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🎨 Improve structure and documentation of the SiDB defects
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@marcelwa
marcelwa committed Nov 22, 2023
1 parent 708f2e7 commit 9f73676
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Showing 4 changed files with 137 additions and 84 deletions.
4 changes: 3 additions & 1 deletion bindings/pyfiction/include/pyfiction/technology/sidb_defects.hpp
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Expand Up @@ -55,7 +55,9 @@ inline void sidb_defects(pybind11::module& m)

;

m.def("is_charged_defect", &fiction::is_charged_defect, "defect"_a, DOC(fiction_is_charged_defect));
m.def("is_charged_defect_type", &fiction::is_charged_defect_type, "defect"_a, DOC(fiction_is_charged_defect));
m.def("is_neutral_defect_type", &fiction::is_neutral_defect_type, "defect"_a, DOC(fiction_is_neutral_defect));

m.def("is_positively_charged_defect", &fiction::is_positively_charged_defect, "defect"_a,
DOC(fiction_is_positively_charged_defect));
m.def("is_negatively_charged_defect", &fiction::is_negatively_charged_defect, "defect"_a,
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22 changes: 12 additions & 10 deletions docs/technology/defects.rst
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Expand Up @@ -15,11 +15,12 @@ SiDB Defect Types
.. doxygenstruct:: fiction::sidb_defect
:members:

.. doxygenfunction:: fiction::is_charged_defect
.. doxygenfunction:: fiction::is_charged_defect_type
.. doxygenfunction:: fiction::is_neutral_defect_type

.. doxygenfunction:: fiction::is_positively_charged_defect
.. doxygenfunction:: fiction::is_negatively_charged_defect
.. doxygenfunction:: fiction::is_neutrally_charged_defect
.. doxygenfunction:: fiction::is_neutral_defect

.. doxygenvariable:: fiction::SIDB_CHARGED_DEFECT_HORIZONTAL_SPACING
.. doxygenvariable:: fiction::SIDB_CHARGED_DEFECT_VERTICAL_SPACING
Expand All @@ -29,19 +30,20 @@ SiDB Defect Types
.. doxygenfunction:: fiction::defect_extent

.. tab:: Python
.. autoclass:: fiction.technology.sidb_defect_type
.. autoclass:: fiction.pyfiction.sidb_defect_type
:members:

.. autoclass:: fiction.technology.sidb_defect
.. autoclass:: fiction.pyfiction.sidb_defect
:members:

.. autofunction:: fiction.technology.is_charged_defect
.. autofunction:: fiction.technology.is_positively_charged_defect
.. autofunction:: fiction.technology.is_negatively_charged_defect
.. autofunction:: fiction.technology.is_neutrally_charged_defect
.. autofunction:: fiction.technology.is_neutral_defect
.. autofunction:: fiction.pyfiction.is_charged_defect_type
.. autofunction:: fiction.pyfiction.is_neutral_defect_type

.. autofunction:: fiction.pyfiction.is_positively_charged_defect
.. autofunction:: fiction.pyfiction.is_negatively_charged_defect
.. autofunction:: fiction.pyfiction.is_neutrally_charged_defect

.. autofunction:: fiction.technology.defect_extent
.. autofunction:: fiction.pyfiction.defect_extent


SiDB Defect Surface
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139 changes: 94 additions & 45 deletions include/fiction/technology/sidb_defects.hpp
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Expand Up @@ -20,20 +20,62 @@ namespace fiction
*/
enum class sidb_defect_type
{
NONE, // H-Si
DB, // an extra dangling bond
SI_VACANCY, // missing silicon
SINGLE_DIHYDRIDE, // double hydrogen passivation
DIHYDRIDE_PAIR, // missing bond between dimers leading to two double hydrogen passivations
ONE_BY_ONE, // collection of dihydride pairs
THREE_BY_ONE, // collection of 1 by 1's
SILOXANE, // oxidized dimer
RAISED_SI, // raised silicon dimer
MISSING_DIMER, // dimer missing altogether
ETCH_PIT, // collection of missing dimers
STEP_EDGE, // break in the surface
GUNK, // residual material
UNKNOWN // unknown defect
/**
* Defect-free H-Si.
*/
NONE,
/**
* A stray dangling bond.
*/
DB,
/**
* A missing silicon atom.
*/
SI_VACANCY,
/**
* Double hydrogen passivation.
*/
SINGLE_DIHYDRIDE,
/**
* A missing bond between dimers that leads to two double hydrogen passivations.
*/
DIHYDRIDE_PAIR,
/**
* A collection of dihydride pairs.
*/
ONE_BY_ONE,
/**
* A collection of 1 by 1's.
*/
THREE_BY_ONE,
/**
* An oxidized dimer.
*/
SILOXANE,
/**
* A raised silicon dimer.
*/
RAISED_SI,
/**
* The dimer is missing altogether.
*/
MISSING_DIMER,
/**
* A collection of missing dimers.
*/
ETCH_PIT,
/**
* A step edge, which is a break in the surface reconstruction.
*/
STEP_EDGE,
/**
* Residual material.
*/
GUNK,
/**
* Unknown defect.
*/
UNKNOWN
};
/**
* In accordance with the paper mentioned above, the `sidb_defect` struct is used to represent a specific defect on the
Expand Down Expand Up @@ -77,75 +119,82 @@ struct sidb_defect
*/
double lambda_tf;
/**
* This operator compares two sidb_defect instances for equality. It checks if the type, charge,
* epsilon_r, and lambda_tf members of the two instances are equal.
* This operator compares two `sidb_defect` instances for equality. It checks if the `type`, `charge`,
* `epsilon_r`, and `lambda_tf` members of the two instances are equal.
*
* @param rhs `sidb_defect` instance to compare against.
*/
constexpr bool operator==(const sidb_defect& rhs) const noexcept
{
return type == rhs.type && charge == rhs.charge && epsilon_r == rhs.epsilon_r && lambda_tf == rhs.lambda_tf;
}
/**
* This operator compares two sidb_defect instances for inequality. It uses the operator== to check
* This operator compares two `sidb_defect` instances for inequality. It uses the `operator==` to check
* if the two instances are equal and returns the negation of the result.
*
* @param rhs `sidb_defect` instance to compare against.
*/
constexpr bool operator!=(const sidb_defect& rhs) const noexcept
{
return !(*this == rhs);
}
};
/**
* Checks whether the given defect is charged. Charged defects are to be avoided by a larger distance.
* Checks whether the given defect type is a charged one. `DB` and `SI_VACANCY` types are charged. Those charged defects
* are to be avoided by a larger distance.
*
* @param defect Defect type to check.
* @return `true` iff defect is charged.
* @param defect Defect to check.
* @return `true` iff `defect` is of a charged type.
*/
[[nodiscard]] static constexpr bool is_charged_defect(const sidb_defect& defect) noexcept
[[nodiscard]] static constexpr bool is_charged_defect_type(const sidb_defect& defect) noexcept
{
return defect.type == sidb_defect_type::DB || defect.type == sidb_defect_type::SI_VACANCY;
}
/**
* Checks whether the given defect is positively charged.
* Checks whether the given defect type is not a charged one. Neutral defects are to be avoided as well, but not by such
* a large distance. Even though the `NONE` defect type is technically neutral, it is not a defect per se which is why
* this function returns false on the `NONE` defect input.
*
* @param defect Defect to check.
* @return `true` iff `defect` is not of a charged type.
*/
[[nodiscard]] static constexpr bool is_neutral_defect_type(const sidb_defect& defect) noexcept
{
return defect.type != sidb_defect_type::NONE && !is_charged_defect_type(defect);
}
/**
* Checks whether the given defect has a positive charge value assigned to it. This function is irrespective of the
* associated defect type.
*
* @param defect Defect to check.
* @return `true` iff defect is positively charged.
* @return `true` iff `defect` has a positive charge value.
*/
[[nodiscard]] static constexpr bool is_positively_charged_defect(const sidb_defect& defect) noexcept
{
return defect.charge > 0;
}
/**
* Checks whether the given defect is negatively charged.
* Checks whether the given defect has a negative charge value assigned to it. This function is irrespective of the
* associated defect type.
*
* @param defect Defect to check.
* @return `true` iff defect is negatively charged.
* @return `true` iff `defect` has a negative charge value.
*/
[[nodiscard]] static constexpr bool is_negatively_charged_defect(const sidb_defect& defect) noexcept
{
return defect.charge < 0;
}
/**
* Checks whether the given defect is neutrally charged.
* Checks whether the given defect has a neutral charge value, i.e., `0`, assigned to it. This function is irrespective
* of the associated defect type.
*
* @param defect Defect to check.
* @return `true` iff defect is neutrally charged.
* @return `true` iff `defect` has a neutral charge value.
*/
[[nodiscard]] static constexpr bool is_neutrally_charged_defect(const sidb_defect& defect) noexcept
{
return defect.charge == 0;
}
/**
* Checks whether the given defect is not charged. Neutral defects are to be avoided but not by such a large distance.
* Even though the `NONE` defect type is technically neutral, it is not a defect per se which is why this function
* returns false on the `NONE` defect input. Additionally, the `UNKNOWN` defect cannot be guaranteed to be either
* neutral or charged which is why this function returns false for `UNKNOWN` defect inputs as well.
*
* @param defect Defect type to check.
* @return `true` iff defect is not charged.
*/
[[nodiscard]] static constexpr bool is_neutral_defect(const sidb_defect& defect) noexcept
{
return defect.type != sidb_defect_type::NONE && !is_charged_defect(defect);
}
/**
* Horizontal distance to keep from charged SiDB defects. The value is to be understood as the number of DB positions
* rather than the number of dimers. This is true even though each defect always affects the entire dimer.
Expand All @@ -167,19 +216,19 @@ inline constexpr const uint16_t SIDB_NEUTRAL_DEFECT_HORIZONTAL_SPACING = 1u;
*/
inline constexpr const uint16_t SIDB_NEUTRAL_DEFECT_VERTICAL_SPACING = 0u;
/**
* Returns the extent of a defect as a pair of SiDB distances in horizontal and vertical direction. If defect is the
* Returns the extent of a defect as a pair of SiDB distances in horizontal and vertical direction. If `defect` has the
* `NONE` defect type, `{0, 0}` is returned.
*
* @param defect Defect type to evaluate.
* @return Number of horizontal and vertical SiDBs that are affected by the given defect type.
* @param defect Defect to evaluate.
* @return Number of horizontal and vertical SiDBs that are affected by the given defect.
*/
[[nodiscard]] static constexpr std::pair<uint16_t, uint16_t> defect_extent(const sidb_defect& defect) noexcept
{
if (is_charged_defect(defect))
if (is_charged_defect_type(defect))
{
return {SIDB_CHARGED_DEFECT_HORIZONTAL_SPACING, SIDB_CHARGED_DEFECT_VERTICAL_SPACING};
}
if (is_neutral_defect(defect))
if (is_neutral_defect_type(defect))
{
return {SIDB_NEUTRAL_DEFECT_HORIZONTAL_SPACING, SIDB_NEUTRAL_DEFECT_VERTICAL_SPACING};
}
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56 changes: 28 additions & 28 deletions test/technology/sidb_defects.cpp
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Expand Up @@ -10,35 +10,35 @@ using namespace fiction;

TEST_CASE("Charged and uncharged defect types", "[sidb-defects]")
{
CHECK(!is_charged_defect(sidb_defect{sidb_defect_type::NONE}));
CHECK(is_charged_defect(sidb_defect{sidb_defect_type::DB}));
CHECK(is_charged_defect(sidb_defect{sidb_defect_type::SI_VACANCY}));
CHECK(!is_charged_defect(sidb_defect{sidb_defect_type::SINGLE_DIHYDRIDE}));
CHECK(!is_charged_defect(sidb_defect{sidb_defect_type::DIHYDRIDE_PAIR}));
CHECK(!is_charged_defect(sidb_defect{sidb_defect_type::ONE_BY_ONE}));
CHECK(!is_charged_defect(sidb_defect{sidb_defect_type::THREE_BY_ONE}));
CHECK(!is_charged_defect(sidb_defect{sidb_defect_type::SILOXANE}));
CHECK(!is_charged_defect(sidb_defect{sidb_defect_type::RAISED_SI}));
CHECK(!is_charged_defect(sidb_defect{sidb_defect_type::MISSING_DIMER}));
CHECK(!is_charged_defect(sidb_defect{sidb_defect_type::ETCH_PIT}));
CHECK(!is_charged_defect(sidb_defect{sidb_defect_type::STEP_EDGE}));
CHECK(!is_charged_defect(sidb_defect{sidb_defect_type::GUNK}));
CHECK(!is_charged_defect(sidb_defect{sidb_defect_type::UNKNOWN}));
CHECK(!is_charged_defect_type(sidb_defect{sidb_defect_type::NONE}));
CHECK(is_charged_defect_type(sidb_defect{sidb_defect_type::DB}));
CHECK(is_charged_defect_type(sidb_defect{sidb_defect_type::SI_VACANCY}));
CHECK(!is_charged_defect_type(sidb_defect{sidb_defect_type::SINGLE_DIHYDRIDE}));
CHECK(!is_charged_defect_type(sidb_defect{sidb_defect_type::DIHYDRIDE_PAIR}));
CHECK(!is_charged_defect_type(sidb_defect{sidb_defect_type::ONE_BY_ONE}));
CHECK(!is_charged_defect_type(sidb_defect{sidb_defect_type::THREE_BY_ONE}));
CHECK(!is_charged_defect_type(sidb_defect{sidb_defect_type::SILOXANE}));
CHECK(!is_charged_defect_type(sidb_defect{sidb_defect_type::RAISED_SI}));
CHECK(!is_charged_defect_type(sidb_defect{sidb_defect_type::MISSING_DIMER}));
CHECK(!is_charged_defect_type(sidb_defect{sidb_defect_type::ETCH_PIT}));
CHECK(!is_charged_defect_type(sidb_defect{sidb_defect_type::STEP_EDGE}));
CHECK(!is_charged_defect_type(sidb_defect{sidb_defect_type::GUNK}));
CHECK(!is_charged_defect_type(sidb_defect{sidb_defect_type::UNKNOWN}));

CHECK(!is_neutral_defect(sidb_defect{sidb_defect_type::NONE}));
CHECK(!is_neutral_defect(sidb_defect{sidb_defect_type::DB}));
CHECK(!is_neutral_defect(sidb_defect{sidb_defect_type::SI_VACANCY}));
CHECK(is_neutral_defect(sidb_defect{sidb_defect_type::SINGLE_DIHYDRIDE}));
CHECK(is_neutral_defect(sidb_defect{sidb_defect_type::DIHYDRIDE_PAIR}));
CHECK(is_neutral_defect(sidb_defect{sidb_defect_type::ONE_BY_ONE}));
CHECK(is_neutral_defect(sidb_defect{sidb_defect_type::THREE_BY_ONE}));
CHECK(is_neutral_defect(sidb_defect{sidb_defect_type::SILOXANE}));
CHECK(is_neutral_defect(sidb_defect{sidb_defect_type::RAISED_SI}));
CHECK(is_neutral_defect(sidb_defect{sidb_defect_type::MISSING_DIMER}));
CHECK(is_neutral_defect(sidb_defect{sidb_defect_type::ETCH_PIT}));
CHECK(is_neutral_defect(sidb_defect{sidb_defect_type::STEP_EDGE}));
CHECK(is_neutral_defect(sidb_defect{sidb_defect_type::GUNK}));
CHECK(is_neutral_defect(sidb_defect{sidb_defect_type::UNKNOWN}));
CHECK(!is_neutral_defect_type(sidb_defect{sidb_defect_type::NONE}));
CHECK(!is_neutral_defect_type(sidb_defect{sidb_defect_type::DB}));
CHECK(!is_neutral_defect_type(sidb_defect{sidb_defect_type::SI_VACANCY}));
CHECK(is_neutral_defect_type(sidb_defect{sidb_defect_type::SINGLE_DIHYDRIDE}));
CHECK(is_neutral_defect_type(sidb_defect{sidb_defect_type::DIHYDRIDE_PAIR}));
CHECK(is_neutral_defect_type(sidb_defect{sidb_defect_type::ONE_BY_ONE}));
CHECK(is_neutral_defect_type(sidb_defect{sidb_defect_type::THREE_BY_ONE}));
CHECK(is_neutral_defect_type(sidb_defect{sidb_defect_type::SILOXANE}));
CHECK(is_neutral_defect_type(sidb_defect{sidb_defect_type::RAISED_SI}));
CHECK(is_neutral_defect_type(sidb_defect{sidb_defect_type::MISSING_DIMER}));
CHECK(is_neutral_defect_type(sidb_defect{sidb_defect_type::ETCH_PIT}));
CHECK(is_neutral_defect_type(sidb_defect{sidb_defect_type::STEP_EDGE}));
CHECK(is_neutral_defect_type(sidb_defect{sidb_defect_type::GUNK}));
CHECK(is_neutral_defect_type(sidb_defect{sidb_defect_type::UNKNOWN}));
}

TEST_CASE("Defect extent", "[sidb-defects]")
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