pair_style dpd T cutoff seed
pair_style dpd 1.0 2.5 34387
Q1) This is an example of writing dpd unit of temperature (the bold one) for lj system where, T* = 1.0 means that T* = TkB/Epsilon = 1.0. In the lammps documentation, it was mentioned that here 1.0 is equivalent to 300K. Now, if I want to use increased temperature, for example 400K, what will be the equivalent non-dimensional number? I am really confused about this conversion. It will be much appreciated if anyone can please help me with an explanation.
Q2) In lammps if I want to mimic the experimental annealing ( e.g. raising temperature to reach equilibrium and then bringing the temperature back to room temperature) can just follow the following steps- a) run the simulation at room temp. b) take the last trajectory of atoms from step (a) and run the simulation at higher temp. and then c) take the last trajectory from step (b) to repeat the step (a) at room temperature. I am wondering if there might be any computational artifact generated due to such change of the temperature or it should mimic the experimental annealing system?
Q3) For the question (Q2), if I use it for systems having pair_coeff (= interation parameter obtained from Chi parameter),how this change of whole system temperature can potentially affect the interaction parameter. Or will it just change the total system temperature leaving the mutual interaction unaffected ?
Thanks a lot in advance !
Yes, I tried asking them as well. Alex replied in his own style that if I care to get the real unit temperature, then why do I even care to use the normalized units ? In LAMMPS the temperature is normalized my Epsilon (energy) as T* = TkB/Epsilon and I think, this energy is system dependent. But, I don't know exactly what will be conversion factor !! I wish if someone could help !
A1) If you want to stay in reduced units, use that epsilon you are using for your lennard jones potential in real units in the equation you have written to get the reduced temperature T* = T*kB/Epsilon.. the right side of this equation will have units cancel out, giving the unit less T*
The example where they said T* = 1 at 300 K is just an example. In that case epsilon in real units is 300 K *kB which is about 4.14E-23 J, at the T=300 K, the reduced temperature T* = TKb/epsilon = (300*kB)/(300*kB) = 1
A2) You can also ramp up the temperature and cool the temperature more gradually. Switching between different temperatures like you described is also done. Equilibration/annealing can be a challenge in molecular simulations, especially with polymers. Here is a link to a paper that talks about a 21-step equilibration for polymers in simulation http://link.springer.com/article/10.1007%2Fs00214-013-1334-z
A3) Chi will only change with temperature if it is temperature dependent..
http://link.springer.com/article/10.1007%2Fs00214-013-1334-z
Great Thanks, Amulya.
A1) I think, you meant 4.14E-21 J. Is that right ? I got the point where you derived how it might be 300K as an example. However, in the lammps unit conversion page (http://lammps.sandia.gov/doc/units.html), they mentioned that, for style lj, both Kb and Epsilon are equal to 1.0 . It made me more confused. If I consider that epsilon is system specific then, honestly, I am not just sure where I am putting the energy as input so that I can potentially use that to obtain the real temperature from the normalized temperature. I am getting the total energy at the equilibrium state in the logfile as output. However, since, those are also normalized quantity, I still need to know what is being used for the normalization so that I can convert those. I will appreciate if you share your ideas on that.
A2 & A3) You have just helped me on a real concern that I did not explicitly mention regarding the gradual/instant temperature ramping. I really appreciate that !
sorry for the typo.. i meant 4.14E-21 J, if you are using lj units everything is scaled by epsilon and sigma, even the epsilon and sigma used in the simulation is scaled by epsilon and sigma, that's why epsilon and sigma will be 1 in lj units. But you can choose in real units epsilon and sigma to be anything that makes sense for your system. Then for the temperature but if you are simulating a real system with a real quantity epsilon, the temperature that will be outputted in lj units will be the reduced temperature, to get the "real" temperature use the real values of epsilon and kB you want to use.
Of course there is always the option of using real units and getting the real temperature from that.
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