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dihedral_helix.cpp
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Thu, Nov 7, 07:28

dihedral_helix.cpp
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/* ----------------------------------------------------------------------
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 authors: Naveen Michaud-Agrawal (Johns Hopkins U) and
Mark Stevens (Sandia)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "mpi.h"
#include "dihedral_helix.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "update.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define TOLERANCE 0.05
#define SMALL 0.001
#define SMALLER 0.00001
/* ---------------------------------------------------------------------- */
DihedralHelix::DihedralHelix(LAMMPS *lmp) : Dihedral(lmp) {}
/* ---------------------------------------------------------------------- */
DihedralHelix::~DihedralHelix()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(aphi);
memory->destroy(bphi);
memory->destroy(cphi);
}
}
/* ---------------------------------------------------------------------- */
void DihedralHelix::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];
domain->minimum_image(vb1x,vb1y,vb1z);
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
domain->minimum_image(vb2x,vb2y,vb2z);
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
domain->minimum_image(vb2xm,vb2ym,vb2zm);
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
// 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;
phi = acos(c);
if (dx < 0.0) phi *= -1.0;
si = sin(phi);
if (fabs(si) < SMALLER) si = SMALLER;
siinv = 1.0/si;
p = aphi[type]*(1.0 - c) + bphi[type]*(1.0 + cos(3.0*phi)) +
cphi[type]*(1.0 + cos(phi + MY_PI4));
pd = -aphi[type] + 3.0*bphi[type]*sin(3.0*phi)*siinv +
cphi[type]*sin(phi + MY_PI4)*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 DihedralHelix::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
memory->create(aphi,n+1,"dihedral:aphi");
memory->create(bphi,n+1,"dihedral:bphi");
memory->create(cphi,n+1,"dihedral:cphi");
memory->create(setflag,n+1,"dihedral:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs from one line in input script
------------------------------------------------------------------------- */
void DihedralHelix::coeff(int narg, char **arg)
{
if (narg != 4) error->all(FLERR,"Incorrect args for dihedral coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
double aphi_one = force->numeric(arg[1]);
double bphi_one = force->numeric(arg[2]);
double cphi_one = force->numeric(arg[3]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
aphi[i] = aphi_one;
bphi[i] = bphi_one;
cphi[i] = cphi_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 DihedralHelix::write_restart(FILE *fp)
{
fwrite(&aphi[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&bphi[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&cphi[1],sizeof(double),atom->ndihedraltypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralHelix::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&aphi[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&bphi[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&cphi[1],sizeof(double),atom->ndihedraltypes,fp);
}
MPI_Bcast(&aphi[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&bphi[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&cphi[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}

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