Would you should me how to use Brenner potential to calculate the total energy and force of a free carbon cluster?

OpenKIM
1

Dear OPENKIM users:

I would like to learn how to calculate the total force and total energy of a free carbon cluster( without substrate) with a second generation Brenner potential( model_ArCHHeXe_BOP_AIREBO__MO_154399806462_000). If possible, can you show me how to modify the existing example, say ex_test_Ar_free_cluster_CLUSTER_F90 and replace the “Ar” with carbon and also change potential to Brenner. If elsewhere has instruction to my question already, would you please show me where is the documents or place so i can learn it. Many thanks.

Best
Peter

2

Hello Peter,

Using openkim-api-v1.5.0, it will be very easy to modify ex_test_Ar_free_cluster_CLUSTER_F03 to work with model_ArCHHeXe_BOP_AIREBO__MO_154399806462_000:

* cp -r ex_test_Ar_free_cluster_CLUSTER_F03 ex_test_C_free_cluster_CLUSTER_F03
* cd ex_test_C_free_cluster_CLUSTER_F03
* mv ex_test_Ar_free_cluster_CLUSTER_F03.F03 ex_test_C_free_cluster_CLUSTER_F03.F03
* Edit the Makefile to change the TEST_NAME
* Edit the descriptor.kim file to change the SUPPORTED_ATOM type from Ar to C
* Update the README file, as appropriate
* Edit ex_test_C_free_cluster_CLUSTER_F03.F03 as follows:
   - Search-and-replace: "Ar" with "C"
   - Change the lattice spacing (FCCspacing) and the crystal structure as
     appropriate for carbon.

That's it!

NOTE: The current version of the API is kim-api-v1.6.0. This is not backward compatible with previous version of the openkim-api package. Thus, we will soon release updated versions of all Models on openkim.org. So, keep an eye out for model_ArCHHeXe_BOP_AIREBO__MO_154399806462_001 (note the _001 version number) and upgrade when it is available.

Cheers,

Ryan S. Elliott

3

Dear Mr. Ryan:
I appreciate your kindness and instructions. May bother you with further questions if necessary.

With Best Regards
Tsung-Wen Yen

RyanElliott於 2014年8月11日星期一UTC+8下午9時21分15秒寫道：

4

Dear Mr.Ryan:
This is the error messages i got following your instructions:

  • Info (KIM_API_model::is_it_match): The following descriptor file line may not match with Test’s descriptor file.
    Neigh_IterAccess flag none []

  • Info (KIM_API_model::is_it_match): The following descriptor file line may not match with model_ArCHHeXe_BOP_AIREBO__MO_154399806462_000’s descriptor file.
    Neigh_BothAccess flag none []

  • Error (KIM_API_model::is_it_match): (virial,particleVirial,hessian,process_d1/2Edr) do not match:
    Do not match model_ArCHHeXe_BOP_AIREBO__MO_154399806462_000 and Test

Would it possible for you to solve it for me? Thank you in advance.

With Best Regards
Tsung-Wen Yen

Peter Yen於 2014年8月19日星期二UTC+8下午11時22分50秒寫道：

5

Hello,

Ah, yes. The model_ArCHHeXe_BOP_AIREBO__MO_154399806462_000 does not support computation of the virial. So, you will need to remove this part of the Test code.

To do so you should delete these lines from ex_test_Ar_free_cluster_CLUSTER_F03

real(c_double), pointer :: virial_global(:); type(c_ptr) :: pvirialglob

        "virial", pvirialglob, 1, &

   call c_f_pointer(pvirialglob, virial_global, [6])

   print '("Global Virial = ",3ES25.15)', (virial_global(I),I=1,3)
   print '(" ",3ES25.15)', (virial_global(I),I=4,6)

and this line from descriptor.kim:

virial double energy [6]

Cheers,

Ryan Elliott