All required dependencies should be automatically taken care of if you install pymatgen using easy_install or pip. Otherwise, these packages should be available on PyPI.
- Python 2.7+ required. New default modules such as json are used, as well as new unittest features in Python 2.7.
- numpy - For array, matrix and other numerical manipulations. Used extensively by all core modules.
- pyhull 1.3.6+: For generation of phase diagrams.
- PyCifRW 3.3+: For reading and writing Crystallographic Information Format (CIF) files.
Optional python libraries that are required if you need certain features
- scipy 0.10+ (highly recommended) - For use in Gaussian smearing.
- matplotlib (highly recommended): For plotting (e.g., Phase Diagrams).
- VTK with Python bindings (http://www.vtk.org/): For visualization of crystal structures using the pymatgen.vis package.
- Atomistic Simulation Environment or ASE : Required for the usage of the adapters in pymatgen.io.aseio between pymatgen's core Structure object and the Atoms object used by ASE. Get it at https://wiki.fysik.dtu.dk/ase/.
- OpenBabel with Python bindings (http://openbabel.org). Required for the usage of the adapters in pymatgen.io.babelio between pymatgen's Molecule and OpenBabel's OBMol. Opens up input and output support for the very large number of input and output formats supported by OpenBabel.
- nose - For complete unittesting. This is not optional for developers!
Optional non-python libraries (because no good pythonic alternative exists at the moment) required only for certain features.
- ffmpeg : Needed for generation of movies (structure_vtk.py). The executable ffmpeg must be in the path. Get it at http://www.ffmpeg.org.
- enum : Needed for the use of EnumerateStructureTransformation and the pymatgen.command_line.enumlib_caller module. This library by Gus Hart provides a robust way to enumerate derivative structures. It can be used to completely enumerate all symmetrically distinct ordered structures of disordered structures via the EnumerateStructureTransformation. The multienum.x and makestr.x executables must be in the path. Get it at http://enum.sourceforge.org and follow the instructions to compile multienum.x and makestr.x.
For the code to generate POTCAR files, it needs to know where the VASP pseudopotential files are. We are not allowed to distribute these under the VASP license. The good news is that we have included a setup script to help you along.
If you cloned the repo directly from GitHub, you should have a run_me_first.sh file in the root directory of your local repo. Otherwise, you can get it directly from our github site at http://github.com/materialsproject/pymatgen. Run the shell script and follow the instructions. If you have done it correctly, you should get a resources directory with the following directory structure:
- psp_resources
|- POT_GGA_PAW_PBE
||- POTCAR.Ac_s.gz
||- POTCAR.Ac.gz
||- POTCAR.Ag.gz
...
|- POT_GGA_PAW_PW91
...After generating the resources directory, you should add a VASP_PSP_DIR environment variable pointing to the generated directory and you should then be able to generate POTCARs.
Alternatively, you can setup the above directly structure manually and set the VASP_PSP_DIR environment variable accordingly.
- Clone the repo at http://github.com/materialsproject/pymatgen.
In your root pymatgen repo directory, type (you may need to do this with root privileges):
python setup.py develop- Install any missing python libraries that are necessary.
I recommend that you start by reading some of the unittests in the tests subdirectory for each package. The unittests demonstrate the expected behavior and functionality of the code.
Please read up on pymatgen's coding guidelines </contributing> before you start coding. It will make integration much easier.
This section provides a guide for installing various optional libraries used in pymatgen. Some of the python libraries are rather tricky to build in certain operating systems, especially for users unfamiliar with building C/C++ code. Please feel free to send in suggestions to update the instructions based on your experiences. In all the instructions, it is assumed that you have standard gcc and other compilers (e.g., Xcode on Macs) already installed.
Typical installation of Xcode with python setup.py install seems to work fine. The pre-compiled binary for OSX 10.6 also seems to work.
This setup assumes you have the latest version of python (2.7 as of this is written) and numpy already installed. You will need to set the compiler flags to build matplotlib from source.
export CFLAGS="-arch x86_64 -I/usr/X11/include -I/usr/X11/include/freetype2"
export LDFLAGS="-arch x86_64 -L/usr/X11/lib"
python setup.py build
sudo python setup.py installFirst install solstudio 12.2. Then put the following code in a shell script and run it.
#!/bin/bash
PATH=/opt/solstudio12.2/bin:/usr/ccs/bin:/usr/bin:/usr/sfw/bin:/usr/sbin; export PATH
ATLAS=None; export ATLAS
BLAS=/opt/solstudio12.2/lib/libsunperf.so; export BLAS
LAPACK=/opt/solstudio12.2/lib/libsunmath.so; export LAPACK
python setup.py build
python setup.py installThe easiest is to install cmake from http://cmake.org/cmake/resources/software.html.
Type the following:
cd VTK (this is the directory you expanded VTK into)
cmake -i (this uses cmake in an interactive manner)For all options, use the defaults, EXCEPT for BUILD_SHARED_LIBS and VTK_WRAP_PYTHON which must be set to ON. You may also need to modify the python paths and library paths if they are in non-standard locations. For example, if you have installed the official version of Python instead of using the Mac-provided version, you will probably need to edit the CMakeCache Python links. Example configuration for Python 2.7 is given below (only variables that need to be modified are shown):
//Path to a program.
PYTHON_EXECUTABLE:FILEPATH=/Library/Frameworks/Python.framework/Versions/2.7/bin/python
//Path to a file.
PYTHON_INCLUDE_DIR:PATH=/Library/Frameworks/Python.framework/Versions/2.7/Headers
//Path to a library.
PYTHON_LIBRARY:FILEPATH=/Library/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib
//Also delete the prefix settings for python, which typically links to the Mac python.After the CMakeCache.txt file is generated, type:
make
sudo make installWith any luck, you should have vtk with the necessary python wrappers installed.
openbabel must be compiled with python bindings for integration with pymatgen. Here are the steps that I took to make it work:
- Install cmake from http://cmake.org/cmake/resources/software.html.
- Download openbabel 2.3.2 source code from http://sourceforge.net/projects/openbabel/files/openbabel/2.3.0/.
- Download Eigen version 3.0 from http://eigen.tuxfamily.org/index.php?title=Main_Page
- Install pkg-config (easiest way is to install homebrew and do the following:
- ::
brew install pkg-config
- Extract your Eigen and openbabel source distributions:
tar -zxvf openbabel-2.3.2.tar.gz
tar -zxvf eigen3.tar.gz- Now you should have two directories. Assuming that your openbabel src is in a directory called "openbabel-2.3.2" and your eigen source is in a directory called "eigen3", do the following steps.
mv openbabel-2.3.2 ob-src
mkdir ob-build
cd ob-build
cmake -DPYTHON_BINDINGS=ON -DEIGEN3_INCLUDE_DIR=../eigen3 ../ob-src 2>&1 |
tee cmake.out
make -j2
sudo make installWith any luck, you should have openbabel with python bindings installed. You can test your installation by trying to import openbabel from the python command line.
There does not seem to be any issues with installation as per the instructions given by the author. For convenience, the steps are reproduced here:
tar -zxvf enum.tar.gz
#Compile the symmetry library. Go to the celib/trunk directory:
cd celib/trunk
#Set an environment variable to identify your fortran compiler
export F90=gfortran
make
Next, make the enumeration library
cd ../../enumlib/trunk
make
# Make the necessary standalone executables
make multienum.x
make makestr.xAfter doing the above, make sure that the multienum.x and makestr.x executables are available in your path.