git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3951 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/fix_nh_sphere.cpp

@@ -0,0 +1,191 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under 
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Mike Brown (SNL)
+------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "fix_nh_sphere.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "group.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define INERTIA 0.4          // moment of inertia for sphere
+
+enum{NOBIAS,BIAS};
+
+/* ---------------------------------------------------------------------- */
+
+FixNHSphere::FixNHSphere(LAMMPS *lmp, int narg, char **arg) :
+  FixNH(lmp, narg, arg)
+{
+  if (!atom->omega_flag || !atom->torque_flag)
+    error->all("Fix nvt/nph/npt sphere requires "
+	       "atom attributes omega, torque");
+  if (!atom->radius_flag && !atom->avec->shape_type)
+    error->all("Fix nvt/nph/npt sphere requires "
+	       "atom attribute radius or shape");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNHSphere::init()
+{
+  int i,itype;
+
+  // check that all particles are finite-size and spherical
+  // no point particles allowed
+
+  if (atom->radius_flag) {
+    double *radius = atom->radius;
+    int *mask = atom->mask;
+    int nlocal = atom->nlocal;
+    if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+    for (i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+	if (radius[i] == 0.0)
+	  error->one("Fix nvt/sphere requires extended particles");
+      }
+
+  } else {
+    double **shape = atom->shape;
+    int *type = atom->type;
+    int *mask = atom->mask;
+    int nlocal = atom->nlocal;
+    if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+    for (i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+	itype = type[i];
+	if (shape[itype][0] == 0.0)
+	  error->one("Fix nvt/sphere requires extended particles");
+	if (shape[itype][0] != shape[itype][1] || 
+	    shape[itype][0] != shape[itype][2])
+	  error->one("Fix nvt/sphere requires spherical particle shapes");
+      }
+  }
+
+  FixNH::init();
+}
+
+/* ----------------------------------------------------------------------
+   perform half-step update of velocities 
+-----------------------------------------------------------------------*/
+
+void FixNHSphere::nve_v()
+{
+  // standard nve_v velocity update
+
+  FixNH::nve_v();
+
+  double **omega = atom->omega;
+  double **torque = atom->torque;
+  double *radius = atom->radius;
+  double *rmass = atom->rmass;
+  double *mass = atom->mass;
+  double **shape = atom->shape;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+  // set timestep here since dt may have changed or come via rRESPA
+
+  double dtfrotate = dtf / INERTIA;
+  double dtirotate;
+  int itype;
+
+  // update omega for all particles
+  // d_omega/dt = torque / inertia
+  // 4 cases depending on radius vs shape and rmass vs mass
+
+  if (radius) {
+    if (rmass) {
+      for (int i = 0; i < nlocal; i++) {    
+	if (mask[i] & groupbit) {
+	  dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
+	  omega[i][0] += dtirotate*torque[i][0];
+	  omega[i][1] += dtirotate*torque[i][1];
+	  omega[i][2] += dtirotate*torque[i][2];
+	}
+      }
+    } else {
+      for (int i = 0; i < nlocal; i++) {    
+	if (mask[i] & groupbit) {
+	  dtirotate = dtfrotate / (radius[i]*radius[i]*mass[type[i]]);
+	  omega[i][0] += dtirotate*torque[i][0];
+	  omega[i][1] += dtirotate*torque[i][1];
+	  omega[i][2] += dtirotate*torque[i][2];
+	}
+      }
+    }
+
+  } else {
+    if (rmass) {
+      for (int i = 0; i < nlocal; i++) {    
+	if (mask[i] & groupbit) {
+	  itype = type[i];
+	  dtirotate = dtfrotate / (shape[itype][0]*shape[itype][0]*rmass[i]);
+	  omega[i][0] += dtirotate*torque[i][0];
+	  omega[i][1] += dtirotate*torque[i][1];
+	  omega[i][2] += dtirotate*torque[i][2];
+	}
+      }
+    } else {
+      for (int i = 0; i < nlocal; i++) {    
+	if (mask[i] & groupbit) {
+	  itype = type[i];
+	  dtirotate = dtfrotate / 
+	    (shape[itype][0]*shape[itype][0]*mass[itype]);
+	  omega[i][0] += dtirotate*torque[i][0];
+	  omega[i][1] += dtirotate*torque[i][1];
+	  omega[i][2] += dtirotate*torque[i][2];
+	}
+      }
+    }
+  }
+
+}
+
+/* ----------------------------------------------------------------------
+   perform half-step scaling of velocities
+-----------------------------------------------------------------------*/
+
+void FixNHSphere::nh_v_temp()
+{
+  // standard nh_v_temp velocity update
+
+  FixNH::nh_v_temp();
+
+  double **omega = atom->omega;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+  // set timestep here since dt may have changed or come via rRESPA
+
+  double factor_rotate = exp(-dthalf*eta_dot[0]);
+
+  for (int i = 0; i < nlocal; i++) {    
+    if (mask[i] & groupbit) {
+      omega[i][0] *= factor_rotate;
+      omega[i][1] *= factor_rotate;
+      omega[i][2] *= factor_rotate;
+    }
+  }
+}