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Re: [lammps-users] Electric_field


From: Mohammad Izadi <izadi0511@...24...>
Date: Thu, 3 Aug 2017 10:02:16 +0430

Dear Axel Kohlmeyer

 

My purpose is also researching and I have known that the mailing list goal is validating and developing models to make confidence about them. I have been investigating on molecular dynamics simulation (exactly on the reactive force field ReaxFF) since four years ago. In my MSc thesis I spend the whole time to investigate the ReaxFF potential functions, it applications. Finally I did some reactive simulations on the Flame Synthesis processes (with and without imposing the constant external electric field on my simulation box). As imposing the external electric field, I have recognized the total energy of the system is not conserved in the ReaxFF Fortran source code. I have extensive research about this phenomenon (e.g. elicit the equation of the electric field from the source code “efih=vfieldx*23.02*c1c*ch(i1)*c(i1,1)”, investigation of this equation and its constant conversion factors, how the external electric field effect on the reactive simulations, contact to experts of this field and also to the developer of the ReaxFF). And in my PhD thesis I have been deciding to use the Lammps/reax/c for my research since about one year ago. So, all of us have similar tasks.

 

I had learned to install and run simulations on Lammps in my own limit and I have read the whole document about electric field command, fix addforce command, compute command, variable command, region command and other related commands which I thing they are relating to the external electric field. In my last email I told you “I know that the external electric field in my simulations is a classical approximation and it just impose electric forces on my charged elements” so I knew that we are not exactly applying an electric field!!

 

By the way, I have some technical questions about this subject in my mind:

 

1- Is my electric field command in the input file correct or not?

 

2- Is the total energy conserve in the lammps/reax/c simulations if we apply an external electric field or not? And what is a solution for this probably problem?

 

3- Is the result of an external electric field in lammps/reax/c runs from this equation “efih=vfieldx*23.02*c1c*ch(i1)*c(i1,1)” in subroutine efield reax code or “F = E.Q” in common lammps command?

I think the second one is the answer since when I compare my results from the serial ReaxFF Fortarn code, the electric field in the lammps run is far weaker than the electric field in the ReaxFF Fortarn code in the absolutely similar conditions.

 

4- If the answer of the last question is the first one, why the electric field in the lammps run is much weaker?

 

5- It is correct that the external electric field cannot include in the charge equilibration scheme in the ReaxFF force field potential but I think the resulted forces on the partial charged particles can cleavage or deform bonds and molecular structures and finally can affect resulted fragments or products of the chemical reactions. So, as the products of a chemical reaction are changed, the charge equilibration of the ReaxFF produce other partial charges for the atoms in molecules due to the change of atomic chemical environments. On the other words, the external electric field can indirectly affect the atomic partial charges in the molecules and fragments!

 

If you can, please answer to this questions and likely other questions that I will ask in lammps-mailing-list and if you cannot, you don’t have to answer my questions.

 

Mohammad Ebrahim Izadi 


On Thu, Aug 3, 2017 at 9:56 AM, Mohammad Izadi <izadi0511@...24...> wrote:

Dear Axel Kohlmeyer

 

My purpose is also researching and I have known that the mailing list goal is validating and developing models to make confidence about them. I have been investigating on molecular dynamics simulation (exactly on the reactive force field ReaxFF) since four years ago. In my MSc thesis I spend the whole time to investigate the ReaxFF potential functions, it applications. Finally I did some reactive simulations on the Flame Synthesis processes (with and without imposing the constant external electric field on my simulation box). As imposing the external electric field, I have recognized the total energy of the system is not conserved in the ReaxFF Fortran source code. I have extensive research about this phenomenon (e.g. elicit the equation of the electric field from the source code “efih=vfieldx*23.02*c1c*ch(i1)*c(i1,1)”, investigation of this equation and its constant conversion factors, how the external electric field effect on the reactive simulations, contact to experts of this field and also to the developer of the ReaxFF). And in my PhD thesis I have been deciding to use the Lammps/reax/c for my research since about one year ago. So, all of us have similar tasks.

 

I had learned to install and run simulations on Lammps in my own limit and I have read the whole document about electric field command, fix addforce command, compute command, variable command, region command and other related commands which I thing they are relating to the external electric field. In my last email I told you “I know that the external electric field in my simulations is a classical approximation and it just impose electric forces on my charged elements” so I knew that we are not exactly applying an electric field!!

By the way, I have some technical questions about this subject in my mind:

1- Is my electric field command in the input file correct or not?

2- Is the total energy conserve in the lammps/reax/c simulations if we apply an external electric field or not? And what is a solution for this probably problem?

3- Is the result of an external electric field in lammps/reax/c runs from this equation “efih=vfieldx*23.02*c1c*ch(i1)*c(i1,1)” in subroutine efield reax code or “F = E.Q” in common lammps command?

I think the second one is the answer since when I compare my results from the serial ReaxFF Fortarn code, the electric field in the lammps run is far weaker than the electric field in the ReaxFF Fortarn code in the absolutely similar conditions.

4- If the answer of the last question is the first one, why the electric field in the lammps run is much weaker?

5- It is correct that the external electric field cannot include in the charge equilibration scheme in the ReaxFF force field potential but I think the resulted forces on the partial charged particles can cleavage or deform bonds and molecular structures and finally can affect resulted fragments or products of the chemical reactions. So, as the products of a chemical reaction are changed, the charge equilibration of the ReaxFF produce other partial charges for the atoms in molecules due to the change of atomic chemical environments. On the other words, the external electric field can indirectly affect the atomic partial charges in the molecules and fragments!

If you can, please answer to this questions and likely other questions that I will ask in lammps-mailing-list and if you cannot, you don’t have to answer my questions.

Mohammad Ebrahim Izadi 


On Thu, Aug 3, 2017 at 4:02 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Wed, Aug 2, 2017 at 1:14 PM, Mohammad Izadi <izadi0511@...24...> wrote:

Dear lammps users,

 

I’m using lammps/reax/c for simulating decomposition of an organic compound under a constant electric field. From outputs (I mean dump.xyz and specie) I recognized that the electric field is worked but I’m not sure that it’s exactly correct or not. Please look into my input file and make recommends if it needs. This is my input file:

​you seem to be confusing the purpose of a mailing list. it is most certainly not an input file approval or debugging/correction service​.
in other words, it is part of the job of a researcher to validate that a chosen model is giving results at the expected level of accuracy and usefulness.

please let me repeat what i have pointed out in an earlier e-mail response. when you are using fix efield, you are not exactly applying an electric field, you are adding a force to all charged atoms, that depends on the product of the (partial) charge of each atom and a given force constant with conversion factor.
this does not include the electric field in the charge equilibration (only indirectly over response to the force generated by fix efield) and there is no screening or other effects taken under consideration.

​axel.​


 

 

echo            both

units                real

dimension 3

boundary  p p p

atom_style       charge

read_data        NBCom.data

#read_restart    restart22

restart 500      restart11 restart22

pair_style         reax/c NULL

pair_coeff        * * ffield.reax.rdx C H O N

compute reax all pair reax/c

variable eb        equal c_reax[1]

variable ea        equal c_reax[2]

variable et         equal c_reax[9]

variable ew       equal c_reax[11]

variable efi       equal c_reax[13]

variable eqeq    equal c_reax[14]

#define a region for efield

region    elecf block 0.0 100.0 0.0 100.0 0.0 100.0 units box

group     elf region elecf

neighbor          2 bin

neigh_modify  every 10 delay 0 check no

velocity        all create 300 235485 mom yes rot yes

fix                    1 all nvt temp 300 300 25    ###########timestep*100=25

fix             2 all qeq/reax 1 0.0 10.0 1e-6 reax/c

fix             3 all reax/c/species 1 50 250 species.txt

fix             4 elf efield 2.0 0.0 0.0 region elecf

fix_modify      4 energy yes

thermo_style    custom   step    atoms   temp   press   vol   etotal   ke   pe   v_eb   v_ea  v_et   v_ew v_efi   v_eqeq

thermo          250

timestep           0.25

dump               1 all atom 30 dump.reax.rdx

dump               2 all xyz  30 dumpnvt.xyz

run    30000


Thanks in advance  

Mohammad Ebrahim Izadi 


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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.