Dear lammps usres
i use reax/c pair_style to simulate dissociation of oxygen molecule on nickel surface at 300 K. i check output temp for oxygen and nickel group in initial steps and i paste here these output:
all |
| oxygen |
| nickel |
- | - | - | - | - |
558.371 |
| 4965.63 |
| 194.934 |
507.158 |
| 4409.14 |
| 185.399 |
305.965 |
| 1671.86 |
| 193.440 |
491.799 |
| 3906.12 |
| 210.292 |
500.338 |
| 3607.36 |
| 244.213 |
404.971 |
| 2364.31 |
| 243.528 |
408.230 |
| 2079.86 |
| 270.545 |
445.102 |
| 2602.96 |
| 267.301 |
442.292 |
| 2442.62 |
| 277.496 |
395.243 |
| 1886.58 |
| 272.435 |
472.325 |
| 2433.50 |
| 310.787 |
449.507 |
| 1996.88 |
| 322.117 |
417.280 |
| 1551.67 |
| 323.963 |
397.574 |
| 1248.73 |
| 327.627 |
384.673 |
| 1079.91 |
| 327.589 |
374.752 |
| 1201.68 |
| 306.786 |
369.889 |
| 1134.60 |
| 307.057 |
377.123 |
| 1218.38 |
| 307.976 |
373.436 |
| 1276.46 |
| 299.185 |
345.520 |
| 983.659 |
| 293.118 |
323.711 |
| 815.297 |
| 283.391 |
326.392 |
| 870.932 |
| 281.702 |
318.260 |
| 824.014 |
| 276.766 |
319.760 |
| 951.530 |
| 267.862 |
334.220 |
| 1101.1 |
| 271.178 |
319.072 |
| 927.373 |
| 269.112 |
316.088 |
| 827.240 |
| 274.146 |
296.53 |
| 721.847 |
| 261.659 |
298.474 |
| 717.161 |
| 264.153 |
300.387 |
| 688.507 |
| 268.591 |
293.527 |
| 704.807 |
| 259.813 |
297.035 |
| 769.953 |
| 258.235 |
296.047 |
| 766.777 |
| 257.426 |
296.900 |
| 719.217 |
| 262.278 |
301.432 |
| 798.412 |
| 260.648 |
290.015 |
| 746.880 |
| 252.534 |
305.997 |
| 863.194 |
| 260.245 |
292.654 |
| 730.857 |
| 256.717 |
314.462 |
| 765.422 |
| 277.489 |
309.284 |
| 846.880 |
| 265.153 |
323.021 |
| 885.192 |
| 276.872 |
318.432 |
| 848.415 |
| 274.938 |
315.162 |
| 995.139 |
| 259.280 |
304.206 |
| 818.294 |
| 262.012 |
313.052 |
| 822.538 |
| 271.245 |
298.417 |
| 702.584 |
| 265.294 |
314.604 |
| 703.472 |
| 282.759 |
298.915 |
| 725.674 |
| 263.928 |
304.668 |
| 756.014 |
| 267.655 |
299.651 |
| 680.282 |
| 268.473 |
300.365 |
| 660.303 |
| 270.896 |
293.049 |
| 628.446 |
| 265.6 |
305.241 |
| 705.316 |
| 272.461 |
303.750 |
| 688.861 |
| 272.205 |
289.438 |
| 759.795 |
| 250.842 |
299.943 |
| 709.615 |
| 266.367 |
305.236 |
| 647.466 |
| 277.233 |
301.097 |
| 693.691 |
| 268.932 |
294.633 |
| 644.537 |
| 265.987 |
298.807 |
| 661.510 |
| 269.109 |
296.476 |
| 584.632 |
| 272.931 |
301.138 |
| 573.225 |
| 278.923 |
302.073 |
| 594.123 |
| 278.211 |
288.875 |
| 560.118 |
| 266.720 |
290.065 |
| 615.749 |
| 263.416 |
295.441 |
| 588.220 |
| 271.513 |
299.620 |
| 655.922 |
| 270.451 |
309.273 |
| 627.710 |
| 283.238 |
299.901 |
| 639.725 |
| 272.092 |
299.768 |
| 654.721 |
| 270.710 |
293.115 |
| 629.826 |
| 265.557 |
304.892 |
| 608.278 |
| 280.096 |
302.126 |
| 723.432 |
| 267.591 |
291.577 |
| 652.077 |
| 262.054 |
304.237 |
| 695.262 |
| 272.204 |
293.455 |
| 587.336 |
| 269.435 |
308.609 |
| 594.049 |
| 285.298 |
284.073 |
| 531.277 |
| 263.899 |
295.199 |
| 621.325 |
| 268.517 |
294.245 |
| 573.902 |
| 271.399 |
287.544 |
| 608.701 |
| 261.266 |
…
and here is my input file:
dimension 3
units real
boundary p p f
atom_style charge
Dear lammps usres
i use reax/c pair_style to simulate dissociation of oxygen molecule on
nickel surface at 300 K. i check output temp for oxygen and nickel group in
initial steps and i paste here these output:
[...]
and here is my input file:
dimension 3
units real
boundary p p f
atom_style charge
###################
read_data data.mix
group nickel type 1
group oxygen type 2
#Potentiel ReaxFF
pair_style reax/c NULL
pair_coeff * * ffield.reax Ni O
fix 2 all qeq/reax 100 0.0 10.0 1.0e-6 reax/c
#############
neighbor 2 bin
neigh_modify delay 0 every 1 check no
#############
compute new3d all temp
compute tempo oxygen temp
compute tempni nickel temp
variable T equal c_new3d
variable T1 equal c_tempo
variable T2 equal c_tempni
fix qq all print 100 "T {T1} ${T2}" screen no file temp.out
fix walls all wall/reflect zhi 21.000000 units box
region lower block -0.79863834 35.098638 -0.74863834 35.148638 -1
2 units box
group lower region lower
group rest subtract all lower
velocity rest create 300 458127641 mom yes rot yes dist gaussian
fix 33 lower setforce 0.0 0.0 0.0
fix qw all nvt temp 300 300 100 drag 2
run 1000000
in fact dissociation of oxygen on surface occur at initial steps and in
these steps temp for oxygen group is high,and the high temp affect reaction
rate.how can i maintain the whole system temp and oxygen and nickel group
temp at 300 K?
sorry, but how can this be a realistic description of a system where an
exothermic reaction is happening? and where there is nothing your atoms in
reality would couple to that they would exchange kinetic energy with? in
fact, even thermostatting the oxygen atoms *at all* is in my personal
opinion a questionable approach (as is the temperature control of the metal
atoms at the surface).
axel.
Dear Axel
Thanks for your suggestion. Do you mean I should just thermostat nickel
slab(no surface atoms or oxygen atom)?
Sent from Yahoo Mail on Android
<Yahoo Mail;
what i mean is that you have to understand the chemistry and
thermodynamics of the process you are simulating and not just make it look
like any regular equilibrium bulk simulation. what is adequate, you need to
decide by yourself and that is best done by looking at the published
literature of similar systems.
my usual recommendation for such slab systems is a bit more elaborate:
bottom layer of metal atoms is immobilized.
the rest of the system is integrated with fix nve.
the lower section (but not the topmost N layers) are thermalized with fix
langevin, or temp/csvr or whatever else tickles your fancy to model the
thermal coupling to the bulk.
the only problem with this setup is that many times, people deposit atoms
faster than what is realistic in an experiment or at a higher density, so
that the simulation doesn't take a very long time. that is where the person
doing the simulation has to decide what is the best compromise for your
specific needs. that is impossible to say from remote, since only you know
what is important in your research.
axel.
Dear Axel
I am trying to use your recommendation setup for my system, as you said
the simulation doesnt take a very long time, but there is one thing i cant
understand, at the beginning of run as expected temperature is rising from
300 to 700 k, and then is decreased and becomes below 100k and because of
this decreasing the reaction does not go on, what causes this temperature
decreasing?
sorry, but i am not a psychic. most likely you either set up your
simulation wrong or are looking at the wrong temperature or both.
axel.