🐍 Minor fixes and change of template parameter of BDL pairs. (#442)

* 🐍 small fixes and change template parameter of bdl pairs.

* 🎨 Incorporated pre-commit fixes

* 🎨 add missing header.

* 🎨 add missing header.

* 🎨 small fix.

* ✅ add python unit test for gate design on 111.

* 🐛 use correct test name.

* 🐛 use correct test name.

* 🐛 use correct test name.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

bindings/pyfiction/include/pyfiction/algorithms/physical_design/design_sidb_gates.hpp

@@ -24,42 +24,47 @@ void design_sidb_gates(pybind11::module& m)
     namespace py = pybind11;
     using namespace py::literals;
 
+    m.def("design_sidb_gates", &fiction::design_sidb_gates<Lyt, py_tt>, "skeleton"_a, "spec"_a,
+          "params"_a = fiction::design_sidb_gates_params<fiction::cell<Lyt>>{}, DOC(fiction_design_sidb_gates));
+}
+
+}  // namespace detail
+
+inline void design_sidb_gates(pybind11::module& m)
+{
+    namespace py = pybind11;
     /**
      * Design approach selector type.
      */
-    pybind11::enum_<typename fiction::design_sidb_gates_params<Lyt>::design_sidb_gates_mode>(
+    pybind11::enum_<typename fiction::design_sidb_gates_params<fiction::offset::ucoord_t>::design_sidb_gates_mode>(
         m, "design_sidb_gates_mode", DOC(fiction_design_sidb_gates_params_design_sidb_gates_mode))
-        .value("EXHAUSTIVE", fiction::design_sidb_gates_params<Lyt>::design_sidb_gates_mode::EXHAUSTIVE,
+        .value("EXHAUSTIVE",
+               fiction::design_sidb_gates_params<fiction::offset::ucoord_t>::design_sidb_gates_mode::EXHAUSTIVE,
                DOC(fiction_design_sidb_gates_params_design_sidb_gates_mode_EXHAUSTIVE))
-        .value("RANDOM", fiction::design_sidb_gates_params<Lyt>::design_sidb_gates_mode::RANDOM,
+        .value("RANDOM", fiction::design_sidb_gates_params<fiction::offset::ucoord_t>::design_sidb_gates_mode::RANDOM,
                DOC(fiction_design_sidb_gates_params_design_sidb_gates_mode_RANDOM));
 
     /**
      * Parameters.
      */
-    py::class_<fiction::design_sidb_gates_params<Lyt>>(m, "design_sidb_gates_params",
-                                                       DOC(fiction_design_sidb_gates_params))
+    py::class_<fiction::design_sidb_gates_params<fiction::offset::ucoord_t>>(m, "design_sidb_gates_params",
+                                                                             DOC(fiction_design_sidb_gates_params))
         .def(py::init<>())
-        .def_readwrite("simulation_parameters", &fiction::design_sidb_gates_params<Lyt>::simulation_parameters,
+        .def_readwrite("simulation_parameters",
+                       &fiction::design_sidb_gates_params<fiction::offset::ucoord_t>::simulation_parameters,
                        DOC(fiction_design_sidb_gates_params))
-        .def_readwrite("design_mode", &fiction::design_sidb_gates_params<Lyt>::design_mode,
+        .def_readwrite("design_mode", &fiction::design_sidb_gates_params<fiction::offset::ucoord_t>::design_mode,
                        DOC(fiction_design_sidb_gates_params_design_mode))
-        .def_readwrite("canvas", &fiction::design_sidb_gates_params<Lyt>::canvas,
+        .def_readwrite("canvas", &fiction::design_sidb_gates_params<fiction::offset::ucoord_t>::canvas,
                        DOC(fiction_design_sidb_gates_params_canvas))
-        .def_readwrite("number_of_sidbs", &fiction::design_sidb_gates_params<Lyt>::number_of_sidbs,
+        .def_readwrite("number_of_sidbs",
+                       &fiction::design_sidb_gates_params<fiction::offset::ucoord_t>::number_of_sidbs,
                        DOC(fiction_design_sidb_gates_params_number_of_sidbs))
-        .def_readwrite("sim_engine", &fiction::design_sidb_gates_params<Lyt>::sim_engine,
+        .def_readwrite("sim_engine", &fiction::design_sidb_gates_params<fiction::offset::ucoord_t>::sim_engine,
                        DOC(fiction_design_sidb_gates_params_sim_engine));
 
-    m.def("design_sidb_gates", &fiction::design_sidb_gates<Lyt, py_tt>, "skeleton"_a, "spec"_a,
-          "params"_a = fiction::design_sidb_gates_params<Lyt>{}, DOC(fiction_design_sidb_gates));
-}
-
-}  // namespace detail
-
-inline void design_sidb_gates(pybind11::module& m)
-{
-    detail::design_sidb_gates<py_sidb_layout>(m);
+    detail::design_sidb_gates<py_sidb_100_lattice>(m);
+    detail::design_sidb_gates<py_sidb_111_lattice>(m);
 }
 
 }  // namespace pyfiction

bindings/pyfiction/include/pyfiction/algorithms/simulation/sidb/critical_temperature.hpp

@@ -88,7 +88,7 @@ inline void critical_temperature(pybind11::module& m)
     // NOTE be careful with the order of the following calls! Python will resolve the first matching overload!
 
     detail::critical_temperature<py_sidb_100_lattice>(m);
-    detail::critical_temperature<py_sidb_100_lattice>(m);
+    detail::critical_temperature<py_sidb_111_lattice>(m);
 }
 
 }  // namespace pyfiction

bindings/pyfiction/include/pyfiction/algorithms/simulation/sidb/detect_bdl_pairs.hpp

@@ -20,22 +20,12 @@ namespace detail
 {
 
 template <typename Lyt>
-void detect_bdl_pairs(pybind11::module& m, const std::string& lattice = "")
+void detect_bdl_pairs(pybind11::module& m)
 {
     namespace py = pybind11;
     using namespace pybind11::literals;
 
-    py::class_<fiction::bdl_pair<Lyt>>(m, fmt::format("bdl_pair{}", lattice).c_str(), DOC(fiction_bdl_pair))
-        .def(py::init<>(), DOC(fiction_bdl_pair_bdl_pair))
-        .def(py::init<fiction::sidb_technology::cell_type, fiction::cell<Lyt>, fiction::cell<Lyt>>(), "t"_a, "u"_a,
-             "l"_a, DOC(fiction_bdl_pair_bdl_pair_2))
-        .def_readonly("type", &fiction::bdl_pair<Lyt>::type, DOC(fiction_bdl_pair_type))
-        .def_readonly("upper", &fiction::bdl_pair<Lyt>::upper, DOC(fiction_bdl_pair_upper))
-        .def_readonly("lower", &fiction::bdl_pair<Lyt>::lower, DOC(fiction_bdl_pair_lower))
-
-        ;
-
-    m.def(fmt::format("detect_bdl_pairs{}", lattice).c_str(), &fiction::detect_bdl_pairs<Lyt>, "lyt"_a, "type"_a,
+    m.def("detect_bdl_pairs", &fiction::detect_bdl_pairs<Lyt>, "lyt"_a, "type"_a,
           "params"_a = fiction::detect_bdl_pairs_params{}, DOC(fiction_detect_bdl_pairs));
 }
 
@@ -44,6 +34,15 @@ void detect_bdl_pairs(pybind11::module& m, const std::string& lattice = "")
 inline void detect_bdl_pairs(pybind11::module& m)
 {
     namespace py = pybind11;
+    using namespace pybind11::literals;
+
+    py::class_<fiction::bdl_pair<fiction::offset::ucoord_t>>(m, "bdl_pair", DOC(fiction_bdl_pair))
+        .def(py::init<>(), DOC(fiction_bdl_pair_bdl_pair))
+        .def(py::init<fiction::sidb_technology::cell_type, fiction::offset::ucoord_t, fiction::offset::ucoord_t>(),
+             "t"_a, "u"_a, "l"_a, DOC(fiction_bdl_pair_bdl_pair_2))
+        .def_readonly("type", &fiction::bdl_pair<fiction::offset::ucoord_t>::type, DOC(fiction_bdl_pair_type))
+        .def_readonly("upper", &fiction::bdl_pair<fiction::offset::ucoord_t>::upper, DOC(fiction_bdl_pair_upper))
+        .def_readonly("lower", &fiction::bdl_pair<fiction::offset::ucoord_t>::lower, DOC(fiction_bdl_pair_lower));
 
     py::class_<fiction::detect_bdl_pairs_params>(m, "detect_bdl_pairs_params", DOC(fiction_detect_bdl_pairs_params))
         .def(py::init<>())
@@ -54,8 +53,8 @@ inline void detect_bdl_pairs(pybind11::module& m)
 
     // NOTE be careful with the order of the following calls! Python will resolve the first matching overload!
 
-    detail::detect_bdl_pairs<py_sidb_100_lattice>(m, "_100");
-    detail::detect_bdl_pairs<py_sidb_111_lattice>(m, "_111");
+    detail::detect_bdl_pairs<py_sidb_100_lattice>(m);
+    detail::detect_bdl_pairs<py_sidb_111_lattice>(m);
 }
 
 }  // namespace pyfiction

bindings/pyfiction/test/algorithms/physical_design/test_design_sidb_gates.py

@@ -1,10 +1,12 @@
 import unittest
+
 from mnt.pyfiction import *
 
+
 class TestDesignSiDBGates(unittest.TestCase):
 
-    def test_siqad_and_gate_skeleton(self):
-        layout = sidb_layout((20, 20))
+    def test_siqad_and_gate_skeleton_100(self):
+        layout = sidb_100_lattice((20, 20))
 
         layout.assign_cell_type((0, 1), sidb_technology.cell_type.INPUT)
         layout.assign_cell_type((2, 3), sidb_technology.cell_type.INPUT)
@@ -40,6 +42,52 @@ def test_siqad_and_gate_skeleton(self):
 
         self.assertEqual(len(designed_gates), 23)
 
+    def test_nor_gate_111(self):
+        layout = sidb_111_lattice((20, 20))
+
+        layout.assign_cell_type((0, 0), sidb_technology.cell_type.INPUT)
+        layout.assign_cell_type((25, 0), sidb_technology.cell_type.INPUT)
+
+        layout.assign_cell_type((23, 3), sidb_technology.cell_type.INPUT)
+        layout.assign_cell_type((1, 3), sidb_technology.cell_type.INPUT)
+
+        layout.assign_cell_type((4, 8), sidb_technology.cell_type.NORMAL)
+        layout.assign_cell_type((21, 4), sidb_technology.cell_type.NORMAL)
+
+        layout.assign_cell_type((5, 11), sidb_technology.cell_type.NORMAL)
+        layout.assign_cell_type((19, 11), sidb_technology.cell_type.NORMAL)
+
+        layout.assign_cell_type((8, 16), sidb_technology.cell_type.NORMAL)
+        layout.assign_cell_type((17, 16), sidb_technology.cell_type.NORMAL)
+
+        layout.assign_cell_type((9, 19), sidb_technology.cell_type.NORMAL)
+        layout.assign_cell_type((15, 19), sidb_technology.cell_type.NORMAL)
+
+        layout.assign_cell_type((15, 43), sidb_technology.cell_type.NORMAL)
+        layout.assign_cell_type((17, 46), sidb_technology.cell_type.NORMAL)
+
+        layout.assign_cell_type((19, 51), sidb_technology.cell_type.OUTPUT)
+        layout.assign_cell_type((21, 54), sidb_technology.cell_type.OUTPUT)
+
+        layout.assign_cell_type((23, 59), sidb_technology.cell_type.NORMAL)
+
+        params = design_sidb_gates_params()
+        params.simulation_parameters.base = 2
+        params.simulation_parameters.mu_minus = -0.32
+        params.design_mode = design_sidb_gates_mode.EXHAUSTIVE
+        params.canvas = [(10, 22), (14, 34)]
+        params.number_of_sidbs = 3
+        params.sim_engine = sidb_simulation_engine.QUICKEXACT
+
+        self.assertEqual(params.simulation_parameters.mu_minus, -0.32)
+        self.assertEqual(params.number_of_sidbs, 3)
+        self.assertEqual(params.canvas[0], (10, 22, 0))
+        self.assertEqual(params.canvas[1], (14, 34))
+
+        designed_gates = design_sidb_gates(layout, [create_nor_tt()], params)
+
+        self.assertEqual(len(designed_gates), 206)
+
 
 if __name__ == '__main__':
     unittest.main()

bindings/pyfiction/test/algorithms/simulation/sidb/test_critical_temperature.py

@@ -8,7 +8,7 @@
 
 class TestCriticalTemperature(unittest.TestCase):
 
-    def test_perturber_and_DB_pair(self):
+    def test_perturber_and_DB_pair_100(self):
         layout = sidb_100_lattice((10, 10))
         layout.assign_cell_type((0, 1), sidb_technology.cell_type.NORMAL)
         layout.assign_cell_type((4, 1), sidb_technology.cell_type.NORMAL)
@@ -26,6 +26,24 @@ def test_perturber_and_DB_pair(self):
         self.assertEqual(stats.algorithm_name, "QuickExact")
         self.assertEqual(stats.num_valid_lyt, 1)
 
+    def test_perturber_and_DB_pair_111(self):
+        layout = sidb_111_lattice((10, 10))
+        layout.assign_cell_type((0, 1), sidb_technology.cell_type.NORMAL)
+        layout.assign_cell_type((4, 1), sidb_technology.cell_type.NORMAL)
+        layout.assign_cell_type((6, 1), sidb_technology.cell_type.NORMAL)
+
+        params = critical_temperature_params()
+        params.engine = simulation_engine.EXACT
+
+        stats = critical_temperature_stats()
+
+        cds = charge_distribution_surface_111(layout)
+
+        self.assertEqual(critical_temperature_non_gate_based(cds, params, stats), 400)
+
+        self.assertEqual(stats.algorithm_name, "QuickExact")
+        self.assertEqual(stats.num_valid_lyt, 1)
+
     def test_gate_based_simulation(self):
         layout = read_sqd_layout_100(dir_path + "/../../../resources/hex_21_inputsdbp_xor_v1.sqd", "xor_gate")
         params = critical_temperature_params()

bindings/pyfiction/test/algorithms/simulation/sidb/test_detect_bdl_pairs.py

@@ -23,15 +23,15 @@ def test_detect_bdl_pairs_100_lattice(self):
 
         params = detect_bdl_pairs_params()
 
-        input_bdl_pairs = detect_bdl_pairs_100(lyt, sidb_technology.cell_type.INPUT, params)
-        output_bdl_pairs = detect_bdl_pairs_100(lyt, sidb_technology.cell_type.OUTPUT, params)
-        normal_bdl_pairs = detect_bdl_pairs_100(lyt, sidb_technology.cell_type.NORMAL, params)
+        input_bdl_pairs = detect_bdl_pairs(lyt, sidb_technology.cell_type.INPUT, params)
+        output_bdl_pairs = detect_bdl_pairs(lyt, sidb_technology.cell_type.OUTPUT, params)
+        normal_bdl_pairs = detect_bdl_pairs(lyt, sidb_technology.cell_type.NORMAL, params)
 
         self.assertEqual(len(input_bdl_pairs), 0)
         self.assertEqual(len(output_bdl_pairs), 0)
         self.assertEqual(len(normal_bdl_pairs), 2)
 
-    def test_detect_bdl_pairs_100_lattice(self):
+    def test_detect_bdl_pairs_111_lattice(self):
         lyt = sidb_111_lattice((7, 0))
 
         lyt = charge_distribution_surface_111(lyt)
@@ -49,9 +49,9 @@ def test_detect_bdl_pairs_100_lattice(self):
 
         params = detect_bdl_pairs_params()
 
-        input_bdl_pairs = detect_bdl_pairs_111(lyt, sidb_technology.cell_type.INPUT, params)
-        output_bdl_pairs = detect_bdl_pairs_111(lyt, sidb_technology.cell_type.OUTPUT, params)
-        normal_bdl_pairs = detect_bdl_pairs_111(lyt, sidb_technology.cell_type.NORMAL, params)
+        input_bdl_pairs = detect_bdl_pairs(lyt, sidb_technology.cell_type.INPUT, params)
+        output_bdl_pairs = detect_bdl_pairs(lyt, sidb_technology.cell_type.OUTPUT, params)
+        normal_bdl_pairs = detect_bdl_pairs(lyt, sidb_technology.cell_type.NORMAL, params)
 
         self.assertEqual(len(input_bdl_pairs), 0)
         self.assertEqual(len(output_bdl_pairs), 0)

docs/algorithms/sidb_simulation.rst

@@ -327,14 +327,11 @@ Binary-dot Logic (BDL) Pair Detection
         .. doxygenfunction:: fiction::detect_bdl_pairs
 
     .. tab:: Python
-        .. autoclass:: mnt.pyfiction.bdl_pair_100
-            :members:
-        .. autoclass:: mnt.pyfiction.bdl_pair_111
+        .. autoclass:: mnt.pyfiction.bdl_pair
             :members:
         .. autoclass:: mnt.pyfiction.detect_bdl_pairs_params
             :members:
-        .. autofunction:: mnt.pyfiction.detect_bdl_pairs_100
-        .. autofunction:: mnt.pyfiction.detect_bdl_pairs_111
+        .. autofunction:: mnt.pyfiction.detect_bdl_pairs
 
 
 Assess Population Stability

docs/io/physical_simulation.rst

@@ -134,7 +134,8 @@ SiQAD
         .. autofunction:: mnt.pyfiction.write_sqd_layout
         .. autofunction:: mnt.pyfiction.write_sqd_sim_result
         .. autofunction:: mnt.pyfiction.write_location_and_ground_state
-        .. autofunction:: mnt.pyfiction.read_sqd_layout
+        .. autofunction:: mnt.pyfiction.read_sqd_layout_100
+        .. autofunction:: mnt.pyfiction.read_sqd_layout_111
 
         .. autoclass:: mnt.pyfiction.sqd_parsing_error
             :members:

include/fiction/algorithms/iter/bdl_input_iterator.hpp

@@ -284,7 +284,7 @@ class bdl_input_iterator
     /**
      * The detected input BDL pairs.
      */
-    const std::vector<bdl_pair<Lyt>> input_pairs;
+    const std::vector<bdl_pair<cell<Lyt>>> input_pairs;
     /**
      * The amount of input BDL pairs.
      */

include/fiction/algorithms/physical_design/design_sidb_gates.hpp

@@ -33,10 +33,10 @@ namespace fiction
 /**
  * This struct contains parameters and settings to design SiDB gates.
  *
- * @tparam Cell-level layout type.
+ * @tparam CellType Cell type.
  *
  */
-template <typename Lyt>
+template <typename CellType>
 struct design_sidb_gates_params
 {
     /**
@@ -64,7 +64,7 @@ struct design_sidb_gates_params
     /**
      * Canvas spanned by the northwest and southeast cell.
      */
-    std::pair<typename Lyt::cell, typename Lyt::cell> canvas{};
+    std::pair<CellType, CellType> canvas{};
     /**
      * Number of SiDBs placed in the canvas to create a working gate.
      */
@@ -90,7 +90,8 @@ class design_sidb_gates_impl
      * @param tt Expected Boolean function of the layout given as a multi-output truth table.
      * @param ps Parameters and settings for the gate designer.
      */
-    design_sidb_gates_impl(const Lyt& skeleton, const std::vector<TT>& tt, const design_sidb_gates_params<Lyt>& ps) :
+    design_sidb_gates_impl(const Lyt& skeleton, const std::vector<TT>& tt,
+                           const design_sidb_gates_params<cell<Lyt>>& ps) :
             skeleton_layout{skeleton},
             truth_table{tt},
             params{ps},
@@ -219,7 +220,7 @@ class design_sidb_gates_impl
     /**
      * Parameters for the *SiDB Gate Designer*.
      */
-    const design_sidb_gates_params<Lyt>& params;
+    const design_sidb_gates_params<cell<Lyt>>& params;
     /**
      * All cells within the canvas.
      */
@@ -305,7 +306,7 @@ class design_sidb_gates_impl
  */
 template <typename Lyt, typename TT>
 [[nodiscard]] std::vector<Lyt> design_sidb_gates(const Lyt& skeleton, const std::vector<TT>& spec,
-                                                 const design_sidb_gates_params<Lyt>& params = {}) noexcept
+                                                 const design_sidb_gates_params<cell<Lyt>>& params = {}) noexcept
 {
     static_assert(is_cell_level_layout_v<Lyt>, "Lyt is not a cell-level layout");
     static_assert(has_sidb_technology_v<Lyt>, "Lyt is not an SiDB layout");
@@ -322,7 +323,7 @@ template <typename Lyt, typename TT>
 
     detail::design_sidb_gates_impl<Lyt, TT> p{skeleton, spec, params};
 
-    if (params.design_mode == design_sidb_gates_params<Lyt>::design_sidb_gates_mode::EXHAUSTIVE)
+    if (params.design_mode == design_sidb_gates_params<cell<Lyt>>::design_sidb_gates_mode::EXHAUSTIVE)
     {
         return p.run_exhaustive_design();
     }

include/fiction/algorithms/simulation/sidb/calculate_energy_and_state_type.hpp

@@ -5,16 +5,19 @@
 #ifndef FICTION_CALCULATE_ENERGY_AND_STATE_TYPE_HPP
 #define FICTION_CALCULATE_ENERGY_AND_STATE_TYPE_HPP
 
-#include "fiction/algorithms/iter/bdl_input_iterator.hpp"
+#include "fiction/algorithms/simulation/sidb/detect_bdl_pairs.hpp"
 #include "fiction/algorithms/simulation/sidb/energy_distribution.hpp"
 #include "fiction/technology/charge_distribution_surface.hpp"
 #include "fiction/technology/physical_constants.hpp"
+#include "fiction/traits.hpp"
 #include "fiction/utils/math_utils.hpp"
 
+#include <kitty/bit_operations.hpp>
+#include <kitty/traits.hpp>
+
+#include <cassert>
 #include <cmath>
 #include <cstdint>
-#include <map>
-#include <string>
 #include <utility>
 #include <vector>
 
@@ -44,7 +47,7 @@ template <typename Lyt, typename TT>
 [[nodiscard]] sidb_energy_and_state_type
 calculate_energy_and_state_type(const sidb_energy_distribution&                      energy_distribution,
                                 const std::vector<charge_distribution_surface<Lyt>>& valid_charge_distributions,
-                                const std::vector<bdl_pair<Lyt>>& output_bdl_pairs, const std::vector<TT>& spec,
+                                const std::vector<bdl_pair<cell<Lyt>>>& output_bdl_pairs, const std::vector<TT>& spec,
                                 const uint64_t input_index) noexcept
 
 {