shapes: fix SimplePore side-sign at lower pore mouth (bug-sweep #13)

src/shapes/src/SimplePore.cpp

@@ -103,7 +103,7 @@ void SimplePore::calculate_dist(const Utils::Vector3d &pos, double &dist,
   } else {
     // smoothing area
     if (std::abs(z) >= c_z) {
-      auto const d_sq = Utils::sqr(r - c_r) + Utils::sqr(z - c_z);
+      auto const d_sq = Utils::sqr(r - c_r) + Utils::sqr(std::abs(z) - c_z);
       if (d_sq > Utils::sqr(m_smoothing_rad)) {
         side = 1;
       }

src/shapes/unit_tests/CMakeLists.txt

@@ -26,5 +26,7 @@ espresso_unit_test(SRC Union_test.cpp DEPENDS espresso::shapes espresso::utils)
 espresso_unit_test(SRC Ellipsoid_test.cpp DEPENDS espresso::shapes
                    espresso::utils)
 espresso_unit_test(SRC Sphere_test.cpp DEPENDS espresso::shapes espresso::utils)
+espresso_unit_test(SRC SimplePore_test.cpp DEPENDS espresso::shapes
+                   espresso::utils)
 espresso_unit_test(SRC NoWhere_test.cpp DEPENDS espresso::shapes
                    espresso::utils)

src/shapes/unit_tests/SimplePore_test.cpp

@@ -0,0 +1,68 @@
+/*
+ * Copyright (C) 2010-2026 The ESPResSo project
+ *
+ * This file is part of ESPResSo.
+ *
+ * ESPResSo is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * ESPResSo is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#define BOOST_TEST_MODULE simple_pore test
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+
+#include <shapes/SimplePore.hpp>
+#include <utils/Vector.hpp>
+
+/*
+ * The pore has mirror symmetry in z about its center (the documented
+ * invariant in SimplePore::calculate_dist). Two probe points at the +z and
+ * -z mouths with identical r and |z| therefore MUST yield the same signed
+ * distance, and a point inside the solid wall material at either mouth must
+ * report a negative (inside) distance.
+ *
+ * Bug #13: the smoothing-area side test used the signed z in
+ * Utils::sqr(z - c_z) instead of Utils::sqr(std::abs(z) - c_z). At the
+ * negative-z mouth this forces side=+1 (outside) even for a point inside the
+ * solid, flipping the sign of the distance.
+ */
+BOOST_AUTO_TEST_CASE(mirror_symmetry_in_z) {
+  Shapes::SimplePore pore;
+  pore.set_axis({0., 0., 1.});
+  pore.set_radius(3.);
+  pore.set_smoothing_radius(0.1);
+  pore.set_length(6.);
+  pore.center() = Utils::Vector3d{10., 10., 10.};
+  /* derived: c_r = 3.1, c_z = 2.9 */
+
+  /* Probe r = 3.05 (x-offset), z = +/-2.95 relative to the center: inside the
+     solid wall material, inside the smoothing fillet at each mouth. r is
+     chosen slightly larger than m_rad so the smoothing branch is exercised. */
+  Utils::Vector3d const center{10., 10., 10.};
+  auto const pos_plus = center + Utils::Vector3d{3.05, 0., 2.95};
+  auto const pos_minus = center + Utils::Vector3d{3.05, 0., -2.95};
+
+  double dist_plus, dist_minus;
+  Utils::Vector3d vec_plus, vec_minus;
+  pore.calculate_dist(pos_plus, dist_plus, vec_plus);
+  pore.calculate_dist(pos_minus, dist_minus, vec_minus);
+
+  /* The signed scalar distance must be mirror-symmetric in z. */
+  BOOST_TEST_INFO("dist(+z)=" << dist_plus << " dist(-z)=" << dist_minus);
+  BOOST_REQUIRE_CLOSE(dist_plus, dist_minus, 1e-9);
+
+  /* The probe lies inside the solid wall material, so both mouths must
+     report a negative (inside) distance. */
+  BOOST_REQUIRE_LT(dist_plus, 0.);
+  BOOST_REQUIRE_LT(dist_minus, 0.);
+}