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changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution

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This commit is contained in:
Steve Plimpton
2017-03-21 08:56:37 -06:00
parent 145e682ad3
commit dcede304df
112 changed files with 912 additions and 534 deletions
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25
src/set.cpp
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@ -295,13 +295,20 @@ void Set::command(int narg, char **arg)
set(DIAMETER);
iarg += 2;
} else if (strcmp(arg[iarg],"density") == 0) {
} else if (strcmp(arg[iarg],"density") == 0 ||
(strcmp(arg[iarg],"density/disc") == 0)) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else dvalue = force->numeric(FLERR,arg[iarg+1]);
if (!atom->rmass_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (dvalue <= 0.0) error->all(FLERR,"Invalid density in set command");
discflag = 0;
if (strcmp(arg[iarg],"density/disc") == 0) {
discflag = 1;
if (domain->dimension != 2)
error->all(FLERR,"Density/disc option requires 2d simulation");
}
set(DENSITY);
iarg += 2;
@ -678,8 +685,8 @@ void Set::set(int keyword)
}
// set rmass via density
// if radius > 0.0, treat as sphere
// if shape > 0.0, treat as ellipsoid
// if radius > 0.0, treat as sphere or disc
// if shape > 0.0, treat as ellipsoid (or ellipse, when uncomment below)
// if length > 0.0, treat as line
// if area > 0.0, treat as tri
// else set rmass to density directly
@ -687,10 +694,18 @@ void Set::set(int keyword)
else if (keyword == DENSITY) {
if (dvalue <= 0.0) error->one(FLERR,"Invalid density in set command");
if (atom->radius_flag && atom->radius[i] > 0.0)
atom->rmass[i] = 4.0*MY_PI/3.0 *
atom->radius[i]*atom->radius[i]*atom->radius[i] * dvalue;
if (discflag)
atom->rmass[i] = MY_PI*atom->radius[i]*atom->radius[i] * dvalue;
else
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;
// enable 2d ellipse (versus 3d ellipsoid) when time integration
// options (fix nve/asphere, fix nh/asphere) are also implemented
// if (discflag)
// atom->rmass[i] = MY_PI*shape[0]*shape[1] * dvalue;
// else
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;