add SCAL file

docs/source/examples/color/steadyState.rst

@@ -1,5 +1,120 @@
-*******************
-Steady-state flow
-*******************
+********************************
+Steady-state flow (color model)
+********************************
+
+In this example we simulate a steady-state flow with a constant driving force. This will enforce a periodic boundary condition
+in all directions. While the driving force may be set in any direction, we will set it in the z-direction to be consistent
+with the convention for pressure and velocity boundary conditions. 
+
+
+For the case considered in ``example/DiscPack`` we specify the following information in the input file
+
+.. code:: c
+
+	  Domain {
+	     Filename = "discs_3x128x128.raw.morphdrain.raw"
+	     ReadType = "8bit"    // data type
+	     N = 3, 128, 128       // size of original image
+	     nproc = 1, 2, 2       // process grid
+	     n = 3, 64, 64         // sub-domain size
+	     voxel_length = 1.0    // voxel length (in microns)
+	     ReadValues = 0, 1, 2  // labels within the original image
+	     WriteValues = 0, 1, 2 // associated labels to be used by LBPM
+	     BC = 0                // fully periodic BC
+	     Sw = 0.35             // target saturation for morphological tools
+	  }
+
+	  Color {
+	     capillary_number = -1e-5           // capillary number for the displacement, positive="oil injection"
+	     timestepMax = 20000              // maximum timtestep
+	     alpha = 0.01                       // controls interfacial tension
+	     rhoA = 1.0                         // controls the density of fluid A
+	     rhoB = 1.0                         // controls the density of fluid B
+	     tauA = 0.7                         // controls the viscosity of fluid A
+	     tauB = 0.7                         // controls the viscosity of fluid B
+	     F = 0, 0, 1e-5                     // body force
+	     WettingConvention = "SCAL" 
+	     ComponentLabels = 0        // image labels for solid voxels
+	     ComponentAffinity = 0.9  // controls the wetting affinity for each label
+	     Restart = false
+	  }
+	  Analysis {
+	     analysis_interval = 1000           // logging interval for timelog.csv
+	     subphase_analysis_interval = 500000  // loggging interval for subphase.csv
+	     N_threads = 4                      // number of analysis threads (GPU version only)
+	     visualization_interval = 10000    // interval to write visualization files
+	     restart_interval = 10000000         // interval to write restart file
+	     restart_file = "Restart"           // base name of restart file
+	  }
+	  Visualization {
+	     format = "hdf5"
+	     write_silo = true        // write SILO databases with assigned variables
+	     save_8bit_raw = true      // write labeled 8-bit binary files with phase assignments
+	     save_phase_field = true  // save phase field within SILO database
+	     save_pressure = true     // save pressure field within SILO database
+	     save_velocity = false     // save velocity field within SILO database
+	  }
+	  FlowAdaptor {
+	  }
+
+	  
+Once this has been set, we launch ``lbpm_color_simulator`` in the same way as other parallel tools
+
+.. code:: bash
+
+	  mpirun -np 4 $LBPM_BIN/lbpm_color_simulator input.db
+
+Successful output looks like the following
+
+
+.. code:: bash
+
+      ********************************************************
+      Running Color LBM	
+      ********************************************************
+      voxel length = 1.000000 micron 
+      voxel length = 1.000000 micron 
+      Input media: discs_3x128x128.raw.morphdrain.raw
+      Relabeling 3 values
+      oldvalue=0, newvalue =0 
+      oldvalue=1, newvalue =1 
+      oldvalue=2, newvalue =2 
+      Dimensions of segmented image: 3 x 128 x 128 
+      Reading 8-bit input data 
+      Read segmented data from discs_3x128x128.raw.morphdrain.raw 
+      Label=0, Count=11862 
+      Label=1, Count=26430 
+      Label=2, Count=10860 
+      Distributing subdomains across 4 processors 
+      Process grid: 1 x 2 x 2 
+      Subdomain size: 3 x 64 x 64 
+      Size of transition region: 0 
+      Media porosity = 0.758667 
+      Initialized solid phase -- Converting to Signed Distance function 
+      Domain set.
+      Create ScaLBL_Communicator 
+      Set up memory efficient layout, 9090 | 9120 | 21780 
+      Allocating distributions 
+      Setting up device map and neighbor list 
+      Component labels: 1 
+	 label=0, affinity=-0.900000, volume fraction==0.417582
+      Initializing distributions 
+      Initializing phase field 
+      Affinities - rank 0:
+      Main: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
+      Thread 1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
+      Thread 2: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
+      Thread 3: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
+      Thread 4: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
+      Affinities - rank 0:
+      Main: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
+      Thread 1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
+      Thread 2: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
+      Thread 3: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
+      Thread 4: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
+      ********************************************************
+      CPU time = 0.001501 
+      Lattice update rate (per core)= 6.074861 MLUPS 
+      Lattice update rate (per MPI process)= 6.074861 MLUPS 
+	 (flatten density field)  
 
-In this example we simulate a steady-state flow with a constant driving force.

docs/source/userGuide/models/mrt/mrt.rst

@@ -225,4 +225,5 @@ Example Input File
       InletLayers = 0, 0, 10 // specify 10 layers along the z-inlet
       BC = 0                 // boundary condition type (0 for periodic)
    }
- 
+   Visualization {
+   }