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Re: [lammps-users] Equilibrate crystal SiO2 at normal pressure and atmosphere
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Re: [lammps-users] Equilibrate crystal SiO2 at normal pressure and atmosphere


From: Julien Guénolé <julien.guenole@...4839...>
Date: Mon, 13 Nov 2017 16:18:19 +0100

To complement this suggestion, you can also ensure that your system is statically relaxed (lower energy and forces, by minimize) and stress-free before running the dynamics. Then slowly increase the temperature by doing a dynamics within the NPT ensemble.

Also I do not see any timestep command in your script. I think one should always provide such value, even if Lammps define a default one.

On 12/11/17 16:54, Chowdhury, Sanjib Chandra wrote:

Make sure that initial crystal structure and force field are correct.

 

From: Bingyu Cui [mailto:hwtray@...8...]
Sent: Sunday, November 12, 2017 7:13 AM
To: Chowdhury, Sanjib Chandra <sanjib@...2437...>
Cc: lammps-users@lists.sourceforge.net
Subject: RE: Equilibrate crystal SiO2 at normal pressure and atmosphere

 

Dear Sanjib,

 

Thank you for your quick reply. As you mentioned, before step 1100 (from step 0 to step 1000), everything goes fine but the pressure fluctuates a lot. However, at step 1100, namely when fix 3 all pressure/berendsen begin to work, model blows up and all particles got lost…

If I fix NPT or NVT between fix NVE&Langevin and fix pressure/berendsen, same problem occurs.

 

I also tried to run fix pressure/berendsen and NPT simultaneously after fix NVE and langevin, however, it then reported unstable simulation-numerical pressure…

 

Regards

Bingyu Cui

From: Chowdhury, Sanjib Chandra
Sent: Sunday, November 12, 2017 12:46 AM
To: 'Bingyu Cui'
Cc: lammps-users@lists.sourceforge.net
Subject: RE: Equilibrate crystal SiO2 at normal pressure and atmosphere

 

Visualize the model just before step 1100 to see what happens. PE =0 means model blows up. This could be for multiple reasons - bad initial structure, bad force field etc.

Did you try with ‘Fix NVT’ and ‘Fix NPT’?

 

Sanjib

 

From: Bingyu Cui [mailto:hwtray@...8...]
Sent: Saturday, November 11, 2017 7:13 PM
To: lammps-users@lists.sourceforge.net
Subject: [lammps-users] Equilibrate crystal SiO2 at normal pressure and atmosphere

 

Dear all,

 

I want to get equilibrated lattice constants of crystal SiO2 at room temperature. I have searched many previous posts but I am still not clear on the procedure to control temperature and atmosphere. The total number of atoms in simulation box is 13500.

 

I firstly run 1000 for quick test. The problem occurs when I fix pressure since I want to relax the structure after the system is in 1 atom. At step 1000, temperature is 297, Potential is -205457, total energy is -204938 and pressure is 28496.

Then at step 1100,

Temp=297, potential energy=0, total energy=519 while pressure, volume and density all becomes -nan

 

I also tried to fix pressure at 1atom before fixing temperature, but then it reported: ORTE_ERROR_LOG:Data unpack would read past end of buffer in file unti/show_help.c at line 500

 

Why does it happen and how to fix the temperature before relaxation the structure?

 

Thanks

Bingyu Cui

 

Here is my script:

#Initialization############################################################

units metal

dimension       3

boundary        p p p

atom_style charge

# Atom definition##########################################################

lattice custom 5.4047 &

a1 0.9092 0.0000 0.0000 &

a2 -0.4546 0.7873 0.0000 &

a3 0.0000 0.0000 1.0000 &

basis 0.4697 0.0000 0.0000 &

basis 0.0000 0.4697 0.6667 &

basis 0.5303 0.5303 0.3333 &

basis 0.4133 0.2672 0.1188 &

basis 0.2672 0.4133 0.5479 &

basis 0.7328 0.1461 0.7855 &

basis 0.5867 0.8539 0.2145 &

basis 0.8539 0.5867 0.4521 &

basis 0.1461 0.7328 0.8812

region simbox block 0.0 10.0 0.0 10.0 0.0 10.0 units lattice

create_box 2 simbox

create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 2 basis 5 2 basis 6 2 basis 7 2 basis 8 2 basis 9 2

mass 1 28.0855

mass 2 15.9994

group           siliconatoms type 1

group           oxygenatoms type 2

set group siliconatoms charge 2.4

set group oxygenatoms charge -1.2

# Atoms interactions settings##################################

# Si type 1, O type 2

pair_style      table linear 10001

pair_coeff      1 1 potential.table SiSi

pair_coeff      1 2 potential.table SiO

pair_coeff      2 2 potential.table OO

#kspace_style pppm 1.0e-4

neigh_modify every 1 delay 0 check yes

pair_write      1 2 9999 r 0.001 10.0 table.txt Si_O 2.4 -1.2

pair_write      2 2 9999 r 0.001 10.0 table.txt O_O -1.2 -1.2

pair_write      1 1 9999 r 0.001 10.0 table.txt Si_Si 2.4 2.4

# Equilibrate ##############################

velocity        all create 298.15 635845 dist gaussian

fix 0 all npt temp 298.15 298.15 0.1 iso 1.01325 1.01325 1.0

unfix 0

fix 1 all nve                                                       

fix 2 all langevin 298.15 298.15 0.1 48279

thermo_style     custom step temp pe etotal press vol density xlat ylat zlat

thermo          100

dump 2 all atom 1000 dump2.qua

run             1000000

unfix 1

unfix 2

fix 3 all pressure/berendsen iso 1.03125 1.03125 1.0

thermo_style     custom step temp pe etotal press vol density xlat ylat zlat

thermo          100

dump 3 all atom 1000 dump3.qua

run             1000000

unfix 3

fix 4 all box/relax iso 0.0 vmax 0.001

 



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