3.10.2. horton.scripts.common – Code shared by several scripts¶
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horton.scripts.common.iter_elements(elements_str)¶ Interpret a string as a list of elements
- elements_str
- A string with comma-separated element numbers. One may add ranges with the format ‘N-M’ where M>N.
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horton.scripts.common.reduce_ugrid(ugrid, stride, chop)¶ Reduce the uniform grid
Arguments:
- ugrid
- The uniform integration grid.
- stride
- The reduction factor.
- chop
- The number of slices to chop of the grid in each direction.
Returns: a reduced ugrid object
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horton.scripts.common.reduce_data(cube_data, ugrid, stride, chop)¶ Reduce the uniform grid data according to stride and chop arguments
Arguments:
- fn_cube
- The cube file with the electron density.
- ugrid
- The uniform integration grid.
- stride
- The reduction factor.
- chop
- The number of slices to chop of the grid in each direction.
Returns: a new array and an updated grid object
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horton.scripts.common.parse_h5(arg_h5, name, path_optional=True)¶ Parse an HDF5 command line argument of the form file.h5:group or file.h5:dataset
Arguments:
- arg_h5
- The command line argument that consists of two parts, the HDF5 filename and a path, separated by a colon. If the path is optional, the default value is the root group.
- name
- The name of the argument to be used in error messages.
Optional arguments:
- path_optional
- Set this to False when a path in the HDF5 is not optional
Returns: the filename and the group
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horton.scripts.common.check_output(fn_h5, grp_name, overwrite)¶ Check if the output is already present in print a warning if –overwrite is not used
Arguments:
- fn_h5
- The output HDF5 file
- grp_name
- The HDF5 group in which the output is stored.
- overwrite
- Whether the user wants to overwrite contents that were already present.
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horton.scripts.common.parse_ewald_args(args)¶
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horton.scripts.common.parse_pbc(spbc)¶
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horton.scripts.common.store_args(args, grp)¶ Convert the command line arguments to hdf5 attributes
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horton.scripts.common.write_part_output(fn_h5, grp_name, part, keys, args)¶ Write the output of horton-wpart.py
Arguments:
- fn_h5
- The filename for the HDF5 output file.
- grp_name
- the destination group
- part
- The partitioning object (instance of subclass of horton.part.base.Part)
- keys
- The keys of the cached items that must go in the HDF5 outut file.
- args
- The results of the command line parser. All arguments are stored as attributes in the HDF5 output file.
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horton.scripts.common.write_script_output(fn_h5, grp_name, results, args)¶ Store the output of a script in an open HDF5 file
Arguments:
- fn_h5
- The HDF5 filename
- grp_name
- The name of the group where the results will be stored.
- results
- A dictionary with results.
- args
- The results of the command line parser. All arguments are stored as attributes in the HDF5 output file.