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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9013 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-10-26 23:01:35 +00:00
parent 8663c92293
commit 8bd8b77489
15 changed files with 2613 additions and 0 deletions
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28
src/USER-MISC/Install.sh
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@ -10,12 +10,19 @@ if (test $1 = 1) then
cp angle_cosine_shift.cpp .. cp angle_cosine_shift.cpp ..
cp angle_cosine_shift_exp.cpp .. cp angle_cosine_shift_exp.cpp ..
cp angle_dipole.cpp .. cp angle_dipole.cpp ..
cp angle_fourier.cpp ..
cp angle_fourier_simple.cpp ..
cp angle_quartic.cpp ..
cp bond_harmonic_shift.cpp .. cp bond_harmonic_shift.cpp ..
cp bond_harmonic_shift_cut.cpp .. cp bond_harmonic_shift_cut.cpp ..
cp compute_ackland_atom.cpp .. cp compute_ackland_atom.cpp ..
cp compute_temp_rotate.cpp .. cp compute_temp_rotate.cpp ..
cp dihedral_cosine_shift_exp.cpp .. cp dihedral_cosine_shift_exp.cpp ..
cp dihedral_fourier.cpp ..
cp dihedral_nharmonic.cpp ..
cp dihedral_quadratic.cpp ..
cp dihedral_table.cpp .. cp dihedral_table.cpp ..
cp improper_fourier.cpp ..
cp fix_addtorque.cpp .. cp fix_addtorque.cpp ..
cp fix_imd.cpp .. cp fix_imd.cpp ..
cp fix_smd.cpp .. cp fix_smd.cpp ..
@ -32,12 +39,19 @@ if (test $1 = 1) then
cp angle_cosine_shift.h .. cp angle_cosine_shift.h ..
cp angle_cosine_shift_exp.h .. cp angle_cosine_shift_exp.h ..
cp angle_dipole.h .. cp angle_dipole.h ..
cp angle_fourier.h ..
cp angle_fourier_simple.h ..
cp angle_quartic.h ..
cp bond_harmonic_shift.h .. cp bond_harmonic_shift.h ..
cp bond_harmonic_shift_cut.h .. cp bond_harmonic_shift_cut.h ..
cp compute_ackland_atom.h .. cp compute_ackland_atom.h ..
cp compute_temp_rotate.h .. cp compute_temp_rotate.h ..
cp dihedral_cosine_shift_exp.h .. cp dihedral_cosine_shift_exp.h ..
cp dihedral_fourier.h ..
cp dihedral_nharmonic.h ..
cp dihedral_quadratic.h ..
cp dihedral_table.h .. cp dihedral_table.h ..
cp improper_fourier.h ..
cp fix_addtorque.h .. cp fix_addtorque.h ..
cp fix_imd.h .. cp fix_imd.h ..
cp fix_smd.h .. cp fix_smd.h ..
@ -55,13 +69,20 @@ elif (test $1 = 0) then
rm -f ../angle_cosine_shift.cpp rm -f ../angle_cosine_shift.cpp
rm -f ../angle_cosine_shift_exp.cpp rm -f ../angle_cosine_shift_exp.cpp
rm -f ../angle_fourier.cpp
rm -f ../angle_fourier_simple.cpp
rm -f ../angle_dipole.cpp rm -f ../angle_dipole.cpp
rm -f ../angle_quartic.cpp
rm -f ../bond_harmonic_shift.cpp rm -f ../bond_harmonic_shift.cpp
rm -f ../bond_harmonic_shift_cut.cpp rm -f ../bond_harmonic_shift_cut.cpp
rm -f ../compute_ackland_atom.cpp rm -f ../compute_ackland_atom.cpp
rm -f ../compute_temp_rotate.cpp rm -f ../compute_temp_rotate.cpp
rm -f ../dihedral_cosine_shift_exp.cpp rm -f ../dihedral_cosine_shift_exp.cpp
rm -f ../dihedral_fourier.cpp
rm -f ../dihedral_nharmonic.cpp
rm -f ../dihedral_quadratic.cpp
rm -f ../dihedral_table.cpp rm -f ../dihedral_table.cpp
rm -f ../improper_fourier.cpp
rm -f ../fix_addtorque.cpp rm -f ../fix_addtorque.cpp
rm -f ../fix_imd.cpp rm -f ../fix_imd.cpp
rm -f ../fix_smd.cpp rm -f ../fix_smd.cpp
@ -79,12 +100,19 @@ elif (test $1 = 0) then
rm -f ../angle_cosine_shift.h rm -f ../angle_cosine_shift.h
rm -f ../angle_cosine_shift_exp.h rm -f ../angle_cosine_shift_exp.h
rm -f ../angle_dipole.h rm -f ../angle_dipole.h
rm -f ../angle_fourier.h
rm -f ../angle_fourier_simple.h
rm -f ../angle_quartic.h
rm -f ../bond_harmonic_shift.h rm -f ../bond_harmonic_shift.h
rm -f ../bond_harmonic_shift_cut.h rm -f ../bond_harmonic_shift_cut.h
rm -f ../compute_ackland_atom.h rm -f ../compute_ackland_atom.h
rm -f ../compute_temp_rotate.h rm -f ../compute_temp_rotate.h
rm -f ../dihedral_cosine_shift_exp.h rm -f ../dihedral_cosine_shift_exp.h
rm -f ../dihedral_fourier.h
rm -f ../dihedral_nharmonic.h
rm -f ../dihedral_quadratic.h
rm -f ../dihedral_table.h rm -f ../dihedral_table.h
rm -f ../improper_fourier.h
rm -f ../fix_addtorque.h rm -f ../fix_addtorque.h
rm -f ../fix_imd.h rm -f ../fix_imd.h
rm -f ../fix_smd.h rm -f ../fix_smd.h

268
src/USER-MISC/angle_fourier.cpp Normal file
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@ -0,0 +1,268 @@
/* ----------------------------------------------------------------------
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: Loukas D. Peristeras (Scienomics SARL)
[ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)]
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "angle_fourier.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
AngleFourier::AngleFourier(LAMMPS *lmp) : Angle(lmp) {}
/* ---------------------------------------------------------------------- */
AngleFourier::~AngleFourier()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
memory->destroy(C0);
memory->destroy(C1);
memory->destroy(C2);
}
}
/* ---------------------------------------------------------------------- */
void AngleFourier::compute(int eflag, int vflag)
{
int i1,i2,i3,n,type;
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
double term;
double rsq1,rsq2,r1,r2,c,c2,a,a11,a12,a22;
eangle = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **anglelist = neighbor->anglelist;
int nanglelist = neighbor->nanglelist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nanglelist; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
// force & energy
c2 = 2.0*c*c-1.0;
term = k[type]*(C0[type]+C1[type]*c+C2[type]*c2);
if (eflag) eangle = term;
a = k[type]*(C1[type]+4.0*C2[type]*c);
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
f3[0] = a22*delx2 + a12*delx1;
f3[1] = a22*dely2 + a12*dely1;
f3[2] = a22*delz2 + a12*delz1;
// apply force to each of 3 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] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
delx1,dely1,delz1,delx2,dely2,delz2);
}
}
/* ---------------------------------------------------------------------- */
void AngleFourier::allocate()
{
allocated = 1;
int n = atom->nangletypes;
memory->create(k,n+1,"angle:k");
memory->create(C0,n+1,"angle:C0");
memory->create(C1,n+1,"angle:C1");
memory->create(C2,n+1,"angle:C2");
memory->create(setflag,n+1,"angle:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void AngleFourier::coeff(int narg, char **arg)
{
if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nangletypes,ilo,ihi);
double k_one = force->numeric(arg[1]);
double C0_one = force->numeric(arg[2]);
double C1_one = force->numeric(arg[3]);
double C2_one = force->numeric(arg[4]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
C0[i] = C0_one;
C1[i] = C1_one;
C2[i] = C2_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
}
/* ---------------------------------------------------------------------- */
double AngleFourier::equilibrium_angle(int i)
{
double ret=MY_PI;
if ( C2[i] != 0.0 ) {
ret = (C1[i]/4.0/C2[i]);
if ( abs(ret) <= 1.0 ) ret = acos(-ret);
}
return ret;
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleFourier::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
fwrite(&C0[1],sizeof(double),atom->nangletypes,fp);
fwrite(&C1[1],sizeof(double),atom->nangletypes,fp);
fwrite(&C2[1],sizeof(double),atom->nangletypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleFourier::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nangletypes,fp);
fread(&C0[1],sizeof(double),atom->nangletypes,fp);
fread(&C1[1],sizeof(double),atom->nangletypes,fp);
fread(&C2[1],sizeof(double),atom->nangletypes,fp);
}
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&C0[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&C1[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&C2[1],atom->nangletypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
double AngleFourier::single(int type, int i1, int i2, int i3)
{
double **x = atom->x;
double delx1 = x[i1][0] - x[i2][0];
double dely1 = x[i1][1] - x[i2][1];
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(delx2,dely2,delz2);
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
double c2 = 2.0*c*c-1.0;
double eng = k[type]*(C0[type]+C1[type]*c+C2[type]*c2);
return eng;
}

48
src/USER-MISC/angle_fourier.h Normal file
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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.
------------------------------------------------------------------------- */
#ifdef ANGLE_CLASS
AngleStyle(fourier,AngleFourier)
#else
#ifndef ANGLE_FOURIER_H
#define ANGLE_FOURIER_H
#include "stdio.h"
#include "angle.h"
namespace LAMMPS_NS {
class AngleFourier : public Angle {
public:
AngleFourier(class LAMMPS *);
virtual ~AngleFourier();
virtual void compute(int, int);
void coeff(int, char **);
double equilibrium_angle(int);
void write_restart(FILE *);
void read_restart(FILE *);
virtual double single(int, int, int, int);
protected:
double *k,*C0,*C1,*C2;
void allocate();
};
}
#endif
#endif

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src/USER-MISC/angle_fourier_simple.cpp Normal file
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@ -0,0 +1,274 @@
/* ----------------------------------------------------------------------
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: Loukas D. Peristeras (Scienomics SARL)
[ based on angle_cosine_quared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)]
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "angle_fourier_simple.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
AngleFourierSimple::AngleFourierSimple(LAMMPS *lmp) : Angle(lmp) {}
/* ---------------------------------------------------------------------- */
AngleFourierSimple::~AngleFourierSimple()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
memory->destroy(C);
memory->destroy(N);
}
}
/* ---------------------------------------------------------------------- */
void AngleFourierSimple::compute(int eflag, int vflag)
{
int i1,i2,i3,n,type;
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
double term,sgn;
double rsq1,rsq2,r1,r2,c,cn,th,nth,a,a11,a12,a22;
eangle = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **anglelist = neighbor->anglelist;
int nanglelist = neighbor->nanglelist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nanglelist; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
// force & energy
th = acos(c);
nth = N[type]*acos(c);
cn = cos(nth);
term = k[type]*(1.0+C[type]*cn);
if (eflag) eangle = term;
// handle sin(n th)/sin(th) singulatiries
if ( abs(c)-1.0 > 0.0001 )
{
a = k[type]*C[type]*N[type]*sin(nth)/sin(th);
} else {
if ( c >= 0.0 ) {
term = 1.0 - c;
sgn = 1.0;
} else {
term = 1.0 + c;
sgn = ( fmodf((float)(N[type]),2.0) == 0.0f )?-1.0:1.0;
}
a = N[type]+N[type]*(1.0-N[type]*N[type])*term/3.0;
a = k[type]*C[type]*N[type]*(double)(sgn)*a;
}
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
f3[0] = a22*delx2 + a12*delx1;
f3[1] = a22*dely2 + a12*dely1;
f3[2] = a22*delz2 + a12*delz1;
// apply force to each of 3 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] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
delx1,dely1,delz1,delx2,dely2,delz2);
}
}
/* ---------------------------------------------------------------------- */
void AngleFourierSimple::allocate()
{
allocated = 1;
int n = atom->nangletypes;
memory->create(k,n+1,"angle:k");
memory->create(C,n+1,"angle:C");
memory->create(N,n+1,"angle:N");
memory->create(setflag,n+1,"angle:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void AngleFourierSimple::coeff(int narg, char **arg)
{
if (narg != 4) error->all(FLERR,"Incorrect args for angle coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nangletypes,ilo,ihi);
double k_one = force->numeric(arg[1]);
double C_one = force->numeric(arg[2]);
double N_one = force->numeric(arg[3]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
C[i] = C_one;
N[i] = N_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
}
/* ---------------------------------------------------------------------- */
double AngleFourierSimple::equilibrium_angle(int i)
{
return (MY_PI/N[i]);
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleFourierSimple::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
fwrite(&C[1],sizeof(double),atom->nangletypes,fp);
fwrite(&N[1],sizeof(double),atom->nangletypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleFourierSimple::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nangletypes,fp);
fread(&C[1],sizeof(double),atom->nangletypes,fp);
fread(&N[1],sizeof(double),atom->nangletypes,fp);
}
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&C[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&N[1],atom->nangletypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
double AngleFourierSimple::single(int type, int i1, int i2, int i3)
{
double **x = atom->x;
double delx1 = x[i1][0] - x[i2][0];
double dely1 = x[i1][1] - x[i2][1];
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(delx2,dely2,delz2);
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
double cn = cos(N[type]*acos(c));
double eng = k[type]*(1.0+C[type]*cn);
return eng;
}

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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.
------------------------------------------------------------------------- */
#ifdef ANGLE_CLASS
AngleStyle(fourier/simple,AngleFourierSimple)
#else
#ifndef ANGLE_FOURIER_SIMPLE_H
#define ANGLE_FOURIER_SIMPLE_H
#include "stdio.h"
#include "angle.h"
namespace LAMMPS_NS {
class AngleFourierSimple : public Angle {
public:
AngleFourierSimple(class LAMMPS *);
virtual ~AngleFourierSimple();
virtual void compute(int, int);
void coeff(int, char **);
double equilibrium_angle(int);
void write_restart(FILE *);
void read_restart(FILE *);
virtual double single(int, int, int, int);
protected:
double *k,*C,*N;
void allocate();
};
}
#endif
#endif

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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: Loukas D. Peristeras (Scienomics SARL)
[ based on angle_harmonic.cpp]
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "angle_quartic.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
AngleQuartic::AngleQuartic(LAMMPS *lmp) : Angle(lmp) {}
/* ---------------------------------------------------------------------- */
AngleQuartic::~AngleQuartic()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k2);
memory->destroy(k3);
memory->destroy(k4);
memory->destroy(theta0);
}
}
/* ---------------------------------------------------------------------- */
void AngleQuartic::compute(int eflag, int vflag)
{
int i1,i2,i3,n,type;
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
double dtheta,dtheta2,dtheta3,dtheta4,tk;
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
eangle = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **anglelist = neighbor->anglelist;
int nanglelist = neighbor->nanglelist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nanglelist; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
// force & energy
dtheta = acos(c) - theta0[type];
dtheta2 = dtheta * dtheta;
dtheta3 = dtheta2 * dtheta;
tk = 2.0 * k2[type] * dtheta + 3.0 * k3[type] * dtheta2 + 4.0 * k4[type] * dtheta3;
if (eflag) {
dtheta4 = dtheta3 * dtheta;
eangle = k2[type] * dtheta2 + k3[type] * dtheta3 + k4[type] * dtheta4;
}
a = -2.0 * tk * s;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
f3[0] = a22*delx2 + a12*delx1;
f3[1] = a22*dely2 + a12*dely1;
f3[2] = a22*delz2 + a12*delz1;
// apply force to each of 3 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] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
delx1,dely1,delz1,delx2,dely2,delz2);
}
}
/* ---------------------------------------------------------------------- */
void AngleQuartic::allocate()
{
allocated = 1;
int n = atom->nangletypes;
memory->create(k2,n+1,"angle:k2");
memory->create(k3,n+1,"angle:k3");
memory->create(k4,n+1,"angle:k4");
memory->create(theta0,n+1,"angle:theta0");
memory->create(setflag,n+1,"angle:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void AngleQuartic::coeff(int narg, char **arg)
{
if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nangletypes,ilo,ihi);
double theta0_one = force->numeric(arg[1]);
double k2_one = force->numeric(arg[2]);
double k3_one = force->numeric(arg[3]);
double k4_one = force->numeric(arg[4]);
// convert theta0 from degrees to radians
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k2[i] = k2_one;
k3[i] = k3_one;
k4[i] = k4_one;
theta0[i] = theta0_one/180.0 * MY_PI;
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
}
/* ---------------------------------------------------------------------- */
double AngleQuartic::equilibrium_angle(int i)
{
return theta0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleQuartic::write_restart(FILE *fp)
{
fwrite(&k2[1],sizeof(double),atom->nangletypes,fp);
fwrite(&k3[1],sizeof(double),atom->nangletypes,fp);
fwrite(&k4[1],sizeof(double),atom->nangletypes,fp);
fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleQuartic::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k2[1],sizeof(double),atom->nangletypes,fp);
fread(&k3[1],sizeof(double),atom->nangletypes,fp);
fread(&k4[1],sizeof(double),atom->nangletypes,fp);
fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
}
MPI_Bcast(&k2[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k3[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k4[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
double AngleQuartic::single(int type, int i1, int i2, int i3)
{
double **x = atom->x;
double delx1 = x[i1][0] - x[i2][0];
double dely1 = x[i1][1] - x[i2][1];
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(delx2,dely2,delz2);
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
double dtheta = acos(c) - theta0[type];
double dtheta2 = dtheta * dtheta;
double dtheta3 = dtheta2 * dtheta;
double dtheta4 = dtheta3 * dtheta;
double tk = 2.0 * k2[type] * dtheta + 3.0 * k3[type] * dtheta2 + 4.0 * k4[type] * dtheta3;
return k2[type] * dtheta2 + k3[type] * dtheta3 + k4[type] * dtheta4;
}

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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.
------------------------------------------------------------------------- */
#ifdef ANGLE_CLASS
AngleStyle(quartic,AngleQuartic)
#else
#ifndef LMP_ANGLE_QUARTIC_H
#define LMP_ANGLE_QUARTIC_H
#include "stdio.h"
#include "angle.h"
namespace LAMMPS_NS {
class AngleQuartic : public Angle {
public:
AngleQuartic(class LAMMPS *);
virtual ~AngleQuartic();
virtual void compute(int, int);
void coeff(int, char **);
double equilibrium_angle(int);
void write_restart(FILE *);
void read_restart(FILE *);
double single(int, int, int, int);
protected:
double *k2, *k3, *k4, *theta0;
void allocate();
};
}
#endif
#endif

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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: Loukas D. Peristeras (Scienomics SARL)
[ based on dihedral_charmm.cpp Paul Crozier (SNL) ]
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "dihedral_fourier.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "pair.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
/* ---------------------------------------------------------------------- */
DihedralFourier::DihedralFourier(LAMMPS *lmp) : Dihedral(lmp) {}
/* ---------------------------------------------------------------------- */
DihedralFourier::~DihedralFourier()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(nterms);
for (int i=1; i<= atom->ndihedraltypes; i++) {
if ( k[i] ) delete [] k[i];
if ( multiplicity[i] ) delete [] multiplicity[i];
if ( shift[i] ) delete [] shift[i];
if ( cos_shift[i] ) delete [] cos_shift[i];
if ( sin_shift[i] ) delete [] sin_shift[i];
}
delete [] k;
delete [] multiplicity;
delete [] shift;
delete [] cos_shift;
delete [] sin_shift;
}
}
/* ---------------------------------------------------------------------- */
void DihedralFourier::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,i,j,m,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 ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double df,df1_,ddf1_,fg,hg,fga,hgb,gaa,gbb;
double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
double c,s,p,p_,sx2,sy2,sz2;
int itype,jtype;
double delx,dely,delz,rsq,r2inv,r6inv;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *atomtype = atom->type;
int **dihedrallist = neighbor->dihedrallist;
int ndihedrallist = neighbor->ndihedrallist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
double qqrd2e = force->qqrd2e;
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);
ax = vb1y*vb2zm - vb1z*vb2ym;
ay = vb1z*vb2xm - vb1x*vb2zm;
az = vb1x*vb2ym - vb1y*vb2xm;
bx = vb3y*vb2zm - vb3z*vb2ym;
by = vb3z*vb2xm - vb3x*vb2zm;
bz = vb3x*vb2ym - vb3y*vb2xm;
rasq = ax*ax + ay*ay + az*az;
rbsq = bx*bx + by*by + bz*bz;
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
rginv = ra2inv = rb2inv = 0.0;
if (rg > 0) rginv = 1.0/rg;
if (rasq > 0) ra2inv = 1.0/rasq;
if (rbsq > 0) rb2inv = 1.0/rbsq;
rabinv = sqrt(ra2inv*rb2inv);
c = (ax*bx + ay*by + az*bz)*rabinv;
s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
// 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 and energy
// p = sum(i=1,nterms) k_i*(1+cos(n_i*phi-d_i)
// dp = dp / dphi
edihedral = 0.0;
df = 0.0;
for (j=0; j<nterms[type]; j++)
{
m = multiplicity[type][j];
p_ = 1.0;
df1_ = 0.0;
for (i = 0; i < m; i++) {
ddf1_ = p_*c - df1_*s;
df1_ = p_*s + df1_*c;
p_ = ddf1_;
}
p_ = p_*cos_shift[type][j] + df1_*sin_shift[type][j];
df1_ = df1_*cos_shift[type][j] - ddf1_*sin_shift[type][j];
df1_ *= -m;
p_ += 1.0;
if (m == 0) {
p_ = 1.0 + cos_shift[type][j];
df1_ = 0.0;
}
if (eflag) edihedral += k[type][j] * p_;
df += (-k[type][j] * df1_);
}
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
fga = fg*ra2inv*rginv;
hgb = hg*rb2inv*rginv;
gaa = -ra2inv*rg;
gbb = rb2inv*rg;
dtfx = gaa*ax;
dtfy = gaa*ay;
dtfz = gaa*az;
dtgx = fga*ax - hgb*bx;
dtgy = fga*ay - hgb*by;
dtgz = fga*az - hgb*bz;
dthx = gbb*bx;
dthy = gbb*by;
dthz = gbb*bz;
sx2 = df*dtgx;
sy2 = df*dtgy;
sz2 = df*dtgz;
f1[0] = df*dtfx;
f1[1] = df*dtfy;
f1[2] = df*dtfz;
f2[0] = sx2 - f1[0];
f2[1] = sy2 - f1[1];
f2[2] = sz2 - f1[2];
f4[0] = df*dthx;
f4[1] = df*dthy;
f4[2] = df*dthz;
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 DihedralFourier::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
memory->create(nterms,n+1,"dihedral:nterms");
k = new double * [n+1];
multiplicity = new int * [n+1];
shift = new int * [n+1];
cos_shift = new double * [n+1];
sin_shift = new double * [n+1];
for (int i = 1; i <= n; i++) {
k[i] = cos_shift[i] = sin_shift[i] = 0;
multiplicity[i] = shift[i] = 0;
}
memory->create(setflag,n+1,"dihedral:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void DihedralFourier::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);
// require integer values of shift for backwards compatibility
// arbitrary phase angle shift could be allowed, but would break
// backwards compatibility and is probably not needed
double k_one;
int multiplicity_one;
int shift_one;
int nterms_one = force->inumeric(arg[1]);
if (nterms_one < 1)
error->all(FLERR,"Incorrect number of terms arg for dihedral coefficients");
if (2+3*nterms_one < narg)
error->all(FLERR,"Incorrect number of arguments for dihedral coefficients");
int count = 0;
for (int i = ilo; i <= ihi; i++) {
nterms[i] = nterms_one;
k[i] = new double [nterms_one];
multiplicity[i] = new int [nterms_one];
shift[i] = new int [nterms_one];
cos_shift[i] = new double [nterms_one];
sin_shift[i] = new double [nterms_one];
for (int j = 0; j<nterms_one; j++) {
int offset = 1+3*j;
k_one = force->numeric(arg[offset+1]);
multiplicity_one = force->inumeric(arg[offset+2]);
shift_one = force->inumeric(arg[offset+3]);
k[i][j] = k_one;
multiplicity[i][j] = multiplicity_one;
shift[i][j] = shift_one;
cos_shift[i][j] = cos(MY_PI*shift_one/180.0);
sin_shift[i][j] = sin(MY_PI*shift_one/180.0);
}
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralFourier::write_restart(FILE *fp)
{
fwrite(&nterms[1],sizeof(int),atom->ndihedraltypes,fp);
for(int i = 1; i <= atom->ndihedraltypes; i++) {
fwrite(k[i],sizeof(double),nterms[i],fp);
fwrite(multiplicity[i],sizeof(int),nterms[i],fp);
fwrite(shift[i],sizeof(int),nterms[i],fp);
}
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralFourier::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0)
fread(&nterms[1],sizeof(int),atom->ndihedraltypes,fp);
MPI_Bcast(&nterms[1],atom->ndihedraltypes,MPI_INT,0,world);
// allocate
for (int i=1; i<=atom->ndihedraltypes; i++) {
k[i] = new double [nterms[i]];
multiplicity[i] = new int [nterms[i]];
shift[i] = new int [nterms[i]];
cos_shift[i] = new double [nterms[i]];
sin_shift[i] = new double [nterms[i]];
}
if (comm->me == 0) {
for (int i=1; i<=atom->ndihedraltypes; i++) {
fread(k[i],sizeof(double),nterms[i],fp);
fread(multiplicity[i],sizeof(int),nterms[i],fp);
fread(shift[i],sizeof(int),nterms[i],fp);
}
}
for (int i=1; i<=atom->ndihedraltypes; i++) {
MPI_Bcast(k[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(multiplicity[i],nterms[i],MPI_INT,0,world);
MPI_Bcast(shift[i],nterms[i],MPI_INT,0,world);
}
for (int i=1; i <= atom->ndihedraltypes; i++) {
setflag[i] = 1;
for (int j = 0; j < nterms[i]; j++) {
cos_shift[i][j] = cos(MY_PI*shift[i][j]/180.0);
sin_shift[i][j] = sin(MY_PI*shift[i][j]/180.0);
}
}
}

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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.
------------------------------------------------------------------------- */
#ifdef DIHEDRAL_CLASS
DihedralStyle(fourier,DihedralFourier)
#else
#ifndef LMP_DIHEDRAL_FOURIER_H
#define LMP_DIHEDRAL_FOURIER_H
#include "stdio.h"
#include "dihedral.h"
namespace LAMMPS_NS {
class DihedralFourier : public Dihedral {
public:
DihedralFourier(class LAMMPS *);
virtual ~DihedralFourier();
virtual void compute(int, int);
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
protected:
double **k,**cos_shift,**sin_shift;
int **multiplicity,**shift;
int *nterms;
int implicit,weightflag;
void allocate();
};
}
#endif
#endif

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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: Loukas D. Peristeras (Scienomics SARL)
[ based on dihedral_multi_harmonic.cpp Mathias Puetz (SNL) and friends ]
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "dihedral_nharmonic.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.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
/* ---------------------------------------------------------------------- */
DihedralNHarmonic::DihedralNHarmonic(LAMMPS *lmp) : Dihedral(lmp) {}
/* ---------------------------------------------------------------------- */
DihedralNHarmonic::~DihedralNHarmonic()
{
if (allocated) {
memory->destroy(setflag);
for (int i = 1; i <= atom->ndihedraltypes; i++)
delete [] a[i];
delete [] a;
delete [] nterms;
}
}
/* ---------------------------------------------------------------------- */
void DihedralNHarmonic::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,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;
// 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);
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,n) a_i * c**(i-1)
// pd = dp/dc
p = this->a[type][0];
pd = this->a[type][1];
for (int i = 1; i < nterms[type]-1; i++) {
p += c * this->a[type][i];
pd += c * static_cast<double>(i+1) * this->a[type][i+1];
c *= c;
}
p += c * this->a[type][nterms[type]-1];
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 DihedralNHarmonic::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
memory->create(nterms,n+1,"dihedral:nt");
a = new double * [n+1];
memory->create(setflag,n+1,"dihedral:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void DihedralNHarmonic::coeff(int narg, char **arg)
{
if (narg < 4 ) error->all(FLERR,"Incorrect args for dihedral coefficients");
int n = force->inumeric(arg[1]);
if (narg != n + 2 ) error->all(FLERR,"Incorrect args for dihedral coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
a[i] = new double [n];
nterms[i] = n;
for (int j = 0; j < n; j++ ) {
a[i][j] = force->numeric(arg[2+i]);
setflag[i] = 1;
}
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralNHarmonic::write_restart(FILE *fp)
{
fwrite(&nterms[1],sizeof(int),atom->ndihedraltypes,fp);
for(int i = 1; i <= atom->ndihedraltypes; i++)
fwrite(a[i],sizeof(double),nterms[i],fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralNHarmonic::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0)
fread(&nterms[1],sizeof(int),atom->ndihedraltypes,fp);
MPI_Bcast(&nterms[1],atom->ndihedraltypes,MPI_INT,0,world);
// allocate
for(int i = 1; i <= atom->ndihedraltypes; i++)
a[i] = new double [nterms[i]];
if (comm->me == 0) {
for(int i = 1; i <= atom->ndihedraltypes; i++)
fread(a[i],sizeof(double),nterms[i],fp);
}
for (int i = 1; i <= atom->ndihedraltypes; i++ )
MPI_Bcast(a[i],nterms[i],MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}

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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.
------------------------------------------------------------------------- */
#ifdef DIHEDRAL_CLASS
DihedralStyle(n/harmonic,DihedralNHarmonic)
#else
#ifndef DIHEDRAL_NHARMONIC_H
#define DIHEDRAL_NHARMONIC_H
#include "stdio.h"
#include "dihedral.h"
namespace LAMMPS_NS {
class DihedralNHarmonic : public Dihedral {
public:
DihedralNHarmonic(class LAMMPS *);
~DihedralNHarmonic();
void compute(int, int);
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
protected:
int *nterms;
double **a;
void allocate();
};
}
#endif
#endif

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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: Loukas D. Peristeras (Scienomics SARL)
[ based on dihedral_helix.cpp Paul Crozier (SNL) ]
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "dihedral_quadratic.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
/* ---------------------------------------------------------------------- */
DihedralQuadratic::DihedralQuadratic(LAMMPS *lmp) : Dihedral(lmp) {}
/* ---------------------------------------------------------------------- */
DihedralQuadratic::~DihedralQuadratic()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
memory->destroy(phi0);
}
}
/* ---------------------------------------------------------------------- */
void DihedralQuadratic::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,i,m,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;
// force & energy
// p = k ( phi- phi0)^2
// pd = dp/dc
phi = acos(c);
if (dx < 0.0) phi *= -1.0;
si = sin(phi);
double dphi = phi-phi0[type];
p = k[type]*dphi;
if (fabs(si) < SMALLER) {
pd = - 2.0 * k[type];
} else {
pd = - 2.0 * p / si;
}
p = p * dphi;
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 DihedralQuadratic::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
memory->create(k,n+1,"dihedral:k");
memory->create(phi0,n+1,"dihedral:phi0");
memory->create(setflag,n+1,"dihedral:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void DihedralQuadratic::coeff(int narg, char **arg)
{
if (narg != 3) error->all(FLERR,"Incorrect args for dihedral coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
double k_one = force->numeric(arg[1]);
double phi0_one= force->numeric(arg[2]);
// require k >= 0
if (k_one < 0.0)
error->all(FLERR,"Incorrect coefficient arg for dihedral coefficients");
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
phi0[i] = phi0_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 DihedralQuadratic::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&phi0[1],sizeof(double),atom->ndihedraltypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralQuadratic::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&phi0[1],sizeof(int),atom->ndihedraltypes,fp);
}
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&phi0[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}

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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.
------------------------------------------------------------------------- */
#ifdef DIHEDRAL_CLASS
DihedralStyle(quadratic,DihedralQuadratic)
#else
#ifndef LMP_DIHEDRAL_QUADRATIC_H
#define LMP_DIHEDRAL_QUADRATIC_H
#include "stdio.h"
#include "dihedral.h"
namespace LAMMPS_NS {
class DihedralQuadratic : public Dihedral {
public:
DihedralQuadratic(class LAMMPS *);
~DihedralQuadratic();
void compute(int, int);
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
protected:
double *k,*phi0;
int *sign,*multiplicity;
void allocate();
};
}
#endif
#endif

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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: Loukas D. Peristeras (Scienomics SARL)
[ based on improper_umbrella.cpp Tod A Pascal (Caltech) ]
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "improper_fourier.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
/* ---------------------------------------------------------------------- */
ImproperFourier::ImproperFourier(LAMMPS *lmp) : Improper(lmp) {}
/* ---------------------------------------------------------------------- */
ImproperFourier::~ImproperFourier()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
memory->destroy(C0);
memory->destroy(C1);
memory->destroy(C2);
}
}
/* ---------------------------------------------------------------------- */
void ImproperFourier::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
int **improperlist = neighbor->improperlist;
int nimproperlist = neighbor->nimproperlist;
for (n = 0; n < nimproperlist; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
// 1st bond
vb1x = x[i2][0] - x[i1][0];
vb1y = x[i2][1] - x[i1][1];
vb1z = x[i2][2] - x[i1][2];
domain->minimum_image(vb1x,vb1y,vb1z);
// 2nd bond
vb2x = x[i3][0] - x[i1][0];
vb2y = x[i3][1] - x[i1][1];
vb2z = x[i3][2] - x[i1][2];
domain->minimum_image(vb2x,vb2y,vb2z);
// 3rd bond
vb3x = x[i4][0] - x[i1][0];
vb3y = x[i4][1] - x[i1][1];
vb3z = x[i4][2] - x[i1][2];
domain->minimum_image(vb3x,vb3y,vb3z);
addone(i1,i2,i3,i4, type,evflag,eflag,
vb1x, vb1y, vb1z,
vb2x, vb2y, vb2z,
vb3x, vb3y, vb3z);
if ( all[type] ) {
addone(i1,i4,i2,i3, type,evflag,eflag,
vb3x, vb3y, vb3z,
vb1x, vb1y, vb1z,
vb2x, vb2y, vb2z);
addone(i1,i3,i4,i2, type,evflag,eflag,
vb2x, vb2y, vb2z,
vb3x, vb3y, vb3z,
vb1x, vb1y, vb1z);
}
}
}
void ImproperFourier::addone(const int &i1,const int &i2,const int &i3,const int &i4,
const int &type,const int &evflag,const int &eflag,
const double &vb1x, const double &vb1y, const double &vb1z,
const double &vb2x, const double &vb2y, const double &vb2z,
const double &vb3x, const double &vb3y, const double &vb3z)
{
int n;
double eimproper,f1[3],f2[3],f3[3],f4[3];
double domega,c,c2,a,s,projhfg,dhax,dhay,dhaz,dahx,dahy,dahz,cotphi;
double ax,ay,az,ra2,rh2,ra,rh,rar,rhr,arx,ary,arz,hrx,hry,hrz;
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
eimproper = 0.0;
// c0 calculation
// A = vb1 X vb2 is perpendicular to IJK plane
ax = vb1y*vb2z-vb1z*vb2y;
ay = vb1z*vb2x-vb1x*vb2z;
az = vb1x*vb2y-vb1y*vb2x;
ra2 = ax*ax+ay*ay+az*az;
rh2 = vb3x*vb3x+vb3y*vb3y+vb3z*vb3z;
ra = sqrt(ra2);
rh = sqrt(rh2);
if (ra < SMALL) ra = SMALL;
if (rh < SMALL) rh = SMALL;
rar = 1/ra;
rhr = 1/rh;
arx = ax*rar;
ary = ay*rar;
arz = az*rar;
hrx = vb3x*rhr;
hry = vb3y*rhr;
hrz = vb3z*rhr;
c = arx*hrx+ary*hry+arz*hrz;
// 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,
"Improper 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) s = 1.0;
if (c < -1.0) s = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
cotphi = c/s;
projhfg = (vb3x*vb1x+vb3y*vb1y+vb3z*vb1z) /
sqrt(vb1x*vb1x+vb1y*vb1y+vb1z*vb1z);
projhfg += (vb3x*vb2x+vb3y*vb2y+vb3z*vb2z) /
sqrt(vb2x*vb2x+vb2y*vb2y+vb2z*vb2z);
if (projhfg > 0.0) {
s *= -1.0;
cotphi *= -1.0;
}
// force and energy
// E = k ( C0 + C1 cos(w) + C2 cos(w)
c2 = 2.0*s*s-1.0;
if (eflag) eimproper = k[type]*(C0[type]+C1[type]*s+C2[type]*c2);
// dhax = diffrence between H and A in X direction, etc
a = k[type]*(C1[type]+4.0*C2[type]*s)*cotphi;
dhax = hrx-c*arx;
dhay = hry-c*ary;
dhaz = hrz-c*arz;
dahx = arx-c*hrx;
dahy = ary-c*hry;
dahz = arz-c*hrz;
f2[0] = (dhay*vb1z - dhaz*vb1y)*rar;
f2[1] = (dhaz*vb1x - dhax*vb1z)*rar;
f2[2] = (dhax*vb1y - dhay*vb1x)*rar;
f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar;
f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar;
f3[2] = (-dhax*vb2y + dhay*vb2x)*rar;
f4[0] = dahx*rhr;
f4[1] = dahy*rhr;
f4[2] = dahz*rhr;
f1[0] = -(f2[0] + f3[0] + f4[0]);
f1[1] = -(f2[1] + f3[1] + f4[1]);
f1[2] = -(f2[2] + f3[2] + f4[2]);
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0]*a;
f[i1][1] += f1[1]*a;
f[i1][2] += f1[2]*a;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f3[0]*a;
f[i2][1] += f3[1]*a;
f[i2][2] += f3[2]*a;
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f2[0]*a;
f[i3][1] += f2[1]*a;
f[i3][2] += f2[2]*a;
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0]*a;
f[i4][1] += f4[1]*a;
f[i4][2] += f4[2]*a;
}
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 ImproperFourier::allocate()
{
allocated = 1;
int n = atom->nimpropertypes;
memory->create(k,n+1,"improper:k");
memory->create(C0,n+1,"improper:C0");
memory->create(C1,n+1,"improper:C1");
memory->create(C2,n+1,"improper:C2");
memory->create(all,n+1,"improper:C2");
memory->create(setflag,n+1,"improper:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void ImproperFourier::coeff(int narg, char **arg)
{
if ( narg != 5 && narg != 6 ) error->all(FLERR,"Incorrect args for improper coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nimpropertypes,ilo,ihi);
double k_one = force->numeric(arg[1]);
double C0_one = force->numeric(arg[2]);
double C1_one = force->numeric(arg[3]);
double C2_one = force->numeric(arg[4]);
int all_one = 1;
if ( narg == 6 ) all_one = force->inumeric(arg[5]);
// convert w0 from degrees to radians
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
C0[i] = C0_one;
C1[i] = C1_one;
C2[i] = C2_one;
all[i] = all_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperFourier::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&C0[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&C1[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&C2[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&all[1],sizeof(int),atom->nimpropertypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperFourier::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
fread(&C0[1],sizeof(double),atom->nimpropertypes,fp);
fread(&C1[1],sizeof(double),atom->nimpropertypes,fp);
fread(&C2[1],sizeof(double),atom->nimpropertypes,fp);
fread(&all[1],sizeof(int),atom->nimpropertypes,fp);
}
MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&C0[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&C1[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&C2[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&all[1],atom->nimpropertypes,MPI_INT,0,world);
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}

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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.
------------------------------------------------------------------------- */
#ifdef IMPROPER_CLASS
ImproperStyle(fourier,ImproperFourier)
#else
#ifndef LMP_IMPROPER_FOURIER_H
#define LMP_IMPROPER_FOURIER_H
#include "stdio.h"
#include "improper.h"
namespace LAMMPS_NS {
class ImproperFourier : public Improper {
public:
ImproperFourier(class LAMMPS *);
~ImproperFourier();
void compute(int, int);
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
protected:
double *k, *C0, *C1, *C2;
int *all;
void addone(const int &i1,const int &i2,const int &i3,const int &i4,
const int &type,const int &evflag,const int &eflag,
const double &vb1x, const double &vb1y, const double &vb1z,
const double &vb2x, const double &vb2y, const double &vb2z,
const double &vb3x, const double &vb3y, const double &vb3z);
void allocate();
};
}
#endif
#endif