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Initialization fix for docstrings #53

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Merged
RaulPPelaez merged 2 commits into from
Jul 21, 2025
Merged

Initialization fix for docstrings #53

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ab835bf
get rid of repeated initialization string w/ incorrect information in…
rykerfish Jul 11, 2025
ecd1606
format
rykerfish Jul 11, 2025
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10 changes: 8 additions & 2 deletions docs/source/solvers.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,14 @@

Available solvers
=================

The following solvers are available in libMobility.
Solvers must be instantiated with the type of boundary in each direction (X, Y, and Z). Each periodicity condition can be one of the following:
- open: No periodicity in the corresponding direction.
- unspecified: The periodicity is not specified.
- single_wall: The system is bounded by a single wall in the corresponding direction.
- two_walls: The system is bounded by two walls in the corresponding direction.
- periodic: The system is periodic in the corresponding direction.

All solvers support a subset of periodicity conditions. The description for each solver below will descript supported periodicities. The following solvers are available in libMobility.

Self Mobility
-------------
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24 changes: 2 additions & 22 deletions include/MobilityInterface/pythonify.h
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Expand Up @@ -144,26 +144,6 @@ auto setup_arrays(Solver &myself, pyarray_c &forces, pyarray_c &torques) {
return std::make_tuple(f, t, mf, mt);
}

const char *constructor_docstring = R"pbdoc(
Initialize the module with a given set of periodicity conditions.

Each periodicity condition can be one of the following:
- open: No periodicity in the corresponding direction.
- unspecified: The periodicity is not specified.
- single_wall: The system is bounded by a single wall in the corresponding direction.
- two_walls: The system is bounded by two walls in the corresponding direction.
- periodic: The system is periodic in the corresponding direction.

Parameters
----------
periodicityX : str
Periodicity condition in the x direction.
periodicityY : str
Periodicity condition in the y direction.
periodicityZ : str
Periodicity condition in the z direction.
)pbdoc";

const char *initialize_docstring = R"pbdoc(
Initialize the module with a given set of parameters.

Expand Down Expand Up @@ -372,8 +352,8 @@ auto define_module_content(
auto solver = py::class_<MODULENAME>(m, name, documentation);

solver
.def(nb::new_(&call_construct<MODULENAME>), constructor_docstring,
"periodicityX"_a, "periodicityY"_a, "periodicityZ"_a)
.def(nb::new_(&call_construct<MODULENAME>), "periodicityX"_a,
"periodicityY"_a, "periodicityZ"_a)
.def("initialize", call_initialize<MODULENAME>, initialize_docstring,
"viscosity"_a, "hydrodynamicRadius"_a, "includeAngular"_a = false,
"tolerance"_a = 1e-4)
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