+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2021, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS 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
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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+ * consider code for inclusion in the official distribution, but
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+ * official version at http://www.gromacs.org.
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+ */
+/*! \internal \file
+ * \brief
+ * Tests for the WholeMoleculeTransform class.
+ *
+ * \author berk Hess <hess@kth.se>
+ * \ingroup module_mdlib
+ */
+#include "gmxpre.h"
+
+#include "gromacs/mdlib/wholemoleculetransform.h"
+
+#include <gtest/gtest.h>
+
+#include "gromacs/domdec/ga2la.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/topology.h"
+
+#include "testutils/testasserts.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+//! The number of atoms for the test molecule
+constexpr int c_numAtoms = 4;
+//! The number of bonds, we use 2 bonds so we have one unbound atom
+constexpr int c_numBonds = 2;
+
+//! Returns a topology with a three atom molecule that is linearly connected
+std::unique_ptr<gmx_mtop_t> triAtomMoleculeSystem()
+{
+ gmx_moltype_t moltype;
+
+ moltype.atoms.nr = c_numAtoms;
+
+ for (int b = 0; b < c_numBonds; b++)
+ {
+ const int parameterType = -1; // value is not actually used
+ const std::array<int, 2> atomIndices = { b, b + 1 };
+ moltype.ilist[F_CONNBONDS].push_back(parameterType, atomIndices);
+ }
+
+ std::unique_ptr<gmx_mtop_t> mtop = std::make_unique<gmx_mtop_t>();
+
+ mtop->moltype.push_back(moltype);
+
+ gmx_molblock_t molblock;
+ molblock.type = 0;
+ molblock.nmol = 1;
+ mtop->molblock.push_back(molblock);
+ mtop->natoms = c_numAtoms;
+
+ return mtop;
+}
+
+
+//! Coordinates, broken over PBC
+const std::array<RVec, c_numAtoms> c_coords = {
+ { { 2.5, 0.5, 1.5 }, { 0.5, 0.5, 1.5 }, { 1.5, 0.5, 1.5 }, { 2.7, 0.5, 1.5 } }
+};
+
+//! A box that works with \p c_coords
+const matrix box = { { 3, 0, 0 }, { 0, 2, 0 }, { 0, 0, 2 } };
+
+TEST(WholeMoleculeTransform, MakesMoleculesWhole)
+{
+ const auto mtop = triAtomMoleculeSystem();
+
+ WholeMoleculeTransform wmt(*mtop, PbcType::Xyz, false);
+
+ wmt.updateForAtomPbcJumps(c_coords, box);
+
+ auto wholeCoords = wmt.wholeMoleculeCoordinates(c_coords, box);
+
+ for (int b = 0; b < c_numBonds; b++)
+ {
+ EXPECT_FLOAT_EQ(std::abs(wholeCoords[b][XX] - wholeCoords[b + 1][XX]), 1);
+ }
+}
+
+TEST(WholeMoleculeTransform, HandlesReordering)
+{
+ const auto mtop = triAtomMoleculeSystem();
+
+ WholeMoleculeTransform wmt(*mtop, PbcType::Xyz, true);
+
+ const std::array<int, c_numAtoms> reordering = { 2, 0, 3, 1 };
+
+ gmx_ga2la_t ga2la(c_numAtoms, c_numAtoms);
+ std::vector<RVec> coords;
+ for (int a = 0; a < c_numAtoms; a++)
+ {
+ ga2la.insert(reordering[a], { a, 0 });
+
+ coords.push_back(c_coords[reordering[a]]);
+ }
+
+ wmt.updateAtomOrder(reordering, ga2la);
+
+ wmt.updateForAtomPbcJumps(coords, box);
+
+ auto wholeCoords = wmt.wholeMoleculeCoordinates(coords, box);
+
+ for (int b = 0; b < c_numBonds; b++)
+ {
+ EXPECT_FLOAT_EQ(
+ std::abs(wholeCoords[ga2la.find(b)->la][XX] - wholeCoords[ga2la.find(b + 1)->la][XX]), 1);
+ }
+}
+
+} // namespace
+
+} // namespace gmx