From b4795c53c011572cd7708dedb26f15058d6c9363 Mon Sep 17 00:00:00 2001
From: micahjohnson150 <micah.johnson150@gmail.com>
Date: Tue, 15 Jul 2014 17:10:47 -0600
Subject: [PATCH] working on problems, found memory leak

---
 problems/2D_full/imported_initial_full.i | 12 +++---------
 problems/2D_full/phi_T_initial.i         | 13 ++++++-------
 python/KaempferPlapp2009.py              |  4 ++--
 src/ics/ChemicalPotentialIC.C            |  9 +--------
 src/kernels/PhaseTransition.C            |  4 +++-
 5 files changed, 15 insertions(+), 27 deletions(-)

diff --git a/problems/2D_full/imported_initial_full.i b/problems/2D_full/imported_initial_full.i
index f37f8b56..ad09cd75 100644
--- a/problems/2D_full/imported_initial_full.i
+++ b/problems/2D_full/imported_initial_full.i
@@ -2,7 +2,6 @@
   type = FileMesh
   file = phi_temp_diffusion_0010_mesh.xdr
   dim = 2
-  uniform_refine = 1
 []
 
 [Variables]
@@ -145,14 +144,6 @@
   [../]
 []
 
-[Preconditioning]
-  [./smp_precond]
-    type = SMP
-    off_diag_row = u
-    off_diag_column = T
-  [../]
-[]
-
 [Executioner]
   # Preconditioned JFNK (default)
   type = Transient
@@ -257,5 +248,8 @@
   temperature = T
   interface_thickness = 1e-5
   temporal_scaling = 1e-4
+  output_properties = 'diffusion_coefficient conductivity latent_heat tau lambda'
+  outputs = all
+  conversion_factor = 1000
 []
 
diff --git a/problems/2D_full/phi_T_initial.i b/problems/2D_full/phi_T_initial.i
index d54bd4f6..db1eb826 100644
--- a/problems/2D_full/phi_T_initial.i
+++ b/problems/2D_full/phi_T_initial.i
@@ -1,11 +1,10 @@
 [Mesh]
   type = GeneratedMesh
   dim = 2
-  nx = 15
-  ny = 15
+  nx = 30
+  ny = 30
   xmax = 5 # mm
   ymax = 5 # mm
-  uniform_refine = 2
   elem_type = QUAD4
 []
 
@@ -127,8 +126,8 @@
 []
 
 [Adaptivity]
-  max_h_level = 6
-  initial_steps = 6
+  max_h_level = 4
+  initial_steps = 4
   initial_marker = phi_marker
   marker = phi_marker
   [./Indicators]
@@ -146,9 +145,9 @@
     active = 'phi_marker'
     [./phi_marker]
       type = ErrorFractionMarker
-      coarsen = .02
+      coarsen = .01
       indicator = phi_grad_indicator
-      refine = .5
+      refine = .8
     [../]
     [./T_marker]
       type = ErrorFractionMarker
diff --git a/python/KaempferPlapp2009.py b/python/KaempferPlapp2009.py
index 33e80691..e0f9dbd5 100755
--- a/python/KaempferPlapp2009.py
+++ b/python/KaempferPlapp2009.py
@@ -59,5 +59,5 @@
 print "rho_vs(268.15) = ", rho_vs.evalf(subs={T: 263.15})
 
 print ""
-print "u_eq(263.15) = ", u_eq.evalf(subs={T: 263.15})
-print "u_eq(268.15) = ", u_eq.evalf(subs={T: 268.15})
+print "u_eq(263.15) = ", u_eq.evalf(subs={T: 264.8})
+print "u_eq(268.15) = ", u_eq.evalf(subs={T: 267.515})
diff --git a/src/ics/ChemicalPotentialIC.C b/src/ics/ChemicalPotentialIC.C
index b1bf19f7..d5efae79 100644
--- a/src/ics/ChemicalPotentialIC.C
+++ b/src/ics/ChemicalPotentialIC.C
@@ -21,12 +21,5 @@ ChemicalPotentialIC::ChemicalPotentialIC(const std::string & name, InputParamete
 Real
 ChemicalPotentialIC::value(const Point & /*p*/)
 {
-  if (_phase[_qp]<0.95)
-  {
-    Real f =  _property_uo.equilibriumConcentration(_temperature[_qp]) * (1.0-_phase[_qp])/2.0;
-    std::cout<<_temperature[_qp]<<' ' <<_phase[_qp]<< ' '<<f<<std::endl; 
-    return f;
-  }    
-  else
-    return 0.0;
+  return _property_uo.equilibriumConcentration(_temperature[_qp]) * (1.0 - _phase[_qp])/2.0;
 }
diff --git a/src/kernels/PhaseTransition.C b/src/kernels/PhaseTransition.C
index b31c7f23..d854fb60 100644
--- a/src/kernels/PhaseTransition.C
+++ b/src/kernels/PhaseTransition.C
@@ -26,8 +26,10 @@ PhaseTransition::computeDFDOP(PFFunctionType type)
 {
   switch (type)
   { 
+  Real f =  -(_lambda[_qp]) * (_s[_qp] - _s_eq[_qp]) * (1.0 - _u[_qp]*_u[_qp])*(1.0 - _u[_qp]*_u[_qp]);
+    std::cout<<f<<std::endl;
     case Residual:
-      return -(_lambda[_qp]) * (_s[_qp] - _s_eq[_qp]) * (1.0 - _u[_qp]*_u[_qp])*(1.0 - _u[_qp]*_u[_qp]);
+     return f;
 
     case Jacobian:
       return  4.0 * _lambda[_qp] * _u[_qp] * (-_u[_qp]*_u[_qp]+1.0) * ( _s[_qp] - (_s_eq[_qp]));