From cd5a34021d03bffefeb3ad256e9eaf6de41f143b Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 21 May 2010 15:23:59 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4172
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/neigh_full.cpp | 18 +++++++++++++++---
src/neigh_half_bin.cpp | 20 ++++++++++++++++----
src/neigh_half_multi.cpp | 20 ++++++++++++++++----
src/neigh_half_nsq.cpp | 17 ++++++++++++++---
src/neigh_respa.cpp | 37 ++++++++++++++++++++++++++++++-------
src/neighbor.cpp | 37 -------------------------------------
src/neighbor.h | 36 ++++++++++++++++++++++++++++++++++--
7 files changed, 125 insertions(+), 60 deletions(-)
diff --git a/src/neigh_full.cpp b/src/neigh_full.cpp
index 31c753579c..de5d576dfc 100644
--- a/src/neigh_full.cpp
+++ b/src/neigh_full.cpp
@@ -30,6 +30,10 @@ void Neighbor::full_nsq(NeighList *list)
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -81,7 +85,7 @@ void Neighbor::full_nsq(NeighList *list)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -116,6 +120,10 @@ void Neighbor::full_bin(NeighList *list)
// loop over each atom, storing neighbors
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -170,7 +178,7 @@ void Neighbor::full_bin(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -208,6 +216,10 @@ void Neighbor::full_multi(NeighList *list)
// loop over each atom, storing neighbors
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -268,7 +280,7 @@ void Neighbor::full_multi(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
diff --git a/src/neigh_half_bin.cpp b/src/neigh_half_bin.cpp
index 570b87307e..3432b4a0d1 100644
--- a/src/neigh_half_bin.cpp
+++ b/src/neigh_half_bin.cpp
@@ -37,6 +37,10 @@ void Neighbor::half_bin_no_newton(NeighList *list)
// loop over each atom, storing neighbors
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -93,7 +97,7 @@ void Neighbor::half_bin_no_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -130,6 +134,10 @@ void Neighbor::half_bin_newton(NeighList *list)
// loop over each atom, storing neighbors
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -188,7 +196,7 @@ void Neighbor::half_bin_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -209,7 +217,7 @@ void Neighbor::half_bin_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -246,6 +254,10 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
// loop over each atom, storing neighbors
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -309,7 +321,7 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
diff --git a/src/neigh_half_multi.cpp b/src/neigh_half_multi.cpp
index bbfff83655..b61a53114d 100644
--- a/src/neigh_half_multi.cpp
+++ b/src/neigh_half_multi.cpp
@@ -39,6 +39,10 @@ void Neighbor::half_multi_no_newton(NeighList *list)
// loop over each atom, storing neighbors
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -101,7 +105,7 @@ void Neighbor::half_multi_no_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -140,6 +144,10 @@ void Neighbor::half_multi_newton(NeighList *list)
// loop over each atom, storing neighbors
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -199,7 +207,7 @@ void Neighbor::half_multi_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -227,7 +235,7 @@ void Neighbor::half_multi_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -266,6 +274,10 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
// loop over each atom, storing neighbors
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -337,7 +349,7 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
diff --git a/src/neigh_half_nsq.cpp b/src/neigh_half_nsq.cpp
index 1f3bf89ae8..0447c3ffd4 100644
--- a/src/neigh_half_nsq.cpp
+++ b/src/neigh_half_nsq.cpp
@@ -31,6 +31,12 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
+ // loop over each atom, storing neighbors
+
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -81,7 +87,7 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -111,8 +117,13 @@ void Neighbor::half_nsq_newton(NeighList *list)
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
- double **x = atom->x;
+ // loop over each atom, storing neighbors
+
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
int *tag = atom->tag;
+
+ double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
@@ -180,7 +191,7 @@ void Neighbor::half_nsq_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
diff --git a/src/neigh_respa.cpp b/src/neigh_respa.cpp
index daed5d6793..a1e0194a33 100644
--- a/src/neigh_respa.cpp
+++ b/src/neigh_respa.cpp
@@ -32,6 +32,12 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
+ // loop over each atom, storing neighbors
+
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -122,7 +128,7 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -184,8 +190,13 @@ void Neighbor::respa_nsq_newton(NeighList *list)
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
- double **x = atom->x;
+ // loop over each atom, storing neighbors
+
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
int *tag = atom->tag;
+
+ double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
@@ -292,7 +303,7 @@ void Neighbor::respa_nsq_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -361,6 +372,10 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
// loop over each atom, storing neighbors
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -456,7 +471,7 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -525,6 +540,10 @@ void Neighbor::respa_bin_newton(NeighList *list)
// loop over each atom, storing neighbors
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -623,7 +642,7 @@ void Neighbor::respa_bin_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -655,7 +674,7 @@ void Neighbor::respa_bin_newton(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
@@ -724,6 +743,10 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
// loop over each atom, storing neighbors
+ int **special = atom->special;
+ int **nspecial = atom->nspecial;
+ int *tag = atom->tag;
+
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
@@ -827,7 +850,7 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
+ if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 1aa2743687..4cd449659f 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -1443,43 +1443,6 @@ void Neighbor::modify_params(int narg, char **arg)
}
}
-/* ----------------------------------------------------------------------
- determine if atom j is in special list of atom i
- if it is not, return 0
- if it is and special flag is 0 (both coeffs are 0.0), return -1
- if it is and special flag is 1 (both coeffs are 1.0), return 0
- if it is and special flag is 2 (otherwise), return 1,2,3
- for which neighbor it is (and which coeff it maps to)
-------------------------------------------------------------------------- */
-
-int Neighbor::find_special(int i, int j)
-{
- int *list = atom->special[i];
- int n1 = atom->nspecial[i][0];
- int n2 = atom->nspecial[i][1];
- int n3 = atom->nspecial[i][2];
- int tag = atom->tag[j];
-
- for (int i = 0; i < n3; i++) {
- if (list[i] == tag) {
- if (i < n1) {
- if (special_flag[1] == 0) return -1;
- else if (special_flag[1] == 1) return 0;
- else return 1;
- } else if (i < n2) {
- if (special_flag[2] == 0) return -1;
- else if (special_flag[2] == 1) return 0;
- else return 2;
- } else {
- if (special_flag[3] == 0) return -1;
- else if (special_flag[3] == 1) return 0;
- else return 3;
- }
- }
- }
- return 0;
-}
-
/* ----------------------------------------------------------------------
bin owned and ghost atoms
------------------------------------------------------------------------- */
diff --git a/src/neighbor.h b/src/neighbor.h
index 5f5951fc37..6a21950af6 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -149,11 +149,44 @@ class Neighbor : protected Pointers {
void bin_atoms(); // bin all atoms
double bin_distance(int, int, int); // distance between binx
int coord2bin(double *); // mapping atom coord to a bin
- int find_special(int, int); // look for special neighbor
+
int exclusion(int, int, int, int, int *, int *); // test for pair exclusion
void choose_build(int, class NeighRequest *);
void choose_stencil(int, class NeighRequest *);
+ // find_special: determine if atom j is in special list of atom i
+ // if it is not, return 0
+ // if it is and special flag is 0 (both coeffs are 0.0), return -1
+ // if it is and special flag is 1 (both coeffs are 1.0), return 0
+ // if it is and special flag is 2 (otherwise), return 1,2,3
+ // for which neighbor it is (and which coeff it maps to)
+
+ inline int find_special(const int *list, const int *nspecial,
+ const int tag) const {
+ const int n1 = nspecial[0];
+ const int n2 = nspecial[1];
+ const int n3 = nspecial[2];
+
+ for (int i = 0; i < n3; i++) {
+ if (list[i] == tag) {
+ if (i < n1) {
+ if (special_flag[1] == 0) return -1;
+ else if (special_flag[1] == 1) return 0;
+ else return 1;
+ } else if (i < n2) {
+ if (special_flag[2] == 0) return -1;
+ else if (special_flag[2] == 1) return 0;
+ else return 2;
+ } else {
+ if (special_flag[3] == 0) return -1;
+ else if (special_flag[3] == 1) return 0;
+ else return 3;
+ }
+ }
+ }
+ return 0;
+ };
+
// pairwise build functions
typedef void (Neighbor::*PairPtr)(class NeighList *);
@@ -236,7 +269,6 @@ class Neighbor : protected Pointers {
BondPtr improper_build; // ptr to improper list functions
void improper_all(); // improper list with all impropers
void improper_partial(); // exclude certain impropers
-
};
}
--
GitLab