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improper_ring.cpp
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improper_ring.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 author: Georgios G. Vogiatzis (CoMSE, NTU Athens),
gvog@chemeng.ntua.gr
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Description: This file implements the improper potential introduced
by Destree et al., in Equation 9 of:
- M. Destree, F. Laupretre, A. Lyulin, and J.-P.
Ryckaert, J. Chem. Phys. 112, 9632 (2000),
and subsequently referred in:
- A.V. Lyulin, M.A.J Michels, Macromolecules, 35, 1463,
(2002)
This potential does not affect small amplitude vibrations
but is used in an ad hoc way to prevent the onset of
accidentially large amplitude fluctuations leading to
the occurrence of a planar conformation of the three
bonds i, i + 1 and i', an intermediate conformation
toward the chiral inversion of a methine carbon.
In the "Impropers" section of data file four atoms:
i, j, k and l are specified with i,j and l lying on the
backbone of the chain and k specifying the chirality
of j.
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include "improper_ring.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathSpecial;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
ImproperRing::ImproperRing(LAMMPS *lmp) : Improper(lmp) {}
/* ---------------------------------------------------------------------- */
ImproperRing::~ImproperRing()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
memory->destroy(chi);
}
}
/* ---------------------------------------------------------------------- */
void ImproperRing::compute(int eflag, int vflag)
{
/* Be careful!: "chi" is the equilibrium angle in radians. */
int i1,i2,i3,i4,n,type;
double eimproper ;
/* Compatibility variables. */
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z;
double f1[3], f3[3], f4[3];
/* Actual computation variables. */
int at1[3], at2[3], at3[3], icomb;
double bvec1x[3], bvec1y[3], bvec1z[3],
bvec2x[3], bvec2y[3], bvec2z[3],
bvec1n[3], bvec2n[3], bend_angle[3];
double angle_summer, angfac, cfact1, cfact2, cfact3;
double cjiji, ckjji, ckjkj, fix, fiy, fiz, fjx, fjy, fjz, fkx, fky, fkz;
eimproper = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
/* References to simulation data. */
double **x = atom->x;
double **f = atom->f;
int **improperlist = neighbor->improperlist;
int nimproperlist = neighbor->nimproperlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
/* A description of the potential can be found in
Macromolecules 35, pp. 1463-1472 (2002). */
for (n = 0; n < nimproperlist; n++)
{
/* Take the ids of the atoms contributing to the improper potential. */
i1 = improperlist[n][0]; /* Atom "1" of Figure 1 from the above reference.*/
i2 = improperlist[n][1]; /* Atom "2" ... */
i3 = improperlist[n][2]; /* Atom "3" ... */
i4 = improperlist[n][3]; /* Atom "9" ... */
type = improperlist[n][4];
/* Calculate the necessary variables for LAMMPS implementation.
if (evflag) ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
Although, they are irrelevant to the calculation of the potential, we keep
them for maximal compatibility. */
vb1x = x[i1][0] - x[i2][0]; vb1y = x[i1][1] - x[i2][1]; vb1z = x[i1][2] - x[i2][2];
vb2x = x[i3][0] - x[i2][0]; vb2y = x[i3][1] - x[i2][1]; vb2z = x[i3][2] - x[i2][2];
vb3x = x[i4][0] - x[i3][0]; vb3y = x[i4][1] - x[i3][1]; vb3z = x[i4][2] - x[i3][2];
/* Pass the atom tags to form the necessary combinations. */
at1[0] = i1; at2[0] = i2; at3[0] = i4; /* ids: 1-2-9 */
at1[1] = i1; at2[1] = i2; at3[1] = i3; /* ids: 1-2-3 */
at1[2] = i4; at2[2] = i2; at3[2] = i3; /* ids: 9-2-3 */
/* Initialize the sum of the angles differences. */
angle_summer = 0.0;
/* Take a loop over the three angles, defined by each triad: */
for (icomb = 0; icomb < 3; icomb ++)
{
/* Bond vector connecting the first and the second atom. */
bvec1x[icomb] = x[at2[icomb]][0] - x[at1[icomb]][0];
bvec1y[icomb] = x[at2[icomb]][1] - x[at1[icomb]][1];
bvec1z[icomb] = x[at2[icomb]][2] - x[at1[icomb]][2];
/* also calculate the norm of the vector: */
bvec1n[icomb] = sqrt( bvec1x[icomb]*bvec1x[icomb]
+ bvec1y[icomb]*bvec1y[icomb]
+ bvec1z[icomb]*bvec1z[icomb]);
/* Bond vector connecting the second and the third atom. */
bvec2x[icomb] = x[at3[icomb]][0] - x[at2[icomb]][0];
bvec2y[icomb] = x[at3[icomb]][1] - x[at2[icomb]][1];
bvec2z[icomb] = x[at3[icomb]][2] - x[at2[icomb]][2];
/* also calculate the norm of the vector: */
bvec2n[icomb] = sqrt( bvec2x[icomb]*bvec2x[icomb]
+ bvec2y[icomb]*bvec2y[icomb]
+ bvec2z[icomb]*bvec2z[icomb]);
/* Calculate the bending angle of the atom triad: */
bend_angle[icomb] = ( bvec2x[icomb]*bvec1x[icomb]
+ bvec2y[icomb]*bvec1y[icomb]
+ bvec2z[icomb]*bvec1z[icomb]);
bend_angle[icomb] /= (bvec1n[icomb] * bvec2n[icomb]);
if (bend_angle[icomb] > 1.0) bend_angle[icomb] -= SMALL;
if (bend_angle[icomb] < -1.0) bend_angle[icomb] += SMALL;
/* Append the current angle to the sum of angle differences. */
angle_summer += (bend_angle[icomb] - chi[type]);
}
if (eflag) eimproper = (1.0/6.0) *k[type] * powint(angle_summer,6);
/*
printf("The tags: %d-%d-%d-%d, of type %d .\n",atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4],type);
// printf("The coordinates of the first: %f, %f, %f.\n", x[i1][0], x[i1][1], x[i1][2]);
// printf("The coordinates of the second: %f, %f, %f.\n", x[i2][0], x[i2][1], x[i2][2]);
// printf("The coordinates of the third: %f, %f, %f.\n", x[i3][0], x[i3][1], x[i3][2]);
// printf("The coordinates of the fourth: %f, %f, %f.\n", x[i4][0], x[i4][1], x[i4][2]);
printf("The angles are: %f / %f / %f equilibrium: %f.\n", bend_angle[0], bend_angle[1], bend_angle[2],chi[type]);
printf("The energy of the improper: %f with prefactor %f.\n", eimproper,(1.0/6.0)*k[type]);
printf("The sum of the angles: %f.\n", angle_summer);
*/
/* Force calculation acting on all atoms.
Calculate the derivatives of the potential. */
angfac = k[type] * powint(angle_summer,5);
f1[0] = 0.0; f1[1] = 0.0; f1[2] = 0.0;
f3[0] = 0.0; f3[1] = 0.0; f3[2] = 0.0;
f4[0] = 0.0; f4[1] = 0.0; f4[2] = 0.0;
/* Take a loop over the three angles, defined by each triad: */
for (icomb = 0; icomb < 3; icomb ++)
{
/* Calculate the squares of the distances. */
cjiji = bvec1n[icomb] * bvec1n[icomb]; ckjkj = bvec2n[icomb] * bvec2n[icomb];
ckjji = bvec2x[icomb] * bvec1x[icomb]
+ bvec2y[icomb] * bvec1y[icomb]
+ bvec2z[icomb] * bvec1z[icomb] ;
cfact1 = angfac / (sqrt(ckjkj * cjiji));
cfact2 = ckjji / ckjkj;
cfact3 = ckjji / cjiji;
/* Calculate the force acted on the thrid atom of the angle. */
fkx = cfact2 * bvec2x[icomb] - bvec1x[icomb];
fky = cfact2 * bvec2y[icomb] - bvec1y[icomb];
fkz = cfact2 * bvec2z[icomb] - bvec1z[icomb];
/* Calculate the force acted on the first atom of the angle. */
fix = bvec2x[icomb] - cfact3 * bvec1x[icomb];
fiy = bvec2y[icomb] - cfact3 * bvec1y[icomb];
fiz = bvec2z[icomb] - cfact3 * bvec1z[icomb];
/* Finally, calculate the force acted on the middle atom of the angle.*/
fjx = - fix - fkx; fjy = - fiy - fky; fjz = - fiz - fkz;
/* Consider the appropriate scaling of the forces: */
fix *= cfact1; fiy *= cfact1; fiz *= cfact1;
fjx *= cfact1; fjy *= cfact1; fjz *= cfact1;
fkx *= cfact1; fky *= cfact1; fkz *= cfact1;
if (at1[icomb] == i1) {f1[0] += fix; f1[1] += fiy; f1[2] += fiz;}
else if (at2[icomb] == i1) {f1[0] += fjx; f1[1] += fjy; f1[2] += fjz;}
else if (at3[icomb] == i1) {f1[0] += fkx; f1[1] += fky; f1[2] += fkz;}
if (at1[icomb] == i3) {f3[0] += fix; f3[1] += fiy; f3[2] += fiz;}
else if (at2[icomb] == i3) {f3[0] += fjx; f3[1] += fjy; f3[2] += fjz;}
else if (at3[icomb] == i3) {f3[0] += fkx; f3[1] += fky; f3[2] += fkz;}
if (at1[icomb] == i4) {f4[0] += fix; f4[1] += fiy; f4[2] += fiz;}
else if (at2[icomb] == i4) {f4[0] += fjx; f4[1] += fjy; f4[2] += fjz;}
else if (at3[icomb] == i4) {f4[0] += fkx; f4[1] += fky; f4[2] += fkz;}
/* Store the contribution to the global arrays: */
/* Take the id of the atom from the at1[icomb] element, i1 = at1[icomb]. */
if (newton_bond || at1[icomb] < nlocal) {
f[at1[icomb]][0] += fix;
f[at1[icomb]][1] += fiy;
f[at1[icomb]][2] += fiz;
}
/* Take the id of the atom from the at2[icomb] element, i2 = at2[icomb]. */
if (newton_bond || at2[icomb] < nlocal) {
f[at2[icomb]][0] += fjx;
f[at2[icomb]][1] += fjy;
f[at2[icomb]][2] += fjz;
}
/* Take the id of the atom from the at3[icomb] element, i3 = at3[icomb]. */
if (newton_bond || at3[icomb] < nlocal) {
f[at3[icomb]][0] += fkx;
f[at3[icomb]][1] += fky;
f[at3[icomb]][2] += fkz;
}
}
if (evflag) ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
/* ---------------------------------------------------------------------- */
void ImproperRing::allocate()
{
allocated = 1;
int n = atom->nimpropertypes;
memory->create(k,n+1,"improper:k");
memory->create(chi,n+1,"improper:chi");
memory->create(setflag,n+1,"improper:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void ImproperRing ::coeff(int narg, char **arg)
{
/* Check whether there exist sufficient number of arguments.
0: type of improper to be applied to
1: energetic constant
2: equilibrium angle in degrees */
if (narg != 3) error->all(FLERR,"Incorrect args for RING improper coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nimpropertypes,ilo,ihi);
double k_one = force->numeric(FLERR,arg[1]);
double chi_one = force->numeric(FLERR,arg[2]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
/* Read the k parameter in kcal/mol. */
k[i] = k_one;
/* "chi_one" stores the equilibrium angle in degrees.
Convert it to radians and store its cosine. */
chi[i] = cos((chi_one/180.0)*MY_PI);
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperRing ::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&chi[1],sizeof(double),atom->nimpropertypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperRing::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
}
MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}

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