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Merge branch 'develop' into dielectric-updates

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This commit is contained in:
Axel Kohlmeyer
2022-04-17 17:47:55 -04:00
parent 9228855257 21f24ef572
commit f40b8f5694
157 changed files with 13436 additions and 3840 deletions
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74
src/set.cpp
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@ -303,7 +303,7 @@ void Set::command(int narg, char **arg)
else zvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp);
if (utils::strmatch(arg[iarg+4],"^v_")) varparse(arg[iarg+4],4);
else wvalue = utils::numeric(FLERR,arg[iarg+4],false,lmp);
if (!atom->ellipsoid_flag && !atom->tri_flag && !atom->body_flag)
if (!atom->ellipsoid_flag && !atom->tri_flag && !atom->body_flag && !atom->quat_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(QUAT);
iarg += 5;
@ -311,7 +311,7 @@ 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 = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->ellipsoid_flag && !atom->tri_flag && !atom->body_flag)
if (!atom->ellipsoid_flag && !atom->tri_flag && !atom->body_flag && !atom->quat_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");
@ -946,31 +946,44 @@ void Set::set(int keyword)
sp[i][3] = dvalue;
}
// set quaternion orientation of ellipsoid or tri or body particle
// set quaternion orientation of ellipsoid or tri or body particle
// set quaternion orientation of ellipsoid or tri or body particle or sphere/bpm
// enforce quat rotation vector in z dir for 2d systems
else if (keyword == QUAT) {
double *quat = nullptr;
double **quat2 = nullptr;
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 if (atom->quat_flag)
quat2 = atom->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");
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);
quat[1] = xvalue * sintheta2;
quat[2] = yvalue * sintheta2;
quat[3] = zvalue * sintheta2;
MathExtra::qnormalize(quat);
const double theta2 = MY_PI2 * wvalue/180.0;
const double sintheta2 = sin(theta2);
double temp[4];
temp[0] = cos(theta2);
temp[1] = xvalue * sintheta2;
temp[2] = yvalue * sintheta2;
temp[3] = zvalue * sintheta2;
MathExtra::qnormalize(temp);
if (atom->quat_flag) {
quat2[i][0] = temp[0];
quat2[i][1] = temp[1];
quat2[i][2] = temp[2];
quat2[i][3] = temp[3];
} else {
quat[0] = temp[0];
quat[1] = temp[1];
quat[2] = temp[2];
quat[3] = temp[3];
}
}
// set theta of line particle
@ -1247,6 +1260,7 @@ void Set::setrandom(int keyword)
} else if (keyword == QUAT_RANDOM) {
int nlocal = atom->nlocal;
double *quat;
double **quat2;
if (domain->dimension == 3) {
double s,t1,t2,theta1,theta2;
@ -1258,6 +1272,8 @@ void Set::setrandom(int keyword)
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 if (atom->quat_flag)
quat2 = atom->quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
@ -1267,10 +1283,17 @@ void Set::setrandom(int keyword)
t2 = sqrt(s);
theta1 = 2.0*MY_PI*ranpark->uniform();
theta2 = 2.0*MY_PI*ranpark->uniform();
quat[0] = cos(theta2)*t2;
quat[1] = sin(theta1)*t1;
quat[2] = cos(theta1)*t1;
quat[3] = sin(theta2)*t2;
if (atom->quat_flag) {
quat2[i][0] = cos(theta2)*t2;
quat2[i][1] = sin(theta1)*t1;
quat2[i][2] = cos(theta1)*t1;
quat2[i][3] = sin(theta2)*t2;
} else {
quat[0] = cos(theta2)*t2;
quat[1] = sin(theta1)*t1;
quat[2] = cos(theta1)*t1;
quat[3] = sin(theta2)*t2;
}
count++;
}
@ -1282,15 +1305,24 @@ void Set::setrandom(int keyword)
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 if (atom->quat_flag)
quat2 = atom->quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
ranpark->reset(seed,x[i]);
theta2 = MY_PI*ranpark->uniform();
quat[0] = cos(theta2);
quat[1] = 0.0;
quat[2] = 0.0;
quat[3] = sin(theta2);
if (atom->quat_flag) {
quat2[i][0] = cos(theta2);
quat2[i][1] = 0.0;
quat2[i][2] = 0.0;
quat2[i][3] = sin(theta2);
} else {
quat[0] = cos(theta2);
quat[1] = 0.0;
quat[2] = 0.0;
quat[3] = sin(theta2);
}
count++;
}
}