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44 lines
2.3 KiB
ReStructuredText
44 lines
2.3 KiB
ReStructuredText
.. _usemap:
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usemap
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======
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.. note::
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.. currentmodule:: apbs.input_file.calculate.generic
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Some instances of this keyword have been ported to the *new APBS syntax* (see :ref:`new_input_format`); see :class:`UseMap`
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.. todo:: Port other uses to new syntax.
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Specify pre-calculated coefficient maps to be used in the Poisson-Boltzmann calculation.
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These must have been input via an earlier READ statement (see :ref:`read_old_input`).
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The syntax for this command is:
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.. code-block:: bash
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usemap {type} {id}
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where the mandatory keywords are:
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``type``
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A string that specifies the type of pre-calculated map to be read in:
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``diel``
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Dielectric function map (as read by :ref:`read_old_input` ``diel``); this causes the :ref:`pdie`, :ref:`sdie`, :ref:`srad`, :ref:`swin`, and :ref:`elecsrfm` parameters and the radii of the biomolecular atoms to be ignored when computing dielectric maps for the Poisson-Boltzmann equation.
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Note that the :ref:`pdie` and :ref:`sdie` values are still used for some boundary condition calculations as specified by :ref:`bcfl`.
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``kappa``
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Mobile ion-accessibility function map (as read by :ref:`read_old_input` ``kappa``); this causes the :ref:`swin` and :ref:`elecsrfm` parameters and the radii of the biomolecular atoms to be ignored when computing mobile ion values for the Poisson-Boltzmann equation.
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The :ref:`ion` parameter is not ignored and will still be used.
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``charge``
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Charge distribution map (as read by :ref:`read_old_input` ``charge``); this causes the :ref:`chgm` parameter and the charges of the biomolecular atoms to be ignored when assembling the fixed charge distribution for the Poisson-Boltzmann equation.
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``pot``
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Potential map (as read by :ref:`read_old_input` ``pot``); this option requires setting :ref:`bcfl` to ``map``.
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``id``
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As described in the READ command documentation (see :ref:`read_old_input`), this integer ID specifies the particular map read in with READ.
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These IDs are assigned sequentially, starting from 1, and incremented independently for each map type read by APBS.
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In other words, a calculation that uses two PQR files, one parameter file, three charge maps, and four dielectric maps would have PQR files with IDs 1-2, a parameter file with ID 1, charge maps with IDs 1-3, and dielectric maps with IDs 1-4.
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