[cig-commits] commit: Lots of input file fixes

Mercurial hg at geodynamics.org
Fri Nov 25 21:01:15 PST 2011


changeset:   436:eaa1483208eb
tag:         tip
user:        Walter Landry <wlandry at caltech.edu>
date:        Fri Nov 25 21:00:58 2011 -0800
files:       input/benchmarks/divergence.json input/benchmarks/thermal_diffusion.json input/benchmarks/thermal_eulerian.json input/cookbook/deforming_bottom.json input/cookbook/extension.json input/cookbook/extension3D.json input/cookbook/file.json input/cookbook/fixed_bottom.json input/cookbook/inflow_outflow.json input/cookbook/multi_material.json input/cookbook/non_newtonian.json input/cookbook/normal_stress.json input/cookbook/sinusoid.json input/cookbook/split.json input/cookbook/template.json input/cookbook/test.topo input/cookbook/thermal.json input/cookbook/thermal_file.json input/cookbook/thermal_only.json input/cookbook/tracers.json input/cookbook/viscous.json input/cookbook/yielding.json
description:
Lots of input file fixes


diff -r 8630c321b820 -r eaa1483208eb input/benchmarks/divergence.json
--- a/input/benchmarks/divergence.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/benchmarks/divergence.json	Fri Nov 25 21:00:58 2011 -0800
@@ -153,9 +153,8 @@
     "maxX": "2",
     "maxY": "2",
     "maxZ": "2",
-    "nx": "4",
-    "ny": "4",
-    "nz": "4",
+    "nx": "16",
+    "ny": "16",
     "particlesPerCell": "40",
     "seed": "13",
     "checkpointEvery": "1"
diff -r 8630c321b820 -r eaa1483208eb input/benchmarks/thermal_diffusion.json
--- a/input/benchmarks/thermal_diffusion.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/benchmarks/thermal_diffusion.json	Fri Nov 25 21:00:58 2011 -0800
@@ -22,7 +22,7 @@
             "Shape": "boxShape",
             "density": "1.0",
             "alpha": "1.0",
-            "diffusivity": "3.14159",
+            "diffusivity": "1.7",
             "heatingElements": [
                 {
                     "Q": "0.0",
@@ -32,6 +32,10 @@
             "Rheology": [
                 "backgroundViscosity"
             ]
+        },
+        "predictorMulticorrector":
+        {
+            "Type": "AdvDiffMulticorrector"
         }
     },
     "velocityICs":
@@ -72,7 +76,7 @@
                 "variables": [
                     {
                         "name": "temperature",
-                        "value": "1.0"
+                        "value": "0.0"
                     }
                 ]
             }
@@ -87,7 +91,7 @@
                 "variables":[
                     {
                         "name": "temperature",
-                        "value": "0.0"
+                        "value": "sin(2*pi*y)*cos(pi*x)"
                     }
                 ]
             }
@@ -99,7 +103,7 @@
     ],
     "enable-stokes": false,
     "enable-thermal": true,
-    "timeIntegratorOrder": "1",
+    // "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
@@ -108,12 +112,17 @@
     "minZ": "0",
     "maxX": "1",
     "maxY": "1",
-    "maxZ": "0.3",
+    "maxZ": "1",
     "nx": "8",
     "ny": "8",
-    "nz": "4",
+    "nz": "8",
     "particlesPerCell": "40",
     "seed": "13",
     "checkpointEvery": "1",
     "gravity": "1.0"
+// ,
+//     "journal.info": "True",
+//     "journal.debug": "True",
+//     "journal-level.info": "2",
+//     "journal-level.debug": "2"
 }
\ No newline at end of file
diff -r 8630c321b820 -r eaa1483208eb input/benchmarks/thermal_eulerian.json
--- a/input/benchmarks/thermal_eulerian.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/benchmarks/thermal_eulerian.json	Fri Nov 25 21:00:58 2011 -0800
@@ -1,20 +1,4 @@
 {
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "T-mesh": "T-mesh",
-                "displacementField": "DisplacementField",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "staticLeft": "True",
-                "staticRight": "True",
-                "staticTop": "True",
-                "staticBottom": "True"
-            }
-        ]
-    },
     "components":
     {
         "boxShape":
@@ -123,7 +107,7 @@
                 "variables":[
                     {
                         "name": "temperature",
-                        "value": "(x<.375 || x>.625 || y<.375 || y>.625) ? 1 : 2"
+                        "value": "(x<.375 || x>1 || y<.375 || y>1) ? 1 : 2"
                     }
                 ]
             }
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/deforming_bottom.json
--- a/input/cookbook/deforming_bottom.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/deforming_bottom.json	Fri Nov 25 21:00:58 2011 -0800
@@ -21,15 +21,10 @@
             "Swarm": "gaussSwarm",
             "gravity": "gravity"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "backgroundViscosity":
         {
@@ -39,7 +34,7 @@
         "viscous":
         {
             "Type": "RheologyMaterial",
-            "Shape": "boxShape",
+            "Shape": "backgroundShape",
             "density": "1.0",
             "Rheology": [
                 "backgroundViscosity",
@@ -64,11 +59,11 @@
                 "variables": [
                     {
                         "name": "vx",
-                        "value": "0.0"
+                        "value": "0"
                     },
                     {
                         "name": "vy",
-                        "value": "0.0"
+                        "value": "0"
                     }
                 ]
             },
@@ -94,7 +89,6 @@
         "VelocityField",
         "PressureField"
     ],
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/extension.json
--- a/input/cookbook/extension.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/extension.json	Fri Nov 25 21:00:58 2011 -0800
@@ -20,15 +20,10 @@
             "Swarm": "gaussSwarm",
             "gravity": "gravity"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "backgroundViscosity":
         {
@@ -38,7 +33,7 @@
         "viscous":
         {
             "Type": "RheologyMaterial",
-            "Shape": "boxShape",
+            "Shape": "backgroundShape",
             "density": "1.0",
             "Rheology": [
                 "backgroundViscosity",
@@ -88,7 +83,6 @@
         "VelocityField",
         "PressureField"
     ],
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/extension3D.json
--- a/input/cookbook/extension3D.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/extension3D.json	Fri Nov 25 21:00:58 2011 -0800
@@ -87,7 +87,7 @@
                 "variables": [
                     {
                         "name": "vx",
-                        "value": "0.0"
+                        "value": "0"
                     }
                 ]
             },
@@ -107,7 +107,7 @@
                 "variables": [
                     {
                         "name": "vy",
-                        "value": "0.0"
+                        "value": "0"
                     }
                 ]
             }
@@ -119,7 +119,6 @@
         "VelocityField",
         "PressureField"
     ],
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "3",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/file.json
--- a/input/cookbook/file.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/file.json	Fri Nov 25 21:00:58 2011 -0800
@@ -20,15 +20,10 @@
             "Swarm": "gaussSwarm",
             "gravity": "gravity"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "backgroundViscosity":
         {
@@ -38,7 +33,7 @@
         "viscous":
         {
             "Type": "RheologyMaterial",
-            "Shape": "boxShape",
+            "Shape": "backgroundShape",
             "density": "1.0",
             "Rheology": [
                 "backgroundViscosity",
@@ -93,7 +88,6 @@
         "VelocityField",
         "PressureField"
     ],
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/fixed_bottom.json
--- a/input/cookbook/fixed_bottom.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/fixed_bottom.json	Fri Nov 25 21:00:58 2011 -0800
@@ -23,15 +23,10 @@
             "Swarm": "gaussSwarm",
             "gravity": "gravity"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "backgroundViscosity":
         {
@@ -41,7 +36,7 @@
         "viscous":
         {
             "Type": "RheologyMaterial",
-            "Shape": "boxShape",
+            "Shape": "backgroundShape",
             "density": "1.0",
             "Rheology": [
                 "backgroundViscosity",
@@ -102,7 +97,6 @@
         "VelocityField",
         "PressureField"
     ],
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/inflow_outflow.json
--- a/input/cookbook/inflow_outflow.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/inflow_outflow.json	Fri Nov 25 21:00:58 2011 -0800
@@ -22,15 +22,10 @@
             "Swarm": "gaussSwarm",
             "gravity": "gravity"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "backgroundViscosity":
         {
@@ -40,7 +35,7 @@
         "viscous":
         {
             "Type": "RheologyMaterial",
-            "Shape": "boxShape",
+            "Shape": "backgroundShape",
             "density": "1.0",
             "Rheology": [
                 "backgroundViscosity",
@@ -94,7 +89,6 @@
         "VelocityField",
         "PressureField"
     ],
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/multi_material.json
--- a/input/cookbook/multi_material.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/multi_material.json	Fri Nov 25 21:00:58 2011 -0800
@@ -20,15 +20,10 @@
             "Swarm": "gaussSwarm",
             "gravity": "gravity"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "sphereShape":
         {
@@ -40,7 +35,7 @@
             "Type": "Intersection",
             "shapes":
             [
-                "boxShape",
+                "backgroundShape",
                 "!sphereShape"
             ]
         },
@@ -118,7 +113,6 @@
         "VelocityField",
         "PressureField"
     ],
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/non_newtonian.json
--- a/input/cookbook/non_newtonian.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/non_newtonian.json	Fri Nov 25 21:00:58 2011 -0800
@@ -23,15 +23,10 @@
             "gravity": "gravity",
             "TemperatureField": "TemperatureField"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "sphereShape":
         {
@@ -43,7 +38,7 @@
             "Type": "Intersection",
             "shapes":
             [
-                "boxShape",
+                "backgroundShape",
                 "!sphereShape"
             ]
         },
@@ -204,7 +199,6 @@
         "PressureField"
     ],
     "enable-thermal": true,
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
@@ -215,7 +209,7 @@
     "maxY": "0.35",
     "maxZ": "0.3",
     "nx": "16",
-    "ny": "4",
+    "ny": "8",
     "nz": "4",
     "particlesPerCell": "40",
     "seed": "13",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/normal_stress.json
--- a/input/cookbook/normal_stress.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/normal_stress.json	Fri Nov 25 21:00:58 2011 -0800
@@ -21,15 +21,10 @@
             "Swarm": "gaussSwarm",
             "gravity": "gravity"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "backgroundViscosity":
         {
@@ -39,7 +34,7 @@
         "viscous":
         {
             "Type": "RheologyMaterial",
-            "Shape": "boxShape",
+            "Shape": "backgroundShape",
             "density": "1.0",
             "Rheology": [
                 "backgroundViscosity",
@@ -64,11 +59,11 @@
                 "variables": [
                     {
                         "name": "vx",
-                        "value": "0.0"
+                        "value": "0"
                     },
                     {
                         "name": "vy",
-                        "value": "0.0"
+                        "value": "0"
                     }
                 ]
             },
@@ -94,7 +89,6 @@
         "VelocityField",
         "PressureField"
     ],
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/sinusoid.json
--- a/input/cookbook/sinusoid.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/sinusoid.json	Fri Nov 25 21:00:58 2011 -0800
@@ -90,7 +90,6 @@
         "VelocityField",
         "PressureField"
     ],
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/split.json
--- a/input/cookbook/split.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/split.json	Fri Nov 25 21:00:58 2011 -0800
@@ -20,15 +20,10 @@
             "Swarm": "gaussSwarm",
             "gravity": "gravity"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "backgroundViscosity":
         {
@@ -38,7 +33,7 @@
         "viscous":
         {
             "Type": "RheologyMaterial",
-            "Shape": "boxShape",
+            "Shape": "backgroundShape",
             "density": "1.0",
             "Rheology": [
                 "backgroundViscosity",
@@ -92,7 +87,6 @@
         "VelocityField",
         "PressureField"
     ],
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/template.json
--- a/input/cookbook/template.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/template.json	Fri Nov 25 21:00:58 2011 -0800
@@ -62,7 +62,6 @@
         "VelocityField",
         "PressureField"
     ],
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/test.topo
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/input/cookbook/test.topo	Fri Nov 25 21:00:58 2011 -0800
@@ -0,0 +1,384 @@
+   0    0   0.080000
+   0    1   0.080000
+   0    2   0.080000
+   0    3   0.080000
+   0    4   0.080000
+   0    5   0.080000
+   0    6   0.080000
+   0    7   0.080000
+   0    8   0.080000
+   0    9   0.080000
+   0   10   0.080000
+   0   11   0.080000
+   1    0   0.080000
+   1    1   0.080000
+   1    2   0.080000
+   1    3   0.080000
+   1    4   0.080000
+   1    5   0.080000
+   1    6   0.080000
+   1    7   0.080000
+   1    8   0.080000
+   1    9   0.080000
+   1   10   0.080000
+   1   11   0.080000
+   2    0   0.080000
+   2    1   0.080000
+   2    2   0.080000
+   2    3   0.080000
+   2    4   0.080000
+   2    5   0.080000
+   2    6   0.080000
+   2    7   0.080000
+   2    8   0.080000
+   2    9   0.080000
+   2   10   0.080000
+   2   11   0.080000
+   3    0   0.080000
+   3    1   0.080000
+   3    2   0.080000
+   3    3   0.080000
+   3    4   0.080000
+   3    5   0.080000
+   3    6   0.080000
+   3    7   0.080000
+   3    8   0.080000
+   3    9   0.080000
+   3   10   0.080000
+   3   11   0.080000
+   4    0   0.067500
+   4    1   0.067500
+   4    2   0.067500
+   4    3   0.067500
+   4    4   0.067500
+   4    5   0.067500
+   4    6   0.067500
+   4    7   0.067500
+   4    8   0.067500
+   4    9   0.067500
+   4   10   0.067500
+   4   11   0.067500
+   5    0   0.055000
+   5    1   0.055000
+   5    2   0.055000
+   5    3   0.055000
+   5    4   0.055000
+   5    5   0.055000
+   5    6   0.055000
+   5    7   0.055000
+   5    8   0.055000
+   5    9   0.055000
+   5   10   0.055000
+   5   11   0.055000
+   6    0   0.052222
+   6    1   0.052222
+   6    2   0.052222
+   6    3   0.052222
+   6    4   0.052222
+   6    5   0.052222
+   6    6   0.052222
+   6    7   0.052222
+   6    8   0.052222
+   6    9   0.052222
+   6   10   0.052222
+   6   11   0.052222
+   7    0   0.049444
+   7    1   0.049444
+   7    2   0.049444
+   7    3   0.049444
+   7    4   0.049444
+   7    5   0.049444
+   7    6   0.049444
+   7    7   0.049444
+   7    8   0.049444
+   7    9   0.049444
+   7   10   0.049444
+   7   11   0.049444
+   8    0   0.046667
+   8    1   0.046667
+   8    2   0.046667
+   8    3   0.046667
+   8    4   0.046667
+   8    5   0.046667
+   8    6   0.046667
+   8    7   0.046667
+   8    8   0.046667
+   8    9   0.046667
+   8   10   0.046667
+   8   11   0.046667
+   9    0   0.043889
+   9    1   0.043889
+   9    2   0.043889
+   9    3   0.043889
+   9    4   0.043889
+   9    5   0.043889
+   9    6   0.043889
+   9    7   0.043889
+   9    8   0.043889
+   9    9   0.043889
+   9   10   0.043889
+   9   11   0.043889
+  10    0   0.041111
+  10    1   0.041111
+  10    2   0.041111
+  10    3   0.041111
+  10    4   0.041111
+  10    5   0.041111
+  10    6   0.041111
+  10    7   0.041111
+  10    8   0.041111
+  10    9   0.041111
+  10   10   0.041111
+  10   11   0.041111
+  11    0   0.038333
+  11    1   0.038333
+  11    2   0.038333
+  11    3   0.038333
+  11    4   0.038333
+  11    5   0.038333
+  11    6   0.038333
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diff -r 8630c321b820 -r eaa1483208eb input/cookbook/thermal.json
--- a/input/cookbook/thermal.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/thermal.json	Fri Nov 25 21:00:58 2011 -0800
@@ -23,15 +23,10 @@
             "gravity": "gravity",
             "TemperatureField": "TemperatureField"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "sphereShape":
         {
@@ -43,7 +38,7 @@
             "Type": "Intersection",
             "shapes":
             [
-                "boxShape",
+                "backgroundShape",
                 "!sphereShape"
             ]
         },
@@ -199,7 +194,6 @@
         "PressureField"
     ],
     "enable-thermal": true,
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/thermal_file.json
--- a/input/cookbook/thermal_file.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/thermal_file.json	Fri Nov 25 21:00:58 2011 -0800
@@ -23,15 +23,10 @@
             "gravity": "gravity",
             "TemperatureField": "TemperatureField"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "sphereShape":
         {
@@ -43,7 +38,7 @@
             "Type": "Intersection",
             "shapes":
             [
-                "boxShape",
+                "backgroundShape",
                 "!sphereShape"
             ]
         },
@@ -200,7 +195,6 @@
         "PressureField"
     ],
     "enable-thermal": true,
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/thermal_only.json
--- a/input/cookbook/thermal_only.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/thermal_only.json	Fri Nov 25 21:00:58 2011 -0800
@@ -15,15 +15,10 @@
     },
     "components":
     {
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "sphereShape":
         {
@@ -35,7 +30,7 @@
             "Type": "Intersection",
             "shapes":
             [
-                "boxShape",
+                "backgroundShape",
                 "!sphereShape"
             ]
         },
@@ -46,19 +41,14 @@
         },
         "viscous":
         {
-            "Type": "RheologyMaterial",
+            "Type": "Material",
             "Shape": "nonsphereShape",
-            "density": "1.0",
-            "alpha": "1.0",
             "diffusivity": "1.0",
             "heatingElements": [
                 {
                     "Q": "1.0",
                     "lambda": "1.0"
                 }
-            ],
-            "Rheology": [
-                "backgroundViscosity"
             ]
         },
         "sphereViscosity":
@@ -68,19 +58,14 @@
         },
         "sphereViscous":
         {
-            "Type": "RheologyMaterial",
+            "Type": "Material",
             "Shape": "sphereShape",
-            "density": "1.0",
-            "alpha": "10.0",
             "diffusivity": "10.0",
             "heatingElements": [
                 {
                     "Q": "1000.0",
                     "lambda": "10.0"
                 }
-            ],
-            "Rheology": [
-                "sphereViscosity"
             ]
         }
     },
@@ -93,11 +78,11 @@
                 "variables":[
                     {
                         "name": "vx",
-                        "value": "0.0"
+                        "value": "0"
                     },
                     {
                         "name": "vy",
-                        "value": "0.0"
+                        "value": "0"
                     }
                 ]
             }
@@ -170,7 +155,6 @@
     ],
     "enable-thermal": true,
     "enable-stokes": false,
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/tracers.json
--- a/input/cookbook/tracers.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/tracers.json	Fri Nov 25 21:00:58 2011 -0800
@@ -23,15 +23,10 @@
             "Swarm": "gaussSwarm",
             "gravity": "gravity"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "backgroundViscosity":
         {
@@ -41,7 +36,7 @@
         "viscous":
         {
             "Type": "RheologyMaterial",
-            "Shape": "boxShape",
+            "Shape": "backgroundShape",
             "density": "1.0",
             "Rheology": [
                 "backgroundViscosity",
@@ -60,7 +55,6 @@
         "pLayout":
         {
             "Type": "ManualParticleLayout",
-            "totalInitialParticles": "1",
             "manualParticlePositions": [
                 "asciidata",
                 ["x", "y"],
@@ -130,7 +124,6 @@
         "PressureField"
     ],
     "enable-tracers": true,
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "100",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/viscous.json
--- a/input/cookbook/viscous.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/viscous.json	Fri Nov 25 21:00:58 2011 -0800
@@ -20,15 +20,10 @@
             "Swarm": "gaussSwarm",
             "gravity": "gravity"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "backgroundViscosity":
         {
@@ -38,7 +33,7 @@
         "viscous":
         {
             "Type": "RheologyMaterial",
-            "Shape": "boxShape",
+            "Shape": "backgroundShape",
             "density": "1.0",
             "Rheology": [
                 "backgroundViscosity",
@@ -88,7 +83,6 @@
         "VelocityField",
         "PressureField"
     ],
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",
diff -r 8630c321b820 -r eaa1483208eb input/cookbook/yielding.json
--- a/input/cookbook/yielding.json	Fri Nov 25 11:01:26 2011 -0800
+++ b/input/cookbook/yielding.json	Fri Nov 25 21:00:58 2011 -0800
@@ -20,15 +20,10 @@
             "Swarm": "gaussSwarm",
             "gravity": "gravity"
         },
-        "boxShape":
+        "backgroundShape":
         {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
+            "Type": "EquationShape",
+            "equation": "1"
         },
         "sphereShape":
         {
@@ -40,7 +35,7 @@
             "Type": "Intersection",
             "shapes":
             [
-                "boxShape",
+                "backgroundShape",
                 "!sphereShape"
             ]
         },
@@ -145,7 +140,6 @@
         "VelocityField",
         "PressureField"
     ],
-    "timeIntegratorOrder": "1",
     "maxTimeSteps": "10",
     "outputPath": "./output",
     "dim": "2",



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