IRCCAR - Revision history

Csheldon: Csheldon moved page Construction:IRCCAR to IRCCAR

2026-06-09T12:32:38Z

Csheldon moved page Construction:IRCCAR to IRCCAR

← Older revision		Revision as of 12:32, 9 June 2026
(No difference)

Csheldon at 12:28, 9 June 2026

2026-06-09T12:28:55Z

← Older revision		Revision as of 12:28, 9 June 2026
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	==References==		==References==

	~~<!--~~[[Category:Files]][[Category:Input files]][[Category:Advanced molecular-dynamics sampling]][[Category:Biased molecular dynamics]][[Category:Transition states]]~~-->~~		[[Category:Files]][[Category:Input files]][[Category:Advanced molecular-dynamics sampling]][[Category:Biased molecular dynamics]][[Category:Transition states]]

Csheldon: /* 1. Extracting basis coordinates from XDATCAR */

2025-07-16T15:30:23Z

1. Extracting basis coordinates from XDATCAR

← Older revision		Revision as of 15:30, 16 July 2025
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	==== 1. Extracting basis coordinates from XDATCAR ====		==== 1. Extracting basis coordinates from XDATCAR ====

	Using the <code>tellcoord.py</code> script, you can compute the values of the basis coordinates ~~making up the path for the negative branch of the IRC~~:		Using the <code>tellcoord.py</code> script, you can compute the values of the basis coordinates defined in {{FILE\|ICONST}}:

	<div class="toccolours mw-customtoggle-script">'''Click to show <code>tellcoord.py</code> script'''</div>		<div class="toccolours mw-customtoggle-script">'''Click to show <code>tellcoord.py</code> script'''</div>

Csheldon at 14:30, 11 July 2025

2025-07-11T14:30:54Z

← Older revision		Revision as of 14:30, 11 July 2025
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	The {{FILE\|IRCCAR}} file defines a discretized transformation path. Usually this is taken from an [[Intrinsic-reaction-coordinate calculations\|intrinsic reaction coordinate]] (IRC - using {{TAG\|IBRION}}=40), projected onto a small set of internal coordinates. It is required to define the path-based coordinates <code>IS</code> and <code>IZ</code> in [[ICONST#In_case_of_complex_coordinates\|ICONST]].		The {{FILE\|IRCCAR}} file defines a discretized transformation path. Usually this is taken from an [[Intrinsic-reaction-coordinate calculations\|intrinsic reaction coordinate]] (IRC) - using {{TAG\|IBRION}}=40, projected onto a small set of internal coordinates. It is required to define the path-based coordinates <code>IS</code> and <code>IZ</code> in [[ICONST#In_case_of_complex_coordinates\|ICONST]] {{Cite\|branduari:parrinello:2007}}.

	However, this ~~IRC~~ is followed during a biased molecular dynamics (MD) simulation, similar to the [[Blue moon ensemble]] method, [[Metadynamics\|metadynamics]], and other [[:Category:Advanced molecular-dynamics sampling\| advanced MD aproaches]] {{Cite\|bucko:book:2025}}. The structure of the file is:		However, this path is followed during a biased molecular dynamics (MD) simulation, similar to the [[Blue moon ensemble]] method, [[Metadynamics\|metadynamics]], and other [[:Category:Advanced molecular-dynamics sampling\| advanced MD aproaches]] {{Cite\|bucko:book:2025}}. The structure of the file is:

	M		M
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	==== 1. Extracting basis coordinates from XDATCAR ====		==== 1. Extracting basis coordinates from XDATCAR ====

	Using the <code>tellcoord.py</code> script, you can compute the values of the basis coordinates for the negative branch of the IRC:		Using the <code>tellcoord.py</code> script, you can compute the values of the basis coordinates making up the path for the negative branch of the IRC:

	<div class="toccolours mw-customtoggle-script">'''Click to show <code>tellcoord.py</code> script'''</div>		<div class="toccolours mw-customtoggle-script">'''Click to show <code>tellcoord.py</code> script'''</div>
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	IS 5.136342611992123 5.136342611992123 0		IS 5.136342611992123 5.136342611992123 0

	If you want to define also the IZ coordinate and use it to prevent side reaction by imposing a [[:Category:Biased_molecular_dynamics\|step-shaped potential]], the following {{FILE\|ICONST}} should be used:		If you want to define also the <code>IZ</code> coordinate and use it to prevent side reaction by imposing a [[:Category:Biased_molecular_dynamics\|step-shaped potential]], the following {{FILE\|ICONST}} should be used:

	R 3 25 0		R 3 25 0
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	{{TAGBL\|FBIAS_D}} = 5.0		{{TAGBL\|FBIAS_D}} = 5.0
	{{TAGBL\|FBIAS_A}} = 5		{{TAGBL\|FBIAS_A}} = 5

	~~For further information, see pages 50-51 of "Investigating chemical reactions with VASP" {{Cite\|bucko:book:2025}}.~~

	==Related tags and articles==		==Related tags and articles==

Csheldon: /* Using IRCCAR */

2025-07-11T08:22:57Z

Using IRCCAR

← Older revision		Revision as of 08:22, 11 July 2025
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	== Using IRCCAR ==		== Using IRCCAR ==

	In the context of following a [[https://www.vasp.at/tutorials/latest/transition_states/part3/\| reaction pathway]], using <code>IS</code> and <code>IZ</code> represent one of the few ways to define collective variables for investigating chemical reactions. The following example covers defining {{FILE\|IRCCAR}} and the corresponding {{FILE\|ICONST}} file.		In the context of following a [https://www.vasp.at/tutorials/latest/transition_states/part3/\| reaction pathway], using <code>IS</code> and <code>IZ</code> represent one of the few ways to define collective variables for investigating chemical reactions. The following example covers defining {{FILE\|IRCCAR}} and the corresponding {{FILE\|ICONST}} file.

	=== Defining IRCCAR ===		=== Defining IRCCAR ===

Csheldon at 08:22, 11 July 2025

2025-07-11T08:22:43Z

← Older revision		Revision as of 08:22, 11 July 2025
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	chi_1(M) chi_2(M) ... chi(r)(M)		chi_1(M) chi_2(M) ... chi(r)(M)

	where <code>M</code> is the number of points in the file and <code>chi_j(i)</code> is <math>\tilde{\chi}_k(i)</math>, the discretized transformation path in terms of internal coordinates.		where <code>M</code> is the number of points in the file and <code>chi_j(i)</code> is <math>\tilde{\chi}_k(i)</math>, the discretized transformation path in terms of internal coordinates, taking values between 0 and 1.

	~~<math>\tilde{\chi}_k(i)</math> can take~~ values between 0 and 1.

	== Using IRCCAR ==		== Using IRCCAR ==

Csheldon: /* Defining ICONST */

2025-07-11T08:22:11Z

Defining ICONST

← Older revision		Revision as of 08:22, 11 July 2025
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	IZ 5.136342611992123 5.136342611992123 4		IZ 5.136342611992123 5.136342611992123 4

	The {{FILE\|INCAR}} file should also have the following tags, adjusting the values to your problem:		The {{FILE\|INCAR}} file should also have the following tags, adjusting the values to your problem, depending on how you want to define the step-function:

	FBIAS_R0 = 0.2		{{TAGBL\|FBIAS_R0}} = 0.2
	FBIAS_D = 5.0		{{TAGBL\|FBIAS_D}} = 5.0
	FBIAS_A = 5		{{TAGBL\|FBIAS_A}} = 5

	For further information, see pages 50-51 of "Investigating chemical reactions with VASP" {{Cite\|bucko:book:2025}}.		For further information, see pages 50-51 of "Investigating chemical reactions with VASP" {{Cite\|bucko:book:2025}}.

	==Related tags and articles==		==Related tags and articles==

Csheldon at 08:19, 11 July 2025

2025-07-11T08:19:10Z

← Older revision		Revision as of 08:19, 11 July 2025
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	{{TAG\|FBIAS_D}},		{{TAG\|FBIAS_D}},
	{{TAG\|FBIAS_A}}		{{TAG\|FBIAS_A}}

			==References==

	<!--[[Category:Files]][[Category:Input files]][[Category:Advanced molecular-dynamics sampling]][[Category:Biased molecular dynamics]][[Category:Transition states]]-->		<!--[[Category:Files]][[Category:Input files]][[Category:Advanced molecular-dynamics sampling]][[Category:Biased molecular dynamics]][[Category:Transition states]]-->

Csheldon at 08:18, 11 July 2025

2025-07-11T08:18:15Z

← Older revision		Revision as of 08:18, 11 July 2025
Line 1:		Line 1:
	The {{FILE\|IRCCAR}} file defines a discretized transformation path. Usually this is taken from an [[Intrinsic-reaction-coordinate calculations\|intrinsic reaction coordinate]] (IRC - using {{TAG\|IBRION}}=40), projected onto a small set of internal coordinates. It is required to define the path-based coordinates <code>IS</code> and <code>IZ</code> in [[ICONST#In_case_of_complex_coordinates\|ICONST]].		The {{FILE\|IRCCAR}} file defines a discretized transformation path. Usually this is taken from an [[Intrinsic-reaction-coordinate calculations\|intrinsic reaction coordinate]] (IRC - using {{TAG\|IBRION}}=40), projected onto a small set of internal coordinates. It is required to define the path-based coordinates <code>IS</code> and <code>IZ</code> in [[ICONST#In_case_of_complex_coordinates\|ICONST]].

	However, this IRC is followed during a biased molecular dynamics (MD) simulation, similar to the [[Blue moon ensemble]] method, metadynamics, and other [[:Category:Advanced molecular-dynamics sampling\| advanced MD aproaches]] {{Cite\|bucko:book:2025}}. The structure of the file is:		However, this IRC is followed during a biased molecular dynamics (MD) simulation, similar to the [[Blue moon ensemble]] method, [[Metadynamics\|metadynamics]], and other [[:Category:Advanced molecular-dynamics sampling\| advanced MD aproaches]] {{Cite\|bucko:book:2025}}. The structure of the file is:

	M		M

Csheldon at 08:15, 11 July 2025

2025-07-11T08:15:21Z

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