Slow-growth approach - Revision history

Huebsch at 13:10, 21 October 2025

2025-10-21T13:10:37Z

← Older revision		Revision as of 13:10, 21 October 2025
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	* For a slow-growth simulation, one has to perform a calcualtion very similar to [[Constrained molecular dynamics]] but additionally the transformation velocity-related {{TAG\|INCREM}} tag for each geometric parameter with <tt>STATUS=0</tt> has to be specified:		* For a slow-growth simulation, one has to perform a calcualtion very similar to [[Constrained molecular dynamics]] but additionally the transformation velocity-related {{TAG\|INCREM}} tag for each geometric parameter with <tt>STATUS=0</tt> has to be specified:
	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}
	#Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}		#Choose a thermostat:
			## Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}
			## Set {{TAG\|MDALGO}}=2, and choose an appropriate setting for {{TAG\|SMASS}}
	#Define geometric constraints in the {{FILE\|ICONST}} file, and set the STATUS parameter for the constrained coordinates to 0		#Define geometric constraints in the {{FILE\|ICONST}} file, and set the STATUS parameter for the constrained coordinates to 0
	#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.		#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.

Huebsch at 12:46, 21 October 2025

2025-10-21T12:46:21Z

← Older revision		Revision as of 12:46, 21 October 2025
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	Detailed description of the simulation protocol that employs Jarzynski's identity		Detailed description of the simulation protocol that employs Jarzynski's identity
	can be found in reference <ref name="oberhofer2005"/>.		can be found in reference <ref name="oberhofer2005"/>.

			== How to ==
			* For a slow-growth simulation, one has to perform a calcualtion very similar to [[Constrained molecular dynamics]] but additionally the transformation velocity-related {{TAG\|INCREM}} tag for each geometric parameter with <tt>STATUS=0</tt> has to be specified:
			#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}
			#Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}
			#Define geometric constraints in the {{FILE\|ICONST}} file, and set the STATUS parameter for the constrained coordinates to 0
			#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.

			<ol start="5">
			<li>Specify the transformation velocity-related {{TAG\|INCREM}}-tag for each geometric parameter with <tt>STATUS=0</tt>.</li>
			</ol>

Karsai at 13:54, 16 October 2024

2024-10-16T13:54:53Z

@@ Line 29: / Line 29: @@
 can be found in reference <ref name="oberhofer2005"/>.
 == References ==
@@ Line 62: / Line 38: @@
 ----
-[[Category:Molecular dynamics]][[Category:Slow-growth approach]][[Category:Theory]][[Category:Howto]]
+[[Category:Advanced molecular-dynamics sampling]][[Category:Theory]]

Huebsch: /* Anderson thermostat */

2024-06-14T06:12:07Z

Anderson thermostat

← Older revision		Revision as of 06:12, 14 June 2024
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	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}
	#Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}		#Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}
	#Define geometric constraints in the {{FILE\|ICONST}}-file, and set the ~~{{TAG\|~~STATUS}} parameter for the constrained coordinates to 0		#Define geometric constraints in the {{FILE\|ICONST}} file, and set the '''STATUS''' parameter for the constrained coordinates to 0
	#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.		#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.

Singraber at 10:27, 16 November 2023

2023-11-16T10:27:20Z

← Older revision		Revision as of 10:27, 16 November 2023
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	In the limit of infinitesimally small <math>\dot{\xi}</math>, the work <math>w^{irrev}_{1 \rightarrow 2}</math>		In the limit of infinitesimally small <math>\dot{\xi}</math>, the work <math>w^{irrev}_{1 \rightarrow 2}</math>
	corresponds to the free-energy difference between the the final and initial state.		corresponds to the free-energy difference between the the final and initial state.
	In the general case, <math>w^{irrev}_{1 \rightarrow 2}$ </math>is the irreversible work related		In the general case, <math>w^{irrev}_{1 \rightarrow 2}</math> is the irreversible work related
	to the free energy via Jarzynski's identity<ref name="jarzynski1997"/>:		to the free energy via Jarzynski's identity<ref name="jarzynski1997"/>:

Ftran at 08:34, 20 October 2023

2023-10-20T08:34:17Z

← Older revision		Revision as of 08:34, 20 October 2023
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	</references>		</references>
	----		----
	~~[[The_VASP_Manual\|Contents]]~~

	[[Category:Molecular dynamics]][[Category:Slow-growth approach]][[Category:Theory]][[Category:Howto]]		[[Category:Molecular dynamics]][[Category:Slow-growth approach]][[Category:Theory]][[Category:Howto]]

Huebsch at 14:30, 7 April 2022

2022-04-07T14:30:10Z

← Older revision		Revision as of 14:30, 7 April 2022
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	can be computed as:		can be computed as:

	<math>		::<math>
	w^{irrev}_{1 \rightarrow 2}=\int_{{\xi(1)}}^{{\xi(2)}} \left ( \frac{\partial {V(q)}} {\partial \xi} \right ) \cdot \dot{\xi}\, dt.		w^{irrev}_{1 \rightarrow 2}=\int_{{\xi(1)}}^{{\xi(2)}} \left ( \frac{\partial {V(q)}} {\partial \xi} \right ) \cdot \dot{\xi}\, dt.
	</math>		</math>
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	to the free energy via Jarzynski's identity<ref name="jarzynski1997"/>:		to the free energy via Jarzynski's identity<ref name="jarzynski1997"/>:

	<math>		::<math>
	exp^{-\frac{\Delta A_{1 \rightarrow 2}}{k_B\,T}}=		exp^{-\frac{\Delta A_{1 \rightarrow 2}}{k_B\,T}}=
	\bigg \langle exp^{-\frac{w^{irrev}_{1 \rightarrow 2}}{k_B\,T}} \bigg\rangle.		\bigg \langle exp^{-\frac{w^{irrev}_{1 \rightarrow 2}}{k_B\,T}} \bigg\rangle.
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	[[The_VASP_Manual\|Contents]]		[[The_VASP_Manual\|Contents]]

	[[Category:Molecular ~~Dynamics~~]][[Category:Slow-growth approach]][[Category:Theory]][[Category:Howto]]		[[Category:Molecular dynamics]][[Category:Slow-growth approach]][[Category:Theory]][[Category:Howto]]

Karsai at 09:03, 14 March 2019

2019-03-14T09:03:38Z

← Older revision		Revision as of 09:03, 14 March 2019
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	<math>		<math>
	~~{\rm~~ exp~~}\left\~~{-\frac{\Delta A_{1 \rightarrow 2}}{k_B\,T} ~~\right \~~}=		exp^{-\frac{\Delta A_{1 \rightarrow 2}}{k_B\,T}}=
	\bigg \langle exp^{-\frac{w^{irrev}_{1 \rightarrow 2}}{k_B\,T}} \bigg\rangle.		\bigg \langle exp^{-\frac{w^{irrev}_{1 \rightarrow 2}}{k_B\,T}} \bigg\rangle.
	</math>		</math>

Karsai at 09:03, 14 March 2019

2019-03-14T09:03:00Z

← Older revision		Revision as of 09:03, 14 March 2019
Line 19:		Line 19:
	<math>		<math>
	{\rm exp}\left\{-\frac{\Delta A_{1 \rightarrow 2}}{k_B\,T} \right \}=		{\rm exp}\left\{-\frac{\Delta A_{1 \rightarrow 2}}{k_B\,T} \right \}=
	\bigg \langle ~~{\rm~~ exp~~} \left \~~{-\frac{w^{irrev}_{1 \rightarrow 2}}{k_B\,T} ~~\right \~~} \bigg\rangle.		\bigg \langle exp^{-\frac{w^{irrev}_{1 \rightarrow 2}}{k_B\,T}} \bigg\rangle.
	</math>		</math>

Karsai: /* Anderson thermostat */

2019-03-13T15:48:12Z

Anderson thermostat

← Older revision		Revision as of 15:48, 13 March 2019
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	== Anderson thermostat ==		== Anderson thermostat ==

	* For a slow-growth simulation, one has to perform a calcualtion very similar to {{TAG\|Constrained molecular dynamics}} but additionally the transformation velocity-related {{TAG\|INCREM}}-tag for each geometric parameter with <tt>STATUS=0</tt> has to be specified:		* For a slow-growth simulation, one has to perform a calcualtion very similar to {{TAG\|Constrained molecular dynamics}} but additionally the transformation velocity-related {{TAG\|INCREM}}-tag for each geometric parameter with <tt>STATUS=0</tt> has to be specified. For a slow-growth approach run with Andersen thermostat, one has to:
	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}
	#Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}		#Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}

← Older revision		Revision as of 13:10, 21 October 2025
Line 32:		Line 32:
	* For a slow-growth simulation, one has to perform a calcualtion very similar to [[Constrained molecular dynamics]] but additionally the transformation velocity-related {{TAG\|INCREM}} tag for each geometric parameter with <tt>STATUS=0</tt> has to be specified:		* For a slow-growth simulation, one has to perform a calcualtion very similar to [[Constrained molecular dynamics]] but additionally the transformation velocity-related {{TAG\|INCREM}} tag for each geometric parameter with <tt>STATUS=0</tt> has to be specified:
	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}
	#Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}		#Choose a thermostat:
			## Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}
			## Set {{TAG\|MDALGO}}=2, and choose an appropriate setting for {{TAG\|SMASS}}
	#Define geometric constraints in the {{FILE\|ICONST}} file, and set the STATUS parameter for the constrained coordinates to 0		#Define geometric constraints in the {{FILE\|ICONST}} file, and set the STATUS parameter for the constrained coordinates to 0
	#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.		#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.

← Older revision		Revision as of 06:12, 14 June 2024
Line 34:		Line 34:
	#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}		#Set the standard MD-related tags: {{TAG\|IBRION}}=0, {{TAG\|TEBEG}}, {{TAG\|POTIM}}, and {{TAG\|NSW}}
	#Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}		#Set {{TAG\|MDALGO}}=1, and choose an appropriate setting for {{TAG\|ANDERSEN_PROB}}
	#Define geometric constraints in the {{FILE\|ICONST}}-file, and set the ~~{{TAG\|~~STATUS}} parameter for the constrained coordinates to 0		#Define geometric constraints in the {{FILE\|ICONST}} file, and set the '''STATUS''' parameter for the constrained coordinates to 0
	#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.		#When the free-energy gradient is to be computed, set {{TAG\|LBLUEOUT}}=.TRUE.