Changeset 6a5eb2 for src/Fragmentation/Summation

Timestamp:

Sep 14, 2016, 6:42:53 PM (8 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

57fda0

Parents:

d56e21

git-author:

Frederik Heber <heber@…> (05/26/16 18:15:19)

git-committer:

Frederik Heber <heber@…> (09/14/16 18:42:53)

Message:

SamplingGrid::downsample() uses padWithZerosForEvenNumberedSamples().

• in the end this requires copying the original grid as we might need to pad it with zeros but should not change the given one.
• Added some debugging information to downsample().

Location:

src/Fragmentation/Summation/SetValues

Files:

• Makefile.am (modified) (1 diff)
• SamplingGrid.cpp (modified) (5 diffs)

src/Fragmentation/Summation/SetValues/Makefile.am

@@ -27 +27 @@
 libMolecuilderFragmentationSetValues_la_LDFLAGS = -ldl ${BOOST_LDFLAGS}
 libMolecuilderFragmentationSetValues_la_LIBADD = \
+        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
         ${CodePatterns_LIBS}
 

src/Fragmentation/Summation/SetValues/SamplingGrid.cpp

@@ -50 +50 @@
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
+
+#include "LinearAlgebra/Vector.hpp"
 
 // static instances
@@ -792 +794 @@
   size_t wnewend_index[NDIM];
   for(size_t i=0;i<NDIM;++i) {
+    LOG(2, "INFO: window[" << i << "] starts at " << wbegin_index[i] << " and ends at "
+        << wend_index[i] << " with length " << wlength_index[i]);
     // We require begin and end of window on even indices (and inside grid).
     wnewbegin_index[i] = wbegin_index[i];
@@ -822 +826 @@
       end_newwindow[i] = begin[i]+delta*wnewend_index[i];
     }
+    LOG(2, "INFO: Original window is " << Vector(begin_window) << " <-> "  << Vector(end_window));
+    LOG(2, "INFO: Padded window is " << Vector(begin_newwindow) << " <-> "  << Vector(end_newwindow));
     // extend window
     extendWindow(begin_newwindow, end_newwindow);
@@ -836 +842 @@
 {
   if (&instance != &other) {
+    LOG(2, "INFO: other's window is " << Vector(other.begin_window)
+        << " <-> " << Vector(other.end_window));
     // take over properties
     static_cast<SamplingGridProperties &>(instance) = other;
     instance.setWindowSize(other.begin_window, other.end_window);
+    LOG(2, "INFO: Set instance's window to " << Vector(instance.begin_window)
+        << " <-> " << Vector(instance.end_window));
     ASSERT( _level <= other.level,
         "SamplingGrid::downsample() - desired level "+toString(_level)
@@ -850 +860 @@
       // have reached the desired one
 
-      // the reference such that we never have to copy the full grid but only
-      // downsampled ones
-      const sampledvalues_t * sourcevalues = &other.sampled_grid;
-      int length_d[3];
-      int length_s[3];
-      getLengthsOfWindow(length_s, other);
+      // we need to copy the other grid because we might need to pad it with zeros anyway
+      SamplingGrid FinerGrid(other);
+      int length_d[NDIM];
+      int length_s[NDIM];
       for (instance.level = other.level-1; instance.level >= _level; --instance.level) {
+        // pad with zeros for even indices and get length of fine grid window
+        FinerGrid.padWithZerosForEvenNumberedSamples();
+        getLengthsOfWindow(length_s, FinerGrid);
+        ASSERT( FinerGrid.getWindowGridPoints() % 8 == 0,
+            "SamplingGrid::downsample() - at level "+toString( instance.level)
+            +" given grid points "+toString(FinerGrid.getWindowGridPoints())+" are not even numbered per axis anymore.");
+        // re-adjust the window (length), get the corresponding window length and downsample
+        instance.setWindow(FinerGrid.begin_window, FinerGrid.end_window);
         getLengthsOfWindow(length_d, instance);
-        // we always have an eighth of the number of sample points as we stop
-        ASSERT( sourcevalues->size() % 8 == 0,
+        ASSERT( instance.sampled_grid.size() == FinerGrid.getWindowGridPoints()/(size_t)8,
             "SamplingGrid::downsample() - at level "+toString( instance.level)
-            +" given grid points "+toString(sourcevalues->size())+" are not even numbered per axis anymore.");
-        sampledvalues_t downsampled(sourcevalues->size()/(size_t)8, 0.);
-        restrictFullWeight(downsampled, length_d, *sourcevalues, length_s);
-        // then copy the downsampled values
-        instance.sampled_grid = downsampled;
-        sourcevalues = &instance.sampled_grid;
-        // and exchange lengths
-        for (size_t i=0;i<3;++i) {
-          length_s[i] = length_d[i];
-        }
+            +" points on coarser grid "+toString(instance.sampled_grid.size())
+            +" and downsampled number on finer grid "
+            +toString(FinerGrid.getWindowGridPoints()/(size_t)8)+" do not match.");
+        restrictFullWeight(instance.sampled_grid, length_d, FinerGrid.sampled_grid, length_s);
+        // then use as new finer grid for next downsampling (if it's not the last level)
+        if (instance.level > _level)
+          FinerGrid = instance;
       }
+      // loop stops at _level-1
       instance.level = _level;