hi!
split is just a command in bash, cutting any ascii file after a " -l
"amount of lines, and appending 000x after the name, where " -d "
creates a number suffix and " -a " says how many digits there should
be. It might not be necessary to use this for jmol anymore, because
the load trajectory per frame or stride appears very memory-efficient,
but it's anyway a handy trick for other analysis.
As in my previous mails, I am currently experimenting with the "load
trajectory" option and the conversion to a movie file within the same
viewing state.
For testing, I just created a trajectory of about 100 atoms, and
actually managed to read in 40000 (>9999!) frames, and after reading
in I could move around between frames, although jmol crashed when I
tried to click on atoms etc. :)
In any case, it is indeed perfectly possible to read in even the
biggest file in little bits:
load trajectory {199000 200000 1} "/WORK/LAMMPS/meam/dump.xyz"
and create a loop around it that increments the first and last frame
of the strides with e.g. 1000 frames.
Now the printing part:
For frames that are counted as x.y, "load trajectory" seems to load
all the timesteps in 1.y, because it is just one file, did I get that
correctly?
Unfortunately for my case, it appears that the easiest image printing
solution via "write frames" only prints images of incrementing files
x and ignores the incrementing frames .y , is that correct?
I did get a bit further with extracting state information to
variables, the only thing I need to do is replace a string, I guess by
calling a fitting javascript command from jmol...
greetings, pim
On 6/23/09, Robert Hanson <hans...@stolaf.edu> wrote:
> Also, Jmol's load TRAJECTORY command allows you to use the same idea to
> load
> only specific trajectories from a set using the first, last, and "stride"
> familiar to AMBER users.
>
> load TRAJECTORY {first last stride} or ({i j k:l m..}) "filename"*
>
> Loads the specified subset of models from the file as a trajectory.
> **In the first syntax, first and last models along with a "stride" (step)
> are specified. Models are then read using an equivalent of for (i = first;
> i
> <= last; i = i + stride). Numbers start with 0 for the first model; -1 for
> last indicates "to the end of the file." For example, load MODELS {0 10 2}
> "..." would load six models, models 0, 2, 4, 6, 8, and 10.*
> *
>
> *So, Pim, can you explain those split command parameters? How do they
> indicate to do this?
>
> Bob
>
>
> On Tue, Jun 23, 2009 at 4:12 AM, pim schravendijk
> <pimli...@googlemail.com>wrote:
>
>> if you really really really would need to perform operations on all
>> the frames, you could also split the xyz before reading them in jmol:
>>
>> Say, if you have 10000 atoms in your system, and you want to split
>> your trajectory in batches of 100 frames, you could use the bash
>> command split:
>>
>> p...@mypc:~> split -a 4 -d -l 1000200 trajectory.xyz
>> trajectory.xyz.split.
>>
>> (in xyz there are probably 2 comment lines in each frame)
>>
>> this gives you trajectory.xyz.split.0001 trajectory.xyz.split.0002
>> etc. You could then load them separately or use a jmol script
>>
>> greetings, Pim
>>
>> On 6/19/09, Nicolas Bock <nicolasb...@gmail.com> wrote:
>> > Hi Bob,
>> >
>> > thanks for clarifying this.
>> >
>> > nick
>> >
>> >
>> > On Thu, Jun 18, 2009 at 22:12, Robert Hanson <hans...@stolaf.edu>
>> > wrote:
>> >
>> >> The maximum number of models in a file is limited by the format for
>> >> describing models:
>> >>
>> >> x.y
>> >>
>> >> where x is the file number and y is the model number in the file. The
>> >> limitation on y is 9999.
>> >>
>> >> If you have more than that number of models in a single file, you
>> >> should
>> >> consider using a trajectory and probably load only, say, every 5th
>> model.
>> >>
>> >> Bob
>> >>
>> >>
>> >> On Thu, Jun 18, 2009 at 8:53 AM, Nicolas Bock
>> >> <nicolasb...@gmail.com>wrote:
>> >>
>> >>> Hello list,
>> >>>
>> >>> I am trying to read an xyz file into Jmol that has a lot of frames.
>> Jmol
>> >>> doesn't load the file and on the java console I get this error
>> >>> message:
>> >>>
>> >>> 34106 models in this collection. Use getProperty "modelInfo" or
>> >>> getProperty "auxiliaryInfo" to inspect them.
>> >>> Exception in thread "QueueThread0"
>> >>> java.lang.ArrayIndexOutOfBoundsException: -32768
>> >>> at org.jmol.modelset.ModelLoader.iterateOverAllNewAtoms(Unknown
>> >>> Source)
>> >>> at org.jmol.modelset.ModelLoader.initializeModelSet(Unknown
>> >>> Source)
>> >>> at org.jmol.modelset.ModelLoader.<init>(Unknown Source)
>> >>> at org.jmol.viewer.ModelManager.setClientFile(Unknown Source)
>> >>> at org.jmol.viewer.Viewer.openClientFile(Unknown Source)
>> >>> at org.jmol.viewer.Viewer.getOpenFileError(Unknown Source)
>> >>> at org.jmol.viewer.Eval.load(Unknown Source)
>> >>> at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source)
>> >>> at org.jmol.viewer.Eval.runEval(Unknown Source)
>> >>> at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
>> >>> at
>> >>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown
>> >>> Source)
>> >>> at
>> >>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown
>> >>> Source)
>> >>> at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown
>> >>> Source)
>> >>> at java.lang.Thread.run(Thread.java:619)
>> >>>
>> >>> My completely uneducated guess is that Jmol uses a short signed int
>> >>> for
>> >>> the number of models and that's why it's failing, but of course I
>> >>> might
>> >>> be
>> >>> completely off here. What is the maximum number of models an xyz file
>> can
>> >>> have? Can one raise this limit?
>> >>>
>> >>> Thanks already, nick
>> >>>
>> >>>
>> >>>
>> >>>
>> ------------------------------------------------------------------------------
>> >>> Crystal Reports - New Free Runtime and 30 Day Trial
>> >>> Check out the new simplified licensing option that enables unlimited
>> >>> royalty-free distribution of the report engine for externally facing
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>> >>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> >>>
>> >>>
>> >>
>> >>
>> >> --
>> >> Robert M. Hanson
>> >> Professor of Chemistry
>> >> St. Olaf College
>> >> 1520 St. Olaf Ave.
>> >> Northfield, MN 55057
>> >> http://www.stolaf.edu/people/hansonr
>> >> phone: 507-786-3107
>> >>
>> >>
>> >> If nature does not answer first what we want,
>> >> it is better to take what answer we get.
>> >>
>> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>> >>
>> >>
>> >>
>> ------------------------------------------------------------------------------
>> >> Crystal Reports - New Free Runtime and 30 Day Trial
>> >> Check out the new simplified licensing option that enables unlimited
>> >> royalty-free distribution of the report engine for externally facing
>> >> server and web deployment.
>> >> http://p.sf.net/sfu/businessobjects
>> >> _______________________________________________
>> >> Jmol-users mailing list
>> >> Jmol-users@lists.sourceforge.net
>> >> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> >>
>> >>
>> >
>>
>>
>> --
>> Greetings, Pim
>> http://www.molmod.com
>>
>>
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>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
--
Greetings, Pim
http://www.molmod.com
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