Merge pull request #324 from ludwig-cf/feature-323-cell-list

Relax cell list constraint for ellipsoids
ludwig-cf · Oct 21, 2024 · 517a3f0 · 517a3f0
2 parents 3d5f18e + 0d3c218
commit 517a3f0
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Showing 3 changed files with 280 additions and 15 deletions.
diff --git a/src/colloids_rt.c b/src/colloids_rt.c
@@ -1202,17 +1202,26 @@ int angle_cosine_init(pe_t * pe, cs_t * cs, rt_t * rt, interact_t * interact) {
  *  3) ncell >= 2       must have at least two cells to separate
  *                      'left-going' and 'right-going' communications.
  *
+ *  There are some edge cases where we can relax these constraints:
+ *
+ *  a) A direction which is non-periodic (eg., has walls)
+ *     and is not decomposed (mpisz == 1) will have no message passing.
+ *     In such a case,  (1) and (2) may be ignored, and (3) is relaxed to
+ *     ncell >= 1. This may be useful for systems which are "narrow" (cf. a0).
+ *
  *****************************************************************************/
 
 int colloids_init_halo_range_check(pe_t * pe, cs_t * cs,
 				   colloids_info_t * cinfo) {
 
   int ifail = 0;
-  int ncolloid;
-  int ncell[3];
-  int nlocal[3];
+  int ncolloid = 0;
+  int ncell[3] = {0};
+  int nlocal[3] = {0};
   int nhalo = 1;       /* Always, for purpose of BBL. */
 
+  int nar[3] = {0};    /* See point (a) above */
+
   double a0max = 0.0;  /* Maximum colloid a0 present */
   double lcell[3];
 
@@ -1228,23 +1237,27 @@ int colloids_init_halo_range_check(pe_t * pe, cs_t * cs,
 
   colloids_info_a0max(cinfo, &a0max);
 
-  if (2.0*a0max >= 1.0*(nlocal[X] - nhalo)) ifail = 1;
-  if (2.0*a0max >= 1.0*(nlocal[Y] - nhalo)) ifail = 1;
-  if (2.0*a0max >= 1.0*(nlocal[Z] - nhalo)) ifail = 1;
+  if (cs->param->periodic[X] == 0 && cs->param->mpi_cartsz[X] == 1) nar[X] = 1;
+  if (cs->param->periodic[Y] == 0 && cs->param->mpi_cartsz[Y] == 1) nar[Y] = 1;
+  if (cs->param->periodic[Z] == 0 && cs->param->mpi_cartsz[Z] == 1) nar[Z] = 1;
+
+  if (nar[X] == 0 && (2.0*a0max >= 1.0*(nlocal[X] - nhalo))) ifail = 1;
+  if (nar[Y] == 0 && (2.0*a0max >= 1.0*(nlocal[Y] - nhalo))) ifail = 1;
+  if (nar[Z] == 0 && (2.0*a0max >= 1.0*(nlocal[Z] - nhalo))) ifail = 1;
   if (ifail == 1) {
     pe_fatal(pe, "Particle diameter larger than (nlocal - 1) domain size\n");
   }
 
-  if (lcell[X] <= a0max) ifail = 1;
-  if (lcell[Y] <= a0max) ifail = 1;
-  if (lcell[Z] <= a0max) ifail = 1;
+  if (nar[X] == 0 && (lcell[X] <= a0max)) ifail = 1;
+  if (nar[Y] == 0 && (lcell[Y] <= a0max)) ifail = 1;
+  if (nar[Z] == 0 && (lcell[Z] <= a0max)) ifail = 1;
   if (ifail == 1) {
     pe_fatal(pe, "Particle a0 > cell width breaks BBL message passing\n");
   }
 
-  if (ncell[X] < 2) ifail = 1;
-  if (ncell[Y] < 2) ifail = 1;
-  if (ncell[Z] < 2) ifail = 1;
+  if (ncell[X] < (2 - nar[X])) ifail = 1;
+  if (ncell[Y] < (2 - nar[Y])) ifail = 1;
+  if (ncell[Z] < (2 - nar[Z])) ifail = 1;
 
   if (ifail == 1) {
     pe_fatal(pe, "Must have two cells minimum\n");
@@ -1254,9 +1267,9 @@ int colloids_init_halo_range_check(pe_t * pe, cs_t * cs,
 
   cs_nhalo(cs, &nhalo);
 
-  if (lcell[X] < (a0max + nhalo - 0.5)) ifail = 1;
-  if (lcell[Y] < (a0max + nhalo - 0.5)) ifail = 1;
-  if (lcell[Z] < (a0max + nhalo - 0.5)) ifail = 1;
+  if (nar[X] == 0 && (lcell[X] < (a0max + nhalo - 0.5))) ifail = 1;
+  if (nar[Y] == 0 && (lcell[Y] < (a0max + nhalo - 0.5))) ifail = 1;
+  if (nar[Z] == 0 && (lcell[Z] < (a0max + nhalo - 0.5))) ifail = 1;
 
   if (ifail == 1) {
     pe_fatal(pe, "Must have cell width > a0_max + nhalo\n");

diff --git a/tests/regression/d3q27/serial-elip-s10.inp b/tests/regression/d3q27/serial-elip-s10.inp
@@ -0,0 +1,94 @@
+##############################################################################
+#
+#  Colloid simple configuration output
+#
+##############################################################################
+
+N_start  0
+N_cycles 10
+
+##############################################################################
+#
+#  System and MPI
+# 
+##############################################################################
+
+size        128_18_18
+periodicity 1_0_0
+
+##############################################################################
+#
+#  Fluid parameters
+#
+##############################################################################
+
+viscosity      0.1
+fluid_rho0     1.0
+
+##############################################################################
+#
+#  Free energy parameters
+#
+###############################################################################
+
+free_energy  none
+
+###############################################################################
+#
+#  Colloid parameters
+#
+###############################################################################
+
+colloid_init        input_one
+colloid_one_shape   ellipsoid
+colloid_one_elabc   9.562082_4.996656_4.996656
+colloid_one_euler   0.0_0.0_0.0 
+colloid_one_r       64.5_9.5_9.5
+
+###############################################################################
+#
+# Colloid-colloid soft-sphere potential parameters
+# The soft sphere is always needed
+#
+###############################################################################
+
+
+colloid_gravity        0.005_0.0_0.0
+
+###############################################################################
+#
+#  Walls / boundaries
+#
+###############################################################################
+
+boundary_walls 0_1_1
+
+###############################################################################
+#
+#  Output frequency and type
+#
+###############################################################################
+
+default_io_mode    mpiio
+default_io_format  binary
+freq_statistics    10
+config_at_end      no
+
+##############################################################################
+#
+#  colloid i/o
+#
+##############################################################################
+
+colloid_io_freq          1000
+colloid_io_format_output ASCII
+
+###############################################################################
+#
+#  Miscellaneous
+#
+#  random_seed  +ve integer is the random number generator seed
+#
+###############################################################################
+
+random_seed 8361435
diff --git a/tests/regression/d3q27/serial-elip-s10.log b/tests/regression/d3q27/serial-elip-s10.log
@@ -0,0 +1,158 @@
+Welcome to: Ludwig v0.22.0 (Serial version running on 1 process)
+Git commit: 9255199534dfc86c44c98ff14cfb3dfa09108af5
+
+Start time: Tue Oct  1 10:00:36 2024
+
+Compiler:
+  name:           Gnu 14.1.0
+  version-string: 14.1.0
+  options:        -O2 -g -Wall -Werror
+
+Note assertions via standard C assert() are on.
+
+Target thread model: OpenMP.
+OpenMP threads: 1; maximum number of threads: 11.
+
+Read 21 user parameters from input
+
+No free energy selected
+
+System details
+--------------
+System size:    128 18 18
+Decomposition:  1 1 1
+Local domain:   128 18 18
+Periodic:       1 0 0
+Halo nhalo:     1
+Reorder:        true
+Initialised:    1
+
+System properties
+----------------
+Mean fluid density:           1.00000e+00
+Shear viscosity               1.00000e-01
+Bulk viscosity                1.00000e-01
+Temperature                   0.00000e+00
+External body force density   0.00000e+00  0.00000e+00  0.00000e+00
+External E-field amplitude    0.00000e+00  0.00000e+00  0.00000e+00
+External E-field frequency    0.00000e+00
+External magnetic field       0.00000e+00  0.00000e+00  0.00000e+00
+
+Lattice Boltzmann distributions
+-------------------------------
+Model:            d3q27  
+SIMD vector len:  1
+Number of sets:   1
+Halo type:        lb_halo_target (full halo)
+Input format:     binary
+Output format:    binary
+I/O grid:         1 1 1
+
+Lattice Boltzmann collision
+---------------------------
+Relaxation time scheme:   M10
+Hydrodynamic modes:       on
+Ghost modes:              on
+Isothermal fluctuations:  off
+Shear relaxation time:    8.00000e-01
+Bulk relaxation time:     8.00000e-01
+Ghost relaxation time:    1.00000e+00
+[User   ] Random number seed: 8361435
+
+Hydrodynamics
+-------------
+Hydrodynamics: on
+
+Boundary walls
+--------------
+Boundary walls:                  - Y Z
+Boundary speed u_x (bottom):     0.0000000e+00
+Boundary speed u_x (top):        0.0000000e+00
+Boundary normal lubrication rc:  0.0000000e+00
+Wall boundary links allocated:   81408
+Memory (total, bytes):           1302528
+Boundary shear initialise:       0
+
+Colloid information
+-------------------
+
+Colloid I/O settings
+--------------------
+Decomposition:                1  1  1
+Number of files:              1
+Input format:                 ascii
+Output format:                ascii
+Single file read flag:        0
+
+Requested one colloid via input:
+colloid_one                   ellipsoid
+colloid_one_r                 6.4500000e+01  9.5000000e+00  9.5000000e+00
+colloid_one_elabc             9.5620820e+00  4.9966560e+00  4.9966560e+00
+colloid_one_euler             0.0000000e+00  0.0000000e+00  0.0000000e+00
+
+Initialised 1 colloid
+
+Colloid cell list information
+-----------------------------
+Input radius maximum:         9.5620820e+00
+Final cell list:              12 1 1
+Final cell lengths:           1.0666667e+01  1.8000000e+01  1.8000000e+01
+
+Sedimentation force on:       yes
+Sedimentation force:          5.0000000e-03  0.0000000e+00  0.0000000e+00
+
+Initial conditions.
+
+Scalars - total mean variance min max
+[rho]       40464.00  1.00000000000  2.2204460e-16  1.00000000000  1.00000000000
+
+Momentum - x y z
+[total   ]  0.0000000e+00  0.0000000e+00  0.0000000e+00
+[fluid   ]  0.0000000e+00  0.0000000e+00  0.0000000e+00
+[colloids]  0.0000000e+00  0.0000000e+00  0.0000000e+00
+[walls   ]  0.0000000e+00  0.0000000e+00  0.0000000e+00
+
+Starting time step loop.
+
+Particle statistics:
+
+Colloid velocities - x y z
+[minimum ]  2.6153937e-05 -5.3604951e-18  1.8203251e-18
+[maximum ]  2.6153937e-05 -5.3604951e-18  1.8203251e-18
+
+Scalars - total mean variance min max
+[rho]       40464.00  1.00000000000  7.4389384e-12  0.99997187102  1.00002812813
+
+Momentum - x y z
+[total   ]  6.2665151e-14  8.8029209e-14 -3.2492556e-14
+[fluid   ] -1.9760295e-02 -1.1450476e-13 -4.4833668e-13
+[colloids]  2.8251562e-02 -3.2562774e-15  2.3560458e-16
+[walls   ] -8.4912674e-03  2.0579025e-13  4.1560852e-13
+
+Velocity - x y z
+[minimum ] -1.9016983e-06 -9.0171214e-06 -9.0171214e-06
+[maximum ]  2.4698222e-05  9.0171214e-06  9.0171214e-06
+
+Completed cycle 10
+
+Timer resolution: 1e-06 second
+
+Timer statistics
+             Section:       tmin       tmax      total
+               Total:      0.499      0.499      0.499   0.498647 (1 call)
+      Time step loop:      0.045      0.058      0.461   0.046146 (10 calls)
+         Propagation:      0.006      0.006      0.059   0.005870 (10 calls)
+    Propagtn (krnl) :      0.006      0.006      0.059   0.005869 (10 calls)
+           Collision:      0.029      0.030      0.293   0.029312 (10 calls)
+   Collision (krnl) :      0.029      0.030      0.293   0.029310 (10 calls)
+       Lattice halos:      0.001      0.002      0.026   0.001299 (20 calls)
+       phi gradients:      0.000      0.000      0.000   0.000000 (10 calls)
+              Forces:      0.000      0.000      0.001   0.000091 (10 calls)
+             Rebuild:      0.001      0.001      0.008   0.000846 (10 calls)
+                 BBL:      0.006      0.006      0.056   0.005586 (10 calls)
+      Particle halos:      0.000      0.000      0.000   0.000003 (10 calls)
+   Force calculation:      0.000      0.000      0.000   0.000000 (10 calls)
+          phi update:      0.000      0.000      0.000   0.000000 (10 calls)
+Diagnostics / output:      0.000      0.013      0.013   0.001299 (10 calls)
+End time: Tue Oct  1 10:00:36 2024
+Ludwig finished normally.