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Re: [lammps-users] COMB3 too slow (compared to Reax/C)
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Re: [lammps-users] COMB3 too slow (compared to Reax/C)

From: Sencer Selcuk <sselcuk@...1683...>
Date: Thu, 30 Nov 2017 21:39:11 -0500

Hi Ray,

Thanks for the answer. Yes I use the real units and the proper timestep value with reax. Also, I don't actually output the fq.out, the second qeq was (and the whole minimization part) was commented out in my tests, as I first did the minimization separately.

I understand that there is nothing obviously wrong in my input file then, right?

On [11/30/17] [10:33pm], Ray Shan wrote:
Factor of 5-10 seems a bit much.  Are you using “real” units and changing >timestep appropriately for ReaxFF?  If you have a slow disk I/O, then not >writing fq.out might help (remove "file fq.out” from fix qeq/comb).


On 11/30/17, 11:04 AM, "Sencer Selcuk" ><sselcuk@...1683...<mailto:sselcuk@...1683...>> wrote:

Dear all,

I am experimenting with the COMB3 potential to model a system of Zn/O/H and >possibly Ti. I started a simulation with <3000 atoms, and it seems to be >running well expect for the fact that it is too slow. When I try simulating >the system with Reax/C (which also has the parameters for Zn/O/H) speed up is >around ~5-10 times of the COMB3. I am wondering if I am doing anything wrong.

I am using lammps-31Mar17 on NERSC resources, and the code is available as a >module.

Here is my input file, and for the qeq/reax I used 1E-6 as the convergence >criterion.

units          metal
atom_style     charge
boundary       p p p

mass           1 1.00
mass           2 16.0
mass           3 65.4

pair_style     comb3 polar_off
pair_coeff     * * ffield.comb3 H O Zn
fix            qeq all qeq/comb 10 1E-3 # tried to speed up, was 1 1E-3

neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes

dump           1 all custom 2000 nano.lammpstrj element x y z
dump_modify    1 sort id element H O Zn append yes

timestep 2E-4

thermo_style   custom step time temp press vol pe etotal enthalpy
thermo_modify  flush yes
thermo         2000

# equilibrate charge first; minimization hangs indefinitely otherwise
fix             1 all nvt temp 300.0 300.0 0.1
thermo          1
run             1
fix             2 all qeq/comb 1 0.003 file fq.out
run             5

# minimize
unfix           1
fix             1 all box/relax aniso 0.0 vmax 0.0002
minimize        1.0E-8 1.0E-10 10000 100000
unfix           1

displace_atoms  all random 0.08 0.08 0.08 328
fix             nvt all nvt temp 300.0 300.0 20
run             1000000


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