From 6bc507cd6aed552d5662ae3aad1a112c73701e03 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Sat, 9 Jul 2016 20:41:07 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15274
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/neigh_gran.cpp | 136 ++++++++++++++++++++++++------------------
src/neigh_request.cpp | 55 ++++++++++++-----
src/neighbor.cpp | 87 ++++++++++++++++++++-------
3 files changed, 182 insertions(+), 96 deletions(-)
diff --git a/src/neigh_gran.cpp b/src/neigh_gran.cpp
index 3549212c51..a537fbae09 100644
--- a/src/neigh_gran.cpp
+++ b/src/neigh_gran.cpp
@@ -11,6 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include <string.h>
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
@@ -30,7 +31,7 @@ using namespace LAMMPS_NS;
void Neighbor::granular_nsq_no_newton(NeighList *list)
{
- int i,j,m,n,nn,bitmask;
+ int i,j,m,n,nn,bitmask,dnum,dnumbytes;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
@@ -75,6 +76,8 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
firstshear = listgranhistory->firstdouble;
ipage_touch = listgranhistory->ipage;
dpage_shear = listgranhistory->dpage;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
}
int inum = 0;
@@ -120,20 +123,17 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
if (partner[i][m] == tag[j]) break;
if (m < npartner[i]) {
touchptr[n] = 1;
- shearptr[nn++] = shearpartner[i][m][0];
- shearptr[nn++] = shearpartner[i][m][1];
- shearptr[nn++] = shearpartner[i][m][2];
+ memcpy(&shearptr[nn],shearpartner[i][m],dnumbytes);
+ nn += dnum;
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
}
@@ -170,7 +170,7 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
void Neighbor::granular_nsq_newton(NeighList *list)
{
- int i,j,m,n,nn,itag,jtag,bitmask;
+ int i,j,m,n,nn,itag,jtag,bitmask,dnum,dnumbytes;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
@@ -215,6 +215,8 @@ void Neighbor::granular_nsq_newton(NeighList *list)
firstshear = listgranhistory->firstdouble;
ipage_touch = listgranhistory->ipage;
dpage_shear = listgranhistory->dpage;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
}
int inum = 0;
@@ -277,20 +279,17 @@ void Neighbor::granular_nsq_newton(NeighList *list)
if (partner[i][m] == tag[j]) break;
if (m < npartner[i]) {
touchptr[n] = 1;
- shearptr[nn++] = shearpartner[i][m][0];
- shearptr[nn++] = shearpartner[i][m][1];
- shearptr[nn++] = shearpartner[i][m][2];
+ memcpy(&shearptr[nn],shearpartner[i][m],dnumbytes);
+ nn += dnum;
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
}
@@ -316,6 +315,18 @@ void Neighbor::granular_nsq_newton(NeighList *list)
list->inum = inum;
}
+/* ----------------------------------------------------------------------
+ granular particles
+ N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
+ shear history must be accounted for when a neighbor pair is added
+ pair added to list if atoms i and j are both owned and i < j
+ pair added if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void Neighbor::granular_nsq_newton_onesided(NeighList *list)
+{
+}
+
/* ----------------------------------------------------------------------
granular particles
binned neighbor list construction with partial Newton's 3rd law
@@ -327,12 +338,13 @@ void Neighbor::granular_nsq_newton(NeighList *list)
void Neighbor::granular_bin_no_newton(NeighList *list)
{
- int i,j,k,m,n,nn,ibin;
+ int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
double *shearptr;
+
NeighList *listgranhistory;
int *npartner;
tagint **partner;
@@ -376,6 +388,8 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
firstshear = listgranhistory->firstdouble;
ipage_touch = listgranhistory->ipage;
dpage_shear = listgranhistory->dpage;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
}
int inum = 0;
@@ -426,20 +440,17 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
if (partner[i][m] == tag[j]) break;
if (m < npartner[i]) {
touchptr[n] = 1;
- shearptr[nn++] = shearpartner[i][m][0];
- shearptr[nn++] = shearpartner[i][m][1];
- shearptr[nn++] = shearpartner[i][m][2];
+ memcpy(&shearptr[nn],shearpartner[i][m],dnumbytes);
+ nn += dnum;
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
}
@@ -476,7 +487,7 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
void Neighbor::granular_bin_newton(NeighList *list)
{
- int i,j,k,m,n,nn,ibin;
+ int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
@@ -525,6 +536,8 @@ void Neighbor::granular_bin_newton(NeighList *list)
firstshear = listgranhistory->firstdouble;
ipage_touch = listgranhistory->ipage;
dpage_shear = listgranhistory->dpage;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
}
int inum = 0;
@@ -579,20 +592,17 @@ void Neighbor::granular_bin_newton(NeighList *list)
if (partner[i][m] == tag[j]) break;
if (m < npartner[i]) {
touchptr[n] = 1;
- shearptr[nn++] = shearpartner[i][m][0];
- shearptr[nn++] = shearpartner[i][m][1];
- shearptr[nn++] = shearpartner[i][m][2];
+ memcpy(&shearptr[nn],shearpartner[i][m],dnumbytes);
+ nn += dnum;
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
}
@@ -623,20 +633,17 @@ void Neighbor::granular_bin_newton(NeighList *list)
if (partner[i][m] == tag[j]) break;
if (m < npartner[i]) {
touchptr[n] = 1;
- shearptr[nn++] = shearpartner[i][m][0];
- shearptr[nn++] = shearpartner[i][m][1];
- shearptr[nn++] = shearpartner[i][m][2];
+ memcpy(&shearptr[nn],shearpartner[i][m],dnumbytes);
+ nn += dnum;
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
}
@@ -663,6 +670,18 @@ void Neighbor::granular_bin_newton(NeighList *list)
list->inum = inum;
}
+/* ----------------------------------------------------------------------
+ granular particles
+ N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
+ shear history must be accounted for when a neighbor pair is added
+ pair added to list if atoms i and j are both owned and i < j
+ pair added if j is ghost (also stored by proc owning j)
+------------------------------------------------------------------------- */
+
+void Neighbor::granular_bin_newton_onesided(NeighList *list)
+{
+}
+
/* ----------------------------------------------------------------------
granular particles
binned neighbor list construction with Newton's 3rd law for triclinic
@@ -673,7 +692,7 @@ void Neighbor::granular_bin_newton(NeighList *list)
void Neighbor::granular_bin_newton_tri(NeighList *list)
{
- int i,j,k,m,n,nn,ibin;
+ int i,j,k,m,n,nn,ibin,dnum,dnumbytes;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
@@ -722,6 +741,8 @@ void Neighbor::granular_bin_newton_tri(NeighList *list)
firstshear = listgranhistory->firstdouble;
ipage_touch = listgranhistory->ipage;
dpage_shear = listgranhistory->dpage;
+ dnum = listgranhistory->dnum;
+ dnumbytes = dnum * sizeof(double);
}
int inum = 0;
@@ -781,20 +802,17 @@ void Neighbor::granular_bin_newton_tri(NeighList *list)
if (partner[i][m] == tag[j]) break;
if (m < npartner[i]) {
touchptr[n] = 1;
- shearptr[nn++] = shearpartner[i][m][0];
- shearptr[nn++] = shearpartner[i][m][1];
- shearptr[nn++] = shearpartner[i][m][2];
+ memcpy(&shearptr[nn],shearpartner[i][m],dnumbytes);
+ nn += dnum;
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
} else {
touchptr[n] = 0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
- shearptr[nn++] = 0.0;
+ memcpy(&shearptr[nn],zeroes,dnumbytes);
+ nn += dnum;
}
}
diff --git a/src/neigh_request.cpp b/src/neigh_request.cpp
index a9c0924387..cc8c0d7c99 100644
--- a/src/neigh_request.cpp
+++ b/src/neigh_request.cpp
@@ -26,23 +26,28 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
id = 0;
unprocessed = 1;
- // default is pair request
+ // class user of list: default is pair request
+ // only one is set to 1
pair = 1;
fix = compute = command = 0;
- // default is half neighbor list
+ // kind of list: default is half neighbor list
+ // only one is set to 1
half = 1;
full = 0;
full_cluster = 0;
- gran = granhistory = 0;
+ gran = 0;
respainner = respamiddle = respaouter = 0;
half_from_full = 0;
+ // combination of settings, mutiple can be set to 1
// default is every reneighboring
// default is use newton_pair setting in force
// default is encode special bond flags
+ // default is no granular history (when gran = 1)
+ // default is no one-sided sphere/surface interactions (when gran = 1)
// default is no auxiliary floating point values
// default is no neighbors of ghosts
// default is no multi-threaded neighbor list build
@@ -52,6 +57,8 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
occasional = 0;
newton = 0;
//special = 1;
+ granhistory = 0;
+ granonesided = 0;
dnum = 0;
ghost = 0;
omp = 0;
@@ -59,7 +66,8 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
kokkos_host = kokkos_device = 0;
ssa = 0;
- // default is no copy or skip
+ // copy/skip/derive info, default is no copy or skip
+ // none or only one option is set
copy = 0;
skip = 0;
@@ -119,7 +127,6 @@ int NeighRequest::identical(NeighRequest *other)
if (half != other->half_original) same = 0;
if (full != other->full) same = 0;
if (gran != other->gran) same = 0;
- if (granhistory != other->granhistory) same = 0;
if (respainner != other->respainner) same = 0;
if (respamiddle != other->respamiddle) same = 0;
if (respaouter != other->respaouter) same = 0;
@@ -128,6 +135,8 @@ int NeighRequest::identical(NeighRequest *other)
if (newton != other->newton) same = 0;
if (occasional != other->occasional) same = 0;
//if (special != other->special) same = 0;
+ if (granhistory != other->granhistory) same = 0;
+ if (granonesided != other->granonesided) same = 0;
if (dnum != other->dnum) same = 0;
if (ghost != other->ghost) same = 0;
if (omp != other->omp) same = 0;
@@ -150,6 +159,10 @@ int NeighRequest::same_kind(NeighRequest *other)
{
int same = 1;
+ // class caller will be same (pair), b/c called by pair hybrid styles
+
+ // kind must be the the same
+
if (half != other->half) same = 0;
if (full != other->full) same = 0;
if (gran != other->gran) same = 0;
@@ -158,12 +171,20 @@ int NeighRequest::same_kind(NeighRequest *other)
if (respamiddle != other->respamiddle) same = 0;
if (respaouter != other->respaouter) same = 0;
if (half_from_full != other->half_from_full) same = 0;
+
+ // settings that must be the same
+ // other settings do not need to be the same (e.g. granonesided)
+
if (newton != other->newton) same = 0;
if (ghost != other->ghost) same = 0;
if (omp != other->omp) same = 0;
if (intel != other->intel) same = 0;
+ if (kokkos_host != other->kokkos_host) same = 0;
+ if (kokkos_device != other->kokkos_device) same = 0;
if (ssa != other->ssa) same = 0;
+ // copy/skip/derive info does not need to be the same
+
return same;
}
@@ -192,26 +213,28 @@ int NeighRequest::same_skip(NeighRequest *other)
}
/* ----------------------------------------------------------------------
- set kind and other values of this request to that of other request
+ set kind and optional values in this request to those of other request
+ not copy/skip/derive values since this may be non-skip parent of child
------------------------------------------------------------------------- */
void NeighRequest::copy_request(NeighRequest *other)
{
- half = 0;
-
- if (other->half) half = 1;
- if (other->full) full = 1;
- if (other->gran) gran = 1;
- if (other->granhistory) granhistory = 1;
- if (other->respainner) respainner = 1;
- if (other->respamiddle) respamiddle = 1;
- if (other->respaouter) respaouter = 1;
- if (other->half_from_full) half_from_full = 1;
+ half = other->half;
+ full = other->full;
+ gran = other->gran;
+ granhistory = other->granhistory;
+ respainner = other->respainner;
+ respamiddle = other->respamiddle;
+ respaouter = other->respaouter;
+ half_from_full = other->half_from_full;
newton = other->newton;
+ granonesided = other->granonesided;
dnum = other->dnum;
ghost = other->ghost;
omp = other->omp;
intel = other->intel;
+ kokkos_host = other->kokkos_host;
+ kokkos_device = other->kokkos_device;
ssa = other->ssa;
}
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index f82a20acd9..307ea10dd8 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -153,6 +153,8 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
old_check = dist_check;
old_cutoff = cutneighmax;
+ zeroes = NULL;
+
// bond lists
maxbond = 0;
@@ -213,6 +215,8 @@ Neighbor::~Neighbor()
for (int i = 0; i < old_nrequest; i++) delete old_requests[i];
memory->sfree(old_requests);
+ delete [] zeroes;
+
memory->destroy(bondlist);
memory->destroy(anglelist);
memory->destroy(dihedrallist);
@@ -582,13 +586,11 @@ void Neighbor::init()
}
// granhistory: set preceeding list's listgranhistory to this list
- // also set preceeding list's ptr to FixShearHistory
+ // also set FH ptr in preceeding list to FSH class created by pair
if (requests[i]->granhistory) {
lists[i-1]->listgranhistory = lists[i];
- for (int ifix = 0; ifix < modify->nfix; ifix++)
- if (strcmp(modify->fix[ifix]->style,"SHEAR_HISTORY") == 0)
- lists[i-1]->fix_history = (FixShearHistory *) modify->fix[ifix];
+ lists[i-1]->fix_history = requests[i]->fix_history;
processed = 1;
// respaouter: point this list at preceeding 1/2 inner/middle lists
@@ -669,11 +671,21 @@ void Neighbor::init()
}
// allocate initial pages for each list, except if listcopy set
+ // allocate dnum vector of zeroes if set
+ int dnummax = 0;
for (i = 0; i < nrequest; i++) {
if (!lists[i]) continue;
- if (!lists[i]->listcopy)
+ if (!lists[i]->listcopy) {
lists[i]->setup_pages(pgsize,oneatom,requests[i]->dnum);
+ dnummax = MAX(dnummax,requests[i]->dnum);
+ }
+ }
+
+ if (dnummax) {
+ delete [] zeroes;
+ zeroes = new double[dnummax];
+ for (i = 0; i < dnummax; i++) zeroes[i] = 0.0;
}
// set ptrs to pair_build and stencil_create functions for each list
@@ -1028,17 +1040,17 @@ int Neighbor::request(void *requestor, int instance)
determine which pair_build function each neigh list needs
based on settings of neigh request
copy -> copy_from function
- skip -> granular function if gran with granhistory,
+ skip -> granular function if gran, several options
respa function if respaouter,
skip_from function for everything else
ssa -> special case for USER-DPD pair styles
half_from_full, half, full, gran, respaouter ->
- choose by newton and rq->newton and tri settings
+ choose by newton and rq->newton and triclinic settings
style NSQ options = newton off, newton on
style BIN options = newton off, newton on and not tri, newton on and tri
stlye MULTI options = same options as BIN
if none of these, ptr = NULL since pair_build is not invoked for this list
- use "else if" b/c skip,copy can be set in addition to half,full,etc
+ use "else if" logic b/c skip,copy can be set in addition to half,full,etc
------------------------------------------------------------------------- */
void Neighbor::choose_build(int index, NeighRequest *rq)
@@ -1050,8 +1062,19 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
if (rq->copy) pb = &Neighbor::copy_from;
else if (rq->skip) {
- if (rq->gran && lists[index]->listgranhistory)
- pb = &Neighbor::skip_from_granular;
+ if (rq->gran) {
+ NeighRequest *otherrq = requests[rq->otherlist];
+ if (otherrq->newton == 0) {
+ pb = &Neighbor::skip_from_granular;
+ } else if (otherrq->newton == 1) {
+ error->all(FLERR,"Neighbor build method not supported");
+ } else if (otherrq->newton == 2) {
+ if (rq->granonesided == 0)
+ pb = &Neighbor::skip_from_granular_off2on;
+ else if (rq->granonesided == 1)
+ pb = &Neighbor::skip_from_granular_off2on_onesided;
+ }
+ }
else if (rq->respaouter) pb = &Neighbor::skip_from_respa;
else pb = &Neighbor::skip_from;
@@ -1145,16 +1168,39 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
}
} else if (rq->gran) {
- if (style == NSQ) {
- if (newton_pair == 0) pb = &Neighbor::granular_nsq_no_newton;
- else if (newton_pair == 1) pb = &Neighbor::granular_nsq_newton;
- } else if (style == BIN) {
- if (newton_pair == 0) pb = &Neighbor::granular_bin_no_newton;
- else if (triclinic == 0) pb = &Neighbor::granular_bin_newton;
- else if (triclinic == 1) pb = &Neighbor::granular_bin_newton_tri;
- } else if (style == MULTI)
- error->all(FLERR,"Neighbor multi not yet enabled for granular");
-
+ if (rq->newton == 0) {
+ if (style == NSQ) {
+ if (newton_pair == 0) pb = &Neighbor::granular_nsq_no_newton;
+ else if (newton_pair == 1) {
+ if (rq->granonesided == 0) pb = &Neighbor::granular_nsq_newton;
+ else pb = &Neighbor::granular_nsq_newton_onesided;
+ }
+ } else if (style == BIN) {
+ if (newton_pair == 0) pb = &Neighbor::granular_bin_no_newton;
+ else if (newton_pair == 1) {
+ if (triclinic == 0) {
+ if (rq->granonesided == 0) pb = &Neighbor::granular_bin_newton;
+ else pb = &Neighbor::granular_bin_newton_onesided;
+ } else if (triclinic == 1) {
+ if (rq->granonesided == 0)
+ pb = &Neighbor::granular_bin_newton_tri;
+ else error->all(FLERR,"Neighbor build method not supported");
+ }
+ }
+ } else if (style == MULTI)
+ error->all(FLERR,"Neighbor multi not yet enabled for granular");
+ } else if (rq->newton == 1) {
+ error->all(FLERR,"Neighbor build method not yet supported");
+ } else if (rq->newton == 2) {
+ if (style == NSQ) pb = &Neighbor::granular_nsq_no_newton;
+ else if (style == BIN) {
+ if (triclinic == 0) pb = &Neighbor::granular_bin_no_newton;
+ else if (triclinic == 1)
+ error->all(FLERR,"Neighbor build method not yet supported");
+ } else if (style == MULTI)
+ error->all(FLERR,"Neighbor multi not yet enabled for granular");
+ }
+
} else if (rq->respaouter) {
if (style == NSQ) {
if (newton_pair == 0) pb = &Neighbor::respa_nsq_no_newton;
@@ -2232,4 +2278,3 @@ int Neighbor::exclude_setting()
{
return exclude;
}
-
--
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