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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@712 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2007-07-02 20:06:44 +00:00
parent c2515c1083
commit 308e8cc12b
13 changed files with 279 additions and 279 deletions
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6
src/MOLECULE/bond_fene.cpp
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@ -233,7 +233,7 @@ void BondFENE::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondFENE::single(int type, double rsq, int i, int j, double rfactor,
void BondFENE::single(int type, double rsq, int i, int j,
int eflag, double &fforce, double &eng)
{
double r0sq = r0[type] * r0[type];
@ -265,8 +265,8 @@ void BondFENE::single(int type, double rsq, int i, int j, double rfactor,
// energy
if (eflag) {
eng = -0.5*rfactor * k[type]*r0sq*log(rlogarg);
eng = -0.5 * k[type]*r0sq*log(rlogarg);
if (rsq < TWO_1_3*sigma[type]*sigma[type])
eng += rfactor * (4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type]);
eng += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
}
}

2
src/MOLECULE/bond_fene.h
View File

@ -28,7 +28,7 @@ class BondFENE : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double, int, double &, double &);
void single(int, double, int, int, int, double &, double &);
private:
double TWO_1_3;

6
src/MOLECULE/bond_fene_expand.cpp
View File

@ -246,7 +246,7 @@ void BondFENEExpand::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondFENEExpand::single(int type, double rsq, int i, int j, double rfactor,
void BondFENEExpand::single(int type, double rsq, int i, int j,
int eflag, double &fforce, double &eng)
{
double r = sqrt(rsq);
@ -281,8 +281,8 @@ void BondFENEExpand::single(int type, double rsq, int i, int j, double rfactor,
// energy
if (eflag) {
eng = -0.5*rfactor * k[type]*r0sq*log(rlogarg);
eng = -0.5 * k[type]*r0sq*log(rlogarg);
if (rshiftsq < TWO_1_3*sigma[type]*sigma[type])
eng += rfactor * (4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type]);
eng += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
}
}

2
src/MOLECULE/bond_fene_expand.h
View File

@ -28,7 +28,7 @@ class BondFENEExpand : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double, int, double &, double &);
void single(int, double, int, int, int, double &, double &);
private:
double TWO_1_3;

4
src/MOLECULE/bond_harmonic.cpp
View File

@ -193,7 +193,7 @@ void BondHarmonic::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondHarmonic::single(int type, double rsq, int i, int j, double rfactor,
void BondHarmonic::single(int type, double rsq, int i, int j,
int eflag, double &fforce, double &eng)
{
double r = sqrt(rsq);
@ -204,5 +204,5 @@ void BondHarmonic::single(int type, double rsq, int i, int j, double rfactor,
if (r > 0.0) fforce = -2.0*rk/r;
else fforce = 0.0;
if (eflag) eng = rfactor * rk*dr;
if (eflag) eng = rk*dr;
}

2
src/MOLECULE/bond_harmonic.h
View File

@ -28,7 +28,7 @@ class BondHarmonic : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double, int, double &, double &);
void single(int, double, int, int, int, double &, double &);
private:
double *k,*r0;

4
src/MOLECULE/bond_hybrid.cpp
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@ -250,11 +250,11 @@ void BondHybrid::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondHybrid::single(int type, double rsq, int i, int j, double rfactor,
void BondHybrid::single(int type, double rsq, int i, int j,
int eflag, double &fforce, double &eng)
{
if (styles[map[type]])
styles[map[type]]->single(type,rsq,i,j,rfactor,eflag,fforce,eng);
styles[map[type]]->single(type,rsq,i,j,eflag,fforce,eng);
}
/* ----------------------------------------------------------------------

436
src/MOLECULE/bond_morse.cpp
View File

@ -1,218 +1,218 @@
/* ----------------------------------------------------------------------
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: Jeff Greathouse (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "bond_morse.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondMorse::BondMorse(LAMMPS *lmp) : Bond(lmp) {}
/* ---------------------------------------------------------------------- */
BondMorse::~BondMorse()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(d0);
memory->sfree(alpha);
memory->sfree(r0);
}
}
/* ---------------------------------------------------------------------- */
void BondMorse::compute(int eflag, int vflag)
{
int i1,i2,n,type,factor;
double delx,dely,delz,rsq,r,dr,fforce,rfactor,ralpha;
energy = 0.0;
if (vflag) for (n = 0; n < 6; n++) virial[n] = 0.0;
double **x = atom->x;
double **f = atom->f;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nbondlist; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
if (newton_bond) factor = 2;
else {
factor = 0;
if (i1 < nlocal) factor++;
if (i2 < nlocal) factor++;
}
rfactor = 0.5 * factor;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
dr = r - r0[type];
ralpha = exp(-alpha[type]*dr);
// force & energy
if (r > 0.0) fforce = -2.0*d0[type]*alpha[type]*(1-ralpha)*ralpha/r;
else fforce = 0.0;
if (eflag) energy += rfactor * d0[type]*(1-ralpha)*(1-ralpha);
// apply force to each of 2 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fforce;
f[i1][1] += dely*fforce;
f[i1][2] += delz*fforce;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fforce;
f[i2][1] -= dely*fforce;
f[i2][2] -= delz*fforce;
}
// virial contribution
if (vflag) {
virial[0] += rfactor*delx*delx*fforce;
virial[1] += rfactor*dely*dely*fforce;
virial[2] += rfactor*delz*delz*fforce;
virial[3] += rfactor*delx*dely*fforce;
virial[4] += rfactor*delx*delz*fforce;
virial[5] += rfactor*dely*delz*fforce;
}
}
}
/* ---------------------------------------------------------------------- */
void BondMorse::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
d0 = (double *) memory->smalloc((n+1)*sizeof(double),"bond:d0");
alpha = (double *) memory->smalloc((n+1)*sizeof(double),"bond:alpha");
r0 = (double *) memory->smalloc((n+1)*sizeof(double),"bond:r0");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void BondMorse::coeff(int narg, char **arg)
{
if (narg != 4) error->all("Incorrect args for bond coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
double d0_one = atof(arg[1]);
double alpha_one = atof(arg[2]);
double r0_one = atof(arg[3]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
d0[i] = d0_one;
alpha[i] = alpha_one;
r0[i] = r0_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for bond coefficients");
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
------------------------------------------------------------------------- */
double BondMorse::equilibrium_distance(int i)
{
return r0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void BondMorse::write_restart(FILE *fp)
{
fwrite(&d0[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&alpha[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void BondMorse::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&d0[1],sizeof(double),atom->nbondtypes,fp);
fread(&alpha[1],sizeof(double),atom->nbondtypes,fp);
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
}
MPI_Bcast(&d0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
void BondMorse::single(int type, double rsq, int i, int j, double rfactor,
int eflag, double &fforce, double &eng)
{
double r = sqrt(rsq);
double dr = r - r0[type];
double ralpha = exp(-alpha[type]*dr);
// force & energy
if (r > 0.0) fforce = -2.0*d0[type]*alpha[type]*(1-ralpha)*ralpha/r;
else fforce = 0.0;
if (eflag) eng = rfactor * d0[type]*(1-ralpha)*(1-ralpha);
}
/* ----------------------------------------------------------------------
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: Jeff Greathouse (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "bond_morse.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondMorse::BondMorse(LAMMPS *lmp) : Bond(lmp) {}
/* ---------------------------------------------------------------------- */
BondMorse::~BondMorse()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(d0);
memory->sfree(alpha);
memory->sfree(r0);
}
}
/* ---------------------------------------------------------------------- */
void BondMorse::compute(int eflag, int vflag)
{
int i1,i2,n,type,factor;
double delx,dely,delz,rsq,r,dr,fforce,rfactor,ralpha;
energy = 0.0;
if (vflag) for (n = 0; n < 6; n++) virial[n] = 0.0;
double **x = atom->x;
double **f = atom->f;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nbondlist; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
if (newton_bond) factor = 2;
else {
factor = 0;
if (i1 < nlocal) factor++;
if (i2 < nlocal) factor++;
}
rfactor = 0.5 * factor;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
dr = r - r0[type];
ralpha = exp(-alpha[type]*dr);
// force & energy
if (r > 0.0) fforce = -2.0*d0[type]*alpha[type]*(1-ralpha)*ralpha/r;
else fforce = 0.0;
if (eflag) energy += rfactor * d0[type]*(1-ralpha)*(1-ralpha);
// apply force to each of 2 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fforce;
f[i1][1] += dely*fforce;
f[i1][2] += delz*fforce;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fforce;
f[i2][1] -= dely*fforce;
f[i2][2] -= delz*fforce;
}
// virial contribution
if (vflag) {
virial[0] += rfactor*delx*delx*fforce;
virial[1] += rfactor*dely*dely*fforce;
virial[2] += rfactor*delz*delz*fforce;
virial[3] += rfactor*delx*dely*fforce;
virial[4] += rfactor*delx*delz*fforce;
virial[5] += rfactor*dely*delz*fforce;
}
}
}
/* ---------------------------------------------------------------------- */
void BondMorse::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
d0 = (double *) memory->smalloc((n+1)*sizeof(double),"bond:d0");
alpha = (double *) memory->smalloc((n+1)*sizeof(double),"bond:alpha");
r0 = (double *) memory->smalloc((n+1)*sizeof(double),"bond:r0");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void BondMorse::coeff(int narg, char **arg)
{
if (narg != 4) error->all("Incorrect args for bond coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
double d0_one = atof(arg[1]);
double alpha_one = atof(arg[2]);
double r0_one = atof(arg[3]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
d0[i] = d0_one;
alpha[i] = alpha_one;
r0[i] = r0_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for bond coefficients");
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
------------------------------------------------------------------------- */
double BondMorse::equilibrium_distance(int i)
{
return r0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void BondMorse::write_restart(FILE *fp)
{
fwrite(&d0[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&alpha[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void BondMorse::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&d0[1],sizeof(double),atom->nbondtypes,fp);
fread(&alpha[1],sizeof(double),atom->nbondtypes,fp);
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
}
MPI_Bcast(&d0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
void BondMorse::single(int type, double rsq, int i, int j,
int eflag, double &fforce, double &eng)
{
double r = sqrt(rsq);
double dr = r - r0[type];
double ralpha = exp(-alpha[type]*dr);
// force & energy
if (r > 0.0) fforce = -2.0*d0[type]*alpha[type]*(1-ralpha)*ralpha/r;
else fforce = 0.0;
if (eflag) eng = d0[type]*(1-ralpha)*(1-ralpha);
}

82
src/MOLECULE/bond_morse.h
View File

@ -1,41 +1,41 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifndef BOND_MORSE_H
#define BOND_MORSE_H
#include "stdio.h"
#include "bond.h"
namespace LAMMPS_NS {
class BondMorse : public Bond {
public:
BondMorse(class LAMMPS *);
~BondMorse();
void compute(int, int);
void coeff(int, char **);
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double, int, double &, double &);
private:
double *d0,*alpha,*r0;
void allocate();
};
}
#endif
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifndef BOND_MORSE_H
#define BOND_MORSE_H
#include "stdio.h"
#include "bond.h"
namespace LAMMPS_NS {
class BondMorse : public Bond {
public:
BondMorse(class LAMMPS *);
~BondMorse();
void compute(int, int);
void coeff(int, char **);
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, int, double &, double &);
private:
double *d0,*alpha,*r0;
void allocate();
};
}
#endif

4
src/MOLECULE/bond_nonlinear.cpp
View File

@ -198,7 +198,7 @@ void BondNonlinear::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondNonlinear::single(int type, double rsq, int i, int j, double rfactor,
void BondNonlinear::single(int type, double rsq, int i, int j,
int eflag, double &fforce, double &eng)
{
double r = sqrt(rsq);
@ -211,5 +211,5 @@ void BondNonlinear::single(int type, double rsq, int i, int j, double rfactor,
// force & energy
fforce = -epsilon[type]/r * 2.0*dr*lamdasq/denomsq;
if (eflag) eng = rfactor * epsilon[type] * drsq / denom;
if (eflag) eng = epsilon[type] * drsq / denom;
}

2
src/MOLECULE/bond_nonlinear.h
View File

@ -28,7 +28,7 @@ class BondNonlinear : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double, int, double &, double &);
void single(int, double, int, int, int, double &, double &);
private:
double *epsilon,*r0,*lamda;

6
src/MOLECULE/bond_quartic.cpp
View File

@ -295,7 +295,7 @@ void BondQuartic::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
void BondQuartic::single(int type, double rsq, int i, int j, double rfactor,
void BondQuartic::single(int type, double rsq, int i, int j,
int eflag, double &fforce, double &eng)
{
double r,dr,r2,ra,rb,sr2,sr6;
@ -334,7 +334,7 @@ void BondQuartic::single(int type, double rsq, int i, int j, double rfactor,
}
if (eflag) {
eng += rfactor*(k[type]*r2*ra*rb + u0[type]);
if (rsq < TWO_1_3) eng += rfactor * (4.0*sr6*(sr6-1.0) + 1.0);
eng += k[type]*r2*ra*rb + u0[type];
if (rsq < TWO_1_3) eng += 4.0*sr6*(sr6-1.0) + 1.0;
}
}

2
src/MOLECULE/bond_quartic.h
View File

@ -29,7 +29,7 @@ class BondQuartic : public Bond {
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, double, int, int, double, int, double &, double &);
void single(int, double, int, int, int, double &, double &);
private:
double TWO_1_3;