Carbil - Revision history

Endel: Replaced content with 'Page has moved to https://ims.ut.ee/mediawiki/index.php/Secure:Carbil'

2010-06-07T13:45:01Z

Replaced content with 'Page has moved to https://ims.ut.ee/mediawiki/index.php/Secure:Carbil'

← Older revision		Revision as of 16:45, 7 June 2010
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	~~= Generation of the simulation box =~~		Page has moved to https://ims.ut.ee/mediawiki/index.php/Secure:Carbil

	~~== Nomenclature of the carbon flakes used ==~~

	~~Carbon flakes were generated by starting with four carbon atoms in fixed positions, forming three 120 degree angles, and consecutively completing three or more carbon atoms on the edge nearest~~ to the centre to a complete hexagonal or pentagonal cycle. The location of the pentagonal cycles (defects) was chosen randomly, but then a manual selection was done and the least symmetric flakes were discarded. Eight types with different locations of defects were chosen to construct the CDC carbon model.
	The flakes were created on a single plane first, keeping only the topology and bond lengths in correspondence with the force field. To get their real 3-dimensional shape, they were equilibrated using a MD simulation 0.1ns long with 0.1fs timestep on room temperature (293K) in vacuo.
	~~The initial (topological) shapes and their shapes after MD simulation are shown below.~~


	~~=== Flake type 0 ===~~

	~~[[Image:carbil-flake0-topo.png\|320px]] [[Image:carbil-flake0.png\|320px]] [[File:carbil-flake0.xyz]] [[File:carbil-flake0.FIELD]]~~

	~~Flat sheet with 24 cycles and no defects.~~

	~~=== Flake type 1 ===~~

	~~[[Image:carbil-flake1-topo.png\|320px]] [[Image:carbil-flake1.png\|320px]] [[File:carbil-flake1.xyz]] [[File:carbil-flake1.FIELD]]~~

	~~Curved sheet with 23 normal hexagon cycles and one defect in the form of a pentagonal cycle in the middle of the flake.~~

	~~=== Flake type 2 ===~~

	~~[[Image:carbil-flake2-topo.png\|320px]] [[Image:carbil-flake2.png\|320px]] [[File:carbil-flake2.xyz]] [[File:carbil-flake2.FIELD]]~~

	~~Sheet with one defect near the edge.~~

	~~=== Flake type 3 ===~~

	~~[[Image:carbil-flake3-topo.png\|320px]] [[Image:carbil-flake3.png\|320px]] [[File:carbil-flake3.xyz]] [[File:carbil-flake3.FIELD]]~~

	~~Sheet with two defects: one on the edge, another near the edge.~~

	~~=== Flake type 4 ===~~

	~~[[Image:carbil-flake4-topo.png\|320px]] [[Image:carbil-flake4.png\|320px]] [[File:carbil-flake4.xyz]] [[File:carbil-flake4.FIELD]]~~

	~~Sheet with three defects located on a straight line - one in the middle, two on the edges.~~

	~~=== Flake type 5 ===~~

	~~[[Image~~:~~carbil-flake5-topo~~.~~png\|320px]] [[Image:carbil-flake5~~.~~png\|320px]] [[File:carbil-flake5~~.~~xyz]] [[File~~:~~carbil-flake5.FIELD]]~~

	~~Two defects near the edges.~~

	~~=== Flake type 6 ===~~

	~~[[Image:carbil-flake6-topo.png\|320px]] [[Image:carbil-flake6.png\|320px]] [[File:carbil-flake6.xyz]] [[File:carbil-flake6.FIELD]]~~

	~~One defect in the middle, two on the edges.~~

	~~=== Flake type 7 ===~~

	~~[[Image:carbil-flake7-topo.png\|320px]] [[Image:carbil-flake7.png\|320px]] [[File:carbil-flake7.xyz]] [[File:carbil-flake7.FIELD]]~~

	~~Sheet with one defect in the middle.~~

Endel: /* Nomenclature of the carbon flakes used */

2010-06-07T13:30:54Z

Nomenclature of the carbon flakes used

← Older revision		Revision as of 16:30, 7 June 2010
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	== Nomenclature of the carbon flakes used ==		== Nomenclature of the carbon flakes used ==

	The ~~CDC carbon model~~ was ~~constructed of carbon sheets~~ with different ~~amount~~ of defects.		Carbon flakes were generated by starting with four carbon atoms in fixed positions, forming three 120 degree angles, and consecutively completing three or more carbon atoms on the edge nearest to the centre to a complete hexagonal or pentagonal cycle. The location of the pentagonal cycles (defects) was chosen randomly, but then a manual selection was done and the least symmetric flakes were discarded. Eight types with different locations of defects were chosen to construct the CDC carbon model.
	~~8 types of carbon sheet~~ were ~~used:~~		The flakes were created on a single plane first, keeping only the topology and bond lengths in correspondence with the force field. To get their real 3-dimensional shape, they were equilibrated using a MD simulation 0.1ns long with 0.1fs timestep on room temperature (293K) in vacuo.
			The initial (topological) shapes and their shapes after MD simulation are shown below.


	=== Flake type 0 ===		=== Flake type 0 ===

Endel: /* Generation of the simulation box */

2010-06-07T13:13:58Z

Generation of the simulation box

← Older revision		Revision as of 16:13, 7 June 2010
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	=== Flake type 0 ===		=== Flake type 0 ===

	[[Image:carbil-flake0-topo.png\|320px]] [[Image:carbil-flake0.png\|320px]] [[File:carbil-flake0.xyz]]		[[Image:carbil-flake0-topo.png\|320px]] [[Image:carbil-flake0.png\|320px]] [[File:carbil-flake0.xyz]] [[File:carbil-flake0.FIELD]]

	Flat sheet with 24 cycles and no defects.		Flat sheet with 24 cycles and no defects.
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	=== Flake type 1 ===		=== Flake type 1 ===

	[[Image:carbil-flake1-topo.png\|320px]] [[Image:carbil-flake1.png\|320px]] [[File:carbil-flake1.xyz]]		[[Image:carbil-flake1-topo.png\|320px]] [[Image:carbil-flake1.png\|320px]] [[File:carbil-flake1.xyz]] [[File:carbil-flake1.FIELD]]

	Curved sheet with 23 normal hexagon cycles and one defect in the form of a pentagonal cycle in the middle of the flake.		Curved sheet with 23 normal hexagon cycles and one defect in the form of a pentagonal cycle in the middle of the flake.
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	=== Flake type 2 ===		=== Flake type 2 ===

	[[Image:carbil-flake2-topo.png\|320px]] [[Image:carbil-flake2.png\|320px]] [[File:carbil-flake2.xyz]]		[[Image:carbil-flake2-topo.png\|320px]] [[Image:carbil-flake2.png\|320px]] [[File:carbil-flake2.xyz]] [[File:carbil-flake2.FIELD]]

	Sheet with one defect near the edge.		Sheet with one defect near the edge.
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	=== Flake type 3 ===		=== Flake type 3 ===

	[[Image:carbil-flake3-topo.png\|320px]] [[Image:carbil-flake3.png\|320px]] [[File:carbil-flake3.xyz]]		[[Image:carbil-flake3-topo.png\|320px]] [[Image:carbil-flake3.png\|320px]] [[File:carbil-flake3.xyz]] [[File:carbil-flake3.FIELD]]

	Sheet with two defects: one on the edge, another near the edge.		Sheet with two defects: one on the edge, another near the edge.
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	=== Flake type 4 ===		=== Flake type 4 ===

	[[Image:carbil-flake4-topo.png\|320px]] [[Image:carbil-flake4.png\|320px]] [[File:carbil-flake4.xyz]]		[[Image:carbil-flake4-topo.png\|320px]] [[Image:carbil-flake4.png\|320px]] [[File:carbil-flake4.xyz]] [[File:carbil-flake4.FIELD]]

	Sheet with three defects located on a straight line - one in the middle, two on the edges.		Sheet with three defects located on a straight line - one in the middle, two on the edges.
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	=== Flake type 5 ===		=== Flake type 5 ===

	[[Image:carbil-flake5-topo.png\|320px]] [[Image:carbil-flake5.png\|320px]] [[File:carbil-flake5.xyz]]		[[Image:carbil-flake5-topo.png\|320px]] [[Image:carbil-flake5.png\|320px]] [[File:carbil-flake5.xyz]] [[File:carbil-flake5.FIELD]]

	Two defects near the edges.		Two defects near the edges.
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	=== Flake type 6 ===		=== Flake type 6 ===

	[[Image:carbil-flake6-topo.png\|320px]] [[Image:carbil-flake6.png\|320px]] [[File:carbil-flake6.xyz]]		[[Image:carbil-flake6-topo.png\|320px]] [[Image:carbil-flake6.png\|320px]] [[File:carbil-flake6.xyz]] [[File:carbil-flake6.FIELD]]

	One defect in the middle, two on the edges.		One defect in the middle, two on the edges.
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	=== Flake type 7 ===		=== Flake type 7 ===

	[[Image:carbil-flake7-topo.png\|320px]] [[Image:carbil-flake7.png\|320px]] [[File:carbil-flake7.xyz]]		[[Image:carbil-flake7-topo.png\|320px]] [[Image:carbil-flake7.png\|320px]] [[File:carbil-flake7.xyz]] [[File:carbil-flake7.FIELD]]

	Sheet with one defect in the middle.		Sheet with one defect in the middle.

Endel at 13:11, 7 June 2010

2010-06-07T13:11:49Z

← Older revision		Revision as of 16:11, 7 June 2010
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	Generation of the simulation box		= Generation of the simulation box =

			== Nomenclature of the carbon flakes used ==

	The CDC carbon model was constructed of carbon sheets with different amount of defects.		The CDC carbon model was constructed of carbon sheets with different amount of defects.

Endel: /* Flake type 7 */

2010-06-07T12:51:32Z

Flake type 7

← Older revision		Revision as of 15:51, 7 June 2010
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	[[Image:carbil-flake7-topo.png\|320px]] [[Image:carbil-flake7.png\|320px]] [[File:carbil-flake7.xyz]]		[[Image:carbil-flake7-topo.png\|320px]] [[Image:carbil-flake7.png\|320px]] [[File:carbil-flake7.xyz]]

	Sheet with ~~some defects~~.		Sheet with one defect in the middle.

Endel: /* Flake type 6 */

2010-06-07T12:50:56Z

Flake type 6

← Older revision		Revision as of 15:50, 7 June 2010
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	[[Image:carbil-flake6-topo.png\|320px]] [[Image:carbil-flake6.png\|320px]] [[File:carbil-flake6.xyz]]		[[Image:carbil-flake6-topo.png\|320px]] [[Image:carbil-flake6.png\|320px]] [[File:carbil-flake6.xyz]]

	~~Sheet with some defects~~.		One defect in the middle, two on the edges.

	=== Flake type 7 ===		=== Flake type 7 ===

Endel: /* Flake type 5 */

2010-06-07T12:50:27Z

Flake type 5

← Older revision		Revision as of 15:50, 7 June 2010
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	[[Image:carbil-flake5-topo.png\|320px]] [[Image:carbil-flake5.png\|320px]] [[File:carbil-flake5.xyz]]		[[Image:carbil-flake5-topo.png\|320px]] [[Image:carbil-flake5.png\|320px]] [[File:carbil-flake5.xyz]]

	~~Sheet with some~~ defects.		Two defects near the edges.

	=== Flake type 6 ===		=== Flake type 6 ===

Endel: /* Flake type 4 */

2010-06-07T12:49:45Z

Flake type 4

← Older revision		Revision as of 15:49, 7 June 2010
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	[[Image:carbil-flake4-topo.png\|320px]] [[Image:carbil-flake4.png\|320px]] [[File:carbil-flake4.xyz]]		[[Image:carbil-flake4-topo.png\|320px]] [[Image:carbil-flake4.png\|320px]] [[File:carbil-flake4.xyz]]

	Sheet with ~~some~~ defects.		Sheet with three defects located on a straight line - one in the middle, two on the edges.

	=== Flake type 5 ===		=== Flake type 5 ===

Endel: /* Flake type 3 */

2010-06-07T12:48:25Z

Flake type 3

← Older revision		Revision as of 15:48, 7 June 2010
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	[[Image:carbil-flake3-topo.png\|320px]] [[Image:carbil-flake3.png\|320px]] [[File:carbil-flake3.xyz]]		[[Image:carbil-flake3-topo.png\|320px]] [[Image:carbil-flake3.png\|320px]] [[File:carbil-flake3.xyz]]

	Sheet with ~~some~~ defects.		Sheet with two defects: one on the edge, another near the edge.

	=== Flake type 4 ===		=== Flake type 4 ===

Endel: /* Flake type 2 */

2010-06-07T12:47:41Z

Flake type 2

← Older revision		Revision as of 15:47, 7 June 2010
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	[[Image:carbil-flake2-topo.png\|320px]] [[Image:carbil-flake2.png\|320px]] [[File:carbil-flake2.xyz]]		[[Image:carbil-flake2-topo.png\|320px]] [[Image:carbil-flake2.png\|320px]] [[File:carbil-flake2.xyz]]

	Sheet with ~~some defects~~.		Sheet with one defect near the edge.

	=== Flake type 3 ===		=== Flake type 3 ===