From 4fbc6f42c05358592df37453f40109401183ad99 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 21 Aug 2008 13:53:19 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2090
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/comm.cpp | 26 +++++++++++++++++++-------
src/comm.h | 1 +
src/delete_atoms.cpp | 4 ++--
src/neighbor.cpp | 40 +++++++++++++++++-----------------------
src/neighbor.h | 5 ++---
5 files changed, 41 insertions(+), 35 deletions(-)
diff --git a/src/comm.cpp b/src/comm.cpp
index a286968810..ae24ab1712 100644
--- a/src/comm.cpp
+++ b/src/comm.cpp
@@ -62,6 +62,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
style = SINGLE;
multilo = multihi = NULL;
cutghostmulti = NULL;
+ cutghostuser = 0.0;
// initialize comm buffers & exchange memory
@@ -215,14 +216,14 @@ void Comm::init()
/* ----------------------------------------------------------------------
setup spatial-decomposition communication patterns
- function of neighbor cutoff(s) and current box size
+ function of neighbor cutoff(s) & cutghostuser & current box size
single style sets slab boundaries (slablo,slabhi) based on max cutoff
multi style sets type-dependent slab boundaries (multilo,multihi)
------------------------------------------------------------------------- */
void Comm::setup()
{
- // cutghost = max distance at which ghost atoms need to be acquired
+ // cutghost[] = max distance at which ghost atoms need to be acquired
// for orthogonal:
// cutghost is in box coords = neigh->cutghost in all 3 dims
// for triclinic:
@@ -235,17 +236,21 @@ void Comm::setup()
int ntypes = atom->ntypes;
double *prd,*sublo,*subhi;
+ double cut = MAX(neighbor->cutneighmax,cutghostuser);
+
if (triclinic == 0) {
prd = domain->prd;
sublo = domain->sublo;
subhi = domain->subhi;
- cutghost[0] = cutghost[1] = cutghost[2] = neighbor->cutghost;
+ cutghost[0] = cutghost[1] = cutghost[2] = cut;
+
if (style == MULTI) {
double *cuttype = neighbor->cuttype;
for (i = 1; i <= ntypes; i++)
cutghostmulti[i][0] = cutghostmulti[i][1] = cutghostmulti[i][2] =
cuttype[i];
}
+
} else {
prd = domain->prd_lamda;
sublo = domain->sublo_lamda;
@@ -253,11 +258,12 @@ void Comm::setup()
double *h_inv = domain->h_inv;
double length0,length1,length2;
length0 = sqrt(h_inv[0]*h_inv[0] + h_inv[5]*h_inv[5] + h_inv[4]*h_inv[4]);
- cutghost[0] = neighbor->cutghost * length0;
+ cutghost[0] = cut * length0;
length1 = sqrt(h_inv[1]*h_inv[1] + h_inv[3]*h_inv[3]);
- cutghost[1] = neighbor->cutghost * length1;
+ cutghost[1] = cut * length1;
length2 = h_inv[2];
- cutghost[2] = neighbor->cutghost * length2;
+ cutghost[2] = cut * length2;
+
if (style == MULTI) {
double *cuttype = neighbor->cuttype;
for (i = 1; i <= ntypes; i++) {
@@ -1524,11 +1530,17 @@ void Comm::set(int narg, char **arg)
if (iarg+2 > narg) error->all("Illegal communicate command");
bordergroup = group->find(arg[iarg+1]);
if (bordergroup < 0)
- error->all("Invalid group ID in communicate command");
+ error->all("Invalid group in communicate command");
if (bordergroup && (atom->firstgroupname == NULL ||
strcmp(arg[iarg+1],atom->firstgroupname) != 0))
error->all("Communicate group != atom_modify first group");
iarg += 2;
+ } else if (strcmp(arg[iarg],"cutoff") == 0) {
+ if (iarg+2 > narg) error->all("Illegal communicate command");
+ cutghostuser = atof(arg[iarg+1]);
+ if (cutghostuser < 0.0)
+ error->all("Invalid cutoff in communicate command");
+ iarg += 2;
} else error->all("Illegal communicate command");
}
}
diff --git a/src/comm.h b/src/comm.h
index 54078ad950..b1b31a60ae 100644
--- a/src/comm.h
+++ b/src/comm.h
@@ -72,6 +72,7 @@ class Comm : protected Pointers {
int map_style; // non-0 if global->local mapping is done
int ***grid2proc; // which proc owns i,j,k loc in 3d grid
int bordergroup; // only communicate this group in borders
+ double cutghostuser; // user-specified ghost cutoff
int *firstrecv; // where to put 1st recv atom in each swap
int **sendlist; // list of atoms to send in each swap
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index ed2b4765b2..03c6cf6f20 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -200,8 +200,8 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
// error check on cutoff
- if (cut > neighbor->cutghost)
- error->all("Delete_atoms cutoff > ghost cutoff");
+ if (cut > neighbor->cutneighmax)
+ error->all("Delete_atoms cutoff > neighbor cutoff");
// setup domain, communication and neighboring
// acquire ghosts
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index e2fe51d4c4..4b75e1ea10 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -201,15 +201,9 @@ void Neighbor::init()
// set neighbor cutoffs (force cutoff + skin)
// trigger determines when atoms migrate and neighbor lists are rebuilt
- // cutneigh and cutneighsq determine what pairs go into neighbor list
- // set to 0 if cutforce = 0
- // cutneighmin/max used for neighbor bin sizes
- // cutghost determines comm distance = max of cutneigh & skin
- // skin is only > cutneighmax when cutneighmax = 0.0 due to pair = NULL
- // in this case, are running a bond-only simulation
- // still need ghost atom communication for bonds and atom exchange
- // triggered by atoms moving 1/2 skin distance, but no neigh lists formed
- // user should set skin big enough to find all bonds
+ // needs to be non-zero for migration distance check
+ // even if pair = NULL and no neighbor lists are used
+ // cutneigh = force cutoff + skin if cutforce > 0, else cutneigh = 0
triggersq = 0.25*skin*skin;
@@ -240,7 +234,6 @@ void Neighbor::init()
cutneighmax = MAX(cutneighmax,cut);
}
}
- cutghost = MAX(cutneighmax,skin);
cutneighmaxsq = cutneighmax * cutneighmax;
// check other classes that can induce reneighboring in decide()
@@ -1053,7 +1046,7 @@ void Neighbor::setup_bins()
{
// bbox lo/hi = bounding box of entire domain
// bbox = size of bbox of entire domain
- // bsubbox lo/hi = bounding box of my subdomain extended by ghost atoms
+ // bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost
// for triclinic:
// bbox bounds all 8 corners of tilted box
// subdomain is in lamda coords
@@ -1061,26 +1054,27 @@ void Neighbor::setup_bins()
// domain->bbox() converts lamda extent to box coords and computes bbox
double bbox[3],bsubboxlo[3],bsubboxhi[3];
+ double *cutghost = comm->cutghost;
if (triclinic == 0) {
bboxlo = domain->boxlo;
bboxhi = domain->boxhi;
- bsubboxlo[0] = domain->sublo[0] - cutghost;
- bsubboxlo[1] = domain->sublo[1] - cutghost;
- bsubboxlo[2] = domain->sublo[2] - cutghost;
- bsubboxhi[0] = domain->subhi[0] + cutghost;
- bsubboxhi[1] = domain->subhi[1] + cutghost;
- bsubboxhi[2] = domain->subhi[2] + cutghost;
+ bsubboxlo[0] = domain->sublo[0] - cutghost[0];
+ bsubboxlo[1] = domain->sublo[1] - cutghost[1];
+ bsubboxlo[2] = domain->sublo[2] - cutghost[2];
+ bsubboxhi[0] = domain->subhi[0] + cutghost[0];
+ bsubboxhi[1] = domain->subhi[1] + cutghost[1];
+ bsubboxhi[2] = domain->subhi[2] + cutghost[2];
} else {
bboxlo = domain->boxlo_bound;
bboxhi = domain->boxhi_bound;
double lo[3],hi[3];
- lo[0] = domain->sublo_lamda[0] - comm->cutghost[0];
- lo[1] = domain->sublo_lamda[1] - comm->cutghost[1];
- lo[2] = domain->sublo_lamda[2] - comm->cutghost[2];
- hi[0] = domain->subhi_lamda[0] + comm->cutghost[0];
- hi[1] = domain->subhi_lamda[1] + comm->cutghost[1];
- hi[2] = domain->subhi_lamda[2] + comm->cutghost[2];
+ lo[0] = domain->sublo_lamda[0] - cutghost[0];
+ lo[1] = domain->sublo_lamda[1] - cutghost[1];
+ lo[2] = domain->sublo_lamda[2] - cutghost[2];
+ hi[0] = domain->subhi_lamda[0] + cutghost[0];
+ hi[1] = domain->subhi_lamda[1] + cutghost[1];
+ hi[2] = domain->subhi_lamda[2] + cutghost[2];
domain->bbox(lo,hi,bsubboxlo,bsubboxhi);
}
diff --git a/src/neighbor.h b/src/neighbor.h
index 233eb3c8bb..a30f174959 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -29,7 +29,8 @@ class Neighbor : protected Pointers {
int oneatom; // max # of neighbors for one atom
double skin; // skin distance
- double cutghost; // distance for acquiring ghost atoms
+ double cutneighmin; // min neighbor cutoff for all type pairs
+ double cutneighmax; // max neighbor cutoff for all type pairs
double *cuttype; // for each type, max neigh cut w/ others
int ncalls; // # of times build has been called
@@ -81,8 +82,6 @@ class Neighbor : protected Pointers {
int *fixchecklist; // which fixes to check
double **cutneighsq; // neighbor cutneigh sq for each type pair
- double cutneighmin; // min neighbor cutoff (for cutforce > 0)
- double cutneighmax; // max neighbor cutoff for all type pairs
double cutneighmaxsq; // cutneighmax squared
double *cuttypesq; // cuttype squared
--
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