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Re: [lammps-users] Temperature control in fix gcmc with fix rigid/nvt/small
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Re: [lammps-users] Temperature control in fix gcmc with fix rigid/nvt/small


From: "Youzhi Hao" <hyzlvxg@...516...>
Date: Mon, 19 Jun 2017 20:19:39 +0800

Hi Mohammad,

         I’ve tested in three simulation scenarios:

1)      Using fix gcmc to fill the clay structure with methane, combined with fix rigid/nvt/small.  During this process, the system temperature was not well controlled.
Specially, the system temperature  was always much higher than the specified temperature, because the large amount of continuous filling of methane molecules.

2)      Unfix gcmc after some time which the system was filled with some methane, then let the fix rigid/nvt/small do the thermostat alone.
However, the temperature was
still not thermostat correctly, i.e. the temperature seemed not affected by this fix.

3)      Then let’s just start with a new simulation, with a methane pre-filled simulation system, by using fix rigid/nvt/small, then the temperature was finely thermostat!

As you can see, this indeed may be related to the fix gcmc command, but I cannot figure out the reason, could someone take a look at this?

 

regards,

Youzhi

 

From: Mohammad Rafat Sadat [mailto:msadat@...12...3324...]
Sent: Monday, June 19, 2017 6:00 PM
To: Youzhi Hao <hyzlvxg@...516...>
Cc: LAMMPS Users Mailing List <lammps-users@lists.sourceforge.net>
Subject: Re: [lammps-users] Temperature control in fix gcmc with fix rigid/nvt/small

 

Hi Youzhi,

 

I also observed similar phenomena for my water adsorption onto silicate systems where the temperature is not controlled as speciefied in gcmc command. However, I went ahead with the simulation and equilibrated the system separately once the final configuration was achieved from the gcmc run. Not really sure if this is to be expected from gcmc. So I look forward for any other user's comments on this. Thanks!

 

 


Mohammad Rafat Sadat

Graduate Assistant (PhD candidate)

Department of Civil Engineering and Engineering Mechanics,
University of Arizona,

PO Box 210072 • 1209 E. Second Street, Room 207A, Tucson, AZ 85721

 

On Mon, Jun 19, 2017 at 1:27 AM, Youzhi Hao <hyzlvxg@...516...> wrote:

hi,

I’m trying to do gcmc simulation of rigid CH4 molecules adsorption isotherms in clay minerals

by using fix gcmc with fix rigid/nvt/small.

The coulomb potential was calculated by PPPM.

The fix rigid/nvt/small was combined with fix_modify dynamic/dof yes

and fix_modify temp as the LAMMPS Manuals says.

 

However, as the simulation going on (after a long time), the CH4 molecules were just kept adding to the system,

leading the pressure far higher than the pressure specified in fix gcmc command.

Also, the system temperature continues increasing up, higher than the specified temperature.

The fix rigid/nvt/small command seems did not thermostat well.

So, what’s the reason lying beneath this unusual phenomenon?

 

Part of my input file is :

variable temp  equal  363.15

variable press  equal  100.00

variable fug_coeff equal 0.934

molecule  ch4  mol.ch4.txt  #full atom methane molecule

compute Temp_methane methane temp/com

compute_modify Temp_methane dynamic/dof yes

fix  mrsnvt  methane  rigid/nvt/small  molecule  temp ${temp} ${temp} 100.0  mol ch4

fix_modify  mrsnvt  dynamic/dof  yes

fix_modify  mrsnvt  temp  Temp_methane

fix  1  methane  gcmc  1000  1000 500 0 2949499 ${temp} -0.28 0.5 mol ch4  &

      maxangle 180 rigid mrsnvt pressure ${press}  fugacity_coeff ${ fug_coeff } full_energy

run 5000000

 

Best regards.

Youzhi Hao

 


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