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replace redundant get_distance() with sqrt(MathExtra::distsqr())

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Also avoid repetitive computation of distance.
This commit is contained in:
Axel Kohlmeyer
2025-06-05 06:15:48 -04:00
parent 8abd42ed2f
commit 4b56fd4cd2
2 changed files with 15 additions and 27 deletions
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39
src/MC/fix_neighbor_swap.cpp
View File

@ -32,6 +32,7 @@
#include "group.h"
#include "improper.h"
#include "kspace.h"
#include "math_extra.h"
#include "math_special.h"
#include "memory.h"
#include "modify.h"
@ -48,6 +49,7 @@
using namespace LAMMPS_NS;
using namespace FixConst;
using MathExtra::distsq3;
static const char cite_fix_neighbor_swap[] =
"fix neighbor/swap command: doi:10.1016/j.commatsci.2022.111929\n\n"
@ -548,16 +550,6 @@ int FixNeighborSwap::pick_j_swap_neighbor(int i)
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
double FixNeighborSwap::get_distance(double *i, double *j)
{
double r = sqrt(MathSpecial::square((i[0] - j[0])) + MathSpecial::square((i[1] - j[1])) +
MathSpecial::square((i[2] - j[2])));
return r;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixNeighborSwap::build_i_neighbor_list(int i_center)
{
int nghost = atom->nghost;
@ -624,13 +616,12 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
// Get distance if own center atom
double r = INFINITY;
if (i_center >= 0) { double r = get_distance(x[temp_j], x[i_center]); }
if (i_center >= 0) { double r = sqrt(distsq3(x[temp_j], x[i_center])); }
// Get local id of ghost center atom when ghost
for (int i = nlocal; i < nlocal + nghost; i++) {
if ((id[i] == id_center) && (get_distance(x[temp_j], x[i]) < r)) {
r = get_distance(x[temp_j], x[i]);
}
double rtmp = sqrt(distsq3(x[temp_j], x[i]));
if ((id[i] == id_center) && (rtmp < r)) r = rtmp;
}
if (rates_flag) {
@ -649,13 +640,12 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
// Calculate distance from i to each j, adjust probability of selection
// Get distance if own center atom
double r = INFINITY;
if (i_center >= 0) { double r = get_distance(x[temp_j], x[i_center]); }
if (i_center >= 0) { double r = sqrt(distsq3(x[temp_j], x[i_center])); }
// Get local id of ghost center atom when ghost
for (int i = nlocal; i < nlocal + nghost; i++) {
if ((id[i] == id_center) && (get_distance(x[temp_j], x[i]) < r)) {
r = get_distance(x[temp_j], x[i]);
}
double rtmp = sqrt(distsq3(x[temp_j], x[i]));
if ((id[i] == id_center) && (rtmp < r)) r = rtmp;
}
if (rates_flag) {
@ -680,12 +670,12 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
// Calculate distance from i to each j, adjust probability of selection
// Get distance if own center atom
double r = INFINITY;
if (i_center >= 0) { r = get_distance(x[temp_j], x[i_center]); }
if (i_center >= 0) { r = sqrt(distsq3(x[temp_j], x[i_center])); }
// Get local id of ghost center atoms
for (int i = nlocal; i < nlocal + nghost; i++) {
if ((id[i] == id_center) && (get_distance(x[temp_j], x[i]) < r))
r = get_distance(x[temp_j], x[i]);
double rtmp = sqrt(distsq3(x[temp_j], x[i]));
if ((id[i] == id_center) && (rtmp < r)) r = rtmp;
}
if (rates_flag) {
@ -705,13 +695,12 @@ void FixNeighborSwap::build_i_neighbor_list(int i_center)
// Calculate distance from i to each j, adjust probability of selection
// Get distance if own center atom
double r = INFINITY;
if (i_center >= 0) { double r = get_distance(x[temp_j], x[i_center]); }
if (i_center >= 0) { double r = sqrt(distsq3(x[temp_j], x[i_center])); }
// Get local id of ghost center atom when ghost
for (int i = nlocal; i < nlocal + nghost; i++) {
if ((id[i] == id_center) && (get_distance(x[temp_j], x[i]) < r)) {
r = get_distance(x[temp_j], x[i]);
}
double rtmp = sqrt(distsq3(x[temp_j], x[i]));
if ((id[i] == id_center) && (rtmp < r)) r = rtmp;
}
if (rates_flag) {

3
src/MC/fix_neighbor_swap.h
View File

@ -47,7 +47,7 @@ class FixNeighborSwap : public Fix {
int niswap, njswap; // # of i,j swap atoms on all procs
int niswap_local, njswap_local; // # of swap atoms on this proc
int niswap_before, njswap_before; // # of swap atoms on procs < this proc
// int global_i_ID; // global id of selected i atom
class Region *region; // swap region
char *idregion; // swap region id
@ -89,7 +89,6 @@ class FixNeighborSwap : public Fix {
double energy_full();
int pick_i_swap_atom();
int pick_j_swap_neighbor(int);
double get_distance(double[3], double[3]);
void build_i_neighbor_list(int);
void update_iswap_atoms_list();
};