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Remove neigh_f2c/c2f, related cleanup

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- neighbour lists now use C indexing
- removed many arr*v() macros
- removed some unneccessary pointers
- minor reformatting
This commit is contained in:
Sebastian Hütter
2017-06-22 19:02:14 +02:00
parent f092da80a9
commit dadd1c8b4d
6 changed files with 310 additions and 382 deletions
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28
src/USER-MEAMC/meam.h
View File

@ -141,20 +141,24 @@ public:
void interpolate_meam(int);
double compute_phi(double, int, int);
public:
void meam_setup_global(int, lattice_t*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*);
void meam_setup_param(int, double, int, int*, int*);
void meam_setup_done(double*);
void meam_dens_setup(int, int, int);
void meam_dens_init(int* i, int* ntype, int* type, int* fmap, double** x,
int* numneigh, int* firstneigh, int* numneigh_full,
void meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* atwt,
double* alpha, double* b0, double* b1, double* b2,
double* b3, double* alat, double* esub, double* asub,
double* t0, double* t1, double* t2, double* t3,
double* rozero, int* ibar);
void meam_setup_param(int which, double value, int nindex, int* index /*index(3)*/, int* errorflag);
void meam_setup_done(double* cutmax);
void meam_dens_setup(int atom_nmax, int nall, int n_neigh);
void meam_dens_init(int i, int ntype, int* type, int* fmap, double** x,
int numneigh, int* firstneigh, int numneigh_full,
int* firstneigh_full, int fnoffset, int* errorflag);
void meam_dens_final(int* nlocal, int* eflag_either, int* eflag_global,
int* eflag_atom, double* eng_vdwl, double* eatom, int* ntype,
void meam_dens_final(int nlocal, int eflag_either, int eflag_global,
int eflag_atom, double* eng_vdwl, double* eatom, int ntype,
int* type, int* fmap, int* errorflag);
void meam_force(int* iptr, int* eflag_either, int* eflag_global,
int* eflag_atom, int* vflag_atom, double* eng_vdwl, double* eatom,
int* ntype, int* type, int* fmap, double** x, int* numneigh,
int* firstneigh, int* numneigh_full, int* firstneigh_full,
void meam_force(int i, int eflag_either, int eflag_global,
int eflag_atom, int vflag_atom, double* eng_vdwl, double* eatom,
int ntype, int* type, int* fmap, double** x, int numneigh,
int* firstneigh, int numneigh_full, int* firstneigh_full,
int fnoffset, double** f, double** vatom,
int* errorflag);
};

108
src/USER-MEAMC/meam_dens_final.cpp
View File

@ -21,8 +21,8 @@ using namespace LAMMPS_NS;
//
void
MEAM::meam_dens_final(int* nlocal, int* eflag_either, int* eflag_global,
int* eflag_atom, double* eng_vdwl, double* eatom, int* ntype,
MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global,
int eflag_atom, double* eng_vdwl, double* eatom, int ntype,
int* type, int* fmap, int* errorflag)
{
int i, elti;
@ -32,56 +32,54 @@ MEAM::meam_dens_final(int* nlocal, int* eflag_either, int* eflag_global,
// Complete the calculation of density
for (i = 1; i <= *nlocal; i++) {
elti = fmap[arr1v(type, i)];
for (i = 0; i < nlocal; i++) {
elti = fmap[type[i]];
if (elti >= 0) {
arr1v(rho1, i) = 0.0;
arr1v(rho2, i) = -1.0 / 3.0 * arr1v(arho2b, i) * arr1v(arho2b, i);
arr1v(rho3, i) = 0.0;
rho1[i] = 0.0;
rho2[i] = -1.0 / 3.0 * arho2b[i] * arho2b[i];
rho3[i] = 0.0;
for (m = 1; m <= 3; m++) {
arr1v(rho1, i) =
arr1v(rho1, i) + arr2v(arho1, m, i) * arr2v(arho1, m, i);
arr1v(rho3, i) = arr1v(rho3, i) -
3.0 / 5.0 * arr2v(arho3b, m, i) * arr2v(arho3b, m, i);
rho1[i] = rho1[i] + arr2v(arho1, m, i+1) * arr2v(arho1, m, i+1);
rho3[i] = rho3[i] - 3.0 / 5.0 * arr2v(arho3b, m, i+1) * arr2v(arho3b, m, i+1);
}
for (m = 1; m <= 6; m++) {
arr1v(rho2, i) =
arr1v(rho2, i) +
this->v2D[m] * arr2v(arho2, m, i) * arr2v(arho2, m, i);
rho2[i] =
rho2[i] +
this->v2D[m] * arr2v(arho2, m, i+1) * arr2v(arho2, m, i+1);
}
for (m = 1; m <= 10; m++) {
arr1v(rho3, i) =
arr1v(rho3, i) +
this->v3D[m] * arr2v(arho3, m, i) * arr2v(arho3, m, i);
rho3[i] =
rho3[i] +
this->v3D[m] * arr2v(arho3, m, i+1) * arr2v(arho3, m, i+1);
}
if (arr1v(rho0, i) > 0.0) {
if (rho0[i] > 0.0) {
if (this->ialloy == 1) {
arr2v(t_ave, 1, i) = arr2v(t_ave, 1, i) / arr2v(tsq_ave, 1, i);
arr2v(t_ave, 2, i) = arr2v(t_ave, 2, i) / arr2v(tsq_ave, 2, i);
arr2v(t_ave, 3, i) = arr2v(t_ave, 3, i) / arr2v(tsq_ave, 3, i);
t_ave[i][0] = t_ave[i][0] / tsq_ave[i][0];
t_ave[i][1] = t_ave[i][1] / tsq_ave[i][1];
t_ave[i][2] = t_ave[i][2] / tsq_ave[i][2];
} else if (this->ialloy == 2) {
arr2v(t_ave, 1, i) = this->t1_meam[elti];
arr2v(t_ave, 2, i) = this->t2_meam[elti];
arr2v(t_ave, 3, i) = this->t3_meam[elti];
t_ave[i][0] = this->t1_meam[elti];
t_ave[i][1] = this->t2_meam[elti];
t_ave[i][2] = this->t3_meam[elti];
} else {
arr2v(t_ave, 1, i) = arr2v(t_ave, 1, i) / arr1v(rho0, i);
arr2v(t_ave, 2, i) = arr2v(t_ave, 2, i) / arr1v(rho0, i);
arr2v(t_ave, 3, i) = arr2v(t_ave, 3, i) / arr1v(rho0, i);
t_ave[i][0] = t_ave[i][0] / rho0[i];
t_ave[i][1] = t_ave[i][1] / rho0[i];
t_ave[i][2] = t_ave[i][2] / rho0[i];
}
}
arr1v(gamma, i) = arr2v(t_ave, 1, i) * arr1v(rho1, i) +
arr2v(t_ave, 2, i) * arr1v(rho2, i) +
arr2v(t_ave, 3, i) * arr1v(rho3, i);
gamma[i] = t_ave[i][0] * rho1[i] +
t_ave[i][1] * rho2[i] +
t_ave[i][2] * rho3[i];
if (arr1v(rho0, i) > 0.0) {
arr1v(gamma, i) = arr1v(gamma, i) / (arr1v(rho0, i) * arr1v(rho0, i));
if (rho0[i] > 0.0) {
gamma[i] = gamma[i] / (rho0[i] * rho0[i]);
}
Z = this->Z_meam[elti];
G_gam(arr1v(gamma, i), this->ibar_meam[elti], &G, errorflag);
G_gam(gamma[i], this->ibar_meam[elti], &G, errorflag);
if (*errorflag != 0)
return;
get_shpfcn(shp, this->lattce_meam[elti][elti]);
@ -90,8 +88,8 @@ MEAM::meam_dens_final(int* nlocal, int* eflag_either, int* eflag_global,
dGbar = 0.0;
} else {
if (this->mix_ref_t == 1) {
gam = (arr2v(t_ave, 1, i) * shp[1] + arr2v(t_ave, 2, i) * shp[2] +
arr2v(t_ave, 3, i) * shp[3]) /
gam = (t_ave[i][0] * shp[1] + t_ave[i][1] * shp[2] +
t_ave[i][2] * shp[3]) /
(Z * Z);
} else {
gam = (this->t1_meam[elti] * shp[1] +
@ -101,15 +99,15 @@ MEAM::meam_dens_final(int* nlocal, int* eflag_either, int* eflag_global,
}
G_gam(gam, this->ibar_meam[elti], &Gbar, errorflag);
}
arr1v(rho, i) = arr1v(rho0, i) * G;
rho[i] = rho0[i] * G;
if (this->mix_ref_t == 1) {
if (this->ibar_meam[elti] <= 0) {
Gbar = 1.0;
dGbar = 0.0;
} else {
gam = (arr2v(t_ave, 1, i) * shp[1] + arr2v(t_ave, 2, i) * shp[2] +
arr2v(t_ave, 3, i) * shp[3]) /
gam = (t_ave[i][0] * shp[1] + t_ave[i][1] * shp[2] +
t_ave[i][2] * shp[3]) /
(Z * Z);
dG_gam(gam, this->ibar_meam[elti], &Gbar, &dGbar);
}
@ -121,57 +119,57 @@ MEAM::meam_dens_final(int* nlocal, int* eflag_either, int* eflag_global,
rho_bkgd = this->rho_ref_meam[elti];
}
}
rhob = arr1v(rho, i) / rho_bkgd;
rhob = rho[i] / rho_bkgd;
denom = 1.0 / rho_bkgd;
dG_gam(arr1v(gamma, i), this->ibar_meam[elti], &G, &dG);
dG_gam(gamma[i], this->ibar_meam[elti], &G, &dG);
arr1v(dgamma1, i) = (G - 2 * dG * arr1v(gamma, i)) * denom;
dgamma1[i] = (G - 2 * dG * gamma[i]) * denom;
if (!iszero(arr1v(rho0, i))) {
arr1v(dgamma2, i) = (dG / arr1v(rho0, i)) * denom;
if (!iszero(rho0[i])) {
dgamma2[i] = (dG / rho0[i]) * denom;
} else {
arr1v(dgamma2, i) = 0.0;
dgamma2[i] = 0.0;
}
// dgamma3 is nonzero only if we are using the "mixed" rule for
// computing t in the reference system (which is not correct, but
// included for backward compatibility
if (this->mix_ref_t == 1) {
arr1v(dgamma3, i) = arr1v(rho0, i) * G * dGbar / (Gbar * Z * Z) * denom;
dgamma3[i] = rho0[i] * G * dGbar / (Gbar * Z * Z) * denom;
} else {
arr1v(dgamma3, i) = 0.0;
dgamma3[i] = 0.0;
}
B = this->A_meam[elti] * this->Ec_meam[elti][elti];
if (!iszero(rhob)) {
if (this->emb_lin_neg == 1 && rhob <= 0) {
arr1v(frhop, i) = -B;
frhop[i] = -B;
} else {
arr1v(frhop, i) = B * (log(rhob) + 1.0);
frhop[i] = B * (log(rhob) + 1.0);
}
if (*eflag_either != 0) {
if (*eflag_global != 0) {
if (eflag_either != 0) {
if (eflag_global != 0) {
if (this->emb_lin_neg == 1 && rhob <= 0) {
*eng_vdwl = *eng_vdwl - B * rhob;
} else {
*eng_vdwl = *eng_vdwl + B * rhob * log(rhob);
}
}
if (*eflag_atom != 0) {
if (eflag_atom != 0) {
if (this->emb_lin_neg == 1 && rhob <= 0) {
arr1v(eatom, i) = arr1v(eatom, i) - B * rhob;
eatom[i] = eatom[i] - B * rhob;
} else {
arr1v(eatom, i) = arr1v(eatom, i) + B * rhob * log(rhob);
eatom[i] = eatom[i] + B * rhob * log(rhob);
}
}
}
} else {
if (this->emb_lin_neg == 1) {
arr1v(frhop, i) = -B;
frhop[i] = -B;
} else {
arr1v(frhop, i) = B;
frhop[i] = B;
}
}
}

192
src/USER-MEAMC/meam_dens_init.cpp
View File

@ -101,18 +101,18 @@ MEAM::meam_dens_setup(int atom_nmax, int nall, int n_neigh)
//
void
MEAM::meam_dens_init(int* i, int* ntype, int* type, int* fmap, double** x,
int* numneigh, int* firstneigh, int* numneigh_full,
MEAM::meam_dens_init(int i, int ntype, int* type, int* fmap, double** x,
int numneigh, int* firstneigh, int numneigh_full,
int* firstneigh_full, int fnoffset, int* errorflag)
{
*errorflag = 0;
// Compute screening function and derivatives
getscreen(*i, &scrfcn[fnoffset], &dscrfcn[fnoffset], &fcpair[fnoffset], x, *numneigh, firstneigh,
*numneigh_full, firstneigh_full, *ntype, type, fmap);
getscreen(i, &scrfcn[fnoffset], &dscrfcn[fnoffset], &fcpair[fnoffset], x, numneigh, firstneigh,
numneigh_full, firstneigh_full, ntype, type, fmap);
// Calculate intermediate density terms to be communicated
calc_rho1(*i, *ntype, type, fmap, x, *numneigh, firstneigh, &scrfcn[fnoffset], &fcpair[fnoffset]);
calc_rho1(i, ntype, type, fmap, x, numneigh, firstneigh, &scrfcn[fnoffset], &fcpair[fnoffset]);
}
// ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
@ -135,24 +135,24 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair,
double rnorm, fc, dfc, drinv;
drinv = 1.0 / this->delr_meam;
elti = fmap[arr1v(type, i)];
elti = fmap[type[i]];
if (elti >= 0) {
xitmp = arr2v(x, 1, i);
yitmp = arr2v(x, 2, i);
zitmp = arr2v(x, 3, i);
xitmp = x[i][0];
yitmp = x[i][1];
zitmp = x[i][2];
for (jn = 1; jn <= numneigh; jn++) {
j = arr1v(firstneigh, jn);
for (jn = 0; jn < numneigh; jn++) {
j = firstneigh[jn];
eltj = fmap[arr1v(type, j)];
eltj = fmap[type[j]];
if (eltj >= 0) {
// First compute screening function itself, sij
xjtmp = arr2v(x, 1, j);
yjtmp = arr2v(x, 2, j);
zjtmp = arr2v(x, 3, j);
xjtmp = x[j][0];
yjtmp = x[j][1];
zjtmp = x[j][2];
delxij = xjtmp - xitmp;
delyij = yjtmp - yitmp;
delzij = zjtmp - zitmp;
@ -171,21 +171,21 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair,
}
// Now compute derivatives
arr1v(dscrfcn, jn) = 0.0;
dscrfcn[jn] = 0.0;
sfcij = sij * fcij;
if (iszero(sfcij) || iszero(sfcij - 1.0))
goto LABEL_100;
rbound = this->ebound_meam[elti][eltj] * rij2;
for (kn = 1; kn <= numneigh_full; kn++) {
k = arr1v(firstneigh_full, kn);
for (kn = 0; kn < numneigh_full; kn++) {
k = firstneigh_full[kn];
if (k == j)
continue;
eltk = fmap[arr1v(type, k)];
eltk = fmap[type[k]];
if (eltk < 0)
continue;
xktmp = arr2v(x, 1, k);
yktmp = arr2v(x, 2, k);
zktmp = arr2v(x, 3, k);
xktmp = x[k][0];
yktmp = x[k][1];
zktmp = x[k][2];
delxjk = xktmp - xjtmp;
delyjk = yktmp - yjtmp;
delzjk = zktmp - zjtmp;
@ -223,16 +223,16 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair,
dfcut(cikj, &sikj, &dfikj);
coef1 = dfikj / (delc * sikj);
dCfunc(rij2, rik2, rjk2, &dCikj);
arr1v(dscrfcn, jn) = arr1v(dscrfcn, jn) + coef1 * dCikj;
dscrfcn[jn] = dscrfcn[jn] + coef1 * dCikj;
}
}
coef1 = sfcij;
coef2 = sij * dfcij / rij;
arr1v(dscrfcn, jn) = arr1v(dscrfcn, jn) * coef1 - coef2;
dscrfcn[jn] = dscrfcn[jn] * coef1 - coef2;
LABEL_100:
arr1v(scrfcn, jn) = sij;
arr1v(fcpair, jn) = fcij;
scrfcn[jn] = sij;
fcpair[jn] = fcij;
}
}
}
@ -252,20 +252,20 @@ MEAM::calc_rho1(int i, int ntype, int* type, int* fmap, double** x,
double ro0i, ro0j;
double rhoa0i, rhoa1i, rhoa2i, rhoa3i, A1i, A2i, A3i;
elti = fmap[arr1v(type, i)];
xtmp = arr2v(x, 1, i);
ytmp = arr2v(x, 2, i);
ztmp = arr2v(x, 3, i);
for (jn = 1; jn <= numneigh; jn++) {
if (!iszero(arr1v(scrfcn, jn))) {
j = arr1v(firstneigh, jn);
sij = arr1v(scrfcn, jn) * arr1v(fcpair, jn);
delij[1] = arr2v(x, 1, j) - xtmp;
delij[2] = arr2v(x, 2, j) - ytmp;
delij[3] = arr2v(x, 3, j) - ztmp;
elti = fmap[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
for (jn = 0; jn < numneigh; jn++) {
if (!iszero(scrfcn[jn])) {
j = firstneigh[jn];
sij = scrfcn[jn] * fcpair[jn];
delij[1] = x[j][0] - xtmp;
delij[2] = x[j][1] - ytmp;
delij[3] = x[j][2] - ztmp;
rij2 = delij[1] * delij[1] + delij[2] * delij[2] + delij[3] * delij[3];
if (rij2 < this->cutforcesq) {
eltj = fmap[arr1v(type, j)];
eltj = fmap[type[j]];
rij = sqrt(rij2);
ai = rij / this->re_meam[elti][elti] - 1.0;
aj = rij / this->re_meam[eltj][eltj] - 1.0;
@ -287,45 +287,27 @@ MEAM::calc_rho1(int i, int ntype, int* type, int* fmap, double** x,
rhoa2i = rhoa2i * this->t2_meam[elti];
rhoa3i = rhoa3i * this->t3_meam[elti];
}
arr1v(rho0, i) = arr1v(rho0, i) + rhoa0j;
arr1v(rho0, j) = arr1v(rho0, j) + rhoa0i;
rho0[i] = rho0[i] + rhoa0j;
rho0[j] = rho0[j] + rhoa0i;
// For ialloy = 2, use single-element value (not average)
if (this->ialloy != 2) {
arr2v(t_ave, 1, i) =
arr2v(t_ave, 1, i) + this->t1_meam[eltj] * rhoa0j;
arr2v(t_ave, 2, i) =
arr2v(t_ave, 2, i) + this->t2_meam[eltj] * rhoa0j;
arr2v(t_ave, 3, i) =
arr2v(t_ave, 3, i) + this->t3_meam[eltj] * rhoa0j;
arr2v(t_ave, 1, j) =
arr2v(t_ave, 1, j) + this->t1_meam[elti] * rhoa0i;
arr2v(t_ave, 2, j) =
arr2v(t_ave, 2, j) + this->t2_meam[elti] * rhoa0i;
arr2v(t_ave, 3, j) =
arr2v(t_ave, 3, j) + this->t3_meam[elti] * rhoa0i;
t_ave[i][0] = t_ave[i][0] + this->t1_meam[eltj] * rhoa0j;
t_ave[i][1] = t_ave[i][1] + this->t2_meam[eltj] * rhoa0j;
t_ave[i][2] = t_ave[i][2] + this->t3_meam[eltj] * rhoa0j;
t_ave[j][0] = t_ave[j][0] + this->t1_meam[elti] * rhoa0i;
t_ave[j][1] = t_ave[j][1] + this->t2_meam[elti] * rhoa0i;
t_ave[j][2] = t_ave[j][2] + this->t3_meam[elti] * rhoa0i;
}
if (this->ialloy == 1) {
arr2v(tsq_ave, 1, i) =
arr2v(tsq_ave, 1, i) +
this->t1_meam[eltj] * this->t1_meam[eltj] * rhoa0j;
arr2v(tsq_ave, 2, i) =
arr2v(tsq_ave, 2, i) +
this->t2_meam[eltj] * this->t2_meam[eltj] * rhoa0j;
arr2v(tsq_ave, 3, i) =
arr2v(tsq_ave, 3, i) +
this->t3_meam[eltj] * this->t3_meam[eltj] * rhoa0j;
arr2v(tsq_ave, 1, j) =
arr2v(tsq_ave, 1, j) +
this->t1_meam[elti] * this->t1_meam[elti] * rhoa0i;
arr2v(tsq_ave, 2, j) =
arr2v(tsq_ave, 2, j) +
this->t2_meam[elti] * this->t2_meam[elti] * rhoa0i;
arr2v(tsq_ave, 3, j) =
arr2v(tsq_ave, 3, j) +
this->t3_meam[elti] * this->t3_meam[elti] * rhoa0i;
tsq_ave[i][0] = tsq_ave[i][0] + this->t1_meam[eltj] * this->t1_meam[eltj] * rhoa0j;
tsq_ave[i][1] = tsq_ave[i][1] + this->t2_meam[eltj] * this->t2_meam[eltj] * rhoa0j;
tsq_ave[i][2] = tsq_ave[i][2] + this->t3_meam[eltj] * this->t3_meam[eltj] * rhoa0j;
tsq_ave[j][0] = tsq_ave[j][0] + this->t1_meam[elti] * this->t1_meam[elti] * rhoa0i;
tsq_ave[j][1] = tsq_ave[j][1] + this->t2_meam[elti] * this->t2_meam[elti] * rhoa0i;
tsq_ave[j][2] = tsq_ave[j][2] + this->t3_meam[elti] * this->t3_meam[elti] * rhoa0i;
}
arr1v(arho2b, i) = arr1v(arho2b, i) + rhoa2j;
arr1v(arho2b, j) = arr1v(arho2b, j) + rhoa2i;
arho2b[i] = arho2b[i] + rhoa2j;
arho2b[j] = arho2b[j] + rhoa2i;
A1j = rhoa1j / rij;
A2j = rhoa2j / rij2;
@ -336,21 +318,21 @@ MEAM::calc_rho1(int i, int ntype, int* type, int* fmap, double** x,
nv2 = 1;
nv3 = 1;
for (m = 1; m <= 3; m++) {
arr2v(arho1, m, i) = arr2v(arho1, m, i) + A1j * delij[m];
arr2v(arho1, m, j) = arr2v(arho1, m, j) - A1i * delij[m];
arr2v(arho3b, m, i) = arr2v(arho3b, m, i) + rhoa3j * delij[m] / rij;
arr2v(arho3b, m, j) = arr2v(arho3b, m, j) - rhoa3i * delij[m] / rij;
arr2v(arho1, m, i+1) = arr2v(arho1, m, i+1) + A1j * delij[m];
arr2v(arho1, m, j+1) = arr2v(arho1, m, j+1) - A1i * delij[m];
arr2v(arho3b, m, i+1) = arr2v(arho3b, m, i+1) + rhoa3j * delij[m] / rij;
arr2v(arho3b, m, j+1) = arr2v(arho3b, m, j+1) - rhoa3i * delij[m] / rij;
for (n = m; n <= 3; n++) {
arr2v(arho2, nv2, i) =
arr2v(arho2, nv2, i) + A2j * delij[m] * delij[n];
arr2v(arho2, nv2, j) =
arr2v(arho2, nv2, j) + A2i * delij[m] * delij[n];
arr2v(arho2, nv2, i+1) =
arr2v(arho2, nv2, i+1) + A2j * delij[m] * delij[n];
arr2v(arho2, nv2, j+1) =
arr2v(arho2, nv2, j+1) + A2i * delij[m] * delij[n];
nv2 = nv2 + 1;
for (p = n; p <= 3; p++) {
arr2v(arho3, nv3, i) =
arr2v(arho3, nv3, i) + A3j * delij[m] * delij[n] * delij[p];
arr2v(arho3, nv3, j) =
arr2v(arho3, nv3, j) - A3i * delij[m] * delij[n] * delij[p];
arr2v(arho3, nv3, i+1) =
arr2v(arho3, nv3, i+1) + A3j * delij[m] * delij[n] * delij[p];
arr2v(arho3, nv3, j+1) =
arr2v(arho3, nv3, j+1) - A3i * delij[m] * delij[n] * delij[p];
nv3 = nv3 + 1;
}
}
@ -379,26 +361,26 @@ MEAM::screen(int i, int j, double** x, double rijsq, double* sij,
double Cmax, Cmin, rbound;
*sij = 1.0;
elti = fmap[arr1v(type, i)];
eltj = fmap[arr1v(type, j)];
elti = fmap[type[i]];
eltj = fmap[type[j]];
// if rjksq > ebound*rijsq, atom k is definitely outside the ellipse
rbound = this->ebound_meam[elti][eltj] * rijsq;
for (nk = 1; nk <= numneigh_full; nk++) {
k = arr1v(firstneigh_full, nk);
eltk = fmap[arr1v(type, k)];
for (nk = 0; nk < numneigh_full; nk++) {
k = firstneigh_full[nk];
eltk = fmap[type[k]];
if (k == j)
continue;
delxjk = arr2v(x, 1, k) - arr2v(x, 1, j);
delyjk = arr2v(x, 2, k) - arr2v(x, 2, j);
delzjk = arr2v(x, 3, k) - arr2v(x, 3, j);
delxjk = x[k][0] - x[j][0];
delyjk = x[k][1] - x[j][1];
delzjk = x[k][2] - x[j][2];
rjksq = delxjk * delxjk + delyjk * delyjk + delzjk * delzjk;
if (rjksq > rbound)
continue;
delxik = arr2v(x, 1, k) - arr2v(x, 1, i);
delyik = arr2v(x, 2, k) - arr2v(x, 2, i);
delzik = arr2v(x, 3, k) - arr2v(x, 3, i);
delxik = x[k][0] - x[i][0];
delyik = x[k][1] - x[i][1];
delzik = x[k][2] - x[i][2];
riksq = delxik * delxik + delyik * delyik + delzik * delzik;
if (riksq > rbound)
continue;
@ -450,10 +432,10 @@ MEAM::dsij(int i, int j, int k, int jn, int numneigh, double rij2,
double rbound, delc, sij, xik, xjk, cikj, sikj, dfc, a;
double Cmax, Cmin, dCikj1, dCikj2;
sij = arr1v(scrfcn, jn) * arr1v(fcpair, jn);
elti = fmap[arr1v(type, i)];
eltj = fmap[arr1v(type, j)];
eltk = fmap[arr1v(type, k)];
sij = scrfcn[jn] * fcpair[jn];
elti = fmap[type[i]];
eltj = fmap[type[j]];
eltk = fmap[type[k]];
Cmax = this->Cmax_meam[elti][eltj][eltk];
Cmin = this->Cmin_meam[elti][eltj][eltk];
@ -462,14 +444,14 @@ MEAM::dsij(int i, int j, int k, int jn, int numneigh, double rij2,
if (!iszero(sij) && !iszero(sij - 1.0)) {
rbound = rij2 * this->ebound_meam[elti][eltj];
delc = Cmax - Cmin;
dxjk = arr2v(x, 1, k) - arr2v(x, 1, j);
dyjk = arr2v(x, 2, k) - arr2v(x, 2, j);
dzjk = arr2v(x, 3, k) - arr2v(x, 3, j);
dxjk = x[k][0] - x[j][0];
dyjk = x[k][1] - x[j][1];
dzjk = x[k][2] - x[j][2];
rjk2 = dxjk * dxjk + dyjk * dyjk + dzjk * dzjk;
if (rjk2 <= rbound) {
dxik = arr2v(x, 1, k) - arr2v(x, 1, i);
dyik = arr2v(x, 2, k) - arr2v(x, 2, i);
dzik = arr2v(x, 3, k) - arr2v(x, 3, i);
dxik = x[k][0] - x[i][0];
dyik = x[k][1] - x[i][1];
dzik = x[k][2] - x[i][2];
rik2 = dxik * dxik + dyik * dyik + dzik * dzik;
if (rik2 <= rbound) {
xik = rik2 / rij2;

300
src/USER-MEAMC/meam_force.cpp
View File

@ -26,14 +26,14 @@ using namespace LAMMPS_NS;
//
void
MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
int* eflag_atom, int* vflag_atom, double* eng_vdwl, double* eatom,
int* ntype, int* type, int* fmap, double** x, int* numneigh,
int* firstneigh, int* numneigh_full, int* firstneigh_full,
MEAM::meam_force(int i, int eflag_either, int eflag_global,
int eflag_atom, int vflag_atom, double* eng_vdwl, double* eatom,
int ntype, int* type, int* fmap, double** x, int numneigh,
int* firstneigh, int numneigh_full, int* firstneigh_full,
int fnoffset, double** f, double** vatom,
int* errorflag)
{
int i, j, jn, k, kn, kk, m, n, p, q;
int j, jn, k, kn, kk, m, n, p, q;
int nv2, nv3, elti, eltj, eltk, ind;
double xitmp, yitmp, zitmp, delij[3 + 1], rij2, rij, rij3;
double delik[3 + 1], deljk[3 + 1], v[6 + 1], fi[3 + 1], fj[3 + 1];
@ -69,29 +69,26 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
third = 1.0 / 3.0;
sixth = 1.0 / 6.0;
//: aliased
i = *iptr;
// Compute forces atom i
elti = fmap[arr1v(type, i)];
elti = fmap[type[i]];
if (elti >= 0) {
xitmp = arr2v(x, 1, i);
yitmp = arr2v(x, 2, i);
zitmp = arr2v(x, 3, i);
xitmp = x[i][0];
yitmp = x[i][1];
zitmp = x[i][2];
// Treat each pair
for (jn = 1; jn <= *numneigh; jn++) {
j = arr1v(firstneigh, jn);
eltj = fmap[arr1v(type, j)];
for (jn = 0; jn < numneigh; jn++) {
j = firstneigh[jn];
eltj = fmap[type[j]];
if (!iszero(arr1v(scrfcn, fnoffset + jn)) && eltj >= 0) {
if (!iszero(scrfcn[fnoffset + jn]) && eltj >= 0) {
sij = arr1v(scrfcn, fnoffset + jn) * arr1v(fcpair, fnoffset + jn);
delij[1] = arr2v(x, 1, j) - xitmp;
delij[2] = arr2v(x, 2, j) - yitmp;
delij[3] = arr2v(x, 3, j) - zitmp;
sij = scrfcn[fnoffset + jn] * fcpair[fnoffset + jn];
delij[1] = x[j][0] - xitmp;
delij[2] = x[j][1] - yitmp;
delij[3] = x[j][2] - zitmp;
rij2 = delij[1] * delij[1] + delij[2] * delij[2] + delij[3] * delij[3];
if (rij2 < this->cutforcesq) {
rij = sqrt(rij2);
@ -116,12 +113,12 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
this->phirar4[ind][kk];
recip = 1.0 / r;
if (*eflag_either != 0) {
if (*eflag_global != 0)
if (eflag_either != 0) {
if (eflag_global != 0)
*eng_vdwl = *eng_vdwl + phi * sij;
if (*eflag_atom != 0) {
arr1v(eatom, i) = arr1v(eatom, i) + 0.5 * phi * sij;
arr1v(eatom, j) = arr1v(eatom, j) + 0.5 * phi * sij;
if (eflag_atom != 0) {
eatom[i] = eatom[i] + 0.5 * phi * sij;
eatom[j] = eatom[j] + 0.5 * phi * sij;
}
}
@ -193,19 +190,19 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
for (p = n; p <= 3; p++) {
for (q = p; q <= 3; q++) {
arg = delij[n] * delij[p] * delij[q] * this->v3D[nv3];
arg1i3 = arg1i3 + arr2v(arho3, nv3, i) * arg;
arg1j3 = arg1j3 - arr2v(arho3, nv3, j) * arg;
arg1i3 = arg1i3 + arr2v(arho3, nv3, i+1) * arg;
arg1j3 = arg1j3 - arr2v(arho3, nv3, j+1) * arg;
nv3 = nv3 + 1;
}
arg = delij[n] * delij[p] * this->v2D[nv2];
arg1i2 = arg1i2 + arr2v(arho2, nv2, i) * arg;
arg1j2 = arg1j2 + arr2v(arho2, nv2, j) * arg;
arg1i2 = arg1i2 + arr2v(arho2, nv2, i+1) * arg;
arg1j2 = arg1j2 + arr2v(arho2, nv2, j+1) * arg;
nv2 = nv2 + 1;
}
arg1i1 = arg1i1 + arr2v(arho1, n, i) * delij[n];
arg1j1 = arg1j1 - arr2v(arho1, n, j) * delij[n];
arg3i3 = arg3i3 + arr2v(arho3b, n, i) * delij[n];
arg3j3 = arg3j3 - arr2v(arho3b, n, j) * delij[n];
arg1i1 = arg1i1 + arr2v(arho1, n, i+1) * delij[n];
arg1j1 = arg1j1 - arr2v(arho1, n, j+1) * delij[n];
arg3i3 = arg3i3 + arr2v(arho3b, n, i+1) * delij[n];
arg3j3 = arg3j3 - arr2v(arho3b, n, j+1) * delij[n];
}
// rho0 terms
@ -218,25 +215,25 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
drho1dr2 = a1 * (drhoa1i - rhoa1i / rij) * arg1j1;
a1 = 2.0 * sij / rij;
for (m = 1; m <= 3; m++) {
drho1drm1[m] = a1 * rhoa1j * arr2v(arho1, m, i);
drho1drm2[m] = -a1 * rhoa1i * arr2v(arho1, m, j);
drho1drm1[m] = a1 * rhoa1j * arr2v(arho1, m, i+1);
drho1drm2[m] = -a1 * rhoa1i * arr2v(arho1, m, j+1);
}
// rho2 terms
a2 = 2 * sij / rij2;
drho2dr1 = a2 * (drhoa2j - 2 * rhoa2j / rij) * arg1i2 -
2.0 / 3.0 * arr1v(arho2b, i) * drhoa2j * sij;
2.0 / 3.0 * arho2b[i] * drhoa2j * sij;
drho2dr2 = a2 * (drhoa2i - 2 * rhoa2i / rij) * arg1j2 -
2.0 / 3.0 * arr1v(arho2b, j) * drhoa2i * sij;
2.0 / 3.0 * arho2b[j] * drhoa2i * sij;
a2 = 4 * sij / rij2;
for (m = 1; m <= 3; m++) {
drho2drm1[m] = 0.0;
drho2drm2[m] = 0.0;
for (n = 1; n <= 3; n++) {
drho2drm1[m] = drho2drm1[m] +
arr2v(arho2, this->vind2D[m][n], i) * delij[n];
arr2v(arho2, this->vind2D[m][n], i+1) * delij[n];
drho2drm2[m] = drho2drm2[m] -
arr2v(arho2, this->vind2D[m][n], j) * delij[n];
arr2v(arho2, this->vind2D[m][n], j+1) * delij[n];
}
drho2drm1[m] = a2 * rhoa2j * drho2drm1[m];
drho2drm2[m] = -a2 * rhoa2i * drho2drm2[m];
@ -260,25 +257,25 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
for (p = n; p <= 3; p++) {
arg = delij[n] * delij[p] * this->v2D[nv2];
drho3drm1[m] = drho3drm1[m] +
arr2v(arho3, this->vind3D[m][n][p], i) * arg;
arr2v(arho3, this->vind3D[m][n][p], i+1) * arg;
drho3drm2[m] = drho3drm2[m] +
arr2v(arho3, this->vind3D[m][n][p], j) * arg;
arr2v(arho3, this->vind3D[m][n][p], j+1) * arg;
nv2 = nv2 + 1;
}
}
drho3drm1[m] =
(a3 * drho3drm1[m] - a3a * arr2v(arho3b, m, i)) * rhoa3j;
(a3 * drho3drm1[m] - a3a * arr2v(arho3b, m, i+1)) * rhoa3j;
drho3drm2[m] =
(-a3 * drho3drm2[m] + a3a * arr2v(arho3b, m, j)) * rhoa3i;
(-a3 * drho3drm2[m] + a3a * arr2v(arho3b, m, j+1)) * rhoa3i;
}
// Compute derivatives of weighting functions t wrt rij
t1i = arr2v(t_ave, 1, i);
t2i = arr2v(t_ave, 2, i);
t3i = arr2v(t_ave, 3, i);
t1j = arr2v(t_ave, 1, j);
t2j = arr2v(t_ave, 2, j);
t3j = arr2v(t_ave, 3, j);
t1i = t_ave[i][0];
t2i = t_ave[i][1];
t3i = t_ave[i][2];
t1j = t_ave[j][0];
t2j = t_ave[j][1];
t3j = t_ave[j][2];
if (this->ialloy == 1) {
@ -288,18 +285,18 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
a2j = 0.0;
a3i = 0.0;
a3j = 0.0;
if (!iszero(arr2v(tsq_ave, 1, i)))
a1i = drhoa0j * sij / arr2v(tsq_ave, 1, i);
if (!iszero(arr2v(tsq_ave, 1, j)))
a1j = drhoa0i * sij / arr2v(tsq_ave, 1, j);
if (!iszero(arr2v(tsq_ave, 2, i)))
a2i = drhoa0j * sij / arr2v(tsq_ave, 2, i);
if (!iszero(arr2v(tsq_ave, 2, j)))
a2j = drhoa0i * sij / arr2v(tsq_ave, 2, j);
if (!iszero(arr2v(tsq_ave, 3, i)))
a3i = drhoa0j * sij / arr2v(tsq_ave, 3, i);
if (!iszero(arr2v(tsq_ave, 3, j)))
a3j = drhoa0i * sij / arr2v(tsq_ave, 3, j);
if (!iszero(tsq_ave[i][0]))
a1i = drhoa0j * sij / tsq_ave[i][0];
if (!iszero(tsq_ave[j][0]))
a1j = drhoa0i * sij / tsq_ave[j][0];
if (!iszero(tsq_ave[i][1]))
a2i = drhoa0j * sij / tsq_ave[i][1];
if (!iszero(tsq_ave[j][1]))
a2j = drhoa0i * sij / tsq_ave[j][1];
if (!iszero(tsq_ave[i][2]))
a3i = drhoa0j * sij / tsq_ave[i][2];
if (!iszero(tsq_ave[j][2]))
a3j = drhoa0i * sij / tsq_ave[j][2];
dt1dr1 = a1i * (this->t1_meam[eltj] -
t1i * pow(this->t1_meam[eltj], 2));
@ -326,11 +323,11 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
} else {
ai = 0.0;
if (!iszero(arr1v(rho0, i)))
ai = drhoa0j * sij / arr1v(rho0, i);
if (!iszero(rho0[i]))
ai = drhoa0j * sij / rho0[i];
aj = 0.0;
if (!iszero(arr1v(rho0, j)))
aj = drhoa0i * sij / arr1v(rho0, j);
if (!iszero(rho0[j]))
aj = drhoa0i * sij / rho0[j];
dt1dr1 = ai * (this->t1_meam[eltj] - t1i);
dt1dr2 = aj * (this->t1_meam[elti] - t1j);
@ -344,32 +341,32 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
get_shpfcn(shpi, this->lattce_meam[elti][elti]);
get_shpfcn(shpj, this->lattce_meam[eltj][eltj]);
drhodr1 =
arr1v(dgamma1, i) * drho0dr1 +
arr1v(dgamma2, i) * (dt1dr1 * arr1v(rho1, i) + t1i * drho1dr1 +
dt2dr1 * arr1v(rho2, i) + t2i * drho2dr1 +
dt3dr1 * arr1v(rho3, i) + t3i * drho3dr1) -
arr1v(dgamma3, i) *
dgamma1[i] * drho0dr1 +
dgamma2[i] * (dt1dr1 * rho1[i] + t1i * drho1dr1 +
dt2dr1 * rho2[i] + t2i * drho2dr1 +
dt3dr1 * rho3[i] + t3i * drho3dr1) -
dgamma3[i] *
(shpi[1] * dt1dr1 + shpi[2] * dt2dr1 + shpi[3] * dt3dr1);
drhodr2 =
arr1v(dgamma1, j) * drho0dr2 +
arr1v(dgamma2, j) * (dt1dr2 * arr1v(rho1, j) + t1j * drho1dr2 +
dt2dr2 * arr1v(rho2, j) + t2j * drho2dr2 +
dt3dr2 * arr1v(rho3, j) + t3j * drho3dr2) -
arr1v(dgamma3, j) *
dgamma1[j] * drho0dr2 +
dgamma2[j] * (dt1dr2 * rho1[j] + t1j * drho1dr2 +
dt2dr2 * rho2[j] + t2j * drho2dr2 +
dt3dr2 * rho3[j] + t3j * drho3dr2) -
dgamma3[j] *
(shpj[1] * dt1dr2 + shpj[2] * dt2dr2 + shpj[3] * dt3dr2);
for (m = 1; m <= 3; m++) {
drhodrm1[m] = 0.0;
drhodrm2[m] = 0.0;
drhodrm1[m] =
arr1v(dgamma2, i) *
dgamma2[i] *
(t1i * drho1drm1[m] + t2i * drho2drm1[m] + t3i * drho3drm1[m]);
drhodrm2[m] =
arr1v(dgamma2, j) *
dgamma2[j] *
(t1j * drho1drm2[m] + t2j * drho2drm2[m] + t3j * drho3drm2[m]);
}
// Compute derivatives wrt sij, but only if necessary
if (!iszero(arr1v(dscrfcn, fnoffset + jn))) {
if (!iszero(dscrfcn[fnoffset + jn])) {
drho0ds1 = rhoa0j;
drho0ds2 = rhoa0i;
a1 = 2.0 / rij;
@ -377,9 +374,9 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
drho1ds2 = a1 * rhoa1i * arg1j1;
a2 = 2.0 / rij2;
drho2ds1 =
a2 * rhoa2j * arg1i2 - 2.0 / 3.0 * arr1v(arho2b, i) * rhoa2j;
a2 * rhoa2j * arg1i2 - 2.0 / 3.0 * arho2b[i] * rhoa2j;
drho2ds2 =
a2 * rhoa2i * arg1j2 - 2.0 / 3.0 * arr1v(arho2b, j) * rhoa2i;
a2 * rhoa2i * arg1j2 - 2.0 / 3.0 * arho2b[j] * rhoa2i;
a3 = 2.0 / rij3;
a3a = 6.0 / (5.0 * rij);
drho3ds1 = a3 * rhoa3j * arg1i3 - a3a * rhoa3j * arg3i3;
@ -393,18 +390,12 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
a2j = 0.0;
a3i = 0.0;
a3j = 0.0;
if (!iszero(arr2v(tsq_ave, 1, i)))
a1i = rhoa0j / arr2v(tsq_ave, 1, i);
if (!iszero(arr2v(tsq_ave, 1, j)))
a1j = rhoa0i / arr2v(tsq_ave, 1, j);
if (!iszero(arr2v(tsq_ave, 2, i)))
a2i = rhoa0j / arr2v(tsq_ave, 2, i);
if (!iszero(arr2v(tsq_ave, 2, j)))
a2j = rhoa0i / arr2v(tsq_ave, 2, j);
if (!iszero(arr2v(tsq_ave, 3, i)))
a3i = rhoa0j / arr2v(tsq_ave, 3, i);
if (!iszero(arr2v(tsq_ave, 3, j)))
a3j = rhoa0i / arr2v(tsq_ave, 3, j);
if (!iszero(tsq_ave[i][0])) a1i = rhoa0j / tsq_ave[i][0];
if (!iszero(tsq_ave[j][0])) a1j = rhoa0i / tsq_ave[j][0];
if (!iszero(tsq_ave[i][1])) a2i = rhoa0j / tsq_ave[i][1];
if (!iszero(tsq_ave[j][1])) a2j = rhoa0i / tsq_ave[j][1];
if (!iszero(tsq_ave[i][2])) a3i = rhoa0j / tsq_ave[i][2];
if (!iszero(tsq_ave[j][2])) a3j = rhoa0i / tsq_ave[j][2];
dt1ds1 = a1i * (this->t1_meam[eltj] -
t1i * pow(this->t1_meam[eltj], 2));
@ -431,11 +422,11 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
} else {
ai = 0.0;
if (!iszero(arr1v(rho0, i)))
ai = rhoa0j / arr1v(rho0, i);
if (!iszero(rho0[i]))
ai = rhoa0j / rho0[i];
aj = 0.0;
if (!iszero(arr1v(rho0, j)))
aj = rhoa0i / arr1v(rho0, j);
if (!iszero(rho0[j]))
aj = rhoa0i / rho0[j];
dt1ds1 = ai * (this->t1_meam[eltj] - t1i);
dt1ds2 = aj * (this->t1_meam[elti] - t1j);
@ -446,44 +437,44 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
}
drhods1 =
arr1v(dgamma1, i) * drho0ds1 +
arr1v(dgamma2, i) * (dt1ds1 * arr1v(rho1, i) + t1i * drho1ds1 +
dt2ds1 * arr1v(rho2, i) + t2i * drho2ds1 +
dt3ds1 * arr1v(rho3, i) + t3i * drho3ds1) -
arr1v(dgamma3, i) *
dgamma1[i] * drho0ds1 +
dgamma2[i] * (dt1ds1 * rho1[i] + t1i * drho1ds1 +
dt2ds1 * rho2[i] + t2i * drho2ds1 +
dt3ds1 * rho3[i] + t3i * drho3ds1) -
dgamma3[i] *
(shpi[1] * dt1ds1 + shpi[2] * dt2ds1 + shpi[3] * dt3ds1);
drhods2 =
arr1v(dgamma1, j) * drho0ds2 +
arr1v(dgamma2, j) * (dt1ds2 * arr1v(rho1, j) + t1j * drho1ds2 +
dt2ds2 * arr1v(rho2, j) + t2j * drho2ds2 +
dt3ds2 * arr1v(rho3, j) + t3j * drho3ds2) -
arr1v(dgamma3, j) *
dgamma1[j] * drho0ds2 +
dgamma2[j] * (dt1ds2 * rho1[j] + t1j * drho1ds2 +
dt2ds2 * rho2[j] + t2j * drho2ds2 +
dt3ds2 * rho3[j] + t3j * drho3ds2) -
dgamma3[j] *
(shpj[1] * dt1ds2 + shpj[2] * dt2ds2 + shpj[3] * dt3ds2);
}
// Compute derivatives of energy wrt rij, sij and rij[3]
dUdrij = phip * sij + arr1v(frhop, i) * drhodr1 + arr1v(frhop, j) * drhodr2;
dUdrij = phip * sij + frhop[i] * drhodr1 + frhop[j] * drhodr2;
dUdsij = 0.0;
if (!iszero(arr1v(dscrfcn, fnoffset + jn))) {
dUdsij = phi + arr1v(frhop, i) * drhods1 + arr1v(frhop, j) * drhods2;
if (!iszero(dscrfcn[fnoffset + jn])) {
dUdsij = phi + frhop[i] * drhods1 + frhop[j] * drhods2;
}
for (m = 1; m <= 3; m++) {
dUdrijm[m] =
arr1v(frhop, i) * drhodrm1[m] + arr1v(frhop, j) * drhodrm2[m];
frhop[i] * drhodrm1[m] + frhop[j] * drhodrm2[m];
}
// Add the part of the force due to dUdrij and dUdsij
force = dUdrij * recip + dUdsij * arr1v(dscrfcn, fnoffset + jn);
force = dUdrij * recip + dUdsij * dscrfcn[fnoffset + jn];
for (m = 1; m <= 3; m++) {
forcem = delij[m] * force + dUdrijm[m];
arr2v(f, m, i) = arr2v(f, m, i) + forcem;
arr2v(f, m, j) = arr2v(f, m, j) - forcem;
f[i][m-1] = f[i][m-1] + forcem;
f[j][m-1] = f[j][m-1] - forcem;
}
// Tabulate per-atom virial as symmetrized stress tensor
if (*vflag_atom != 0) {
if (vflag_atom != 0) {
fi[1] = delij[1] * force + dUdrijm[1];
fi[2] = delij[2] * force + dUdrijm[2];
fi[3] = delij[3] * force + dUdrijm[3];
@ -494,47 +485,46 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
v[5] = -0.25 * (delij[1] * fi[3] + delij[3] * fi[1]);
v[6] = -0.25 * (delij[2] * fi[3] + delij[3] * fi[2]);
arr2v(vatom, 1, i) = arr2v(vatom, 1, i) + v[1];
arr2v(vatom, 2, i) = arr2v(vatom, 2, i) + v[2];
arr2v(vatom, 3, i) = arr2v(vatom, 3, i) + v[3];
arr2v(vatom, 4, i) = arr2v(vatom, 4, i) + v[4];
arr2v(vatom, 5, i) = arr2v(vatom, 5, i) + v[5];
arr2v(vatom, 6, i) = arr2v(vatom, 6, i) + v[6];
arr2v(vatom, 1, j) = arr2v(vatom, 1, j) + v[1];
arr2v(vatom, 2, j) = arr2v(vatom, 2, j) + v[2];
arr2v(vatom, 3, j) = arr2v(vatom, 3, j) + v[3];
arr2v(vatom, 4, j) = arr2v(vatom, 4, j) + v[4];
arr2v(vatom, 5, j) = arr2v(vatom, 5, j) + v[5];
arr2v(vatom, 6, j) = arr2v(vatom, 6, j) + v[6];
vatom[i][0] = vatom[i][0] + v[1];
vatom[i][1] = vatom[i][1] + v[2];
vatom[i][2] = vatom[i][2] + v[3];
vatom[i][3] = vatom[i][3] + v[4];
vatom[i][4] = vatom[i][4] + v[5];
vatom[i][5] = vatom[i][5] + v[6];
vatom[j][0] = vatom[j][0] + v[1];
vatom[j][1] = vatom[j][1] + v[2];
vatom[j][2] = vatom[j][2] + v[3];
vatom[j][3] = vatom[j][3] + v[4];
vatom[j][4] = vatom[j][4] + v[5];
vatom[j][5] = vatom[j][5] + v[6];
}
// Now compute forces on other atoms k due to change in sij
if (iszero(sij) || iszero(sij - 1.0))
continue; //: cont jn loop
for (kn = 1; kn <= *numneigh_full; kn++) {
k = arr1v(firstneigh_full, kn);
eltk = fmap[arr1v(type, k)];
for (kn = 0; kn < numneigh_full; kn++) {
k = firstneigh_full[kn];
eltk = fmap[type[k]];
if (k != j && eltk >= 0) {
dsij(i, j, k, jn, *numneigh, rij2, &dsij1, &dsij2, *ntype,
dsij(i, j, k, jn, numneigh, rij2, &dsij1, &dsij2, ntype,
type, fmap, x, &scrfcn[fnoffset], &fcpair[fnoffset]);
if (!iszero(dsij1) || !iszero(dsij2)) {
force1 = dUdsij * dsij1;
force2 = dUdsij * dsij2;
for (m = 1; m <= 3; m++) {
delik[m] = arr2v(x, m, k) - arr2v(x, m, i);
deljk[m] = arr2v(x, m, k) - arr2v(x, m, j);
delik[m] = arr2v(x, m, k+1) - arr2v(x, m, i+1);
deljk[m] = arr2v(x, m, k+1) - arr2v(x, m, j+1);
}
for (m = 1; m <= 3; m++) {
arr2v(f, m, i) = arr2v(f, m, i) + force1 * delik[m];
arr2v(f, m, j) = arr2v(f, m, j) + force2 * deljk[m];
arr2v(f, m, k) =
arr2v(f, m, k) - force1 * delik[m] - force2 * deljk[m];
arr2v(f, m, i+1) = arr2v(f, m, i+1) + force1 * delik[m];
arr2v(f, m, j+1) = arr2v(f, m, j+1) + force2 * deljk[m];
arr2v(f, m, k+1) = arr2v(f, m, k+1) - force1 * delik[m] - force2 * deljk[m];
}
// Tabulate per-atom virial as symmetrized stress tensor
if (*vflag_atom != 0) {
if (vflag_atom != 0) {
fi[1] = force1 * delik[1];
fi[2] = force1 * delik[2];
fi[3] = force1 * delik[3];
@ -551,24 +541,24 @@ MEAM::meam_force(int* iptr, int* eflag_either, int* eflag_global,
v[6] = -sixth * (delik[2] * fi[3] + deljk[2] * fj[3] +
delik[3] * fi[2] + deljk[3] * fj[2]);
arr2v(vatom, 1, i) = arr2v(vatom, 1, i) + v[1];
arr2v(vatom, 2, i) = arr2v(vatom, 2, i) + v[2];
arr2v(vatom, 3, i) = arr2v(vatom, 3, i) + v[3];
arr2v(vatom, 4, i) = arr2v(vatom, 4, i) + v[4];
arr2v(vatom, 5, i) = arr2v(vatom, 5, i) + v[5];
arr2v(vatom, 6, i) = arr2v(vatom, 6, i) + v[6];
arr2v(vatom, 1, j) = arr2v(vatom, 1, j) + v[1];
arr2v(vatom, 2, j) = arr2v(vatom, 2, j) + v[2];
arr2v(vatom, 3, j) = arr2v(vatom, 3, j) + v[3];
arr2v(vatom, 4, j) = arr2v(vatom, 4, j) + v[4];
arr2v(vatom, 5, j) = arr2v(vatom, 5, j) + v[5];
arr2v(vatom, 6, j) = arr2v(vatom, 6, j) + v[6];
arr2v(vatom, 1, k) = arr2v(vatom, 1, k) + v[1];
arr2v(vatom, 2, k) = arr2v(vatom, 2, k) + v[2];
arr2v(vatom, 3, k) = arr2v(vatom, 3, k) + v[3];
arr2v(vatom, 4, k) = arr2v(vatom, 4, k) + v[4];
arr2v(vatom, 5, k) = arr2v(vatom, 5, k) + v[5];
arr2v(vatom, 6, k) = arr2v(vatom, 6, k) + v[6];
vatom[i][0] = vatom[i][0] + v[1];
vatom[i][1] = vatom[i][1] + v[2];
vatom[i][2] = vatom[i][2] + v[3];
vatom[i][3] = vatom[i][3] + v[4];
vatom[i][4] = vatom[i][4] + v[5];
vatom[i][5] = vatom[i][5] + v[6];
vatom[j][0] = vatom[j][0] + v[1];
vatom[j][1] = vatom[j][1] + v[2];
vatom[j][2] = vatom[j][2] + v[3];
vatom[j][3] = vatom[j][3] + v[4];
vatom[j][4] = vatom[j][4] + v[5];
vatom[j][5] = vatom[j][5] + v[6];
vatom[k][0] = vatom[k][0] + v[1];
vatom[k][1] = vatom[k][1] + v[2];
vatom[k][2] = vatom[k][2] + v[3];
vatom[k][3] = vatom[k][3] + v[4];
vatom[k][4] = vatom[k][4] + v[5];
vatom[k][5] = vatom[k][5] + v[6];
}
}
}

62
src/USER-MEAMC/pair_meamc.cpp
View File

@ -129,24 +129,17 @@ void PairMEAMC::compute(int eflag, int vflag)
int *type = atom->type;
int ntype = atom->ntypes;
// change neighbor list indices to Fortran indexing
neigh_c2f(inum_half,ilist_half,numneigh_half,firstneigh_half);
neigh_c2f(inum_half,ilist_half,numneigh_full,firstneigh_full);
// 3 stages of MEAM calculation
// loop over my atoms followed by communication
int ifort;
int offset = 0;
errorflag = 0;
for (ii = 0; ii < inum_half; ii++) {
i = ilist_half[ii];
ifort = i+1;
meam_inst->meam_dens_init(&ifort,&ntype,type,map,x,
&numneigh_half[i],firstneigh_half[i],
&numneigh_full[i],firstneigh_full[i],
meam_inst->meam_dens_init(i,ntype,type,map,x,
numneigh_half[i],firstneigh_half[i],
numneigh_full[i],firstneigh_full[i],
offset,
&errorflag);
if (errorflag) {
@ -159,8 +152,8 @@ void PairMEAMC::compute(int eflag, int vflag)
comm->reverse_comm_pair(this);
meam_inst->meam_dens_final(&nlocal,&eflag_either,&eflag_global,&eflag_atom,
&eng_vdwl,eatom,&ntype,type,map,
meam_inst->meam_dens_final(nlocal,eflag_either,eflag_global,eflag_atom,
&eng_vdwl,eatom,ntype,type,map,
&errorflag);
if (errorflag) {
char str[128];
@ -181,11 +174,10 @@ void PairMEAMC::compute(int eflag, int vflag)
for (ii = 0; ii < inum_half; ii++) {
i = ilist_half[ii];
ifort = i+1;
meam_inst->meam_force(&ifort,&eflag_either,&eflag_global,&eflag_atom,
&vflag_atom,&eng_vdwl,eatom,&ntype,type,map,x,
&numneigh_half[i],firstneigh_half[i],
&numneigh_full[i],firstneigh_full[i],
meam_inst->meam_force(i,eflag_either,eflag_global,eflag_atom,
vflag_atom,&eng_vdwl,eatom,ntype,type,map,x,
numneigh_half[i],firstneigh_half[i],
numneigh_full[i],firstneigh_full[i],
offset,
f,vptr,&errorflag);
if (errorflag) {
@ -196,11 +188,6 @@ void PairMEAMC::compute(int eflag, int vflag)
offset += numneigh_half[i];
}
// change neighbor list indices back to C indexing
neigh_f2c(inum_half,ilist_half,numneigh_half,firstneigh_half);
neigh_f2c(inum_half,ilist_half,numneigh_full,firstneigh_full);
if (vflag_fdotr) virial_fdotr_compute();
}
@ -806,34 +793,3 @@ void PairMEAMC::neigh_strip(int inum, int *ilist,
for (j = 0; j < jnum; j++) jlist[j] &= NEIGHMASK;
}
}
/* ----------------------------------------------------------------------
toggle neighbor list indices between zero- and one-based values
needed for access by MEAM Fortran library
------------------------------------------------------------------------- */
void PairMEAMC::neigh_f2c(int inum, int *ilist, int *numneigh, int **firstneigh)
{
int i,j,ii,jnum;
int *jlist;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
jlist = firstneigh[i];
jnum = numneigh[i];
for (j = 0; j < jnum; j++) jlist[j]--;
}
}
void PairMEAMC::neigh_c2f(int inum, int *ilist, int *numneigh, int **firstneigh)
{
int i,j,ii,jnum;
int *jlist;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
jlist = firstneigh[i];
jnum = numneigh[i];
for (j = 0; j < jnum; j++) jlist[j]++;
}
}

2
src/USER-MEAMC/pair_meamc.h
View File

@ -54,8 +54,6 @@ class PairMEAMC : public Pair {
void allocate();
void read_files(char *, char *);
void neigh_strip(int, int *, int *, int **);
void neigh_f2c(int, int *, int *, int **);
void neigh_c2f(int, int *, int *, int **);
};
}