If you are a workshop attendee, the instructions are here. Please proceed to install the software.
First install git
and
and follow the compile instructions below.
First, open a terminal and clone the repository:
git clone --recursive https://github.com/dylan-jayatilaka/tonto.git
While waiting, in another terminal window, or using your software package manager, install:
perl
gfortran
make
blas
lapack
openmpi-3.0
(for parallel)python3
(recommended for testing)gnuplot
(recommended)
To compile Tonto, first enter the tonto
directory downloaded with
git
:
cd tonto
Then make a build
directory (name is up to you) and enter that :
mkdir build && cd build
Use cmake to generate the build (default uses Makefiles), and compile the programs :
cmake ..
make -j
If you want a specific compiler, use :
cmake .. -DCMAKE_Fortran_COMPILER=<insert-your-compiler-here>
make -j
where you should replace with the
command for your fortran compiler. We recommend gfortran-6
.
If you want a static executable for redistribution set the build type to RELEASE-STATIC as follows:
cmake .. -DCMAKE_BUILD_TYPE=RELEASE-STATIC
make -j
To make an MPI parallel version (e.g. using openmpi) , type :
cmake .. -DCMAKE_Fortran_COMPILER=mpifort -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DMPI=1
make -j
To change build type (e.g. make a DEBUG version) use this option :
cmake .. -DCMAKE_BUILD_TYPE=Debug
make -j
In the case you do NOT have lapack and blas installed, there is a packaged lapack included in tonto, which you can also request manually:
cmake .. -DCOMPILE_LAPACK=ON
make -j
By default the tonto
program is built with Release flags.
The executable program is located at:
build/tonto(.exe)
The standalone Hirshfeld atom refinement terminal (HARt) program will be located at:
build/hart(.exe)
Copy the program build/hart
anywhere you like
For help type hart -help
.
The tests use the test.py
script located in scripts
to check the difference between outputs. This should
defer to sbftool
for SBF formatted files, and will
overcome small numerical differences.
To run all tests, in the build directory type:
ctest
Or you may use ctest
directly and run only tests matching
certain labels or regular expressions; or specify the number
of processors to use when running tests :
ctest -L short # this will run all tests with the label short.
ctest -R h2o # this will run all tests with h2o in their name.
ctest -L long -j4 # this will run all long tests with 4 jobs at a time.
You should get mostly the passed
message --- but there may be small
numerical differences which lead to pseudo-failures. If you are keen
you may check for true failed tests.
To check failures go into the tests/
folder and then from there into the
folder with the same name as the job that failed. You should see there
pairs of files called <file>
and <file>.bad
. You have to compare
the reference <file>
and alleged failed output file <file.bad>
using your favourite tool e.g.
vimdiff stdout stdout.bad
Let me know at
dylan.jayatilaka@gmail.com
See the wiki for details.