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1. vvvrvrvvrvvwanwnvroyvryvyvryvrvrvrvyv gt Magnetic Field gt F Spreadsheet a gt Streamline Derived D Subset dist_fn gt Tensor CPUs gt ri gt a time_derivative a Pera operators gt eee Once an SDF file has been successfully loaded the Add menu item will become un greyed and the cycle numbers for each file in the virtual database will be displayed If we navigate to one of the plot types we are able to select the variable to plot from a drop down list 7 5 Contour Plots in Visit We will now replicate each of the plots which we generated using IDL in earlier sections For reasons which will soon become clear we begin with the contour plot and move on to the 1D plot in the next section 83 Having opened the same dataset we were using in the IDL discussion we now select the Add menu item Notice that many of the plot types listed here are greyed out and cannot be selected This is because many of the plots are dependent on the type or dimensionality of the variable to be plotted If our dataset contains no variables which match the required properties for a plot the plot menu will be disabled For the current dataset there is no Boundary plot available since this requires multi material data and none of our variables meet that criteria The list contains a menu item for a Contour plot We are not going to select this item since it only generates a contour p
2. 0 2 2 2 000 B 2 Additions to the input deck B 3 Changes in behaviour which are not due to changes in the input deck References 92 92 92 93 93 93 93 94 95 96 1 FAQs 1 1 Is this manual up to date Whenever a new milestone version of EPOCH is finalised the version number is changed and this manual is updated accordingly The version number of the manual should match the first two digits for that of the EPOCH source code This version number is printed to screen when you run the code The line looks something like the following Welcome to EPOCH2D Version 4 3 3 commit v4 3 3 3 g3ed1a0e clean Here only the number 4 3 is important Since version 3 1 of the manual new additions and changes are mentioned in the appendix 1 2 What is EPOCH EPOCH is a plasma physics simulation code which uses the Particle in Cell PIC method In this method collections of physical particles are represented using a smaller number of pseudoparticles and the fields generated by the motion of these pseudoparticles are calculated using a finite difference time domain technique on an underlying grid of fixed spatial resolution The forces on the pseudoparticles due to the calculated fields are then used to update the pseudoparticle velocities and these velocities are then used to update the pseudoparticle positions This leads to a scheme which can reproduce the full range of classical micro scale behaviour of a collectio
3. dt_snapshot Sets the interval between normal output dumps in simulation seconds Setting zero or negative means that the code will output every step of the core solver The code does NOT guarantee that outputs will be exactly dt_snapshot apart what is guaranteed is that the next output 30 will be after the first iteration which takes the simulation to a time gt dt_snapshot from the last output As with other variables which specify a unit of time it can be specified in more convenient unit by using a multiplication factor see Section 8 15 1 For example dt_snapshot 5 femto will set it to be 5 femtoseconds The default value is a large number which will never trigger an output nstep_snapshot Sets the number of timesteps between normal output dumps Setting zero or negative means that the code will output every step of the core solver If dt_snapshot is also specified then both conditions are considered and output will be generated when either condition is met The default value is a large integer which will never trigger an output full dump_every The number of normal output dumps between full output dumps Setting to zero makes every dump a full dump Setting to a negative number stops the code from producing any full dumps This is the default restart_dump every The number of normal output dumps between restart dumps Setting to zero makes every dump a restart dump Setting to a negative number stops the code from p
4. has been considered For example if the output block contains distribution functions full and the dist_fn block see Section 3 9 contains dumpmask always then the distribution function will only be output at full dumps particle_probes Dumpmask for outputting particle probes specified in the input deck Each individual particle probe can have its own dumpmask and these will be applied after the value of particle_probes has been considered For example if the output block contains particle_probes always and the dist_fn block contains dumpmask full then the particle probe will only be output at full dumps absorption This is a two valued output variable It accepts a dumpmask in the same manner as other output variables When selected two numbers will be calculated and written to file 34 1 Absorption Laser_enTotal The total amount of energy injected into the simulation by laser boundaries 2 Absorption Abs_frac The fraction of the total laser energy being absorbed by the open bound aries total_energy_sum This is also a two valued output variable It accepts a dumpmask in the same manner as other output variables When selected the following two numbers will be calculated and written to file 1 Total Particle Energy in Simulation J 2 Total Field Energy in Simulation J 3 7 7 Data Averaging EPOCH can accumulate an average value for field variables to
5. Sometimes it is useful to reconstruct part of the full phase space for one or more particle species This functionality is provided through a dist_fn block The distribution function is integrated over all dimensions which are not axes of the distribution function Calculating distribution functions requires some degree of integration of data leading to various possible ways of normalising the resulting distribution function In EPOCH distribution functions are normalised so that the value at every point of the distribution function is the number of particles within that cell of the distribution function ignoring all phase space directions which are not considered as an axis of the distribution function Summing the distribution function should give the total number of real particles as opposed to computational pseudoparticles in the simulation An example dist fn block is given below 39 dist_fn block begin dist_fn name X_px ndims 2 dumpmask always directionl dir_x direction2 dir_px range is ignored for spatial coordinates rangel 1 1 range2 50 0e 20 50 0e 20 resolution is ignored for spatial coordinates resolutioni 1 resolution2 5000 restrict_py 3 0e 20 3 0e 20 include_species Electron include_species Carbon end dist_fn name The name of the distribution function when it is output This name is appended with the name of each species for which the data is output and so for example wh
6. The range between which this axis should run This is in the form of minimum maximum Any particle which exceeds the range is ignored In the current version of EPOCH the rangen parameter is ignored when applied to a spatial direction For momentum directions this parameter is specified in kg ms If the range of a momentum direction is set so that the maximum and the minimum are equal then the code will automatically set the range to exactly span the range of particle momenta at the point of writing the dump 40 NOTE Currently the range parameters have to be simple floating point numbers and NOT maths parser expressions resolutionn The number of gridpoints in a given direction Once again this is ignored for spatial dimensions where the resolution is always the same as the resolution of the underlying simulation include_species Specifies a species which should be included in the output This is useful since it is rare that momentum limits are appropriate for both electrons and ions so usually for a given dist_fn block only electrons or ions are considered It is possible to have two dist_fn blocks with the same name but different momentum ranges and different include_species settings produce the effect of a single diagnostic for all species in the output file restrict_ x y z px py pZ Restrictions are specified in the same way as ranges but have a subtly different behaviour Ranges specify the range of a visible axis on
7. cpml laser is used to attach a laser to an otherwise absorbing boundary condition There are also four configurable parameters cpml_thickness The thickness of the CPML boundary in terms of the number of grid cells The default value is 6 cpml_kappa_max cpml_a_max cpml_sigma_max These are tunable parameters which affect the behaviour of the absorbing media The notation follows that used in the two references quoted above Note that the cpml_sigma_max parameter is normalised by opt which is taken to be 3 2 dx see Taflove and Hagness 4 for details These are real valued parameters which take the following default values cpml_kappa_max 20 cpml_a_max 0 15 cpml_sigma_max 0 7 An example usage is as follows begin boundaries cpml_thickness 16 cpml_kappa_max cpml_a_max 0 cpml_sigma_max 20 I N I on bc_x_min cpml_laser bc_x_max cpml_outflow bc_y_min cpml_outflow bc_y_max cpml_outflow end boundaries 3 2 2 Thermal boundaries Thermal boundary conditions have been added to the boundaries block These simulate the existence of a thermal bath of particles in the domain adjacent to the boundary When a particle leaves the simulation it is replace with an incoming particle sampled from a Maxwellian of a temperature 18 corresponding to that of the initial conditions It is requested using the keyword thermal For example begin boundaries bc_x_min laser bc_x_max thermal
8. to the end of input deck and removing the import line The final output from this simulation is shown in Figure 5 2 Structured density profile in EPOCH2D Time 0 sec Pseudocolor Var Derived Number_Density Electron Units 1 m43 2 115e 19 1 5868 19 1 057e 19 5 287e 18 0 000 Max 2 115e 19 5 Min 0 000 Y x10 6 m o 5 5 0 5 X x10 6 m Figure 8 Complex 2D density structure A simple but useful example for EPOCH2D is to have a highly structured initial condition to show that this is still easy to implement in EPOCH A good example initial condition would be input deck begin control nx 500 ny nx x_min 10 micron x_max Xx_min y_min x_min y_max X_max nsteps 0 npart 40 nx ny end control begin boundaries bc_x_min bc_x_max bc_y_min periodic periodic periodic 66 bc_y_max periodic end boundaries begin constant den_peak 1 0e19 end constant begin species name Electron density den_peak sin 4 0 pixx length_xtpi 4 sin 8 0 pixy length_y 1 density_min 0 1 den_peak chargel 50 mass 1 0 frac 0 5 end species begin species name Proton density density Electron charge 1 0 mass 1836 2 frac 0 5 end species begin output number_density always species end output The species block for Electron is specified first setting up the electron density to be a structured 2D sinus
9. 0 2 multiply density by real particle density density density s1 100 0 Set the temperature to be zero temp x 0 0 temp_y temp_x s1 Set the minimum density for this species density_min 0 3 100 0 end species begin species Just copy the density for species s1 density density s1 51 Just copy the temperature from species s1 temp_x temp_x s1 temp_y temp_y s1 Set the minimum density for this species density_min 0 3 100 0 end species An important point to notice is that the two parts of the logical expressions in the input deck are enclosed within their own brackets This helps to remove some ambiguities in the functioning of the input deck parser It is hoped that this will soon be fixed but at present ALWAYS enclose logical expressions in brackets 4 2 Manually overriding particle parameters set by the autoloader Since not all problems in plasma physics can be described in terms of an initial distribution of thermal plasma it is also possible to manually control properties of each individual pseudoparticle for an initial condition This takes place in the subroutine manual_load in the file user_interaction ic_module f90 Manual loading takes place after all the autoloader phase to allow manual tweaking of autoloader specified initial conditions 4 2 1 EPOCH internal representation of particles Before we can go about manipulating particle properties in manual_load we first need an ov
10. CURRENT 2D Plain variable 10 WEIGHT_ELECTRON PARTICLES 1D Point variable 11 WEIGHT_PROTON PARTICLES 1D Point variable 12 PX_ELECTRON PARTICLES 1D Point variable 13 PX_PROTON PARTICLES 1D Point variable 14 GRID_ELECTRON GRID 2D Point mesh 15 GRID_PROTON GRID 2D Point mesh 16 EKBAR DERIVED 2D Plain variable 17 EKBAR_ELECTRON DERIVED 2D Plain variable 18 EKBAR_PROTON DERIVED 2D Plain variable 19 CHARGE_DENSITY DERIVED 2D Plain variable 72 20 NUMBER_DENSITY DERIVED 2D Plain variable 21 NUMBER_DENSITY_ELECTRON DERIVED 2D Plain variable 22 NUMBER_DENSITY_PROTON DERIVED 2D Plain variable 23 GRID GRID 2D Plain mesh 24 GRID_EN_ELECTRON GRID 1D Plain mesh 25 EN_ELECTRON DIST_FN 3D Plain variable 26 GRID_X_EN_ELECTRON GRID 2D Plain mesh 27 X_EN_ELECTRON DIST_FN 3D Plain variable 28 GRID_X_PX_ELECTRON GRID 2D Plain mesh 29 X_PX_ELECTRON DIST_FN 3D Plain variable IDL gt Each variable in the SDF self describing file format is assigned a name and a class as well as being defined by a given variable type The list variables procedure prints out the variable name followed by the variable s class in parenthesis Following the colon is a description of the variable type To retrieve the data you must use the getdata function call The function must be passed a snapshot number either as the first argument or as a keyword parameter sna
11. The EPOCH codes are written using MPI for parallelism but have no other libraries or dependencies Currently the codes are written to only require MPI1 2 compatible libraries although this may change to require full MPI2 compliance in the future Current versions of both MPICH and OpenMPI implement the MPI2 standard and are known to work with this code The SCALI MPI implementation is only compliant with the MPI1 2 specification and may loose support soon There are no plans to write a version of EPOCH which does not require the MPI libraries The code is supplied with a standard GNU make Makefile which is also compatible with most other forms of the make utility In theory it is possible to compile the code without a make utility but it is much easier to compile the code using the supplied makefile 2 3 Compiling and running EPOCH To compile EPOCH in the supplied state you must first change to the correct working directory As explained in Section 2 1 the root directory for EPOCH contains several subdirectories including separate directories for each of the 1D 2D and 3D versions of the code To compile the 2D version of the code you first switch to the epoch2d directory using the command cd HOME epoch epoch2d and then type make and the code will compile There are certain options within the code which are controlled by compiler preprocessors and are described in the next section When the code is compiled it creates a new directo
12. but all lasers with the same id will have the same time profile This parameter is optional and is not used under normal conditions omega Angular frequency rad s not Hz for the laser frequency Ordinary frequency Hz not rad s for the laser lambda Wavelength in a vacuum for the laser specified in m If you want to specify in wm then you can multiply by the constant micron One of lambda or omega or frequency is a required parameter pol_angle Polarisation angle for the electric field of the laser in radians This parameter is optional and has a value of zero by default The angle is measured with respect to the right hand triad of propagation direction electric and magnetic fields Although the 1D code has no y or z spatial axis the fields still have y and z components If the laser is on x min then the default E field is in the y direction and the B field is the z direction The polarisation angle is measured clockwise about the x axis with zero along the direction If the laser is on x_max then the angle is anti clockwise Similarly for propagation directions y min angle about y axis zero along z axis z min angle about z axis zero along x axis y_max angle anti clockwise about y axis zero along z axis z max angle anti clockwise about z axis zero along x axis pol This is identical to pol_angle with the angle specified in degrees rather than radians If both are specified then the last one is used phas
13. end species begin species name s2 Just copy the density for species s1 density density s1 Just copy the temperature from species s1 temp_x temp_x s1 temp_y temp_y s1 Set the minimum density for this species density_min 0 3 particle_density end species This changes the code to run with a Gaussian density profile rather then a step function Again this can be extended as far as required 5 Basic examples of using EPOCH In this section we outline a few worked examples of setting up problems using the EPOCH input deck 5 1 Electron two stream instability An obvious simple test problem to do with EPOCH is the electron two stream instability An example of a nice dramatic two stream instability can be obtained using EPOCHID by setting the code with the following input deck files input deck begin control nx 400 npart 20000 63 Hfinal time of simulation t_end 1 5e 1 size of domain x_min 0 x_max 5 0e5 end control begin boundaries bc_x_min periodic bc_x_max periodic end boundaries begin constant drift_p 2 5e 24 temp 273 dens 10 end constant begin species Rightwards travelling electrons name Right charge 1 mass 1 0 mas gt 0 8 temp_x temp drift_x drift_p rho dens end species begin species Leftwards travelling electrons name Left charge 1 mass 1 0 frac 0 5 temp_x temp driftix drift p rho dens end
14. end boundaries 3 3 species block The next section of the input deck describes the particle species used in the code An example species block for any EPOCH code is given below species block begin species name Electron charge 1 0 mass 1O frac 0 5 npart 2000 100 tracer F density 1 e4 temp 1e6 temp_x 0 0 temp_y temp_x Electron density_min 0 1 den_max density if abs x lt thick den_max 0 0 density if x gt thick and abs y gt 2e 6 0 0 density Carbon end species begin species name Carbon charge 4 0 mass 1836 0 12 frac 0 5 density 0 25 density Electron temp_x temp_x Electron temp_y temp_x Electron dumpmask full end species Each species block accepts the following parameters name This specifies the name of the particle species defined in the current block This name can include any alphanumeric characters in the basic ASCII set The name is used to identify the species in any consequent input block and is also used for labelling species data in any output dumps It is a mandatory parameter 19 NOTE IT IS IMPOSSIBLE TO SET TWO SPECIES WITH THE SAME NAME charge This sets the charge of the species in multiples of the electron charge Negative numbers are used for negatively charged particles This is a mandatory parameter mass This sets the mass of the species in multiples of the electron mass Cannot be negative This is a mandat
15. Array 1 GRID_X_PX_ELECTRON STRUCT gt lt Anonymous gt Array 1 IDL gt help gridclass grid structures Structure lt 1701168 gt 5 tags length 12376 data length 12376 refs 2 X DOUBLE Array 1025 Y DOUBLE Array 513 LABELS STRING Array 2 UNITS STRING Array 2 NPTS LONG Array 2 Here we have used IDL s built in help routine and passed the structures keyword which prints information about a structure s contents rather than just the structure itself Since Grid is a class name all variables of that class have been loaded into the returned data structure It is a nested type so many of the variables returned are structures themselves and those variables may contain structures of their own The Grid variable itself contains x and y arrays containing the x and y coordinates of the 2D cartesian grid The other variables in the Grid structure are metadata used to identify the type and properties of the variable In order to access the Grid variable contained within the gridclass data structure we have used the operator In a similar way we would access the x array contained within the Grid variable using the identifier gridclass grid x 6 2 Getting Help in IDL IDL is a fairly sophisticated scripting environment with a large library of tools for manipulating data Fortunately it comes with a fairly comprehensive array of documentation This can
16. Functions o sc reu rkr da ak e da ea ea a e E a a aa ee a a a Sak nas oa a A 4 1 Specifying initial conditions for particles using the input deck 4 1 1 Setting autoloader properties from the input deck TER AA tee nee nes ba a ut Peas Ee ee AA A eo eG padel A A 4 4 laser blocks in multiple dimensions o ade e o dec nee AR RNE ee ee TOES 5 Basic examples of using EPOCH 5 1 Electron two stream instability o oo a a a A A E RA E e a a ee A a Pade a ee aes a O a Se tl a ee AE A EII 6 2 Getting Help in ID se c s pee Ge eee BHR REE a RAE A A sis ee o o es ae Gea ty Bag ee e 64 TD Plotting m MOL 2 64464 nee nadreda 244464 SRG AAA Te ee ee a a ee ee A ee a 6 6 Contour Plots in IDL 0 0 0 0020 000000000 a 6 7 Shaded Surface Plots in IDL de A e be ae A EA ees 6 8 Interactive Plo blocs 2 a E e a RAE A A eg ee AS AMAIA A E S 7 2 Obtaining And Installing VislIt o o ee as o A o o e 7 4 Loading Data Into Vis 22 lt 4 a224 5 ae bes bea ries da a a 7 5 Contour Plots in VisIt 2 a TO ID Plotting in Vislt s ss s rosita A A T Shaded Surface Plots in Visit oaoa a aaa a a Es a e ee A Ee a A 1 9 Creating Movies aa a ido a ra A id e AN AA A IN e O A e en ee ee ee ee A Changes between version 3 1 and 4 0 A EN A rt o 4 ew ek R B Changes between version 4 0 and 4 3 C B 1 Changes to the Makefile
17. K K 2K K 2K 2K 3K 3K 3K 3K 3K 3K 3K 2K 2K 2K IK 2K 2K 2K 2K 2K 2K Code is running on 1 processing elements Specify output directory At which point the end user should simply type in the name of the directory where the code output is to be placed This directory must also include the file input deck which controls the code setup specifies how to set the initial conditions and controls the I O Writing an input deck for EPOCH is 11 fairly time consuming and so the code is supplied with some example input decks which include all the necessary sections for the code to run 3 The EPOCH input deck Most of the control of EPOCH is through a text file called input deck The input deck file must be in the output directory which is passed to the code at runtime and contains all the basic information which is needed to set up the code including the size and subdivision of the domain the boundary conditions the species of particles to simulate and the output settings for the code For most users this will be capable of specifying all the initial conditions and output options they need More complicated initial conditions will be handled in later sections The input deck is a structured file which is split into separate blocks with each block containing several parameter value pairs The pairs can be present in any order and not all possible pairs must be present in any given input deck If a required pair is missing the code wil
18. Of particular help here is the Getting VisIt to run in parallel section and the How VisIt Launching works entry in the Developer documentation section 91 A Changes between version 3 1 and 4 0 A 1 Changes to the Makefile Some changes have been made to the Makefile These are documented in Section The following compile time defines have been added to the Makefile e NO IO e PARTICLE_ID e PARTICLE_ID4 e COLLISIONS TEST e PHOTONS e TRIDENT_PHOTONS e PREFETCH The following compile time defines have been removed from the Makefile e COLLISIONS e SPLIT PARTICLES AFTER PUSH e PARTICLE_IONISE A 2 Major features and new blocks added to the input deck e CPML boundary conditions See Section 3 2 1 e Thermal boundary conditions See Section 3 2 2 e Collisions See Section 3 11 e QED See Section 3 12 e Subsets See Section 3 13 e lonisation See Section 3 3 2 e Single precision output See Section 3 7 8 e Multiple output blocks See Section 3 7 9 e Particle migration See Section 3 3 1 92 A 3 Additional output block parameters The following parameters have also been added to the output block see Section 3 7 2 e dump first e dump_last e force_first_to_be_restartable e ejected_particles e absorption e id e name e restartable A 4 Other additions to the input deck e npart_per_cell See Section 3 3 e dir_ xy yz zx _ angle See Section 3 9 e particle tstart Se
19. The following parameters cannot be used in conjunction with the new style of output block e full dump every e restart_dump every e force first to be restartable e force_last_to_be_restartable e use_offset_grid The file _prefix parameter warrants some further discussion This parameter prepends the given prefix to all files generated by the output block in which it is specified For example if file_prefix aa is set then files generated by the output block will be named aa0000 sdf etc instead of just 0000 sdf This also allows different variables to different files at the same time step For example here are two output blocks which do not use file prefixes begin output name ol nstep_snapshot charge_density end output begin output name 02 dump_at_nsteps restartable T end output With this input deck we want to have the charge_density derived variable at every snapshot and then periodically write a restart dump The problem is that the dump file 0010 sdf contains both the restart information and the charge_density variable At the end of the run we can t just delete the large restart dumps without losing the smaller variables at that time step With the new version we would add a prefix to one or both blocks begin output name ol file_prefix small nstep_snapshot 1 charge_density always end output begin output name 02 37 nstep_snapshot 10
20. a UNIX machine and the desktop used for visualisation is running Windows It is sometimes possible to run a graphical tool on the remote machine and tunnel the X server session through to the local machine but this can be quite slow and unstable When connecting to a remote VisIt instance the only data which needs to be sent between machines is the pre rendered image and a few simple plotting commands Naturally this can be a much faster approach Also as mentioned before it is possible to use a machine on which the reader plugin is difficult or impossible to compile for and connect to a machine on which the reader is already installed In order to use the remote visualisation facility you must first set up a Host profile for the remote machine using the Options Host profiles menu item The pre compiled binaries are shipped with a long list of pre defined host profiles These are unnecessary for anyone not affiliated and can safely be removed by deleting the directory HOME visit current visit assuming you have unpacked the Vislt tarball into your home directory 89 eoo Host profiles Biosie E Launch Profiles minerva Machine Host nickname minerva Remote host name minervalogin1 csc warwick ac uk Host name aliases minerva o C Maximum nodes 1 _ Maximum processors 1 Path to Visit installation 1 home space phsiav INSTALL visit Account Username phsiav Connection Share batch job with Metada
21. archive commonly referred to as a tarball is downloaded and unpacked into the user s HOME directory then the extracted contents will consist of a directory named HOME epoch 4 3 3 with 4 3 3 substituted by the current version number and the subdirectories and files listed below Alternatively if the code is checked out from the CCPForge subversion repository with the command svn checkout username lt user gt http ccpforge cse rl ac uk svn epoch then the directory will be SHOME epoch trunk In this case the directories SHOME epoch branches and HOME epoch tags will also be created These two directories are entirely unnecessary You can avoid creating them by checking out the subversion repository using the following command svn co username lt user gt http ccpforge cse rl ac uk svn epoch trunk epoch All the required source code will then be contained in a directory named HOME epoch Once the code has been obtained the top level directory will contain the following 5 directories and two files e epochld Source code and other files required for the 1D version of EPOCH e epoch2d Source code and other files required for the 2D version of EPOCH e epoch3d Source code and other files required for the 3D version of EPOCH e MatLab The files for creating a plug in for the Mathworks MatLab visualisation tool for reading SDF files generated by an EPOCH run e Vislt The files for creating a pl
22. be accessed by typing at the IDL prompt IDL gt ONLINE_HELP Starting the online help browser IDL gt 74 800 Help IDL Workbench gt ff 127 0 0 1 50320 help index jsp wis Search Sd RR Search scope All topics Contents r g go Go fle ao o l About IDL IDL Help Welcome to the IDL 7 1 help system This home page provides links to information on important IDL topics including IDL 7 1 News E IDL Help Home El N What s New in IDL 7 1 G IDL 7 1 Release Notes W Installation and Licensing Guide B Legal Notices IDL Workbench Guide E IDL API Reference Guides IDL Users Guides El IDL Programmers Guides supplemental IDL Guides What s New in IDL 7 1 e IDL Release Notes Popular Help Topics IDL Workbench Super Quick Start Getting Started with IDL e List of IDL Routines by Functional Area e A tour of the IDL Workbench interface Using the IDL help system e IDL Tutorials IDL Workbench Tips and Tricks On the Web ITT Visual Information Solutions Home Page IDL Home Page The documentation is divided into books aimed at users or developers and is fully searchable and cross indexed 6 3 Manipulating And Plotting Data Once the data has been loaded from the SDF file we will want to extract the specific data we wish to analyse perhaps perform some mathematical operations on it and then plot the result
23. dumps Only the average value of ekbar will be written at full dumps Only field and derived variables can be averaged currently in EPOCH Particle properties distribu tion functions and particle probes cannot currently be averaged 3 7 8 Single precision output By default EPOCH is compiled and run using double precision arithmetic This is the only method which has been fully tested and the method that we recommend to other users of the code However this also means that data files can get very large To avoid this problem it is possible to run the code in double precision but convert the data to single precision when writing to disk This is done by adding the single field the the dumpmask of an output variable It can be specified on a per variable basis 35 begin output dt_snapshot 8 femto grid always ex always ey always single end output In this example the grid variable ex will be written as a double precision array and ey will be converted to single precision Dumping variable averages adds an extra field variable for each average requested These take up memory during runtime but do not influence the simulation behaviour in any way For this reason if the average is to be written out in single precision then it may as well be stored in a single precision variable This behaviour can be requested using the average single dumpmask flag 3 7 9 Multiple output blocks In mo
24. e PARTICLE_ID When this option is enabled all particles are assigned a unique identification number when writing particle data to file This number can then be used to track the progress of a particle during the simulation e PARTICLE_ID4 This does the same as the previous option except it uses a 4 byte integer instead of an 8 byte one Whilst this saves storage space care must be taken that the number does not overflow e PHOTONS This enables support for photon particle types in the code These are a pre requisite for modelling synchrotron emission radiation reaction and pair production see Section 3 12 e TRIDENT PHOTONS This enables support for virtual photons which are used by the Trident process for pair production e PARTICLE_ COUNT_UPDATE Makes the code keep global particle counts for each species on each processor This information isn t needed by the core algorithm but can be useful for develop ing some types of additional physics packages It does require one additional MPIALL_REDUCE per species per timestep so it is not activated by default e PREFETCH This enables an Intel specific code optimisation e PARSER_DEBUG The code outputs more detailed information whilst parsing the input deck This is a debug mode for code development e PARTICLE_DEBUG Each particle is additionally tagged with information about which processor it is currently on and which processor it started on This is a debug mode for code
25. requested If this flag is set to T then EPOCH will continue to run and leave some of the requested CPUs idle If set to F then code will exit if all CPUs cannot be utilised The default value is T check_stop file frequency Integer parameter controlling automatic halting of the code The frequency is specified as number of simulation cycles Refer to description later in this section The default value is 10 stop_at_walltime Floating point parameter controlling automatic halting of the code Refer to description later in this section The default value is 1 0 stop_at_walltime_file String parameter controlling automatic halting of the code Refer to description later in this section The default value is an empty string simplify _deck If this logical flag is set to T then the deck parser will attempt to simplify the maths expressions encountered after the first pass This can significantly improve the speed of evaluation for some input deck blocks The default value is F print_constants If this logical flag is set to T deck constants are printed to the deck status file as they are parsed The default value is F use_migration Logical flag which determines whether or not to use particle migration The default is F See Section 3 3 1 migration interval The number of timesteps between each migration event The default is 1 migrate at every timestep See Section M
26. restartable T end output Now the charge density will be written to small0000 sdf etc At step 10 two files will be written small0010 sdf containing just the charge_density and 0000 sdf containing all the restart variables Note that some care must be taken since if the same variable is in the output block for multiple file prefixes then multiple copies will be written to file This obviously uses more disk space and is more time consuming than necessary It should also be noted that if multiple output blocks use the same file stem then their output will be combined eg begin output name ol file_prefix a dump_at_nsteps 2 4 ex always end output begin output name 02 file_prefix a dump_at_nsteps 3 4 ey always end output begin output name 03 file_prefix b dump_at_nsteps 4 ez always end output In this example at step 2 a0000 sdf contains ex step 3 a0001 sdf contains ey step 4 a0002 sdf contains ex ey and b0000 sdf contains ez 3 8 output_global block With the introduction of multiple output blocks there are now a few parameters that only make sense to be applied globally across all output blocks To accommodate this a new block named output_global has been added Most of the parameters accepted by this block have the same meaning as those in the output block except that they are applied to all output blocks The parameters that can be spec
27. script just type unpack_source_from_restart lt sdf_filename gt at the command line If this logical flag is set to false then the feature will be disabled The default value is T dump_input_decks If this logical flag is set to true then a copy of the input decks for the currently running simulation is written into the restart dumps The default value is T dt_average When averaged variables are being output to file this parameter specifies the simulation time period over which averaging is to occur averaging period is accepted as a synonym nstep_average When averaged variables are being output to file this parameter specifies the number of time steps over which averaging is to occur min_cycles_per_average is accepted as a synonym If both dt_average and nstep_ average are specified the code will use the one which gives the longest simulation time span use_offset_grid When using moving windows some visualisation programs notably Vislt show the motion of the window by moving the visualisation window rather than by changing the x axis Setting this option to T causes the code to write another grid which always gives the offset relative to the left hand edge of the window rather than the true origin Performs no function when not using the moving window The default value is F filesystem String parameter Some filesystems can be unreliable when performing parallel I O Often this is fixable b
28. sensible defaults eg 1 grid cell 1 metre thick etc Automatic byte swapping is carried out by the SDF library The library now checks the endianness of the SDF file and byte swaps the data if required qed blocks may now be present even if the code was not compiled using the DPHOTONS flag The code will only halt if use_qed T inside the qed block The code now checks for the Data directory in a file named USE_DATA DIRECTORY before prompting at the command line This allows the code to be run without waiting for input at the command line The field and particle grids are now automatically written to SDF output files if they are needed The Data directory may now contain a character 95 C References 1 T D Arber K Bennett C S Brady A Lawrence Douglas M G Ramsay N J Sircombe P Gillies R G Evans H Schmitz A R Bell and C P Ridgers A particle in cell code for laser plasma interactions test problems convergence and accuracy J Comput Phys submitted 2014 C Ridgers J Kirk R Duclous T Blackburn C Brady K Bennett T Arber and A Bell Mod elling gamma ray photon emission and pair production in high intensity lasermatter interactions J Comput Phys vol 260 pp 273 285 2014 O Buneman TRISTAN The 3 D Electromagnetic Particle Code in Computer Space Plasma Physics Simulations Techniques and Software 1993 A Taf
29. species begin output number of timesteps between output dumps dt_snapshot 1 5e 3 Number of dt_snapshot between full dumps full_dump_every 1 64 Properties at particle positions particles always px always Properties on grid grid always ex always ey always ez always bx always by always bz always jx always ekbar always mass_density never species charge_density always number_density always species temperature always species extended io distribution_functions always end output Time 0 15 sec Particles Px kg m s FAA AA 35 5 5 1 17 0 2 0 4 0 6 Grid Particles X m Figure 7 The final state of the electron phase space for the two stream instability example While the input deck file is rather long most of it is the basic standard input deck that is supplied with EPOCH with only the length of the domain the final time and the time between snapshots 65 specific to this problem ic deck the initial conditions file is very simple indeed The first block sets up constants for the momentum space drift the temperature and the electron number density The second and third blocks set up the two drifting Maxwellian distributions and the constant density profile Note that we have written this example as two separate files simply to demonstrate how this is done The same result would be obtained by appending the contents of ic deck
30. then no clipping is performed This is the default mass_density Particle mass density in kgm The same as density but multiplied by the particle mass If you wish to use units of gem then append the appropriate multiplication factor For example mass_density 2 1e3 cc temp_ x y z The temperature in each direction for a thermal distribution in Kelvin temp Sets an isotropic temperature distribution in Kelvin If both temp and a specific temp_x temp_y temp_z parameter is specified then the last to appear in the deck has precedence If neither are given then the species will have a default temperature of zero Kelvin temp_ x y z ev temp_ev These are the same as the temperature parameters described above except the units are given in electronvolts rather than Kelvin drift_ x y z Specifies a momentum space offset in kg ms to the distribution function for this species By default the drift is zero offset File offset See below for details It is also possible to set initial conditions for a particle species using an external file Instead of specifying the initial conditions mathematically in the input deck you specify in quotation marks the filename of a simple binary file containing the information required external initial conditions begin species name Electron density Data ic dat offset 80000 temp_x Data ic dat end species An additional ele
31. time at which to stop considering output for the block The default value is the largest possible float nstep_start Integer parameter which specifies the step number at which to start considering output for the block The default value is 0 nstep stop Integer parameter which specifies the step number at which to stop considering output for the block The default value is the largest possible integer dump_cycle If this is set to a positive integer then the output file number will be reset to zero after the specified cycle number is reached eg if dump cycle 2 then the sequence of output dumps will be 0000 sdf 0001 sdf 0002 sdf 0000 sdf 0001 sdf etc The default is 0 so dump cycling never occurs 31 dump_cycle_first_index If this is set to a positive integer then the value is used as the first index to use when cycling output dumps due to the dump cycle parameter For example if dump cycle 2 and dump cycle first index 1 then the sequence of output dumps will be 0000 sdf 0001 sdf 0002 sdf 0001 sdf 0002 sdf 0001 sdf etc The default is 0 dump_source_code EPOCH has the ability to write its own source code into restart dumps This is generated at compile time and embedded into the binary and so is guaranteed to match that corresponding to the running code EPOCH comes with a script called unpack_source_from restart which can be used to unpack the source code from a restart dump To use this
32. time dependance is given separately The default value of t_profile is just the real constant value of 1 0 t_start Start time for the laser in seconds Can be set to the string start to start at the beginning of the simulation This is the default value When using this parameter the laser start is 25 hard To get a soft start use the t_profile parameter to ramp the laser up to full strength t_end End time for the laser in seconds can be set to the string end to end at the end of the simulation This is the default value When using this parameter the laser end is clipped straight to zero at t gt t_end To get a soft end use the t_profile parameter to ramp the laser down to zero If you add multiple laser blocks to the initial conditions file then the multiple lasers will be additively combined on the boundary In theory any laser time profile required is possible but the core FDTD solver for the EM fields in EPOCH produces spurious results if sudden changes in the field intensity occur This is shown in Figures iJand 2 The pulse shown in Figure I used a constant t profile and used t_end to stop the laser after 8fs Since the stopping time was not an exact multiple of the period the result was to introduce spurious oscillations behind the pulse If the laser had a finite phase shift so that the amplitude did not start at zero a similar effect would be observed on the front of the pulse t_profile 1 t_end 8e 15 F
33. to 2D simply replace the line r sqrt y 2 z 2 with the liner abs y The actual work in these initial conditions is done by the three lines inside the block for the Proton species Each of these lines performs a very specific function 1 Creates the outer cone Simply tests whether r is within the range of radii which corresponds to the thickness of the cone and if so fills it with the given density Since the inner radius is x dependent this produces a cone rather than a cylinder On its own this line produces a pair of cones joined at the tip 2 Creates the solid tip of the cone This line just tests whether the point in space is within the outer radius of the cone and within a given range in x and fills it with the given density if true 68 3 Cuts off all of the cone beyond the solid tip Simply tests if x is greater than the end of the cone tip and sets the density to zero if so Pseudocolor Var Derived Number_Density electron Units 1 mA3 1 141e 22 8 555e 21 5 703e 21 2 852e 21 0 000 Max 1 141e 22 Min 0 000 Figure 9 Cone initial conditions in 3D Pseudocolor Var Derived Number_Density electron Units 1 mM 3 1 124e 22 8 429e 21 5 619e 21 2 810e 21 0 000 Max 1 124e 22 5 Min 0 000 Y x10 6 m o 5 5 0 5 X x10 6 m Figure 10 Cone initial conditions in 2D 69 This deck produces and initial condition which looks like Figure 9 and Figure 10 in 3D an
34. to enable the use of mathematical expressions in the input deck Further information about this facility can be found in Section 3 15 1 10 I am an advanced user but I want to set up the code so that less experienced users can use it How do I do that See 4 6 Section 4 6 1 11 I want to develop an addition to EPOCH How do I do that A slightly outdate developers manual exists which should be sufficient to cover most aspects of the code functionality However the code is written in a fairly modular and consistent manner so reading through that is the best source of information If you get stuck then you can post questions on the CCPForge forums 1 12 I want to have a full understanding of how EPOCH works How do I do that If you really want to understand EPOCH in full the only way is to read all of this manual and then read through the code Most of it is commented 2 EPOCH for end users This manual aims to give a complete description of how to set up and run EPOCH as an end user Further details on the design and implemetation of the code may be found in Arber et al I and Ridgers et al 2 We begin by giving a brief overview of the EPOCH code base how to compile and run the code Note that throughout this user manual instructions are given assuming that you are typing commands at a UNIX terminal 2 1 Structure of the EPOCH codes When obtained the EPOCH codes all have a similar structure If the tarred and gzipped
35. using dump _source_code F and dump _input deck F in the output block However the functionality is difficult to build on some platforms so the Makefile contains a line for bypassing this section of the build process Just below all the DEFINE flags there is the following line ENCODED_SOURCE dummy_encoded_source o Just uncomment this line and source code in restart dumps will be permanently disabled 2 5 Running EPOCH and basic control of EPOCH1D When the code is run the output is Command line output CHHHHHHHHP d HHHHHHHD HHHHHHD AHHHHHHH d HP d P AHHHHHHHHP d HHHHHHHHHH AHHHHHHHHHHH HEHHHHHHHH dP d P S os e556 555 gt P AHHHHHHHHP d HHH HHHP HHH HHHH dHHHP AHHHHHHHHHHHHP AHHHHHHHHP GHHHHHHHHHP HHHH HHHP HHHH AHHHHHHHHHHHHP d P dH P HEH AHHH HHH di P d P CHHHHHHHHP ARHP HHHHHHH HHH P HHHHHHHHHHP dH P d P GHHHHHHHHP dit P dAHHHHHHP HHHHHHP d P d P Welcome to EPOCH2D Version 4 3 3 commit v4 3 3 3 g3ed1a0e clean The code was compiled with the following compile time options KKK KK K aK aK aK 2A 3K 3K 3K K K K aK aK 3K 3K 3K 2K 3K K K K 2K 3K 3K 3K 3K K aK K 2A 2K 3K 3K 3K 3K K K K K K 3K 3K 3K 3K 3K K K K K 2K 3K 3K 2K 2K K Per particle weighting DPER_PARTICLE_WEIGHT Tracer particle support DTRACER_PARTICLES Particle probe support DPARTICLE_PROBES 3K aK ak ak aK aK aK K K K 2K 2K 3K 2K 3K 3K 3K 3K 3K 3K 3K ak 2 2 2 2 2K 2K aK gt K K
36. you to browse directories along with the options to filter the results according to a given regular expression and grouping options By default VisIt will attempt to group all files containing the same suffix and some kind of numbering system into a sort of virtual database The right hand pane of this window shows a list of selected files which will appear in the main Vislt window when you are finished An alternative method of specifying the data file to open is to pass a command line option when the tool is launched An example of this method is visit o Data 0000 sdf When the file is specified in this manner the list of files shown in the VisIt window will also include the full list of files in the 82 dataset s subdirectory and all the files in the current working directory The other SDF files will be grouped together in a virtual database Yet another method for selecting the dataset to use is by opening a previously saved session file We will discuss this further in a later section e00 Visit 2 7 1 Global Active window 1 gt _ Auto apply Sources ra amp Open Close Reopen Replace Overlay Active source sdf database a gt Time e gt 0000 dl 4 EP lA Plots opts gt Addy Operators Delete Hide Show Draw Variables Boundary Contour Curve D Filled Boundary Histogram Label E Mesh Molecule MultiCurve FN Parallel Coordinates Pseudocolor
37. AINMESH Compiled module SDFGETLAGRANMESH Compiled module SDFGETPOINTMESH Compiled module SDFGETPLAINVAR Compiled module SDFGETPOINTVAR Compiled module SDFGETCONSTANT Compiled module SDFCHECKNAME Compiled module INIT_SDFHELP Compiled module GETDATA Compiled module GETSTRUCT Compiled module EXPLORE_DATA Compiled module EXPLORE_STRUCT Compiled module LIST_VARIABLES Compiled module QUICK_VIEW Compiled module GET_WKDIR Compiled module SET_WKDIR Compiled module INIT_STARTPIC Compiled module SWAPCHR Compiled module CHECKNAME Compiled module RETURNIDLUSABLE Compiled module RETURNFRIENDLYTYPENAME Compiled module INIT_CFDHELP Compiled module INIT_WIDGET Compiled module GENERATE_FILENAME Compiled module COUNT_FILES Compiled module LOAD_RAW 71 Compiled module GET_SDF_METATEXT Compiled module VIEWER_EVENT_HANDLER Compiled module EXPLORER_EVENT_HANDLER Compiled module XLOADCT_CALLBACK Compiled module LOAD_DATA Compiled module DRAW_IMAGE Compiled module LOAD_META_AND_POPULATE_SDF Compiled module CLEAR_DRAW_SURFACE Compiled module SDF_EXPLORER Compiled module EXPLORER_LOAD_NEW_FILE Compiled module CREATE_SDF_VISUALIZER Compiled module VIEWER_LOAD_NEW_FILE Compiled module LOADCT Compiled module FILEPATH LOADCT Loading table RED TEMPERATURE IDL gt Ds c o o c om c c o S c c So c oo This starts up the IDL interpreter and loads in all of the lib
38. EM wave source to a boundary which is set as simple laser laser block begin laser boundary x_min id 1 intensity_w_cm2 1 0e15 lambda 1 06 micron pol_angle 0 0 phase 0 t_profile gauss time 40 0e 15 40 0e 15 t_start 0 0 t_end 80 0e 15 end laser As already mentioned in the discussion of laser boundaries in the boundaries block lasers are attached to compatible boundaries here in the initial conditions deck boundary The boundary on which to attach the laser In 1D the directions can be either x_min or x_max left and right are accepted as a synonyms In 2D y_min and y max may also be specified These have synonyms of down and up Finally 3D adds z min and z max with synonyms of back and front amp The amplitude of the E field of the laser in V m intensity The intensity of the laser in W m There is no need to specify both intensity and amp and the last specified in the block is the value used It is mandatory to specify at least one The ampli tude of the laser is calculated from intensity using the formula amp sqrt 2 intensity c epsilono irradiance is accepted as a synonym 24 intensity_w_cm2 This is identical to the intensity parameter described above except that the units are specified in W cm id An id code for the laser Used if you specify the laser time profile in the EPOCH source rather than in the input deck Does not have to be unique
39. EPOC An open source PIC code for high energy density physics CFSA pee Fa SA SON A EFOCI UNIVERSITY OF WARWICK Users Manual for the EPOCH PIC codes Last manual revision by Keith BENNETT EPOCH written by Chris BRADY Keith BENNETT Holger SCHMITZ Christopher RIDGERS Project coordinators Tony ARBER Roger EVANS Tony BELL September 10 2015 EPOCH Version 4 3 4 Contents 4 LL Is this manual up to date cross rss we HO 4 12 Whats EPOCH doe ea ocas eS Be ee Ee BE G 4 1 2 1 Features of RCM ao of ke ka rea eee be ele OE we eb ee 4 oS ier ENE ee ee eae 4 1 4 What normalisations are used in EPOCH 2 ee 4 1 5 What are those num things doing everywhere 0 2 00 00520 eee 5 1 6 What is an input eck se ea eros ERE GRABER RSE OR oe EERE Se RES 5 1 7 I just want to use the code as a black box or I m just starting How do I do that 5 1 8 What is the auto loader 4 64 ih G6 6 omo cir A 5 1 9 What is a maths parser ce cae a E A ds a ee Ye Hs 5 a ks eg a A ANA 5 1 11 I want to develop an addition to EPOCH How do I do that 6 1 12 I want to have a full understanding of how EPOCH works How do I do that 6 2 EPOCH for end users 7 2 1 Structure of the EPOCH codes 22 4 64444 6445 a 7 free gy a eS ee A eee ee a 8 2 3 Compiling and running EPOCH osorno de bs ede bole Cal es 8 a seo os ee Seis oe at es e tes a 9 wd ee pits pda eo i 3 The EP
40. GE_MASS is specified this is still populated from the input deck and now refers to the reference charge for the species e mass The mass in kg e weight The per species particle weight e count The global number of particles of this species NOTE may not be accurate This will only ever be the number of particles on this processor when running on a single processor While this property will be accurate when setting up initial conditions it is only guaranteed to be accurate for the rest of the code if the code is compiled with the correct preprocessor options e attached_list The list of particles which belong to this species The last three entries are only used by the particle injection model 4 2 2 Setting the particle properties The details of exactly what a linked list means in EPOCH requires a more in depth study of the source code For now all we really need to know is that each species has a list of particles A pointer to the first particle in the list is contained in species_list ispecies Zattached_list head Once you have a pointer to a particle eg current you advance to the next pointer in the list with current gt current next After all the descriptions of the types actually setting the properties of the particles is fairly simple The following is an example which positions the particles uniformly in 1D space but doesn t set any momentum 54 SUBROUTINE manual_load TYPE particle POINTER current
41. INTEGER ispecies REAL num rpos dx DO ispecies 1 n_species current gt species_list ispecies hattached_list head dx length_x species_list ispecies fattached_list count rpos x_min DO WHILE ASSOCIATED current current part_pos rpos current weight 1 0_num rpos rpos dx current gt current next ENDDO ENDDO END SUBROUTINE manual_load This will take the particles which have been placed at random positions by the autoloader and repositions them in a uniform manner In order to adjust the particle positions you need to know about the grid used in EPOCH In this example we only required the length of the domain length x and the minimum value of x x_min A more exhaustive list is given in the following section Note that I completely ignored the question of domain decomposition when setting up the particles The code automatically moves the particles onto the correct processor without user interaction In the above example note that particle momentum was not specified and particle weight was set to be a simple constant Setting particle weight can be very simple if you can get the pseudoparticle distribution to match the real particle distribution or quite tricky if this isn t possible The weight of a pseudoparticle is calculated such that the number of pseudoparticles in a cell multiplied by their weights equals the number of physical particles in that cell This can be quite tricky to get righ
42. OCH input deck 12 31 trol block lt s e rasta a Rs ES 13 3 1 1 Dynamic Load Balancing soo 4 oe oe ek oe eS ee e Wwe a a eX 16 sp eth is Ge ih He eB di 16 0 2 bo ndaries Dlock s sr poe pi oe ER WER Oe AREA ERA A 16 pe de Be duck de dde BE Ee de a 18 3 2 2 Thermal boundaries examina ae RARA PEE S 18 3 3 species DIO III 19 3 3 1 Particle migration between species o o ee 22 3 3 2 onisation AI 22 gA laser block spes Ase aw O A A a 24 3 5 fields IOC 4 amp a ee A ares AE a 26 36 wind w A 27 al OM ONGC arado pa a a a de ee o R ee ee a ea 28 a Ll D mpma sk ses caos a o e e ke e a eee oS 30 AAA A TR RNA 30 3 7 3 Particle Variables pia E as a a 32 324 Grid Variables s oso kOe e aed A A egi 33 3 45 Derived Variables 4 462 heb eed cbr AR AAA 34 5 00 Other Variables xsara as a E BOO 34 l Data Averaging amp lt so secos ah fogan kon Goi He ee hae wee ee awe Rm SG 35 3 7 8 almele precision GUEPUL aceros esa e A 35 Ad da ad A Re 36 3 8 sept Sie Block e s e sti ee Se ee a a AA 38 E A oe SG es S ASR HE GO RE eS 39 3 10 probe bl ck 2 iy ew oe tw eR eed OL EG eee g RES Re ROE Le Seeds 41 3 11 collisions DIGG o s gonca 2 eco dd a A ERED EES 42 312 MIO nasos de ee ogee a Be EO OG ee eee RAP EE G 43 3 13 subset block 3 14 constant bloek ok are la ke ea ee el eS OS ee A eg EO ee ee O oe ne ee ee ee ee ee ee ee ae 3 15 1 Constants 1 aaa a a a a 3 15 2
43. S Gives the option to specify one or more species as tracer particles Tracer particles are specified like normal particles and move about as would a normal particle with the same charge and mass but tracer particles do not generate any current and are therefore passive elements in the simulation Any attempt to add particle collision effects should remember that tracer species should not interact through collisions The implementation of tracer particles requires an additional IF clause in the particle push so it is not activated by default e PARTICLE_PROBES For laser plasma interaction studies it can sometimes be useful to be able to record information about particles which cross a plane in the simulation Since this requires the code to check whether each particles has crossed the plane in the particles pusher and also to store copies of particles until the next output dump it is a heavyweight diagnostic Therefore this diagnostic is only enabled when the code is compiled with this directive e PARTICLE SHAPE _TOPHAT By default the code uses a first order b spline triangle shape function to represent particles giving third order particle weighting Using this flag changes the particle representation to that of a top hat function Oth order b spline yielding a second order weighting e PARTICLE SHAPE BSPLINE3 This flag changes the particle representation to that of a 3rd order b spline shape function 5th order weighting
44. SION was unreliable so EPOCH uses kind tags to specify the precision of the code The _num suffixes and the associated definition of REALs as REAL num are these kind tags in operation The num tags force numerical constants to match the precision of the code preventing errors due to precision conversion The important thing is that all numerical constants should be tagged with an _num tag and all REALs should be defined as REAL num 1 6 What is an input deck An input deck is text file which can be used to set simulation parameters for EPOCH without needing to edit or recompile the source code It consists of a list of blocks which start as begin blockname and end with end blockname Within the body of each block is a list of key value pairs one per line with key and value separated by an equals sign Most aspects of a simulation can be controlled using an input deck such as the number of grid points in the simulation domain the initial distribution of particles and initial electromagnetic field configuration It is designed to be relatively easy to read and edit For most projects it should be possible to set up a simulation without editing the source code at all For more details read 3 Section 3 1 7 I just want to use the code as a black box or I m just starting How do I do that Begin by reading 5 Section B There s quite a lot to learn in order to get started so you should plan to read through all of this sec
45. The following parameter has been added to the collisions block of the input deck see Section 3 11 collisional_ionisation The following parameter has been added to the qed block of the input deck see Section 3 12 use_radiation_reaction The following parameter has been added to the species block of the input deck see Section 3 3 immobile The following parameters were changed in the laser block of the input deck see Section 3 4p The phase parameter can now be time varying The profile parameter can now be time varying The following parameters have been added to the list of pre defined constants see Section 3 15 1 nproc_ x y z nsteps t_end CC There has also been a new output_global block added to the input deck This is documented in Section 3 8 B 3 Changes in behaviour which are not due to changes in the input deck The species drift property is now applied to particles whilst the moving window model is active In previous versions of the code this property was ignored once the moving window began Ionisation species now inherit their dumpmask See Section for details Default values for ignorable directions were added This change allows submitting 3D or 2D input decks to a 1D version of EPOCH and 3D input decks to a 2D version of EPOCH Any references to y z will be set equal to zero unless overridden by a deck constant Other y z values also assume
46. This can only be used with named output blocks The values are given as a comma separated list eg dump_at_time 0 0 15 1 1 The name times_dump is accepted as a synonym By default the list is empty dump at _nsteps Integer parameter which specifies a set of step numbers at which to write the current output block This can only be used with named output blocks The values are given as a comma separated list eg dump_at_nsteps 5 11 15 The name nsteps_dump is accepted as a synonym By default the list is empty file_prefix String parameter It is sometimes useful to distinguish between dumps generated by the different output blocks This parameter allows the user to supply a file prefix to be prepended to all dumps generated by the current output block See below for further details The default value is an empty string 36 rolling restart Logical flag If set to T this sets the parameters required for performing rolling restarts on the current block It is a shorthand for setting the following flags dump cycle 1 restartable T and file prefix roll With rolling restarts enabled the first file will be named roll0000 sdf and the second will be roll0001 sdf The third dump will again be named roll0000 sdf overwriting the first one In this way restart dumps can be generated throughout the duration of the simulation whilst limiting the amount of disk space used
47. a Electronvolt micron A convenience symbol for specifying wavelength in microns rather than metres milli 1073 micro 1076 nano 107 pico 104 femto 107 atto 10718 cc A convenience symbol for converting from cubic metres to cubic centimetres ie 1076 time Initial simulation time x y z Grid coordinates in the x y z direction ix iy iz Grid index in the x y z direction nx ny nz Number of grid points in the x y z direction dx dy dz Grid spacing in the x y z direction x y z min Grid coordinate of the minimum x y z boundary x y z max Grid coordinate of the maximum x y z boundary length_ x y z The length of the simulation box in the x y z direction nproc_ x y z The number of processes in the x y z directions nsteps The number of timesteps requested t_end The end time of the simulation It is also possible for an end user to specify custom constants both within the code and from the input deck These topics are covered later in this subsection An example of using a constant would be lengthx pi 48 3 15 2 Functions The maths parser in EPOCH has the following functions abs a Absolute value floor a Convert real to integer rounding down ceil a Convert real to integer rounding up nint a Convert real to integer rounding to nearest integer sqrt a Square root sin a Sine cos a Cosine tan a Tangent acos a Arccosine atan a Arct
48. ain VisIt pane 7 7 Shaded Surface Plots in VisIt Again we will confusingly refuse to pick the obvious plot type for this task There is Surface plot listed in the menu However most of the time the Elevator operator does what we want and also gives us more flexibility The first step is to do a Pseudocolor plot of Number_Density as we did before Next select the Operator Attributes Transforms gt Elevate menu item In the pop up dialogue click on the Elevation height relative to XY limits and then Apply Click Yes when the warning dialogue pops up 86 ea indow 1 k 42 daa dD Been Pseudocolor Var Derived Number_Density Units 1 mA3 1 9088 27 40 1 4318 27 IN 9 5380 26 4 7698 26 301 0 000 Max 1 908e 27 Min 0 000 To make this plot look similar to the one generated by IDL we have changed the colour table using Controls Color table We also changed the axis appearance with the annotations menu discussed earlier and changed the height of the elevation using the min and max operator attributes 7 8 Creating User Defined Expressions VisIt comes with an extremely powerful method of manipulating data before visualising the results The basic idea is that an array is transformed by applying a set of mathematical functions on all its elements and then the result is defined as a new variable Once defined this variable behaves in exactl
49. ak down complicated expressions using constants or by other means in order to make the deck look more readable Constants are persistent for the entire runtime of the code allowing them to be used when specifying time profiles for lasers and also allowing developers to use maths parser expressions for other internal parts of the code where needed In the above example several pre defined constants have been used pi and c and also several functions critical exp gauss and sqrt These are described in Section 3 15 1 and Section 3 15 2 3 15 The maths parser A discussion of the input deck for EPOCH would not be complete without consideration of the maths parser The maths parser is the code which reads the input decks The parser makes it possible that any parameter taking a numerical value integer or real can be input as a mathematical expression rather than as a numerical constant The maths parser is fairly extensive and includes a range of mathematical functions physical and simulation constants and appropriately prioritised mathematical operators 3 15 1 Constants The maths parser in EPOCH has the following constants e pi The ratio of the circumference of a circle to its diameter e kb Boltzmann s constant 47 me Mass of an electron qe Charge of an electron c Speed of light epsilonO Permeability of free space mul Permittivity of free space ev Electronvolt kev Kilo Electronvolt mev Meg
50. angent sinh a Hyperbolic sine cosh a Hyperbolic cosine exp a Exponential loge a Natural logarithm log10 a Base 10 logarithm log base a b Base b logarithm gauss Z zo w Calculate a Gaussian profile in variable z centred on xy with a characteristic width w f x exp x 29 w In this expression the full width at half maximum is given by fwhm 2wyln 2 supergauss Z zp w n This is identical to gauss except it takes a fourth parameter n which is the power to raise the exponential argument to semigauss t A Ag w Calculate a semi Gaussian profile in variable t with maximum amplitude A amplitude at t 0 Ap and width w The parameter Ap is used to calculate ty the point at which the Gaussian reaches its maximum value For t less than to the profile is Gaussian and for t greater than to it is the constant A to w ln 4p 4 f t hake ty uyP t lt to A otherwise interpolate interp_var n pairs Linear interpolation function explained later if a b c Conditional function If a 0 the function returns b otherwise the function returns c 49 e density a Returns the density for species a e temp x y z a Returns temperature in the x y or z direction for species a e temp a Returns the isotropic temperature for species a e e x y z x y z Returns the x y or z component of the electric field at the specified location e b x y z x y z R
51. articles to store information about Set to 0 for no minimum kinetic energy ek max The maximum kinetic energy of particles to store information about Set to 1 for no maximum kinetic energy dumpmask The dump code for this particle probe This is the same as that for the main output controls in input deck Note that the code has to store copies of particles which pass through the probe until a dump occurs This means that the code s memory requirements can increase drastically if this code only dumps probe information infrequently If this is set to never then the code effectively never uses the probe 3 11 collisions block EPOCH has a particle collision routine based on the model presented by Sentoku and Kemp 6 This adds a new output block named collisions which accepts the following three parameters use collisions This is a logical flag which determines whether or not to call the collision routine If omitted the default is T if any of the frequency factors are non zero see below and F otherwise coulomb_log This may either be set to a real value specifying the Coulomb logarithm to use when scattering the particles or to the special value auto If auto is used then the routine will calculate a value based on the local temperature and density of the particle species being scattered along with the two particle charges If omitted the default value is auto 42 collide This sets up a s
52. at s New Index Contact VisIt Executables This page contains links to download VisIt executables for Unix Windows and Mac OS X systems The page contains several versions of VisIt organized from the most recent to the oldest The unix and Mac OS X executables require downloading an install script along with the file containing the executable The Windows executables are packaged in a self contained installer Instructions for installing VisIt can be found in the install notes Md5 and shal checksums as well as file sizes are provided for checking that the files were properly downloaded if corruption of the files is suspected during the download process VisIt 2 7 1 VisIt release notes VisIt install script a Visit install notes VisIt md5 checksums VisIt shal checksums VisIt sha256 checksums Visit file sizes executable Windows Xp Vista 7 8 64 bit Visual Studio 2010 download Mac OS X Intel 64 bit Darwin 10 6 3 Darwin Kernel Version 10 3 0 gcc 4 2 1 MPICH Y download Includes parallel VisIt with self contained MPICH MPI Linux x86_64 64 bit Redhat Enterprise Linux 6 kickit llnl gov 2 6 32 358 18 1 el6 x86_64 1 SMP gcc 4 4 7 download Will work on many Linux x86_64 systems Linux x86_64 64 bit There are full instructions for compiling the project from source code along with build scripts written to help ease the process However this is not recommended as it is an ext
53. be used by name later in the deck Constants are simply maths parser expressions which are assigned to a name as shown above When the name is used on the right hand side of a deck expression it is replaced by the expression it was assigned with This expression may be a simple numerical constant a mathematical expression or a function Constants may contain spatially varying information without having to pre calculate them at every location in the domain To those familiar with FORTRAN codes which use statement functions 46 parameters appearing in the constant block are fairly similar If a constant name is reused in a constant block then the old constant is deleted and replaced with the new one This happens without warning constant block begin constant lambda 1 06 micron omega 2 0 pixc lambda den_crit critical omega scale 3 5 micron den_max 5 0 den_crit thick 300e 9 pplength 6000e 9 widscale 5 0e 6 t_wid 10 0e 6 c amax 1 0 wy 1e 6 y 0 0 slope exp 2 0 y wy 2 blob gauss sqrt x 2 y72 0 0 1 0e 6 end constant Using constants can be very helpful when dealing with long complicated expressions since they allow the expression to be broken down into much simpler parts They can also be used to get around the FORTRAN string length limitation built into many compilers which prevents deck lines being longer then 512 characters long As a general rule it is a good idea to bre
54. be written to output dumps These may be requested by using the average keyword when specifying a dump variable The non averaged variable will still be written to restart dumps where required for restarting the code but not full or normal dumps If you also want the non averaged variable to be written then you can add the snapshot option The period of time over which averaging occurs can be specified using the dt_average keyword Alternatively you may specify the number of cycles over which to perform the averaging using the nstep_average keyword If both dt_average and nstep average are specified then the averaging will be performed over the longest of the two intervals Note that previous versions of the code would alter the time step to ensure that there were enough cycles between output dumps to satisfy the nstep_average parameter However since it affects the accuracy of the result this is no longer the case and only a warning message is issued The following shows an example use of averaging in the output block begin output dt_snapshot 1 0e 15 full_dump_every 10 dt_average 1 0e 17 charge_density always average snapshot mass_density full average snapshot ekbar full average end output With this configuration charge density will be written in both normal and averaged form at normal full and restart dumps mass density will be written in both forms at full
55. collide spec2 spec3 0 1 end collisions With this block collisions are turned on and the Coulomb logarithm is automatically calculated All values of the frequency array are set to one except specl spec2 is set to minus one and also spec2 specl and spec2 spec3 is set to 0 1 3 12 qed block EPOCH can model QED pair production synchrotron emission and radiation reaction as described in Duclous et al 7 It is enabled using the compiler flag DPHOTONS Additionally the Trident process is enabled using DTRIDENT_PHOTONS A new input deck block named ged has been added which accepts the following parameters use_qed Logical flag which turns QED on or off The default is F qed_start_time Floating point value specifying the time after which QED effects should be turned on The default is 0 produce_photons Logical flag which specifies whether to track the photons generated by synchrotron emission If this is F then the radiation reaction force is calculated but the properties of the emitted photons are not tracked The default is F photon_energy min Minimum energy of produced photons Radiation reaction is calculated for photons of all energies but photons with energy below this cutoff are not tracked The default is 0 photon_dynamics Logical flag which specifies whether to push photons If F then photons are generated but their motion through the domain is not simulated and t
56. d 2D respectively The details presented above are a first rough guide to using EPOCH To clearly understand EPOCH it is best to now try some simple examples To view the results you will have to jump forward to 6 Section 6 70 6 Using IDL to visualise data The EPOCH distribution comes with procedures for loading and inspecting SDF self describing data files The IDL routines are held in the IDL directory for each of the epoch d directories There is also a procedure named Start pro in each of the epoch d directories which is used to set up the IDL environment To load data into IDL navigate to one of the base directories eg epoch trunk epoch2d where epoch is the directory in which you have checked out the Subversion repository and type the following gt idl Start IDL Version 7 1 1 Mac OS X darwin x86_64 m64 c 2009 ITT Visual Informat Installation number Licensed for use by STAR404570 32University of Warwick Compiled module PARTICLEPHASEPLANE Compiled module TRACKEX_EVENT Compiled module ISOPLOT Compiled module READVAR Compiled module LOADCFDFILE Compiled module HANDLEBLOCK Compiled module GETMESH Compiled module GETMESHVAR Compiled module GETSNAPSHOT Compiled module READVAR Compiled module LOADSDFFILE Compiled module SDFHANDLEBLOCK Compiled module SDFGETPL
57. dary is significant This is most clearly explained through a couple of examples In these examples the spatial profile of the laser is set to vary between a flat uniform profile profile 1 and a Gaussian profile in y profile gauss y 0 2 5e 6 The difference between these profiles is obvious but the important point is that a laser travelling parallel to the x direction has a profile in the y direction Similarly a laser propagating in the y direction has 57 Van Blech Field Ey Time 5 00428e 14 8 66e 10 4 34e 10 1 08e 08 4 31e 10 Max 8 66e 10 Min 8 64e 10 Y o x10 6 m 0 X x10 6 m Figure 4 Gaussian laser profile a profile in the x direction In 3D this is extended so that a laser propagating in a specified direction has a profile in both orthogonal directions So a laser travelling parallel to the x axis in 3D would have a profile in y and z Since 3D lasers are very similar to 2D lasers they will not be considered here in greater detail but in 3D it is possible to freely specify the laser profile across the entire face where a laser is attached phase Phase shift for the laser in radians This is a spatial variable which is also defined across the whole of the boundary on which the laser is attached This allows a user to add a laser travelling at an angle to a boundary as shown in Figure 5 The setup for this is not entirely straightforward and requires a little bit of explanation Figure 6 ill
58. development e MPI_DEBUG This option installs an error handler for MPI calls which should aid tracking down some MPI related errors e NOJO This option disables all file I O which can be useful when doing benchmarking e PER_PARTICLE_CHARGE_MASS By default the particle charge and mass are specified on a per species basis With this flag enabled charge and mass become a per particle property This is a legacy flag which will be removed soon If a user requests an option which the code has not been compiled to support then the code will give an error message as follows 10 WARNING The element particle_probes of block output cannot be set because the code has not been compiled with the correct preprocessor options Code will continue but to use selected features please recompile with the DPARTICLE_PROBES option It is also possible to pass other flags to the compiler In Makefile there is a line which reads FFLAGS 03 fast The two commands to the right are compiler flags and are passed unaltered to the FORTRAN compiler Change this line to add any additional flags required by your compiler By default EPOCH will write a copy of the source code and input decks into each restart dump This can be very useful since a restart dump contains an exact copy of the code which was used to generate it ensuring that you can always regenerate the data or continue running from a restart The output can be prevented by
59. e The phase profile of the laser wavefront given in radians Phase may be a function of both space and time The laser is driven using sin wt and phase is the parameter There is zero phase shift applied by default profile The spatial profile of the laser This should be a spatial function not including any values in the direction normal to the boundary on which the laser is attached and the expression will be evaluated at the boundary It may also be time dependant The laser field is multiplied by the profile to give its final amplitude so the intention is to use a value between zero and one By default it is a unit constant and therefore has no affect on the laser amplitude This parameter is redundant in 1D and is only included for consistency with 2D and 3D versions of the code t_profile Used to specify the time profile for the laser amplitude Like profile the laser field is multiplied by this parameter but it is only a function of time and not space In a similar manner to profile it is best to use a value between zero and one Setting values greater than one is possible but will cause the maximum laser intensity to grow beyond amp In previous versions of EPOCH the profile parameter was only a function of space and this parameter was used to impose time dependance Since profile can now vary in time t_profile is no longer needed but it has been kept to facilitate backwards compatibility It can also make input decks clearer if the
60. e To use particle probes the code must be compiled with the DPARTICLE PROBES compiler option This is a fairly heavyweight diagnostic since each parti cle position must be tested from within the particle push The code will run faster if it is not compiled in The probe is specified in terms of a point in the plane and the normal vector to the plane which is to be monitored Particles are only recorded if they cross the plane in the direction given by the normal vector If you want to record particles travelling in both directions then use two particle probes one with an opposite signed normal vector to the other 41 begin probe name electron_back_probe point 50 0e 6 50 0e 6 normal 1 0 0 0 ek_min 0 0 ek_max 1 0 include_species s1 dumpmask always end probe name The name that the probe should have in output dumps Output variables are then named this as a prefix For example the block shown above will result in the name electron_back_probe_px for the x momentum The particle positions would just be called electron back probe point An arbitrary point in the plane of the probe normal A vector normal to the plane of the probe in the direction of crossings you wish to monitor include_species The species to which this probe should be applied To probe several species use several probe blocks in the input deck probe_species is accepted as a synonym ek_min The minimum kinetic energy of p
61. e Section 3 1 e identify See Section Finally the input deck now has a method for writing continuation lines If the deck contains a character then the rest of the line is ignored and the next line becomes a continuation of the current one B Changes between version 4 0 and 4 3 B 1 Changes to the Makefile Some changes have been made to the Makefile These are documented in Section The following compile time define has been added to the Makefile e MPLDEBUG The following compile time define has been removed from the Makefile e FIELD DEBUG 93 B 2 Additions to the input deck The following parameters have been added to the control block of the input deck see Section 8 1 e nproc x y z e smooth_currents e field ionisation e use_exact_restart e allow_cpu reduce e check stop file frequency e stop_at_walltime e stop_at_walltime file e simplify_deck e print_constants e The restart_snapshot parameter now accepts filenames The following parameters have been added to the output block of the input deck see Section 3 7 e disabled e time start e time_stop e nstep start e nstep stop e dump_at_times e dump_at_nsteps e dump cycle e dump cycle first_index e filesystem e file prefix e rolling restart e particle_ energy e relativistic_mass e gamma e total_energy_sum e optical depth 94 qed_energy trident_optical_depth The default value of dump_first is now T
62. e flag DPER PARTICLE CHARGE MASS see Section 2 4 The synonym rest_mass may also be used particle_weight The dumpmask for the weighting function which describes how many real particles each pseudoparticle represents Restart variable ejected particles If requested then all the particles which have left the simulation domain since the last output dump of this type are included in the output The list of ejected particles is treated as if it were a separate species and the particle variables which get written are requested using the other particle variable flags ie particle_grid etc Once the data has been written the ejected particle lists are reset and will accumulate particles until the next requested output dump particle_energy The dumpmask for per particle kinetic energy relativistic_mass The dumpmask for per particle relativistic mass ie not rest mass gamma The dumpmask for per particle relativistic gamma ie 1 v c 14 optical_depth The dumpmask for per particle optical depth Restart variable This option is only supplied for debugging purposes and should not be required by most users trident_optical depth The dumpmask for per particle optical depth used by the Trident model Restart variable This option is only supplied for debugging purposes and should not be required by most users qed energy The dumpmask for per particle QED related particle energy Restart variable This o
63. e particle migration The default is F migration_interval The number of timesteps between each migration event The default is 1 migrate at every timestep The following parameters are added to the species block migrate Logical flag which determines whether or not to consider this species for migration The default is F promote_to The name of the species to promote particles to demote_to The name of the species to demote particles to promote_multiplier The particle is promoted when its energy is greater than pro mote_multiplier times the local average The default value is 1 demote_multiplier The particle is demoted when its energy is less than demote_multiplier times the local average The default value is 1 promote_density The particle is only considered for promotion when the local density is less than promote_density The default value is the largest floating point number demote_density The particle is only considered for demotion when the local density is greater than demote_density The default value is 0 3 3 2 Ionisation EPOCH now includes field ionisation which can be activated by defining ionisation energies and an electron for the ionising species This is done via the species block using the following parameters 22 ionisation_energies This is an array of ionisation energies in Joules starting from the outermost shell It expects to be given all e
64. e species of particles which are used in the code Also details of how these are initialised e laser Contains information about laser boundary sources e fields Contains information about the EM fields specified at the start of the simulation e window Contains information about the moving window if the code is used in that fashion e output Contains information about when and how to dump output files e output_global Contains parameters which should be applied to all output blocks e dist_fn Contains information about distribution functions that should be calculated for output e probe Contains information about particle probes used for output 12 e collisions Contains information about particle collisions e qed Contains information about QED pair production e subset Contains configuration for filters which can be used to modify the data to be output e constant Contains information about user defined constants and expressions These are designed to simplify the initial condition setup 3 1 control block The control block sets up the basic code properties for the domain the end time of the code the load balancer and the types of initial conditions to use The control block of a valid input deck for EPOCH2D reads as follows control block begin control global number of gridpoints nx 512 in X ny 512 in y global number of particles npart 10 nx ny final time of simulation t_
65. e way of setting up initial conditions in EPOCH is to load in a previous output dump and use it to specify initial conditions for the code The effect of this is to restart the code from the state that it was in when the dump was made To do this you just set the field restart snapshot to the number of the output dump from which you want the code to restart Because of the way in which the code is written you cannot guarantee that the code will successfully restart from any output dump To restart properly the following must have been dumped 59 e Particle positions e Particle momenta e Particle species e Particle weights e Relevant parts of the electric field If for example it is known that ez 0 then it is not needed e Relevant parts of the magnetic field It is possible to use the manual particle control part of the initial conditions to make changes to a restarted initial condition after the restart dump is loaded The output files don t include all of the information needed to restart the code fully since some of this information is contained in the input deck However a restart dump also contains a full copy of the input deck used and this can be unpacked before running the code If specific restart dumps are specified in the input deck or the force final_to_be_restartable flag is set then in some cases the output is forced to contain enough information to output all the data These restart dumps can be ver
66. en applied to a species named carbon the output is called x px Carbon The Cartesian grid which describes the axes of the distribution function would then be called grid _x px Carbon ndims The number of dimensions in this phase space reconstruction Due to difficulties in visualising data in more than three dimensions this is restricted to being 1 2 or 3 dumpmask Determines which output dumps will include this distribution function The dumpmask has the same semantics as those used by variables in the output block described in Section The dumpmask from distribution functions in the output block is applied first and then this one is applied afterwards For example if the dist_fn block contains dumpmask full and the output block contains distribution functions always then this distribution function will be only be dumped at full dumps The default dumpmask is always directionn This is the phase space to sample along axis n This can be any one of dir_x dir_y dir_z dir_px dir_py dir_pz dir_en dir_gamma_m1l dir_xy_angle dir_yz_angle dir_zx_angle with spatial codes only being available in dimensionalities of the code which have that direction Therefore dir_z does not exist in EPOCH1D or EPOCH2D and dir_y does not exist in EPOCHID The flags dir_xy_angle dir_yz_angle and dir_zx_angle calculate the distribution of particle momentum directions in the X Y Y Z and Z X planes rangen
67. end 1 0e 12 nsteps 1 size of domain x_min 0 1e 6 x_max 400 0e 6 y_min 400 0e 6 y_max 400 0e 6 dt_multiplier dlb_threshold restart_snapshot field_order 2 stdout_frequency end control As illustrated in the above code block the symbol is treated as a comment character and the code ignores everything on a line following this character The allowed entries are as follows nx ny nz Number of grid points in the x y z direction This parameter is mandatory npart The global number of pseudoparticles in the simulation This parameter does not need to be given if a specific number of particles is supplied for each particle species by using the npart directive in each species block see Section 3 3 If both are given then the value in the control block will be ignored 13 nsteps The number of iterations of the core solver before the code terminates Negative numbers instruct the code to only terminate at t_end If nsteps is not specified then t_end must be given t end The final simulation time in simulation seconds before the code terminates If t end is not specified then nsteps must be given If they are both specified then the first time restriction to be satisfied takes precedence Sometimes it is more useful to specify the time in picoseconds or femtoseconds To accomplish this just append the appropriate multiplication factor For example t_end 3 femto specifie
68. eps required for installing your own copy of VisIt when you have no other choice Vislt is an extremely large program so if a version is already available then it is usually better to use the installed version The machines at Warwick have a recent version of VisIt installed which is available via the modules system To make use of it you must first issue the command module load visit 7 3 Compiling The Reader Plugin One piece of compilation which is almost always necessary is that of the SDF reader plugin This is shipped as source code in a subdirectory of the EPOCH repository It is located in the VisIt subdirectory of the main epoch directory The reader will work for any SDF file generated by any code which uses the SDF I O routines You do not need a separate reader for each version of EPOCH 81 To compile first navigate to one of the epoch d directories in your EPOCH repository Just type make visit and the build scripts should take care of the rest The SDF reader plugin will be installed into the directory HOME visit linux intel plugins databases on your system Note that the linux intel component will vary depending on your machine operating system and architecture Each time you install a new version of VisIt you must recompile the reader to match the new installation It will also occasionally be necessary to recompile when changes occur to the SDF data format or the reader plugin itself The developers will notify u
69. erview of how the particles are defined in EPOCH Inside the code particles are represented by a Fortran90 TYPE called particle The current definition of this type in 2D is TYPE particle REAL num DIMENSION 3 part_p REAL num DIMENSION c_ndims part_pos ifdef PER_PARTICLE_WEIGHT REAL num weight endif ifdef PER_PARTICLE_CHARGE_MASS REAL num charge REAL num mass ttendif TYPE particle POINTER next prev ifdef PARTICLE_DEBUG INTEGER processor INTEGER processor_at_t0 endif END TYPE particle Note the presence of the preprocessor directives meaning that charge and mass only exist if the DPER_PARTICLE_CHARGE_MASS define was put in the makefile If you want to access a property that does not seem to be present check the preprocessor defines The particle properties can be explained as follows e part_p The momentum in 3 dimensions for the particle This is always of size 3 e part_pos The position of the particle in space This is of the same size as the dimensionality of the code 52 e weight The weight of this particle The number of real particles represented by this pseudoparticle e charge The particle charge If the code was compiled without per particle charge then the code uses the charge property from TYPE particle species e mass The particle rest mass If the code was compiled without per particle mass then the code uses the mass property from TYPE par
70. eter see Section 3 2 1 There are ten boundary types in EPOCH and each boundary of the domain can have one and only one of these boundaries attached to it These boundary types are periodic A simple periodic boundary condition Fields and or particles reaching one edge of the domain are wrapped round to the opposite boundary If either boundary condition is set to periodic then the boundary condition on the matching boundary at the other side of the box is also assumed periodic simple_laser A characteristic based boundary condition to which one or more EM wave sources can be attached EM waves impinging on a simple_laser boundary are transmitted with as little reflection as possible Particles are fully transmitted The field boundary condition works by allowing outflowing characteristics to propagate through the boundary while using the attached lasers to specify the inflowing characteristics The particles are simply removed from the simulation when they reach the boundary simple_outflow A simplified version of simple_laser which has the same properties of transmitting incident waves and particles but which cannot have EM wave sources attached to it These boundaries are about 5 more computationally efficient than simple laser boundaries with no attached sources This boundary condition again allows outflowing characteristics to flow unchanged but this time the inflowing characteristics are set to zero The particles are again simply
71. eturns the x y or z component of the magnetic field at the specified location e critical w Returns the critical density for the given frequency w ie New w 2moeo e It is also possible for an end user to specify custom functions within the code An example of using a function would be length x exp pi The use of most of these functions is fairly simple but interpolate requires some additional expla nation This function allows a user to specify a set of position value pairs and have the code linearly interpolate the values between these control points This function is mainly intended for ease of convert ing initial conditions from other existing PIC codes and the same effect can usually be obtained more elegantly using the if command The structure of the interpolate command is as follows The first parameter is the variable which is to be used as the axis over which to interpolate the values This can in general be any valid expression but will normally just be a coordinate axis The next 2n entries are the position value pairs and the final parameter is the number of position value pairs The slightly clunky syntax of this command is unfortunately necessary to allow it to work with some fairly fundamental features of the maths parser used in EPOCH 3 15 3 Operators The maths parser in EPOCH allows the following operators e a b Addition operator e a b Subtraction operator or unary negation operator auto de
72. g the initial conditions rather simpler In this case entire parts of the initial conditions are moved into a spatially varying constant in order to make changing them at a later date easier For example begin constant particle_density 100 0 Particle number density profile_x if x gt 1 and x 1t 1 1 0 0 2 profile_y if y gt 1 and y lt 1 1 0 0 2 end constant begin species name sl multiply density by real particle density density particle_density profile_x profile_y Set the temperature to be zero temp_x 0 0 temp_y temp_x s1 Set the minimum density for this species density_min 0 3 particle_density end species begin species name s2 Just copy the density for species s1 density density s1 Just copy the temperature from species s1 temp_x temp_x s1 temp_y temp_y s1 Set the minimum density for this species density_min 0 3 particle_density end species This creates the same output as before It is now trivial to modify the profiles later For example 62 begin constant particle_density 100 0 Particle number density profile_x gauss x 0 0 1 0 profile_y gauss y 0 0 1 0 end constant begin species name sl multiply density by real particle density density particle_density profile_x profile_y Set the temperature to be zero temp_x 0 0 temp_y temp_x s1 Set the minimum density for this species density_min 0 3 particle_density
73. h as recent versions of OpenMPI this can be achieved with the following echo Data mpirun np 2 bin epoch2d Some cluster setups accept the following instead mpirun np 2 bin epoch2d lt deck file where deck file is a file containing the name of the output directory Some cluster queueing systems do not allow the use of input pipes to mpirun In this case there is usually a stdin command line option to specify an input file See your cluster documentation for more details As of version 4 2 12 EPOCH now checks for the existence of a file named USE DATA_DIRECTORY in the current working directory before it prompts the user for a Data directory If such a file exists it reads it to obtain the name of the data directory to use and does not prompt the user If no such file exists it prompts for a data directory name as before This is useful for cluster setups in which it is difficult or impossible to pipe in the directory name using a job script The Makefile supplied with EPOCH is setup to use the Intel compiler by default However it also contains configurations for gfortran pgi g95 hector and ibm the compiler suite used on IBM s BlueGene machines In order to compile using one of the listed configurations add the COMPILER option to the make command For example make COMPILER gfortran will compile the code using the gfortran compiler and appropriate compiler flags You can also compile the code w
74. h denotes the X server and ps which is the postscript device Once the desired device has been selected various attributes of its behaviour can be altered using the device procedure For example we can set the output file to use for the postscript plot By default a file with the name idl ps is used Note that this file is not fully written until the postscript device is closed using the device close command When we have finished our plot we can resume plotting to screen by setting the device back lbg to x set_plot ps device filename out ps plot data x data number_density 256 xtitle x ytitle number density charsize 1 5 device close set_plot x This set of commands results in the following plot being written to a file named out ps 2 0x10 T 1 5x107 gt 1 Z o c 1 0K1077F Oo O E y E 5 0x10 0 x By default IDL draws its own set of fonts called Hershey vector fonts Much better looking results can be obtained by using a postscript font instead These options are passed as parameters to the device procedure More details can be found in the on line documentation under Reference Guides gt IDL Reference Guide gt Appendices Fonts 6 6 Contour Plots in IDL Whilst 1D plots are excellent tools for quantitive analysis of data we can often get a better qualitative overview of the data using 2D or 3D plots One comm
75. he most commonly performed plot and perhaps the most useful data analysis tool is the 1D plot In IDL this is performed by issuing the command plot x y where x and y are one dimensional arrays of equal length For each element x i plotted on the x axis the corresponding value y i is plotted along the y axis As a simple example 75 IDES plo toral 245 Gives rise to the following plot POSF IDLO we will now take a one dimensional slice through the 2D As a more concrete example In this example we will give the x Number_Density array read in from our SDF data file and y axes labels by passing extra parameters to the plot routine A full list of parameters can be found in the on line documentation In this example we also make use of the symbol which is IDL s line continuation character IDL gt data getdata 0 IDL gt plot data x data number_density 256 xtitle x IDL gt ytitle number density This command generates the following plot OO IDLO 76 6 5 Postscript Plots The plots shown so far have just been screen shots of the interactive IDL plotting window These are fairly low quality and could included as figures in a paper In order to generate publication quality plots we must output to the postscript device IDL maintains a graphics context which is set using the set plot command The two most commonly used output devices are x whic
76. hey stay where they were 43 generated The default is F produce pairs Logical flag which determines whether or not to simulate the process of pair generation from gamma ray photons Both produce photons and photon dynamics must be T for this to work The default is F qed_table_location EPOCH s QED routines use lookup tables to calculate gamma ray emission and pair production If you want to use tables in a different location from the default specify the new location using this parameter The default is src physics_packages TABLES use_radiation_reaction Logical flag which determines whether or not to calculate the radiation reaction force If set to F then the force is not calculated This should nearly always be enabled when using the QED model It is only provided for testing purposes The default value is T QED also requires that the code now know which species are electrons positrons and photons The species type is specified using a single identify tag in a species block To specify an electron the block in the deck would look like begin species name electron frac 0 5 rho 1 7829 identify electron end species Once the identity of a species is set then the code automatically assigns mass and charge states for the species Possible identities are electron A normal electron species All species of electrons in the simulation must be identified in this way or they wi
77. ified in the output_global block are as follows force_first_to_be_restartable Logical flag which determines whether the file written at time zero is a restart dump The default value is F force_last_to_be restartable Force the code to override other output settings and make the last output dump it writes be a restart dump Any internal condition which causes the code to terminate will make the code write a restart dump but code crashes or scheduler terminations will not cause the code to write a restart dump force_final_to_be_restartable is accepted as a synonym The 38 default value is T dump first Logical flag which determines whether to write an output file immediately after initialising the simulation The default is F dump_last Logical flag which determines whether to write an output file just before ending the simulation The default is T if an output block exists in the input deck and F otherwise dump final is accepted as a synonym time start Floating point parameter which specifies the simulation time at which to start considering output for the block Note that if dump_first or dump_last are set to true for this block then dumps will occur at the first or last timestep regardless of the value of this parameter This also applies to the three following parameters The default value is 0 time stop Floating point parameter which specifies the simulat
78. ified using restart_snapshot 12 or alternatively it can be specified using restart_snapshot 0012 sdf This syntax is required if output file prefixes have been used see Section 3 7 field_order Order of the finite difference scheme used for solving Maxwell s equations Can be 2 4 or 6 If not specified the default is to use a second order scheme stdout_frequency If specified then the code will print a one line status message to stdout after every given number or timesteps The default is to print nothing to screen ie stdout_frequency 0 use random seed The initial particle distribution is generated using a random number generator By default EPOCH uses a fixed value for the random generator seed so that results are repeatable If this flag is set to T then the seed will be generated using the system clock nproc x y z Number of processes in the x y z directions By default EPOCH will try to pick the best method of splitting the domain amongst the available processors but occasionally the user may wish to override this choice smooth_currents This is a logical flag If set to T then a smoothing function is applied to the current generated during the particle push This can help to reduce noise and self heating in a simula tion The smoothing function used is the same as that outlined in Buneman 3 The default value is F 14 field _ionisation Logical flag which turns on fie
79. igure 1 A laser pulse with a sharp cutoff shows numerical artefacts behind the pulse Figure 2 instead used a Gaussian window function with a characteristic width of 8fs as well as using t_end to introduce a hard cutoff It can clearly be seen that there are no spurious oscillations and the wave packet propagates correctly showing only some dispersive features There is no hard and fast rule as to how rapid the rise or fall for a laser can be and the best advice is to simply test the problem and see whether any problems occur If they do then there are various solutions Essentially the timestep must be reduced to the point where the sharp change in amplitude can be accommodated The best solution for this is to increase the spatial resolution with a comparable increase in the number of pseudoparticles thus causing the timestep to drop via the CFL condition This is computationally expensive and so a cheaper option is simply to decrease the input deck option dt_multiplier This artificially decreases the timestep below the timestep calculated from the internal stability criteria and allows the resolution of sharp temporal gradients This is an inferior solution since the FDTD scheme has increased error as the timestep is reduced from that for EM waves EPOCH includes a high order field solver to attempt to reduce this 3 5 fields block The next type of block in the EPOCH input deck is the fields block This allows you to specify the electric a
80. inimum density for this species density_min 0 3 100 0 end species The particle density 100 0 is hard coded into the deck file in several places It would be easier if this was given to a new user as begin constant particle_density 100 0 Particle number density end constant begin species name sl first set density in the range 0 gt 1 cut down density in x direction density if x gt 1 and x 1t 1 1 0 0 2 cut down density in y direction density if y gt 1 and y 1t 1 density s1 0 2 multiply density by real particle density density density s1 particle_density Set the temperature to be zero temp_x 0 0 temp_y temp_x s1 Set the minimum density for this species density_min 0 3 particle_density end species begin species name s2 Just copy the density for species s1 density density s1 Just copy the temperature from species s1 temp_x temp_x s1 temp_y temp_y s1 Set the minimum density for this species 61 density_min 0 3 particle_density end species It is also possible to parameterise other elements of initial conditions in a similar fashion This is generally a good idea since it makes the initial conditions easier to read an maintain 4 7 Using spatially varying functions to further parameterise initial con ditions Again this is just a readability change to the normal input deck file but it also makes changing and understandin
81. input deck file This allows any initial condition which can be specified everywhere in space by a number density and a drifting Maxwellian distribution function These are built up using the normal maths expressions by setting the density and temperature for each species which is then used by the autoloader to actually position the particles The elements of the species block used for setting initial conditions are density Particle number density in m73 As soon as a density line has been read the values are calculated for the whole domain and are available for reuse on the right hand side of an expression This is seen in the above example in the first two lines for the Electron species where the density is first set and then corrected If you wish to specify the density in parts per cubic metre then you can divide by the cc constant see Section 8 15 1 This parameter is mandatory density_min Minimum particle number density in m When the number density in a cell falls below density_min the autoloader does not load any pseudoparticles into that cell to minimise the number of low weight unimportant particles If set to 0 then all cells are loaded with particles This is the default density_max Maximum particle number density in m When the number density in a cell rises above density_max the autoloader clips the density to density_max allowing easy implementation of exponential rises to plateaus If it is a negative value
82. ion time at which to stop considering output for the block The default value is the largest possible float nstep_start Integer parameter which specifies the step number at which to start considering output for the block The default value is 0 nstep_stop Integer parameter which specifies the step number at which to stop considering output for the block The default value is the largest possible integer sdf buffer size Integer parameter When writing particle data to an SDF file the data is first transferred into an output buffer The size of this buffer can have a big impact on the overall speed of writing dump files This parameter allows the size of the buffer to be specified in bytes The default value is 67108864 64 MB filesystem String parameter Some filesystems can be unreliable when performing parallel I O Often this is fixable by prefixing the filename with ufs or nfs This parameter supplies the prefix to be used The default value is an empty string use_offset_grid When using moving windows some visualisation programs notably Vislt show the motion of the window by moving the visualisation window rather than by changing the x axis Setting this option to T causes the code to write another grid which always gives the offset relative to the left hand edge of the window rather than the true origin Performs no function when not using the moving window The default value is F 3 9 dist fn block
83. ith debugging flags by adding MODE debug and can compile using more than one processor by using j lt n gt where lt n gt is the number of processors to use Note that this is just to speed up the compilation process the resulting binary can be run on any number of processors 2 4 Compiler flags and preprocessor defines As already stated some features of the code are controlled by compiler preprocessor directives The flags for these preprocessor directives are specified in Makefile and are placed on lines which look like the following DEFINES D PER_PARTICLE_WEIGHT On most machines D just means D but the variable is required to accommodate more exotic setups Most of the flags provided in the Makefile are commented out by prepending them with a symbol the make system s comment character To turn on the effect controlled by a given preprocessor directive just uncomment the appropriate DEFINES line by deleting this symbol The options currently controlled by the preprocessor are e PER_PARTICLE_WEIGHT Instead of running the code where each pseudoparticle represents the same number of real particles each pseudoparticle can represent a different number of real particles Many of the codes more advanced features require this and it is turned on by default It can be turned off to save on memory but this is recommended only for advanced users e TRACER PARTICLE
84. l exit with an error message The blocks themselves can also appear in any order The input deck is case sensitive so true is always T false is always F and the names of the parameters are al ways lower case Parameter values are evaluated using a maths parser which is described in Section 3 15 If the deck contains a A character then the rest of the line is ignored and the next line becomes a continuation of the current one Also the comment character is tt if the character is used anywhere on a line then the remainder of that line is ignored There are three input deck directive commands which are e begin block Begin the block named block e end block Ends the block named block e import filename Includes another file called filename into the input deck at the point where the directive is encountered The input deck parser reads the included file exactly as if the contents of the included file were pasted directly at the position of the import directive Each block must be surrounded by valid begin and end directives or the input deck will fail There are currently fourteen valid blocks hard coded into the input deck reader but it is possible for end users to extend the input deck The fourteen built in blocks are e control Contains information about the general code setup e boundaries Contains information about the boundary conditions for this run e species Contains information about th
85. l tool but it also comes with a fairly hefty price tag If you are not part of an organisation that will buy it for you then you may wish to look into a free alternative It is also a proprietary tool and you may not wish to work within the restrictions that this imposes There are a number of free tools available which offer similar functionality to that of IDL occasionally producing superior results For a simple drop in replacement the GDL project aims to be fully compatible and works with the existing EPOCH IDL libraries after a couple of small changes Other tools worth investigating are yorick and python with the SciPy libraries At present there is no SDF reader for either of these utilities but one may be developed if there is sufficient demand 7 Using VisIt to visualise data 7 1 LLNL Visit LLNL s VisIt software is a parallel data visualisation package https wci 11n1 gov codes visit EPOCH comes with source code for the plug in needed to allow VisIt to load the SDF output files which are generated by EPOCH There are full manuals for VisIt which can be downloaded from the above link so no further details will be given here To build the plug in first ensure that the visit binary is in the PATH environment variable Then simply type make visit in one of the epoch 1 2 3 d directories For more experienced users of Vislt the xml file which is used to generate the plug in is supplied in the VisIt subdirectory ca
86. ld ionisation See Section 3 3 2 use bsi Logical flag which turns on barrier suppression ionisation correction to the tunnelling ionisation model for high intensity lasers See Section This flag should always be enabled when using field ionisation and is only supplied for testing purposes The default is T use_multiphoton Logical flag which turns on modelling ionisation by multiple photon absorption This should be set to F if there is no laser attached to a boundary as it relies on laser frequency See Section 3 3 2 This flag should always be enabled when using field ionisation and is only supplied for testing purposes The default is T particle_tstart Specifies the time at which to start pushing particles This allows the field to evolve using the Maxwell solver for a specified time before beginning to move the particles use_exact_restart Logical flag which makes a simulation restart using exactly the same configuration as the original simulation If set to IT then the domain split amongst processors will be identical along with the seeds for the random number generators Note that the flag will be ig nored if the number of processors does not match that used in the original run The default value is F allow_cpu_reduce Logical flag which allows the number of CPUs used to be reduced from the number specified In some situations it may not be possible to divide the simulation amongst all the processors
87. led and shaded one As we can see from the following example many of IDL s plotting routines accept the same parameters and keywords The first command shown here loadct 3 asks IDL to load the third colour table which is RED TEMPERATURE IDL gt loadct 3 IDL gt shade_surf data number_density data x data y xstyle 1 IDL gt ystyle 1 xtitle x ytitle y ztitle number density charsize 3 78 X IDL O 6 8 Interactive Plotting Finally in recent versions of IDL it is now possible to perform all of these plot types in an interac tive graphical user interface The corresponding procedures are launched with the commands iplot icontour and isurface IDL gt iplot data x data number_density 256 X IDL iPlot File Edit Insert Operations Window Help 0548 BR joo a for ANDOGY o o o ETETE EETA EEA EAT PEET EET EEA TTT TNT Ty 27 1 5x10 27 1 0x1 PH Q A O O IDL iPlot Visualization Bro g Plot Po m Nane Plot ay HH Description Plot Show True 26 Vertex color table Edit color table 5 0x10 e Plot transparency 0 PF Color Mito 0 01 Line style Thickness 1 Hininun value o Maxinun value ga aiii istogran prot Felse o 0 1x10 2 x10 4 Points to average 1 Polar plot False Fill plot False 4 Click on item to select or click amp drag selection box 472 677 y 79 IDL is an extremely usefu
88. ll not generate photons positron A normal positron species All species of positron in the simulation must be identified in this way or they will not generate photons photon A normal photon species One species of this type is needed for photon production to work If multiple species are present then generated photons will appear in the first species of this type bw_electron The electron species for pair production by the Breit Wheeler process If a species of this type exists then electrons from the pair production module will be created in this species If no species of this type is specified then pair electrons will be generated in the first electron species bw_positron As above but for positrons trident_electron The electron species for pair production by the Trident process If a species of this type exists then electrons from the pair production module will be created in this species If no species of this type is specified then pair electrons will be generated in the first electron species trident_positron As above but for positrons proton A normal proton species This is for convenience only and is not required by the pair production routines 44 A species should be identified only once so a bw_electron species does not need to also be identified as an electron species If the code is running with produce_photons T then a photon species must be created by the user and identified If the code is
89. lled SDF2 xml Whilst IDL is an excellent tool for visualising 1D and 2D datasets it is extremely poor when it comes to dealing with 3D data For this purpose we recommend the use of the VisIt visualisation tool The other great advantage that VisIt has over IDL is the ability to render in parallel enabling the visualisation of huge datasets which IDL would be incapable of dealing with e Initially developed by the Department of Energy DOE Advanced Simulation and Computing Initiative ASCI e Now developed and maintained by the Lawrence Livermore National Laboratory along with a group of external contributors e Written in C and supports python and Java interfaces e Available for UNIX Irix Tru64 AIX Linux Solaris Mac OS X 10 3 10 9 and Windows platforms e Open source and freely available under the BSD license e Plots operators and database readers are implemented as plugins allowing the VisIt to be dynam ically extended at run time e Powerful set of tools for manipulating analysing and visualising 3D datasets e Parallel and distributed architecture for visualising huge data sets 7 2 Obtaining And Installing VisIt Both the source code and pre compiled binaries are available for download from the projects web page which is found at the URL https wci 11n1 gov codes visit home html 80 eoe Visit Executables e a gt e 19 EM A hups wei lini gov A Reade lo Downloads Documentation Wh
90. logint csc warwick ac uk y Path Igpfs home space phsiav epoch epoch2d Data Filter Y Use current working directory by default Fil i Smart 2 Remove paths C Show dot files ee i Directories Files current directory y ae waite i o S go up 1 directory level ee Open file as type Guess from file name extension Set default open options X Refresh OK Cancel 7 11 Parallel Visualisation Parallel visualisation is performed in almost exactly the same manner as remote visualisation Again you must create a host profile for the purpose except this time you need to set up a parallel launch profile in the Launch Profiles tab pane Click the New Profile button give the profile a name and then set the required options in the Parallel tab on the bottom section of the page Selecting the Launch parallel engine radio button will allow you to set the various launch options which relate to the cluster on which the job will run The major difference now is due to the fact that VisIt must be launched by an external job script which fits in with the queueing system used by the parallel machine Usually you will need to consult with the system administrator of the cluster to confirm which launch method and arguments to use The details of job launch can be better understood by reading through the User documentation section provided at http www visitusers org
91. lot with lines indicating each contour level and not a filled version Instead we choose Add gt Pseudocolor Derived Number_Density and then hit the Draw button Pseudocolor Var Derived Number_Density Units 1 mA3 1 908e 27 1 431e 27 9 5388 26 4 7698 26 0 000 10 Max 1 9088 27 Min 0 000 Y x107 6 m o 0 10 20 30 X x10 6 m There are many settings which can alter the visual appearance of plots generated by VisIt The first point of call is usually to open up the Plot Attributes or Operator Attributes dialogue corresponding to the plot in question A simpler method for accomplishing this task is to double click on the plot in the main VisIt menu pane which will launch the corresponding Plot Attributes dialogue If it is the operator attributes you wish to change click on the white arrow on the left hand side of the plot in the main VisIt menu pane This will drop down to reveal a list containing the plot and all operators acting on it Double clicking on an operator will launch the corresponding Operator Attributes dialogue e fm D Add Operators Delete Hide Show Draw Variables w Derived Number_Density Pseudocolor 84 Another important tool for controlling the appearance of plots can be found in Controls gt An notation from the VisIt menu bar This allows all of the plot annotations to be modified such as the legend title axi
92. love and S C Hagness Computational Electrodynamics The Finite Difference Time Domain Method Artech House 2000 J Roden and S Gedney Convolution pml cpml An efficient fdtd implementation of the cfs pml for arbitrary media Microw Opt Technol Lett 2000 Y Sentoku and A J Kemp Numerical methods for particle simulations at extreme densities and temperatures Weighted particles relativistic collisions and reduced currents J Comput Phys 2008 R Duclous J G Kirk and A R Bell Monte carlo calculations of pair production in high intensity laserplasma interactions Plasma Phys Contr F vol 53 no 1 p 015009 2011 96
93. mation in a normal dump and if they coincide with the timing for a full dump will also contain the full dump information Information will never be written into a file twice even if two conditions for it being written are satisfied i e even if px should be dumped both because it is a full dump and a restart dump px will only be written once 29 Note that these dump levels only really make sense for the traditional style of output block and are not really required when the new style is used 3 7 1 Dumpmask When specifying which type of output dump to write a variable to there are eight options which can be specified for each variable and can be combined by addition Some combinations make no sense but are formally valid The first four options specify at which output types the variable is to be dumped never If the variable is not a required restart variable then it will never be written If it is a required restart variable then it will be written only at restart dumps full This variable will be written at full dumps only always This variable will be written at full normal and restart dumps restart This variable will be written at restart dumps only Note that variables required for restarting the code are always written to restart dumps This flag is to enable the writing of additional variables into such dump files For grid variables derived from summing over particles ie ekbar mass_density charge_den
94. ment is also introduced the offset element This is the offset in bytes from the start of the file to where the data should be read from As a given line in the block executes the file 21 is opened the file handle is moved to the point specified by the offset parameter the data is read and the file is then closed Therefore unless the offset value is changed between data reading lines the same data will be read into all the variables The data is read in as soon as a line is executed and so it is perfectly possible to load data from a file and then modify the data using a mathematical expression The file should be a simple binary file consisting of floating point numbers of the same precision as _num in the core EPOCH code For multidimensional arrays the data is assumed to be written according to FORTRAN array ordering rules ie column major order NOTE The files that are expected by this block are SIMPLE BINARY files NOT FORTRAN unformatted files It is possible to read FORTRAN unformatted files using the offset element but care must be taken 3 3 1 Particle migration between species It is sometimes useful to separate particle species into separate energy bands and to migrate particles between species when they become more or less energetic A method to achieve this functionality has been implemented It is specified using two parameters to the control block use_migration Logical flag which determines whether or not to us
95. menu item This pops up a movie wizard which will walk you through the process of generating a simple linear movie based on the time advancing snapshots represented by your virtual database of files Alternatively you can select one of the pre defined movie templates which manipulate the currently selected plot and create a movie from that Creating a simple time advancing movie is as simple as walking through the wizard dialogue and selecting from the self explanatory options presented to you For many uses the wizard will give exactly the desired results However it is occasionally useful to have a little more control over how the movie is created In such cases it can be useful to specify an image format such as PNG to save to rather than MPEG VisIt will then generate one image per frame and number them consecutively At the end of the process the images can be converted into a movie using whatever tool best accomplishes the task 88 e090 Save movie wizard Choose format Choose movie formats and resolutions Format and resolution Output Format PNG images t Format Resolution Use current window size Scale 1 Specify movie size Width nsse gt M lock aspect Height 1492 saa _ Stereo movie Stereo type Left Right Use Screen Capture GoBack Continue Cancel Another useful tip is to select the Later tell me the command to run radio button This will output a long co
96. mmand which can run from a UNIX terminal screen The advantage is that no X session is required so the command can be run in the background It also becomes a simple task to interrupt the job at any point and resume it from where it left off at a later date In a similar manner it is easy to resume a job which crashes half way through for any reason More complex movies can be created by using VisIt s keyframing facility which allows you to change animation attributes such as view or plot attributes as the animation progresses Further information about this somewhat complex task can be found in the on line help Finally you can use VisIt s python scripting interface to programmatically describe the details of each frame as the movie progresses This approach offers far more flexibility in what can be achieved but is also much more involved and time consuming than the previous two methods Again further information on this subject can be found in the on line help system 7 10 Remote Visualisation It was mentioned earlier that it is possible to perform remote visualisation using VisIt This is a process in which the data files being interrogated reside on a different machine to the one on which the Vislt GUI runs and where the results are plotted This method of working can be extremely useful when the data is generated on a powerful machine located in an external environment such as a large cluster Another common use is when EPOCH is executed on
97. n and introduces new particles at the right hand edge The new particles are placed by re evaluating the species density temperature and drift using the new time and spatial coordinates The block looks like 27 begin window move_window T window_v_x 3 0e8 window_start_time 7 0e 13 bc_x_min_after_move simple_outflow bc_x_max_after_move simple_outflow end window move_window Logical flag determining whether or not to move the window If the window block is absent then this is the same as setting move_window to F window_v_x The speed in m s of the window window start_time The time in seconds at which the window should start moving bc_x_min_after_move The boundary condition which should apply to the left boundary after the window has started moving This is to allow the swapping of a laser boundary to a simple outflow boundary Boundary codes are the same as when just specifying normal boundaries If a boundary value isn t specified then it is assumed that the boundary isn t changed when the window starts moving xbc_left_after_move is accepted as a synonym bc_x_max_after_move The boundary condition which should apply to the right boundary after the window has started moving xbc_right_after_move is accepted as a synonym 3 7 output block Output in EPOCH is handled using the custom designed SDF file format Self Describing Format A detailed specification of this format is available el
98. n of charged particles 1 2 1 Features of EPOCH e MPI parallelised explicit second order relativistic PIC code e Dynamic load balancing option for making optimal use of all processors when run in parallel e MPI IO based output allowing restart on an arbitrary number of processors e Data analysis and visualisation options include ITT IDL LLNL VisIt and Mathworks MatLab e Control of setup and runs of EPOCH through a customisable input deck 1 3 The origins of the code The EPOCH family of PIC codes is based on the older PSC code written by Hartmut Ruhl and retains almost the same core algorithm for the field updates and particle push routines EPOCH was written to add more modern features and to structure the code in such a way that future expansion of the code is made as easy as possible 1 4 What normalisations are used in EPOCH Since the idea from the start was that EPOCH would be used by a large number of different users and that it should be as easy as possible to plug in different modules from different people into a given copy of the code it was decided to write EPOCH in SI units There are a few places in the code where some quantities are given in other units for convenience for example charges are specified in multiples of the electron charge but the entire core of the code is written in SI units 1 5 What are those _num things doing everywhere Historically using the compiler auto promotion of REAL to DOUBLE PRECI
99. n space to reproduce the number density profile that was requested It then sets the momentum components of the particles to approximate a Maxwell Boltzmann distribution corresponding to the temperature profile Sometimes this is not the desired behaviour for example you may wish to model a bump on tail velocity distribution It is currently not possible to specify these initial conditions from the input deck and the particles must be setup by modifying the source code There are two stages to the particle setup in EROCH e auto_load This routine is called after reading and parsing the input deck It takes care of allocating particles and setting up their initial positions and momenta using the initial conditions supplied in deck file It is not necessary to recompile the code or even have access to the source to change the initial conditions using this method e manual_load Once particles have been allocated they can have their properties altered in this routine By default it is an empty routine which does nothing 4 1 1 Setting autoloader properties from the input deck To illustrate using the autoloader in practice we present an example for setting up an isolated plasma block in 2D This would look like begin species name sl first set density in the range 0 gt 1 cut down density in x direction density if x gt 1 and x 1t 1 1 0 0 2 cut down density in y direction density if y gt 1 and y 1t 1 density s1
100. nd magnetic fields at any point in the domain An example block is shown below 26 t_profile gauss time 4e 15 4e 15 t_end 14e 15 Figure 2 A laser pulse with a smooth temporal profile shows no artefacts fields block begin fields ex sin pi x length_x ey cos pi x length_x CA bx 1 0 by 1 0 bz 0 end fields Once again this is a very simple block needing only limited explanation All field variables are accessible by name and can be read back using the appropriate commands from the maths parser see Section 3 15 The possible parameters are as follows ex ey ez The electric field vectors pointing in all three directions The default value is zero bx by bz The magnetic field vectors pointing in all three directions The default value is zero offset File offset The field values may also be specified using a binary file in a similar way to that used for species variables See Section 3 3 for more details Any valid maths parser expression can be used to set up the fields and no check is made to ensure that the V B 0 is satisfied 3 6 window block EPOCH can include an optional block which causes the simulation domain to operate as a moving window At present it is only possible to have the window moving at a constant speed parallel to the x direction although the window does not have to start moving at t 0 When the window moves the code removes particles from the left hand edge of the domai
101. nergies down to the fully ionised ion if the user wishes to exclude some inner shell ionisation for some reason they need to give this a very large number Note that the ionisation model assumes that the outermost electron ionises first always and that the orbitals are filled assuming ground state When this parameter is specified it turns on ionisation modelling If you wish to specify the values in Electron Volts add the ev multiplication factor see Section 3 15 1 ionisation_electron_species Name of the electron species This can be specified as an array in the event that the user wishes some levels to have a different electron species which can be handy for monitoring ionisation at specific levels electron and electron_species are accepted as synonyms For example ionising carbon species might appear in the input deck as begin species charge 0 0 mass 1837 2 name carbon ionisation_energies 11 26x ev 24 38x ev 47 89 ev 64 49 ev 392 1x ev 490 0 ev ionisation_electron_species electron electron electron fourth electron electron rho den_gas end species begin species charge 1 0 mass 1 0 name electron rho 0 0 end species begin species echarpe O mass 1 0 name fourth rho 0 0 end species If ionisation electron species is not specified then the electron species are created automatically and are named according to the ionising species name with a number appended For e
102. oidal profile The species block for Proton is then set to match the density of Electron enforcing charge neutrality On its own this initial condition does nothing and so only needs to run for 0 timesteps nsteps 0 in input deck The resulting electron number density should look like Figure 5 3 A hollow cone in 3D A more useful example of an initial condition is to create a hollow cone This is easy to do in both 2D and 3D but is presented here in 3D form input deck begin control nx 250 ny nx nz nx npart 2 nx ny nz x_min 10 micron X_max x_min y_min x_min y_max X_max z_ min x_min z_max X_max nsteps 0 end control 67 begin boundaries bc_x_min simple_laser bc_x_max simple_outflow bc_y_min periodic bc_y_max periodic bc_z_min periodic bc_z_max periodic end boundaries begin output number_density always species end output begin constant den_cone 1 0e22 ri abs x 5 0e 6 0 5e 6 ro abs x 5 0e 6 0 5e 6 xi 3 0e 6 0 5e 6 xo 3 0e 6 0 5e 6 r sqrt y 2 2 2 end constant begin species name proton charge 1 0 mass 1836 2 frac 0 5 rho if r gt ri and r 1t ro den _cone 0 0 rho if x gt xi and x 1t xo and r lt ri den_cone rho proton rho if x gt xo 0 0 rho proton end species begin species name electron charge 10 mass 1 0 mae 0 8 rho rho proton end species To convert this
103. only the input deck It is not necessary to normalise the distribution function as this is done automatically by the sample dist_function function 4 3 Lasers EPOCH has the ability to add EM wave sources such as lasers at boundaries To use lasers set the boundary that you wish to have a laser on to be of type simple laser and then specify one or more lasers attached to that boundary Lasers may be specified anywhere initial conditions are specified 4 4 laser blocks in multiple dimensions Var Beste Fekl Ey Time 5 00428e 14 4 68e 10 1 95e 09 4 29e 10 8 77e 10 Max 9 16e 10 Min 8 77e 10 y o x10 6 m 0 X x10 6 m Figure 3 Constant laser profile When running EPOCH in 2D or 3D the laser can be modified spatially via the profile and phase parameters These are briefly outlined in Section 3 4 but in this section we will describe them in a little more depth profile The spatial profile for the laser This is essentially an array defined along the edge or surface that the laser is attached to It is clear that the spatial profile is only meaningful perpendicular to the laser s direction of travel and so it is just a single constant in 1D The laser profile is evaluated as an initial condition and so cannot include any temporal information which must be encoded in t_profile The spatial profile is evaluated at the boundary where the laser is attached and so only spatial information in the plane of the boun
104. only used plot for 2D is the contour plot The aptly named contour z x y procedure 66 takes a 2D array of data values z and plots them against x and y axes which are specified in the 1D TT Uy Uno x and y arrays The number of contour lines to plot is specified by the nlevels parameter If the fi11 parameter is used then IDL will fill each contour level with a solid colour rather than just drawing a line at the contour value The example given below plots a huge number of levels so that a smooth looking plot is produced xstyle 1 requests that the x axes drawn exactly matches the data in the x variable rather than just using a nearby rounded value and similarly for ystyle 1 IDL gt n 100 IDL gt levels max data number_density findgen n n 1 IDL gt colors 253 findgen n n 1 1 IDL gt contour data number_density data x data y xstyle 1 ystyle 1 IDL gt levels levels fill c_colors colors Issuing these commands gives us the contour plot shown below Note that the colour table used is not the default one but has been constructed to be similar to the one used by Vislt 000 X IDLO 6 7 Shaded Surface Plots in IDL Another method for visualising 2D datasets is to produce a 3D plot in which the data is elevated in the z direction by a height proportional to its value IDL has two versions of the surface plot surface produces a wireframe plot and shade surf produces a fil
105. ory parameter npart This specifies the number of pseudoparticles which should be loaded into the simulation domain for this species block Using this parameter is the most convenient way of loading particles for simulations which contain multiple species with different number densities If npart is specified in a species block then any value given for npart in the control block is ignored npart should not be specified at the same time as frac within a species block frac This specifies what fraction of npart the global number of particles specified in the control block should be assigned to the species NOTE frac should not be specified at the same time as npart for a given species npart_per_cell Integer parameter which specifies the number of particles per cell to use for the initial particle loading At a later stage this may be extended to allow npart_per cell to be a spatially varying function If per species weighting is used then the value of npart_per cell will be the average number of particles per cell If npart or frac have also been specified for a species then they will be ignored To avoid confusion there is no globally used npart_per_species If you want to have a single value to change in the input deck then this can be achieved using a constant block dumpmask Determines which output dumps will include this particle species The dumpmask has the same semantics as those used by variable
106. ost of the control block is self explanatory but there are two parts which need further description 15 3 1 1 Dynamic Load Balancing The first is the dlb_threshold flag dlb stands for Dynamic Load Balancing and when turned on it allows the code to rearrange the internal domain boundaries to try and balance the workload on each processor This rearrangement is an expensive operation so it is only performed when the maximum load imbalance reaches a given critical point This critical point is given by the parameter dlb_threshold which is the ratio of the workload on the least loaded processor to the most loaded processor When the calculated load imbalance is less than dlb_threshold the code performs a re balancing sweep so if dlb threshold 1 0 is set then the code will keep trying to re balance the workload at almost every timestep At present the workload on each processor is simply calculated from the number of particles on each processor but this will probably change in future If the dlb_threshold parameter is not specified then the code will only be load balanced at initialisation time 3 1 2 Automatic halting of a simulation It is sometimes useful to be able to halt an EPOCH simulation midway through execution and generate a restart dump Two methods have been implemented to enable this The first method is to check for the existence of a STOP file Throughout execution EPOCH will check for the exi
107. pshot It also accepts the wkdir as either the second argument or the keyword parameter wkdir If it is omitted alltogether the current global default is used Finally it accepts a list of variables or class of variables to load Since it is a function the result must be assigned to a variable The object returned is an IDL data structure containing a list of named variables To load either a specific variable or a class of variables specify the name prefixed by a forward slash It should be noted here that the IDL scripting language is not case sensitive so P can be specified as either Px or px We will now load and inspect the Grid class this time omitting the optional wkdir parameter This time we will load from the third dump file generated by the EPOCH run which is found in the file 0002 sdf since the dump files are numbered starting from zero 73 6 1 Inspecting Data IDL gt gridclass getdata 1 grid IDL gt help gridclass structures Structure lt 22806408 gt 11 tags length 536825024 data length 536825016 refs 1 FILENAME STRING Data 0001 sdf TIMESTEP LONG 43 TIME DOUBLE 5 0705572e 15 GRID_ELECTRON STRUCT gt lt Anonymous gt Array 1 GRID_PROTON STRUCT gt lt Anonymous gt Array 1 GRID STRUCT gt lt Anonymous gt Array 1 X DOUBLE Array 1024 Y DOUBLE Array 512 GRID_EN_ELECTRON STRUCT gt lt Anonymous gt Array 1 GRID_X_EN_ELECTRON STRUCT gt lt Anonymous gt
108. ption is only supplied for debugging purposes and should not be required by most users id Global particle ID See below for details Particle IDs are useful if you want to track the progress of each particle throughout the simulation Since they increase the size of each particle data structure they are disabled by default and must be enabled using a compiler flag The PARTICLE ID flag will use an 8 byte integer to represent the ID and PARTICLE_ID4 uses a 4 byte integer They are written to file using the id flag Note In the current implementation the particle IDs are passed between processors and written to file using REAL numbers This means that in double precision the maximum particle ID is 253 101 This should be ample for the foreseeable future However if the code is compiled for single precision then the maximum ID is 2 16777216 Probably not big enough 3 7 4 Grid Variables The next set of parameters specify properties which are defined on a regular cartesian mesh All entries have a default dumpmask of never 33 grid The dumpmask for the Cartesian grid which defines the locations of the grid variables No grid variables can be plotted in VisIt unless this variable is output If any grid variables are written then the grid is automatically written unless grid never is specified The synonym field grid may also be used ex ey ez The electric field vectors pointing in all
109. raries for loading and inspecting SDF files We begin by inspecting SDF file contents and finding out what variables it contains To do this we execute the list_variables procedure call which is provided by the EPOCH IDL library At each timestep for which EPOCH is instructed to dump a set of variables a new data file is created These files take the form 0000 sdf For each new dump the number is incremented The procedure call accepts up to two arguments The first argument is mandatory and specifies the number of the SDF file to be read in This argument can be any integer from 0 to 9999 It is padded with zeros and the suffix sdf appended to the end to give the name of the data file eg 99 gt 0099 sdf The next arguments is optional The keyword wkdir specifies the directory in which the data files are located If this argument is omitted then the currently defined global default is used Initially this takes the value Data but this can be changed using the set _wkdir procedure and queried using the get wkdir function IDL gt list_variables 0 Data Available elements are 1 EX ELECTRIC_FIELD 2D Plain variable 2 EY ELECTRIC_FIELD 2D Plain variable 3 EZ ELECTRIC_FIELD 2D Plain variable 4 BX MAGNETIC_FIELD 2D Plain variable 5 BY MAGNETIC_FIELD 2D Plain variable 6 BZ MAGNETIC_FIELD 2D Plain variable 7 JX CURRENT 2D Plain variable 8 JY CURRENT 2D Plain variable 9 JZ
110. re recent versions of EPOCH it is now possible to have multiple output blocks in the input deck each with their own dt_snapshot or nstep_snapshot and their own set of output variables The syntax remains the same as the original output block syntax with the addition of name and restartable fields The name field specifies the file name to use for the output list Each time EPOCH generates an output dump it writes an entry into the file lt name gt visit This can be used to find all the output dumps of a specific output block It is named with a visit suffix to enable its use as a file grouping list in the VisIt data analysis tool but it is just a plain text file so it can equally be used by any other program If two output blocks are written at the same time the output will be combined into a single file The restartable field specifies that the output block should generate output dumps containing all the information necessary to restart a simulation The following parameters are supported by the new style of output block in addition to those for the traditional style name Identifies the output block with a name which is required when multiple output blocks are used restartable Specifies whether or not the output for this block is a restartable dump dump_at_times Floating point parameter which specifies a set of simulation times at which to write the current output block
111. remely large tool and the compilation takes hours to complete It is usually far easier to download a pre compiled binary which matches your system architecture However occasionally compilation may be a necessary step Linux in particular is a moving target and it is not always possible to find a binary which matches the particular combination of libraries installed on your system The easiest way to install the VisIt tool is to ask the system administrator to do it for you However this may not always be the best option The system in question may be run by someone who is not concerned with your particular software needs or has insufficient skills to deal with the task In any case VisIt has a fairly rapid release schedule and you may find that some functionality you need is not present in the version installed on the machine Fortunately for all these scenarios it is usually quite easy to install a copy in your own home directory Just find a binary on the web page https wci 11n1 gov codes visit executables html which closely matches your machine and download it This can be unpacked into your home directory with the command tar xzf visit2_7_1 linux x86_64 tar gz The actual name of the file will vary depending on which version you downloaded This will unpack the VisIt binary into a subdirectory named visit Now all that is necessary is to add this to your search path eg export PATH HOME visit bin PATH These instructions illustrate the st
112. removed from the simulation when they reach the boundary reflect This applies reflecting boundary conditions to particles When specified for fields all field components are clamped to zero conduct This applies perfectly conducting boundary conditions to the field When specified for particles the particles are reflected open When applied to fields EM waves outflowing characteristics propagate through the 17 boundary Particles are transmitted through the boundary and removed from the system cpml laser See Section 3 2 1 cpml_outflow See Section 3 2 1 thermal See Section 3 2 2 NOTE If simple laser simple outflow cpml laser cpml outflow or open are specified on one or more boundaries then the code will no longer necessarily conserve mass Note also that it is possible for the user to specify contradictory unphysical boundary conditions It is the users responsibility that these flags are set correctly 3 2 1 CPML boundary conditions There are now Convolutional Perfectly Matched Layer boundary conditions in EPOCH The implemen tation closely follows that outlined in the book Computational Electrodynamics The Finite Difference Time Domain Method by Taflove and Hagness 1 See also Roden and Gedney 5 CPML boundaries are specified in the input deck by specifying either cpml_outflow or cpml laser in the boundaries block cpml outflow specifies an absorbing boundary condition whereas
113. roducing any restart dumps This is the default force first to be restartable Logical flag which determines whether the file written at time zero is a restart dump The default value is F force_last_to_be_restartable Force the code to override other output settings and make the last output dump it writes be a restart dump Any internal condition which causes the code to terminate will make the code write a restart dump but code crashes or scheduler terminations will not cause the code to write a restart dump force final to be restartable is accepted as a synonym The default value is T dump first Logical flag which determines whether to write an output file immediately after initialising the simulation The default is T dump_last Logical flag which determines whether to write an output file just before ending the simulation The default is T if an output block exists in the input deck and F otherwise dump final is accepted as a synonym time start Floating point parameter which specifies the simulation time at which to start considering output for the block Note that if dump_first or dump_last are set to true for this block then dumps will occur at the first or last timestep regardless of the value of the time_start parameter This also applies to the three following parameters The default value is 0 time stop Floating point parameter which specifies the simulation
114. rs to be attached to a boundary Lasers are attached at the initial conditions stage An example boundary block for EPOCH2D is as follows boundaries block begin boundaries bc_x_min simple_laser bc_x_max_field simple_outflow bc_x_max_particle simple_outflow bc_y_min periodic bc_y_max periodic end boundaries The boundaries accepts the following parameters 16 be_ x y z min The condition for the lower boundary for both fields and particles xbc_left ybc_down and zbc_back are accepted as a synonyms bc x y z min _ field particle The condition for the lower boundary for fields particles xbe_left_ field particle ybc_down_ field particle and zbc_back_ field particle are accepted as a synonyms bc_ x y z _ max The condition for the upper boundary for both fields and particles xbc right ybc_up and zbc front are accepted as a synonyms bc_ x y z _max field particle The condition for the upper boundary for fields particles xbe_right_ field particle ybc_up_ field particle and zbc_front_ field particle are accepted as a synonyms cpml_thickness The thickness of the CPML boundary in terms of the number of grid cells see Section 3 2 1 The default value is 6 cpml_kappa_max A tunable CPML parameter see Section 3 2 1 cpml a max A tunable CPML parameter see Section 3 2 1 cpml_sigma_max A tunable CPML param
115. running with produce_pairs T then the code must specify at least one electron or bw_electron species and one positron or bw_positron species These species will usually be defined with zero particles from the start of the simulation and will accumulate particles as the simulation progresses The code will fail to run if the needed species are not specified The basic input deck has now been considered fully but it is possible for an end user to add new blocks to the input deck As a result a version of the code which you have obtained from a source other than CCPForge may include other input deck blocks These should be described in additional documentation provided with the version of the code that you have 3 13 subset block It is possible to restrict the number of particles written to file according to various criteria For example you can now output the momentum of all particles which have a gamma lower than 1 8 or the positions of a randomly chosen subset of a given species A new input deck block named subset is defined which accepts the following parameters name The name given to this subset This is used to identify the subset in the output block and is also used when labelling the data in the SDF files include_species Add the given particle species to the set of particles that this subset applies to By default no particle species are included dumpmask The dumpmask to use when considering this subset in an outpu
116. ry called bin containing the compiled binary which will be called epochid epoch2d or epoch3d To run the code just execute the binary file by typing bin epoch2d or whatever the correct binary is for the dimensionality of the code that you have You should be given a screen which begins with the EPOCH logo and then reads Welcome to EPOCH2D Version 4 3 3 commit v4 3 3 3 g3ed1a0e clean The code was compiled with the following compile time options 2K 2K aK ak k aK K K K K 3K 2K 3K 2K 3K 3K 3K 3K 3K 2K 2K aK 2 2k 2 2 2K 2K aK K K K K 2K K 2K 2K 3K 3K 3K 3K 3K 3K 3K 2K 2K 2K 2K 2K 2K K IK 2K 2K 2K 2K 2K 2k Per particle weighting DPER_PARTICLE_WEIGHT Tracer particle support DTRACER_PARTICLES Particle probe support DPARTICLE_PROBES KKK KK K aK aK aK 2 3K 3K 3K K K K 2 2K 3K K K K K 3K 3K 3K 3K K K K 2A K 3K 3K 3K 3K K K K aK K 3K 3K 3K 3K 3K K K K AC 3K 2K 2K K Code is running on 1 processing elements Specify output directory At this point the user simply types in the name of the already existing output directory and the code will read the input deck files inside the specified directory and start running To run the code in parallel just use the normal mpirun or mpiexec scripts supplied by your MPI implementation If you want the code to run unattended then you will need to pipe in the output directory name to be used The method for doing this varies between MPI implementations For many MPI implementations suc
117. s To do this we must learn a few basic essentials about the IDL scripting language Since we are all familiar with the basic concepts shared by all computer programming languages I will just provide a brief overview of the essentials and leave other details to the excellent on line documentation IDL supports multidimensional arrays similar to those found in the FORTRAN programming lan guage Whole array operations are supported such as 5 array to multiply every element of array by 5 Also matrix operations such as addition and multiplication are supported The preferred method for indexing arrays is to use brackets It is possible to use parenthesis instead but this usage is deprecated Column ordering is the same as that used by FORTRAN so to access the i 7 k th element of an array you would use array i j k IDL arrays also support ranges so array 5 10 3 4 will return a one dimensional array with five elements array 5 specifies elements five to n of an n element array array 3 picks out the third row of an array There are also a wide range of routines for querying and transforming arrays of data For example finding minimum and maximum values performing FFTs etc These details can all be found by searching the on line documentation Finally IDL is a full programming language so you can write your own functions and procedures for processing the data to suit your needs 6 4 1D Plotting in IDL T
118. s 3 femtoseconds A list of multiplication factors is supplied in Section 3 15 1 x y z min Minimum grid position of the domain in metres These are required parameters Can be negative x y z start is accepted as a synonym In a similar manner to that described above distances can be specified in microns using a multiplication constant eg x_min 4 micron specifies a distance of 4um x y z max Maximum grid position of the domain in metres These are required parameters Must be greater than x y z min fx y z _end is accepted as a synonym dt_multiplier Factor by which the timestep is multiplied before it is applied in the code ie a multiplying factor applied to the CFL condition on the timestep Must be less than one If no value is given then the default of 0 95 is used dlb_threshold The minimum ratio of the load on the least loaded processor to that on the most loaded processor allowed before the code load balances Set to 1 means always balance set to O means never balance If this parameter is not specified then the code will only be load balanced at initialisation time restart_snapshot The number of a previously written restart dump to restart the code from If not specified then the initial conditions from the input deck are used Note that as of version 4 2 5 this parameter can now also accept a filename in place of a number If you want to restart from 0012 sdf then it can either be spec
119. s in the output block described in Section The actual dumpmask from the output block is applied first and then this one is applied afterwards For example if the species block contains dumpmask full and the output block contains vx always then the particle velocity will be only be dumped at full dumps for this particle species The default dumpmask is always dump This logical flag is provided for backwards compatibility If set to F it has the same meaning as dumpmask never If set to T it has the same meaning as dumpmask always tracer Logical flag switching the particle species into tracer particles Tracer particles are enabled with the correct precompiler option and when set for a given species make that species move correctly for its charge and mass but contribute no current This means that these particles are passive tracers in the plasma tracer F is the default value identify Used to identify the type of particle Currently this is used primarily by the QED routines See Section for details immobile Logical flag If this parameter is set to T then the species will be ignored during the particle push The default value is F The species blocks are also used for specifying initial conditions for the particle species The initial conditions in EPOCH can be specified in various ways but the easiest way is to specify the initial 20 conditions in the
120. s labels etc ex Annotation 2D 3D Array Colors Objects M Legend No annotations Y Database Path Expansion File Font name Arial Fontscale 1 Bold Italic 7 6 1D Plotting in Visit Mal ak Jud ED LY GAU Bt AS ES a a et aD et A Le 5 v Use foreground color E ans 400 M Time Time scale factor 1 Time offset 0 Y User information Font name Arial Fontscale 1 Bold Italic m Usa i dnd Golar MGAL JR DAE el BL J E n d he aha 15 BEJ HN eet JU ee m 1 Make default Reset ARON en fe Fh Diners A 1D plot in VisIt is called a Curve plot We already mentioned that this was greyed out because we have no one dimensional variables in our data file The solution to this dilemma is the lineout operator which extracts a one dimensional array from a 2D or 3D variable This operator is selected by pressing the button with red and blue lines located at the top of the plot window A pan a Once the button has been pressed we can click and drag anywhere in the Pseudocolor plot window When we release the mouse button a new plot window pops up containing a Curve plot of the data just selected 85 Value x10 27 1 m 3 T TT T T T TT T rere fo T rr te Tr 7 T rr TT TT T Gr 10 20 30 40 Distance x10 6 m In order to change the attributes for this plot we must first select Active window number 2 in the m
121. sers if this is the case although it does no harm to regularly recompile the reader as a matter of course We will see later that it is possible to do remote data visualisation with VisIt in which the GUI is launched and interacted with on one machine and the data files are located on a separate machine entirely In this situation the reader must be installed on the remote machine and must match the setup there The setup on the local machine is unimportant In fact it is not even necessary to have the plugin installed on the local machine This is particularly useful when using a Windows environment to analyse data located on a remote UNIX workstation 7 4 Loading Data Into Visit eoo File open MH Host localhost y y Path Users phsiav dev epoch epoch2d Data ly Filter Y Use current working directory by default Remove paths Show dot files File grouping Smat Directories Files current directory gm sd database go up 1 directory level 82 antol iac deck status epoch2d dat full visit Open file as type Guess from file name extension a Set default open options ideal Refresh OK Cancel The most straightforward method for loading data into VisIt is to start the application and then browse the filesystem for the dataset you are interested in This is done by selecting File Open file from the VisIt menu bar A file selection dialogue will appear allowing
122. sewhere although this is only of interest to developers wishing to write new libraries EPOCH comes with readers for ITT IDL LLNL VisIt and Mathworks MatLab The IDL reader is also compatible with the open source GDL tool There are two styles of output block supported by EPOCH The first style which will be referred to as the traditional style is the method that has been supported by EPOCH since its inception With this method a single output block governs all the output dumps which are to be performed There are a few levels of output which give some small amount of flexibility over what gets dumped but these do not allow for a very fine grained control In version 4 0 of EPOCH a new style was introduced in which multiple named output blocks may be specified allowing for much greater flexibility The existence of a name parameter is what determines that an output block is the new style rather than the traditional style Most of the parameters are shared by both styles The following sections document the traditional style of output block and any differences between the two styles are described in Section 3 7 9 What the code should output and when it should output it is specified in the output block of the input deck An example output block is shown below output block begin output If use_offset_grid is true then the code dumps a grid which displays positions relative to the left hand edge of the window use_offse
123. sity number density temperature the following two parameters also apply species The derived variable should be output on a species by species basis It is combined with a dumpmask code by addition as in charge density always species no_sum The output for this derived variable should not be summed over all species By default derived variables are summed over all species If you don t want to include this sum you must use the no_sum flag It is combined with a dumpmask code by addition as in charge density always species no_sum Most grid variables may be averaged over time A more detailed description of this is given in Section 3 7 7 Data averaging is specified using the following dumpmask parameters average The output for this variable should be averaged over time The time span over which the variable will be averaged is controlled using flags described in Section 8 7 2 snapshot By default the average parameter replaces the variable with an averaged version of the data Adding this flag specifies that the non averaged variable should also be dumped to file When applied to a variable these codes are referred to as a dumpmask 3 7 2 Directives The first set of options control the type and frequency of output dumps They are used as follows disabled Logical flag If this is set to T then the block is ignored and never generates any output The default value is F
124. stence of a file named either STOP or STOP_NODUMP in the simulation output directory The check is performed at regular intervals and if such a file is found then the code exits immediately If STOP is found then a restart dump is written before exiting If STOP_NODUMP is found then no I O is performed The interval between checks is controlled by the integer parameter check stop frequency which can be specified in the control block of the input deck If it is less than or equal to zero then the check is never performed The next method for automatically halting the code is to stop execution after a given elapsed wall time If a positive value for stop_at_walltime is specified in the control block of an input deck then the code will halt once this time is exceeded and write a restart dump The parameter takes a real argument which is the time in seconds since the start of the simulation An alternative method of specifying this time is to write it into a separate text file stop_at_walltime_file is the filename from which to read the value for stop_at_walltime Since the walltime will often be found by querying the queueing system in a job script it may be more convenient to pipe this value into a text file rather than modifying the input deck 3 2 boundaries block The boundaries block sets the boundary conditions of each boundary of the domain Some types of boundaries allow EM wave sources lase
125. t so in more complicated cases it is probably better to use the autoloader than to manually set up the number density distribution 4 2 3 Grid coordinates used in EPOCH When setting up initial conditions within the EPOCH source rather than using the input deck there are several constants that you may need to use These constants are e nx Number of gridpoints on the local processor in the x direction e ny Number of gridpoints on the local processor in the y direction 2D and 3D e nz Number of gridpoints on the local processor in the z direction 3D e length x y z Length of domain in the x y z directions e x y z _ min Minimum value of x y z for the whole domain e x y z max Maximum value of x y z for the whole domain e n species The number of species in the code There are also up to three arrays which are available for use 59 e x 2 nx 3 Position of a given gridpoint in real units in the x direction e y 2 ny 3 Position of a given gridpoint in real units in the y direction 2D and 3D e z 2 nz 3 Position of a given gridpoint in read units in the z direction 3D 4 2 4 Loading a non thermal particle distribution While the autoloader is capable of dealing with most required initial thermal distributions you may want to set up non thermal initial conditions The code includes a helper function to select a point from an arbitrary distribution function which can be used to deal with mos
126. t block This takes the same form as the output block dumpmask The default value is always random fraction Select a random percentage of the particle species This is a real value between zero and one If 0 is specified no particles are selected If 1 is specified all the particles are selected If 0 2 is specified 20 of the particles are selected px py pz weight charge mass gamma _min Select only the particles with momen tum weight charge mass or gamma which is greater than the given value px py pz weight charge mass gamma _Max Select only the particles with momen tum weight charge mass or gamma which is less than the given value x y z min Select only the particles whose position lies above the given value x y z max Select only the particles whose position lies below the given value id_min max Select only the particles whose id is greater than or less than the given values The id field is explained below Once a subset has been defined the subset name can then be used in place of or in addition to the dumpmask in an output block For example 45 begin subset name background random_fraction 0 1 include_species electron include_species proton end subset begin subset name high gamma gamma_min 1 3 include_species electron end subset begin output particles background high_gamma always px background high_gamma py background pz alwa
127. t non thermal distributions To use the helper function you need to define two 1D arrays which are the x and y axes for the distribution function An example of using the helper function is given below SUBROUTINE manual_load TYPE particle POINTER current INTEGER PARAMETER np_local 1000 INTEGER ispecies ip REAL num temperature stdev2 tail_width tail_height tail_drift REAL num frac tail_frac min ip max p dp_local p2 tail_p2 REAL num DIMENSION np_local p_axis distfn_axis temperature 1e4_num tail_width 0 05_num tail_height 0 2_num tail_drift 0 5_num DO ispecies 1 n_species stdev2 kb temperature species_list ispecies mass frac 1 0_num 2 0_num stdev2 tail_frac 1 0_num 2 0_num stdev2 tail_width max_p 5 0_num SQRT stdev2 min_p max_p dp_local max_p min_p REAL mp_local 1 num DO ip 1 np_local p_axis ip min_p ip 1 dp_local p2 p_axis ip 2 tail_p2 p_axis ip tail_drift max_p x 2 distfn_axis ip EXP p2 frac amp tail_height EXP tail_p2 tail_frac ENDDO current gt species_list ispecies Zattached_list head DO WHILE ASSOCIATED current current part_p 1 sample_dist_function p_axis distfn_axis current gt current next ENDDO ENDDO END SUBROUTINE manual_load 56 This example will set the particles to have a bump on tail velocity distribution a setup which is not possible to do using
128. t_grid F number of timesteps between output dumps dt_snapshot 1 0e 14 Number of dt_snapshot between full dumps full_dump_every 10 28 restart_dump_every 1 force_final_to_be_restartable T Properties at particle positions particles never px never py never pz never vx never vy never vz never charge never mass never particle_weight never Properties on grid grid always ex always ey always ez always bx always by always bz always jx always jy always ekbar always species mass_density never species charge_density always number_density always species temperature always species distribution_functions always particle_probes never end output There are three types of output dump in EPOCH which are used for different purposes These types are e normal The most frequent type of output dump in EPOCH is a normal dump e full A full dump is usually written every 10 or so normal dumps A full dump contains all the data that a normal dump contains and should also contain any information which is needed only infrequently whether this is the full particle information or a large distribution function It is possible to turn off full dumps completely e restart A restart dump is a dump where the code guarantees to write enough data to allow the code to restart from the output Output dumps are guaranteed to contain all the infor
129. ta Server Y Tunnel data connections through SSH Method used to determine local host name when not tunneling Use local machine name Parse from SSH_CLIENT environment variable Remote Profiles Specify manually C SSH command ssh _ SSH port 22 _ Use gateway New Host Delete Host Copy Host Export Host Apply Post Dismiss Create a new profile by clicking on the New Host button and filling out some of the form fields The important ones to change are Host nickname Remote host name Host name aliases and Username If the visit binary is not in your default search path on the remote machine then you must specify its location by filling in the Path to VisIt installation field Now click Apply and Dismiss followed by the Options Save Settings menu item to ensure that the profile is saved for future sessions Data on the remote machine can now be loaded by selecting File Open file and picking the desired host profile from the drop down list of Hosts VisIt will wait for the remote process to launch and then continue with the file selection procedure but now displaying files located on the remote machine rather than the local one From this point on everything should work as before except you should see the name of the remote machine in the Selected files dialogue 90 eoo File open Host minerva
130. tected e a b Multiplication operator e a b Division operator e a b Power raise operator e ae b Power of ten operator 1 0e3 1000 e alt b Less than operator Returns 1 if a lt b otherwise returns 0 Intended for use with if e a gt b Greater than operator Returns 1 if a gt b otherwise returns 0 e a eq b Equality operator Returns 1 if a b otherwise returns 0 e a and b Logical and operator Returns 1 if a 0 and b 0 otherwise returns 0 e aor b Logical or operator Returns 1 if a 0 or b 0 otherwise returns 0 These follow the usual rules for operator precedence although it is best to surround more complex expressions in parenthesis if the precedence is important It is not possible at this time to specify custom operators without major changes to the code An example of using an operator would be length_x 10 0 12 0 50 4 EPOCH use in practice 4 1 Specifying initial conditions for particles using the input deck If the initial conditions for the plasma you wish to model can be described by a number density and temperature profile on the underlying grid then EPOCH can create an appropriate particle distribution for you The set of routines which accomplish this task are known as the autoloader For many users this functionality is sufficient to make use of the code and there is no need to deal with the internal representation of particles in EPOCH The autoloader randomly loads particles i
131. the resulting distribution function whereas restrictions allow you to specify minimum and maximum values for each spatial and momentum direction and use only particles which fall within this range when calculating the distribution function Restrictions can be specified even for properties which are not being used as axes It is possible to set a restriction that is more restrictive than the range applied This is not trapped as an error and such parts of the distribution function are guaranteed to be empty The available spatial restrictions depend on the dimensionality of the code Therefore attempting to set restrict_z in EPOCH1D will produce a warning At present the code to calculate the distribution functions has one limitation it ignores particle shape functions when calculating properties on the spatial axis meaning that the result is less smooth than normal properties from the code 3 10 probe block Sometimes it is useful to consider all the properties of particle which pass through a point line plane depending on dimension in the simulation To allow this it is possible to specify one or more Particle Probe blocks in the input deck These record copies of all particles which cross a point line plane in a given direction which meet minimum and maximum kinetic energy criteria and output the particle properties into the normal output files Particle probes record the positions momenta and weight of all particles passing through the plan
132. ther Fortran TYPE this time called particle species This represents all the properties which are common to all particles in a species There are lots of entries which are only compiled in when compile time flags are specified The definition without any such flags is TYPE particle_species Core properties CHARACTER string_length name TYPE particle_species POINTER next prev INTEGER id INTEGER dumpmask REAL num charge 93 REAL num mass REAL num weight INTEGER KIND 8 count TYPE particle_list attached_list Injection of particles INTEGER KIND 8 npart_per_cell REAL num DIMENSION POINTER density REAL num DIMENSION POINTER temperature END TYPE particle_species This definition is for the 2D version of the code The only difference for the other two versions is the number of dimensions in the density and temperature arrays e name The name of the particle species used in the output dumps etc e next prev Particle species are also linked together in a linked list This is used internally by the output dump routines but should not be used by end users e id The species number for this species This is the same number as is used in the input deck to designate the species e dumpmask Determine when to include this species in output dumps Note that the flag is ignored for restart dumps e charge The charge in Coulombs Even if PER PARTICLE CHAR
133. three directions Restart variables bx by bz The magnetic field vectors pointing in all three directions Restart variables In 1D bx is a trivial variable because of the Solenoidal condition It is included simply for symmetry with higher dimension codes JX JY JZ The current densities pointing in all three directions Restart variables 3 7 5 Derived Variables The final set of parameters specify properties which are not variables used in the code but are derived from them The first six variables are derived by summing properties of all the particles in each grid cell The resulting quantities are defined on the regular cartesian mesh used for grid variables All entries have a default dumpmask of never ekbar Mean kinetic energy on grid Can have species dumpmask ekflux Mean kinetic energy flux in each direction on the grid Can have species dumpmask mass_density Mass density on grid Can have species dumpmask charge_density Charge density on grid Can have species dumpmask number_density Number density on grid Can have species dumpmask temperature Isotropic temperature on grid Can have species dumpmask poynt_flux Poynting flux in each direction 3 7 6 Other Variables distribution_functions Dumpmask for outputting distribution functions specified in the input deck Each individual distribution function can have its own dumpmask and these will be applied after the value of distribution functions
134. ticle_species e next prev The next and previous particle in the linked list which represents the particles in the current species This will be explained in more detail later e processor The rank of the processor which currently holds the particle e processor_at_t0 The rank of the processor on which the particle started Collections of particles are represented by another Fortran TYPE called particle list This type represents all the properties of a collection of particles and is used behind the scenes to deal with inter processor communication of particles The definition of the type is TYPE particle_list TYPE particle POINTER head TYPE particle POINTER tail INTEGER KIND 8 count Pointer is safe if the particles in it are all unambiguously linked LOGICAL safe TYPE particle last POINTER next prev END TYPE particle_list e head The first particle in the linked list e tail The last particle in the linked list e count The number of particles in the list Note that this is NOT MPI aware so reading count only gives you the number of particles on the local processor e safe Any particle list which a user should come across will be a safe particle list Don t change this property e next prev For future expansion it is possible to attach particle_lists together in another linked list This is not currently used anywhere in the code An entire species of particles is represented by ano
135. tion You will also need to refer to 8 Section 3 Next look at the code and have a play with some test problems After that re read this section This should be enough for testing simple problems 1 8 What is the auto loader Throughout this document we will often refer to the auto loader when setting up the initial particle distribution In the input deck it is possible to specify a functional form for the density and temperature of a particle species EPOCH will then place the particles to match the density function and set the velocities of the particles so that they match the Maxwellian thermal distribution for the temperature The code which performs this particle set up is called the auto loader At present there is no way to specify a non Maxwellian particle distribution from within the input deck In such cases it is necessary to edit and recompile the EPOCH source code The recommended method for setting the initial particle properties is to use the manual_load function as described in Section 1 9 What is a maths parser As previously mentioned the behaviour of EPOCH is controlled using an input deck which contains a list of key value pairs The value part of the pair is not restricted to simple constants but can be a complex mathematical expression It is evaluated at run time using a section of code called the maths parser There is no need for the end user to know anything about this code It is just there
136. ug in for the LLNL VisIt parallel visualisation tool for reading SDF files generated by an EPOCH run e CODING_STYLE This document contains the conventions which must be used for any code being submitted for inclusion in the EPOCH project e epoch tarball ssh This is a shell script which is used for creating the tarred and gzipped archives of EPOCH which are posted to CCPForge each time a new release is made The three EPOCH subdirectories all have a similar structure Inside each of the epoch 1 2 3 d directories there are 4 sub directories e src The EPOCH source code e IDL The IDL routines needed to open the SDF files which the code outputs e example_decks A sample data directory containing example input deck files e Data This is an empty directory to use for running simulations there are also 5 files e COMMIT Contains versioning information for the code 7 e Changelog txt A brief overview of the change history for each released version of EPOCH e Makefile A standard makefile e Start pro An IDL script which starts the IDL visualisation routines Execute it using idl Start e unpack_source_from_restart Restart dumps can be written to contain a copy of the input decks and source code used to generate them This script can be used to unpack that information from a given restart dump It is run from the command line and must be passed the name of the restart dump file 2 2 Libraries and requirements
137. ustrates a laser being driven at an angle on the x_min boundary Different wave fronts cross the y axis at different places and this forms a sinusoidal profile along y that represents the phase The wavelength of this profile is given by Ag A sin0 where A is the wavelength of the laser and is the angle of the propagation direction with respect to the x axis The actual phase to use will be y kgy 27y A It is negative because the phase of the wave is propagating in the positive y direction It is also necessary to alter the wavelength of the driver since this is given in the direction perpendicular to the boundary The new wavelength to use will be cos Figure 5 shows the resulting E field for a laser driven at an angle of 7 8 Note that since the boundary conditions in the code are derived for propagation perpendicular to the boundary there will be artefacts on the scale of the grid for lasers driven at an angle Using this technique it is also possible to focus a laser This is done by using the same technique as above but making the angle of propagation 0 a function of y such that the laser is focused to a point along the x axis 58 Var Heche Fek Ey Time 5 00428e 14 4 18e 10 1 41e 07 4 19e 10 8 378 10 Max 8 37e 10 Min 8 37e 10 Y o x10 6 m 0 X x10 6 m Figure 5 Angled laser profile Figure 6 Laser at an angle 4 5 Restarting EPOCH from previous output dumps Another possibl
138. xample begin species name Helium ionisation_energies 24 6 ev 54 4 ev dump F end species With this species block the electron species named Helium1 and Helium are automatically created These species will also inherit the dump parameter from their parent species so in this example they will both have dump F set This behaviour can be overridden by explicitly adding a species block of the same name with a differing dumpmask eg 23 begin species name Heliumi dump T end species Field ionisation consists of three distinct regimes multiphoton in which ionisation is best described as absorption of multiple photons tunnelling in which deformation of the atomic Coulomb potential is the dominant factor and barrier suppression ionisation in which the electric field is strong enough for an electron to escape classically It is possible to turn off multiphoton or barrier suppression ionisation through the input deck using the following control block parameters use_multiphoton Logical flag which turns on modelling ionisation by multiple photon absorption This should be set to F if there is no laser attached to a boundary as it relies on laser frequency The default is T use_bsi Logical flag which turns on barrier suppression ionisation correction to the tunnelling ionisation model for high intensity lasers The default is T 3 4 laser block Laser blocks attach an
139. y large and also override the dumpmask parameter specified for a species and output the data for that species anyway 4 6 Parameterising input decks The simplest way to allow someone to use EPOCH as a black box is to give them the input deck files that control the setup and initial conditions of the code The input deck is simple enough that a quick read through of the relevant section of the manual should make it fairly easy for a new user to control those features of the code but the initial conditions can be complex enough to be require significant work on the part of an unfamiliar user to understand In this case it can be helpful to use the ability to specify constants in an input deck to parameterise the file So to go back to a slight variation on an earlier example begin species name sl first set density in the range 0 gt 1 cut down density in x direction density if x gt 1 and x 1t 1 1 0 0 2 cut down density in y direction density if y gt 1 and y 1t 1 density s1 0 2 multiply density by real particle density density density s1 100 0 Set the temperature to be zero temp_x 0 0 temp_y temp_x s1 Set the minimum density for this species density_min 0 3 100 0 end species begin species 60 name s2 Just copy the density for species s1 density density s1 Just copy the temperature from species s1 temp_x temp_x s1 temp_y temp_y s1 Set the m
140. y prefixing the filename with ufs or nfs This parameter supplies the prefix to be used The default value is an empty string file_prefix Although this parameter is supported by the traditional style of output block its primary purpose is for use with multiple output blocks so it is documented in Section 3 7 9 A few additional parameters have been added for use with the new style of output block These are documented in Section 3 7 9 3 7 3 Particle Variables The next set are per particle properties If you wish to plot these according to their spatial positions you must include the particle_grid in your output variables All entries have a default dumpmask of never particle_grid Requests the output of particle positions This is a restart variable No particle variables can be plotted in VisIt unless this is dumped If any particle variables are written then the particle_grid is automatically written unless particle_grid never is specified The synonym particles may also be used 32 PX Py PZ The dumpmasks for the particle momenta Restart variable VX Vy VZ The dumpmasks for the particle velocities charge The dumpmask for the charge of a given particle This has no effect if the code is not compiled with the flag DPER PARTICLE CHARGE_MASS see Section 2 4 mass The dumpmask for the mass of a given particles This has no effect if the code is not compiled with th
141. y the same way as any of the variables read from the data file As an example we can combine the three components of electric field to generate a single electric field vector 87 e oo Expressions Expression List Definition Electric Field Vector Name Electric Field Vector Type Vector Mesh Variable V Show variable in plot menus Python Expression Editor Definition lt Electric Field Ex gt lt Electric Field Eyp lt Electric Field Ez gt New Delete Insert Function w Insert Variable y _ Display expressions from database Load Save Apply Post Dismiss Now when we return to the Add menu we see that the Vector and Streamline plot types now have an entry for our newly defined vector 7 9 Creating Movies A compelling visualisation of numerically generated data is often made by combining a series of images into a movie This can be an invaluable method for illustrating the basic behaviour of a system as it changes over time Alternatively rotating around a 3D scene can sometimes give a much better idea of the structure in the model being presented There can also be much to gain by constructing visual fly throughs of a scene dynamically slicing through sets of data or combinations of all these techniques VisIt provides several facilities for generating movies from your data The simplest of these is to select the File Save movie
142. ymmetric square matrix of size nspecies x nspecies containing the collision frequency factors to use between particle species The element s1 s2 gives the frequency factor used when colliding species s1 with species s2 If the factor is less than zero no collisions are performed If it is equal to one collisions are performed normally For any value between zero and one the collisions are performed using a frequency multiplied by the given factor If collide has a value of all then all elements of the matrix are set to one If it has a value of none then all elements are set to minus one If the syntax speciesl species2 lt value gt is used then the speciesl species2 element of the matrix is set to the factor lt value gt This may either be a real number or the special value on or off The collide parameter may be used multiple times The default value is all ie all elements of the matrix are set to one collisional_ionisation If this logical flag is set to T then the collisional ionisation model is enabled This process is independent of field ionisation Section 3 3 2 However in order to set up collisional ionisation you must also specify ionisation energies and electrons in a species block see Section 3 3 2 The default value is F For example collisions begin collisions use_collisions T coulomb_log auto collide all collide speci spec2 off
143. ys end output In this example three px blocks will be written Particles background electron Px Parti cles background proton Px and Particles high gamma electron Px The background blocks will contain 10 of the each species randomly selected The high gamma block will contain all the electrons with a gamma greater than 1 3 There will also be Particles background electron Py and Particles background proton Py block containing y momentum for the same 10 random subset of particles Finally the Parti cles All electron Pz and Particles All proton Pz will contain the z momentum for all particles The final selection criteria given in the list above is id_min and id_max As of EPOCH version 4 0 the code can now assign a unique ID field to every particle in the simulation This can be useful for tracking specific particles as they move through a simulation As this field adds extra memory require ments to the particles it is disabled by default and must be compiled in using the DPARTICLE_ID compiler flag Particle IDs can be written to file using the id variable name in the output block Eg begin output particles always id always end output 3 14 constant block The constant block type helps to make the input deck more flexible and maintainable It allows you to define constants and maths parser expressions see Section 3 15 which can

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