Merge branch 'master' into nc-jump

CMakeLists.txt

@@ -9,25 +9,30 @@ include(testing)
 
 option(ENABLE_UNIT_TESTS "Enable unit testing" OFF)
 option(AutodetectMPI "Automatically detect MPI" ON)
+option(ENABLE_CEDAR "Enable Cedar solver" OFF)
 
 enable_language(C CXX Fortran)
 
-find_package(PETSc REQUIRED)
-#if(PETSC_VERSION VERSION_LESS 3.7.0)
-  #message(FATAL_ERROR "ERROR: stella requires PETSc 3.7.0 or newer.")
-#endif()
-
 set(req-lib ${PETSC_LIBRARIES} m)
 set(req-inc ${PETSC_INCLUDES})
-set(req-def PETSC_OPTIONS_TAKES_DATABASE)
+set(req-def "")
+
+find_package(PETSc REQUIRED)
+list(APPEND req-def PETSC_OPTIONS_TAKES_DATABASE)
+# if(PETSC_VERSION)
+#   if(NOT (${PETSC_VERSION} VERSION_LESS 3.7.0))
+# 	list(APPEND req-def PETSC_OPTIONS_TAKES_DATABASE)
+#   endif()
+# endif()
 
 if(AutodetectMPI)
   find_package(MPI REQUIRED)
   list(APPEND req-lib ${MPI_C_LIBRARIES})
   list(APPEND req-inc ${MPI_C_INCLUDE_PATH})
 endif()
-find_package(cedar QUIET)
-if (cedar_FOUND)
+
+if(ENABLE_CEDAR)
+  find_package(cedar REQUIRED)
   list(APPEND req-inc ${CEDAR_INCLUDE_DIR})
   list(APPEND req-lib cedar)
   list(APPEND req-def WITH_CEDAR)

src/CMakeLists.txt

@@ -1,4 +1,4 @@
-set(stella_sources
+set(sources
   ${CMAKE_CURRENT_SOURCE_DIR}/stella_bc.c
   ${CMAKE_CURRENT_SOURCE_DIR}/stella_boundary.c
   ${CMAKE_CURRENT_SOURCE_DIR}/stella_dirichlet.c
@@ -15,6 +15,10 @@ set(stella_sources
   ${CMAKE_CURRENT_SOURCE_DIR}/stella_stencil.c
   ${CMAKE_CURRENT_SOURCE_DIR}/stella_signals.c
   ${CMAKE_CURRENT_SOURCE_DIR}/stella_classify.c
-  ${CMAKE_CURRENT_SOURCE_DIR}/stella_util.c
-  ${CMAKE_CURRENT_SOURCE_DIR}/stella_cedar.c
-  PARENT_SCOPE)
+  ${CMAKE_CURRENT_SOURCE_DIR}/stella_util.c)
+
+if (ENABLE_CEDAR)
+  list(APPEND sources ${CMAKE_CURRENT_SOURCE_DIR}/stella_cedar.c)
+endif()
+
+set(stella_sources ${sources} PARENT_SCOPE)

src/stella_io.c

@@ -57,7 +57,7 @@ PetscErrorCode stella_io_print(MPI_Comm comm, char *msg)
 {
 	PetscErrorCode ierr;
 
-	ierr = PetscPrintf(comm, "PlasComCM: %s\n", msg);CHKERRQ(ierr);
+	ierr = PetscPrintf(comm, "stella: %s\n", msg);CHKERRQ(ierr);
 
 	return 0;
 }

src/stella_solver.c

@@ -318,13 +318,6 @@ PetscErrorCode stella_solve(stella *slv)
 	// Update external array with solution
 	ierr = update_solution(slv);CHKERRQ(ierr);
 
-	if (stella_log(slv, STELLA_LOG_PROBLEM)) {
-		PetscViewer vout;
-		ierr = PetscViewerBinaryOpen(slv->comm, "sol.dat", FILE_MODE_WRITE, &vout);CHKERRQ(ierr);
-		ierr = VecView(slv->x, vout);CHKERRQ(ierr);
-		ierr = PetscViewerDestroy(&vout);CHKERRQ(ierr);
-	}
-
 	return 0;
 }
 

tools/single-block/config.json

@@ -0,0 +1,16 @@
+{
+	"log": ["status","error"],
+	"solver":
+	{
+		"cycle":
+		{
+			"nrelax-pre": 2,
+			"nrelax-post": 1
+		},
+		"relaxation": "point",
+		"tol": 1e-10,
+		"max-iter": 10,
+		"min-coarse": 3,
+		"cg-solver": "LU"
+	}
+}

tools/single-block/grid.c

@@ -156,27 +156,23 @@ grid *grid_create(double startx, double endx, int nx,
 	grd->hy = (endy - starty) / (grd->num_global[1] - 1);
 	grd->hz = (endz - startz) / (grd->num_global[2] - 1);
 
-	startx = startx + (grd->is[0]-1)*grd->hx - grd->ibeg[0]*grd->hx;
-	starty = starty + (grd->is[1]-1)*grd->hy - grd->ibeg[1]*grd->hy;
-	startz = startz + (grd->is[2]-1)*grd->hz - grd->ibeg[2]*grd->hz;
-
 	if (grd->nd == 3) {
 		for (k = 0; k < grd->len[2]; k++) {
 			for (j = 0; j < grd->len[1]; j++) {
 				for (i = 0; i < grd->len[0]; i++) {
 					ind = k*grd->len[0]*grd->len[1] + j*grd->len[0] + i;
-					grd->x[ind] = startx + i*grd->hx;
-					grd->y[ind] = starty + j*grd->hy;
-					grd->z[ind] = startz + k*grd->hz;
+					grd->x[ind] = startx + (grd->is[0]-1-grd->ibeg[0]+i)*grd->hx;
+					grd->y[ind] = starty + (grd->is[1]-1-grd->ibeg[1]+j)*grd->hy;
+					grd->z[ind] = startz + (grd->is[2]-1-grd->ibeg[2]+k)*grd->hz;
 				}
 			}
 		}
 	} else {
 		for (j = 0; j < grd->len[1]; j++) {
 			for (i = 0; i < grd->len[0]; i++) {
 				ind = j*grd->len[0] + i;
-				grd->x[ind] = startx + i*grd->hx;
-				grd->y[ind] = starty + j*grd->hy;
+				grd->x[ind] = startx + (grd->is[0]-1-grd->ibeg[0]+i)*grd->hx;
+				grd->y[ind] = starty + (grd->is[1]-1-grd->ibeg[1]+j)*grd->hy;
 			}
 		}
 	}