Python库 | ninia-0.0.41.tar.gz

# Ninia A small Python wrapper for setting up Quantum Espresso input files. More functionality may be added later. <p>Currently, there is only assumed support for hexagonal close packed (HCP) crystal structures. Support for other structures may be tested but <b>should not</b> be expected.</p> > Note: The ```calc.create_bash()``` function (described later) assumes a Torque/PBS structure and sets up script to run in parallel using MPI. It also assumes an already built Quantum Espresso package and that ```pw.x``` can be run from the command-line. > > For tips on how to install Quantum Espresso on an HPC cluster, go to [Espresso Installation](/espresso_installation.md). --- ### Behind the Name  **Ninia** is a genus of snakes, also known as **coffee snakes**, that are native to parts of Central and South America. The choice of name is a play on **Python** and Quantum **Espresso**. --- #### Example usage: ```python # Import necessary modules: from ase.build import molecule, add_adsorbate, hcp0001 from ase.visualize import view # Set up geometry using ASE: surface = hcp0001('Ru', size=(4, 2, 4), a=2.7059, c=4.2815) ad = molecule('NH2') ad.rotate(180, 'x') add_adsorbate(surface, ad, 2.0, 'hcp') view(surface, viewer='x3d') # Specific viewer for use in Jupyter ``` <p>This will display a view of the geometry we have created. More information about ASE (Atomic Simulation Environment) can be found at their homepage: <a href="https://wiki.fysik.dtu.dk/ase/">https://wiki.fysik.dtu.dk/ase/</a></p> Then you can start using ninia to convert this geometry into an input file: ```python from ninia import relax calc = relax.Relax(prefix='Ru_test', functional='beef') calc.set_directories(outputdir='/home/ajs0201/workQE/output', pseudodir='/home/ajs0201/workQE/pseudo') # Ninia assumes the current script directory as the input directory # if none is given. calc.load_geometry(surface) calc.set_parameters(mixing_beta=0.15) calc.create_input() calc.create_job(hours=20) # This will create both an input (.i) file and bash (.sh) for the geometry above ``` --- If you do not specify the **prefix** and **functional** during the initialization step, the program will give warnings. Additionally, the pseudopotential directory ***must*** be set before the ```calc.load_geometry()``` step. In the ```calc.set_directories()``` step, you can set the following directories: * The directory to place input and bash files (**inputdir**) * The directory to place output files created by Quantum Espresso (**outputdir**) * The directory that contains pseudopotentials relevant to the calculation (**pseudodir**) > Note: The output directory, post calculation, will contain wave function files (.wfc) and save directories (.save/). This ***does not*** include output files (.out), which will be place in the input directory, unless explicitly changed. In the ```calc.set_parameters()``` step, you can set the following parameters [default]: * Plane wave cutoff energy (ecutwfc) [30.0] * Plane wave cutoff density (ecutrho) [4*ecutwfc] * Convergence threshold (conv_thr) [1e-8] * Electron mixing beta (mixing_beta) [0.7] * Number of k-points (k_points) [[4, 4, 4, 0, 0, 0]] * Functional (functional) [beef] In the ```calc.create_job()``` step, you can set the following parameters [default]: * Job type [```pbs.sh```] (other option ```slurm.sh```) * Partition/queue [```general```] * Memory used by calculation in GB (memory) [50] * Number of CPUs used by calculation (cpus) [8] * Walltime allowed for execution in hours (hours) [30]