Error in computing rdf using rerun: Fix ave/time missed timestep

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1

Dear all lammps users

We want compute the rdf for our copolymer system. During main run, but we get zero numbers for most of the pairs. Like this:

Time-averaged data for fix rdf

TimeStep Number-of-rows

Row c_rdf4[1] c_rdf4[2] c_rdf4[3] c_rdf4[4] c_rdf4[5] c_rdf4[6] c_rdf4[7] c_rdf4[8] c_rdf4[9] c_rdf4[10] c_rdf4[11] c_rdf4[12] c_rdf4[13]

15502000 50
1 0.1 0 0 0 0 0 0 0 0 0 0 0 0
2 0.3 0 0 0 0 0 0 0 0 0 0 0 0
3 0.5 0 0 0 0 0 0 0 0 0 0 0 0
4 0.7 0 0 0 0 0 0 0 0 0 0 0 0
5 0.9 0 0 0 0 0 0 0 0 0 0 0 0
6 1.1 0 0 0 0 0 0 0 0 0 0 0 0
7 1.3 0 0 0 0 0 0 0 0 0 0 0 0
8 1.5 0 0 0.134701 8.33333e-05 0 0 0 0 0 0 0 0
9 1.7 0 0 4.32212 0.00351667 0 0 0 0 0 0 0 0
10 1.9 0 0 22.4621 0.0258 0 0 0 0 0 0 0 0
11 2.1 0 0 16.341 0.0456 0 0 0 0 0 0 0 0
12 2.3 0 0 14.5533 0.06675 0 0 0 0 0 0 0 0
13 2.5 0 0 10.5426 0.08485 0 0 0 0 0 0 0 0
14 2.7 0 0 10.9037 0.106683 0 0 0 0 0 0 0 0
15 2.9 0 0 36.2717 0.190467 0 0 0 0 0 0 2.00588 0.00463333
16 3.1 0 0 361.05 1.1434 0 0 0 0 0 0 5.48117 0.0191
17 3.3 0 0 23.1936 1.21277 0 0 0 0 0 0 13.0513 0.0581333
18 3.5 0 0 18.281 1.27427 0 0 0 0 0 0 14.8725 0.108167

This maybe be of special bonds according the IMPORTANT NOTE in compute rdf in manual.

This step we want use rerun and modify special bonds and see what happen. We have problem with rerun. We never reset the time step, but we see this error:

ERROR: Fix ave/time missed timestep
(You cannot reset the timestep to a value beyond where the fix expects to next perform averaging. )

I use this commands for rerun:

read_data data.CPVC
read_dump CPVC.lammpstrj 5000 x y z

compute rdf all rdf 50 7 9 7 5 5 10 9 10 5 9 5 5
fix rdf all ave/time 1 5000 5000 c_rdf file rdf.lammps mode vector

thermo 5000

rerun CPVC.lammpstrj first 0 every 5000 last 4000000 dump x y z box yes scaled yes

It is interesting that when we use this command:
fix rdf all ave/time 1 5000 200000 c_rdf file rdf.lammps mode vector

Run continues to 200000, and again we see the same error. But again there is no thing in the rdf file.

Would someone please help solve this problem. Sorry that it become long.

2

You mention a couple different problems.

This maybe be of special bonds according the IMPORTANT NOTE in compute rdf in manual.

that is probably the reason you get 0.0 values for some RDF pairs

This step we want use rerun and modify special bonds and see what happen.

The lines you showed for your rerun script, do not modify special bonds.

fix rdf all ave/time 1 5000 5000 c_rdf file rdf.lammps mode vector
rerun CPVC.lammpstrj first 0 every 5000 last 4000000 dump x y z box yes scaled yes

The rerun command indicates the dump file has a snapshot every 5000 steps.

The fix ave/time command, is requiring 5000 snapshots, 1 every step, for 5000
steps to produce an output. Those snapshots don’t exist. That is why you get the error.

It is interesting that when we use this command:
fix rdf all ave/time 1 5000 200000 c_rdf file rdf.lammps mode vector

Run continues to 200000, and again we see the same error.

It’s the same problem. You don’t have 5000 snapshots in the file, spaced
one timestep apart.

Please read the fix ave/time doc page carefully to understand what those 3 numeric

params (1 5000 200000) mean.

Steve