mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@685 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
67fcb1a3bd
commit
f8d06291c9
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@ -271,7 +271,8 @@ in the command's documentation.
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<P>Actions:
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</P>
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<P><A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
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<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "minimize.html">minimize</A>,
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<A HREF = "displace_atoms.html">displace_atoms</A>,
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<A HREF = "displace_box.html">displace_box</A>, <A HREF = "minimize.html">minimize</A>,
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<A HREF = "run.html">run</A>, <A HREF = "temper.html">temper</A>
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</P>
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<P>Miscellaneous:
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@ -298,16 +299,16 @@ in the command's documentation.
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<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD><TD ><A HREF = "bond_style.html">bond_style</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "communicate.html">communicate</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD><TD ><A HREF = "create_atoms.html">create_atoms</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "create_box.html">create_box</A></TD><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "dimension.html">dimension</A></TD><TD ><A HREF = "dipole.html">dipole</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "echo.html">echo</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix.html">fix</A></TD><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "if.html">if</A></TD><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD><TD ><A HREF = "improper_style.html">improper_style</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD><TD ><A HREF = "label.html">label</A></TD><TD ><A HREF = "lattice.html">lattice</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "shape.html">shape</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
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<TR ALIGN="center"><TD ><A HREF = "dimension.html">dimension</A></TD><TD ><A HREF = "dipole.html">dipole</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD><TD ><A HREF = "displace_box.html">displace_box</A></TD><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "echo.html">echo</A></TD><TD ><A HREF = "fix.html">fix</A></TD><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "if.html">if</A></TD><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD><TD ><A HREF = "label.html">label</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD><TD ><A HREF = "min_style.html">min_style</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shape.html">shape</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
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</TD></TR></TABLE></DIV>
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<HR>
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@ -268,7 +268,8 @@ Output:
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Actions:
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"delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html,
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"displace_atoms"_displace_atoms.html, "minimize"_minimize.html,
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"displace_atoms"_displace_atoms.html,
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"displace_box"_displace_box.html, "minimize"_minimize.html,
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"run"_run.html, "temper"_temper.html
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Miscellaneous:
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@ -312,6 +313,7 @@ in the command's documentation.
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"dimension"_dimension.html,
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"dipole"_dipole.html,
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"displace_atoms"_displace_atoms.html,
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"displace_box"_displace_box.html,
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"dump"_dump.html,
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"dump_modify"_dump_modify.html,
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"echo"_echo.html,
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@ -74,18 +74,20 @@ units. <I>Lattice</I> means distance units are in lattice spacings. The
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<A HREF = "lattice.html">lattice</A> command must have been previously used to
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define the lattice spacing.
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</P>
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<HR>
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<P>Care should be taken not to move atoms on top of other atoms. After
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the move, atoms are remapped into the periodic simulation box if
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needed.
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</P>
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<P>Atoms can be moved arbitrarily long distances by this command.
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However if the box is non-periodic, this can change the shape of the
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simulation box. This is not a problem, except that the mapping of
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processors to the simulation box is not changed from its initial 3d
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configuration by this command; see the <A HREF = "processors.html">processors</A>
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command. Thus, if the box shape changes dramatically, the simulation
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may not be as well load-balanced (atoms per processor) as the initial
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mapping tried to achieve.
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<P>Atoms can be moved arbitrarily long distances by this command. If the
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simulation box is non-periodic, this can change its size or shape.
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This is not a problem, except that the mapping of processors to the
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simulation box is not changed by this command from its initial 3d
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configuration; see the <A HREF = "processors.html">processors</A> command. Thus, if
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the box size or shape changes dramatically, the simulation may not be
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as well load-balanced (atoms per processor) as the initial mapping
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tried to achieve.
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</P>
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<P><B>Restrictions:</B>
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</P>
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|
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@ -66,18 +66,20 @@ units. {Lattice} means distance units are in lattice spacings. The
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"lattice"_lattice.html command must have been previously used to
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define the lattice spacing.
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:line
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Care should be taken not to move atoms on top of other atoms. After
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the move, atoms are remapped into the periodic simulation box if
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needed.
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Atoms can be moved arbitrarily long distances by this command.
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However if the box is non-periodic, this can change the shape of the
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simulation box. This is not a problem, except that the mapping of
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processors to the simulation box is not changed from its initial 3d
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configuration by this command; see the "processors"_processors.html
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command. Thus, if the box shape changes dramatically, the simulation
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may not be as well load-balanced (atoms per processor) as the initial
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mapping tried to achieve.
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Atoms can be moved arbitrarily long distances by this command. If the
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simulation box is non-periodic, this can change its size or shape.
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This is not a problem, except that the mapping of processors to the
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simulation box is not changed by this command from its initial 3d
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configuration; see the "processors"_processors.html command. Thus, if
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the box size or shape changes dramatically, the simulation may not be
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as well load-balanced (atoms per processor) as the initial mapping
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tried to achieve.
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[Restrictions:]
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@ -0,0 +1,191 @@
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<HTML>
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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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</CENTER>
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<HR>
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<H3>displace_box command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>displace_box group-ID parameter args ... keyword value ...
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</PRE>
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<UL><LI>group-ID = ID of group of atoms to displace
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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>volume</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>volume</I> value = none = adjust this dim to preserve volume of system
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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>
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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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</PRE>
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<LI>zero or more keyword/value pairs may be appended to the args
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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>none</I>
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x = remap coords of atoms in group into deforming box
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none = no remapping of coords
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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>displace_box all xy final -2.0 z final 0.0 5.0 units box
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displace_box all x scale 1.1 y volume z volume
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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. Orthogonal
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simulation boxes have 3 adjustable parameters (x,y,z). Triclinic
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(non-orthogonal) simulation boxes have 6 adjustable parameters
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(x,y,z,xy,xz,yz). Any or all of them can be adjusted independently
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and simultaneously by this command. This fix can be used to expand or
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contract a box, or to apply a shear strain to a non-orthogonal box.
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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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"xy", "xz", and "yz" this means both affected dimensions must be
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periodic, e.g. x and y for "xy". Dimensions not varied by this
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command can be periodic or non-periodic.
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</P>
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<P>The size and shape of the initial simulation box are 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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or they are the values from the end of the previous run. The
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<A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read data</A>, and
|
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<A HREF = "read_restart.html">read_restart</A> 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. If the displace_box command
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changes the xy,xz,yz tilt factors, then the simulation box must be
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triclinic, even if its initial tilt factors are 0.0.
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</P>
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<HR>
|
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|
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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>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 discsussion 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>
|
||||
<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
|
||||
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
|
||||
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 by this command, it may be physically undesirable to hold the
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other 2 box lengths constant (unspecified by this command) since that
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implies a density change. Using the <I>volume</I> style for those 2
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dimensions to keep the box volume constant may make more physical
|
||||
sense, but may also not be correct for materials and potentials whose
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Poisson ratio is not 0.5.
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</P>
|
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<P>For the <I>scale</I> and <I>volume</I> styles, the box length is expanded or
|
||||
compressed around its mid point.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>For the <I>xy</I>, <I>xz</I>, and <I>yz</I> parameters, this is the meaning of their
|
||||
styles and values. Note that changing the tilt factors of a triclinic
|
||||
box does not change its volume.
|
||||
</P>
|
||||
<P>For style <I>final</I>, the final tilt factor is specified. The value
|
||||
can be in lattice or box distance units. See the discussion of the
|
||||
units keyword below.
|
||||
</P>
|
||||
<P>For style <I>delta</I>, a plus or minus change in the tilt factor is
|
||||
specified. The value can be in lattice or box distance units. See
|
||||
the discsussion of the units keyword below.
|
||||
</P>
|
||||
<P>All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
|
||||
tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half
|
||||
the distance of the parallel box length. For example, if xlo = 2 and
|
||||
xhi = 12, then the x box length is 10 and the xy tilt factor must be
|
||||
between -5 and 5. Similarly, both xz and yz must be between
|
||||
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
|
||||
since if the maximum tilt factor is 5 (as in this example), then
|
||||
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
|
||||
equivalent. Any tilt factor specified by this command must be within
|
||||
these limits.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>remap</I> keyword determines whether atom positions are re-mapped to
|
||||
the new box. If <I>remap</I> is set to <I>x</I> (the default), atoms in the fix
|
||||
group are re-mapped; otherwise they are not. If <I>remap</I> is set to
|
||||
<I>none</I>, then this remapping does not take place.
|
||||
</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.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The simulation box size or shape can be changed by arbitrarily large
|
||||
amounts by this command. This is not a problem, except that the
|
||||
mapping of processors to the simulation box is not changed by this
|
||||
command from its initial 3d configuration; see the
|
||||
<A HREF = "processors.html">processors</A> command. Thus, if the box size or shape
|
||||
changes dramatically, the simulation may not be as well load-balanced
|
||||
(atoms per processor) as the initial mapping tried to achieve.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>Any box dimension varied by this fix must be periodic.
|
||||
</P>
|
||||
<P>This command requires inter-processor communication to migrate atoms
|
||||
once they have moved. This means that your system must be ready to
|
||||
perform a simulation before using this command (force fields are
|
||||
setup, atom masses are set, etc).
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_deform.html">fix deform</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The option defaults are remap = x and units = lattice.
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,181 @@
|
|||
"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
|
||||
|
||||
displace_box command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
displace_box group-ID parameter args ... keyword value ... :pre
|
||||
|
||||
group-ID = ID of group of atoms to displace :ulb,l
|
||||
one or more parameter/arg pairs may be appended :l
|
||||
parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
|
||||
{x}, {y}, {z} args = style value(s)
|
||||
style = {final} or {delta} or {scale} or {volume}
|
||||
{final} values = lo hi
|
||||
lo hi = box boundaries at end of run (distance units)
|
||||
{delta} values = dlo dhi
|
||||
dlo dhi = change in box boundaries at end of run (distance units)
|
||||
{scale} values = factor
|
||||
factor = multiplicative factor for change in box length at end of run
|
||||
{volume} value = none = adjust this dim to preserve volume of system
|
||||
{xy}, {xz}, {yz} args = style value
|
||||
style = {final} or {delta}
|
||||
{final} value = tilt
|
||||
tilt = tilt factor at end of run (distance units)
|
||||
{delta} value = dtilt
|
||||
dtilt = change in tilt factor at end of run (distance units) :pre
|
||||
|
||||
zero or more keyword/value pairs may be appended to the args :l
|
||||
keyword = {remap} or {units} :l
|
||||
{remap} value = {x} or {none}
|
||||
x = remap coords of atoms in group into deforming box
|
||||
none = no remapping of coords
|
||||
{units} value = {lattice} or {box}
|
||||
lattice = distances are defined in lattice units
|
||||
box = distances are defined in simulation box units :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
displace_box all xy final -2.0 z final 0.0 5.0 units box
|
||||
displace_box all x scale 1.1 y volume z volume :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Change the volume and/or shape of the simulation box. Orthogonal
|
||||
simulation boxes have 3 adjustable parameters (x,y,z). Triclinic
|
||||
(non-orthogonal) simulation boxes have 6 adjustable parameters
|
||||
(x,y,z,xy,xz,yz). Any or all of them can be adjusted independently
|
||||
and simultaneously by this command. This fix can be used to expand or
|
||||
contract a box, or to apply a shear strain to a non-orthogonal box.
|
||||
|
||||
Any parameter varied by this command must refer to a periodic
|
||||
dimension - see the "boundary"_boundary.html command. For parameters
|
||||
"xy", "xz", and "yz" this means both affected dimensions must be
|
||||
periodic, e.g. x and y for "xy". Dimensions not varied by this
|
||||
command can be periodic or non-periodic.
|
||||
|
||||
The size and shape of the initial simulation box are specified by the
|
||||
"create_box"_create_box.html or "read_data"_read_data.html or
|
||||
"read_restart"_read_restart.html command used to setup the simulation,
|
||||
or they are the values from the end of the previous run. The
|
||||
"create_box"_create_box.html, "read data"_read_data.html, and
|
||||
"read_restart"_read_restart.html commands also determine whether the
|
||||
simulation box is orthogonal or triclinic and their doc pages explain
|
||||
the meaning of the xy,xz,yz tilt factors. If the displace_box command
|
||||
changes the xy,xz,yz tilt factors, then the simulation box must be
|
||||
triclinic, even if its initial tilt factors are 0.0.
|
||||
|
||||
:line
|
||||
|
||||
For the {x}, {y}, and {z} parameters, this is the meaning of their
|
||||
styles and values.
|
||||
|
||||
For style {final}, the final lo and hi box boundaries of a dimension
|
||||
are specified. The values can be in lattice or box distance units.
|
||||
See the discsussion of the units keyword below.
|
||||
|
||||
For style {delta}, plus or minus changes in the lo/hi box boundaries
|
||||
of a dimension are specified. The values can be in lattice or box
|
||||
distance units. See the discussion of the units keyword below.
|
||||
|
||||
For style {scale}, a multiplicative factor to apply to the box length
|
||||
of a dimension is specified. For example, if the initial box length
|
||||
is 10, and the factor is 1.1, then the final box length will be 11. A
|
||||
factor less than 1.0 means compression.
|
||||
|
||||
The {volume} style changes the specified dimension in such a way that
|
||||
the box volume remains constant while other box dimensions are changed
|
||||
explicitly via the styles discussed above. For example, "x scale 1.1
|
||||
y scale 1.1 z volume" will shrink the z box length as the x,y box
|
||||
lengths increase, to keep the volume constant (product of x,y,z
|
||||
lengths). If "x scale 1.1 z volume" is specified and parameter {y} is
|
||||
unspecified, then the z box length will shrink as x increases to keep
|
||||
the product of x,z lengths constant. If "x scale 1.1 y volume z
|
||||
volume" is specified, then both the y,z box lengths will shrink as x
|
||||
increases to keep the volume constant (product of x,y,z lengths). In
|
||||
this case, the y,z box lengths shrink so as to keep their relative
|
||||
aspect ratio constant.
|
||||
|
||||
For solids or liquids, note that when one dimension of the box is
|
||||
expanded by this command, it may be physically undesirable to hold the
|
||||
other 2 box lengths constant (unspecified by this command) since that
|
||||
implies a density change. Using the {volume} style for those 2
|
||||
dimensions to keep the box volume constant may make more physical
|
||||
sense, but may also not be correct for materials and potentials whose
|
||||
Poisson ratio is not 0.5.
|
||||
|
||||
For the {scale} and {volume} styles, the box length is expanded or
|
||||
compressed around its mid point.
|
||||
|
||||
:line
|
||||
|
||||
For the {xy}, {xz}, and {yz} parameters, this is the meaning of their
|
||||
styles and values. Note that changing the tilt factors of a triclinic
|
||||
box does not change its volume.
|
||||
|
||||
For style {final}, the final tilt factor is specified. The value
|
||||
can be in lattice or box distance units. See the discussion of the
|
||||
units keyword below.
|
||||
|
||||
For style {delta}, a plus or minus change in the tilt factor is
|
||||
specified. The value can be in lattice or box distance units. See
|
||||
the discsussion of the units keyword below.
|
||||
|
||||
All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
|
||||
tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half
|
||||
the distance of the parallel box length. For example, if xlo = 2 and
|
||||
xhi = 12, then the x box length is 10 and the xy tilt factor must be
|
||||
between -5 and 5. Similarly, both xz and yz must be between
|
||||
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
|
||||
since if the maximum tilt factor is 5 (as in this example), then
|
||||
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
|
||||
equivalent. Any tilt factor specified by this command must be within
|
||||
these limits.
|
||||
|
||||
:line
|
||||
|
||||
The {remap} keyword determines whether atom positions are re-mapped to
|
||||
the new box. If {remap} is set to {x} (the default), atoms in the fix
|
||||
group are re-mapped; otherwise they are not. If {remap} is set to
|
||||
{none}, then this remapping does not take place.
|
||||
|
||||
The {units} keyword determines the meaning of the distance units used
|
||||
to define various arguments. A {box} value selects standard distance
|
||||
units as defined by the "units"_units.html command, e.g. Angstroms for
|
||||
units = real or metal. A {lattice} value means the distance units are
|
||||
in lattice spacings. The "lattice"_lattice.html command must have
|
||||
been previously used to define the lattice spacing.
|
||||
|
||||
:line
|
||||
|
||||
The simulation box size or shape can be changed by arbitrarily large
|
||||
amounts by this command. This is not a problem, except that the
|
||||
mapping of processors to the simulation box is not changed by this
|
||||
command from its initial 3d configuration; see the
|
||||
"processors"_processors.html command. Thus, if the box size or shape
|
||||
changes dramatically, the simulation may not be as well load-balanced
|
||||
(atoms per processor) as the initial mapping tried to achieve.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Any box dimension varied by this fix must be periodic.
|
||||
|
||||
This command requires inter-processor communication to migrate atoms
|
||||
once they have moved. This means that your system must be ready to
|
||||
perform a simulation before using this command (force fields are
|
||||
setup, atom masses are set, etc).
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix deform"_fix_deform.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are remap = x and units = lattice.
|
||||
|
|
@ -130,7 +130,7 @@ See the discsussion of the units keyword below.
|
|||
</P>
|
||||
<P>For style <I>delta</I>, plus or minus changes in the lo/hi box boundaries
|
||||
of a dimension are specified. The values can be in lattice or box
|
||||
distance units. See the discsussion of the units keyword below.
|
||||
distance units. See the discussion of the units keyword below.
|
||||
</P>
|
||||
<P>For style <I>scale</I>, a multiplicative factor to apply to the box length
|
||||
of a dimension is specified. For example, if the initial box length
|
||||
|
|
|
|||
|
|
@ -119,7 +119,7 @@ See the discsussion of the units keyword below.
|
|||
|
||||
For style {delta}, plus or minus changes in the lo/hi box boundaries
|
||||
of a dimension are specified. The values can be in lattice or box
|
||||
distance units. See the discsussion of the units keyword below.
|
||||
distance units. See the discussion of the units keyword below.
|
||||
|
||||
For style {scale}, a multiplicative factor to apply to the box length
|
||||
of a dimension is specified. For example, if the initial box length
|
||||
|
|
|
|||
Loading…
Reference in New Issue