Trajectory Looping - Revision history

Redaktor at 21:17, 8 May 2023

2023-05-08T21:17:22Z

← Older revision		Revision as of 23:17, 8 May 2023
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	In order to change simulation parameters or define a new system of chemical reactions, one has to modify and recompile the source code of Looper.		In order to change simulation parameters or define a new system of chemical reactions, one has to modify and recompile the source code of Looper.

	<div class="toccolours mw-collapsible mw-collapsed" data-expandtext="Show detailed ~~instrucitons~~" data-collapsetext="Hide detailed ~~instrucitons~~" style="float:left"><div class="mw-collapsible-content">		<div class="toccolours mw-collapsible mw-collapsed" data-expandtext="Show detailed instructions" data-collapsetext="Hide detailed instructions" style="float:left"><div class="mw-collapsible-content">
	<h4>Defining a reaction system</h4>		<h4>Defining a reaction system</h4>

Redaktor at 21:17, 8 May 2023

2023-05-08T21:17:00Z

← Older revision		Revision as of 23:17, 8 May 2023
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	=== Modifying the source code ===		=== Modifying the source code ===

	In order to change simulation parameters or define a new system		In order to change simulation parameters or define a new system of chemical reactions, one has to modify and recompile the source code of Looper.
	of chemical reactions, one has to modify and recompile the source
	code of Looper.		<div class="toccolours mw-collapsible mw-collapsed" data-expandtext="Show detailed instrucitons" data-collapsetext="Hide detailed instrucitons" style="float:left"><div class="mw-collapsible-content">
	<~~accordion parent~~="~~accordion~~" ~~heading~~="~~Detailed instructions~~">		<h4>Defining a reaction system</h4>
	=== Defining a reaction system ~~===~~

	In file Chemistry.hpp there are already two systems of reactions: <code>ChemistrySystem1</code>		In file Chemistry.hpp there are already two systems of reactions: <code>ChemistrySystem1</code>
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	is pointed in Settings.hpp with a type alias <code>chemistry_t</code>.		is pointed in Settings.hpp with a type alias <code>chemistry_t</code>.

			<h4>Various settings</h4>
	~~===~~ Various settings ~~===~~

	'''Simulation duration:'''		'''Simulation duration:'''
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	<code>kWriteToChemStateFileEverySteps</code> in Settings.hpp		<code>kWriteToChemStateFileEverySteps</code> in Settings.hpp

			<h4>Building</h4>

	~~=== Building ===~~		'''Compiler.'''  A decent and recent C++ compiler that supports C++14 standard is required. The code has been confirmed to compile successfully under Linux with GNU

	'''Compiler.'''  A decent and recent C++ compiler that supports C++14 standard is required.
	The code has been confirmed to compile successfully under Linux with GNU
	g++ 8.0 and Clang++ 6.0.		g++ 8.0 and Clang++ 6.0.

	'''Toolchain.'''  Compilation is managed by CMake. To build Looper under Linux, it should be		'''Toolchain.'''  Compilation is managed by CMake. To build Looper under Linux, it should be sufficient to enter the build directory and execute <code>./build_release.sh</code>.
	sufficient to enter the build directory and execute <code>./build_release.sh</code>.

			<h4>Usage</h4>

	~~===Usage ===~~		Invoke simply as:

	Invoke simply as:

	./Looper trajectory chemprefix		./Looper trajectory chemprefix


	'''Multiple input trajectories.'''		'''Multiple input trajectories.'''
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	The order of the use of multiple trajectories is random. The trajectories		The order of the use of multiple trajectories is random. The trajectories
	should have the same number of molecules and the same time step.		should have the same number of molecules and the same time step.


	'''Multiple simulations – seed.'''		'''Multiple simulations – seed.'''
	If more than one simulation is to be performed (by setting appropriately		If more than one simulation is to be performed (by setting appropriately
	variable <code>kNumOfReplicas</code> in file Settings.hpp), each simulation is seeded		variable <code>kNumOfReplicas</code> in file Settings.hpp), each simulation is seeded
	sequentially starting from the value assigned to <code>kSimulationSeedsBase</code> (file		sequentially starting from the value assigned to <code>kSimulationSeedsBase</code> (file Settings.hpp). This value can be overridden by setting the environmental
	Settings.hpp). This value can be overridden by setting the environmental
	variable <code>LOOPER_SEED_BASE</code> prior to Looper invocation.		variable <code>LOOPER_SEED_BASE</code> prior to Looper invocation.


	'''Multiple simulations – multi-threading.'''		'''Multiple simulations – multi-threading.'''
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	hardware capabilities. If necessary, this behavior can be tweaked manually		hardware capabilities. If necessary, this behavior can be tweaked manually
	using variable <code>kNumOfThreads</code> (in file Settings.hpp).		using variable <code>kNumOfThreads</code> (in file Settings.hpp).
	</~~accordion~~>		<br/><br/>
			</div></div>
			<br/>


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	A conceptually equivalent approach (published nearly in parallel):		A conceptually equivalent approach (published nearly in parallel):
	* <span class="pmbm">Bednarek X</span>, <span class="pmbm">Martin S</span>, <span class="pmbm">Ndiaye A</span>, <span class="pmbm">Peres V</span>, <span class="pmbm">Bonnefoy O</span>. '''Extrapolation of DEM simulations to large time scale. Application to the mixing of powder in a conical screw mixer''', ''Chem Eng Sci'' <u>197</u>:223–234 (2019) [https://doi.org/10.1016/j.ces.2018.12.022 CrossRef]		* <span class="pmbm">Bednarek X</span>, <span class="pmbm">Martin S</span>, <span class="pmbm">Ndiaye A</span>, <span class="pmbm">Peres V</span>, <span class="pmbm">Bonnefoy O</span>. '''Extrapolation of DEM simulations to large time scale. Application to the mixing of powder in a conical screw mixer''', ''Chem Eng Sci'' <u>197</u>:223–234 (2019) [https://doi.org/10.1016/j.ces.2018.12.022 CrossRef]


	An interesting application of trajectory looping:		An interesting application of trajectory looping:
	* <span class="pmbm">Lichtenegger T</span> and <span class="pmbm">Miethlinger T</span>. '''On the connection between Lagrangian and Eulerian metrics for recurrent particulate flows''', ''Phys Fluids'' <u>32</u>:113308 (2020) [https://doi.org/10.1063/5.0025597 CrossRef]		* <span class="pmbm">Lichtenegger T</span> and <span class="pmbm">Miethlinger T</span>. '''On the connection between Lagrangian and Eulerian metrics for recurrent particulate flows''', ''Phys Fluids'' <u>32</u>:113308 (2020) [https://doi.org/10.1063/5.0025597 CrossRef]

Redaktor at 21:50, 18 November 2020

2020-11-18T21:50:30Z

← Older revision		Revision as of 23:50, 18 November 2020
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	===Related methods and applications===		===Related methods and applications===
	A conceptually equivalent approach ~~has been~~ published nearly in parallel:		A conceptually equivalent approach (published nearly in parallel):
	* <span class="pmbm">Bednarek X</span>, <span class="pmbm">Martin S</span>, <span class="pmbm">Ndiaye A</span>, <span class="pmbm">Peres V</span>, <span class="pmbm">Bonnefoy O</span>. '''Extrapolation of DEM simulations to large time scale. Application to the mixing of powder in a conical screw mixer''', ''Chem Eng Sci'' <u>197</u>:223–234 (2019) [https://doi.org/10.1016/j.ces.2018.12.022 CrossRef]		* <span class="pmbm">Bednarek X</span>, <span class="pmbm">Martin S</span>, <span class="pmbm">Ndiaye A</span>, <span class="pmbm">Peres V</span>, <span class="pmbm">Bonnefoy O</span>. '''Extrapolation of DEM simulations to large time scale. Application to the mixing of powder in a conical screw mixer''', ''Chem Eng Sci'' <u>197</u>:223–234 (2019) [https://doi.org/10.1016/j.ces.2018.12.022 CrossRef]

	An interesting application of trajectory looping:		An interesting application of trajectory looping:
	* <span class="pmbm">Lichtenegger T</span> and <span class="pmbm">Miethlinger T</span>. '''On the connection between Lagrangian and Eulerian metrics for recurrent particulate flows''', ''Phys Fluids'' <u>32</u>:113308 (2020) [https://doi.org/10.1063/5.0025597 CrossRef]		* <span class="pmbm">Lichtenegger T</span> and <span class="pmbm">Miethlinger T</span>. '''On the connection between Lagrangian and Eulerian metrics for recurrent particulate flows''', ''Phys Fluids'' <u>32</u>:113308 (2020) [https://doi.org/10.1063/5.0025597 CrossRef]

Redaktor at 08:44, 17 November 2020

2020-11-17T08:44:35Z

← Older revision		Revision as of 10:44, 17 November 2020
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	===Related methods and applications===		===Related methods and applications===
	A conceptually equivalent approach has been published nearly in parallel:		A conceptually equivalent approach has been published nearly in parallel:
	* <span class="pmbm">Bednarek X</span>, <span class="pmbm">Martin S</span>, <span class="pmbm">Ndiaye A</span>, <span class="pmbm">Peres V</span>, <span class="pmbm">Bonnefoy O</span>. '''Extrapolation of DEM simulations to large time scale. Application to the mixing of powder in a conical screw mixer''', ''Chem Eng Sci'' <u>197</u>:223–234 (2019) [https://doi.org/10.1016/j.ces.2018.12.022 CrossRef]		* <span class="pmbm">Bednarek X</span>, <span class="pmbm">Martin S</span>, <span class="pmbm">Ndiaye A</span>, <span class="pmbm">Peres V</span>, <span class="pmbm">Bonnefoy O</span>. '''Extrapolation of DEM simulations to large time scale. Application to the mixing of powder in a conical screw mixer''', ''Chem Eng Sci'' <u>197</u>:223–234 (2019) [https://doi.org/10.1016/j.ces.2018.12.022 CrossRef]

	An interesting application of trajectory looping:		An interesting application of trajectory looping:
	* <span class="pmbm">Lichtenegger T</span> and <span class="pmbm">Miethlinger T</span>. '''On the connection between Lagrangian and Eulerian metrics for recurrent particulate flows''', ''Phys ~~Fluid~~'' <u>32</u>:113308 (2020) [https://doi.org/10.1063/5.0025597 CrossRef]		* <span class="pmbm">Lichtenegger T</span> and <span class="pmbm">Miethlinger T</span>. '''On the connection between Lagrangian and Eulerian metrics for recurrent particulate flows''', ''Phys Fluids'' <u>32</u>:113308 (2020) [https://doi.org/10.1063/5.0025597 CrossRef]

Redaktor at 08:43, 17 November 2020

2020-11-17T08:43:38Z

← Older revision		Revision as of 10:43, 17 November 2020
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	===~~Similar~~ methods===		===Related methods and applications===
	A conceptually equivalent approach has been published nearly in parallel:		A conceptually equivalent approach has been published nearly in parallel:
	* <span class="pmbm">Bednarek X</span>, <span class="pmbm">Martin S</span>, <span class="pmbm">Ndiaye A</span>, <span class="pmbm">Peres V</span>, <span class="pmbm">Bonnefoy O</span>. '''Extrapolation of DEM simulations to large time scale. Application to the mixing of powder in a conical screw mixer''', ''Chem Eng Sci'' <u>197</u>:223–234 (2019) [https://doi.org/10.1016/j.ces.2018.12.022 CrossRef]		* <span class="pmbm">Bednarek X</span>, <span class="pmbm">Martin S</span>, <span class="pmbm">Ndiaye A</span>, <span class="pmbm">Peres V</span>, <span class="pmbm">Bonnefoy O</span>. '''Extrapolation of DEM simulations to large time scale. Application to the mixing of powder in a conical screw mixer''', ''Chem Eng Sci'' <u>197</u>:223–234 (2019) [https://doi.org/10.1016/j.ces.2018.12.022 CrossRef]

	An interesting application of trajectory looping:		An interesting application of trajectory looping:
	* <span class="pmbm">Lichtenegger  T</span> ~~&~~ <span class="pmbm">Miethlinger T</span>. '''On the connection between Lagrangian and Eulerian metrics for recurrent particulate flows''', ''Phys Fluid'' <u>32</u>:113308 (2020) [https://doi.org/10.1063/5.0025597 CrossRef]		* <span class="pmbm">Lichtenegger T</span> and <span class="pmbm">Miethlinger T</span>. '''On the connection between Lagrangian and Eulerian metrics for recurrent particulate flows''', ''Phys Fluid'' <u>32</u>:113308 (2020) [https://doi.org/10.1063/5.0025597 CrossRef]

Redaktor at 22:15, 14 November 2020

2020-11-14T22:15:05Z

← Older revision		Revision as of 00:15, 15 November 2020
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	using variable <code>kNumOfThreads</code> (in file Settings.hpp).		using variable <code>kNumOfThreads</code> (in file Settings.hpp).
	</accordion>		</accordion>


			===Similar methods===
			A conceptually equivalent approach has been published nearly in parallel:
			* <span class="pmbm">Bednarek X</span>, <span class="pmbm">Martin S</span>, <span class="pmbm">Ndiaye A</span>, <span class="pmbm">Peres V</span>, <span class="pmbm">Bonnefoy O</span>. '''Extrapolation of DEM simulations to large time scale. Application to the mixing of powder in a conical screw mixer''', ''Chem Eng Sci'' <u>197</u>:223–234 (2019) [https://doi.org/10.1016/j.ces.2018.12.022 CrossRef]

			An interesting application of trajectory looping:
			* <span class="pmbm">Lichtenegger  T</span> & <span class="pmbm">Miethlinger T</span>. '''On the connection between Lagrangian and Eulerian metrics for recurrent particulate flows''', ''Phys Fluid'' <u>32</u>:113308 (2020) [https://doi.org/10.1063/5.0025597 CrossRef]

Redaktor at 18:56, 1 August 2018

2018-08-01T18:56:31Z

← Older revision		Revision as of 20:56, 1 August 2018
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	the intermediary looped contacts trajectory, whose desired length may be		the intermediary looped contacts trajectory, whose desired length may be
	hard to guess. When using the second way, a stop condition can be defined		hard to guess. When using the second way, a stop condition can be defined
	depending on the chemical state ~~of the~~ of the system or based on the already		depending on the chemical state of the system or based on the already
	collected chemical event statistics. '''Looper''' has been written according to the second way.		collected chemical event statistics.

			'''Looper''' has been written according to the second way.

Redaktor at 14:58, 1 August 2018

2018-08-01T14:58:50Z

← Older revision		Revision as of 16:58, 1 August 2018
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	=== Downloads ===		=== Downloads ===
	* [http://pmbm.ippt.pan.pl/software/looping/looper-~~v20180415~~.tar.gz '''Looper''' – an implementation of the method in C++]		* [http://pmbm.ippt.pan.pl/software/looping/looper-v20180801.tar.gz '''Looper''' – an implementation of the method in C++]
	* [http://pmbm.ippt.pan.pl/software/looping/n_500__f_0.2__eps_0.05.trajectory Example input trajectory] (~2.4 GB, parameters: <i>N</i>=500, φ=20%, ε=0.05, θ=100τ<sub>B</sub>)		* [http://pmbm.ippt.pan.pl/software/looping/n_500__f_0.2__eps_0.05.trajectory Example input trajectory] (~2.4 GB, parameters: <i>N</i>=500, φ=20%, ε=0.05, θ=100τ<sub>B</sub>)

Redaktor at 14:51, 1 August 2018

2018-08-01T14:51:42Z

← Older revision		Revision as of 16:51, 1 August 2018
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	<span id="RefZukEtAl"></span>		<span id="RefZukEtAl"></span>
	=== Reference ===		=== Reference ===
	* <span class="pmbm">Żuk PJ</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Lipniacki T</span>. '''Sampling rare events in stochastic reaction–diffusion systems within trajectory looping''', ''Physical Review E'' (2018) [http://doi.org/10.1103/PhysRevE.98.022401 CrossRef] \| [http://pmbm.ippt.pan.pl/publications/Zuk-2018-PhysRevE-MS.pdf PDF-ms]		* <span class="pmbm">Żuk PJ</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Lipniacki T</span>. '''Sampling rare events in stochastic reaction–diffusion systems within trajectory looping''', ''Physical Review E'' <u>98</u>:022401 (2018) [http://doi.org/10.1103/PhysRevE.98.022401 CrossRef] \| [http://pmbm.ippt.pan.pl/publications/Zuk-2018-PhysRevE-MS.pdf PDF-ms]

Redaktor at 14:49, 1 August 2018

2018-08-01T14:49:04Z

← Older revision		Revision as of 16:49, 1 August 2018
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	<span id="RefZukEtAl"></span>		<span id="RefZukEtAl"></span>
	=== Reference ===		=== Reference ===
	* <span class="pmbm">Żuk PJ</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Lipniacki T</span>. '''Sampling rare events in stochastic reaction–diffusion systems within trajectory looping''', ''Physical Review~~ E'' ''Phys Rev~~ E'' (2018) [http://doi.org/10.1103/PhysRevE.98.022401 CrossRef] \| [http://pmbm.ippt.pan.pl/publications/Zuk-2018-PhysRevE-MS.pdf PDF-ms]		* <span class="pmbm">Żuk PJ</span>, <span class="pmbm">Kochańczyk M</span>, <span class="pmbm">Lipniacki T</span>. '''Sampling rare events in stochastic reaction–diffusion systems within trajectory looping''', ''Physical Review E'' (2018) [http://doi.org/10.1103/PhysRevE.98.022401 CrossRef] \| [http://pmbm.ippt.pan.pl/publications/Zuk-2018-PhysRevE-MS.pdf PDF-ms]