Add temperature to finite_difference.

This commit is contained in:
Nathan Baker
2021-06-15 14:41:49 -07:00
parent 0265719f49
commit ffc4dea698
2 changed files with 23 additions and 4 deletions

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@@ -716,6 +716,7 @@ class FiniteDifference(InputFile):
* ``solvent radius``: see :func:`solvent_radius`
* ``surface method``: see :func:`surface_method`
* ``surface spline window``: see :func:`surface_spline_window`
* ``temperature``: see :func:`temperature`
.. todo:: finish this
"""
@@ -736,11 +737,28 @@ class FiniteDifference(InputFile):
self._solvent_radius = None
self._surface_method = None
self._surface_spline_window = None
self._temperature = None
super().__init__(dict_=dict_, yaml=yaml, json=json)
@property
def temperature(self) -> float:
"""Temperature for the calculation in Kelvin.
:raises ValueError: if not a positive number (no violations of the
3rd Law!)
"""
return self._temperature
@temperature.setter
def temperature(self, value):
if check.is_positive_definite(value):
self._temperature = value
else:
raise ValueError(f"{value} is not a positive number.")
@property
def surface_spline_window(self) -> float:
"""Window for spline-based surface definitions.
"""Window for spline-based surface definitions (not needed otherwise).
This is the distance (in Å) over which the spline transitions from the
solvent dielectric value to the solute dielectric value. A typical

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@@ -7,11 +7,12 @@ temp
Some versions of this command have been ported to the *new APBS syntax* (see :ref:`new_input_format`):
.. currentmodule:: apbs.input_file.calculate
* Nonpolar calculations:
.. currentmodule:: apbs.input_file.calculate.nonpolar
* Finite difference calculations: See :func:`finite_difference.FiniteDifference.temperature`.
* Nonpolar calculations: See :func:`nonpolar.Nonpolar.temperature`.
See :func:`Nonpolar.temperature` for more information.
.. todo:: add other uses to new syntax
This keyword specifies the temperature for the calculation.
The syntax is: