added regression tests and function descriptions

demo/richards/richards-driver-snes-initial-cond-anisotropic-k.regression.gold

@@ -0,0 +1,5 @@
+-- PRESSURE: Liquid Pressure --
+      Max:   9.9000539440768e+04
+      Min:   9.9000489163783e+04
+     Mean:   9.9000513212237e+04
+        0:   9.9000489163783e+04

demo/richards/richards-driver-snes-initial-cond-isotropic-k.regression.gold

@@ -0,0 +1,5 @@
+-- PRESSURE: Liquid Pressure --
+      Max:   9.9000582419508e+04
+      Min:   9.9000529724118e+04
+     Mean:   9.9000555854316e+04
+        0:   9.9000529724118e+04

demo/richards/richards.cfg

@@ -1,6 +1,8 @@
 [suites]
 standard=
 	richards-driver-snes-prob1
+	richards-driver-snes-initial-cond-isotropic-k
+	richards-driver-snes-initial-cond-anisotropic-k
 	#richards-driver-ts-prob1
 
 standard_parallel=
@@ -25,3 +27,8 @@ np=4
 timeout=300.
 input_arguments=-dim 3 -Nx 3 -Ny 3 -Nz 3 -tdy_water_density exponential -tdy_regression_test -tdy_regression_test_num_cells_per_process 1 -tdy_regression_test_filename richards-driver-ts-prob1-np4 -tdy_final_time 3.1536e3 -tdy_dt_max 600. -tdy_dt_growth_factor 1.5 -tdy_timers -tdy_init_with_random_field -tdy_time_integration_method TS
 
+[richards-driver-snes-initial-cond-isotropic-k]
+input_arguments=-dim 3 -Nx 5 -Ny 4 -Nz 3 -tdy_water_density exponential -tdy_regression_test -tdy_regression_test_num_cells_per_process 1 -tdy_regression_test_filename richards-driver-snes-initial-cond-isotropic-k -tdy_final_time 3.1536e3 -tdy_dt_max 600. -tdy_dt_growth_factor 1.5 -tdy_time_integration_method SNES -init_permeability_file initial.h5 -ic_file initial.h5
+
+[richards-driver-snes-initial-cond-anisotropic-k]
+input_arguments=-dim 3 -Nx 5 -Ny 4 -Nz 3 -tdy_water_density exponential -tdy_regression_test -tdy_regression_test_num_cells_per_process 1 -tdy_regression_test_filename richards-driver-snes-initial-cond-anisotropic-k -tdy_final_time 3.1536e3 -tdy_dt_max 600. -tdy_dt_growth_factor 1.5 -tdy_time_integration_method SNES -init_porosity_file initial.h5 -init_permeability_file initial.h5 -anisotropic_perm -ic_file initial.h5 -ic_dataset fields/IC

src/tdyio.c

@@ -87,6 +87,11 @@ PetscErrorCode TDyIOSetPrintIntermediate(TDyIO io, PetscBool flag){
   PetscFunctionReturn(0);
 }
 
+/* -------------------------------------------------------------------------- */
+/// Reads in and sets initial permeability for the TDy solver
+///
+/// @param [inout] tdy A TDy struct
+/// @returns 0 on success, or a non-zero error code on failure
 PetscErrorCode TDyIOReadPermeability(TDy tdy){
   PetscFunctionBegin;
   PetscInt cStart,cEnd,ncell,c,n,BlockSize;
@@ -162,6 +167,11 @@ PetscErrorCode TDyIOReadPermeability(TDy tdy){
   PetscFunctionReturn(0);
 }
 
+/* -------------------------------------------------------------------------- */
+/// Reads in and sets initial porosity for the TDy solver
+///
+/// @param [inout] tdy A TDy struct
+/// @returns 0 on success, or a non-zero error code on failure
 PetscErrorCode TDyIOReadPorosity(TDy tdy){
   PetscFunctionBegin;
   PetscInt cStart,cEnd,ncell,c;
@@ -192,6 +202,11 @@ PetscErrorCode TDyIOReadPorosity(TDy tdy){
   PetscFunctionReturn(0);
 }
 
+/* -------------------------------------------------------------------------- */
+/// Reads in and sets initial condition for the TDy solver
+///
+/// @param [inout] tdy A TDy struct
+/// @returns 0 on success, or a non-zero error code on failure
 PetscErrorCode TDyIOReadIC(TDy tdy){
   PetscFunctionBegin;
   PetscInt cStart,cEnd,ncell,c;
@@ -209,20 +224,28 @@ PetscErrorCode TDyIOReadIC(TDy tdy){
     strcpy(VariableName, tdy->io->ic_dataset);
   }
 
-  ierr = DMPlexGetHeightStratum(tdy->dm,0,&cStart,&cEnd);CHKERRQ(ierr);
-  ncell = (cEnd-cStart);
   ierr = VecCreate(PETSC_COMM_WORLD,&u);
-  ierr = VecSetSizes(u,ncell,PETSC_DECIDE);
 
   ierr = PetscObjectSetName((PetscObject) u, VariableName);
 
   ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD,tdy->io->ic_filename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
   ierr = VecLoad(u,viewer);CHKERRQ(ierr);
+
   ierr = TDyNaturaltoLocal(tdy->dm,u,&u_local);CHKERRQ(ierr);
+
   ierr = TDySetInitialCondition(tdy,u_local);CHKERRQ(ierr);
   PetscFunctionReturn(0); 
 }
 
+/* -------------------------------------------------------------------------- */
+/// Reads in and sets initial permeability for the TDy solver
+///
+/// @param [inout] tdy A TDy struct
+/// @param [in] VariableName A char that is set as the variable name for the
+///                          PETSc vector read in from the HDF5 file
+/// @param [in] filename A char that is the filename of the HDF5 file
+/// @param [inout] variable A pointer to the values read in from HDF5 file 
+/// @returns 0 on success, or a non-zero error code on failure
 PetscErrorCode TDyIOReadVariable(TDy tdy, char *VariableName, char *filename, PetscReal **variable){
   PetscFunctionBegin;
   PetscErrorCode ierr;
@@ -237,8 +260,9 @@ PetscErrorCode TDyIOReadVariable(TDy tdy, char *VariableName, char *filename, Pe
 
   ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
   ierr = VecLoad(u,viewer);CHKERRQ(ierr);
-
+  
   ierr = TDyNaturaltoLocal(tdy->dm,u,&u_local);CHKERRQ(ierr);
+
   ierr = VecGetArray(u_local,&ptr);CHKERRQ(ierr);
   ierr = VecGetSize(u_local,&n);CHKERRQ(ierr);