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README.md

molsturm

Build Status Licence

molsturm is a modular electronic structure theory program, which tries to employ concepts like lazy matrices and orthogonal programming to achieve a versatile structure. Our motto is flexibility first, but speed second, even though we are probably very far from either of the two still.

Note that this is a very young project. Things may change in incompatible ways at any time.

Dependencies

molsturm consists of a set of compiled C++ libraries as well as a python module, which the user may use to setup and drive the calculations.

For building molsturm the following things are required:

  • cmake >= 3.0.0

  • A compiler supporting C++11: clang starting from clang-3.5 and gcc starting from gcc-5 should work.

  • swig >= 2.0.11

  • python >= 3.4, including the development headers

  • The regular build process mentioned below will automatically build the lazyten linear algebra library as well. This requires further

    See github.com/lazyten/lazyten for more details about lazyten's dependencies.

  • If you want to use Gaussian integrals from libint you further need

    • Eigen3
    • Autoconf
    • GNU Multiprecision library

In order to actually use the molsturm-module once it has been built the following python packages are required:

On a recent Debian/Ubuntu you can install all the aforementioned dependencies by running

apt-get install cmake swig python3-dev libopenblas-dev liblapack-dev libarmadillo-dev \
                python3-h5py python3-yaml python3-numpy python3-scipy libeigen3-dev \
                autoconf libgmp-dev

as root.

Optional dependencies

The dependencies in this section are only needed for some extra functionality. molsturm will work without them, but the mentioned features will be unavailable.

  • pyscf for full-configuration interaction (FCI)

Building molsturm

The recommended build enables Edward Valeev's libint library as an integral backend for Gaussian-type basis functions and installs molsturm to $HOME/opt of the local user:

# Fully download molsturm repository and dependent submodules
git clone https://github.com/molsturm/molsturm molsturm
cd molsturm
git submodule update --init --recursive

# Configure inside build directory
mkdir build && cd build
cmake -DCMAKE_INSTALL_PREFIX=~/opt -DAUTOCHECKOUT_MISSING_REPOS=ON -DGINT_ENABLE_LIBINT=ON ..
cmake --build .

# Test and install the build
ctest
cmake --build . --target install

Note, that this will automatically download and build libint as well as rapidcheck and Catch as well. The latter two libraries are only needed for testing molsturm and are not installed to $HOME/opt

Installing molsturm is still experimental and might not work properly in all cases. Please let us know about any problems. Every other feedback to improve the process is welcomed as well.

Configure options

In order to configure the build further there are a number of options, which can be passed to the first invocation of cmake in the instructions above. For example

  • -DCMAKE_INSTALL_PREFIX=<dir>: Choose a different installation directory for molsturm (if you remove the option entirely, the default is /usr/local)
  • -DENABLE_TESTS=OFF: Disable building the unit test executables
  • -DENABLE_EXAMPLES=OFF: Disable building the example executables
  • -DENABLE_DOCUMENTATION=ON: Build and install the sparse doxygen-generated in-source documentation.
  • -DGINT_ENABLE_LIBCINT=ON: Enable Gaussian integrals via the libcint library.
  • -DGINT_ENABLE_STURMINT=ON: Enable the Coulomb-Sturmian basis functions via sturmint (This library is not yet publicly available, but will be released soon.)

Using molsturm from python

Given that you followed the build procedure sketched above, you just need to make sure that your python interpreter finds molsturm in the installation directory. This is done by modifying the PYTHONPATH. For example if you chose the CMAKE_INSTALL_PREFIX of ~/opt as we shown above, you need to type

# Find out the major and minor version of your python interpreter:
VERSION=$(python3 -c 'import sys; print(str(sys.version_info.major) + "." + str(sys.version_info.minor))')
export PYTHONPATH="$PYTHONPATH:$HOME/opt/lib/python${VERSION}/site-packages"

to setup your environment for molsturm.

You might need to change python3 to python in the first line if your operating system uses python to refer to the binary of your python version 3 interpreter.

Running calculations

To get started with molsturm take a look at the examples subfolder. Good entry points are especially the single_point scripts.

In principle a calculation is a sequence of calls to python functions of the molsturm module. For example the snippet

import molsturm
hfres = molsturm.hartree_fock("Be", basis_type="gaussian",
                              basis_set_name="6-31g")
print("Be HF energy", hfres["energy_ground_state"])

just performs a Hartree-Fock calculation on a beryllium atom and prints the resulting SCF energy.