diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index 15a4b0a61..074c8bf15 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -1,341 +1,355 @@ /* ---------------------------------------------------------------------- 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: Mark Stevens (SNL) ------------------------------------------------------------------------- */ #include "math.h" #include "stdlib.h" #include "dihedral_opls.h" #include "atom.h" #include "comm.h" #include "neighbor.h" #include "domain.h" #include "force.h" #include "update.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; #define TOLERANCE 0.05 #define SMALL 0.001 #define SMALLER 0.00001 /* ---------------------------------------------------------------------- */ -DihedralOPLS::DihedralOPLS(LAMMPS *lmp) : Dihedral(lmp) {} +DihedralOPLS::DihedralOPLS(LAMMPS *lmp) : Dihedral(lmp) +{ + writedata = 1; +} /* ---------------------------------------------------------------------- */ DihedralOPLS::~DihedralOPLS() { if (allocated) { memory->destroy(setflag); memory->destroy(k1); memory->destroy(k2); memory->destroy(k3); memory->destroy(k4); } } /* ---------------------------------------------------------------------- */ void DihedralOPLS::compute(int eflag, int vflag) { int i1,i2,i3,i4,n,type; double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm; double edihedral,f1[3],f2[3],f3[3],f4[3]; double sb1,sb2,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2; double b2mag,b3mag2,b3mag,ctmp,r12c1,c1mag,r12c2; double c2mag,sc1,sc2,s1,s12,c,p,pd,a,a11,a22; double a33,a12,a13,a23,sx2,sy2,sz2; double s2,cx,cy,cz,cmag,dx,phi,si,siinv,sin2; edihedral = 0.0; if (eflag || vflag) ev_setup(eflag,vflag); else evflag = 0; double **x = atom->x; double **f = atom->f; int **dihedrallist = neighbor->dihedrallist; int ndihedrallist = neighbor->ndihedrallist; int nlocal = atom->nlocal; int newton_bond = force->newton_bond; for (n = 0; n < ndihedrallist; n++) { i1 = dihedrallist[n][0]; i2 = dihedrallist[n][1]; i3 = dihedrallist[n][2]; i4 = dihedrallist[n][3]; type = dihedrallist[n][4]; // 1st bond vb1x = x[i1][0] - x[i2][0]; vb1y = x[i1][1] - x[i2][1]; vb1z = x[i1][2] - x[i2][2]; // 2nd bond vb2x = x[i3][0] - x[i2][0]; vb2y = x[i3][1] - x[i2][1]; vb2z = x[i3][2] - x[i2][2]; vb2xm = -vb2x; vb2ym = -vb2y; vb2zm = -vb2z; // 3rd bond vb3x = x[i4][0] - x[i3][0]; vb3y = x[i4][1] - x[i3][1]; vb3z = x[i4][2] - x[i3][2]; // c0 calculation sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z); sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z); sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z); rb1 = sqrt(sb1); rb3 = sqrt(sb3); c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3; // 1st and 2nd angle b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z; b1mag = sqrt(b1mag2); b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z; b2mag = sqrt(b2mag2); b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z; b3mag = sqrt(b3mag2); ctmp = vb1x*vb2x + vb1y*vb2y + vb1z*vb2z; r12c1 = 1.0 / (b1mag*b2mag); c1mag = ctmp * r12c1; ctmp = vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z; r12c2 = 1.0 / (b2mag*b3mag); c2mag = ctmp * r12c2; // cos and sin of 2 angles and final c sin2 = MAX(1.0 - c1mag*c1mag,0.0); sc1 = sqrt(sin2); if (sc1 < SMALL) sc1 = SMALL; sc1 = 1.0/sc1; sin2 = MAX(1.0 - c2mag*c2mag,0.0); sc2 = sqrt(sin2); if (sc2 < SMALL) sc2 = SMALL; sc2 = 1.0/sc2; s1 = sc1 * sc1; s2 = sc2 * sc2; s12 = sc1 * sc2; c = (c0 + c1mag*c2mag) * s12; cx = vb1y*vb2z - vb1z*vb2y; cy = vb1z*vb2x - vb1x*vb2z; cz = vb1x*vb2y - vb1y*vb2x; cmag = sqrt(cx*cx + cy*cy + cz*cz); dx = (cx*vb3x + cy*vb3y + cz*vb3z)/cmag/b3mag; // error check if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) { int me; MPI_Comm_rank(world,&me); if (screen) { char str[128]; sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d", me,update->ntimestep, atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]); error->warning(FLERR,str,0); fprintf(screen," 1st atom: %d %g %g %g\n", me,x[i1][0],x[i1][1],x[i1][2]); fprintf(screen," 2nd atom: %d %g %g %g\n", me,x[i2][0],x[i2][1],x[i2][2]); fprintf(screen," 3rd atom: %d %g %g %g\n", me,x[i3][0],x[i3][1],x[i3][2]); fprintf(screen," 4th atom: %d %g %g %g\n", me,x[i4][0],x[i4][1],x[i4][2]); } } if (c > 1.0) c = 1.0; if (c < -1.0) c = -1.0; // force & energy // p = sum (i=1,4) k_i * (1 + (-1)**(i+1)*cos(i*phi) ) // pd = dp/dc phi = acos(c); if (dx < 0.0) phi *= -1.0; si = sin(phi); if (fabs(si) < SMALLER) si = SMALLER; siinv = 1.0/si; p = k1[type]*(1.0 + c) + k2[type]*(1.0 - cos(2.0*phi)) + k3[type]*(1.0 + cos(3.0*phi)) + k4[type]*(1.0 - cos(4.0*phi)) ; pd = k1[type] - 2.0*k2[type]*sin(2.0*phi)*siinv + 3.0*k3[type]*sin(3.0*phi)*siinv - 4.0*k4[type]*sin(4.0*phi)*siinv; if (eflag) edihedral = p; a = pd; c = c * a; s12 = s12 * a; a11 = c*sb1*s1; a22 = -sb2 * (2.0*c0*s12 - c*(s1+s2)); a33 = c*sb3*s2; a12 = -r12c1 * (c1mag*c*s1 + c2mag*s12); a13 = -rb1*rb3*s12; a23 = r12c2 * (c2mag*c*s2 + c1mag*s12); sx2 = a12*vb1x + a22*vb2x + a23*vb3x; sy2 = a12*vb1y + a22*vb2y + a23*vb3y; sz2 = a12*vb1z + a22*vb2z + a23*vb3z; f1[0] = a11*vb1x + a12*vb2x + a13*vb3x; f1[1] = a11*vb1y + a12*vb2y + a13*vb3y; f1[2] = a11*vb1z + a12*vb2z + a13*vb3z; f2[0] = -sx2 - f1[0]; f2[1] = -sy2 - f1[1]; f2[2] = -sz2 - f1[2]; f4[0] = a13*vb1x + a23*vb2x + a33*vb3x; f4[1] = a13*vb1y + a23*vb2y + a33*vb3y; f4[2] = a13*vb1z + a23*vb2z + a33*vb3z; f3[0] = sx2 - f4[0]; f3[1] = sy2 - f4[1]; f3[2] = sz2 - f4[2]; // apply force to each of 4 atoms if (newton_bond || i1 < nlocal) { f[i1][0] += f1[0]; f[i1][1] += f1[1]; f[i1][2] += f1[2]; } if (newton_bond || i2 < nlocal) { f[i2][0] += f2[0]; f[i2][1] += f2[1]; f[i2][2] += f2[2]; } if (newton_bond || i3 < nlocal) { f[i3][0] += f3[0]; f[i3][1] += f3[1]; f[i3][2] += f3[2]; } if (newton_bond || i4 < nlocal) { f[i4][0] += f4[0]; f[i4][1] += f4[1]; f[i4][2] += f4[2]; } if (evflag) ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4, vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z); } } /* ---------------------------------------------------------------------- */ void DihedralOPLS::allocate() { allocated = 1; int n = atom->ndihedraltypes; memory->create(k1,n+1,"dihedral:k1"); memory->create(k2,n+1,"dihedral:k2"); memory->create(k3,n+1,"dihedral:k3"); memory->create(k4,n+1,"dihedral:k4"); memory->create(setflag,n+1,"dihedral:setflag"); for (int i = 1; i <= n; i++) setflag[i] = 0; } /* ---------------------------------------------------------------------- set coeffs for one type ------------------------------------------------------------------------- */ void DihedralOPLS::coeff(int narg, char **arg) { if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients"); if (!allocated) allocate(); int ilo,ihi; force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi); double k1_one = force->numeric(FLERR,arg[1]); double k2_one = force->numeric(FLERR,arg[2]); double k3_one = force->numeric(FLERR,arg[3]); double k4_one = force->numeric(FLERR,arg[4]); // store 1/2 factor with prefactor int count = 0; for (int i = ilo; i <= ihi; i++) { k1[i] = 0.5*k1_one; k2[i] = 0.5*k2_one; k3[i] = 0.5*k3_one; k4[i] = 0.5*k4_one; setflag[i] = 1; count++; } if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); } /* ---------------------------------------------------------------------- proc 0 writes out coeffs to restart file ------------------------------------------------------------------------- */ void DihedralOPLS::write_restart(FILE *fp) { fwrite(&k1[1],sizeof(double),atom->ndihedraltypes,fp); fwrite(&k2[1],sizeof(double),atom->ndihedraltypes,fp); fwrite(&k3[1],sizeof(double),atom->ndihedraltypes,fp); fwrite(&k4[1],sizeof(double),atom->ndihedraltypes,fp); } /* ---------------------------------------------------------------------- proc 0 reads coeffs from restart file, bcasts them ------------------------------------------------------------------------- */ void DihedralOPLS::read_restart(FILE *fp) { allocate(); if (comm->me == 0) { fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp); fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp); fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp); fread(&k4[1],sizeof(double),atom->ndihedraltypes,fp); } MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); MPI_Bcast(&k2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); MPI_Bcast(&k3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); MPI_Bcast(&k4[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1; } + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void DihedralOPLS::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ndihedraltypes; i++) + fprintf(fp,"%d %g %g %g %g\n",i,2.0*k1[i],2.0*k2[i],2.0*k3[i],2.0*k4[i]); +} + diff --git a/src/MOLECULE/dihedral_opls.h b/src/MOLECULE/dihedral_opls.h index 500a5927a..238a67cf3 100644 --- a/src/MOLECULE/dihedral_opls.h +++ b/src/MOLECULE/dihedral_opls.h @@ -1,59 +1,60 @@ -/* ---------------------------------------------------------------------- +/* -*- 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. ------------------------------------------------------------------------- */ #ifdef DIHEDRAL_CLASS DihedralStyle(opls,DihedralOPLS) #else #ifndef LMP_DIHEDRAL_OPLS_H #define LMP_DIHEDRAL_OPLS_H #include "stdio.h" #include "dihedral.h" namespace LAMMPS_NS { class DihedralOPLS : public Dihedral { public: DihedralOPLS(class LAMMPS *); virtual ~DihedralOPLS(); virtual void compute(int, int); void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); + void write_data(FILE *); protected: double *k1,*k2,*k3,*k4; void allocate(); }; } #endif #endif /* ERROR/WARNING messages: W: Dihedral problem: %d %ld %d %d %d %d Conformation of the 4 listed dihedral atoms is extreme; you may want to check your simulation geometry. E: Incorrect args for dihedral coefficients Self-explanatory. Check the input script or data file. */