Working with MainInput¶

In [1]:

import genesis.version4 as g4

%config InlineBackend.figure_format = 'retina' # Nicer plots

import genesis.version4 as g4 %config InlineBackend.figure_format = 'retina' # Nicer plots

Load an existing main input file¶

You can load Genesis4-format main input directly from a file by using from_file:

In [2]:

input = g4.MainInput.from_file("data/basic4/cu_hxr.in")

input = g4.MainInput.from_file("data/basic4/cu_hxr.in")

In [3]:

input.namelists

input.namelists

Out[3]:

[Setup(
   rootname='LCLS2_HXR_9keV',
   lattice='hxr.lat',
   beamline='HXR',
   gamma0=19174.0776,
   lambda0=1.3789244869952112e-10,
   delz=0.026,
   seed=84672,
   npart=1024,
 ),
 Time(slen=1.5e-05, sample=200),
 Field(dgrid=0.0001, ngrid=101, accumulate=True),
 ProfileFile(
   label='beamcurrent',
   xdata='beam_current.h5/s',
   ydata='beam_current.h5/current',
 ),
 ProfileFile(label='beamgamma', xdata='beam_gamma.h5/s', ydata='beam_gamma.h5/gamma'),
 Beam(
   gamma='@beamgamma',
   delgam=3.97848,
   current='@beamcurrent',
   ex=4e-07,
   ey=4e-07,
   betax=7.910909406464387,
   betay=16.881178621346898,
   alphax=-0.7393217413918415,
   alphay=1.3870723536888105,
 ),
 Track(zstop=10.0)]

This input object is a convenient dataclass which contains all of the namelists and offers some convenience methods.

We can see the Genesis 4 representation of a namelist by looking at namelist.to_genesis():

In [4]:

print(input.setup.to_genesis())

print(input.setup.to_genesis())

&setup
  rootname = LCLS2_HXR_9keV
  lattice = hxr.lat
  beamline = HXR
  gamma0 = 19174.0776
  lambda0 = 1.3789244869952112e-10
  delz = 0.026
  seed = 84672
  npart = 1024
&end

The parser also works directly with strings if you prefer with .from_contents. Try the following:

In [5]:

input = g4.MainInput.from_contents(
    """
&setup
  rootname = LCLS2_HXR_9keV
  lattice = hxr.lat
  beamline = HXR
  gamma0 = 19174.0776
  lambda0 = 1.3789244869952112e-10
  delz = 0.026
  seed = 84672
  npart = 1024
&end
"""
)

input = g4.MainInput.from_contents( """ &setup rootname = LCLS2_HXR_9keV lattice = hxr.lat beamline = HXR gamma0 = 19174.0776 lambda0 = 1.3789244869952112e-10 delz = 0.026 seed = 84672 npart = 1024 &end """ )

In [6]:

input.setup

input.setup

Out[6]:

Setup(
  rootname='LCLS2_HXR_9keV',
  lattice='hxr.lat',
  beamline='HXR',
  gamma0=19174.0776,
  lambda0=1.3789244869952112e-10,
  delz=0.026,
  seed=84672,
  npart=1024,
)

In [7]:

input

input

Out[7]:

MainInput(
  namelists=[
    Setup(
      rootname='LCLS2_HXR_9keV',
      lattice='hxr.lat',
      beamline='HXR',
      gamma0=19174.0776,
      lambda0=1.3789244869952112e-10,
      delz=0.026,
      seed=84672,
      npart=1024,
    ),
  ],
  filename=pathlib.Path('unknown'),
)

You can see full descriptions of all parameters and values in a table format:

In [8]:

input.to_table()

input.to_table()

Out[8]:

Copy to clipboard

Attribute	Value	Type	Description
0	Copy to clipboard Attribute Value Type Description type setup str rootname LCLS2_HXR_9keV str The basic string, with which all output files will start, unless the output filename is directly overwritten (see `write` namelist) outputdir str Output directory name. lattice hxr.lat str The name of the file which contains the undulator lattice description. This can also include some relative paths if the lattice file is not in the same directory as the input file. beamline HXR str The name of the beamline, which has to be defined within the lattice file. For more information on the lattice file, see the next chapter. gamma0 19174.0776 float The reference energy in unites of the electron rest mass. This is the reference energy which is used in the code at various place, mostly in the calculation of the matching condition, the reference focusing strength of quadrupoles and undulator as well as the default value if an electron distribution is generated. lambda0 1.3789244869952112e-10 float The reference wavelength in meter, which is used as the wavelength in steady-state simulation or for defining the sample distance in time- dependent runs. It also acts as the default value when field distributions are generated. delz 0.026 float Preferred integration stepsize in meter. Note that this is not a strict value because Genesis tries to optimized the stepsize according to the elements it can resolve. E.g. if an undulator is 1.99 m long but the preferred stepsize is 2 cm than it uses a stepsize which is the closest to preserve the number of integration step. In this case the preferred stepsize gives 99.5 steps which is than rounded to 100 and thus resulting in an actual stepsize of 1.99 cm. Note that outside of the undulator, which are free drifts for the radiation field, Genesis progresses the electron beam and radiation field in larger steps, namely one step per resolved element (drift, quadrupole, phase shifter). seed 84672 int Seed to initialize the random number generator, which is used for shot noise calculation and undulator lattice errors, though it is recommended that the random number generator seed is redefined explicitly for undulator errors in its corresponding namelist. npart 1024 int Number of macro particles per slice. Note that the number must be a multiple of the used bins `nbins` otherwise Genesis will exit with an error. If one-for-one simulations are used, this parameter has no meaning. nbins 4 int Number of macro particles, which are grouped into beamlets for gener ating the correct shot noise. For one-for-one simulations this parameter has no meaning one4one False bool Flag to enable or disable resolving each electron in the simulation. This is mandatory for certain features, such as sorting or slicing of particle distributions. If set to `true` other parameters such as `npart` and `nbins` are obsolete and do not need to be defined. It is recommended to estimate the number of electrons, which are generated in the simulations, because this can easily required memory beyond what is available on the computer. shotnoise True bool Flag to enable the calculation of shotnoise per each slice during generation of the electron distribution. It is recommended to set the value to `false` for steady-state or scan simulations. beam_global_stat False bool Flag to enable extra output of beam parameters of the entire bunch, such as energy, energy spread etc. The data are placed in the HDF group ”Global” within the group ”Beam” of the output file field_global_stat False bool Flag for the field output, similar to `beam_global_stat`. exclude_spatial_output False bool Flag to suppress the datasets in the output file for the x- and y-position and size (both Beam and Field) and px- and py-position (Beam only). This might be useful to reduce the file size of the output file, if these datasets are not needed for the post-processing exclude_fft_output False bool Flag to suppress the datasets in the output file for the field divergence and pointing. Since it also disable the FFT calculation of the 2D wavefronts it speeds up the execution time slightly. If the code has been compiled without the support of the FFTW library this parametr has no effect. exclude_intensity_output False bool Flag to suppress the datasets for the near and farfield intensity and phase for the radiation field. If excluded the output file size becomes smaller but no post-processing calculation of the spectra is possible. exclude_energy_output False bool Flag to suppress the datasets in the output file for the mean energy and energy spread of the electron beam. exclude_aux_output False bool Flag to suppress the auxiliary datasets in the output file. In the moment it is the long-range longitudinal electric field as seen by the electrons. exclude_current_output True bool Flag to reduce the size of the current dataset for the electron beam. Under most circumstances the current profile is constant and only the initial current profile is written out. However, simulation with one-4-one set to `true` and sorting events the current profile might change. Example are ESASE/HGHG schemes. By setting the flag to false the current profile is written out at each output step similar to radiation power and bunching profile. exclude_twiss_output True bool Flag to reduce the size of the twiss (emittance, beta and alpha values) dataset for the electron beam. Under most circumstances the twiss parameters are constant and only the initial values are written out. However, simulation with one-4-one set to `true` and sorting events the twiss parameters might change. Example are ESASE/HGHG schemes. By setting the flag to false the twiss values written out at each output step similar to radiation power and bunching profile. exclude_field_dump False bool Exclude the field dump to `.fld.h5`. write_meta_file False bool Write a metadata file. semaphore_file_name str Providing a file name for the semaphore file always switches on writing the 'done' semaphore file, overriding 'write_semaphore_file' flag. This allows to switch on semaphore functionality just by specifying corresponding command line argument -- no modification of G4 input file needed. write_semaphore_file False bool Write a semaphore file when the simulation has completed. write_semaphore_file_done False bool Alias for `write_semaphore_file`. This takes precedence over `write_semaphore_file` if both are specified. write_semaphore_file_started False bool Write a semaphore file at startup, after the setup block is parsed.