Merge pull request #94 from ludwig-cf/ludwig-0.11.0

Ludwig 0.11.0

.gitattributes

@@ -0,0 +1,4 @@
+# An attempt to prevent mislabeling of .h files as C++
+# See https://github.com/github/linguist
+
+*.h linguist-language=C

CHANGES.md

@@ -1,6 +1,15 @@
 
 ### Changes
 
+
+version 0.11.0
+- Add external chemical potential gradient in Cahn Hilliard for
+  free energy symmetric. Thanks to Jurij Sablic (jurij.sablic@gmail.com).
+- Add Arrhenius viscosity model for compositional order parameter
+- Add the ability to run both subgrid and fully resolved particles at
+  the same time. Thanks to Qi Kai (kai.qi@epfl.ch) for this.
+- Various code quality updates
+
 version 0.10.0
 - Added an option to fix colloid position or velocity on a per-direction
   basis, e.g.

README.md

@@ -3,7 +3,7 @@
 
 A lattice Boltzmann code for complex fluids
 
-[![Build Status](https://travis-ci.com/ludwig-cf/ludwig.svg?branch=develop)](https://travis-ci.com/ludwig-cf/ludwig)
+[![Build Status](https://travis-ci.com/ludwig-cf/ludwig.svg?branch=master)](https://travis-ci.com/ludwig-cf/ludwig)
 [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/1998/badge)](https://bestpractices.coreinfrastructure.org/projects/1998)
 
 

src/advection.c

@@ -21,7 +21,7 @@
  *  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 (kevin@epcc.ed.ac.uk)
@@ -35,7 +35,7 @@
 #include "field_s.h"
 #include "advection_s.h"
 #include "psi_gradients.h"
-#include "hydro_s.h"
+#include "hydro.h"
 #include "timer.h"
 
 __host__
@@ -158,10 +158,10 @@ __host__ int advflux_create(pe_t * pe, cs_t * cs, lees_edw_t * le, int nf,
   obj->nf = nf;
   obj->nsite = nsites;
 
-  obj->fe = (double *) calloc(nsites*nf, sizeof(double));
-  obj->fw = (double *) calloc(nsites*nf, sizeof(double));
-  obj->fy = (double *) calloc(nsites*nf, sizeof(double));
-  obj->fz = (double *) calloc(nsites*nf, sizeof(double));
+  obj->fe = (double *) calloc((size_t) nsites*nf, sizeof(double));
+  obj->fw = (double *) calloc((size_t) nsites*nf, sizeof(double));
+  obj->fy = (double *) calloc((size_t) nsites*nf, sizeof(double));
+  obj->fz = (double *) calloc((size_t) nsites*nf, sizeof(double));
 
   if (obj->fe == NULL) pe_fatal(pe, "calloc(advflux->fe) failed\n");
   if (obj->fw == NULL) pe_fatal(pe, "calloc(advflux->fw) failed\n");
@@ -179,19 +179,21 @@ __host__ int advflux_create(pe_t * pe, cs_t * cs, lees_edw_t * le, int nf,
   else {
     cs_t * cstarget = NULL;
     lees_edw_t * letarget = NULL;
+    size_t nsz = (size_t) nsites*nf*sizeof(double);
 
     tdpMalloc((void **) &obj->target, sizeof(advflux_t));
     tdpMemset(obj->target, 0, sizeof(advflux_t));
-    tdpMalloc((void **) &tmp, nf*nsites*sizeof(double));
+
+    tdpMalloc((void **) &tmp, nsz);
     tdpMemcpy(&obj->target->fe, &tmp, sizeof(double *), tdpMemcpyHostToDevice);
 
-    tdpMalloc((void **) &tmp, nf*nsites*sizeof(double));
+    tdpMalloc((void **) &tmp, nsz);
     tdpMemcpy(&obj->target->fw, &tmp, sizeof(double *), tdpMemcpyHostToDevice);
 
-    tdpMalloc((void **) &tmp, nf*nsites*sizeof(double));
+    tdpMalloc((void **) &tmp, nsz);
     tdpMemcpy(&obj->target->fy, &tmp, sizeof(double *), tdpMemcpyHostToDevice);
 
-    tdpMalloc((void **) &tmp, nf*nsites*sizeof(double));
+    tdpMalloc((void **) &tmp, nsz);
     tdpMemcpy(&obj->target->fz, &tmp, sizeof(double *), tdpMemcpyHostToDevice);
 
     tdpMemcpy(&obj->target->nf, &obj->nf, sizeof(int), tdpMemcpyHostToDevice);

src/bbl.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 (kevin@epcc.ed.ac.uk)
@@ -212,6 +212,8 @@ static int bbl_active_conservation(bbl_t * bbl, colloids_info_t * cinfo) {
 
   for ( ; pc; pc = pc->nextall) {
 
+    if (pc->s.type != COLLOID_TYPE_ACTIVE) continue;
+
     pc->sump /= pc->sumw;
     p_link = pc->lnk;
 
@@ -324,7 +326,7 @@ __global__ void bbl_pass0_kernel(kernel_ctxt_t * ktxt, cs_t * cs, lb_t * lb,
 
     pc = cinfo->map_new[index];
 
-    if (pc) { 
+    if (pc && pc->s.type != COLLOID_TYPE_SUBGRID) { 
       cs_nlocal_offset(cs, noffset);
       r[X] = 1.0*(noffset[X] + ic);
       r[Y] = 1.0*(noffset[Y] + jc);
@@ -400,6 +402,8 @@ static int bbl_pass1(bbl_t * bbl, lb_t * lb, colloids_info_t * cinfo) {
 
   for ( ; pc; pc = pc->nextall) {
 
+    if (pc->s.type == COLLOID_TYPE_SUBGRID) continue;
+
     p_link = pc->lnk;
 
     for (i = 0; i < 21; i++) {
@@ -603,6 +607,8 @@ static int bbl_pass2(bbl_t * bbl, lb_t * lb, colloids_info_t * cinfo) {
 
   for ( ; pc; pc = pc->nextall) {
 
+    if (pc->s.type == COLLOID_TYPE_SUBGRID) continue;
+
     /* Set correction for phi arising from previous step */
 
     dgtm1 = pc->s.deltaphi;
@@ -716,6 +722,7 @@ static int bbl_pass2(bbl_t * bbl, lb_t * lb, colloids_info_t * cinfo) {
     bbl->deltag += pc->s.deltaphi;
   }
 
+
   return 0;
 }
 
@@ -760,6 +767,8 @@ int bbl_update_colloids(bbl_t * bbl, wall_t * wall, colloids_info_t * cinfo) {
 
   for ( ; pc; pc = pc->nextall) {
 
+    if (pc->s.type == COLLOID_TYPE_SUBGRID) continue;
+
     /* Set up the matrix problem and solve it here. */
 
     /* Mass and moment of inertia are those of a hard sphere

src/blue_phase_beris_edwards.c

@@ -31,7 +31,7 @@
  *  Edinburgh Soft Matter and Statistical Physics Group and
  *  Edinburgh Parallel Computing Centre
  *
- *  (c) 2009-2018 The University of Edinburgh
+ *  (c) 2009-2020 The University of Edinburgh
  *
  *  Contributing authors:
  *  Kevin Stratford (kevin@epcc.ed.ac.uk)
@@ -53,7 +53,6 @@
 #include "blue_phase.h"
 #include "blue_phase_beris_edwards.h"
 #include "advection_s.h"
-#include "hydro_s.h"
 #include "field_s.h"
 #include "field_grad_s.h"
 #include "colloids_s.h"
@@ -234,11 +233,12 @@ __host__ int beris_edw_param_commit(beris_edw_t * be) {
  *
  *****************************************************************************/
 
-__host__ int beris_edw_param_set(beris_edw_t * be, beris_edw_param_t vals) {
+__host__ int beris_edw_param_set(beris_edw_t * be, beris_edw_param_t * vals) {
 
   assert(be);
+  assert(vals);
 
-  *be->param = vals;
+  *be->param = *vals;
 
   return 0;
 }

src/blue_phase_beris_edwards.h

@@ -2,19 +2,18 @@
  *
  *  blue_phase_beris_edwards.h
  *
- *  $Id$
  *
  *  Edinburgh Soft Matter and Statistical Physics Group and
  *  Edinburgh Parallel Computing Centre
  *
  *  Kevin Stratford (kevin@epcc.ed.ac.uk)
  *
- *  (c) 2009-2017 The University of Edinburgh
+ *  (c) 2009-2020 The University of Edinburgh
  *
  *****************************************************************************/
 
-#ifndef BLUE_PHASE_BERIS_EDWARDS_H
-#define BLUE_PHASE_BERIS_EDWARDS_H
+#ifndef LUDWIG_BLUE_PHASE_BERIS_EDWARDS_H
+#define LUDWIG_BLUE_PHASE_BERIS_EDWARDS_H
 
 #include "coords.h"
 #include "leesedwards.h"
@@ -40,7 +39,7 @@ __host__ int beris_edw_create(pe_t * pe, cs_t * cs, lees_edw_t * le,
 			      beris_edw_t ** pobj);
 __host__ int beris_edw_free(beris_edw_t * be);
 __host__ int beris_edw_memcpy(beris_edw_t * be, int flag);
-__host__ int beris_edw_param_set(beris_edw_t * be, beris_edw_param_t values);
+__host__ int beris_edw_param_set(beris_edw_t * be, beris_edw_param_t * values);
 __host__ int beris_edw_param_commit(beris_edw_t * be);
 
 __host__ int beris_edw_update(beris_edw_t * be, fe_t * fe, field_t * fq,

src/blue_phase_rt.c

@@ -9,7 +9,7 @@
  *  Edinburgh Soft Matter and Statistical Physics Group and
  *  Edinburgh Parallel Computing Centre
  *
- *  (c) 2009-2018 The University of Edinburgh
+ *  (c) 2009-2020 The University of Edinburgh
  *
  *  Contributing authors:
  *  Kevin Stratford (kevin@epcc.ed.ac.uk)
@@ -318,7 +318,7 @@ __host__ int blue_phase_init_rt(pe_t * pe, rt_t *rt,
   else {
     be_param.gamma = gamma;
     be_param.xi = fe_param.xi;
-    beris_edw_param_set(be, be_param);
+    beris_edw_param_set(be, &be_param);
     pe_info(pe, "Rotational diffusion const = %14.7e\n", gamma);
   }
 

src/bond_fene.c

@@ -16,7 +16,7 @@
  *  Edinburgh Soft Matter and Statistical Physics Group and
  *  Edinburgh Parallel Computing Centre
  *
- *  (c) 2014-2017 The University of Edinburgh
+ *  (c) 2014-2020 The University of Edinburgh
  *
  *  Contributing authors:
  *  Kevin Stratford (kevin@epcc.ed.ac.uk)
@@ -165,6 +165,8 @@ int bond_fene_compute(colloids_info_t * cinfo, void * self) {
   obj->bondlocal = 0.0;
 
   for (; pc; pc = pc->nextlocal) {
+
+    if (pc->s.nbonds == 0) continue;
 
     for (n = 0; n < pc->s.nbonds; n++) {
       assert(pc->bonded[n]);
@@ -191,7 +193,6 @@ int bond_fene_compute(colloids_info_t * cinfo, void * self) {
       pc->bonded[n]->force[Y] += f*r12[Y];
       pc->bonded[n]->force[Z] += f*r12[Z];
     }
-
   }
 
   obj->rminlocal = sqrt(r2min);

src/build.c

@@ -9,7 +9,7 @@
  *  Edinburgh Soft Matter and Statisitical Physics Group and
  *  Edinburgh Parallel Computing Centre
  *
- *  (c) 2006-2019 The University of Edinburgh
+ *  (c) 2006-2020 The University of Edinburgh
  *
  *  Contributing authors:
  *  Kevin Stratford (kevin@epcc.ed.ac.uk)
@@ -142,7 +142,9 @@ int build_update_map(cs_t * cs, colloids_info_t * cinfo, map_t * map) {
 
 	/* For each colloid in this cell, check solid/fluid status */
 
-	while (p_colloid != NULL) {
+	for ( ; p_colloid; p_colloid = p_colloid->next) {
+
+          if (p_colloid->s.type == COLLOID_TYPE_SUBGRID) continue;
 
 	  /* Set actual position and radius */
 
@@ -212,7 +214,6 @@ int build_update_map(cs_t * cs, colloids_info_t * cinfo, map_t * map) {
 	      }
 
 	  /* Next colloid */
-	  p_colloid = p_colloid->next;
 	}
 
 	/* Next cell */
@@ -253,7 +254,9 @@ int build_update_links(cs_t * cs, colloids_info_t * cinfo, wall_t * wall,
 
 	colloids_info_cell_list_head(cinfo, ic, jc, kc, &pc);
 
-	while (pc) {
+	for (; pc; pc = pc->next) {
+
+          if (pc->s.type == COLLOID_TYPE_SUBGRID) continue;
 
 	  pc->sumw   = 0.0;
 	  for (ia = 0; ia < 3; ia++) {
@@ -276,7 +279,6 @@ int build_update_links(cs_t * cs, colloids_info_t * cinfo, wall_t * wall,
 	  /* Next colloid */
 
 	  pc->s.rebuild = 0;
-	  pc = pc->next;
 	}
 
 	/* Next cell */