trying to read dump file with wrapped coordinates, process for 0 time_steps, and write out unwrapped coordinates

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1

I have a dump file from a triclinic box and unwrapped coordinates that I wish to read in and process using 0 time steps (if possible) then write out using unwrapped coordinates. My intention is to convert the dump file coordinate from wrapped to unwrapped coordinatesusing for some post processing. I can only get it to work using a time increment of 1 (time_step of 0.001 femtosecond here). It seems to have worked, but I have still moved it slightly, I think. Is there a way to do this without changing the true atom positions?

Here is my file I ran. I could see at least 1 atom that moved from 1 side of the borders to the other in the simulation when I compared the dump file, so I think it did unwrap the coordinates. The dump file here contains atom positions and atom properties from a series of stress controlled experiments from 0 stress to failure as the sample was sheared. The original dump files were written with x y x coordinates and pbc set as yes. I am trying to figure out if the atom positions in an unwrapped condition can be determined by converting the cooridnates to xu yu zu without rerunning the entire simulation sequence from scratch.

Here is an example I could get to run. the 240000 refers to the dumped time step and the stress was -0.2 gpa. There are actually many others starting a 0 gpa stress and being increased to break point. I cant get it to run with time_npt3 value as 0

read_restart restart.equil remap
pair_style eam/alloy
pair_coeff * * PdH_Zhou.eam.alloy Pd H
# ------------------------ VARIABLES -----------------------------
variable time_step equal 0.001
variable time_npt3 equal 1
variable tdamp equal "v_time_step*100"
variable pdamp equal "v_time_step*1000"
# temp1 is 100 and read into file from lammps call as input variable
reset_timestep 240000
read_dump dump_-0.2gpa_${temp1}K.240000.custom 240000 x y z

fix 1 all npt temp \{temp1\} {temp1} \{tdamp\} x 0\.0 0\.0 {pdamp} y 0.0 0.0 \{pdamp\} z 0\.0 0\.0 {pdamp} xy 0.0 0.0 \{pdamp\} xz 0\.0 0\.0 {pdamp} yz 0.0 0.0 ${pdamp} flip yes

dump 3 all custom 240000 dump_-0.2gpa_\{temp1\}K\.240000\.uwt\.custom id xu yu zu dump\_modify 3 sort id dump\_modify 3 pbc no run {time_npt3}
unfix 1
undump 3

# SIMULATION DONE
print "All done"

2

this is a very long and complex description, but the situation is rather simple: you cannot get information back, that isn’t there.
for the unwrapping to work, you need to a) have the image flag information in your original dump file and b) read it back when using read_dump. from your input it doesn’t show that you are doing b), and i cannot tell if you have a) since you didn’t provide a sample of your trajectory file header.
when the trajectory was generated with a variable cell simulation (e.g. using fix npt), then you also need to tell read_dump to read the box dimensions from the trajectory file (or else the application of the image flags would be incorrect).

the dump_modify pbc yes/no option has a completely different meaning from what you seem to infer. please read the documentation of that option again and with more attention to detail.

axel.