Illegal variable substitution when creating dump from temper command

LAMMPS LAMMPS Mailing List Mirror
1

Hello,

My version of LAMMPS is 16 Feb 2016. I am trying to implement replica exchange on my MD simulation using the temper command, but I cannot get it to create dump files due to a “Substitution for Illegal Variable” error. This is coming from these commands:

variable rep world 0 1 2 3 4 5 6 7 8 9 (NO ERROR)

dump 1 all custom 1000 temper.$rep.xyz id type mol x y z (ERROR HERE)

When I run temper alone without trying to create dump files, there doesn’t appear to be a problem. I obtain 10 log files and 10 screen files, with the command line showing the expected exchange schema.

LAMMPS (16 Feb 2016)

Running on 10 partitions of processors

Setting up tempering …

Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9

100000000 0 1 2 3 4 5 6 7 8 9

100001000 0 1 2 3 4 5 6 7 8 9

100002000 0 1 2 3 4 5 6 7 8 9

100003000 0 1 2 3 4 5 6 7 8 9

100004000 0 1 2 3 4 5 6 7 8 9

100005000 0 1 2 3 4 6 5 7 8 9

100006000 0 1 2 3 4 6 5 7 8 9

100007000 0 1 2 3 4 6 5 7 8 9

100008000 0 1 2 3 4 6 5 7 8 9

100009000 0 1 2 3 5 6 4 7 8 9

100010000 0 1 2 3 5 6 4 7 8 9

However, then I cannot look at my trajectories. I tried the exact command from the LAMMPS documentation, as well:

dump 1 all atom 1000 dump.temper.$rep

This also throws the same error. If I try to create a restart file using this rep variable, I also get the illegal variable error:

write_restart restart1prod60.$rep.rest

write_data restart1prod60.$rep.data

(This syntax for the restart files I might be messing up because this is not in the documentation. In fact, I’m not sure how to create the restart files from each replica.)

My temper command looks like this:

Temper 10000 1000 $t thermostat 1206 1825

with the temperature variable defined as thus:

variable t world 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0

I’m using a Langevin thermostat; based on the log files, it looks like the temperature is being maintained reliably for each replica and after exchange. To run my tempering simulation, I’m using the following command line input:

mpirun –np 10 /share/apps/bin/lammps_REPLICA –partition 10x1 –in in.temper

Any insight into why I cannot create my dump files is much appreciated. Please let me know if additional info on my simulation is needed.

Thank you,

Helen

2

Hello,

My version of LAMMPS is 16 Feb 2016. I am trying to implement replica exchange on my MD simulation using the temper command, but I cannot get it to create dump files due to a “Substitution for Illegal Variable” error. This is coming from these commands:

variable rep world 0 1 2 3 4 5 6 7 8 9 (NO ERROR)

dump 1 all custom 1000 temper.$rep.xyz id type mol x y z (ERROR HERE)

When I run temper alone without trying to create dump files, there doesn’t appear to be a problem. I obtain 10 log files and 10 screen files, with the command line showing the expected exchange schema.

LAMMPS (16 Feb 2016)

Running on 10 partitions of processors

Setting up tempering …

Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9

100000000 0 1 2 3 4 5 6 7 8 9

100001000 0 1 2 3 4 5 6 7 8 9

100002000 0 1 2 3 4 5 6 7 8 9

100003000 0 1 2 3 4 5 6 7 8 9

100004000 0 1 2 3 4 5 6 7 8 9

100005000 0 1 2 3 4 6 5 7 8 9

100006000 0 1 2 3 4 6 5 7 8 9

100007000 0 1 2 3 4 6 5 7 8 9

100008000 0 1 2 3 4 6 5 7 8 9

100009000 0 1 2 3 5 6 4 7 8 9

100010000 0 1 2 3 5 6 4 7 8 9

However, then I cannot look at my trajectories. I tried the exact command from the LAMMPS documentation, as well:

dump 1 all atom 1000 dump.temper.$rep

This also throws the same error. If I try to create a restart file using this rep variable, I also get the illegal variable error:

write_restart restart1prod60.$rep.rest

write_data restart1prod60.$rep.data

(This syntax for the restart files I might be messing up because this is not in the documentation. In fact, I’m not sure how to create the restart files from each replica.)

My temper command looks like this:

Temper 10000 1000 $t thermostat 1206 1825

with the temperature variable defined as thus:

variable t world 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0

I’m using a Langevin thermostat; based on the log files, it looks like the temperature is being maintained reliably for each replica and after exchange. To run my tempering simulation, I’m using the following command line input:

mpirun –np 10 /share/apps/bin/lammps_REPLICA –partition 10x1 –in in.temper

Any insight into why I cannot create my dump files is much appreciated. Please let me know if additional info on my simulation is needed.

Thank you,

Helen