Hi Everybody
I had a question about using run_style verlet/split. To summarize, I am running a NPT simulation using a series of two fix npt (first is to equilibrate and the second for production).
The equilibration run works flawlessly for an indefinite number of time steps. When I start the production run, the simulation always fails at the 1st time step with a message - ERROR on abc-Kspace-processor: Bond atoms missing on xyz-Rspace-processor or similar. This happens for every Kspace processor. I don’t believe physics is a problem because the simulation can run using the first fix indefinitely. It appears that as the atoms migrate from one Kspace processor to another, the original run can continue alright but attempting to start a new run fails. If I run the first fix for just one time step, the simulation proceeds from the first fix to the second smoothly.
I first observed this problem in a much larger and complex system but I am now using toluene as an example. I am running this system on 16 (4X2X2) processors for the real space and 2 processors (2X1X1) for the k space. I did not observe this error if I used just one k_space processor (i.e. 8 (2X2X2) processors for real space and 1 (1X1X1) processor for k_space). I have attached pasted the input script file and screen file for the k_space partition. (the log files do not show the error)
Maybe I missing something obvious, but I have been trying to figure this out for some time and I am going in circles. Any help would be appreciated.
Thanks
Ketan
---------------------------------Input script-------------------------------------
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
pair_style lj/cut/coul/long/opt 9
pair_modify mix arithmetic
pair_modify tail yes
kspace_style pppm 1e-4
boundary p p p
processors * * * part 1 2 multiple
read_data data.Toluene600
replicate 2 1 1
timestep 1
run_style verlet/split
variable mass_g equal mass(all)/6.02e23
variable vol_cm3 equal vol*1.0e-24
variable Density equal v_mass_g/v_vol_cm3
variable SpecificVolume equal 1.0/v_Density
thermo_style custom step temp press vol etotal epair emol evdwl ecoul elong ebond eangle enthalpy pe ke v_Density v_SpecificVolume lx ly lz cpu
thermo 100
fix 1 all npt temp 300 300 100.0 iso 1.0 1.0 1000.0
run 4000 #fs
unfix 1
fix 1 all npt temp 300 300 100.0 iso 1.0 1.0 1000.0
run 1 #fs
unfix 1
write_restart restart.EndofRun
data.Toluene600 (1.53 MB)