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[lammps-users] Fwd: Fwd: [lammps-user]Conversion of VMD files to lammps file -Continued
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[lammps-users] Fwd: Fwd: [lammps-user]Conversion of VMD files to lammps file -Continued


From: sumit nagar <sn971489@...24...>
Date: Sun, 24 Sep 2017 13:49:17 +0530

Axel,

Thanks for your support and help i could get the entire file generated in VMD to be read by Lammps code by read_data command.The trick was to specify "atom_style full" before reading the VMD converted file .

Now i want to check the fracture strength of graphene in  "x" direction . I want a hint about the commands that i can use from the lammps documentation .Please also send me the link of good books that i need for learning about Molecular dynamics simulation .

With your patience and expertise i can easily solve my task .

Sumit ,Nagar
M.Tech (Production engg)
B.E (Production and Ind Engg)
MCSA 70-290 ,SQL (Oracle z -007)
ITIL certified ,MCAD 70-306
GATE 2006,2013

---------- Forwarded message ----------
From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sat, Sep 23, 2017 at 9:16 PM
Subject: Re: [lammps-users] Fwd: [lammps-user]Conversion of VMD files to lammps file -Continued
To: sumit nagar <sn971489@...24...>
Cc: LAMMPS Users Mailing List <lammps-users@lists.sourceforge.net>


On Sat, Sep 23, 2017 at 1:15 AM, sumit nagar <sn971489@...24...> wrote:
> Sir,
>
> Currently i am getting the error "Unexpected end of data file " while
> reading this file with read_data command  .This error means lammps hit the
> end of the data file while attempting to read a section. Something went
> wrong with the format of data file .I have checked the header information is
> correct and to the best of my knowledge the file also has correct body
> structure in accordance with atom_style"full" as all the information like
> atom ID,molecule ID,atom type q(charge on atom) and its x,y,z coordinates is
> present .What needs to be done to solve this problem ?

what i wrote in my previous response still applies, provided you do
not manually edit the VMD generated data file, as you are writing in
other e-mails to this mailing list.

axel.

> Sumit ,Nagar
> M.Tech (Production engg)
> B.E (Production and Ind Engg)
> MCSA 70-290 ,SQL (Oracle z -007)
> ITIL certified ,MCAD 70-306
> GATE 2006,2013
>
> ---------- Forwarded message ----------
> From: Axel Kohlmeyer <akohlmey@...24...>
> Date: Fri, Sep 22, 2017 at 8:21 PM
> Subject: Re: [lammps-users] [lammps-user]Conversion of VMD files to lammps
> file -Continued
> To: sumit nagar <sn971489@...43...4...>
> Cc: LAMMPS Users Mailing List <lammps-users@...396...sourceforge.net>
>
>
> On Fri, Sep 22, 2017 at 6:36 AM, sumit nagar <sn971489@...24...> wrote:
>> Sir,
>>
>> This time i have not included any bonds,dihedrals,impropers and angles in
>> my
>> graphene sheet created from  VMD and converted to lammps data by tk
>> console
>> .The data file looks like the attached file.It is giving  a error
>> Incorrect
>> atom format in data file.The documentation says this error comes when
>> number
>> of values per atom line in the data file is not consistent with atom style
>> .What needs to be changed in the data file ? Will i have to manually edit
>> it
>
> as explained in the documentation for read_data, the file format is
> dependent on the choice of atom style.
> the error message you quote indicates that this is not given in your
> data file. either you have to change the atom style in your LAMMPS
> input to match the format that you requested when generating the data
> file in VMD, or you have to tell VMD to write out the data file in a
> format consistent with the atom style you are using in LAMMPS.
> please refer to the relevant documentation for the commands in question.
>
> axel.
>
>> .
>>
>> Sumit ,Nagar
>> M.Tech (Production engg)
>> B.E (Production and Ind Engg)
>> MCSA 70-290 ,SQL (Oracle z -007)
>> ITIL certified ,MCAD 70-306
>> GATE 2006,2013
>>
>>
>> ------------------------------------------------------------------------------
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>>
>
>
>
> --
> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.