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Re: [ESPResSo-users] Fwd: Problem with output
From: |
Ulf Schiller |
Subject: |
Re: [ESPResSo-users] Fwd: Problem with output |
Date: |
Wed, 4 May 2016 13:07:45 -0400 |
User-agent: |
Mozilla/5.0 (X11; Linux i686; rv:38.0) Gecko/20100101 Thunderbird/38.1.0 |
Hi,
Please find in the user's guide how to set the seed for ESPResSo's
(pseudo-)random number generator. Hint: Look up the command 't_random'.
Hope this helps,
Ulf
On 05/04/2016 11:05 AM, Nairhita Samanta wrote:
> Please find the attached code (MWE), which is producing the same
> trajectory over and over again.
>
> On Wed, May 4, 2016 at 4:56 PM, Peter Košovan
> <address@hidden <mailto:address@hidden>> wrote:
>
> Dear Nairitha,
>
> please check the following link:
> https://en.wikipedia.org/wiki/Minimal_Working_Example
>
> peter
>
> On Wed, May 4, 2016 at 1:17 PM, Nairhita Samanta
> <address@hidden <mailto:address@hidden>> wrote:
>
> This is how I place the polymer
>
> for {set i 0} {$i < $n_poly} {incr i} {
> polymer 1 $n_mono $l_poly start [expr
> ((($fact+1)*$n_janus)+$i*$n_mono)] mode SAW 0.5 5000000 types 3
> FENE 0
> }
>
> Even if the polymers are not placed randomly initially, after
> warm up, they should follow sufficiently distinct trajectory in
> different run.
>
>
> On Wed, May 4, 2016 at 4:42 PM, Peter Košovan
> <address@hidden
> <mailto:address@hidden>> wrote:
>
> Please provide a minimal working example, otherwise we can
> only speculate about the possible reasons.
>
> Greetings,
>
> peter
>
> On Wed, May 4, 2016 at 1:11 PM, Rohit Goswami
> <address@hidden <mailto:address@hidden>> wrote:
>
> Perhaps the polymer placement loop has no incorporation
> of the random variable?
>
> Rohit Goswami
> B.Tech II
> Dept. Of Chemical Engineering
> HBTI Kanpur
>
> On Wed, May 04, 2016 at 4:39 PM, Nairhita Samanta
> <address@hidden <mailto:address@hidden>> wrote:
>
> Hi Peter!
>
> This problem was not arising when I had a simpler
> system. However if I have many polymers in a system,
> this is happening. Although the volume fraction is
> same from the system with simple particles.
>
> Regards,
> Nairhita
>
> On Wed, May 4, 2016 at 4:30 PM, Peter Košovan
> <address@hidden
> <mailto:address@hidden>> wrote:
>
> Yes, there is something you might do:
> 1. reduce your simulation script to a minimal
> working example which reproduces the problem
> 2. attach it to your mailing
>
> If you start with different seeds, you certainly
> get different trajectories. But there could be
> other reasons why your script is not doing what
> you want it to.
>
> Greetings,
>
> peter
>
> On Wed, May 4, 2016 at 12:53 PM, Nairhita
> Samanta <address@hidden
> <mailto:address@hidden>> wrote:
>
>
> Hi everyone!
>
> I am providing seed to the code in the
> following way
>
> expr srand ([pid])
>
> But the configurations are still coming to
> be identical every time. Is there anything
> else I have to do?
>
> Regards,
> Nairhita
>
>
> On Sun, May 1, 2016 at 11:12 AM, Nairhita
> Samanta <address@hidden
> <mailto:address@hidden>> wrote:
>
> Thank you everyone for your quick
> response. I will look into this book and
> the script. If the problem still
> persists, I will mail again.
>
> Regards,
> Nairhita
>
> On Apr 30, 2016 9:22 PM, "Florian Weik"
> <address@hidden
> <mailto:address@hidden>> wrote:
>
> Hi,
> if you do not set a seed, Espresso
> and the random numbers provided by
> Espresso in TCL (by the t_random
> command) behave deterministically,
> which means that if you do not set a
> different seed, the script will
> produce the same output. I am not
> sure how rand, which is provided by
> TCL behaves.
>
> If you are not sure about PRNGs and
> their meaning for MD simulations you
> should look that up in a standard
> textbook like Frenkel and Smit.
>
> Hope that helps,
> Florian
>
> On Apr 30, 2016 3:34 PM, "Nairhita
> Samanta" <address@hidden
> <mailto:address@hidden>> wrote:
>
> Hi all!
>
> I have this strange
> problem with my code. Whenever I
> am running a code, it is giving
> me the exact same output, i.e.
> the position and velocity of
> each particle at each time step
> coming to be identical from my
> previous run. I have changed the
> name of the input and output
> files, but every time I am
> seeing the same problem. If you
> have any solution regarding this
> problem, please suggest.
>
> Regards,
> Nairhita
>
>
>
>
>
>
> --
> Dr. Peter Košovan
>
> Department of Physical and Macromolecular Chemistry
> Faculty of Science, Charles University in
> Prague, Czech Republic
>
> Katedra fyzikální a makromolekulární chemie
> Přírodovědecká fakulta Univerzity Karlovy v Praze
>
> www.natur.cuni.cz/chemistry/fyzchem/
> <http://www.natur.cuni.cz/chemistry/fyzchem/>
> Tel. +420221951290 <tel:%2B420221951290>
> Fax +420224919752
>
>
>
>
>
> --
> Dr. Peter Košovan
>
> Department of Physical and Macromolecular Chemistry
> Faculty of Science, Charles University in Prague, Czech Republic
>
> Katedra fyzikální a makromolekulární chemie
> Přírodovědecká fakulta Univerzity Karlovy v Praze
>
> www.natur.cuni.cz/chemistry/fyzchem/
> <http://www.natur.cuni.cz/chemistry/fyzchem/>
> Tel. +420221951290 <tel:%2B420221951290>
> Fax +420224919752
>
>
>
>
>
> --
> Dr. Peter Košovan
>
> Department of Physical and Macromolecular Chemistry
> Faculty of Science, Charles University in Prague, Czech Republic
>
> Katedra fyzikální a makromolekulární chemie
> Přírodovědecká fakulta Univerzity Karlovy v Praze
>
> www.natur.cuni.cz/chemistry/fyzchem/
> <http://www.natur.cuni.cz/chemistry/fyzchem/>
> Tel. +420221951290
> Fax +420224919752
>
>
--
Dr. Ulf D. Schiller
Assistant Professor
Department of Materials Science and Engineering
Clemson University
161 Sirrine Hall
Clemson, SC 29634
Office: 299c Sirrine Hall
Phone: 1-864-656-2669
Fax: 1-864-656-5973
- Re: [ESPResSo-users] Problem with output, (continued)
- Re: [ESPResSo-users] Problem with output, Nairhita Samanta, 2016/05/03
- Re: [ESPResSo-users] Problem with output, Ulf Schiller, 2016/05/03
- [ESPResSo-users] Fwd: Problem with output, Nairhita Samanta, 2016/05/04
- Re: [ESPResSo-users] Fwd: Problem with output, Peter Košovan, 2016/05/04
- Re: [ESPResSo-users] Fwd: Problem with output, Nairhita Samanta, 2016/05/04
- Re: [ESPResSo-users] Fwd: Problem with output, Rohit Goswami, 2016/05/04
- Re: [ESPResSo-users] Fwd: Problem with output, Peter Košovan, 2016/05/04
- Re: [ESPResSo-users] Fwd: Problem with output, Nairhita Samanta, 2016/05/04
- Re: [ESPResSo-users] Fwd: Problem with output, Peter Košovan, 2016/05/04
- Re: [ESPResSo-users] Fwd: Problem with output, Nairhita Samanta, 2016/05/04
- Re: [ESPResSo-users] Fwd: Problem with output,
Ulf Schiller <=