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


From: "Youzhi Hao" <hyzlvxg@...516...>
Date: Sun, 2 Jul 2017 15:14:55 +0800

hi Aidan,
I have installed the latest development LAMMPS version 23 June 2017 and tested it.
Now the fix gcmc with fix rigid/nvt/small works fine with my system, the temperature 
is thermostatted well.
Thanks!

Best regards,
Youzhi

-----Original Message-----
From: Thompson, Aidan [mailto:athomps@...3...]
Sent: Thursday, June 29, 2017 6:37 AM
To: hyzlvxg@...516...
Cc: lammps/lammps LAMMPS Users List <lammps-users@lists.sourceforge.net>
Subject: Re: [EXTERNAL] Fwd: [lammps-users] Temperature control in fix gcmc
with fix rigid/nvt/small

There were some recent improvements made to fix gcmc that might resolve the
issues you describe here. If not, please post a *small* example that
demonstrates the problem.

Aidan


---------- Forwarded message ----------
From: Youzhi Hao <hyzlvxg@...516...>
Date: Thu, Jun 22, 2017 at 9:36 PM
Subject: Re: [lammps-users] Temperature control in fix gcmc with fix
rigid/nvt/small
To: Mohammad Rafat Sadat <msadat@...3324...>
Cc: LAMMPS Users Mailing List <lammps-users@lists.sourceforge.net>

Hi Mohammad,
   This is update information for the question as I mentioned before as:
“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.”

Recently, I tried a different way to tackle the problem described above:
When unfix gcmc, also unfix  rigid/nvt/small, then create a new fix
rigid/nvt/small.
By doing this, the system is well thermostated. It seems that fix
rigid/nvt/small functions well when fully detached from fix gcmc.

However, this question still troubles me:
Fix gcmc combined with fix rigid/nvt/small does not thermostat the system as
user-specified temperature T.
This leads the system temperature differs greatly from the ideal gas
reservoir’s temperature, which is not a uvt ensemble.


From: Youzhi Hao [mailto:hyzlvxg@...516...]
Sent: Monday, June 19, 2017 8:20 PM
To: 'Mohammad Rafat Sadat' <msadat@...3324...>

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 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@...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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