Dear all
I am modelling a cis-polyisoprene network to atmospheric conditions - periodic in all directions). It involves many intermediate annealings - NVT and minimisations. At the end there is an NPT equilibration at atmospheric temperature and pressure, which changes the box limits.
In the output I see that, some of the atom coordinates (x, y, z) and outside the final box dimension (xlo-xhi, ylo-yhi, zlo-zhi). I would like to get a proper box dimension which is capable of holding all atoms, and which is the right repeating unit of the bulk. Could anyone help me how to get this?
Thank you
Jeeno Jose
Dear all
I am modelling a cis-polyisoprene network to atmospheric conditions - periodic in all directions). It involves many intermediate annealings - NVT and minimisations. At the end there is an NPT equilibration at atmospheric temperature and pressure, which changes the box limits.
In the output I see that, some of the atom coordinates (x, y, z) and outside the final box dimension (xlo-xhi, ylo-yhi, zlo-zhi). I would like to get a proper box dimension which is capable of holding all atoms, and which is the right repeating unit of the bulk. Could anyone help me how to get this?
Your box is correct as it is. Please see the ‘important notes’ in the dump documentation about reneighboring and atom not always being fully wrapped back into the principal simulation cell.
Axel
Dear all,
Even though I have set every 1, check no, and delay 0 in neigh_modify, minimize command makes check yes. Since I am ending the simulation with a minimization I cannot expect all atoms within simulation box.
I need to unwrap each of my polymer chain, and for that I need to know the true box dimensions that fully contains all the atoms. So, please anyone let me know what is the LAMMPS rule of modifying the xlo xhi ylo yhi zlo zhi during the course of simulation. (my simulation contains minimization, NVT, minimization, NPT, minimization, in order). Is that by taking the min(xi) and max(xi) - that won’t be accurate, if something else, what is the method of modifying the simulation box parameter?
Thank you
Jeeno
Dear all,
Even though I have set every 1, check no, and delay 0 in neigh_modify,
Which means that you are likely wasting time on needlessly recomputing your neighbor lists.
minimize command makes check yes. Since I am ending the simulation with a minimization I cannot expect all atoms within simulation box.
So what?
I need to unwrap each of my polymer chain, and for that I need to know the true box dimensions that fully contains all the atoms. So, please anyone let me
Like I already explained, you do get the proper box dimensions and those are definitely the dimensions to be used for unwrapping.
know what is the LAMMPS rule of modifying the xlo xhi ylo yhi zlo zhi during the course of simulation. (my simulation contains minimization, NVT, minimization, NPT, minimization, in order). Is that by taking the min(xi) and max(xi) - that won’t be accurate, if something else, what is the method of modifying the simulation box parameter?
What you say here makes no sense.
Axel