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sjplimp
2012-06-01 16:41:20 +00:00
parent 75d99d30f5
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12 changed files with 506 additions and 28 deletions
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2
doc/Manual.html
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@ -41,7 +41,7 @@ describe the version you have.
<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated <LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want about once per month. This is because it is large, and we don't want
it to be part of very patch. it to be part of every patch.
<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc <LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
directory, which describes the internal structure and algorithms of directory, which describes the internal structure and algorithms of

2
doc/Manual.txt
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@ -38,7 +38,7 @@ describe the version you have. :l
The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want about once per month. This is because it is large, and we don't want
it to be part of very patch. :l it to be part of every patch. :l
There is also a "Developer.pdf"_Developer.pdf file in the doc There is also a "Developer.pdf"_Developer.pdf file in the doc
directory, which describes the internal structure and algorithms of directory, which describes the internal structure and algorithms of

17
doc/Section_commands.html
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@ -245,8 +245,8 @@ in the command's documentation.
</P> </P>
<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "create_box.html">create_box</A>, <P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "create_box.html">create_box</A>,
<A HREF = "lattice.html">lattice</A>, <A HREF = "read_data.html">read_data</A>, <A HREF = "lattice.html">lattice</A>, <A HREF = "read_data.html">read_data</A>,
<A HREF = "read_restart.html">read_restart</A>, <A HREF = "region.html">region</A>, <A HREF = "read_dump.html">read_dump</A>, <A HREF = "read_restart.html">read_restart</A>,
<A HREF = "replicate.html">replicate</A> <A HREF = "region.html">region</A>, <A HREF = "replicate.html">replicate</A>
</P> </P>
<P>Force fields: <P>Force fields:
</P> </P>
@ -323,11 +323,11 @@ in the command's documentation.
<TR ALIGN="center"><TD ><A HREF = "label.html">label</A></TD><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></TR> <TR ALIGN="center"><TD ><A HREF = "label.html">label</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "neb.html">neb</A></TD><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></TR> <TR ALIGN="center"><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "neb.html">neb</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "package.html">package</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><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "partition.html">partition</A></TD></TR> <TR ALIGN="center"><TD ><A HREF = "package.html">package</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><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "partition.html">partition</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "prd.html">prd</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "quit.html">quit</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD></TR> <TR ALIGN="center"><TD ><A HREF = "prd.html">prd</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "quit.html">quit</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_dump.html">read_dump</A></TD></TR>
<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> <TR ALIGN="center"><TD ><A HREF = "read_restart.html">read_restart</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "suffix.html">suffix</A></TD><TD ><A HREF = "tad.html">tad</A></TD><TD ><A HREF = "temper.html">temper</A></TD></TR> <TR ALIGN="center"><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "suffix.html">suffix</A></TD><TD ><A HREF = "tad.html">tad</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "thermo.html">thermo</A></TD><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></TR> <TR ALIGN="center"><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><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></TR>
<TR ALIGN="center"><TD ><A HREF = "unfix.html">unfix</A></TD><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> <TR ALIGN="center"><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><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>
</TD></TR></TABLE></DIV> </TD></TR></TABLE></DIV>
<HR> <HR>
@ -607,7 +607,8 @@ built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>. package</A>.
</P> </P>
<DIV ALIGN=center><TABLE BORDER=1 > <DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_class2.html">class2/omp</A></TD><TD WIDTH="100"><A HREF = "improper_cvff.html">cvff/omp</A></TD><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic/omp</A></TD><TD WIDTH="100"><A HREF = "improper_umbrella.html">umbrella/omp</A> <TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_class2.html">class2/omp</A></TD><TD WIDTH="100"><A HREF = "improper_cossq.html">cossq/omp</A></TD><TD WIDTH="100"><A HREF = "improper_cvff.html">cvff/omp</A></TD><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_ring.html">ring/omp</A></TD><TD WIDTH="100"><A HREF = "improper_umbrella.html">umbrella/omp</A>
</TD></TR></TABLE></DIV> </TD></TR></TABLE></DIV>
<HR> <HR>

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doc/Section_commands.txt
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@ -241,8 +241,8 @@ Atom definition:
"create_atoms"_create_atoms.html, "create_box"_create_box.html, "create_atoms"_create_atoms.html, "create_box"_create_box.html,
"lattice"_lattice.html, "read_data"_read_data.html, "lattice"_lattice.html, "read_data"_read_data.html,
"read_restart"_read_restart.html, "region"_region.html, "read_dump"_read_dump.html, "read_restart"_read_restart.html,
"replicate"_replicate.html "region"_region.html, "replicate"_replicate.html
Force fields: Force fields:
@ -368,6 +368,7 @@ in the command's documentation.
"processors"_processors.html, "processors"_processors.html,
"quit"_quit.html, "quit"_quit.html,
"read_data"_read_data.html, "read_data"_read_data.html,
"read_dump"_read_dump.html,
"read_restart"_read_restart.html, "read_restart"_read_restart.html,
"region"_region.html, "region"_region.html,
"replicate"_replicate.html, "replicate"_replicate.html,
@ -1006,8 +1007,10 @@ built with the "appropriate accelerated
package"_Section_accelerate.html. package"_Section_accelerate.html.
"class2/omp"_improper_class2.html, "class2/omp"_improper_class2.html,
"cossq/omp"_improper_cossq.html,
"cvff/omp"_improper_cvff.html, "cvff/omp"_improper_cvff.html,
"harmonic/omp"_improper_harmonic.html, "harmonic/omp"_improper_harmonic.html,
"ring/omp"_improper_ring.html,
"umbrella/omp"_improper_umbrella.html :tb(c=4,ea=c,w=100) "umbrella/omp"_improper_umbrella.html :tb(c=4,ea=c,w=100)
:line :line

12
doc/compute_temp_region.html
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@ -73,11 +73,13 @@ fixes can operate on a geometric region of atoms, as defined by this
compute. compute.
</P> </P>
<P>Unlike other compute styles that calculate temperature, this compute <P>Unlike other compute styles that calculate temperature, this compute
does NOT currently subtract out degrees-of-freedom due to fixes that does not subtract out degrees-of-freedom due to fixes that constrain
constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and <A HREF = "fix_rigid.html">fix
<A HREF = "fix_rigid.html">fix rigid</A>. If needed the subtracted rigid</A>. This is because those degrees of freedom
degrees-of-freedom can be altered using the <I>extra</I> option of the (e.g. a constrained bond) can straddle the region boundary, and hence
<A HREF = "compute_modify.html">compute_modify</A> command. the concept is somewhat ill-defined. If needed the number of
subtracted degrees-of-freedom can be set explicitly using the <I>extra</I>
option of the <A HREF = "compute_modify.html">compute_modify</A> command.
</P> </P>
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for <P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
a discussion of different ways to compute temperature and perform a discussion of different ways to compute temperature and perform

12
doc/compute_temp_region.txt
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@ -70,11 +70,13 @@ fixes can operate on a geometric region of atoms, as defined by this
compute. compute.
Unlike other compute styles that calculate temperature, this compute Unlike other compute styles that calculate temperature, this compute
does NOT currently subtract out degrees-of-freedom due to fixes that does not subtract out degrees-of-freedom due to fixes that constrain
constrain molecular motion, such as "fix shake"_fix_shake.html and molecular motion, such as "fix shake"_fix_shake.html and "fix
"fix rigid"_fix_rigid.html. If needed the subtracted rigid"_fix_rigid.html. This is because those degrees of freedom
degrees-of-freedom can be altered using the {extra} option of the (e.g. a constrained bond) can straddle the region boundary, and hence
"compute_modify"_compute_modify.html command. the concept is somewhat ill-defined. If needed the number of
subtracted degrees-of-freedom can be set explicitly using the {extra}
option of the "compute_modify"_compute_modify.html command.
See "this howto section"_Section_howto.html#howto_16 of the manual for See "this howto section"_Section_howto.html#howto_16 of the manual for
a discussion of different ways to compute temperature and perform a discussion of different ways to compute temperature and perform

3
doc/read_data.html
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@ -824,7 +824,8 @@ LAMMPS</A> section of the documentation.
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>
<P><A HREF = "read_restart.html">read_restart</A>, <A HREF = "create_atoms.html">create_atoms</A> <P><A HREF = "read_dump.html">read_dump</A>, <A HREF = "read_restart.html">read_restart</A>,
<A HREF = "create_atoms.html">create_atoms</A>
</P> </P>
<P><B>Default:</B> none <P><B>Default:</B> none
</P> </P>

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doc/read_data.txt
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@ -731,6 +731,7 @@ LAMMPS"_Section_start.html#start_2 section of the documentation.
[Related commands:] [Related commands:]
"read_restart"_read_restart.html, "create_atoms"_create_atoms.html "read_dump"_read_dump.html, "read_restart"_read_restart.html,
"create_atoms"_create_atoms.html
[Default:] none [Default:] none

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doc/read_dump.html Normal file
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@ -0,0 +1,240 @@
<HTML>
<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>
</CENTER>
<HR>
<H3>read_dump command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>read_dump file Nstep field1 field2 ... keyword values ...
</PRE>
<UL><LI>file = name of dump file to read
<LI>Nstep = snapshot timestep to read from file
<LI>one or more fields may be appended
<PRE>field = <I>x</I> or <I>y</I> or <I>z</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>ix</I> or <I>iy</I> or <I>iz</I>
<I>x</I>,<I>y</I>,<I>z</I> = atom coordinates
<I>vx</I>,<I>vy</I>,<I>vz</I> = velocity components
<I>ix</I>,<I>iy</I>,<I>iz</I> = image flags in each dimension
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>box</I> or <I>replace</I> or <I>purge</I> or <I>trim</I> or <I>add</I> or <I>label</I> or <I>scaled</I> or <I>format</I>
<PRE> <I>box</I> value = <I>yes</I> or <I>no</I> = replace simulation box with dump box
<I>replace</I> value = <I>yes</I> or <I>no</I> = overwrite atoms with dump atoms
<I>purge</I> value = <I>yes</I> or <I>no</I> = delete all atoms before adding dump atoms
<I>trim</I> value = <I>yes</I> or <I>no</I> = trim atoms not in dump snapshot
<I>add</I> value = <I>yes</I> or <I>no</I> = add new dump atoms to system
<I>label</I> value = field column
field = one of the listed fields or <I>id</I> or <I>type</I>
column = label on corresponding column in dump file
<I>scaled</I> value = <I>yes</I> or <I>no</I> = coords in dump file are scaled/unscaled
<I>format</I> value = <I>native</I> = format of dump file
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>read_dump dump.file 5000 x y z
read_dump dump.file 5000 x y vx vy trim yes
read_dump ../run7/dump.file.gz 10000 x y z box yes
</PRE>
<P><B>Description:</B>
</P>
<P>Read atom information from a dump file to overwrite the current atom
coordinates, and optionally the atom velocities and image flags and
the simluation box dimensions. This is useful for restarting a run
from a particular snapshot in a dump file. See the
<A HREF = "read_restart.html">read_restart</A> and <A HREF = "read_data.html">read_data</A>
commands and the <A HREF = "Section_tools.html#restart">restart2data</A> tool for
alternative methods to do this.
</P>
<P>Note that a simulation box must already be defined before using the
read_dump command. This can be done by the
<A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read_data</A>, or
<A HREF = "read_restart.html">read_restart</A> commands. The read_dump command can
reset the simulation box dimensions, as explained below.
</P>
<P>Also note that reading per-atom information from a dump snapshot is
limited to the atom coordinates, velocities and image flags, as
explained below. Other atom properties, which may be necessary to run
a valid simulation, such as atom charge, or bond topology information
for a molecular system, are not read from (or even contained in) dump
files. Thus this auxiliary information should be defined in the usual
way, e.g. in a data file read in by a <A HREF = "read_data.html">read_data</A>
command, before using the read_dump command, or by the <A HREF = "set.html">set</A>
command, after the dump snapshot is read.
</P>
<HR>
<P>The dump file must be in native LAMMPS format, meaning it was written
with a "dump atom".html or <A HREF = "dump.html">dump custom</A> command. Support
for other dump file formats may be added in the future. These will be
added as options to the <I>format</I> keyword.
</P>
<P>If the filename ends with ".gz", the dump file is read in gzipped
format. You cannot (yet) read a dump file that was written in binary
format with a ".bin" suffix, or to multiple files via the "%" option
in the dump file name. See the <A HREF = "dump.html">dump</A> command for details.
</P>
<P>The dump file is scanned for a snapshot with a time stamp that matches
the specified <I>Nstep</I>. The dimensions of the simulation box for that
snapshot are also read; see the <I>box</I> keyword discussion below. An
error is generated if the snapshot is for a triclinic box and the
current simulation box is orthogonal or vice versa. A warning will be
generated if the snapshot box boundary conditions (periodic,
shrink-wrapped, etc) do not match the current simulation boundary
conditions, but the boundary condition information in the snapshot is
otherwise ignored. See the "boundary" command for more details.
</P>
<P>Per-atom information from the dump file snapshot is then read in,
corresponding to the specified <I>fields</I> listed in the read_dump
command. It is an error to specify a z-dimension field (<I>z</I>, <I>vz</I>,
<I>iz</I>) for a 2d simulation.
</P>
<P>For dump files in native LAMMPS format, each column of per-atom data
has a text label which is listed in the file. A matching label for
each field must appear, e.g. the label "vy" for the field <I>vy</I>. For
the <I>x</I>, <I>y</I>, <I>z</I> fields any of the following labels are considered a
match:
</P>
<PRE>x, xs, xu, xsu for field <I>x</I>
y, ys, yu, ysu for field <I>y</I>
z, zs, zu, zsu for field <I>z</I>
</PRE>
<P>The meaning of xs (scaled), xu (unwrapped), and xsu (scaled and
unwrapped) is explained on the <A HREF = "dump.html">dump</A> command doc page.
These labels are searched for in the list of column labels in the dump
file, in order, until a match is found.
</P>
<P>The dump file must also contain atom IDs, with a column label of "id".
</P>
<P>If a column label in the dump file is not a match to a specified
field, the <I>label</I> keyword can be used to specify which column label
to associate with that field. An example is if a time-averaged
coordinate is written to the dump file via the <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command. The column will then have a
label corresponding to the fix-ID rather than "x" or "xs". The
<I>label</I> keyword can also be used to specify new column labels for
fields <I>id</I> and <I>type</I>. Information for atom types is needed from the
dump file shapshot when the <I>add</I> keyword is used; see the discussion
below.
</P>
<HR>
<P>Information from the dump file snapshot is used to overwrite or
replace properties of the current system. There are various options
for how this is done, determined by the specified fields and optional
keywords.
</P>
<P>The timestep of the snapshot becomes the current timestep for the
simulation. See the <A HREF = "reset_timestep.html">reset_timestep</A> command if
you wish to change this after the dump snapshot is read.
</P>
<P>If the <I>box</I> keyword is specified with a <I>yes</I> value, then the current
simulation box dimensions are replaced by the dump snapshot box
dimensions. If the <I>box</I> keyword is specified with a <I>no</I> value, the
current simulatoin box is unchanged.
</P>
<P>If the <I>purge</I> keyword is specified with a <I>yes</I> value, then all
current atoms in the system are deleted before any of the operations
invoked by the <I>replace</I>, <I>trim</I>, or <I>add</I> keywords take place.
</P>
<P>If the <I>replace</I> keyword is specified with a <I>yes</I> value, then atoms
with IDs that are in both the current system and the dump snapshot
have their properties overwritten by field values. If the <I>replace</I>
keyword is specified with a <I>no</I> value, atoms with IDs that are in
both the current system and the dump snapshot are not modified.
</P>
<P>If the <I>trim</I> keyword is specified with a <I>yes</I> value, then atoms with
IDs that are in the current system but not in the dump snapshot are
deleted. These atoms are unaffected if the <I>trim</I> keyword is
specified with a <I>no</I> value.
</P>
<P>If the <I>add</I> keyword is specified with a <I>yes</I> value, then atoms with
IDs that are in the dump snapshot, but not in the current system are
added to the system. These dump atoms ignored if the <I>add</I> keyword is
specified with a <I>no</I> value.
</P>
<P>Note that atoms added via the <I>add</I> keyword will have only the
attributes read from the dump file due to the <I>field</I> arguments. If
<I>x</I> or <I>y</I> or <I>z</I> is not specified as a field, a value of 0.0 is used
for added atoms. Added atoms must have an atom type, so this per-atom
attribute must also appear in the dump file snapshot, with a column
label of "type". Any other attributes (e.g. charge or particle
diameter for spherical particles) will be set to default values, the
same as if the <A HREF = "create_atoms.html">create_atoms</A> command were used.
</P>
<P>Note that atom IDs are not preserved for new dump snapshot atoms added
via the <I>add</I> keyword. The procedure for assigning new atom IDS to
added atoms is the same as is described for the
<A HREF = "create_atoms.html">create_atoms</A> command.
</P>
<HR>
<P>Atom coordinates read from the dump file are converted into absolute,
unscaled coordinates, relative to the box dimensions of the snapshot.
These coordinates may then be assigned to an existing or new atom in
the current simulation. The coordinates will be remapped to the
simulation box, whether it is the original box or the dump snapshot
box. If periodic boundary conditiona apply, this means the atom will
be remapped back into the box if necessary. If shrink-wrap boundary
conditions apply, the new coordinates may change the current box
dimensions. If fixed boundary conditions apply, the atom will be lost
if it is outside the simulation box.
</P>
<P>The 3 xyz image flags for an atom in the dump file are set to values
in the dump file if the <I>ix</I>, <I>iy</I>, <I>iz</I> fields are specified. If not
specified, the image flags for replaced atoms are not changed and
image flags for new atoms are set to default values. The remapping
procedure described in the previous paragraph can change images flags
for all atoms (old and new) if periodic boundary conditions are
applied to remap an atom back into the simulation box. Note that
inconsistent image flag values can result if you use image flag fields
from the dump file but do not also use the dump file box parameters.
</P>
<P>LAMMPS knows how to compute absolute, unscaled coordinates for the
snapshot column labels discussed above, e.g. <I>x</I>, <I>xs</I>, <I>xu</I>, <I>xsu</I>.
If another column label is assigned to the <I>x</I> or <I>y</I> or <I>z</I> field via
the <I>label</I> keyword, e.g. for coordinates output by the <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command, then LAMMPS needs to know whether
the coordinate information in the dump file is scaled or unscaled.
This can be set via the <I>scaled</I> keyword. The value of the <I>scaled</I>
keyword is ignored for field <I>x</I> or <I>y</I> or <I>z</I> if the <I>label</I> keyword
is not used to assign a column label to that field.
</P>
<P>The scaled vs unscaled setting must be consistent for any of the <I>x</I>,
<I>y</I>, <I>z</I> fields that are specified. If the dump file coordinates are
scaled and the simulation box is triclinic, then all 3 of the <I>x</I>,
<I>y</I>, <I>z</I> fields must be specified, since they are all needed to
generate absolute, unscaled coordinates.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>To read gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
LAMMPS</A> section of the documentation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump</A>, <A HREF = "read_data.html">read_data</A>,
<A HREF = "read_restart.html">read_restart</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are box = yes, replace = yes, purge = no, trim =
no, add = no, scaled = no, and format = native.
</P>
</HTML>

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@ -0,0 +1,228 @@
"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
read_dump command :h3
[Syntax:]
read_dump file Nstep field1 field2 ... keyword values ... :pre
file = name of dump file to read :ulb,l
Nstep = snapshot timestep to read from file :l
one or more fields may be appended :l
field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {ix} or {iy} or {iz}
{x},{y},{z} = atom coordinates
{vx},{vy},{vz} = velocity components
{ix},{iy},{iz} = image flags in each dimension :pre
zero or more keyword/value pairs may be appended :l
keyword = {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {format} :l
{box} value = {yes} or {no} = replace simulation box with dump box
{replace} value = {yes} or {no} = overwrite atoms with dump atoms
{purge} value = {yes} or {no} = delete all atoms before adding dump atoms
{trim} value = {yes} or {no} = trim atoms not in dump snapshot
{add} value = {yes} or {no} = add new dump atoms to system
{label} value = field column
field = one of the listed fields or {id} or {type}
column = label on corresponding column in dump file
{scaled} value = {yes} or {no} = coords in dump file are scaled/unscaled
{format} value = {native} = format of dump file :pre
:ule
[Examples:]
read_dump dump.file 5000 x y z
read_dump dump.file 5000 x y vx vy trim yes
read_dump ../run7/dump.file.gz 10000 x y z box yes :pre
[Description:]
Read atom information from a dump file to overwrite the current atom
coordinates, and optionally the atom velocities and image flags and
the simluation box dimensions. This is useful for restarting a run
from a particular snapshot in a dump file. See the
"read_restart"_read_restart.html and "read_data"_read_data.html
commands and the "restart2data"_Section_tools.html#restart tool for
alternative methods to do this.
Note that a simulation box must already be defined before using the
read_dump command. This can be done by the
"create_box"_create_box.html, "read_data"_read_data.html, or
"read_restart"_read_restart.html commands. The read_dump command can
reset the simulation box dimensions, as explained below.
Also note that reading per-atom information from a dump snapshot is
limited to the atom coordinates, velocities and image flags, as
explained below. Other atom properties, which may be necessary to run
a valid simulation, such as atom charge, or bond topology information
for a molecular system, are not read from (or even contained in) dump
files. Thus this auxiliary information should be defined in the usual
way, e.g. in a data file read in by a "read_data"_read_data.html
command, before using the read_dump command, or by the "set"_set.html
command, after the dump snapshot is read.
:line
The dump file must be in native LAMMPS format, meaning it was written
with a "dump atom".html or "dump custom"_dump.html command. Support
for other dump file formats may be added in the future. These will be
added as options to the {format} keyword.
If the filename ends with ".gz", the dump file is read in gzipped
format. You cannot (yet) read a dump file that was written in binary
format with a ".bin" suffix, or to multiple files via the "%" option
in the dump file name. See the "dump"_dump.html command for details.
The dump file is scanned for a snapshot with a time stamp that matches
the specified {Nstep}. The dimensions of the simulation box for that
snapshot are also read; see the {box} keyword discussion below. An
error is generated if the snapshot is for a triclinic box and the
current simulation box is orthogonal or vice versa. A warning will be
generated if the snapshot box boundary conditions (periodic,
shrink-wrapped, etc) do not match the current simulation boundary
conditions, but the boundary condition information in the snapshot is
otherwise ignored. See the "boundary" command for more details.
Per-atom information from the dump file snapshot is then read in,
corresponding to the specified {fields} listed in the read_dump
command. It is an error to specify a z-dimension field ({z}, {vz},
{iz}) for a 2d simulation.
For dump files in native LAMMPS format, each column of per-atom data
has a text label which is listed in the file. A matching label for
each field must appear, e.g. the label "vy" for the field {vy}. For
the {x}, {y}, {z} fields any of the following labels are considered a
match:
x, xs, xu, xsu for field {x}
y, ys, yu, ysu for field {y}
z, zs, zu, zsu for field {z} :pre
The meaning of xs (scaled), xu (unwrapped), and xsu (scaled and
unwrapped) is explained on the "dump"_dump.html command doc page.
These labels are searched for in the list of column labels in the dump
file, in order, until a match is found.
The dump file must also contain atom IDs, with a column label of "id".
If a column label in the dump file is not a match to a specified
field, the {label} keyword can be used to specify which column label
to associate with that field. An example is if a time-averaged
coordinate is written to the dump file via the "fix
ave/atom"_fix_ave_atom.html command. The column will then have a
label corresponding to the fix-ID rather than "x" or "xs". The
{label} keyword can also be used to specify new column labels for
fields {id} and {type}. Information for atom types is needed from the
dump file shapshot when the {add} keyword is used; see the discussion
below.
:line
Information from the dump file snapshot is used to overwrite or
replace properties of the current system. There are various options
for how this is done, determined by the specified fields and optional
keywords.
The timestep of the snapshot becomes the current timestep for the
simulation. See the "reset_timestep"_reset_timestep.html command if
you wish to change this after the dump snapshot is read.
If the {box} keyword is specified with a {yes} value, then the current
simulation box dimensions are replaced by the dump snapshot box
dimensions. If the {box} keyword is specified with a {no} value, the
current simulatoin box is unchanged.
If the {purge} keyword is specified with a {yes} value, then all
current atoms in the system are deleted before any of the operations
invoked by the {replace}, {trim}, or {add} keywords take place.
If the {replace} keyword is specified with a {yes} value, then atoms
with IDs that are in both the current system and the dump snapshot
have their properties overwritten by field values. If the {replace}
keyword is specified with a {no} value, atoms with IDs that are in
both the current system and the dump snapshot are not modified.
If the {trim} keyword is specified with a {yes} value, then atoms with
IDs that are in the current system but not in the dump snapshot are
deleted. These atoms are unaffected if the {trim} keyword is
specified with a {no} value.
If the {add} keyword is specified with a {yes} value, then atoms with
IDs that are in the dump snapshot, but not in the current system are
added to the system. These dump atoms ignored if the {add} keyword is
specified with a {no} value.
Note that atoms added via the {add} keyword will have only the
attributes read from the dump file due to the {field} arguments. If
{x} or {y} or {z} is not specified as a field, a value of 0.0 is used
for added atoms. Added atoms must have an atom type, so this per-atom
attribute must also appear in the dump file snapshot, with a column
label of "type". Any other attributes (e.g. charge or particle
diameter for spherical particles) will be set to default values, the
same as if the "create_atoms"_create_atoms.html command were used.
Note that atom IDs are not preserved for new dump snapshot atoms added
via the {add} keyword. The procedure for assigning new atom IDS to
added atoms is the same as is described for the
"create_atoms"_create_atoms.html command.
:line
Atom coordinates read from the dump file are converted into absolute,
unscaled coordinates, relative to the box dimensions of the snapshot.
These coordinates may then be assigned to an existing or new atom in
the current simulation. The coordinates will be remapped to the
simulation box, whether it is the original box or the dump snapshot
box. If periodic boundary conditiona apply, this means the atom will
be remapped back into the box if necessary. If shrink-wrap boundary
conditions apply, the new coordinates may change the current box
dimensions. If fixed boundary conditions apply, the atom will be lost
if it is outside the simulation box.
The 3 xyz image flags for an atom in the dump file are set to values
in the dump file if the {ix}, {iy}, {iz} fields are specified. If not
specified, the image flags for replaced atoms are not changed and
image flags for new atoms are set to default values. The remapping
procedure described in the previous paragraph can change images flags
for all atoms (old and new) if periodic boundary conditions are
applied to remap an atom back into the simulation box. Note that
inconsistent image flag values can result if you use image flag fields
from the dump file but do not also use the dump file box parameters.
LAMMPS knows how to compute absolute, unscaled coordinates for the
snapshot column labels discussed above, e.g. {x}, {xs}, {xu}, {xsu}.
If another column label is assigned to the {x} or {y} or {z} field via
the {label} keyword, e.g. for coordinates output by the "fix
ave/atom"_fix_ave_atom.html command, then LAMMPS needs to know whether
the coordinate information in the dump file is scaled or unscaled.
This can be set via the {scaled} keyword. The value of the {scaled}
keyword is ignored for field {x} or {y} or {z} if the {label} keyword
is not used to assign a column label to that field.
The scaled vs unscaled setting must be consistent for any of the {x},
{y}, {z} fields that are specified. If the dump file coordinates are
scaled and the simulation box is triclinic, then all 3 of the {x},
{y}, {z} fields must be specified, since they are all needed to
generate absolute, unscaled coordinates.
:line
[Restrictions:]
To read gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option - see the "Making
LAMMPS"_Section_start.html#start_2 section of the documentation.
[Related commands:]
"dump"_dump.html, "read_data"_read_data.html,
"read_restart"_read_restart.html
[Default:]
The option defaults are box = yes, replace = yes, purge = no, trim =
no, add = no, scaled = no, and format = native.

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@ -136,8 +136,8 @@ output, <A HREF = "region.html">geometric regions</A>, etc.
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>
<P><A HREF = "read_data.html">read_data</A>, <A HREF = "write_restart.html">write_restart</A>, <P><A HREF = "read_data.html">read_data</A>, <A HREF = "read_dump.html">read_dump</A>,
<A HREF = "restart.html">restart</A> <A HREF = "write_restart.html">write_restart</A>, <A HREF = "restart.html">restart</A>
</P> </P>
<P><B>Default:</B> none <P><B>Default:</B> none
</P> </P>

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doc/read_restart.txt
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@ -133,7 +133,7 @@ output, "geometric regions"_region.html, etc.
[Related commands:] [Related commands:]
"read_data"_read_data.html, "write_restart"_write_restart.html, "read_data"_read_data.html, "read_dump"_read_dump.html,
"restart"_restart.html "write_restart"_write_restart.html, "restart"_restart.html
[Default:] none [Default:] none