Dipoles and polarization

[Paolo Pegolo]

Hello,

I would like to compute total and molecular dipoles of MB-pol water.

Is it possible to obtain these quantities from LAMMPS simulations? 

Thank you,

Paolo

[CH HO]

Hi Paolo,

Yes it is possible. In order to print this, you need to run the simulations with fix mbx command. The fix mbx command is something like this:

fix             3 all mbx 2 352 dp1 19 h2o json mbx.json print/settings print/dipoles

(The first "3" is the fix index. I have 352 point charges and 19 water molecules described by MB-pol.)

Put the following lines after the fix mbx command:

variable dipx atom f_3[7]/0.2081943
variable dipy atom f_3[8]/0.2081943
variable dipz atom f_3[9]/0.2081943
variable dipnorm atom sqrt(f_3[7]*f_3[7]+f_3[8]*f_3[8]+f_3[9]*f_3[9])/0.2081943

Lastly, we need to dump it into some output file. The command is something like this:

dump            dip all custom 20 dump.dipoles id type v_dipx v_dipy v_dipz v_dipnorm

-Hank

Paolo Pegolo 在 2023年2月21日 星期二下午5:08:36 [UTC-8] 的信中寫道：

[Paolo Pegolo]

Dear Hank,

Thank you for your answer.

I tried the above commands for a system of 277 water molecules. My input thus contains the following lines:

fix 2 all mbx 1 277 h2o print/settings json "mbx.json" print/dipoles

variable dipx atom f_2[7]/0.2081943
variable dipy atom f_2[8]/0.2081943
variable dipz atom f_2[9]/0.2081943

variable dipnorm atom sqrt(f_3[7]*f_3[7]+f_3[8]*f_3[8]+f_3[9]*f_3[9])/0.2081943

dump            1 all custom ${dump_freq} dump.lammpstrj id mol type q x y z v_dipx v_dipy v_dipz

I have some more questions.

I see that only oxygen atoms have a nonzero dipole. Is that the total dipole associated with the water molecule (including both the contribution of point charges and induced dipoles)?

If so, the total dipole of the system would be just the sum of the dipoles of each oxygen atom in the simulation, right?

What are the units of the dipoles printed with the commands above?

Thanks again.

Best regards,

Paolo

[CH HO]

Hi Paolo,

Yes, the dipole moment of an oxygen atom corresponds to the dipole moment of the water molecule which it belongs to. It includes both induced dipole and permanent dipole (i.e. the one from point changes of a water molecule). Therefore, the total dipole moment of the system is the sum of all dipole moments of oxygen atoms.

The unit is in Debye.

Thank you!

-Hank

Paolo Pegolo 在 2023年2月22日 星期三清晨7:53:25 [UTC-8] 的信中寫道：