17.1.1.18. pysisyphus.wrapper package

17.1.1.18.1. Submodules

17.1.1.18.2. pysisyphus.wrapper.jmol module

pysisyphus.wrapper.jmol.arrow(from_, to_)[source]

Jmol cmd to create arrow between two points.

Return type:

str

pysisyphus.wrapper.jmol.call_jmol(spt_str, show=False)[source]
pysisyphus.wrapper.jmol.render_cdd_cube(cdd_cube, isoval=0.001, orient='')[source]
pysisyphus.wrapper.jmol.render_geom_and_charges(geom, point_charges)[source]
pysisyphus.wrapper.jmol.to_point(point)[source]

Convert 3d point to Jmol point '{x, y, z}'

Return type:

str

pysisyphus.wrapper.jmol.view_cdd_cube(cdd_cube, isoval=0.001, orient='')[source]

17.1.1.18.3. pysisyphus.wrapper.mwfn module

pysisyphus.wrapper.mwfn.call_mwfn(inp_fn, stdin, cwd=None)[source]
pysisyphus.wrapper.mwfn.get_mwfn_exc_str(energies, Xa, Ya=None, Xb=None, Yb=None, thresh=0.001)[source]

Write plain text input for MWFN according to 3.21.

As of version 3.8 MWFN does not seem to handle this file when spin labels are present, even though it is given as an example in the manual.

pysisyphus.wrapper.mwfn.log(msg)[source]
pysisyphus.wrapper.mwfn.make_cdd(inp_fn, state, log_fn, cwd=None, keep=False, quality=2, prefix='S')[source]

Create CDD cube in cwd.

Parameters:

  • inp_fn (str) -- Filename of a .molden/.fchk file.

  • state (int) -- CDD cubes will be generated up to this state.

  • log_fn (str) -- Filename of the .log file.

  • cwd (str or Path, optional) -- If a different cwd should be used.

  • keep (bool) -- Wether to keep electron.cub and hole.cub, default is False.

  • quality (int) -- Quality of the cube. (1=low, 2=medium, 3=high).

pysisyphus.wrapper.mwfn.wrap_stdin(stdin)[source]

17.1.1.18.4. pysisyphus.wrapper.packmol module

pysisyphus.wrapper.packmol.call_packmol(inp)[source]
pysisyphus.wrapper.packmol.make_input(output_fn, solvent_fn, solvent_num, sphere_radius, solute_fn=None, solute_num=None, tolerance=2.0)[source]

17.1.1.18.5. Module contents