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Re: [lammps-users] Fwd: pcff force field
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Re: [lammps-users] Fwd: pcff force field


From: Rajesh <creativeidleminds@...24...>
Date: Wed, 4 Oct 2017 20:07:33 +0530

Dear Andrew,
Also when I put a graphene sheet inside a polymer and use msi2lmp to convert ,car file to lammps data file, I get errors regarding inconsistent number of connect with atom x type x. Any advice?

On Wed, Oct 4, 2017 at 7:12 AM, Rajesh <creativeidleminds@...24...> wrote:
Dear Andrew,
Thank you for your valuable efforts. I want know. 

On Oct 4, 2017 00:10, "Andrew Jewett" <jewett@...12...1937...> wrote:
Although not directly relevant to the original post, I wanted to
follow up on this thread for others who browse to it from the search
engine links.  I believe the COMPASS force field is now working in
moltemplate, but it is experimental.  There are some simple examples
with alkane chains in the "examples" directory.  Now that I have a
script that can convert MSI's .FRC files into moltemplate, I'll try
converting PCFF and CVFF next

Cheers
Andrew

   -- other caveats ---

   The moltemplate implementation of COMPASS (and later PCFF, and
CVFF) currently relies on the same incomplete force-field files (FRC
files) that "msi2lmp" uses.  Unfortunately this means that many force
field parameters and some atom types (such as sp2-carbons) have not
(yet) been publicly released and are not available.
    Currently you should run the "cleanup_moltemplate.sh" script after
running "moltemplate.sh system.lt".  Then manually check that the
"system.in.settings" and "system.in.charges" files which remain make
sense.  Specifically, you must check that the angle_coeff,
dihedral_coeff, bond_coeff commands are not full of zeros (in places
where they should not be zero.  This is another consequence of the
fact that the .FRC files I mentioned above are incomplete.)  It's a
good idea to also check that the charges in the "system.in.charges"
file seem reasonable (ie. not all zeros).  (There is a list of
warnings at the end of the "compass_published.lt" file.  You can check
to see if any of the bonds in your system are covered by these
warnings.)  Later on hopefully I'll add some automated way to warn
users when these problems arise, but now you should check for them
manually.

On Wed, Aug 23, 2017 at 8:19 PM, Andrew Jewett <jewett@...1937...> wrote:
> Currently, it's difficult to use PCFF.
>
> EMC (or msi2lmp+MaterialsStudio) might be your only options.  However,
> unfortunately both PCFF and CVFF use a complicated system
> "auto_equivalences" for looking up force field parameters according to
> atom type.  "msi2lmp" does not handle these correctly, and I suspect
> EMC might not either, but I could be wrong.  (Please correct me if I'm
> wrong.  People have complained to me about using both tools with PCFF
> force field.)
>
> About 6 months ago, we attempted to convert COMPASS PCFF and CVFF into
> moltemplate format, but it was taking a lot of time to figure out how
> to handle "auto_equivalences" correctly.  (A LOT of time.  A -month-
> of time devoted to this specific issue.)
> http://lammps.sandia.gov/threads/msg66954.html
> With Marcus Martin's help, I think we figured out how to solve the
> issue I still probably need another week to get this working, and I
> have other projects of much greater urgency (which threaten my
> livelihood) to work on.  I hope to get this working some time early
> next year when things have settled down.
>
> If you want to use a class2 force field, perhaps you will have better
> luck with COMPASS.  For now, try using EMC (or msi2lmp) with the
> compass force field.  COMPASS does not use "auto_equivalences"
>
> Good luck
>
> Andrew
>
>
>
> On Wed, Aug 23, 2017 at 7:58 PM, Vanessa Oklejas <voklejas@...24...> wrote:
>> Please, always email the lammps user list when responding.
>>
>> What version of lammps are you using? I believe the most current stable
>> version for download (17 August 2017) lists a force field file (*.frc) for
>> pcff in ./tools/msi2lmp/frc_files/. So I imagine that producing a
>> lammps-style data files using types from the pcff force field should be
>> possible. There are a few places where you might run into stumbling blocks
>> that I can think of off the top of my head: (1) I think pcff is a class 2
>> type force field, which I think requires a special flag when you invoke
>> msi2lmp. (2) It's possible MS might have additional atom types in their
>> version of pcff that are not present in the pcff.frc file that is part of
>> the lammps distribution.
>>
>> ---------- Forwarded message ---------
>> From: Rajesh <creativeidleminds@...24...>
>> Date: Wed, Aug 23, 2017 at 7:37 PM
>> Subject: Re: [lammps-users] pcff force field
>> To: Vanessa Oklejas <voklejas@...24...>
>>
>>
>> Dear Vanessa,
>> I tried with msi2lmp tool but it is inconsistent with pcff force field. Cant
>> we use vmd or moltemplate for the same?
>>
>> On Wed, Aug 23, 2017 at 10:55 PM, Rajesh <creativeidleminds@...24...>
>> wrote:
>>>
>>> Thank you Vanessa, will give it a try.
>>>
>>> On Wed, Aug 23, 2017 at 10:28 PM, Vanessa Oklejas <voklejas@...24...>
>>> wrote:
>>>>
>>>> See the msi2lmp tool located in the tools directory of your LAMMPS
>>>> package. You need to build this tool before you use it, but that's
>>>> relatively straightforward. See the README file in the msi2lmp directory for
>>>> specific instructions.
>>>>
>>>> On Wed, Aug 23, 2017 at 9:50 AM Rajesh <creativeidleminds@...24...>
>>>> wrote:
>>>>>
>>>>> Dear Dr Shan
>>>>>
>>>>> Thank you for your reply. Is there any tool that can convert material
>>>>> studio files to lammps input with all coefficients defined automatically.?
>>>>>
>>>>>
>>>>> Thanks
>>>>>
>>>>> On Wed, Aug 23, 2017 at 10:12 PM, Ray Shan <rshan@...1795...>
>>>>> wrote:
>>>>>>
>>>>>> Like anyother valence force fields, pcff is invoked via a combination
>>>>>> of pair, bond, angle, dihedral, and improper styles.  Pcff belongs to the
>>>>>> class2 family, so check the doc page with anything that is “class2”.
>>>>>>
>>>>>>
>>>>>>
>>>>>> Ray
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> From: Rajesh <creativeidleminds@...24...>
>>>>>> Date: Wednesday, August 23, 2017 at 9:37 AM
>>>>>> To: LAMMPS Users Mailing List <lammps-users@...7146.....e.net>
>>>>>> Subject: Re: [lammps-users] pcff force field
>>>>>>
>>>>>>
>>>>>>
>>>>>> Dear lammps users
>>>>>>
>>>>>>
>>>>>>
>>>>>> I am trying to simulate a polymer in lammps with pcff. Is there any
>>>>>> option for pcff field in lammps? How can I achieve this? I didn't find
>>>>>> anything in manual on pcff. Any help will be appreciated. I found some file
>>>>>> pcff.frc in lammps folder. I think pcff in not included a pair_style in
>>>>>> lammps?
>>>>>>
>>>>>>
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>>
>>>>>>
>>>>>> Rajesh
>>>>>
>>>>>
>>>>>
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