[ADF-LIST] reaxff simulation

Praveen Kumar pravink068 at gmail.com
Wed Sep 20 13:22:11 CEST 2017

Dear Fedor,

Thanks a lot for your kind help, it works for me. I am not able to get new
python script. Could you please provide me the python script file or link
of the script file?


Regards,
Praveen

On Wed, Sep 20, 2017 at 4:18 PM, Fedor Goumans <goumans at scm.com> wrote:

> Dear Praveen,
>
> Sorry again. My colleague Michal pointed out this is a python2 script
> while we're currently shipping a python 3 stack.
> He has updated the script, which you can download from the same place.
> Attached is the cleaned up force field file, but please also check if the
> new script works for you, too.
>
> Best wishes,
> Fedor
>
>
> On 9/20/2017 11:40 AM, Praveen Kumar wrote:
>
> 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
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>>>>
>>>>
>>>
>>>
>>> --
>>> 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
>
>
> _______________________________________________
> 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
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