Adjust colloid I/O to ensure backward compatability; use reference in…

… write calls

CHANGES.md

@@ -1,6 +1,11 @@
 
 ### Changes
 version 0.10.0
+- Added an option to fix colloid position or velocity on a per-direction
+  basis, e.g.
+    colloid_isfixedrxyz  1_1_0
+  allows movement in z-direction only. Any value is overridden by
+  colloid_isfixedr. An analogous option colloid_isfixedvxyz is available.
 - Added target thread model information to output
 - Refactored d_ij and e_ijk from char to int8_t to avoid potential
   pitfalls with default unsigned char.

src/colloid.c

@@ -9,7 +9,7 @@
  *  Edinburgh Parallel Computing Centre
  *
  *  Kevin Stratford ([email protected])
- *  (c) 2010-2014 The University of Edinburgh
+ *  (c) 2010-2020 The University of Edinburgh
  *
  *****************************************************************************/
 
@@ -33,7 +33,6 @@ int colloid_state_read_ascii(colloid_state_t * ps, FILE * fp) {
   int ifail = 0;
 
   const char * isformat = "%24d\n";
-  const char * ivformat = "%24d %24d %24d\n";
   const char * sformat  = "%24le\n";
   const char * vformat  = "%24le %24le %24le\n";
 
@@ -45,9 +44,7 @@ int colloid_state_read_ascii(colloid_state_t * ps, FILE * fp) {
   nread += fscanf(fp, isformat, &ps->nbonds);
   nread += fscanf(fp, isformat, &ps->nangles);
   nread += fscanf(fp, isformat, &ps->isfixedr);
-  nread += fscanf(fp, ivformat, &ps->isfixedrxyz[0], &ps->isfixedrxyz[1], &ps->isfixedrxyz[2]);
   nread += fscanf(fp, isformat, &ps->isfixedv);
-  nread += fscanf(fp, ivformat, &ps->isfixedvxyz[0], &ps->isfixedvxyz[1], &ps->isfixedvxyz[2]);
   nread += fscanf(fp, isformat, &ps->isfixedw);
   nread += fscanf(fp, isformat, &ps->isfixeds);
   nread += fscanf(fp, isformat, &ps->type);
@@ -58,6 +55,12 @@ int colloid_state_read_ascii(colloid_state_t * ps, FILE * fp) {
 
   nread += fscanf(fp, isformat, &ps->rng);
 
+  for (n = 0; n < 3; n++) {
+    nread += fscanf(fp, isformat, ps->isfixedrxyz + n);
+  }
+  for (n = 0; n < 3; n++) {
+    nread += fscanf(fp, isformat, ps->isfixedvxyz + n);
+  }
   for (n = 0; n < NPAD_INT; n++) {
     nread += fscanf(fp, isformat, &ps->intpad[n]);
   }
@@ -133,66 +136,74 @@ int colloid_state_read_binary(colloid_state_t * ps, FILE * fp) {
  *
  *****************************************************************************/
 
-int colloid_state_write_ascii(colloid_state_t s, FILE * fp) {
+int colloid_state_write_ascii(const colloid_state_t * s, FILE * fp) {
 
   int n;
   int nwrite = 0;
   int ifail = 0;
 
   const char * isformat = "%24d\n";
-  const char * ivformat = "%24d %24d %24d\n";
   const char * sformat  = "%24.15e\n";
   const char * vformat  = "%24.15e %24.15e %24.15e\n";
 
+  assert(s);
   assert(fp);
 
-  nwrite += fprintf(fp, isformat, s.index);
-  nwrite += fprintf(fp, isformat, s.rebuild);
-  nwrite += fprintf(fp, isformat, s.nbonds);
-  nwrite += fprintf(fp, isformat, s.nangles);
-  nwrite += fprintf(fp, isformat, s.isfixedr);
-  nwrite += fprintf(fp, ivformat, s.isfixedrxyz[0], s.isfixedrxyz[1], s.isfixedrxyz[2]);
-  nwrite += fprintf(fp, isformat, s.isfixedv);
-  nwrite += fprintf(fp, ivformat, s.isfixedvxyz[0], s.isfixedvxyz[1], s.isfixedvxyz[2]);
-  nwrite += fprintf(fp, isformat, s.isfixedw);
-  nwrite += fprintf(fp, isformat, s.isfixeds);
-  nwrite += fprintf(fp, isformat, s.type);
+  nwrite += fprintf(fp, isformat, s->index);
+  nwrite += fprintf(fp, isformat, s->rebuild);
+  nwrite += fprintf(fp, isformat, s->nbonds);
+  nwrite += fprintf(fp, isformat, s->nangles);
+  nwrite += fprintf(fp, isformat, s->isfixedr);
+  nwrite += fprintf(fp, isformat, s->isfixedv);
+  nwrite += fprintf(fp, isformat, s->isfixedw);
+  nwrite += fprintf(fp, isformat, s->isfixeds);
+  nwrite += fprintf(fp, isformat, s->type);
 
   for (n = 0; n < NBOND_MAX; n++) {
-    nwrite += fprintf(fp, isformat, s.bond[n]);
+    nwrite += fprintf(fp, isformat, s->bond[n]);
   }
 
-  nwrite += fprintf(fp, isformat, s.rng);
+  nwrite += fprintf(fp, isformat, s->rng);
+
+  /* isfixedrxyz and isfixedvxyz are writen as 3 x scalars as they
+   * have replaced padding */
+
+  for (n = 0; n < 3; n++) {
+    nwrite += fprintf(fp, isformat, s->isfixedrxyz[n]);
+  }
+  for (n = 0; n < 3; n++) {
+    nwrite += fprintf(fp, isformat, s->isfixedvxyz[n]);
+  }
 
   for (n = 0; n < NPAD_INT; n++) {
-    nwrite += fprintf(fp, isformat, s.intpad[n]);
+    nwrite += fprintf(fp, isformat, s->intpad[n]);
   }
 
-  nwrite += fprintf(fp, sformat, s.a0);
-  nwrite += fprintf(fp, sformat, s.ah);
-  nwrite += fprintf(fp, vformat, s.r[0], s.r[1], s.r[2]);
-  nwrite += fprintf(fp, vformat, s.v[0], s.v[1], s.v[2]);
-  nwrite += fprintf(fp, vformat, s.w[0], s.w[1], s.w[2]);
-  nwrite += fprintf(fp, vformat, s.s[0], s.s[1], s.s[2]);
-  nwrite += fprintf(fp, vformat, s.m[0], s.m[1], s.m[2]);
-  nwrite += fprintf(fp, sformat, s.b1);
-  nwrite += fprintf(fp, sformat, s.b2);
-  nwrite += fprintf(fp, sformat, s.c);
-  nwrite += fprintf(fp, sformat, s.h);
-  nwrite += fprintf(fp, vformat, s.dr[0], s.dr[1], s.dr[2]);
-  nwrite += fprintf(fp, sformat, s.deltaphi);
-
-  nwrite += fprintf(fp, sformat, s.q0);
-  nwrite += fprintf(fp, sformat, s.q1);
-  nwrite += fprintf(fp, sformat, s.epsilon);
-
-  nwrite += fprintf(fp, sformat, s.deltaq0);
-  nwrite += fprintf(fp, sformat, s.deltaq1);
-  nwrite += fprintf(fp, sformat, s.sa);
-  nwrite += fprintf(fp, sformat, s.saf);
+  nwrite += fprintf(fp, sformat, s->a0);
+  nwrite += fprintf(fp, sformat, s->ah);
+  nwrite += fprintf(fp, vformat, s->r[0], s->r[1], s->r[2]);
+  nwrite += fprintf(fp, vformat, s->v[0], s->v[1], s->v[2]);
+  nwrite += fprintf(fp, vformat, s->w[0], s->w[1], s->w[2]);
+  nwrite += fprintf(fp, vformat, s->s[0], s->s[1], s->s[2]);
+  nwrite += fprintf(fp, vformat, s->m[0], s->m[1], s->m[2]);
+  nwrite += fprintf(fp, sformat, s->b1);
+  nwrite += fprintf(fp, sformat, s->b2);
+  nwrite += fprintf(fp, sformat, s->c);
+  nwrite += fprintf(fp, sformat, s->h);
+  nwrite += fprintf(fp, vformat, s->dr[0], s->dr[1], s->dr[2]);
+  nwrite += fprintf(fp, sformat, s->deltaphi);
+
+  nwrite += fprintf(fp, sformat, s->q0);
+  nwrite += fprintf(fp, sformat, s->q1);
+  nwrite += fprintf(fp, sformat, s->epsilon);
+
+  nwrite += fprintf(fp, sformat, s->deltaq0);
+  nwrite += fprintf(fp, sformat, s->deltaq1);
+  nwrite += fprintf(fp, sformat, s->sa);
+  nwrite += fprintf(fp, sformat, s->saf);
 
   for (n = 0; n < NPAD_DBL; n++) {
-    nwrite += fprintf(fp, sformat, s.dpad[n]);
+    nwrite += fprintf(fp, sformat, s->dpad[n]);
   }
 
   /* ... should be NTOT_VAR items of format + 1 characters */
@@ -213,13 +224,14 @@ int colloid_state_write_ascii(colloid_state_t s, FILE * fp) {
  *
  *****************************************************************************/
 
-int colloid_state_write_binary(colloid_state_t s, FILE * fp) {
+int colloid_state_write_binary(const colloid_state_t * s, FILE * fp) {
 
   int nwrite;
 
+  assert(s);
   assert(fp);
 
-  nwrite = fwrite(&s, sizeof(colloid_state_t), 1, fp);
+  nwrite = fwrite(s, sizeof(colloid_state_t), 1, fp);
 
   return (1 - nwrite);
 }

src/colloid.h

@@ -48,10 +48,8 @@ struct colloid_state_type {
   int nbonds;           /* Number of bonds e.g. fene (to NBOND_MAX) */
   int nangles;          /* Number of angles, e.g., fene (1 at the moment) */
 
-  int isfixedr;         /* Set to 1 for no position update in all coordinate directions */
-  int isfixedrxyz[3];   /* Set vector for no position update in specific coordinate directions */
-  int isfixedv;         /* Set to 1 for no velocity update in all coordinate directions */
-  int isfixedvxyz[3];   /* Set vector for no velocity update in specific coordinate directions */
+  int isfixedr;         /* Set to 1 for no position update */
+  int isfixedv;         /* Set to 1 for no velocity update */
   int isfixedw;         /* Set to 1 for no angular velocity update */
   int isfixeds;         /* Set to zero for no s, m update */
 
@@ -60,6 +58,12 @@ struct colloid_state_type {
 
   int rng;              /* Random number state */
 
+  int isfixedrxyz[3];   /* Position update in specific coordinate directions */
+  int isfixedvxyz[3];   /* Velocity update in specific coordinate directions */
+
+  /* New integer additions can be immediately before the padding */
+  /* This should allow existing binary files to be read correctly */
+
   int intpad[NPAD_INT]; /* I'm going to pad to 32 ints to allow for future
 			 * expansion. Additions should be appended here,
 			 * and the padding reduced appropriately. */
@@ -100,7 +104,7 @@ struct colloid_state_type {
 
 int colloid_state_read_ascii(colloid_state_t * ps, FILE * fp);
 int colloid_state_read_binary(colloid_state_t * ps, FILE * fp);
-int colloid_state_write_ascii(colloid_state_t ps, FILE * fp);
-int colloid_state_write_binary(colloid_state_t ps, FILE * fp);
+int colloid_state_write_ascii(const colloid_state_t * ps, FILE * fp);
+int colloid_state_write_binary(const colloid_state_t * ps, FILE * fp);
 
 #endif

src/colloid_io.c

@@ -7,7 +7,7 @@
  *  Edinburgh Soft Matter and Statistical Physics Group and
  *  Edinburgh Parallel Computing Centre
  *
- *  (c) 2010-2018 The University of Edinburgh
+ *  (c) 2010-2020 The University of Edinburgh
  *
  *  Contributing authors:
  *  Kevin Stratford ([email protected])
@@ -391,7 +391,7 @@ int colloid_io_write_buffer_ascii(FILE * fp, int nc, colloid_state_t * buf) {
   assert(buf);
 
   for (n = 0; n < nc; n++) {
-    ifail += colloid_state_write_ascii(buf[n], fp);
+    ifail += colloid_state_write_ascii(buf + n, fp);
   }
 
   return ifail;
@@ -556,7 +556,7 @@ static int colloid_io_write_list_ascii(colloid_io_t * cio,
   colloids_info_cell_list_head(cio->info, ic, jc, kc, &pc);
 
   while (pc) {
-    ifail += colloid_state_write_ascii(pc->s, fp);
+    ifail += colloid_state_write_ascii(&pc->s, fp);
     pc = pc->next;
   }
 
@@ -614,7 +614,7 @@ static int colloid_io_write_list_binary(colloid_io_t * cio,
   colloids_info_cell_list_head(cio->info, ic, jc, kc, &pc);
 
   while (pc) {
-    colloid_state_write_binary(pc->s, fp);
+    colloid_state_write_binary(&pc->s, fp);
     pc = pc->next;
   }
 

src/colloids.c

@@ -7,7 +7,7 @@
  *  Edinburgh Soft Matter and Statistical Physics Group and
  *  Edinburgh Parallel Computing Centre
  *
- *  (c) 2010-2018 The University of Edinburgh
+ *  (c) 2010-2020 The University of Edinburgh
  *
  *  Contributing authors:
  *  Kevin Stratford ([email protected])
@@ -1059,7 +1059,7 @@ __host__ int colloids_info_position_update(colloids_info_t * cinfo) {
 	    if (ifail == 1) {
 	      pe_verbose(cinfo->pe, "Colloid velocity exceeded max %14.7e\n",
 			 cinfo->drmax);
-	      colloid_state_write_ascii(coll->s, stdout);
+	      colloid_state_write_ascii(&coll->s, stdout);
 	      pe_fatal(cinfo->pe, "Stopping\n");
 	    }
 	  }