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I am trying to simulate the Zinc oxide bulk structure (periodic) at constant pressure(0.0 ~ 20.0 GPa) to observe phase transition with LAMMPS.

However, I approached a problem that the fluctuating pressure in each step of optimisation and importantly the final step of the optimisation does not have the value of pressure that I set.

*5th-edit: the problem is solved *

The last step of the pressure is not the exact the pressure that I set for which presumably a form of showing residual force of minimisation. Basically, it went down to the basin but not exactly the lowest point of the basin with a certain tolerance.

Primarily the calculation went wrong because I have used wrongly formatted structure data in the read_data command. The wrong data file was produced by three different software... which was very unlucky...

I sincerely apologise for the question as I made many people confused.

Here is my input:

units       metal
atom_style  charge
dimension   3
boundary    p p p

#box tilt large                          # allow lammps to have large tilt facotr (xy yz xz)
read_data       data.3_iso0.0
#replicate       3 3 3

pair_style  comb3 polar_off
pair_coeff  * * ./lammps_ip Zn O

neighbor        2.0 bin
neigh_modify every 1 delay 0 check yes

set type 1    charge  2.0  # Zn
set type 2    charge -2.0  # O

##############################################################
#                   type of output data                      #
##############################################################

fix             1 all qeq/comb 2 0.00003 file fq.out
fix             2 all box/relax iso 0.0                 # Pressure = unit [bars], 1 GPa = 10,000 bars, Constant pressure


thermo          1
thermo_style    custom step press temp enthalpy etotal pe ke evdwl ecoul cella cellb cellc cellalpha cellbeta cellgamma

#min_style cg
minimize 0 0.0 10000 10000
min_modify line quadratic

write_data data.*        #produce file for "read_data" command
print " All done "

The corresponding output data is: Step Press c_1 v_press Temp v_etot v_relax TotEng PotEng KinEng

    1157   -186.71231   -186.71231   -186.71231            0  -2.9709191            0   -2.9709191   -2.9709191            0
    1158    -128.7401    -128.7401    -128.7401            0   -2.9709192            0   -2.9709192   -2.9709192            0
    1159   -124.22057   -124.22057   -124.22057            0   -2.9709192            0   -2.9709192   -2.9709192            0
 Loop time of 464.543 on 1 procs for 1159 steps with 216 atoms

 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

 Minimization stats:
   Stopping criterion = linesearch alpha is zero
   Energy initial, next-to-last, final =
         -2.25448773082     -2.97091924357     -2.97091924466
   Force two-norm initial, final = 351.736 2.00988
   Force max component initial, final = 342.312 0.805865
   Final line search alpha, max atom move = 4.67711e-07 3.76912e-07
   Iterations, force evaluations = 1159 1175
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    $\begingroup$ What would you like to achieve, perfect non-fluctuating pressure? You write yourself that the pressure will fluctuate during an NPT simulations. This is usually acceptable and the fluctuations typically go down when the system is properly equilibrated. $\endgroup$
    – Fabian
    May 26, 2020 at 13:13
  • $\begingroup$ Nice first question. Welcome to the site and we hope to see more of you! $\endgroup$
    – Nike Dattani
    May 26, 2020 at 13:15
  • $\begingroup$ @Fabian Thank you for the comment. Yes, I understand that NPT simulation will provides pressure fluctuation, but what I trying to do is just simple global optimisation with constant pressure. Is this considered as NPT simulations? $\endgroup$
    – DGKang
    May 26, 2020 at 13:34
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    $\begingroup$ @CodyAldaz I will take your advice in next posts. Apologies for the inconveniences. $\endgroup$
    – DGKang
    May 27, 2020 at 15:36
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    $\begingroup$ In your last edit you have said that you solved the problem. I think instead of putting the answer into the question, you should write an "answer" to your own question. $\endgroup$
    – Nike Dattani
    Jun 12, 2020 at 15:08

1 Answer 1

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However, I am not clear which command have to be used to optimise the structure at a certain pressure to have the constant pressure at the final step.

For this you need to perform a time integration from the Isobaric Isothermal ($NPT$) ensemble. Essentially performing these dynamics, you equilibrate the systems at certain $T$ and $P$. In LAMMPS documentation you can find the necessary commands for $NPT$ simulation. A very generic example is given below.

fix 1 all npt temp 300.0 300.0 $(100.0*dt) iso 0.0 0.0 $(1000.0*dt)
run 1000000

After equilibration, plot $E(timestep)$. If the slope becomes zero, your system is properly equilibrated at that $T$ and $P$, if you plot the $P(timestep)$ after equilibration, it should always fluctuate around Final $P$ as per your input.

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  • $\begingroup$ Thank you for the advice. However, what I want to do is geometry optimisation (H=E + pv) not MD simulation. (minimisation enthalpy) $\endgroup$
    – DGKang
    Jun 10, 2020 at 9:45
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    $\begingroup$ Is there any specific reason to run optimization only via LAMMPS "minimize" command? May I ask what is the purpose of your work? "Optimization" doesn't need to adhere to "minimize" command just because "minimize" command is designed to minimize something. $\endgroup$
    – exsonic01
    Jun 12, 2020 at 2:33
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    $\begingroup$ Sometimes I also run very low-temperature (like 0.1K) NPT MD or NVT MD to optimize the system energy and geometry, or sometimes I use minimize command and very short NPT or NVT or NVE MD to stabilize the system. The choice of procedure usually depends on my goal or target of the simulation. $\endgroup$
    – exsonic01
    Jun 12, 2020 at 2:34
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    $\begingroup$ Also, if you want to really "optimize" something only with "minimize" command, then you can test other minimize algorithms with different criteria conditions. $\endgroup$
    – exsonic01
    Jun 12, 2020 at 2:35
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    $\begingroup$ You may know about this, but don't forget to monitor system PE, not only pressure, to judge if your system is optimized or not. $\endgroup$
    – exsonic01
    Jun 12, 2020 at 2:58

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