Commit cd52d034 authored by gsell's avatar gsell

Merge branch '25-fix-links-in-gitlab-environment' into 'master'

Resolve "Fix links in gitlab environment"

Closes #25

See merge request OPAL/documentation/manual!85
parents 685e8fa5 581ec963
......@@ -7,8 +7,15 @@ ifdef::backend-docbook5,backend-html5[]
:description: _OPAL_ User Manual
:keywords: _OPAL_
:revdate: @REVDATE@
:adoc: adoc
endif::[]
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[cols="<19,<27,<.^27,<27",frame="none",grid="none"]
......@@ -25,15 +32,6 @@ ifdef::backend-html5[]
endif::[]
ifdef::env-gitlab[]
:adoc: asciidoc
endif::[]
ifdef::backend-docbook5,backend-html5[]
:adoc: adoc
endif::[]
include::Manual.macros[]
:sectnums!:
== Preliminary note
......@@ -68,36 +66,37 @@ flavours.
ifdef::env-gitlab[]
:sectnums!:
== Table of Contents
. {baseurl}/introduction.{adoc}[Introduction]
. {baseurl}/conventions.{adoc}[Conventions]
. {baseurl}/pitfalls.{adoc}[Pitfalls and Limitations]
. {baseurl}/tutorial.{adoc}[Tutorial]
. {baseurl}/opalt.{adoc}[OPAL-T]
. {baseurl}/opalcycl.{adoc}[OPAL-CYCL]
. {baseurl}/opalmap.{adoc}[OPAL-MAP]
. {baseurl}/format.{adoc}[Command Format]
. {baseurl}/control.{adoc}[Control Statements]
. {baseurl}/elements.{adoc}[Elements]
. {baseurl}/field-output.{adoc}[Field Output Commands]
. {baseurl}/lines.{adoc}[Beam Lines]
. {baseurl}/beam-command.{adoc}[Beam Command]
. {baseurl}/distribution.{adoc}[Distribution Command]
. {baseurl}/fieldsolvers.{adoc}[Field Solver]
. {baseurl}/track.{adoc}[Tracking]
. {baseurl}/wakefields.{adoc}[Wakefields]
. {baseurl}/geometry.{adoc}[Geometry]
. {baseurl}/partmatter.{adoc}[Physics Models Used in the Particle Matter Interaction Model]
. {baseurl}/optimiser.{adoc}[Multi Objective Optimization]
. {baseurl}/sampler.{adoc}[Sampler]
. {link_manual_src}/introduction.{adoc}[Introduction]
. {link_manual_src}/conventions.{adoc}[Conventions]
. {link_manual_src}/pitfalls.{adoc}[Pitfalls and Limitations]
. {link_manual_src}/tutorial.{adoc}[Tutorial]
. {link_manual_src}/opalt.{adoc}[OPAL-T]
. {link_manual_src}/opalcycl.{adoc}[OPAL-CYCL]
. {link_manual_src}/opalmap.{adoc}[OPAL-MAP]
. {link_manual_src}/format.{adoc}[Command Format]
. {link_manual_src}/control.{adoc}[Control Statements]
. {link_manual_src}/elements.{adoc}[Elements]
. {link_manual_src}/field-output.{adoc}[Field Output Commands]
. {link_manual_src}/lines.{adoc}[Beam Lines]
. {link_manual_src}/beam-command.{adoc}[Beam Command]
. {link_manual_src}/distribution.{adoc}[Distribution Command]
. {link_manual_src}/fieldsolvers.{adoc}[Field Solver]
. {link_manual_src}/track.{adoc}[Tracking]
. {link_manual_src}/wakefields.{adoc}[Wakefields]
. {link_manual_src}/geometry.{adoc}[Geometry]
. {link_manual_src}/partmatter.{adoc}[Physics Models Used in the Particle Matter Interaction Model]
. {link_manual_src}/optimiser.{adoc}[Multi Objective Optimization]
. {link_manual_src}/sampler.{adoc}[Sampler]
.Appendices
[upperalpha]
. {baseurl}/syntax.{adoc}[OPAL Language Syntax]
. {baseurl}/fieldmaps.{adoc}[OPAL-T Field Maps]
. {baseurl}/opal-madx.{adoc}[OPAL-MADX Conversion Guide]
. {baseurl}/autophase.{adoc}[Auto-phasing Algorithm]
. {baseurl}/benchmarks.{adoc}[Benchmarks]
. {link_manual_src}/syntax.{adoc}[OPAL Language Syntax]
. {link_manual_src}/fieldmaps.{adoc}[OPAL-T Field Maps]
. {link_manual_src}/opal-madx.{adoc}[OPAL-MADX Conversion Guide]
. {link_manual_src}/autophase.{adoc}[Auto-phasing Algorithm]
. {link_manual_src}/benchmarks.{adoc}[Benchmarks]
endif::[]
ifdef::backend-docbook5,backend-html5[]
......
:OPAL_version: 2.5
:branch_OPAL: master
//:branch_manual: master
:branch_manual: 25-fix-links-in-gitlab-environment
:branch_reg_tests: master
:host_git: https://gitlab.psi.ch
:host_amas: http://amas.web.psi.ch
:link_manual: {host_git}/OPAL/documentation/manual
:link_manual_src: {link_manual}/blob/{branch_manual}
:baseurl: {link_manual}/blob/{branch_manual}
:link_OPAL_doc: {host_amas}/opal/Documentation/{branch_OPAL}
:link_OPAL: {host_git}/OPAL/src
:link_OPAL_wiki: {link_OPAL}/wikis
:link_pyOPALTools: {host_git}/OPAL/pyOPALTools
:link_pyOPALTools_wiki: {link_pyOPALTools}/wikis
:link_PSI_Ring: {host_git}/AMAS-BDModels/PSI-Ring
:link_RRI2_0038Y1: {link_PSI_Ring}/blob/master/RawData/RRI2-0038Y17.peaks[file].
:link_opt_pilot: {host_git}/OPAL/opt-pilot/
:link_opt_pilot_wiki: {link_opt_pilot}/wikis
:link_H5hut: {host_git}/H5hut/src
:link_H5hut_wiki: {link_H5hut}/wikis/home
:link_doxygen_doc: {host_amas}/docs/opal/master-doxygen/
:link_ipac2017: http://accelconf.web.cern.ch/AccelConf/ipac2017
:link_ipac2017_thpab077: {link_ipac2017}/papers/thpab077.pdf
:link_reg_tests: {host_git}/OPAL/regression-tests
:link_reg_tests_src: {link_reg_tests}/blob/{branch_reg_tests}/RegressionTests
:link_regtest_MAP_FODO: {link_reg_tests_src}/MAP-FODO
:link_regtest_LaserEmission_1: {link_reg_tests_src}/LaserEmission-1
:link_regtest_RingCyclotronMatched: {link_reg_tests_src}/RingCyclotronMatched
:host: https://gitlab.psi.ch/
:project: OPAL/documentation/manual
:repository: {host}/{project}
:branch: master
:baseurl: {host}/{project}/blob/{branch}
:website: http://amas.web.psi.ch/opal/Documentation
:OPAL_version: 2.5
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......@@ -568,10 +562,10 @@ The `SYSTEM` command can also be used to execute an external script.
Below is an example that generates a random seed with python.
The python script
{website}/{branch}/examples/gen_seed.py[gen_seed.py]
{link_OPAL_doc}/examples/gen_seed.py[gen_seed.py]
is called with the `SYSTEM` command.
This scripts writes the seed to a file
{website}/{branch}/examples/gen_seed.opal[gen_seed.opal]
{link_OPAL_doc}/examples/gen_seed.opal[gen_seed.opal]
that can be read with the `CALL` command.
----
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......@@ -741,7 +738,7 @@ imposed on the flat top, latexmath:[t_\mathrm{flattop}], in
|`LASERPROFFN` | |None |File name containing measured laser image.
|`IMAGENAME` | |None |Used for h5 files. Name of the groups containing the laser image, see https://gitlab.psi.ch/OPAL/regression-tests/blob/master/RegressionTests/LaserEmission-1/LaserEmission-1.in[regression test].
|`IMAGENAME` | |None |Used for h5 files. Name of the groups containing the laser image, see {link_regtest_LaserEmission_1}/LaserEmission-1.in[regression test].
|`INTENSITYCUT` |0.0 |None |Parameter defining floor of the background
to be subtracted from the laser image in percent of the maximum
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......@@ -1311,7 +1308,7 @@ model includes fringe fields. The detailed description can be found at:
https://gitlab.psi.ch/OPAL/src/uploads/0d3fc561b57e8962ed79a57cd6115e37/8FBB32A4-7FA1-4084-A4A7-CDDB1F949CD3_psi.ch.pdf.
----
label:MULTIPOLET, L=real, ANGLE=real, VAPERT=real, HAPERT=real,
Label:MULTIPOLET, L=real, ANGLE=real, VAPERT=real, HAPERT=real,
LFRINGE=real, RFRINGE=real, TP=real-vector, VARRADIUS=bool;
----
......@@ -1511,7 +1508,7 @@ ring: Cyclotron, TYPE="RING", CYHARMON=6, PHIINIT=0.0,
----
If TYPE is set to BANDRF, the 3D electric field map of RF cavity will be
read from external https://gitlab.psi.ch/H5hut/src/wikis/home[H5Hut] file and the following extra arguments need to specified:
read from external {link_H5hut_wiki}[H5Hut] file and the following extra arguments need to specified:
RFMAPFN::
The file name(s) for the electric field map(s) in H5Hut binary format.
......@@ -1576,7 +1573,7 @@ TYPE::
Separate functions can be given for the radial and azimuthal direction.
These functions are multiplied together for the function.
If a function in a direction is not specified it is the identity 1.
The PSI-BFIELD-MIRRORED type is described in http://accelconf.web.cern.ch/AccelConf/ipac2017/papers/thpab077.pdf
The PSI-BFIELD-MIRRORED type is described in {link_ipac2017_thpab077}.
RMIN::
Inner radius of the trim coil [mm]
RMAX::
......
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......@@ -61,7 +58,7 @@ since we are convinced that adequate documentation is a key factor in
the usefulness of a code like _OPAL_ to study present and future
particle accelerators. Using tools such as a source code version control
system (https://git-scm.com[git]), source code documentation using
Doxygen (found http://amas.web.psi.ch/docs/opal/master-doxygen/[here]) and the
Doxygen (found {link_doxygen_doc}[here]) and the
extensive user manual you are now enjoying, we are committed to
providing users as well as co-developers with state-of-the-art
documentation to _OPAL_.
......@@ -94,7 +91,7 @@ to a file with extension .stat. The frequency with which this data is
written can be controlled with the `OPTION` statement
see link:control#sec.control.option[Option Statement] with the flag `STATDUMPFREQ`.
For postprocessing we recommend to use the https://gitlab.psi.ch/OPAL/pyOPALTools/wikis/home[pyOPALTools]
For postprocessing we recommend to use the {link_pyOPALTools_wiki}/home[pyOPALTools]
Python package which contains many tools for pre- and postprocessing, and analysing and plotting output data.
In addition to the output files, note that important information is displayed on the _stdout_ i.e. the _terminal_.
......@@ -107,13 +104,13 @@ image::figures/H5rootPicture.png[scaledwidth=18cm,width=90%]
[[sec.introduction.change-history]]
=== Change History
See https://gitlab.psi.ch/OPAL/src/wikis/ReleaseNotes[Release Notes]
See {link_OPAL_wiki}/ReleaseNotes[Release Notes]
for a detailed list of changes in _OPAL_.
[[sec.introduction.known-issues-and-limitations]]
=== Known Issues and Limitations
See the https://gitlab.psi.ch/OPAL/src/issues[issue list] in the repository.
See the {link_OPAL}/issues[issue list] in the repository.
See also link:pitfalls#chp.pitfalls[pitfalls and limitations].
......
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......@@ -608,7 +602,7 @@ mrad.
A bash script _tuning.sh_ is shown on the next page, to execute
_OPAL-cycl_ for tune calculations.
{website}/{branch}/examples/tuning.sh[tuning.sh]
{link_OPAL_doc}/examples/tuning.sh[tuning.sh]
To start execution, just run
_tuning.sh_ which uses the input file _testcycl.in_ and the auxiliary
......@@ -716,14 +710,14 @@ given in the output.
[[sec.opalcycl.input-file]]
===== Input file
https://gitlab.psi.ch/OPAL/regression-tests/blob/master/RegressionTests/RingCyclotronMatched/RingCyclotronMatched.in[matchedDistribution.in]
{link_regtest_RingCyclotronMatched}/RingCyclotronMatched.in[matchedDistribution.in]
All supplementary files can be found in https://gitlab.psi.ch/OPAL/regression-tests/tree/master/RegressionTests/RingCyclotronMatched[the matched distribution regression test].
All supplementary files can be found in {link_regtest_RingCyclotronMatched}[the matched distribution regression test].
[[sec.opalcycl.output-1]]
===== Output
https://gitlab.psi.ch/OPAL/regression-tests/blob/master/RegressionTests/RingCyclotronMatched/reference/RingCyclotronMatched.out[matchedDistribution.output]
{link_regtest_RingCyclotronMatched}/reference/RingCyclotronMatched.out[matchedDistribution.output]
[[sec.opalcycl.bibliography]]
=== References
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......@@ -163,9 +160,9 @@ _OPAL-map_ is the new flavour of _OPAL_ and currently just contains the fundamen
[[sec.opalmap.example]]
=== Example
FODO lattice: https://gitlab.psi.ch/OPAL/regression-tests/blob/master/RegressionTests/MAP-FODO/MAP-FODO.in[MAP-FODO.in]
FODO lattice: {link_regtest_MAP_FODO}/MAP-FODO.in[MAP-FODO.in]
Input distribution (to be put in directory `data`): https://gitlab.psi.ch/OPAL/regression-tests/blob/master/RegressionTests/MAP-FODO/data/FODO_DIST.dat[FODO_DIST.dat]
Input distribution (to be put in directory `data`): {link_regtest_MAP_FODO}/data/FODO_DIST.dat[FODO_DIST.dat]
To `RUN` _OPAL-map_, the `METHOD` attribute gets set to `THICK`.
----
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......@@ -25,7 +22,10 @@ In this chapter we introduce multi-objective optimization problems and
discuss techniques for their solution with an emphasis on evolutionary
algorithms.
NOTE: For multi-objective optimization OPAL uses https://gitlab.psi.ch/OPAL/opt-pilot/[`opt-pilot`] developed by Y. Ineichen. `opt-pilot` has been fully integrated into OPAL. Instructions can be found on the https://gitlab.psi.ch/OPAL/opt-pilot/wikis/home[`opt-pilot` wiki page].
NOTE: For multi-objective optimization OPAL uses
{link_opt_pilot}[`opt-pilot`] developed by Y. Ineichen. `opt-pilot`
has been fully integrated into OPAL. Instructions can be found on the
{link_opt_pilot_wiki}/home[`opt-pilot` wiki page].
[[sec.optimiser.definition]]
=== Definition
......@@ -319,8 +319,7 @@ There are several methods to access output data:
(measurement_i - value_i)^2}]
| radialPeak(<file>, <turn>)
| A simple expression to get the n-th peak of a radial probe
https://gitlab.psi.ch/AMAS-BDModels/PSI-Ring/blob/master/RawData/RRI2-0038Y17.peaks[file].
| A simple expression to get the n-th peak of a radial probe {link_RRI2_0038Y1}.
| sumErrSqRadialPeak(<meas_file>, <sim_file>, <begin>, <end>)
| A simple expression computing the sum of all peak errors (given as
......
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......@@ -400,7 +394,7 @@ track it as in a drift and put it back to the main bunch when finishing
[[sec.partmatter.example-of-an-input-file]]
=== Example of an Input File
{website}/{branch}/examples/particlematterinteraction.in[particlematterinteraction.in]
{link_OPAL_doc}/examples/particlematterinteraction.in[particlematterinteraction.in]
FX5 is a slit in x direction, the `APERTURE` is *POSITIVE*, the first
value in `APERTURE` is the left part, the second value is the right
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......@@ -17,7 +11,7 @@ endif::[]
This chapter will provide a jump start describing some of the most
common used features of _OPAL_. The complete set of examples can be
found and downloaded at https://gitlab.psi.ch/OPAL/src/wikis/home. All
found and downloaded at {link_OPAL_wiki}/home. All
examples are requiring a small amount of computing resources and run on
a single core, but can be used efficiently on up to 8 cores. _OPAL_
scales in the weak sense, hence for a higher concurrency one has to
......@@ -139,9 +133,9 @@ with the first entry defining the number of cavities in the simulation.
[[sec.tutorial.obla]]
==== Laser emission, OBLA (SwissFEL test facility) 4 MeV Gun and Beamline
https://gitlab.psi.ch/OPAL/regression-tests/blob/master/RegressionTests/LaserEmission-1/LaserEmission-1.in[LaserEmission-1.in]
{link_regtest_LaserEmission_1}/LaserEmission-1.in[LaserEmission-1.in]
All supplementary files can be found in https://gitlab.psi.ch/OPAL/regression-tests/tree/master/RegressionTests/LaserEmission-1[the laser emission regression test].
All supplementary files can be found in {link_regtest_LaserEmission_1}[the laser emission regression test].
[[sec.tutorial.inj2]]
==== PSI Injector II Cyclotron
......@@ -155,16 +149,16 @@ two single-gap flat-top cavities.
Following is an input file of *Single Particle Tracking mode* for PSI
Injector II cyclotron.
{website}/{branch}/examples/Injector2.in[Injector2.in]
{link_OPAL_doc}/examples/Injector2.in[Injector2.in]
The supplementary files should be placed in the same directory.
* {website}/{branch}/examples/Fieldmaps/Cav1.dat[Cav1.dat]
* {website}/{branch}/examples/Fieldmaps/Cav3.dat[Cav3.dat]
* {website}/{branch}/examples/Fieldmaps/ZYKL9Z.NAR[ZYKL9Z.NAR]
* {website}/{branch}/examples/Distribution/scdist.opal[scdist.opal]
* {website}/{branch}/examples/Distribution/spdist.opal[spdist.opal]
* {website}/{branch}/examples/Distribution/tdist.opal[tdist.opal]
* {link_OPAL_doc}/examples/Fieldmaps/Cav1.dat[Cav1.dat]
* {link_OPAL_doc}/examples/Fieldmaps/Cav3.dat[Cav3.dat]
* {link_OPAL_doc}/examples/Fieldmaps/ZYKL9Z.NAR[ZYKL9Z.NAR]
* {link_OPAL_doc}/examples/Distribution/scdist.opal[scdist.opal]
* {link_OPAL_doc}/examples/Distribution/spdist.opal[spdist.opal]
* {link_OPAL_doc}/examples/Distribution/tdist.opal[tdist.opal]
To run opal on a single node, just use this command:
......@@ -211,7 +205,7 @@ the biggest amplitude is the betatron tune value at the given energy.
Following is the input file for single bunch tracking with space charge
effects in Injector II.
{website}/{branch}/examples/Injector2-sc.in[Injector2-sc.in]
{link_OPAL_doc}/examples/Injector2-sc.in[Injector2-sc.in]
For the supplementary files see above, <<sec.tutorial.inj2>>
......