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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: Ray Shan <rshan@...1795...>
Date: Fri, 1 Dec 2017 04:20:59 +0000

Hi Sencer,



No real problem with your script, but please note that the last instance of a command is the effective one, therefore the following line is the effective “fix qeq/comb” for your minimization and long-time production NVT run:

fix             2 all qeq/comb 1 0.003 file fq.out


So you didn’t actually use a larger Nfreq and turn off writing the fq.out file.

Ray

On 11/30/17, 6:39 PM, "Sencer Selcuk" <sselcuk@...1683...> wrote:

>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?
>
>Best,
>Sencer
>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).
>>
>>Ray
>>
>>
>>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
>>read_data      data.in
>>
>>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
>>write_data      data.in
>>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
>>
>>Best,
>>Sencer
>>
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