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Input file for GaAs geometry optimization
From NWChem
Viewed 2092 times, With a total of 10 Posts


10:19:50 PM PDT  Sun, May 29th 2011 

Hi all,
can you suggest an input file to do DFT geometry optimization for GaAs? I can't get it working (something about the choice of basis set, functional). Thank you!




Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop


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3:53:24 PM PDT  Wed, Jun 1st 2011 

Gaussian DFT or plane waves? Could you copy the input file in a post so we have some information we can use to help you?
Thanks,
Bert
Quote: May 30th 6:19 amHi all,
can you suggest an input file to do DFT geometry optimization for GaAs? I can't get it working (something about the choice of basis set, functional). Thank you!





1:19:27 AM PDT  Thu, Jun 2nd 2011 

GaAs

Hi Bert,
My trial input looks like:
Jun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local Time~
title "GaAs"
geometry units angstroms
Ga 0.0 0.0 2.5
As 0.0 0.0 2.5
end
basis
Ga library sto3g
As library sto3g
end
dft; direct; end
task dft optimize
Jun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local Time192.122.131.20
The goal is to optimize accurately the GaAs structure (using quality DFT functional). Either PW or Gaussian (any would do,
or as required by accuracy goal).




Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop


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2:55:33 PM PDT  Fri, Jun 3rd 2011 

Well, a couple of things here. Having a Ga and As separated by 5 angstroms is creating some of your problems, try a more realistic bond length like 2.0, i.e.
geometry units angstroms
Ga 0.0 0.0 1.0
As 0.0 0.0 1.0
end
You will need to increase the number of iterations:
dft; iterations 300; direct; end
Also, I hope you're going to use a reasonable basis set and not the minimal sto3g.
You hinted at the calculation not being able to find a basis set. If this is another issue, you should set NWCHEM_BASIS_LIBRARY to point to the location where the NWChem basis sets are on your machine (if you build from source it will be in <nwchempath>/src/basis/libraries)
setenv NWCHEM_BASIS_LIBRARY <nwchempath>/src/basis/libraries/
Hope this helps,
Bert
Quote: Jun 2nd 9:19 amHi Bert,
My trial input looks like:
Jun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local Time~
title "GaAs"
geometry units angstroms
Ga 0.0 0.0 2.5
As 0.0 0.0 2.5
end
basis
Ga library sto3g
As library sto3g
end
dft; direct; end
task dft optimize
Jun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local TimeJun 2nd 9:19 am Local Time192.122.131.20
The goal is to optimize accurately the GaAs structure (using quality DFT functional). Either PW or Gaussian (any would do,
or as required by accuracy goal).




Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop


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Threads 4
Posts 148


7:14:33 PM PDT  Sat, Jun 4th 2011 

Hi,
Are you trying to do perform a periodic or molecular calculation ?
Our Gaussian basis DFT module is for molecular systems while the planewave module can handle periodic systems. Your input specifications above will invoke the Gaussian DFT module. In other words, the calculation will only be performed on 2 atoms.
Best,
Niri
niri.govind@pnnl.gov





10:14:44 PM PDT  Sun, Jun 5th 2011 

Progress on GaAs

Hi Bert and Niri,
thanks for your quick replays. I reply to each below in detail. Additionally, do you know any way in NWChem to access 1) the band occupation numbers (ie, to change them at will) and 2) to calculate dipole transition moments (ie, <kmx,y,zk'n> or momentum operator transitions)? Even to have the wave functions numerically could help by doing the dipole elements with quadrature (though not so accurately).
For Bert:
I went to 2 Angstr for the bond length. I tried some augccpvdz. Not much success. Could you suggest a suitable basis set for GaAs? At this point, I would be happy to see a converged calculation (ground state energy) at a given bond length (say 2 Angstrom).
For Niri:
A molecular calculation is wanted. As you can see above, I am missing some good basis set for GaAs. Basically, i would like to see a converged energy calculation at fixed bond length.
Thank you!




Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop


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2:47:30 PM PDT  Thu, Jun 9th 2011 

The input deck below works fine for me:
title "GaAs"
geometry units angstroms
Ga 0.0 0.0 1.5
As 0.0 0.0 1.5
end
basis
Ga library augccpvdz
As library augccpvdz
end
dft
iterations 300
end
task dft optimize
The first DFT converges in 29 steps. The geometry optimization converges in 7 steps to a bond length of 2.15429 Angstrom.
If you cannot reproduce this I wonder if something is up with your binary.
Bert
Quote: Jun 6th 6:14 amHi Bert and Niri,
thanks for your quick replays. I reply to each below in detail. Additionally, do you know any way in NWChem to access 1) the band occupation numbers (ie, to change them at will) and 2) to calculate dipole transition moments (ie, <kmx,y,zk'n> or momentum operator transitions)? Even to have the wave functions numerically could help by doing the dipole elements with quadrature (though not so accurately).
For Bert:
I went to 2 Angstr for the bond length. I tried some augccpvdz. Not much success. Could you suggest a suitable basis set for GaAs? At this point, I would be happy to see a converged calculation (ground state energy) at a given bond length (say 2 Angstrom).
For Niri:
A molecular calculation is wanted. As you can see above, I am missing some good basis set for GaAs. Basically, i would like to see a converged energy calculation at fixed bond length.
Thank you!





10:00:35 PM PDT  Thu, Jun 9th 2011 

Working well so far...

Hi Bert,
this one is working indeed . Thank you!
Once optimized, is it now difficult to do a band structure plot? Or is that not implemented in NWChem? I saw that one can give the individual k point when asking for the energy levels (even then, I am not sure i know where to read for the energy levels at that given k point). Here is what I used (and working):
title "GaAs"
geometry units angstroms
Ga 0.0 0.0 0
As 0.0 0.0 2.15429
end
basis
Ga library augccpvdz
As library augccpvdz
end
dft
iterations 300
end
task dft energy
NWPW
BRILLOUIN_ZONE
ZONE_NAME zone_1
KVECTOR 0.0 0.0 0.0 1.0
END
END




Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop


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Threads 4
Posts 148


4:53:28 AM PDT  Fri, Jun 10th 2011 

Hi,
You performed a Gaussian basis set DFT calculation. Our Gaussian basis set module is purely for molecular or finite systems. If you want a band structure, you need to run the plane wave module for this system
Check the following tutorial in the Plane Wave DFT documentation page. It shows you how to performa band structure calculation on diamond.
http://www.nwchemsw.org/index.php/NWPW#Using_BAND_to_Calculate_the_Band_Structures_of_Dia...
Best,
Niri





11:41:51 PM PDT  Sun, Jun 12th 2011 

Thank you. For the PW approach, I encounter some difficulties with running the script. I put below the file for the band structure (inspired from the diamond example). At some points, it crashes
"0:0:cpsi_data_alloc: out of heap memory:: 0 ..."
Jun 13th 7:41 am Local TimeJun 13th 7:41 am Local Time192.122.131.20
title "GaAs"
permanent_dir ./
start GaAs
memory 3000 mb
geometry center noautosym noautoz print
system crystal
lat_a 5.4d0
lat_b 5.4d0
lat_c 5.4d0
alpha 90.0d0
beta 90.0d0
gamma 90.0d0
end
Ga 0.00000d0 0.00000d0 0.00000d0
As 0.25000d0 0.25000d0 0.25000d0
end
nwpw
ewald_rcut 3.0
ewald_ncut 8 #The default value of 1 needs to be increased
lmbfgs
xc pbe96
monkhorstpack 9 9 9
end
task band energy
nwpw
virtual 16
brillouin_zone
zone_name fccpath
path fcc l gamma x w k gamma
end
zone_structure_name fccpath
end
task band structure
Jun 13th 7:41 am Local TimeJun 13th 7:41 am Local Time192.122.131.20




Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop


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Threads 5
Posts 598


1:28:33 PM PDT  Mon, Jul 18th 2011 

Try "memory heap 1400 stack 1500 global 100 mb"
Bert
Quote: Jun 13th 7:41 amThank you. For the PW approach, I encounter some difficulties with running the script. I put below the file for the band structure (inspired from the diamond example). At some points, it crashes
"0:0:cpsi_data_alloc: out of heap memory:: 0 ..."
Jun 13th 7:41 am Local TimeJun 13th 7:41 am Local Time192.122.131.20
title "GaAs"
permanent_dir ./
start GaAs
memory 3000 mb
geometry center noautosym noautoz print
system crystal
lat_a 5.4d0
lat_b 5.4d0
lat_c 5.4d0
alpha 90.0d0
beta 90.0d0
gamma 90.0d0
end
Ga 0.00000d0 0.00000d0 0.00000d0
As 0.25000d0 0.25000d0 0.25000d0
end
nwpw
ewald_rcut 3.0
ewald_ncut 8 #The default value of 1 needs to be increased
lmbfgs
xc pbe96
monkhorstpack 9 9 9
end
task band energy
nwpw
virtual 16
brillouin_zone
zone_name fccpath
path fcc l gamma x w k gamma
end
zone_structure_name fccpath
end
task band structure
Jun 13th 7:41 am Local TimeJun 13th 7:41 am Local Time192.122.131.20



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