Graphite TS binding energy - Revision history

Karsai: /* References */

2019-11-14T13:25:44Z

References

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	{{Template:Bulk_systems}}		{{Template:Bulk_systems}}

	~~Back to the [[The_VASP_Manual\|main page]].~~

	[[Category:Examples]]		[[Category:Examples]]

Karsai: /* Download */

2019-11-14T08:37:05Z

Download

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	== Download ==		== Download ==
	[~~http~~:~~//www.vasp.at/vasp-workshop/examples/graphiteBinding_ts~~.tgz graphiteBinding_ts.tgz]		[[Media:GraphiteBinding ts.tgz\| graphiteBinding_ts.tgz]]

	== References ==		== References ==

Vaspmaster: /* Running this example */

2019-06-24T21:24:08Z

Running this example

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	(N.B.: for the latter ''python'' needs to be available.)		(N.B.: for the latter ''python'' needs to be available.)

	Even though the TS method predicts a reasonable geometry (see the [[~~Graphite_interlayer_distance~~]] example) it overestimates the energetics strongly:		Even though the TS method predicts a reasonable geometry (see the [[Graphite interlayer distance]] example) it overestimates the energetics strongly:
	the computed binding energy of -0.083 eV/atom is too large compared to the RPA reference of 0.048 eV/atom.		the computed binding energy of -0.083 eV/atom is too large compared to the RPA reference of 0.048 eV/atom.
	This overestimation is - at least in part - due to neglecting the many-body interactions (see example [[Graphite MBD binding energy]]).		This overestimation is - at least in part - due to neglecting the many-body interactions (see example [[Graphite MBD binding energy]]).

Vaspmaster: /* Running this example */

2019-06-24T21:23:49Z

Running this example

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	(N.B.: for the latter ''python'' needs to be available.)		(N.B.: for the latter ''python'' needs to be available.)

	Even though the TS method predicts a reasonable geometry it overestimates the energetics strongly:		Even though the TS method predicts a reasonable geometry (see the [[Graphite_interlayer_distance]] example) it overestimates the energetics strongly:
	the computed binding energy of -0.083 eV/atom is too large compared to the RPA reference of 0.048 eV/atom.		the computed binding energy of -0.083 eV/atom is too large compared to the RPA reference of 0.048 eV/atom.
	This overestimation is - at least in part - due to neglecting the many-body interactions (see example [[Graphite MBD binding energy]]).		This overestimation is - at least in part - due to neglecting the many-body interactions (see example [[Graphite MBD binding energy]]).

Vaspmaster: /* Running this example */

2019-06-24T21:06:05Z

Running this example

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	Note that the calculation is performed in two steps (two separate single-point calculations) in which the energy for bulk graphite and for graphene are obtained.		Note that the calculation is performed in two steps (two separate single-point calculations) in which the energy for bulk graphite and for graphene are obtained.
	The binding energy is computed automatically and it is written in the file <code>results.dat</code>.		The binding energy is computed automatically and it is written in the file <code>results.dat</code>.
	(N.B.: ''python'' needs to be available.)		(N.B.: for the latter ''python'' needs to be available.)

	Even though the TS method predicts a reasonable geometry it overestimates the energetics strongly:		Even though the TS method predicts a reasonable geometry it overestimates the energetics strongly:

Vaspmaster: /* Running this example */

2019-06-24T21:05:24Z

Running this example

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	Note that the calculation is performed in two steps (two separate single-point calculations) in which the energy for bulk graphite and for graphene are obtained.		Note that the calculation is performed in two steps (two separate single-point calculations) in which the energy for bulk graphite and for graphene are obtained.
	The binding energy is computed automatically and it is written in the file <code>results.dat</code>.		The binding energy is computed automatically and it is written in the file <code>results.dat</code>.
			(N.B.: ''python'' needs to be available.)

	Even though the TS method predicts a reasonable geometry it overestimates the energetics strongly:		Even though the TS method predicts a reasonable geometry it overestimates the energetics strongly:

Vaspmaster: /* Running this example */

2019-06-24T21:03:23Z

Running this example

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	To run this example, execute the <code>run.sh</code> bash-script:		To run this example, execute the <code>run.sh</code> bash-script:

	~~./run.sh~~

	<pre>		<pre>
	#		#

Vaspmaster: /* Running this example */

2019-06-24T21:02:55Z

Running this example

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	To run this example, execute the <code>run.sh</code> bash-script:		To run this example, execute the <code>run.sh</code> bash-script:

			./run.sh

	<pre>		<pre>
	#		#
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	</pre>		</pre>

	~~The~~ calculation is performed in two steps (two separate single-point calculations) in which the energy for bulk graphite and for graphene are obtained.		Note that the calculation is performed in two steps (two separate single-point calculations) in which the energy for bulk graphite and for graphene are obtained.
	The binding energy is computed automatically and it is written in the file results.dat.		The binding energy is computed automatically and it is written in the file <code>results.dat</code>.

	Even though the TS method predicts a reasonable geometry it overestimates the energetics strongly:		Even though the TS method predicts a reasonable geometry it overestimates the energetics strongly:

Vaspmaster at 21:01, 24 June 2019

2019-06-24T21:01:34Z

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	== Task ==		== Task ==

	~~Determine~~ the interlayer binding energy of graphite in its experimental structure using the method		In this example you will determine the interlayer binding energy of graphite in its experimental structure using the method
	of Tchatchenko and Scheffler to account for van der Waals interactions.		of Tchatchenko and Scheffler to account for van der Waals interactions.

			Semilocal DFT at the GGA level underestimates long-range dispersion interactions.
			In the case of graphite, PBE predicts the interlayer binding energy of ~1 meV/atom which is too small compared to the RPA reference of 0.048 eV/atom <ref name="lebegue"/>.

			In this example, the interlayer binding energy of graphite in its experimental structure is determined using the {{TAG\|Tkatchenko-Scheffler method}},
			which performs well in description of the structure of graphite (see e.g. example [[graphite interlayer distance]]).

	----		----

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	There is no interaction of layers in z-direction for graphene so we need only 1 k point in this direction.		There is no interaction of layers in z-direction for graphene so we need only 1 k point in this direction.

	== ~~Calculation~~ ==		== Running this example ==

			To run this example, execute the <code>run.sh</code> bash-script:
			<pre>
			#
			# To run VASP this script calls $vasp_std
			# (or posibly $vasp_gam and/or $vasp_ncl).
			# These variables can be defined by sourcing vaspcmd
			. vaspcmd 2> /dev/null

			#
			# When vaspcmd is not available and $vasp_std,
			# $vasp_gam, and/or $vasp_ncl are not set as environment
			# variables, you can specify them here
			[ -z "`echo $vasp_std`" ] && vasp_std="mpirun -np 8 /path-to-your-vasp/vasp_std"
			[ -z "`echo $vasp_gam`" ] && vasp_gam="mpirun -np 8 /path-to-your-vasp/vasp_gam"
			[ -z "`echo $vasp_ncl`" ] && vasp_ncl="mpirun -np 8 /path-to-your-vasp/vasp_ncl"

			#
			# The real work starts here
			#

			rm results.dat

			drct=$(pwd)

			for i in graphene graphite
			do
			cd $drct/$i
			$vasp_std
			done

			cd $drct

	~~Semilocal DFT at the GGA level underestimates~~		# obtain total energy for graphite
	~~long~~-~~range dispersion interactions.~~		en2=$(grep "free ene" graphite/OUTCAR \|tail -1\|awk '{print $5}')
	~~In the case of graphite, PBE predicts the~~
	~~interlayer binding~~ energy ~~of ~1 meV/atom~~		# obtain total energy for graphene
	~~which is too small compared to the RPA~~		en1=$(grep "free ene" graphene/OUTCAR \|tail -1\|awk '{print $5}')
	~~reference of 0.048 eV/atom~~
	~~<ref name~~="~~lebegue~~"/>.		# compute interlayer binding energy (eV/atom)
			deltaE=$(echo print $en2/4 - $en1/2 \|python)
	~~In this example, the~~ interlayer binding energy
	~~of graphite in its experimental structure is~~		echo "Binding energy (eV/atom): " $deltaE >results.dat
	~~determined using the {{TAG~~\|~~Tkatchenko-Scheffler method}},~~		</pre>
	~~which performs well in description of the~~
	~~structure of graphite~~ (~~see e~~.~~g. example~~
	~~{{TAG\|graphite interlayer distance}}).~~

	The calculation is performed in two steps (single-point		The calculation is performed in two steps (two separate single-point calculations) in which the energy for bulk graphite and for graphene are obtained.
	calculations) in which the energy for bulk graphite		The binding energy is computed automatically and it is written in the file results.dat.
	and for graphene are obtained. The binding energy
	is computed automatically and it is written in the
	file results.dat.

	Even though the TS method predicts a reasonable geometry		Even though the TS method predicts a reasonable geometry it overestimates the energetics strongly:
	it overestimates the energetics strongly:		the computed binding energy of -0.083 eV/atom is too large compared to the RPA reference of 0.048 eV/atom.
	the computed binding energy of -0.083 eV/atom is too		This overestimation is - at least in part - due to neglecting the many-body interactions (see example [[Graphite MBD binding energy]]).
	large compared to the RPA reference of 0.048 eV/atom.
	This overestimation is - at least in part - due to
	neglecting the many-body interactions (see example
	~~{{TAG\|~~Graphite MBD binding energy}}).

	== Download ==		== Download ==

Vaspmaster: /* Calculation */

2019-06-23T20:29:58Z

Calculation

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	{{TAG\|graphite interlayer distance}}).		{{TAG\|graphite interlayer distance}}).

	The calculation is performed in two steps (~~sigle~~-point		The calculation is performed in two steps (single-point
	calculations) in which the energy for bulk graphite		calculations) in which the energy for bulk graphite
	and for graphene are obtained. The binding energy		and for graphene are obtained. The binding energy