Merge pull request #165 from ludwig-cf/feature-lb-halo

Add field halo switch for lc droplet

CHANGES.md

@@ -3,10 +3,18 @@
 
 version 0.16.0
 
+- Improved host halo swaps are available.
+  The implementation of the reduced distribution halo has been replaced
+  with one that will work in all circumstances for a single distribution.
+  See https://ludwig.epcc.ed.ac.uk/inputs/index.html Parallelism for details.
+  No user action is required if you are not interested.
+
 - Reinstated the boundary (wall) - colloid soft sphere potential.
   See https://ludwig.epcc.ed.ac.uk/inputs/colloid.html
   Thanks to Rishish Mishra for spotting this problem.
 
+- Various minor updates.
+
 version 0.15.0
 
 - Active stress implementation is updated to conform to the documented

mpi_s/mpi_serial.c

@@ -660,7 +660,7 @@ int MPI_Type_indexed(int count, int * array_of_blocklengths,
   assert(newtype);
 
   {
-    data_t dt = {};
+    data_t dt = {0};
 
     dt.handle  = MPI_DATATYPE_NULL;
     dt.bytes   = 0;
@@ -685,7 +685,7 @@ int MPI_Type_contiguous(int count, MPI_Datatype old, MPI_Datatype * newtype) {
   assert(newtype);
 
   {
-    data_t dt = {};
+    data_t dt = {0};
 
     dt.handle  = MPI_DATATYPE_NULL;
     dt.bytes   = mpi_sizeof(old)*count;  /* contiguous */
@@ -756,7 +756,7 @@ int MPI_Type_vector(int count, int blocklength, int stride,
   assert(newtype);
 
   {
-    data_t dt = {};
+    data_t dt = {0};
 
     dt.handle = MPI_DATATYPE_NULL;
     dt.bytes  = 0;
@@ -1164,7 +1164,7 @@ int MPI_Type_create_resized(MPI_Datatype oldtype, MPI_Aint lb, MPI_Aint extent,
   assert(newtype);
 
   {
-    data_t dt = {};
+    data_t dt = {0};
 
     dt.handle  = MPI_DATATYPE_NULL;
     dt.bytes   = extent;
@@ -1198,7 +1198,7 @@ int MPI_Type_create_struct(int count, int array_of_blocklengths[],
 
 
   {
-    data_t dt = {};
+    data_t dt = {0};
 
     dt.handle  = MPI_DATATYPE_NULL;
     dt.bytes   = 0;

mpi_s/mpi_tests.c

@@ -253,10 +253,10 @@ int test_mpi_type_create_struct(void) {
 
   {
     /* Commit */
-    test_t data = {};
+    test_t data = {0};
     int count = 2;
     int blocklengths[2] = {1, 1};
-    MPI_Aint displacements[3] = {};
+    MPI_Aint displacements[3] = {0};
     MPI_Datatype datatypes[2] = {MPI_INT, MPI_DOUBLE};
 
     MPI_Get_address(&data,   displacements + 0);

src/blue_phase_beris_edwards.c

@@ -31,7 +31,7 @@
  *  Edinburgh Soft Matter and Statistical Physics Group and
  *  Edinburgh Parallel Computing Centre
  *
- *  (c) 2009-2021 The University of Edinburgh
+ *  (c) 2009-2022 The University of Edinburgh
  *
  *  Contributing authors:
  *  Kevin Stratford ([email protected])
@@ -322,7 +322,7 @@ __host__ int beris_edw_update_host(beris_edw_t * be, fe_t * fe, field_t * fq,
   double gamma;
 
   double chi[NQAB], chi_qab[3][3];
-  double tmatrix[3][3][NQAB] = {};
+  double tmatrix[3][3][NQAB] = {0};
   double var = 0.0;
 
   const double dt = 1.0;

src/blue_phase_init.c

@@ -10,7 +10,7 @@
  *  Edinburgh Soft Matter and Statistical Physics Group and
  *  Edinburgh Parallel Computing Centre
  *
- *  (c) 2012-2021 The University of Edinburgh
+ *  (c) 2012-2022 The University of Edinburgh
  *
  *  Contributing authors:
  *  Oliver Henrich ([email protected])
@@ -64,7 +64,7 @@ int blue_phase_O8M_init(cs_t * cs, fe_lc_param_t * param, field_t * fq,
   double root2;
   double q0;
   double amplitude0;
-  rotation_t rot = {};
+  rotation_t rot = {0};
 
   assert(cs);
   assert(fq);
@@ -82,7 +82,7 @@ int blue_phase_O8M_init(cs_t * cs, fe_lc_param_t * param, field_t * fq,
   /* So we add a sign here. */
 
   {
-    double angles[3]  = {}; /* radians */
+    double angles[3]  = {0}; /* radians */
     PI_DOUBLE(pi);
 
     angles[0] = -1.0*pi*euler_angles[0]/180.0;
@@ -98,7 +98,7 @@ int blue_phase_O8M_init(cs_t * cs, fe_lc_param_t * param, field_t * fq,
       double y = noffset[Y] + jc;
       for (int kc = 1; kc <= nlocal[Z]; kc++) {
 	double z = noffset[Z] + kc;
-	double r[3] = {};
+	double r[3] = {0};
 
 	/* Rotate around the centre */
 	r[X] = x - 0.5*ntotal[X];
@@ -119,7 +119,7 @@ int blue_phase_O8M_init(cs_t * cs, fe_lc_param_t * param, field_t * fq,
 	  double sinx = sin(root2*q0*r[X]);
 	  double siny = sin(root2*q0*r[Y]);
 	  double sinz = sin(root2*q0*r[Z]);
-	  double q[3][3] = {};
+	  double q[3][3] = {0};
 
 	  q[X][X] = amplitude0*( -2.0*cosy*sinz +       sinx*cosz + cosx*siny);
 	  q[X][Y] = amplitude0*(root2*cosy*cosz + root2*sinx*sinz - sinx*cosy);
@@ -159,7 +159,7 @@ int blue_phase_O2_init(cs_t * cs, fe_lc_param_t * param, field_t * fq,
 
   double q0;
   double amplitude0;
-  rotation_t rot = {};
+  rotation_t rot = {0};
 
   assert(cs);
   assert(fq);
@@ -176,7 +176,7 @@ int blue_phase_O2_init(cs_t * cs, fe_lc_param_t * param, field_t * fq,
   /* Hence the factor of -1.0 below. */
 
   {
-    double angles[3] = {}; /* radians */
+    double angles[3] = {0}; /* radians */
     PI_DOUBLE(pi);
 
     angles[0] = -1.0*pi*euler_angles[0]/180.0;
@@ -192,7 +192,7 @@ int blue_phase_O2_init(cs_t * cs, fe_lc_param_t * param, field_t * fq,
       double y = noffset[Y] + jc;
       for (int kc = 1; kc <= nlocal[Z]; kc++) {
 	double z = noffset[Z] + kc;
-	double r[3] = {};
+	double r[3] = {0};
 
 	r[X] = x - 0.5*ntotal[X];
 	r[Y] = y - 0.5*ntotal[Y];
@@ -212,7 +212,7 @@ int blue_phase_O2_init(cs_t * cs, fe_lc_param_t * param, field_t * fq,
 	  double sinx = sin(2.0*q0*r[X]);
 	  double siny = sin(2.0*q0*r[Y]);
 	  double sinz = sin(2.0*q0*r[Z]);
-	  double q[3][3] = {};
+	  double q[3][3] = {0};
 
 	  q[X][X] = amplitude0*(cosz - cosy);
 	  q[X][Y] = amplitude0*sinz;

src/blue_phase_rt.c

@@ -9,7 +9,7 @@
  *  Edinburgh Soft Matter and Statistical Physics Group and
  *  Edinburgh Parallel Computing Centre
  *
- *  (c) 2009-2021 The University of Edinburgh
+ *  (c) 2009-2022 The University of Edinburgh
  *
  *  Contributing authors:
  *  Kevin Stratford ([email protected])
@@ -72,7 +72,7 @@ __host__ int blue_phase_init_rt(pe_t * pe, rt_t *rt,
   pe_info(pe, "Blue phase free energy selected.\n");
 
   {
-    char description[BUFSIZ] = {};
+    char description[BUFSIZ] = {0};
     rt_string_parameter(rt, "free_energy", description, BUFSIZ);
     fe_is_lc_droplet = (strcmp(description, "lc_droplet") == 0);
   }

src/cahn_hilliard_stats.c

@@ -5,7 +5,7 @@
  *  Edinburgh Soft Matter and Statistical Physics Group and
  *  Edinburgh Parallel Computing Centre
  *
- *  (c) 2021 The University of Edinburgh
+ *  (c) 2021-2022 The University of Edinburgh
  *
  *  Contributions:
  *  Kevin Stratford ([email protected])
@@ -59,7 +59,7 @@ __global__ void cahn_stats_min_kernel(kernel_ctxt_t * ktx, field_t * phi,
 __host__ int cahn_hilliard_stats_time0(phi_ch_t * pch, field_t * phi,
 				       map_t * map) {
 
-  phi_stats_t stats = {};
+  phi_stats_t stats = {0};
   MPI_Comm comm = MPI_COMM_NULL;
 
   assert(pch);
@@ -83,8 +83,8 @@ __host__ int cahn_hilliard_stats_time0(phi_ch_t * pch, field_t * phi,
 
 __host__ int cahn_hilliard_stats(phi_ch_t * pch, field_t * phi, map_t * map) {
 
-  phi_stats_t stats = {.sum1 = {},
-		       .sum2 = {},
+  phi_stats_t stats = {.sum1 = {0},
+		       .sum2 = {0},
 		       .sum  = 0.0,
 		       .var  = 0.0,
 		       .min  = +FLT_MAX,
@@ -123,7 +123,7 @@ __host__ int cahn_hilliard_stats(phi_ch_t * pch, field_t * phi, map_t * map) {
 __host__ int cahn_stats_reduce(phi_ch_t * pch, field_t * phi,
 			       map_t * map, phi_stats_t * stats,
 			       int root, MPI_Comm comm) {
-  phi_stats_t local = {};
+  phi_stats_t local = {0};
   phi_stats_t * stats_d = NULL;
 
   int nlocal[3];

src/colloid_io.c

@@ -7,7 +7,7 @@
  *  Edinburgh Soft Matter and Statistical Physics Group and
  *  Edinburgh Parallel Computing Centre
  *
- *  (c) 2010-2021 The University of Edinburgh
+ *  (c) 2010-2022 The University of Edinburgh
  *
  *  Contributing authors:
  *  Kevin Stratford ([email protected])
@@ -429,7 +429,7 @@ int colloid_io_write_buffer_binary(FILE * fp, int nc, colloid_state_t * buf) {
 int colloid_io_read(colloid_io_t * cio, const char * filename) {
 
   int    ngroup;
-  char   filename_io[FILENAME_MAX] = {};
+  char   filename_io[FILENAME_MAX] = {0};
   FILE * fp_state;
 
   assert(cio->f_header_read);

src/colloids_rt.c

@@ -814,10 +814,10 @@ int pair_ss_cut_ij_init(pe_t * pe, cs_t * cs, rt_t * rt, interact_t * intrct) {
   if (ison) {
     int ntypes = 0;
     int nsymm  = 0;
-    double epsilon[BUFSIZ] = {};
-    double sigma[BUFSIZ] = {};
-    double nu[BUFSIZ] = {};
-    double hc[BUFSIZ] = {};
+    double epsilon[BUFSIZ] = {0};
+    double sigma[BUFSIZ] = {0};
+    double nu[BUFSIZ] = {0};
+    double hc[BUFSIZ] = {0};
     pair_ss_cut_ij_t * pair = NULL;
 
     rt_key_required(rt, "pair_ss_cut_ij_ntypes",  RT_FATAL);
@@ -1092,7 +1092,7 @@ int wall_ss_cut_init(pe_t * pe, cs_t * cs, rt_t * rt, wall_t * wall,
   if (have_wall_ss_cut) {
 
     wall_ss_cut_t * wall_ss_cut = NULL;
-    wall_ss_cut_options_t opts = {};
+    wall_ss_cut_options_t opts = {0};
 
     rt_key_required(rt, "wall_ss_cut_epsilon", RT_FATAL);
     rt_key_required(rt, "wall_ss_cut_sigma", RT_FATAL);

src/compiler.c

@@ -7,7 +7,7 @@
  *  Edinburgh Soft Matter and Statistical Phyiscs Group and
  *  Edinburgh Parallel Computing Centre
  *
- *  (c) 2021 The University of Edinburgh
+ *  (c) 2021-2022 The University of Edinburgh
  *
  *  Contributing authors:
  *  Kevin Stratford ([email protected])
@@ -109,7 +109,7 @@ int compiler_id(compiler_info_t * compiler) {
   compiler->major = __GNUC__;
   compiler->minor = __GNUC_MINOR__;
   compiler->patchlevel = __GNUC_PATCHLEVEL__;
-  strncpy(compiler->version, __VERSION__, 1 + strnlen(__VERSION__, BUFSIZ-1));
+  strncpy(compiler->version, __VERSION__, 1 + strlen(__VERSION__));
   sprintf(compiler->name, "%s", "Gnu");
   ierr = 0;
 

src/coords.c

@@ -546,14 +546,14 @@ static __host__ int cs_rectilinear_decomposition(cs_t * cs) {
   int idim;
   int n, ntot, nremainder;
   int ntotal[3];
-  int mpisz[3] = {};
+  int mpisz[3] = {0};
 
   assert(cs);
 
   {
-    int dims[3] = {};
-    int coords[3] = {};
-    int periods[3] = {};
+    int dims[3] = {0};
+    int coords[3] = {0};
+    int periods[3] = {0};
     MPI_Cart_get(cs->commcart, 3, dims, coords, periods);
     mpisz[X] = dims[X]; mpisz[Y] = dims[Y]; mpisz[Z] = dims[Z];
   }