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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9542 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-02-20 15:21:22 +00:00
parent 1a354ef5f5
commit 4ff021e8f4
106 changed files with 2384 additions and 2369 deletions
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50
src/USER-OMP/angle_charmm_omp.cpp
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@ -90,40 +90,40 @@ void AngleCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
double delxUB,delyUB,delzUB,rsqUB,rUB,dr,rk,forceUB;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
// Urey-Bradley bond
delxUB = x[i3][0] - x[i1][0];
delyUB = x[i3][1] - x[i1][1];
delzUB = x[i3][2] - x[i1][2];
delxUB = x[i3].x - x[i1].x;
delyUB = x[i3].y - x[i1].y;
delzUB = x[i3].z - x[i1].z;
rsqUB = delxUB*delxUB + delyUB*delyUB + delzUB*delzUB;
rUB = sqrt(rsqUB);
@ -173,21 +173,21 @@ void AngleCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,

44
src/USER-OMP/angle_class2_omp.cpp
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@ -91,31 +91,31 @@ void AngleClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22,b1,b2;
double vx11,vx12,vy11,vy12,vz11,vz12,vx21,vx22,vy21,vy22,vz21,vz22;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
@ -217,21 +217,21 @@ void AngleClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,

44
src/USER-OMP/angle_cosine_delta_omp.cpp
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@ -88,31 +88,31 @@ void AngleCosineDeltaOMP::eval(int nfrom, int nto, ThrData * const thr)
double eangle,f1[3],f3[3];
double rsq1,rsq2,r1,r2,c,a,cot,a11,a12,a22,b11,b12,b22,c0,s0,s;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
@ -166,21 +166,21 @@ void AngleCosineDeltaOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,

44
src/USER-OMP/angle_cosine_omp.cpp
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@ -88,31 +88,31 @@ void AngleCosineOMP::eval(int nfrom, int nto, ThrData * const thr)
double eangle,f1[3],f3[3];
double rsq1,rsq2,r1,r2,c,a,a11,a12,a22;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
@ -143,21 +143,21 @@ void AngleCosineOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,

44
src/USER-OMP/angle_cosine_periodic_omp.cpp
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@ -91,31 +91,31 @@ void AngleCosinePeriodicOMP::eval(int nfrom, int nto, ThrData * const thr)
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
double tn,tn_1,tn_2,un,un_1,un_2;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
@ -183,21 +183,21 @@ void AngleCosinePeriodicOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,

44
src/USER-OMP/angle_cosine_shift_exp_omp.cpp
View File

@ -89,31 +89,31 @@ void AngleCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
double rsq1,rsq2,r1,r2,c,s,a11,a12,a22;
double exp2,aa,uumin,cccpsss,cssmscc;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
@ -164,21 +164,21 @@ void AngleCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,

44
src/USER-OMP/angle_cosine_shift_omp.cpp
View File

@ -88,32 +88,32 @@ void AngleCosineShiftOMP::eval(int nfrom, int nto, ThrData * const thr)
double f1[3],f3[3];
double rsq1,rsq2,r1,r2,c,s,cps,a11,a12,a22;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
double eangle = 0.0;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
@ -149,21 +149,21 @@ void AngleCosineShiftOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,

44
src/USER-OMP/angle_cosine_squared_omp.cpp
View File

@ -89,31 +89,31 @@ void AngleCosineSquaredOMP::eval(int nfrom, int nto, ThrData * const thr)
double dcostheta,tk;
double rsq1,rsq2,r1,r2,c,a,a11,a12,a22;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
@ -148,21 +148,21 @@ void AngleCosineSquaredOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,

44
src/USER-OMP/angle_fourier_omp.cpp
View File

@ -89,31 +89,31 @@ void AngleFourierOMP::eval(int nfrom, int nto, ThrData * const thr)
double term;
double rsq1,rsq2,r1,r2,c,c2,a,a11,a12,a22;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
@ -148,21 +148,21 @@ void AngleFourierOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,

44
src/USER-OMP/angle_fourier_simple_omp.cpp
View File

@ -89,31 +89,31 @@ void AngleFourierSimpleOMP::eval(int nfrom, int nto, ThrData * const thr)
double term,sgn;
double rsq1,rsq2,r1,r2,c,cn,th,nth,a,a11,a12,a22;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
@ -165,21 +165,21 @@ void AngleFourierSimpleOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,

44
src/USER-OMP/angle_harmonic_omp.cpp
View File

@ -89,31 +89,31 @@ void AngleHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
double dtheta,tk;
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
@ -152,21 +152,21 @@ void AngleHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,

44
src/USER-OMP/angle_quartic_omp.cpp
View File

@ -89,31 +89,31 @@ void AngleQuarticOMP::eval(int nfrom, int nto, ThrData * const thr)
double dtheta,dtheta2,dtheta3,dtheta4,tk;
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
@ -157,21 +157,21 @@ void AngleQuarticOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,

50
src/USER-OMP/angle_sdk_omp.cpp
View File

@ -91,31 +91,31 @@ void AngleSDKOMP::eval(int nfrom, int nto, ThrData * const thr)
double dtheta,tk;
double rsq1,rsq2,rsq3,r1,r2,c,s,a,a11,a12,a22;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
@ -142,9 +142,9 @@ void AngleSDKOMP::eval(int nfrom, int nto, ThrData * const thr)
if (repflag) {
delx3 = x[i1][0] - x[i3][0];
dely3 = x[i1][1] - x[i3][1];
delz3 = x[i1][2] - x[i3][2];
delx3 = x[i1].x - x[i3].x;
dely3 = x[i1].y - x[i3].y;
delz3 = x[i1].z - x[i3].z;
rsq3 = delx3*delx3 + dely3*dely3 + delz3*delz3;
const int type1 = atom->type[i1];
@ -203,21 +203,21 @@ void AngleSDKOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of the 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0] + f13*delx3;
f[i1][1] += f1[1] + f13*dely3;
f[i1][2] += f1[2] + f13*delz3;
f[i1].x += f1[0] + f13*delx3;
f[i1].y += f1[1] + f13*dely3;
f[i1].z += f1[2] + f13*delz3;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0] - f13*delx3;
f[i3][1] += f3[1] - f13*dely3;
f[i3][2] += f3[2] - f13*delz3;
f[i3].x += f3[0] - f13*delx3;
f[i3].y += f3[1] - f13*dely3;
f[i3].z += f3[2] - f13*delz3;
}
if (EVFLAG) {

44
src/USER-OMP/angle_table_omp.cpp
View File

@ -89,31 +89,31 @@ void AngleTableOMP::eval(int nfrom, int nto, ThrData * const thr)
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
double theta,u,mdu; //mdu: minus du, -du/dx=f
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const anglelist = neighbor->anglelist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
@ -152,21 +152,21 @@ void AngleTableOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 3 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,

30
src/USER-OMP/bond_class2_omp.cpp
View File

@ -83,19 +83,19 @@ void BondClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
double delx,dely,delz,ebond,fbond;
double rsq,r,dr,dr2,dr3,dr4,de_bond;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const bondlist = neighbor->bondlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int3_t * _noalias const bondlist = (int3_t *) neighbor->bondlist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
i1 = bondlist[n].a;
i2 = bondlist[n].b;
type = bondlist[n].t;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
delx = x[i1].x - x[i2].x;
dely = x[i1].y - x[i2].y;
delz = x[i1].z - x[i2].z;
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
@ -115,15 +115,15 @@ void BondClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 2 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
f[i1].x += delx*fbond;
f[i1].y += dely*fbond;
f[i1].z += delz*fbond;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
f[i2].x -= delx*fbond;
f[i2].y -= dely*fbond;
f[i2].z -= delz*fbond;
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,

30
src/USER-OMP/bond_fene_expand_omp.cpp
View File

@ -85,20 +85,20 @@ void BondFENEExpandOMP::eval(int nfrom, int nto, ThrData * const thr)
double rsq,r0sq,rlogarg,sr2,sr6;
double r,rshift,rshiftsq;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const bondlist = neighbor->bondlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int3_t * _noalias const bondlist = (int3_t *) neighbor->bondlist[0];
const int nlocal = atom->nlocal;
const int tid = thr->get_tid();
for (n = nfrom; n < nto; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
i1 = bondlist[n].a;
i2 = bondlist[n].b;
type = bondlist[n].t;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
delx = x[i1].x - x[i2].x;
dely = x[i1].y - x[i2].y;
delz = x[i1].z - x[i2].z;
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
@ -145,15 +145,15 @@ void BondFENEExpandOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 2 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
f[i1].x += delx*fbond;
f[i1].y += dely*fbond;
f[i1].z += delz*fbond;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
f[i2].x -= delx*fbond;
f[i2].y -= dely*fbond;
f[i2].z -= delz*fbond;
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,

30
src/USER-OMP/bond_fene_omp.cpp
View File

@ -84,20 +84,20 @@ void BondFENEOMP::eval(int nfrom, int nto, ThrData * const thr)
double delx,dely,delz,ebond,fbond;
double rsq,r0sq,rlogarg,sr2,sr6;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const bondlist = neighbor->bondlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int3_t * _noalias const bondlist = (int3_t *) neighbor->bondlist[0];
const int nlocal = atom->nlocal;
const int tid = thr->get_tid();
for (n = nfrom; n < nto; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
i1 = bondlist[n].a;
i2 = bondlist[n].b;
type = bondlist[n].t;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
delx = x[i1].x - x[i2].x;
dely = x[i1].y - x[i2].y;
delz = x[i1].z - x[i2].z;
rsq = delx*delx + dely*dely + delz*delz;
r0sq = r0[type] * r0[type];
@ -141,15 +141,15 @@ void BondFENEOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 2 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
f[i1].x += delx*fbond;
f[i1].y += dely*fbond;
f[i1].z += delz*fbond;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
f[i2].x -= delx*fbond;
f[i2].y -= dely*fbond;
f[i2].z -= delz*fbond;
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,

30
src/USER-OMP/bond_harmonic_omp.cpp
View File

@ -82,19 +82,19 @@ void BondHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
double delx,dely,delz,ebond,fbond;
double rsq,r,dr,rk;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const bondlist = neighbor->bondlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int3_t * _noalias const bondlist = (int3_t *) neighbor->bondlist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
i1 = bondlist[n].a;
i2 = bondlist[n].b;
type = bondlist[n].t;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
delx = x[i1].x - x[i2].x;
dely = x[i1].y - x[i2].y;
delz = x[i1].z - x[i2].z;
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
@ -111,15 +111,15 @@ void BondHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 2 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
f[i1].x += delx*fbond;
f[i1].y += dely*fbond;
f[i1].z += delz*fbond;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
f[i2].x -= delx*fbond;
f[i2].y -= dely*fbond;
f[i2].z -= delz*fbond;
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,

30
src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
View File

@ -82,19 +82,19 @@ void BondHarmonicShiftCutOMP::eval(int nfrom, int nto, ThrData * const thr)
double delx,dely,delz,ebond,fbond;
double rsq,r,dr,rk;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const bondlist = neighbor->bondlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int3_t * _noalias const bondlist = (int3_t *) neighbor->bondlist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
i1 = bondlist[n].a;
i2 = bondlist[n].b;
type = bondlist[n].t;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
delx = x[i1].x - x[i2].x;
dely = x[i1].y - x[i2].y;
delz = x[i1].z - x[i2].z;
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
@ -115,15 +115,15 @@ void BondHarmonicShiftCutOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 2 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
f[i1].x += delx*fbond;
f[i1].y += dely*fbond;
f[i1].z += delz*fbond;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
f[i2].x -= delx*fbond;
f[i2].y -= dely*fbond;
f[i2].z -= delz*fbond;
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,

30
src/USER-OMP/bond_harmonic_shift_omp.cpp
View File

@ -82,19 +82,19 @@ void BondHarmonicShiftOMP::eval(int nfrom, int nto, ThrData * const thr)
double delx,dely,delz,ebond,fbond;
double rsq,r,dr,rk;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const bondlist = neighbor->bondlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int3_t * _noalias const bondlist = (int3_t *) neighbor->bondlist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
i1 = bondlist[n].a;
i2 = bondlist[n].b;
type = bondlist[n].t;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
delx = x[i1].x - x[i2].x;
dely = x[i1].y - x[i2].y;
delz = x[i1].z - x[i2].z;
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
@ -112,15 +112,15 @@ void BondHarmonicShiftOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 2 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
f[i1].x += delx*fbond;
f[i1].y += dely*fbond;
f[i1].z += delz*fbond;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
f[i2].x -= delx*fbond;
f[i2].y -= dely*fbond;
f[i2].z -= delz*fbond;
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,

30
src/USER-OMP/bond_morse_omp.cpp
View File

@ -82,19 +82,19 @@ void BondMorseOMP::eval(int nfrom, int nto, ThrData * const thr)
double delx,dely,delz,ebond,fbond;
double rsq,r,dr,ralpha;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const bondlist = neighbor->bondlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int3_t * _noalias const bondlist = (int3_t *) neighbor->bondlist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
i1 = bondlist[n].a;
i2 = bondlist[n].b;
type = bondlist[n].t;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
delx = x[i1].x - x[i2].x;
dely = x[i1].y - x[i2].y;
delz = x[i1].z - x[i2].z;
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
@ -112,15 +112,15 @@ void BondMorseOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 2 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
f[i1].x += delx*fbond;
f[i1].y += dely*fbond;
f[i1].z += delz*fbond;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
f[i2].x -= delx*fbond;
f[i2].y -= dely*fbond;
f[i2].z -= delz*fbond;
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,

30
src/USER-OMP/bond_nonlinear_omp.cpp
View File

@ -82,19 +82,19 @@ void BondNonlinearOMP::eval(int nfrom, int nto, ThrData * const thr)
double delx,dely,delz,ebond,fbond;
double rsq,r,dr,drsq,lamdasq,denom,denomsq;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const bondlist = neighbor->bondlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int3_t * _noalias const bondlist = (int3_t *) neighbor->bondlist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
i1 = bondlist[n].a;
i2 = bondlist[n].b;
type = bondlist[n].t;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
delx = x[i1].x - x[i2].x;
dely = x[i1].y - x[i2].y;
delz = x[i1].z - x[i2].z;
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
@ -112,15 +112,15 @@ void BondNonlinearOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 2 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
f[i1].x += delx*fbond;
f[i1].y += dely*fbond;
f[i1].z += delz*fbond;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
f[i2].x -= delx*fbond;
f[i2].y -= dely*fbond;
f[i2].z -= delz*fbond;
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,

30
src/USER-OMP/bond_table_omp.cpp
View File

@ -83,19 +83,19 @@ void BondTableOMP::eval(int nfrom, int nto, ThrData * const thr)
double rsq,r;
double u,mdu;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const bondlist = neighbor->bondlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int3_t * _noalias const bondlist = (int3_t *) neighbor->bondlist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
i1 = bondlist[n].a;
i2 = bondlist[n].b;
type = bondlist[n].t;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
delx = x[i1].x - x[i2].x;
dely = x[i1].y - x[i2].y;
delz = x[i1].z - x[i2].z;
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
@ -109,15 +109,15 @@ void BondTableOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 2 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
f[i1].x += delx*fbond;
f[i1].y += dely*fbond;
f[i1].z += delz*fbond;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
f[i2].x -= delx*fbond;
f[i2].y -= dely*fbond;
f[i2].z -= delz*fbond;
}
if (EVFLAG) ev_tally_thr(this,i1,i2,nlocal,NEWTON_BOND,

86
src/USER-OMP/dihedral_charmm_omp.cpp
View File

@ -104,32 +104,32 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
edihedral = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * const atomtype = atom->type;
const int * const * const dihedrallist = neighbor->dihedrallist;
const int5_t * _noalias const dihedrallist = (int5_t *) neighbor->dihedrallist[0];
const double qqrd2e = force->qqrd2e;
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
i1 = dihedrallist[n].a;
i2 = dihedrallist[n].b;
i3 = dihedrallist[n].c;
i4 = dihedrallist[n].d;
type = dihedrallist[n].t;
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
vb1x = x[i1].x - x[i2].x;
vb1y = x[i1].y - x[i2].y;
vb1z = x[i1].z - x[i2].z;
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
vb2xm = -vb2x;
vb2ym = -vb2y;
@ -137,9 +137,9 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
// c,s calculation
@ -176,13 +176,13 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
@ -253,27 +253,27 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)
@ -286,9 +286,9 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
itype = atomtype[i1];
jtype = atomtype[i4];
delx = x[i1][0] - x[i4][0];
dely = x[i1][1] - x[i4][1];
delz = x[i1][2] - x[i4][2];
delx = x[i1].x - x[i4].x;
dely = x[i1].y - x[i4].y;
delz = x[i1].z - x[i4].z;
rsq = delx*delx + dely*dely + delz*delz;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
@ -305,14 +305,14 @@ void DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
}
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += delx*fpair;
f[i1][1] += dely*fpair;
f[i1][2] += delz*fpair;
f[i1].x += delx*fpair;
f[i1].y += dely*fpair;
f[i1].z += delz*fpair;
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] -= delx*fpair;
f[i4][1] -= dely*fpair;
f[i4][2] -= delz*fpair;
f[i4].x -= delx*fpair;
f[i4].y -= dely*fpair;
f[i4].z -= delz*fpair;
}
if (EVFLAG) ev_tally_thr(force->pair,i1,i4,nlocal,NEWTON_BOND,

66
src/USER-OMP/dihedral_class2_omp.cpp
View File

@ -99,29 +99,29 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
edihedral = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const dihedrallist = neighbor->dihedrallist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const dihedrallist = (int5_t *) neighbor->dihedrallist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
i1 = dihedrallist[n].a;
i2 = dihedrallist[n].b;
i3 = dihedrallist[n].c;
i4 = dihedrallist[n].d;
type = dihedrallist[n].t;
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
vb1x = x[i1].x - x[i2].x;
vb1y = x[i1].y - x[i2].y;
vb1z = x[i1].z - x[i2].z;
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
vb2xm = -vb2x;
vb2ym = -vb2y;
@ -129,9 +129,9 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
// distances
@ -188,13 +188,13 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
@ -500,27 +500,27 @@ void DihedralClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += fabcd[0][0];
f[i1][1] += fabcd[0][1];
f[i1][2] += fabcd[0][2];
f[i1].x += fabcd[0][0];
f[i1].y += fabcd[0][1];
f[i1].z += fabcd[0][2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += fabcd[1][0];
f[i2][1] += fabcd[1][1];
f[i2][2] += fabcd[1][2];
f[i2].x += fabcd[1][0];
f[i2].y += fabcd[1][1];
f[i2].z += fabcd[1][2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += fabcd[2][0];
f[i3][1] += fabcd[2][1];
f[i3][2] += fabcd[2][2];
f[i3].x += fabcd[2][0];
f[i3].y += fabcd[2][1];
f[i3].z += fabcd[2][2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += fabcd[3][0];
f[i4][1] += fabcd[3][1];
f[i4][2] += fabcd[3][2];
f[i4].x += fabcd[3][0];
f[i4].y += fabcd[3][1];
f[i4].z += fabcd[3][2];
}
if (EVFLAG)

66
src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
View File

@ -94,29 +94,29 @@ void DihedralCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
edihedral = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const dihedrallist = neighbor->dihedrallist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const dihedrallist = (int5_t *) neighbor->dihedrallist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
i1 = dihedrallist[n].a;
i2 = dihedrallist[n].b;
i3 = dihedrallist[n].c;
i4 = dihedrallist[n].d;
type = dihedrallist[n].t;
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
vb1x = x[i1].x - x[i2].x;
vb1y = x[i1].y - x[i2].y;
vb1z = x[i1].z - x[i2].z;
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
vb2xm = -vb2x;
vb2ym = -vb2y;
@ -124,9 +124,9 @@ void DihedralCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
// c,s calculation
@ -163,13 +163,13 @@ void DihedralCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
@ -232,27 +232,27 @@ void DihedralCosineShiftExpOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)

66
src/USER-OMP/dihedral_fourier_omp.cpp
View File

@ -93,29 +93,29 @@ void DihedralFourierOMP::eval(int nfrom, int nto, ThrData * const thr)
edihedral = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const dihedrallist = neighbor->dihedrallist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const dihedrallist = (int5_t *) neighbor->dihedrallist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
i1 = dihedrallist[n].a;
i2 = dihedrallist[n].b;
i3 = dihedrallist[n].c;
i4 = dihedrallist[n].d;
type = dihedrallist[n].t;
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
vb1x = x[i1].x - x[i2].x;
vb1y = x[i1].y - x[i2].y;
vb1z = x[i1].z - x[i2].z;
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
vb2xm = -vb2x;
vb2ym = -vb2y;
@ -123,9 +123,9 @@ void DihedralFourierOMP::eval(int nfrom, int nto, ThrData * const thr)
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
ax = vb1y*vb2zm - vb1z*vb2ym;
ay = vb1z*vb2xm - vb1x*vb2zm;
@ -160,13 +160,13 @@ void DihedralFourierOMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
@ -244,27 +244,27 @@ void DihedralFourierOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)

66
src/USER-OMP/dihedral_harmonic_omp.cpp
View File

@ -93,29 +93,29 @@ void DihedralHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
edihedral = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const dihedrallist = neighbor->dihedrallist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const dihedrallist = (int5_t *) neighbor->dihedrallist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
i1 = dihedrallist[n].a;
i2 = dihedrallist[n].b;
i3 = dihedrallist[n].c;
i4 = dihedrallist[n].d;
type = dihedrallist[n].t;
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
vb1x = x[i1].x - x[i2].x;
vb1y = x[i1].y - x[i2].y;
vb1z = x[i1].z - x[i2].z;
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
vb2xm = -vb2x;
vb2ym = -vb2y;
@ -123,9 +123,9 @@ void DihedralHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
// c,s calculation
@ -162,13 +162,13 @@ void DihedralHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
@ -239,27 +239,27 @@ void DihedralHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)

66
src/USER-OMP/dihedral_helix_omp.cpp
View File

@ -97,29 +97,29 @@ void DihedralHelixOMP::eval(int nfrom, int nto, ThrData * const thr)
edihedral = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const dihedrallist = neighbor->dihedrallist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const dihedrallist = (int5_t *) neighbor->dihedrallist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
i1 = dihedrallist[n].a;
i2 = dihedrallist[n].b;
i3 = dihedrallist[n].c;
i4 = dihedrallist[n].d;
type = dihedrallist[n].t;
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
vb1x = x[i1].x - x[i2].x;
vb1y = x[i1].y - x[i2].y;
vb1z = x[i1].z - x[i2].z;
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
vb2xm = -vb2x;
vb2ym = -vb2y;
@ -127,9 +127,9 @@ void DihedralHelixOMP::eval(int nfrom, int nto, ThrData * const thr)
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
// c0 calculation
@ -194,13 +194,13 @@ void DihedralHelixOMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
@ -252,27 +252,27 @@ void DihedralHelixOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)

66
src/USER-OMP/dihedral_multi_harmonic_omp.cpp
View File

@ -94,29 +94,29 @@ void DihedralMultiHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
edihedral = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const dihedrallist = neighbor->dihedrallist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const dihedrallist = (int5_t *) neighbor->dihedrallist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
i1 = dihedrallist[n].a;
i2 = dihedrallist[n].b;
i3 = dihedrallist[n].c;
i4 = dihedrallist[n].d;
type = dihedrallist[n].t;
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
vb1x = x[i1].x - x[i2].x;
vb1y = x[i1].y - x[i2].y;
vb1z = x[i1].z - x[i2].z;
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
vb2xm = -vb2x;
vb2ym = -vb2y;
@ -124,9 +124,9 @@ void DihedralMultiHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
// c0 calculation
@ -184,13 +184,13 @@ void DihedralMultiHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
@ -239,27 +239,27 @@ void DihedralMultiHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)

66
src/USER-OMP/dihedral_nharmonic_omp.cpp
View File

@ -93,29 +93,29 @@ void DihedralNHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
edihedral = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const dihedrallist = neighbor->dihedrallist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const dihedrallist = (int5_t *) neighbor->dihedrallist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
i1 = dihedrallist[n].a;
i2 = dihedrallist[n].b;
i3 = dihedrallist[n].c;
i4 = dihedrallist[n].d;
type = dihedrallist[n].t;
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
vb1x = x[i1].x - x[i2].x;
vb1y = x[i1].y - x[i2].y;
vb1z = x[i1].z - x[i2].z;
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
vb2xm = -vb2x;
vb2ym = -vb2y;
@ -123,9 +123,9 @@ void DihedralNHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
// c0 calculation
@ -184,13 +184,13 @@ void DihedralNHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
@ -243,27 +243,27 @@ void DihedralNHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)

66
src/USER-OMP/dihedral_opls_omp.cpp
View File

@ -95,29 +95,29 @@ void DihedralOPLSOMP::eval(int nfrom, int nto, ThrData * const thr)
edihedral = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const dihedrallist = neighbor->dihedrallist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const dihedrallist = (int5_t *) neighbor->dihedrallist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
i1 = dihedrallist[n].a;
i2 = dihedrallist[n].b;
i3 = dihedrallist[n].c;
i4 = dihedrallist[n].d;
type = dihedrallist[n].t;
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
vb1x = x[i1].x - x[i2].x;
vb1y = x[i1].y - x[i2].y;
vb1z = x[i1].z - x[i2].z;
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
vb2xm = -vb2x;
vb2ym = -vb2y;
@ -125,9 +125,9 @@ void DihedralOPLSOMP::eval(int nfrom, int nto, ThrData * const thr)
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
// c0 calculation
@ -192,13 +192,13 @@ void DihedralOPLSOMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
@ -255,27 +255,27 @@ void DihedralOPLSOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)

66
src/USER-OMP/dihedral_quadratic_omp.cpp
View File

@ -94,29 +94,29 @@ void DihedralQuadraticOMP::eval(int nfrom, int nto, ThrData * const thr)
edihedral = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const dihedrallist = neighbor->dihedrallist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const dihedrallist = (int5_t *) neighbor->dihedrallist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
i1 = dihedrallist[n].a;
i2 = dihedrallist[n].b;
i3 = dihedrallist[n].c;
i4 = dihedrallist[n].d;
type = dihedrallist[n].t;
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
vb1x = x[i1].x - x[i2].x;
vb1y = x[i1].y - x[i2].y;
vb1z = x[i1].z - x[i2].z;
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
vb2xm = -vb2x;
vb2ym = -vb2y;
@ -124,9 +124,9 @@ void DihedralQuadraticOMP::eval(int nfrom, int nto, ThrData * const thr)
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
// c0 calculation
@ -191,13 +191,13 @@ void DihedralQuadraticOMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
@ -256,27 +256,27 @@ void DihedralQuadraticOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)

10
src/USER-OMP/domain_omp.cpp
View File

@ -21,7 +21,7 @@
using namespace LAMMPS_NS;
typedef struct { double x,y,z; } vec3_t;
typedef struct { double x,y,z; } dbl3_t;
#if defined(__GNUC__)
#define _noalias __restrict
#else
@ -41,8 +41,8 @@ typedef struct { double x,y,z; } vec3_t;
void DomainOMP::pbc()
{
vec3_t * _noalias const x = (vec3_t *)&atom->x[0][0];
vec3_t * _noalias const v = (vec3_t *)&atom->v[0][0];
dbl3_t * _noalias const x = (dbl3_t *)&atom->x[0][0];
dbl3_t * _noalias const v = (dbl3_t *)&atom->v[0][0];
const double * _noalias const lo = (triclinic == 0) ? boxlo : boxlo_lamda;
const double * _noalias const hi = (triclinic == 0) ? boxhi : boxhi_lamda;
const double * _noalias const period = (triclinic == 0) ? prd : prd_lamda;
@ -146,7 +146,7 @@ void DomainOMP::pbc()
void DomainOMP::lamda2x(int n)
{
vec3_t * _noalias const x = (vec3_t *)&atom->x[0][0];
dbl3_t * _noalias const x = (dbl3_t *)&atom->x[0][0];
const int num = n;
int i;
@ -167,7 +167,7 @@ void DomainOMP::lamda2x(int n)
void DomainOMP::x2lamda(int n)
{
vec3_t * _noalias const x = (vec3_t *)&atom->x[0][0];
dbl3_t * _noalias const x = (dbl3_t *)&atom->x[0][0];
const int num = n;
int i;

79
src/USER-OMP/fix_omp.cpp
View File

@ -65,12 +65,13 @@ static int get_tid()
/* ---------------------------------------------------------------------- */
FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg)
: Fix(lmp, narg, arg),
thr(NULL), last_omp_style(NULL), last_pair_hybrid(NULL),
_nthr(-1), _neighbor(true), _newton(false)
_nthr(-1), _neighbor(true), _mixed(false)
{
if ((narg < 4) || (narg > 6)) error->all(FLERR,"Illegal fix OMP command");
if (strcmp(arg[1],"all") != 0) error->all(FLERR,"Illegal fix OMP command");
if ((narg < 4) || (narg > 7)) error->all(FLERR,"Illegal package omp command");
if (strcmp(arg[1],"all") != 0) error->all(FLERR,"fix OMP has to operate on group 'all'");
int nthreads = 1;
if (narg > 3) {
@ -84,64 +85,59 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
}
if (nthreads < 1)
error->all(FLERR,"Illegal number of threads requested.");
error->all(FLERR,"Illegal number of OpenMP threads requested");
if (nthreads != comm->nthreads) {
#if defined(_OPENMP)
omp_set_num_threads(nthreads);
#endif
comm->nthreads = nthreads;
if (comm->me == 0) {
if (screen)
fprintf(screen," reset %d OpenMP thread(s) per MPI task\n", nthreads);
if (logfile)
fprintf(logfile," reset %d OpenMP thread(s) per MPI task\n", nthreads);
}
}
if (narg > 4) {
if (strcmp(arg[4],"force/neigh") == 0)
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"force/neigh") == 0)
_neighbor = true;
else if (strcmp(arg[4],"force") == 0)
else if (strcmp(arg[iarg],"force") == 0)
_neighbor = false;
else if (strcmp(arg[iarg],"mixed") == 0)
_mixed = true;
else if (strcmp(arg[iarg],"double") == 0)
_mixed = false;
else
error->all(FLERR,"Illegal fix omp mode requested.");
error->all(FLERR,"Illegal package omp mode requested");
}
// print summary of settings
if (comm->me == 0) {
const char * const mode = _neighbor ? "OpenMP capable" : "serial";
const char * const nmode = _neighbor ? "OpenMP capable" : "serial";
const char * const kmode = _mixed ? "mixed" : "double";
if (screen)
fprintf(screen," using %s neighbor list subroutines\n", mode);
if (logfile)
fprintf(logfile," using %s neighbor list subroutines\n", mode);
}
}
#if 0 /* to be enabled when we can switch between half and full neighbor lists */
if (narg > 5) {
if (strcmp(arg[5],"neigh/half") == 0)
_newton = true;
else if (strcmp(arg[5],"neigh/full") == 0)
_newton = false;
if (screen) {
fprintf(screen," reset %d OpenMP thread(s) per MPI task\n", nthreads);
fprintf(screen," using %s neighbor list subroutines\n", nmode);
if (_mixed)
fputs(" using mixed precision OpenMP force kernels where available\n", screen);
else
error->all(FLERR,"Illegal fix OMP command");
fputs(" using double precision OpenMP force kernels\n", screen);
}
if (comm->me == 0) {
const char * const mode = _newton ? "half" : "full";
if (screen)
fprintf(screen," using /omp styles with %s neighbor list builds\n", mode);
if (logfile)
fprintf(logfile," using /omp styles with %s neighbor list builds\n", mode);
if (logfile) {
fprintf(logfile," reset %d OpenMP thread(s) per MPI task\n", nthreads);
fprintf(logfile," using %s neighbor list subroutines\n", nmode);
if (_mixed)
fputs(" using mixed precision OpenMP force kernels where available\n", logfile);
else
fputs(" using double precision OpenMP force kernels\n", logfile);
}
}
#endif
// allocate list for per thread accumulator manager class instances
// and then have each thread create an instance of this class to
// encourage the OS to use storage that is "close" to each thread's CPU.
thr = new ThrData *[nthreads];
_nthr = nthreads;
_clearforce = true;
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
@ -286,10 +282,11 @@ void FixOMP::init()
fprintf(logfile,"Last active /omp style is %s_style %s\n",
last_force_name, last_omp_name);
} else {
_clearforce = false;
if (screen)
fprintf(screen,"No /omp style for force computation currently active\n");
if (logfile)
fprintf(screen,"No /omp style for force computation currently active\n");
fprintf(logfile,"No /omp style for force computation currently active\n");
}
}
}
@ -325,6 +322,7 @@ void FixOMP::pre_force(int)
double *de = atom->de;
double *drho = atom->drho;
if (_clearforce) {
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(f,torque,erforce,de,drho)
#endif
@ -333,6 +331,9 @@ void FixOMP::pre_force(int)
thr[tid]->check_tid(tid);
thr[tid]->init_force(nall,f,torque,erforce,de,drho);
}
} else {
thr[0]->init_force(nall,f,torque,erforce,de,drho);
}
}
/* ---------------------------------------------------------------------- */

23
src/USER-OMP/fix_omp.h
View File

@ -37,17 +37,14 @@ class FixOMP : public Fix {
virtual void init();
virtual void pre_force(int);
virtual void setup_pre_force(int vflag) { pre_force(vflag); };
virtual void min_setup_pre_force(int vflag) { pre_force(vflag); };
virtual void min_pre_force(int vflag) { pre_force(vflag); };
virtual void setup_pre_force_respa(int vflag,int) { pre_force(vflag); };
virtual void pre_force_respa(int vflag,int,int) { pre_force(vflag); };
virtual void setup_pre_force(int vflag) { pre_force(vflag); }
virtual void min_setup_pre_force(int vflag) { pre_force(vflag); }
virtual void min_pre_force(int vflag) { pre_force(vflag); }
virtual void setup_pre_force_respa(int vflag,int) { pre_force(vflag); }
virtual void pre_force_respa(int vflag,int,int) { pre_force(vflag); }
virtual double memory_usage();
ThrData *get_thr(int tid) { return thr[tid]; };
int get_nthr() const { return _nthr; }
protected:
ThrData **thr;
void *last_omp_style; // pointer to the style that needs
@ -56,13 +53,17 @@ class FixOMP : public Fix {
// to call virial_fdot_compute()
public:
bool get_neighbor() const {return _neighbor;};
bool get_newton() const {return _newton;};
ThrData *get_thr(int tid) { return thr[tid]; }
int get_nthr() const { return _nthr; }
bool get_neighbor() const { return _neighbor; }
bool get_mixed() const { return _mixed; }
private:
int _nthr; // number of currently active ThrData object
bool _neighbor; // en/disable threads for neighbor list construction
bool _newton; // en/disable newton's 3rd law for local atoms.
bool _clearforce; // whether to clear per thread data objects
bool _mixed; // whether to use a mixed precision compute kernel
void set_neighbor_omp();
};

124
src/USER-OMP/improper_class2_omp.cpp
View File

@ -105,9 +105,9 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
eimproper = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const improperlist = neighbor->improperlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const improperlist = (int5_t *) neighbor->improperlist[0];
const int nlocal = atom->nlocal;
for (i = 0; i < 3; i++)
@ -120,27 +120,27 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
}
for (n = nfrom; n < nto; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
i1 = improperlist[n].a;
i2 = improperlist[n].b;
i3 = improperlist[n].c;
i4 = improperlist[n].d;
type = improperlist[n].t;
if (k0[type] == 0.0) continue;
// difference vectors
delr[0][0] = x[i1][0] - x[i2][0];
delr[0][1] = x[i1][1] - x[i2][1];
delr[0][2] = x[i1][2] - x[i2][2];
delr[0][0] = x[i1].x - x[i2].x;
delr[0][1] = x[i1].y - x[i2].y;
delr[0][2] = x[i1].z - x[i2].z;
delr[1][0] = x[i3][0] - x[i2][0];
delr[1][1] = x[i3][1] - x[i2][1];
delr[1][2] = x[i3][2] - x[i2][2];
delr[1][0] = x[i3].x - x[i2].x;
delr[1][1] = x[i3].y - x[i2].y;
delr[1][2] = x[i3].z - x[i2].z;
delr[2][0] = x[i4][0] - x[i2][0];
delr[2][1] = x[i4][1] - x[i2][1];
delr[2][2] = x[i4][2] - x[i2][2];
delr[2][0] = x[i4].x - x[i2].x;
delr[2][1] = x[i4].y - x[i2].y;
delr[2][2] = x[i4].z - x[i2].z;
// bond lengths and associated values
@ -173,13 +173,13 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
}
@ -468,27 +468,27 @@ void ImproperClass2OMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += fabcd[0][0];
f[i1][1] += fabcd[0][1];
f[i1][2] += fabcd[0][2];
f[i1].x += fabcd[0][0];
f[i1].y += fabcd[0][1];
f[i1].z += fabcd[0][2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += fabcd[1][0];
f[i2][1] += fabcd[1][1];
f[i2][2] += fabcd[1][2];
f[i2].x += fabcd[1][0];
f[i2].y += fabcd[1][1];
f[i2].z += fabcd[1][2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += fabcd[2][0];
f[i3][1] += fabcd[2][1];
f[i3][2] += fabcd[2][2];
f[i3].x += fabcd[2][0];
f[i3].y += fabcd[2][1];
f[i3].z += fabcd[2][2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += fabcd[3][0];
f[i4][1] += fabcd[3][1];
f[i4][2] += fabcd[3][2];
f[i4].x += fabcd[3][0];
f[i4].y += fabcd[3][1];
f[i4].z += fabcd[3][2];
}
if (EVFLAG)
@ -522,31 +522,31 @@ void ImproperClass2OMP::angleangle_thr(int nfrom, int nto, ThrData * const thr)
eimproper = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const improperlist = neighbor->improperlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const improperlist = (int5_t *) neighbor->improperlist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
i1 = improperlist[n].a;
i2 = improperlist[n].b;
i3 = improperlist[n].c;
i4 = improperlist[n].d;
type = improperlist[n].t;
// difference vectors
delxAB = x[i1][0] - x[i2][0];
delyAB = x[i1][1] - x[i2][1];
delzAB = x[i1][2] - x[i2][2];
delxAB = x[i1].x - x[i2].x;
delyAB = x[i1].y - x[i2].y;
delzAB = x[i1].z - x[i2].z;
delxBC = x[i3][0] - x[i2][0];
delyBC = x[i3][1] - x[i2][1];
delzBC = x[i3][2] - x[i2][2];
delxBC = x[i3].x - x[i2].x;
delyBC = x[i3].y - x[i2].y;
delzBC = x[i3].z - x[i2].z;
delxBD = x[i4][0] - x[i2][0];
delyBD = x[i4][1] - x[i2][1];
delzBD = x[i4][2] - x[i2][2];
delxBD = x[i4].x - x[i2].x;
delyBD = x[i4].y - x[i2].y;
delzBD = x[i4].z - x[i2].z;
// bond lengths
@ -667,27 +667,27 @@ void ImproperClass2OMP::angleangle_thr(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += fabcd[0][0];
f[i1][1] += fabcd[0][1];
f[i1][2] += fabcd[0][2];
f[i1].x += fabcd[0][0];
f[i1].y += fabcd[0][1];
f[i1].z += fabcd[0][2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += fabcd[1][0];
f[i2][1] += fabcd[1][1];
f[i2][2] += fabcd[1][2];
f[i2].x += fabcd[1][0];
f[i2].y += fabcd[1][1];
f[i2].z += fabcd[1][2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += fabcd[2][0];
f[i3][1] += fabcd[2][1];
f[i3][2] += fabcd[2][2];
f[i3].x += fabcd[2][0];
f[i3].y += fabcd[2][1];
f[i3].z += fabcd[2][2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += fabcd[3][0];
f[i4][1] += fabcd[3][1];
f[i4][2] += fabcd[3][2];
f[i4].x += fabcd[3][0];
f[i4].y += fabcd[3][1];
f[i4].z += fabcd[3][2];
}
if (EVFLAG)

66
src/USER-OMP/improper_cossq_omp.cpp
View File

@ -90,34 +90,34 @@ void ImproperCossqOMP::eval(int nfrom, int nto, ThrData * const thr)
eimproper = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const improperlist = neighbor->improperlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const improperlist = (int5_t *) neighbor->improperlist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
i1 = improperlist[n].a;
i2 = improperlist[n].b;
i3 = improperlist[n].c;
i4 = improperlist[n].d;
type = improperlist[n].t;
/* separation vector between i1 and i2, (i2-i1) */
vb1x = x[i2][0] - x[i1][0];
vb1y = x[i2][1] - x[i1][1];
vb1z = x[i2][2] - x[i1][2];
vb1x = x[i2].x - x[i1].x;
vb1y = x[i2].y - x[i1].y;
vb1z = x[i2].z - x[i1].z;
rjisq = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z ;
rji = sqrt(rjisq);
/* separation vector between i2 and i3 (i3-i2) */
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
/* separation vector between i3 and i4, (i4-i3) */
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
rlksq = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z ;
rlk = sqrt(rlksq);
@ -134,13 +134,13 @@ void ImproperCossqOMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
@ -236,27 +236,27 @@ void ImproperCossqOMP::eval(int nfrom, int nto, ThrData * const thr)
/* Apply force to each of 4 atoms */
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)

66
src/USER-OMP/improper_cvff_omp.cpp
View File

@ -92,29 +92,29 @@ void ImproperCvffOMP::eval(int nfrom, int nto, ThrData * const thr)
eimproper = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const improperlist = neighbor->improperlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const improperlist = (int5_t *) neighbor->improperlist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
i1 = improperlist[n].a;
i2 = improperlist[n].b;
i3 = improperlist[n].c;
i4 = improperlist[n].d;
type = improperlist[n].t;
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
vb1x = x[i1].x - x[i2].x;
vb1y = x[i1].y - x[i2].y;
vb1z = x[i1].z - x[i2].z;
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
vb2xm = -vb2x;
vb2ym = -vb2y;
@ -122,9 +122,9 @@ void ImproperCvffOMP::eval(int nfrom, int nto, ThrData * const thr)
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
// c0 calculation
@ -181,13 +181,13 @@ void ImproperCvffOMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
@ -268,27 +268,27 @@ void ImproperCvffOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)

66
src/USER-OMP/improper_harmonic_omp.cpp
View File

@ -91,31 +91,31 @@ void ImproperHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
eimproper = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const improperlist = neighbor->improperlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const improperlist = (int5_t *) neighbor->improperlist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
i1 = improperlist[n].a;
i2 = improperlist[n].b;
i3 = improperlist[n].c;
i4 = improperlist[n].d;
type = improperlist[n].t;
// geometry of 4-body
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
vb1x = x[i1].x - x[i2].x;
vb1y = x[i1].y - x[i2].y;
vb1z = x[i1].z - x[i2].z;
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
ss1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
ss2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
@ -154,13 +154,13 @@ void ImproperHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
@ -210,27 +210,27 @@ void ImproperHarmonicOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
f[i1].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)

66
src/USER-OMP/improper_umbrella_omp.cpp
View File

@ -90,35 +90,35 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
eimproper = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const improperlist = neighbor->improperlist;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int5_t * _noalias const improperlist = (int5_t *) neighbor->improperlist[0];
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
i1 = improperlist[n].a;
i2 = improperlist[n].b;
i3 = improperlist[n].c;
i4 = improperlist[n].d;
type = improperlist[n].t;
// 1st bond
vb1x = x[i2][0] - x[i1][0];
vb1y = x[i2][1] - x[i1][1];
vb1z = x[i2][2] - x[i1][2];
vb1x = x[i2].x - x[i1].x;
vb1y = x[i2].y - x[i1].y;
vb1z = x[i2].z - x[i1].z;
// 2nd bond
vb2x = x[i3][0] - x[i1][0];
vb2y = x[i3][1] - x[i1][1];
vb2z = x[i3][2] - x[i1][2];
vb2x = x[i3].x - x[i1].x;
vb2y = x[i3].y - x[i1].y;
vb2z = x[i3].z - x[i1].z;
// 3rd bond
vb3x = x[i4][0] - x[i1][0];
vb3y = x[i4][1] - x[i1][1];
vb3z = x[i4][2] - x[i1][2];
vb3x = x[i4].x - x[i1].x;
vb3y = x[i4].y - x[i1].y;
vb3z = x[i4].z - x[i1].z;
// c0 calculation
// A = vb1 X vb2 is perpendicular to IJK plane
@ -156,13 +156,13 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
me,x[i1].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
me,x[i4].x,x[i4].y,x[i4].z);
}
}
@ -226,27 +226,27 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0]*a;
f[i1][1] += f1[1]*a;
f[i1][2] += f1[2]*a;
f[i1].x += f1[0]*a;
f[i1].y += f1[1]*a;
f[i1].z += f1[2]*a;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f3[0]*a;
f[i2][1] += f3[1]*a;
f[i2][2] += f3[2]*a;
f[i2].x += f3[0]*a;
f[i2].y += f3[1]*a;
f[i2].z += f3[2]*a;
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f2[0]*a;
f[i3][1] += f2[1]*a;
f[i3][2] += f2[2]*a;
f[i3].x += f2[0]*a;
f[i3].y += f2[1]*a;
f[i3].z += f2[2]*a;
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0]*a;
f[i4][1] += f4[1]*a;
f[i4][2] += f4[2]*a;
f[i4].x += f4[0]*a;
f[i4].y += f4[1]*a;
f[i4].z += f4[2]*a;
}
if (EVFLAG)

45
src/USER-OMP/msm_omp.cpp
View File

@ -115,42 +115,44 @@ void MSMOMP::direct(int n)
}
template <int EFLAG_GLOBAL, int VFLAG_GLOBAL, int VFLAG_ATOM>
void MSMOMP::direct_eval(const int n)
void MSMOMP::direct_eval(const int nn)
{
double * const * const * const egridn = egrid[n];
const double * const * const * const qgridn = qgrid[n];
const double * const g_directn = g_direct[n];
const double * const v0_directn = v0_direct[n];
const double * const v1_directn = v1_direct[n];
const double * const v2_directn = v2_direct[n];
const double * const v3_directn = v3_direct[n];
const double * const v4_directn = v4_direct[n];
const double * const v5_directn = v5_direct[n];
double * _noalias const * _noalias const * _noalias const egridn = egrid[nn];
const double * _noalias const * _noalias const * _noalias const qgridn = qgrid[nn];
const double * _noalias const g_directn = g_direct[nn];
const double * _noalias const v0_directn = v0_direct[nn];
const double * _noalias const v1_directn = v1_direct[nn];
const double * _noalias const v2_directn = v2_direct[nn];
const double * _noalias const v3_directn = v3_direct[nn];
const double * _noalias const v4_directn = v4_direct[nn];
const double * _noalias const v5_directn = v5_direct[nn];
double v0,v1,v2,v3,v4,v5,emsm;
v0 = v1 = v2 = v3 = v4 = v5 = emsm = 0.0;
const int alphan = alpha[n];
const int betaxn = betax[n];
const int betayn = betay[n];
const int betazn = betaz[n];
const int alphan = alpha[nn];
const int betaxn = betax[nn];
const int betayn = betay[nn];
const int betazn = betaz[nn];
const int nx = nxhi_direct - nxlo_direct + 1;
const int ny = nyhi_direct - nylo_direct + 1;
// merge three outer loops into one for better threading
const int nzlo_inn = nzlo_in[n];
const int nylo_inn = nylo_in[n];
const int nxlo_inn = nxlo_in[n];
const int numz = nzhi_in[n] - nzlo_inn + 1;
const int numy = nyhi_in[n] - nylo_inn + 1;
const int numx = nxhi_in[n] - nxlo_inn + 1;
const int nzlo_inn = nzlo_in[nn];
const int nylo_inn = nylo_in[nn];
const int nxlo_inn = nxlo_in[nn];
const int numz = nzhi_in[nn] - nzlo_inn + 1;
const int numy = nyhi_in[nn] - nylo_inn + 1;
const int numx = nxhi_in[nn] - nxlo_inn + 1;
const int inum = numz*numy*numx;
const int zper = domain->zperiodic;
const int yper = domain->yperiodic;
const int xper = domain->xperiodic;
const int n=nn;
#if defined(_OPENMP)
#pragma omp parallel default(none) reduction(+:v0,v1,v2,v3,v4,v5,emsm)
#endif
@ -188,8 +190,9 @@ void MSMOMP::direct_eval(const int n)
for (iy = jmin; iy <= jmax; iy++) {
const int jj = icy+iy;
const int zyk = (zk + iy + nyhi_direct)*nx;
const double * _noalias const qgridnkj = & qgridn[kk][jj][icx];
for (ix = imin; ix <= imax; ix++) {
qtmp = qgridn[kk][jj][icx+ix];
qtmp = qgridnkj[ix];
k = zyk + ix + nxhi_direct;
esum += g_directn[k] * qtmp;

102
src/USER-OMP/pair_adp_omp.cpp
View File

@ -110,11 +110,11 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
double * const rho_t = thr->get_rho();
double * const * const mu_t = thr->get_mu();
double * const * const lambda_t = thr->get_lambda();
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
double * _noalias const rho_t = thr->get_rho();
dbl3_t * _noalias const mu_t = (dbl3_t *) thr->get_mu()[0];
double * const * _noalias const lambda_t = thr->get_lambda();
const int tid = thr->get_tid();
int *type = atom->type;
@ -132,9 +132,9 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -143,9 +143,9 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
@ -159,9 +159,9 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
rho_t[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = u2r_spline[type2u2r[jtype][itype]][m];
u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
mu_t[i][0] += u2*delx;
mu_t[i][1] += u2*dely;
mu_t[i][2] += u2*delz;
mu_t[i].x += u2*delx;
mu_t[i].y += u2*dely;
mu_t[i].z += u2*delz;
coeff = w2r_spline[type2w2r[jtype][itype]][m];
w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
lambda_t[i][0] += w2*delx*delx;
@ -177,9 +177,9 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
rho_t[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = u2r_spline[type2u2r[itype][jtype]][m];
u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
mu_t[j][0] -= u2*delx;
mu_t[j][1] -= u2*dely;
mu_t[j][2] -= u2*delz;
mu_t[j].x -= u2*delx;
mu_t[j].y -= u2*dely;
mu_t[j].z -= u2*delz;
coeff = w2r_spline[type2w2r[itype][jtype]][m];
w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
lambda_t[j][0] += w2*delx*delx;
@ -200,9 +200,9 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
if (NEWTON_PAIR) {
// reduce per thread density
data_reduce_thr(&(rho[0]), nall, comm->nthreads, 1, tid);
data_reduce_thr(&(mu[0][0]), nall, comm->nthreads, 3, tid);
data_reduce_thr(&(lambda[0][0]), nall, comm->nthreads, 6, tid);
data_reduce_thr(&(rho_t[0]), nall, comm->nthreads, 1, tid);
data_reduce_thr(&(mu_t[0].x), nall, comm->nthreads, 3, tid);
data_reduce_thr(&(lambda_t[0][0]), nall, comm->nthreads, 6, tid);
// wait until reduction is complete
sync_threads();
@ -217,9 +217,9 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
} else {
// reduce per thread density
data_reduce_thr(&(rho[0]), nlocal, comm->nthreads, 1, tid);
data_reduce_thr(&(mu[0][0]), nlocal, comm->nthreads, 3, tid);
data_reduce_thr(&(lambda[0][0]), nlocal, comm->nthreads, 6, tid);
data_reduce_thr(&(rho_t[0]), nlocal, comm->nthreads, 1, tid);
data_reduce_thr(&(mu_t[0].x), nlocal, comm->nthreads, 3, tid);
data_reduce_thr(&(lambda_t[0][0]), nlocal, comm->nthreads, 6, tid);
// wait until reduction is complete
sync_threads();
@ -239,13 +239,13 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2];
if (EFLAG) {
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
phi += 0.5*(mu[i][0]*mu[i][0]+mu[i][1]*mu[i][1]+mu[i][2]*mu[i][2]);
phi += 0.5*(lambda[i][0]*lambda[i][0]+lambda[i][1]*
lambda[i][1]+lambda[i][2]*lambda[i][2]);
phi += 1.0*(lambda[i][3]*lambda[i][3]+lambda[i][4]*
lambda[i][4]+lambda[i][5]*lambda[i][5]);
phi -= 1.0/6.0*(lambda[i][0]+lambda[i][1]+lambda[i][2])*
(lambda[i][0]+lambda[i][1]+lambda[i][2]);
phi += 0.5*(mu_t[i].x*mu_t[i].x+mu_t[i].y*mu_t[i].y+mu_t[i].z*mu_t[i].z);
phi += 0.5*(lambda_t[i][0]*lambda_t[i][0]+lambda_t[i][1]*
lambda_t[i][1]+lambda_t[i][2]*lambda_t[i][2]);
phi += 1.0*(lambda_t[i][3]*lambda_t[i][3]+lambda_t[i][4]*
lambda_t[i][4]+lambda_t[i][5]*lambda_t[i][5]);
phi -= 1.0/6.0*(lambda_t[i][0]+lambda_t[i][1]+lambda_t[i][2])*
(lambda_t[i][0]+lambda_t[i][1]+lambda_t[i][2]);
e_tally_thr(this,i,i,nlocal,/* newton_pair */ 1, phi, 0.0, thr);
}
}
@ -268,9 +268,9 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
fxtmp = fytmp = fztmp = 0.0;
@ -281,9 +281,9 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
@ -329,16 +329,16 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
psip = fp[i]*rhojp + fp[j]*rhoip + phip;
fpair = -psip*recip;
delmux = mu[i][0]-mu[j][0];
delmuy = mu[i][1]-mu[j][1];
delmuz = mu[i][2]-mu[j][2];
delmux = mu_t[i].x-mu_t[j].x;
delmuy = mu_t[i].y-mu_t[j].y;
delmuz = mu_t[i].z-mu_t[j].z;
trdelmu = delmux*delx+delmuy*dely+delmuz*delz;
sumlamxx = lambda[i][0]+lambda[j][0];
sumlamyy = lambda[i][1]+lambda[j][1];
sumlamzz = lambda[i][2]+lambda[j][2];
sumlamyz = lambda[i][3]+lambda[j][3];
sumlamxz = lambda[i][4]+lambda[j][4];
sumlamxy = lambda[i][5]+lambda[j][5];
sumlamxx = lambda_t[i][0]+lambda_t[j][0];
sumlamyy = lambda_t[i][1]+lambda_t[j][1];
sumlamzz = lambda_t[i][2]+lambda_t[j][2];
sumlamyz = lambda_t[i][3]+lambda_t[j][3];
sumlamxz = lambda_t[i][4]+lambda_t[j][4];
sumlamxy = lambda_t[i][5]+lambda_t[j][5];
tradellam = sumlamxx*delx*delx+sumlamyy*dely*dely+
sumlamzz*delz*delz+2.0*sumlamxy*delx*dely+
2.0*sumlamxz*delx*delz+2.0*sumlamyz*dely*delz;
@ -363,9 +363,9 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += fy;
fztmp += fz;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= fx;
f[j][1] -= fy;
f[j][2] -= fz;
f[j].x -= fx;
f[j].y -= fy;
f[j].z -= fz;
}
if (EFLAG) evdwl = phi;
@ -373,9 +373,9 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
fx,fy,fz,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

34
src/USER-OMP/pair_beck_omp.cpp
View File

@ -86,8 +86,8 @@ void PairBeckOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
@ -102,9 +102,9 @@ void PairBeckOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -115,9 +115,9 @@ void PairBeckOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -138,13 +138,13 @@ void PairBeckOMP::eval(int iifrom, int iito, ThrData * const thr)
fpair = factor_lj*force_beck*rinv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[i].x += delx*fpair;
f[i].y += dely*fpair;
f[i].z += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -158,9 +158,9 @@ void PairBeckOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_born_coul_long_omp.cpp
View File

@ -92,10 +92,10 @@ void PairBornCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@ -112,9 +112,9 @@ void PairBornCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -126,9 +126,9 @@ void PairBornCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -159,9 +159,9 @@ void PairBornCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -180,9 +180,9 @@ void PairBornCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_born_coul_msm_omp.cpp
View File

@ -85,10 +85,10 @@ void PairBornCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@ -105,9 +105,9 @@ void PairBornCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -119,9 +119,9 @@ void PairBornCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -150,9 +150,9 @@ void PairBornCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -171,9 +171,9 @@ void PairBornCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_born_coul_wolf_omp.cpp
View File

@ -88,10 +88,10 @@ void PairBornCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@ -115,9 +115,9 @@ void PairBornCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -133,9 +133,9 @@ void PairBornCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -166,9 +166,9 @@ void PairBornCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -187,9 +187,9 @@ void PairBornCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

28
src/USER-OMP/pair_born_omp.cpp
View File

@ -81,8 +81,8 @@ void PairBornOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
@ -97,9 +97,9 @@ void PairBornOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -110,9 +110,9 @@ void PairBornOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -129,9 +129,9 @@ void PairBornOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -144,9 +144,9 @@ void PairBornOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

30
src/USER-OMP/pair_buck_coul_cut_omp.cpp
View File

@ -82,9 +82,9 @@ void PairBuckCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
@ -102,9 +102,9 @@ void PairBuckCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -116,9 +116,9 @@ void PairBuckCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -142,9 +142,9 @@ void PairBuckCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -162,9 +162,9 @@ void PairBuckCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

30
src/USER-OMP/pair_buck_coul_long_omp.cpp
View File

@ -93,9 +93,9 @@ void PairBuckCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
@ -113,9 +113,9 @@ void PairBuckCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -127,9 +127,9 @@ void PairBuckCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -159,9 +159,9 @@ void PairBuckCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -180,9 +180,9 @@ void PairBuckCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

30
src/USER-OMP/pair_buck_coul_msm_omp.cpp
View File

@ -86,9 +86,9 @@ void PairBuckCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
@ -106,9 +106,9 @@ void PairBuckCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -120,9 +120,9 @@ void PairBuckCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -150,9 +150,9 @@ void PairBuckCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -171,9 +171,9 @@ void PairBuckCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

28
src/USER-OMP/pair_buck_omp.cpp
View File

@ -81,8 +81,8 @@ void PairBuckOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
@ -97,9 +97,9 @@ void PairBuckOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -110,9 +110,9 @@ void PairBuckOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -131,9 +131,9 @@ void PairBuckOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -146,9 +146,9 @@ void PairBuckOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

54
src/USER-OMP/pair_cdeam_omp.cpp
View File

@ -148,15 +148,15 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
double * const rho_t = thr->get_rho();
double * const rhoB_t = thr->get_rhoB();
double * const D_values_t = thr->get_D_values();
const int tid = thr->get_tid();
const int nthreads = comm->nthreads;
const int * const type = atom->type;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
@ -174,9 +174,9 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -185,9 +185,9 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
if(rsq < cutforcesq) {
@ -299,9 +299,9 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
// Compute intermediate value D_i for each atom.
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -320,9 +320,9 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
// This code line is required for ternary alloys.
if(jtype != speciesA && jtype != speciesB) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
if(rsq < cutforcesq) {
@ -382,9 +382,9 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
// Compute force acting on each atom.
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
fxtmp = fytmp = fztmp = 0.0;
@ -417,9 +417,9 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
if(rsq < cutforcesq) {
@ -504,9 +504,9 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if(NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if(EFLAG) evdwl = phi;
@ -514,9 +514,9 @@ void PairCDEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_colloid_omp.cpp
View File

@ -85,12 +85,12 @@ void PairColloidOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const int tid = thr->get_tid();
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
@ -102,9 +102,9 @@ void PairColloidOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -115,9 +115,9 @@ void PairColloidOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -203,17 +203,17 @@ void PairColloidOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,fpair,delx,dely,delz,thr);
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

34
src/USER-OMP/pair_coul_cut_omp.cpp
View File

@ -83,12 +83,12 @@ void PairCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * _noalias const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -102,9 +102,9 @@ void PairCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -115,9 +115,9 @@ void PairCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -131,9 +131,9 @@ void PairCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG)
@ -143,9 +143,9 @@ void PairCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
0.0,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

34
src/USER-OMP/pair_coul_debye_omp.cpp
View File

@ -83,12 +83,12 @@ void PairCoulDebyeOMP::eval(int iifrom, int iito, ThrData * const thr)
ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * _noalias const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -102,9 +102,9 @@ void PairCoulDebyeOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -115,9 +115,9 @@ void PairCoulDebyeOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -133,9 +133,9 @@ void PairCoulDebyeOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG)
@ -145,9 +145,9 @@ void PairCoulDebyeOMP::eval(int iifrom, int iito, ThrData * const thr)
0.0,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

34
src/USER-OMP/pair_coul_diel_omp.cpp
View File

@ -83,12 +83,12 @@ void PairCoulDielOMP::eval(int iifrom, int iito, ThrData * const thr)
ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * _noalias const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -102,9 +102,9 @@ void PairCoulDielOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -116,9 +116,9 @@ void PairCoulDielOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -136,9 +136,9 @@ void PairCoulDielOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -150,9 +150,9 @@ void PairCoulDielOMP::eval(int iifrom, int iito, ThrData * const thr)
0.0,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

34
src/USER-OMP/pair_coul_long_omp.cpp
View File

@ -94,12 +94,12 @@ void PairCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * _noalias const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -113,9 +113,9 @@ void PairCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -126,9 +126,9 @@ void PairCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -164,9 +164,9 @@ void PairCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -183,9 +183,9 @@ void PairCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
0.0,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

34
src/USER-OMP/pair_coul_msm_omp.cpp
View File

@ -87,12 +87,12 @@ void PairCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * _noalias const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -106,9 +106,9 @@ void PairCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -119,9 +119,9 @@ void PairCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -155,9 +155,9 @@ void PairCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -174,9 +174,9 @@ void PairCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
0.0,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

34
src/USER-OMP/pair_coul_wolf_omp.cpp
View File

@ -88,12 +88,12 @@ void PairCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * _noalias const special_coul = force->special_coul;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -114,9 +114,9 @@ void PairCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
jlist = firstneigh[i];
jnum = numneigh[i];
fxtmp=fytmp=fztmp=0.0;
@ -130,9 +130,9 @@ void PairCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_coulsq) {
@ -150,9 +150,9 @@ void PairCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -166,9 +166,9 @@ void PairCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
0.0,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

108
src/USER-OMP/pair_dipole_cut_omp.cpp
View File

@ -85,15 +85,15 @@ void PairDipoleCutOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
double * const * const torque = thr->get_torque();
const double * const q = atom->q;
const double * const * const mu = atom->mu;
const int * const type = atom->type;
const double * _noalias const q = atom->q;
const dbl4_t * _noalias const mu = (dbl4_t *) atom->mu[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp,t1tmp,t2tmp,t3tmp;
@ -106,9 +106,9 @@ void PairDipoleCutOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
qtmp = q[i];
itype = type[i];
jlist = firstneigh[i];
@ -121,9 +121,9 @@ void PairDipoleCutOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -149,64 +149,64 @@ void PairDipoleCutOMP::eval(int iifrom, int iito, ThrData * const thr)
forcecoulz += pre1*delz;
}
if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
if (mu[i].w > 0.0 && mu[j].w > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
r7inv = r5inv*r2inv;
pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
pdotp = mu[i].x*mu[j].x + mu[i].y*mu[j].y + mu[i].z*mu[j].z;
pidotr = mu[i].x*delx + mu[i].y*dely + mu[i].z*delz;
pjdotr = mu[j].x*delx + mu[j].y*dely + mu[j].z*delz;
pre1 = 3.0*r5inv*pdotp - 15.0*r7inv*pidotr*pjdotr;
pre2 = 3.0*r5inv*pjdotr;
pre3 = 3.0*r5inv*pidotr;
pre4 = -1.0*r3inv;
forcecoulx += pre1*delx + pre2*mu[i][0] + pre3*mu[j][0];
forcecouly += pre1*dely + pre2*mu[i][1] + pre3*mu[j][1];
forcecoulz += pre1*delz + pre2*mu[i][2] + pre3*mu[j][2];
forcecoulx += pre1*delx + pre2*mu[i].x + pre3*mu[j].x;
forcecouly += pre1*dely + pre2*mu[i].y + pre3*mu[j].y;
forcecoulz += pre1*delz + pre2*mu[i].z + pre3*mu[j].z;
crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
crossx = pre4 * (mu[i].y*mu[j].z - mu[i].z*mu[j].y);
crossy = pre4 * (mu[i].z*mu[j].x - mu[i].x*mu[j].z);
crossz = pre4 * (mu[i].x*mu[j].y - mu[i].y*mu[j].x);
tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
tixcoul += crossx + pre2 * (mu[i].y*delz - mu[i].z*dely);
tiycoul += crossy + pre2 * (mu[i].z*delx - mu[i].x*delz);
tizcoul += crossz + pre2 * (mu[i].x*dely - mu[i].y*delx);
tjxcoul += -crossx + pre3 * (mu[j].y*delz - mu[j].z*dely);
tjycoul += -crossy + pre3 * (mu[j].z*delx - mu[j].x*delz);
tjzcoul += -crossz + pre3 * (mu[j].x*dely - mu[j].y*delx);
}
if (mu[i][3] > 0.0 && q[j] != 0.0) {
if (mu[i].w > 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pidotr = mu[i].x*delx + mu[i].y*dely + mu[i].z*delz;
pre1 = 3.0*q[j]*r5inv * pidotr;
pre2 = q[j]*r3inv;
forcecoulx += pre2*mu[i][0] - pre1*delx;
forcecouly += pre2*mu[i][1] - pre1*dely;
forcecoulz += pre2*mu[i][2] - pre1*delz;
tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
forcecoulx += pre2*mu[i].x - pre1*delx;
forcecouly += pre2*mu[i].y - pre1*dely;
forcecoulz += pre2*mu[i].z - pre1*delz;
tixcoul += pre2 * (mu[i].y*delz - mu[i].z*dely);
tiycoul += pre2 * (mu[i].z*delx - mu[i].x*delz);
tizcoul += pre2 * (mu[i].x*dely - mu[i].y*delx);
}
if (mu[j][3] > 0.0 && qtmp != 0.0) {
if (mu[j].w > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
pjdotr = mu[j].x*delx + mu[j].y*dely + mu[j].z*delz;
pre1 = 3.0*qtmp*r5inv * pjdotr;
pre2 = qtmp*r3inv;
forcecoulx += pre1*delx - pre2*mu[j][0];
forcecouly += pre1*dely - pre2*mu[j][1];
forcecoulz += pre1*delz - pre2*mu[j][2];
tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
forcecoulx += pre1*delx - pre2*mu[j].x;
forcecouly += pre1*dely - pre2*mu[j].y;
forcecoulz += pre1*delz - pre2*mu[j].z;
tjxcoul += -pre2 * (mu[j].y*delz - mu[j].z*dely);
tjycoul += -pre2 * (mu[j].z*delx - mu[j].x*delz);
tjzcoul += -pre2 * (mu[j].x*dely - mu[j].y*delx);
}
}
@ -235,9 +235,9 @@ void PairDipoleCutOMP::eval(int iifrom, int iito, ThrData * const thr)
t3tmp += fq*tizcoul;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= fx;
f[j][1] -= fy;
f[j][2] -= fz;
f[j].x -= fx;
f[j].y -= fy;
f[j].z -= fz;
torque[j][0] += fq*tjxcoul;
torque[j][1] += fq*tjycoul;
torque[j][2] += fq*tjzcoul;
@ -246,11 +246,11 @@ void PairDipoleCutOMP::eval(int iifrom, int iito, ThrData * const thr)
if (EFLAG) {
if (rsq < cut_coulsq[itype][jtype]) {
ecoul = qtmp*q[j]*rinv;
if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
if (mu[i].w > 0.0 && mu[j].w > 0.0)
ecoul += r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr;
if (mu[i][3] > 0.0 && q[j] != 0.0)
if (mu[i].w > 0.0 && q[j] != 0.0)
ecoul += -q[j]*r3inv*pidotr;
if (mu[j][3] > 0.0 && qtmp != 0.0)
if (mu[j].w > 0.0 && qtmp != 0.0)
ecoul += qtmp*r3inv*pjdotr;
ecoul *= factor_coul*qqrd2e;
} else ecoul = 0.0;
@ -266,9 +266,9 @@ void PairDipoleCutOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fx,fy,fz,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
torque[i][0] += t1tmp;
torque[i][1] += t2tmp;
torque[i][2] += t3tmp;

108
src/USER-OMP/pair_dipole_sf_omp.cpp
View File

@ -89,15 +89,15 @@ void PairDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
double * const * const torque = thr->get_torque();
const double * const q = atom->q;
const double * const * const mu = atom->mu;
const int * const type = atom->type;
const double * _noalias const q = atom->q;
const dbl4_t * _noalias const mu = (dbl4_t *) atom->mu[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp,t1tmp,t2tmp,t3tmp;
@ -110,9 +110,9 @@ void PairDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
qtmp = q[i];
itype = type[i];
jlist = firstneigh[i];
@ -125,9 +125,9 @@ void PairDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -154,14 +154,14 @@ void PairDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
forcecoulz += pre1*delz;
}
if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
if (mu[i].w > 0.0 && mu[j].w > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
pdotp = mu[i].x*mu[j].x + mu[i].y*mu[j].y + mu[i].z*mu[j].z;
pidotr = mu[i].x*delx + mu[i].y*dely + mu[i].z*delz;
pjdotr = mu[j].x*delx + mu[j].y*dely + mu[j].z*delz;
afac = 1.0 - rsq*rsq * rcutcoul2inv*rcutcoul2inv;
pre1 = afac * ( pdotp - 3.0 * r2inv * pidotr * pjdotr );
@ -172,9 +172,9 @@ void PairDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
bfac = 1.0 - 4.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv) +
3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
presf = 2.0 * r2inv * pidotr * pjdotr;
bforcecoulx = bfac * (pjdotr*mu[i][0]+pidotr*mu[j][0]-presf*delx);
bforcecouly = bfac * (pjdotr*mu[i][1]+pidotr*mu[j][1]-presf*dely);
bforcecoulz = bfac * (pjdotr*mu[i][2]+pidotr*mu[j][2]-presf*delz);
bforcecoulx = bfac * (pjdotr*mu[i].x+pidotr*mu[j].x-presf*delx);
bforcecouly = bfac * (pjdotr*mu[i].y+pidotr*mu[j].y-presf*dely);
bforcecoulz = bfac * (pjdotr*mu[i].z+pidotr*mu[j].z-presf*delz);
forcecoulx += 3.0 * r5inv * ( aforcecoulx + bforcecoulx );
forcecouly += 3.0 * r5inv * ( aforcecouly + bforcecouly );
@ -184,52 +184,52 @@ void PairDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
pre3 = 3.0 * bfac * r5inv * pidotr;
pre4 = -bfac * r3inv;
crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
crossx = pre4 * (mu[i].y*mu[j].z - mu[i].z*mu[j].y);
crossy = pre4 * (mu[i].z*mu[j].x - mu[i].x*mu[j].z);
crossz = pre4 * (mu[i].x*mu[j].y - mu[i].y*mu[j].x);
tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
tixcoul += crossx + pre2 * (mu[i].y*delz - mu[i].z*dely);
tiycoul += crossy + pre2 * (mu[i].z*delx - mu[i].x*delz);
tizcoul += crossz + pre2 * (mu[i].x*dely - mu[i].y*delx);
tjxcoul += -crossx + pre3 * (mu[j].y*delz - mu[j].z*dely);
tjycoul += -crossy + pre3 * (mu[j].z*delx - mu[j].x*delz);
tjzcoul += -crossz + pre3 * (mu[j].x*dely - mu[j].y*delx);
}
if (mu[i][3] > 0.0 && q[j] != 0.0) {
if (mu[i].w > 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pidotr = mu[i].x*delx + mu[i].y*dely + mu[i].z*delz;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pre1 = 3.0 * q[j] * r5inv * pidotr * (1-rsq*rcutcoul2inv);
pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
pre2 = q[j] * r3inv * pqfac;
forcecoulx += pre2*mu[i][0] - pre1*delx;
forcecouly += pre2*mu[i][1] - pre1*dely;
forcecoulz += pre2*mu[i][2] - pre1*delz;
tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
forcecoulx += pre2*mu[i].x - pre1*delx;
forcecouly += pre2*mu[i].y - pre1*dely;
forcecoulz += pre2*mu[i].z - pre1*delz;
tixcoul += pre2 * (mu[i].y*delz - mu[i].z*dely);
tiycoul += pre2 * (mu[i].z*delx - mu[i].x*delz);
tizcoul += pre2 * (mu[i].x*dely - mu[i].y*delx);
}
if (mu[j][3] > 0.0 && qtmp != 0.0) {
if (mu[j].w > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
pjdotr = mu[j].x*delx + mu[j].y*dely + mu[j].z*delz;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pre1 = 3.0 * qtmp * r5inv * pjdotr * (1-rsq*rcutcoul2inv);
qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
pre2 = qtmp * r3inv * qpfac;
forcecoulx += pre1*delx - pre2*mu[j][0];
forcecouly += pre1*dely - pre2*mu[j][1];
forcecoulz += pre1*delz - pre2*mu[j][2];
tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
forcecoulx += pre1*delx - pre2*mu[j].x;
forcecouly += pre1*dely - pre2*mu[j].y;
forcecoulz += pre1*delz - pre2*mu[j].z;
tjxcoul += -pre2 * (mu[j].y*delz - mu[j].z*dely);
tjycoul += -pre2 * (mu[j].z*delx - mu[j].x*delz);
tjzcoul += -pre2 * (mu[j].x*dely - mu[j].y*delx);
}
}
@ -264,9 +264,9 @@ void PairDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
t3tmp += fq*tizcoul;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= fx;
f[j][1] -= fy;
f[j][2] -= fz;
f[j].x -= fx;
f[j].y -= fy;
f[j].z -= fz;
torque[j][0] += fq*tjxcoul;
torque[j][1] += fq*tjycoul;
torque[j][2] += fq*tjzcoul;
@ -277,11 +277,11 @@ void PairDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
ecoul = (1.0-sqrt(rsq)/sqrt(cut_coulsq[itype][jtype]));
ecoul *= ecoul;
ecoul *= qtmp * q[j] * rinv;
if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
if (mu[i].w > 0.0 && mu[j].w > 0.0)
ecoul += bfac * (r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr);
if (mu[i][3] > 0.0 && q[j] != 0.0)
if (mu[i].w > 0.0 && q[j] != 0.0)
ecoul += -q[j] * r3inv * pqfac * pidotr;
if (mu[j][3] > 0.0 && qtmp != 0.0)
if (mu[j].w > 0.0 && qtmp != 0.0)
ecoul += qtmp * r3inv * qpfac * pjdotr;
ecoul *= factor_coul*qqrd2e;
} else ecoul = 0.0;
@ -299,9 +299,9 @@ void PairDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fx,fy,fz,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
torque[i][0] += t1tmp;
torque[i][1] += t2tmp;
torque[i][2] += t3tmp;

44
src/USER-OMP/pair_dpd_omp.cpp
View File

@ -113,10 +113,10 @@ void PairDPDOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
const double * const * const v = atom->v;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
const dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double *special_lj = force->special_lj;
const double dtinvsqrt = 1.0/sqrt(update->dt);
@ -132,12 +132,12 @@ void PairDPDOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
vxtmp = v[i][0];
vytmp = v[i][1];
vztmp = v[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
vxtmp = v[i].x;
vytmp = v[i].y;
vztmp = v[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -148,9 +148,9 @@ void PairDPDOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_dpd = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -158,9 +158,9 @@ void PairDPDOMP::eval(int iifrom, int iito, ThrData * const thr)
r = sqrt(rsq);
if (r < EPSILON) continue; // r can be 0.0 in DPD systems
rinv = 1.0/r;
delvx = vxtmp - v[j][0];
delvy = vytmp - v[j][1];
delvz = vztmp - v[j][2];
delvx = vxtmp - v[j].x;
delvy = vytmp - v[j].y;
delvz = vztmp - v[j].z;
dot = delx*delvx + dely*delvy + delz*delvz;
wd = 1.0 - r/cut[itype][jtype];
randnum = rng.gaussian();
@ -178,9 +178,9 @@ void PairDPDOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -195,9 +195,9 @@ void PairDPDOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

44
src/USER-OMP/pair_dpd_tstat_omp.cpp
View File

@ -111,10 +111,10 @@ void PairDPDTstatOMP::eval(int iifrom, int iito, ThrData * const thr)
double rsq,r,rinv,dot,wd,randnum,factor_dpd;
int *ilist,*jlist,*numneigh,**firstneigh;
const double * const * const x = atom->x;
const double * const * const v = atom->v;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
const dbl3_t * _noalias const v = (dbl3_t *) atom->v[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double *special_lj = force->special_lj;
const double dtinvsqrt = 1.0/sqrt(update->dt);
@ -142,12 +142,12 @@ void PairDPDTstatOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
vxtmp = v[i][0];
vytmp = v[i][1];
vztmp = v[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
vxtmp = v[i].x;
vytmp = v[i].y;
vztmp = v[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -158,9 +158,9 @@ void PairDPDTstatOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_dpd = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -168,9 +168,9 @@ void PairDPDTstatOMP::eval(int iifrom, int iito, ThrData * const thr)
r = sqrt(rsq);
if (r < EPSILON) continue; // r can be 0.0 in DPD systems
rinv = 1.0/r;
delvx = vxtmp - v[j][0];
delvy = vytmp - v[j][1];
delvz = vztmp - v[j][2];
delvx = vxtmp - v[j].x;
delvy = vytmp - v[j].y;
delvz = vztmp - v[j].z;
dot = delx*delvx + dely*delvy + delz*delvz;
wd = 1.0 - r/cut[itype][jtype];
randnum = rng.gaussian();
@ -186,18 +186,18 @@ void PairDPDTstatOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
0.0,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

42
src/USER-OMP/pair_eam_omp.cpp
View File

@ -101,13 +101,13 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
double * const rho_t = thr->get_rho();
const int tid = thr->get_tid();
const int nthreads = comm->nthreads;
const int * const type = atom->type;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
@ -122,9 +122,9 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -133,9 +133,9 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
@ -221,9 +221,9 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
fxtmp = fytmp = fztmp = 0.0;
@ -234,9 +234,9 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
@ -276,9 +276,9 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) evdwl = phi;
@ -286,9 +286,9 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

72
src/USER-OMP/pair_edip_omp.cpp
View File

@ -147,9 +147,9 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
double *pre_thrPow2B_ij = prePow2B_ij + tid * leadDimInteractionList;
double *pre_thrForceCoord = preForceCoord + tid * leadDimInteractionList;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
inum = list->inum;
@ -165,9 +165,9 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
itype = map[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
jlist = firstneigh[i];
jnum = numneigh[i];
@ -180,9 +180,9 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
double dr_ij[3], r_ij;
dr_ij[0] = xtmp - x[j][0];
dr_ij[1] = ytmp - x[j][1];
dr_ij[2] = ztmp - x[j][2];
dr_ij[0] = xtmp - x[j].x;
dr_ij[1] = ytmp - x[j].y;
dr_ij[2] = ztmp - x[j].z;
r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2];
jtype = map[type[j]];
@ -297,9 +297,9 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
j = jlist[neighbor_j];
j &= NEIGHMASK;
dr_ij[0] = x[j][0] - xtmp;
dr_ij[1] = x[j][1] - ytmp;
dr_ij[2] = x[j][2] - ztmp;
dr_ij[0] = x[j].x - xtmp;
dr_ij[1] = x[j].y - ytmp;
dr_ij[2] = x[j].z - ztmp;
r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2];
jtype = map[type[j]];
@ -334,13 +334,13 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
f_ij[1] = forceMod2B * directorCos_ij_y;
f_ij[2] = forceMod2B * directorCos_ij_z;
f[j][0] -= f_ij[0];
f[j][1] -= f_ij[1];
f[j][2] -= f_ij[2];
f[j].x -= f_ij[0];
f[j].y -= f_ij[1];
f[j].z -= f_ij[2];
f[i][0] += f_ij[0];
f[i][1] += f_ij[1];
f[i][2] += f_ij[2];
f[i].x += f_ij[0];
f[i].y += f_ij[1];
f[i].z += f_ij[2];
// potential energy
@ -360,9 +360,9 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
ikparam = elem2param[itype][ktype][ktype];
ijkparam = elem2param[itype][jtype][ktype];
dr_ik[0] = x[k][0] - xtmp;
dr_ik[1] = x[k][1] - ytmp;
dr_ik[2] = x[k][2] - ztmp;
dr_ik[0] = x[k].x - xtmp;
dr_ik[1] = x[k].y - ytmp;
dr_ik[2] = x[k].z - ztmp;
r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
if (r_ik > params[ikparam].cutsq) continue;
@ -426,17 +426,17 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
forceModCoord += (forceMod3B_factor2 *
(tauFunctionDerived - 0.5 * mu * cosTetaDiff));
f[j][0] += f_ij[0];
f[j][1] += f_ij[1];
f[j][2] += f_ij[2];
f[j].x += f_ij[0];
f[j].y += f_ij[1];
f[j].z += f_ij[2];
f[k][0] += f_ik[0];
f[k][1] += f_ik[1];
f[k][2] += f_ik[2];
f[k].x += f_ik[0];
f[k].y += f_ik[1];
f[k].z += f_ik[2];
f[i][0] -= f_ij[0] + f_ik[0];
f[i][1] -= f_ij[1] + f_ik[1];
f[i][2] -= f_ij[2] + f_ik[2];
f[i].x -= f_ij[0] + f_ik[0];
f[i].y -= f_ij[1] + f_ik[1];
f[i].z -= f_ij[2] + f_ik[2];
// potential energy
@ -464,13 +464,13 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
f_ij[1] = forceModCoord_ij * dr_ij[1];
f_ij[2] = forceModCoord_ij * dr_ij[2];
f[j][0] -= f_ij[0];
f[j][1] -= f_ij[1];
f[j][2] -= f_ij[2];
f[j].x -= f_ij[0];
f[j].y -= f_ij[1];
f[j].z -= f_ij[2];
f[i][0] += f_ij[0];
f[i][1] += f_ij[1];
f[i][2] += f_ij[2];
f[i].x += f_ij[0];
f[i].y += f_ij[1];
f[i].z += f_ij[2];
// potential energy

54
src/USER-OMP/pair_eim_omp.cpp
View File

@ -102,14 +102,14 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
double * const rho_t = thr->get_rho();
double * const fp_t = thr->get_fp();
const int tid = thr->get_tid();
const int nthreads = comm->nthreads;
const int * const type = atom->type;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
@ -124,9 +124,9 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -135,9 +135,9 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq[itype][jtype]) {
@ -195,9 +195,9 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -207,9 +207,9 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq[itype][jtype]) {
@ -279,9 +279,9 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
fxtmp = fytmp = fztmp = 0.0;
@ -292,9 +292,9 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq[itype][jtype]) {
@ -328,9 +328,9 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) evdwl = phi-q0[itype]*q0[jtype]*coul;
@ -338,9 +338,9 @@ void PairEIMOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_gauss_cut_omp.cpp
View File

@ -81,11 +81,11 @@ void PairGaussCutOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
@ -97,9 +97,9 @@ void PairGaussCutOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -111,9 +111,9 @@ void PairGaussCutOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -127,9 +127,9 @@ void PairGaussCutOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -141,9 +141,9 @@ void PairGaussCutOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_gauss_omp.cpp
View File

@ -86,11 +86,11 @@ double PairGaussOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
@ -102,9 +102,9 @@ double PairGaussOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -115,9 +115,9 @@ double PairGaussOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -137,9 +137,9 @@ double PairGaussOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -152,9 +152,9 @@ double PairGaussOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
return occ;
}

42
src/USER-OMP/pair_gayberne_omp.cpp
View File

@ -83,13 +83,13 @@ void PairGayBerneOMP::eval(int iifrom, int iito, ThrData * const thr)
int *ilist,*jlist,*numneigh,**firstneigh;
double *iquat,*jquat;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
double * const * const tor = thr->get_torque();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
dbl3_t * _noalias const tor = (dbl3_t *) thr->get_torque()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const int * const ellipsoid = atom->ellipsoid;
const double * _noalias const special_lj = force->special_lj;
const int * _noalias const ellipsoid = atom->ellipsoid;
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
@ -126,9 +126,9 @@ void PairGayBerneOMP::eval(int iifrom, int iito, ThrData * const thr)
// r12 = center to center vector
r12[0] = x[j][0]-x[i][0];
r12[1] = x[j][1]-x[i][1];
r12[2] = x[j][2]-x[i][2];
r12[0] = x[j].x-x[i].x;
r12[1] = x[j].y-x[i].y;
r12[2] = x[j].z-x[i].z;
rsq = MathExtra::dot3(r12,r12);
jtype = type[j];
@ -196,12 +196,12 @@ void PairGayBerneOMP::eval(int iifrom, int iito, ThrData * const thr)
rtor[0] *= factor_lj;
rtor[1] *= factor_lj;
rtor[2] *= factor_lj;
f[j][0] -= fforce[0];
f[j][1] -= fforce[1];
f[j][2] -= fforce[2];
tor[j][0] += rtor[0];
tor[j][1] += rtor[1];
tor[j][2] += rtor[2];
f[j].x -= fforce[0];
f[j].y -= fforce[1];
f[j].z -= fforce[2];
tor[j].x += rtor[0];
tor[j].y += rtor[1];
tor[j].z += rtor[2];
}
if (EFLAG) evdwl = factor_lj*one_eng;
@ -211,12 +211,12 @@ void PairGayBerneOMP::eval(int iifrom, int iito, ThrData * const thr)
-r12[0],-r12[1],-r12[2],thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
tor[i][0] += t1tmp;
tor[i][1] += t2tmp;
tor[i][2] += t3tmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
tor[i].x += t1tmp;
tor[i].y += t2tmp;
tor[i].z += t3tmp;
}
}

50
src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
View File

@ -124,10 +124,10 @@ void PairHbondDreidingLJOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const double * const special_lj = force->special_lj;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const double * _noalias const special_lj = force->special_lj;
const int * const * const nspecial = atom->nspecial;
const int * const * const special = atom->special;
double fxtmp,fytmp,fztmp;
@ -156,9 +156,9 @@ void PairHbondDreidingLJOMP::eval(int iifrom, int iito, ThrData * const thr)
jnum = numneigh[i];
fxtmp=fytmp=fztmp=0.0;
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
@ -168,9 +168,9 @@ void PairHbondDreidingLJOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (!acceptor[jtype]) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
for (kk = 0; kk < knum; kk++) {
@ -182,16 +182,16 @@ void PairHbondDreidingLJOMP::eval(int iifrom, int iito, ThrData * const thr)
const Param &pm = params[m];
if (rsq < pm.cut_outersq) {
delr1[0] = xtmp - x[k][0];
delr1[1] = ytmp - x[k][1];
delr1[2] = ztmp - x[k][2];
delr1[0] = xtmp - x[k].x;
delr1[1] = ytmp - x[k].y;
delr1[2] = ztmp - x[k].z;
domain->minimum_image(delr1);
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
r1 = sqrt(rsq1);
delr2[0] = x[j][0] - x[k][0];
delr2[1] = x[j][1] - x[k][1];
delr2[2] = x[j][2] - x[k][2];
delr2[0] = x[j].x - x[k].x;
delr2[1] = x[j].y - x[k].y;
delr2[2] = x[j].z - x[k].z;
domain->minimum_image(delr2);
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
r2 = sqrt(rsq2);
@ -258,13 +258,13 @@ void PairHbondDreidingLJOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += fi[1];
fztmp += fi[2];
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
f[j].x += fj[0];
f[j].y += fj[1];
f[j].z += fj[2];
f[k][0] -= vx1 + vx2;
f[k][1] -= vy1 + vy2;
f[k][2] -= vz1 + vz2;
f[k].x -= vx1 + vx2;
f[k].y -= vy1 + vy2;
f[k].z -= vz1 + vz2;
// KIJ instead of IJK b/c delr1/delr2 are both with respect to k
@ -277,9 +277,9 @@ void PairHbondDreidingLJOMP::eval(int iifrom, int iito, ThrData * const thr)
}
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
const int tid = thr->get_tid();
hbcount_thr[tid] = static_cast<double>(hbcount);

50
src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
View File

@ -123,10 +123,10 @@ void PairHbondDreidingMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const double * const special_lj = force->special_lj;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const double * _noalias const special_lj = force->special_lj;
const int * const * const nspecial = atom->nspecial;
const int * const * const special = atom->special;
double fxtmp,fytmp,fztmp;
@ -155,9 +155,9 @@ void PairHbondDreidingMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
jnum = numneigh[i];
fxtmp=fytmp=fztmp=0.0;
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
@ -167,9 +167,9 @@ void PairHbondDreidingMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
jtype = type[j];
if (!acceptor[jtype]) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
for (kk = 0; kk < knum; kk++) {
@ -181,16 +181,16 @@ void PairHbondDreidingMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
const Param &pm = params[m];
if (rsq < pm.cut_outersq) {
delr1[0] = xtmp - x[k][0];
delr1[1] = ytmp - x[k][1];
delr1[2] = ztmp - x[k][2];
delr1[0] = xtmp - x[k].x;
delr1[1] = ytmp - x[k].y;
delr1[2] = ztmp - x[k].z;
domain->minimum_image(delr1);
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
r1 = sqrt(rsq1);
delr2[0] = x[j][0] - x[k][0];
delr2[1] = x[j][1] - x[k][1];
delr2[2] = x[j][2] - x[k][2];
delr2[0] = x[j].x - x[k].x;
delr2[1] = x[j].y - x[k].y;
delr2[2] = x[j].z - x[k].z;
domain->minimum_image(delr2);
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
r2 = sqrt(rsq2);
@ -256,13 +256,13 @@ void PairHbondDreidingMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += fi[1];
fztmp += fi[2];
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
f[j].x += fj[0];
f[j].y += fj[1];
f[j].z += fj[2];
f[k][0] -= vx1 + vx2;
f[k][1] -= vy1 + vy2;
f[k][2] -= vz1 + vz2;
f[k].x -= vx1 + vx2;
f[k].y -= vy1 + vy2;
f[k].z -= vz1 + vz2;
// KIJ instead of IJK b/c delr1/delr2 are both with respect to k
@ -275,9 +275,9 @@ void PairHbondDreidingMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
}
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
const int tid = thr->get_tid();
hbcount_thr[tid] = static_cast<double>(hbcount);

32
src/USER-OMP/pair_lj96_cut_omp.cpp
View File

@ -82,11 +82,11 @@ void PairLJ96CutOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
@ -98,9 +98,9 @@ void PairLJ96CutOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -111,9 +111,9 @@ void PairLJ96CutOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -129,9 +129,9 @@ void PairLJ96CutOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -144,9 +144,9 @@ void PairLJ96CutOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

36
src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
View File

@ -84,13 +84,13 @@ void PairLJCharmmCoulCharmmImplicitOMP::eval(int iifrom, int iito, ThrData * con
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -106,9 +106,9 @@ void PairLJCharmmCoulCharmmImplicitOMP::eval(int iifrom, int iito, ThrData * con
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -120,9 +120,9 @@ void PairLJCharmmCoulCharmmImplicitOMP::eval(int iifrom, int iito, ThrData * con
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -162,9 +162,9 @@ void PairLJCharmmCoulCharmmImplicitOMP::eval(int iifrom, int iito, ThrData * con
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -193,9 +193,9 @@ void PairLJCharmmCoulCharmmImplicitOMP::eval(int iifrom, int iito, ThrData * con
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

36
src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
View File

@ -84,13 +84,13 @@ void PairLJCharmmCoulCharmmOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -106,9 +106,9 @@ void PairLJCharmmCoulCharmmOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -120,9 +120,9 @@ void PairLJCharmmCoulCharmmOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -162,9 +162,9 @@ void PairLJCharmmCoulCharmmOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -193,9 +193,9 @@ void PairLJCharmmCoulCharmmOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

36
src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
View File

@ -78,12 +78,12 @@ template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairLJCharmmCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
{
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
const double inv_denom_lj = 1.0/denom_lj;
@ -99,9 +99,9 @@ void PairLJCharmmCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
const int i = ilist[ii];
const int itype = type[i];
const double qtmp = q[i];
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
const double xtmp = x[i].x;
const double ytmp = x[i].y;
const double ztmp = x[i].z;
double fxtmp,fytmp,fztmp;
fxtmp=fytmp=fztmp=0.0;
@ -115,9 +115,9 @@ void PairLJCharmmCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
const int sbindex = sbmask(jlist[jj]);
const int j = jlist[jj] & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double delx = xtmp - x[j].x;
const double dely = ytmp - x[j].y;
const double delz = ztmp - x[j].z;
const double rsq = delx*delx + dely*dely + delz*delz;
const int jtype = type[j];
@ -197,18 +197,18 @@ void PairLJCharmmCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

36
src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp
View File

@ -79,12 +79,12 @@ template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairLJCharmmCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
{
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
const double inv_denom_lj = 1.0/denom_lj;
@ -100,9 +100,9 @@ void PairLJCharmmCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
const int i = ilist[ii];
const int itype = type[i];
const double qtmp = q[i];
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
const double xtmp = x[i].x;
const double ytmp = x[i].y;
const double ztmp = x[i].z;
double fxtmp,fytmp,fztmp;
fxtmp=fytmp=fztmp=0.0;
@ -116,9 +116,9 @@ void PairLJCharmmCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
const int sbindex = sbmask(jlist[jj]);
const int j = jlist[jj] & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double delx = xtmp - x[j].x;
const double dely = ytmp - x[j].y;
const double delz = ztmp - x[j].z;
const double rsq = delx*delx + dely*dely + delz*delz;
const int jtype = type[j];
@ -190,18 +190,18 @@ void PairLJCharmmCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

36
src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
View File

@ -84,13 +84,13 @@ void PairLJClass2CoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -104,9 +104,9 @@ void PairLJClass2CoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -118,9 +118,9 @@ void PairLJClass2CoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -146,9 +146,9 @@ void PairLJClass2CoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -166,9 +166,9 @@ void PairLJClass2CoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

36
src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
View File

@ -92,13 +92,13 @@ void PairLJClass2CoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -112,9 +112,9 @@ void PairLJClass2CoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -126,9 +126,9 @@ void PairLJClass2CoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -160,9 +160,9 @@ void PairLJClass2CoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -182,9 +182,9 @@ void PairLJClass2CoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_lj_class2_omp.cpp
View File

@ -81,11 +81,11 @@ void PairLJClass2OMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
@ -97,9 +97,9 @@ void PairLJClass2OMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -110,9 +110,9 @@ void PairLJClass2OMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -128,9 +128,9 @@ void PairLJClass2OMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -143,9 +143,9 @@ void PairLJClass2OMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_lj_cubic_omp.cpp
View File

@ -83,11 +83,11 @@ void PairLJCubicOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
@ -99,9 +99,9 @@ void PairLJCubicOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -112,9 +112,9 @@ void PairLJCubicOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -135,9 +135,9 @@ void PairLJCubicOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -154,9 +154,9 @@ void PairLJCubicOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

36
src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
View File

@ -83,13 +83,13 @@ void PairLJCutCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -103,9 +103,9 @@ void PairLJCutCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -117,9 +117,9 @@ void PairLJCutCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -144,9 +144,9 @@ void PairLJCutCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -164,9 +164,9 @@ void PairLJCutCoulCutOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

36
src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
View File

@ -84,13 +84,13 @@ void PairLJCutCoulDebyeOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -104,9 +104,9 @@ void PairLJCutCoulDebyeOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -118,9 +118,9 @@ void PairLJCutCoulDebyeOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -147,9 +147,9 @@ void PairLJCutCoulDebyeOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -167,9 +167,9 @@ void PairLJCutCoulDebyeOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

36
src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
View File

@ -94,13 +94,13 @@ void PairLJCutCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -114,9 +114,9 @@ void PairLJCutCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -128,9 +128,9 @@ void PairLJCutCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -175,9 +175,9 @@ void PairLJCutCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -202,9 +202,9 @@ void PairLJCutCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

36
src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp
View File

@ -87,13 +87,13 @@ void PairLJCutCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -107,9 +107,9 @@ void PairLJCutCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -121,9 +121,9 @@ void PairLJCutCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -166,9 +166,9 @@ void PairLJCutCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -193,9 +193,9 @@ void PairLJCutCoulMSMOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

73
src/USER-OMP/pair_lj_cut_omp.cpp
View File

@ -75,34 +75,38 @@ void PairLJCutOMP::compute(int eflag, int vflag)
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairLJCutOMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcelj,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const double * _noalias const special_lj = force->special_lj;
const int * _noalias const ilist = list->ilist;
const int * _noalias const numneigh = list->numneigh;
const int * const * const firstneigh = list->firstneigh;
double xtmp,ytmp,ztmp,delx,dely,delz,fxtmp,fytmp,fztmp;
double rsq,r2inv,r6inv,forcelj,factor_lj,evdwl,fpair;
const int nlocal = atom->nlocal;
int j,jj,jnum,jtype;
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ++ii) {
for (int ii = iifrom; ii < iito; ++ii) {
const int i = ilist[ii];
const int itype = type[i];
const int * _noalias const jlist = firstneigh[i];
const double * _noalias const cutsqi = cutsq[itype];
const double * _noalias const offseti = offset[itype];
const double * _noalias const lj1i = lj1[itype];
const double * _noalias const lj2i = lj2[itype];
const double * _noalias const lj3i = lj3[itype];
const double * _noalias const lj4i = lj4[itype];
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
jnum = numneigh[i];
fxtmp=fytmp=fztmp=0.0;
@ -111,30 +115,29 @@ void PairLJCutOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
if (rsq < cutsqi[jtype]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj = r6inv * (lj1i[jtype]*r6inv - lj2i[jtype]);
fpair = factor_lj*forcelj*r2inv;
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])
- offset[itype][jtype];
evdwl = r6inv*(lj3i[jtype]*r6inv-lj4i[jtype]) - offseti[jtype];
evdwl *= factor_lj;
}
@ -142,9 +145,9 @@ void PairLJCutOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

15
src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
View File

@ -329,8 +329,10 @@ void PairLJCutTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
// virial = sum(r x F) where each water's atoms are near xi and xj
// vlist stores 2,4,6 atoms whose forces contribute to virial
if (EVFLAG) {
n = 0;
key = 0;
}
if (itype != typeO) {
fxtmp += delx * cforce;
@ -345,10 +347,10 @@ void PairLJCutTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
v[4] = x[i].x * delz * cforce;
v[5] = x[i].y * delz * cforce;
}
vlist[n++] = i;
if (EVFLAG) vlist[n++] = i;
} else {
key++;
if (EVFLAG) key++;
fdx = delx*cforce;
fdy = dely*cforce;
@ -385,10 +387,12 @@ void PairLJCutTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
v[4] = x[i].x*fOz + xH1[0]*fHz + xH2[0]*fHz;
v[5] = x[i].y*fOz + xH1[1]*fHz + xH2[1]*fHz;
}
if (EVFLAG) {
vlist[n++] = i;
vlist[n++] = iH1;
vlist[n++] = iH2;
}
}
if (jtype != typeO) {
f[j].x -= delx * cforce;
@ -403,10 +407,10 @@ void PairLJCutTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
v[4] -= x[j].x * delz * cforce;
v[5] -= x[j].y * delz * cforce;
}
vlist[n++] = j;
if (EVFLAG) vlist[n++] = j;
} else {
key += 2;
if (EVFLAG) key += 2;
fdx = -delx*cforce;
fdy = -dely*cforce;
@ -443,10 +447,12 @@ void PairLJCutTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
v[4] += x[j].x*fOz + xH1[0]*fHz + xH2[0]*fHz;
v[5] += x[j].y*fOz + xH1[1]*fHz + xH2[1]*fHz;
}
if (EVFLAG) {
vlist[n++] = j;
vlist[n++] = jH1;
vlist[n++] = jH2;
}
}
if (EFLAG) {
if (CTABLE || rsq <= tabinnersq)
@ -468,7 +474,6 @@ void PairLJCutTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
}
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
compute position xM of fictitious charge site for O atom and 2 H atoms
return it as xM

4
src/USER-OMP/pair_lj_cut_tip4p_long_omp.h
View File

@ -41,8 +41,8 @@ class PairLJCutTIP4PLongOMP : public PairLJCutTIP4PLong, public ThrOMP {
private:
dbl3_t *newsite_thr;
int3_t *hneigh_thr;
template <int CFLAG, int EVFLAG, int EFLAG, int VFLAG>
void eval(int ifrom, int ito, ThrData * const thr);
template < int, int, int, int > void eval(int, int, ThrData *const);
void compute_newsite_thr(const dbl3_t &, const dbl3_t &,
const dbl3_t &, dbl3_t &) const;
};

32
src/USER-OMP/pair_lj_expand_omp.cpp
View File

@ -82,11 +82,11 @@ void PairLJExpandOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
@ -98,9 +98,9 @@ void PairLJExpandOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -111,9 +111,9 @@ void PairLJExpandOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -130,9 +130,9 @@ void PairLJExpandOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -145,9 +145,9 @@ void PairLJExpandOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

36
src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
View File

@ -84,13 +84,13 @@ void PairLJGromacsCoulGromacsOMP::eval(int iifrom, int iito, ThrData * const thr
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp;
@ -104,9 +104,9 @@ void PairLJGromacsCoulGromacsOMP::eval(int iifrom, int iito, ThrData * const thr
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -118,9 +118,9 @@ void PairLJGromacsCoulGromacsOMP::eval(int iifrom, int iito, ThrData * const thr
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -161,9 +161,9 @@ void PairLJGromacsCoulGromacsOMP::eval(int iifrom, int iito, ThrData * const thr
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -191,9 +191,9 @@ void PairLJGromacsCoulGromacsOMP::eval(int iifrom, int iito, ThrData * const thr
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_lj_gromacs_omp.cpp
View File

@ -82,11 +82,11 @@ void PairLJGromacsOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
@ -98,9 +98,9 @@ void PairLJGromacsOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -111,9 +111,9 @@ void PairLJGromacsOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -134,9 +134,9 @@ void PairLJGromacsOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -153,9 +153,9 @@ void PairLJGromacsOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

36
src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
View File

@ -79,12 +79,12 @@ template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
{
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * _noalias const type = atom->type;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
const int * const ilist = list->ilist;
@ -99,9 +99,9 @@ void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
const int i = ilist[ii];
const int itype = type[i];
const double qtmp = q[i];
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
const double xtmp = x[i].x;
const double ytmp = x[i].y;
const double ztmp = x[i].z;
double fxtmp,fytmp,fztmp;
fxtmp=fytmp=fztmp=0.0;
@ -115,9 +115,9 @@ void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
const int sbindex = sbmask(jlist[jj]);
const int j = jlist[jj] & NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double delx = xtmp - x[j].x;
const double dely = ytmp - x[j].y;
const double delz = ztmp - x[j].z;
const double rsq = delx*delx + dely*dely + delz*delz;
const int jtype = type[j];
@ -209,18 +209,18 @@ void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_lj_sdk_omp.cpp
View File

@ -86,11 +86,11 @@ void PairLJSDKOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
const int * const ilist = list->ilist;
@ -102,9 +102,9 @@ void PairLJSDKOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
fxtmp=fytmp=fztmp=0.0;
const int itype = type[i];
@ -116,9 +116,9 @@ void PairLJSDKOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -159,9 +159,9 @@ void PairLJSDKOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) evdwl *= factor_lj;
@ -169,9 +169,9 @@ void PairLJSDKOMP::eval_thr(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_lj_sf_omp.cpp
View File

@ -81,11 +81,11 @@ void PairLJShiftedForceOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
@ -97,9 +97,9 @@ void PairLJShiftedForceOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -110,9 +110,9 @@ void PairLJShiftedForceOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -129,9 +129,9 @@ void PairLJShiftedForceOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -144,9 +144,9 @@ void PairLJShiftedForceOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_lj_smooth_linear_omp.cpp
View File

@ -82,11 +82,11 @@ void PairLJSmoothLinearOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
@ -98,9 +98,9 @@ void PairLJSmoothLinearOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -111,9 +111,9 @@ void PairLJSmoothLinearOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -130,9 +130,9 @@ void PairLJSmoothLinearOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -146,9 +146,9 @@ void PairLJSmoothLinearOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_lj_smooth_omp.cpp
View File

@ -82,11 +82,11 @@ void PairLJSmoothOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
@ -98,9 +98,9 @@ void PairLJSmoothOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -111,9 +111,9 @@ void PairLJSmoothOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -137,9 +137,9 @@ void PairLJSmoothOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -157,9 +157,9 @@ void PairLJSmoothOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

32
src/USER-OMP/pair_morse_omp.cpp
View File

@ -81,11 +81,11 @@ void PairMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
@ -97,9 +97,9 @@ void PairMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -110,9 +110,9 @@ void PairMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -126,9 +126,9 @@ void PairMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG) {
@ -141,9 +141,9 @@ void PairMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

46
src/USER-OMP/pair_resquared_omp.cpp
View File

@ -82,12 +82,12 @@ void PairRESquaredOMP::eval(int iifrom, int iito, ThrData * const thr)
int *ilist,*jlist,*numneigh,**firstneigh;
RE2Vars wi,wj;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
double * const * const tor = thr->get_torque();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
dbl3_t * _noalias const tor = (dbl3_t *) thr->get_torque()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp,t1tmp,t2tmp,t3tmp;
@ -117,9 +117,9 @@ void PairRESquaredOMP::eval(int iifrom, int iito, ThrData * const thr)
// r12 = center to center vector
r12[0] = x[j][0]-x[i][0];
r12[1] = x[j][1]-x[i][1];
r12[2] = x[j][2]-x[i][2];
r12[0] = x[j].x-x[i].x;
r12[1] = x[j].y-x[i].y;
r12[2] = x[j].z-x[i].z;
rsq = MathExtra::dot3(r12,r12);
jtype = type[j];
@ -147,9 +147,9 @@ void PairRESquaredOMP::eval(int iifrom, int iito, ThrData * const thr)
precompute_i(j,wj);
if (NEWTON_PAIR || j < nlocal) {
one_eng = resquared_lj(j,i,wj,r12,rsq,fforce,rtor,true);
tor[j][0] += rtor[0]*factor_lj;
tor[j][1] += rtor[1]*factor_lj;
tor[j][2] += rtor[2]*factor_lj;
tor[j].x += rtor[0]*factor_lj;
tor[j].y += rtor[1]*factor_lj;
tor[j].z += rtor[2]*factor_lj;
} else
one_eng = resquared_lj(j,i,wj,r12,rsq,fforce,rtor,false);
break;
@ -168,9 +168,9 @@ void PairRESquaredOMP::eval(int iifrom, int iito, ThrData * const thr)
t2tmp += ttor[1]*factor_lj;
t3tmp += ttor[2]*factor_lj;
if (NEWTON_PAIR || j < nlocal) {
tor[j][0] += rtor[0]*factor_lj;
tor[j][1] += rtor[1]*factor_lj;
tor[j][2] += rtor[2]*factor_lj;
tor[j].x += rtor[0]*factor_lj;
tor[j].y += rtor[1]*factor_lj;
tor[j].z += rtor[2]*factor_lj;
}
break;
}
@ -183,9 +183,9 @@ void PairRESquaredOMP::eval(int iifrom, int iito, ThrData * const thr)
fztmp += fforce[2];
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= fforce[0];
f[j][1] -= fforce[1];
f[j][2] -= fforce[2];
f[j].x -= fforce[0];
f[j].y -= fforce[1];
f[j].z -= fforce[2];
}
if (EFLAG) evdwl = factor_lj*one_eng;
@ -195,12 +195,12 @@ void PairRESquaredOMP::eval(int iifrom, int iito, ThrData * const thr)
-r12[0],-r12[1],-r12[2],thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
tor[i][0] += t1tmp;
tor[i][1] += t2tmp;
tor[i][2] += t3tmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
tor[i].x += t1tmp;
tor[i].y += t2tmp;
tor[i].z += t3tmp;
}
}

32
src/USER-OMP/pair_soft_omp.cpp
View File

@ -85,11 +85,11 @@ void PairSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
const double * _noalias const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
@ -101,9 +101,9 @@ void PairSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -114,9 +114,9 @@ void PairSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
@ -131,9 +131,9 @@ void PairSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
}
if (EFLAG)
@ -143,9 +143,9 @@ void PairSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,fpair,delx,dely,delz,thr);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

62
src/USER-OMP/pair_sw_omp.cpp
View File

@ -78,10 +78,10 @@ void PairSWOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const tag = atom->tag;
const int * const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int * _noalias const tag = atom->tag;
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
ilist = list->ilist;
@ -97,9 +97,9 @@ void PairSWOMP::eval(int iifrom, int iito, ThrData * const thr)
i = ilist[ii];
itag = tag[i];
itype = map[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
fxtmp = fytmp = fztmp = 0.0;
// two-body interactions, skip half of them
@ -117,16 +117,16 @@ void PairSWOMP::eval(int iifrom, int iito, ThrData * const thr)
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
if (x[j].z < ztmp) continue;
if (x[j].z == ztmp && x[j].y < ytmp) continue;
if (x[j].z == ztmp && x[j].y == ytmp && x[j].x < xtmp) continue;
}
jtype = map[type[j]];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
ijparam = elem2param[itype][jtype][jtype];
@ -137,9 +137,9 @@ void PairSWOMP::eval(int iifrom, int iito, ThrData * const thr)
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j].x -= delx*fpair;
f[j].y -= dely*fpair;
f[j].z -= delz*fpair;
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,
evdwl,0.0,fpair,delx,dely,delz,thr);
@ -152,9 +152,9 @@ void PairSWOMP::eval(int iifrom, int iito, ThrData * const thr)
j &= NEIGHMASK;
jtype = map[type[j]];
ijparam = elem2param[itype][jtype][jtype];
delr1[0] = x[j][0] - xtmp;
delr1[1] = x[j][1] - ytmp;
delr1[2] = x[j][2] - ztmp;
delr1[0] = x[j].x - xtmp;
delr1[1] = x[j].y - ytmp;
delr1[2] = x[j].z - ztmp;
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
if (rsq1 > params[ijparam].cutsq) continue;
@ -168,9 +168,9 @@ void PairSWOMP::eval(int iifrom, int iito, ThrData * const thr)
ikparam = elem2param[itype][ktype][ktype];
ijkparam = elem2param[itype][jtype][ktype];
delr2[0] = x[k][0] - xtmp;
delr2[1] = x[k][1] - ytmp;
delr2[2] = x[k][2] - ztmp;
delr2[0] = x[k].x - xtmp;
delr2[1] = x[k].y - ytmp;
delr2[2] = x[k].z - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (rsq2 > params[ikparam].cutsq) continue;
@ -183,19 +183,19 @@ void PairSWOMP::eval(int iifrom, int iito, ThrData * const thr)
fjxtmp += fj[0];
fjytmp += fj[1];
fjztmp += fj[2];
f[k][0] += fk[0];
f[k][1] += fk[1];
f[k][2] += fk[2];
f[k].x += fk[0];
f[k].y += fk[1];
f[k].z += fk[2];
if (EVFLAG) ev_tally3_thr(this,i,j,k,evdwl,0.0,fj,fk,delr1,delr2,thr);
}
f[j][0] += fjxtmp;
f[j][1] += fjytmp;
f[j][2] += fjztmp;
f[j].x += fjxtmp;
f[j].y += fjytmp;
f[j].z += fjztmp;
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
}

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