From 82aa6401464f01d61710ee3cbbd2b73cc686d2ea Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 10 Aug 2010 14:24:51 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4474 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/read_dump.txt | 106 ---------------------------------------------- 1 file changed, 106 deletions(-) delete mode 100644 doc/read_dump.txt diff --git a/doc/read_dump.txt b/doc/read_dump.txt deleted file mode 100644 index 852c172676..0000000000 --- a/doc/read_dump.txt +++ /dev/null @@ -1,106 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -read_dump command :h3 - -[Syntax:] - -read_dump filename N col1 col2 ... keyword value ... :pre - -filename = name of dump file to read snapshot from :ulb,l -N = timestamp to read in :l -col1, col2, ... = {x} or {y} or {z} or {xs} or {ys} or {zs} or {xu} or {yu} or {zu} or {ix} or {iy} or {iz} or {vx} or {vy} or {vz} :l -zero or more keyword/value pairs may be appended :l -keyword = {procs} or {box} :l - {procs} value = P - P = number of processors that wrote out dump file - {box} value = {reset} or {ignore} :pre -:ule - -[Examples:] - -read_dump dump.run 1000 x y z -read_dump dump.poly.% 50000 xs ys zs vx vy vz procs 100 :pre - -[Description:] - -Read a snapshot at timestamp N from the specified dump file and use -the specified per-atom column information from the snapshot to -overwrite current per-atom values. The dump file must be in the -native LAMMPS format, as produced by an {atom} or {custom} style -"dump"_dump.html command. - -The specified filename can contain the "%" wild-card character. This -means that individual dump files were written by each of the P -processors the original simulation was running on, where "%" is -replaced by the processor ID from 0 to P-1. If the current simulation -is not running on the same number of processors, then the {procs} -keyword must be used to specify what P was in the original simulation, -so that the current simulation knows which files to read. If the "%" -wild-card character is not used, or the current simulation is running -on the same number of processors, then the {procs} keyword should not -be used. - -{N} is the timestamp of the snapshot that will be read from the dump -file. The file will be scanned until the snapshot with that timestamp -is found. The timestep of the current simulation will not be reset to -{N}. Use the "reset_timestep"_reset_timestep.html command if this is -desired. - -The dump file snapshot defines a simulation box size via its ITEM: BOX -BOUNDS field. If the setting for the optional {box} keyword is -{ignore} then the box size settings are ignored. If the setting for -the {box} keyword is {reset} then the current simulation box size is -reset to the values in the dump snapshot. Note that due to the finite -precision at which numeric values are written into a dump file, box -sizes values which are identical to the current box size may be read -in as slightly different values. Hence you should not reset the box -size if you expect it to be the same. - -The dump file snapshot defines the number of atom in the snapshot via -its ITEM: NUMBER OF ATOMS field. If this number does not match the -number of atoms in the current simulation, then a WARNING is printed. - -The dump file snapshot defines a list of per-atom quantities via its -ITEM: ATOMS field. Any of the quantities listed above may be -specified, in which case that per-atom quantity is read from the dump -file and overwrites the corresponding current quantity. See the -"dump"_dump.html command for an explanation of these quantities. - -Atom IDs must also appear in the dump file. They are used to map -read-in atoms to current atoms one by one. Note that if some current -atoms do not appear in the dump file, their values are not -overwritten. Likewise if atom IDs appear in the dump file which do -not exist in the current simulation, their read-in values are ignored. - -The various flavors of atom coordinates that can appear in the dump -file ({x} or {xs} or {xu}) are all converted into internal LAMMPS -coordinates (equivalent to {x}). Each atom is also remapped to the -current simulation box, if it is outside periodic boundaries. Note -that the current simulation box size may have been reset to the dump -snapshot box size before this takes place. - -IMPORTANT NOTE: Image flags from the dump file ({ix}, {iy}, {iz}) -should only be read-in if the corresponding coordinates are of the {x} -or {xs} form. In this case, the remap of each atom to the (new) -periodic box should update its read-in image flags correctly. If the -read-in coordinates are of the {xu} form, then no corresponding image -flags should be read-in. This is because the image flags are -initialized to 0 when {xu} style coordinates are read. The remap of -atoms to the (new) periodic box should update the re-initialized image -flags correctly. - -[Restrictions:] none - -[Related commands:] - -"read_data"_read_data.html, "read_restart"_read_restart.html - -[Default:] - -The option defaults are box = ignore.