digichem-core 6.0.0rc1__py3-none-any.whl

digichem/data/config/digichem.yaml

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+# Master silico config file. Uncomment and change options here to affect everyone.
+#
+# Options for controlling the appearance of simulated UV-Vis like absorption spectra.
+# required: False
+#absorption_spectrum:
+#   Set to False to disable image rendering.
+#   type: wrapper_type, default: True, required: False
+#  enable_rendering: true
+#    
+#   The method used to set the min/max limits of the Y axis.
+#   Possible options are:
+#     - 'auto': Limits are set automatically so all peaks are clearly visible.
+#     - a list of [y_min, y_max], where y_min is the most negative value on the Y axis, and y_max is
+#    the most positive value on the Y axis (both in oscillator strength).
+#   type: wrapper_type, default: auto, required: False
+#  y_limits: auto
+#    
+#   The method used to set the min/max limits of the X axis.
+#   Possible options are:
+#     - 'auto': Limits are set automatically so all peaks are clearly visible.
+#     - a list of [x_min, x_max], where x_min is the most negative value on the X axis, and x_max is
+#    the most positive value on the X axis (both in nm).
+#   type: wrapper_type, default: auto, required: False
+#  x_limits: auto
+#    
+#   The maximum image width in pixels.
+#   Absorption graphs will grow/shrink their width to fit available data, keeping a constant scale 
+#   (constant pixels to nm ratio) but only up to this maximum.
+#   To disable the maximum width, set to null.
+#   type: wrapper_type, default: 1200, required: False
+#  max_width: 1200
+#    
+#   The minimum oscillator strength that a peak must have to be shown in the graph, as a fraction 
+#   ofthe highest peak.
+#   Set to 0 for no cutoff (all peaks shown), which may results in the graph being extended well 
+#   beyond the drawn peaks (because many peaks are too small to see).
+#   This option has no effect when using manual x limits.
+#   type: wrapper_type, default: 0.01, required: False
+#  peak_cutoff: 0.01
+#    
+#   The amount (in nm) to extend the x axis past the highest/lowest energy peak.
+#   type: wrapper_type, default: 40, required: False
+#  x_padding: 40
+#    
+#   The full-width at half-maximum; changes how wide the drawn peaks are. Note that the choice of 
+#   peak width is essentially arbitrary; only the peak height is given by calculation. Units are eV.
+#   type: wrapper_type, default: 0.4, required: False
+#  fwhm: 0.4
+#    
+#   The minimum y value to plot using the Gaussian function (controls how close to the x axis we 
+#   draw the gaussian) as a fraction of the max peak height.
+#   type: wrapper_type, default: 0.001, required: False
+#  gaussian_cutoff: 0.001
+#    
+#   The spacing between x values to plot using the Gaussian function, in eV. Values that are too 
+#   large will result in 'curves' made up of a series of straight edges.
+#   type: wrapper_type, default: 0.01, required: False
+#  gaussian_resolution: 0.01
+#    
+#   Whether or not to use the jacobian transformation to correctly scale the y-axis (see J. Phys. 
+#   Chem. Lett. 2014, 5, 20, 3497)
+#   type: wrapper_type, default: True, required: False
+#  use_jacobian: true
+#    
+#   Whether to plot vertical bars for each excited state.
+#   type: wrapper_type, default: True, required: False
+#  plot_bars: true
+#    
+#   Whether to plot individual Gaussian functions for each excited state.
+#   type: wrapper_type, default: False, required: False
+#  plot_peaks: false
+#    
+#   Whether to plot the sum of all Gaussian functions (most closely simulates a real spectrum).
+#   type: wrapper_type, default: True, required: False
+#  plot_cumulative_peak: true
+#    
+# The default alignment method to use, MIN: minimal, FAP: furthest atom pair, AA: average angle, 
+# AAA: advanced average angle.
+# default: MIN, choices: ['MIN', 'FAP', 'AA', 'AAA'], required: False
+#alignment: MIN
+#  
+# The default angle units to use, deg: degrees, rad: radians.
+# default: deg, choices: ['deg', 'rad'], required: False
+#angle_units: deg
+#  
+# A list of database configs.
+# type: wrapper_type, list_type: list, default: [<silico.config.silico.Database_config object at 
+# 0x7f668619f970>], required: False
+#databases:
+#- name: main
+#  path: ~/.silico/silico.main.db
+#  
+# Options for controlling the appearance of simulated emission spectra. 'emission_spectrum' and 
+# 'absorption_spectrum 'take the same options.
+# required: False
+#emission_spectrum:
+#   Set to False to disable image rendering.
+#   type: wrapper_type, default: True, required: False
+#  enable_rendering: true
+#    
+#   The method used to set the min/max limits of the Y axis.
+#   Possible options are:
+#     - 'auto': Limits are set automatically so all peaks are clearly visible.
+#     - a list of [y_min, y_max], where y_min is the most negative value on the Y axis, and y_max is
+#    the most positive value on the Y axis (both in oscillator strength).
+#   type: wrapper_type, default: auto, required: False
+#  y_limits: auto
+#    
+#   The method used to set the min/max limits of the X axis.
+#   Possible options are:
+#     - 'auto': Limits are set automatically so all peaks are clearly visible.
+#     - a list of [x_min, x_max], where x_min is the most negative value on the X axis, and x_max is
+#    the most positive value on the X axis (both in nm).
+#   type: wrapper_type, default: auto, required: False
+#  x_limits: auto
+#    
+#   The maximum image width in pixels.
+#   Absorption graphs will grow/shrink their width to fit available data, keeping a constant scale 
+#   (constant pixels to nm ratio) but only up to this maximum.
+#   To disable the maximum width, set to null.
+#   type: wrapper_type, default: 1200, required: False
+#  max_width: 1200
+#    
+#   The minimum oscillator strength that a peak must have to be shown in the graph, as a fraction 
+#   ofthe highest peak.
+#   Set to 0 for no cutoff (all peaks shown), which may results in the graph being extended well 
+#   beyond the drawn peaks (because many peaks are too small to see).
+#   This option has no effect when using manual x limits.
+#   type: wrapper_type, default: 0.01, required: False
+#  peak_cutoff: 0.01
+#    
+#   The amount (in nm) to extend the x axis past the highest/lowest energy peak.
+#   type: wrapper_type, default: 40, required: False
+#  x_padding: 40
+#    
+#   The full-width at half-maximum; changes how wide the drawn peaks are. Note that the choice of 
+#   peak width is essentially arbitrary; only the peak height is given by calculation. Units are eV.
+#   type: wrapper_type, default: 0.4, required: False
+#  fwhm: 0.4
+#    
+#   The minimum y value to plot using the Gaussian function (controls how close to the x axis we 
+#   draw the gaussian) as a fraction of the max peak height.
+#   type: wrapper_type, default: 0.001, required: False
+#  gaussian_cutoff: 0.001
+#    
+#   The spacing between x values to plot using the Gaussian function, in eV. Values that are too 
+#   large will result in 'curves' made up of a series of straight edges.
+#   type: wrapper_type, default: 0.01, required: False
+#  gaussian_resolution: 0.01
+#    
+#   Whether or not to use the jacobian transformation to correctly scale the y-axis (see J. Phys. 
+#   Chem. Lett. 2014, 5, 20, 3497)
+#   type: wrapper_type, default: True, required: False
+#  use_jacobian: true
+#    
+#   Whether to plot vertical bars for each excited state.
+#   type: wrapper_type, default: True, required: False
+#  plot_bars: true
+#    
+#   Whether to plot individual Gaussian functions for each excited state.
+#   type: wrapper_type, default: False, required: False
+#  plot_peaks: false
+#    
+#   Whether to plot the sum of all Gaussian functions (most closely simulates a real spectrum).
+#   type: wrapper_type, default: True, required: False
+#  plot_cumulative_peak: true
+#    
+# Options that control the appearance of excited states energy diagrams.
+# required: False
+#excited_states_diagram:
+#   Set to False to disable image rendering.
+#   type: wrapper_type, default: True, required: False
+#  enable_rendering: true
+#    
+#   The method used to set the min/max limits of the Y axis.
+#   Possible options are:
+#     - 'all': Limits are set so all excited states are visible.
+#     - 'auto': Limits are set automatically so the lowest excited state of each multiplicity is 
+#   clearly visible (S1, D1, T1, Q1... N1 etc).
+#     - a list of [y_min, y_max], where y_min is the most negative value on the Y axis, and y_max is
+#    the most positive value on the Y axis (both in eV).
+#   type: wrapper_type, default: all, required: False
+#  y_limits: all
+#    
+#   Whether or not to show the dE(ST) label.
+#   type: wrapper_type, default: True, required: False
+#  show_dest: true
+#    
+# Options specifying paths to various external programs that silico may use. If no path is given, 
+# then these programs will simply be executed by name (so relying on OS path resolution to find the 
+# necessary executables, which is normally fine.)
+# required: False
+#external:
+#   Gaussian's formchk utility https://gaussian.com/formchk/
+#   default: formchk, required: False
+#  formchk: formchk
+#    
+#   Gaussian's cubegen utility https://gaussian.com/cubegen/
+#   default: cubegen, required: False
+#  cubegen: cubegen
+#    
+# Options for controlling the appearance of simulated IR like vibrational frequency spectra.
+# required: False
+#IR_spectrum:
+#   Set to False to disable image rendering.
+#   type: wrapper_type, default: True, required: False
+#  enable_rendering: true
+#    
+#   The method used to set the min/max limits of the Y axis.
+#   Possible options are:
+#     - 'auto': Limits are set automatically so all peaks are clearly visible.
+#     - a list of [y_min, y_max], where y_min is the most negative value on the Y axis, and y_max is
+#    the most positive value on the Y axis (both in km/mol).
+#   type: wrapper_type, default: auto, required: False
+#  y_limits: auto
+#    
+#   The method used to set the min/max limits of the X axis.
+#   Possible options are:
+#     - 'auto': Limits are set automatically so all peaks are clearly visible.
+#     - a list of [x_min, x_max], where x_min is the most negative value on the X axis, and x_max is
+#    the most positive value on the X axis (both in cm-1).
+#   type: wrapper_type, default: auto, required: False
+#  x_limits: auto
+#    
+#   The full-width at half-maximum; changes how wide the drawn peaks are. Note that the choice of 
+#   peak width is essentially arbitrary; only the peak height is given by calculation. Units are 
+#   cm-1.
+#   type: wrapper_type, default: 80, required: False
+#  fwhm: 80
+#    
+#   The maximum image width in pixels.
+#   IR spectra will grow/shrink their width to fit available data, keeping a constant scale 
+#   (constant pixels to nm ratio) but only up to this maximum.
+#   To disable the maximum width, set to null.
+#   type: wrapper_type, default: 1500, required: False
+#  max_width: 1500
+#    
+#   The minimum y value to plot using the Gaussian function (controls how close to the x axis we 
+#   draw the gaussian) as a fraction of the max peak height.
+#   type: wrapper_type, default: 0.001, required: False
+#  gaussian_cutoff: 0.001
+#    
+#   The spacing between x values to plot using the Gaussian function, in eV. Values that are too 
+#   large will result in 'curves' made up of a series of straight edges.
+#   type: wrapper_type, default: 1.0, required: False
+#  gaussian_resolution: 1.0
+#    
+# Options relating to output of error messages. Note that the final logging level is determined by 
+# combining both 'log_level' and 'verbose', so a 'log_level' of 'OFF' and 'verbose' of '2' is equal 
+# to 'ERROR'.
+# required: False
+#logging:
+#   The level of messages to output, one of OFF (no logging at all), CRITICAL (fewest messages), 
+#   ERROR, WARNING, INFO or DEBUG (most messages)
+#   default: INFO, choices: ['OFF', 'CRITICAL', 'ERROR', 'WARNING', 'INFO', 'DEBUG'], required: 
+#   False
+#  log_level: INFO
+#    
+#   Increase the verbosity of the program by this amount. Each integer increase of verbosity will 
+#   increase 'log_level' by 1 degree.
+#   type: wrapper_type, default: 0, required: False
+#  verbose: 0
+#    
+#   Whether to print output from render engines.
+#   type: wrapper_type, default: False, required: False
+#  render_logging: false
+#    
+# Options for controlling simulated NMR spectra
+# required: False
+#nmr:
+#   Set to False to disable image rendering.
+#   type: wrapper_type, default: True, required: False
+#  enable_rendering: true
+#    
+#   Discard J coupling that is below this threshold (in Hz)
+#   type: wrapper_type, default: 1, required: False
+#  coupling_filter: 1
+#    
+#   The full-width at half-maximum; changes how wide the drawn peaks are. Note that the choice of 
+#   peak width is essentially arbitrary; only the peak height is given by calculation. Units are 
+#   ppm.
+#   type: wrapper_type, default: 0.01, required: False
+#  fwhm: 0.01
+#    
+#   The minimum y value to plot using the Gaussian function (controls how close to the x axis we 
+#   draw the gaussian) as a fraction of the max peak height.
+#   type: wrapper_type, default: 0.001, required: False
+#  gaussian_cutoff: 0.001
+#    
+#   The spacing between x values to plot using the Gaussian function, in ppm. Values that are too 
+#   large will result in 'curves' made up of a series of straight edges.
+#   type: wrapper_type, default: 0.001, required: False
+#  gaussian_resolution: 0.001
+#    
+#   The frequency to run the simulated spectrometer at. Larger values will result in narrower 
+#   coupling. Units are MHz
+#   type: wrapper_type, default: 100, required: False
+#  frequency: 100
+#    
+#   The threshold within which similar peaks will be merged together, before they are split by 
+#   coupling. This option typically results in faster execution, but more error, compared to 
+#   post_merge. Units in ppm.
+#   type: wrapper_type, default: 0.01, required: False
+#  pre_merge: 0.01
+#    
+#   The threshold within which similar peaks will be merged together. Units in ppm.
+#   type: wrapper_type, required: False
+#  post_merge: null
+#    
+#   The chemical shift of a standard reference peak (in ppm) to use to adjust the spectrum. One for 
+#   each element.
+#   type: wrapper_type, default: B: 111.27199999999999
+#   C: 197.90316666666664
+#   F: 183.2779999999999
+#   H: 31.68766666666667
+#   P: 290.8630000000001
+#   , required: False
+#  standards: 'B: 111.27199999999999
+#    C: 197.90316666666664
+#    F: 183.2779999999999
+#    H: 31.68766666666667
+#    P: 290.8630000000001
+#    '
+#    
+#   Whether to plot vertical bars for each NMR shift
+#   type: wrapper_type, default: False, required: False
+#  plot_bars: false
+#    
+#   Whether to plot vertical bars for each NMR shift in zoomed spectra
+#   type: wrapper_type, default: True, required: False
+#  plot_zoom_bars: true
+#    
+#   Isotope specific options. Each key should consist of a tuple of (proton_number, isotope).
+#   type: wrapper_type, default: 11B:
+#     frequency: 128.3
+#   13C:
+#     frequency: 100.6
+#   19F:
+#     frequency: 376.5
+#   1H:
+#     coupling_filter: 0.001
+#     frequency: 400
+#     fwhm: 0.005
+#     gaussian_resolution: 0.0005
+#     pre_merge: 0.0005
+#   31P:
+#     frequency: 162.0
+#   , required: False
+#  isotopes: "11B:\n  frequency: 128.3\n13C:\n  frequency: 100.6\n19F:\n  frequency:\
+#    \ 376.5\n1H:\n  coupling_filter: 0.001\n  frequency: 400\n  fwhm: 0.005\n  gaussian_resolution:\
+#    \ 0.0005\n  pre_merge: 0.0005\n31P:\n  frequency: 162.0\n"
+#    
+# Options that control the appearance of orbital energy diagrams.
+# required: False
+#orbital_diagram:
+#   Set to False to disable image rendering.
+#   type: wrapper_type, default: True, required: False
+#  enable_rendering: true
+#    
+#   The method used to set the min/max limits of the Y axis.
+#   Possible options are:
+#     - 'all': Limits are set so all orbitals are visible.
+#     - 'auto': Limits are set automatically so the 0 point (ie, 'X' axis), HOMO and LUMO are 
+#   clearly visible.
+#     - 'center': Like 'auto' except the lower limit is set more negative so the HOMO-LUMO are 
+#   closer to the middle of the diagram.
+#     - a list of [y_min, y_max], where y_min is the most negative value on the Y axis, and y_max is
+#    the most positive value on the Y axis (both in eV).
+#   type: wrapper_type, default: auto, required: False
+#  y_limits: auto
+#    
+#   If True, black lines are drawn around the boarder of the diagram. If False, a line is drawn for 
+#   the Y axis but not for the other 3 sides of the diagram.
+#   type: wrapper_type, default: False, required: False
+#  full_axis_lines: false
+#    
+# Options for controlling the appearance of 3D molecule images.
+# required: False
+#render:
+#   Set to False to disable image rendering.
+#   type: wrapper_type, default: True, required: False
+#  enable_rendering: true
+#    
+#   The rendering engine to use
+#   default: batoms, choices: ['vmd', 'batoms'], required: False
+#  engine: batoms
+#    
+#   VMD specific options (only applies if engine == 'vmd'
+#   required: False
+#  vmd:
+#     Path to the VMD (Visual Molecular Dynamics) executable
+#     default: vmd, required: False
+#    executable: vmd
+#      
+#     The tachyon ray-tracing library, performs the actual rendering. Tachyon is typically packaged 
+#     with VMD, but often isn't added to the path automatically
+#     default: tachyon, required: False
+#    tachyon: tachyon
+#      
+#     The render/display mode, changes the appearance of rendered molecules/orbitals.
+#     Possible options are:
+#      pastel: The default style, uses light, pastel-ish colours for orbitals with low transparency.
+#      Normal atom colours.
+#      light-pastel: Similar to pastel, but with lighter orbital colours.
+#      dark-pastel: Similar to pastel, but with darker orbital colours, reminiscant of the 'sharp' 
+#     style.
+#      sharp: Orbitals are darkly coloured around their edge but have high transparency in their 
+#     center. Normal atom colours.
+#      gaussian: A style attempting to mimic that of GaussView.
+#      vesta: A style attempting to mimic that of VESTA.
+#     default: pastel, choices: ['pastel', 'light-pastel', 'dark-pastel', 'sharp', 'gaussian', 
+#     'vesta'], required: False
+#    rendering_style: pastel
+#      
+#   Beautiful Atoms/Blender specific options (only applies if engine == 'batoms'
+#   required: False
+#  batoms:
+#     Path to the blender executable, in which beautiful atoms should be installed
+#     required: False
+#    blender: null
+#      
+#     The number of CPUs/threads to use. This option is overridden if running in a calculation 
+#     environemnt (where it uses the same number of CPUs as the calculation did)
+#     type: wrapper_type, default: 1, required: False
+#    cpus: 1
+#      
+#     The number of render samples (or passes) to use. Higher values result in higher image quality 
+#     and greater render times
+#     type: wrapper_type, default: 256, required: False
+#    render_samples: 256
+#      
+#     The perspective mode
+#     default: orthographic, choices: ['orthographic', 'perspective'], required: False
+#    perspective: orthographic
+#      
+#   If True, previously created files will be reused. If False, new images will rendered, replacing 
+#   the old.
+#   This is on by default for 3D rendered images because they are expensive (time-consuming) to 
+#   render.
+#   type: wrapper_type, default: True, required: False
+#  use_existing: true
+#    
+#   Whether to enable  automatic cropping of excess whitespace around the border of generated 
+#   images.  If False, overall image rendering is likely to take less time, but molecules may only 
+#   occupy a small portion of the true image.
+#   type: wrapper_type, default: True, required: False
+#  auto_crop: true
+#    
+#   The target resolution for rendered images. Higher values will increase image quality, at the 
+#   cost of increased render time and file size.
+#   type: wrapper_type, default: 512, required: False
+#  resolution: 512
+#    
+#   Specific options for orbital density plots.
+#   required: False
+#  orbital:
+#     The size of grid used to generate cube files.
+#     Densities are plotted on a 3D grid of points, this option controls how many points there are 
+#     in the grid (per dimension).
+#     In addition to an integer number of points (~100 is often sufficient), any of the following 
+#     keywords can also be specified:
+#     Tiny, Small, Medium, Large, Huge or Default.
+#     type: wrapper_type, default: Default, required: False
+#    cube_grid_size: Default
+#      
+#     The isovalue to use for rendering orbital density.
+#     type: wrapper_type, default: 0.02, required: False
+#    isovalue: 0.02
+#      
+#   Specific options for spin density plots.
+#   required: False
+#  spin:
+#     The size of the grid use to plot cube data. As cubes of this type are rendered with a smaller 
+#     isovalue, it is often necessary to use a larger grid size than normal to maintain quality.
+#     type: wrapper_type, default: Large, required: False
+#    cube_grid_size: Large
+#      
+#     The isovalue to use for plotting spin density.
+#     type: wrapper_type, default: 0.0004, required: False
+#    isovalue: 0.0004
+#      
+#   Specific options for total density plots.
+#   required: False
+#  density:
+#     The size of the grid use to plot cube data.
+#     type: wrapper_type, default: Large, required: False
+#    cube_grid_size: Large
+#      
+#     The isovalue to use for plotting total density.
+#     type: wrapper_type, default: 0.02, required: False
+#    isovalue: 0.02
+#      
+#   Specific options for excited states difference density plots.
+#   required: False
+#  difference_density:
+#     The size of the grid use to plot cube data.
+#     type: wrapper_type, default: Default, required: False
+#    cube_grid_size: Default
+#      
+#     The isovalue to use for difference density plots.
+#     type: wrapper_type, default: 0.001, required: False
+#    isovalue: 0.001
+#      
+#   Specific options for NTO plots.
+#   required: False
+#  natural_transition_orbital:
+#     The size of the grid use to plot cube data.
+#     type: wrapper_type, default: Default, required: False
+#    cube_grid_size: Default
+#      
+#     The isovalue to use for NTO plots.
+#     type: wrapper_type, default: 0.02, required: False
+#    isovalue: 0.02
+#      
+#   Specific options for permanent dipole moment plots.
+#   required: False
+#  dipole_moment:
+#     The value (x) to scale the TDM by, where 1 D = x Å.
+#     type: wrapper_type, default: 1.0, required: False
+#    scaling: 1.0
+#      
+#   Specific options for transition dipole moment plots.
+#   required: False
+#  transition_dipole_moment:
+#     The value (x) to scale the TEDM by, where 1 D = x Å.
+#     type: wrapper_type, default: 5.0, required: False
+#    electric_scaling: 5.0
+#      
+#     The value (x) to scale the TMDM by, where 1 au = x Å.
+#     type: wrapper_type, default: 10.0, required: False
+#    magnetic_scaling: 10.0
+#      
+# Options for controlling the generation of calculation reports.
+# required: False
+#report:
+#   The image to use for the front page of the report.
+#   default: rendered, choices: ['skeletal', 'rendered'], required: False
+#  front_page_image: rendered
+#    
+#   Options that control the running of Turbomole calculations to generate cube files from completed
+#    calculations. Note that when reports are created automatically following calculation completion
+#    these options will be overridden with the specifics of that calculation.
+#   required: False
+#  turbomole:
+#     The number of CPUs with which to run.
+#     type: wrapper_type, default: 1, required: False
+#    num_cpu: 1
+#      
+#     The amount of memory with which to run.
+#     type: wrapper_type, default: 1GB, required: False
+#    memory: 1GB
+#      
+#     A program definition from the internal library to run.
+#     type: type_func, required: False
+#    program: null
+#      
+#   Options that control the running of Gaussian calculations to generate NTO cube files from 
+#   completed calculations. Note that when reports are created automatically following calculation 
+#   completion these options will be overridden with the specifics of that calculation.
+#   required: False
+#  gaussian:
+#     The number of CPUs with which to run.
+#     type: wrapper_type, default: 1, required: False
+#    num_cpu: 1
+#      
+#     The amount of memory with which to run.
+#     type: wrapper_type, default: 1GB, required: False
+#    memory: 1GB
+#      
+#     A program definition from the internal library to run.
+#     type: type_func, required: False
+#    program: null
+#      
+#     Path to the top of the scratch directory.
+#     default: /scratch, required: False
+#    scratch_path: /scratch
+#      
+#   Options that control the running of orca_plot to generate cube files from completed 
+#   calculations. Note that when reports are created automatically following calculation completion 
+#   these options will be overridden with the specifics of that calculation.
+#   required: False
+#  orca:
+#     The amount of memory with which to run. If left blank, no maximum will be specified.
+#     type: wrapper_type, required: False
+#    memory: null
+#      
+#     A program definition from the internal library to run.
+#     type: type_func, required: False
+#    program: null
+#      
+#   Whether to delete intermediate files that are written during the report generation process.
+#   Intermediate files include:
+#      - .cube files.
+#      - .fchk files.
+#      - .html files.
+#      - .css files.
+#   Note that this option will only delete new files written by the program; existing files given by
+#    the user are never deleted.
+#   type: wrapper_type, default: True, required: False
+#  cleanup: true
+#    
+#   Options which control how many orbitals to print in the MO table.
+#   These numbers are relative to the HOMO for both the min and max.
+#   null can be specified for either/both the min/max to print all available orbitals in that 
+#   direction.
+#   If both alpha and beta orbitals are available (for unrestricted calculations, for example), then
+#    additional orbitals may be printed outside of the given min/max to ensure the given value is 
+#   met for both sets of orbitals. This is common for triplet calculations, where the alpha and beta
+#    frontier MOs are at different levels.
+#   Examples:
+#     min: -10, max: 16: From HOMO-10 to LUMO+15 inclusive (total of 27 orbitals).
+#     min: null, max: 11: All orbitals with energy less than or equal to LUMO+10.
+#     min: 0, max: 1: HOMO and LUMO only.
+#   required: False
+#  orbital_table:
+#     The highest orbital to show in the molecular orbital table.
+#     type: wrapper_type, default: 16, required: False
+#    max: 16
+#      
+#     The lowest orbital to show in the molecular orbital table.
+#     type: wrapper_type, default: -15, required: False
+#    min: -15
+#      
+#   Options which specify which orbitals to render 3D images of. The default is the HOMO and LUMO.
+#   Orbitals can be specified by level (an index starting at 1 for the most negative orbital, useful
+#    if you want images of a particular orbital) and/or by distance from the HOMO (useful for more 
+#   day-to-day operation.
+#   In addition, excited_state_transition_threshold: can be used to add orbitals that are involved 
+#   in an excited state transition with a probability above a certain threshold.
+#   Duplicates will be automatically ignored, as will orbitals specified here that are not actually 
+#   available in the calculation result file.
+#   Alpha and beta are set separately. Beta will be ignored if there are no beta orbitals available.
+#    
+#   Example:
+#      orbital_levels:
+#        - 5
+#      orbital_distance:
+#        - -1
+#        - 0
+#        - 1
+#      excited_state_transition_threshold: 0.1
+#      Would render orbital 5, HOMO-1, HOMO, LUMO and any orbitals involved in an excited state 
+#   transition with a probability 0.1 or greater.
+#   required: False
+#  orbital_image:
+#     Include orbitals involved in an excited state transition with a probability of this value or 
+#     greater.
+#     type: wrapper_type, default: 0.1, required: False
+#    et_transition_threshold: 0.1
+#      
+#     Include normal/alpha orbitals by level.
+#     type: wrapper_type, list_type: list, required: False
+#    orbital_levels: []
+#      
+#     Include beta orbitals by level.
+#     type: wrapper_type, list_type: list, required: False
+#    beta_levels: []
+#      
+#     Include normal/alpha orbitals by distance from the HOMO.
+#     type: wrapper_type, list_type: list, default: [0, 1], required: False
+#    orbital_distances:
+#    - 0
+#    - 1
+#      
+#     Include beta orbitals by distance from the HOMO.
+#     type: wrapper_type, list_type: list, default: [0, 1], required: False
+#    beta_distances:
+#    - 0
+#    - 1
+#      
+#   Options that control how many vibrational frequencies to list in the frequencies table. 
+#   required: False
+#  frequency_table:
+#     The most negative frequency to show in the table (remember that frequencies can be negative). 
+#     'null' is for no limit. Units are cm-1.
+#     type: wrapper_type, required: False
+#    min_frequency: null
+#      
+#     The most positive frequency to show in the table. 'null' is for no limit. Units are cm-1.
+#     type: wrapper_type, required: False
+#    max_frequency: null
+#      
+#     The maximum number of frequencies to show in the table.
+#     type: wrapper_type, required: False
+#    max_num: null
+#      
+#   Options which specify which NMR spectra to render.
+#   required: False
+#  nmr_image:
+#     If True, at least one experiment will be included for each element and isotope pair (for which
+#      NMR data is available). If no expt is explicitly requested (via codes), then the spectra will
+#      be the one with the least decoupling.
+#     type: wrapper_type, default: True, required: False
+#    auto: true
+#      
+#     Explicitly include certain NMR experiments.
+#     type: wrapper_type, list_type: list, default: ['13C{1H}'], required: False
+#    codes:
+#    - 13C{1H}
+#      
+# Options for controlling the rendering of 2D skeletal images.
+# required: False
+#skeletal_image:
+#   The resolution for rendered images
+#   required: False
+#  resolution:
+#     The output resolution (x and y) in pixels
+#     type: wrapper_type, required: False
+#    absolute: null
+#      
+#     The output resolution (x and y) in multiples of the length of the molecule
+#     type: wrapper_type, default: 100, required: False
+#    relative: 100
+#