Hi all,
I have simulated linear polymers, while production run, I am using NVE ensemble with sorting ID in the dump command. I am getting overlapping coordinates of the particles. Can anyone suggest the solution?
Here I am showing the script.
FENE beadspring benchmark
units lj
atom_style bond
special_bonds fene
read_restart poly.restart.5000
neighbor 0.4 bin
neigh_modify every 1 delay 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 2.50
pair_modify shift no
pair_coeff 1 1 1.0 1.0 2.5
fix 1 all nve
dump 2 all custom 25 crd.xyz.* id xu yu zu ix iy iz vx vy vz
dump_modify 2 sort id
compute 3 all pressure thermo_temp
thermo 100
timestep 0.0020
reset_timestep 0
restart 15000 poly.restart
run 75000
Hi all,
I have simulated linear polymers, while production run, I am using NVE ensemble with sorting ID in the dump command. I am getting overlapping coordinates of the particles. Can anyone suggest the solution?
there is not enough information here to even confirm, that there is a problem, let alone suggest a solution.
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always state which version of LAMMPS you are using and what platform you are running on. if possible, try to update LAMMPS to the latest patch and see, if the issue persists
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ideally, provide a small test case, that makes it easy to reproduce and debug the issue
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please explain and provide ways to prove the issue, i.e. how exactly did you conclude, that you have overlapping particles?
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make some tests yourself that narrow down the issue. e.g. you say that you changed to nve and trajectory sorting. so by undoing those changes one by one which of those is the actual issue.
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you are outputting unwrapped coordinates and image flags. isn’t that redundant?
axel.
Hi Axel,
(1) Actually, I had saved the dumped trajectories from LAMMPS into the large files, e.g., 20MB and then I was calculating radial distribution function (RDF), in which I am having the statement if distance between two monomers is less than 0.25 (LJ units), then it will exit by showing the error for overlap. I am using lammps 12 Dec 2018
(2) Earlier with the NVT simulations production run, without sorting IDs of the particles, I was getting exact RDF.
(3) Yes, I have to dump only the unwrapped coordinates that I realized later when I checked that I can calculate minimum images from the unwrapped crds only and the images are not required further.
(4) I am debugging it, using NVT with sorting IDs and NVE without sorting IDs.
Regards
Jalim
What you are saying does not make much sense. Sorting the IDs in the dump file should have no influence on any dynamics whatsoever, since it only determines the order in which the atoms are written to the dump file. Therefore, the RDF should be the same regardless of sorting your dump file. Secondly, overlap might happen initially so I do not think it is a good idea to abort a simulation just because there is overlap at some point. Finally, this statement you mention now is absent from your original script. Please post the exact input deck that produces the issue so we can actually help you properly, rather than guessing around. Also, if your script includes other files, you should send those as well (your restart file in this case, although they tend to not be compatible between various versions so it might not help much).
Hi Axel,
(1) Actually, I had saved the dumped trajectories from LAMMPS into the large files, e.g., 20MB and then I was calculating radial distribution function (RDF), in which I am having the statement if distance between two monomers is less than 0.25 (LJ units), then it will exit by showing the error for overlap. I am using lammps 12 Dec 2018
i assume that means you are using your own code to compute the RDF, not the compute included in LAMMPS or from some other MD analysis tool. have you considered, that there may be a bug in that RDF code, e.g. by incorrectly setting/importing box dimensions? seems much more likely than an issue with sorting in dump or fix nve.
axel.
Hi Axel,
Yes, you are right, I am using my own code for trajectory storing dumped from LAMMPS and calculate RDF, I have cross checked all these parameters many times, already. The box length, number of snapshots, etc. Let me again check them and let you know the outcome.
Sorry for the presenting problem in abstract way.
Regards
Jalim
Hi Axel,
Sorry for the spamming, there was a problem in my trajectory reading code. I found it, but lately. Thanks a lot for your help.
Regards
Jalim