[ADF-LIST] reaxff simulation

Praveen Kumar pravink068 at gmail.com
Wed Sep 20 11:40:37 CEST 2017

Dear Fedor,

I tried to sort out this problem, but I am not able to resolve it (as i am
getting following error with every forcefield, as i tried it with the
advanced workshop materilas also).








*startpython cleanreaxffforcefield.py -i water.ff -o new  File
"cleanreaxffforcefield.py", line 36    print "Forcefield File contains %i
lines" %(nlines)                                            ^SyntaxError:
invalid syntax*
I am sending the same forcefield parameter file with this e-mail. Please
find the attachment.



Regards,
Praveen






On Wed, Sep 20, 2017 at 2:27 PM, Fedor Goumans <goumans at scm.com> wrote:

> Dear Praveen,
>
> My mistake. The script for cleaning up the force field is called
> cleanreaxffforcefield.py and I can't find it in our standard distribution
> in the scripting directories, but it is available in the ReaxFF advanced
> workshop materials.
> For your convenience I've uploaded it here:
> https://www.scm.com/wp-content/uploads/cleanreaxffforcefield.py
> You would run it as:
>  $ADFBIN/startpython cleanreaxffforcefield.py -i [input ffield] -o
> [output ffield]
>
> If you still have problems, please send us the force field file (
> support at scm.com) and maybe we can help you figure it out.
>
> Best wishes,
> Fedor
>
>
> On 9/20/2017 10:35 AM, Praveen Kumar wrote:
>
> Dear Fedor,
>
> I checked all the things as you mentioned in your previous e-mail. But, I
> am getting the same error.
>
>
> When I ran the python script by using this command* "startpython
> checkreaxffforcefield.py H.ff"*
> Then I got this:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *ForceField file: H.ff ngenparams: 39 natoms: 3 atoms: H O X dummyatoms:
> X nbonds: 3 defined bonds: H-H O-O H-O missing bonds: noffdiags: 1 defined
> offdiags: H-O missing offdiags: nangles: 6 defined angles: H-H-H O-O-O
> H-O-O H-O-H O-H-O H-H-O missing angles: ndihedrals: 6 defined dihedrals:
> H-O-O-H H-O-O-O O-O-O-O *-H-H-* *-H-O-* *-O-O-* missing dihedrals: nhbonds:
> 1 defined hbonds: O-H-O missing hbonds: H-H-H H-H-O*
>
> and when I am running my calculation, then I am getting an error:
>
>
> *Error reading forcefield file ERROR DETECTED*
>
> These parameters are taken from one of the previous study named as "*Second-Generation
> ReaxFF Water Force Field: Improvements in the Description of Water Density
> and OH-Anion Diffusion*".
>
> I am using the trial version of ADF (is error coming due to that reason?).
>
>
> Any suggestion will be helpful.
>
>
>
> Regards,
> Praveen
>
>
>
>
>
>
> On Wed, Sep 20, 2017 at 1:23 PM, Praveen Kumar <pravink068 at gmail.com>
> wrote:
>
>> Dear Fedor,
>>
>> Thanks a lot.
>>
>> Regards,
>> Praveen
>>
>> On Wed, Sep 20, 2017 at 1:15 PM, Fedor Goumans <goumans at scm.com> wrote:
>>
>>> Dear Praveen,
>>>
>>> The current ReaxFF implementation is very sensitive to the formatting of
>>> the force field file, for historical reasons from Prof. van Duin's original
>>> standalone ReaxFF code.
>>> We ship a python script that can help you with checking the format of
>>> your file. You can find it in your ADFHOME in the scripting directory. It
>>> is called checkreaxffforcefield.py
>>> Use $ADFBIN/startphyton to use the python stack we ship.
>>>
>>> It is advisable to use this script it whenever you save or modify your
>>> own force field. See also the advanced ReaxFF workshop materials on
>>> https://www.scm.com/adf-modeling-suite/adf-hands-on-workshop
>>> s/advanced-2-day-reaxff-workshop/
>>>
>>> Best wishes,
>>> Fedor
>>>
>>>
>>> On 9/20/2017 8:59 AM, Praveen Kumar wrote:
>>>
>>> Hi,
>>>
>>> I want to simulate water model using Reaxff. I have all the forcefield
>>> parameter. But if  I am including these parameters as mentioned in SCM
>>> included forcefield *"So if you have the force field information from
>>> somewhere else you can just use it (save it in a text file, and select it
>>> in ADFinput via the Other... option)." *I am getting the following
>>> error.
>>>
>>> Error reading forcefield file
>>> ERROR DETECTED
>>>
>>>
>>> Please help me to sort out this problem.
>>>
>>> Regards
>>> PRAVEEN KUMAR
>>> Research scholar
>>> INDIAN INSTITUTE OF SCIENCE
>>> EDUCATION AND RESEARCH PUNE, INDIA
>>>
>>>
>>> _______________________________________________
>>> ADFlist mailing listADFlist at scm.comhttps://lists.scm.com/mailman/listinfo/adflist
>>>
>>>
>>> --
>>> Dr. T. P. M. (Fedor) Goumans
>>> Business Developer
>>> Software for Chemistry & Materials
>>> Vrije Universiteit, FEW, Theoretical Chemistry
>>> De Boelelaan 1083
>>> 1081 HV Amsterdam, The Netherlands
>>> T +31 20 598 7625https://www.scm.comhttps://twitter.com/SCM_Amsterdamhttps://www.linkedin.com/company/software-for-chemistry-&-materials
>>>
>>>
>>> _______________________________________________
>>> ADFlist mailing list
>>> ADFlist at scm.com
>>> https://lists.scm.com/mailman/listinfo/adflist
>>>
>>>
>>
>>
>> --
>> PRAVEEN KUMAR
>> Research scholar
>> INDIAN INSTITUTE OF SCIENCE
>> EDUCATION AND RESEARCH PUNE
>>
>
>
>
> --
> PRAVEEN KUMAR
> Research scholar
> INDIAN INSTITUTE OF SCIENCE
> EDUCATION AND RESEARCH PUNE
>
>
> _______________________________________________
> ADFlist mailing listADFlist at scm.comhttps://lists.scm.com/mailman/listinfo/adflist
>
>
> --
> Dr. T. P. M. (Fedor) Goumans
> Business Developer
> Software for Chemistry & Materials
> Vrije Universiteit, FEW, Theoretical Chemistry
> De Boelelaan 1083
> 1081 HV Amsterdam, The Netherlands
> T +31 20 598 7625https://www.scm.comhttps://twitter.com/SCM_Amsterdamhttps://www.linkedin.com/company/software-for-chemistry-&-materials
>
>
> _______________________________________________
> ADFlist mailing list
> ADFlist at scm.com
> https://lists.scm.com/mailman/listinfo/adflist
>
>


-- 
PRAVEEN KUMAR
Research scholar
INDIAN INSTITUTE OF SCIENCE
EDUCATION AND RESEARCH PUNE
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.scm.com/pipermail/adflist/attachments/20170920/47042fcf/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: water.ff
Type: application/octet-stream
Size: 4489 bytes
Desc: not available
URL: <https://lists.scm.com/pipermail/adflist/attachments/20170920/47042fcf/attachment-0001.obj>


More information about the ADFlist mailing list