[ADF-LIST] reaxff simulation

Fedor Goumans goumans at scm.com
Wed Sep 20 12:48:14 CEST 2017

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 
> <mailto: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
>     <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 <mailto: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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>>>             ADFlist at scm.com <mailto:ADFlist at scm.com>
>>>             https://lists.scm.com/mailman/listinfo/adflist
>>>             <https://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 7625
>>             https://www.scm.com
>>             https://twitter.com/SCM_Amsterdam
>>             <https://twitter.com/SCM_Amsterdam>
>>             https://www.linkedin.com/company/software-for-chemistry-&-materials
>>             <https://www.linkedin.com/company/software-for-chemistry-&-materials>
>>
>>               
>>
>>
>>             _______________________________________________
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>>             <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 list
>>     ADFlist at scm.com <mailto:ADFlist at scm.com>
>>     https://lists.scm.com/mailman/listinfo/adflist
>>     <https://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 7625
>     https://www.scm.com
>     https://twitter.com/SCM_Amsterdam <https://twitter.com/SCM_Amsterdam>
>     https://www.linkedin.com/company/software-for-chemistry-&-materials
>     <https://www.linkedin.com/company/software-for-chemistry-&-materials>
>
>       
>
>
>     _______________________________________________
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>     https://lists.scm.com/mailman/listinfo/adflist
>     <https://lists.scm.com/mailman/listinfo/adflist>
>
>
>
>
> -- 
> 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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 Water-2017 model
 39       ! Number of general parameters
   50.0000 !Overcoordination parameter
    9.5469 !Overcoordination parameter
   26.5405 !Valency angle conjugation parameter
    1.7224 !Triple bond stabilisation parameter
    6.8702 !Triple bond stabilisation parameter
   60.4850 !C2-correction
    1.0588 !Undercoordination parameter
    4.6000 !Triple bond stabilisation parameter
   12.1176 !Undercoordination parameter
   13.3056 !Undercoordination parameter
  -70.5044 !Triple bond stabilization energy
    0.0000 !Lower Taper-radius
   10.0000 !Upper Taper-radius
    2.8793 !Not used
   33.8667 !Valency undercoordination
    6.0891 !Valency angle/lone pair parameter
    1.0563 !Valency angle
    2.0384 !Valency angle parameter
    6.1431 !Not used
    6.9290 !Double bond/angle parameter
    0.3989 !Double bond/angle parameter: overcoord
    3.9954 !Double bond/angle parameter: overcoord
   -2.4837 !Not used
    5.7796 !Torsion/BO parameter
   10.0000 !Torsion overcoordination
    1.9487 !Torsion overcoordination
   -1.2327 !Conjugation 0 (not used)
    2.1645 !Conjugation
    1.5591 !vdWaals shielding
    0.1000 !Cutoff for bond order (*100)
    2.1365 !Valency angle conjugation parameter
    0.6991 !Overcoordination parameter
   50.0000 !Overcoordination parameter
    1.8512 !Valency/lone pair parameter
    0.5000 !Not used
   20.0000 !Not used
    5.0000 !Molecular energy (not used)
    0.0000 !Molecular energy (not used)
    2.6962 !Valency angle conjugation parameter
  3    ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;#
            alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u.
            cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u.
            ov/un;val1;n.u.;val3,vval4
 H    0.8930   1.0000   1.0080   1.3550   0.0930   0.8203  -0.1000   1.0000
      8.2180  33.2894   1.0000   0.0000 121.1250   3.7248   9.6093   1.0000
     -0.1000   0.0000  61.6606   3.0408   2.4197   0.0003   1.0698   0.0000
    -19.4571   4.2733   1.0338   1.0000   2.8793   0.0000   0.0000   0.0000
 O    1.2450   2.0000  15.9990   2.3808   0.1038   1.0950   1.0548   6.0000
      9.7942  11.7301   4.0000  37.5000 116.0768   8.5000   8.3134   2.0000
      0.9049   0.1000  59.0626   3.5357   0.6653   0.0021   0.9745   0.0000
     -3.6039   2.7952   1.0493   4.0000   2.9225   0.0000   0.0000   0.0000
 X   -0.1000   2.0000   1.0080   2.0000   0.0000   1.0000  -0.1000   6.0000
     10.0000   2.5000   4.0000   0.0000   0.0000   8.5000   1.5000   0.0000
     -0.1000   0.0000  -2.3700   8.7410  13.3640   0.6690   0.9745   0.0000
    -11.0000   2.7466   1.0338   2.0000   2.8793   0.0000   0.0000   0.0000
  3    ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6
                        pbe2;pbo3;pbo4;n.u.;pbo1;pbo2;ovcorr
  1  1 153.3934   0.0000   0.0000  -0.4600   0.0000   1.0000   6.0000   0.7300
         6.2500   1.0000   0.0000   1.0000  -0.0790   6.0552   0.0000   0.0000
  2  2 142.2858 145.0000  50.8293   0.2506  -0.1000   1.0000  29.7503   0.6051
         0.3451  -0.1055   9.0000   1.0000  -0.1225   5.5000   1.0000   0.0000
  1  2 167.2086   0.0000   0.0000  -0.5770   0.0000   1.0000   6.0000   0.6019
         1.1413   1.0000   0.0000   0.0000  -0.0924   4.2778   0.0000   0.0000
  1    ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2
  1  2   0.0320   1.2896  10.9108   0.9215  -1.0000  -1.0000
  6    ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2
  1  1  1   0.0000  27.9213   5.8635   0.0000   0.0000   0.0000   1.0400
  2  2  2  80.7324  30.4554   0.9953   0.0000   1.6310  50.0000   1.0783
  1  2  2  75.6935  50.0000   2.0000   0.0000   1.0000   0.0000   1.1680
  1  2  1  85.1864   8.5843   2.2985   0.0000   2.9142   0.0000   2.0521
  2  1  2   0.0000  11.8475   2.7571   0.0000   0.0000   0.0000   2.9000
  1  1  2   0.0000   6.4269   2.8500   0.0000   0.0000   0.0000   1.0772
  6    ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n
  1  2  2  1   2.5000  -4.0000   0.9000  -2.5000  -1.0000   0.0000   0.0000
  1  2  2  2   0.8302  -4.0000  -0.7763  -2.5000  -1.0000   0.0000   0.0000
  2  2  2  2  -2.5000  -4.0000   1.0000  -2.5000  -1.0000   0.0000   0.0000
  0  1  1  0   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000
  0  1  2  0   0.0000   0.1000   0.0200  -2.5415   0.0000   0.0000   0.0000
  0  2  2  0   0.5511  25.4150   1.1330  -5.1903  -1.0000   0.0000   0.0000
  1    ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1
  2  1  2   2.1653  -3.6983   1.7831  17.0964


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