2006-09-22 00:22:34 +08:00
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<HTML>
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2009-09-14 22:32:20 +08:00
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<CENTER> <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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2006-09-22 00:22:34 +08:00
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</CENTER>
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<HR>
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<H3>dump command
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</H3>
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2011-04-12 03:49:41 +08:00
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<H3><A HREF = "dump_image.html">dump image</A> command
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</H3>
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2013-11-22 04:53:41 +08:00
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<H3><A HREF = "dump_image.html">dump movie</A> command
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</H3>
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2012-06-13 06:54:32 +08:00
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<H3><A HREF = "dump_molfile.html">dump molfile</A> command
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</H3>
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2006-09-22 00:22:34 +08:00
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<P><B>Syntax:</B>
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</P>
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<PRE>dump ID group-ID style N file args
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</PRE>
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<UL><LI>ID = user-assigned name for the dump
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<LI>group-ID = ID of the group of atoms to be dumped
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2012-06-13 06:54:32 +08:00
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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>image</I> or <I>molfile</I> or <I>local</I> or <I>custom</I>
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2006-09-22 00:22:34 +08:00
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<LI>N = dump every this many timesteps
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<LI>file = name of file to write dump info to
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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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2009-09-03 00:20:52 +08:00
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<I>cfg</I> args = same as <I>custom</I> args, see below
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2007-02-10 05:37:30 +08:00
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<I>dcd</I> args = none
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2008-01-18 02:29:47 +08:00
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<I>xtc</I> args = none
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2009-12-18 07:33:42 +08:00
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<I>xyz</I> args = none
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</PRE>
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2011-04-12 03:49:41 +08:00
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<PRE> <I>image</I> args = discussed on <A HREF = "dump_image.html">dump image</A> doc page
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</PRE>
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2012-06-13 06:54:32 +08:00
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<PRE> <I>molfile</I> args = discussed on <A HREF = "dump_molfile.html">dump molfile</A> doc page
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</PRE>
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2009-12-18 07:33:42 +08:00
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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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2011-05-30 23:46:25 +08:00
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possible attributes = id, mol, type, element, mass,
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2011-04-30 07:38:34 +08:00
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x, y, z, xs, ys, zs, xu, yu, zu,
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xsu, ysu, zsu, ix, iy, iz,
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2007-02-10 05:37:30 +08:00
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vx, vy, vz, fx, fy, fz,
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2011-04-14 05:39:34 +08:00
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q, mux, muy, muz, mu,
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2011-05-30 23:46:25 +08:00
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radius, diameter, omegax, omegay, omegaz,
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2011-04-16 07:14:41 +08:00
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angmomx, angmomy, angmomz, tqx, tqy, tqz,
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2010-08-25 23:35:46 +08:00
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spin, eradius, ervel, erforce,
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2009-12-18 01:28:42 +08:00
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c_ID, c_ID[N], f_ID, f_ID[N], v_name
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</PRE>
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<PRE> id = atom ID
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2006-09-22 00:22:34 +08:00
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mol = molecule ID
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type = atom type
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2011-05-30 23:46:25 +08:00
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element = name of atom element, as defined by <A HREF = "dump_modify.html">dump_modify</A> command
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2009-12-16 01:39:43 +08:00
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mass = atom mass
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2006-09-22 00:22:34 +08:00
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x,y,z = unscaled atom coordinates
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xs,ys,zs = scaled atom coordinates
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xu,yu,zu = unwrapped atom coordinates
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2011-04-30 07:38:34 +08:00
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xsu,ysu,zsu = scaled unwrapped atom coordinates
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2006-10-03 06:11:58 +08:00
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ix,iy,iz = box image that the atom is in
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2006-09-22 00:22:34 +08:00
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vx,vy,vz = atom velocities
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fx,fy,fz = forces on atoms
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q = atom charge
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2011-04-14 05:39:34 +08:00
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mux,muy,muz = orientation of dipole moment of atom
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mu = magnitude of dipole moment of atom
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2011-05-30 23:46:25 +08:00
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radius,diameter = radius,diameter of spherical particle
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2013-02-01 03:46:51 +08:00
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omegax,omegay,omegaz = angular velocity of spherical particle
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angmomx,angmomy,angmomz = angular momentum of aspherical particle
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tqx,tqy,tqz = torque on finite-size particles
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2010-08-21 04:47:28 +08:00
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spin = electron spin
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eradius = electron radius
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2010-08-25 23:35:46 +08:00
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ervel = electron radial velocity
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erforce = electron radial force
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2009-12-18 07:33:42 +08:00
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c_ID = per-atom vector calculated by a compute with ID
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2009-12-05 05:04:00 +08:00
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c_ID[N] = Nth column of per-atom array calculated by a compute with ID
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2009-12-18 07:33:42 +08:00
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f_ID = per-atom vector calculated by a fix with ID
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2009-12-05 05:04:00 +08:00
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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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2006-09-22 00:22:34 +08:00
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>dump myDump all atom 100 dump.atom
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dump 2 subgroup atom 50 dump.run.bin
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2009-01-06 06:26:31 +08:00
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dump 4a all custom 100 dump.myforce.* id type x y vx fx
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dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
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2013-11-05 00:59:03 +08:00
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dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
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dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress<B>2</B>
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2010-08-21 04:47:28 +08:00
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dump 1 all xtc 1000 file.xtc
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dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce
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2006-09-22 00:22:34 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Dump a snapshot of atom quantities to one or more files every N
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2011-04-12 03:49:41 +08:00
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timesteps in one of several styles. The <I>image</I> style is the
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exception; it creates a JPG or PPM image file of the atom
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configuration every N timesteps, as discussed on the <A HREF = "dump_image.html">dump
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2012-06-09 00:00:54 +08:00
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image</A> doc page. The timesteps on which dump output
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2013-11-20 23:14:48 +08:00
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is written can also be controlled by a variable; see the <A HREF = "dump_modify.html">dump_modify
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every</A> command for details.
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2011-04-12 03:49:41 +08:00
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</P>
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<P>Only information for atoms in the specified group is dumped. The
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<A HREF = "dump_modify.html">dump_modify thresh and region</A> commands can also
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alter what atoms are included. Not all styles support all these
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options; see details below.
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</P>
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<P>As described below, the filename determines the kind of output (text
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or binary or gzipped, one big file or one per timestep, one big file
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2013-11-20 23:14:48 +08:00
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or multiple smaller files).
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2006-09-22 00:22:34 +08:00
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</P>
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2008-01-17 03:17:20 +08:00
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<P>IMPORTANT NOTE: Because periodic boundary conditions are enforced only
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2008-01-03 03:25:15 +08:00
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on timesteps when neighbor lists are rebuilt, the coordinates of an
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atom written to a dump file may be slightly outside the simulation
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box.
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2006-09-22 00:22:34 +08:00
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</P>
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2010-09-16 06:15:54 +08:00
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<P>IMPORTANT NOTE: Unless the <A HREF = "dump_modify.html">dump_modify sort</A> option
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is invoked, the lines of atom information written to dump files
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2010-09-03 07:27:22 +08:00
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(typically one line per atom) will be in an indeterminate order for
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2010-09-16 06:15:54 +08:00
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each snapshot. This is even true when running on a single processor,
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if the <A HREF = "atom_modify.html">atom_modify sort</A> option is on, which it is
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by default. In this case atoms are re-ordered periodically during a
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simulation, due to spatial sorting. It is also true when running in
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parallel, because data for a single snapshot is collected from
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2013-11-20 23:14:48 +08:00
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multiple processors, each of which owns a subset of the atoms.
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2010-09-16 06:15:54 +08:00
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</P>
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<P>For the <I>atom</I>, <I>custom</I>, <I>cfg</I>, and <I>local</I> styles, sorting is off by
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2012-06-13 06:54:32 +08:00
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default. For the <I>dcd</I>, <I>xtc</I>, <I>xyz</I>, and <I>molfile</I> styles, sorting by
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atom ID is on by default. See the <A HREF = "dump_modify.html">dump_modify</A> doc
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page for details.
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2006-09-22 00:22:34 +08:00
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</P>
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<HR>
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<P>The <I>style</I> keyword determines what atom quantities are written to the
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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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2009-12-18 07:33:42 +08:00
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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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2007-04-13 07:23:28 +08:00
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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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2012-06-09 01:08:04 +08:00
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<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A>, work with this
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2012-11-30 23:23:04 +08:00
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format, as does the <A HREF = "rerun.html">rerun</A> command.
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2009-03-17 06:44:23 +08:00
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</P>
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2013-02-01 01:24:45 +08:00
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<P>For post-processing purposes the <I>atom</I>, <I>local</I>, and <I>custom</I> text
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files are self-describing in the following sense.
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2010-10-12 00:45:51 +08:00
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</P>
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2010-10-14 05:58:00 +08:00
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<P>The dimensions of the simulation box are included in each snapshot.
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2010-10-15 07:23:43 +08:00
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For an orthogonal simulation box this information is is formatted as:
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2010-10-12 00:45:51 +08:00
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</P>
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2011-04-12 03:49:41 +08:00
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<PRE>ITEM: BOX BOUNDS xx yy zz
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2010-10-12 00:45:51 +08:00
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xlo xhi
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ylo yhi
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zlo zhi
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</PRE>
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2010-10-14 05:58:00 +08:00
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<P>where xlo,xhi are the maximum extents of the simulation box in the
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2011-04-12 03:49:41 +08:00
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x-dimension, and similarly for y and z. The "xx yy zz" represent 6
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characters that encode the style of boundary for each of the 6
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2011-04-14 05:56:07 +08:00
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simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi). Each of
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the 6 characters is either p = periodic, f = fixed, s = shrink wrap,
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or m = shrink wrapped with a minimum value. See the
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2013-03-11 22:52:39 +08:00
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<A HREF = "boundary.html">boundary</A> command for details.
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2010-10-12 00:45:51 +08:00
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</P>
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2010-10-15 07:23:43 +08:00
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<P>For triclinic simulation boxes (non-orthogonal), an orthogonal
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bounding box which encloses the triclinic simulation box is output,
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along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
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formatted as follows:
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2010-10-12 00:45:51 +08:00
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</P>
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2011-04-14 05:56:07 +08:00
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<PRE>ITEM: BOX BOUNDS xy xz yz xx yy zz
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2010-10-12 00:45:51 +08:00
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xlo_bound xhi_bound xy
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ylo_bound yhi_bound xz
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zlo_bound zhi_bound yz
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</PRE>
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2011-04-14 05:56:07 +08:00
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<P>The presence of the text "xy xz yz" in the ITEM line indicates that
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the 3 tilt factors will be included on each of the 3 following lines.
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This bounding box is convenient for many visualization programs. The
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meaning of the 6 character flags for "xx yy zz" is the same as above.
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</P>
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<P>Note that the first two numbers on each line are now xlo_bound instead
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2011-08-26 01:01:01 +08:00
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of xlo, etc, since they repesent a bounding box. See <A HREF = "Section_howto.html#howto_12">this
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2011-04-14 05:56:07 +08:00
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section</A> of the doc pages for a geometric
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description of triclinic boxes, as defined by LAMMPS, simple formulas
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for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
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calculated from the triclinic parameters, and how to transform those
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parameters to and from other commonly used triclinic representations.
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2010-10-15 07:23:43 +08:00
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</P>
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2010-10-12 00:45:51 +08:00
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<P>The "ITEM: ATOMS" line in each snapshot lists column descriptors for
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the per-atom lines that follow. For example, the descriptors would be
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"id type xs ys zs" for the default <I>atom</I> style, and would be the atom
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attributes you specify in the dump command for the <I>custom</I> style.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>For style <I>atom</I>, atom coordinates are written to the file, along with
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the atom ID and atom type. By default, atom coords are written in a
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scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom
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is at a location 1/4 of the distance from xlo to xhi of the box
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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>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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2007-12-14 02:16:20 +08:00
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listed above and will appear in the order specified. You cannot
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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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2006-09-22 00:22:34 +08:00
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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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2009-12-18 07:33:42 +08:00
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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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2012-01-07 00:58:21 +08:00
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and <A HREF = "fix.html">fixes</A> is used to generate lines of output that is
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2009-12-18 07:33:42 +08:00
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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,
|
|
|
|
|
it is possible to generate information on bonds, angles, etc that can
|
|
|
|
|
be cut and pasted directly into a data file read by the
|
|
|
|
|
<A HREF = "read_data.html">read_data</A> command.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2009-09-03 00:20:52 +08:00
|
|
|
<P>Style <I>cfg</I> has the same command syntax as style <I>custom</I> and writes
|
|
|
|
|
extended CFG format files, as used by the
|
|
|
|
|
<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization
|
|
|
|
|
package. Since the extended CFG format uses a single snapshot of the
|
2011-03-15 22:36:35 +08:00
|
|
|
system per file, a wildcard "*" must be included in the filename, as
|
2009-09-03 00:20:52 +08:00
|
|
|
discussed below. The list of atom attributes for style <I>cfg</I> must
|
2013-11-09 06:12:10 +08:00
|
|
|
begin with either "mass type xs ys zs" or "mass type xsu ysu zsu"
|
|
|
|
|
since these quantities are needed to write the CFG files in the
|
|
|
|
|
appropriate format (though the "mass" and "type" fields do not appear
|
|
|
|
|
explicitly in the file). Any remaining attributes will be stored as
|
|
|
|
|
"auxiliary properties" in the CFG files. Note that you will typically
|
|
|
|
|
want to use the <A HREF = "dump_modify.html">dump_modify element</A> command with
|
|
|
|
|
CFG-formatted files, to associate element names with atom types, so
|
|
|
|
|
that AtomEye can render atoms appropriately. When unwrapped
|
|
|
|
|
coordinates <I>xsu</I>, <I>ysu</I>, and <I>zsu</I> are requested, the nominal AtomEye
|
|
|
|
|
periodic cell dimensions are expanded by a large factor UNWRAPEXPAND =
|
|
|
|
|
10.0, which ensures atoms that are displayed correctly for up to
|
|
|
|
|
UNWRAPEXPAND/2 periodic boundary crossings in any direction. Beyond
|
|
|
|
|
this, AtomEye will rewrap the unwrapped coordinates. The expansion
|
|
|
|
|
causes the atoms to be drawn farther away from the viewer, but it is
|
|
|
|
|
easy to zoom the atoms closer, and the interatomic distances are
|
|
|
|
|
unaffected.
|
2009-09-03 00:20:52 +08:00
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P>The <I>dcd</I> style writes DCD files, a standard atomic trajectory format
|
|
|
|
|
used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
|
|
|
|
|
files are binary and thus may not be portable to different machines.
|
2010-09-16 06:15:54 +08:00
|
|
|
The number of atoms per snapshot cannot change with the <I>dcd</I> style.
|
|
|
|
|
The <I>unwrap</I> option of the <A HREF = "dump_modify.html">dump_modify</A> command
|
|
|
|
|
allows DCD coordinates to be written "unwrapped" by the image flags
|
2010-10-06 23:58:26 +08:00
|
|
|
for each atom. Unwrapped means that if the atom has passed through
|
|
|
|
|
a periodic boundary one or more times, the value is printed for what
|
|
|
|
|
the coordinate would be if it had not been wrapped back into the
|
|
|
|
|
periodic box. Note that these coordinates may thus be far outside
|
|
|
|
|
the box size stored with the snapshot.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P>The <I>xtc</I> style writes XTC files, a compressed trajectory format used
|
2007-02-23 00:52:24 +08:00
|
|
|
by the GROMACS molecular dynamics package, and described
|
2010-10-06 23:58:26 +08:00
|
|
|
<A HREF = "http://manual.gromacs.org/current/online/xtc.html">here</A>.
|
2008-01-18 02:29:47 +08:00
|
|
|
The precision used in XTC files can be adjusted via the
|
|
|
|
|
<A HREF = "dump_modify.html">dump_modify</A> command. The default value of 1000
|
|
|
|
|
means that coordinates are stored to 1/1000 nanometer accuracy. XTC
|
2010-10-06 23:58:26 +08:00
|
|
|
files are portable binary files written in the NFS XDR data format,
|
|
|
|
|
so that any machine which supports XDR should be able to read them.
|
|
|
|
|
The number of atoms per snapshot cannot change with the <I>xtc</I> style.
|
|
|
|
|
The <I>unwrap</I> option of the <A HREF = "dump_modify.html">dump_modify</A> command allows
|
2010-09-16 06:15:54 +08:00
|
|
|
XTC coordinates to be written "unwrapped" by the image flags for each
|
|
|
|
|
atom. Unwrapped means that if the atom has passed thru a periodic
|
|
|
|
|
boundary one or more times, the value is printed for what the
|
|
|
|
|
coordinate would be if it had not been wrapped back into the periodic
|
|
|
|
|
box. Note that these coordinates may thus be far outside the box size
|
|
|
|
|
stored with the snapshot.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P>The <I>xyz</I> style writes XYZ files, which is a simple text-based
|
2012-05-23 23:52:08 +08:00
|
|
|
coordinate format that many codes can read. Specifically it has
|
|
|
|
|
a line with the number of atoms, then a comment line that is
|
|
|
|
|
usually ignored followed by one line per atom with the atom type
|
|
|
|
|
and the x-, y-, and z-coordinate of that atom. You can use the
|
|
|
|
|
<A HREF = "dump_modify.html">dump_modify element</A> option to change the output
|
|
|
|
|
from using the (numerical) atom type to an element name (or some
|
|
|
|
|
other label). This will help many visualization programs to guess
|
|
|
|
|
bonds and colors.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2013-11-20 23:14:48 +08:00
|
|
|
<P>Note that <I>atom</I>, <I>custom</I>, <I>dcd</I>, <I>xtc</I>, and <I>xyz</I> style dump files
|
|
|
|
|
can be read directly by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>, a
|
|
|
|
|
popular molecular viewing program. See <A HREF = "Section_tools.html#vmd">Section
|
|
|
|
|
tools</A> of the manual and the
|
|
|
|
|
tools/lmp2vmd/README.txt file for more information about support in
|
|
|
|
|
VMD for reading and visualizing LAMMPS dump files.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2006-12-16 06:53:57 +08:00
|
|
|
<P>Dumps are performed on timesteps that are a multiple of N (including
|
|
|
|
|
timestep 0) and on the last timestep of a minimization if the
|
2010-03-03 06:52:34 +08:00
|
|
|
minimization converges. Note that this means a dump will not be
|
|
|
|
|
performed on the initial timestep after the dump command is invoked,
|
|
|
|
|
if the current timestep is not a multiple of N. This behavior can be
|
|
|
|
|
changed via the <A HREF = "dump_modify.html">dump_modify first</A> command, which
|
2012-11-10 09:17:45 +08:00
|
|
|
can also be useful if the dump command is invoked after a minimization
|
2010-03-03 06:52:34 +08:00
|
|
|
ended on an arbitrary timestep. N can be changed between runs by
|
|
|
|
|
using the <A HREF = "dump_modify.html">dump_modify every</A> command (not allowed
|
2012-06-08 07:52:27 +08:00
|
|
|
for <I>dcd</I> style). The <A HREF = "dump_modify.html">dump_modify every</A> command
|
|
|
|
|
also allows a variable to be used to determine the sequence of
|
2012-11-10 09:17:45 +08:00
|
|
|
timesteps on which dump files are written. In this mode a dump on the
|
|
|
|
|
first timestep of a run will also not be written unless the
|
|
|
|
|
<A HREF = "dump_modify.html">dump_modify first</A> command is used.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P>The specified filename determines how the dump file(s) is written.
|
|
|
|
|
The default is to write one large text file, which is opened when the
|
|
|
|
|
dump command is invoked and closed when an <A HREF = "undump.html">undump</A>
|
|
|
|
|
command is used or when LAMMPS exits. For the <I>dcd</I> and <I>xtc</I> styles,
|
|
|
|
|
this is a single large binary file.
|
|
|
|
|
</P>
|
2011-03-15 22:36:35 +08:00
|
|
|
<P>Dump filenames can contain two wildcard characters. If a "*"
|
2006-09-22 00:22:34 +08:00
|
|
|
character appears in the filename, then one file per snapshot is
|
|
|
|
|
written and the "*" character is replaced with the timestep value.
|
|
|
|
|
For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000,
|
|
|
|
|
tmp.dump.20000, etc. This option is not available for the <I>dcd</I> and
|
2011-04-12 03:49:41 +08:00
|
|
|
<I>xtc</I> styles. Note that the <A HREF = "dump_modify.html">dump_modify pad</A>
|
|
|
|
|
command can be used to insure all timestep numbers are the same length
|
|
|
|
|
(e.g. 00010), which can make it easier to read a series of dump files
|
2013-11-20 23:14:48 +08:00
|
|
|
in order with some post-processing tools.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2013-04-02 23:15:35 +08:00
|
|
|
<P>If a "%" character appears in the filename, then each of P processors
|
|
|
|
|
writes a portion of the dump file, and the "%" character is replaced
|
|
|
|
|
with the processor ID from 0 to P-1. For example, tmp.dump.% becomes
|
2006-09-22 00:22:34 +08:00
|
|
|
tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc. This creates smaller
|
|
|
|
|
files and can be a fast mode of output on parallel machines that
|
|
|
|
|
support parallel I/O for output. This option is not available for the
|
|
|
|
|
<I>dcd</I>, <I>xtc</I>, and <I>xyz</I> styles.
|
|
|
|
|
</P>
|
2013-04-02 23:15:35 +08:00
|
|
|
<P>By default, P = the number of processors meaning one file per
|
|
|
|
|
processor, but P can be set to a smaller value via the <I>nfile</I> or
|
|
|
|
|
<I>fileper</I> keywords of the <A HREF = "dump_modify.html">dump_modify</A> command.
|
|
|
|
|
These options can be the most efficient way of writing out dump files
|
|
|
|
|
when running on large numbers of processors.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Note that using the "*" and "%" characters together can produce a
|
2006-09-22 00:22:34 +08:00
|
|
|
large number of small dump files!
|
|
|
|
|
</P>
|
|
|
|
|
<P>If the filename ends with ".bin", the dump file (or files, if "*" or
|
|
|
|
|
"%" is also used) is written in binary format. A binary dump file
|
|
|
|
|
will be about the same size as a text version, but will typically
|
|
|
|
|
write out much faster. Of course, when post-processing, you will need
|
|
|
|
|
to convert it back to text format (see the <A HREF = "Section_tools.html#binary">binary2txt
|
|
|
|
|
tool</A>) or write your own code to read the
|
|
|
|
|
binary file. The format of the binary file can be understood by
|
|
|
|
|
looking at the tools/binary2txt.cpp file. This option is only
|
|
|
|
|
available for the <I>atom</I> and <I>custom</I> styles.
|
|
|
|
|
</P>
|
|
|
|
|
<P>If the filename ends with ".gz", the dump file (or files, if "*" or "%"
|
|
|
|
|
is also used) is written in gzipped format. A gzipped dump file will
|
|
|
|
|
be about 3x smaller than the text version, but will also take longer
|
|
|
|
|
to write. This option is not available for the <I>dcd</I> and <I>xtc</I>
|
|
|
|
|
styles.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2009-12-18 07:33:42 +08:00
|
|
|
<P>This section explains the local attributes that can be specified as
|
|
|
|
|
part of the <I>local</I> style.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The <I>index</I> 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.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The <I>c_ID</I> and <I>c_ID[N]</I> attributes allow local vectors or arrays
|
|
|
|
|
calculated by a <A HREF = "compute.html">compute</A> 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
|
|
|
|
|
<A HREF = "compute.html">compute</A> command for details. There are computes for
|
|
|
|
|
calculating local information such as indices, types, and energies for
|
|
|
|
|
bonds and angles.
|
|
|
|
|
</P>
|
|
|
|
|
<P>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 <A HREF = "thermo_style.html">thermo_style
|
|
|
|
|
custom</A> command, and per-atom quantities can be
|
|
|
|
|
output by the dump custom command.
|
|
|
|
|
</P>
|
|
|
|
|
<P>If <I>c_ID</I> is used as a attribute, then the local vector calculated 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 local
|
|
|
|
|
array calculated by the compute.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The <I>f_ID</I> and <I>f_ID[N]</I> attributes allow local vectors or arrays
|
|
|
|
|
calculated by a <A HREF = "fix.html">fix</A> 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.
|
|
|
|
|
</P>
|
|
|
|
|
<P>If <I>f_ID</I> is used as a attribute, then the local 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 local
|
|
|
|
|
array calculated by the fix.
|
|
|
|
|
</P>
|
2011-12-22 23:33:47 +08:00
|
|
|
<P>Here is an example of how to dump bond info for a system,
|
|
|
|
|
including the distance and energy of each bond:
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>compute 1 all property/local batom1 batom2 btype
|
|
|
|
|
compute 2 all bond/local dist eng
|
2012-10-15 22:18:13 +08:00
|
|
|
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
|
2011-12-22 23:33:47 +08:00
|
|
|
</PRE>
|
2009-12-18 07:33:42 +08:00
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P>This section explains the atom attributes that can be specified as
|
2009-09-03 00:20:52 +08:00
|
|
|
part of the <I>custom</I> and <I>cfg</I> styles.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2011-05-30 23:46:25 +08:00
|
|
|
<P>The <I>id</I>, <I>mol</I>, <I>type</I>, <I>element</I>, <I>mass</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
|
2009-12-18 07:33:42 +08:00
|
|
|
<I>fz</I>, <I>q</I> attributes are self-explanatory.
|
2009-01-13 23:40:11 +08:00
|
|
|
</P>
|
|
|
|
|
<P><I>Id</I> is the atom ID. <I>Mol</I> is the molecule ID, included in the data
|
2011-05-30 23:46:25 +08:00
|
|
|
file for molecular systems. <I>Type</I> is the atom type. <I>Element</I> is
|
|
|
|
|
typically the chemical name of an element, which you must assign to
|
|
|
|
|
each type via the <A HREF = "dump_modify.html">dump_modify element</A> command.
|
|
|
|
|
More generally, it can be any string you wish to associated with an
|
|
|
|
|
atom type. <I>Mass</I> is the atom mass. <I>Vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
|
|
|
|
|
<I>fz</I>, and <I>q</I> are components of atom velocity and force and atomic
|
|
|
|
|
charge.
|
2009-01-13 23:40:11 +08:00
|
|
|
</P>
|
|
|
|
|
<P>There are several options for outputting atom coordinates. The <I>x</I>,
|
2009-12-18 07:33:42 +08:00
|
|
|
<I>y</I>, <I>z</I> attributes write atom coordinates "unscaled", in the
|
2007-09-28 07:25:52 +08:00
|
|
|
appropriate distance <A HREF = "units.html">units</A> (Angstroms, sigma, etc). Use
|
|
|
|
|
<I>xs</I>, <I>ys</I>, <I>zs</I> if you want the coordinates "scaled" to the box size,
|
2011-04-30 07:38:34 +08:00
|
|
|
so that each value is 0.0 to 1.0. If the simulation box is triclinic
|
2009-01-13 23:40:11 +08:00
|
|
|
(tilted), then all atom coords will still be between 0.0 and 1.0. Use
|
|
|
|
|
<I>xu</I>, <I>yu</I>, <I>zu</I> if you want the coordinates "unwrapped" by the image
|
|
|
|
|
flags for each atom. Unwrapped means that if the atom has passed thru
|
|
|
|
|
a periodic boundary one or more times, the value is printed for what
|
|
|
|
|
the coordinate would be if it had not been wrapped back into the
|
|
|
|
|
periodic box. Note that using <I>xu</I>, <I>yu</I>, <I>zu</I> means that the
|
2009-03-18 00:11:05 +08:00
|
|
|
coordinate values may be far outside the box bounds printed with the
|
2011-04-30 07:38:34 +08:00
|
|
|
snapshot. Using <I>xsu</I>, <I>ysu</I>, <I>zsu</I> is similar to using <I>xu</I>, <I>yu</I>, <I>zu</I>,
|
|
|
|
|
except that the unwrapped coordinates are scaled by the box size. Atoms
|
|
|
|
|
that have passed through a periodic boundary will have the corresponding
|
|
|
|
|
cooordinate increased or decreased by 1.0.
|
|
|
|
|
</P>
|
2013-07-31 05:01:14 +08:00
|
|
|
<P>The image flags can be printed directly using the <I>ix</I>, <I>iy</I>, <I>iz</I>
|
|
|
|
|
attributes. For periodic dimensions, they specify which image of the
|
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|
|
|
simulation box the atom is considered to be in. An image of 0 means
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|
it is inside the box as defined. A value of 2 means add 2 box lengths
|
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|
|
|
to get the true value. A value of -1 means subtract 1 box length to
|
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|
|
|
get the true value. LAMMPS updates these flags as atoms cross
|
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periodic boundaries during the simulation.
|
2007-02-10 05:37:30 +08:00
|
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</P>
|
2009-12-18 07:33:42 +08:00
|
|
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<P>The <I>mux</I>, <I>muy</I>, <I>muz</I> attributes are specific to dipolar systems
|
2007-04-20 07:25:27 +08:00
|
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|
defined with an atom style of <I>dipole</I>. They give the orientation of
|
2011-04-14 05:39:34 +08:00
|
|
|
the atom's point dipole moment. The <I>mu</I> attribute gives the
|
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|
|
|
magnitude of the atom's dipole moment.
|
2007-04-20 07:25:27 +08:00
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|
</P>
|
2013-02-01 08:24:05 +08:00
|
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<P>The <I>radius</I> and <I>diameter</I> attributes are specific to spherical
|
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particles that have a finite size, such as those defined with an atom
|
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|
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|
style of <I>sphere</I>.
|
2008-04-29 07:51:08 +08:00
|
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|
</P>
|
2011-04-14 05:39:34 +08:00
|
|
|
<P>The <I>omegax</I>, <I>omegay</I>, and <I>omegaz</I> attributes are specific to
|
2013-02-01 08:24:05 +08:00
|
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|
finite-size spherical particles that have an angular velocity. Only
|
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|
|
|
certain atom styles, such as <I>sphere</I> define this quantity.
|
2008-04-29 07:51:08 +08:00
|
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|
</P>
|
2009-12-18 07:33:42 +08:00
|
|
|
<P>The <I>angmomx</I>, <I>angmomy</I>, and <I>angmomz</I> attributes are specific to
|
2013-02-01 08:24:05 +08:00
|
|
|
finite-size aspherical particles that have an angular momentum. Only
|
2009-01-09 05:03:05 +08:00
|
|
|
the <I>ellipsoid</I> atom style defines this quantity.
|
2008-06-25 01:28:12 +08:00
|
|
|
</P>
|
2013-02-01 08:24:05 +08:00
|
|
|
<P>The <I>tqx</I>, <I>tqy</I>, <I>tqz</I> attributes are for finite-size particles that
|
|
|
|
|
can sustain a rotational torque due to interactions with other
|
|
|
|
|
particles.
|
2007-02-10 05:37:30 +08:00
|
|
|
</P>
|
2010-08-25 23:35:46 +08:00
|
|
|
<P>The <I>spin</I>, <I>eradius</I>, <I>ervel</I>, and <I>erforce</I> attributes are for
|
2010-08-21 04:47:28 +08:00
|
|
|
particles that represent nuclei and electrons modeled with the
|
|
|
|
|
electronic force field (EFF). See <A HREF = "atom_style.html">atom_style
|
|
|
|
|
electron</A> and <A HREF = "pair_eff.html">pair_style eff</A> for more
|
|
|
|
|
details.
|
|
|
|
|
</P>
|
2009-12-18 07:33:42 +08:00
|
|
|
<P>The <I>c_ID</I> and <I>c_ID[N]</I> attributes allow per-atom vectors or arrays
|
|
|
|
|
calculated by a <A HREF = "compute.html">compute</A> 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
|
|
|
|
|
<A HREF = "compute.html">compute</A> command for details. There are computes for
|
|
|
|
|
calculating the per-atom energy, stress, centro-symmetry parameter,
|
|
|
|
|
and coordination number of individual atoms.
|
|
|
|
|
</P>
|
|
|
|
|
<P>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
|
|
|
|
|
<A HREF = "thermo_style.html">thermo_style custom</A> command, and local quantities
|
|
|
|
|
can be output by the dump local command.
|
|
|
|
|
</P>
|
|
|
|
|
<P>If <I>c_ID</I> is used as a attribute, then the per-atom vector calculated
|
|
|
|
|
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
|
|
|
|
|
per-atom array calculated by the compute.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The <I>f_ID</I> and <I>f_ID[N]</I> attributes allow vector or array per-atom
|
2007-12-14 02:16:20 +08:00
|
|
|
quantities calculated by a <A HREF = "fix.html">fix</A> to be output. The ID in the
|
2009-12-18 07:33:42 +08:00
|
|
|
attribute should be replaced by the actual ID of the fix that has been
|
2008-01-04 07:28:08 +08:00
|
|
|
defined previously in the input script. The <A HREF = "fix_ave_atom.html">fix
|
|
|
|
|
ave/atom</A> command is one that calculates per-atom
|
|
|
|
|
quantities. Since it can time-average per-atom quantities produced by
|
|
|
|
|
any <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or atom-style
|
2007-12-14 02:16:20 +08:00
|
|
|
<A HREF = "variable.html">variable</A>, this allows those time-averaged results to
|
|
|
|
|
be written to a dump file.
|
2007-09-28 07:25:52 +08:00
|
|
|
</P>
|
2009-12-18 07:33:42 +08:00
|
|
|
<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> 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.
|
2007-12-14 02:16:20 +08:00
|
|
|
</P>
|
2011-12-14 04:35:35 +08:00
|
|
|
<P>See <A HREF = "Section_modify.html">Section_modify</A> of the manual for information
|
2008-01-03 03:25:15 +08:00
|
|
|
on how to add new compute and fix styles to LAMMPS to calculate
|
2007-12-14 02:16:20 +08:00
|
|
|
per-atom quantities which could then be output into dump files.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
|
</P>
|
2008-01-18 07:46:30 +08:00
|
|
|
<P>To write gzipped dump files, you must compile LAMMPS with the
|
2011-08-26 00:46:23 +08:00
|
|
|
-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
|
|
|
|
|
LAMMPS</A> section of the documentation.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2011-08-27 02:53:00 +08:00
|
|
|
<P>The <I>xtc</I> style is part of the XTC package. It is only enabled if
|
2011-08-26 00:46:23 +08:00
|
|
|
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
|
|
|
|
LAMMPS</A> section for more info. This is
|
|
|
|
|
because some machines may not support the low-level XDR data format
|
|
|
|
|
that XTC files are written with, which will result in a compile-time
|
|
|
|
|
error when a low-level include file is not found. Putting this style
|
|
|
|
|
in a package makes it easy to exclude from a LAMMPS build for those
|
|
|
|
|
machines. However, the XTC package also includes two compatibility
|
|
|
|
|
header files and associated functions, which should be a suitable
|
|
|
|
|
substitute on machines that do not have the appropriate native header
|
|
|
|
|
files. This option can be invoked at build time by adding
|
|
|
|
|
-DLAMMPS_XDR to the CCFLAGS variable in the appropriate low-level
|
|
|
|
|
Makefile, e.g. src/MAKE/Makefile.foo. This compatibility mode has
|
|
|
|
|
been tested successfully on Cray XT3/XT4/XT5 and IBM BlueGene/L
|
|
|
|
|
machines and should also work on IBM BG/P, and Windows XP/Vista/7
|
|
|
|
|
machines.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
2011-04-12 03:49:41 +08:00
|
|
|
<P><A HREF = "dump_image.html">dump image</A>, <A HREF = "dump_modify.html">dump_modify</A>,
|
|
|
|
|
<A HREF = "undump.html">undump</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B>
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2011-04-12 03:49:41 +08:00
|
|
|
<P>The defaults for the image style are listed on the <A HREF = "dump_image.html">dump
|
|
|
|
|
image</A> doc page.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
</HTML>
|
