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Cleaned up atom->x and atom->f deferences.

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This commit is contained in:
DallasTrinkle
2017-05-03 16:56:07 -05:00
parent 11cb0212b7
commit 7409c6d781
1 changed files with 39 additions and 32 deletions
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67
src/USER-MISC/pair_meam_spline.cpp
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@ -170,14 +170,15 @@ double PairMEAMSpline::pair_density(int i)
{
double rho_value = 0;
MEAM2Body* nextTwoBodyInfo = twoBodyInfo;
double** const x = atom->x;
for(int jj = 0; jj < listfull->numneigh[i]; jj++) {
int j = listfull->firstneigh[i][jj];
j &= NEIGHMASK;
double jdelx = atom->x[j][0] - atom->x[i][0];
double jdely = atom->x[j][1] - atom->x[i][1];
double jdelz = atom->x[j][2] - atom->x[i][2];
double jdelx = x[j][0] - x[i][0];
double jdely = x[j][1] - x[i][1];
double jdelz = x[j][2] - x[i][2];
double rij_sq = jdelx*jdelx + jdely*jdely + jdelz*jdelz;
double rij = sqrt(rij_sq);
@ -196,6 +197,7 @@ double PairMEAMSpline::three_body_density(int i)
{
double rho_value = 0;
int numBonds=0;
double** const x = atom->x;
MEAM2Body* nextTwoBodyInfo = twoBodyInfo;
@ -203,9 +205,9 @@ double PairMEAMSpline::three_body_density(int i)
int j = listfull->firstneigh[i][jj];
j &= NEIGHMASK;
double jdelx = atom->x[j][0] - atom->x[i][0];
double jdely = atom->x[j][1] - atom->x[i][1];
double jdelz = atom->x[j][2] - atom->x[i][2];
double jdelx = x[j][0] - x[i][0];
double jdely = x[j][1] - x[i][1];
double jdelz = x[j][2] - x[i][2];
double rij_sq = jdelx*jdelx + jdely*jdely + jdelz*jdelz;
if(rij_sq < cutoff*cutoff) {
@ -239,14 +241,15 @@ double PairMEAMSpline::three_body_density(int i)
double PairMEAMSpline::compute_three_body_contrib_to_charge_density(int i, int& numBonds) {
double rho_value = 0;
MEAM2Body* nextTwoBodyInfo = twoBodyInfo;
double** const x = atom->x;
for(int jj = 0; jj < listfull->numneigh[i]; jj++) {
int j = listfull->firstneigh[i][jj];
j &= NEIGHMASK;
double jdelx = atom->x[j][0] - atom->x[i][0];
double jdely = atom->x[j][1] - atom->x[i][1];
double jdelz = atom->x[j][2] - atom->x[i][2];
double jdelx = x[j][0] - x[i][0];
double jdely = x[j][1] - x[i][1];
double jdelz = x[j][2] - x[i][2];
double rij_sq = jdelx*jdelx + jdely*jdely + jdelz*jdelz;
if(rij_sq < cutoff*cutoff) {
@ -296,6 +299,7 @@ double PairMEAMSpline::compute_embedding_energy_and_deriv(int eflag, int i, doub
void PairMEAMSpline::compute_three_body_contrib_to_forces(int i, int numBonds, double Uprime_i) {
double forces_i[3] = {0, 0, 0};
double** forces = atom->f;
for(int jj = 0; jj < numBonds; jj++) {
const MEAM2Body bondj = twoBodyInfo[jj];
@ -345,9 +349,9 @@ void PairMEAMSpline::compute_three_body_contrib_to_forces(int i, int numBonds, d
forces_i[2] -= fk[2];
int k = bondk->tag;
atom->f[k][0] += fk[0];
atom->f[k][1] += fk[1];
atom->f[k][2] += fk[2];
forces[k][0] += fk[0];
forces[k][1] += fk[1];
forces[k][2] += fk[2];
if(evflag) {
double delta_ij[3];
@ -362,20 +366,23 @@ void PairMEAMSpline::compute_three_body_contrib_to_forces(int i, int numBonds, d
}
}
atom->f[i][0] -= forces_j[0];
atom->f[i][1] -= forces_j[1];
atom->f[i][2] -= forces_j[2];
atom->f[j][0] += forces_j[0];
atom->f[j][1] += forces_j[1];
atom->f[j][2] += forces_j[2];
forces[i][0] -= forces_j[0];
forces[i][1] -= forces_j[1];
forces[i][2] -= forces_j[2];
forces[j][0] += forces_j[0];
forces[j][1] += forces_j[1];
forces[j][2] += forces_j[2];
}
atom->f[i][0] += forces_i[0];
atom->f[i][1] += forces_i[1];
atom->f[i][2] += forces_i[2];
forces[i][0] += forces_i[0];
forces[i][1] += forces_i[1];
forces[i][2] += forces_i[2];
}
void PairMEAMSpline::compute_two_body_pair_interactions() {
double** const x = atom->x;
double** forces = atom->f;
for(int ii = 0; ii < listhalf->inum; ii++) {
int i = listhalf->ilist[ii];
@ -384,9 +391,9 @@ void PairMEAMSpline::compute_two_body_pair_interactions() {
j &= NEIGHMASK;
double jdel[3];
jdel[0] = atom->x[j][0] - atom->x[i][0];
jdel[1] = atom->x[j][1] - atom->x[i][1];
jdel[2] = atom->x[j][2] - atom->x[i][2];
jdel[0] = x[j][0] - x[i][0];
jdel[1] = x[j][1] - x[i][1];
jdel[2] = x[j][2] - x[i][2];
double rij_sq = jdel[0]*jdel[0] + jdel[1]*jdel[1] + jdel[2]*jdel[2];
if(rij_sq < cutoff*cutoff) {
@ -405,12 +412,12 @@ void PairMEAMSpline::compute_two_body_pair_interactions() {
fpair /= rij;
atom->f[i][0] += jdel[0]*fpair;
atom->f[i][1] += jdel[1]*fpair;
atom->f[i][2] += jdel[2]*fpair;
atom->f[j][0] -= jdel[0]*fpair;
atom->f[j][1] -= jdel[1]*fpair;
atom->f[j][2] -= jdel[2]*fpair;
forces[i][0] += jdel[0]*fpair;
forces[i][1] += jdel[1]*fpair;
forces[i][2] += jdel[2]*fpair;
forces[j][0] -= jdel[0]*fpair;
forces[j][1] -= jdel[1]*fpair;
forces[j][2] -= jdel[2]*fpair;
if (evflag) ev_tally(i, j, atom->nlocal, force->newton_pair,
pair_pot, 0.0, -fpair, jdel[0], jdel[1], jdel[2]);
}