forked from lijiext/lammps
383 lines
15 KiB
Plaintext
383 lines
15 KiB
Plaintext
.. index:: change_box
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change_box command
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==================
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Syntax
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""""""
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.. parsed-literal::
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change_box group-ID parameter args ... keyword args ...
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* group-ID = ID of group of atoms to (optionally) displace
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* one or more parameter/arg pairs may be appended
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.. parsed-literal::
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parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *boundary* or *ortho* or *triclinic* or *set* or *remap*
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*x*\ , *y*\ , *z* args = style value(s)
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style = *final* or *delta* or *scale* or *volume*
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*final* values = lo hi
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lo hi = box boundaries after displacement (distance units)
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*delta* values = dlo dhi
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dlo dhi = change in box boundaries after displacement (distance units)
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*scale* values = factor
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factor = multiplicative factor for change in box length after displacement
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*volume* value = none = adjust this dim to preserve volume of system
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*xy*\ , *xz*\ , *yz* args = style value
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style = *final* or *delta*
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*final* value = tilt
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tilt = tilt factor after displacement (distance units)
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*delta* value = dtilt
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dtilt = change in tilt factor after displacement (distance units)
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*boundary* args = x y z
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x,y,z = *p* or *s* or *f* or *m*\ , one or two letters
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*p* is periodic
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*f* is non-periodic and fixed
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*s* is non-periodic and shrink-wrapped
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*m* is non-periodic and shrink-wrapped with a minimum value
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*ortho* args = none = change box to orthogonal
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*triclinic* args = none = change box to triclinic
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*set* args = none = store state of current box
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*remap* args = none = remap atom coords from last saved state to current box
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* zero or more keyword/value pairs may be appended
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* keyword = *units*
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.. parsed-literal::
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*units* value = *lattice* or *box*
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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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Examples
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""""""""
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.. parsed-literal::
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change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
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change_box all x scale 1.1 y volume z volume remap
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Description
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"""""""""""
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Change the volume and/or shape and/or boundary conditions for the
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simulation box. Orthogonal simulation boxes have 3 adjustable size
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parameters (x,y,z). Triclinic (non-orthogonal) simulation boxes have
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6 adjustable size/shape parameters (x,y,z,xy,xz,yz). Any or all of
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them can be adjusted independently by this command. Thus it can be
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used to expand or contract a box, or to apply a shear strain to a
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non-orthogonal box. It can also be used to change the boundary
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conditions for the simulation box, similar to the
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:doc:`boundary <boundary>` command.
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The size and shape of the initial simulation box are specified by the
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:doc:`create_box <create_box>` or :doc:`read_data <read_data>` or
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:doc:`read_restart <read_restart>` command used to setup the simulation.
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The size and shape may be altered by subsequent runs, e.g. by use of
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the :doc:`fix npt <fix_nh>` or :doc:`fix deform <fix_deform>` commands.
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The :doc:`create_box <create_box>`, :doc:`read data <read_data>`, and
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:doc:`read_restart <read_restart>` commands also determine whether the
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simulation box is orthogonal or triclinic and their doc pages explain
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the meaning of the xy,xz,yz tilt factors.
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See :ref:`Section_howto 12 <howto_12>` of the doc pages
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for a geometric description of triclinic boxes, as defined by LAMMPS,
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and how to transform these parameters to and from other commonly used
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triclinic representations.
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The keywords used in this command are applied sequentially to the
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simulation box and the atoms in it, in the order specified.
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Before the sequence of keywords are invoked, the current box
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size/shape is stored, in case a *remap* keyword is used to map the
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atom coordinates from a previously stored box size/shape to the
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current one.
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After all the keywords have been processed, any shrink-wrap boundary
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conditions are invoked (see the :doc:`boundary <boundary>` command)
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which may change simulation box boundaries, and atoms are migrated to
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new owning processors.
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.. note::
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This means that you cannot use the change_box command to enlarge
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a shrink-wrapped box, e.g. to make room to insert more atoms via the
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:doc:`create_atoms <create_atoms>` command, because the simulation box
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will be re-shrink-wrapped before the change_box command completes.
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Instead you could do something like this, assuming the simulation box
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is non-periodic and atoms extend from 0 to 20 in all dimensions:
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.. parsed-literal::
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change_box all x final -10 20
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create_atoms 1 single -5 5 5 # this will fail to insert an atom
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.. parsed-literal::
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change_box all x final -10 20 boundary f s s
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create_atoms 1 single -5 5 5
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change_box boundary s s s # this will work
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.. note::
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Unlike the earlier "displace_box" version of this command, atom
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remapping is NOT performed by default. This command allows remapping
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to be done in a more general way, exactly when you specify it (zero or
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more times) in the sequence of transformations. Thus if you do not
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use the *remap* keyword, atom coordinates will not be changed even if
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the box size/shape changes. If a uniformly strained state is desired,
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the *remap* keyword should be specified.
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.. note::
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It is possible to lose atoms with this command. E.g. by
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changing the box without remapping the atoms, and having atoms end up
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outside of non-periodic boundaries. It is also possible to alter
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bonds between atoms straddling a boundary in bad ways. E.g. by
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converting a boundary from periodic to non-periodic. It is also
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possible when remapping atoms to put them (nearly) on top of each
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other. E.g. by converting a boundary from non-periodic to periodic.
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All of these will typically lead to bad dynamics and/or generate error
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messages.
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.. note::
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The simulation box size/shape can be changed by arbitrarily
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large amounts by this command. This is not a problem, except that the
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mapping of processors to the simulation box is not changed from its
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initial 3d configuration; see the :doc:`processors <processors>`
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command. Thus, if the box size/shape changes dramatically, the
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mapping of processors to the simulation box may not end up as optimal
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as the initial mapping attempted to be.
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.. note::
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Because the keywords used in this command are applied one at a
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time to the simulation box and the atoms in it, care must be taken
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with triclinic cells to avoid exceeding the limits on skew after each
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transformation in the sequence. If skew is exceeded before the final
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transformation this can be avoided by changing the order of the
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sequence, or breaking the transformation into two or more smaller
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transformations. For more information on the allowed limits for box
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skew see the discussion on triclinic boxes on :ref:`this page <howto_12>`.
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----------
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For the *x*\ , *y*\ , and *z* parameters, this is the meaning of their
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styles and values.
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For style *final*\ , 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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For style *delta*\ , 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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For style *scale*\ , 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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The *volume* style changes the specified dimension in such a way that
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the overall box volume remains constant with respect to the operation
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performed by the preceding keyword. The *volume* style can only be
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used following a keyword that changed the volume, which is any of the
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*x*\ , *y*\ , *z* keywords. If the preceding keyword "key" had a *volume*
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style, then both it and the current keyword apply to the keyword
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preceding "key". I.e. this sequence of keywords is allowed:
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.. parsed-literal::
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change_box all x scale 1.1 y volume z volume
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The *volume* style changes the associated dimension so that the
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overall box volume is unchanged relative to its value before the
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preceding keyword was invoked.
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If the following command is used, then the z box length will shrink by
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the same 1.1 factor the x box length was increased by:
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.. parsed-literal::
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change_box all x scale 1.1 z volume
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If the following command is used, then the y,z box lengths will each
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shrink by sqrt(1.1) to keep the volume constant. In this case, the
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y,z box lengths shrink so as to keep their relative aspect ratio
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constant:
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.. parsed-literal::
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change_box all"x scale 1.1 y volume z volume
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If the following command is used, then the final box will be a factor
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of 10% larger in x and y, and a factor of 21% smaller in z, so as to
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keep the volume constant:
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.. parsed-literal::
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change_box all x scale 1.1 z volume y scale 1.1 z volume
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.. note::
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For solids or liquids, when one dimension of the box is
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expanded, it may be physically undesirable to hold the other 2 box
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lengths constant since that implies a density change. For solids,
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adjusting the other dimensions via the *volume* style may make
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physical sense (just as for a liquid), but may not be correct for
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materials and potentials whose Poisson ratio is not 0.5.
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For the *scale* and *volume* styles, the box length is expanded or
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compressed around its mid point.
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----------
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For the *xy*\ , *xz*\ , and *yz* 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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For style *final*\ , 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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For style *delta*\ , 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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All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
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tilt factors (xy,xz,yz) for triclinic boxes are required to be no more
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than half the distance of the parallel box length. For example, if
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xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
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factor must be between -5 and 5. Similarly, both xz and yz must be
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between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a
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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. Any tilt factor specified by this command
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must be within these limits.
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----------
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The *boundary* keyword takes arguments that have exactly the same
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meaning as they do for the :doc:`boundary <boundary>` command. In each
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dimension, a single letter assigns the same style to both the lower
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and upper face of the box. Two letters assigns the first style to the
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lower face and the second style to the upper face.
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The style *p* means the box is periodic; the other styles mean
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non-periodic. For style *f*\ , the position of the face is fixed. For
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style *s*\ , the position of the face is set so as to encompass the
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atoms in that dimension (shrink-wrapping), no matter how far they
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move. For style *m*\ , shrink-wrapping occurs, but is bounded by the
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current box edge in that dimension, so that the box will become no
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smaller. See the :doc:`boundary <boundary>` command for more
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explanation of these style options.
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Note that the "boundary" command itself can only be used before the
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simulation box is defined via a :doc:`read_data <read_data>` or
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:doc:`create_box <create_box>` or :doc:`read_restart <read_restart>`
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command. This command allows the boundary conditions to be changed
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later in your input script. Also note that the
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:doc:`read_restart <read_restart>` will change boundary conditions to
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match what is stored in the restart file. So if you wish to change
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them, you should use the change_box command after the read_restart
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command.
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----------
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The *ortho* and *triclinic* keywords convert the simulation box to be
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orthogonal or triclinic (non-orthongonal). See :ref:`this section <howto_13>` for a discussion of how non-orthongal
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boxes are represented in LAMMPS.
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The simulation box is defined as either orthogonal or triclinic when
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it is created via the :doc:`create_box <create_box>`,
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:doc:`read_data <read_data>`, or :doc:`read_restart <read_restart>`
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commands.
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These keywords allow you to toggle the existing simulation box from
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orthogonal to triclinic and vice versa. For example, an initial
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equilibration simulation can be run in an orthogonal box, the box can
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be toggled to triclinic, and then a :ref:`non-equilibrium MD (NEMD) simulation <howto_13>` can be run with deformation
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via the :doc:`fix deform <fix_deform>` command.
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If the simulation box is currently triclinic and has non-zero tilt in
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xy, yz, or xz, then it cannot be converted to an orthogonal box.
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----------
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The *set* keyword saves the current box size/shape. This can be
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useful if you wish to use the *remap* keyword more than once or if you
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wish it to be applied to an intermediate box size/shape in a sequence
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of keyword operations. Note that the box size/shape is saved before
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any of the keywords are processed, i.e. the box size/shape at the time
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the create_box command is encountered in the input script.
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The *remap* keyword remaps atom coordinates from the last saved box
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size/shape to the current box state. For example, if you stretch the
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box in the x dimension or tilt it in the xy plane via the *x* and *xy*
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keywords, then the *remap* commmand will dilate or tilt the atoms to
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conform to the new box size/shape, as if the atoms moved with the box
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as it deformed.
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Note that this operation is performed without regard to periodic
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boundaries. Also, any shrink-wrapping of non-periodic boundaries (see
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the :doc:`boundary <boundary>` command) occurs after all keywords,
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including this one, have been processed.
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Only atoms in the specified group are remapped.
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----------
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The *units* keyword determines the meaning of the distance units used
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to define various arguments. A *box* value selects standard distance
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units as defined by the :doc:`units <units>` command, e.g. Angstroms for
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units = real or metal. A *lattice* value means the distance units are
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in lattice spacings. The :doc:`lattice <lattice>` command must have
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been previously used to define the lattice spacing.
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----------
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Restrictions
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""""""""""""
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If you use the *ortho* or *triclinic* keywords, then at the point in
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the input script when this command is issued, no :doc:`dumps <dump>` can
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be active, nor can a :doc:`fix deform <fix_deform>` be active. This is
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because these commands test whether the simulation box is orthogonal
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when they are first issued. Note that these commands can be used in
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your script before a change_box command is issued, so long as an
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:doc:`undump <undump>` or :doc:`unfix <unfix>` command is also used to
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turn them off.
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Related commands
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""""""""""""""""
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:doc:`fix deform <fix_deform>`, :doc:`boundary <boundary>`
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Default
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"""""""
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The option default is units = lattice.
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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