1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
|
/* ----------------------------------------------------------------------
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: Naveen Michaud-Agrawal (Johns Hopkins U)
Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_spring_rg.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "respa.h"
#include "domain.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixSpringRG::FixSpringRG(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 5) error->all(FLERR,"Illegal fix spring/rg command");
k = atof(arg[3]);
rg0_flag = 0;
if (strcmp(arg[4],"NULL") == 0) rg0_flag = 1;
else rg0 = atof(arg[4]);
}
/* ---------------------------------------------------------------------- */
int FixSpringRG::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixSpringRG::init()
{
masstotal = group->mass(igroup);
// if rg0 was specified as NULL, compute current Rg
// only occurs on 1st run
if (rg0_flag) {
double xcm[3];
group->xcm(igroup,masstotal,xcm);
rg0 = group->gyration(igroup,masstotal,xcm);
rg0_flag = 0;
}
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixSpringRG::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixSpringRG::post_force(int vflag)
{
// compute current Rg and center-of-mass
double xcm[3];
group->xcm(igroup,masstotal,xcm);
double rg = group->gyration(igroup,masstotal,xcm);
// apply restoring force to atoms in group
// f = -k*(r-r0)*mass/masstotal
double dx,dy,dz,term1;
double **f = atom->f;
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
double *mass = atom->mass;
int nlocal = atom->nlocal;
double massfrac;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
int xbox,ybox,zbox;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
term1 = 2.0 * k * (1.0 - rg0/rg);
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = (x[i][0] + xbox*xprd) - xcm[0];
dy = (x[i][1] + ybox*yprd) - xcm[1];
dz = (x[i][2] + zbox*zprd) - xcm[2];
massfrac = mass[type[i]]/masstotal;
f[i][0] -= term1*dx*massfrac;
f[i][1] -= term1*dy*massfrac;
f[i][2] -= term1*dz*massfrac;
}
}
/* ---------------------------------------------------------------------- */
void FixSpringRG::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
|
