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update to fix orient/eco from the authors

This commit is contained in:
Axel Kohlmeyer 2020-06-09 14:38:55 -04:00
parent ee5e479343
commit 89fb194f51
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GPG Key ID: D9B44E93BF0C375A
3 changed files with 63 additions and 132 deletions
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5
doc/src/fix_orient_eco.rst
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@ -76,10 +76,7 @@ grain boundaries, it might be beneficial to increase the cutoff in order to get
precise identification of the atoms surrounding. However, computation time will
increase as more atoms are considered in the order parameter and force computation.
It is also worth noting that the cutoff radius must not exceed the communication
distance for ghost atoms in LAMMPS. Currently however, the method stores results
for order parameter and force computations in statically allocated arrays to
increase efficiency such that the user is limited to 24 nearest neighbors.
This is more than enough in most applications. With orientationsFile, the
distance for ghost atoms in LAMMPS. With orientationsFile, the
6 oriented crystal basis vectors is specified. Each line of the input file
contains the three components of a primitive lattice vector oriented according to
the grain orientation in the simulation box. The first (last) three lines correspond

186
src/USER-MISC/fix_orient_eco.cpp
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@ -53,15 +53,10 @@ static const char cite_fix_orient_eco[] =
" url = {https://doi.org/10.1016/j.commatsci.2020.109774}\n"
"}\n\n";
#define FIX_ORIENT_ECO_MAX_NEIGH 24
struct FixOrientECO::Nbr {
int n; // # of neighbors
int id[FIX_ORIENT_ECO_MAX_NEIGH]; // IDs of each neighbor
double duchi; // potential derivative
double delta[FIX_ORIENT_ECO_MAX_NEIGH][3]; // difference vectors
double real_phi[2][3]; // real part of wave function
double imag_phi[2][3]; // imaginary part of wave function
double duchi; // potential derivative
double real_phi[2][3]; // real part of wave function
double imag_phi[2][3]; // imaginary part of wave function
};
/* ---------------------------------------------------------------------- */
@ -132,8 +127,7 @@ FixOrientECO::FixOrientECO(LAMMPS *lmp, int narg, char **arg) :
MPI_Bcast(&inv_eta, 1, MPI_DOUBLE, 0, world); // communicate inverse threshold
// set comm size needed by this Fix
comm_forward = 2 + 4 * FIX_ORIENT_ECO_MAX_NEIGH; // data of Nbr struct that needs to be communicated in any case
if (u_0 != 0) comm_forward += 12; // real_phi and imag_phi needed for force computation
if (u_0 != 0) comm_forward = sizeof(Nbr) / sizeof(double);
added_energy = 0.0; // initial energy
@ -229,11 +223,9 @@ void FixOrientECO::post_force(int /* vflag */) {
int k; // variable to loop over 3 reciprocal directions
int lambda; // variable to loop over 2 crystals
int dim; // variable to loop over 3 spatial components
int n; // stores current number of neighbors
double dx, dy, dz; // stores current interatomic vector
double squared_distance; // stores current squared distance
double chi; // stores current order parameter
double *delta; // pointer to current interatomic vector (POSSIBLY OMIT)
double weight; // stores current weight function
double scalar_product; // stores current scalar product
double omega; // phase of sine transition
@ -267,16 +259,20 @@ void FixOrientECO::post_force(int /* vflag */) {
array_atom = order;
}
// loop over owned atoms and build Nbr data structure of neighbors
// use full neighbor list
// loop over owned atoms and compute order parameter
for (ii = 0; ii < inum; ++ii) {
i = ilist[ii];
jlist = firstneigh[i];
jnum = numneigh[i];
// initializations
chi = 0.0;
for (k = 0; k < 3; ++k) {
nbr[i].real_phi[0][k] = nbr[i].real_phi[1][k] = 0.0;
nbr[i].imag_phi[0][k] = nbr[i].imag_phi[1][k] = 0.0;
}
// loop over all neighbors of atom i
// for those within squared_cutoff, store id and delta vectors
n = 0;
for (jj = 0; jj < jnum; ++jj) {
j = jlist[jj];
j &= NEIGHMASK;
@ -288,43 +284,15 @@ void FixOrientECO::post_force(int /* vflag */) {
squared_distance = dx * dx + dy * dy + dz * dz;
if (squared_distance < squared_cutoff) {
if (n >= FIX_ORIENT_ECO_MAX_NEIGH) {
error->one(FLERR, "Fix orient/eco maximal number of neighbors exceeded");
}
nbr[i].id[n] = j;
nbr[i].delta[n][0] = dx;
nbr[i].delta[n][1] = dy;
nbr[i].delta[n][2] = dz;
++n;
}
}
nbr[i].n = n;
}
squared_distance *= inv_squared_cutoff;
weight = squared_distance * (squared_distance - 2.0) + 1.0;
// loop over owned atoms and compute order parameter
// use short neighbor lists
for (ii = 0; ii < inum; ++ii) {
i = ilist[ii];
// initializations
n = nbr[i].n;
chi = 0.0;
for (k = 0; k < 3; ++k) {
nbr[i].real_phi[0][k] = nbr[i].real_phi[1][k] = 0.0;
nbr[i].imag_phi[0][k] = nbr[i].imag_phi[1][k] = 0.0;
}
// loop over all neighbors of atom i
for (j = 0; j < n; ++j) {
delta = &nbr[i].delta[j][0];
squared_distance = (delta[0] * delta[0] + delta[1] * delta[1] + delta[2] * delta[2]) * inv_squared_cutoff;
weight = squared_distance * (squared_distance - 2.0) + 1.0;
for (k = 0; k < 3; ++k) {
for (lambda = 0; lambda < 2; ++lambda) {
scalar_product = reciprocal_vectors[lambda][k][0] * delta[0] + reciprocal_vectors[lambda][k][1] * delta[1] + reciprocal_vectors[lambda][k][2] * delta[2];
nbr[i].real_phi[lambda][k] += weight * cos(scalar_product);
nbr[i].imag_phi[lambda][k] += weight * sin(scalar_product);
for (k = 0; k < 3; ++k) {
scalar_product = reciprocal_vectors[lambda][k][0] * dx + reciprocal_vectors[lambda][k][1] * dy + reciprocal_vectors[lambda][k][2] * dz;
nbr[i].real_phi[lambda][k] += weight * cos(scalar_product);
nbr[i].imag_phi[lambda][k] += weight * sin(scalar_product);
}
}
}
}
@ -370,7 +338,6 @@ void FixOrientECO::post_force(int /* vflag */) {
double gradient_ii_sin[2][3][3]; // gradient ii sine term
double gradient_ij_vec[2][3][3]; // gradient ij vector term
double gradient_ij_sca[2][3]; // gradient ij scalar term
int idj; // stores id of neighbor j
double weight_gradient_prefactor; // gradient prefactor
double weight_gradient[3]; // gradient of weight
double cos_scalar_product; // cosine of scalar product
@ -383,12 +350,15 @@ void FixOrientECO::post_force(int /* vflag */) {
if (u_0 != 0.0) {
// communicate to acquire nbr data for ghost atoms
comm->forward_comm_fix(this);
// loop over owned atoms and compute force
// use short neighbor lists
// loop over all atoms
for (ii = 0; ii < inum; ++ii) {
i = ilist[ii];
jlist = firstneigh[i];
jnum = numneigh[i];
const bool no_boundary_atom = (nbr[i].duchi == 0.0);
// skip atoms not in group
if (!(mask[i] & groupbit)) continue;
@ -403,41 +373,46 @@ void FixOrientECO::post_force(int /* vflag */) {
gradient_ij_sca[lambda][k] = 0.0;
}
}
n = nbr[i].n;
const bool boundary_atom = (nbr[i].duchi != 0.0);
// loop over all neighbors of atom i
for (j = 0; j < n; ++j) {
idj = nbr[i].id[j];
// compute force on atom i if it is close to boundary
if ((nbr[idj].duchi != 0.0) || boundary_atom) {
delta = &nbr[i].delta[j][0];
squared_distance = (delta[0] * delta[0] + delta[1] * delta[1] + delta[2] * delta[2]) * inv_squared_cutoff;
// for those within squared_cutoff, compute force
for (jj = 0; jj < jnum; ++jj) {
j = jlist[jj];
j &= NEIGHMASK;
// do not compute force on atom i if it is far from boundary
if ((nbr[j].duchi == 0.0) && no_boundary_atom) continue;
// vector difference
dx = x[i][0] - x[j][0];
dy = x[i][1] - x[j][1];
dz = x[i][2] - x[j][2];
squared_distance = dx * dx + dy * dy + dz * dz;
if (squared_distance < squared_cutoff) {
// compute force on atom i
// need weight and its gradient
squared_distance *= inv_squared_cutoff;
weight = squared_distance * (squared_distance - 2.0) + 1.0;
weight_gradient_prefactor = 4.0 * (squared_distance - 1.0) * inv_squared_cutoff;
for (dim = 0; dim < 3; ++dim) {
weight_gradient[dim] = weight_gradient_prefactor * delta[dim];
}
weight_gradient[0] = weight_gradient_prefactor * dx;
weight_gradient[1] = weight_gradient_prefactor * dy;
weight_gradient[2] = weight_gradient_prefactor * dz;
// (1) compute scalar product and sine and cosine of it
// (2) compute product of sine and cosine with gradient of weight function
// (3) compute gradient_ii_cos and gradient_ii_sin by summing up result of (2)
// (4) compute gradient_ij_vec and gradient_ij_sca
for (k = 0; k < 3; ++k) {
for (lambda = 0; lambda < 2; ++lambda) {
scalar_product = reciprocal_vectors[lambda][k][0] * delta[0] + reciprocal_vectors[lambda][k][1] * delta[1] + reciprocal_vectors[lambda][k][2] * delta[2];
for (lambda = 0; lambda < 2; ++lambda) {
for (k = 0; k < 3; ++k) {
scalar_product = reciprocal_vectors[lambda][k][0] * dx + reciprocal_vectors[lambda][k][1] * dy + reciprocal_vectors[lambda][k][2] * dz;
cos_scalar_product = cos(scalar_product);
sin_scalar_product = sin(scalar_product);
for (dim = 0; dim < 3; ++dim) {
gradient_ii_cos[lambda][k][dim] += (gcos_scalar_product = weight_gradient[dim] * cos_scalar_product);
gradient_ii_sin[lambda][k][dim] += (gsin_scalar_product = weight_gradient[dim] * sin_scalar_product);
gradient_ij_vec[lambda][k][dim] += (nbr[idj].real_phi[lambda][k] * gcos_scalar_product - nbr[idj].imag_phi[lambda][k] * gsin_scalar_product);
gradient_ij_vec[lambda][k][dim] += (nbr[j].real_phi[lambda][k] * gcos_scalar_product - nbr[j].imag_phi[lambda][k] * gsin_scalar_product);
}
gradient_ij_sca[lambda][k] += weight * (nbr[idj].real_phi[lambda][k] * sin_scalar_product + nbr[idj].imag_phi[lambda][k] * cos_scalar_product);
gradient_ij_sca[lambda][k] += weight * (nbr[j].real_phi[lambda][k] * sin_scalar_product + nbr[j].imag_phi[lambda][k] * cos_scalar_product);
}
}
}
@ -470,38 +445,14 @@ double FixOrientECO::compute_scalar() {
/* ---------------------------------------------------------------------- */
int FixOrientECO::pack_forward_comm(int n, int *list, double *buf,
int /* pbc_flag */, int * /* pbc */) {
int ii, i, jj, j, k, num;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
int FixOrientECO::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int */*pbc*/) {
int i, j;
int m = 0;
for (i = 0; i < n; ++i) {
k = list[i];
num = nbr[k].n;
buf[m++] = num;
buf[m++] = nbr[k].duchi;
if (u_0 != 0.0) {
for (ii = 0; ii < 2; ++ii) {
for (jj = 0; jj < 3; ++jj) {
buf[m++] = nbr[i].real_phi[ii][jj];
buf[m++] = nbr[i].imag_phi[ii][jj];
}
}
}
for (j = 0; j < num; ++j) {
buf[m++] = nbr[k].delta[j][0];
buf[m++] = nbr[k].delta[j][1];
buf[m++] = nbr[k].delta[j][2];
// id stored in buf needs to be global ID
buf[m++] =ubuf(tag[nbr[k].id[j]]).i;
}
j = list[i];
*((Nbr*)&buf[m]) = nbr[j];
m += sizeof(Nbr)/sizeof(double);
}
return m;
@ -510,30 +461,13 @@ int FixOrientECO::pack_forward_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
void FixOrientECO::unpack_forward_comm(int n, int first, double *buf) {
int ii, i, jj, j, num;
int i;
int last = first + n;
int m = 0;
for (i = first; i < last; ++i) {
nbr[i].n = num = static_cast<int> (buf[m++]);
nbr[i].duchi = buf[m++];
if (u_0 != 0.0) {
for (ii = 0; ii < 2; ++ii) {
for (jj = 0; jj < 3; ++jj) {
nbr[i].real_phi[ii][jj] = buf[m++];
nbr[i].imag_phi[ii][jj] = buf[m++];
}
}
}
for (j = 0; j < num; ++j) {
nbr[i].delta[j][0] = buf[m++];
nbr[i].delta[j][1] = buf[m++];
nbr[i].delta[j][2] = buf[m++];
// convert from global to closest local id
nbr[i].id[j] = domain->closest_image(i,atom->map(ubuf(buf[m++]).i));
}
nbr[i] = *((Nbr*) &buf[m]);
m += sizeof(Nbr) / sizeof(double);
}
}

4
src/USER-MISC/fix_orient_eco.h
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@ -40,7 +40,7 @@ class FixOrientECO : public Fix {
double memory_usage();
private:
struct Nbr; // private struct for managing precomputed terms
struct Nbr; // forward declaration. private struct for managing precomputed terms
int me; // this processors rank
int nmax; // maximal # of owned + ghost atoms on this processor
@ -66,7 +66,7 @@ class FixOrientECO : public Fix {
double norm_fac; // normalization constant
double inv_norm_fac; // inverse normalization constant
Nbr *nbr; // pointer on array of Nbr structs
Nbr *nbr; // pointer on array of precomputed terms
class NeighList *list; // LAMMPS' neighbor list
void get_reciprocal(); // calculate reciprocal lattice vectors