add "transrot" style to fix move that allows to do translation and rotation at the same time

doc/src/fix_move.rst

@@ -12,7 +12,7 @@ Syntax
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * move = style name of this fix command
-* style = *linear* or *wiggle* or *rotate* or *variable*
+* style = *linear* or *wiggle* or *rotate* or *transrot* or *variable*
 
   .. parsed-literal::
 
@@ -25,6 +25,11 @@ Syntax
          Px,Py,Pz = origin point of axis of rotation (distance units)
          Rx,Ry,Rz = axis of rotation vector
          period = period of rotation (time units)
+       *transrot* args = Vx Vy Vz Px Py Pz Rx Ry Rz period
+         Vx,Vy,Vz = components of velocity vector (velocity units)
+         Px,Py,Pz = origin point of axis of rotation (distance units)
+         Rx,Ry,Rz = axis of rotation vector
+         period = period of rotation (time units)
        *variable* args = v_dx v_dy v_dz v_vx v_vy v_vz
          v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
          v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL
@@ -44,6 +49,7 @@ Examples
    fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
    fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
    fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL
+   fix 3 boundary move transrot 0.1 0.1 0.0 0.0 0.0 0.0 0.0 0.0 1.0 5.0 units box
 
 Description
 """""""""""
@@ -55,15 +61,17 @@ whose movement can influence nearby atoms.
 
 .. note::
 
-   The atoms affected by this fix should not normally be time
+   The atoms affected by this fix should not normally be time integrated
-   integrated by other fixes (e.g. :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`), since that will change their positions and
+   by other fixes (e.g. :doc:`fix nve <fix_nve>`, :doc:`fix nvt
-   velocities twice.
+   <fix_nh>`), since that will change their positions and velocities
+   twice.
 
 .. note::
 
    As atoms move due to this fix, they will pass through periodic
    boundaries and be remapped to the other side of the simulation box,
-   just as they would during normal time integration (e.g. via the :doc:`fix nve <fix_nve>` command).  It is up to you to decide whether
+   just as they would during normal time integration (e.g. via the
+   :doc:`fix nve <fix_nve>` command).  It is up to you to decide whether
    periodic boundaries are appropriate with the kind of atom motion you
    are prescribing with this fix.
 
@@ -73,11 +81,11 @@ whose movement can influence nearby atoms.
    position at the time the fix is specified.  These initial coordinates
    are stored by the fix in "unwrapped" form, by using the image flags
    associated with each atom.  See the :doc:`dump custom <dump>` command
-   for a discussion of "unwrapped" coordinates.  See the Atoms section of
+   for a discussion of "unwrapped" coordinates.  See the Atoms section
-   the :doc:`read_data <read_data>` command for a discussion of image flags
+   of the :doc:`read_data <read_data>` command for a discussion of image
-   and how they are set for each atom.  You can reset the image flags
+   flags and how they are set for each atom.  You can reset the image
-   (e.g. to 0) before invoking this fix by using the :doc:`set image <set>`
+   flags (e.g. to 0) before invoking this fix by using the :doc:`set
-   command.
+   image <set>` command.
 
 ----------
 
@@ -118,13 +126,13 @@ notation as
 
 where *X0* = (x0,y0,z0) is their position at the time the fix is
 specified, *A* is the specified amplitude vector with components
-(Ax,Ay,Az), *omega* is 2 PI / *period*, and *delta* is the time
+(Ax,Ay,Az), *omega* is 2 PI / *period*, and *delta* is the time elapsed
-elapsed since the fix was specified.  This style also sets the
+since the fix was specified.  This style also sets the velocity of each
-velocity of each atom to the time derivative of this expression.  If
+atom to the time derivative of this expression.  If any of the amplitude
-any of the amplitude components is specified as NULL, then the
+components is specified as NULL, then the position and velocity of that
-position and velocity of that component is time integrated the same as
+component is time integrated the same as the :doc:`fix nve <fix_nve>`
-the :doc:`fix nve <fix_nve>` command would perform, using the
+command would perform, using the corresponding force component on the
-corresponding force component on the atom.
+atom.
 
 Note that the *wiggle* style is identical to using the *variable*
 style with :doc:`equal-style variables <variable>` that use the
@@ -139,21 +147,29 @@ swiggle() and cwiggle() functions.  E.g.
    variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
    fix 1 boundary move variable v_x NULL NULL v_v NULL NULL
 
-The *rotate* style rotates atoms around a rotation axis *R* =
+The *rotate* style rotates atoms around a rotation axis *R* = (Rx,Ry,Rz)
-(Rx,Ry,Rz) that goes through a point *P* = (Px,Py,Pz).  The *period* of
+that goes through a point *P* = (Px,Py,Pz).  The *period* of the
-the rotation is also specified.  The direction of rotation for the
+rotation is also specified.  The direction of rotation for the atoms
-atoms around the rotation axis is consistent with the right-hand rule:
+around the rotation axis is consistent with the right-hand rule: if your
-if your right-hand thumb points along *R*, then your fingers wrap
+right-hand thumb points along *R*, then your fingers wrap around the
-around the axis in the direction of rotation.
+axis in the direction of rotation.
 
 This style also sets the velocity of each atom to (omega cross Rperp)
 where omega is its angular velocity around the rotation axis and Rperp
 is a perpendicular vector from the rotation axis to the atom.  If the
 defined :doc:`atom_style <atom_style>` assigns an angular velocity or
-angular momentum or orientation to each atom (:doc:`atom styles <atom_style>` sphere, ellipsoid, line, tri, body), then
+angular momentum or orientation to each atom (:doc:`atom styles
+<atom_style>` sphere, ellipsoid, line, tri, body), then
 those properties are also updated appropriately to correspond to the
 atom's motion and rotation over time.
 
+The *transrot* style combines the effects of *rotate* and *linear* so
+that it is possible to prescribe a rotating group of atoms that also
+moves at a constant velocity.  The arguments are for the translation
+first and then for the rotation.  Since the rotation affects all
+coordinate components, it is not possible to set any of the
+translation vector components to NULL.
+
 The *variable* style allows the position and velocity components of
 each atom to be set by formulas specified via the
 :doc:`variable <variable>` command.  Each of the 6 variables is
@@ -165,10 +181,10 @@ Each variable must be of either the *equal* or *atom* style.
 a function of the timestep as well as of other simulation values.
 *Atom*\ -style variables compute a numeric quantity for each atom, that
 can be a function per-atom quantities, such as the atom's position, as
-well as of the timestep and other simulation values.  Note that this
+well as of the timestep and other simulation values.  Note that this fix
-fix stores the original coordinates of each atom (see note below) so
+stores the original coordinates of each atom (see note below) so that
-that per-atom quantity can be used in an atom-style variable formula.
+per-atom quantity can be used in an atom-style variable formula.  See
-See the :doc:`variable <variable>` command for details.
+the :doc:`variable <variable>` command for details.
 
 The first 3 variables (v_dx,v_dy,v_dz) specified for the *variable*
 style are used to calculate a displacement from the atom's original
@@ -206,8 +222,9 @@ spacings can be different in x,y,z.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the original coordinates of moving atoms to :doc:`binary restart files <restart>`, as well as the initial timestep, so that
+This fix writes the original coordinates of moving atoms to :doc:`binary
-the motion can be continuous in a restarted simulation.  See the
+restart files <restart>`, as well as the initial timestep, so that the
+motion can be continuous in a restarted simulation.  See the
 :doc:`read_restart <read_restart>` command for info on how to re-specify
 a fix in an input script that reads a restart file, so that the
 operation of the fix continues in an uninterrupted fashion.
@@ -224,11 +241,12 @@ fix.
 
 This fix produces a per-atom array which can be accessed by various
 :doc:`output commands <Howto_output>`.  The number of columns for each
-atom is 3, and the columns store the original unwrapped x,y,z coords
+atom is 3, and the columns store the original unwrapped x,y,z coords of
-of each atom.  The per-atom values can be accessed on any timestep.
+each atom.  The per-atom values can be accessed on any timestep.
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 For :doc:`rRESPA time integration <run_style>`, this fix adjusts the
 position and velocity of atoms on the outermost rRESPA level.