Download and installation

System Requirements

• Atomic Simulation Environment (ASE)
• BLAS & LAPACK libraries
  • basic linear algebra operations (matrix vector multiplication etc.)
  • solving (generalized) eigenvalue problem
• numpy
  • for numerical arrays, some linear algebra, etc.
• scipy
  • fitting, interpolation, non-linear equation solving, etc.
• [matplotlib](http://matplotlib.sourceforge.net/ matplotlib)
  • not explicitly needed for production calculations
  • hotbit works, in principle, without matplotlib
  • for plotting

Using git

For svn checkout (different options):

# initial checkout 
~>git clone https://github.com/pekkosk/hotbit.git

Installation

1. Download the code to some location (e.g. ~/hb):

~>git clone https://github.com/pekkosk/hotbit.git

2. Run python's setup.py script.

~/hb>python setup.py install --home=<my-directory>

This will compile the C-extensions and copy data files (parametrizations) to <my-directory>.

3. Setup environmental variables HOTBIT_DIR and HOTBIT_PARAMETERS, append HOTBIT_DIR to PYTHONPATH so that python can find hotbit and box modules, and append HOTBIT_DIR/hotbit to PATH to provide access Hotbit shell guide.

export HOTBIT_DIR="<my-directory>/lib64/python" #the name "lib64" can vary
export PATH="<my-directory>:$PATH"
export HOTBIT_PARAMETERS="<my-directory>/param"
export PYTHONPATH="$PYTHONPATH:$HOTBIT_DIR"

4. Run tests

• Run script test.py in $HOTBIT_DIR/hotbit/test. This will take a minute or so, depending on the machine.

Organization of the code

• Source code

• hotbit module for python in HOTBIT_DIR folder
• contains Fortran code that needs to be compiled (in hotbit/fortran)
• hotbit comes together with box python module
  • box contains auxiliary python stuff, and hotbit needs it
  • interpolation, plotting, file input/output, molecular dynamics stuff, timing

• Files containing element data: .elm-files

• By default in HOTBIT_PARAMETERS folder
• Contains on-site energies, Hubbard U parameters,...
• Customized .elm-files can be anywhere (given explicitly to calculator)

• Parametrization files: .par-files

• By default in HOTBIT_PARAMETERS
• Contains all pair-wise data: Slater-Koster tables and short-range repulsions
• Customized .par-files can be anywhere (given explicitly to calculator)