fix move command¶
Syntax¶
fix ID group-ID move style args keyword values ...
ID, group-ID are documented in fix command
move = style name of this fix command
style = linear or wiggle or rotate or variable
linear args = Vx Vy Vz Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL wiggle args = Ax Ay Az period Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL period = period of oscillation (time units) rotate args = Px Py Pz Rx Ry Rz period 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
zero or more keyword/value pairs may be appended
keyword = units
units value = box or lattice
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
Description¶
Perform updates of position and velocity for atoms in the group each timestep using the specified settings or formulas, without regard to forces on the atoms. This can be useful for boundary or other atoms, whose movement can influence nearby atoms.
Note
The atoms affected by this fix should not normally be time integrated by other fixes (e.g. fix nve, fix nvt), 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 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.
Note
As discussed below, atoms are moved relative to their initial 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 dump custom command for a discussion of “unwrapped” coordinates. See the Atoms section of the read_data command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this fix by using the set image command.
The linear style moves atoms at a constant velocity, so that their position X = (x,y,z) as a function of time is given in vector notation as
X(t) = X0 + V * delta
where X0 = (x0,y0,z0) is their position at the time the fix is specified, V is the specified velocity vector with components (Vx,Vy,Vz), and delta is the time elapsed since the fix was specified. This style also sets the velocity of each atom to V = (Vx,Vy,Vz). If any of the velocity components is specified as NULL, then the position and velocity of that component is time integrated the same as the fix nve command would perform, using the corresponding force component on the atom.
Note that the linear style is identical to using the variable style with an equal-style variable that uses the vdisplace() function. E.g.
variable V equal 10.0
variable x equal vdisplace(0.0,$V)
fix 1 boundary move variable v_x NULL NULL v_V NULL NULL
The wiggle style moves atoms in an oscillatory fashion, so that their position X = (x,y,z) as a function of time is given in vector notation as
X(t) = X0 + A sin(omega*delta)
where X0 = (x0,y0,z0) is their position at the time the fix is specified, A is the specified amplitude vector with components (Ax,Ay,Az), omega is 2 PI / period, and delta is the time elapsed since the fix was specified. This style also sets the velocity of each atom to the time derivative of this expression. If any of the amplitude components is specified as NULL, then the position and velocity of that component is time integrated the same as the fix nve command would perform, using the corresponding force component on the atom.
Note that the wiggle style is identical to using the variable style with equal-style variables that use the swiggle() and cwiggle() functions. E.g.
variable A equal 10.0
variable T equal 5.0
variable omega equal 2.0*PI/$T
variable x equal swiggle(0.0,$A,$T)
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 = (Rx,Ry,Rz) that goes through a point P = (Px,Py,Pz). The period of the rotation is also specified. The direction of rotation for the atoms around the rotation axis is consistent with the right-hand rule: if your right-hand thumb points along R, then your fingers wrap around the 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 atom_style assigns an angular velocity or angular momentum or orientation to each atom (atom styles sphere, ellipsoid, line, tri, body), then those properties are also updated appropriately to correspond to the atom’s motion and rotation over time.
The variable style allows the position and velocity components of each atom to be set by formulas specified via the variable command. Each of the 6 variables is specified as an argument to the fix as v_name, where name is the variable name that is defined elsewhere in the input script.
Each variable must be of either the equal or atom style. Equal-style variables compute a single numeric quantity, that can be 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 fix stores the original coordinates of each atom (see note below) so that per-atom quantity can be used in an atom-style variable formula. See the 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 position at the time the fix was specified. The second 3 variables (v_vx,v_vy,v_vz) specified are used to compute a velocity for each atom.
Any of the 6 variables can be specified as NULL. If both the displacement and velocity variables for a particular x,y,z component are specified as NULL, then the position and velocity of that component is time integrated the same as the fix nve command would perform, using the corresponding force component on the atom. If only the velocity variable for a component is specified as NULL, then the displacement variable will be used to set the position of the atom, and its velocity component will not be changed. If only the displacement variable for a component is specified as NULL, then the velocity variable will be used to set the velocity of the atom, and the position of the atom will be time integrated using that velocity.
The units keyword determines the meaning of the distance units used to define the linear velocity and wiggle amplitude and rotate origin. This setting is ignored for the variable style. A box value selects standard units as defined by the units command, e.g. velocity in Angstroms/fs and amplitude and position in Angstroms for units = real. A lattice value means the velocity units are in lattice spacings per time and the amplitude and position are in lattice spacings. The lattice command must have been previously used to define the lattice spacing. Each of these 3 quantities may be dependent on the x,y,z dimension, since the lattice 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 binary restart files, as well as the initial timestep, so that the motion can be continuous in a restarted simulation. See the 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.
Note
Because the move positions are a function of the current timestep and the initial timestep, you cannot reset the timestep to a different value after reading a restart file, if you expect a fix move command to work in an uninterrupted fashion.
None of the fix_modify options are relevant to this fix.
This fix produces a per-atom array which can be accessed by various output commands. The number of columns for each atom is 3, and the columns store the original unwrapped x,y,z coords of 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 run command. This fix is not invoked during energy minimization.
For rRESPA time integration, this fix adjusts the position and velocity of atoms on the outermost rRESPA level.
Restrictions¶
none