Changeset 3690e4 for src/Actions

Timestamp:

Feb 2, 2016, 5:50:29 PM (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_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:

9ae11c

Parents:

d1831e (diff), 62d092 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'Enhancing_Interdistance' into Candidate_v1.5.1

Location:

src/Actions/FragmentationAction

Files:

• AnalyseFragmentationResultsAction.cpp (modified) (7 diffs)
• FragmentationAction.cpp (modified) (1 diff)
• FragmentationAutomationAction.cpp (modified) (3 diffs)
• FragmentationAutomationAction.def (modified) (2 diffs)

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

@@ -72 +72 @@
 #include "Fragmentation/Summation/SetValues/Eigenvalues.hpp"
 #include "Fragmentation/Summation/SetValues/Fragment.hpp"
+#include "Fragmentation/Summation/SetValues/FragmentForces.hpp"
 #include "Fragmentation/Summation/SetValues/Histogram.hpp"
 #include "Fragmentation/Summation/SetValues/IndexedVectors.hpp"
@@ -240 +241 @@
     const FragmentationLongRangeResults &results)
 {
-  // print tables (without eigenvalues, they go extra)
+  // print tables per keyset(without grids, they go extra)
 
   {
@@ -252 +253 @@
   }
 
+  if (results.hasLongRangeForces()) {
+    const std::string forceresult =
+        writeTable<VMGDataForceMap_t, VMGDataForceVector_t>()(
+            results.Result_ForceLongRange_fused, results.getMaxLevel());
+    LOG(2, "DEBUG: Force table is \n" << forceresult);
+    std::string filename;
+    filename += FRAGMENTPREFIX + std::string("_VMGForces.dat");
+    writeToFile(filename, forceresult);
+  }
+
   {
     const std::string gridresult =
@@ -260 +271 @@
     filename += FRAGMENTPREFIX + std::string("_LongRangeEnergy.dat");
     writeToFile(filename, gridresult);
+  }
+
+  if (results.hasLongRangeForces()) {
+    const std::string forceresult =
+        writeTable<VMGDataLongRangeForceMap_t, VMGDataLongRangeForceVector_t >()(
+            results.Result_ForcesLongRangeIntegrated_fused, results.getMaxLevel(), 1);
+    LOG(2, "DEBUG: ForcesLongRange table is \n" << forceresult);
+    std::string filename;
+    filename += FRAGMENTPREFIX + std::string("_LongRangeForces.dat");
+    writeToFile(filename, forceresult);
   }
 }
@@ -325 +346 @@
 
       // obtain potential distribution
-      std::map<IndexSet::ptr, std::pair< VMGDataMap_t, VMGDataMap_t> >::const_iterator potentialiter
-          = longrangeresults.Result_perIndexSet_LongRange.find(index);
-      ASSERT( potentialiter != longrangeresults.Result_perIndexSet_LongRange.end(),
+      std::map<IndexSet::ptr, std::pair< VMGDataGridMap_t, VMGDataGridMap_t> >::const_iterator potentialiter
+          = longrangeresults.Result_perIndexSet_LongRange_Grid.find(index);
+      ASSERT( potentialiter != longrangeresults.Result_perIndexSet_LongRange_Grid.end(),
           "appendToHomologyFile() - cannot find index "+toString(*index)
           +" in FragmentResults.");
       // add e+n potentials
-      value.potential_distribution = boost::fusion::at_key<VMGDataFused::both_sampled_potential>(potentialiter->second.second); // contributions
+      value.potential_distribution =
+          boost::fusion::at_key<VMGDataFused::both_sampled_potential>(potentialiter->second.second); // contributions
 //      // and re-average to zero (integral is times volume_element which we don't need here)
 //      const double sum =
@@ -625 +647 @@
   if (DoLongrange) {
     if ( const_cast<const World &>(World::getInstance()).getAllAtoms().size() == 0) {
-      STATUS("Please load the full molecule intostd::map<JobId_t, VMGData> longrangeData the world before starting this action.");
+      STATUS("Please load the full molecule into std::map<JobId_t, VMGData> longrangeData the world before starting this action.");
       return Action::failure;
     }
@@ -635 +657 @@
     // remove full solution corresponding to full_sample from map (must be highest ids), has to be treated extra
     std::map<JobId_t, VMGData>::iterator iter = longrangeData.end();
-    for (size_t i=0;i<full_sample.size();++i)
-      --iter;
+    std::advance(iter, -full_sample.size());
     std::map<JobId_t, VMGData>::iterator remove_iter = iter;
     std::vector<VMGData> fullsolutionData;
     for (; iter != longrangeData.end(); ++iter)
       fullsolutionData.push_back(iter->second);
-    longrangeData.erase(remove_iter, longrangeData.end());
+    if (longrangeData.size() > 1) // when there's just a single fragment, it corresponds to full solution
+      longrangeData.erase(remove_iter, longrangeData.end());
 
     // Final phase: sum up and print result

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -259 +259 @@
         << params.InterOrder.get() << " and distance of "
         << params.distance.get() << ".");
+    const enum HydrogenTreatment treatment =
+        params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
+    const double UpperBound = std::max(10., params.distance.get());
     Interfragmenter fragmenter(TotalGraph);
-    const enum HydrogenTreatment treatment =  params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
+
+    // check the largest Rcut that causes no additional inter-fragments
+    const double Min_Rcut =
+        fragmenter.findLargestCutoff(params.InterOrder.get(), UpperBound, treatment);
+
+    // if we smear out electronic charges, warn when non-overlapping criterion does not hold
+    if (params.InterOrder.get() < Min_Rcut)
+      ELOG(2, "Inter-order is too low to cause any additional fragments.");
+
+    // then add fragments
     fragmenter(params.InterOrder.get(), params.distance.get(), treatment);
+
     LOG(0, "STATUS: There are now " << TotalGraph.size() << " fragments after interfragmenting.");
   }

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -260 +260 @@
         params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly,
         params.DoPrintDebug.get(),
-        OpenBoundaryConditions)) {
+        OpenBoundaryConditions,
+        params.DoSmearCharges.get())) {
       STATUS("Could not create long-range jobs for electronic charge distribution.");
       return Action::failure;
@@ -290 +291 @@
           params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly,
           params.DoPrintDebug.get(),
-          OpenBoundaryConditions)) {
+          OpenBoundaryConditions,
+          params.DoSmearCharges.get())) {
         STATUS("Could not create long-range jobs for nuclei charge distribution.");
         return Action::failure;
@@ -316 +318 @@
         destiter->second.both_sampled_potential = srciter->second.sampled_potential;
         destiter->second.nuclei_long = srciter->second.nuclei_long;
+        destiter->second.forces = srciter->second.forces;
+        destiter->second.hasForces = srciter->second.hasForces;
       }
     }

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)
-#define paramtokens ("server-address")("server-port")("fragment-executable")("grid-level")("near-field-cells")("interpolation-degree")("DoLongrange")("fragment-resultfile")("DoValenceOnly")("DoPrintDebug")
-#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") 
-#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"))
-#define paramreferences (host)(port)(executable)(level)(near_field_cells)(interpolation_degree)(DoLongrange)(resultsfile)(DoValenceOnly)(DoPrintDebug)
+#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 paramvalids \
 (DummyValidator< std::string >()) \
@@ -32 +32 @@
 (DummyValidator< bool >()) \
 (DummyValidator< boost::filesystem::path >()) \
+(DummyValidator< bool >()) \
 (DummyValidator< bool >()) \
 (DummyValidator< bool >())