/* ---------------------------------------------------------------------- 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 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. ------------------------------------------------------------------------- */ #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" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ PairMEAMSpline::PairMEAMSpline(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; restartinfo = 0; one_coeff = 1; manybody_flag = 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 [] map; } } /* ---------------------------------------------------------------------- */ void PairMEAMSpline::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); nmax = atom->nmax; memory->create(Uprime_values,nmax,"pair:Uprime"); } 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; 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; nextTwoBodyInfo->tag = j; nextTwoBodyInfo->r = rij; 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); } rho_value += nextTwoBodyInfo->f * partial_sum; 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; Uprime_values[i] = Uprime_i; if(eflag) { if(eflag_global) eng_vdwl += embeddingEnergy; if(eflag_atom) eatom[i] += embeddingEnergy; } 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 = 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 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); 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 PairMEAMSpline::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 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 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/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 PairMEAMSpline::read_file(const char* filename) { if(comm->me == 0) { FILE *fp = force->open_potential(filename); 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); 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); // 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(); // 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)"); } /* ---------------------------------------------------------------------- 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); 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 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) { 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; ione(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 (). * 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. ------------------------------------------------------------------------- */