diff --git a/doc/src/compute_property_local.txt b/doc/src/compute_property_local.txt index e4e6f1ef1efc913be2a4c8aad3417e4a7686644c..c4ad0afc95cd3fcf7655d5861c66a3f488683519 100644 --- a/doc/src/compute_property_local.txt +++ b/doc/src/compute_property_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -48,10 +48,10 @@ compute 1 all property/local atype aatom2 :pre Define a computation that stores the specified attributes as local data so it can be accessed by other "output -commands"_Section_howto.html#howto_15. If the input attributes refer -to bond information, then the number of datums generated, aggregated -across all processors, equals the number of bonds in the system. -Ditto for pairs, angles, etc. +commands"_Howto_output.html. If the input attributes refer to bond +information, then the number of datums generated, aggregated across +all processors, equals the number of bonds in the system. Ditto for +pairs, angles, etc. If multiple attributes are specified then they must all generate the same amount of information, so that the resulting local array has the @@ -140,8 +140,8 @@ the array is the number of bonds, angles, etc. If a single input is specified, a local vector is produced. If two or more inputs are specified, a local array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command -that uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +that uses local values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector or array values will be integers that correspond to the diff --git a/src/balance.cpp b/src/balance.cpp index ed44e3ee0e9f3a9dd98187adf84e7f5d138005c7..2a953caf477acc84863fa3f39e4ad54e518128cd 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -28,7 +28,6 @@ #include "rcb.h" #include "irregular.h" #include "domain.h" -#include "neighbor.h" #include "force.h" #include "update.h" #include "group.h" @@ -351,13 +350,13 @@ void Balance::command(int narg, char **arg) domain->set_local_box(); // move particles to new processors via irregular() + // set disable = 0, so weights migrate with atoms for imbfinal calculation if (domain->triclinic) domain->x2lamda(atom->nlocal); Irregular *irregular = new Irregular(lmp); if (wtflag) fixstore->disable = 0; if (style == BISECTION) irregular->migrate_atoms(1,1,rcb->sendproc); else irregular->migrate_atoms(1); - if (wtflag) fixstore->disable = 1; delete irregular; if (domain->triclinic) domain->lamda2x(atom->nlocal); @@ -378,9 +377,11 @@ void Balance::command(int narg, char **arg) } // imbfinal = final imbalance + // set disable = 1, so weights no longer migrate with atoms double maxfinal; double imbfinal = imbalance_factor(maxfinal); + if (wtflag) fixstore->disable = 1; // stats output @@ -541,6 +542,8 @@ void Balance::weight_storage(char *prefix) fixstore = (FixStore *) modify->fix[modify->nfix-1]; } else fixstore = (FixStore *) modify->fix[ifix]; + // do not carry weights with atoms during normal atom migration + fixstore->disable = 1; if (prefix) delete [] fixargs[0]; @@ -644,17 +647,19 @@ int *Balance::bisection(int sortflag) double *shrinklo = &shrinkall[0]; double *shrinkhi = &shrinkall[3]; - // ensure that that the box has at least some extent. - const double nproc_rt = domain->dimension == 3 ? - cbrt(static_cast<double>(comm->nprocs)) : - sqrt(static_cast<double>(comm->nprocs)); - const double min_extent = ceil(nproc_rt)*neighbor->skin; - for (int i = 0; i < domain->dimension; i++) { - if (shrinkall[3+i]-shrinkall[i] < min_extent) { - const double mid = 0.5*(shrinkall[3+i]+shrinkall[i]); - shrinkall[3+i] = std::min(mid + min_extent*0.5, boxhi[i]); - shrinkall[i] = std::max(mid - min_extent*0.5, boxlo[i]); - } + // if shrink size in any dim is zero, use box size in that dim + + if (shrinklo[0] == shrinkhi[0]) { + shrinklo[0] = boxlo[0]; + shrinkhi[0] = boxhi[0]; + } + if (shrinklo[1] == shrinkhi[1]) { + shrinklo[1] = boxlo[1]; + shrinkhi[1] = boxhi[1]; + } + if (shrinklo[2] == shrinkhi[2]) { + shrinklo[2] = boxlo[2]; + shrinkhi[2] = boxhi[2]; } // invoke RCB diff --git a/src/rcb.cpp b/src/rcb.cpp index 4ea70ee9141e6230ecdf6ca758a3bde9e40c98a8..13e27b6fbfda836c53b381db8171f59f4b921e0d 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -241,6 +241,8 @@ void RCB::compute(int dimension, int n, double **x, double *wt, // dim_select = selected cut dimension // valuehalf_select = valuehalf in that dimension // dotmark_select = dot markings in that dimension + // initialize largest = -1.0 to insure a cut in some dim is accepted + // e.g. if current recursed box is size 0 in all dims int dim_select = -1; double largest = -1.0;