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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3135 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2009-09-02 16:20:52 +00:00
parent 14254f023a
commit e8f3ce6b35
4 changed files with 212 additions and 134 deletions
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26
doc/dump.txt
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@ -14,12 +14,13 @@ 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 {dcd} or {xtc} or {xyz} or {custom} :l
style = {atom} or {bond} or {cfg} or {dcd} or {xtc} or {xyz} 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
@ -61,6 +62,8 @@ dump myDump all atom 100 dump.atom
dump 2 subgroup atom 50 dump.run.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg id type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.*.cfg id type xs ys zs id type c_Stress[2]
dump 1 all xtc 1000 file.xtc :pre
[Description:]
@ -86,7 +89,9 @@ collected from multiple processors. This is always the case for the
{atom}, {bond}, 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}.
So does the {xyz} style if the dump group is {all}. The {cfg} style
supports the {sort} option of the "dump_modify"_dump_modify.html
command which allows for allows sorting to be turned on or off.
:line
@ -142,6 +147,21 @@ attributes will include effects due to fixes that are applied during
the timestep. An explanation of the dump custom quantities is given
below.
Style {cfg} has the same command syntax as style {custom} and writes
extended CFG format files, as used by the
"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualization
package. Since the extended CFG format uses a single snapshot of the
system per file, a wild-card "*" must be included in the filename, as
discussed below. The list of atom attributes for style {cfg} must
begin with "id tag xs ys zs", since these quantities are needed to
write the CFG files in the appropriate format (though the "id" 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 "dump_modify
element"_dump_modify.html command with CFG-formatted files, to
associate element names with atom types, so that AtomEye can render
atoms appropriately.
The {dcd} 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.
@ -233,7 +253,7 @@ styles.
:line
This section explains the atom quantities that can be specified as
part of the {custom} style.
part of the {custom} and {cfg} styles.
The {id}, {mol}, {type}, {vx}, {vy}, {vz}, {fx}, {fy},
{fz}, {q} keywords are self-explanatory.