Genesis Manual

GENESIS 1.
3
User Manual
Oct-02
Contents
About this Manual
About GENESIS 1.3
The Particle Equations .
The Field Equations . .
Time-Dependent Effects
Pre- and Postprocessors
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Compilation, Installation and Execution

Compilation of the FORTRAN Source Code
Compilation of the C++ Source Code . . .
Installation . . . . . . . . . . . . . . . . . .
SDDS . . . . . . . . . . . . . . . . .
XML . . . . . . . . . . . . . . . . . .
HDF5 . . . . . . . . . . . . . . . . . .
MPI . . . . . . . . . . . . . . . . . .
Running GENESIS 1.3 . . . . . . . . . . . .
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Setting-up Simulations
Step I - The Magnetic Lattice . . . . . . . . . .
Step II - The Electron Beam . . . . . . . . . . .
Step III - The Radiation Field . . . . . . . . . .
Step IV - Optimization Using the SCAN-Feature
Step V - Time-dependent Simulation . . . . . .
Step VI - External Input for the Magnetic Field .
General Tips . . . . . . . . . . . . . . . . . . .
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Input Parameters
Undulator Parameters . . . .
Electron Beam Parameters .
Radiation Parameters . . . .
Particle Loading Parameters .
Mesh Parameters . . . . . .
Focusing Parameters . . . . .
Time-Dependence Parameters
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Simulation Control Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Scan Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Input and Output Control Parameters . . . . . . . . . . . . . . . . . . . . . . . . . .
Input and Output Files
The Main Input File . . . . . . . . . . . . . . . . . . . . . . . .
The Main Output File . . . . . . . . . . . . . . . . . . . . . . .
The Radiation and Particle Output File . . . . . . . . . . . . . .
The Log File . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Reading-in and Dumping the Particle and Radiation Distribution .
The Magnet Description Input and Output File . . . . . . . . . .
The Beam Description File . . . . . . . . . . . . . . . . . . . .
The External Distribution File . . . . . . . . . . . . . . . . . . .
The Time-Record File . . . . . . . . . . . . . . . . . . . . . . .
The SDDS File Format . . . . . . . . . . . . . . . . . . . . . .
The XML File Format . . . . . . . . . . . . . . . . . . . . . . .
The HDF5 File Format . . . . . . . . . . . . . . . . . . . . . .
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The GENESIS 1.3 Algorithm
49
Where to Find Further Information
51
About this Manual
This manual covers the FEL simulation code GENESIS 1.3. It explains how to set-up an
input deck as well as how to extend the capability by using additional input files. The central
part of this document is the reference list of all input parameters, which are accepted by
GENESIS 1.3. Further information about the code can be found at the website
http://pbpl.physics.ucla.edu/genesis
In particular the novice user of GENESIS 1.3 can find there sample input files, which is a
good starting point for setting-up his own input decks. Anyhow a basic understanding of
FEL physics is recommended for a successful operation of GENESIS 1.3.
Throughout this document different fonts are used to distinguish text from the plain text of
the manual. The italic font and Greek symbols refer to mathematical and physical constants
or expression, e.g.
E = mc2
Sample input and output files as well as all names referring directly to GENESIS 1.3 are
written in typewriter-style such as GAMMA0 or XLAMD.
The manual has a short section on the algorithm of GENESIS 1.3. Its purpuse is to let user
understand, what is calculated and what are the capabilities and limits of GENESIS 1.3. It
is not written to encourage people to modify or extend the code. Anyhow the code is not
perfect. If there is a demand to extend the code, please notefy the authors of the code.
GENESIS 1.3 Manual
About GENESIS 1.3
GENESIS 1.3 is a time-dependent three-dimensional FEL code. It is focused to simulate

single-pass free-electron lasers, both FEL amplifier and SASE FEL, although the flexible
input can be used to easily extend the capacity of GENESIS 1.3 to cover FEL oscillators or
multistage set-ups.
GENESIS 1.3 bears its origin in the steady-state 2D code TDA3D, although they have
nothing in common except for some naming convention. GENESIS 1.3 has all the features
of TDA3D and is intendent as a replacement, in particular that there is no more support
for TDA3D. For an easier transition GENESIS 1.3 adopted most of the input and output
format of TDA3D. TDA3D input file will most likely not work.
The code was written by Sven Reiche as a part of the Ph.D. thesis at DESY, Germany, and
then further extended at UCLA and DESY.
The Particle Equations

Macro particles represent the electron beam in all dimension of the 6D phase space. For
convenience the longitudinal position is replaced by the ponderomotive phase of the particle
and the transverse momenta are normalized to mc. The equations of motion are
d
dz
d
dz
dx
dz
dpx
dz
dy
dz
dpy
dz
1
= k 1
+ ku
z
kfc ar au
=
sin( + ) Ez
z
px
=
z
s
= qx x + bx + py
py
=
z
s
= qy y + by px
(1)
(2)
(3)
(4)
(5)
(6)
where z is the electron velocity in z, normalized to the speed of light, k is the radiation wave
number, ku is the undulator wave number, fc the coupling factor, ar and au are the scalar,
7
GENESIS 1.3 Manual
normalized amplitudes of the radiation and undulator field, is the phase of the radiation
field, Ez is the electrostatic field, bx and by are the normalized dipole strengths in x and y,
qx and qy are the quadrupole field strengths in x and y and s is the solenoid field strength.
The differential equations for energy and phase are solved by a 4th order Runge-Kutta
solver, where the field amplitude of the discretized radiation field and electrostatic field is
interpolated to the particle position.
Distinct to the main undulator field au , the quadrupole and dipole fields combines many field
sources such as the natural focusing of the undulator, strong focusing quadrupoles, undulator
field errors and corrector magnets (steering magnets). Per integration step their strength is
fixed and the differential equations for the transverse motion is solved analytically. Because
these equations depend on the particle energy, a higher precision requires to split the pushing
of the transverse variables into two half-steps. While the first step relies on the energy value
of the previous iteration, the second uses the updated values of the Runge-Kutta solver for
this iteration.
The Field Equations

Electro-static and electro-magnetic fields are discretized within GENESIS 1.3. The radiation
field is described in the paraxial approximation, where the field is separated into a dominant,
fast oscillating term and an amplitude, which slowly varies in magnitude and phase. The
partial differential equation
"
e2 0 X
fc au ij
+ 2ik
u=i
(~r ~rj )
e
z
m j
j
#
is of parabolic type where u = -iar exp[i] is the complex representation of the radiation field.
Note that there is no explicit dependence on t in the differential equation. Time-dependence
effects are discussed below. The transverse profile of the field is discretized on a Cartesian
grid with uniform spacing. The Alternating Direction Implicit (ADI) solver guarantees an
unconditional stable, fast and memory-efficient method to advance the radiation field one
integration step.
Only the longitudinal component of the electro-static field is taken into account within
GENESIS 1.3, because it acts as a repulsive force during the formation of the micro bunching.
On the scope of a single radiation wavelength the field can be assumed to be periodic in the
ponderomotive phase of the electrons. In the Fourier series expansion of the longitudinal
field the partial different equation of the l coefficient is
"
l2 k 2 (1 + a2u )
ec2 0 lk(1 + a2u ) X
+
E
=
i
(~r ~rj )eilj
z,l
R2
R2
j
#
About GENESIS 1.3
9
q
where the resonant energy is defined as R = k(1 + a2u )/2k. With a radial grid centered
to the electron beam centroid position and the azimuthal decomposition of the Fourier
coefficients Ez,l the matrix representation of the partial differential equation is reduced to
a tridiagonal matrix, where a fast and memory-efficient solver is applied to. Long-term
electro-static fields (e.g. wake fields) must be calculated externally. They can be imported
into GENESIS 1.3 and applied to equations of motion for the macro particles.
Time-Dependent Effects
GENESIS 1.3 supports two modes of calculations: steady-state and time-dependent simulations. Steady-state simulations are base on the assumption of an infinite long electron bunch
and radiation field with no longitudinal variation of any parameter. The partial derivative
with respect to the time drops out of the field equations resulting in the parabolic equation
shown above. The longitudinal description can be reduced to a single wavelength (bucket)
with periodic boundary condition in the ponderomotive phase of the macro particles.
Time-dependent simulations would require to keep the entire radiation field and electron
bunch at whole in memory, which easily exceeds the capability of todays best single processor
machines. For a solution, which is not bounded to memory constraints, GENESIS 1.3
discretizes the radiation field and electron beam in t, referring to them as slices. Because
information on the local electron distribution is carried by the radiation field only in the
forward direction (slippage) time-dependent simulations rolls over the electron bunch starting
from the back. Advancing the radiation field is split into two parts: solving the steady-state
field equation and copying the field to the next slice. Using the method only a single slice
of an electron beam and the radiation field over the total slippage length, which can be
significantly shorter than the bunch length, needs to be kept in memory. Although the
spacing of the slices can freely be chosen with GENESIS 1.3, some conditions have to be
fulfilled for a valid time-dependent simulation.
The propagation of the radiation field has to be done frequently to avoid collective instabilities of the steady-state field solver per integration step within a single slice. The characteristic
parameter of the FEL interaction is
au fc
1
=
4ku b
!2
Ip
IA
where b is the electron beam radius, Ip is the peak current and IA = 17 kA. The resulting
limitation for the integration step size, being much smaller than the gain length, is
z
1
2ku
10
GENESIS 1.3 Manual
Similar arguments are valid for the separation t of the slices, which is related to the
integration step size by the inequity ct (ku /k)z. The constraint for the t-discretization
is therefore
t
1
2ck
On the other hand each slice has a thickness of one radiation wavelength . The time discretization must be ct to avoid overlapping slices. Conflicts might arise if approaches
unity. Anyhow in this case the entire FEL model, on which GENESIS 1.3 is based, is not
valid anymore and other simulation tools need to be used to solve this problem.
Very often the time-window T, which is spawn by all slices, covers only a subsection of the
electron beam. Because GENESIS 1.3 does not know anything about the field, which slips
through the back of the time-window, it suppresses the output over the first slippage length.
To obtain valid output the time window must be at least as long as the slippage length Ts ,
yielding the constraint
T Ts =
k u Lu
k c
where Lu is the length of the undulator. In practice the time-window should be significantly
larger than the limit given above to allow a frequency analysis of the radiation. The typical
width of the FEL spectrum is . To resolve the spectrum the time-window must fulfill the
more stringent constraint
T
+ Ts
c
Once GENESIS 1.3 has allocated enough memory to hold the radiation field over one slippage
length there is no computational limitation imposed on the maximum size of the timewindow.
Pre- and Postprocessors

One of GENESIS 1.3 key feature is the extensive support of additional input files as well the
import of modified or process output files of GENESIS 1.3. The generation or processing
of these files can be done in the simplest case by hand or by external programs. Although
the GENESIS 1.3 website offers several programs for pre- and post-processing they do not
officially belong to the GENESIS 1.3 distribution. Experience shows that these programs
About GENESIS 1.3
11
are mostly customized and specifically bound to a given project or experiment. With the
description of the GENESIS 1.3 input and output files in this manual and the 3rd party
programs it should be fairly easy to write programs which fulfills the individual needs of the
user.
GENESIS 1.3 does not support the graphical preparation of the output data due to two
reasons. First, subroutines and function would rely on graphic libraries, which makes it
more difficult to write a platform independent source code. At least for the FORTRAN
version, using the original file format, it is the idea to have a code independent on any
library. In addition several graphic packages needs to be supported. Otherwise it would
force the user to use a graphic package, which does not necessary agree with his choice.
Second, time-dependent simulations generate typically more data than useful to be plotted.
It should be possible for the user to filter out the data, he needs. In addition some data
have to be prepared (e.g. Fourier transformation, averaging, binning for histogram plots) for
further information on the simulated FEL process. To help the GENESIS 1.3 offers several
programs, which can be the base for the users individual postprocessor.
12
GENESIS 1.3 Manual
The C++ version is currently under development. The manual will be

updated, when the source code has been written.
GENESIS 1.3 is distributed as executables for the Linux and Windows platform, as well as
the source code and can be obtained from the official website
http://pbpl.physics.ucla.edu/genesis
GENESIS 1.3 is originally written in FORTRAN but the limit capability of FORTRAN to
handle various input and output formats and a restricted string processing, resulted in a
C++ version of the code. The simulated physics of both the C++ and FORTRAN version
is the same and the only difference is in the extended set of file formats, supported by C++.
The support of the Fortran stops with the release of the current version.
The compilation section is only important for those who are building GENESIS 1.3 from
the source code. However the distributed executable might depend on addition libraries not
included in the distribution. The section on the installion lists all required libraries and
enviroment variables for running GENESIS 1.3
Compilation of the FORTRAN Source Code

After unpacking the .tar-archive the directory genesis contains the subdirectory base and
extension. The base directory has all the source code, which is needed to run GENESIS
1.3, supporting only the original fileformat for input and output. Additional source files are
located n the extension directory. For FORTRAN only two two extensions are supported:
the SDDS file format and the parallelized version, using MPI. By default all extensions are
disabled.
The source code has three different types of source files, indicated by their extension. Files
with the extension .f contain all functions, subroutine and local variables, while variables
used in more than one subroutine are grouped into common blocks in the files with the
extension .cmn. The last type of files is the single file genesis.def which defines constants
and function prototypes.
The memory requirement of GENESIS 1.3 can be demanding if time-dependen simulation are
performed or external distribution are imported and kept in memory. The file timerec.cmn
holds the information of the time records of the slippage field. NTMAX is the total record
13
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GENESIS 1.3 Manual
length, if the slippage filed is stored in memory. If simulation encounters the case that
this size is too small (GENESIS 1.3 will give an error message) NTMAX has to be increased.
Another possible way is to export the slippage field to a file. It is done by setting NOFILE
and NTMAX to unity. The file will be deleted at the end of the run. The default setting has a
time-record, which demands 160 MByte of free memory - equivalent to 700 records of a grid
with 121 times 121 grid points.
The default settings of GENESIS 1.3 is that the external distribution is read from a file
for every slice. Due to the processing of the input file it can be time-consuming. To keep
the distribution in memory after the first processing two parameters in genesis.def have to
be change. KEEPDIST has to be set to unity while NDMAX defines the maximum number of
particles GENESIS 1.3 can hold in memory. Note that 100000 particles correspond to an
additional memory demand of 5 MByte.
The FORTRAN follows in general the F77 standard although it is not fully ANSI-F77
compliant. This requires to set specific flags while invoking the compiler. Because compiler
option and flags are compiler specific the following list of recommended option just gives a
general description. Please refer to the manual of your compiler. The distribution contains a
Makefile, which works with the Absoft FORTRAN compiler under linux. If might be used
as a template for setting up the compiler and linking instruction.
Optimization should be turned on. In addition if the linker supports a library of
optimized mathematical function it should be used
The compiler should warn or preferable generate an error, if variables are not defined
explicitly.
In general it is a good idea that the compiler issues all warning, but due to the function
prototyping in genesis.def the warning of unused variable should be disabled.
GENESIS 1.3 relies on intrinsic double-precision complex numbers for assignment such
as A=DCMPLX(1.d0,0.d0). Most FORTRAN compilers support this by a special VAX
or complex option. As an alternative method the DCMPLX(...,...) statements must
be replaced by CMPLX(...,... kind=8) statements by hand.
It is recommended to generate a symbolic table (debugger option)
Some compilers do not automatically treat variables in DATA blocks as static, but
GENESIS relies on it. Either enable this option or, as an alternative, make all local
variables static (the size of the executable is increased only by a small amount).
GENESIS is not written consistently with the same case of all variables through out
the source code. A compiler option should fold all variable and function names to lower
or upper case letters if the compiler is case-sensitive.
The SDDS extension of GENESIS 1.3 is in the directory extension/SDDS. Compilation requires that the SDDS libraries are installed on the computer. In addition the FORTRAN
wrapper of SDDS must be linked to the executable to make GENESIS 1.3 work. Unfortunately FORTRAN compilers do not support compiler instructions as C++ compiler do. As
15
a consequnce the base source code must be edited to enable calls to the SDDS part of the
program. Which files and where to edit are described in the README.SDDS file in the root
directory of the genesis distribution.
The MPI version is under development. The manual will be updated, when
the source code has been finished.
Compilation of the C++ Source Code

The C++ version is under development. The manual will be updated,
when the source code has been finished.
Installation
The FORTRAN version of GENESIS is a single executable and can be located anywhere.
Under Linux it is preferable in the directory /usr/local/bin.
The C++ version is under development. The manual will be updated,
when the source code has been finished.
Both versions can rely on additional libraries, which have to be installed prior to running
GENESIS 1.3. The following lists all possible extensions and links, where further information
can be obtained.
SDDS
The Self-Describing Data Set (SDDS) is a file format, where a header defines the properties
of the following data section. The SDDS toolkit allows processing and displaying content of
SDDS files. The offical link is
http://www.aps.anl.gov/asd/oag/oagPackages.shtml
XML
The eXtensible Markup Language (XML) is a popular file format for platform independent
data, mainly in ASCII. XML files can be checked with any XML reader (e.g. Internet
Explorer) whether the file does not violates the basic syntax of XML. In addition files can
16
GENESIS 1.3 Manual
be validated, so that the data has to fulfill user-defined contraints. The standard for XML
and is associated formats can be found at
http://www.w3c.org
GENESIS 1.3 is build with the Xerces XML libraries of the Apache distribution. The libraries
can be downloaded from the Xerces website
http://xml.apache.org
HDF5
The Hirachial Data Format (HDF5) is a standard for platform independent binary data. It is
benefical to GENESIS 1.3 because it also allows parallel computation and data compression.
The offical website is
http://hdf.ncsa.uiuc.edu/HDF5/
MPI
The Message-Passing Interface is a standard for portable code for parralel computer architecture.
http://www-unix.mcs.anl.gov/mpi/
Running GENESIS 1.3

GENESIS 1.3 requires at least one argument, which is the name of the main input file.
In the C++ version it is a command line argument, while the FORTRAN version promt
for the filename. If additional information is needed the program will propt for the missing
information. The progress as well as warning and error messages are directed to the standard
output channel or redirect to a file if the ILOG parameter is set.
The C++ versions allows addition comand line arguments for more flexability
The C++ version is currently under development. The manual will be
updated when the source code has been finished.
On UNIX and LINUX platforms GENESIS 1.3 can be easily executed in the background by
redirecting the standard input, output and error to files such as
17
[prompt]$ genesis < GENINPUT > GENOUTPUT 2 >&1 &
where GENINPUT contains line by line all file name, which are normally be prompted for
by GENESIS. Any output and error message will be written to the file GENOUTPUT. If ILOG
is set a log-file is created and GENOUTPUT remains empty.
18
GENESIS 1.3 Manual
This section is a guideline for the novice user of GENESIS 1.3 to set up the main input
correctly so that reasonable results can be obtained. It does not cover all aspects of GENESIS
1.3. For a more complete reference please check the sections on the input parameters of the
main input deck and the usage of additional input and output files. Certain parameters are
not mentioned in this section. If they are omitted in the input deck they fall back to their
default values. To obtain a valid input deck in the first place start GENESIS 1.3 and type at
the prompt the filename of a non-existing file. The template file template.in is generated,
which can be edited by any text-editor.
Step I - The Magnetic Lattice

The coarse layout of the undulator is defined by the undulator period length (XLAMD), the
number of periods (NWIG) and number of modules (NSEC). In this coarse lattice the FODO
lattice has to fit in a way that a new undulator module starts after the last FODO cell of
the section is complete. The length of a FODO cell is determined by FL + DL +2*DRL. Thus
the number of FODO cells per undulator section is given by the next higher integer of the
ratio between NWIG and the FODO-cell length. As an example with NWIG = 100, NSEC = 2,
FL = 4.0, DL = 4.0 and DRL = 8.0 there are 5 FODO cells per section and the two undulator
modules are separated by a gap of 20 undulator periods. If F1ST is set to half the value of
FL the FODO cell starts in the center of the first quadrupole, which simplifies the matching
of the electron beam (ALPHAX, ALPHAY=0).
Set AWD to the same value as AW0. Similar XKX and XKY should agree with the definition of
the undulator (0.0, 1.0 for planar undulator (IWITYP = 0) or 0.5, 0.5 for helical undulator
(IWITYP = 1)). It is recommended that the coupling factor is calculated automatically by
setting FBESS0 to zero. Disable tapering and undulator field errors.
Finally set the integration step with DELZ so that it can resolve FL, DL, DRL and F1ST. In the
example above possible choices are 0.5, 1.0 or 2.0.
Step II - The Electron Beam

After the energy, energy spread and emittances are defined a good value for the beam size
and the twiss parameters ALPHAX, ALPHAY are critical for a good performance. GENESIS 1.3
does not support matching and these values have to be found by external programs. Anyhow
19
20
GENESIS 1.3 Manual
if the FODO lattice start with half a quadrupole or the field strength of all quadrupoles is set
to zero than the beam is going through a waist at the undulator entrance for best matching
(ALPHAX, ALPHAY=0). In this case initial runs of GENESIS 1.3 allows for an iterative method
to find the right values for the beam size while ignoring the radiation results.
It is recommended that the number of macro particles (NPART) is at least 2048 (powers of
two numbers allows a better performance). For simulation of wavelengths below 10 nm the
number must be even higher to exclude numerical noise.
Step III - The Radiation Field

In an FEL oscillator the radiation parameter are well defined by the seeding radiation field
and the enclosing cavity. Otherwise (FEL amplifier or SASE FEL) they typically need to be
optimized. Although SASE simulation significantly reduces the impact of the waist position
ZWAIST and the Rayleigh length ZRAYL parameters it is recommended as a pre-optimization
step to run steady-state simulation (ITDP = 0). Thus the following is valid for both, FEL
amplifier and SASE FEL.
A good estimate of the radiation wavelength is given by the resonant formula

u
2
1
+
a
u
2 2
with =XLAMDS, =GAMMA0, u =XLAMD and au =AW0. Anyhow diffraction or emittance effects
might slightly change the resonant wavelength. The Raylength length should be chosen so
that the initial beam size is similar to the beam size of the gain-guided radiation field in
the exponential amplification regime. If the radiation
q waist is at the undulator entrance
(ZWAIST=0) the initial beam size is simply given by zr / with zr =ZRAYL.
While the input radiation power is a well-defined input parameter for an FEL amplifier
its value has to be estimated for steady-state simulation modelling SASE FELs. With the
definition of the FEL parameter
1
au fc u
=
8b
!2
Ip
IA
an approximation of an equivalent input power (shot noise power) of the SASE FEL is
Pin = 6 2
Pb
q
N log(N/)
21
with fc =FBESS0 or the value GENESIS 1.3 would calculate in the case that FBESS0 is set to
zero in the input deck, b =(RXBEAM + RYBEAM)/2, Ip = CURPEAK, IA = 17 kA, Pb =Ip mc2 /e as
the electron beam power and N=Ip /ce as the number of electronsper radiation wavelength.
With the parameters for the magnetic field, electron beam and radiation field a run of
GENESIS 1.3 should produce some gain. If the results are satisfying the input deck can
be used for more advanced simulation (field errors, time-dependent simulation). Otherwise
further optimization of the input parameters is needed.
Step IV - Optimization Using the SCAN-Feature

It can be tedious to find the optimum set of beam energy and radiation wavelength for
maximum gain. The scan feature of GENESIS 1.3 helps by performing several runs for
different wavelength or energies. To start a scan the scan parameter has to be defined. It is
simply done be assigning the name of the parameter to be scanned to SCAN. As an example
SCAN = XLAMDS scans over the radiation wavelength. Only two other parameters are needed
to complete the input for a scan-run. NSCAN defines the number of runs of the scan while
SVAR limits the scan range. As an example SVAR = 0.1 and NSCAN = 5 will result in five
runs at wavelengths of 90%, 95%, 100%, 105% and 110% of the input wavelength XLAMDS.
The scan feature will automatically adjust the input deck internally to start with the same
initial conditions at each run.
Step V - Time-dependent Simulation

To enable time-dependence simply set ITDP to one. In addition IALL should be zero,
SHOTNOISE 1.0 and PRAD0 zero for SASE simulations. The start-up regime has typically
modes with strong diffraction. Therefore it is recommended to increase the grid size RMAX0
or DGRID by roughly 50-100%. To compensate the coarser grid NCAR can be increased as
well.
The desired time-window requires some minor calculations. For easier calculation time is
scaled by the speed of light (s=ct). Assuming a time-window, which starts at the tail s0 and
ends at the head s1 the required number of slices is NSLICE = (s1 -s0 )/(ZSEP*XLAMDS). The
first slice has the position s0 . Therefore NTAIL is s0 /(ZSEP*XLAMDS). Note that in the frame
of GENESIS 1.3 s0 has to be smaller than s1 .
The parameter IOTAIL is an indication for GENESIS 1.3 whether radiation is generated
outside the time-window but might slip at s0 into the time-window while the beam propagates
through the undulator. This is the case if only a subsection of the electron beam is simulated.
Because GENESIS 1.3 can do only a wild guess about the radiation field which slips into
the time-window the tail part of the time-window is physically incorrect. To exclude these
22
GENESIS 1.3 Manual
slices in the output IOTAIL should be set to zero. The number of suppressed slices is simply
the number of undulator periods of the entire undulator divided by ZSEP.
As an example we assume a Gaussian beam profile with an rms length of 1 mm (CURLEN =
1.e-3) and a radiation wavelength of 5 m for an undulator with 200 periods. The spacing
between the slices is ZSEP=2.0. The output should be between -2 mm and 2 mm which
cuts out a part of the bunch (IOTAIL=0). The total number of slices is 400 slice of output
plus 100 suppressed slices (NSLICES=500). The first simulated slices is NTAIL=-300 which is
equivalent to s0 =-3mm.
In this example the time-window is actually very close to cover the entire beam. With s0 =-3
mm the local beam current is only 1% of the peak current. It is a good assumption that
the tail s<s0 will not significantly amplify any radiation. With only 100 more slices the
entire bunch can be simulated. The parameters would be now: NSLICE=600, NTAIL=-300
and IOTAIL=1.
Step VI - External Input for the Magnetic Field

One of the strength of GENESIS 1.3 is the usage of external input files for a more flexible
description of the FEL such as a more complicated magnetic lattice. The best way to start
using magnetic field input files is to generate one by GENESIS 1.3. This is done by specifying
in MAGOUTFILE the name of the file to be generated. This file can be edited to set up the
undulator. Using the two section undulator from above (AWD=0.85, XLAMD=0.02) the file
contains the lines
...
AW 8.5000E-01
AW 0.0000E-01
AW 8.5000E-01
AW 0.0000E-01
...
2.0000E-02 100
2.0000E-02 20
2.0000E-02 100
2.0000E-02 20
Example: To remove the gaps and to taper the second module so that the field strength is
5% smaller change the lines to
...
AW 8.5000E-01
AW 8.0750E-01
...
2.0000E-02 120
2.0000E-02 120
23
The modified file can then be loaded into GENESIS 1.3 for the next run. The filename of the
edited file is assigned to MAGINFILE. It is recommended to remove the parameter MAGOUTFILE
from the input deck or change the assigned filename before running the simulation. Otherwise
the file is overwritten again. In this case it does not matter but there are some cases (e.g.
field errors) where there are subtle difference in the file used for the input and the overwritten
output. For more information refer to the section on input and output files.
General Tips
At the end of this section some general hints and tips are listed. There are in no particular
order or relation to each other.
Time-dependent simulations are very CPU-expensive. To optimize an input deck, try
to do it in steady-state mode (ITDP=0).
The calculation of the diffraction angle of the radiation field as part of the diagnostic
is CPU intensive and not needed for the simulation itself. To speed up the execution
it is better to save the radiation field at various locations along the undulator. The
diffraction angle can then be obtained in a post-processing step.
The output of the particle and field distributions can generate huge output files. Although GENESIS 1.3 warns about large output files it does not check the available
space of the hard disk. Either run GENESIS 1.3, check for warning about large output
files and stop the program (if the space is not available) or reduce the size of the output
file by increasing the value of IPRADI, ISRADI, IPPART and/or ISPART.
Avoid to use the same parameter several times in the input deck. GENESIS 1.3 will
use the last occurrence in the input deck or might even report an error and quit.
Check whether space charge has a significant impact on the result of the steady-state
case. Space charge can be disabled by setting NSCZ to zero. If the results are not
effected by the space charge routine time-dependent simulations excluding the space
charge routine run faster.
For runs with different field errors change the value of ISEED before each run. The
same is valid for the phase fluctuation in SASE simulations where IPSEED has to be
changed.
Although the loading parameters ILDPSI, ILDGAM, ILDX, ILDY, ILDPX and ILDPY need
hardly to be changed at all, do not assign the same number to more than one parameter.
It is recommended to set the VERSION parameter to the latest version number to avoid
unexpected behavior (e.g. IDUMP=1 will not dump the particle distribution if VERSION
is smaller than 1.0).
ZRAYL and ZWAIST are needed to calculated the grid size for the simulation although
their primary meanings are obsolete for SASE simulation. If DGRID is used and PRAD0
is very small than indeed they have no impact on the simulation. Still ZRAYL is required
to be larger than 0.
24
GENESIS 1.3 Manual
Input Parameters
The main input file of GENESIS 1.3 is controlled by roughly 100 parameters. Some of
them become obsolete if additional input files are used. In the case that the main input file
cannot be found GENESIS 1.3 creates a template for the main input file and terminates.
Parameters, which are not included in the input file, fall back on their default values. All
allowed input parameters and their default values, formats and units are listed below.
Undulator Parameters
AW0 (0.735 float unitless)
The normalized, dimensionless rms undulator parameter, defined by AW0 = (e/mc)(Bu /ku ),
where e is the electron charge, m is electron mass, c is speed of light, ku =2/u is the
undulator wave number, u is the undulator period. Bu is the rms undulator field with Bu
= Bp /2 for a planar undulator and Bu = Bp for a helical undulator, where Bp is the on-axis
peak field.
IWITYP (0 integer unitless)

Flag indicating the undulator type. A value of zero indicates a planar undulator, any other
value a helical one.
XKX (0.0 float unitless)

Normalized natural focusing of the undulator in x. Common values are XKX = 0.0, XKY = 1.0
for a planar undulator or XKX, XKY = 0.5 for a helical undulator, but might vary if focusing
by curved pole faces is simulated. The values should fulfill the constraint XKX + XKY = 1.0.
XKY (1.0 float unitless)

Normalized natural focusing of the undulator in x. See XKX for more information.
FBESS0 (0.0 float unitless)

The coupling factor of the electron beam to the radiation field due to the longitudinal wiggle
motion of the electrons. It is 1.0 for a helical undulator and J0 (x) - J1 (x) for a planar
undulator where J0 (x), J1 (x) are Bessel functions and x = AW02 /2(1+AW02 ). If FBESS0 is set
to 0.0 GENESIS 1.3 calculates the value.
XLAMD (2.05e-2 float meter)

The undulator period length.
NWIG (98 integer unitless)

The number of periods within a single undulator module. The product of NWIG and XLAMD
defines the length of the undulator module.
25
26
GENESIS 1.3 Manual
NSEC (1 integer unitless)

The number of sections of the undulator. Note that a section length in not automatically
identical with the undulator module length. GENESIS 1.3 aligns modules to the FODOlattice. If a module ends within a FODO cell the next module starts with the beginning
of the next cell. Sometimes this results in a longitudinal gap between adjacent undulator
modules.
AWD (0.735 float unitless)

A virtual undulator parameter for the gap between undulator modules. The only purpose
of this parameter is to delay the longitudinal motion of the electrons in the same manner as
AW0 does within the undulator modules. It is used to keep the electron and radiation phases
synchronize up to the point when the interaction at the next undulator module starts again.
AWD has typically the same value as AW0, but might vary for optimum matching between the
modules.
WCOEFZ(1) (0.0 float meter)

Start of undulator tapering. Note that tapering is applied, even the magnetic lattice is
defined by an external file.
WCOEFZ(2) (0.0 float unitless)

The relative change of the undulator field over the entire taper length (AW(exit) = (1 WCOEFZ(2)) AW(entrance)). In the case of a multi section undulator GENESIS 1.3 tapers
the magnetic field over the gaps as well, resulting in a jump of the magnetic field AW(z)
between two modules.
WCOEFZ(3) (0.0 float unitless)

The taper model:
= 1 for linear taper,
= 2 for quadratic taper,
or no taper otherwise.
IERTYP (0 integer unitless)

Type of undulator field errors. Either a uniform (+/-1) or Gaussian (+/- 2) distribution can
be chosen. If IERTYP is negative the errors are correlated to minimize the first and second
field integral. IERTYP =0 disables field errors. Field errors requires a integration step size of
half an undulator period (DELZ = 0.5). Note that field errors are applied even if the magnetic
lattice is defined by an external file.
DELAW (0.0 float unitless)

RMS value of the undulator field error distribution. A value of zero disables field errors.
ISEED (-1 integer unitless)

The initial seeding of the random number generator for field errors.
Input Parameters
27
Electron Beam Parameters

NPART (8192 integer unitless)
The number of macro particles per slice. NPART must be a multiple of 4*NBINS and smaller
than NPMAX defined in the source file genesis.def.
GAMMA0 (35.2 float unitless)

The mean energy of the electron beam in terms of the electron rest mass energy.
DELGAM (5.0e-3 float unitless)

The RMS value of the energy distribution in terms of electron rest mass energy.
RXBEAM (112.1e-6 float meter)

The rms value in x of the transverse, spatial distribution.
RYBEAM (112.1e-6 float meter)

The rms value in y of the transverse, spatial distribution.
EMITX (2.0e-6 float meter)

The normalized rms emittance in x .
EMITY (2.0e-6 float meter)

The normalized rms emittance in y.
ALPHAX (0.0 float unitless)

Rotation of the transverse phase space distribution in x according to the standard definition
ALPHAX = -<xx> GAMMA0 / EMITX.
ALPHAY (0.0 float unitless)

Rotation of the transverse phase space distribution in y. See ALPHAX for more information.
XBEAM (0.0 float meter)

Transverse position in x of the electron beam at the undulator entrance with respect to the
undulator axis.
YBEAM (0.0 float meter)

Transverse position in y of the electron beam at the undulator entrance with respect to the
undulator axis.
PXBEAM (0.0 float unitless)

Average normalized transverse momentum x of the electron beam at the undulator entrance.
The momenta are defined as PXBEAM = x where x = cvx is the average transverse velocity
and the Lorenz factor of the electron energy.
PYBEAM (0.0 float unitless)

Average normalized transverse momentum in y of the electron beam at the undulator entrance. See PXBEAM for more information.
28
GENESIS 1.3 Manual
CURPEAK (250.0 float Amperes)

Peak current of the electron beam. Time-independent simulations enforces a constant current.
CUTTAIL (-1.0 float unitless)

Cut in the transverse phase space in measures of the rms size to collimate transverse beam
tails/halos. The cut is applied after the loading and beam current is set accordingly to the
reduced number of macro particles. It is disabled if the value is negative or the electron
beam is imported from an external file.
Radiation Parameters
XLAMDS (12.852e-6 float meter)
The resonant radiation wavelength. Due to the bandwidth of time-dependent simulation
SASE simulations do not require a very precise value for XLAMDS.
PRAD0 (10.0 float Watt)

The input power of the radiation field. For SASE simulation PRAD0 should be set to zero
value or at least well below the shot noise level.
ZRAYL (0.5 float meter)

The Rayleigh length of the seeding radiation field. ZRAYL is defined as w0 2 /XLAMDS where
w0 is the radius of the optical beam waist. The Rayleigh length is a measure for the diffraction w(z)2 = w0 2 (1 + (z - ZWAIST)2 /ZRAYL2 ) and is needed to calculate the size and divergence/convergence of the seeding field at the undulator entrance. Because the field size can
determine the grid size it is strongly recommended to supply reasonable numbers for ZRAYL
and ZWAIST even for simulation starting from noise.
ZWAIST (0.0 float meter)

Position of the waist of the seeding radiation field with respect to the undulator entrance.
ZWAIST is needed in combination with ZRAYL to calculate the initial radiation field. Note
that a waist position within the undulator (ZWAIST > 0) is only used to determine the initial
convergence. The FEL interaction might significantly change the beam size and diffraction
of the radiation field (gain guiding).
Particle Loading Parameters

ILDPSI (7 integer unitless)
Indices of the Hammersley sequence bases for loading the particle phase. GENESIS 1.3 uses
the first 26 prime numbers as bases. To avoid correlation between the variables each base
should be different.
Input Parameters
29
ILDGAM (5 integer unitless)

Hammersley base for loading the energy distribution. See ILDPSI for more information.
Note that the loading of the energy distribution is Gaussian and uses two bases (ILDGAM and
ILDGAM + 1).
ILDX (1 integer unitless)

Hammersley base for loading the distribution in x. See ILDPSI for more information.
ILDY (2 integer unitless)

Hammersley base for loading the distribution in y. See ILDPSI for more information.
ILDPX (3 integer unitless)

Hammersley base for loading the distribution in px . See ILDPSI for more information.
ILDPY (4 integer unitless)

Hammersley base for loading the distribution in py . See ILDPSI for more information.
ITGAUS (1 integer unitless)

Defines distribution profile in the transverse variables. The available distributions are:
- Gaussian (ITGAUS=1)
- Uniform (ITGAUS=2)
- Parabolic (otherwise)
IALL (0 integer unitless)

A non-zero value of IALL enforces that all slices are starting with the same element of the
Hammersley sequences. It is recommend for time-dependent simulation excluding shot noise.
IALL is set automatically for scans.
IPSEED (-1 integer unitless)

Initial seed for the random number generator used for particle phase fluctuation (shot noise).
GENESIS 1.3 requires a re-initialization of the random number generator to guarantee the
same loading whether magnetic field errors are used or not.
NBINS (4 integer unitless)

Number of bins in the particle phase. The value has to be at least 4 or larger than (2+2n),
depending on whether the bunching at the nth harmonics is needed for space charge calculations or output.
Mesh Parameters
NCAR (151 integer unitless)
The number of grid points for the radiation field along a single axis. The total number for
the mesh is NCAR2 . NCAR must be an odd number to cover the undulator axis with one grid
point. Do not exceed NCMAX defined in the source file genesis.def.
30
GENESIS 1.3 Manual
LBC (0 integer unitless)

Flag to set the boundary condition for the field solver. The options are Direchlet boundary
condition (LBC = 0) and Neumann boundary condition (otherwise). Anyhow the grid should
be chosen large enough so that the choice of LBC should not change the results.
RMAX0 (9.0 float unitless)

GENESIS 1.3 estimates the size of the grid on which the radiation field is discretized by
scaling the averages size of the initial radiation field and beam size with RMAX0. The explicit
size is [-DGRID,DGRID] in both dimensions with DGRID = RMAX0( r,beam + r,f ield ). The electron
beam size is the rms sum of RXBEAM and RYBEAM while the radiation field size is calculated
with ZRAYL and ZWAIST.
DGRID (0.0 float meter)

Any value larger than zero explicitly sets the grid size, overruling the calculation by the
RMAX0-parameter.
NSCZ (1 integer unitless)

Number of longitudinal Fourier components for space charge calculation. NSCZ must be
greater than 0 to include space charge but less than (2NBINS+2) for valid results.
NSCR (1 integer unitless)

Number of azimuthal modes for space charge calculation.
NPTR (40 integer unitless)

Number of radial grid points, on which the space charge field is evaluated. The radial axis is
automatically chosen by GENESIS 1.3 to be twice as long as the maximum offset of macro
particles relative to the center of the electron beam. This excludes effects of the boundary
condition even for the case of narrow beams.
Focusing Parameters
QUADF (1.23 float Tesla/meter)
The field strength of (F-)quadrupoles, focusing in the x-plane.
QUADD (0.0 float Tesla/meter)

The fields strength of (D-)quadrupoles, defocusing in the x-plane. GENESIS 1.3 automatically applies the correct signs to QUADF and QUADD indicating the alternating focusing in the
FODO-lattice.
FL (98.0 float unitless)

Length of the F-quadrupoles in measures of the undulator period. The integration step size
DELZ must resolve the quadrupole length.
DL (0.0 float unitless)

Length of the D-quadrupoles in measures of the undulator period.
Input Parameters
31
DRL (0.0 float unitless)

Drift length between F- and D-quadrupoles in measures of undulator period.
F1ST (0.0 float unitless)

Position within a FODO cell, where GENESIS 1.3 starts the FODO cell lattice. To start
with a full F-quadrupole set F1ST to zero while a value of FL/2 begins the cell in the middle
of the focusing quadrupole.
QFDX (0.0 float meter)

Maximum transverse misplacement of the quadrupoles in x-direction. A random offset between [-QDFX,QDFX] in x is applied to every quadrupole. Quadrupole position errors are
generated even if the magnetic field is defined by an external file.
QFDY (0.0 float meter)

Maximum transverse misplacement of the quadrupoles in y-direction, respectively. See QFDX
for more information.
SOLEN (0.0 float Tesla)

On-axis field strength of a superimposed solenoid field.
SL (0.0 float unitless)

Length of solenoid field in measures of undulator period. The solenoid is aligned to the
beginning of each undulator section.
Time-Dependence Parameters
ITDP (0 integer unitless)
A non-zero value enables time-dependent simulation. Time-dependence is not allowed if the
scan-feature is enabled.
CURLEN (1.0e-3 float meter)

Bunch length of the current profile. If CURLEN is positive a Gaussian distribution is generated
with an rms length given by CURLEN. A negative or zero value yield a constant profile.
ZSEP (1.0 float unitless)

Separation of beam slices in measures of the radiation wavelength. ZSEP must be a multiple
of DELZ.
NSLICE (408 float unitless)

Total number of simulated slices. It defines the time window of the simulation with NSLICE
* ZSEP * XLAMDS/c. Note that the output does not start with the first slice unless the
parameter IOTAIL is set. If NSLICE set to zero it automatically adjust NSLICE and NTAIL
to the time-window given by the external input files (BEAMFILE or DISTFILE). It assumes
32
GENESIS 1.3 Manual
6 standard deviation for a Gaussian distribution or the absolute value of CURLEN for a step
profile.
NTAIL (-253 integer unitless)

Position of the first simulated slice in measures of ZSEP*XLAMDS. GENESIS 1.3 starts with
the tail side of the time window, progressing towards the head. Thus a negative or positive
value shifts the slices towards the tail or head region of the beam, respectively. For a constant
profile (CURLEN < 0) NTAIL has no impact.
SHOTNOISE (1.0 float unitless)

GENESIS 1.3 applies a random offset to each macro particle phase to generate the correct
statistic for the bunching factor. Each offset is scaled prior by SHOTNOISE, thus SHOTNOISE
can be set to zero to disable shot noise.
Simulation Control Parameters

DELZ (1.0 float unitless)
Integration step size in measure of the undulator period length.
ZSTOP (0.0 float meter)

Defines the total integration length. If the undulator length is shorter than ZSTOP or ZSTOP
is zero or negative, the parameter is ignored and the integration is performed over the entire
undulator.
IORB (0 integer unitless)

Flag for orbit correction. For any non-zero value the offset due to the wiggle motion is taken
into account for the interaction between electron beam and radiation field. The correction
is not included in the output values for the beam centroid position.
ISRAVG (0 integer unitless)

If set to a non-zero value the energy loss due to spontaneous synchrotron radiation is included
in the calculation.
ISRSIG (0 integer unitless)

If set to a non-zero value the increase of the energy spread due to the quantum fluctuation
of the spontaneous synchrotron radiation is included in the calculation.
ELOSS (0.0 float eVolt/meter)

Externally applied energy loss of the electron beam.
VERSION (0.1 float unitless)

Used for backward compatibility of the input decks. Some parameters might change their
behavior for older versions of GENESIS 1.3. The current version is 1.0.
Input Parameters
33
Scan Parameters
ISCAN (0 integer unitless)
Selects the parameter for a scan over a certain range of its value:
1. GAMMA0
2. DELGAM
3. CURPEAK
4. XLAMDS
5. AW0
6. ISEED
7. PXBEAM
8. PYBEAM
9. XBEAM
10. YBEAM
11. RXBEAM
12. RYBEAM
13. XLAMD
14. DELAW
15. ALPHAX
16. ALPHAY
17. EMITX
18. EMITY
19. PRAD0
20. ZRAYL
21. ZWAIST
22. AWD
23. BEAMFILE
24. BEAMOPT
25. BEAMGAM
The last two enable a user-defined scan, where a steady-state run is performed for each
entry of the supplied BEAMFILE. BEAMOPT differs from BEAMFILE that it automatically adjust
XLAMDS according to the resonance condition and the beam energy, defined in the BEAMFILE.
The BEAMGAM option is similar to BEAMFILE, but overwrites the value of energy with GAMMA0
from the main input file.
34
GENESIS 1.3 Manual
SCAN ( string)
By supplying the parameter name to scan over it overrules the setting of ISCAN.
NSCAN (3 integer unitless)

Number of steps per scan.
SVAR (0.01 float unitless)

Defines the scan range of the selected scan parameter. The parameter is varied between
(1-SVAR) and (1+SVAR) of its initial value. One exception is the scan over ISEED where the
random number generator is not reinitialized.
Input and Output Control Parameters

IPHSTY (1 integer unitless)
Generate output in the main output file at each IPHSTYth integration step. To disable output
set IPHSTY to zero.
ISHSTY (1 integer unitless)

Generate output in the main output file for each ISHSTYth slice.
IPPART (0 integer unitless)

Write the particle distribution to file at each IPPARTth integration step. To disable output
set IPPART to zero. The filename is the same of the main outputfile + the extension .par.
ISPART (0 integer unitless)

Write the particle distribution to file for every ISPART slice.
IPRADI (0 integer unitless)

Write the field distribution to file at each IPRADIth integration step. To disable output set
IPRADI to zero. The filename is the same of the main outputfile + the extension .fld.
ISRADI (0 integer unitless)

Write the field distribution to file for every ISRADI slice.
IOTAIL (0 integer unitless)

If set to a non-zero value the output time window is the same as the simulated time window.
Otherwise the output for the first slices covered by the slippage length is subpressed. Needed
for bunches which are completely covered by the time-window.
OUTPUTFILE ( string)
The name of the main output file. The prompt for the output filename at the beginning of
a GENESIS 1.3 run will be suppressed.
Input Parameters
35
MAGIN (0 integer unitless)

If set to a non-zero value the user is prompted to type in the file name containing a explicit
description of the magnetic field.
MAGOUT (0 integer unitless)

Similar to MAGIN to write out the magnetic field lattice used for the simulation.
MAGINFILE ( string)
Defines a file, which contains the magnetic field description, bypassing the interactive request
of MAGIN.
MAGOUTFILE ( string)
Defines the file to which the magnetic field lattice is written to, bypassing the interactive
request of MAGOUT.
IDUMP (0 integer unitless)

If set to a non-zero value the complete particle and field distribution is dumped at the
undulator exit into two outputfiles. The filenames are the filename of the main output file
plus the extension .dpa and .dfl, respectively.
IDMPFLD (0 integer unitless)

Similar to IDUMP but only for the field distribution.
IDMPPAR (0 integer unitless)

Similar to IDUMP but only for the particle distribution.
BEAMFILE ( string)
Specifying a file containing a lookup table for the electron beam parameters at different
position along the bunch.
DISTFILE ( string)
If DISTFILE is defined, the 6d distribution is imported into GENESIS 1.3 and used to load
the phase space. The quiet start algorithm is bypassed.
NDCUT (0 integer unitless)

When loading a slice, only particles of the external distribution are used, which falls within
a small time-window centered around the current position of the slice. If NDCUT has a
value larger than zero the width is calculated by (tmax -tmin )/NDCUT, where tmax and tmin are
determined, while scanning through the particle distribution. If NDCUT is zero, the timewindow is adjusted, so that in average NPART/NBIN particles fall in each slice.
FIELDFILE ( string)
Defines the file containing the field distribution. The distribution is directly imported into
the arrays, holding the field and the time-records.
PARTFILE ( string)
Defines the file containing the particle distribution. The distribution is directly imported
into the arrays holding the particle variables.
36
GENESIS 1.3 Manual
ILOG (0 integer unitless)

If set to a non-zero value all further run-information and error messages are redirect to a log
file. The name is the main output file name plus the extension .log.
FILETYPE (ORIGINAL string)

Indication of the file type of all output files.
NHARM (1 integer unitless)

Defines the number of harmonics in the bunching factor to be calculated for output purposes.
LOUT (1 1 1 1 1 0 1 1 1 1 1 0 0 0 0 0 0 0 0 array of integers unitless)

Defines, which parameter is included in the main output file:
1. radiation power
2. logarithmic derivative of the power growth
3. power density at the undulator axis
4. radiation phase at the undulator axis
5. transverse radiation size
6. rms diffraction angle of the radiation
7. beam energy
8. bunching factor
9. beam size in x
10. beam size in y
11. error in energy conservation
12. beam position in x
13. beam position in y
14. energy spread
15. on-axis field intensity in the far field zone
16. bunching at the 2nd harmonic
17. bunching at the 3rd harmonic
18. bunching at the 4th harmonic
19. bunching at the 5th harmonic
Note that the calculation of the diffraction angle is very CPU intensive. It is recommended
to save some radiation profile distributions and apply the Fourier transformation in the
post-processing part.
FFSPEC (0 integer unitless)

If set to zero the on-axis phase is calculated in the near field zone. Otherwise the far-field
zone is used.
The capability of GENESIS 1.3 can widely be extended by additional input and output files.
In total GENESIS 1.3 depends on up to 14 files including such files containing the magnetic
field or a sample phase space distribution of the electron beam.
For all runs the main input file is mandatory. It contains the vast majority of the information
needed to run the simulation. Besides the main output file, which is always created, the main
input files defines, whether additional input and output files are read or written. All output
files except for the magnetic output file, uses the filename of the main output file as the
root for their filenames and appends a three letter filename extension. Input files can have
independent filenames, which are defined in the main input. The main output file and the
magnetic input and output files are not needed to be specified in the input file. GENESIS
prompts for the name if necessary.
Genesis 1.3 has support for different file formats, depending on the programming language
and built of the executable. The original file format is always supported. Input files are
automatically checked for file formats, which are supported by the executable. If GENESIS
1.3 cannot identify any special format, it assumes the original file format and starts processing
the file. The file format of output files are set by the input parameter FILETYPE. Request
for unsupported file formats will cause an error message and the termination of GENESIS
1.3
Besides the principle support of a specific file format, certain input and output files are not
suitable for all file formats. The following table lists all files and the implicit support for
them. The last column is the default filetype of output files for the C++ version of Genesis
if the filetype is not explicitly defined. If that file format is not supported GENESIS 1.3 falls
back to the original file format as default. The FORTRAN default is the original format for
all output files.
It is strongly recommended that the original file format is not used, because it is of all
formats the least platform-independent format. Also if more than one record of the electron
or field distribution is written, the SDDS and HDF5 file formats yield much smaller file sizes.
The XML output is always ASCII and the base64 encoding is not supported.
In the following all individual file are described for the original file format. All other file
formats share the same content of information as the original but might have also additional
information for more self-consistent sets of data files. The differnece and addition for the
other file formats are explained in the last sections of this chapter.
37
38
GENESIS 1.3 Manual

File
Main Input
Main Output
Particle Output
Field Output
Particle Dump
Field Dump
Particle Input
Field Input
Beam Description
Beam Distribution
Magnet Input
Magnet Output
Log File
Time Record
Original SDDS XML HDF5 Default

yes
no
yes
no
yes
yes
yes
yes
XML
yes
yes
yes
yes
HDF5
yes
yes
yes
yes
HDF5
yes
yes
yes
yes
HDF5
yes
yes
yes
yes
HDF5
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
no
yes
no
yes
no
yes
no
XML
yes
no
yes
no
XML
yes
no
no
no
-
The Main Input File

All input parameters are contained by a FORTRAN namelist. The namelist has to fulfill
a specific syntax, otherwise GENESIS 1.3 reports an error message and quits. The error
support for namelist is minimal and does not help to identify the problem.
The first character of every line must be blank.
The namelist starts with $newrun and ends with $end. Any text outside the namelist
is ignored.
The format of an entry in a namelist is: parameter name, equal sign, value (e.g. NPART
= 2048).
Parameter names and name list names are case insensitve
Arrays element are either defined by the index (LOUT(4) = 1) or by a list of several
elements separated by spaces (LOUT =1 1 0 0), starting with the first element in the
array.
Strings are assigned by using single, double or no quotation marks at all (e.g. BEAMFILE
= beam.dat, MAGINFILE = undulator.lattice).
Multiple entries per line have to be separated by commas.
The Main Output File

The main output file is in ASCII format and is split into three parts: the header, the
global parameters and the parameters for each slice. After some information about version,
39
platform and name of the input file, a namelist repeats all input parameters. It is possible
to rerun GENESIS 1.3 with the output file because the header fulfills the requirement of a
valid input file. Still header part several auxiliary parameters are listed which describes the
following data set as well as some information about additional output for the radiation field
and particle distribution (see below). These information can be used by any postprocessor
to correctly read the output files.
The global parameters are mainly the position along the undulator for each output and the
corresponding undulator and quadrupole field at that position.
For each slice an entire table is written containing a header and the main body. The header
lists the slice number, the local current and the column names. In scan mode the current
is replaced by the value of the scan parameter. The data follows directly the header. The
rows correspond to the z-positions given in the block of the global parameters. The size of
the table is controlled by the LOUT parameter.
The Radiation and Particle Output File

As an addition to the main output file the distribution of the radiation field or the electron
beam can be written to binary files. The file names are derived from the file name of the
main output file by adding the extension .fld and .par, respectively. In most cases these
files are large even in their binary format (ASCII output would increase the file size by
roughly a factor of 3). The output order is similar to the output of the main output file with
a consecutive output along the undulator. The output for a single slice at a certain position
within the undulator is referred to as a record in z. All zrecords of a single slices form a
record in t. The total number of z- and t-records are given in the header of the main output
file.
Each particle record in z starts with the energy of all particles followed by the output of
the particle phases, positions in x and y and the momenta in x and y. The momenta are
normalized to mc.
The radiation field record contains the real part of the discretized field and then the imaginary
part. The field is normalized so that the square sum of the real and imaginary part yields
the field intensity with respect to a unit area. To obtain the real intensity each value has to
be devided by the area each grid point covers. The order of the grid points starts with the
lower left corner (x,y < 0) along the x-axis. At the end of each row in x it jumps back in x
and advance y by one step.
40
GENESIS 1.3 Manual
The Log File

If the log feature is enables any output of genesis to the screen is redirect into a log-file.
The purpose of the log-file is to support background calculation of GENESIS 1.3. Thus the
execution will be terminated if GENESIS 1.3 needs further information (e.g. file names for
additional input files). The log feature is more reasonable for the C++-version of GENESIS
1.3 because the input file name can by supplied as a command line argument while starting
GENESIS 1.3. The FORTRAN version still needs to request the input file name thus defying
the purpose of a background job. Anyhow to start it as a background job type the command:
genesis < geninput > genoutput 2>&1 &
where geninput is a simple ASCII file containing the file name of the input file. The file
genoutput will catch any output, which cannot be handled by the log file (e.g. error messages). In the ideal case genoutput contains only the initial text lines for requesting the
input file name.
Reading-in and Dumping the Particle and Radiation Distribution

With the parameters IDMPFLD and IDMPPAR set to a non-zero value the field and particle
distribution is written to binary files for each slice at the end of the undulator. The file format
is similar to that of the particle and field output file (see above) with a few differences. The
particle phase is absolute and not relative to the radiation phase. The radiation field has
the same format as in the radiation output files (see above), representing the intensity if
real and imaginary parts are summed in square, but instead listing real and imaginary part
separately, the field dump has the complex value listed instead (pairs of real and imaginary
part). The radiation field escaping the last slice is added to the output so that the radiation
field, escaping first, is the last record in t. Note that there is only one record in z for both
files.
These files can be used to simulate the effect of a bunch compressor or a monochromator and
then reused as an input for a consecutive run of GENESIS 1.3. To indicate GENESIS 1.3
to skip the internal generation of the radiation field or particle distribution the file names of
these files are given as the input values for FIELDFILE and PARTFILE.
There are some restrictions of using these files.
The number of slices must be equal or smaller than the number of t-records in the
particle file
The grid spacing and the radiation wavelength must be the same to guarantee energy
conservation of the radiation field.
The number of slices plus the length of the slippage field record must be smaller than
the number of t-records in the field file.
41
While the first point is obvious the second needs some explanation. Because the radiation
slips through several electron slices the time-window of the radiation field must be larger
than the time-window of the simulated electron beam. It is extended by the slippage length
NSLP, which is the number of radiation slices which slips through a single electron beam slice
over the entire undulator length. The length is the undulator length divided by XLAMD and
ZSEP and rounded to the lower integer. The radiation initially seen by the first beam slice
is the NSLP+1 record of the radiation input file. The records between the first and NSLPth
slice are copied in the time-record. During the integration these slices are pushed into the
location of the simulated electron slice. Generally speaking the time window of the radiation
field is shifted forwards with respect to the time window of the electron beam during the
integration. In the case that the second GENESIS 1.3 run uses a longer undulator than
the first run, which dumped the radiation field and beam distribution, the number of beam
slices has to reduced to match the file length of the input radiation field.
Note that Genesis does not check for consistency. The field dump is associated to a certain
grid size and radiation wavelength. If a field is imported for a simulation, where these values
differs, the energy of the field is not conserved.
The Magnet Description Input and Output File

The magnet description file is in ASCII format and contains the explicit profile of all magnetic components or a subset of it. After processing the file GENESIS 1.3 recalculates the
undulator length and adjusts the number of integration steps. Field errors and tapering is
always enforced, when the corresponding parameters in the main input file are set. This
allows that different sets of field errors or taper gradients can be simulated while using only
a single input file. The output of the magnetic lattice, if requested, includes the field lattice,
seen by particle of the simulation. Even if field error and taper is disabled the output file
might differ from the input file in the format, but not in the content.
If any line of the input file starts with a space the content of the entire line is treated as a
comment. Also any character beyond the 30th position is ignored. These two restrictions
does not apply for the C++ version. In general the processing of the file is case insensitive.
Each line is categorized either as
content line,
comment line,
command line,
information line.
The content line actually holds information about the magnetic structure. The format of
each line depends on the version of the input file. There is a difference between the current
42
GENESIS 1.3 Manual
version 1.0 and earlier versions (<1.0). The version number is defined by an information line
in the header of the file. If omitted GENESIS 1.3 assumes a version prior to 1.0.
Each line hast four elements, where the first two are version independent. The first element
is a two-character string, indicating the type of structure. Following types are supported
AW - Main magnetic field
AD - Drift section
QF - Quadrupole strength
QX - Quadrupole offset in x
QY - Quadrupole offset in y
SL - Solenoid strength
CX - Corrector strength in x
CY - Corrector strength in y
Next the strength/offset value of that structure is specified.
For earlier version the next two numbers define the length of the structure. The first of those
is a unit length, common for all structure. Typically it is the undulator period length. The
second number is the length of the structure in measure of the unit length. As an example
the following lines descibe a 1 m long undulator with an rms strength of 1.30:
AW 1.3 2.e-2 50
Note that for a file version < 1.0 the absence of any structure must be included in the input
file as well. The strength/offset value is zero. Thus a two cell FODO lattice with a 4 cm
quadrupole length and a drift length of 8 cm is defined by
QF 2.5e+1 2.e-2 2
QF 0.0e+0 2.e-2 4
QF -2.5e+1 2.e-2 2
QF 0.0e+0 2.e-2 4
QF 2.5e+1 2.e-2 2
QF 0.0e+0 2.e-2 4
QF -2.5e+1 2.e-2 2
QF 0.0e+0 2.e-2 4
43
For the latest version the unit length is declared once in the header of the file and is mandatory. The third number is the length of the structure in measure of the unit length, while
the last number is the distance to the previous element of the same kind, again inmeasure
of the unit length. The definition of the FODO cell becomes now
? VERSION=1.0
? UNITLENGTH=2.e-2
QF 2.5e+1 2 0
QF -2.5e+1 2 4
QF 2.5e+1 2 4
QF -2.5e+1 2 4
The usage of the lines, starting with the question marks, are explainded below. A comment
line is indicated by a -sign as its first character. The remaining content of the line is ignored.
Similar lines, which do not contain any printable characters (spaces excluded) are treated as
comment lines.
A command line starts with an exclamation mark. For the magnetic field only two commands
are recognized. The first command !LOOP = x marks the beginning of a loop where x is
the number of loops to be performed. Note that there can be an arbitrary number of spaces
on both sides of the equal sign as long as the entire line is no longer than 30 characters. The
end of the loop is indicated by !ENDLOOP. Loops cannot be nested and starting a new loop
before the current loop is not closed will cause an error and the termination of GENESIS
1.3. The following lines define the same FODO lattice as above but this time with 10 cells
? VERSION=1.0
? UNITLENGTH=2.e-2
QF 2.5e+1 2 0
! LOOP=9
QF -2.5e+1 2 4
QF 2.5e+1 2 4
! ENDLOOP
QF -2.5e+1 2 4
The last class of input lines is information lines, which helps GENESIS 1.3 to process the file
correctly. These lines have to start with a question mark. One example is to set the version
number with ?VERSION = n.m for compatibility reason, where m.n is the version number.
Currently only versions below 1.0 and below are supported. The remaining other option is
44
GENESIS 1.3 Manual
setting the unitlength with ? UNITLENGTH = x, where x is the numeric value of the length
in meter. As for the command line spaces can seperate keyword, equal sign and value.
Note that GENESIS 1.3 stops processing a line, once it obtained all needed information.
This allows, also not recommended, to add comments at the end of each line.
The Beam Description File

The beam description file contains a table of beam parameters such as emittance and energy
at certain positions along the bunch. The positions listed in the file must be ordered starting
with the tail. In GENESIS 1.3 smaller number refers to a position towards the tail of the
bunch. Note that you have to adjust the simulation time-window in GENESIS 1.3 (ZSEP,
NSLICE and NTAIL) to the range, defined in the beam description file. Genesis 1.3 uses
relative positions within the time-window, starting at zero for the first entry in the beam
description file. This corresponds to NTAIL = 0.
Each line can contain up to 15 parameters: corresponding to the input parameters of the
main input deck:
ZPOS or TPOS
GAMMA0
DELGAM
EMITX
EMITY
RXBEAM or BETAX
RYBEAM or BETAY
XBEAM
YBEAM
PXBEAM
PYBEAM
ALPHAX
ALPHAY
CURPEAK
ELOSS
45
Besides ZPOS and TPOS, which refers to the position within the bunch, most of the remaining
parameters correspond to the input parameter of the main input file. If BETAX is defined
instead of RXBEAM the beam size is calculated, using the specified beam energy and emittance.
The same is valid for BETAY.
If a time coordinate specifies the position (TPOS) instead of a space coordinate (ZPOS), Genesis
1.3 enforces the convention that time and space coordinate differ with a relative sign. For
the right order in the beam description file the ZPOS values should increment, while the TPOS
should decremnt
The format of the beam description file is similar to the magnetic field input file. All
numbers are given in ASCII format. The input file can contain content lines, comment lines
and information lines. Commands lines are not needed and thus not supported.
Empty lines and lines starting with a #-sign are treated as comment lines. They are ignored
while processing the beam description file.
A question mark indicates an information line. The VERSION-keyword is the same as in the
magnetic field input file, defining the version of the input file. Note that there is a difference
between earlier versions (<1.0) and the current version 1.0 (see below). The SIZE parameter
is optional. It should contain the number of information lines in the input file. At the end of
processing the file GENESIS 1.3 compares the number of valid lines with the number defined
by SIZE and prints out a warning message if the two numbers differs. If no SIZE statement
is included the check is omitted.
The last information keyword is COLUMNS. It controls the number and order of columns in
the beam description file by simply adding the parameter names after the COLUMNS keyword.
Parameters, which are excluded in the beam description file, fall back to their default value,
defined in the main input deck. Omitting the current results in a step profile. The column
ZPOS is mandatory and GENESIS 1.3 with given an error message when it is not specified
in the COLUMN information line. If no COLUMNS-statement is given all input parameter are
required in the order as they appear in the list above.
As an example the following line describes a 100 m long, uniform beam with an energy
chirp of 1% along the beam.
? VERSION=1.0
? SIZE=2
? COLUMNS ZPOS GAMMA0
-50.0e-6 99.5
50.0e-6 100.5
Any version before 1.0 required that the number of input lines, containing the beam parameters, must be listed in the beginning of the file as the first information line before the actual
46
GENESIS 1.3 Manual
data lines started. To guarantee backwards compatibility this is still valid if the version is
no defined to be 1.0 and the SIZE-statement is omitted. The example above would be then
? COLUMNS ZPOS GAMMA0

2
-50.0e-6 99.5
50.0e-6 100.5
Again the specified value (here 2) is only used to check with the number of data lines, which
is processed by GENESIS 1.3 without any error.
The beam description file can also be used for a scan (NSCAN = 23,24). Each line correspond
to a run of the scan. The meaning of the ZPOS column becomes obsolete. However it is still
required for a correct parsing of the file.
The External Distribution File

GENESIS 1.3 support external phase space distribution, generate by other simulation codes
(e.g. ELEGANT). To enable the feature the input parameter DISTFILE points to a file,
which contains the particle distribution of the entire bunch.
The format is ASCII and for each particle all 6 coordinates must be supplied per line.
Additional information can be added per particle (such as particle ID), which is ignored by
GENESIS 1.3 in the current version.
Similar to the beam description file and the magnetic field input file the functionality is
extended by additional file information or comments.
Lines starting with the #-sign and empty lines are ignored. The question mark indicates
information lines. The VERSION and the SIZE keywords are the same as in the beam description file. Again if the version is smaller than 1.0 and the SIZE keyword is omitted the first
line, containing data, must be the size of the following data set. This value is used to check
for consistency and completeness of the distribution file. A required information the charge
in Coulombs, defined by the CHARGE keyword
The order of the 6 coordinates and additional values is set by the COLUMNS keyword followed
by the names of each column in the data set. In the current version the total number of
columns is limited to ten, but only those columns are used where the column name matches
one of the following recognized keywords:
47
X - position in x in meters
PX or XPRIME - momentum in x normalized to mc or divergence in x, respectively
Y - position in y in meters
PY or YPRIME - momentum in y normalized to mc or divergence in y, respectively
T or Z - longitudinal position in seconds or meters, respectively
P or GAMMA - total momentum or energy, normalized to mc or mcit2 , respectively.
The longitudinal position has to be defined exclusive either to be T or Z. The same is valid for
the other pairs listed above. If not all 6 dimensions are given GENESIS 1.3 will terminate
and report an error message. Note that GENESIS follows the rule that the longitudinal
position is reversed if a time is specified by the T column. In this case smaller numbers
correspond to particle in the tail of the distribution.
The default behavior of GENESIS 1.3 corresponds to the lines:
? VERSION = 0.1
? COLUMNS X PX Y PY T P
Note that with this default behaviour the first data line must be the number of particles (=
information lines) in the distribution file.
The Time-Record File

This is an file, which is created by GENESIS if the NOFILE parameter is set to a non-zero
value in the file timerec.cmn. It is only for internal use and will be deleted, when GENESIS
1.3 terminates.
The SDDS File Format

Currently not implemented. The manual will be updated, when the source
code, supporting new file formats, has been written
The XML File Format

48
GENESIS 1.3 Manual
The HDF5 File Format

The GENESIS 1.3 Algorithm
Has to be written
49
50
GENESIS 1.3 Manual
Where to Find Further Information
GENESIS 1.3
S. Reiche, Numerical Studies for a Single Pass High Gain Free-Electron Laser, DESY
print, DESY-THESIS-2000-012 (2000)
http://pbpl.physics.ucla.edu/genesis (official website)
FEL Basics
E.L. Saldin, E.A. Schneidmiller and M.V.Yurkov, The Physics of Free Electron Lasers,
Springer, (2000)
J.B. Murphy and C. Pellegrini, Introduction to the Physics of the FEL, Proceedings of
the South Padre Island Conference, Springer (1986) 163
Numeric Basics
W.H. Press, S.A. Teukolsky, W.T. Vetterling and B.P. Flannery, Numerical Recipes in
FORTRAN, Cambridge University Press, (1988)
W.F. Ames, Numerical Methods for Partial Differential Equations, Academic Press (1996)
FORTRAN, C++
J.M. Ortega, An Introduction to FORTRAN for Scientific Computing, Oxford University
Press (1994)
B. Stroustrup, C++ Programming Language, Addison-Wesley (1997)
XML, SDDS
M. Birbeck et al., Professional XML, Wrox (2001)
M. Borland, Users Guide for SDDS Toolkit Version 1.20,
http://www.aps.anl.gov/asd/oag/manuals/SDDStoolkit
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What is GENESIS 1.3?

What is GENESIS 1.3?

What are the main sections/chapters covered in the manual?

What are the main sections/chapters covered in the manual?

GENESIS 1.

Compilation, Installation and Execution

The GENESIS 1.3 Algorithm

Where to Find Further Information

About this Manual

GENESIS 1.3 Manual

About GENESIS 1.3

GENESIS 1.3 is a time-dependent three-dimensional FEL code. It is focused to simulate

The Particle Equations

GENESIS 1.3 Manual

The Field Equations

About GENESIS 1.3

GENESIS 1.3 Manual

Pre- and Postprocessors

About GENESIS 1.3

GENESIS 1.3 Manual

Compilation, Installation and Execution

The C++ version is currently under development. The manual will be

Compilation of the FORTRAN Source Code

GENESIS 1.3 Manual

Compilation, Installation and Execution

Compilation of the C++ Source Code

GENESIS 1.3 Manual

Running GENESIS 1.3

Compilation, Installation and Execution

[prompt]$ genesis < GENINPUT > GENOUTPUT 2 >&1 &

GENESIS 1.3 Manual

Step I - The Magnetic Lattice

Step II - The Electron Beam

GENESIS 1.3 Manual

Step III - The Radiation Field

Step IV - Optimization Using the SCAN-Feature

Step V - Time-dependent Simulation

GENESIS 1.3 Manual

Step VI - External Input for the Magnetic Field

GENESIS 1.3 Manual

IWITYP (0 integer unitless)

XKX (0.0 float unitless)

XKY (1.0 float unitless)

FBESS0 (0.0 float unitless)

XLAMD (2.05e-2 float meter)

NWIG (98 integer unitless)

GENESIS 1.3 Manual

NSEC (1 integer unitless)

AWD (0.735 float unitless)

WCOEFZ(1) (0.0 float meter)

WCOEFZ(2) (0.0 float unitless)

WCOEFZ(3) (0.0 float unitless)

IERTYP (0 integer unitless)

DELAW (0.0 float unitless)

ISEED (-1 integer unitless)

Electron Beam Parameters

GAMMA0 (35.2 float unitless)

DELGAM (5.0e-3 float unitless)

RXBEAM (112.1e-6 float meter)