spycci.tools sub-module
split_multixyz function
- spycci.tools.split_multixyz(mol, file, suffix='', charge=None, spin=None, engine=None, remove_xyz_files=False)
Splits a .xyz file containing multiple structures into individual structures.
- Parameters:
mol (System object) – Input molecule, giving the charge/spin (if not defined) and name of the output molecules
file (str) – .xyz file containing the multiple structures
suffix (str, optional) – suffix to add to the new molecule names. By default, empty.
charge (int, optional) – Charge of the output molecules, by default the same as the input molecule
spin (int, optional) – Spin of the output molecules, by default the same as the input molecule
engine (Engine, optional) – The engine used to produce the multiple xyz file (If given and if available, the energies included in the comment line will be added to each system parsed)
remove_xyz_files (bool) – If set to True will remove the temporary .xyz files used in generating the System list
- Returns:
molecules_list – List containing the individual System object, whose structure is taken from the .xyz file
- Return type:
list
compress_dftb_trajectory function
- spycci.tools.compress_dftb_trajectory(filename, md_out='md.out', geo_xyz='geo_end.xyz')
Parses a geo_end.xyz trajectory and an md.out file to export a single compressed trajectory file also containing the energies for all frames
- Parameters:
filename (str) – name of the output trajectory files
md_out (str, optional) – path to the md.out file containing energy info (by default, ./md.out)
geo_xyz (str, optional) – path to the geo_end.xyz file containing energy info (by default, ./geo_end.xyz)
maxdist function
cyclization_check function
- spycci.tools.cyclization_check(start_file, end_file)
Checks if a cyclization has occurred (e.g., during a geometry optimization), or if a ring opening has occurred.
- Parameters:
start_file (str) – .xyz file containing the starting geometry
end_file (str) – .xyz file containing the final geometry
- Return type:
If a change in the number of rings is detected, returns True.
dissociation_check function
- spycci.tools.dissociation_check()
Checks if a dissociation has occurred (e.g., during a geometry optimization). Requires the presence of a .mol file in the current directory.
- Returns:
True, if a dissociation is detected
False, if a dissociation is not detected
process_output function
- spycci.tools.process_output(mol, method, calc, charge=None, spin=None, save_cubes=False)
Processes the output of a calculation, copying the output files to a safe directory (output_files) in the parent directory tree, and cleans the temporary directory if requested.
- Parameters:
mol (System object) – Systems processed in the calculation
method (str) – String indicating the level of theory for the calculation
calc (str) – Type of calculation
charge (int, optional) – Charge of the molecule in the calculation
spin (int, optional) – Spin of the molecule in the calculation
save_cubes (bool) – If set to true will copy the .cube files in a safe directory (output_densities) in the parent directory tree
save_dftb_trajectory function
- spycci.tools.save_dftb_trajectory(output_prefix)
Saves the geo_end.xyz and md.out files to a temporary directory where an MDTrajectory object can go read the data it needs.
- Parameters:
output_prefix (str) – name of the output trajectory files prefix
reorder_energies function
- spycci.tools.reorder_energies(system_list, ncores=None, maxcore=350, method_opt=None, method_el=None, method_vib=None)
Reorders a System list (generated by a CREST routine such as deprotonation) at a different level of theory.
- Parameters:
system_list (list(System)) – list containing the System objects to be reordered (e.g., generated by a CREST routine)
ncores (int, optional) – number of cores, by default all available cores
maxcore (int, optional) – memory per core, in MB, by default 350
method_opt (XtbInput/OrcaInput, optional) – level of theory for the geometry optimization. By default converted to gfn2
method_el (XtbInput/OrcaInput, optional) – level of theory for the electronic part of the energy. By default converted to M06-2X
method_vib (XtbInput/OrcaInput, optional) – level of theory for the vibronic contribution to the energy. By default converted to gfn2
- Returns:
molecule_list – System list, reordered at the new level of theory.
- Return type:
list(System)
spycci.tools.vmdtools sub-module
- spycci.tools.vmdtools.render_condensed_fukui(cubfile, resolution=4800, shadows=True, ambientocclusion=True, dof=True, VMD_PATH=None)
Given the path to a Fukui function cube file saves a .bmp render of the condensed Fukui functions.
- Parameters:
cubefile (str) – The path to the .fukui.cube file that must be rendered.
resolution (int) – The resolution of the output image (default: 4800).
shadows (bool) – If set to True will enable the vmd shadows option
ambientocclusion (bool) – If set to True will enable the vmd ambientocclusion option
dof (bool) – If set to True will enable the vmd dof option
VMD_PATH (str) – The path to the vmd folder. Is set to None (default), will automatically search vmd in the system PATH.
cubfile (str) –
- Return type:
None
- spycci.tools.vmdtools.render_fukui_cube(cubfile, isovalue=0.003, include_negative=False, resolution=4800, shadows=True, ambientocclusion=True, dof=True, VMD_PATH=None)
Given the path to a Fukui function cube file saves a .bmp render the volumetric Fukui function.
- Parameters:
cubefile (str) – The path to the .fukui.cube file that must be rendered.
isovalue (float) – The isovalue at which the contour must be plotted (default: 0.003).
include_negative (bool) – If set to True, will render also the negative part of the Fukui function. (default: False)
resolution (int) – The resolution of the output image (default: 4800).
shadows (bool) – If set to True will enable the vmd shadows option
ambientocclusion (bool) – If set to True will enable the vmd ambientocclusion option
dof (bool) – If set to True will enable the vmd dof option
VMD_PATH (str) – The path to the vmd folder. Is set to None (default), will automatically search vmd in the system PATH.
cubfile (str) –
- Return type:
None
- spycci.tools.vmdtools.render_spin_density_cube(cubfile, isovalue=0.005, resolution=4800, shadows=True, ambientocclusion=True, dof=True, VMD_PATH=None)
Given the path to a spin density cube file saves a .bmp render the function.
- Parameters:
cubefile (str) – The path to the .fukui.cube file that must be rendered.
isovalue (float) – The isovalue at which the contour must be plotted (default: 0.003).
resolution (int) – The resolution of the output image (default: 4800).
shadows (bool) – If set to True will enable the vmd shadows option
ambientocclusion (bool) – If set to True will enable the vmd ambientocclusion option
dof (bool) – If set to True will enable the vmd dof option
VMD_PATH (str) – The path to the vmd folder. Is set to None (default), will automatically search vmd in the system PATH.
cubfile (str) –
- Return type:
None