Dump Data

Hi all,

I am running a simulation to deform a polymer. Now, I want to dump
the data in the logarithmic scale time steps. I mean, I want to
dump the data in those time steps which will be expressed as power
of '2' . Can you kindly share any way out ?

Thanking you,

Best,

Hi all,

I am running a simulation to deform a polymer. Now, I want to dump
the data in the logarithmic scale time steps. I mean, I want to
dump the data in those time steps which will be expressed as power
of '2' . Can you kindly share any way out ?

as always, please start by reading the documentation, particularly the
description of the "dump_modify every" command.

axel.

Hello,

I hope it is okay if I ask a similar question; indeed, having read the documentation, "dump_modify every" gives a possibility of having dump files written at defined timesteps, which is great. However, what can be done to the thermo output- for instance the etotal as a function of time? Is there a way of having thermo output printed in the same way, or perhaps just writing a text file with logarithmic time and etotal, for example, without all the unnecessary (for this specific case) dump file attributes?

With best wishes,
Anna

Hi Anna,

The thermo command accepts variables in the same way as dump_modify every. (http://lammps.sandia.gov/doc/thermo.html)

Thanks for that Niall, I think I was so confused about all the possible options that did not notice the elephant.

With best wishes,
Anna

Hi all,

I am running a simulation to deform a polymer. Now, I want to dump
the data in the logarithmic scale time steps. I mean, I want to
dump the data in those time steps which will be expressed as power
of '2' . Can you kindly share any way out ?

as always, please start by reading the documentation, particularly the
description of the "dump_modify every" command.

Thanks Axel.
I have just gone through the documentation and aptly follow the same
command lines which have been listed there. Which is the following :

"
variable f file tmp.times
variable s equal next(f)
dump 2 all atom 100 tmp.dump
dump_modify 2 every v_s
"

where my tmp.times file looks like

   1
   2
   4
   8
  16
  32
  64
128
256
512
1024

That is, I want to dump the configurations in those time steps that are
listed in the 'tmp.times' file. When I am trying to run it, it gives an
error message :
"ERROR: Dump every variable returned a bad timestep (output.cpp:310)"

Now, according to the documentations
provided in the 'dump' page it says.

"dump 2 all atom 100 tmp.dump " means it has to dump after every
  100 time steps whereas I want to dump them according the steps that are
  tabulated in the 'tmp'times' file. So are not they self contradictory ?

Thanking you,

Best,
******************
Saikat Basu
Senior Research Fellow
Room no:C/312,Centenary Building
Department of Solid State Physics
Indian Association for the Cultivation of Science,
Jadavpur
Kolkata-700032
Ph no- 03324734971(extn- 2114)

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--
Dr. Axel Kohlmeyer akohlme[email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

Thanking you,

Best,

Hi all,

I am running a simulation to deform a polymer. Now, I want to dump
the data in the logarithmic scale time steps. I mean, I want to
dump the data in those time steps which will be expressed as power
of '2' . Can you kindly share any way out ?

as always, please start by reading the documentation, particularly the
description of the "dump_modify every" command.

Thanks Axel.
I have just gone through the documentation and aptly follow the same
command lines which have been listed there. Which is the following :

"
variable f file tmp.times
variable s equal next(f)
dump 2 all atom 100 tmp.dump
dump_modify 2 every v_s
"

where my tmp.times file looks like

   1
   2
   4
   8
  16
  32
  64
128
256
512
1024

That is, I want to dump the configurations in those time steps that are
listed in the 'tmp.times' file. When I am trying to run it, it gives an
error message :
"ERROR: Dump every variable returned a bad timestep (output.cpp:310)"

it works fine for me, when i add this to the melt example, for
instance. that being said, using a file based variable seems overkill
for such a simple scale of steps. why don't you just use the logfreq()
function, that was added specifically for this purpose?

Now, according to the documentations
provided in the 'dump' page it says.

"dump 2 all atom 100 tmp.dump " means it has to dump after every
  100 time steps whereas I want to dump them according the steps that are
  tabulated in the 'tmp'times' file. So are not they self contradictory ?

what the hell has this got to do with it? and where is the
contradiction? you define the dump with a fixed frequency and *then*
you *modify* its frequency. seems very straightforward to me.

axel.

Hi all,

I am running a simulation to deform a polymer. Now, I want to dump
the data in the logarithmic scale time steps. I mean, I want to
dump the data in those time steps which will be expressed as power
of '2' . Can you kindly share any way out ?

as always, please start by reading the documentation, particularly the
description of the "dump_modify every" command.

Thanks Axel.
I have just gone through the documentation and aptly follow the same
command lines which have been listed there. Which is the following :

"
variable f file tmp.times
variable s equal next(f)
dump 2 all atom 100 tmp.dump
dump_modify 2 every v_s
"

where my tmp.times file looks like

   1
   2
   4
   8
  16
  32
  64
128
256
512
1024

That is, I want to dump the configurations in those time steps that are
listed in the 'tmp.times' file. When I am trying to run it, it gives an
error message :
"ERROR: Dump every variable returned a bad timestep (output.cpp:310)"

it works fine for me, when i add this to the melt example, for
instance. that being said, using a file based variable seems overkill
for such a simple scale of steps. why don't you just use the logfreq()
function, that was added specifically for this purpose?

The next(f) suffices my purpose. It's working fine now. Thanks very much.

Now, according to the documentations
provided in the 'dump' page it says.

"dump 2 all atom 100 tmp.dump " means it has to dump after
every
  100 time steps whereas I want to dump them according the steps that
are
  tabulated in the 'tmp'times' file. So are not they self contradictory
?

what the hell has this got to do with it? and where is the
contradiction? you define the dump with a fixed frequency and *then*
you *modify* its frequency. seems very straightforward to me.

Yes, I was thinking in the wrong way. I did not specify two more timesteps
than my required run length. that is why it was not working. Now its
working fine .

thanks a lot.

Thanking you,

Best,
******************
Saikat Basu
Senior Research Fellow
Room no:C/312,Centenary Building
Department of Solid State Physics
Indian Association for the Cultivation of Science,
Jadavpur
Kolkata-700032
Ph no- 03324734971(extn- 2114)

------------------------------------------------------------------------------
LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
1,500+ hours of tutorials including VisualStudio 2012, Windows 8,
SharePoint
2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack
includes
Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/22/13.
http://pubads.g.doubleclick.net/gampad/clk?id=64545871&iu=/4140/ostg.clktrk
_______________________________________________
lammps-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/lammps-users

--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

Thanking you,

Best,
******************
Saikat Basu
Senior Research Fellow
Room no:C/312,Centenary Building
Department of Solid State Physics
Indian Association for the Cultivation of Science,
Jadavpur
Kolkata-700032
Ph no- 03324734971(extn- 2114)

--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

Thanking you,

Best,