Commit b79b71dd authored by ext-calvo_p's avatar ext-calvo_p
Browse files

Merge branch '60-description-of-eb-out-and-gnu-out' into 'master'

Resolve "Description of eb.out and gnu.out"

Closes #60

See merge request OPAL/documentation/manual!130
parents 7b0c93ce 2f6b731b
......@@ -183,4 +183,4 @@ DT::
T_STEPS::
Number of steps in time. It is an error if `T_STEPS` is non-integer or less than 1.
// EOF
\ No newline at end of file
// EOF
......@@ -41,9 +41,9 @@ FFAs.
[[sec.opalcycl.tracking-modes]]
=== Tracking modes
According to the number of particles defined by the argument `npart` in
`beam` see Chapter link:beam-command#chp.beam-command[Beam Command], _OPAL-cycl_ works in one of the following
three operation modes automatically.
According to the number of particles defined by the argument `NPART` in
`BEAM` (see Chapter link:beam-command#chp.beam-command[Beam Command]),
_OPAL-cycl_ works in one of the following three operation modes automatically.
[[sec.opalcycl.single-particle-tracking-mode]]
==== Single Particle Tracking mode
......@@ -54,8 +54,8 @@ preliminary design phase of a cyclotron.
The 6D parameters of a single particle in the initial local frame must
be read from a file. To do this, in the _OPAL_ input file, the command
line `DISTRIBUTION` see Chapter link:distribution#chp.distribution[Distribution] should be defined like
this:
line `DISTRIBUTION` (see Chapter link:distribution#chp.distribution[Distribution])
should be defined like this:
----
Dist1: DISTRIBUTION, TYPE=fromfile, FNAME="PartDatabase.dat";
......@@ -146,19 +146,18 @@ The independent variable is: *t* [s].
==== The initial distribution in the local reference frame
The initial distribution of the bunch, either read from file or
generated by a distribution generator (see Chapter link:distribution#chp.distribution[Distribution]), is
specified in the local reference frame of the _OPAL-cycl_ Cartesian
coordinate system see <<sec.opalcycl.variables>>. At the beginning of the
generated by a distribution generator (see Chapter link:distribution#chp.distribution[Distribution]),
is specified in the local reference frame of the _OPAL-cycl_ Cartesian
coordinate system (see <<sec.opalcycl.variables>>). At the beginning of the
run, the 6 phase space variables latexmath:[(x, y, z, p_x, p_y, p_z)]
are transformed to the global Cartesian coordinates latexmath:[(X, Y, Z, PX, PY, PZ)] using the starting
coordinates latexmath:[r_0] (`RINIT`), latexmath:[\phi_0]
(`PHIINIT`), and latexmath:[z_0] (`ZINIT`), and the starting momenta
latexmath:[p_{total}] (defined by the beam energy specified in the link:beam-command#sec.beam-command.beam-energy[Beam Command]),
latexmath:[p_{r0}] (`PRINIT`), and latexmath:[p_{z0}] (`PZINIT`) of
the reference particle, defined in the `CYCLOTRON` element
see link:elements#sec.elements.cyclotron[Cyclotron]. Note that latexmath:[p_{\phi 0}] is
calculated automatically from latexmath:[p_{total}],
latexmath:[p_{r0}], and latexmath:[p_{z0}].
the reference particle, defined in the `link:elements#sec.elements.cyclotron[CYCLOTRON]`
element. Note that latexmath:[p_{\phi 0}] is calculated automatically from
latexmath:[p_{total}], latexmath:[p_{r0}], and latexmath:[p_{z0}].
[latexmath]
++++
......@@ -191,12 +190,11 @@ latexmath:[B_z], can be measured on the median plane (latexmath:[z=0]).
by using measurement equipment. Since the magnetic field outside the
median plane is required to compute trajectories with latexmath:[z \neq 0],
the field needs to be expanded in the latexmath:[z] direction.
According to the approach given by Gordon and Taivassalo by
According to the approach given by Gordon and Taivassalo <<bib.gordon1985>> by
using a magnetic potential and measured latexmath:[B_z] on the median
plane at the point latexmath:[(r,\theta, z)] in cylindrical polar
coordinates, the third order field can be written as
coordinates, the third order field can be written as:
.Third order field
[latexmath#eq-Bfield]
++++
\begin{aligned}
......@@ -233,7 +231,7 @@ at large distances from the median plane i.e. a full 3D field map can be calcula
In the current version, we implemented three specific type
field-read functions _Cyclotron::getFieldFromFile()_ of the median plane
fields. Which function is used is controlled by the parameters
`TYPE` of `CYCLOTRON` see  link:elements#sec.elements.cyclotron[Cyclotron] in the input file.
`TYPE` of `link:elements#sec.elements.cyclotron[CYCLOTRON]` in the input file.
[[sec.opalcycl.carboncycl-type]]
==== CARBONCYCL type
......@@ -628,16 +626,15 @@ The intermediate phase space data is stored in an ASCII file which can
be used to plot the orbit. The file’s name is combined by input file
name (without extension) and _-trackOrbit.dat_. The data are stored in
the global Cartesian coordinates. The frequency of the data output can
be set using the option `SPTDUMPFREQ` of `OPTION` statement
see  link:control#sec.control.option[Option Statement].
be set using the option `SPTDUMPFREQ` of link:control#sec.control.option[`OPTION` statement].
The phase space data per `STEPSPERTURN` (a parameter in the `TRACK`
The phase space data per `STEPSPERTURN` (a parameter in the `link:track#chp.track[TRACK]`
command) steps is stored in an ASCII file. The file's is named
_<input_file_name >-afterEachTurn.dat_. The data is stored in the global cylindrical
coordinate system. Please note that if the field map is ideally
isochronous, the reference particle of a given energy take exactly one
revolution in `STEPPERTURN` steps; Otherwise, the particle may not go
through a full 360 degrees in `STEPPERTURN` steps.
revolution in `STEPSPERTURN` steps; Otherwise, the particle may not go
through a full 360latexmath:[\degree] in `STEPSPERTURN` steps.
There are 3 ASCII files which store the phase space data around
latexmath:[0], latexmath:[\pi/8] and latexmath:[\pi/4] azimuths.
......@@ -660,8 +657,7 @@ parameters, including RMS envelop size, RMS emittance, external field,
time, energy, length of path, number of bunches and tracking step, are
stored in the H5hut file-format <<bib.howison2010>> and can be analyzed
using H5root <<bib.schietinger>>. The frequency of the data output can
be set using the `PSDUMPFREQ` option of `OPTION` statement
see link:control#sec.control.option[Option Statement].
be set using the `PSDUMPFREQ` option of link:control#sec.control.option[`OPTION` statement].
The file is named _<input_file_name >.h5_.
This output can be switched on or off with the option `ENABLEHDF5`.
......@@ -669,7 +665,28 @@ The intermediate phase space data of central particle (with ID of 0) and
an off-centering particle (with ID of 1) are stored in an ASCII file.
The file is named _<input_file_name >-trackOrbit.dat_.
The frequency of the data output can be set using
the `SPTDUMPFREQ` option of `OPTION` statement see link:control#sec.control.option[Option Statement].
the `SPTDUMPFREQ` option of link:control#sec.control.option[`OPTION` statement].
[[sec.opalcycl.fields-maps-1]]
==== Field maps
The magnetic field map read by _OPAL_ could be saved into an output file called
_gnu.out_. This file stores the magnetic field latexmath:[B_z] data in the
median plane in cylindrical coordinates following the sequence shown in
<<fig_CYCLField>>. This output file is available in the cyclotron field types
`CARBONCYCL`, `BANDRF`, `FFA` and `AVFEQ`.
In case of `CARBONCYCL` or `BANDRF` an additional output field file an
additional output field file is saved (_eb.out_), storing three vectors with
the position, electric field and the magnetic field.
Writing these output files is enabled when _OPAL_ is run on single node, and
it can be switched on or off with the `INFO` option of
link:control#sec.control.option[`OPTION` statement].
Moreover, `DUMPFIELDS` and `DUMPEMFIELDS` routines (see Chapter link:field-output#chp.field_output[Field Output])
can be employed to write out the external field used in _OPAL-cycl_ in a
different grid than the input field maps.
[[sec.opalcycl.matched-distribution]]
=== Matched Distribution
......@@ -723,6 +740,9 @@ All supplementary files can be found in {link_regtest_RingCyclotronMatched}[the
[[sec.opalcycl.bibliography]]
=== References
anchor:bib.gordon1985[[{counter:bib-cnt}\]]
<<bib.gordon1985>> M. M. Gordon and V. Taivassalo, https://ieeexplore.ieee.org/document/4333942[_Nonlinear Effects of Focusing Bars Used in the Extraction Systems of Superconducting Cyclotrons_], in IEEE Transactions on Nuclear Science (1985), 32, pp. 2447-2449.
anchor:bib.howison2010[[{counter:bib-cnt}\]]
<<bib.howison2010>> M. Howison et al., http://dx.doi.org/10.1109/CLUSTERWKSP.2010.5613098[_H5hut: A High-Performance I/O Library for Particle-based Simulations_], in IEEE International Conference on Cluster Computing Workshops and Posters (2010), pp. 1–8, 10 . 1109 / CLUSTERWKSP.2010.5613098.
......
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