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Re: [lammps-users] How to raise the temperature after box relaxation at 0K?
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Re: [lammps-users] How to raise the temperature after box relaxation at 0K?


From: Meral Sharkas <eng_meral.sh10@...16...>
Date: Tue, 22 Aug 2017 22:29:23 +0000 (UTC)

Thank you Stefan for your help.

so how can i know if there are atoms not moving?


#                                                  ****System identification****


units         metal
atom_style    charge
boundary      p p p
#read_data     data.cryst
#replicate     2 2 2 




lattice custom 1 a1 6.607 0 0 a2 0 6.607 0 a3 0 0 5.982 basis 0.0 0.75 0.125 basis 0.0 0.25 0.875 basis 0.5 0.75 0.375 basis 0.5 0.25 0.625 basis 0.0 0.75 0.625 basis 0.0 0.25 0.375 basis 0.5 0.75 0.875 basis 0.5 0.25 0.125 basis 0.0 0.0658 0.1955 basis 0.0 0.9342 0.8045 basis 0.5  0.0658 0.3045 basis 0.5 0.9342 0.6955 basis 0.0 0.5658 0.8045 basis 0.0 0.4342 0.1955 basis 0.5 0.5658 0.6955 basis 0.5 0.4342 0.3045 basis 0.6842 0.25 0.9455 basis 0.8158 0.75 0.4455 basis 0.8158 0.25 0.5545 basis 0.6842 0.75 0.0545 basis 0.1842 0.25 0.5545 basis 0.3158 0.75 0.0545 basis 0.3158 0.25 0.9455 basis 0.1842 0.75 0.4455

region R1 block -1 1 -1 1 -1 1

create_box    3 R1
 

create_atoms 3 region R1 basis 1 1 basis 2 1 basis 3 1 basis 4 1 basis 5 2 basis 6 2 basis 7 2 basis 8 2 basis 9 3 basis 10 3 basis 11 3 basis 12 3 basis 13 3 basis 14 3 basis 15 3 basis 16 3 basis 17 3 basis 18 3 basis 19 3 #basis 20 3 basis 21 3 basis 22 3 basis 23 3 basis 24 3



mass          1 91.224
mass          2 28
mass          3 16
group         1 type 1   # zircon
group         2 type 2   # silicon
group         3 type 3   # oxygen

set group     1 type 1 charge 3.8
set group     2 type 2 charge  2.0
set group     3 type 3 charge -1.45

velocity      all create 1 7928459 dist gaussian

dump atom     all custom 1000 dump.coordinates id type x y z

#                                               ****System interatomic potential****

kspace_style ewald 5e-3

pair_style born/coul/long 10

#pair_style hybrid/overlay table linear 9999 ewald coul/long 10


pair_coeff 1 3   1967.0 0.305004 0.0 0.0 0.0
pair_coeff 2 3   1277.0 0.227225 0.0 0.0 0.0 
pair_coeff 3 3   1755.0 0.306820 0.0 0.0 0.0 
pair_coeff 1 2   0.0 0.306820 0.0 0.0 0.0 
pair_coeff 2 2   0.0 0.306820 0.0 0.0 0.0 
pair_coeff 1 1   0.0 0.306820 0.0 0.0 0.0  

timestep 0.001
thermo 100

compute me all pressure thermo_temp
thermo_style custom step atoms temp press c_me vol lx ly lz density


fix 1 all nve
run 1000
unfix 1

fix 1 all nve/limit 1
run 1000
unfix 1    


fix 2 all nve/limit 0.8
run 1000

unfix 2

fix 3 all nve/limit 0.6
run 1000
unfix 3

fix 4 all nve/limit 0.4
run 1000   
unfix 4

fix 1 all nve/limit 0.2
run 1000   
unfix 1   

fix 1 all nve/limit 0.1
run 1000   
unfix 1   

fix 1 all nve/limit 0.07
run 1000   
unfix 1   


fix 1 all nve/limit 0.04
run 1000   
unfix 1
   
   
fix 1 all nve/limit 0.02
run 1000   
unfix 1   

fix 1 all nve/limit 0.01
run 1000   
unfix 1   


fix 1 all box/relax iso 0.0

min_style cg
minimize 1e-25 1e-25 5000 100000

run 100
unfix 1

#Equilibration
fix                     2 all npt temp 1 300.0 100 iso 0.0 0.0 1000
run 100000


On Tuesday, August 22, 2017 11:49 PM, Meral Sharkas <eng_meral.sh10@...16...> wrote:


Dear all,

Apologies but the temperature doesn't exceed 30 K and I tried several Tdamp and Pdamp. May I ask what could be the reason of that ?

Thank you




On Tuesday, August 22, 2017 11:10 PM, Meral Sharkas <eng_meral.sh10@...16...> wrote:


Dear Michal,

It worked .. Thank you very much I really appreciate it... 

Regards


On Wed, Aug 23, 2017 at 12:04 AM, Michał Kański
<michal.kanski@...2460...> wrote:
Try starting from 1K instead of 0K.

Michal

From: Meral Sharkas via lammps-users
Sent: ‎2017-‎08-‎22 22:59
To: lammps-users@lists.sourceforge.net
Subject: [lammps-users] How to raise the temperature after box relaxation at 0K?

Dear Team,

I wander if you can help me with my question.

I am trying to relax my box at 0K to decrease pressure as much as I can as a start then I want to run my equilibration at 300 K and constant NPT ensemble.

When I ran the "fix/Npt" , I got Nans.

I suppose that the problem was "raising the temperature", so if that is the case, how can I raise the temperature to 300 K for equilibration?


timestep 0.0001
thermo 100
velocity      all create 0 7928459 dist gaussian
fix 1 all box/relax iso 0.0

#minimization

min_style cg
minimize 1e-25 1e-25 5000 100000
run 1000

#Equilibration
fix                     1 all npt temp 0 300.0 100 iso 0.0 0.0 1000
run 100000

Thank you in advance

Regards,