Finished spliting growth variables into groups #11

include/kernels/SinkGrowth.h

@@ -22,15 +22,17 @@ class SinkGrowth : public Kernel
   Real calcLosses();
   Real calcGains();
 
-  std::vector<Real> _atoms;
+  std::vector<VariableValue *> _c;
+  std::vector<Real> _avgsize;
+  std::vector<Real> _maxsize;
+  std::vector<Real> _jumpsize;
   VariableValue & _temp;
+
   int _g;
+  int _G;
   int _N_nuc;
 
   MaterialProperty<Real> & _atomic_diffusivity;
 
-  int _G;
-  std::vector<VariableValue *> _c;
-
 };
 #endif //SINKGROWTH_H

src/actions/ClustersActionBase.C

@@ -1,5 +1,7 @@
 #include "ClustersActionBase.h"
 
+#include "BuckUtils.h"
+
 template<>
 InputParameters validParams<ClustersActionBase>()
 {
@@ -29,18 +31,21 @@ ClustersActionBase::ClustersActionBase(const std::string & name, InputParameters
 void
 ClustersActionBase::setup()
 {
-  if ( _G < _N_max )
-    mooseError("From ClustersActionBase: G must be equal to or greater than N_max.");
+  // if ( _G < _N_max )
+  //   mooseError("From ClustersActionBase: G must be equal to or greater than N_max.");
   if ( _N_nuc > _N_max )
     mooseError("From ClustersActionBase: N_max must be equal to or greater than N_nuc.");
 
   varNamesFromG( _vars, _var_name_base, _G);
   avgSizeFromGroup( _atoms, _G, getParam<Real>("N_max"), getParam<int>("N_nuc"), getParam<bool>("log") );
+
+  Buck::iterateAndDisplay("vars", _vars);
+  Buck::iterateAndDisplay("atoms", _atoms);
 }
 
 
 void
-ClustersActionBase::avgSizeFromGroup(std::vector<Real> & avgs, const Real G, const Real N_max, const int N_nuc, const bool log)
+ClustersActionBase::avgSizeFromGroup(std::vector<Real> & sizes, const Real G, const Real N_max, const int N_nuc, const bool log)
 {
   // Determines maximum cluster size for a given group.
   // G = Max number of groups
@@ -49,8 +54,6 @@ ClustersActionBase::avgSizeFromGroup(std::vector<Real> & avgs, const Real G, con
 
   // First setup nucleation clusters, which consist of N_nuc groups with one atom each
 
-  std::vector<Real> sizes;
-
   for ( int g=1; g<N_nuc+1; ++g )
     sizes.push_back(g);
 
@@ -62,7 +65,7 @@ ClustersActionBase::avgSizeFromGroup(std::vector<Real> & avgs, const Real G, con
     b = N_nuc;
     m = (N_max - N_nuc) / (G - N_nuc);
 
-    for ( int g=N_nuc; g<G+1; ++g )
+    for ( int g=N_nuc; g<G; ++g )
       sizes.push_back( b + m * (g-N_nuc+1) );
   }
   else
@@ -71,16 +74,16 @@ ClustersActionBase::avgSizeFromGroup(std::vector<Real> & avgs, const Real G, con
     b = N_nuc - 1;
     m = std::log10(N_max - N_nuc +1) / (G - N_nuc);
 
-    for ( int g=N_nuc; g<G+1; ++g )
+    for ( int g=N_nuc; g<G; ++g )
       sizes.push_back( b+ std::pow( 10, m * (g-N_nuc+1) ) );
   }
 
-  avgs.push_back(1.0);
-  for ( int g=0; g<N_max-1; ++g )
-  {
-    Real tempavg = 0.5*sizes[g] + 0.5*sizes[g+1];
-    avgs.push_back( ceil(tempavg) );
-  }
+  // avgs.push_back(1.0);
+  // for ( int g=0; g<N_max-1; ++g )
+  // {
+  //   Real tempavg = 0.5*sizes[g] + 0.5*sizes[g+1];
+  //   avgs.push_back( ceil(tempavg) );
+  // }
 }
 
 

src/actions/GrowthKernelsAction.C

@@ -33,7 +33,7 @@ GrowthKernelsAction::act()
       InputParameters p = _factory.getValidParams("SinkGrowth");
       p.set<NonlinearVariableName>("variable") = var_name;
       p.set<std::vector<VariableName> >("coupled_conc") = _vars;
-      p.set<std::vector<Real> >("coupled_conc_atoms") = _atoms;
+      p.set<std::vector<Real> >("coupled_maxsize") = _atoms;
       p.set<int>("N_nuc") = _N_nuc;
 
       p.addCoupledVar("temp", "");

src/kernels/SinkGrowth.C

@@ -1,15 +1,15 @@
 #include "SinkGrowth.h"
 
-// #include "MooseException.h"
 #include "MaterialXeBubble.h"
+#include "BuckUtils.h"
 
 template<>
 InputParameters validParams<SinkGrowth>()
 {
   InputParameters params = validParams<Kernel>();
 
   params.addRequiredCoupledVar("coupled_conc", "List of coupled concentration variables.");
-  params.addRequiredParam<std::vector<Real> >("coupled_conc_atoms", "List of coupled concentration variables.");
+  params.addRequiredParam<std::vector<Real> >("coupled_maxsize", "List of coupled concentration variables.");
   params.addRequiredCoupledVar("temp", "Coupled Temperature");
   params.addRequiredParam<int>("g", "Group number");
   params.addRequiredParam<int>("N_nuc", "Largest cluster size in nucleation model");
@@ -19,7 +19,7 @@ InputParameters validParams<SinkGrowth>()
 
 SinkGrowth::SinkGrowth(const std::string & name, InputParameters parameters)
   :Kernel(name,parameters),
-  _atoms(getParam<std::vector<Real> >("coupled_conc_atoms")),
+  _maxsize(getParam<std::vector<Real> >("coupled_maxsize")),
   _temp(coupledValue("temp")),
   _g(getParam<int>("g") - 1),
   _N_nuc(getParam<int>("N_nuc")),
@@ -29,11 +29,33 @@ SinkGrowth::SinkGrowth(const std::string & name, InputParameters parameters)
 {
 	_G = coupledComponents("coupled_conc");
 
+  if ( _maxsize.size() != _G )
+    mooseError("In SinkGrowth: coupled_conc and coupled_maxsize must be the same size!");
+
+  for ( int i=0; i<_G; ++i )
+  {
+    if ( _maxsize[i] <= _N_nuc )
+      _avgsize.push_back(_maxsize[i]);
+    else
+      _avgsize.push_back( ( _maxsize[i] + _maxsize[i-1] + 1.0 ) /2.0 );
+  }
+
+  for ( int i=0; i<_G-1; ++i )
+  {
+    if ( _maxsize[i] < _N_nuc )
+      _jumpsize.push_back(0);
+    else if ( _maxsize[i] == _N_nuc )
+      _jumpsize.push_back( _maxsize[i+1]*0.5 - _maxsize[i]*0.5 + 0.5 );
+    else
+      _jumpsize.push_back( 0.5*_maxsize[i+1] - 0.5*_maxsize[i-1] );
+  }
+
   for ( int i=0; i<_G; ++i)
     _c.push_back( &coupledValue("coupled_conc", i) );
 
-  if ( _atoms.size() != _c.size() )
-    mooseError("In SinkGrowth: coupled_conc.size() != coupled_conc_atoms.size()");
+  // Buck::iterateAndDisplay("avg", _avgsize);
+  // Buck::iterateAndDisplay("max", _maxsize);
+  // Buck::iterateAndDisplay("jumpsize", _jumpsize);
 }
 
 Real
@@ -48,7 +70,7 @@ SinkGrowth::computeQpResidual()
   Real gains(0);
 
   losses = calcLosses();
-  if ( _atoms[_g] > _N_nuc )
+  if ( _avgsize[_g] > _N_nuc )
     gains = calcGains();
 
   return -( gains - losses * _u[_qp] ) * _test[_i][_qp];
@@ -80,19 +102,20 @@ SinkGrowth::calcLosses()
   {
     for ( int i=1; i<_G-1; ++i ) // iterate through clusters, except for largest size
     {
-      if ( _atoms[i] >= _N_nuc )
+      if ( _avgsize[i] >= _N_nuc ) // don't allow losses from nucleation model bubbles, except for N_nuc concentration
       {
-        radius = 1.0e9 * MaterialXeBubble::VDW_MtoR( _atoms[i], _temp[_qp], sigma );
-        losses += KoverR * radius * (*_c[i])[_qp]; // *_u[_qp] below
+        radius = 1.0e9 * MaterialXeBubble::VDW_MtoR( _avgsize[i], _temp[_qp], sigma );
+        losses += KoverR * radius * (*_c[i])[_qp] * _jumpsize[i]; // *_u[_qp] below
+        // std::cout << "i: " << i << " size: " << _avgsize[i] << " width: " << _width[i] << " width/2: " << ceil(_width[i]/2) << std::endl;
       }
     }
   }
   else // if bubble
   {
     // Losses due to this cluster absorbing atoms
-    if ( _g < _G-1 && _atoms[_g] >= _N_nuc ) // make sure it's not the largest bubble size
+    if ( _g < _G-1 && _avgsize[_g] >= _N_nuc ) // make sure it's not the largest bubble size
     {
-      radius = 1.0e9 * MaterialXeBubble::VDW_MtoR( _atoms[_g], _temp[_qp], sigma );
+      radius = 1.0e9 * MaterialXeBubble::VDW_MtoR( _avgsize[_g], _temp[_qp], sigma );
       losses += KoverR * radius * (*_c[0])[_qp]; // *_u[_qp] below
     }
   }
@@ -110,7 +133,7 @@ SinkGrowth::calcGains()
 
   Real KoverR = 4.0 * M_PI * _atomic_diffusivity[_qp]; // reaction co-efficient divided by radius
 
-  radius = 1.0e9 * MaterialXeBubble::VDW_MtoR( _atoms[_g-1], _temp[_qp], sigma );
+  radius = 1.0e9 * MaterialXeBubble::VDW_MtoR( _avgsize[_g-1], _temp[_qp], sigma );
   gain = KoverR * radius * (*_c[0])[_qp] * (*_c[_g-1])[_qp];
 
   return gain;

tests/clustersaction_growth/spacedout.i

@@ -0,0 +1,125 @@
+# Test for SinkGrowth action.
+# Sum should always be 400
+#
+# This should be exactly the same as tests/sinkgrowth/spacedout.i
+#
+# +----------------+----------------+----------------+----------------+----------------+----------------+----------------+
+# | time           | c1_conc        | c2_conc        | c3_conc        | c4_conc        | c5_conc        | sum            |
+# +----------------+----------------+----------------+----------------+----------------+----------------+----------------+
+# |   1.000000e+02 |   9.908314e-01 |   0.000000e+00 |   9.957639e-01 |   4.214605e-03 |   2.147220e-05 |   4.000000e+00 |
+# |   2.000000e+02 |   9.816081e-01 |   0.000000e+00 |   9.915849e-01 |   8.351485e-03 |   6.362455e-05 |   4.000000e+00 |
+# |   3.000000e+02 |   9.723358e-01 |   0.000000e+00 |   9.874625e-01 |   1.241178e-02 |   1.256786e-04 |   4.000000e+00 |
+# |   4.000000e+02 |   9.630203e-01 |   0.000000e+00 |   9.833965e-01 |   1.639663e-02 |   2.068700e-04 |   4.000000e+00 |
+# |   5.000000e+02 |   9.536671e-01 |   0.000000e+00 |   9.793864e-01 |   2.030718e-02 |   3.064487e-04 |   4.000000e+00 |
+# |   6.000000e+02 |   9.442816e-01 |   0.000000e+00 |   9.754317e-01 |   2.414458e-02 |   4.236794e-04 |   4.000000e+00 |
+# |   7.000000e+02 |   9.348690e-01 |   0.000000e+00 |   9.715322e-01 |   2.790998e-02 |   5.578416e-04 |   4.000000e+00 |
+# |   8.000000e+02 |   9.254344e-01 |   0.000000e+00 |   9.676872e-01 |   3.160452e-02 |   7.082301e-04 |   4.000000e+00 |
+# |   9.000000e+02 |   9.159826e-01 |   0.000000e+00 |   9.638965e-01 |   3.522935e-02 |   8.741551e-04 |   4.000000e+00 |
+# |   1.000000e+03 |   9.065184e-01 |   0.000000e+00 |   9.601595e-01 |   3.878560e-02 |   1.054942e-03 |   4.000000e+00 |
+# +----------------+----------------+----------------+----------------+----------------+----------------+----------------+
+
+[GlobalParams]
+  N_max = 20
+  G = 5
+  log = true
+  N_nuc = 3
+  temp = temp
+[]
+
+
+[Mesh]
+  type = GeneratedMesh
+  dim = 1
+[]
+
+
+[Clusters]
+  [./Growth]
+  [../]
+[]
+
+
+[ICs]
+  [./c3_ic]
+    type = ConstantIC
+    variable = c3
+    value = 1
+  [../]
+  [./c1_ic]
+    type = ConstantIC
+    variable = c1
+    value = 1
+  [../]
+[]
+
+
+[AuxVariables]
+  [./temp]
+    order = CONSTANT
+    family = MONOMIAL
+  [../]
+[]
+
+
+[AuxKernels]
+  [./temp_aux]
+    type = ConstantAux
+    variable = temp
+    value = 1000
+  [../]
+[]
+
+
+[Materials]
+  [./c1_diff]
+    type = AtomicDiffusionCoef
+    model = 1
+    factor = 1
+    block = 0
+  [../]
+[]
+
+
+[Executioner]
+  type = Transient
+
+  solve_type = PJFNK
+
+  num_steps = 10
+  dt = 100
+[]
+
+
+[Postprocessors]
+  [./c1_conc]
+    type = ElementIntegralVariablePostprocessor
+    variable = c1
+  [../]
+  [./c2_conc]
+    type = ElementIntegralVariablePostprocessor
+    variable = c2
+  [../]
+  [./c3_conc]
+    type = ElementIntegralVariablePostprocessor
+    variable = c3
+  [../]
+  [./c4_conc]
+    type = ElementIntegralVariablePostprocessor
+    variable = c4
+  [../]
+  [./c5_conc]
+    type = ElementIntegralVariablePostprocessor
+    variable = c5
+  [../]
+  [./sum]
+    type = SumOfPostprocessors
+    postprocessors = 'c1_conc c2_conc c3_conc c4_conc c5_conc'
+    factors = '1 2 3 5.12132 13.62132'
+  [../]
+[]
+
+[Outputs]
+  console = true
+  exodus = true
+  interval = 1
+[]

tests/clustersaction_growth/tests

@@ -4,4 +4,9 @@
     input = '3species.i'
     exodiff = '3species_out.e'
   [../]
+  [./spacedout]
+    type = 'Exodiff'
+    input = 'spacedout.i'
+    exodiff = 'spacedout_out.e'
+  [../]
 []

tests/sinkgrowth/3species.i

@@ -18,7 +18,7 @@
 
 [GlobalParams]
   coupled_conc = 'c1 c5 c6'
-  coupled_conc_atoms = '1 5 6'
+  coupled_maxsize = '1 5 6'
   N_nuc = 5
   temp = 1000
 []