2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2013,2014, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
37 * Implements test helper routines from toputils.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
46 #include "gromacs/math/vec.h"
47 #include "gromacs/fileio/tpxio.h"
48 #include "gromacs/fileio/trx.h"
49 #include "gromacs/fileio/trxio.h"
50 #include "gromacs/topology/atoms.h"
51 #include "gromacs/topology/topology.h"
52 #include "gromacs/utility/gmxassert.h"
53 #include "gromacs/utility/smalloc.h"
55 #include "testutils/testfilemanager.h"
62 TopologyManager::TopologyManager()
63 : top_(NULL), frame_(NULL)
67 TopologyManager::~TopologyManager()
71 free_t_atoms(&top_->atoms, TRUE);
85 void TopologyManager::requestFrame()
87 GMX_RELEASE_ASSERT(top_ == NULL,
88 "Frame must be requested before initializing topology");
95 void TopologyManager::requestVelocities()
97 GMX_RELEASE_ASSERT(frame_ != NULL,
98 "Velocities requested before requesting a frame");
100 if (frame_->natoms > 0)
102 snew(frame_->v, frame_->natoms);
106 void TopologyManager::requestForces()
108 GMX_RELEASE_ASSERT(frame_ != NULL,
109 "Forces requested before requesting a frame");
111 if (frame_->natoms > 0)
113 snew(frame_->f, frame_->natoms);
117 void TopologyManager::loadTopology(const char *filename)
124 GMX_RELEASE_ASSERT(top_ == NULL, "Topology initialized more than once");
126 read_tps_conf(gmx::test::TestFileManager::getInputFilePath(filename).c_str(),
127 title, top_, &ePBC, frame_ != NULL ? &xtop : NULL,
132 frame_->flags = TRX_NEED_X;
133 frame_->natoms = top_->atoms.nr;
135 snew(frame_->x, frame_->natoms);
136 std::memcpy(frame_->x, xtop, sizeof(*frame_->x) * frame_->natoms);
138 copy_mat(box, frame_->box);
144 void TopologyManager::initAtoms(int count)
146 GMX_RELEASE_ASSERT(top_ == NULL, "Topology initialized more than once");
148 init_t_atoms(&top_->atoms, count, FALSE);
149 for (int i = 0; i < count; ++i)
151 top_->atoms.atom[i].m = (i % 3 == 0 ? 2.0 : 1.0);
155 frame_->flags = TRX_NEED_X;
156 frame_->natoms = count;
158 snew(frame_->x, count);
161 snew(frame_->v, count);
165 snew(frame_->f, count);
170 void TopologyManager::initAtomTypes(int count, const char *const types[])
172 GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
173 atomtypes_.reserve(count);
174 for (int i = 0; i < count; ++i)
176 atomtypes_.push_back(strdup(types[i]));
178 snew(top_->atoms.atomtype, top_->atoms.nr);
179 for (int i = 0, j = 0; i < top_->atoms.nr; ++i, ++j)
185 top_->atoms.atomtype[i] = &atomtypes_[j];
189 void TopologyManager::initUniformResidues(int residueSize)
191 GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
192 int residueIndex = -1;
193 for (int i = 0; i < top_->atoms.nr; ++i)
195 if (i % residueSize == 0)
199 top_->atoms.atom[i].resind = residueIndex;
203 void TopologyManager::initUniformMolecules(int moleculeSize)
205 GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
207 top_->mols.nalloc_index = (top_->atoms.nr + moleculeSize - 1) / moleculeSize + 1;
208 snew(top_->mols.index, top_->mols.nalloc_index);
210 while (index < top_->atoms.nr)
212 top_->mols.index[top_->mols.nr] = index;
214 index += moleculeSize;
216 top_->mols.index[top_->mols.nr] = top_->atoms.nr;