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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14440 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2016-01-14 22:33:46 +00:00
parent cd1f4ae7f0
commit 09fb68df71
10 changed files with 588 additions and 117 deletions
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286
src/fix_move.cpp
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@ -26,7 +26,12 @@
#include "respa.h"
#include "input.h"
#include "variable.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "atom_vec_body.h"
#include "math_const.h"
#include "math_extra.h"
#include "memory.h"
#include "error.h"
@ -37,6 +42,8 @@ using namespace MathConst;
enum{LINEAR,WIGGLE,ROTATE,VARIABLE};
enum{EQUAL,ATOM};
#define INERTIA 0.2 // moment of inertia prefactor for ellipsoid
/* ---------------------------------------------------------------------- */
FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
@ -216,7 +223,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
// set omega_rotate from period
if (mstyle == WIGGLE || mstyle == ROTATE) omega_rotate = 2.0*MY_PI / period;
if (mstyle == WIGGLE || mstyle == ROTATE) omega_rotate = MY_2PI / period;
// runit = unit vector along rotation axis
@ -229,24 +236,54 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
runit[2] = axis[2]/len;
}
// set omega_flag if particles store omega
// set flags for extra attributes particles may store
// relevant extra attributes = omega, angmom, theta, quat
omega_flag = atom->omega_flag;
angmom_flag = atom->angmom_flag;
radius_flag = atom->radius_flag;
ellipsoid_flag = atom->ellipsoid_flag;
line_flag = atom->line_flag;
tri_flag = atom->tri_flag;
body_flag = atom->body_flag;
theta_flag = quat_flag = 0;
if (line_flag) theta_flag = 1;
if (ellipsoid_flag || tri_flag || body_flag) quat_flag = 1;
extra_flag = 0;
if (omega_flag || angmom_flag || theta_flag || quat_flag) extra_flag = 1;
// perform initial allocation of atom-based array
// register with Atom class
xoriginal = NULL;
toriginal = NULL;
qoriginal = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
displace = velocity = NULL;
// AtomVec pointers to retrieve per-atom storage of extra quantities
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
avec_line = (AtomVecLine *) atom->style_match("line");
avec_tri = (AtomVecTri *) atom->style_match("tri");
avec_body = (AtomVecBody *) atom->style_match("body");
// xoriginal = initial unwrapped positions of atoms
// toriginal = initial theta of lines
// qoriginal = initial quat of extended particles
double **x = atom->x;
imageint *image = atom->image;
int *ellipsoid = atom->ellipsoid;
int *line = atom->line;
int *tri = atom->tri;
int *body = atom->body;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -255,6 +292,45 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
}
if (theta_flag) {
for (int i = 0; i < nlocal; i++) {
if ((mask[i] & groupbit) && line[i] >= 0)
toriginal[i] = avec_line->bonus[line[i]].theta;
else toriginal[i] = 0.0;
}
}
if (quat_flag) {
double *quat;
for (int i = 0; i < nlocal; i++) {
quat = NULL;
if (mask[i] & groupbit) {
if (ellipsoid_flag && ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[ellipsoid[i]].quat;
else if (tri_flag && tri[i] >= 0)
quat = avec_tri->bonus[tri[i]].quat;
else if (body_flag && body[i] >= 0)
quat = avec_body->bonus[body[i]].quat;
}
if (quat) {
qoriginal[i][0] = quat[0];
qoriginal[i][1] = quat[1];
qoriginal[i][2] = quat[2];
qoriginal[i][3] = quat[3];
} else qoriginal[i][0] = qoriginal[i][1] =
qoriginal[i][2] = qoriginal[i][3] = 0.0;
}
}
// nrestart = size of per-atom restart data
// nrestart = 1 + xorig + torig + qorig
nrestart = 4;
if (theta_flag) nrestart++;
if (quat_flag) nrestart += 4;
// time origin for movement = current timestep
time_origin = update->ntimestep;
}
@ -270,6 +346,8 @@ FixMove::~FixMove()
// delete locally stored arrays
memory->destroy(xoriginal);
memory->destroy(toriginal);
memory->destroy(qoriginal);
memory->destroy(displace);
memory->destroy(velocity);
@ -381,9 +459,12 @@ void FixMove::init()
void FixMove::initial_integrate(int vflag)
{
double dtfm;
double xold[3],a[3],b[3],c[3],d[3],disp[3];
int flag;
double ddotr,dx,dy,dz;
double dtfm,theta_new;
double xold[3],a[3],b[3],c[3],d[3],disp[3],w[3],ex[3],ey[3],ez[3];
double inertia_ellipsoid[3],qrotate[4];
double *quat,*inertia,*shape;
double delta = (update->ntimestep - time_origin) * dt;
@ -391,10 +472,17 @@ void FixMove::initial_integrate(int vflag)
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **angmom = atom->angmom;
double *radius = atom->radius;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *ellipsoid = atom->ellipsoid;
int *line = atom->line;
int *tri = atom->tri;
int *body = atom->body;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// for linear: X = X0 + V*dt
@ -553,17 +641,89 @@ void FixMove::initial_integrate(int vflag)
v[i][0] = omega_rotate * (runit[1]*disp[2] - runit[2]*disp[1]);
v[i][1] = omega_rotate * (runit[2]*disp[0] - runit[0]*disp[2]);
v[i][2] = omega_rotate * (runit[0]*disp[1] - runit[1]*disp[0]);
if (omega_flag) {
omega[i][0] = omega_rotate*runit[0];
omega[i][1] = omega_rotate*runit[1];
omega[i][2] = omega_rotate*runit[2];
}
// set any extra attributes affected by rotation
if (extra_flag) {
// omega for spheres and lines
if (omega_flag) {
flag = 0;
if (radius_flag && radius[i] > 0.0) flag = 1;
if (line_flag && line[i] >= 0.0) flag = 1;
if (flag) {
omega[i][0] = omega_rotate*runit[0];
omega[i][1] = omega_rotate*runit[1];
omega[i][2] = omega_rotate*runit[2];
}
}
// angmom for ellipsoids, tris, and bodies
if (angmom_flag) {
quat = inertia = NULL;
if (ellipsoid_flag && ellipsoid[i] >= 0) {
quat = avec_ellipsoid->bonus[ellipsoid[i]].quat;
shape = avec_ellipsoid->bonus[ellipsoid[i]].shape;
inertia_ellipsoid[0] =
INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
inertia_ellipsoid[1] =
INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
inertia_ellipsoid[2] =
INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
inertia = inertia_ellipsoid;
} else if (tri_flag && tri[i] >= 0) {
quat = avec_tri->bonus[tri[i]].quat;
inertia = avec_tri->bonus[tri[i]].inertia;
} else if (body_flag && body[i] >= 0) {
quat = avec_body->bonus[body[i]].quat;
inertia = avec_body->bonus[body[i]].inertia;
}
if (quat) {
w[0] = omega_rotate*runit[0];
w[1] = omega_rotate*runit[1];
w[2] = omega_rotate*runit[2];
MathExtra::q_to_exyz(quat,ex,ey,ez);
MathExtra::omega_to_angmom(w,ex,ey,ez,inertia,angmom[i]);
}
}
// theta for lines
if (theta_flag && line[i] >= 0.0) {
theta_new = fmod(toriginal[i]+arg,MY_2PI);
avec_line->bonus[atom->line[i]].theta = theta_new;
}
// quats for ellipsoids, tris, and bodies
if (quat_flag) {
quat = NULL;
if (ellipsoid_flag && ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[ellipsoid[i]].quat;
else if (tri_flag && tri[i] >= 0)
quat = avec_tri->bonus[tri[i]].quat;
else if (body_flag && body[i] >= 0)
quat = avec_body->bonus[body[i]].quat;
if (quat) {
qrotate[0] = cosine;
qrotate[1] = runit[0]*sine;
qrotate[2] = runit[1]*sine;
qrotate[3] = runit[2]*sine;
MathExtra::quatquat(qrotate,qoriginal[i],quat);
}
}
}
domain->remap_near(x[i],xold);
}
}
// for variable: compute x,v from variables
// NOTE: also allow for changes to extra attributes?
// omega, angmom, theta, quat
// only necessary if prescribed motion involves rotation
} else if (mstyle == VARIABLE) {
@ -809,6 +969,8 @@ void FixMove::final_integrate_respa(int ilevel, int iloop)
double FixMove::memory_usage()
{
double bytes = atom->nmax*3 * sizeof(double);
if (theta_flag) bytes += atom->nmax * sizeof(double);
if (quat_flag) bytes += atom->nmax*4 * sizeof(double);
if (displaceflag) bytes += atom->nmax*3 * sizeof(double);
if (velocityflag) bytes += atom->nmax*3 * sizeof(double);
return bytes;
@ -850,6 +1012,8 @@ void FixMove::restart(char *buf)
void FixMove::grow_arrays(int nmax)
{
memory->grow(xoriginal,nmax,3,"move:xoriginal");
if (theta_flag) memory->grow(toriginal,nmax,"move:toriginal");
if (quat_flag) memory->grow(qoriginal,nmax,4,"move:qoriginal");
array_atom = xoriginal;
}
@ -862,6 +1026,13 @@ void FixMove::copy_arrays(int i, int j, int delflag)
xoriginal[j][0] = xoriginal[i][0];
xoriginal[j][1] = xoriginal[i][1];
xoriginal[j][2] = xoriginal[i][2];
if (theta_flag) toriginal[j] = toriginal[i];
if (quat_flag) {
qoriginal[j][0] = qoriginal[i][0];
qoriginal[j][1] = qoriginal[i][1];
qoriginal[j][2] = qoriginal[i][2];
qoriginal[j][3] = qoriginal[i][3];
}
}
/* ----------------------------------------------------------------------
@ -870,8 +1041,15 @@ void FixMove::copy_arrays(int i, int j, int delflag)
void FixMove::set_arrays(int i)
{
double theta;
double *quat;
double **x = atom->x;
imageint *image = atom->image;
int *ellipsoid = atom->ellipsoid;
int *line = atom->line;
int *tri = atom->tri;
int *body = atom->body;
int *mask = atom->mask;
// particle not in group
@ -932,6 +1110,33 @@ void FixMove::set_arrays(int i)
xoriginal[i][0] = point[0] + c[0] + disp[0];
xoriginal[i][1] = point[1] + c[1] + disp[1];
xoriginal[i][2] = point[2] + c[2] + disp[2];
// set theta and quat extra attributes affected by rotation
if (extra_flag) {
// theta for lines
if (theta_flag && line[i] >= 0.0) {
theta = avec_line->bonus[atom->line[i]].theta;
toriginal[i] = theta - 0.0; // NOTE: edit this line
}
// quats for ellipsoids, tris, and bodies
if (quat_flag) {
quat = NULL;
if (ellipsoid_flag && ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[ellipsoid[i]].quat;
else if (tri_flag && tri[i] >= 0)
quat = avec_tri->bonus[tri[i]].quat;
else if (body_flag && body[i] >= 0)
quat = avec_body->bonus[body[i]].quat;
if (quat) {
// qoriginal = f(quat,-delta); // NOTE: edit this line
}
}
}
}
}
@ -941,10 +1146,18 @@ void FixMove::set_arrays(int i)
int FixMove::pack_exchange(int i, double *buf)
{
buf[0] = xoriginal[i][0];
buf[1] = xoriginal[i][1];
buf[2] = xoriginal[i][2];
return 3;
int n = 0;
buf[n++] = xoriginal[i][0];
buf[n++] = xoriginal[i][1];
buf[n++] = xoriginal[i][2];
if (theta_flag) buf[n++] = toriginal[i];
if (quat_flag) {
buf[n++] = qoriginal[i][0];
buf[n++] = qoriginal[i][1];
buf[n++] = qoriginal[i][2];
buf[n++] = qoriginal[i][3];
}
return n;
}
/* ----------------------------------------------------------------------
@ -953,10 +1166,18 @@ int FixMove::pack_exchange(int i, double *buf)
int FixMove::unpack_exchange(int nlocal, double *buf)
{
xoriginal[nlocal][0] = buf[0];
xoriginal[nlocal][1] = buf[1];
xoriginal[nlocal][2] = buf[2];
return 3;
int n = 0;
xoriginal[nlocal][0] = buf[n++];
xoriginal[nlocal][1] = buf[n++];
xoriginal[nlocal][2] = buf[n++];
if (theta_flag) toriginal[nlocal] = buf[n++];
if (quat_flag) {
qoriginal[nlocal][0] = buf[n++];
qoriginal[nlocal][1] = buf[n++];
qoriginal[nlocal][2] = buf[n++];
qoriginal[nlocal][3] = buf[n++];
}
return n;
}
/* ----------------------------------------------------------------------
@ -965,11 +1186,19 @@ int FixMove::unpack_exchange(int nlocal, double *buf)
int FixMove::pack_restart(int i, double *buf)
{
buf[0] = 4;
buf[1] = xoriginal[i][0];
buf[2] = xoriginal[i][1];
buf[3] = xoriginal[i][2];
return 4;
int n = 1;
buf[n++] = xoriginal[i][0];
buf[n++] = xoriginal[i][1];
buf[n++] = xoriginal[i][2];
if (theta_flag) buf[n++] = toriginal[i];
if (quat_flag) {
buf[n++] = qoriginal[i][0];
buf[n++] = qoriginal[i][1];
buf[n++] = qoriginal[i][2];
buf[n++] = qoriginal[i][3];
}
buf[0] = n;
return n;
}
/* ----------------------------------------------------------------------
@ -989,6 +1218,13 @@ void FixMove::unpack_restart(int nlocal, int nth)
xoriginal[nlocal][0] = extra[nlocal][m++];
xoriginal[nlocal][1] = extra[nlocal][m++];
xoriginal[nlocal][2] = extra[nlocal][m++];
if (theta_flag) toriginal[nlocal] = extra[nlocal][m++];
if (quat_flag) {
qoriginal[nlocal][0] = extra[nlocal][m++];
qoriginal[nlocal][1] = extra[nlocal][m++];
qoriginal[nlocal][2] = extra[nlocal][m++];
qoriginal[nlocal][3] = extra[nlocal][m++];
}
}
/* ----------------------------------------------------------------------
@ -997,7 +1233,7 @@ void FixMove::unpack_restart(int nlocal, int nth)
int FixMove::maxsize_restart()
{
return 4;
return nrestart;
}
/* ----------------------------------------------------------------------
@ -1006,7 +1242,7 @@ int FixMove::maxsize_restart()
int FixMove::size_restart(int nlocal)
{
return 4;
return nrestart;
}
/* ---------------------------------------------------------------------- */