[ADF-LIST] reaxff simulation

Fedor Goumans goumans at scm.com
Wed Sep 20 10:57:13 CEST 2017

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 
> <mailto: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
>     <mailto: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-workshops/advanced-2-day-reaxff-workshop/
>         <https://www.scm.com/adf-modeling-suite/adf-hands-on-workshops/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
>>
>>
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>
>         -- 
>         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 7625
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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
>
>
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-- 
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 7625
https://www.scm.com
https://twitter.com/SCM_Amsterdam
https://www.linkedin.com/company/software-for-chemistry-&-materials

  

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