Re: [ESPResSo-users] Fwd: Problem with output

[Ulf Schiller]

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
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