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doc/dump.html
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doc/dump.html
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@ -19,7 +19,7 @@
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<LI>group-ID = ID of the group of atoms to be dumped
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<LI>style = <I>atom</I> or <I>bond</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>custom</I>
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<LI>style = <I>atom</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>local</I> or <I>custom</I>
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<LI>N = dump every this many timesteps
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@ -28,12 +28,20 @@
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<LI>args = list of arguments for a particular style
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<PRE> <I>atom</I> args = none
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<I>bond</I> args = none
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<I>cfg</I> args = same as <I>custom</I> args, see below
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<I>dcd</I> args = none
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<I>xtc</I> args = none
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<I>xyz</I> args = none
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<I>custom</I> args = list of atom attributes
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<I>xyz</I> args = none
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</PRE>
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<PRE> <I>local</I> args = list of local attributes
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possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N]
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index = enumeration of local values
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c_ID = local vector calculated by a compute with ID
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c_ID[N] = Nth column of local array calculated by a compute with ID
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f_ID = local vector calculated by a fix with ID
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f_ID[N] = Nth column of local array calculated by a fix with ID
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</PRE>
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<PRE> <I>custom</I> args = list of atom attributes
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possible attributes = id, mol, type, mass,
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x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
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vx, vy, vz, fx, fy, fz,
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@ -60,9 +68,9 @@
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angmomx,angmomy,angmomz = angular momentum of extended particle
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quatw,quati,quatj,quatk = quaternion components for aspherical particles
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tqx,tqy,tqz = torque on extended particles
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c_ID = per-atom vector value calculated by a compute with ID
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c_ID = per-atom vector calculated by a compute with ID
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c_ID[N] = Nth column of per-atom array calculated by a compute with ID
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f_ID = per-atom vector value calculated by a fix with ID
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f_ID = per-atom vector calculated by a fix with ID
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f_ID[N] = Nth column of per-atom array calculated by a fix with ID
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v_name = per-atom vector calculated by an atom-style variable with name
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</PRE>
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@ -98,7 +106,7 @@ box.
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dump files (typically one line per atom) may be written in an
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indeterminate order. This is because data for a single snapshot is
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collected from multiple processors. This is always the case for the
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<I>atom</I>, <I>bond</I>, and <I>custom</I> styles. It is also the case for the
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<I>atom</I>, <I>local</I>, and <I>custom</I> styles. It is also the case for the
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<I>xyz</I> style if the dump group is not <I>all</I>. It is not the case for
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the <I>dcd</I> and <I>xtc</I> styles which always write atoms in sorted order.
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So does the <I>xyz</I> style if the dump group is <I>all</I>. The <I>cfg</I> style
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@ -112,7 +120,7 @@ file and in what format. Settings made via the
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<A HREF = "dump_modify.html">dump_modify</A> command can also alter the format of
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individual values and the file itself.
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</P>
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<P>The <I>atom</I>, <I>bond</I>, and <I>custom</I> styles create files in a simple text
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<P>The <I>atom</I>, <I>local</I>, and <I>custom</I> styles create files in a simple text
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format that is self-explanatory when viewing a dump file. Many of the
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LAMMPS <A HREF = "Section_tools.html">post-processing tools</A>, including
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<A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A>, work with
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@ -139,16 +147,6 @@ boundaries. The format can be changed to unscaled coords via the
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<A HREF = "dump_modify.html">dump_modify</A> settings. Image flags can also be
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added for each atom via dump_modify.
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</P>
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<P>For style <I>bond</I>, the bond topology between atoms is written, in the
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same format specified in data files read in by the
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<A HREF = "read_data.html">read_data</A> command. Both atoms in the bond must be in
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the dump group for the bond to be written. Any bonds that have been
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broken (see the <A HREF = "bond_style.html">bond_style</A> command) by setting their
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bond type to 0 are not written. Bonds that have been turned off (see
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the <A HREF = "fix_shake.html">fix shake</A> or <A HREF = "delete_bonds.html">delete_bonds</A>
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commands) by setting their bond type negative are written into the
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file.
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</P>
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<P>Style <I>custom</I> allows you to specify a list of atom attributes to be
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written to the dump file for each atom. Possible attributes are
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listed above and will appear in the order specified. You cannot
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@ -156,8 +154,20 @@ specify a quantity that is not defined for a particular simulation -
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such as <I>q</I> for atom style <I>bond</I>, since that atom style doesn't
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assign charges. Dumps occur at the very end of a timestep, so atom
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attributes will include effects due to fixes that are applied during
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the timestep. An explanation of the dump custom quantities is given
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below.
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the timestep. An explanation of the possible dump custom attributes
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is given below.
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</P>
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<P>For style <I>local</I>, local output generated by <A HREF = "compute.html">computes</A>
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and <A HREF = "fix.html">fixes</A> is used to gnerate lines of output that is
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written to the dump file. This local data is typically calculated by
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each processor based on the atoms it owns, but there may be zero or
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more entities per atom, e.g. a list of bond distances. An explanation
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of the possible dump local attributes is given below. Note that by
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using input from the <A HREF = "compute_property_local.html">compute
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property/local</A> command with dump local,
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it is possible to generate information on bonds, angles, etc that can
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be cut and pasted directly into a data file read by the
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<A HREF = "read_data.html">read_data</A> command.
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</P>
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<P>Style <I>cfg</I> has the same command syntax as style <I>custom</I> and writes
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extended CFG format files, as used by the
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@ -264,11 +274,54 @@ styles.
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</P>
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<HR>
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<P>This section explains the atom quantities that can be specified as
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<P>This section explains the local attributes that can be specified as
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part of the <I>local</I> style.
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</P>
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<P>The <I>index</I> attribute can be used to generate an index number from 1
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to N for each line written into the dump file, where N is the total
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number of local datums from all processors, or lines of output that
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will appear in the snapshot. Note that because data from different
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processors depend on what atoms they currently own, and atoms migrate
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between processor, there is no guarantee that the same index will be
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used for the same info (e.g. a particular bond) in successive
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snapshots.
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</P>
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<P>The <I>c_ID</I> and <I>c_ID[N]</I> attributes allow local vectors or arrays
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calculated by a <A HREF = "compute.html">compute</A> to be output. The ID in the
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attribute should be replaced by the actual ID of the compute that has
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been defined previously in the input script. See the
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<A HREF = "compute.html">compute</A> command for details. There are computes for
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calculating local information such as indices, types, and energies for
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bonds and angles.
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</P>
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<P>Note that computes which calculate global or per-atom quantities, as
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opposed to local quantities, cannot be output in a dump local command.
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Instead, global quantities can be output by the <A HREF = "thermo_style.html">thermo_style
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custom</A> command, and per-atom quantities can be
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output by the dump custom command.
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</P>
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<P>If <I>c_ID</I> is used as a attribute, then the local vector calculated by
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the compute is printed. If <I>c_ID[N]</I> is used, then N must be in the
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range from 1-M, which will print the Nth column of the M-length local
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array calculated by the compute.
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</P>
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<P>The <I>f_ID</I> and <I>f_ID[N]</I> attributes allow local vectors or arrays
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calculated by a <A HREF = "fix.html">fix</A> to be output. The ID in the attribute
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should be replaced by the actual ID of the fix that has been defined
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previously in the input script.
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</P>
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<P>If <I>f_ID</I> is used as a attribute, then the local vector calculated by
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the fix is printed. If <I>f_ID[N]</I> is used, then N must be in the
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range from 1-M, which will print the Nth column of the M-length local
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array calculated by the fix.
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</P>
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<HR>
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<P>This section explains the atom attributes that can be specified as
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part of the <I>custom</I> and <I>cfg</I> styles.
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</P>
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<P>The <I>id</I>, <I>mol</I>, <I>type</I>, <I>mass</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
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<I>fz</I>, <I>q</I> keywords are self-explanatory.
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<I>fz</I>, <I>q</I> attributes are self-explanatory.
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</P>
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<P><I>Id</I> is the atom ID. <I>Mol</I> is the molecule ID, included in the data
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file for molecular systems. <I>Type</I> is the atom type. <I>Mass</I> is the
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@ -276,7 +329,7 @@ atom mass. <I>Vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>, <I>fz</I>, an
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of atom velocity and force and atomic charge.
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</P>
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<P>There are several options for outputting atom coordinates. The <I>x</I>,
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<I>y</I>, <I>z</I> keywords write atom coordinates "unscaled", in the
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<I>y</I>, <I>z</I> attributes write atom coordinates "unscaled", in the
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appropriate distance <A HREF = "units.html">units</A> (Angstroms, sigma, etc). Use
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<I>xs</I>, <I>ys</I>, <I>zs</I> if you want the coordinates "scaled" to the box size,
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so that each value is 0.0 to 1.0. If the simluation box is triclinic
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@ -288,57 +341,58 @@ the coordinate would be if it had not been wrapped back into the
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periodic box. Note that using <I>xu</I>, <I>yu</I>, <I>zu</I> means that the
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coordinate values may be far outside the box bounds printed with the
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snapshot. The image flags can be printed directly using the <I>ix</I>,
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<I>iy</I>, <I>iz</I> keywords. The <A HREF = "dump_modify.html">dump_modify</A> command
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<I>iy</I>, <I>iz</I> attributes. The <A HREF = "dump_modify.html">dump_modify</A> command
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describes in more detail what is meant by scaled vs unscaled
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coordinates and the image flags.
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</P>
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<P>The <I>mux</I>, <I>muy</I>, <I>muz</I> keywords are specific to dipolar systems
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<P>The <I>mux</I>, <I>muy</I>, <I>muz</I> attributes are specific to dipolar systems
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defined with an atom style of <I>dipole</I>. They give the orientation of
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the atom's point dipole moment.
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</P>
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<P>The <I>radius</I> keyword is specific to extended spherical particles
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<P>The <I>radius</I> attribute is specific to extended spherical particles
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that have a finite size, such as granular particles defined with
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an atom style of <I>granular</I>.
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</P>
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<P>The <I>omegax</I>, <I>omegay</I>, and <I>omegaz</I> keywords are specific to extended
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<P>The <I>omegax</I>, <I>omegay</I>, and <I>omegaz</I> attributes are specific to extended
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spherical or aspherical particles that have an angular velocity. Only
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certain atom styles, such as <I>granular</I> or <I>dipole</I> define this
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quantity.
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</P>
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<P>The <I>angmomx</I>, <I>angmomy</I>, and <I>angmomz</I> keywords are specific to
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<P>The <I>angmomx</I>, <I>angmomy</I>, and <I>angmomz</I> attributes are specific to
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extended aspherical particles that have an angular momentum. Only
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the <I>ellipsoid</I> atom style defines this quantity.
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</P>
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<P>The <I>quatw</I>, <I>quati</I>, <I>quatj</I>, <I>quatk</I> keywords are for aspherical
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<P>The <I>quatw</I>, <I>quati</I>, <I>quatj</I>, <I>quatk</I> attributes are for aspherical
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particles defined with an atom style of <I>ellipsoid</I>. They are the
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components of the quaternion that defines the orientation of the
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particle.
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</P>
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<P>The <I>tqx</I>, <I>tqy</I>, <I>tqz</I> keywords are for extended spherical or
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<P>The <I>tqx</I>, <I>tqy</I>, <I>tqz</I> attributes are for extended spherical or
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aspherical particles that can sustain a rotational torque due
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to interactions with other particles.
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</P>
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<P>The <I>c_ID</I> and <I>c_ID[N]</I> keywords allow scalar or vector per-atom
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quantities calculated by a <A HREF = "compute.html">compute</A> to be output. The
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ID in the keyword should be replaced by the actual ID of the compute
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that has been defined previously in the input script. See the
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<A HREF = "compute.html">compute</A> command for details. There are per-atom
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computes for calculating the energy, stress, centro-symmetry
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parameter, and coordination number of individual atoms.
|
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<P>The <I>c_ID</I> and <I>c_ID[N]</I> attributes allow per-atom vectors or arrays
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calculated by a <A HREF = "compute.html">compute</A> to be output. The ID in the
|
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attribute should be replaced by the actual ID of the compute that has
|
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been defined previously in the input script. See the
|
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<A HREF = "compute.html">compute</A> command for details. There are computes for
|
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calculating the per-atom energy, stress, centro-symmetry parameter,
|
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and coordination number of individual atoms.
|
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</P>
|
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<P>Note that computes which calculate global scalar and vector
|
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quantities, as opposed to per-atom quantities, cannot be output in a
|
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dump. Instead, these quantities can be output by the <A HREF = "thermo_style.html">thermo_style
|
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custom</A> command.
|
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<P>Note that computes which calculate global or local quantities, as
|
||||
opposed to per-atom quantities, cannot be output in a dump custom
|
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command. Instead, global quantities can be output by the
|
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<A HREF = "thermo_style.html">thermo_style custom</A> command, and local quantities
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can be output by the dump local command.
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</P>
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<P>If <I>c_ID</I> is used as a keyword, then the scalar per-atom quantity
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calculated by the compute is printed. If <I>c_ID[N]</I> is used, then N
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must be in the range from 1-M, which will print the Nth column of
|
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the M-length per-atom array calculated by the compute.
|
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<P>If <I>c_ID</I> is used as a attribute, then the per-atom vector calculated
|
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by the compute is printed. If <I>c_ID[N]</I> is used, then N must be in
|
||||
the range from 1-M, which will print the Nth column of the M-length
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||||
per-atom array calculated by the compute.
|
||||
</P>
|
||||
<P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow scalar or vector per-atom
|
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<P>The <I>f_ID</I> and <I>f_ID[N]</I> attributes allow vector or array per-atom
|
||||
quantities calculated by a <A HREF = "fix.html">fix</A> to be output. The ID in the
|
||||
keyword should be replaced by the actual ID of the fix that has been
|
||||
attribute should be replaced by the actual ID of the fix that has been
|
||||
defined previously in the input script. The <A HREF = "fix_ave_atom.html">fix
|
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ave/atom</A> command is one that calculates per-atom
|
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quantities. Since it can time-average per-atom quantities produced by
|
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|
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@ -346,20 +400,21 @@ any <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or atom-
|
|||
<A HREF = "variable.html">variable</A>, this allows those time-averaged results to
|
||||
be written to a dump file.
|
||||
</P>
|
||||
<P>If <I>f_ID</I> is used as a keyword, then the scalar per-atom quantity
|
||||
calculated by the fix is printed. If <I>f_ID[N]</I> is used, then N must
|
||||
be in the range from 1-M, which will print the Nth column of the
|
||||
M-length per-atom array calculated by the fix.
|
||||
<P>If <I>f_ID</I> is used as a attribute, then the per-atom vector calculated
|
||||
by the fix is printed. If <I>f_ID[N]</I> is used, then N must be in the
|
||||
range from 1-M, which will print the Nth column of the M-length
|
||||
per-atom array calculated by the fix.
|
||||
</P>
|
||||
<P>The <I>v_name</I> keyword allows per-atom quantities calculated by a
|
||||
<A HREF = "variable.html">variable</A> to be output. The name in the keyword should
|
||||
be replaced by the actual name of the variable that has been defined
|
||||
previously in the input script. Only an atom-style variable can be
|
||||
referenced, since it is the only style that generates per-atom values.
|
||||
Variables of style <I>atom</I> can reference individual atom attributes,
|
||||
per-atom atom attributes, thermodynamic keywords, or invoke other
|
||||
computes, fixes, or variables when they are evaluated, so this is a
|
||||
very general means of creating quantities to output to a dump file.
|
||||
<P>The <I>v_name</I> attribute allows per-atom vectors calculated by a
|
||||
<A HREF = "variable.html">variable</A> to be output. The name in the attribute
|
||||
should be replaced by the actual name of the variable that has been
|
||||
defined previously in the input script. Only an atom-style variable
|
||||
can be referenced, since it is the only style that generates per-atom
|
||||
values. Variables of style <I>atom</I> can reference individual atom
|
||||
attributes, per-atom atom attributes, thermodynamic keywords, or
|
||||
invoke other computes, fixes, or variables when they are evaluated, so
|
||||
this is a very general means of creating quantities to output to a
|
||||
dump file.
|
||||
</P>
|
||||
<P>See <A HREF = "Section_modify.html">this section</A> of the manual for information
|
||||
on how to add new compute and fix styles to LAMMPS to calculate
|
||||
|
|
@ -373,10 +428,6 @@ per-atom quantities which could then be output into dump files.
|
|||
-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#2_2">Making LAMMPS</A>
|
||||
section of the documentation.
|
||||
</P>
|
||||
<P>The <I>bond</I> style is part of the "molecular" package. It is only
|
||||
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P>The <I>xtc</I> style is part of the "xtc" package. It is only enabled if
|
||||
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
|
||||
LAMMPS</A> section for more info. This is because
|
||||
|
|
|
|||
177
doc/dump.txt
177
doc/dump.txt
|
|
@ -14,16 +14,24 @@ dump ID group-ID style N file args :pre
|
|||
|
||||
ID = user-assigned name for the dump :ulb,l
|
||||
group-ID = ID of the group of atoms to be dumped :l
|
||||
style = {atom} or {bond} or {cfg} or {dcd} or {xtc} or {xyz} or {custom} :l
|
||||
style = {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} :l
|
||||
N = dump every this many timesteps :l
|
||||
file = name of file to write dump info to :l
|
||||
args = list of arguments for a particular style :l
|
||||
{atom} args = none
|
||||
{bond} args = none
|
||||
{cfg} args = same as {custom} args, see below
|
||||
{dcd} args = none
|
||||
{xtc} args = none
|
||||
{xyz} args = none
|
||||
{xyz} args = none :pre
|
||||
|
||||
{local} args = list of local attributes
|
||||
possible attributes = index, c_ID, c_ID\[N\], f_ID, f_ID\[N\]
|
||||
index = enumeration of local values
|
||||
c_ID = local vector calculated by a compute with ID
|
||||
c_ID\[N\] = Nth column of local array calculated by a compute with ID
|
||||
f_ID = local vector calculated by a fix with ID
|
||||
f_ID\[N\] = Nth column of local array calculated by a fix with ID :pre
|
||||
|
||||
{custom} args = list of atom attributes
|
||||
possible attributes = id, mol, type, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
|
||||
|
|
@ -51,9 +59,9 @@ args = list of arguments for a particular style :l
|
|||
angmomx,angmomy,angmomz = angular momentum of extended particle
|
||||
quatw,quati,quatj,quatk = quaternion components for aspherical particles
|
||||
tqx,tqy,tqz = torque on extended particles
|
||||
c_ID = per-atom vector value calculated by a compute with ID
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector value calculated by a fix with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name :pre
|
||||
:ule
|
||||
|
|
@ -88,7 +96,7 @@ When LAMMPS is running in parallel, the atom information written to
|
|||
dump files (typically one line per atom) may be written in an
|
||||
indeterminate order. This is because data for a single snapshot is
|
||||
collected from multiple processors. This is always the case for the
|
||||
{atom}, {bond}, and {custom} styles. It is also the case for the
|
||||
{atom}, {local}, and {custom} styles. It is also the case for the
|
||||
{xyz} style if the dump group is not {all}. It is not the case for
|
||||
the {dcd} and {xtc} styles which always write atoms in sorted order.
|
||||
So does the {xyz} style if the dump group is {all}. The {cfg} style
|
||||
|
|
@ -102,7 +110,7 @@ file and in what format. Settings made via the
|
|||
"dump_modify"_dump_modify.html command can also alter the format of
|
||||
individual values and the file itself.
|
||||
|
||||
The {atom}, {bond}, and {custom} styles create files in a simple text
|
||||
The {atom}, {local}, and {custom} styles create files in a simple text
|
||||
format that is self-explanatory when viewing a dump file. Many of the
|
||||
LAMMPS "post-processing tools"_Section_tools.html, including
|
||||
"Pizza.py"_http://www.cs.sandia.gov/~sjplimp/pizza.html, work with
|
||||
|
|
@ -129,16 +137,6 @@ boundaries. The format can be changed to unscaled coords via the
|
|||
"dump_modify"_dump_modify.html settings. Image flags can also be
|
||||
added for each atom via dump_modify.
|
||||
|
||||
For style {bond}, the bond topology between atoms is written, in the
|
||||
same format specified in data files read in by the
|
||||
"read_data"_read_data.html command. Both atoms in the bond must be in
|
||||
the dump group for the bond to be written. Any bonds that have been
|
||||
broken (see the "bond_style"_bond_style.html command) by setting their
|
||||
bond type to 0 are not written. Bonds that have been turned off (see
|
||||
the "fix shake"_fix_shake.html or "delete_bonds"_delete_bonds.html
|
||||
commands) by setting their bond type negative are written into the
|
||||
file.
|
||||
|
||||
Style {custom} allows you to specify a list of atom attributes to be
|
||||
written to the dump file for each atom. Possible attributes are
|
||||
listed above and will appear in the order specified. You cannot
|
||||
|
|
@ -146,8 +144,20 @@ specify a quantity that is not defined for a particular simulation -
|
|||
such as {q} for atom style {bond}, since that atom style doesn't
|
||||
assign charges. Dumps occur at the very end of a timestep, so atom
|
||||
attributes will include effects due to fixes that are applied during
|
||||
the timestep. An explanation of the dump custom quantities is given
|
||||
below.
|
||||
the timestep. An explanation of the possible dump custom attributes
|
||||
is given below.
|
||||
|
||||
For style {local}, local output generated by "computes"_compute.html
|
||||
and "fixes"_fix.html is used to gnerate lines of output that is
|
||||
written to the dump file. This local data is typically calculated by
|
||||
each processor based on the atoms it owns, but there may be zero or
|
||||
more entities per atom, e.g. a list of bond distances. An explanation
|
||||
of the possible dump local attributes is given below. Note that by
|
||||
using input from the "compute
|
||||
property/local"_compute_property_local.html command with dump local,
|
||||
it is possible to generate information on bonds, angles, etc that can
|
||||
be cut and pasted directly into a data file read by the
|
||||
"read_data"_read_data.html command.
|
||||
|
||||
Style {cfg} has the same command syntax as style {custom} and writes
|
||||
extended CFG format files, as used by the
|
||||
|
|
@ -254,11 +264,54 @@ styles.
|
|||
|
||||
:line
|
||||
|
||||
This section explains the atom quantities that can be specified as
|
||||
This section explains the local attributes that can be specified as
|
||||
part of the {local} style.
|
||||
|
||||
The {index} attribute can be used to generate an index number from 1
|
||||
to N for each line written into the dump file, where N is the total
|
||||
number of local datums from all processors, or lines of output that
|
||||
will appear in the snapshot. Note that because data from different
|
||||
processors depend on what atoms they currently own, and atoms migrate
|
||||
between processor, there is no guarantee that the same index will be
|
||||
used for the same info (e.g. a particular bond) in successive
|
||||
snapshots.
|
||||
|
||||
The {c_ID} and {c_ID\[N\]} attributes allow local vectors or arrays
|
||||
calculated by a "compute"_compute.html to be output. The ID in the
|
||||
attribute should be replaced by the actual ID of the compute that has
|
||||
been defined previously in the input script. See the
|
||||
"compute"_compute.html command for details. There are computes for
|
||||
calculating local information such as indices, types, and energies for
|
||||
bonds and angles.
|
||||
|
||||
Note that computes which calculate global or per-atom quantities, as
|
||||
opposed to local quantities, cannot be output in a dump local command.
|
||||
Instead, global quantities can be output by the "thermo_style
|
||||
custom"_thermo_style.html command, and per-atom quantities can be
|
||||
output by the dump custom command.
|
||||
|
||||
If {c_ID} is used as a attribute, then the local vector calculated by
|
||||
the compute is printed. If {c_ID\[N\]} is used, then N must be in the
|
||||
range from 1-M, which will print the Nth column of the M-length local
|
||||
array calculated by the compute.
|
||||
|
||||
The {f_ID} and {f_ID\[N\]} attributes allow local vectors or arrays
|
||||
calculated by a "fix"_fix.html to be output. The ID in the attribute
|
||||
should be replaced by the actual ID of the fix that has been defined
|
||||
previously in the input script.
|
||||
|
||||
If {f_ID} is used as a attribute, then the local vector calculated by
|
||||
the fix is printed. If {f_ID\[N\]} is used, then N must be in the
|
||||
range from 1-M, which will print the Nth column of the M-length local
|
||||
array calculated by the fix.
|
||||
|
||||
:line
|
||||
|
||||
This section explains the atom attributes that can be specified as
|
||||
part of the {custom} and {cfg} styles.
|
||||
|
||||
The {id}, {mol}, {type}, {mass}, {vx}, {vy}, {vz}, {fx}, {fy},
|
||||
{fz}, {q} keywords are self-explanatory.
|
||||
{fz}, {q} attributes are self-explanatory.
|
||||
|
||||
{Id} is the atom ID. {Mol} is the molecule ID, included in the data
|
||||
file for molecular systems. {Type} is the atom type. {Mass} is the
|
||||
|
|
@ -266,7 +319,7 @@ atom mass. {Vx}, {vy}, {vz}, {fx}, {fy}, {fz}, and {q} are components
|
|||
of atom velocity and force and atomic charge.
|
||||
|
||||
There are several options for outputting atom coordinates. The {x},
|
||||
{y}, {z} keywords write atom coordinates "unscaled", in the
|
||||
{y}, {z} attributes write atom coordinates "unscaled", in the
|
||||
appropriate distance "units"_units.html (Angstroms, sigma, etc). Use
|
||||
{xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size,
|
||||
so that each value is 0.0 to 1.0. If the simluation box is triclinic
|
||||
|
|
@ -278,57 +331,58 @@ the coordinate would be if it had not been wrapped back into the
|
|||
periodic box. Note that using {xu}, {yu}, {zu} means that the
|
||||
coordinate values may be far outside the box bounds printed with the
|
||||
snapshot. The image flags can be printed directly using the {ix},
|
||||
{iy}, {iz} keywords. The "dump_modify"_dump_modify.html command
|
||||
{iy}, {iz} attributes. The "dump_modify"_dump_modify.html command
|
||||
describes in more detail what is meant by scaled vs unscaled
|
||||
coordinates and the image flags.
|
||||
|
||||
The {mux}, {muy}, {muz} keywords are specific to dipolar systems
|
||||
The {mux}, {muy}, {muz} attributes are specific to dipolar systems
|
||||
defined with an atom style of {dipole}. They give the orientation of
|
||||
the atom's point dipole moment.
|
||||
|
||||
The {radius} keyword is specific to extended spherical particles
|
||||
The {radius} attribute is specific to extended spherical particles
|
||||
that have a finite size, such as granular particles defined with
|
||||
an atom style of {granular}.
|
||||
|
||||
The {omegax}, {omegay}, and {omegaz} keywords are specific to extended
|
||||
The {omegax}, {omegay}, and {omegaz} attributes are specific to extended
|
||||
spherical or aspherical particles that have an angular velocity. Only
|
||||
certain atom styles, such as {granular} or {dipole} define this
|
||||
quantity.
|
||||
|
||||
The {angmomx}, {angmomy}, and {angmomz} keywords are specific to
|
||||
The {angmomx}, {angmomy}, and {angmomz} attributes are specific to
|
||||
extended aspherical particles that have an angular momentum. Only
|
||||
the {ellipsoid} atom style defines this quantity.
|
||||
|
||||
The {quatw}, {quati}, {quatj}, {quatk} keywords are for aspherical
|
||||
The {quatw}, {quati}, {quatj}, {quatk} attributes are for aspherical
|
||||
particles defined with an atom style of {ellipsoid}. They are the
|
||||
components of the quaternion that defines the orientation of the
|
||||
particle.
|
||||
|
||||
The {tqx}, {tqy}, {tqz} keywords are for extended spherical or
|
||||
The {tqx}, {tqy}, {tqz} attributes are for extended spherical or
|
||||
aspherical particles that can sustain a rotational torque due
|
||||
to interactions with other particles.
|
||||
|
||||
The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector per-atom
|
||||
quantities calculated by a "compute"_compute.html to be output. The
|
||||
ID in the keyword should be replaced by the actual ID of the compute
|
||||
that has been defined previously in the input script. See the
|
||||
"compute"_compute.html command for details. There are per-atom
|
||||
computes for calculating the energy, stress, centro-symmetry
|
||||
parameter, and coordination number of individual atoms.
|
||||
The {c_ID} and {c_ID\[N\]} attributes allow per-atom vectors or arrays
|
||||
calculated by a "compute"_compute.html to be output. The ID in the
|
||||
attribute should be replaced by the actual ID of the compute that has
|
||||
been defined previously in the input script. See the
|
||||
"compute"_compute.html command for details. There are computes for
|
||||
calculating the per-atom energy, stress, centro-symmetry parameter,
|
||||
and coordination number of individual atoms.
|
||||
|
||||
Note that computes which calculate global scalar and vector
|
||||
quantities, as opposed to per-atom quantities, cannot be output in a
|
||||
dump. Instead, these quantities can be output by the "thermo_style
|
||||
custom"_thermo_style.html command.
|
||||
Note that computes which calculate global or local quantities, as
|
||||
opposed to per-atom quantities, cannot be output in a dump custom
|
||||
command. Instead, global quantities can be output by the
|
||||
"thermo_style custom"_thermo_style.html command, and local quantities
|
||||
can be output by the dump local command.
|
||||
|
||||
If {c_ID} is used as a keyword, then the scalar per-atom quantity
|
||||
calculated by the compute is printed. If {c_ID\[N\]} is used, then N
|
||||
must be in the range from 1-M, which will print the Nth column of
|
||||
the M-length per-atom array calculated by the compute.
|
||||
If {c_ID} is used as a attribute, then the per-atom vector calculated
|
||||
by the compute is printed. If {c_ID\[N\]} is used, then N must be in
|
||||
the range from 1-M, which will print the Nth column of the M-length
|
||||
per-atom array calculated by the compute.
|
||||
|
||||
The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector per-atom
|
||||
The {f_ID} and {f_ID\[N\]} attributes allow vector or array per-atom
|
||||
quantities calculated by a "fix"_fix.html to be output. The ID in the
|
||||
keyword should be replaced by the actual ID of the fix that has been
|
||||
attribute should be replaced by the actual ID of the fix that has been
|
||||
defined previously in the input script. The "fix
|
||||
ave/atom"_fix_ave_atom.html command is one that calculates per-atom
|
||||
quantities. Since it can time-average per-atom quantities produced by
|
||||
|
|
@ -336,20 +390,21 @@ any "compute"_compute.html, "fix"_fix.html, or atom-style
|
|||
"variable"_variable.html, this allows those time-averaged results to
|
||||
be written to a dump file.
|
||||
|
||||
If {f_ID} is used as a keyword, then the scalar per-atom quantity
|
||||
calculated by the fix is printed. If {f_ID\[N\]} is used, then N must
|
||||
be in the range from 1-M, which will print the Nth column of the
|
||||
M-length per-atom array calculated by the fix.
|
||||
If {f_ID} is used as a attribute, then the per-atom vector calculated
|
||||
by the fix is printed. If {f_ID\[N\]} is used, then N must be in the
|
||||
range from 1-M, which will print the Nth column of the M-length
|
||||
per-atom array calculated by the fix.
|
||||
|
||||
The {v_name} keyword allows per-atom quantities calculated by a
|
||||
"variable"_variable.html to be output. The name in the keyword should
|
||||
be replaced by the actual name of the variable that has been defined
|
||||
previously in the input script. Only an atom-style variable can be
|
||||
referenced, since it is the only style that generates per-atom values.
|
||||
Variables of style {atom} can reference individual atom attributes,
|
||||
per-atom atom attributes, thermodynamic keywords, or invoke other
|
||||
computes, fixes, or variables when they are evaluated, so this is a
|
||||
very general means of creating quantities to output to a dump file.
|
||||
The {v_name} attribute allows per-atom vectors calculated by a
|
||||
"variable"_variable.html to be output. The name in the attribute
|
||||
should be replaced by the actual name of the variable that has been
|
||||
defined previously in the input script. Only an atom-style variable
|
||||
can be referenced, since it is the only style that generates per-atom
|
||||
values. Variables of style {atom} can reference individual atom
|
||||
attributes, per-atom atom attributes, thermodynamic keywords, or
|
||||
invoke other computes, fixes, or variables when they are evaluated, so
|
||||
this is a very general means of creating quantities to output to a
|
||||
dump file.
|
||||
|
||||
See "this section"_Section_modify.html of the manual for information
|
||||
on how to add new compute and fix styles to LAMMPS to calculate
|
||||
|
|
@ -363,10 +418,6 @@ To write gzipped dump files, you must compile LAMMPS with the
|
|||
-DLAMMPS_GZIP option - see the "Making LAMMPS"_Section_start.html#2_2
|
||||
section of the documentation.
|
||||
|
||||
The {bond} style is part of the "molecular" package. It is only
|
||||
enabled if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
|
||||
The {xtc} style is part of the "xtc" package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info. This is because
|
||||
|
|
|
|||
Loading…
Reference in New Issue