a question about temper

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1

I am attempting to use replica exchange on the University of Texas TACC Lonestar cluster, and I am having trouble getting each processor to output the restart file so that I may get accurate restarts. I am wondering if I have some error in my input file, or if it is on the job submission file. The following is my in file. Thanks

Single chain P3HT_PtBA

units real

atom_style full

pair_style lj/cut/coul/cut 12.0

bond_style harmonic

angle_style harmonic

dihedral_style hybrid oplsmod1 oplsmod2 opls

improper_style harmonic

special_bonds lj/coul 0 0 0.5

read_data data.P3HT_PtBA_sc

dihedral_coeff 1 oplsmod1 0 7.25 0 0 0

dihedral_coeff 2 oplsmod1 0 7.25 0 0 0

dihedral_coeff 3 oplsmod1 0 7.25 0 0 0

dihedral_coeff 4 oplsmod1 0 7.25 0 0 0

dihedral_coeff 5 oplsmod1 0 7.25 0 0 0

dihedral_coeff 6 oplsmod1 0 7.25 0 0 0

dihedral_coeff 7 oplsmod2 0.596 -4.039 0.252 0.861 0.128

dihedral_coeff 8 oplsmod2 0.596 -4.039 0.252 0.861 0.128

dihedral_coeff 9 oplsmod2 0.596 -4.039 0.252 0.861 0.128

dihedral_coeff 10 oplsmod1 0 7.25 0 0 0

dihedral_coeff 11 oplsmod1 0 7.25 0 0 0

dihedral_coeff 12 oplsmod1 0 7.25 0 0 0

dihedral_coeff 13 oplsmod1 0 7.25 0 0 0

dihedral_coeff 14 oplsmod1 0 7.25 0 0 0

dihedral_coeff 15 oplsmod1 0 7.25 0 0 0

dihedral_coeff 16 oplsmod2 -0.292 0.004 -0.914 -0.111 0

dihedral_coeff 17 oplsmod2 -0.292 0.004 -0.914 -0.111 0

dihedral_coeff 18 oplsmod2 -0.292 0.004 -0.914 -0.111 0

dihedral_coeff 19 oplsmod2 -0.292 0.004 -0.914 -0.111 0

dihedral_coeff 20 oplsmod1 1.3 -0.05 0.2 0 0

dihedral_coeff 21 oplsmod1 1.3 -0.05 0.2 0 0

dihedral_coeff 22 oplsmod1 0 7.25 0 0 0

dihedral_coeff 23 oplsmod1 1.3 -0.05 0.2 0 0

dihedral_coeff 24 oplsmod1 1.3 -0.05 0.2 0 0

dihedral_coeff 25 oplsmod1 0 7.25 0 0 0

dihedral_coeff 26 oplsmod1 1.3 -0.05 0.2 0 0

dihedral_coeff 27 oplsmod1 0 7.25 0 0 0

dihedral_coeff 28 oplsmod1 0 7.25 0 0 0

dihedral_coeff 29 oplsmod1 0 7.25 0 0 0

dihedral_coeff 30 oplsmod1 0 7.25 0 0 0

dihedral_coeff 31 oplsmod1 0 7.25 0 0 0

dihedral_coeff 32 oplsmod1 0 7.25 0 0 0

dihedral_coeff 33 oplsmod1 0 7.25 0 0 0

dihedral_coeff 34 oplsmod1 0 7.25 0 0 0

dihedral_coeff 35 oplsmod2 -0.292 0.004 -0.914 -0.111 0

dihedral_coeff 36 oplsmod2 -0.292 0.004 -0.914 -0.111 0

dihedral_coeff 37 opls 0 0 0.251 0

dihedral_coeff 38 opls 1.3095 -0.31 0.129 0

dihedral_coeff 39 opls 0 0 0.159 0

dihedral_coeff 40 opls 0 0 0.183 0

dihedral_coeff 41 opls 0 0 0.183 0

dihedral_coeff 42 opls 0 0 0.183 0

dihedral_coeff 43 opls 0 0 0.183 0

dihedral_coeff 44 opls 0.87 -0.0785 0.1395 0

dihedral_coeff 45 opls 0 0 0 0

dihedral_coeff 46 opls 0 0 0 0

dihedral_coeff 47 opls 0 0.583 0 0

dihedral_coeff 48 opls -0.1385 0.614 -0.347 0

dihedral_coeff 49 opls 0 0 0.183 0

dihedral_coeff 50 opls 0.87 -0.0785 0.1395 0

dihedral_coeff 51 opls -1.03 -0.1565 0.1575 0

dihedral_coeff 52 opls -0.287 -0.4985 0 0

dihedral_coeff 53 opls 0.325 -0.125 0.335 0

dihedral_coeff 54 opls 0.325 -0.125 0.335 0

dihedral_coeff 55 opls 0 0 0 0

dihedral_coeff 56 opls 0 0 0.183 0

dihedral_coeff 57 opls 0 0 0.183 0

dihedral_coeff 58 opls 0.87 -0.0785 0.1395 0

dihedral_coeff 59 opls 0 0.583 0 0

dihedral_coeff 60 opls -0.1385 0.614 -0.347 0

dihedral_coeff 61 opls 0 0 0.251 0

dihedral_coeff 62 oplsmod2 -0.292 0.004 -0.914 -0.111 0

dihedral_coeff 63 opls 1.3095 -0.31 0.129 0

dihedral_coeff 64 oplsmod2 -0.292 0.004 -0.914 -0.111 0

dihedral_coeff 65 opls 1.3095 -0.31 0.129 0

dihedral_coeff 66 opls -1.03 -0.1565 0.1575 0

dihedral_coeff 67 oplsmod1 0 7.25 0 0 0

dihedral_coeff 68 oplsmod1 0 7.25 0 0 0

dihedral_coeff 69 oplsmod1 0 7.25 0 0 0

dihedral_coeff 70 oplsmod1 0 7.25 0 0 0

neighbor 2.0 bin

neigh_modify delay 1000

timestep 0.1

thermo 1000

thermo_style custom step temp evdwl ecoul pe ke etotal press

variable t world 300.0 333.0 367.0 400.0 433.0 467.0 500.0 533.0 567.0 600.0 633.0 667.0

variable w world 9 3 11 10 6 1 5 8 2 4 0 7

fix myfix all langevin $t $t 1000.0 19191

fix 2 all nve

dump 1 all atom 10000 dump.P3HT_PtBA.%

restart 100000 restart.P3HT_PtBA.%.*

temper 8000000 10000 $t myfix 3847 20000 $w

2

What is the nature of the problem? Are you getting
no restart files output, or something else? Can you
reproduce the problem with a simpler script, in less
timesteps?

Steve

3

I am getting back two restart files for each output step, one with a label 0
for the 0 processor and then one labeled base so I do not think time steps
is the issue. I was under the impression that with the % label it would
output a restart file for each processor.

4

If you're not running tempering, the normal output
for a restart file with a % char, is to have one
small file with the "base" name, and then one per
processor, e.g. 0,1,2,3 if running on 4 procs.

For tempering, you are really running a bunch of
1-processor jobs, so each will write their own restart
file. So you would get a "base" and a "0" file
for each replica. If you didn't otherwise give them
separate names via a world-style variable, they
would step on each other.

I think for tempering, you don't want to use the "%'.
You will get one restart file (w/out the base file)
for each replica regardless. Just use a world-style
variable in the file name to distinguish them.

Steve