From cbbb66194cebc013fc4d313a77d2176689ffda7e Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 25 Oct 2011 16:17:27 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7196
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/MANYBODY/pair_airebo.cpp | 172 ++++++++++++-----------------------
src/MANYBODY/pair_airebo.h | 86 ++++++++++++++----
2 files changed, 129 insertions(+), 129 deletions(-)
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index 6f8ef42511..c2625072cc 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -13,6 +13,8 @@
/* ----------------------------------------------------------------------
Contributing author: Ase Henry (MIT)
+ Bugfixes and optimizations:
+ Marcel Fallet & Steve Stuart (Clemson), Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "math.h"
@@ -45,7 +47,6 @@ using namespace MathConst;
PairAIREBO::PairAIREBO(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
- restartinfo = 0;
one_coeff = 1;
ghostneigh = 1;
@@ -221,7 +222,7 @@ void PairAIREBO::init_style()
pgsize = neighbor->pgsize;
oneatom = neighbor->oneatom;
- if (maxpage == 0) add_pages(0);
+ if (maxpage == 0) add_pages();
}
/* ----------------------------------------------------------------------
@@ -304,7 +305,7 @@ void PairAIREBO::REBO_neigh()
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
- if (nall > maxlocal) {
+ if (atom->nmax > maxlocal) {
maxlocal = atom->nmax;
memory->destroy(REBO_numneigh);
memory->sfree(REBO_firstneigh);
@@ -325,7 +326,7 @@ void PairAIREBO::REBO_neigh()
// store all REBO neighs of owned and ghost atoms
// scan full neighbor list of I
- npage = 0;
+ int npage = 0;
int npnt = 0;
for (ii = 0; ii < allnum; ii++) {
@@ -334,7 +335,7 @@ void PairAIREBO::REBO_neigh()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage) add_pages(npage);
+ if (npage == maxpage) add_pages();
}
neighptr = &pages[npage][npnt];
n = 0;
@@ -1196,60 +1197,6 @@ void PairAIREBO::TORSION(int eflag, int vflag)
}
}
-// ----------------------------------------------------------------------
-// S'(t) and S(t) cutoff functions
-// ----------------------------------------------------------------------
-
-/* ----------------------------------------------------------------------
- cutoff function Sprime
- return cutoff and dX = derivative
-------------------------------------------------------------------------- */
-
-double PairAIREBO::Sp(double Xij, double Xmin, double Xmax, double &dX)
-{
- double cutoff;
-
- double t = (Xij-Xmin) / (Xmax-Xmin);
- if (t <= 0.0) {
- cutoff = 1.0;
- dX = 0.0;
- }
- else if (t >= 1.0) {
- cutoff = 0.0;
- dX = 0.0;
- }
- else {
- cutoff = 0.5 * (1.0+cos(MY_PI*t));
- dX = (-MY_PI2*sin(MY_PI*t)) / (Xmax-Xmin);
- }
- return cutoff;
-}
-
-/* ----------------------------------------------------------------------
- LJ cutoff function Sp2
- return cutoff and dX = derivative
-------------------------------------------------------------------------- */
-
-double PairAIREBO::Sp2(double Xij, double Xmin, double Xmax, double &dX)
-{
- double cutoff;
-
- double t = (Xij-Xmin) / (Xmax-Xmin);
- if (t <= 0.0) {
- cutoff = 1.0;
- dX = 0.0;
- }
- if (t >= 1.0) {
- cutoff = 0.0;
- dX = 0.0;
- }
- if (t>0.0 && t<1.0) {
- cutoff = (1.0-(t*t*(3.0-2.0*t)));
- dX = 6.0*(t*t-t) / (Xmax-Xmin);
- }
- return cutoff;
-}
-
/* ----------------------------------------------------------------------
Bij function
------------------------------------------------------------------------- */
@@ -2123,11 +2070,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
NjiC = nC[atomj]-(wij*kronecker(itype,0));
NjiH = nH[atomj]-(wij*kronecker(itype,1));
- rij[0] = rij0[0];
- rij[1] = rij0[1];
- rij[2] = rij0[2];
- rijmag = rij0mag;
-
bij = 0.0;
tmp = 0.0;
tmp2 = 0.0;
@@ -3133,7 +3075,7 @@ double PairAIREBO::PijSpline(double NijC, double NijH, int typei, int typej,
if (typei == 0 && typej == 1){
if (NijC < pCHdom[0][0]) NijC=pCHdom[0][0];
if (NijC > pCHdom[0][1]) NijC=pCHdom[0][1];
- if (NijH < pCHdom[0][0]) NijH=pCHdom[1][0];
+ if (NijH < pCHdom[1][0]) NijH=pCHdom[1][0];
if (NijH > pCHdom[1][1]) NijH=pCHdom[1][1];
if (fabs(NijC-floor(NijC)) < TOL && fabs(NijH-floor(NijH)) < TOL) {
@@ -3338,27 +3280,17 @@ double PairAIREBO::TijSpline(double Nij, double Nji,
}
/* ----------------------------------------------------------------------
- Kronecker delta function
+ add pages to REBO neighbor list
------------------------------------------------------------------------- */
-double PairAIREBO::kronecker(int a, int b)
-{
- double kd;
- if (a == b) kd = 1.0;
- else kd = 0.0;
- return kd;
-}
-
-/* ----------------------------------------------------------------------
- add pages to REBO neighbor list, starting at npage
-------------------------------------------------------------------------- */
-
-void PairAIREBO::add_pages(int npage)
+void PairAIREBO::add_pages()
{
+ int toppage = maxpage;
maxpage += PGDELTA;
+
pages = (int **)
memory->srealloc(pages,maxpage*sizeof(int *),"AIREBO:pages");
- for (int i = npage; i < maxpage; i++)
+ for (int i = toppage; i < maxpage; i++)
memory->create(pages[i],pgsize,"AIREBO:pages[i]");
}
@@ -3954,17 +3886,23 @@ void PairAIREBO::read_file(char *filename)
double PairAIREBO::Sp5th(double x, double coeffs[6], double *df)
{
- double f;
- int i;
- i = 0;
- f = 0.0;
- *df = 0.0;
-
- for (i = 0; i<6; i++) {
- f += coeffs[i]*pow(x,((double) i));
- if (i > 0) *df += coeffs[i]*((double) i)*pow(x,((double) i-1.0));
- }
-
+ double f, d;
+ const double x2 = x*x;
+ const double x3 = x2*x;
+
+ f = coeffs[0];
+ f += coeffs[1]*x;
+ d = coeffs[1];
+ f += coeffs[2]*x2;
+ d += 2.0*coeffs[2]*x;
+ f += coeffs[3]*x3;
+ d += 3.0*coeffs[3]*x2;
+ f += coeffs[4]*x2*x2;
+ d += 4.0*coeffs[4]*x3;
+ f += coeffs[5]*x2*x3;
+ d += 5.0*coeffs[5]*x2*x2;
+
+ *df = d;
return f;
}
@@ -3975,25 +3913,28 @@ double PairAIREBO::Sp5th(double x, double coeffs[6], double *df)
double PairAIREBO::Spbicubic(double x, double y,
double coeffs[16], double df[2])
{
- double f;
- int i,j,cn;
+ double f,xn,yn,xn1,yn1,c;
+ int i,j;
f = 0.0;
df[0] = 0.0;
df[1] = 0.0;
- cn = 0;
+ xn = 1.0;
for (i = 0; i < 4; i++) {
+ yn = 1.0;
for (j = 0; j < 4; j++) {
- f += coeffs[cn]*pow(x,((double) i))*pow(y,((double) j));
- if (i > 0) df[0] +=
- (coeffs[cn]*((double) i)*pow(x,((double) i-1.0)) *
- pow(y,((double) j)));
- if (j > 0) df[1] +=
- (coeffs[cn]*((double) j)*pow(x,((double) i)) *
- pow(y,((double) j-1.0)));
- cn++;
+ c = coeffs[i*4+j];
+
+ f += c*xn*yn;
+ if (i > 0) df[0] += c * ((double) i) * xn1 * yn;
+ if (j > 0) df[1] += c * ((double) j) * xn * yn1;
+
+ yn1 = yn;
+ yn *= y;
}
+ xn1 = xn;
+ xn *= x;
}
return f;
@@ -4006,31 +3947,36 @@ double PairAIREBO::Spbicubic(double x, double y,
double PairAIREBO::Sptricubic(double x, double y, double z,
double coeffs[64], double df[3])
{
- double f,ir,jr,kr;
- int i,j,k,cn;
+ double f,ir,jr,kr,xn,yn,zn,xn1,yn1,zn1,c;
+ int i,j,k;
f = 0.0;
df[0] = 0.0;
df[1] = 0.0;
df[2] = 0.0;
- cn = 0;
+ xn = 1.0;
for (i = 0; i < 4; i++) {
ir = (double) i;
+ yn = 1.0;
for (j = 0; j < 4; j++) {
jr = (double) j;
+ zn = 1.0;
for (k = 0; k < 4; k++) {
kr = (double) k;
- f += (coeffs[cn]*pow(x,ir)*pow(y,jr)*pow(z,kr));
- if (i > 0) df[0] +=
- (coeffs[cn]*ir*pow(x,ir-1.0)*pow(y,jr)*pow(z,kr));
- if (j > 0) df[1] +=
- (coeffs[cn]*jr*pow(x,ir)*pow(y,jr-1.0)*pow(z,kr));
- if (k > 0) df[2] +=
- (coeffs[cn]*kr*pow(x,ir)*pow(y,jr)*pow(z,kr-1.0));
- cn++;
+ c = coeffs[16*i+4*j+k];
+ f += c*xn*yn*zn;
+ if (i > 0) df[0] += c * ir * xn1 * yn * zn;
+ if (j > 0) df[1] += c * jr * xn * yn1 * zn;
+ if (k > 0) df[2] += c * kr * xn * yn * zn1;
+ zn1 = zn;
+ zn *= z;
}
+ yn1 = yn;
+ yn *= y;
}
+ xn1 = xn;
+ xn *= x;
}
return f;
diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h
index 166e1ed4ed..0c4795ab0d 100644
--- a/src/MANYBODY/pair_airebo.h
+++ b/src/MANYBODY/pair_airebo.h
@@ -21,6 +21,8 @@ PairStyle(airebo,PairAIREBO)
#define LMP_PAIR_AIREBO_H
#include "pair.h"
+#include "math.h"
+#include "math_const.h"
namespace LAMMPS_NS {
@@ -28,7 +30,7 @@ class PairAIREBO : public Pair {
public:
PairAIREBO(class LAMMPS *);
virtual ~PairAIREBO();
- void compute(int, int);
+ virtual void compute(int, int);
virtual void settings(int, char **);
void coeff(int, char **);
void init_style();
@@ -36,15 +38,15 @@ class PairAIREBO : public Pair {
double memory_usage();
protected:
+ int **pages; // neighbor list pages
+ int *map; // 0 (C), 1 (H), or -1 (NULL) for each type
+
int me;
int ljflag,torflag; // 0/1 if LJ,torsion terms included
int maxlocal; // size of numneigh, firstneigh arrays
- int **pages; // neighbor list pages
int maxpage; // # of pages currently allocated
int pgsize; // size of neighbor page
int oneatom; // max # of neighbors for one atom
- int npage; // current page in page list
- int *map; // 0 (C), 1 (H), or -1 (NULL) for each type
double cutlj; // user-specified LJ cutoff
double cutljrebosq; // cut for when to compute
@@ -77,12 +79,12 @@ class PairAIREBO : public Pair {
double PCCf[5][5],PCCdfdx[5][5],PCCdfdy[5][5],PCHf[5][5];
double PCHdfdx[5][5],PCHdfdy[5][5];
- double piCCf[5][5][10],piCCdfdx[5][5][10];
- double piCCdfdy[5][5][10],piCCdfdz[5][5][10];
- double piCHf[5][5][10],piCHdfdx[5][5][10];
- double piCHdfdy[5][5][10],piCHdfdz[5][5][10];
- double piHHf[5][5][10],piHHdfdx[5][5][10];
- double piHHdfdy[5][5][10],piHHdfdz[5][5][10];
+ double piCCf[5][5][11],piCCdfdx[5][5][11];
+ double piCCdfdy[5][5][11],piCCdfdz[5][5][11];
+ double piCHf[5][5][11],piCHdfdx[5][5][11];
+ double piCHdfdy[5][5][11],piCHdfdz[5][5][11];
+ double piHHf[5][5][11],piHHdfdx[5][5][11];
+ double piHHdfdy[5][5][11],piHHdfdz[5][5][11];
double Tf[5][5][10],Tdfdx[5][5][10],Tdfdy[5][5][10],Tdfdz[5][5][10];
void REBO_neigh();
@@ -94,17 +96,12 @@ class PairAIREBO : public Pair {
double bondorderLJ(int, int, double *, double, double,
double *, double, double **, int);
- double Sp(double, double, double, double &);
- double Sp2(double, double, double, double &);
-
double gSpline(double, double, int, double *, double *);
double PijSpline(double, double, int, int, double *);
double piRCSpline(double, double, double, int, int, double *);
double TijSpline(double, double, double, double *);
- double kronecker(int, int);
-
- void add_pages(int);
+ void add_pages();
void read_file(char *);
double Sp5th(double, double *, double *);
@@ -113,6 +110,63 @@ class PairAIREBO : public Pair {
void spline_init();
void allocate();
+
+ // ----------------------------------------------------------------------
+ // S'(t) and S(t) cutoff functions
+ // added to header for inlining
+ // ----------------------------------------------------------------------
+
+ /* ----------------------------------------------------------------------
+ cutoff function Sprime
+ return cutoff and dX = derivative
+ no side effects
+ ------------------------------------------------------------------------- */
+
+ inline double Sp(double Xij, double Xmin, double Xmax, double &dX) const {
+ double cutoff;
+
+ double t = (Xij-Xmin) / (Xmax-Xmin);
+ if (t <= 0.0) {
+ cutoff = 1.0;
+ dX = 0.0;
+ } else if (t >= 1.0) {
+ cutoff = 0.0;
+ dX = 0.0;
+ } else {
+ cutoff = 0.5 * (1.0+cos(t*MathConst::MY_PI));
+ dX = (-0.5*MathConst::MY_PI*sin(t*MathConst::MY_PI)) / (Xmax-Xmin);
+ }
+ return cutoff;
+ };
+
+ /* ----------------------------------------------------------------------
+ LJ cutoff function Sp2
+ return cutoff and dX = derivative
+ no side effects
+ ------------------------------------------------------------------------- */
+
+ inline double Sp2(double Xij, double Xmin, double Xmax, double &dX) const {
+ double cutoff;
+
+ double t = (Xij-Xmin) / (Xmax-Xmin);
+ if (t <= 0.0) {
+ cutoff = 1.0;
+ dX = 0.0;
+ } else if (t >= 1.0) {
+ cutoff = 0.0;
+ dX = 0.0;
+ } else {
+ cutoff = (1.0-(t*t*(3.0-2.0*t)));
+ dX = 6.0*(t*t-t) / (Xmax-Xmin);
+ }
+ return cutoff;
+ };
+
+ /* kronecker delta function returning a double */
+ inline double kronecker(const int a, const int b) const {
+ return (a == b) ? 1.0 : 0.0;
+ };
+
};
}
--
GitLab