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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7146 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-10-20 14:56:49 +00:00
parent 83b55b844c
commit ca8dfd3d7c
11 changed files with 1688 additions and 568 deletions
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136
src/set.cpp
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@ -19,6 +19,8 @@
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "domain.h"
#include "region.h"
#include "group.h"
@ -35,8 +37,8 @@ using namespace LAMMPS_NS;
using namespace MathConst;
enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT};
enum{TYPE,TYPE_FRACTION,MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,
DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,
enum{TYPE,TYPE_FRACTION,MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,LENGTH,TRI,
DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,THETA,ANGMOM,
DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER,
MESO_E,MESO_CV,MESO_RHO};
@ -150,6 +152,22 @@ void Set::command(int narg, char **arg)
}
set(SHAPE);
iarg += 4;
} else if (strcmp(arg[iarg],"length") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->line_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (dvalue < 0.0) error->all(FLERR,"Invalid length in set command");
set(LENGTH);
iarg += 2;
} else if (strcmp(arg[iarg],"tri") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->tri_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (dvalue < 0.0) error->all(FLERR,"Invalid length in set command");
set(TRI);
iarg += 2;
} else if (strcmp(arg[iarg],"dipole") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
xvalue = atof(arg[iarg+1]);
@ -177,19 +195,36 @@ void Set::command(int narg, char **arg)
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
wvalue = atof(arg[iarg+4]);
if (!atom->ellipsoid_flag)
if (!atom->ellipsoid_flag && !atom->tri_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(QUAT);
iarg += 5;
} else if (strcmp(arg[iarg],"quat/random") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (!atom->ellipsoid_flag)
if (!atom->ellipsoid_flag && !atom->tri_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0)
error->all(FLERR,"Invalid random number seed in set command");
setrandom(QUAT_RANDOM);
iarg += 2;
} else if (strcmp(arg[iarg],"theta") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
dvalue *= MY_PI/180.0;
if (!atom->line_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(THETA);
iarg += 2;
} else if (strcmp(arg[iarg],"angmom") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (!atom->ellipsoid_flag && !atom->tri_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(ANGMOM);
iarg += 4;
} else if (strcmp(arg[iarg],"diameter") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
@ -385,6 +420,8 @@ void Set::set(int keyword)
{
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
selection(atom->nlocal);
@ -405,23 +442,49 @@ void Set::set(int keyword)
else if (keyword == MESO_CV) atom->cv[i] = dvalue;
else if (keyword == MESO_RHO) atom->rho[i] = dvalue;
// set shape
// set shape of ellipsoidal particle
else if (keyword == SHAPE)
avec_ellipsoid->set_shape(i,0.5*xvalue,0.5*yvalue,0.5*zvalue);
// set length of line particle
else if (keyword == LENGTH)
avec_line->set_length(i,dvalue);
// set corners of tri particle
else if (keyword == TRI)
avec_tri->set_equilateral(i,dvalue);
// set rmass via density
// if radius > 0.0, treat as sphere
// if shape > 0.0, treat as ellipsoid
// if length > 0.0, treat as line
// if area > 0.0, treat as tri
// else set rmass to density directly
else if (keyword == DENSITY) {
if (atom->radius_flag && atom->radius[i] > 0.0)
atom->rmass[i] = 4.0*MY_PI*THIRD *
atom->rmass[i] = 4.0*MY_PI/3.0 *
atom->radius[i]*atom->radius[i]*atom->radius[i] * dvalue;
else if (atom->ellipsoid_flag && atom->ellipsoid[i] >= 0) {
double *shape = avec_ellipsoid->bonus[atom->ellipsoid[i]].shape;
atom->rmass[i] = 4.0*MY_PI*THIRD * shape[0]*shape[1]*shape[2] * dvalue;
atom->rmass[i] = 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2] * dvalue;
} else if (atom->line_flag && atom->line[i] >= 0) {
double length = avec_line->bonus[atom->line[i]].length;
atom->rmass[i] = length * dvalue;
} else if (atom->tri_flag && atom->tri[i] >= 0) {
double *c1 = avec_tri->bonus[atom->tri[i]].c1;
double *c2 = avec_tri->bonus[atom->tri[i]].c2;
double *c3 = avec_tri->bonus[atom->tri[i]].c3;
double c2mc1[2],c3mc1[3];
MathExtra::sub3(c2,c1,c2mc1);
MathExtra::sub3(c3,c1,c3mc1);
double norm[3];
MathExtra::cross3(c2mc1,c3mc1,norm);
double area = 0.5 * MathExtra::len3(norm);
atom->rmass[i] = area * dvalue;
} else atom->rmass[i] = dvalue;
// reset any or all of 3 image flags
@ -446,13 +509,17 @@ void Set::set(int keyword)
mu[i][3] = sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] +
mu[i][2]*mu[i][2]);
// set quaternion orientation
// set quaternion orientation of ellipsoid or tri particle
} else if (keyword == QUAT) {
if (atom->ellipsoid[i] < 0)
error->one(FLERR,
"Cannot set quaternion for atom that is not an ellipsoid");
double *quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
double *quat;
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
else if (avec_tri && atom->tri[i] >= 0)
quat = avec_tri->bonus[atom->tri[i]].quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
double theta2 = MY_PI2 * wvalue/180.0;
double sintheta2 = sin(theta2);
quat[0] = cos(theta2);
@ -460,7 +527,22 @@ void Set::set(int keyword)
quat[2] = yvalue * sintheta2;
quat[3] = zvalue * sintheta2;
MathExtra::qnormalize(quat);
// set theta of line particle
} else if (keyword == THETA) {
if (atom->line[i] < 0)
error->one(FLERR,"Cannot set theta for atom that is not a line");
avec_line->bonus[atom->line[i]].theta = dvalue;
// set angmom of ellipsoidal or tri particle
} else if (keyword == ANGMOM) {
atom->angmom[i][0] = xvalue;
atom->angmom[i][1] = yvalue;
atom->angmom[i][2] = zvalue;
}
count++;
}
}
@ -475,6 +557,11 @@ void Set::setrandom(int keyword)
{
int i;
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
selection(atom->nlocal);
RanPark *random = new RanPark(lmp,1);
double **x = atom->x;
@ -535,13 +622,10 @@ void Set::setrandom(int keyword)
}
// set quaternions to random orientations in 3d or 2d
// no need to normalize quats since creations algorithms already do
} else if (keyword == QUAT_RANDOM) {
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
int *ellipsoid = atom->ellipsoid;
int *tri = atom->tri;
int nlocal = atom->nlocal;
double *quat;
@ -549,10 +633,13 @@ void Set::setrandom(int keyword)
double s,t1,t2,theta1,theta2;
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (ellipsoid[i] < 0)
error->one(FLERR,"Cannot set quaternion for atom "
"that is not an ellipsoid");
quat = bonus[ellipsoid[i]].quat;
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
else if (avec_tri && atom->tri[i] >= 0)
quat = avec_tri->bonus[atom->tri[i]].quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
random->reset(seed,x[i]);
s = random->uniform();
t1 = sqrt(1.0-s);
@ -570,10 +657,11 @@ void Set::setrandom(int keyword)
double theta2;
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (ellipsoid[i] < 0)
error->one(FLERR,"Cannot set quaternion for atom "
"that is not an ellipsoid");
quat = bonus[ellipsoid[i]].quat;
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
random->reset(seed,x[i]);
theta2 = MY_PI*random->uniform();
quat[0] = cos(theta2);