forked from lijiext/lammps
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23 KiB
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461 lines
23 KiB
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>fix deform command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID deform N parameter args ... keyword value ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>deform = style name of this fix command
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<LI>N = perform box deformation every this many timesteps
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<LI>one or more parameter/arg pairs may be appended
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<PRE>parameter = <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>xz</I> or <I>yz</I>
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<I>x</I>, <I>y</I>, <I>z</I> args = style value(s)
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style = <I>final</I> or <I>delta</I> or <I>scale</I> or <I>vel</I> or <I>erate</I> or <I>trate</I> or <I>volume</I> or <I>wiggle</I>
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<I>final</I> values = lo hi
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lo hi = box boundaries at end of run (distance units)
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<I>delta</I> values = dlo dhi
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dlo dhi = change in box boundaries at end of run (distance units)
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<I>scale</I> values = factor
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factor = multiplicative factor for change in box length at end of run
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<I>vel</I> value = V
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V = change box length at this velocity (distance/time units),
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effectively an engineering strain rate
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<I>erate</I> value = R
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R = engineering strain rate (1/time units)
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<I>trate</I> value = R
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R = true strain rate (1/time units)
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<I>volume</I> value = none = adjust this dim to preserve volume of system
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<I>wiggle</I> value = A Tp
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A = amplitude of oscillation (distance units)
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Tp = period of oscillation (time units)
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<I>xy</I>, <I>xz</I>, <I>yz</I> args = style value
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style = <I>final</I> or <I>delta</I> or <I>vel</I> or <I>erate</I> or <I>trate</I> or <I>wiggle</I>
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<I>final</I> value = tilt
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tilt = tilt factor at end of run (distance units)
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<I>delta</I> value = dtilt
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dtilt = change in tilt factor at end of run (distance units)
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<I>vel</I> value = V
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V = change tilt factor at this velocity (distance/time units),
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effectively an engineering shear strain rate
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<I>erate</I> value = R
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R = engineering shear strain rate (1/time units)
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<I>trate</I> value = R
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R = true shear strain rate (1/time units)
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<I>wiggle</I> value = A Tp
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A = amplitude of oscillation (distance units)
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Tp = period of oscillation (time units)
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</PRE>
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>remap</I> or <I>units</I>
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<PRE> <I>remap</I> value = <I>x</I> or <I>v</I> or <I>none</I>
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x = remap coords of atoms in group into deforming box
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v = remap velocities of all atoms when they cross periodic boundaries
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none = no remapping of x or v
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<I>units</I> value = <I>lattice</I> or <I>box</I>
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lattice = distances are defined in lattice units
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box = distances are defined in simulation box units
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all deform 1 x final 0.0 9.0 z final 0.0 5.0 units box
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fix 1 all deform 1 x trate 0.1 y volume z volume
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fix 1 all deform 1 xy erate 0.001 remap v
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fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Change the volume and/or shape of the simulation box during a dynamics
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run. Orthogonal simulation boxes have 3 adjustable parameters
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(x,y,z). Triclinic (non-orthogonal) simulation boxes have 6
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adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be
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adjusted independently and simultaneously by this command. This fix
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can be used to perform non-equilibrium MD (NEMD) simulations of a
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continuously strained system. See the <A HREF = "fix_nvt_sllod.html">fix
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nvt/sllod</A> and <A HREF = "compute_temp_deform.html">compute
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temp/deform</A> commands for more details.
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</P>
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<P>Any parameter varied by this command must refer to a periodic
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dimension - see the <A HREF = "boundary.html">boundary</A> command. For parameters
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<I>xy</I>, <I>xz</I>, and <I>yz</I>, the 2nd dimension must be periodic, e.g. <I>y</I> for
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<I>xy</I>. Dimensions not varied by this command can be periodic or
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non-periodic. Dimensions corresponding to unspecified parameters can
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also be controlled by a <A HREF = "fix_nh.html">fix npt</A> or <A HREF = "fix_nh.html">fix nph</A>
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command.
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</P>
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<P>The size and shape of the simulation box at the beginning of the
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simulation run were either specified by the
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<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> or
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<A HREF = "read_restart.html">read_restart</A> command used to setup the simulation
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initially if it is the first run, or they are the values from the end
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of the previous run. The <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read
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data</A>, and <A HREF = "read_restart.html">read_restart</A> commands
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specify whether the simulation box is orthogonal or non-orthogonal
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(triclinic) and explain the meaning of the xy,xz,yz tilt factors. If
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fix deform changes the xy,xz,yz tilt factors, then the simulation box
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must be triclinic, even if its initial tilt factors are 0.0.
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</P>
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<P>As described below, the desired simulation box size and shape at the
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end of the run are determined by the parameters of the fix deform
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command. Every Nth timestep during the run, the simulation box is
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expanded, contracted, or tilted to ramped values between the initial
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and final values.
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</P>
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<HR>
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<P>For the <I>x</I>, <I>y</I>, and <I>z</I> parameters, this is the meaning of their
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styles and values.
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</P>
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<P>The <I>final</I>, <I>delta</I>, <I>scale</I>, <I>vel</I>, and <I>erate</I> styles all change
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the specified dimension of the box via "constant displacement" which
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is effectively a "constant engineering strain rate". This means the
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box dimension changes linearly with time from its initial to final
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value.
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</P>
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<P>For style <I>final</I>, the final lo and hi box boundaries of a dimension
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are specified. The values can be in lattice or box distance units.
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See the discussion of the units keyword below.
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</P>
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<P>For style <I>delta</I>, plus or minus changes in the lo/hi box boundaries
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of a dimension are specified. The values can be in lattice or box
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distance units. See the discussion of the units keyword below.
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</P>
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<P>For style <I>scale</I>, a multiplicative factor to apply to the box length
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of a dimension is specified. For example, if the initial box length
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is 10, and the factor is 1.1, then the final box length will be 11. A
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factor less than 1.0 means compression.
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</P>
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<P>For style <I>vel</I>, a velocity at which the box length changes is
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specified in units of distance/time. This is effectively a "constant
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engineering strain rate", where rate = V/L0 and L0 is the initial box
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length. The distance can be in lattice or box distance units. See
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the discussion of the units keyword below. For example, if the
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initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then
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after 10 psec, the box length will have doubled. After 20 psec, it
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will have tripled.
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</P>
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<P>The <I>erate</I> style changes a dimension of the the box at a "constant
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engineering strain rate". The units of the specified strain rate are
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1/time. See the <A HREF = "units.html">units</A> command for the time units
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associated with different choices of simulation units,
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e.g. picoseconds for "metal" units). Tensile strain is unitless and
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is defined as delta/L0, where L0 is the original box length and delta
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is the change relative to the original length. The box length L as a
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function of time will change as
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</P>
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<PRE>L(t) = L0 (1 + erate*dt)
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</PRE>
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<P>where dt is the elapsed time (in time units). Thus if <I>erate</I> R is
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specified as 0.1 and time units are picoseconds, this means the box
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length will increase by 10% of its original length every picosecond.
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I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.2, etc. R =
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-0.01 means the box length will shrink by 1% of its original length
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every picosecond. Note that for an "engineering" rate the change is
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based on the original box length, so running with R = 1 for 10
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picoseconds expands the box length by a factor of 11 (strain of 10),
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which is different that what the <I>trate</I> style would induce.
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</P>
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<P>The <I>trate</I> style changes a dimension of the box at a "constant true
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strain rate". Note that this is not an "engineering strain rate", as
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the other styles are. Rather, for a "true" rate, the rate of change
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is constant, which means the box dimension changes non-linearly with
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time from its initial to final value. The units of the specified
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strain rate are 1/time. See the <A HREF = "units.html">units</A> command for the
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time units associated with different choices of simulation units,
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e.g. picoseconds for "metal" units). Tensile strain is unitless and
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is defined as delta/L0, where L0 is the original box length and delta
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is the change relative to the original length.
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</P>
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<P>The box length L as a function of time will change as
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</P>
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<PRE>L(t) = L0 exp(trate*dt)
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</PRE>
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<P>where dt is the elapsed time (in time units). Thus if <I>trate</I> R is
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specified as ln(1.1) and time units are picoseconds, this means the
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box length will increase by 10% of its current (not original) length
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every picosecond. I.e. strain after 1 psec = 0.1, strain after 2 psec
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= 0.21, etc. R = ln(2) or ln(3) means the box length will double or
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triple every picosecond. R = ln(0.99) means the box length will
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shrink by 1% of its current length every picosecond. Note that for a
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"true" rate the change is continuous and based on the current length,
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so running with R = ln(2) for 10 picoseconds does not expand the box
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length by a factor of 11 as it would with <I>erate</I>, but by a factor of
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1024 since the box length will double every picosecond.
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</P>
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<P>Note that to change the volume (or cross-sectional area) of the
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simulation box at a constant rate, you can change multiple dimensions
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via <I>erate</I> or <I>trate</I>. E.g. to double the box volume in a picosecond
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picosecond, you could set "x erate M", "y erate M", "z erate M", with
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M = pow(2,1/3) - 1 = 0.26, since if each box dimension grows by 26%,
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the box volume doubles. Or you could set "x trate M", "y trate M", "z
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trate M", with M = ln(1.26) = 0.231, and the box volume would double
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every picosecond.
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</P>
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<P>The <I>volume</I> style changes the specified dimension in such a way that
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the box volume remains constant while other box dimensions are changed
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explicitly via the styles discussed above. For example, "x scale 1.1
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y scale 1.1 z volume" will shrink the z box length as the x,y box
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lengths increase, to keep the volume constant (product of x,y,z
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lengths). If "x scale 1.1 z volume" is specified and parameter <I>y</I> is
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unspecified, then the z box length will shrink as x increases to keep
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the product of x,z lengths constant. If "x scale 1.1 y volume z
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volume" is specified, then both the y,z box lengths will shrink as x
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increases to keep the volume constant (product of x,y,z lengths). In
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this case, the y,z box lengths shrink so as to keep their relative
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aspect ratio constant.
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</P>
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<P>For solids or liquids, note that when one dimension of the box is
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expanded via fix deform (i.e. tensile strain), it may be physically
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undesirable to hold the other 2 box lengths constant (unspecified by
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fix deform) since that implies a density change. Using the <I>volume</I>
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style for those 2 dimensions to keep the box volume constant may make
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more physical sense, but may also not be correct for materials and
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potentials whose Poisson ratio is not 0.5. An alternative is to use
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<A HREF = "fix_nh.html">fix npt aniso</A> with zero applied pressure on those 2
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dimensions, so that they respond to the tensile strain dynamically.
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</P>
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<P>The <I>wiggle</I> style oscillates the specified box length dimension
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sinusoidally with the specified amplitude and period. I.e. the box
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length L as a function of time is given by
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</P>
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<PRE>L(t) = L0 + A sin(2*pi t/Tp)
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</PRE>
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<P>where L0 is its initial length. If the amplitude A is a positive
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number the box initially expands, then contracts, etc. If A is
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negative then the box initially contracts, then expands, etc. The
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amplitude can be in lattice or box distance units. See the discussion
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of the units keyword below.
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</P>
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<P>For the <I>scale</I>, <I>vel</I>, <I>erate</I>, <I>trate</I>, <I>volume</I>, and <I>wiggle</I>
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styles, the box length is expanded or compressed around its mid point.
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</P>
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<HR>
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<P>For the <I>xy</I>, <I>xz</I>, and <I>yz</I> parameters, this is the meaning of their
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styles and values. Note that changing the tilt factors of a triclinic
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box does not change its volume.
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</P>
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<P>The <I>final</I>, <I>delta</I>, <I>vel</I>, and <I>erate</I> styles all change the shear
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strain at a "constant engineering shear strain rate". This means the
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tilt factor changes linearly with time from its initial to final
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value.
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</P>
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<P>For style <I>final</I>, the final tilt factor is specified. The value
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can be in lattice or box distance units. See the discussion of the
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units keyword below.
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</P>
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<P>For style <I>delta</I>, a plus or minus change in the tilt factor is
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specified. The value can be in lattice or box distance units. See
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the discussion of the units keyword below.
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</P>
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<P>For style <I>vel</I>, a velocity at which the tilt factor changes is
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specified in units of distance/time. This is effectively an
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"engineering shear strain rate", where rate = V/L0 and L0 is the
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initial box length perpendicular to the direction of shear. The
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distance can be in lattice or box distance units. See the discussion
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of the units keyword below. For example, if the initial tilt factor
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is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the
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tilt factor will be 15 Angstroms. After 2 psec, it will be 25
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Angstroms.
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</P>
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<P>The <I>erate</I> style changes a tilt factor at a "constant engineering
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shear strain rate". The units of the specified shear strain rate are
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1/time. See the <A HREF = "units.html">units</A> command for the time units
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associated with different choices of simulation units,
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e.g. picoseconds for "metal" units). Shear strain is unitless and is
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defined as offset/length, where length is the box length perpendicular
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to the shear direction (e.g. y box length for xy deformation) and
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offset is the displacement distance in the shear direction (e.g. x
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direction for xy deformation) from the unstrained orientation.
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</P>
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<P>The tilt factor T as a function of time will change as
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</P>
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<PRE>T(t) = T0 + erate*dt
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</PRE>
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<P>where T0 is the initial tilt factor and dt is the elapsed time (in
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time units). Thus if <I>erate</I> R is specified as 0.1 and time units are
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picoseconds, this means the shear strain will increase by 0.1 every
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picosecond. I.e. if the xy shear strain was initially 0.0, then
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strain after 1 psec = 0.1, strain after 2 psec = 0.2, etc. Thus the
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tilt factor would be 0.0 at time 0, 0.1*ybox at 1 psec, 0.2*ybox at 2
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psec, etc, where ybox is the original y box length. R = 1 or 2 means
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the tilt factor will increase by 1 or 2 every picosecond. R = -0.01
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means a decrease in shear strain by 0.01 every picosecond.
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</P>
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<P>The <I>trate</I> style changes a tilt factor at a "constant true shear
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strain rate". Note that this is not an "engineering shear strain
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rate", as the other styles are. Rather, for a "true" rate, the rate
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of change is constant, which means the tilt factor changes
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non-linearly with time from its initial to final value. The units of
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the specified shear strain rate are 1/time. See the
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<A HREF = "units.html">units</A> command for the time units associated with
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different choices of simulation units, e.g. picoseconds for "metal"
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units). Shear strain is unitless and is defined as offset/length,
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where length is the box length perpendicular to the shear direction
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(e.g. y box length for xy deformation) and offset is the displacement
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distance in the shear direction (e.g. x direction for xy deformation)
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from the unstrained orientation.
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</P>
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<P>The tilt factor T as a function of time will change as
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</P>
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<PRE>T(t) = T0 exp(trate*dt)
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</PRE>
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<P>where T0 is the initial tilt factor and dt is the elapsed time (in
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time units). Thus if <I>trate</I> R is specified as ln(1.1) and time units
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are picoseconds, this means the shear strain or tilt factor will
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increase by 10% every picosecond. I.e. if the xy shear strain was
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initially 0.1, then strain after 1 psec = 0.11, strain after 2 psec =
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0.121, etc. R = ln(2) or ln(3) means the tilt factor will double or
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triple every picosecond. R = ln(0.99) means the tilt factor will
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shrink by 1% every picosecond. Note that the change is continuous, so
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running with R = ln(2) for 10 picoseconds does not change the tilt
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factor by a factor of 10, but by a factor of 1024 since it doubles
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every picosecond. Note that the initial tilt factor must be non-zero
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to use the <I>trate</I> option.
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</P>
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<P>Note that shear strain is defined as the tilt factor divided by the
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perpendicular box length. The <I>erate</I> and <I>trate</I> styles control the
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tilt factor, but assume the perpendicular box length remains constant.
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If this is not the case (e.g. it changes due to another fix deform
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parameter), then this effect on the shear strain is ignored.
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</P>
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<P>The <I>wiggle</I> style oscillates the specified tilt factor sinusoidally
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with the specified amplitude and period. I.e. the tilt factor T as a
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function of time is given by
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</P>
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<PRE>T(t) = T0 + A sin(2*pi t/Tp)
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</PRE>
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<P>where T0 is its initial value. If the amplitude A is a positive
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number the tilt factor initially becomes more positive, then more
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negative, etc. If A is negative then the tilt factor initially
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becomes more negative, then more positive, etc. The amplitude can be
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in lattice or box distance units. See the discussion of the units
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keyword below.
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</P>
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<P>All of these styles change the xy, xz, yz tilt factors during a
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simulation. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes
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are always bounded by half the distance of the parallel box length.
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For example, if xlo = 2 and xhi = 12, then the x box length is 10 and
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the xy tilt factor must be between -5 and 5. Similarly, both xz and
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yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is
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not a limitation, since if the maximum tilt factor is 5 (as in this
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example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
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... are all equivalent.
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</P>
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<P>To obey this constraint and allow for large shear deformations to be
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applied via the <I>xy</I>, <I>xz</I>, or <I>yz</I> parameters, the following
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algorithm is used. If <I>prd</I> is the associated parallel box length (10
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in the example above), then if the tilt factor exceeds the accepted
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range of -5 to 5 during the simulation, then the box is re-shaped to
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|
the other limit (an equivalent box) and the simulation continues.
|
|
Thus for this example, if the initial xy tilt factor was 0.0 and "xy
|
|
final 100.0" was specified, then during the simulation the xy tilt
|
|
factor would increase from 0.0 to 5.0, the box would be re-shaped so
|
|
that the tilt factor becomes -5.0, the tilt factor would increase from
|
|
-5.0 to 5.0, the box would be re-shaped again, etc. The re-shaping
|
|
would occur 10 times and the final tilt factor at the end of the
|
|
simulation would be 0.0. During each re-shaping event, atoms are
|
|
remapped into the new box in the appropriate manner.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>Each time the box size or shape is changed, the <I>remap</I> keyword
|
|
determines whether atom positions are remapped to the new box. If
|
|
<I>remap</I> is set to <I>x</I> (the default), atoms in the fix group are
|
|
remapped; otherwise they are not. Note that their velocities are not
|
|
changed, just their positions are altered. If <I>remap</I> is set to <I>v</I>,
|
|
then any atom in the fix group that crosses a periodic boundary will
|
|
have a delta added to its velocity equal to the difference in
|
|
velocities between the lo and hi boundaries. Note that this velocity
|
|
difference can include tilt components, e.g. a delta in the x velocity
|
|
when an atom crosses the y periodic boundary. If <I>remap</I> is set to
|
|
<I>none</I>, then neither of these remappings take place.
|
|
</P>
|
|
<P>Conceptually, setting <I>remap</I> to <I>x</I> forces the atoms to deform via an
|
|
affine transformation that exactly matches the box deformation. This
|
|
setting is typically appropriate for solids. Note that though the
|
|
atoms are effectively "moving" with the box over time, it is not due
|
|
to their having a velocity that tracks the box change, but only due to
|
|
the remapping. By contrast, setting <I>remap</I> to <I>v</I> is typically
|
|
appropriate for fluids, where you want the atoms to respond to the
|
|
change in box size/shape on their own and acquire a velocity that
|
|
matches the box change, so that their motion will naturally track the
|
|
box without explicit remapping of their coordinates.
|
|
</P>
|
|
<P>IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are
|
|
performed using this fix, the option "remap v" should normally be
|
|
used. This is because <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> adjusts the
|
|
atom positions and velocities to induce a velocity profile that
|
|
matches the changing box size/shape. Thus atom coordinates should NOT
|
|
be remapped by fix deform, but velocities SHOULD be when atoms cross
|
|
periodic boundaries, since that is consistent with maintaining the
|
|
velocity profile already created by fix nvt/sllod. LAMMPS will warn
|
|
you if the <I>remap</I> setting is not consistent with fix nvt/sllod.
|
|
</P>
|
|
<P>IMPORTANT NOTE: If a <A HREF = "fix_rigid.html">fix rigid</A> is defined for rigid
|
|
bodies, and <I>remap</I> is set to <I>x</I>, then the center-of-mass coordinates
|
|
of rigid bodies will be remapped to the changing simulation box. This
|
|
will be done regardless of whether atoms in the rigid bodies are in
|
|
the fix deform group or not. The velocity of the centers of mass are
|
|
not remapped even if <I>remap</I> is set to <I>v</I>, since <A HREF = "fix_nvt_sllod.html">fix
|
|
nvt/sllod</A> does not currently do anything special
|
|
for rigid particles. If you wish to perform a NEMD simulation of
|
|
rigid particles, you can either thermostat them independently or
|
|
include a background fluid and thermostat the fluid via <A HREF = "fix_nvt_sllod.html">fix
|
|
nvt/sllod</A>.
|
|
</P>
|
|
<P>The <I>units</I> keyword determines the meaning of the distance units used
|
|
to define various arguments. A <I>box</I> value selects standard distance
|
|
units as defined by the <A HREF = "units.html">units</A> command, e.g. Angstroms for
|
|
units = real or metal. A <I>lattice</I> value means the distance units are
|
|
in lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have
|
|
been previously used to define the lattice spacing. Note that the
|
|
units choice also affects the <I>vel</I> style parameters since it is
|
|
defined in terms of distance/time.
|
|
</P>
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
|
</P>
|
|
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
|
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
|
are relevant to this fix. No global or per-atom quantities are stored
|
|
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
|
|
commands</A>.
|
|
</P>
|
|
<P>This fix can perform deformation over multiple runs, using the <I>start</I>
|
|
and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
|
|
<A HREF = "run.html">run</A> command for details of how to do this.
|
|
</P>
|
|
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
|
|
</P>
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>Any box dimension varied by this fix must be periodic.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "displace_box.html">displace_box</A>
|
|
</P>
|
|
<P><B>Default:</B>
|
|
</P>
|
|
<P>The option defaults are remap = x and units = lattice.
|
|
</P>
|
|
</HTML>
|