git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10812 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -21,14 +21,15 @@
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<LI>one or more fields may be appended
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<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>
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<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>q</I> or <I>ix</I> or <I>iy</I> or <I>iz</I>
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<I>x</I>,<I>y</I>,<I>z</I> = atom coordinates
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<I>vx</I>,<I>vy</I>,<I>vz</I> = velocity components
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<I>q</I> = charge
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<I>ix</I>,<I>iy</I>,<I>iz</I> = image flags in each dimension
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</PRE>
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>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>
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<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>wrapped</I> or <I>format</I>
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<PRE> <I>box</I> value = <I>yes</I> or <I>no</I> = replace simulation box with dump box
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<I>replace</I> value = <I>yes</I> or <I>no</I> = overwrite atoms with dump atoms
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@ -39,6 +40,7 @@
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field = one of the listed fields or <I>id</I> or <I>type</I>
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column = label on corresponding column in dump file
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<I>scaled</I> value = <I>yes</I> or <I>no</I> = coords in dump file are scaled/unscaled
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<I>wrapped</I> value = <I>yes</I> or <I>no</I> = coords in dump file are wrapped/unwrapped
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<I>format</I> values = format of dump file, must be last keyword if used
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<I>native</I> = native LAMMPS dump file
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<I>xyz</I> = XYZ file
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@ -157,9 +159,9 @@ always work perfectly.
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<HR>
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<P>Per-atom information from the dump file snapshot is then read from the
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dump file snapshot. This corresponds tot the specified <I>fields</I>
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listed in the read_dump command. It is an error to specify a
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z-dimension field, namely <I>z</I>, <I>vz</I>, or <I>iz</I>, for a 2d simulation.
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dump file snapshot. This corresponds to the specified <I>fields</I> listed
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in the read_dump command. It is an error to specify a z-dimension
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field, namely <I>z</I>, <I>vz</I>, or <I>iz</I>, for a 2d simulation.
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</P>
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<P>For dump files in <I>native</I> format, each column of per-atom data has a
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text label listed in the file. A matching label for each field must
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@ -181,14 +183,14 @@ file, in order, until a match is found.
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below, the dump file must contain atom types, with a column label of
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"type".
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</P>
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<P>If a column label in the dump file is not a match to a specified
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field, the <I>label</I> keyword can be used to specify which column label
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to associate with that field. An example is if a time-averaged
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coordinate is written to the dump file via the <A HREF = "fix_ave_atom.html">fix
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ave/atom</A> command. The column will then have a
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label corresponding to the fix-ID rather than "x" or "xs". The
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<I>label</I> keyword can also be used to specify new column labels for
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fields <I>id</I> and <I>type</I>.
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<P>If a column label you want to read from the dump file is not a match
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to a specified field, the <I>label</I> keyword can be used to specify the
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specific column label from the dump file to associate with that field.
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An example is if a time-averaged coordinate is written to the dump
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file via the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command. The column
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will then have a label corresponding to the fix-ID rather than "x" or
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"xs". The <I>label</I> keyword can also be used to specify new column
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labels for fields <I>id</I> and <I>type</I>.
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</P>
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<P>For dump files in <I>xyz</I> format, only the <I>x</I>, <I>y</I>, and <I>z</I> fields are
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supported. The dump file does not store atom IDs, so these are
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@ -261,43 +263,53 @@ added atoms is the same as is described for the
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</P>
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<HR>
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<P>Atom coordinates read from the dump file are converted into absolute,
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<P>Atom coordinates read from the dump file are first converted into
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unscaled coordinates, relative to the box dimensions of the snapshot.
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These coordinates may then be assigned to an existing or new atom in
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the current simulation. The coordinates will be remapped to the
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These coordinates are then be assigned to an existing or new atom in
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the current simulation. The coordinates will then be remapped to the
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simulation box, whether it is the original box or the dump snapshot
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box. If periodic boundary conditiona apply, this means the atom will
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be remapped back into the box if necessary. If shrink-wrap boundary
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conditions apply, the new coordinates may change the current box
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dimensions. If fixed boundary conditions apply, the atom will be lost
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if it is outside the simulation box.
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box. If periodic boundary conditions apply, this means the atom will
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be remapped back into the simulation box if necessary. If shrink-wrap
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boundary conditions apply, the new coordinates may change the
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simulation box dimensions. If fixed boundary conditions apply, the
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atom will be lost if it is outside the simulation box.
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</P>
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<P>For <I>native</I> format dump files, the 3 xyz image flags for an atom in
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the dump file are set to the corresponding values appearing in the
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dump file if the <I>ix</I>, <I>iy</I>, <I>iz</I> fields are specified. If not
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specified, the image flags for replaced atoms are not changed and
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image flags for new atoms are set to default values. The remapping
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procedure described in the previous paragraph can change images flags
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for all atoms (old and new) if periodic boundary conditions are
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applied to remap an atom back into the simulation box. Note that
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inconsistent image flag values can result if you use image flag fields
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from the dump file but do not also use the dump file box parameters.
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image flags for new atoms are set to default values. If coordinates
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read from the dump file are in unwrapped format (e.g. <I>xu</I>) then the
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image flags for read-in atoms are also set to default values. The
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remapping procedure described in the previous paragraph will then
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change images flags for all atoms (old and new) if periodic boundary
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conditions are applied to remap an atom back into the simulation box.
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</P>
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<P>LAMMPS knows how to compute absolute, unscaled coordinates for the
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<P>IMPORTANT NOTE: If you get a warning about inconsistent image flags
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after reading in a dump snapshot, it means one or more pairs of bonded
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atoms now have inconsistent image flags. As discussed in <A HREF = "Section_errors.html">Section
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errors</A> this may or may not cause problems for
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subsequent simulations, One way this can happen is if you read image
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flag fields from the dump file but do not also use the dump file box
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parameters.
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</P>
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<P>LAMMPS knows how to compute unscaled and remapped coordinates for the
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snapshot column labels discussed above, e.g. <I>x</I>, <I>xs</I>, <I>xu</I>, <I>xsu</I>.
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If another column label is assigned to the <I>x</I> or <I>y</I> or <I>z</I> field via
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the <I>label</I> keyword, e.g. for coordinates output by the <A HREF = "fix_ave_atom.html">fix
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ave/atom</A> command, then LAMMPS needs to know whether
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the coordinate information in the dump file is scaled or unscaled.
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This can be set via the <I>scaled</I> keyword. The value of the <I>scaled</I>
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keyword is ignored for field <I>x</I> or <I>y</I> or <I>z</I> if the <I>label</I> keyword
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is not used to assign a column label to that field.
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the coordinate information in the dump file is scaled and/or wrapped.
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This can be set via the <I>scaled</I> and <I>wrapped</I> keywords. Note that
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the value of the <I>scaled</I> and <I>wrapped</I> keywords is ignored for fields
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<I>x</I> or <I>y</I> or <I>z</I> if the <I>label</I> keyword is not used to assign a
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column label to that field.
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</P>
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<P>The scaled vs unscaled setting must be consistent for any of the <I>x</I>,
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<I>y</I>, <I>z</I> fields that are specified. If the dump file coordinates are
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scaled and the simulation box is triclinic, then all 3 of the <I>x</I>,
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<I>y</I>, <I>z</I> fields must be specified, since they are all needed to
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generate absolute, unscaled coordinates.
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<P>The scaled/unscaled and wrapped/unwrapped setting must be identical
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for any of the <I>x</I>, <I>y</I>, <I>z</I> fields that are specified. Thus you
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cannot read <I>xs</I> and <I>yu</I> from the dump file. Also, if the dump file
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coordinates are scaled and the simulation box is triclinic, then all 3
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of the <I>x</I>, <I>y</I>, <I>z</I> fields must be specified, since they are all
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needed to generate absolute, unscaled coordinates.
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</P>
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<HR>
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@ -320,6 +332,6 @@ They are only enabled if LAMMPS was built with that packages. See the
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<P><B>Default:</B>
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</P>
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<P>The option defaults are box = yes, replace = yes, purge = no, trim =
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no, add = no, scaled = no, and format = native.
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no, add = no, scaled = no, wrapped = yes, and format = native.
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</P>
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</HTML>
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@ -15,12 +15,13 @@ read_dump file Nstep field1 field2 ... keyword values ... :pre
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file = name of dump file to read :ulb,l
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Nstep = snapshot timestep to read from file :l
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one or more fields may be appended :l
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field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {ix} or {iy} or {iz}
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field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {q} or {ix} or {iy} or {iz}
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{x},{y},{z} = atom coordinates
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{vx},{vy},{vz} = velocity components
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{q} = charge
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{ix},{iy},{iz} = image flags in each dimension :pre
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zero or more keyword/value pairs may be appended :l
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keyword = {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {format} :l
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keyword = {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {wrapped} or {format} :l
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{box} value = {yes} or {no} = replace simulation box with dump box
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{replace} value = {yes} or {no} = overwrite atoms with dump atoms
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{purge} value = {yes} or {no} = delete all atoms before adding dump atoms
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@ -30,6 +31,7 @@ keyword = {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled
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field = one of the listed fields or {id} or {type}
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column = label on corresponding column in dump file
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{scaled} value = {yes} or {no} = coords in dump file are scaled/unscaled
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{wrapped} value = {yes} or {no} = coords in dump file are wrapped/unwrapped
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{format} values = format of dump file, must be last keyword if used
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{native} = native LAMMPS dump file
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{xyz} = XYZ file
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@ -147,9 +149,9 @@ always work perfectly.
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:line
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Per-atom information from the dump file snapshot is then read from the
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dump file snapshot. This corresponds tot the specified {fields}
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listed in the read_dump command. It is an error to specify a
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z-dimension field, namely {z}, {vz}, or {iz}, for a 2d simulation.
|
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dump file snapshot. This corresponds to the specified {fields} listed
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in the read_dump command. It is an error to specify a z-dimension
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field, namely {z}, {vz}, or {iz}, for a 2d simulation.
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For dump files in {native} format, each column of per-atom data has a
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text label listed in the file. A matching label for each field must
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@ -171,14 +173,14 @@ If the {add} keyword is specified with a value of {yes}, as discussed
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below, the dump file must contain atom types, with a column label of
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"type".
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If a column label in the dump file is not a match to a specified
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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
|
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{label} keyword can also be used to specify new column labels for
|
||||
fields {id} and {type}.
|
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If a column label you want to read from the dump file is not a match
|
||||
to a specified field, the {label} keyword can be used to specify the
|
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specific column label from the dump file 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
|
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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
|
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labels for fields {id} and {type}.
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|
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For dump files in {xyz} format, only the {x}, {y}, and {z} fields are
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supported. The dump file does not store atom IDs, so these are
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@ -251,43 +253,53 @@ added atoms is the same as is described for the
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:line
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Atom coordinates read from the dump file are converted into absolute,
|
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Atom coordinates read from the dump file are first converted into
|
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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
|
||||
These coordinates are then be assigned to an existing or new atom in
|
||||
the current simulation. The coordinates will then 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.
|
||||
box. If periodic boundary conditions apply, this means the atom will
|
||||
be remapped back into the simulation box if necessary. If shrink-wrap
|
||||
boundary conditions apply, the new coordinates may change the
|
||||
simulation box dimensions. If fixed boundary conditions apply, the
|
||||
atom will be lost if it is outside the simulation box.
|
||||
|
||||
For {native} format dump files, the 3 xyz image flags for an atom in
|
||||
the dump file are set to the corresponding values appearing 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.
|
||||
image flags for new atoms are set to default values. If coordinates
|
||||
read from the dump file are in unwrapped format (e.g. {xu}) then the
|
||||
image flags for read-in atoms are also set to default values. The
|
||||
remapping procedure described in the previous paragraph will then
|
||||
change images flags for all atoms (old and new) if periodic boundary
|
||||
conditions are applied to remap an atom back into the simulation box.
|
||||
|
||||
LAMMPS knows how to compute absolute, unscaled coordinates for the
|
||||
IMPORTANT NOTE: If you get a warning about inconsistent image flags
|
||||
after reading in a dump snapshot, it means one or more pairs of bonded
|
||||
atoms now have inconsistent image flags. As discussed in "Section
|
||||
errors"_Section_errors.html this may or may not cause problems for
|
||||
subsequent simulations, One way this can happen is if you read image
|
||||
flag fields from the dump file but do not also use the dump file box
|
||||
parameters.
|
||||
|
||||
LAMMPS knows how to compute unscaled and remapped 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 coordinate information in the dump file is scaled and/or wrapped.
|
||||
This can be set via the {scaled} and {wrapped} keywords. Note that
|
||||
the value of the {scaled} and {wrapped} keywords is ignored for fields
|
||||
{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.
|
||||
The scaled/unscaled and wrapped/unwrapped setting must be identical
|
||||
for any of the {x}, {y}, {z} fields that are specified. Thus you
|
||||
cannot read {xs} and {yu} from the dump file. Also, 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
|
||||
|
||||
@ -310,4 +322,4 @@ They are only enabled if LAMMPS was built with that packages. See the
|
||||
[Default:]
|
||||
|
||||
The option defaults are box = yes, replace = yes, purge = no, trim =
|
||||
no, add = no, scaled = no, and format = native.
|
||||
no, add = no, scaled = no, wrapped = yes, and format = native.
|
||||
|
||||
Reference in New Issue
Block a user