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


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 25 Sep 2017 09:24:41 -0400

On Sun, Sep 24, 2017 at 4:19 AM, sumit nagar <sn971489@...24...> wrote:
> 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 .

if you are asking a new question, please follow common mailing list
courtesy and don't reply to an existing discussion, but post a new
e-mail with a new, matching subject line.

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

you seem to be thinking, that i can fill in for your adviser and
explain to you how to do your research. i won't.
i will respond to questions, that are specific to how LAMMPS is
implemented and that cover topics i am interested in.

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: 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@...24...>
>> Cc: LAMMPS Users Mailing List <lammps-users@lists.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
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> lammps-users mailing list
>>> lammps-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>>
>>
>>
>>
>> --
>> 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
>> _______________________________________________
>> lammps-users mailing list
>> lammps-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>
>
>
>
> --
> 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
> _______________________________________________
> lammps-users mailing list
> lammps-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>



-- 
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.