Merge branch 'doc_velo' into 'master'

Update velociraptor doc

See merge request !696

configure.ac

@@ -941,7 +941,7 @@ if test "x$with_velociraptor" != "xno"; then
    AC_PROG_FC
    AC_FC_LIBRARY_LDFLAGS
    if test "x$with_velociraptor" != "xyes" -a "x$with_velociraptor" != "x"; then
-      VELOCIRAPTOR_LIBS="-L$with_velociraptor -lstf -lstdc++ -lhdf5_cpp"
+      VELOCIRAPTOR_LIBS="-L$with_velociraptor -lvelociraptor -lstdc++ -lhdf5_cpp"
       CFLAGS="$CFLAGS -fopenmp"
    else
       VELOCIRAPTOR_LIBS=""
@@ -950,7 +950,7 @@ if test "x$with_velociraptor" != "xno"; then
    have_velociraptor="yes"
 
    AC_CHECK_LIB(
-      [stf],
+      [velociraptor],
       [InitVelociraptor],
       [AC_DEFINE([HAVE_VELOCIRAPTOR],1,[The VELOCIraptor library appears to be present.])],
       [AC_MSG_ERROR(Cannot find VELOCIraptor library at $with_velociraptor)],

doc/RTD/source/VELOCIraptorInterface/stfalone.rst

@@ -23,24 +23,18 @@ git repository as::
   git clone https://github.com/pelahi/VELOCIraptor-STF
 
 Similar to the SWIFT with VELOCIraptor configuration, we can use the 
-swift-interface branch to analyse individual snapshots. We can use this branch
+master to analyse individual snapshots. We can use this branch
 by doing::
 
   cd VELOCIraptor-STF
   git fetch
-  git checkout swift-interface
 
-Again we need to copy the default SWIFT config file to a other config file by
-doing::
+Again we need to configure VELOCIraptor::
 
-  cd stf
-  cp Makefile.config.SWIFT-template Makefile.config
+  cmake . -DVR_USE_GAS=ON
 
-Similar to configuring VELOCIraptor with swift we need to change the first 20
-lines of ``Makefile.config`` to work with our compiler, but we also need to 
-change the fact that we do not use the swift-interface but the standalone 
-version of the code, so change ``SWIFTINTERFACE="on"`` to 
-``SWIFTINTERFACE="off"``.
+In this case, we do not need the SWIFT interface, therefore we can drop
+this option (disabled by default).
 
 Compiling VELOCIraptor
 ----------------------
@@ -50,9 +44,7 @@ configuration with SWIFT. In this case we can compile the code as::
 
   make 
 
-After this an additional folder is created in ``VELOCIraptor-stf/stf`` called
-``bin``, in which the binary files of ``stf-gas`` is present (assuming you 
-run a simulation with SPH [#nosph]_)
+After this an executable is created (``VELOCIraptor-stf/stf``).
 
 Running VELOCIraptor on a Snapshot
 ----------------------------------
@@ -61,10 +53,12 @@ After the code is compile the next step is using VELOCIraptor on a single
 snapshot of a simulation. The code has several options which can be used, which
 can be displayed by running a terminal command of an invalid letter like::
 
-  ./stf-gas -h
+  ./stf -h
 
 which gives the information about the usage of the command::
 
+  VELOCIraptor/STF running with MPI. Number of mpi threads: 1
+  VELOCIraptor/STF running with OpenMP. Number of openmp threads: 8
   USAGE:
 
   -C <configuration file (overrides other options)> 
@@ -80,13 +74,6 @@ which gives the information about the usage of the command::
    ===== EXTRA OPTIONS REQUIRED FOR RAMSES INPUT ====== 
   -t <ramses snapnumber>
 
-After this we can run a VELOCIraptor on a snapshot as::
+After this we can run VELOCIraptor on a snapshot as::
   
-  ./stf-gas -i input -o output -C configfile.txt
-
-
-.. [#nosph] In the case that in the ``Makefile.config`` it is indicate that the 
-   simulation does only contain dark matter this will reflect back on the 
-   generated binary file. So ``stf-gas`` will change to ``stf`` in the case of 
-   a dark matter only simulation.
-
+  ./stf -i input -o output -C configfile.txt

doc/RTD/source/VELOCIraptorInterface/stfwithswift.rst

@@ -22,23 +22,17 @@ VELOCIraptor. This can be done by cloning the repository on GitHub_::
 
   git clone https://github.com/pelahi/VELOCIraptor-STF
 
-Currently the best version that works with SWIFT is the swift-interface branch
+Currently the best version that works with SWIFT is the master
 of VELOCIraptor, to get this branch use::
 
   cd VELOCIraptor-STF 
   git fetch 
-  git checkout swift-interface
 
-To get the default that works with SWIFT simply copy the SWIFT template file in
-the ``Makefile.config``::
+To get VELOCIraptor working with SWIFT simply use::
 
-  cd stf 
-  cp Makefile.config.SWIFT-template Makefile.config
-
-Depending on your compiler you want to change the first 20 lines of your
-``Makefile.config`` to work with your compiler and whether you want to use MPI
-or not. 
+  cmake . -DVR_USE_SWIFT_INTERFACE=ON -DCMAKE_CXX_FLAGS="-fPIC" -DVR_USE_GAS=ON
 
+If you wish to run swift without MPI, you will need to add ``-DVR_MPI=OFF``.
 
 Compiling VELOCIraptor
 ----------------------
@@ -46,13 +40,11 @@ Compiling VELOCIraptor
 After we downloaded the files and made a configuration file we can compile
 VELOCIraptor as follows::
 
-  make lib 
-  make libstf
+  make -j 4
 
-After the compilation of your code, there is an additional folder created in
-the ``VELOCIraptor-stf/stf`` directory called ``lib`` this directory has the
-library of VELOCIraptor and is required to run SWIFT with
-VELOCIraptor. Note that VELOCIraptor needs a serial version of the
+After the compilation of your code, you will find a static library ``libvelociraptor.a``,
+that is required to run SWIFT with VELOCIraptor.
+Note that VELOCIraptor needs a serial version of the
 HDF5 library, not a parallel build.
 
 Compiling SWIFT
@@ -61,7 +53,7 @@ The next part is compiling SWIFT with VELOCIraptor and assumes you already
 downloaded SWIFT from the GitLab_, this can be done by running::
 
   ./autogen.sh 
-  ./configure --with-velociraptor=/path/to/VELOCIraptor-STF/stf/lib 
+  ./configure --with-velociraptor=/path/to/VELOCIraptor-STF/src 
   make 
 
 In which ``./autogen.sh`` only needs to be run once after the code is cloned