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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6651 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-08-08 22:58:28 +00:00
parent c4606286b8
commit 4107844f7a
4 changed files with 16 additions and 37 deletions
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2
src/USER-MISC/angle_cosine_shift.cpp
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@ -17,7 +17,7 @@
#include "math.h"
#include "stdlib.h"
#include "angle_cosineshift.h"
#include "angle_cosine_shift.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"

2
src/USER-MISC/angle_cosine_shift_exp.cpp
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@ -17,7 +17,7 @@
#include "math.h"
#include "stdlib.h"
#include "angle_cosineshiftexp.h"
#include "angle_cosine_shift_exp.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"

16
src/USER-MISC/dihedral_cosine_shift_exp.cpp
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@ -19,7 +19,7 @@
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "dihedral_cosineshiftexp.h"
#include "dihedral_cosine_shift_exp.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
@ -36,11 +36,11 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
DihedralCosShiftExp::DihedralCosShiftExp(LAMMPS *lmp) : Dihedral(lmp) {}
DihedralCosineShiftExp::DihedralCosineShiftExp(LAMMPS *lmp) : Dihedral(lmp) {}
/* ---------------------------------------------------------------------- */
DihedralCosShiftExp::~DihedralCosShiftExp()
DihedralCosineShiftExp::~DihedralCosineShiftExp()
{
if (allocated) {
memory->destroy(setflag);
@ -56,7 +56,7 @@ DihedralCosShiftExp::~DihedralCosShiftExp()
/* ---------------------------------------------------------------------- */
void DihedralCosShiftExp::compute(int eflag, int vflag)
void DihedralCosineShiftExp::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;
@ -250,7 +250,7 @@ void DihedralCosShiftExp::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
void DihedralCosShiftExp::allocate()
void DihedralCosineShiftExp::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
@ -271,7 +271,7 @@ void DihedralCosShiftExp::allocate()
set coeffs for one type
------------------------------------------------------------------------- */
void DihedralCosShiftExp::coeff(int narg, char **arg)
void DihedralCosineShiftExp::coeff(int narg, char **arg)
{
if (narg != 4) error->all("Incorrect args for dihedral coefficients");
if (!allocated) allocate();
@ -305,7 +305,7 @@ void DihedralCosShiftExp::coeff(int narg, char **arg)
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralCosShiftExp::write_restart(FILE *fp)
void DihedralCosineShiftExp::write_restart(FILE *fp)
{
fwrite(&umin[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&a[1],sizeof(double),atom->ndihedraltypes,fp);
@ -318,7 +318,7 @@ void DihedralCosShiftExp::write_restart(FILE *fp)
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralCosShiftExp::read_restart(FILE *fp)
void DihedralCosineShiftExp::read_restart(FILE *fp)
{
allocate();

33
src/USER-MISC/dihedral_cosine_shift_exp.h
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@ -11,45 +11,24 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/*
The torsion angle is defined such that a straight bond has costheta=180.
U(theta,theta0,umin,a) = -Umin[Exp(-a U)-1]/[[Exp(a)-1]]
with U = (-1-cos[theta-theta0])/2 = -Cos((theta-theta0)/2)^2
potential has minimum at theta=theta0 where U() = -Umin
potential has maximum at theta=theta0+180 where U() = 0
The spring constant around the minimum is controlled by a and
is given by k = a exp(a) Umin/[ 2(Exp[a]-1) ] for a=0
the spring constant is k=Umin/2 and the potential reduces to
the cosineshifted potential.
The potential is implemented such that for a<0.001 a series
expansion to linear order is used instead of the expression
above. This ensures a precision of about 1e-5 or better for
energies and forces, and ensures the potential is well
behaved for a=0
*/
#ifdef DIHEDRAL_CLASS
DihedralStyle(cosineshiftexp,DihedralCosShiftExp)
DihedralStyle(cosine/shift/exp,DihedralCosShiftExp)
#else
#ifndef LMP_DIHEDRAL_COSINESHIFTEDEXP_H
#define LMP_DIHEDRAL_COSINESHIFTEDEXP_H
#ifndef LMP_DIHEDRAL_COSINE_SHIFT_EXP_H
#define LMP_DIHEDRAL_COSINE_SHIFT_EXP_H
#include "stdio.h"
#include "dihedral.h"
namespace LAMMPS_NS {
class DihedralCosShiftExp : public Dihedral {
class DihedralCosineShiftExp : public Dihedral {
public:
DihedralCosShiftExp(class LAMMPS *);
~DihedralCosShiftExp();
DihedralCosineShiftExp(class LAMMPS *);
~DihedralCosineShiftExp();
void compute(int, int);
void coeff(int, char **);
void write_restart(FILE *);