{
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        "author": "Ignacio Fdez. Galv\u00e1n",
        "author_email": "jellby@yahoo.com",
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        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Environment :: X11 Applications :: Qt",
            "Intended Audience :: Science/Research",
            "Topic :: Multimedia :: Graphics :: 3D Rendering",
            "Topic :: Scientific/Engineering :: Chemistry",
            "Topic :: Scientific/Engineering :: Visualization"
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        "description": "Pegamoid\n========\n\nPegamoid is an orbital viewer especially suited for use with\n[OpenMolcas](https://gitlab.com/Molcas/OpenMolcas). It can be used to view\norbitals and quickly select active spaces for use in CASSCF or RASSCF\ncalculations.\n\nFeatures\n--------\n\nThe following formats can be opened:\n\n* HDF5 files, as generated by some (Open)Molcas modules like SCF or RASSCF, if compiled with HDF5 support.\n\n* InpOrb files, generated by some (Open)Molcas modules like SCF or RASSCF, provided an HDF5 file for the same system was opened first.\n\n* [Molden](http://www.cmbi.ru.nl/molden/) files.\n\n* [Luscus](http://luscus.sourceforge.net/) files, generated by the GRID_IT module.\n\n* Grid files (ASCII), generated by the GRID_IT module.\n\n* [Cube](http://paulbourke.net/dataformats/cube/) files (formatted).\n\nFor HDF5, InpOrb and Molden files, orbitals are computed on the fly from the\nbasis set, and it is possible to change the sampling resolution and shape and\nsize of the sampled volume. Luscus, grid and cube files contain precomputed\nvolumetric data and only the existing data can be displayed.\n\nDepending on availability in the input file, the following features and objects\nare supported:\n\n* Selection of orbital.\n\n* Selection of spin.\n\n* Selection of symmetry irrep.\n\n* Natural average or state-specific orbitals.\n\n* Electron density and Laplacian.\n\n* Natural average or state-specific spin orbitals.\n\n* Spin density.\n\n* Natural difference orbitals.\n\n* Difference, attachment and detachment density.\n\n* Natural transition orbitals.\n\n* Hole and particle density.\n\nFor any orbital or density, gradient lines can be computed and displayed\n(particularly significant for the electron density). Densities can be computed\nfor reduced subsets of orbitals (for instance, only for the active orbitals),\nand the user can write arbitrary notes for each orbital.\n\nThe value, opacity, colors and texture properties used to display isurfaces can\nbe adjusted and the display of the following elements can be toggled:\n\n* Positive and negative parts of the isosurface.\n\n* Nodal surfaces.\n\n* Nuclei and bonds.\n\n* Atom labels.\n\n* Volume box.\n\nFinally, the type of orbital (inactive, active...) can be changed and the\norbitals saved in the following formats usable in the (Open)Molcas programs:\n\n* HDF5 format.\n\n* InpOrb format.\n\nor the current volumetric data or snapshot can be saved as:\n\n* Cube format.\n\n* PNG image.\n\nInstallation\n------------\n\nThe recommended way to install Pegamoid is by using the [`pip` package\nmanager](https://packaging.python.org/tutorials/installing-packages/#use-pip-for-installing):\n\n    pip install Pegamoid\n\n(you may also want to add the flags `--upgrade` and/or `--user`).\n\nThen you just run:\n\n    pegamoid.py [filename]\n\nwhere ``[filename]`` is an optional supported file to open. In the case of\nInpOrb files, you can supply two filenames (in any order): the InpOrb file and\na corresponding HDF5 file.\n\nThere are other ways to get Pegamoid. One is cloning the git repository, e.g.\n\n    git clone https://gitlab.com/Jellby/Pegamoid.git\n\nAnother way, since Pegamoid is contained in a single python script, is\ndownloading only the script file\n[pegamoid.py](https://gitlab.com/Jellby/Pegamoid/raw/master/pegamoid.py?inline=false).\n\nOnce the program is fetched, it can be run directly or through a python\ninterpreter, no installation is needed, i.e.\n\n    ./pegamoid.py [filename]\n\nor\n\n    python pegamoid.py [filename]\n\nHowever, the script has some requirements (this should be taken care of by\n`pip`, if you use it) that must be installed for it to work:\n\n* Python 2 or python 3 (at least versions 2.7 and 3.4 have been tested).\n\n* Qt with python bindings. PyQt 4, PyQt 5 and PySide have been tested. It is\n  recommended to install the python module qtpy (needed for PySide).\n\n* VTK with python bindings. Version 8.1.0 has been tested, earlier versions\n  will most likely not work.\n\n* The numpy and h5py python modules.\n\n* Other python modules that may not be installed by default, it should be clear\n  which ones, if any, are needed when trying to run Pegamoid.\n\nUse of scratch disk space\n-------------------------\n\nTo speed up the display of several orbitals and the computation of densities,\nPegamoid uses some scratch disk space to store the computed basis functions. A\nfile named ``pegamoid.cache`` will be created in a temporary location (typically\ninside the ``/tmp`` directory). For grids with many points and with many basis\nfunctions, this file could grow very large and even use up all available disk\nspace. The maximum scratch size is by default 1 GiB, but it can be configured in\n\"File > Set scratch\", or through the environment variable\n``PEGAMOID_MAXSCRATCH``, e.g.:\n\n    PEGAMOID_MAXSCRATCH=100MB ./pegamoid.py\n\nfor a maximum size of 100 MB. If the scratch size is not enough to hold all\nbasis functions at the current resolution, it will only be used when computing\nthe densities. In the \"Set scratch\" window you can also find the\ninstance-specific temporary path, as well as the maximum cache size, the scratch\nsize currently in use, and the recommended size to allow keeping a cache of all\nbasis functions. The scratch file and directory are removed on a clean exit, but\nif the program crashes or is otherwise abnormally interrupted, they may be left\nbehind.\n\nUse with a remote connection\n----------------------------\n\nProduction calculations are usually not run on the local machine, but on some\nremote server like a supercomputer. To view/save/modify orbital files, it is\nalways possible to transfer the files between the local and remote machines. It\nis, however, more convenient to run Pegamoid directly on the remote machine and\nhave the graphical interface display in the local machine. Unfortunately, there\nare some difficulties that make this nontrivial.\n\nFirst, the different requirements may not be installed in the remote system. A\npossible solution is installing them for the user account with e.g.\n``pip install --user``. In this case it will probably be easier to install qtpy\nand PySide instead of PyQt.\n\nThen, the VTK visualization uses some advanced OpenGL features that may not be\navailable with all graphical drivers and it could be challenging to make it\nwork through a remote connection. We have had success running Pegamoid with\n``vglrun`` inside a\n[ThinLinc](https://www.cendio.com/thinlinc/what-is-thinlinc) session, or a VNC\nsession opened directly from an ssh connection. The specific needs and working\nsolution will probably depend on the hardware and software available in the\nremote computer.\n\nKnown problems\n--------------\n\nIn some systems there are display issues in the 3D window, where some elements\nare wrongly drawn \"on top\" of others (this does not refer to the atom names,\nwhich are always on top). This problem has been seen with PyQt 5, and it's\nusually solved by switching to PyQt 4 or installing QtOpenGL support (in the\n\"About\" dialog, check if the \"Qt API\" line says \"with QtOpenGL\").\n\nIssues with the \"Transform\" and \"Texture\" windows not appearing have also been\nreported in some PyQt 4 versions. It is unclear at the moment what is the\nreason for this.\n\nWhen running in KDE Plasma 5, some shortcuts may not work because KDE tries to\nbe smart and overwrites them (see\n[here](https://stackoverflow.com/a/32711483/1538701) for example). To fix this,\nyou can add to the ``~/.config/kdeglobals`` file:\n\n    [Development]\n    AutoCheckAccelerators=false\n\n\n",
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