystem::path)(unsigned int)(unsigned int)(unsigned int)(bool)(boost::filesystem::path)(bool)(bool)(bool)(bool)
+#define paramtokens ("server-address")("server-port")("fragment-executable")("grid-level")("near-field-cells")("interpolation-degree")("DoLongrange")("fragment-resultfile")("DoValenceOnly")("DoPrintDebug")("DoSmearElectronicCharges")("UseImplicitCharges")
+#define paramdescriptions ("hostname of server")("controller port of server")("executable to launch on clients")("resolution of multigrid")("number of cells used in smearing out core charge")("interpolation degree for getting the nuclei potential from the grid")("whether to calculate long-range contributions")("parse fragment results from the given file")("whether the sampling uses only the valence electron and nuclei charge")("whether to print grids for debug visualization")("whether to smear out electronic charge distributions with bsplines or not")("whether to model any non-selected atoms by partial charges implicitly") 
+#define paramdefaults (PARAM_DEFAULT("127.0.0.1"))(NOPARAM_DEFAULT)(PARAM_DEFAULT("mpqc"))(PARAM_DEFAULT(5))(PARAM_DEFAULT(3))(PARAM_DEFAULT(3))(PARAM_DEFAULT("0"))(PARAM_DEFAULT(""))(PARAM_DEFAULT("0"))(PARAM_DEFAULT("0"))(PARAM_DEFAULT("0"))(PARAM_DEFAULT("0"))
+#define paramreferences (host)(port)(executable)(level)(near_field_cells)(interpolation_degree)(DoLongrange)(resultsfile)(DoValenceOnly)(DoPrintDebug)(DoSmearCharges)(UseImplicitCharges)
 #define paramvalids \
 (DummyValidator< std::string >()) \
@@ -32 +32 @@
 (DummyValidator< bool >()) \
 (DummyValidator< boost::filesystem::path >()) \
+(DummyValidator< bool >()) \
 (DummyValidator< bool >()) \
 (DummyValidator< bool >()) \

src/Fragmentation/Automation/VMGFragmentController.cpp

@@ -47 +47 @@
 #include "Jobs/VMGJob.hpp"
 #include "molecule.hpp"
+#include "Potentials/Particles/Particle.hpp"
+#include "Potentials/Particles/ParticleRegistry.hpp"
 #include "World.hpp"
 
@@ -77 +79 @@
     const bool _DoPrintDebug,
     const bool _OpenBoundaryConditions,
-    const bool _DoSmearCharges)
+    const bool _DoSmearCharges,
+    const bool _UseImplicitCharges)
 {
   std::vector<FragmentJob::ptr> jobs;
@@ -110 +113 @@
   std::vector< std::vector<double> > positions;
   std::vector<double> charges;
+  const World &world = const_cast<const World &>(World::getInstance());
+  const ParticleRegistry &registry = const_cast<const ParticleRegistry &>(ParticleRegistry::getInstance());
   {
-    const World::ConstAtomComposite &atoms = const_cast<const World &>(World::getInstance()).
-        getAllAtoms();
+    const World::ConstAtomComposite &atoms = world.getAllAtoms();
     positions.reserve(atoms.size());
     charges.reserve(atoms.size());
@@ -118 +122 @@
     for (World::ConstAtomComposite::const_iterator iter = atoms.begin();
         iter != atoms.end(); ++iter) {
+      // set position for this atom
       const Vector &pos = (*iter)->getPosition();
       // convert positions to atomic length units
-      for (size_t i=0;i<3;++i) position[i] = pos[i]/AtomicLengthToAngstroem;
-      positions.push_back(position);
-      int charge = (*iter)->getElement().getAtomicNumber();
-      // subtract core electron charge from nuclei charge if only valence sampled
-      if (_DoValenceOnly == MPQCData::DoSampleValenceOnly)
-        charge -= getCoreElectrons(charge);
-      charges.push_back((double)charge);
+      for (size_t i=0;i<3;++i)
+        position[i] = pos[i]/AtomicLengthToAngstroem;
+
+      // use partial charges ...
+      const atomId_t atomid = (*iter)->getId();
+      if ((!world.isAtomSelected(atomid)) && (_UseImplicitCharges)) {
+        // ... for all unselected particles ...
+        const std::string &symbol = (*iter)->getElement().getSymbol();
+        if (registry.isPresentByName(symbol)) {
+          // ... that are present in ParticleRegistry
+          const Particle * const particle = registry.getByName(symbol);
+          LOG(3, "DEBUG: Using implicit charge " << particle->charge << " for atom " << atomid);
+          positions.push_back(position);
+          charges.push_back(particle->charge);
+        }
+      } else {
+        double charge = (*iter)->getElement().getAtomicNumber();
+        // subtract core electron charge from nuclei charge if only valence sampled
+        if (_DoValenceOnly == MPQCData::DoSampleValenceOnly)
+          charge -= getCoreElectrons(charge);
+        positions.push_back(position);
+        charges.push_back((double)charge);
+      }
     }
   }

src/Fragmentation/Automation/VMGFragmentController.hpp

@@ -64 +64 @@
    *        boundary conditions
    * \param _DoSmearCharges whether to smear out electronic charge distributions with bsplines or not
+   * \param _UseImplicitCharges use implicit charges in potential storage if
+   *            element is found
    */
   bool createLongRangeJobs(
@@ -75 +77 @@
       const bool _DoPrintDebug,
       const bool _OpenBoundaryConditions = false,
-      const bool _DoSmearCharges = false);
+      const bool _DoSmearCharges = false,
+      const bool _UseImplicitCharges = false);
 
   void waitforResults(const size_t NoExpectedResults)

tests/Python/AllActions/options.dat

@@ -252 +252 @@
 unselect-molecules-by-name      "water"
 unselect-shape-by-name  "cube42"
+UseImplicitCharges      "1"
 verbose "3"
 verlet-integration      "forces.dat"