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DallasTrinkle authoredDallasTrinkle authored
pair_meam_spline.cpp 27.53 KiB
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Alexander Stukowski (LLNL), alex@stukowski.com
Will Tipton (Cornell), wwt26@cornell.edu
Dallas R. Trinkle (UIUC), dtrinkle@illinois.edu
Pinchao Zhang (UIUC)
see LLNL copyright notice at bottom of file
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
* File history of changes:
* 25-Oct-10 - AS: First code version.
* 17-Feb-11 - AS: Several optimizations (introduced MEAM2Body struct).
* 25-Mar-11 - AS: Fixed calculation of per-atom virial stress.
* 11-Apr-11 - AS: Adapted code to new memory management of LAMMPS.
* 24-Sep-11 - AS: Adapted code to new interface of Error::one() function.
* 20-Jun-13 - WT: Added support for multiple species types
* 25-Apr-17 - DRT/PZ: Modified format of multiple species type to
conform with pairing, updated to LAMMPS style
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_meam_spline.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include <iostream>
using namespace std;
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairMEAMSpline::PairMEAMSpline(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
restartinfo = 0;
one_coeff = 1;
nelements = 0;
elements = NULL;
Uprime_values = NULL;
nmax = 0;
maxNeighbors = 0;
twoBodyInfo = NULL;
comm_forward = 1; comm_reverse = 0;
}
/* ---------------------------------------------------------------------- */
PairMEAMSpline::~PairMEAMSpline()
{
if (elements)
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
delete[] twoBodyInfo;
memory->destroy(Uprime_values);
if(allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete[] phis;
delete[] Us;
delete[] rhos;
delete[] fs;
delete[] gs;
delete[] zero_atom_energies;
delete [] map;
}
}
/* ---------------------------------------------------------------------- */
void PairMEAMSpline::compute(int eflag, int vflag)
{
double** const x = atom->x;
double** forces = atom->f;
if (eflag || vflag) {
ev_setup(eflag, vflag);
} else {
evflag = vflag_fdotr = eflag_global = 0;
vflag_global = eflag_atom = vflag_atom = 0;
}
// Grow per-atom array if necessary
if (atom->nmax > nmax) {
memory->destroy(Uprime_values);
nmax = atom->nmax;
memory->create(Uprime_values,nmax,"pair:Uprime");
}
// Determine the maximum number of neighbors a single atom has
int newMaxNeighbors = 0;
for(int ii = 0; ii < listfull->inum; ii++) {
int jnum = listfull->numneigh[listfull->ilist[ii]];
if(jnum > newMaxNeighbors)
newMaxNeighbors = jnum;
}
// Allocate array for temporary bond info
if(newMaxNeighbors > maxNeighbors) {
maxNeighbors = newMaxNeighbors;
delete[] twoBodyInfo;
twoBodyInfo = new MEAM2Body[maxNeighbors];
}
// Sum three-body contributions to charge density and // the embedding energy
for(int ii = 0; ii < listfull->inum; ii++) {
int i = listfull->ilist[ii];
int numBonds = 0;
// compute charge density and numBonds
// double rho_value = compute_three_body_contrib_to_charge_density(i, numBonds);
MEAM2Body* nextTwoBodyInfo = twoBodyInfo;
double rho_value = 0;
for(int jj = 0; jj < listfull->numneigh[i]; jj++) {
int j = listfull->firstneigh[i][jj];
j &= NEIGHMASK;
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) {
double rij = sqrt(rij_sq);
double partial_sum = 0;
nextTwoBodyInfo->tag = j;
nextTwoBodyInfo->r = rij;
nextTwoBodyInfo->f = fs[i_to_potl(j)].eval(rij, nextTwoBodyInfo->fprime);
nextTwoBodyInfo->del[0] = jdelx / rij;
nextTwoBodyInfo->del[1] = jdely / rij;
nextTwoBodyInfo->del[2] = jdelz / rij;
for(int kk = 0; kk < numBonds; kk++) {
const MEAM2Body& bondk = twoBodyInfo[kk];
double cos_theta = (nextTwoBodyInfo->del[0]*bondk.del[0] +
nextTwoBodyInfo->del[1]*bondk.del[1] +
nextTwoBodyInfo->del[2]*bondk.del[2]);
partial_sum += bondk.f * gs[ij_to_potl(j,bondk.tag)].eval(cos_theta);
}
rho_value += nextTwoBodyInfo->f * partial_sum;
rho_value += rhos[i_to_potl(j)].eval(rij);
numBonds++;
nextTwoBodyInfo++;
}
}
// Compute embedding energy and its derivative
// double Uprime_i = compute_embedding_energy_and_deriv(eflag, i, rho_value);
double Uprime_i;
double embeddingEnergy = Us[i_to_potl(i)].eval(rho_value, Uprime_i)
- zero_atom_energies[i_to_potl(i)];
Uprime_values[i] = Uprime_i;
if(eflag) {
if(eflag_global)
eng_vdwl += embeddingEnergy;
if(eflag_atom)
eatom[i] += embeddingEnergy;
}
// Compute three-body contributions to force
// compute_three_body_contrib_to_forces(i, numBonds, Uprime_i);
double forces_i[3] = {0, 0, 0};
for(int jj = 0; jj < numBonds; jj++) {
const MEAM2Body bondj = twoBodyInfo[jj];
double rij = bondj.r;
int j = bondj.tag;
double f_rij_prime = bondj.fprime;
double f_rij = bondj.f;
double forces_j[3] = {0, 0, 0};
MEAM2Body const* bondk = twoBodyInfo;
for(int kk = 0; kk < jj; kk++, ++bondk) {
double rik = bondk->r;
double cos_theta = (bondj.del[0]*bondk->del[0] +
bondj.del[1]*bondk->del[1] +
bondj.del[2]*bondk->del[2]);
double g_prime;
double g_value = gs[ij_to_potl(j,bondk->tag)].eval(cos_theta, g_prime);
double f_rik_prime = bondk->fprime;
double f_rik = bondk->f;
double fij = -Uprime_i * g_value * f_rik * f_rij_prime;
double fik = -Uprime_i * g_value * f_rij * f_rik_prime;
double prefactor = Uprime_i * f_rij * f_rik * g_prime;
double prefactor_ij = prefactor / rij;
double prefactor_ik = prefactor / rik;
fij += prefactor_ij * cos_theta;
fik += prefactor_ik * cos_theta;
double fj[3], fk[3];
fj[0] = bondj.del[0] * fij - bondk->del[0] * prefactor_ij;
fj[1] = bondj.del[1] * fij - bondk->del[1] * prefactor_ij;
fj[2] = bondj.del[2] * fij - bondk->del[2] * prefactor_ij;
forces_j[0] += fj[0];
forces_j[1] += fj[1];
forces_j[2] += fj[2];
fk[0] = bondk->del[0] * fik - bondj.del[0] * prefactor_ik;
fk[1] = bondk->del[1] * fik - bondj.del[1] * prefactor_ik;
fk[2] = bondk->del[2] * fik - bondj.del[2] * prefactor_ik;
forces_i[0] -= fk[0];
forces_i[1] -= fk[1];
forces_i[2] -= fk[2];
int k = bondk->tag;
forces[k][0] += fk[0];
forces[k][1] += fk[1];
forces[k][2] += fk[2];
if(evflag) {
double delta_ij[3];
double delta_ik[3];
delta_ij[0] = bondj.del[0] * rij;
delta_ij[1] = bondj.del[1] * rij;
delta_ij[2] = bondj.del[2] * rij;
delta_ik[0] = bondk->del[0] * rik;
delta_ik[1] = bondk->del[1] * rik;
delta_ik[2] = bondk->del[2] * rik;
ev_tally3(i, j, k, 0.0, 0.0, fj, fk, delta_ij, delta_ik);
}
}
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];
}
forces[i][0] += forces_i[0]; forces[i][1] += forces_i[1];
forces[i][2] += forces_i[2];
}
// Communicate U'(rho) values
comm->forward_comm_pair(this);
// Compute two-body pair interactions
// compute_two_body_pair_interactions();
for(int ii = 0; ii < listhalf->inum; ii++) {
int i = listhalf->ilist[ii];
for(int jj = 0; jj < listhalf->numneigh[i]; jj++) {
int j = listhalf->firstneigh[i][jj];
j &= NEIGHMASK;
double jdel[3];
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) {
double rij = sqrt(rij_sq);
double rho_prime_i,rho_prime_j;
rhos[i_to_potl(i)].eval(rij,rho_prime_i);
rhos[i_to_potl(j)].eval(rij,rho_prime_j);
double fpair = rho_prime_j * Uprime_values[i] + rho_prime_i*Uprime_values[j];
double pair_pot_deriv;
double pair_pot = phis[ij_to_potl(i,j)].eval(rij, pair_pot_deriv);
fpair += pair_pot_deriv;
// Divide by r_ij to get forces from gradient
fpair /= rij;
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]);
}
}
}
if(vflag_fdotr)
virial_fdotr_compute();
}
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 = 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);
if(rij_sq < cutoff*cutoff) {
double rij = sqrt(rij_sq);
rho_value += rhos[i_to_potl(j)].eval(rij);
}
}
return rho_value;
}
double PairMEAMSpline::three_body_density(int i)
{
double rho_value = 0;
int numBonds=0;
double** const x = atom->x;
MEAM2Body* nextTwoBodyInfo = twoBodyInfo;
for(int jj = 0; jj < listfull->numneigh[i]; jj++) {
int j = listfull->firstneigh[i][jj];
j &= NEIGHMASK;
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) {
double rij = sqrt(rij_sq);
double partial_sum = 0;
nextTwoBodyInfo->tag = j;
nextTwoBodyInfo->r = rij;
nextTwoBodyInfo->f = fs[i_to_potl(j)].eval(rij, nextTwoBodyInfo->fprime);
nextTwoBodyInfo->del[0] = jdelx / rij;
nextTwoBodyInfo->del[1] = jdely / rij;
nextTwoBodyInfo->del[2] = jdelz / rij;
for(int kk = 0; kk < numBonds; kk++) {
const MEAM2Body& bondk = twoBodyInfo[kk];
double cos_theta = (nextTwoBodyInfo->del[0]*bondk.del[0] +
nextTwoBodyInfo->del[1]*bondk.del[1] +
nextTwoBodyInfo->del[2]*bondk.del[2]);
partial_sum += bondk.f * gs[ij_to_potl(j,bondk.tag)].eval(cos_theta);
}
rho_value += nextTwoBodyInfo->f * partial_sum;
numBonds++;
nextTwoBodyInfo++;
}
}
return rho_value;
}
/* ----------------------------------------------------------------------
helper functions to map atom types to potential array indices
------------------------------------------------------------------------- */
int PairMEAMSpline::ij_to_potl(int i, int j) {
int n = atom->ntypes;
int itype = atom->type[i];
int jtype = atom->type[j];
return jtype - 1 + (itype-1)*n - (itype-1)*itype/2;
}
int PairMEAMSpline::i_to_potl(int i) {
int itype = atom->type[i];
return itype - 1;
}
/* ---------------------------------------------------------------------- */
void PairMEAMSpline::allocate()
{
allocated = 1;
int n = nelements;
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
int nmultichoose2 = n*(n+1)/2;
//Change the functional form
//f_ij->f_i
//g_i(cos\theta_ijk)->g_jk(cos\theta_ijk)
phis = new SplineFunction[nmultichoose2];
Us = new SplineFunction[n];
rhos = new SplineFunction[n];
fs = new SplineFunction[n];
gs = new SplineFunction[nmultichoose2];
zero_atom_energies = new double[n];
map = new int[n+1];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairMEAMSpline::settings(int narg, char **arg)
{
if(narg != 0) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairMEAMSpline::coeff(int narg, char **arg)
{
int i,j,n;
if (!allocated)
allocate();
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// insure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read potential file: also sets the number of elements.
read_file(arg[2]);
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
// nelements = # of unique elements
// elements = list of element names
if ((nelements == 1) && (strlen(elements[0]) == 0)) {
// old style: we only have one species, so we're either "NULL" or we match.
for (i = 3; i < narg; i++)
if (strcmp(arg[i],"NULL") == 0) map[i-2] = -1;
else
map[i-2] = 0;
} else {
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < nelements; j++)
if (strcmp(arg[i],elements[j]) == 0)
break;
if (j < nelements) map[i-2] = j;
else error->all(FLERR,"No matching element in EAM potential file");
}
}
// clear setflag since coeff() called once with I,J = * *
n = atom->ntypes;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
// set setflag i,j for type pairs where both are mapped to elements
int count = 0;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
#define MAXLINE 1024
void PairMEAMSpline::read_file(const char* filename)
{
int nmultichoose2; // = (n+1)*n/2;
if(comm->me == 0) {
FILE *fp = fopen(filename, "r");
if(fp == NULL) {
char str[1024];
sprintf(str,"Cannot open spline MEAM potential file %s", filename);
error->one(FLERR,str);
}
// Skip first line of file. It's a comment.
char line[MAXLINE];
fgets(line, MAXLINE, fp);
// Second line holds potential type (currently just "meam/spline") in new potential format.
bool isNewFormat;
long loc = ftell(fp);
fgets(line, MAXLINE, fp);
if (strncmp(line, "meam/spline", 11) == 0) {
isNewFormat = true;
// parse the rest of the line!
char *linep = line+12, *word;
const char *sep = " ,;:-\t\n"; // overkill, but safe
word = strsep(&linep, sep);
if (! *word)
error->one(FLERR, "Need to include number of atomic species on meam/spline line in potential file");
int n = atoi(word);
if (n<1)
error->one(FLERR, "Invalid number of atomic species on meam/spline line in potential file");
nelements = n; elements = new char*[n];
for (int i=0; i<n; ++i) {
word = strsep(&linep, sep);
if (! *word)
error->one(FLERR, "Not enough atomic species in meam/spline\n");
elements[i] = new char[strlen(word)+1];
strcpy(elements[i], word);
}
} else {
isNewFormat = false;
nelements = 1; // old format only handles one species anyway; this is for backwards compatibility
elements = new char*[1];
elements[0] = new char[1];
strcpy(elements[0], "");
fseek(fp, loc, SEEK_SET);
}
nmultichoose2 = ((nelements+1)*nelements)/2;
// allocate!!
allocate();
// Parse spline functions.
for (int i = 0; i < nmultichoose2; i++)
phis[i].parse(fp, error, isNewFormat);
for (int i = 0; i < nelements; i++)
rhos[i].parse(fp, error, isNewFormat);
for (int i = 0; i < nelements; i++)
Us[i].parse(fp, error, isNewFormat);
for (int i = 0; i < nelements; i++)
fs[i].parse(fp, error, isNewFormat);
for (int i = 0; i < nmultichoose2; i++)
gs[i].parse(fp, error, isNewFormat);
fclose(fp);
}
// Transfer spline functions from master processor to all other processors.
MPI_Bcast(&nelements, 1, MPI_INT, 0, world);
MPI_Bcast(&nmultichoose2, 1, MPI_INT, 0, world);
// allocate!!
if (comm->me != 0) {
allocate();
elements = new char*[nelements];
}
for (int i = 0; i < nelements; ++i) {
int n;
if (comm->me == 0)
n = strlen(elements[i]);
MPI_Bcast(&n, 1, MPI_INT, 0, world);
if (comm->me != 0)
elements[i] = new char[n+1];
MPI_Bcast(elements[i], n+1, MPI_CHAR, 0, world);
}
for (int i = 0; i < nmultichoose2; i++)
phis[i].communicate(world, comm->me);
for (int i = 0; i < nelements; i++)
rhos[i].communicate(world, comm->me);
for (int i = 0; i < nelements; i++)
fs[i].communicate(world, comm->me);
for (int i = 0; i < nelements; i++)
Us[i].communicate(world, comm->me);
for (int i = 0; i < nmultichoose2; i++)
gs[i].communicate(world, comm->me);
// Calculate 'zero-point energy' of single atom in vacuum.
for (int i = 0; i < nelements; i++)
zero_atom_energies[i] = Us[i].eval(0.0);
// Determine maximum cutoff radius of all relevant spline functions. cutoff = 0.0;
for (int i = 0; i < nmultichoose2; i++)
if(phis[i].cutoff() > cutoff)
cutoff = phis[i].cutoff();
for (int i = 0; i < nelements; i++)
if(rhos[i].cutoff() > cutoff)
cutoff = rhos[i].cutoff();
for (int i = 0; i < nelements; i++)
if(fs[i].cutoff() > cutoff)
cutoff = fs[i].cutoff();
// Set LAMMPS pair interaction flags.
for(int i = 1; i <= atom->ntypes; i++) {
for(int j = 1; j <= atom->ntypes; j++) {
// setflag[i][j] = 1;
cutsq[i][j] = cutoff;
}
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairMEAMSpline::init_style()
{
if(force->newton_pair == 0)
error->all(FLERR,"Pair style meam/spline requires newton pair on");
// Need both full and half neighbor list.
int irequest_full = neighbor->request(this,instance_me);
neighbor->requests[irequest_full]->id = 1;
neighbor->requests[irequest_full]->half = 0;
neighbor->requests[irequest_full]->full = 1;
int irequest_half = neighbor->request(this,instance_me);
neighbor->requests[irequest_half]->id = 2;
// neighbor->requests[irequest_half]->half = 1;
// neighbor->requests[irequest_half]->halffull = 1;
// neighbor->requests[irequest_half]->halffulllist = irequest_full;
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
half or full
------------------------------------------------------------------------- */
void PairMEAMSpline::init_list(int id, NeighList *ptr)
{
if(id == 1) listfull = ptr;
else if(id == 2) listhalf = ptr;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairMEAMSpline::init_one(int i, int j)
{
return cutoff;
}
/* ---------------------------------------------------------------------- */
int PairMEAMSpline::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int* list_iter = list;
int* list_iter_end = list + n;
while(list_iter != list_iter_end)
*buf++ = Uprime_values[*list_iter++];
return n;
}
/* ---------------------------------------------------------------------- */
void PairMEAMSpline::unpack_forward_comm(int n, int first, double *buf)
{
memcpy(&Uprime_values[first], buf, n * sizeof(buf[0]));
}
/* ---------------------------------------------------------------------- */
int PairMEAMSpline::pack_reverse_comm(int n, int first, double *buf)
{
return 0;
}
/* ---------------------------------------------------------------------- */
void PairMEAMSpline::unpack_reverse_comm(int n, int *list, double *buf)
{
}
/* ----------------------------------------------------------------------
Returns memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairMEAMSpline::memory_usage()
{
return nmax * sizeof(double); // The Uprime_values array.
}
/// Parses the spline knots from a text file.
void PairMEAMSpline::SplineFunction::parse(FILE* fp, Error* error, bool isNewFormat)
{
char line[MAXLINE];
// If new format, read the spline format. Should always be "spline3eq" for now.
if (isNewFormat)
fgets(line, MAXLINE, fp);
// Parse number of spline knots.
fgets(line, MAXLINE, fp);
int n = atoi(line);
if(n < 2)
error->one(FLERR,"Invalid number of spline knots in MEAM potential file");
// Parse first derivatives at beginning and end of spline.
fgets(line, MAXLINE, fp);
double d0 = atof(strtok(line, " \t\n\r\f"));
double dN = atof(strtok(NULL, " \t\n\r\f"));
init(n, d0, dN);
// Skip line in old format
if (!isNewFormat)
fgets(line, MAXLINE, fp);
// Parse knot coordinates.
for(int i=0; i<n; i++) {
fgets(line, MAXLINE, fp);
double x, y, y2;
if(sscanf(line, "%lg %lg %lg", &x, &y, &y2) != 3) {
error->one(FLERR,"Invalid knot line in MEAM potential file");
}
setKnot(i, x, y);
}
prepareSpline(error);
}
/// Calculates the second derivatives at the knots of the cubic spline.
void PairMEAMSpline::SplineFunction::prepareSpline(Error* error)
{ xmin = X[0];
xmax = X[N-1];
isGridSpline = true;
h = (xmax-xmin)/(N-1);
hsq = h*h;
double* u = new double[N];
Y2[0] = -0.5;
u[0] = (3.0/(X[1]-X[0])) * ((Y[1]-Y[0])/(X[1]-X[0]) - deriv0);
for(int i = 1; i <= N-2; i++) {
double sig = (X[i]-X[i-1]) / (X[i+1]-X[i-1]);
double p = sig * Y2[i-1] + 2.0;
Y2[i] = (sig - 1.0) / p;
u[i] = (Y[i+1]-Y[i]) / (X[i+1]-X[i]) - (Y[i]-Y[i-1])/(X[i]-X[i-1]);
u[i] = (6.0 * u[i]/(X[i+1]-X[i-1]) - sig*u[i-1])/p;
if(fabs(h*i+xmin - X[i]) > 1e-8)
isGridSpline = false;
}
double qn = 0.5;
double un = (3.0/(X[N-1]-X[N-2])) * (derivN - (Y[N-1]-Y[N-2])/(X[N-1]-X[N-2]));
Y2[N-1] = (un - qn*u[N-2]) / (qn * Y2[N-2] + 1.0);
for(int k = N-2; k >= 0; k--) {
Y2[k] = Y2[k] * Y2[k+1] + u[k];
}
delete[] u;
#if !SPLINE_MEAM_SUPPORT_NON_GRID_SPLINES
if(!isGridSpline)
error->one(FLERR,"Support for MEAM potentials with non-uniform cubic splines has not been enabled in the MEAM potential code. Set SPLINE_MEAM_SUPPORT_NON_GRID_SPLINES in pair_spline_meam.h to 1 to enable it");
#endif
// Shift the spline to X=0 to speed up interpolation.
for(int i = 0; i < N; i++) {
Xs[i] = X[i] - xmin;
#if !SPLINE_MEAM_SUPPORT_NON_GRID_SPLINES
if(i < N-1) Ydelta[i] = (Y[i+1]-Y[i])/h;
Y2[i] /= h*6.0;
#endif
}
xmax_shifted = xmax - xmin;
}
/// Broadcasts the spline function parameters to all processors.
void PairMEAMSpline::SplineFunction::communicate(MPI_Comm& world, int me)
{
MPI_Bcast(&N, 1, MPI_INT, 0, world);
MPI_Bcast(&deriv0, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&derivN, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&xmin, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&xmax, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&xmax_shifted, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&isGridSpline, 1, MPI_INT, 0, world);
MPI_Bcast(&h, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&hsq, 1, MPI_DOUBLE, 0, world);
if(me != 0) {
X = new double[N];
Xs = new double[N];
Y = new double[N];
Y2 = new double[N];
Ydelta = new double[N];
}
MPI_Bcast(X, N, MPI_DOUBLE, 0, world);
MPI_Bcast(Xs, N, MPI_DOUBLE, 0, world);
MPI_Bcast(Y, N, MPI_DOUBLE, 0, world);
MPI_Bcast(Y2, N, MPI_DOUBLE, 0, world);
MPI_Bcast(Ydelta, N, MPI_DOUBLE, 0, world);}
/// Writes a Gnuplot script that plots the spline function.
///
/// This function is for debugging only!
void PairMEAMSpline::SplineFunction::writeGnuplot(const char* filename, const char* title) const
{
FILE* fp = fopen(filename, "w");
fprintf(fp, "#!/usr/bin/env gnuplot\n");
if(title) fprintf(fp, "set title \"%s\"\n", title);
double tmin = X[0] - (X[N-1] - X[0]) * 0.05;
double tmax = X[N-1] + (X[N-1] - X[0]) * 0.05;
double delta = (tmax - tmin) / (N*200);
fprintf(fp, "set xrange [%f:%f]\n", tmin, tmax);
fprintf(fp, "plot '-' with lines notitle, '-' with points notitle pt 3 lc 3\n");
for(double x = tmin; x <= tmax+1e-8; x += delta) {
double y = eval(x);
fprintf(fp, "%f %f\n", x, y);
}
fprintf(fp, "e\n");
for(int i = 0; i < N; i++) {
fprintf(fp, "%f %f\n", X[i], Y[i]);
}
fprintf(fp, "e\n");
fclose(fp);
}
/* ----------------------------------------------------------------------
* Spline-based Modified Embedded Atom method (MEAM) potential routine.
*
* Copyright (2011) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
* Written by Alexander Stukowski (<alex@stukowski.com>).
* LLNL-CODE-525797 All rights reserved.
*
* This program is free software; you can redistribute it and/or modify it under
* the terms of the GNU General Public License (as published by the Free
* Software Foundation) version 2, dated June 1991.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the
* GNU General Public License for more details.
*
* Our Preamble Notice
* A. This notice is required to be provided under our contract with the
* U.S. Department of Energy (DOE). This work was produced at the
* Lawrence Livermore National Laboratory under Contract No.
* DE-AC52-07NA27344 with the DOE.
*
* B. Neither the United States Government nor Lawrence Livermore National
* Security, LLC nor any of their employees, makes any warranty, express or
* implied, or assumes any liability or responsibility for the accuracy,
* completeness, or usefulness of any information, apparatus, product, or
* process disclosed, or represents that its use would not infringe
* privately-owned rights.
*
* C. Also, reference herein to any specific commercial products, process,
* or services by trade name, trademark, manufacturer or otherwise does not
* necessarily constitute or imply its endorsement, recommendation, or
* favoring by the United States Government or Lawrence Livermore National
* Security, LLC. The views and opinions of authors expressed herein do not
* necessarily state or reflect those of the United States Government or
* Lawrence Livermore National Security, LLC, and shall not be used for
* advertising or product endorsement purposes.
------------------------------------------------------------------------- */