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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7039 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-10-06 17:55:48 +00:00
parent f70a2f8937
commit 15203cb792
81 changed files with 432 additions and 280 deletions
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22
src/set.cpp
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@ -30,7 +30,10 @@
#include "math_extra.h"
#include "error.h"
#include "math_const.h"
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,
@ -42,13 +45,6 @@ enum{TYPE,TYPE_FRACTION,MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,
/* ---------------------------------------------------------------------- */
Set::Set(LAMMPS *lmp) : Pointers(lmp)
{
PI = 4.0*atan(1.0);
}
/* ---------------------------------------------------------------------- */
void Set::command(int narg, char **arg)
{
if (domain->box_exist == 0)
@ -415,11 +411,11 @@ void Set::set(int keyword)
else if (keyword == DENSITY) {
if (atom->radius_flag && atom->radius[i] > 0.0)
atom->rmass[i] = 4.0*PI/3.0 *
atom->rmass[i] = 4.0*MY_PI*THIRD *
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*PI/3.0 * shape[0]*shape[1]*shape[2] * dvalue;
atom->rmass[i] = 4.0*MY_PI*THIRD * shape[0]*shape[1]*shape[2] * dvalue;
} else atom->rmass[i] = dvalue;
// reset any or all of 3 image flags
@ -450,7 +446,7 @@ void Set::set(int keyword)
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 theta2 = 0.5 * PI * wvalue/180.0;
double theta2 = MY_PI2 * wvalue/180.0;
double sintheta2 = sin(theta2);
quat[0] = cos(theta2);
quat[1] = xvalue * sintheta2;
@ -554,8 +550,8 @@ void Set::setrandom(int keyword)
s = random->uniform();
t1 = sqrt(1.0-s);
t2 = sqrt(s);
theta1 = 2.0*PI*random->uniform();
theta2 = 2.0*PI*random->uniform();
theta1 = 2.0*MY_PI*random->uniform();
theta2 = 2.0*MY_PI*random->uniform();
quat[0] = cos(theta2)*t2;
quat[1] = sin(theta1)*t1;
quat[2] = cos(theta1)*t1;
@ -572,7 +568,7 @@ void Set::setrandom(int keyword)
"that is not an ellipsoid");
quat = bonus[ellipsoid[i]].quat;
random->reset(seed,x[i]);
theta2 = PI*random->uniform();
theta2 = MY_PI*random->uniform();
quat[0] = cos(theta2);
quat[1] = 0.0;
quat[2] = 0.0;