git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15369 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -21,9 +21,13 @@
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#include "atom_vec.h"
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#include "group.h"
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#include "error.h"
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#include "force.h"
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#include "math_vector.h"
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#include "math_extra.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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using namespace MathExtra;
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#define INERTIA 0.4 // moment of inertia prefactor for sphere
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@ -50,7 +54,7 @@ void FixNHSphere::init()
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (radius[i] == 0.0)
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error->one(FLERR,"Fix nvt/sphere requires extended particles");
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error->one(FLERR,"Fix nvt/npt/nph/sphere require extended particles");
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FixNH::init();
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}
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@ -102,28 +106,133 @@ void FixNHSphere::nve_x()
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FixNH::nve_x();
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// update mu for dipoles
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// d_mu/dt = omega cross mu
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// renormalize mu to dipole length
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if (dipole_flag) {
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double msq,scale,g[3];
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double **mu = atom->mu;
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double **omega = atom->omega;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (mu[i][3] > 0.0) {
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g[0] = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
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g[1] = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
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g[2] = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
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msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
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scale = mu[i][3]/sqrt(msq);
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mu[i][0] = g[0]*scale;
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mu[i][1] = g[1]*scale;
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mu[i][2] = g[2]*scale;
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if (dlm_flag == 0){
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// d_mu/dt = omega cross mu
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// renormalize mu to dipole length
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double msq,scale,g[3];
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (mu[i][3] > 0.0) {
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g[0] = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
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g[1] = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
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g[2] = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
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msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
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scale = mu[i][3]/sqrt(msq);
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mu[i][0] = g[0]*scale;
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mu[i][1] = g[1]*scale;
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mu[i][2] = g[2]*scale;
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}
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} else {
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// Integrate orientation following Dullweber-Leimkuhler-Maclachlan scheme
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vector w, w_temp, a;
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matrix Q, Q_temp, R;
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double scale,s2,inv_len_mu;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit && mu[i][3] > 0.0) {
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// Construct Q from dipole:
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// Q is the rotation matrix from space frame to body frame
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// i.e. v_b = Q.v_s
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// Define mu to lie along the z axis in the body frame
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// We take the unit dipole to avoid getting a scaling matrix
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inv_len_mu = 1.0/mu[i][3];
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a[0] = mu[i][0]*inv_len_mu;
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a[1] = mu[i][1]*inv_len_mu;
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a[2] = mu[i][2]*inv_len_mu;
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// v = a x [0 0 1] - cross product of mu in space and body frames
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// s = |v|
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// c = a.[0 0 1] = a[2]
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// vx = [ 0 -v[2] v[1]
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// v[2] 0 -v[0]
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// -v[1] v[0] 0 ]
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// then
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// Q = I + vx + vx^2 * (1-c)/s^2
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s2 = a[0]*a[0] + a[1]*a[1];
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if (s2 != 0.0){ // i.e. the vectors are not parallel
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scale = (1.0 - a[2])/s2;
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Q[0][0] = 1.0 - scale*a[0]*a[0]; Q[0][1] = -scale*a[0]*a[1]; Q[0][2] = -a[0];
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Q[1][0] = -scale*a[0]*a[1]; Q[1][1] = 1.0 - scale*a[1]*a[1]; Q[1][2] = -a[1];
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Q[2][0] = a[0]; Q[2][1] = a[1]; Q[2][2] = 1.0 - scale*(a[0]*a[0] + a[1]*a[1]);
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} else { // if parallel then we just have I or -I
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Q[0][0] = 1.0/a[2]; Q[0][1] = 0.0; Q[0][2] = 0.0;
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Q[1][0] = 0.0; Q[1][1] = 1.0/a[2]; Q[1][2] = 0.0;
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Q[2][0] = 0.0; Q[2][1] = 0.0; Q[2][2] = 1.0/a[2];
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}
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// Local copy of this particle's angular velocity (in space frame)
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w[0] = omega[i][0]; w[1] = omega[i][1]; w[2] = omega[i][2];
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// Transform omega into body frame: w_temp= Q.w
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matvec(Q,w,w_temp);
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// Construct rotation R1
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BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
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// Apply R1 to w: w = R.w_temp
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matvec(R,w_temp,w);
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// Apply R1 to Q: Q_temp = R^T.Q
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transpose_times3(R,Q,Q_temp);
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// Construct rotation R2
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BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
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// Apply R2 to w: w_temp = R.w
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matvec(R,w,w_temp);
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// Apply R2 to Q: Q = R^T.Q_temp
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transpose_times3(R,Q_temp,Q);
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// Construct rotation R3
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BuildRzMatrix(R, 2.0*dtf/force->ftm2v*w_temp[2]);
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// Apply R3 to w: w = R.w_temp
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matvec(R,w_temp,w);
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// Apply R3 to Q: Q_temp = R^T.Q
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transpose_times3(R,Q,Q_temp);
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// Construct rotation R4
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BuildRyMatrix(R, dtf/force->ftm2v*w[1]);
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// Apply R4 to w: w_temp = R.w
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matvec(R,w,w_temp);
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// Apply R4 to Q: Q = R^T.Q_temp
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transpose_times3(R,Q_temp,Q);
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// Construct rotation R5
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BuildRxMatrix(R, dtf/force->ftm2v*w_temp[0]);
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// Apply R5 to w: w = R.w_temp
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matvec(R,w_temp,w);
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// Apply R5 to Q: Q_temp = R^T.Q
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transpose_times3(R,Q,Q_temp);
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// Transform w back into space frame w_temp = Q^T.w
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transpose_matvec(Q_temp,w,w_temp);
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omega[i][0] = w_temp[0]; omega[i][1] = w_temp[1]; omega[i][2] = w_temp[2];
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// Set dipole according to updated Q: mu = Q^T.[0 0 1] * |mu|
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mu[i][0] = Q_temp[2][0] * mu[i][3];
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mu[i][1] = Q_temp[2][1] * mu[i][3];
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mu[i][2] = Q_temp[2][2] * mu[i][3];
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}
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}
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}
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}
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}
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