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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9021 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-10-26 23:25:24 +00:00
parent 547a7df937
commit cfcf3b5bcf
4 changed files with 1510 additions and 0 deletions
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4
src/USER-MISC/Install.sh
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@ -34,6 +34,7 @@ if (test $1 = 1) then
cp pair_gauss_cut.cpp ..
cp pair_lj_sf.cpp ..
cp pair_meam_spline.cpp ..
cp pair_meam_sw_spline.cpp ..
cp pair_tersoff_table.cpp ..
cp angle_cosine_shift.h ..
@ -63,6 +64,7 @@ if (test $1 = 1) then
cp pair_gauss_cut.h ..
cp pair_lj_sf.h ..
cp pair_meam_spline.h ..
cp pair_meam_sw_spline.h ..
cp pair_tersoff_table.h ..
elif (test $1 = 0) then
@ -95,6 +97,7 @@ elif (test $1 = 0) then
rm -f ../pair_gauss_cut.cpp
rm -f ../pair_lj_sf.cpp
rm -f ../pair_meam_spline.cpp
rm -f ../pair_meam_sw_spline.cpp
rm -f ../pair_tersoff_table.cpp
rm -f ../angle_cosine_shift.h
@ -125,6 +128,7 @@ elif (test $1 = 0) then
rm -f ../pair_gauss_cut.h
rm -f ../pair_lj_sf.h
rm -f ../pair_meam_spline.h
rm -f ../pair_meam_sw_spline.h
rm -f ../pair_tersoff_table.h
fi

10
src/USER-MISC/README
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@ -20,17 +20,24 @@ about the feature or its coding.
angle_style cosine/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
angle_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
angle_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
angle_style fourier/simple, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
angle_style dipole, Mario Orsi, orsimario at gmail.com, 10 Jan 12
angle_style quartic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
bond_style harmonic/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007
compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
dihedral_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
dihedral_style nharmonic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
dihedral_style quadratic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12
fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009
fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008
improper_style cossq, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12
improper_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
improper_style ring, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12
pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
@ -39,4 +46,7 @@ pair_style eam/cd, Alexander Stukowski, stukowski at mm.tu-darmstadt.de, 7 Nov 0
pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style lj/sf, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12
pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12
pair_style tersoff/table, Luca Ferraro, luca.ferraro@caspur.it, 1 Dec 11

989
src/USER-MISC/pair_meam_sw_spline.cpp Normal file
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@ -0,0 +1,989 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
* Spline-based Modified Embedded Atom Method plus Stillinger-Weber (MEAM+SW) potential routine.
*
* Copyright (2012) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
* Written by Robert E. Rudd (<robert.rudd@llnl.gov>).
* Based on the spline-based MEAM routine written by
* Alexander Stukowski (<alex@stukowski.com>).
* LLNL-CODE-588032 All rights reserved.
*
* The spline-based MEAM+SW format was first devised and used to develop
* potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,
* and Hyoungki Park at The Ohio State University.
*
* 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
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* or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the
* GNU General Public License for more details.
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* 01-Aug-12 - RER: First code version.
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_meam_sw_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"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairMEAMSWSpline::PairMEAMSWSpline(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
restartinfo = 0;
one_coeff = 1;
nelements = 0;
elements = NULL;
Uprime_values = NULL;
//ESWprime_values = NULL;
nmax = 0;
maxNeighbors = 0;
twoBodyInfo = NULL;
comm_forward = 1;
comm_reverse = 0;
}
/* ---------------------------------------------------------------------- */
PairMEAMSWSpline::~PairMEAMSWSpline()
{
if (elements)
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
delete[] twoBodyInfo;
memory->destroy(Uprime_values);
//memory->destroy(ESWprime_values);
if(allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] map;
}
}
/* ---------------------------------------------------------------------- */
void PairMEAMSWSpline::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag, vflag);
else evflag = vflag_fdotr =
eflag_global = vflag_global = eflag_atom = vflag_atom = 0;
double cutforcesq = cutoff*cutoff;
// Grow per-atom array if necessary
if (atom->nmax > nmax) {
memory->destroy(Uprime_values);
//memory->destroy(ESWprime_values);
nmax = atom->nmax;
memory->create(Uprime_values,nmax,"pair:Uprime");
//memory->create(ESWprime_values,nmax,"pair:ESWprime");
}
double** const x = atom->x;
double** forces = atom->f;
int nlocal = atom->nlocal;
bool newton_pair = force->newton_pair;
int inum_full = listfull->inum;
int* ilist_full = listfull->ilist;
int* numneigh_full = listfull->numneigh;
int** firstneigh_full = listfull->firstneigh;
// Determine the maximum number of neighbors a single atom has
int newMaxNeighbors = 0;
for(int ii = 0; ii < inum_full; ii++) {
int jnum = numneigh_full[ilist_full[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
// compute embedding energies
for(int ii = 0; ii < inum_full; ii++) {
int i = ilist_full[ii];
double xtmp = x[i][0];
double ytmp = x[i][1];
double ztmp = x[i][2];
int* jlist = firstneigh_full[i];
int jnum = numneigh_full[i];
double rho_value = 0;
double rhoSW_value = 0;
int numBonds = 0;
MEAM2Body* nextTwoBodyInfo = twoBodyInfo;
for(int jj = 0; jj < jnum; jj++) {
int j = jlist[jj];
j &= NEIGHMASK;
double jdelx = x[j][0] - xtmp;
double jdely = x[j][1] - ytmp;
double jdelz = x[j][2] - ztmp;
double rij_sq = jdelx*jdelx + jdely*jdely + jdelz*jdelz;
if(rij_sq < cutforcesq) {
double rij = sqrt(rij_sq);
double partial_sum = 0;
double partial_sum2 = 0;
nextTwoBodyInfo->tag = j;
nextTwoBodyInfo->r = rij;
nextTwoBodyInfo->f = f.eval(rij, nextTwoBodyInfo->fprime);
nextTwoBodyInfo->F = F.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 * g.eval(cos_theta);
partial_sum2 += bondk.F * G.eval(cos_theta);
}
rho_value += nextTwoBodyInfo->f * partial_sum;
rhoSW_value += nextTwoBodyInfo->F * partial_sum2;
rho_value += rho.eval(rij);
numBonds++;
nextTwoBodyInfo++;
}
}
// Compute embedding energy and its derivative
double Uprime_i;
double embeddingEnergy = U.eval(rho_value, Uprime_i) - zero_atom_energy;
double SWEnergy = rhoSW_value;
double ESWprime_i = 1.0;
Uprime_values[i] = Uprime_i;
// ESWprime_values[i] = ESWprime_i;
if(eflag) {
if(eflag_global) eng_vdwl += embeddingEnergy + SWEnergy;
if(eflag_atom) eatom[i] += embeddingEnergy + SWEnergy;
}
double forces_i[3] = {0, 0, 0};
// Compute three-body contributions to force
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_prime = bondj.Fprime;
double f_rij = bondj.f;
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 = g.eval(cos_theta, g_prime);
double G_prime;
double G_value = G.eval(cos_theta, G_prime);
double f_rik_prime = bondk->fprime;
double f_rik = bondk->f;
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 Fij = -ESWprime_i * G_value * F_rik * F_rij_prime;
double Fik = -ESWprime_i * G_value * F_rij * F_rik_prime;
double prefactor = Uprime_i * f_rij * f_rik * g_prime;
double prefactor2 = ESWprime_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 prefactor2_ij = prefactor2 / rij;
double prefactor2_ik = prefactor2 / rik;
Fij += prefactor2_ij * cos_theta;
Fik += prefactor2_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;
fj[0] += bondj.del[0] * Fij - bondk->del[0] * prefactor2_ij;
fj[1] += bondj.del[1] * Fij - bondk->del[1] * prefactor2_ij;
fj[2] += bondj.del[2] * Fij - bondk->del[2] * prefactor2_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;
fk[0] += bondk->del[0] * Fik - bondj.del[0] * prefactor2_ik;
fk[1] += bondk->del[1] * Fik - bondj.del[1] * prefactor2_ik;
fk[2] += bondk->del[2] * Fik - bondj.del[2] * prefactor2_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);
int inum_half = listhalf->inum;
int* ilist_half = listhalf->ilist;
int* numneigh_half = listhalf->numneigh;
int** firstneigh_half = listhalf->firstneigh;
// Compute two-body pair interactions
for(int ii = 0; ii < inum_half; ii++) {
int i = ilist_half[ii];
double xtmp = x[i][0];
double ytmp = x[i][1];
double ztmp = x[i][2];
int* jlist = firstneigh_half[i];
int jnum = numneigh_half[i];
for(int jj = 0; jj < jnum; jj++) {
int j = jlist[jj];
j &= NEIGHMASK;
double jdel[3];
jdel[0] = x[j][0] - xtmp;
jdel[1] = x[j][1] - ytmp;
jdel[2] = x[j][2] - ztmp;
double rij_sq = jdel[0]*jdel[0] + jdel[1]*jdel[1] + jdel[2]*jdel[2];
if(rij_sq < cutforcesq) {
double rij = sqrt(rij_sq);
double rho_prime;
rho.eval(rij, rho_prime);
double fpair = rho_prime * (Uprime_values[i] + Uprime_values[j]);
double pair_pot_deriv;
double pair_pot = phi.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, nlocal, newton_pair,
pair_pot, 0.0, -fpair, jdel[0], jdel[1], jdel[2]);
}
}
}
if(vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairMEAMSWSpline::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
map = new int[n+1];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairMEAMSWSpline::settings(int narg, char **arg)
{
if(narg != 0) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairMEAMSWSpline::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 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 (elements) {
for (i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
}
elements = new char*[atom->ntypes];
for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
nelements = 0;
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;
map[i-2] = j;
if (j == nelements) {
n = strlen(arg[i]) + 1;
elements[j] = new char[n];
strcpy(elements[j],arg[i]);
nelements++;
}
}
// for now, only allow single element
if (nelements > 1)
error->all(FLERR,
"Pair meam/sw/spline only supports single element potentials");
// read potential file
read_file(arg[2]);
// 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");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
#define MAXLINE 1024
void PairMEAMSWSpline::read_file(const char* filename)
{
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.
char line[MAXLINE];
fgets(line, MAXLINE, fp);
// Parse spline functions.
phi.parse(fp, error);
F.parse(fp, error);
G.parse(fp, error);
rho.parse(fp, error);
U.parse(fp, error);
f.parse(fp, error);
g.parse(fp, error);
fclose(fp);
}
// Transfer spline functions from master processor to all other processors.
phi.communicate(world, comm->me);
rho.communicate(world, comm->me);
f.communicate(world, comm->me);
U.communicate(world, comm->me);
g.communicate(world, comm->me);
F.communicate(world, comm->me);
G.communicate(world, comm->me);
// Calculate 'zero-point energy' of single atom in vacuum.
zero_atom_energy = U.eval(0.0);
// Determine maximum cutoff radius of all relevant spline functions.
cutoff = 0.0;
if(phi.cutoff() > cutoff) cutoff = phi.cutoff();
if(rho.cutoff() > cutoff) cutoff = rho.cutoff();
if(f.cutoff() > cutoff) cutoff = f.cutoff();
if(F.cutoff() > cutoff) cutoff = F.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;
}
}
// phi.writeGnuplot("phi.gp", "Phi(r)");
// rho.writeGnuplot("rho.gp", "Rho(r)");
// f.writeGnuplot("f.gp", "f(r)");
// U.writeGnuplot("U.gp", "U(rho)");
// g.writeGnuplot("g.gp", "g(x)");
// F.writeGnuplot("F.gp", "F(r)");
// G.writeGnuplot("G.gp", "G(x)");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairMEAMSWSpline::init_style()
{
if(force->newton_pair == 0)
error->all(FLERR,"Pair style meam/sw/spline requires newton pair on");
// Need both full and half neighbor list.
int irequest_full = neighbor->request(this);
neighbor->requests[irequest_full]->id = 1;
neighbor->requests[irequest_full]->half = 0;
neighbor->requests[irequest_full]->full = 1;
int irequest_half = neighbor->request(this);
neighbor->requests[irequest_half]->id = 2;
neighbor->requests[irequest_half]->half = 0;
neighbor->requests[irequest_half]->half_from_full = 1;
neighbor->requests[irequest_half]->otherlist = irequest_full;
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
half or full
------------------------------------------------------------------------- */
void PairMEAMSWSpline::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 PairMEAMSWSpline::init_one(int i, int j)
{
return cutoff;
}
/* ---------------------------------------------------------------------- */
int PairMEAMSWSpline::pack_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 1;
}
/* ---------------------------------------------------------------------- */
void PairMEAMSWSpline::unpack_comm(int n, int first, double *buf)
{
memcpy(&Uprime_values[first], buf, n * sizeof(buf[0]));
}
/* ---------------------------------------------------------------------- */
int PairMEAMSWSpline::pack_reverse_comm(int n, int first, double *buf)
{
return 0;
}
/* ---------------------------------------------------------------------- */
void PairMEAMSWSpline::unpack_reverse_comm(int n, int *list, double *buf)
{
}
/* ----------------------------------------------------------------------
Returns memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairMEAMSWSpline::memory_usage()
{
return nmax * sizeof(double); // The Uprime_values array.
}
/// Parses the spline knots from a text file.
void PairMEAMSWSpline::SplineFunction::parse(FILE* fp, Error* error)
{
char line[MAXLINE];
// 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.
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 PairMEAMSWSpline::SplineFunction::prepareSpline(Error* error)
{
xmin = X[0];
xmax = X[N-1];
isGridSpline = true;
h = (xmax-xmin)/((double)(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 PairMEAMSWSpline::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 PairMEAMSWSpline::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);
}

507
src/USER-MISC/pair_meam_sw_spline.h Normal file
View File

@ -0,0 +1,507 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
* Spline-based Modified Embedded Atom Method plus Stillinger-Weber (MEAM+SW) potential routine.
*
* Copyright (2012) Lawrence Livermore National Security, LLC.
* Produced at the Lawrence Livermore National Laboratory.
* Written by Robert E. Rudd (<robert.rudd@llnl.gov>).
* Based on the spline MEAM routine written by Alexander Stukowski
* (<alex@stukowski.com>).
* LLNL-CODE-588032 All rights reserved.
*
* The spline-based MEAM+SW format was first devised and used to develop
* potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,
* and Hyoungki Park at The Ohio State University.
*
* 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.
*
* The precise terms and conditions for copying, distribution and modification
* follows.
*
* GNU Terms and Conditions for Copying, Distribution, and Modification
*
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* translation is included without limitation in the term "modification".)
* Each licensee is addressed as "you."
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* See file 'pair_meam_sw_spline.cpp' for history of changes.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(meam/sw/spline,PairMEAMSWSpline)
#else
#ifndef LMP_PAIR_MEAM_SW_SPLINE_H
#define LMP_PAIR_MEAM_SW_SPLINE_H
#include "pair.h"
namespace LAMMPS_NS {
/// Set this to 1 if you intend to use MEAM potentials with non-uniform spline knots.
/// Set this to 0 if you intend to use only MEAM potentials with spline knots on a uniform grid.
///
/// With SUPPORT_NON_GRID_SPLINES == 0, the code runs about 50% faster.
#define SPLINE_MEAMSW_SUPPORT_NON_GRID_SPLINES 0
class PairMEAMSWSpline : public Pair
{
public:
PairMEAMSWSpline(class LAMMPS *);
virtual ~PairMEAMSWSpline();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
void init_list(int, class NeighList *);
double init_one(int, int);
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
double memory_usage();
protected:
char **elements; // names of unique elements
int *map; // mapping from atom types to elements
int nelements; // # of unique elements
class SplineFunction {
public:
/// Default constructor.
SplineFunction() : X(NULL), Xs(NULL), Y(NULL), Y2(NULL), Ydelta(NULL), N(0) {}
/// Destructor.
~SplineFunction() {
delete[] X;
delete[] Xs;
delete[] Y;
delete[] Y2;
delete[] Ydelta;
}
/// Initialization of spline function.
void init(int _N, double _deriv0, double _derivN) {
N = _N;
deriv0 = _deriv0;
derivN = _derivN;
delete[] X;
delete[] Xs;
delete[] Y;
delete[] Y2;
delete[] Ydelta;
X = new double[N];
Xs = new double[N];
Y = new double[N];
Y2 = new double[N];
Ydelta = new double[N];
}
/// Adds a knot to the spline.
void setKnot(int n, double x, double y) { X[n] = x; Y[n] = y; }
/// Returns the number of knots.
int numKnots() const { return N; }
/// Parses the spline knots from a text file.
void parse(FILE* fp, Error* error);
/// Calculates the second derivatives of the cubic spline.
void prepareSpline(Error* error);
/// Evaluates the spline function at position x.
inline double eval(double x) const
{
x -= xmin;
if(x <= 0.0) { // Left extrapolation.
return Y[0] + deriv0 * x;
}
else if(x >= xmax_shifted) { // Right extrapolation.
return Y[N-1] + derivN * (x - xmax_shifted);
}
else {
#if SPLINE_MEAMSW_SUPPORT_NON_GRID_SPLINES
// Do interval search.
int klo = 0;
int khi = N-1;
while(khi - klo > 1) {
int k = (khi + klo) / 2;
if(Xs[k] > x) khi = k;
else klo = k;
}
double h = Xs[khi] - Xs[klo];
// Do spline interpolation.
double a = (Xs[khi] - x)/h;
double b = 1.0 - a; // = (x - X[klo])/h
return a * Y[klo] + b * Y[khi] + ((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi])*(h*h)/6.0;
#else
// For a spline with grid points, we can directly calculate the interval X is in.
//
int klo = (int)(x / h);
if ( klo > N - 2 ) klo = N - 2;
int khi = klo + 1;
double a = Xs[khi] - x;
double b = h - a;
return Y[khi] - a * Ydelta[klo] + ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
#endif
}
}
/// Evaluates the spline function and its first derivative at position x.
inline double eval(double x, double& deriv) const
{
x -= xmin;
if(x <= 0.0) { // Left extrapolation.
deriv = deriv0;
return Y[0] + deriv0 * x;
}
else if(x >= xmax_shifted) { // Right extrapolation.
deriv = derivN;
return Y[N-1] + derivN * (x - xmax_shifted);
}
else {
#if SPLINE_MEAMSW_SUPPORT_NON_GRID_SPLINES
// Do interval search.
int klo = 0;
int khi = N-1;
while(khi - klo > 1) {
int k = (khi + klo) / 2;
if(Xs[k] > x) khi = k;
else klo = k;
}
double h = Xs[khi] - Xs[klo];
// Do spline interpolation.
double a = (Xs[khi] - x)/h;
double b = 1.0 - a; // = (x - X[klo])/h
deriv = (Y[khi] - Y[klo]) / h + ((3.0*b*b - 1.0) * Y2[khi] - (3.0*a*a - 1.0) * Y2[klo]) * h / 6.0;
return a * Y[klo] + b * Y[khi] + ((a*a*a - a) * Y2[klo] + (b*b*b - b) * Y2[khi]) * (h*h) / 6.0;
#else
// For a spline with grid points, we can directly calculate the interval X is in.
int klo = (int)(x / h);
if ( klo > N - 2 ) klo = N - 2;
int khi = klo + 1;
double a = Xs[khi] - x;
double b = h - a;
deriv = Ydelta[klo] + ((3.0*b*b - hsq) * Y2[khi] - (3.0*a*a - hsq) * Y2[klo]);
return Y[khi] - a * Ydelta[klo] + ((a*a - hsq) * a * Y2[klo] + (b*b - hsq) * b * Y2[khi]);
#endif
}
}
/// Returns the number of bytes used by this function object.
double memory_usage() const { return sizeof(*this) + sizeof(X[0]) * N * 3; }
/// Returns the cutoff radius of this function.
double cutoff() const { return X[N-1]; }
/// Writes a Gnuplot script that plots the spline function.
void writeGnuplot(const char* filename, const char* title = NULL) const;
/// Broadcasts the spline function parameters to all processors.
void communicate(MPI_Comm& world, int me);
private:
double* X; // Positions of spline knots
double* Xs; // Shifted positions of spline knots
double* Y; // Function values at spline knots
double* Y2; // Second derivatives at spline knots
double* Ydelta; // If this is a grid spline, Ydelta[i] = (Y[i+1]-Y[i])/h
int N; // Number of spline knots
double deriv0; // First derivative at knot 0
double derivN; // First derivative at knot (N-1)
double xmin; // The beginning of the interval on which the spline function is defined.
double xmax; // The end of the interval on which the spline function is defined.
int isGridSpline; // Indicates that all spline knots are on a regular grid.
double h; // The distance between knots if this is a grid spline with equidistant knots.
double hsq; // The squared distance between knots if this is a grid spline with equidistant knots.
double xmax_shifted; // The end of the spline interval after it has been shifted to begin at X=0.
};
/// Helper data structure for potential routine.
struct MEAM2Body {
int tag;
double r;
double f, fprime;
double F, Fprime;
double del[3];
};
SplineFunction phi; // Phi(r_ij)
SplineFunction rho; // Rho(r_ij)
SplineFunction f; // f(r_ij)
SplineFunction U; // U(rho)
SplineFunction g; // g(cos_theta)
SplineFunction F; // F(r_ij)
SplineFunction G; // G(cos_theta)
double zero_atom_energy; // Shift embedding energy by this value to make it zero for a single atom in vacuum.
double cutoff; // The cutoff radius
double* Uprime_values; // Used for temporary storage of U'(rho) values
int nmax; // Size of temporary array.
int maxNeighbors; // The last maximum number of neighbors a single atoms has.
MEAM2Body* twoBodyInfo; // Temporary array.
void read_file(const char* filename);
void allocate();
};
}
#endif
#endif