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Requirements 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. • Python 2.7-3.x supported. It is highly recommended that you use latest Python 3.x unless you know you need other dependencies that works with Python 2.x only.
This does a user installation to prevent breaking any system-wide packages. If pipenv isn’t available in your shell after installation, you’ll need to add the user base’s binary directory to your PATH. Download powerpoint 2010 for mac. On Linux and macOS you can find the user base binary directory by running python-m site--user-base and adding bin to the end. Conda install scikit-learn. If you don’t already have a python installation with numpy and scipy, we recommend to install either via your package manager or via a python bundle. To upgrade or uninstall scikit-learn installed with Anaconda or conda you should not use the pip command.
Pip, and Jupyter installation. Use brew to install conda, run below command. Python -m ipykernel. I came across the 'brew install' solution too but while installing Homebrew before running this comand, Homebrew asked for changing the permissions on certain system folders. Sudo apt-get install libboost-all-dev I'm on a Mac, and I installed cmake with conda and boost with brew: conda install cmake brew install boost. Python Conda Installation.
• numpy>=1.14 • scipy>=1.0.1 • matplotlib>=1.5+ • monty>=0.9.6 • requests>=2.0+ • pybtex • pyyaml • tabulate • six Most of these are fairly easy to install. The well-established numpy and scipy should have ready-made installation packages for all platforms. The rest are pure/semi-pure Python packages that installs without any issues with pip and easy_install.
Optional dependencies Optional libraries that are required if you need certain features. • sympy: For defect generation and analysis. • VTK with Python bindings 5.8+ (): For visualization of crystal structures using the pymatgen.vis package. Note that the VTK package is incompatible with Python 3.x at the moment. • Atomistic Simulation Environment or ASE 3.6+: Required for the usage of the adapters in pymatgen.io.aseio between pymatgen’s core Structure object and the Atoms object used by ASE. Note that the ASE package is incompatible with Python 3.x at the moment. • OpenBabel with Python bindings (): Required for the usage of the adapters in pymatgen.io.babelio between pymatgen’s Molecule and OpenBabel’s OBMol.
Windows® • Adobe® Acrobat® 5.05, 6.x, 7.x • Microsoft® Windows® 2000 with service pack 4 • Microsoft® Windows® XP Professional or Home Edition Macintosh® • Mac OS® 9.x on PowerPC™ – Adobe® Acrobat® 5.05 • Mac OS X v.10.2.8, 10.3 or 10.4 – Adobe Acrobat 6.x, 7.x Hardware • Minimum 64 MB of RAM (128MB recommended) • 1.024x768 screen resolution Color Management To enable Color Management you must have a Color Management enabled operating system. Macintosh® • Adobe® Acrobat® 4.05 • Adobe® Acrobat® 5.0 • MacOS 8.6 or 9.x Hardware • Minimum 32 MB of RAM Color Management To enable Color Management you must have a Color Management enabled operating system. Windows® • Adobe® Acrobat® 4.05 • Adobe® Acrobat® 5.0 • Microsoft® Windows 98 or higher, • Microsoft® Windows NT 4.0 on x86 (with Service Pack 5 or later) • Microsoft® Windows 2000/XP. Enfocus PitStop Professional is compatible with ICM on Microsoft® Windows® Windows® 2000, Windows® XP or higher and with Apple® ColorSync® 2.5 and higher on Mac OS. What is the newest version of adobe acrobat pro for mac.
Opens up input and output support for the very large number of input and output formats supported by OpenBabel. • networkx: For graph analysis associated with critic2 topological analysis of electron charge densities, pygraphviz is also required for visualization. • nose - For unittesting. Not optional for developers.
Optional non-Python programs Optional non-python libraries (because no good python alternative exists at the moment) required only for certain features: • ffmpeg: For generation of movies in structure_vtk.py. The executable ffmpeg must be in the path.
• enum: For the use of pymatgen.transformations.advanced_transformations.EnumerateStructureTransformation and 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 EnumerateStructureTransformation. Many other advanced transformations (e.g., MagOrderingTransformation) use EnumerateStructureTransformation. The enum.x and makestr.x executables must be in the path. Get it at and follow the instructions to compile multienum.x and makestr.x. • bader: For use with. This library by Henkelmann et al.
Provides a robust way to calculate the Bader analysis from a CHGCAR. The bader executable must be in the path. • gulp: For use with, which is in turn used extensively by to compute empirical defect energies. • aconvasp: For use with the.
• Zeo++ (): For defect structure generation. This is required in addition to installing the zeo Python package. • critic2 (): For topological analysis of critical points from electronic charge density. Provides more detailed information compared to bader. For use with.
• graphviz (): For visualization of graphs generated using critic2. Cd VTK ( this is the directory you expanded VTK into ) mkdir build cd build ccmake. ( this uses cmake in an interactive manner ) Press “t” to toggle advanced mode.
Then press “c” to do an initial configuration. After the list of parameters come out, ensure that the PYTHON_VERSION is set to 3, the VTK_WRAP_PYTHON is set to ON, and BUILD_SHARED_LIBS is 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 3.5 installed using conda is given below (only variables that need to be modified/checked are shown).
PYTHON_EXECUTABLE: FILEPATH =/ Users // miniconda3 / bin / python3 PYTHON_INCLUDE_DIR: PATH =/ Users // miniconda3 / include / python3. 5 m PYTHON_LIBRARY: FILEPATH =/ Users // miniconda3 / lib / libpython3. Dylib VTK_INSTALL_PYTHON_MODULE_DIR: PATH =/ Users // miniconda3 / lib / python3. 5 / site - packages VTK_PYTHON_VERSION: STRING = 3 VTK_WRAP_PYTHON: BOOL = ON Then press “c” again to configure and finally “g” to generate the required make files After the CMakeCache.txt file is generated, type. Mkdir ob - build cd ob - build cmake - DPYTHON_BINDINGS = ON - DRUN_SWIG = ON - DEIGEN3_INCLUDE_DIR =./ eigen3./ ob - src 2 >& 1 tee cmake. Out • Before proceeding further, similar to the VTK installation process in the previous section, you may also need to modify the CMakeCache.txt file by hand if your 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.
Mac OS X comes with Python 2.7 out of the box.
You do not need to install or configure anything else to use Python 2. Theseinstructions document the installation of Python 3.
The version of Python that ships with OS X is great for learning, but it’s notgood for development. The version shipped with OS X may be out of date from theofficial current Python release,which is considered the stable production version.
Doing it Right¶
Best Python Installation For Mac Brew Conda Command
Let’s install a real version of Python.
Before installing Python, you’ll need to install GCC. GCC can be obtainedby downloading Xcode, the smallerCommand Line Tools (must have anApple account) or the even smaller OSX-GCC-Installerpackage.
Note
If you already have Xcode installed, do not install OSX-GCC-Installer.In combination, the software can cause issues that are difficult todiagnose.
Note
If you perform a fresh install of Xcode, you will also need to add thecommandline tools by running
xcode-select--install
on the terminal.While OS X comes with a large number of Unix utilities, those familiar withLinux systems will notice one key component missing: a package manager.Homebrew fills this void.
To install Homebrew, open
Terminal
oryour favorite OS X terminal emulator and runThe script will explain what changes it will make and prompt you before theinstallation begins.Once you’ve installed Homebrew, insert the Homebrew directory at the topof your
PATH
environment variable. You can do this by adding the followingline at the bottom of your ~/.profile
fileIf you have OS X 10.12 (Sierra) or older use this line instead
Now, we can install Python 3:
This will take a minute or two.
Pip¶
Homebrew installs
pip
pointing to the Homebrew’d Python 3 for you.Working with Python 3¶
At this point, you have the system Python 2.7 available, potentially theHomebrew version of Python 2 installed, and the Homebrewversion of Python 3 as well.
will launch the Homebrew-installed Python 3 interpreter.
will launch the Homebrew-installed Python 2 interpreter (if any).
will launch the Homebrew-installed Python 3 interpreter.
If the Homebrew version of Python 2 is installed then
pip2
will point to Python 2.If the Homebrew version of Python 3 is installed then pip
will point to Python 3.The rest of the guide will assume that
python
references Python 3.Pipenv & Virtual Environments¶
The next step is to install Pipenv, so you can install dependencies and manage virtual environments.
Best Python Installation For Mac Brew Condado
A Virtual Environment is a tool to keep the dependencies required by different projectsin separate places, by creating virtual Python environments for them. It solves the“Project X depends on version 1.x but, Project Y needs 4.x” dilemma, and keepsyour global site-packages directory clean and manageable.
For example, you can work on a project which requires Django 1.10 while alsomaintaining a project which requires Django 1.8.
So, onward! To the Pipenv & Virtual Environments docs!
This page is a remixed version of another guide,which is available under the same license.