Welcome to Tonto!

And welcome to IUCR23 workshop people! Read on.

If you are a workshop attendee, the instructions are here. Please proceed to install the software.

1. Get ready ...

First install git and and follow the compile instructions below.

On Linux

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)

On MacOS

See Building on MacOS

On Windows

See Building on Windows

2. Get set ...

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.

3. Go!

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

Problems, bugs, contributions

Let me know at

   dylan.jayatilaka@gmail.com

How to run tonto

See the wiki for details.