no output in rdf file with rerun - regd

Dear LAMMPS users,

I am using “compute rdf” & “compute ave/time” in my rerun to compute rdf. In my original run I have dumped coordinates for every 2000 time steps in DCD format using dump dcd and using following lines in my rerun input script to compute rdf

compute 2 all rdf 200 1 1
fix 2 all ave/time 2000 1 2000 c_2 file rdf.lammps mode vector

with these lines job is running fine but not writing anything in the output file other than header lines. I know that problem is in choosing Nevery, Nrepat & Nfreq parameters. I have tried with other options like 2000 2 4000 but in vain.

can anybody help me in this regard.

Thank you,

Dear LAMMPS users,

              I am using "compute rdf" & "compute ave/time" in my rerun to
compute rdf. In my original run I have dumped coordinates for every 2000
time steps in DCD format using dump dcd and using following lines in my
rerun input script to compute rdf

compute 2 all rdf 200 1 1
fix 2 all ave/time 2000 1 2000 c_2 file rdf.lammps
mode vector

with these lines job is running fine but not writing anything in the output
file other than header lines. I know that problem is in choosing Nevery,
Nrepat & Nfreq parameters. I have tried with other options like 2000 2 4000
but in vain.
can anybody help me in this regard.

please re-read the rerun documentation carefully and observe the time
step numbers printed to the screen output. when reading from a file
format that doesn't support storing time step number (like dcd or any
format read through molfile plugins actually), your time steps will be
renumbered.

Dear Axel,

Thank you very much for your reply, I have noticed the re-numbering in times steps of dcd file in rerun. Actually I have 51 frames with time step numbering from 0 to 50, so have taken fix ave/time command as

fix 2 all ave/time 1 5 10 c_2 file rdf.lammps mode vector

According to my understanding above fix should do averages at 10, 20, 30, 40 & 50 steps and at each 10th step it should use its preceding 5 time steps which are successive (as Nrepeat=5 & Nevery=1) for averaging (i.e., for 10th step it should use 6 7 8 9 10 steps),
As molfile giving successive time step numbers with difference of 1 to my frames I have expected output other than headers but its not the case.

I have tried some other possible combinations also but none of the attempts writing the output file (even Nevery=1 , Nrepeat=1 & Nfreq=1).

As a test I have run a 100 steps MD run and dumped coordinates in every time step and used fix ave/time as

fix 1 all ave/time 1 1 10 c_1 file rdf.lammps mode vector

In this case it is writing output file perfectly.
Here I didn’t understand what I am missing in earlier case.

Thank you in advance,

Best,

Ramesh

Dear Axel,

       Thank you very much for your reply, I have noticed the re-numbering
in times steps of dcd file in rerun. Actually I have 51 frames with time
step numbering from 0 to 50, so have taken fix ave/time command as

  fix 2 all ave/time 1 5 10 c_2 file rdf.lammps mode vector

According to my understanding above fix should do averages at 10, 20, 30,
40 & 50 steps and at each 10th step it should use its preceding 5 time
steps which are successive (as Nrepeat=5 & Nevery=1) for averaging (i.e.,
for 10th step it should use 6 7 8 9 10 steps),
As molfile giving successive time step numbers with difference of 1 to my
frames I have expected output other than headers but its not the case.
I have tried some other possible combinations also but none of the attempts
writing the output file (even Nevery=1 , Nrepeat=1 & Nfreq=1).

As a test I have run a 100 steps MD run and dumped coordinates in every time
step and used fix ave/time as
fix 1 all ave/time 1 1 10 c_1 file rdf.lammps mode vector
In this case it is writing output file perfectly.
Here I didn't understand what I am missing in earlier case.

you must be doing something wrong. it works fine for me.
if i add the following lines to the LAMMPS melt example to output a
trajectory and compute g(r)s:

dump d1 all dcd 5 dump.dcd
dump_modify d1 unwrap yes

compute c1 all rdf 100
fix f1 all ave/time 5 10 50 c_c1 file rdf1.dat mode vector

or if i then delete them and instead use:

compute c1 all rdf 100
fix f1 all ave/time 1 10 10 c_c1 file rdf2.dat mode vector

rerun dump.dcd first 0 last 1000 every 0 dump x y z box yes scaled no
format molfile dcd .

i get essentially the same output in rdf1.dat and rdf2.dat not
counting the differences in time steps and from floating point
truncation.