Generic Analyzer - Revision history

Administrator at 19:53, 29 April 2025

2025-04-29T19:53:40Z

← Older revision		Revision as of 14:53, 29 April 2025
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	* [https://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_static.zip Linux executable (try if regular version does not work; static binary that should be suitable for most x86_64 Linux installations)]		* [https://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_static.zip Linux executable (try if regular version does not work; static binary that should be suitable for most x86_64 Linux installations)]
	* [https://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_osx.zip OS X executable (compiled on OS X 10.9.3, also works on OS X 10.10)]		* [https://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_osx.zip OS X executable (compiled on OS X 10.9.3, also works on OS X 10.10)]
	* [https://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_windows.zip Windows executable (tested on Windows 10)] Note: since a standard installation of Windows does not provide gzip, you must install [http://~~ariadne~~.ms.northwestern.edu/Download/Generic_analyzer/gzip.zip gzip.exe] in a folder listed in your %PATH% if you wish to read compressed files.		* [https://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_windows.zip Windows executable (tested on Windows 10)] Note: since a standard installation of Windows does not provide gzip, you must install [http://pergamon.ms.northwestern.edu/Download/Generic_analyzer/gzip.zip gzip.exe] in a folder listed in your %PATH% if you wish to read compressed files.

	=== Copyright ===		=== Copyright ===

Administrator: /* Download (Linux and OS X) */

2021-08-14T15:09:39Z

Download (Linux and OS X)

← Older revision		Revision as of 10:09, 14 August 2021
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	The current version is dated 06/24/2014. It is strongly recommended that you upgrade from any earlier version. You can download binary versions of this program here, but note that this was created for internal lab use - we cannot provide any support.		The current version is dated 06/24/2014. It is strongly recommended that you upgrade from any earlier version. You can download binary versions of this program here, but note that this was created for internal lab use - we cannot provide any support.

	* [~~http~~://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga.zip Linux executable (recommended version; compiled on OpenSuSE 13.1, 64-bit)]		* [https://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga.zip Linux executable (recommended version; compiled on OpenSuSE 13.1, 64-bit)]
	* [~~http~~://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_static.zip Linux executable (try if regular version does not work; static binary that should be suitable for most x86_64 Linux installations)]		* [https://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_static.zip Linux executable (try if regular version does not work; static binary that should be suitable for most x86_64 Linux installations)]
	* [~~http~~://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_osx.zip OS X executable (compiled on OS X 10.9.3, also works on OS X 10.10)]		* [https://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_osx.zip OS X executable (compiled on OS X 10.9.3, also works on OS X 10.10)]
	* [~~http~~://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_windows.zip Windows executable (tested on Windows 10)] Note: since a standard installation of Windows does not provide gzip, you must install [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/gzip.zip gzip.exe] in a folder listed in your %PATH% if you wish to read compressed files.		* [https://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_windows.zip Windows executable (tested on Windows 10)] Note: since a standard installation of Windows does not provide gzip, you must install [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/gzip.zip gzip.exe] in a folder listed in your %PATH% if you wish to read compressed files.

	=== Copyright ===		=== Copyright ===

Administrator: /* Download (Linux and OS X) */

2021-08-14T15:08:10Z

Download (Linux and OS X)

← Older revision		Revision as of 10:08, 14 August 2021
Line 86:		Line 86:
	The current version is dated 06/24/2014. It is strongly recommended that you upgrade from any earlier version. You can download binary versions of this program here, but note that this was created for internal lab use - we cannot provide any support.		The current version is dated 06/24/2014. It is strongly recommended that you upgrade from any earlier version. You can download binary versions of this program here, but note that this was created for internal lab use - we cannot provide any support.

	* [http://~~ariadne~~.ms.northwestern.edu/Download/Generic_analyzer/ga.zip Linux executable (recommended version; compiled on OpenSuSE 13.1, 64-bit)]		* [http://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga.zip Linux executable (recommended version; compiled on OpenSuSE 13.1, 64-bit)]
	* [http://~~ariadne~~.ms.northwestern.edu/Download/Generic_analyzer/ga_static.zip Linux executable (try if regular version does not work; static binary that should be suitable for most x86_64 Linux installations)]		* [http://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_static.zip Linux executable (try if regular version does not work; static binary that should be suitable for most x86_64 Linux installations)]
	* [http://~~ariadne~~.ms.northwestern.edu/Download/Generic_analyzer/ga_osx.zip OS X executable (compiled on OS X 10.9.3, also works on OS X 10.10)]		* [http://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_osx.zip OS X executable (compiled on OS X 10.9.3, also works on OS X 10.10)]
	* [http://~~ariadne~~.ms.northwestern.edu/Download/Generic_analyzer/ga_windows.zip Windows executable (tested on Windows 10)] Note: since a standard installation of Windows does not provide gzip, you must install [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/gzip.zip gzip.exe] in a folder listed in your %PATH% if you wish to read compressed files.		* [http://pergamon.ms.northwestern.edu/Download/Generic_analyzer/ga_windows.zip Windows executable (tested on Windows 10)] Note: since a standard installation of Windows does not provide gzip, you must install [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/gzip.zip gzip.exe] in a folder listed in your %PATH% if you wish to read compressed files.

	=== Copyright ===		=== Copyright ===

Administrator: /* Download (Linux and OS X) */

2020-08-10T16:48:35Z

Download (Linux and OS X)

← Older revision		Revision as of 11:48, 10 August 2020
Line 89:		Line 89:
	* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_static.zip Linux executable (try if regular version does not work; static binary that should be suitable for most x86_64 Linux installations)]		* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_static.zip Linux executable (try if regular version does not work; static binary that should be suitable for most x86_64 Linux installations)]
	* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_osx.zip OS X executable (compiled on OS X 10.9.3, also works on OS X 10.10)]		* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_osx.zip OS X executable (compiled on OS X 10.9.3, also works on OS X 10.10)]
	* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_windows.zip Windows executable (tested on Windows 10)] Note: since a standard installation of Windows does not provide gzip, you must install [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/gzip.zip gzip.exe] in a folder listed in your %PATH%.		* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_windows.zip Windows executable (tested on Windows 10)] Note: since a standard installation of Windows does not provide gzip, you must install [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/gzip.zip gzip.exe] in a folder listed in your %PATH% if you wish to read compressed files.

	=== Copyright ===		=== Copyright ===

Administrator: /* Download (Linux and OS X) */

2020-08-10T14:27:02Z

Download (Linux and OS X)

← Older revision		Revision as of 09:27, 10 August 2020
Line 89:		Line 89:
	* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_static.zip Linux executable (try if regular version does not work; static binary that should be suitable for most x86_64 Linux installations)]		* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_static.zip Linux executable (try if regular version does not work; static binary that should be suitable for most x86_64 Linux installations)]
	* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_osx.zip OS X executable (compiled on OS X 10.9.3, also works on OS X 10.10)]		* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_osx.zip OS X executable (compiled on OS X 10.9.3, also works on OS X 10.10)]
	* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_windows.zip Windows executable (tested on Windows 10)] Note: since a standard installation of Windows does not provide gzip, you must install [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/gzip.~~exe~~ gzip.exe] in a folder listed in your %PATH%.		* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_windows.zip Windows executable (tested on Windows 10)] Note: since a standard installation of Windows does not provide gzip, you must install [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/gzip.zip gzip.exe] in a folder listed in your %PATH%.

	=== Copyright ===		=== Copyright ===

Administrator: /* Download (Linux and OS X) */

2020-08-10T14:24:25Z

Download (Linux and OS X)

← Older revision		Revision as of 09:24, 10 August 2020
Line 89:		Line 89:
	* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_static.zip Linux executable (try if regular version does not work; static binary that should be suitable for most x86_64 Linux installations)]		* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_static.zip Linux executable (try if regular version does not work; static binary that should be suitable for most x86_64 Linux installations)]
	* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_osx.zip OS X executable (compiled on OS X 10.9.3, also works on OS X 10.10)]		* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_osx.zip OS X executable (compiled on OS X 10.9.3, also works on OS X 10.10)]
			* [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/ga_windows.zip Windows executable (tested on Windows 10)] Note: since a standard installation of Windows does not provide gzip, you must install [http://ariadne.ms.northwestern.edu/Download/Generic_analyzer/gzip.exe gzip.exe] in a folder listed in your %PATH%.

	Within the CSML, GA is available on all [[hardware\|local machines]].

	=== Copyright ===		=== Copyright ===

Administrator: /* History */

2020-03-03T18:37:02Z

History

← Older revision		Revision as of 13:37, 3 March 2020
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	=== History ===		=== History ===

	In the late 1980s/early 1990s, Henk Blöte at [http://www.tudelft.nl Delft University of Technology] incorporated techniques for the careful analysis of statistical uncertainties and correlations in Monte Carlo codes for spin models (notably used in a [http://csml.northwestern.edu/resources/Reprints/jpa1.pdf large-scale study of the 3D Ising universality class]). To use this analysis method for Monte Carlo data of polymer blends (simulated via the bond-fluctuation model), Erik Luijten implemented it in C in 1999 (the original subroutines were written in Fortran). This code was combined with a function for binning energy and density data for use in the multiple-histogram reweighting technique. After adapting the code again in 2000 for the analysis of the [http://csml.northwestern.edu/resources/Reprints/prl6.pdf critical point of the Restricted Primitive Model electrolyte], he decided that it would be more efficient to incorporate the routines in a general data analysis program, which became the "generic analyzer" in January 2002. Since then, the code was extended to allow testing of inconsistencies in input files, permit a variable number of columns, offer flexible memory allocation, etc. (see [[Generic_Analyzer#Options\|Options]] below).		In the late 1980s/early 1990s, [https://www.universiteitleiden.nl/en/staffmembers/henk-blote Henk Blöte] at [http://www.tudelft.nl Delft University of Technology] incorporated techniques for the careful analysis of statistical uncertainties and correlations in Monte Carlo codes for spin models (notably used in a [http://csml.northwestern.edu/resources/Reprints/jpa1.pdf large-scale study of the 3D Ising universality class]). To use this analysis method for Monte Carlo data of polymer blends (simulated via the bond-fluctuation model), Erik Luijten implemented it in C in 1999 (the original subroutines were written in Fortran). This code was combined with a function for binning energy and density data for use in the multiple-histogram reweighting technique. After adapting the code again in 2000 for the analysis of the [http://csml.northwestern.edu/resources/Reprints/prl6.pdf critical point of the Restricted Primitive Model electrolyte], he decided that it would be more efficient to incorporate the routines in a general data analysis program, which became the "generic analyzer" in January 2002. Since then, the code was extended to allow testing of inconsistencies in input files, permit a variable number of columns, offer flexible memory allocation, etc. (see [[Generic_Analyzer#Options\|Options]] below).

	=== General usage ===		=== General usage ===

Administrator: /* General usage */

2018-04-29T12:01:27Z

General usage

← Older revision		Revision as of 07:01, 29 April 2018
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	<tt>filename</tt> is a plain text file. Lines starting with a '#' will be ignored (use this feature to insert column descriptions and other information into your simulation data). If <tt>filename</tt> ends with '<tt>.gz</tt>' the file is assumed to be compressed with [http://en.wikipedia.org/wiki/Gzip gzip] and will be decompressed by GA on the fly. Note that this happens in memory; no decompressed version of the file is written to disk. This has the advantage that no additional disk space is required and that no additional time is required to compress the data again after the analysis.		<tt>filename</tt> is a plain text file. Lines starting with a '#' will be ignored (use this feature to insert column descriptions and other information into your simulation data). If <tt>filename</tt> ends with '<tt>.gz</tt>' the file is assumed to be compressed with [http://en.wikipedia.org/wiki/Gzip gzip] and will be decompressed by GA on the fly. Note that this happens in memory; no decompressed version of the file is written to disk. This has the advantage that no additional disk space is required and that no additional time is required to compress the data again after the analysis.

	If the number of <tt>columns</tt> ~~is not provided~~, GA will determine it from the first non-comment line in the file. Otherwise, only the number of columns indicated will be analyzed. Also note the [[#c-option\|<tt>-c</tt>]] option below.		Typically, the user does not specify the number of <tt>columns</tt>, but GA will determine it from the first non-comment line in the file. Otherwise, only the number of columns indicated will be analyzed. Also note the [[#c-option\|<tt>-c</tt>]] option below.

	To read from standard input instead of a file, specify ''STDIN'' as the filename.		To read from standard input instead of a file, specify ''STDIN'' as the filename.

Administrator: /* Overview */

2018-04-29T11:59:30Z

Overview

← Older revision		Revision as of 06:59, 29 April 2018
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	The "generic analyzer" (GA) is a command-line driven program that allows rapid statistical analysis of typical simulation data. It is particularly useful for processing output from Monte Carlo and molecular dynamics simulations.		The "generic analyzer" (GA) is a command-line driven program that allows rapid statistical analysis of typical simulation data. It is particularly useful for processing output from Monte Carlo and molecular dynamics simulations.

	Data files are expected to be arranged in columns, and the GA will provide the average of each column, along with its standard deviation and correlation coefficient. As a rule of thumb, if the correlation coefficient is above 0.1, the data are considered correlated and the standard deviation is underestimated. This is typical for simulation data when sampling takes place more often than the autocorrelation time. To address this, GA will group the data in blocks and make another pass. The number of data points is now decreased, generally reducing the correlation coefficient. This is procedure is repeated with iteratively larger block sizes.		Data files are expected to be arranged in columns, and the GA will provide the average of each column, along with its standard deviation and correlation coefficient. As a rule of thumb, if the correlation coefficient is above 0.1 (i.e., more than 10% correlation), the data are considered correlated and the standard deviation is underestimated. This is typical for simulation data when sampling takes place more often than the autocorrelation time. To address this, GA will group the data in blocks and make another pass. The number of data points is now decreased, generally reducing the correlation coefficient. This is procedure is repeated with iteratively larger block sizes.

	=== History ===		=== History ===

Administrator: /* Copyright */

2018-04-29T11:59:06Z

← Older revision		Revision as of 06:59, 29 April 2018
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	=== Copyright ===		=== Copyright ===

	You are free to download this program and use it for your research. However, please note that the copyright for this code is retained by Erik Luijten, 1999-~~2016~~.		You are free to download this program and use it for your research. However, please note that the copyright for this code is retained by Erik Luijten, 1999-2018.