Hi!
I am working on studying the radiation damage on a material. To that end, I am running an MD simulation using NVE ensemble. I turned off the temperature and I set the velocity of all atoms based on the previous MD simulation. Then, I increased the velocity of one atom. The code complins that the temperature is too small. So, I turned on the temperature(300 K), but it seems that the temperature overridden the velocity I assigned, and bring it down to a value corresponding to T=300 K . As if I did not increase the atom’s velocity. How can I set the Temperature without overridden the assigned velocity
Thank you
Hi Omar,
Without seeing your input it’s hard to absolutely sure what is going on, but here is my best guess. By default, GULP applies velocity rescaling during the equilibration phase and then this is turned off during production since for NVT/NPT simulations this is most sensible thing to do. If you want to control the initial velocities without reference to the temperature, as is the case in radiation damage, then you need to skip the equilibration phase and make sure you don’t turn on velocity rescaling.
Hope that helps,
Julian
Dear Prof. Gale,
Thank you for your response. Indeed, both equilibration and tscale are turned off already.
I am trying to attach my input, but somehow I can’t because I am a new user. So, I am copying part of my input file. The remaining parts of the input are just the rest of the atoms and the ReaxFF potentials.
Thank you
Keywords:
md conv nosym
Options:
name T14_REAXFF
vectors
26.578431476 -0.125298980 0.719097124
-13.039091459 18.752817686 -0.346763513
-0.541723346 0.097091186 28.080602503
cartesian
Ca core 10.39086513 11.74685888 22.33234387
Ca core 6.241058608 17.95922921 22.07416632
Ca core 14.83011344 5.497146557 22.42520313
Ca core -2.713023634 11.87466356 22.19230001
Ca core -7.198639856 18.04237950 21.82491393
Ca core 1.492238045 5.596768026 22.08509276
Ca core 8.538935599 15.34440836 6.179786372
Ca core 17.31818918 2.957573371 6.266793736
Ca core 12.86436181 9.204141768 6.300807853
Ca core -4.669900064 15.43801224 5.841242959
Ca core 3.963187013 2.891396432 5.991604598
Ca core -0.277705849 9.256736418 5.940452753
Ca core 14.02055179 12.26469021 8.406125338
Ca core 9.606809127 18.49833796 8.367294783
Ca core 18.36695138 6.021818367 8.615601697
Ca core 0.789978072 12.32904042 8.135284946
Ca core -3.500402137 18.55983824 8.148523037
Ca core 5.020353183 6.055490186 8.201386987
Ca core 11.71504756 14.81525815 20.22048682
velocities angs/ps
1 0.958917596 -.372277347 -1.43624301
2 0.643108123 -.555628381 1.61860808
3 -.825631537E-01 -.736951189 0.659430171
4 -.559566370 1.71819527 1.22303027
5 0.145204335E-01 -1.61311591 2.22884687
6 -.442488288 0.392679986 1.11165715
7 -.643651347 1.49404159 -.136258886
8 -.465446482 -.828247543 1.36570731
9 -.408391788 0.568852488 0.433310323E-01
10 -.644880710 1.98459944 0.348620383
11 0.632067055 -1.08302549 -2.20456001
12 0.181276505 -1.47721738 -.202491185
13 -.744101216 -1.84080144 -2.77828507
14 -1.03631741 -.335787391 1.81512712
15 -1.01007010 -.489618617 -1.81710722
16 -.548078493 -.600472052 0.605184479
17 1.25022651 2.09252234 4.41706832
18 0.877969331 -.769350681 -.676516703
19 -.668604013 0.600469431 1.09043703
temperature 300.000
integrator leapfrog verlet
ensemble NVE
timestep 0.0000100 ps
production 2.00000 ps
sample 0.00001000 ps
write_MD 0.00001000 ps
Thank you.
Hi Omar,
Thanks for your input. There is one big issue here, which is that you don’t have any potential parameters and so there is no potential energy or forces. I’d recommend fixing that first.
However, there is an issue in the code that it is trapping the temperature being zero even though velocities are specified. I’ll have to look into this. One thing you should be able to do is to perform a quick run (even a few timesteps) at 300 K to create a restart file. If you then edit the restart file to set the velocities you want then it should be OK since the code ought not overwrite the velocities.
Regards,
Julian
Hi Omar,
A further update. I’ve just uploaded a modified version of GULP-6.1 that will now allow the temperature to be ignored if you input your own velocities at the start. Be aware that your input is likely to give lots of ******* in the output since the initial velocities are high, but this seems to settle down once the potential energy contribution kicks in (at least for the dummy potential I added to your input).
Regards,
Julian
Dear prof. Gale,
Thank you, I did what you mentioned and it works fine with me.
Regarding version update, this is highly appreciated.
Best Regards,
Omar