Pegamoid 2.11

Orbital viewer for OpenMolcas

Pegamoid

Pegamoid is an orbital viewer especially suited for use with OpenMolcas. It can be used to view orbitals and quickly select active spaces for use in CASSCF or RASSCF calculations.

Features

The following formats can be opened:

• HDF5 files, as generated by some (Open)Molcas modules like SCF or RASSCF, if compiled with HDF5 support.

• InpOrb files, generated by some (Open)Molcas modules like SCF or RASSCF, provided an HDF5 file for the same system was opened first.

• Molden files.

• Luscus files, generated by the GRID_IT module.

• Grid files (ASCII), generated by the GRID_IT module.

• Cube files (formatted).

For HDF5, InpOrb and Molden files, orbitals are computed on the fly from the basis set, and it is possible to change the sampling resolution and shape and size of the sampled volume. Luscus, grid and cube files contain precomputed volumetric data and only the existing data can be displayed.

Depending on availability in the input file, the following features and objects are supported:

• Selection of orbital.

• Selection of spin.

• Selection of symmetry irrep.

• Natural average or state-specific orbitals.

• Electron density and Laplacian.

• Natural average or state-specific spin orbitals.

• Spin density.

• Natural difference orbitals.

• Difference, attachment and detachment density.

• Natural transition orbitals.

• Transition, hole, particle and unrelaxed difference density.

For any orbital or density, gradient lines can be computed and displayed (particularly significant for the electron density). Densities can be computed for reduced subsets of orbitals (for instance, only for the active orbitals), and the user can write arbitrary notes for each orbital.

The value, opacity, colors and texture properties used to display isurfaces can be adjusted and the display of the following elements can be toggled:

• Positive and negative parts of the isosurface.

• Nodal surfaces.

• Nuclei and bonds.

• Atom labels.

• Volume box.

Finally, the type of orbital (inactive, active...) can be changed and the orbitals saved in the following formats usable in the (Open)Molcas programs:

• HDF5 format.

• InpOrb format.

or the current volumetric data or snapshot can be saved as:

• Cube format.

• PNG image.

Tips for OpenMolcas

Use the TDM keyword in a RASSCF calculation to include transition densities in the HDF5 file.

Use the TRD1 keyword in a RASSI calculation to include state and transition densities in the HDF5 file. Use the SUBSET keyword to reduce the number of transition densities stored.

Use the WFA module for more detailed analysis.

Installation

The recommended way to install Pegamoid is by using the pip package manager:

pip install Pegamoid

(you may also want to add the flags --upgrade and/or --user).

Then you just run:

pegamoid.py [filename]

where [filename] is an optional supported file to open. In the case of InpOrb files, you can supply two filenames (in any order): the InpOrb file and a corresponding HDF5 file.

There are other ways to get Pegamoid. One is cloning the git repository, e.g.

git clone https://gitlab.com/Jellby/Pegamoid.git

Another way, since Pegamoid is contained in a single python script, is downloading only the script file pegamoid.py.

Once the program is fetched, it can be run directly or through a python interpreter, no installation is needed, i.e.

./pegamoid.py [filename]

or

python pegamoid.py [filename]

However, the script has some requirements (this should be taken care of by pip, if you use it) that must be installed for it to work:

• Python 2 or python 3 (at least versions 2.7 and 3.4 have been tested).

• Qt with python bindings. PyQt 4, PyQt 5 and PySide have been tested. It is recommended to install the python module qtpy (needed for PySide).

• VTK with python bindings. Version 8.1.0 has been tested, earlier versions will most likely not work.

• The numpy and h5py python modules.

• Other python modules that may not be installed by default, it should be clear which ones, if any, are needed when trying to run Pegamoid.

Use of scratch disk space

To speed up the display of several orbitals and the computation of densities, Pegamoid uses some scratch disk space to store the computed basis functions. A file named pegamoid.cache will be created in a temporary location (typically inside the /tmp directory). For grids with many points and with many basis functions, this file could grow very large and even use up all available disk space. The maximum scratch size is by default 1 GiB, but it can be configured in "File > Set scratch", or through the environment variable PEGAMOID_MAXSCRATCH, e.g.:

PEGAMOID_MAXSCRATCH=100MB ./pegamoid.py

for a maximum size of 100 MB. If the scratch size is not enough to hold all basis functions at the current resolution, it will only be used when computing the densities. In the "Set scratch" window you can also find the instance-specific temporary path, as well as the maximum cache size, the scratch size currently in use, and the recommended size to allow keeping a cache of all basis functions. The scratch file and directory are removed on a clean exit, but if the program crashes or is otherwise abnormally interrupted, they may be left behind.

Use with a remote connection

Production calculations are usually not run on the local machine, but on some remote server like a supercomputer. To view/save/modify orbital files, it is always possible to transfer the files between the local and remote machines. It is, however, more convenient to run Pegamoid directly on the remote machine and have the graphical interface display in the local machine. Unfortunately, there are some difficulties that make this nontrivial.

First, the different requirements may not be installed in the remote system. A possible solution is installing them for the user account with e.g. pip install --user. In this case it will probably be easier to install qtpy and PySide instead of PyQt.

Then, the VTK visualization uses some advanced OpenGL features that may not be available with all graphical drivers and it could be challenging to make it work through a remote connection. We have had success running Pegamoid with vglrun inside a ThinLinc session, or a VNC session opened directly from an ssh connection. The specific needs and working solution will probably depend on the hardware and software available in the remote computer.

Known problems

In some systems there are display issues in the 3D window, where some elements are wrongly drawn "on top" of others (this does not refer to the atom names, which are always on top). This problem has been seen with PyQt 5, and it's usually solved by switching to PyQt 4 or installing QtOpenGL support (in the "About" dialog, check if the "Qt API" line says "with QtOpenGL"). To disable QtOpenGL detection, define the environment variable PEGAMOID_NO_QGL=1.

Another reported issue is that the orbital/density isosurfaces completely disappear, while the "molecule" (nuclei and bonds) are normally displayed. This is probably a driver problem. As a workaround, defining the environment variable PEGAMOID_DISABLE_OPACITY=1 will completely disable the opacity slider and hopefully allow the isosurfaces to be shown. However, the rendering of textures with transparency may be affected by artifacts.

Issues with the "Transform" and "Texture" windows not appearing have also been reported in some PyQt 4 versions. It is unclear at the moment what is the reason for this.

When running in KDE Plasma 5, some shortcuts may not work because KDE tries to be smart and overwrites them (see here for example). To fix this, you can add to the ~/.config/kdeglobals file:

[Development]
AutoCheckAccelerators=false