Merge branch 'master' of carpetgit@carpetcode.org:carpet

5 files changed, 41 insertions, 6 deletions

diff --git a/Carpet/CarpetLib/src/mem.cc b/Carpet/CarpetLib/src/mem.cc
index 89d8fb211..df374ae3e 100644
--- a/Carpet/CarpetLib/src/mem.cc
+++ b/Carpet/CarpetLib/src/mem.cc
@@ -105,6 +105,7 @@ mem (size_t const vectorlength, size_t const nelems,
       size_t const max_cache_linesize = get_max_cache_linesize();
       size_t const vector_size = CCTK_REAL_VEC_SIZE * sizeof(T);
       size_t const alignment = align_up(max_cache_linesize, vector_size);
+      assert(alignment >= 1);
       // Safety check
       assert(alignment <= 1024);
       // Assume optimistically that operator new returns well-aligned
@@ -123,7 +124,8 @@ mem (size_t const vectorlength, size_t const nelems,
       } else {
       allocate_with_alignment:
         // Operator new needs manual alignment
-        size_t const max_padding = alignment / sizeof(T) - 1;
+        size_t const max_padding = div_up(alignment, sizeof(T));
+        assert(ptrdiff_t(max_padding) >= 0);
         storage_base_ = new T [vectorlength * nelems + max_padding];
         storage_ = (T*) (size_t(storage_base_ + max_padding) & ~(alignment-1));
         assert(size_t(storage_) >= size_t(storage_base_              ) and
diff --git a/Carpet/CarpetReduce/src/mask_coords.c b/Carpet/CarpetReduce/src/mask_coords.c
index 0a07bc854..afdc79410 100644
--- a/Carpet/CarpetReduce/src/mask_coords.c
+++ b/Carpet/CarpetReduce/src/mask_coords.c
@@ -1,4 +1,5 @@
 #include <assert.h>
+#include <stdlib.h>
 
 #include <cctk.h>
 #include <cctk_Arguments.h>
@@ -21,6 +22,7 @@ CoordBase_SetupMask (CCTK_ARGUMENTS)
   CCTK_INT is_internal[2*cctk_dim];
   CCTK_INT is_staggered[2*cctk_dim];
   CCTK_INT shiftout[2*cctk_dim];
+  CCTK_INT is_periodic[2*cctk_dim];
   
   int bnd_points[2*cctk_dim];   /* points outside the domain */
   int int_points[cctk_dim];     /* global interior points */
@@ -52,6 +54,28 @@ CoordBase_SetupMask (CCTK_ARGUMENTS)
   
   
   
+  for (int d=0; d<cctk_dim; ++d) {
+    for (int f=0; f<2; ++f) {
+      is_periodic[2*d+f] = 0;
+    }
+  }
+  CCTK_INT const *const periodic =
+    CCTK_ParameterGet("periodic", "PeriodicCarpet", NULL);
+  CCTK_INT const *const periodic_x =
+    CCTK_ParameterGet("periodic_x", "PeriodicCarpet", NULL);
+  CCTK_INT const *const periodic_y =
+    CCTK_ParameterGet("periodic_x", "PeriodicCarpet", NULL);
+  CCTK_INT const *const periodic_z =
+    CCTK_ParameterGet("periodic_x", "PeriodicCarpet", NULL);
+  is_periodic[0] = is_periodic[1] =
+    (periodic && *periodic) || (periodic_x && *periodic_x);
+  is_periodic[2] = is_periodic[3] =
+    (periodic && *periodic) || (periodic_y && *periodic_y);
+  is_periodic[4] = is_periodic[5] =
+    (periodic && *periodic) || (periodic_z && *periodic_z);
+ 
+  
+  
   /* Calculate the number of boundary points. This excludes points
      that are directly on the boundary. */
   for (int d=0; d<cctk_dim; ++d) {
@@ -62,8 +86,12 @@ CoordBase_SetupMask (CCTK_ARGUMENTS)
         bnd_points[2*d+f] = shiftout[2*d+f];
       } else {
         /* The boundary extends outwards */
-        bnd_points[2*d+f] =
-          nboundaryzones[2*d+f] + shiftout[2*d+f] + is_staggered[2*d+f] - 1;
+        if (is_periodic[2*d+f]) {
+          bnd_points[2*d+f] = nboundaryzones[2*d+f];
+        } else{ 
+          bnd_points[2*d+f] =
+            nboundaryzones[2*d+f] + shiftout[2*d+f] + is_staggered[2*d+f] - 1;
+        }
       }
       
     }
@@ -130,9 +158,9 @@ CoordBase_SetupMask (CCTK_ARGUMENTS)
           iweight[ind] = 0;
         } CCTK_ENDLOOP3(CoordBase_SetupMask_boundary);
         
-        /* When the boundary is not staggered, then give the points
-           directly on the boundary the weight 1/2 */
-        if (! is_staggered[2*d+f]) {
+        /* When the boundary is neither staggered nor periodic, then
+           give the points directly on the boundary the weight 1/2 */
+        if (! is_staggered[2*d+f] && ! is_periodic[2*d+f]) {
           
           /* Since we are going to cut off 1/2 at each boundary, the
              domain size must be at least 1 to begin with */
diff --git a/Carpet/Requirements/src/Requirements.cc b/Carpet/Requirements/src/Requirements.cc
index 1401b7bc4..235acfa04 100644
--- a/Carpet/Requirements/src/Requirements.cc
+++ b/Carpet/Requirements/src/Requirements.cc
@@ -8,6 +8,7 @@
 
 #include <iostream>
 #include <vector>
+#include <cstdlib>
 
 #include <all_clauses.hh>
 #include <util.hh>
diff --git a/Carpet/Requirements/src/all_state.cc b/Carpet/Requirements/src/all_state.cc
index 419379e29..19fa0c1eb 100644
--- a/Carpet/Requirements/src/all_state.cc
+++ b/Carpet/Requirements/src/all_state.cc
@@ -6,6 +6,8 @@
 #include <clauses.hh>
 #include <util.hh>
 
+#include <cstdlib>
+
 using namespace std;
 
 namespace Requirements {
diff --git a/Carpet/Requirements/src/gridpoint.cc b/Carpet/Requirements/src/gridpoint.cc
index 122970c8e..c351eec21 100644
--- a/Carpet/Requirements/src/gridpoint.cc
+++ b/Carpet/Requirements/src/gridpoint.cc
@@ -6,6 +6,8 @@
 #include <gridpoint.hh>
 #include <util.hh>
 
+#include <cstdlib>
+
 namespace Requirements {
 
   using namespace std;