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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14416 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2016-01-11 21:59:49 +00:00
parent 173d4861a2
commit b5086e3d69
2 changed files with 90 additions and 39 deletions
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65
src/set.cpp
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@ -21,6 +21,7 @@
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "atom_vec_body.h"
#include "domain.h"
#include "region.h"
#include "group.h"
@ -41,7 +42,7 @@ 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,LENGTH,TRI,
DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,THETA,ANGMOM,OMEGA,
DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,THETA,THETA_RANDOM,ANGMOM,OMEGA,
DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER,
MESO_E,MESO_CV,MESO_RHO,SMD_MASS_DENSITY,SMD_CONTACT_RADIUS,INAME,DNAME};
@ -221,7 +222,7 @@ void Set::command(int narg, char **arg)
else zvalue = force->numeric(FLERR,arg[iarg+3]);
if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) varparse(arg[iarg+4],4);
else wvalue = force->numeric(FLERR,arg[iarg+4]);
if (!atom->ellipsoid_flag && !atom->tri_flag)
if (!atom->ellipsoid_flag && !atom->tri_flag && !atom->body_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(QUAT);
iarg += 5;
@ -229,7 +230,7 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"quat/random") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = force->inumeric(FLERR,arg[iarg+1]);
if (!atom->ellipsoid_flag && !atom->tri_flag)
if (!atom->ellipsoid_flag && !atom->tri_flag && !atom->body_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");
@ -248,6 +249,16 @@ void Set::command(int narg, char **arg)
set(THETA);
iarg += 2;
} else if (strcmp(arg[iarg],"theta/random") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = force->inumeric(FLERR,arg[iarg+1]);
if (!atom->line_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");
set(THETA_RANDOM);
iarg += 2;
} else if (strcmp(arg[iarg],"angmom") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
@ -256,7 +267,7 @@ void Set::command(int narg, char **arg)
else yvalue = force->numeric(FLERR,arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zvalue = force->numeric(FLERR,arg[iarg+3]);
if (!atom->ellipsoid_flag && !atom->tri_flag)
if (!atom->angmom_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(ANGMOM);
iarg += 4;
@ -269,7 +280,7 @@ void Set::command(int narg, char **arg)
else yvalue = force->numeric(FLERR,arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zvalue = force->numeric(FLERR,arg[iarg+3]);
if (!atom->sphere_flag)
if (!atom->omega_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(OMEGA);
iarg += 4;
@ -558,6 +569,7 @@ void Set::set(int keyword)
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
AtomVecBody *avec_body = (AtomVecBody *) atom->style_match("body");
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
@ -604,8 +616,9 @@ void Set::set(int keyword)
else if (keyword == MESO_E) atom->e[i] = dvalue;
else if (keyword == MESO_CV) atom->cv[i] = dvalue;
else if (keyword == MESO_RHO) atom->rho[i] = dvalue;
else if (keyword == SMD_MASS_DENSITY) { // set mass from volume and supplied mass density
atom->rmass[i] = atom->vfrac[i] * dvalue;
else if (keyword == SMD_MASS_DENSITY) {
// set mass from volume and supplied mass density
atom->rmass[i] = atom->vfrac[i] * dvalue;
}
else if (keyword == SMD_CONTACT_RADIUS) atom->contact_radius[i] = dvalue;
@ -678,17 +691,23 @@ void Set::set(int keyword)
mu[i][2]*mu[i][2]);
}
// set quaternion orientation of ellipsoid or tri particle
// set quaternion orientation of ellipsoid or tri or body particle
// enforce quat rotation vector in z dir for 2d systems
else if (keyword == 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 if (avec_body && atom->body[i] >= 0)
quat = avec_body->bonus[atom->body[i]].quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
if (domain->dimension == 2 && (xvalue != 0.0 || yvalue != 0.0))
error->one(FLERR,"Cannot set quaternion with xy components "
"for 2d system");
double theta2 = MY_PI2 * wvalue/180.0;
double sintheta2 = sin(theta2);
quat[0] = cos(theta2);
@ -706,7 +725,7 @@ void Set::set(int keyword)
avec_line->bonus[atom->line[i]].theta = dvalue;
}
// set angmom of ellipsoidal or tri particle
// set angmom or omega of particle
else if (keyword == ANGMOM) {
atom->angmom[i][0] = xvalue;
@ -720,7 +739,6 @@ void Set::set(int keyword)
atom->omega[i][2] = zvalue;
}
// reset any or all of 3 image flags
else if (keyword == IMAGE) {
@ -768,7 +786,9 @@ void Set::setrandom(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");
AtomVecBody *avec_body = (AtomVecBody *) atom->style_match("body");
RanPark *random = new RanPark(lmp,1);
double **x = atom->x;
@ -828,7 +848,7 @@ void Set::setrandom(int keyword)
}
}
// set quaternions to random orientations in 3d or 2d
// set quaternions to random orientations in 3d and 2d
} else if (keyword == QUAT_RANDOM) {
int nlocal = atom->nlocal;
@ -842,6 +862,8 @@ void Set::setrandom(int keyword)
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 if (avec_body && atom->body[i] >= 0)
quat = avec_body->bonus[atom->body[i]].quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
@ -864,6 +886,8 @@ void Set::setrandom(int keyword)
if (select[i]) {
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
else if (avec_body && atom->body[i] >= 0)
quat = avec_body->bonus[atom->body[i]].quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
@ -876,6 +900,21 @@ void Set::setrandom(int keyword)
count++;
}
}
// set theta to random orientation in 2d
} else if (keyword == QUAT_RANDOM) {
int nlocal = atom->nlocal;
double theta;
for (i = 0; i < nlocal; i++) {
if (select[i]) {
if (atom->line[i] < 0)
error->one(FLERR,"Cannot set theta for atom that is not a line");
random->reset(seed,x[i]);
avec_line->bonus[atom->line[i]].theta = MY_2PI*random->uniform();
count++;
}
}
}
delete random;