Changeset 3690e4 for src/Jobs

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/Jobs

Files:

• ChargeSmearer.cpp (added)
• ChargeSmearer.hpp (added)
• InterfaceVMGJob.cpp (modified) (6 diffs)
• InterfaceVMGJob.hpp (modified) (3 diffs)
• MPQCCommandJob.cpp (modified) (2 diffs)
• Makefile.am (modified) (3 diffs)
• VMGJob.cpp (modified) (4 diffs)
• VMGJob.hpp (modified) (4 diffs)
• WindowGrid_converter.cpp (modified) (7 diffs)
• WindowGrid_converter.hpp (modified) (1 diff)

src/Jobs/InterfaceVMGJob.cpp

@@ -57 +57 @@
 #include "CodePatterns/Log.hpp"
 
+#include "Fragmentation/Summation/SetValues/FragmentForces.hpp"
 #include "Jobs/WindowGrid_converter.hpp"
+#include "Jobs/ChargeSmearer.hpp"
 
 using namespace VMG;
@@ -74 +76 @@
     const ImportParticles_t _ImportParticles,
     const bool _DoPrintDebug,
+    const bool _DoSmearCharges,
     int coarseningSteps,
     double alpha) :
   VMG::Interface(boundary, levelMin, levelMax,
       _box_begin, _box_end, coarseningSteps, alpha),
-  spl(near_field_cells, Extent(MaxLevel()).MeshWidth().Max()),
+  nfc(near_field_cells),
+  meshwidth(Extent(MaxLevel()).MeshWidth().Max()),
+  spl(nfc, meshwidth),
   sampled_input(_sampled_input),
   returndata(_returndata),
@@ -84 +89 @@
   ImportParticles(_ImportParticles),
   DoPrintDebug(_DoPrintDebug),
-  OpenBoundaryCondition(boundary[0] == VMG::Open)
+  OpenBoundaryCondition(boundary[0] == VMG::Open),
+  DoSmearCharges(_DoSmearCharges)
 {
   for (size_t i=0;i<3;++i) {
@@ -158 +164 @@
 
   // add sampled electron charge density onto grid
+  if (DoSmearCharges) {
+    ChargeSmearer &smearer = ChargeSmearer::getInstance();
+    smearer.initializeSplineArray(spl, nfc, meshwidth);
+  }
   WindowGrid_converter::addWindowOntoGrid(
       grid,
       sampled_input,
       1.,
-      OpenBoundaryCondition);
+      OpenBoundaryCondition,
+      DoSmearCharges);
 
   if (DoPrintDebug) {
@@ -318 +329 @@
         const vmg_float length = dir.Length();
 
-        if (length < r_cut) {
+        if ((length < r_cut) && (length > std::numeric_limits<double>::epsilon())) {
 
           (*p1)->Pot() += (*p2)->Charge() / length * (1.0 + spl.EvaluatePotential(length));
@@ -331 +342 @@
       }
 
+  const vmg_int& num_particles_local = factory.GetObjectStorageVal<vmg_int>("PARTICLE_NUM_LOCAL");
+
   /* Remove average force term */
+//  if (!particles.empty()) {
+//    Vector average_force = 0.0;
+//    for (std::list<Particle::Particle>::const_iterator iter=particles.begin(); iter!=particles.end(); ++iter)
+//      average_force += iter->Charge() * iter->Field();
+//    const vmg_int num_particles_global = comm.GlobalSum(num_particles_local);
+//    average_force /= (double)num_particles_global;
+//    comm.GlobalSumArray(average_force.vec(), 3);
+//    for (std::list<Particle::Particle>::iterator iter=particles.begin(); iter!=particles.end(); ++iter)
+//      iter->Field() -= average_force / iter->Charge();
+//    comm.PrintOnce(Debug, "Average force term is:         %e %e %e", average_force[0], average_force[1], average_force[2]);
+//  }
+
+  comm.CommParticlesBack(particles);
+
+  vmg_float* q = factory.GetObjectStorageArray<vmg_float>("PARTICLE_CHARGE_ARRAY");
+  const vmg_float* p = factory.GetObjectStorageArray<vmg_float>("PARTICLE_POTENTIAL_ARRAY");
+  const vmg_float* f = factory.GetObjectStorageArray<vmg_float>("PARTICLE_FIELD_ARRAY");
+
+  // extract forces
   if (!particles.empty()) {
-    Vector average_force = 0.0;
-    for (std::list<Particle::Particle>::const_iterator iter=particles.begin(); iter!=particles.end(); ++iter)
-      average_force += iter->Charge() * iter->Field();
-    const vmg_int& npl = MG::GetFactory().GetObjectStorageVal<vmg_int>("PARTICLE_NUM_LOCAL");
-    const vmg_int num_particles_global = comm.GlobalSum(npl);
-    average_force /= num_particles_global;
-    comm.GlobalSumArray(average_force.vec(), 3);
-    for (std::list<Particle::Particle>::iterator iter=particles.begin(); iter!=particles.end(); ++iter)
-      iter->Field() -= average_force / iter->Charge();
-  }
-
-  comm.CommParticlesBack(particles);
-
-  vmg_float* q = factory.GetObjectStorageArray<vmg_float>("PARTICLE_CHARGE_ARRAY");
-  const vmg_int& num_particles_local = factory.GetObjectStorageVal<vmg_int>("PARTICLE_NUM_LOCAL");
-  const vmg_float* p = factory.GetObjectStorageArray<vmg_float>("PARTICLE_POTENTIAL_ARRAY");
-//  const vmg_float* f = factory.GetObjectStorageArray<vmg_float>("PARTICLE_FIELD_ARRAY");
-
+    size_t index = 0;
+    returndata.forces.resize(
+        num_particles_local, FragmentForces::force_t(3, 0.) );
+    for (FragmentForces::forces_t::iterator iter = returndata.forces.begin();
+        iter != returndata.forces.end(); ++iter) {
+      comm.PrintOnce(Debug, "%d force vector:        %e %e %e", (index/3)+1, f[index+0], f[index+1], f[index+2]);
+      for (size_t i=0;i<3;++i)
+          (*iter)[i] = f[index++];
+    }
+    returndata.hasForces = true;
+  }
 
   e_long = comm.GlobalSumRoot(e_long);

src/Jobs/InterfaceVMGJob.hpp

@@ -53 +53 @@
       const ImportParticles_t _ImportParticles=DoImportParticles,
       const bool _DoPrintDebug=false,
+      const bool _DoSmearCharges=false,
       int coarseningSteps=9,
       double alpha=1.6
@@ -63 +64 @@
 
 protected:
+  unsigned int nfc;
+  const double meshwidth;
   VMG::Particle::BSpline spl;
 
@@ -88 +91 @@
   //!> open boundary conditions or not
   const bool OpenBoundaryCondition;
+
+  //!> whether to smear out electronic charge distributions with bsplines or not
+  const bool DoSmearCharges;
 };
 

src/Jobs/MPQCCommandJob.cpp

@@ -51 +51 @@
 
 #include "LinearAlgebra/defs.hpp"
+
+#include "Fragmentation/Summation/SetValues/FragmentForces.hpp"
 
 const std::string MPQCCommandJob::keyword_hartreefock_energy("total scf energy");
@@ -110 +112 @@
         tok_iter++;
         tok_iter++;
-        MPQCData::vector_type forcevector(NDIM);
+        FragmentForces::force_t forcevector(NDIM);
         try { // first col is index, second is element
           for (size_t index = 0;index < NDIM; ++index)

src/Jobs/Makefile.am

@@ -17 +17 @@
 if CONDVMG
 JOBSSOURCE += \
+        Jobs/ChargeSmearer.cpp \
         Jobs/InterfaceVMGDebugGridJob.cpp \
         Jobs/InterfaceVMGJob.cpp \
@@ -43 +44 @@
 if CONDVMG
 JOBSHEADER += \
+        Jobs/ChargeSmearer.hpp \
         Jobs/InterfaceVMGDebugGridJob.hpp \
         Jobs/InterfaceVMGJob.hpp \
@@ -121 +123 @@
 nodist_libMolecuilderJobs_libinclude_HEADERS = $(top_builddir)/libmolecuilder_config.h
 
-## Install the generated pkg-config file (.pc) into the expected location for
-## architecture-dependent package configuration information.  Occasionally,
-## pkg-config files are also used for architecture-independent data packages,
-## in which case the correct install location would be $(datadir)/pkgconfig.
-#pkgconfigdir = $(libdir)/pkgconfig
-#pkgconfig_DATA = $(top_builddir)/MoleCuilder.pc
-

src/Jobs/VMGJob.cpp

@@ -92 +92 @@
     const bool _DoImportParticles,
     const bool _DoPrintDebug,
-    const bool _OpenBoundaryConditions) :
+    const bool _OpenBoundaryConditions,
+    const bool _DoSmearCharges) :
   FragmentJob(_JobId),
   density_grid(_density_grid),
@@ -102 +103 @@
   DoPrintDebug(_DoPrintDebug),
   OpenBoundaryConditions(_OpenBoundaryConditions),
+  DoSmearCharges(_DoSmearCharges),
   returndata(static_cast<const SamplingGridProperties &>(_density_grid)),
   particles()
@@ -113 +115 @@
   DoPrintDebug(false),
   OpenBoundaryConditions(false),
+  DoSmearCharges(false),
   particles()
 {}
@@ -246 +249 @@
           VMGInterfaces::InterfaceVMGJob::DoImportParticles
           : VMGInterfaces::InterfaceVMGJob::DontImportParticles,
-      DoPrintDebug);
+      DoPrintDebug,
+      DoSmearCharges);
   const int cycle_type = 1; // V-type
   if (OpenBoundaryConditions) {

src/Jobs/VMGJob.hpp

@@ -44 +44 @@
    * @param _DoImportParticles whether we import particles (true) or evaluate only
    * @param _DoPrintDebug whether we do print grid for debug visualization or not
+   * @param _OpenBoundaryConditions whether we have open (true) boundary conditions or periodic (false)
+   * @param _DoSmearCharges whether to smear out electronic charge distributions with bsplines or not
    */
   VMGJob(const JobId_t _JobId,
@@ -53 +55 @@
       const bool _DoImportParticles=true,
       const bool _DoPrintDebug=false,
-      const bool _OpenBoundaryConditions=false
+      const bool _OpenBoundaryConditions=false,
+      const bool _DoSmearCharges=false
       );
   virtual ~VMGJob();
@@ -81 +84 @@
   //!> whether we have open (true) boundary conditions or periodic (false)
   const bool OpenBoundaryConditions;
+  //!> whether to smear out electronic charge distributions with bsplines or not
+  const bool DoSmearCharges;
 
 private:
@@ -134 +139 @@
     ar & const_cast< bool &>(DoPrintDebug);
     ar & const_cast< bool &>(OpenBoundaryConditions);
+    ar & const_cast< bool &>(DoSmearCharges);
     ar & returndata;
   }

src/Jobs/WindowGrid_converter.cpp

@@ -50 +50 @@
 
 #include "Fragmentation/Summation/SetValues/SamplingGrid.hpp"
+#include "Jobs/ChargeSmearer.hpp"
 
 void WindowGrid_converter::addGridOntoWindow(
@@ -178 +179 @@
     const SamplingGrid &grid,
     const double prefactor,
-    const bool OpenBoundaryConditions)
+    const bool OpenBoundaryConditions,
+    const bool DoSmearCharges)
 {
 #ifndef NDEBUG
@@ -244 +246 @@
   }
 
+  /// reset grid to zero everywhere
+
   VMG::Grid::iterator griditer = window.Iterators().Local().Begin();
 //  griditer.advance(pre_offset[0]*total[1]*total[2]);
+  for(N[0]=0; N[0] < total[0]; ++N[0])
+    for(N[1]=0; N[1] < total[1]; ++N[1])
+      for(N[2]=0; N[2] < total[2]; ++N[2]) {
+        ASSERT( griditer != window.Iterators().Local().End(),
+            "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
+        window(*griditer++) = 0.;
+      }
+
+#ifndef NDEBUG
+  ASSERT( griditer == window.Iterators().Local().End(),
+      "InterfaceVMGJob::addWindowOntoGrid() - griditer is not at end of window.");
+#endif
+
+  /// then apply charges onto grid
+
+  griditer = window.Iterators().Local().Begin();
+  SamplingGrid::sampledvalues_t::const_iterator copyiter = grid.sampled_grid.begin();
+  const ChargeSmearer &smearer = ChargeSmearer::getInstance();
+  // NOTE: GridIterator::operator+=()'s implementation in vmg is broken. DON'T USE!
+//  griditer += pre_offset[0] * total[1] * total[2];
   for(N[0]=0; N[0] < pre_offset[0]; ++N[0])
     for(N[1]=0; N[1] < total[1]; ++N[1])
@@ -251 +275 @@
         ASSERT( griditer != window.Iterators().Local().End(),
             "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-        window(*griditer++) = 0.;
-      }
-  SamplingGrid::sampledvalues_t::const_iterator copyiter = grid.sampled_grid.begin();
+        griditer++;
+      }
   for(N[0]=0; N[0] < length[0]; ++N[0]) {
-//    griditer.advance(pre_offset[1]*total[2]);
+//    griditer += pre_offset[1] * total[2];
       for(N[1]=0; N[1] < pre_offset[1]; ++N[1])
         for(N[2]=0; N[2] < total[2]; ++N[2]) {
           ASSERT( griditer != window.Iterators().Local().End(),
               "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-          window(*griditer++) = 0.;
+          griditer++;
         }
     for(N[1]=0; N[1] < length[1]; ++N[1]) {
-//      griditer.advance(pre_offset[2]);
-      for(N[2]=0; N[2] < pre_offset[2]; ++N[2])
-        window(*griditer++) = 0.;
+//      griditer += pre_offset[2];
+      for(N[2]=0; N[2] < pre_offset[2]; ++N[2]) {
+        griditer++;
+      }
+
       for(N[2]=0; N[2] < length[2]; ++N[2]) {
         ASSERT( griditer != window.Iterators().Local().End(),
@@ -271 +296 @@
         ASSERT( copyiter != grid.sampled_grid.end(),
             "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-        window(*griditer++) += prefactor*(*copyiter++);
-      }
-//      griditer.advance(post_offset[2]);
+        // either smear out charges or not.
+        if (DoSmearCharges) {
+          smearer(window, griditer++, prefactor*(*copyiter++));
+        } else {
+          window(*griditer++) += prefactor*(*copyiter++);
+        }
+      }
+//      griditer += post_offset[2];
       for(N[2]=0; N[2] < post_offset[2]; ++N[2]) {
         ASSERT( griditer != window.Iterators().Local().End(),
             "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-        window(*griditer++) = 0.;
+        griditer++;
       }
     }
-//    griditer.advance(post_offset[1]*total[2]);
+//    griditer += post_offset[1] * total[2];
     for(N[1]=0; N[1] < post_offset[1]; ++N[1])
       for(N[2]=0; N[2] < total[2]; ++N[2]) {
         ASSERT( griditer != window.Iterators().Local().End(),
             "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-        window(*griditer++) = 0.;
-      }
-  }
-  //  griditer.advance(post_offset[0]*total[1]*total[2]);
+        griditer++;
+      }
+  }
+//  griditer += post_offset[0] * total[1] * total[2];
   for(N[0]=0; N[0] < post_offset[0]; ++N[0])
     for(N[1]=0; N[1] < total[1]; ++N[1])
@@ -294 +324 @@
         ASSERT( griditer != window.Iterators().Local().End(),
             "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-        window(*griditer++) = 0.;
+        griditer++;
       }
 #ifndef NDEBUG
@@ -302 +332 @@
       "InterfaceVMGJob::addWindowOntoGrid() - copyiter is not at end of window.");
 #endif
-//  LOG(2, "DEBUG: Grid after adding other is " << grid << ".");
+
+  //  LOG(2, "DEBUG: Grid after adding other is " << grid << ".");
 }

src/Jobs/WindowGrid_converter.hpp

@@ -49 +49 @@
       const SamplingGrid &grid,
       const double prefactor,
-      const bool OpenBoundaryConditions = false);
+      const bool OpenBoundaryConditions = false,
+      const bool DoSmearCharges = false);
 
 };