Intrinsic-reaction-coordinate calculations - Revision history

Karsai at 12:10, 19 September 2025

2025-09-19T12:10:34Z

← Older revision		Revision as of 12:10, 19 September 2025
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	ML_LMLFF = .TRUE. # invoke MLFF		ML_LMLFF = .TRUE. # invoke MLFF
	~~ML_ISTART~~ = 2 # sets the mode of MLFF to production		ML_MODE = RUN # sets the mode of MLFF to production

	The {{TAG\|INCAR}} file located in directory p should differ from that in directory m only in the value of parameter {{TAG\|IRC_DIRECTION }}, which should be set to positive 1.		The {{TAG\|INCAR}} file located in directory p should differ from that in directory m only in the value of parameter {{TAG\|IRC_DIRECTION }}, which should be set to positive 1.

Hampel: /* Practical example */

2025-07-31T07:10:06Z

Practical example

@@ Line 67: / Line 67: @@
 [[File:IrcExample1.png|thumb|Potential energy profile along intrinsic reaction coordinate generated in this practical example for the SN<sub>2</sub> reaction of CH<sub>3</sub>Cl with Cl<sup>-</sup>.]]
 Both calculations can be finished in just a few seconds and the potential energy profile along IRC shown on the figure, can be obtained by a simple post-processing. For instance, this simple  bash script ircShift.sh:
   #!/usr/bin/bash

Tbucko: /* Practical example */

2023-11-30T16:13:18Z

Practical example

← Older revision		Revision as of 16:13, 30 November 2023
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	ML_ISTART = 2 # sets the mode of MLFF to production		ML_ISTART = 2 # sets the mode of MLFF to production

	The {{TAG\|INCAR}} file located in directory p should differ from that in directory m only in the value of parameter IRC_DIRECTION, which should be set to positive 1.		The {{TAG\|INCAR}} file located in directory p should differ from that in directory m only in the value of parameter {{TAG\|IRC_DIRECTION }}, which should be set to positive 1.

	[[File:IrcExample1.png\|thumb\|Potential energy profile along intrinsic reaction coordinate generated in this practical example for the SN<sub>2</sub> reaction of CH<sub>3</sub>Cl with Cl<sup>-</sup>.]]		[[File:IrcExample1.png\|thumb\|Potential energy profile along intrinsic reaction coordinate generated in this practical example for the SN<sub>2</sub> reaction of CH<sub>3</sub>Cl with Cl<sup>-</sup>.]]

Tbucko: /* Practical example */

2023-11-30T16:12:05Z

Practical example

← Older revision		Revision as of 16:12, 30 November 2023
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	0. 0. 0.		0. 0. 0.

	The INCAR file located in directory m should contain the following lines:		The {{TAG\|INCAR}} file located in directory m should contain the following lines:

	IBRION = 40 # invokes the IRC calculation		IBRION = 40 # invokes the IRC calculation
Line 63:		Line 63:
	ML_ISTART = 2 # sets the mode of MLFF to production		ML_ISTART = 2 # sets the mode of MLFF to production

	The INCAR file located in directory p should differ from that in directory m only in the value of parameter IRC_DIRECTION, which should be set to positive 1.		The {{TAG\|INCAR}} file located in directory p should differ from that in directory m only in the value of parameter IRC_DIRECTION, which should be set to positive 1.

	[[File:IrcExample1.png\|thumb\|Potential energy profile along intrinsic reaction coordinate generated in this practical example for the SN<sub>2</sub> reaction of CH<sub>3</sub>Cl with Cl<sup>-</sup>.]]		[[File:IrcExample1.png\|thumb\|Potential energy profile along intrinsic reaction coordinate generated in this practical example for the SN<sub>2</sub> reaction of CH<sub>3</sub>Cl with Cl<sup>-</sup>.]]

Tbucko: /* Practical example */

2023-11-30T16:11:25Z

Practical example

← Older revision		Revision as of 16:11, 30 November 2023
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	== Practical example ==		== Practical example ==
	As practical example, let us consider the SN2 reaction of CH<sub>3</sub>Cl with Cl<sup>-</sup> for which we wish to determine potential energy profile along IRC using machine learned forcefield trained to reproduce PBE density functional approximation. The IRC calculation consists of two independent simulations corresponding to parts of path linking transition state with reactant and with product, respectively. For practical reasons, we shall therefore run the simulations in two different directories called, say, m and p, both of which should contain POSCAR, KPOINTS, POTCAR, INCAR and ML_FF files. The POSCAR file:		As practical example, let us consider the SN2 reaction of CH<sub>3</sub>Cl with Cl<sup>-</sup> for which we wish to determine potential energy profile along IRC using machine learned forcefield trained to reproduce PBE density functional approximation. The IRC calculation consists of two independent simulations corresponding to parts of path linking transition state with reactant and with product, respectively. For practical reasons, we shall therefore run the simulations in two different directories called, say, m and p, both of which should contain {{TAG\|POSCAR}}, {{TAG\|KPOINTS}}, {{TAG\|POTCAR}}, {{TAG\|INCAR}} and {{TAG\|ML_FF}} files. The {{TAG\|POSCAR}} file:

	transition state for the SN2 reaction of CH3Cl with Cl-		transition state for the SN2 reaction of CH3Cl with Cl-
Line 37:		Line 37:
	-0.19166655E+00 0.19728353E+00 -0.20233630E+00 ! components for atom N		-0.19166655E+00 0.19728353E+00 -0.20233630E+00 ! components for atom N

	is simply a copy of a CONTCAR file from a well converged improved dimer calculation. Notice that besides usual structural input, POSCAR must contain unstable direction that is needed to initialize the algorithm. To obtain the ML_FF used in this example, the data included in compressed directory [[File:GenerateMLFF.zip]] should be used. The POTCAR file should be prepared for atoms C, H, and Cl and the KPOINTS file		is simply a copy of a {{TAG\|CONTCAR}} file from a well converged improved dimer calculation. Notice that besides usual structural input, {{TAG\|POSCAR}} must contain unstable direction that is needed to initialize the algorithm. To obtain the {{TAG\|ML_FF}} used in this example, the data included in compressed directory [[File:GenerateMLFF.zip]] should be used. The POTCAR file should be prepared for atoms C, H, and Cl and the {{TAG\|KPOINTS}} file

	Automatic		Automatic

Tbucko at 16:08, 30 November 2023

2023-11-30T16:08:50Z

← Older revision		Revision as of 16:08, 30 November 2023
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			Both calculations can be finished in just a few seconds and the potential energy profile along IRC:

	Both calculations can be finished in just a few seconds and the potential energy profile along IRC:		Both calculations can be finished in just a few seconds and the potential energy profile along IRC:

Tbucko: /* Practical example */

2023-11-30T16:07:58Z

Practical example

← Older revision		Revision as of 16:07, 30 November 2023
Line 65:		Line 65:
	The INCAR file located in directory p should differ from that in directory m only in the value of parameter IRC_DIRECTION, which should be set to positive 1.		The INCAR file located in directory p should differ from that in directory m only in the value of parameter IRC_DIRECTION, which should be set to positive 1.

	[[~~Media~~:IrcExample1.png]]		[[File:IrcExample1.png\|thumb\|Potential energy profile along intrinsic reaction coordinate generated in this practical example for the SN<sub>2</sub> reaction of CH<sub>3</sub>Cl with Cl<sup>-</sup>.]]













	Both calculations can be finished in just a few seconds and the potential energy profile along IRC:		Both calculations can be finished in just a few seconds and the potential energy profile along IRC:

	shown on the figure ~~below~~, can be obtained by a simple post-processing. For instance, this simple bash script ircShift.sh:		shown on the figure above, can be obtained by a simple post-processing. For instance, this simple bash script ircShift.sh:

	#!/usr/bin/bash		#!/usr/bin/bash

Tbucko: /* Practical example */

2023-11-30T16:04:34Z

Practical example

← Older revision		Revision as of 16:04, 30 November 2023
Line 65:		Line 65:
	The INCAR file located in directory p should differ from that in directory m only in the value of parameter IRC_DIRECTION, which should be set to positive 1.		The INCAR file located in directory p should differ from that in directory m only in the value of parameter IRC_DIRECTION, which should be set to positive 1.

			[[Media:IrcExample1.png]]

	Both calculations can be finished in just a few seconds and the potential energy profile along IRC:		Both calculations can be finished in just a few seconds and the potential energy profile along IRC:
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	sort -n tmp.tmp >ircShift.dat		sort -n tmp.tmp >ircShift.dat
	executed in a directory one level above directories m and p generates the file ircShift.dat containing data in two-column format that can be visualized using gnuplot, xmgrace, origin, or many other popular visualization tools.		executed in a directory one level above directories m and p generates the file ircShift.dat containing data in two-column format that can be visualized using gnuplot, xmgrace, origin, or many other popular visualization tools.

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

Tbucko: /* Practical example */

2023-11-30T16:02:25Z

Practical example

← Older revision		Revision as of 16:02, 30 November 2023
Line 66:		Line 66:


	Both calculations can be finished in just a few seconds and the potential energy profile along IRC, shown on the figure below, can be obtained by a simple post-processing. For instance, this simple bash script ircShift.sh:
			Both calculations can be finished in just a few seconds and the potential energy profile along IRC:

			shown on the figure below, can be obtained by a simple post-processing. For instance, this simple bash script ircShift.sh:

	#!/usr/bin/bash		#!/usr/bin/bash

Tbucko: /* Practical example */

2023-11-30T15:55:59Z

Practical example

← Older revision		Revision as of 15:55, 30 November 2023
Line 66:		Line 66:


	Both calculations can be finished in just a few seconds and the potential energy profile along IRC, ~~show~~ on the figure below, can be obtained by ~~executing~~ a simple bash script ircShift.sh:		Both calculations can be finished in just a few seconds and the potential energy profile along IRC, shown on the figure below, can be obtained by a simple post-processing. For instance, this simple bash script ircShift.sh:

	#!/usr/bin/bash		#!/usr/bin/bash
Line 76:		Line 76:

	sort -n tmp.tmp >ircShift.dat		sort -n tmp.tmp >ircShift.dat
			executed in a directory one level above directories m and p generates the file ircShift.dat containing data in two-column format that can be visualized using gnuplot, xmgrace, origin, or many other popular visualization tools.

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