Renamed fix active to fix propel/self

doc/src/fix_propel_self.txt

@@ -0,0 +1,50 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix active command  :pre
+
+[Syntax:]
+
+fix ID group-ID magnitude
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+addforce = style name of this fix command :l
+magnitude = magnitude of the active force :l
+:ule
+
+[Examples:]
+
+fix active_group all active 1.0
+fix constant_velocity all viscous 1.0
+
+[Description:]
+
+Adds a force of a constant magnitude to each atom in the group. The direction
+of the force is along the axis obtained by rotating the z-axis along the atom's
+quaternion. In other words, the force is along the z-axis in the atom's body
+frame.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+This fix is not imposed  during minimization.
+
+[Restrictions:]
+
+This fix makes use of per-atom quaternions to take into
+account the fact that the orientation can rotate and hence the direction
+of the active force can change. Therefore, this fix only works with
+ellipsoidal particles.
+
+[Related commands:]
+
+"fix setforce"_fix_setforce.html, "fix addforce"_fix_addforce.html

src/USER-MISC/fix_propel_self.cpp

@@ -0,0 +1,147 @@
+/* ----------------------------------------------------------------------
+   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.
+   ------------------------------------------------------------------------- */
+
+/*  -----------------------------------------------------------------------
+   Contributed by Stefan Paquay @ Brandeis University
+
+   Thanks to Liesbeth Janssen @ Eindhoven University for useful discussions!
+   ----------------------------------------------------------------------- */
+
+
+#include <stdio.h>
+#include <string.h>
+
+#include "fix_propel_self.h"
+
+#include "atom.h"
+#include "atom_vec_ellipsoid.h"
+#include "citeme.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "group.h"
+#include "math.h"
+#include "math_const.h"
+#include "math_extra.h"
+#include "math_vector.h"
+#include "modify.h"
+#include "random_mars.h"
+#include "respa.h"
+#include "update.h"
+
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+using namespace MathConst;
+
+
+static constexpr const bool debug_out = false;
+
+
+FixPropelSelf::FixPropelSelf( LAMMPS *lmp, int narg, char **argv )
+  : Fix(lmp, narg, argv)
+{
+  // if( lmp->citeme) lmp->citeme->add(cite_fix_active);
+  if( narg < 4 ) error->all(FLERR, "Illegal fix propel/self command");
+  
+  AtomVecEllipsoid *av = static_cast<AtomVecEllipsoid*>(atom->avec);
+  if (!av) error->all(FLERR, "FixPropelSelf requires atom_style ellipsoid");
+
+  if( debug_out && comm->me == 0 ){
+    fprintf(screen, "This is fix active, narg is %d\n", narg );
+    fprintf(screen, "args:");
+    for( int i = 0; i < narg; ++i ){
+      fprintf(screen, " %s", argv[i]);
+    }
+    fprintf(screen, "\n");
+  }
+
+  // args: fix ID all active magnitude prop1 prop2 prop3
+  // Optional args are
+  magnitude = force->numeric( FLERR, argv[3] );
+}
+
+
+FixPropelSelf::~FixPropelSelf()
+{}
+
+
+int FixPropelSelf::setmask()
+{
+  int mask = 0;
+  mask |= POST_FORCE;
+
+  return mask;
+}
+
+
+double FixPropelSelf::memory_usage()
+{
+  double bytes = 0.0;
+  return bytes;
+}
+
+
+
+void FixPropelSelf::post_force(int /* vflag */ )
+{
+  // Then do the rest:
+  double **f = atom->f;
+
+  AtomVecEllipsoid *av = static_cast<AtomVecEllipsoid*>(atom->avec);
+
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+  AtomVecEllipsoid::Bonus *bonus = av->bonus;
+  // Add the active force to the atom force:
+  for( int i = 0; i < nlocal; ++i ){
+    if( mask[i] & groupbit ){
+      double f_act[3] = { 0.0, 0.0, 1.0 };
+      double f_rot[3];
+
+      int* ellipsoid = atom->ellipsoid;
+      double *quat  = bonus[ellipsoid[i]].quat;
+      tagint *tag = atom->tag;
+
+      double Q[3][3];
+      MathExtra::quat_to_mat( quat, Q );
+      MathExtra::matvec( Q, f_act, f_rot );
+
+      if (debug_out && comm->me == 0) {
+        // Magical reference particle:
+        if (tag[i] == 12) {
+          fprintf(screen, "rotation quaternion: (%f %f %f %f)\n",
+                  quat[0], quat[1], quat[2], quat[3]);
+          fprintf(screen, "rotation matrix: / %f %f %f \\\n",
+                  Q[0][0] ,Q[0][1], Q[0][2]);
+          fprintf(screen, "                 | %f %f %f |\n",
+                  Q[1][0] ,Q[1][1], Q[1][2]);
+          fprintf(screen, "                 \\ %f %f %f /\n",
+                  Q[2][0] ,Q[2][1], Q[2][2]);
+
+          fprintf(screen, "Active force on atom %d: (%f %f %f)\n",
+                  tag[i], f_rot[0], f_rot[1], f_rot[2]);
+          fprintf(screen, "  Total force before: (%f %f %f)\n",
+                  f[i][0], f[i][1], f[i][2]);
+        }
+      }
+
+      f[i][0] += magnitude * f_rot[0];
+      f[i][1] += magnitude * f_rot[1];
+      f[i][2] += magnitude * f_rot[2];
+
+    }
+  }
+}

src/USER-MISC/fix_propel_self.h

@@ -0,0 +1,55 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(propel/self,FixPropelSelf)
+
+#else
+
+#ifndef LMP_FIX_PROPEL_SELF_H
+#define LMP_FIX_PROPEL_SELF_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixPropelSelf : public Fix {
+ public:
+  FixPropelSelf(class LAMMPS *, int, char **);
+  virtual ~FixPropelSelf();
+  virtual int setmask();
+  virtual void post_force(int);
+  // virtual void post_force_respa(int, int, int);
+
+  double memory_usage();
+
+protected:
+  double magnitude;
+  int thermostat_orient;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+*/