2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2013, by the GROMACS development team, led by
5 * David van der Spoel, Berk Hess, Erik Lindahl, and including many
6 * others, as listed in the AUTHORS file in the top-level source
7 * 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 * Tests the position mapping engine.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
42 #include <gtest/gtest.h>
46 #include "gromacs/legacyheaders/smalloc.h"
47 #include "gromacs/legacyheaders/typedefs.h"
48 #include "gromacs/legacyheaders/vec.h"
50 #include "gromacs/selection/indexutil.h"
51 #include "gromacs/selection/poscalc.h"
52 #include "gromacs/selection/position.h"
54 #include "testutils/refdata.h"
61 /********************************************************************
62 * PositionCalculationTest
65 class PositionCalculationTest : public ::testing::Test
68 PositionCalculationTest();
69 ~PositionCalculationTest();
71 void generateCoordinates();
73 gmx_ana_poscalc_t *createCalculation(e_poscalc_t type, int flags);
74 void setMaximumGroup(gmx_ana_poscalc_t *pc,
75 int count, const int atoms[]);
76 gmx_ana_pos_t *initPositions(gmx_ana_poscalc_t *pc, const char *name);
78 void checkInitialized();
79 void updateAndCheck(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p,
80 int count, const int atoms[],
81 gmx::test::TestReferenceChecker *checker,
84 void testSingleStatic(e_poscalc_t type, int flags, bool bExpectTop,
85 int atomCount, const int atoms[]);
86 void testSingleDynamic(e_poscalc_t type, int flags, bool bExpectTop,
87 int initCount, const int initAtoms[],
88 int evalCount, const int evalAtoms[]);
91 void setMaximumGroup(gmx_ana_poscalc_t *pc, const int (&atoms)[count])
93 setMaximumGroup(pc, count, atoms);
96 void updateAndCheck(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p,
97 const int (&atoms)[count],
98 gmx::test::TestReferenceChecker *checker,
101 updateAndCheck(pc, p, count, atoms, checker, name);
103 template <int atomCount>
104 void testSingleStatic(e_poscalc_t type, int flags, bool bExpectTop,
105 const int (&atoms)[atomCount])
107 testSingleStatic(type, flags, bExpectTop, atomCount, atoms);
109 template <int initCount, int evalCount>
110 void testSingleDynamic(e_poscalc_t type, int flags, bool bExpectTop,
111 const int (&initAtoms)[initCount],
112 const int (&evalAtoms)[evalCount])
114 testSingleDynamic(type, flags, bExpectTop,
115 initCount, initAtoms, evalCount, evalAtoms);
118 gmx::test::TestReferenceData data_;
119 gmx::test::TestReferenceChecker checker_;
120 gmx::test::TopologyManager topManager_;
121 gmx::PositionCalculationCollection pcc_;
126 PositionTest() : pos(NULL), pc(NULL), name(NULL) {}
127 PositionTest(gmx_ana_pos_t *pos, gmx_ana_poscalc_t *pc,
129 : pos(pos), pc(pc), name(name)
134 gmx_ana_poscalc_t *pc;
138 typedef std::vector<PositionTest> PositionTestList;
140 void setTopologyIfRequired();
141 void checkPositions(gmx::test::TestReferenceChecker *checker,
142 const char *name, gmx_ana_pos_t *p,
145 std::vector<gmx_ana_poscalc_t *> pcList_;
146 PositionTestList posList_;
150 PositionCalculationTest::PositionCalculationTest()
151 : checker_(data_.rootChecker()), bTopSet_(false)
153 topManager_.requestFrame();
156 PositionCalculationTest::~PositionCalculationTest()
158 std::vector<gmx_ana_poscalc_t *>::reverse_iterator pci;
159 for (pci = pcList_.rbegin(); pci != pcList_.rend(); ++pci)
161 gmx_ana_poscalc_free(*pci);
164 PositionTestList::iterator pi;
165 for (pi = posList_.begin(); pi != posList_.end(); ++pi)
167 gmx_ana_pos_free(pi->pos);
171 void PositionCalculationTest::generateCoordinates()
173 t_topology *top = topManager_.topology();
174 t_trxframe *frame = topManager_.frame();
175 for (int i = 0; i < top->atoms.nr; ++i)
178 frame->x[i][YY] = top->atoms.atom[i].resind;
179 frame->x[i][ZZ] = 0.0;
182 copy_rvec(frame->x[i], frame->v[i]);
183 frame->v[i][ZZ] = 1.0;
187 copy_rvec(frame->x[i], frame->f[i]);
188 frame->f[i][ZZ] = -1.0;
194 PositionCalculationTest::createCalculation(e_poscalc_t type, int flags)
196 pcList_.reserve(pcList_.size() + 1);
197 pcList_.push_back(pcc_.createCalculation(type, flags));
198 return pcList_.back();
201 void PositionCalculationTest::setMaximumGroup(gmx_ana_poscalc_t *pc,
202 int count, const int atoms[])
204 setTopologyIfRequired();
207 g.index = const_cast<int *>(atoms);
208 gmx_ana_poscalc_set_maxindex(pc, &g);
212 PositionCalculationTest::initPositions(gmx_ana_poscalc_t *pc, const char *name)
214 posList_.reserve(posList_.size() + 1);
217 posList_.push_back(PositionTest(p, pc, name));
218 gmx_ana_poscalc_init_pos(pc, p);
222 void PositionCalculationTest::checkInitialized()
224 gmx::test::TestReferenceChecker compound(
225 checker_.checkCompound("InitializedPositions", NULL));
226 PositionTestList::const_iterator pi;
227 for (pi = posList_.begin(); pi != posList_.end(); ++pi)
229 checkPositions(&compound, pi->name, pi->pos, false);
233 void PositionCalculationTest::updateAndCheck(
234 gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p, int count, const int atoms[],
235 gmx::test::TestReferenceChecker *checker, const char *name)
237 // TODO: The group reference may get stored in p and stays there after this
241 g.index = const_cast<int *>(atoms);
242 gmx_ana_poscalc_update(pc, p, &g, topManager_.frame(), NULL);
243 checkPositions(checker, name, p, true);
246 void PositionCalculationTest::testSingleStatic(
247 e_poscalc_t type, int flags, bool bExpectTop,
248 int atomCount, const int atoms[])
250 t_trxframe *frame = topManager_.frame();
253 flags |= POS_VELOCITIES;
259 gmx_ana_poscalc_t *pc = createCalculation(type, flags);
260 EXPECT_EQ(bExpectTop, gmx_ana_poscalc_requires_top(pc));
261 setMaximumGroup(pc, atomCount, atoms);
262 gmx_ana_pos_t *p = initPositions(pc, NULL);
265 pcc_.initEvaluation();
267 generateCoordinates();
268 gmx::test::TestReferenceChecker frameCompound(
269 checker_.checkCompound("EvaluatedPositions", "Frame0"));
270 updateAndCheck(pc, p, atomCount, atoms, &frameCompound, NULL);
274 void PositionCalculationTest::testSingleDynamic(
275 e_poscalc_t type, int flags, bool bExpectTop,
276 int initCount, const int initAtoms[],
277 int evalCount, const int evalAtoms[])
279 gmx_ana_poscalc_t *pc = createCalculation(type, flags | POS_DYNAMIC);
280 EXPECT_EQ(bExpectTop, gmx_ana_poscalc_requires_top(pc));
281 setMaximumGroup(pc, initCount, initAtoms);
282 gmx_ana_pos_t *p = initPositions(pc, NULL);
285 pcc_.initEvaluation();
287 generateCoordinates();
288 gmx::test::TestReferenceChecker frameCompound(
289 checker_.checkCompound("EvaluatedPositions", "Frame0"));
290 updateAndCheck(pc, p, evalCount, evalAtoms, &frameCompound, NULL);
294 void PositionCalculationTest::setTopologyIfRequired()
300 std::vector<gmx_ana_poscalc_t *>::const_iterator pci;
301 for (pci = pcList_.begin(); pci != pcList_.end(); ++pci)
303 if (gmx_ana_poscalc_requires_top(*pci))
306 pcc_.setTopology(topManager_.topology());
312 void PositionCalculationTest::checkPositions(
313 gmx::test::TestReferenceChecker *checker,
314 const char *name, gmx_ana_pos_t *p, bool bCoordinates)
316 EXPECT_EQ(p->nr, p->m.nr);
317 EXPECT_EQ(p->nr, p->m.mapb.nr);
318 ASSERT_TRUE(p->g != NULL);
319 gmx::test::TestReferenceChecker compound(
320 checker->checkCompound("Positions", name));
321 compound.checkInteger(p->nr, "Count");
322 const char *type = "???";
325 case INDEX_UNKNOWN: type = "unknown"; break;
326 case INDEX_ATOM: type = "atoms"; break;
327 case INDEX_RES: type = "residues"; break;
328 case INDEX_MOL: type = "molecules"; break;
329 case INDEX_ALL: type = "single"; break;
331 compound.checkString(type, "Type");
332 compound.checkSequenceArray(p->nr + 1, p->m.mapb.index, "Block");
333 for (int i = 0; i < p->nr; ++i)
335 gmx::test::TestReferenceChecker posCompound(
336 compound.checkCompound("Position", NULL));
337 // Always true; should satisfy clang.
340 posCompound.checkSequence(&p->g->index[p->m.mapb.index[i]],
341 &p->g->index[p->m.mapb.index[i+1]],
344 posCompound.checkInteger(p->m.refid[i], "RefId");
347 posCompound.checkVector(p->x[i], "Coordinates");
349 if (bCoordinates && p->v != NULL)
351 posCompound.checkVector(p->v[i], "Velocity");
353 if (bCoordinates && p->f != NULL)
355 posCompound.checkVector(p->f[i], "Force");
357 int originalIdIndex = (p->m.refid[i] != -1 ? p->m.refid[i] : i);
358 EXPECT_EQ(p->m.orgid[originalIdIndex], p->m.mapid[i]);
362 /********************************************************************
366 TEST_F(PositionCalculationTest, ComputesAtomPositions)
368 const int group[] = { 0, 1, 2, 3 };
369 topManager_.requestVelocities();
370 topManager_.requestForces();
371 topManager_.initAtoms(4);
372 testSingleStatic(POS_ATOM, 0, false, group);
375 TEST_F(PositionCalculationTest, ComputesResidueCOGPositions)
377 const int group[] = { 0, 1, 2, 3, 4, 8 };
378 topManager_.requestVelocities();
379 topManager_.requestForces();
380 topManager_.initAtoms(9);
381 topManager_.initUniformResidues(3);
382 testSingleStatic(POS_RES, 0, true, group);
385 TEST_F(PositionCalculationTest, ComputesResidueCOMPositions)
387 const int group[] = { 0, 1, 2, 3, 4, 8 };
388 topManager_.requestVelocities();
389 topManager_.requestForces();
390 topManager_.initAtoms(9);
391 topManager_.initUniformResidues(3);
392 testSingleStatic(POS_RES, POS_MASS, true, group);
395 TEST_F(PositionCalculationTest, ComputesGroupCOGPositions)
397 const int group[] = { 0, 1, 2, 3, 4, 5, 6, 7, 8 };
398 topManager_.requestVelocities();
399 topManager_.requestForces();
400 topManager_.initAtoms(9);
401 // Topology (masses) is requires for computing the force
402 testSingleStatic(POS_ALL, 0, true, group);
405 TEST_F(PositionCalculationTest, ComputesGroupCOMPositions)
407 const int group[] = { 0, 1, 2, 3, 4, 5, 6, 7, 8 };
408 topManager_.requestVelocities();
409 topManager_.requestForces();
410 topManager_.initAtoms(9);
411 testSingleStatic(POS_ALL, POS_MASS, true, group);
414 TEST_F(PositionCalculationTest, ComputesPositionsWithCompleteWhole)
416 const int group[] = { 0, 1, 2, 3, 4, 8 };
417 topManager_.initAtoms(9);
418 topManager_.initUniformResidues(3);
419 testSingleStatic(POS_RES, POS_COMPLWHOLE, true, group);
422 TEST_F(PositionCalculationTest, ComputesPositionsWithCompleteMax)
424 const int maxGroup[] = { 0, 1, 4, 5, 6, 8 };
425 const int evalGroup[] = { 0, 1, 5, 6 };
426 topManager_.initAtoms(9);
427 topManager_.initUniformResidues(3);
428 testSingleDynamic(POS_RES, POS_COMPLMAX, true, maxGroup, evalGroup);
431 TEST_F(PositionCalculationTest, ComputesPositionMask)
433 const int maxGroup[] = { 0, 1, 2, 3, 4, 5 };
434 const int evalGroup[] = { 1, 2, 4 };
435 topManager_.initAtoms(6);
436 testSingleDynamic(POS_ATOM, POS_MASKONLY, false, maxGroup, evalGroup);
439 // TODO: Check for POS_ALL_PBC
441 TEST_F(PositionCalculationTest, HandlesIdenticalStaticCalculations)
443 const int group[] = { 0, 1, 4, 5, 6, 7 };
444 topManager_.initAtoms(9);
445 topManager_.initUniformResidues(3);
447 gmx_ana_poscalc_t *pc1 = createCalculation(POS_RES, 0);
448 gmx_ana_poscalc_t *pc2 = createCalculation(POS_RES, 0);
449 gmx_ana_poscalc_t *pc3 = createCalculation(POS_RES, 0);
450 setMaximumGroup(pc1, group);
451 setMaximumGroup(pc2, group);
452 setMaximumGroup(pc3, group);
453 gmx_ana_pos_t *p1 = initPositions(pc1, "Positions");
454 gmx_ana_pos_t *p2 = initPositions(pc2, "Positions");
455 gmx_ana_pos_t *p3 = initPositions(pc3, "Positions");
458 pcc_.initEvaluation();
460 generateCoordinates();
461 gmx::test::TestReferenceChecker frameCompound(
462 checker_.checkCompound("EvaluatedPositions", "Frame0"));
463 updateAndCheck(pc1, p1, group, &frameCompound, "Positions");
464 updateAndCheck(pc2, p2, group, &frameCompound, "Positions");
465 updateAndCheck(pc3, p3, group, &frameCompound, "Positions");
469 TEST_F(PositionCalculationTest, HandlesOverlappingStaticCalculations)
471 const int group1[] = { 0, 1, 4, 5 };
472 const int group2[] = { 4, 5, 7, 8 };
473 topManager_.initAtoms(9);
474 topManager_.initUniformResidues(3);
476 gmx_ana_poscalc_t *pc1 = createCalculation(POS_RES, 0);
477 gmx_ana_poscalc_t *pc2 = createCalculation(POS_RES, 0);
478 setMaximumGroup(pc1, group1);
479 setMaximumGroup(pc2, group2);
480 gmx_ana_pos_t *p1 = initPositions(pc1, "P1");
481 gmx_ana_pos_t *p2 = initPositions(pc2, "P2");
484 pcc_.initEvaluation();
486 generateCoordinates();
487 gmx::test::TestReferenceChecker frameCompound(
488 checker_.checkCompound("EvaluatedPositions", "Frame0"));
489 updateAndCheck(pc1, p1, group1, &frameCompound, "P1");
490 updateAndCheck(pc2, p2, group2, &frameCompound, "P2");
494 // TODO: Check for handling of more multiple calculation cases