Software/BDSIM - Revision history

JamesChappell: /* Running BDSIM Simulations */

2018-11-27T09:34:25Z

Running BDSIM Simulations

← Older revision		Revision as of 09:34, 27 November 2018
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	This sets up all the required EasyBuild modules and environment variables. The version of BDSIM that is used within this script is not the latest build (v1.1.0 instead of v1.2.+) but should be stable. If a newer version is required then contact James Chappell and he will compile a newer version for you to use.		This sets up all the required EasyBuild modules and environment variables. The version of BDSIM that is used within this script is not the latest build (v1.1.0 instead of v1.2.+) but should be stable. If a newer version is required then contact James Chappell and he will compile a newer version for you to use.

			Now your system is ready to use <code>BDSIM</code>. To check that it is working correctly, test the built-in help function:

			<pre>
			$ bdsim --help
			</pre>

			This should produce an output explaining all the possible options that can be used within <code>BDSIM</code>.

	=== Running on the UCL HEP Linux Cluster (Old) ===		=== Running on the UCL HEP Linux Cluster (Old) ===

JamesChappell: /* Running BDSIM Simulations */

2018-11-27T09:32:50Z

Running BDSIM Simulations

@@ Line 17: / Line 17: @@
 In order to use the UCL HEP Linux cluster, you will need a HEP account: please contact Dr. Simon Jolly for more details.
-=== Running on the UCL HEP Linux Cluster ===
+=== Running on the UCL HEP Linux Cluster (EasyBuild) ===
 In order to run <code>BDSIM</code> simulations on the UCL HEP Cluster, you must first source the development version of the PBT environment from a system within the cluster that is running either CentOS7 or Scientific Linux V6. This can be done using the following command:

JamesChappell at 11:41, 7 March 2018

2018-03-07T11:41:09Z

← Older revision		Revision as of 11:41, 7 March 2018
Line 172:		Line 172:
	Batch mode has no interactive interface, but as a consequence is much faster and exits the program once it has finished. For simulations with large numbers of particles within the beam, this is the preferred method of use.		Batch mode has no interactive interface, but as a consequence is much faster and exits the program once it has finished. For simulations with large numbers of particles within the beam, this is the preferred method of use.

	== ~~Basic~~ AWAKE Spectrometer Simulation ==		== AWAKE Spectrometer Simulation ==

	A ~~simple~~ model of the AWAKE spectrometer is available at <code>/unix/pdpwa/AWAKE_spectrometer/spectrometer</code>. This model (<code>spectrometer.gmad</code>) describes ~~the first part of~~ the spectrometer, downstream of the plasma cell, and includes the quadrupole magnets ~~and~~ drift sections ~~up until~~ the ~~dipole magnet~~. Also included in this folder are:		A model of the AWAKE spectrometer is available at <code>/unix/pdpwa/AWAKE_spectrometer/spectrometer</code>. This model (<code>spectrometer.gmad</code>) describes the spectrometer, downstream of the plasma cell, and includes the quadrupole magnets, drift sections and the spectrometer. Also included in this folder are:

	* <code>options.gmad</code> - includes definitions of constants used within the spectrometer model.		* <code>options.gmad</code> - includes definitions of constants used within the spectrometer model.
	* <code>analysisConfig.txt</code> - a simple <code>rebdsim</code> script that is used to produce histograms describing the position and momentum distributions at different points along the beam line. More information can be found at http://www.pp.rhul.ac.uk/bdsim/manual/output_analysis.html .		* <code>spec_test.C</code> - a ROOT macro that plots and fits the Energy vs. position on the screen for particles that pass through the spectrometer.
	* <code>plot_xy.C</code> - a ROOT macro that plots ~~histograms describing~~ the position ~~and momentum distributions at different points along~~ the ~~beam line~~.		* <code>vis.mac</code> - settings for the interactive BDSIM GUI.
	*<code>vis.mac</code> - settings for the interactive BDSIM GUI.		* <code>README</code> - instructions on running the simulation.
	*<code>README</code> - instructions on running the simulation.

	=== Running the Simulation ===		=== Running the Simulation ===

	First source the BDSIM environment as described [[#Running on the UCL HEP Linux Cluster\| above]]. To run the simulation using the ~~default supplied~~ electron beam (E = ~~1.3+/~~-~~0.4~~ GeV), use the command:		First source the BDSIM environment as described [[#Running on the UCL HEP Linux Cluster\| above]]. To run the simulation using the test electron beam (E = 0 -> 10 GeV), use the command:

	<pre>		<pre>
	$ bdsim --file=spectrometer.gmad --batch		$ bdsim --file=spectrometer.gmad --outfile=output --batch
	</pre>		</pre>

	The output is then stored in a file called <code>~~output_event~~.root</code>. There ~~are two~~ supplied ~~scripts~~ for analysis of this output: <code>~~analysisConfig.txt</code> and <code>plot_xy~~.C</code>.		The output is then stored in a file called <code>output.root</code>. There one supplied script for analysis of this output: <code>spec_test.C</code>.

	==== ~~REBDSIM~~ ====		==== ROOT Macro ====

	The ~~first~~ analysis script ~~uses <code>rebdsim</code>,~~ a ~~set~~ of ~~analysis codes that are compiled into a library~~ that is ~~supplied with BDSIM~~. It can be used via:		The analysis script provided is a ROOT Macro that automatically plots the energy of the particle against the x-position on the screen and then fits this curve for comparison to the analytic model. It allows easy confirmation that the simulation is working as expected. It can be used via:

	<pre>		<pre>
	$ ~~rebdsim analysisConfig~~.~~txt output_event~~.~~root analysis.root~~		$ root
			root > .x spec_test.C
	</pre>		</pre>

	~~where the third option, <code>analysis.root</code>, is the desired name of the output file. This can then be opened in ROOT:~~		=== Python Scripts - Creating Field Maps ===

	~~<pre>~~
	~~$ root analysis.root~~
	~~root > TBrowser a;~~
	~~</pre>~~

	~~The second command opens~~ a <code>~~TBrowser~~</code> ~~session~~. <code>~~TBrowser~~</code> ~~is an interactive GUI provided by ROOT that~~ can be used to ~~visualise data. The histograms produced by the <code>rebdsim</code> analysis~~ can be ~~found under <code>EventHistograms;1</code>~~.		There is a directory called <code>python_scripts</code> within the AWAKE spectrometer example directory on the UCL HEP cluster. The script <code>uniformfield.py</code> can be used to generate uniform magnetic field maps that can be used within the AWAKE spectrometer simulation.

	==== ~~ROOT Macro~~ ====		==== Setting up pyBDSIM ====

	~~The second analysis script provided is~~ a ~~ROOT Macro~~ that ~~automatically plots the position~~ and ~~momentum distributions at different points within~~ the ~~beam line in two separate canvasses~~. ~~It allows easy visualisation of the evolution of the~~ beam. It can be ~~used via~~:		BDSIM comes with a group of python modules that can be used to create and visualise aspects of the simulation, e.g. beam distributions and field maps. More information on these modules can be found at http://www.pp.rhul.ac.uk/bdsim/manual/python_modules.html. To download these modules from bitbucket, use the following commands from within your BDSIM source directory:

	<pre>		<pre>
	$ ~~root~~		$ git pull
	~~root > .x plot_xy.C~~		$ git submodule init
			$ git submodule update
	</pre>		</pre>

	~~The output should look similar to~~ the ~~following images~~:		To compile the modules, use:

	~~'''Position Evolution:'''~~		<pre>
			$ cd utils
	~~[[File:position.png \| 900px]]~~		$ make
			</pre>

	~~'''Momentum Evolution~~:~~'''~~		This compilation assumes you are using a python environment with <code>pip</code> installed. If you are running this on the UCL HEP cluster, then follow the instructions on https://www.hep.ucl.ac.uk/twiki/bin/view/Computing/UsingPython to create a virtual environment in which you can install the modules.

	~~[[File:momentum.png \| 900px]]~~		==== Creating a uniform magnetic field map ====

			To create a uniform magnetic field map, you can use the python script <code>uniformfield.py</code> in the following way from the command line:

	<!--~~== References ==~~-->		<pre>
			$ python uniformfield.py --fieldstrength <fieldstrength> --length <length>
			</pre>

	<~~!--{{cite web \|url=https:~~//~~twiki~~.ph.~~rhul~~.ac.uk/twiki/bin/view/PP/JAI/BdSim \|title=BDSIM - Accelerator Beamline Simulation Tool \|last=Nevay \|first=Laurence \|date=30 August 2017 \|website=Royal Holloway Physics TWiki \|access-date=17 October 2017}}-->		where you insert your desired values for the field strength (in T) and length (in m). The length variable must equal the length value given to <code>spectrometer.gmad</code> when defining the <code>awakespectrometer</code> class. It is required due to the way the spectrometer field map is defined within the source code. If you do not give the same length value, the field will be placed in the wrong position within the simulation and the results will be incorrect.

JamesChappell: /* Running on the UCL HEP Linux Cluster */

2018-03-07T11:00:43Z

Running on the UCL HEP Linux Cluster

← Older revision		Revision as of 11:00, 7 March 2018
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	<pre>		<pre>
	$ source /unix/pbt/software/scripts/~~centos7_pbt~~.sh -vd		$ source /unix/pbt/software/scripts/pbt.sh -vd
	</pre>		</pre>

JamesChappell: /* Running on the UCL HEP Linux Cluster */

2018-01-31T16:10:54Z

Running on the UCL HEP Linux Cluster

← Older revision		Revision as of 16:10, 31 January 2018
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	=== Running on the UCL HEP Linux Cluster ===		=== Running on the UCL HEP Linux Cluster ===

	In order to run <code>BDSIM</code> simulations on the UCL HEP Cluster, you must first source the development version of the PBT environment from a system within the cluster that is running Scientific Linux V6. This can be done using the following command:		In order to run <code>BDSIM</code> simulations on the UCL HEP Cluster, you must first source the development version of the PBT environment from a system within the cluster that is running either CentOS7 or Scientific Linux V6. This can be done using the following command:

	<pre>		<pre>
	$ source /unix/pbt/software/scripts/~~pbt~~.sh -vd		$ source /unix/pbt/software/scripts/centos7_pbt.sh -vd
	</pre>		</pre>

	'''Note:''' the '-d' flag is essential as this sources the script that links the latest development software available on the PBT section of the cluster.		'''Note:''' the '-d' flag is essential as this sources the script that links the latest development software available on the PBT section of the cluster.

	~~Following this, a second script must be sourced in order to create the environment required to run <code>BDSIM</code>:~~

	~~<pre>~~
	~~$ source /unix/pbt/software/scripts/bdsim_setup.sh~~
	~~</pre>~~

	Now your system is ready to use <code>BDSIM</code>. To check that it is working correctly, test the built-in help function:		Now your system is ready to use <code>BDSIM</code>. To check that it is working correctly, test the built-in help function:

JamesChappell at 14:16, 25 October 2017

2017-10-25T14:16:43Z

← Older revision		Revision as of 14:16, 25 October 2017
Line 180:		Line 180:
	== Basic AWAKE Spectrometer Simulation ==		== Basic AWAKE Spectrometer Simulation ==

	A simple model of the AWAKE spectrometer is available at <code>/unix/pdpwa/AWAKE_spectrometer</code>. This model (<code>spectrometer.gmad</code>) describes the first part of the spectrometer, downstream of the plasma cell, and includes the quadrupole magnets and drift sections up until the dipole magnet. Also included in this folder are:		A simple model of the AWAKE spectrometer is available at <code>/unix/pdpwa/AWAKE_spectrometer/spectrometer</code>. This model (<code>spectrometer.gmad</code>) describes the first part of the spectrometer, downstream of the plasma cell, and includes the quadrupole magnets and drift sections up until the dipole magnet. Also included in this folder are:

	* <code>options.gmad</code> - includes definitions of constants used within the spectrometer model.		* <code>options.gmad</code> - includes definitions of constants used within the spectrometer model.

JamesChappell at 14:14, 25 October 2017

2017-10-25T14:14:27Z

← Older revision		Revision as of 14:14, 25 October 2017
Line 22:		Line 22:

	<pre>		<pre>
	source /unix/pbt/software/scripts/pbt.sh -vd		$ source /unix/pbt/software/scripts/pbt.sh -vd
	</pre>		</pre>

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	<pre>		<pre>
	source /unix/pbt/software/scripts/bdsim_setup.sh		$ source /unix/pbt/software/scripts/bdsim_setup.sh
	</pre>		</pre>

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	<pre>		<pre>
	bdsim --help		$ bdsim --help
	</pre>		</pre>

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	The BDSIM source code can be downloaded from its git repository using:		The BDSIM source code can be downloaded from its git repository using:

	<pre> git clone --recursive <nowiki>https://bitbucket.org/jairhul/bdsim</nowiki> </pre>		<pre> $ git clone --recursive <nowiki>https://bitbucket.org/jairhul/bdsim</nowiki> </pre>

	This creates a <code>/bdsim</code> folder within your current folder. This folder contains all the code, examples, documentation and associated Python packages.		This creates a <code>/bdsim</code> folder within your current folder. This folder contains all the code, examples, documentation and associated Python packages.
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	'''Note:''' When installing <code>BDSIM</code>, all the <code>Geant4</code> environment variables must be available. This can be tested using the following command:		'''Note:''' When installing <code>BDSIM</code>, all the <code>Geant4</code> environment variables must be available. This can be tested using the following command:

	<pre> echo $G4 <tab> </pre>		<pre> $ echo $G4 <tab> </pre>

	If the <code>Geant4</code> environment variables are available, you should see an output similar to:		If the <code>Geant4</code> environment variables are available, you should see an output similar to:
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	<pre>		<pre>
	cd /unix/pbt/software/build		$ cd /unix/pbt/software/build
	mkdir bdsim		$ mkdir bdsim
	cd bdsim		$ cd bdsim
	mkdir bdsim-0.9.9.2-build		$ mkdir bdsim-0.9.9.2-build
	cd bdsim-0.9.9.2-build		$ cd bdsim-0.9.9.2-build
	</pre>		</pre>

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	<pre>		<pre>
	cmake ../../../src/bdsim/bdsim-bitbucket/		$ cmake ../../../src/bdsim/bdsim-bitbucket/

	ccmake .		$ ccmake .
	</pre>		</pre>

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	<pre>		<pre>
	make		$ make
	make install		$ make install
	</pre>		</pre>

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	<pre>		<pre>
	cd /unix/pbt/software/build/bdsim/bdsim-0.92-dev/bdsim-build-updated/examples		$ cd /unix/pbt/software/build/bdsim/bdsim-0.92-dev/bdsim-build-updated/examples
	cd simpleMachine		$ cd simpleMachine
	</pre>		</pre>

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	<pre>		<pre>
	bdsim --file=sm.gmad		$ bdsim --file=sm.gmad
	</pre>		</pre>

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	<pre>		<pre>
	bdsim --file=sm.gmad --outfile=output		$ bdsim --file=sm.gmad --outfile=output
	</pre>		</pre>

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	<pre>		<pre>
	bdsim --file=sm.gmad --outfile=output --batch		$ bdsim --file=sm.gmad --outfile=output --batch
	</pre>		</pre>

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	The output should look similar to the following images:		The output should look similar to the following images:

			'''Position Evolution:'''

	~~{{multiple image~~		[[File:position.png \| 900px]]
	~~\| width = 80~~
	~~\| footer =~~		'''Momentum Evolution:'''
	~~\| image1 =~~ position.png
	~~\| alt1 = Position evolution~~		[[File:momentum.png \| 900px]]
	~~\| caption1 = Position~~
	~~\| image2 =~~ momentum.png
	~~\| alt2 = Momentum evolution~~
	\| ~~caption2 = Momentum~~
	}}

	<!--== References ==-->		<!--== References ==-->

	<!--{{cite web \|url=https://twiki.ph.rhul.ac.uk/twiki/bin/view/PP/JAI/BdSim \|title=BDSIM - Accelerator Beamline Simulation Tool \|last=Nevay \|first=Laurence \|date=30 August 2017 \|website=Royal Holloway Physics TWiki \|access-date=17 October 2017}}-->		<!--{{cite web \|url=https://twiki.ph.rhul.ac.uk/twiki/bin/view/PP/JAI/BdSim \|title=BDSIM - Accelerator Beamline Simulation Tool \|last=Nevay \|first=Laurence \|date=30 August 2017 \|website=Royal Holloway Physics TWiki \|access-date=17 October 2017}}-->

JamesChappell at 14:08, 25 October 2017

2017-10-25T14:08:29Z

@@ Line 178: / Line 178: @@
 Batch mode has no interactive interface, but as a consequence is much faster and exits the program once it has finished. For simulations with large numbers of particles within the beam, this is the preferred method of use.
 <!--== References ==-->
 <!--{{cite web |url=https://twiki.ph.rhul.ac.uk/twiki/bin/view/PP/JAI/BdSim |title=BDSIM - Accelerator Beamline Simulation Tool |last=Nevay |first=Laurence |date=30 August 2017 |website=Royal Holloway Physics TWiki |access-date=17 October 2017}}-->

JamesChappell at 16:16, 19 October 2017

2017-10-19T16:16:15Z

Show changes

JamesChappell at 13:51, 17 October 2017

2017-10-17T13:51:14Z

← Older revision		Revision as of 13:51, 17 October 2017
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			Work in progress (JChappell 17/10/17)

	== BDSIM ==		== BDSIM ==