SHAKE problem

LAMMPS LAMMPS Mailing List Mirror
1

Dear LAMMPS-USERS,

I tried to simulate a small model (lx=ly=lz=10) consists of 2 SPC/E water model inside two carbon atoms walls. When I run the simulation it works fine with SHAKE algorithm.

But, when I want to run a big simulation model (lx=ly=30, lz=20) with 800 SPC/E water I come across to the error as

fix ensemble_set all nvt temp 300.0 300.0 0.05
fix spce_model water shake 0.0001 20 0 b 1 a 1#
ERROR: Unknown fix style (…/modify.cpp:762)

Please share your comments.

Thanks in advance

My input

***************** Initialization *********************

units real
dimension 3
boundary p p p
atom_style full
read_data atm_data.dat

group oxygen type 1
group hydrogen type 2
group carbon type 3
group water type 1 2

set group oxygen charge -0.8476
set group hydrogen charge 0.4238
set group carbon charge 0.0000

#pair_style dpd/tstat 300.0 300.0 10.0 34387
#comm_style brick
#comm_modify vel yes

#pair_style hybrid lj/cut/coul/long 10.0 10.0 tersoff
pair_style lj/cut/coul/long 10.0 10.0
pair_coeff 1 1 0.155300 3.16900 #lj/cut/coul/long
pair_coeff 1 2 0.00000 0.00000
pair_coeff 1 3 0.093627 3.1900
pair_coeff 2 2 0.000000 0.0000
pair_coeff 2 3 0.000000 0.0000
pair_coeff 3 3 0.000000 0.0000
#pair_coeff * * tersoff SiC_1994.tersoff NULL NULL C

bond_style harmonic
bond_coeff 1 529.581 1.0
angle_style harmonic
angle_coeff 1 37.95 109.47

fix force_zero carbon setforce 0.0 0.0 0.0
fix vel_zero carbon move linear 0.0 0.0 0.0 units lattice

#velocity oxygen create 300.0 34387 rot yes dist gaussian # for Oxygen
#velocity hydrogen create 300.0 34387 rot yes dist gaussian # for Hydrogen
#velocity water create 300.0 34387 rot yes dist gaussian # for water

kspace_style ewald 1.0e-6

*************** Setting ******************************

neighbor 2.0 bin
neigh_modify delay 0 every 10 check yes

reset_timestep 0

thermo 100
thermo_style custom step elapsed dt time atoms
thermo_modify norm no flush yes

fix ensemble_set all nvt temp 300.0 300.0 0.05
fix spce_model water shake 0.0001 20 0 b 1 a 1#

#compute 1 all pe/atom
#minimize 1.0e-4 1.0e-6 100 1000
#min_style cg

dump trj all cfg 100 wat_lammpstrj.*.cfg id type xs ys zs
dump_modify trj element O H C

#write_data waterinfo.data
#write_restart waterinfo.restart

timestep 0.2
run 1000

2

2015-01-16 10:04 GMT+01:00 Majid Shahbabaei <[email protected]...>:

Dear LAMMPS-USERS,

I tried to simulate a small model (lx=ly=lz=10) consists of 2 SPC/E water
model inside two carbon atoms walls. When I run the simulation it works
fine with SHAKE algorithm.
But, when I want to run a big simulation model (lx=ly=30, lz=20) with 800
SPC/E water I come across to the error as

fix ensemble_set all nvt temp 300.0 300.0 0.05
fix spce_model water shake 0.0001 20 0 b 1 a 1#
ERROR: Unknown fix style (../modify.cpp:762)

fix shake is in the RIGID package, so you probably didn't make LAMMPS with
that package

Kristof

3

It seems highly unlikely that fix shake would stop working by only changing the simulation size. Are you running both simulations on the same machine?

4

Dear Stefan and Kristof,

Yes. I am using a same machine.

Meanwhile, I added the RIGID package and made LAMMPS. Even though it works well with small size.

5

In that case I have no clue. If you also post the data file people could try to reproduce the problem to figure out what the problem is.

6

Dear Stefan,

Thank you very much. If any body has a free time I would be appreciated to try my data. The third one works well but first one (atm_data.dat) does not work.

Thanks in advance

atm_data.dat (410 KB)

in.test (2.1 KB)

atmdata-ggg.dat (6.33 KB)

7

In my case the only error is
ERROR: Dump cfg arguments must start with ‘mass type xs ys zs’ or ‘mass type xsu ysu zsu’ (…/dump_cfg.cpp:54)

If I fix the line everything works fine. I concur with Kristof, if LAMMPS says “unknown fix style” you must be missing the rigid package. Does shake show up if you do run lmp_ -h?

8

Dear Stefan and Kristof,

Thank you very much for your helps. When I use lmp_serial -h I find that shake is available. Please see the following lines

* Fix styles

adapt addforce ave/atom ave/correlate aveforce
ave/histo ave/spatial ave/time balance box/relax
deform drag dt/reset enforce2d external
gravity heat indent langevin lineforce
momentum move nph nph/sphere npt
npt/sphere nve nve/limit nve/noforce nve/sphere
nvt nvt/sllod nvt/sphere planeforce press/berendsen
print property/atom qeq/comb recenter restrain
rigid rigid/nph rigid/nph/small rigid/npt rigid/npt/small
rigid/nve rigid/nve/small rigid/nvt rigid/nvt/small rigid/small
setforce shake spring spring/rg spring/self
store/force store/state temp/berendsen temp/csvr temp/rescale
tmd tune/kspace vector viscous wall/colloid
wall/harmonic wall/lj1043 wall/lj126 wall/lj93 wall/reflect
wall/region

Thanks in advance

9

Dear Kristof and Stefan,

I tried to run that simulation with another machine (Leo cluster). Currently I am using Ubuntu 12.04.
Through that machine (Leo cluster) the script works well.

Anyway, thank you very much for your valuable time.

Thanks in advance

10

Which version of LAMMPS are you using? When I try with (26 Nov 14) I get the same result as Stefan.

11

Dear Niall,

Thank you for your attention. I am using LAMMPS 22Dec-14.

12

Dear Niall,

Thank you for your attention. I am using LAMMPS 22Dec-14.

you *have* to be providing inconsistent data. nobody can debug this,
if what you tell us is not consistent with the files you provide.
your input fails due to the incorrect dump command line with that
version (and many newer and older versions, since this feature has not
been changed in a pretty long time) but it does not fail due to the
shake fix.

axel.