git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6033 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -26,6 +26,8 @@
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using namespace LAMMPS_NS;
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enum{ROTATE,ALL};
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#define INERTIA 0.4 // moment of inertia for sphere
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/* ---------------------------------------------------------------------- */
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@ -33,8 +35,7 @@ using namespace LAMMPS_NS;
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ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg != 3 && narg != 4)
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error->all("Illegal compute temp/sphere command");
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if (narg < 3) error->all("Illegal compute temp/sphere command");
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scalar_flag = vector_flag = 1;
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size_vector = 6;
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@ -44,11 +45,24 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
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tempbias = 0;
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id_bias = NULL;
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if (narg == 4) {
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tempbias = 1;
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int n = strlen(arg[3]) + 1;
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id_bias = new char[n];
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strcpy(id_bias,arg[3]);
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mode = ALL;
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"bias") == 0) {
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if (iarg+2 > narg) error->all("Illegal compute temp/sphere command");
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tempbias = 1;
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int n = strlen(arg[iarg+1]) + 1;
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id_bias = new char[n];
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strcpy(id_bias,arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"dof") == 0) {
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if (iarg+2 > narg) error->all("Illegal compute temp/sphere command");
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if (strcmp(arg[iarg+1],"rotate") == 0) mode = ROTATE;
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else if (strcmp(arg[iarg+1],"all") == 0) mode = ALL;
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else error->all("Illegal compute temp/sphere command");
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iarg += 2;
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} else error->all("Illegal compute temp/sphere command");
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}
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vector = new double[6];
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@ -100,27 +114,34 @@ void ComputeTempSphere::dof_compute()
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// 6 or 3 dof for extended/point particles for 3d
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// 3 or 2 dof for extended/point particles for 2d
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// which dof are included also depends on mode
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// assume full rotation of extended particles
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// user should correct this via compute_modify if needed
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int dimension = domain->dimension;
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double *radius = atom->radius;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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count = 0;
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if (dimension == 3) {
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if (domain->dimension == 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 (radius[i] == 0.0) count += 3;
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else count += 6;
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if (radius[i] == 0.0) {
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if (mode == ALL) count += 3;
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} else {
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if (mode == ALL) count += 6;
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else count += 3;
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}
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}
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} else {
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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) count += 2;
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else count += 3;
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if (radius[i] == 0.0) {
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if (mode == ALL) count += 2;
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} else {
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if (mode == ALL) count += 3;
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else count += 1;
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}
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}
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}
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@ -130,28 +151,38 @@ void ComputeTempSphere::dof_compute()
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// additional adjustments to dof
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if (tempbias == 1) {
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double natoms = group->count(igroup);
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dof -= tbias->dof_remove(-1) * natoms;
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if (mode == ALL) {
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double natoms = group->count(igroup);
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dof -= tbias->dof_remove(-1) * natoms;
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}
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} else if (tempbias == 2) {
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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count = 0;
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if (dimension == 3) {
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if (domain->dimension == 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 (tbias->dof_remove(i)) {
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if (radius[i] == 0.0) count += 3;
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else count += 6;
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if (radius[i] == 0.0) {
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if (mode == ALL) count += 3;
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} else {
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if (mode == ALL) count += 6;
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else count += 3;
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}
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}
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}
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (tbias->dof_remove(i)) {
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if (radius[i] == 0.0) count += 2;
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else count += 3;
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if (radius[i] == 0.0) {
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if (mode == ALL) count += 2;
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} else {
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if (mode == ALL) count += 3;
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else count += 1;
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}
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}
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}
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}
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@ -187,12 +218,19 @@ double ComputeTempSphere::compute_scalar()
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double t = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
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t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
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omega[i][2]*omega[i][2]) * INERTIA*radius[i]*radius[i]*rmass[i];
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}
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if (mode == ALL) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
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t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
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omega[i][2]*omega[i][2]) * INERTIA*rmass[i]*radius[i]*radius[i];
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}
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
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omega[i][2]*omega[i][2]) * INERTIA*rmass[i]*radius[i]*radius[i];
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}
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if (tempbias) tbias->restore_bias_all();
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@ -225,25 +263,38 @@ void ComputeTempSphere::compute_vector()
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double massone,inertiaone,t[6];
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for (int i = 0; i < 6; i++) t[i] = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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massone = rmass[i];
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t[0] += massone * v[i][0]*v[i][0];
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t[1] += massone * v[i][1]*v[i][1];
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t[2] += massone * v[i][2]*v[i][2];
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t[3] += massone * v[i][0]*v[i][1];
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t[4] += massone * v[i][0]*v[i][2];
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t[5] += massone * v[i][1]*v[i][2];
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inertiaone = INERTIA*radius[i]*radius[i]*rmass[i];
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t[0] += inertiaone * omega[i][0]*omega[i][0];
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t[1] += inertiaone * omega[i][1]*omega[i][1];
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t[2] += inertiaone * omega[i][2]*omega[i][2];
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t[3] += inertiaone * omega[i][0]*omega[i][1];
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t[4] += inertiaone * omega[i][0]*omega[i][2];
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t[5] += inertiaone * omega[i][1]*omega[i][2];
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}
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if (mode == ALL) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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massone = rmass[i];
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t[0] += massone * v[i][0]*v[i][0];
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t[1] += massone * v[i][1]*v[i][1];
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t[2] += massone * v[i][2]*v[i][2];
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t[3] += massone * v[i][0]*v[i][1];
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t[4] += massone * v[i][0]*v[i][2];
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t[5] += massone * v[i][1]*v[i][2];
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inertiaone = INERTIA*rmass[i]*radius[i]*radius[i];
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t[0] += inertiaone * omega[i][0]*omega[i][0];
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t[1] += inertiaone * omega[i][1]*omega[i][1];
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t[2] += inertiaone * omega[i][2]*omega[i][2];
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t[3] += inertiaone * omega[i][0]*omega[i][1];
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t[4] += inertiaone * omega[i][0]*omega[i][2];
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t[5] += inertiaone * omega[i][1]*omega[i][2];
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}
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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inertiaone = INERTIA*rmass[i]*radius[i]*radius[i];
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t[0] += inertiaone * omega[i][0]*omega[i][0];
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t[1] += inertiaone * omega[i][1]*omega[i][1];
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t[2] += inertiaone * omega[i][2]*omega[i][2];
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t[3] += inertiaone * omega[i][0]*omega[i][1];
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t[4] += inertiaone * omega[i][0]*omega[i][2];
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t[5] += inertiaone * omega[i][1]*omega[i][2];
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}
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}
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if (tempbias) tbias->restore_bias_all();
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MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
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