diff --git a/src/USER-FEP/Install.sh b/src/USER-FEP/Install.sh index 695d2baf69c056172a18d82e269d261247a6e4eb..f6535f48175dd8d699e94b5e3589e4fc069951f3 100644 --- a/src/USER-FEP/Install.sh +++ b/src/USER-FEP/Install.sh @@ -46,8 +46,6 @@ action pair_lj_cut_soft.cpp action pair_lj_cut_soft.h action pair_lj_cut_tip4p_long_soft.cpp pppm_tip4p.cpp action pair_lj_cut_tip4p_long_soft.h pppm_tip4p.cpp -action pair_morse_soft.cpp -action pair_morse_soft.h action pair_tip4p_long_soft.cpp pppm_tip4p.cpp action pair_tip4p_long_soft.h pppm_tip4p.cpp diff --git a/src/USER-FEP/README b/src/USER-FEP/README index 8c942a90d8d667fbc3e702aece4eb9ca275f3de0..967f8e6efe9bdfd784d6fd8a4b70a59f35b1081b 100644 --- a/src/USER-FEP/README +++ b/src/USER-FEP/README @@ -11,8 +11,3 @@ There are auxiliary tools for using this package in tools/fep. The person who created this package is Agilio Padua at Université Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr) Contact him directly if you have questions. - -Pair style morse/soft was contributed by Stefan Paquay, s.paquay at tue.nl -Applied Physics/Theory of Polymers and Soft Matter, -Eindhoven University of Technology (TU/e), The Netherlands -Contact him in case of problems with this pair style. diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp deleted file mode 100644 index 9b0080788e209a78dd63e61501531553ddb3fac6..0000000000000000000000000000000000000000 --- a/src/USER-FEP/pair_morse_soft.cpp +++ /dev/null @@ -1,350 +0,0 @@ -/* ---------------------------------------------------------------------- - 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. -------------------------------------------------------------------------- */ - -#include <math.h> -#include <stdio.h> -#include <stdlib.h> -#include <string.h> -#include "pair_morse_soft.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- - Contributing author: Stefan Paquay (TU/e) -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- */ - -PairMorseSoft::~PairMorseSoft() -{ - if(allocated){ - memory->destroy(lambda); - } -} - -/* ---------------------------------------------------------------------- */ - -void PairMorseSoft::compute(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; - double rsq,r,dr,dexp,factor_lj; - double dp,la,Vp,Vp2,Vpp; - - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; - - double **x = atom->x; - double **f = atom->f; - int *type = atom->type; - int nlocal = atom->nlocal; - double *special_lj = force->special_lj; - int newton_pair = force->newton_pair; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // loop over neighbors of my atoms - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - factor_lj = special_lj[sbmask(j)]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - jtype = type[j]; - - if (rsq < cutsq[itype][jtype]) { - r = sqrt(rsq); - dr = r - r0[itype][jtype]; - dexp = exp(alpha[itype][jtype] * dr); // Careful, 1/(original thing)! - - la = 1.0 - lambda[itype][jtype]; - la *= la; - la *= alpha[itype][jtype]; - - Vp = 1.0 / ( la + dexp ); - Vpp = alpha[itype][jtype]*dexp; - Vp2 = Vp*Vp; - - dp = d0[itype][jtype]*pow(lambda[itype][jtype],power); - - fpair = dp*2.0*Vp2*( Vp - 1.0 ); - fpair *= factor_lj*Vpp/r; - - f[i][0] += delx*fpair; - f[i][1] += dely*fpair; - f[i][2] += delz*fpair; - if (newton_pair || j < nlocal) { - f[j][0] -= delx*fpair; - f[j][1] -= dely*fpair; - f[j][2] -= delz*fpair; - } - - if (eflag) { - evdwl = dp*Vp*(Vp - 2.0); - evdwl *= factor_lj; - } - - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,0.0,fpair,delx,dely,delz); - } - } - } - - if (vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairMorseSoft::allocate() -{ - PairMorse::allocate(); - int n = atom->ntypes; - memory->create(lambda,n+1,n+1,"pair:lambda"); - -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairMorseSoft::coeff(int narg, char **arg) -{ - if (narg < 6 || narg > 7) error->all(FLERR,"Incorrect args for pair coefficients"); - if (!allocated) allocate(); - - int ilo,ihi,jlo,jhi; - force->bounds(arg[0],atom->ntypes,ilo,ihi); - force->bounds(arg[1],atom->ntypes,jlo,jhi); - - double d0_one = force->numeric(FLERR,arg[2]); - double alpha_one = force->numeric(FLERR,arg[3]); - double r0_one = force->numeric(FLERR,arg[4]); - double lambda_one = force->numeric(FLERR,arg[5]); - - double cut_one = cut_global; - if (narg == 7) cut_one = force->numeric(FLERR,arg[6]); - - int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - d0[i][j] = d0_one; - alpha[i][j] = alpha_one; - r0[i][j] = r0_one; - lambda[i][j] = lambda_one; - cut[i][j] = cut_one; - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - -/* ---------------------------------------------------------------------- - Set global stuff. -------------------------------------------------------------------------- */ - -void PairMorseSoft::settings(int narg, char **arg) -{ - if (narg != 3) error->all(FLERR,"Illegal pair_style command"); - - power = force->inumeric(FLERR,arg[0]); - scale = force->numeric(FLERR,arg[1]); - cut_global = force->numeric(FLERR,arg[2]); - - // reset cutoffs that have been explicitly set - - if (allocated) { - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i+1; j <= atom->ntypes; j++) - if (setflag[i][j]) cut[i][j] = cut_global; - } -} - - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairMorseSoft::init_one(int i, int j) -{ - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - - morse1[i][j] = 2.0*d0[i][j]*alpha[i][j]; - - if (offset_flag) { - double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]); - offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr)); - } else offset[i][j] = 0.0; - - d0[j][i] = d0[i][j]; - alpha[j][i] = alpha[i][j]; - r0[j][i] = r0[i][j]; - morse1[j][i] = morse1[i][j]; - lambda[j][i] = lambda[i][j]; - offset[j][i] = offset[i][j]; - - return cut[i][j]; -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairMorseSoft::write_restart(FILE *fp) -{ - write_restart_settings(fp); - - int i,j; - for (i = 1; i <= atom->ntypes; i++) { - for (j = i; j <= atom->ntypes; j++) { - fwrite(&setflag[i][j],sizeof(int),1,fp); - if (setflag[i][j]) { - fwrite(&d0[i][j],sizeof(double),1,fp); - fwrite(&alpha[i][j],sizeof(double),1,fp); - fwrite(&r0[i][j],sizeof(double),1,fp); - fwrite(&lambda[i][j],sizeof(double),1,fp); - fwrite(&cut[i][j],sizeof(double),1,fp); - } - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairMorseSoft::read_restart(FILE *fp) -{ - read_restart_settings(fp); - - allocate(); - - int i,j; - int me = comm->me; - for (i = 1; i <= atom->ntypes; i++) { - for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); - MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); - if (setflag[i][j]) { - if (me == 0) { - fread(&d0[i][j],sizeof(double),1,fp); - fread(&alpha[i][j],sizeof(double),1,fp); - fread(&r0[i][j],sizeof(double),1,fp); - fread(&lambda[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); - } - MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); - } - } - } -} - - -/* ---------------------------------------------------------------------- - proc 0 writes to data file -------------------------------------------------------------------------- */ - -void PairMorseSoft::write_data(FILE *fp) -{ - for (int i = 1; i <= atom->ntypes; i++) - fprintf(fp,"%d %g %g %g %g\n",i,d0[i][i],alpha[i][i],r0[i][i], - lambda[i][i]); -} - -/* ---------------------------------------------------------------------- - proc 0 writes all pairs to data file -------------------------------------------------------------------------- */ - -void PairMorseSoft::write_data_all(FILE *fp) -{ - for (int i = 1; i <= atom->ntypes; i++) - for (int j = i; j <= atom->ntypes; j++) - fprintf(fp,"%d %g %g %g %g\n",i,d0[i][j],alpha[i][j],r0[i][j], - lambda[i][j]); -} - -/* ---------------------------------------------------------------------- */ - -double PairMorseSoft::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, - double &fforce) -{ - double r,dr,dexp,phi; - double dp,la,Vp,Vp2,Vpp; - - r = sqrt(rsq); - dr = r - r0[itype][jtype]; - dexp = exp(alpha[itype][jtype] * dr); // Careful, 1/(the original thing)! - - la = 1.0 - lambda[itype][jtype]; - la *= la; - la *= alpha[itype][jtype]; - - Vp = 1.0 / ( la + dexp ); - Vpp = alpha[itype][jtype]*dexp; - Vp2 = Vp*Vp; - - dp = d0[itype][jtype]*pow(lambda[itype][jtype],power); - - fforce = dp*2.0*Vp2*( Vp - 1.0 ); - fforce *= factor_lj*Vpp; - - phi = dp*Vp*(Vp - 2.0); - - return factor_lj*phi; -} - -/* ---------------------------------------------------------------------- */ - -void *PairMorseSoft::extract(const char *str, int &dim) -{ - dim = 2; - if (strcmp(str,"d0") == 0) return (void *) d0; - if (strcmp(str,"r0") == 0) return (void *) r0; - if (strcmp(str,"alpha") == 0) return (void *) alpha; - if (strcmp(str,"lambda") == 0) return (void *) lambda; - return NULL; -} diff --git a/src/USER-FEP/pair_morse_soft.h b/src/USER-FEP/pair_morse_soft.h deleted file mode 100644 index d7be3774832439cb03019d49c3da75e903ab14a2..0000000000000000000000000000000000000000 --- a/src/USER-FEP/pair_morse_soft.h +++ /dev/null @@ -1,59 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - 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: Stefan Paquay (Eindhoven University of Technology) -------------------------------------------------------------------------- */ - -#ifdef PAIR_CLASS - -PairStyle(morse/soft,PairMorseSoft) - -#else - -#ifndef LMP_PAIR_MORSE_SOFT_H -#define LMP_PAIR_MORSE_SOFT_H - -#include "pair_morse.h" - -namespace LAMMPS_NS { - -class PairMorseSoft : public PairMorse { - public: - PairMorseSoft(class LAMMPS *lmp) : PairMorse(lmp) {}; - virtual ~PairMorseSoft(); - virtual void compute(int, int); - - virtual void settings(int, char **); - virtual void coeff(int, char **); - virtual double init_one(int, int); - virtual void write_restart(FILE *); - virtual void read_restart(FILE *); - - void write_data(FILE *); - void write_data_all(FILE *); - virtual double single(int, int, int, int, double, double, double, double &); - void *extract(const char *, int &); - - protected: - double **lambda; - - int power; - double scale; - - void allocate(); -}; - -} - -#endif -#endif