Qbox Computing Bulk Modulus of Au - Revision history

Caiwei: /* Computing Bulk Modulus of Au */

2008-12-31T20:56:25Z

Computing Bulk Modulus of Au

← Older revision		Revision as of 20:56, 31 December 2008
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	== Computing Bulk Modulus of Au ==		== Qbox: Computing Bulk Modulus of Au ==

	This part of the tutorial is dedicated to a non trivial calculation of Bulk modulus with Qbox.		This part of the tutorial is dedicated to a non trivial calculation of Bulk modulus with Qbox.

Caiwei: Computing Bulk Modulus of Au by Qbox moved to Qbox Computing Bulk Modulus of Au

2008-12-31T20:55:29Z

Computing Bulk Modulus of Au by Qbox moved to Qbox Computing Bulk Modulus of Au

← Older revision	Revision as of 20:55, 31 December 2008
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Kwkang: Protected "Computing Bulk Modulus of Au by Qbox" [edit=Qbox:move=Qbox:read=Qbox]

2008-11-12T21:49:59Z

Protected "Computing Bulk Modulus of Au by Qbox" [edit=Qbox:move=Qbox:read=Qbox]

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Kwkang: Protected "Computing Bulk Modulus of Au by Qbox" [edit=Qbox:move=Qbox:read=Qbox] (expires 08:00, 11 November 2008 (UTC))

2008-11-10T22:57:21Z

Protected "Computing Bulk Modulus of Au by Qbox" [edit=Qbox:move=Qbox:read=Qbox] (expires 08:00, 11 November 2008 (UTC))

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Caiwei: /* Computing Bulk Modulus of Au */

2008-11-08T09:25:21Z

Computing Bulk Modulus of Au

← Older revision		Revision as of 09:25, 8 November 2008
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	We will compute the bulk modulus by computing stress at two different volumes and taking finite differences.		We will compute the bulk modulus by computing stress at two different volumes and taking finite differences.
	The calculation will be done with one atom per cell and many k-points. Qbox does not ~~checks~~ for convergence so it is our responsability to verify for this, including energy cutoff, iteration convergence, k-point grid, system size, and pseudopotential quality. Other ways of calculating bulk modulus and convergence tests are left as exercises.		The calculation will be done with one atom per cell and many k-points. Qbox does not check for convergence so it is our responsability to verify for this, including energy cutoff, iteration convergence, k-point grid, system size, and pseudopotential quality. Other ways of calculating bulk modulus and convergence tests are left as exercises.

	For computing the bulk modulus of gold we will need at least three files (1) a pseudopotential for Gold, (2) input files for defining cell parameters and other calculation specifications (3) a list of k-points for the FCC cell. We will put all of them in one empty directory:		For computing the bulk modulus of gold we will need at least three files (1) a pseudopotential for Gold, (2) input files for defining cell parameters and other calculation specifications (3) a list of k-points for the FCC cell. We will put all of them in one empty directory:
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	wget http://micro.stanford.edu/mediawiki-1.11.0/images/Au_bulk_au-pbe.TM.xml.txt -O au-pbe.TM.xml		wget http://micro.stanford.edu/mediawiki-1.11.0/images/Au_bulk_au-pbe.TM.xml.txt -O au-pbe.TM.xml

	Qbox was designed to be an interactive code, so each input line y actually a command given to the Qbox engine to set internal variables or perform a wavefunction optimization. The input file we will use is this [[media:au_bulk_au_stress.i.txt \| au_bulk/au_stress.i ]]. This input file calls another input file with the k-point sampling set [[media:au_bulk_kp8881fcc.i.txt \| au_bulk/kp8881fcc.i]].		Qbox was designed to be an interactive code, so each input line is actually a command given to the Qbox engine to set internal variables or perform a wavefunction optimization. The input file we will use is this [[media:au_bulk_au_stress.i.txt \| au_bulk/au_stress.i ]]. This input file calls another input file with the k-point sampling set [[media:au_bulk_kp8881fcc.i.txt \| au_bulk/kp8881fcc.i]].

	wget http://micro.stanford.edu/mediawiki-1.11.0/images/Au_bulk_au_stress.i.txt -O au_stress.i		wget http://micro.stanford.edu/mediawiki-1.11.0/images/Au_bulk_au_stress.i.txt -O au_stress.i

Caiwei: /* Computing Bulk Modulus of Au */

2008-11-08T09:18:45Z

Computing Bulk Modulus of Au

← Older revision		Revision as of 09:18, 8 November 2008
Line 2:		Line 2:

	This part of the tutorial is dedicated to a non trivial calculation of Bulk modulus with Qbox.		This part of the tutorial is dedicated to a non trivial calculation of Bulk modulus with Qbox.
	We performed this calculation on a dual-core Ubuntu installation (see ~~above~~).		We performed this calculation on a dual-core Ubuntu installation (see [http://micro.stanford.edu/wiki/How_to_compile_Qbox#Quick_compilation_in_Ubuntu tutorial]).

	We will compute the bulk modulus by computing stress at two different volumes and taking finite differences.		We will compute the bulk modulus by computing stress at two different volumes and taking finite differences.

Caiwei at 09:03, 8 November 2008

2008-11-08T09:03:19Z

← Older revision		Revision as of 09:03, 8 November 2008
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	* Change the k-point grid, k-point grids can be generated or just converted from other codes k-point grid outputs. For example from VASP, the only difference is that the k-point weights (see last column in 'au_bulk/kpt8881fcc.i') must be normalized to one.		* Change the k-point grid, k-point grids can be generated or just converted from other codes k-point grid outputs. For example from VASP, the only difference is that the k-point weights (see last column in 'au_bulk/kpt8881fcc.i') must be normalized to one.
	* Use a different pseudopotential, for example this one (see details inside the file) [[media:au_bulk_Au_PBE_11e.xml.txt \| au_bulk/Au_PBE_11e.xml]]		* Use a different pseudopotential, for example this one (see details inside the file) [[media:au_bulk_Au_PBE_11e.xml.txt \| au_bulk/Au_PBE_11e.xml]]

	(end of compilation tutorial)

Caiwei: New page: == Computing Bulk Modulus of Au == This part of the tutorial is dedicated to a non trivial calculation of Bulk modulus with Qbox. We performed this calculation on a dual-core Ubuntu insta...

2008-11-08T09:02:48Z

New page: == Computing Bulk Modulus of Au == This part of the tutorial is dedicated to a non trivial calculation of Bulk modulus with Qbox. We performed this calculation on a dual-core Ubuntu insta...

New page

== Computing Bulk Modulus of Au ==

This part of the tutorial is dedicated to a non trivial calculation of Bulk modulus with Qbox.
We performed this calculation on a dual-core Ubuntu installation (see above).

We will compute the bulk modulus by computing stress at two different volumes and taking finite differences.
The calculation will be done with one atom per cell and many k-points. Qbox does not checks for convergence so it is our responsability to verify for this, including energy cutoff, iteration convergence, k-point grid, system size, and pseudopotential quality. Other ways of calculating bulk modulus and convergence tests are left as exercises.

For computing the bulk modulus of gold we will need at least three files (1) a pseudopotential for Gold, (2) input files for defining cell parameters and other calculation specifications (3) a list of k-points for the FCC cell. We will put all of them in one empty directory:

mkdir au_bulk
cd au_bulk

We will omit the generation of the pseudopotential, we will only mention that the pseudopotential has to be consistent with the functional choosen (in this case GGA-PBE). The file is directly given here: [[media:au_bulk_au-pbe.TM.xml.txt | au_bulk/au-pbe.TM.xml]]

wget http://micro.stanford.edu/mediawiki-1.11.0/images/Au_bulk_au-pbe.TM.xml.txt -O au-pbe.TM.xml

Qbox was designed to be an interactive code, so each input line y actually a command given to the Qbox engine to set internal variables or perform a wavefunction optimization. The input file we will use is this [[media:au_bulk_au_stress.i.txt | au_bulk/au_stress.i ]]. This input file calls another input file with the k-point sampling set [[media:au_bulk_kp8881fcc.i.txt | au_bulk/kp8881fcc.i]].

wget http://micro.stanford.edu/mediawiki-1.11.0/images/Au_bulk_au_stress.i.txt -O au_stress.i
wget http://micro.stanford.edu/mediawiki-1.11.0/images/Au_bulk_kp8881fcc.i.txt -O kp8881fcc.i

What follows is a explanation line by line of the input file au_bulk/au_stress.i. Pound sign '#' indicate comment lines.

(begin of au_stress.i)

## this input file compute the stress tensor for FCC Au
# define cell
set cell 3.9 3.9 0.000 0.000 3.9 3.9 3.9 0.000 3.9

# define reference cell (always larger than cell),
# meant to smooth out discrete changes on pw basis on volume change
set ref_cell 4 4 0 0 4 4 4 0 4

# declare a pseudopotential file and give name to such species
species gold au-pbe.TM.xml

# add one atom to the cell
atom Au gold 0 0 0

# set number of empty states, needed for metals, nempty is 0 by default.
set nempty 8

# energy cut off, always check convergece against this variable.
set ecut 90

# define kpoints using file kp8881fcc.i
# this will call an external file that should be in the current directory
# if file is not found Qbox will ignore the line and continue!
kp8881fcc.i

# activates the calculation of stress tensor.
set stress ON

# effective cutoff for stress calculation, improves smoothness relative to change in pw basis set
set ecuts 85

# set functional, default is LDA
set xc PBE

#set optimization algorithm in non-selfconsistent loop
set wf_dyn PSD

# energy cutoff for the wf optimization algorith
# must be lower than actual ecut,
# lower values can accelerate converge but increase instabilities
set ecutprec 10

# real calculations start here
# randomize initial wavefunction
randomize_wf

# updating of charge density self consistent loop, can improve convergence
set charge_mix_coeff 0.2

# set smearing of fermi surface, can improve convergence for metals
set fermi_temp 300

# run 10 series of 5 self consistent loops with 5 non-self consistent loop
run 10 5 5

# save atom position and wavefunction for later use
save gs.xml

(end of au_stress.i)

Now we can run the calculation or submit it to a queue.

mpirun -np 2 ~/soft/qbox-1.45.0/src/qbox au_stress.i | tee au_stress.o

'au_bulk/au_stress.o' will contain all the output from qbox, exploring this file is the only way to check for convergence. The simplest check is to see (and plot) how the total energy converged:

grep etotal au_stress.o

Other checks can include stress tensor or electron occupancy. Once we checked converge we can look at the final output of the stress tensor. For example in our case we will see

$ grep '<sigma_xx' au_stress_a3.9.o -A 5 | tail -6
<sigma_xx> 4.85104411 </sigma_xx>
<sigma_yy> 4.85104541 </sigma_yy>
<sigma_zz> 4.85104410 </sigma_zz>
<sigma_xy> 0.00000018 </sigma_xy>
<sigma_yz> 0.00000010 </sigma_yz>
<sigma_xz> -0.00000064 </sigma_xz>

That means that the resulting stress is diagonal (as it should be) and the magnitude is 4.85104~GPa. The we can rerun an input file with a slightly different cell:

set cell 3.855 3.855 0.000 0.000 3.855 3.855 3.855 0.000 3.855

Then read the final stress in the same way. In this way we have two volumes 114.58 and 118.64 and obtained two corresponding pressures 11.441950 and 4.85104411 Gpa. The volumes are given in atomic units but we do not need the volume units for this. A numerical approximation of the bulf modulus is simply

(11.441950-4.85104411)/(114.58 - 118.64)* ((114.58 + 118.64)/2)

which results numerically in 189.30 in units of GPa.

Possible improvements not shown here for simplicity:

(1) It is possible to write a script (bash or otherwise) to automatize the process.
(2) It is possible to reuse the wavefunction of the first calculation in the second
by loading the gs.xml wavefunction before resetting the cell size (and removing the 'randomize_wf' line)

load gs.xml
set cell 3.855 3.855 0 3.855 0 3.855 0 0 3.855
# randomize_wf

(3) In the same way it is possible to save wavefunctions in case the calculation is interrupted

run 3 5 5
save gs_checkpoint.xml
run 3 5 5
save gs_checkpoint.xml
run 3 5 5

Further (home)work to convert this tutorial in a serious result:

* Check that the result is converged by increasing the value of ecut.
* Try duplicating the number of iteration 'run 20 5 5' to improve convergence.
* Take finite differences with smaller volume differences and near zero pressure.
* Calculate the bulk modulus using total energies at three different volumes instead of pressures or by fitting to more point near equilibrium volume.
* Change the k-point grid, k-point grids can be generated or just converted from other codes k-point grid outputs. For example from VASP, the only difference is that the k-point weights (see last column in 'au_bulk/kpt8881fcc.i') must be normalized to one.
* Use a different pseudopotential, for example this one (see details inside the file) [[media:au_bulk_Au_PBE_11e.xml.txt | au_bulk/Au_PBE_11e.xml]]

(end of compilation tutorial)