/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
* David van der Spoel, Berk Hess, Erik Lindahl, and including many
* others, as listed in the AUTHORS file in the top-level source
* directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gromacs/selection/centerofmass.h"
+
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/pbc.h"
#include "gromacs/legacyheaders/vec.h"
-#include "gromacs/selection/centerofmass.h"
-
/*!
* \param[in] top Topology structure (unused, can be NULL).
* \param[in] x Position vectors of all atoms.
* \param[in] index Indices of atoms.
* \param[out] fout Force on the COG position for the indexed atoms.
* \returns 0 on success, EINVAL if \p top is NULL.
- *
- * No special function is provided for calculating the force on the center of
- * mass, because this can be achieved with gmx_calc_cog().
*/
int
gmx_calc_cog_f(t_topology *top, rvec f[], int nrefat, atom_id index[], rvec fout)
}
mtot += mass;
}
- svmul(mtot, fout, fout);
+ svmul(mtot / nrefat, fout, fout);
+ return 0;
+}
+
+/*!
+ * \param[in] top Topology structure (unused, can be NULL).
+ * \param[in] f Forces on all atoms.
+ * \param[in] nrefat Number of atoms in the index.
+ * \param[in] index Indices of atoms.
+ * \param[out] fout Force on the COM position for the indexed atoms.
+ * \returns 0 on success.
+ */
+int
+gmx_calc_com_f(t_topology *top, rvec f[], int nrefat, atom_id index[], rvec fout)
+{
+ clear_rvec(fout);
+ for (int m = 0; m < nrefat; ++m)
+ {
+ const int ai = index[m];
+ rvec_inc(fout, f[ai]);
+ }
return 0;
}
* \param[out] fout Force on the COM/COG position for the indexed atoms.
* \returns 0 on success, EINVAL if \p top is NULL and \p bMass is false.
*
- * Calls either gmx_calc_cog() or gmx_calc_cog_f() depending on the value of
+ * Calls either gmx_calc_cog_f() or gmx_calc_com_f() depending on the value of
* \p bMass.
* Other parameters are passed unmodified to these functions.
*/
{
if (bMass)
{
- return gmx_calc_cog(top, f, nrefat, index, fout);
+ return gmx_calc_com_f(top, f, nrefat, index, fout);
}
else
{
}
mtot += mass;
}
- svmul(mtot, fb, fout[b]);
+ svmul(mtot / (block->index[b+1] - block->index[b]), fb, fout[b]);
+ }
+ return 0;
+}
+
+/*!
+ * \param[in] top Topology structure (unused, can be NULL).
+ * \param[in] f Forces on all atoms.
+ * \param[in] block t_block structure that divides \p index into blocks.
+ * \param[in] index Indices of atoms.
+ * \param[out] fout \p block->nr Forces on COM positions.
+ * \returns 0 on success.
+ */
+int
+gmx_calc_com_f_block(t_topology *top, rvec f[], t_block *block, atom_id index[],
+ rvec fout[])
+{
+ for (int b = 0; b < block->nr; ++b)
+ {
+ rvec fb;
+ clear_rvec(fb);
+ for (int i = block->index[b]; i < block->index[b+1]; ++i)
+ {
+ const int ai = index[i];
+ rvec_inc(fb, f[ai]);
+ }
+ copy_rvec(fb, fout[b]);
}
return 0;
}
* \param[out] fout \p block->nr forces on the COM/COG positions.
* \returns 0 on success, EINVAL if \p top is NULL and \p bMass is true.
*
- * Calls either gmx_calc_com_block() or gmx_calc_cog_block() depending on the
- * value of \p bMass.
+ * Calls either gmx_calc_com_f_block() or gmx_calc_cog_f_block() depending on
+ * the value of \p bMass.
* Other parameters are passed unmodified to these functions.
*/
int
{
if (bMass)
{
- return gmx_calc_cog_block(top, f, block, index, fout);
+ return gmx_calc_com_f_block(top, f, block, index, fout);
}
else
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2013, by the GROMACS development team, led by
* David van der Spoel, Berk Hess, Erik Lindahl, and including many
* others, as listed in the AUTHORS file in the top-level source
* directory and at http://www.gromacs.org.
/** Calculate force on a single center of geometry. */
int
gmx_calc_cog_f(t_topology *top, rvec f[], int nrefat, atom_id index[], rvec fout);
+/** Calculate force on a single center of mass. */
+int
+gmx_calc_com_f(t_topology *top, rvec f[], int nrefat, atom_id index[], rvec fout);
/** Calculate a single center of mass/geometry. */
int
gmx_calc_comg(t_topology *top, rvec x[], int nrefat, atom_id index[],
int
gmx_calc_cog_f_block(t_topology *top, rvec f[], t_block *block,
atom_id index[], rvec fout[]);
+/** Calculate forces on centers of mass for a blocked index. */
+int
+gmx_calc_com_f_block(t_topology *top, rvec f[], t_block *block,
+ atom_id index[], rvec fout[]);
/** Calculate centers of mass/geometry for a blocked index. */
int
gmx_calc_comg_block(t_topology *top, rvec x[], t_block *block,
bool
gmx_ana_poscalc_requires_top(gmx_ana_poscalc_t *pc)
{
- if ((pc->flags & POS_MASS) || pc->type == POS_RES || pc->type == POS_MOL)
+ if ((pc->flags & POS_MASS) || pc->type == POS_RES || pc->type == POS_MOL
+ || ((pc->flags & POS_FORCES) && pc->type != POS_ATOM))
{
return true;
}
{
g = &pc->gmax;
}
- gmx_ana_pos_set_evalgrp(p, g);
/* Update the index map */
if (pc->flags & POS_DYNAMIC)
{
+ gmx_ana_pos_set_evalgrp(p, g);
gmx_ana_indexmap_update(&p->m, g, false);
p->nr = p->m.nr;
}
}
if (p->f && fr->bF)
{
- gmx_calc_comg_blocka(top, fr->f, &pc->b, bMass, p->f);
+ gmx_calc_comg_f_blocka(top, fr->f, &pc->b, bMass, p->f);
}
break;
}
gmx_add_unit_test(SelectionUnitTests selection-test
indexutil.cpp
nbsearch.cpp
+ poscalc.cpp
selectioncollection.cpp
selectionoption.cpp
toputils.cpp)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2013, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, 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.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests the position mapping engine.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_selection
+ */
+#include <gtest/gtest.h>
+
+#include <vector>
+
+#include "gromacs/legacyheaders/smalloc.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vec.h"
+
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/poscalc.h"
+#include "gromacs/selection/position.h"
+
+#include "testutils/refdata.h"
+
+#include "toputils.h"
+
+namespace
+{
+
+/********************************************************************
+ * PositionCalculationTest
+ */
+
+class PositionCalculationTest : public ::testing::Test
+{
+ public:
+ PositionCalculationTest();
+ ~PositionCalculationTest();
+
+ void generateCoordinates();
+
+ gmx_ana_poscalc_t *createCalculation(e_poscalc_t type, int flags);
+ void setMaximumGroup(gmx_ana_poscalc_t *pc,
+ int count, const int atoms[]);
+ gmx_ana_pos_t *initPositions(gmx_ana_poscalc_t *pc, const char *name);
+
+ void checkInitialized();
+ void updateAndCheck(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p,
+ int count, const int atoms[],
+ gmx::test::TestReferenceChecker *checker,
+ const char *name);
+
+ void testSingleStatic(e_poscalc_t type, int flags, bool bExpectTop,
+ int atomCount, const int atoms[]);
+ void testSingleDynamic(e_poscalc_t type, int flags, bool bExpectTop,
+ int initCount, const int initAtoms[],
+ int evalCount, const int evalAtoms[]);
+
+ template <int count>
+ void setMaximumGroup(gmx_ana_poscalc_t *pc, const int (&atoms)[count])
+ {
+ setMaximumGroup(pc, count, atoms);
+ }
+ template <int count>
+ void updateAndCheck(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p,
+ const int (&atoms)[count],
+ gmx::test::TestReferenceChecker *checker,
+ const char *name)
+ {
+ updateAndCheck(pc, p, count, atoms, checker, name);
+ }
+ template <int atomCount>
+ void testSingleStatic(e_poscalc_t type, int flags, bool bExpectTop,
+ const int (&atoms)[atomCount])
+ {
+ testSingleStatic(type, flags, bExpectTop, atomCount, atoms);
+ }
+ template <int initCount, int evalCount>
+ void testSingleDynamic(e_poscalc_t type, int flags, bool bExpectTop,
+ const int (&initAtoms)[initCount],
+ const int (&evalAtoms)[evalCount])
+ {
+ testSingleDynamic(type, flags, bExpectTop,
+ initCount, initAtoms, evalCount, evalAtoms);
+ }
+
+ gmx::test::TestReferenceData data_;
+ gmx::test::TestReferenceChecker checker_;
+ gmx::test::TopologyManager topManager_;
+ gmx::PositionCalculationCollection pcc_;
+
+ private:
+ struct PositionTest
+ {
+ PositionTest() : pos(NULL), pc(NULL), name(NULL) {}
+ PositionTest(gmx_ana_pos_t *pos, gmx_ana_poscalc_t *pc,
+ const char *name)
+ : pos(pos), pc(pc), name(name)
+ {
+ }
+
+ gmx_ana_pos_t *pos;
+ gmx_ana_poscalc_t *pc;
+ const char *name;
+ };
+
+ typedef std::vector<PositionTest> PositionTestList;
+
+ void setTopologyIfRequired();
+ void checkPositions(gmx::test::TestReferenceChecker *checker,
+ const char *name, gmx_ana_pos_t *p,
+ bool bCoordinates);
+
+ std::vector<gmx_ana_poscalc_t *> pcList_;
+ PositionTestList posList_;
+ bool bTopSet_;
+};
+
+PositionCalculationTest::PositionCalculationTest()
+ : checker_(data_.rootChecker()), bTopSet_(false)
+{
+ topManager_.requestFrame();
+}
+
+PositionCalculationTest::~PositionCalculationTest()
+{
+ std::vector<gmx_ana_poscalc_t *>::reverse_iterator pci;
+ for (pci = pcList_.rbegin(); pci != pcList_.rend(); ++pci)
+ {
+ gmx_ana_poscalc_free(*pci);
+ }
+
+ PositionTestList::iterator pi;
+ for (pi = posList_.begin(); pi != posList_.end(); ++pi)
+ {
+ gmx_ana_pos_free(pi->pos);
+ }
+}
+
+void PositionCalculationTest::generateCoordinates()
+{
+ t_topology *top = topManager_.topology();
+ t_trxframe *frame = topManager_.frame();
+ for (int i = 0; i < top->atoms.nr; ++i)
+ {
+ frame->x[i][XX] = i;
+ frame->x[i][YY] = top->atoms.atom[i].resind;
+ frame->x[i][ZZ] = 0.0;
+ if (frame->bV)
+ {
+ copy_rvec(frame->x[i], frame->v[i]);
+ frame->v[i][ZZ] = 1.0;
+ }
+ if (frame->bF)
+ {
+ copy_rvec(frame->x[i], frame->f[i]);
+ frame->f[i][ZZ] = -1.0;
+ }
+ }
+}
+
+gmx_ana_poscalc_t *
+PositionCalculationTest::createCalculation(e_poscalc_t type, int flags)
+{
+ pcList_.reserve(pcList_.size() + 1);
+ pcList_.push_back(pcc_.createCalculation(type, flags));
+ return pcList_.back();
+}
+
+void PositionCalculationTest::setMaximumGroup(gmx_ana_poscalc_t *pc,
+ int count, const int atoms[])
+{
+ setTopologyIfRequired();
+ gmx_ana_index_t g;
+ g.isize = count;
+ g.index = const_cast<int *>(atoms);
+ gmx_ana_poscalc_set_maxindex(pc, &g);
+}
+
+gmx_ana_pos_t *
+PositionCalculationTest::initPositions(gmx_ana_poscalc_t *pc, const char *name)
+{
+ posList_.reserve(posList_.size() + 1);
+ gmx_ana_pos_t *p;
+ snew(p, 1);
+ posList_.push_back(PositionTest(p, pc, name));
+ gmx_ana_poscalc_init_pos(pc, p);
+ return p;
+}
+
+void PositionCalculationTest::checkInitialized()
+{
+ gmx::test::TestReferenceChecker compound(
+ checker_.checkCompound("InitializedPositions", NULL));
+ PositionTestList::const_iterator pi;
+ for (pi = posList_.begin(); pi != posList_.end(); ++pi)
+ {
+ checkPositions(&compound, pi->name, pi->pos, false);
+ }
+}
+
+void PositionCalculationTest::updateAndCheck(
+ gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p, int count, const int atoms[],
+ gmx::test::TestReferenceChecker *checker, const char *name)
+{
+ // TODO: The group reference may get stored in p and stays there after this
+ // function returns.
+ gmx_ana_index_t g;
+ g.isize = count;
+ g.index = const_cast<int *>(atoms);
+ gmx_ana_poscalc_update(pc, p, &g, topManager_.frame(), NULL);
+ checkPositions(checker, name, p, true);
+}
+
+void PositionCalculationTest::testSingleStatic(
+ e_poscalc_t type, int flags, bool bExpectTop,
+ int atomCount, const int atoms[])
+{
+ t_trxframe *frame = topManager_.frame();
+ if (frame->bV)
+ {
+ flags |= POS_VELOCITIES;
+ }
+ if (frame->bF)
+ {
+ flags |= POS_FORCES;
+ }
+ gmx_ana_poscalc_t *pc = createCalculation(type, flags);
+ EXPECT_EQ(bExpectTop, gmx_ana_poscalc_requires_top(pc));
+ setMaximumGroup(pc, atomCount, atoms);
+ gmx_ana_pos_t *p = initPositions(pc, NULL);
+ checkInitialized();
+ {
+ pcc_.initEvaluation();
+ pcc_.initFrame();
+ generateCoordinates();
+ gmx::test::TestReferenceChecker frameCompound(
+ checker_.checkCompound("EvaluatedPositions", "Frame0"));
+ updateAndCheck(pc, p, atomCount, atoms, &frameCompound, NULL);
+ }
+}
+
+void PositionCalculationTest::testSingleDynamic(
+ e_poscalc_t type, int flags, bool bExpectTop,
+ int initCount, const int initAtoms[],
+ int evalCount, const int evalAtoms[])
+{
+ gmx_ana_poscalc_t *pc = createCalculation(type, flags | POS_DYNAMIC);
+ EXPECT_EQ(bExpectTop, gmx_ana_poscalc_requires_top(pc));
+ setMaximumGroup(pc, initCount, initAtoms);
+ gmx_ana_pos_t *p = initPositions(pc, NULL);
+ checkInitialized();
+ {
+ pcc_.initEvaluation();
+ pcc_.initFrame();
+ generateCoordinates();
+ gmx::test::TestReferenceChecker frameCompound(
+ checker_.checkCompound("EvaluatedPositions", "Frame0"));
+ updateAndCheck(pc, p, evalCount, evalAtoms, &frameCompound, NULL);
+ }
+}
+
+void PositionCalculationTest::setTopologyIfRequired()
+{
+ if (bTopSet_)
+ {
+ return;
+ }
+ std::vector<gmx_ana_poscalc_t *>::const_iterator pci;
+ for (pci = pcList_.begin(); pci != pcList_.end(); ++pci)
+ {
+ if (gmx_ana_poscalc_requires_top(*pci))
+ {
+ bTopSet_ = true;
+ pcc_.setTopology(topManager_.topology());
+ return;
+ }
+ }
+}
+
+void PositionCalculationTest::checkPositions(
+ gmx::test::TestReferenceChecker *checker,
+ const char *name, gmx_ana_pos_t *p, bool bCoordinates)
+{
+ EXPECT_EQ(p->nr, p->m.nr);
+ EXPECT_EQ(p->nr, p->m.mapb.nr);
+ ASSERT_TRUE(p->g != NULL);
+ gmx::test::TestReferenceChecker compound(
+ checker->checkCompound("Positions", name));
+ compound.checkInteger(p->nr, "Count");
+ const char *type = "???";
+ switch (p->m.type)
+ {
+ case INDEX_UNKNOWN: type = "unknown"; break;
+ case INDEX_ATOM: type = "atoms"; break;
+ case INDEX_RES: type = "residues"; break;
+ case INDEX_MOL: type = "molecules"; break;
+ case INDEX_ALL: type = "single"; break;
+ }
+ compound.checkString(type, "Type");
+ compound.checkSequenceArray(p->nr + 1, p->m.mapb.index, "Block");
+ for (int i = 0; i < p->nr; ++i)
+ {
+ gmx::test::TestReferenceChecker posCompound(
+ compound.checkCompound("Position", NULL));
+ // Always true; should satisfy clang.
+ if (p->g != NULL)
+ {
+ posCompound.checkSequence(&p->g->index[p->m.mapb.index[i]],
+ &p->g->index[p->m.mapb.index[i+1]],
+ "Atoms");
+ }
+ posCompound.checkInteger(p->m.refid[i], "RefId");
+ if (bCoordinates)
+ {
+ posCompound.checkVector(p->x[i], "Coordinates");
+ }
+ if (bCoordinates && p->v != NULL)
+ {
+ posCompound.checkVector(p->v[i], "Velocity");
+ }
+ if (bCoordinates && p->f != NULL)
+ {
+ posCompound.checkVector(p->f[i], "Force");
+ }
+ int originalIdIndex = (p->m.refid[i] != -1 ? p->m.refid[i] : i);
+ EXPECT_EQ(p->m.orgid[originalIdIndex], p->m.mapid[i]);
+ }
+}
+
+/********************************************************************
+ * Actual tests
+ */
+
+TEST_F(PositionCalculationTest, ComputesAtomPositions)
+{
+ const int group[] = { 0, 1, 2, 3 };
+ topManager_.requestVelocities();
+ topManager_.requestForces();
+ topManager_.initAtoms(4);
+ testSingleStatic(POS_ATOM, 0, false, group);
+}
+
+TEST_F(PositionCalculationTest, ComputesResidueCOGPositions)
+{
+ const int group[] = { 0, 1, 2, 3, 4, 8 };
+ topManager_.requestVelocities();
+ topManager_.requestForces();
+ topManager_.initAtoms(9);
+ topManager_.initUniformResidues(3);
+ testSingleStatic(POS_RES, 0, true, group);
+}
+
+TEST_F(PositionCalculationTest, ComputesResidueCOMPositions)
+{
+ const int group[] = { 0, 1, 2, 3, 4, 8 };
+ topManager_.requestVelocities();
+ topManager_.requestForces();
+ topManager_.initAtoms(9);
+ topManager_.initUniformResidues(3);
+ testSingleStatic(POS_RES, POS_MASS, true, group);
+}
+
+TEST_F(PositionCalculationTest, ComputesGroupCOGPositions)
+{
+ const int group[] = { 0, 1, 2, 3, 4, 5, 6, 7, 8 };
+ topManager_.requestVelocities();
+ topManager_.requestForces();
+ topManager_.initAtoms(9);
+ // Topology (masses) is requires for computing the force
+ testSingleStatic(POS_ALL, 0, true, group);
+}
+
+TEST_F(PositionCalculationTest, ComputesGroupCOMPositions)
+{
+ const int group[] = { 0, 1, 2, 3, 4, 5, 6, 7, 8 };
+ topManager_.requestVelocities();
+ topManager_.requestForces();
+ topManager_.initAtoms(9);
+ testSingleStatic(POS_ALL, POS_MASS, true, group);
+}
+
+TEST_F(PositionCalculationTest, ComputesPositionsWithCompleteWhole)
+{
+ const int group[] = { 0, 1, 2, 3, 4, 8 };
+ topManager_.initAtoms(9);
+ topManager_.initUniformResidues(3);
+ testSingleStatic(POS_RES, POS_COMPLWHOLE, true, group);
+}
+
+TEST_F(PositionCalculationTest, ComputesPositionsWithCompleteMax)
+{
+ const int maxGroup[] = { 0, 1, 4, 5, 6, 8 };
+ const int evalGroup[] = { 0, 1, 5, 6 };
+ topManager_.initAtoms(9);
+ topManager_.initUniformResidues(3);
+ testSingleDynamic(POS_RES, POS_COMPLMAX, true, maxGroup, evalGroup);
+}
+
+TEST_F(PositionCalculationTest, ComputesPositionMask)
+{
+ const int maxGroup[] = { 0, 1, 2, 3, 4, 5 };
+ const int evalGroup[] = { 1, 2, 4 };
+ topManager_.initAtoms(6);
+ testSingleDynamic(POS_ATOM, POS_MASKONLY, false, maxGroup, evalGroup);
+}
+
+// TODO: Check for POS_ALL_PBC
+
+TEST_F(PositionCalculationTest, HandlesIdenticalStaticCalculations)
+{
+ const int group[] = { 0, 1, 4, 5, 6, 7 };
+ topManager_.initAtoms(9);
+ topManager_.initUniformResidues(3);
+
+ gmx_ana_poscalc_t *pc1 = createCalculation(POS_RES, 0);
+ gmx_ana_poscalc_t *pc2 = createCalculation(POS_RES, 0);
+ gmx_ana_poscalc_t *pc3 = createCalculation(POS_RES, 0);
+ setMaximumGroup(pc1, group);
+ setMaximumGroup(pc2, group);
+ setMaximumGroup(pc3, group);
+ gmx_ana_pos_t *p1 = initPositions(pc1, "Positions");
+ gmx_ana_pos_t *p2 = initPositions(pc2, "Positions");
+ gmx_ana_pos_t *p3 = initPositions(pc3, "Positions");
+ checkInitialized();
+ {
+ pcc_.initEvaluation();
+ pcc_.initFrame();
+ generateCoordinates();
+ gmx::test::TestReferenceChecker frameCompound(
+ checker_.checkCompound("EvaluatedPositions", "Frame0"));
+ updateAndCheck(pc1, p1, group, &frameCompound, "Positions");
+ updateAndCheck(pc2, p2, group, &frameCompound, "Positions");
+ updateAndCheck(pc3, p3, group, &frameCompound, "Positions");
+ }
+}
+
+TEST_F(PositionCalculationTest, HandlesOverlappingStaticCalculations)
+{
+ const int group1[] = { 0, 1, 4, 5 };
+ const int group2[] = { 4, 5, 7, 8 };
+ topManager_.initAtoms(9);
+ topManager_.initUniformResidues(3);
+
+ gmx_ana_poscalc_t *pc1 = createCalculation(POS_RES, 0);
+ gmx_ana_poscalc_t *pc2 = createCalculation(POS_RES, 0);
+ setMaximumGroup(pc1, group1);
+ setMaximumGroup(pc2, group2);
+ gmx_ana_pos_t *p1 = initPositions(pc1, "P1");
+ gmx_ana_pos_t *p2 = initPositions(pc2, "P2");
+ checkInitialized();
+ {
+ pcc_.initEvaluation();
+ pcc_.initFrame();
+ generateCoordinates();
+ gmx::test::TestReferenceChecker frameCompound(
+ checker_.checkCompound("EvaluatedPositions", "Frame0"));
+ updateAndCheck(pc1, p1, group1, &frameCompound, "P1");
+ updateAndCheck(pc2, p2, group2, &frameCompound, "P2");
+ }
+}
+
+// TODO: Check for handling of more multiple calculation cases
+
+} // namespace
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <InitializedPositions>
+ <Positions>
+ <Int Name="Count">4</Int>
+ <String Name="Type">atoms</String>
+ <Sequence Name="Block">
+ <Int Name="Length">5</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>0</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>1</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>2</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>3</Int>
+ </Sequence>
+ <Int Name="RefId">3</Int>
+ </Position>
+ </Positions>
+ </InitializedPositions>
+ <EvaluatedPositions Name="Frame0">
+ <Positions>
+ <Int Name="Count">4</Int>
+ <String Name="Type">atoms</String>
+ <Sequence Name="Block">
+ <Int Name="Length">5</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>0</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">0.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ <Vector Name="Velocity">
+ <Real Name="X">0.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">1.000000</Real>
+ </Vector>
+ <Vector Name="Force">
+ <Real Name="X">0.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">-1.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>1</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">1.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ <Vector Name="Velocity">
+ <Real Name="X">1.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">1.000000</Real>
+ </Vector>
+ <Vector Name="Force">
+ <Real Name="X">1.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">-1.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>2</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">2.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ <Vector Name="Velocity">
+ <Real Name="X">2.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">1.000000</Real>
+ </Vector>
+ <Vector Name="Force">
+ <Real Name="X">2.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">-1.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>3</Int>
+ </Sequence>
+ <Int Name="RefId">3</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">3.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ <Vector Name="Velocity">
+ <Real Name="X">3.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">1.000000</Real>
+ </Vector>
+ <Vector Name="Force">
+ <Real Name="X">3.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">-1.000000</Real>
+ </Vector>
+ </Position>
+ </Positions>
+ </EvaluatedPositions>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <InitializedPositions>
+ <Positions>
+ <Int Name="Count">1</Int>
+ <String Name="Type">single</String>
+ <Sequence Name="Block">
+ <Int Name="Length">2</Int>
+ <Int>0</Int>
+ <Int>9</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">9</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ </Position>
+ </Positions>
+ </InitializedPositions>
+ <EvaluatedPositions Name="Frame0">
+ <Positions>
+ <Int Name="Count">1</Int>
+ <String Name="Type">single</String>
+ <Sequence Name="Block">
+ <Int Name="Length">2</Int>
+ <Int>0</Int>
+ <Int>9</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">9</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">4.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ <Vector Name="Velocity">
+ <Real Name="X">4.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">1.000000</Real>
+ </Vector>
+ <Vector Name="Force">
+ <Real Name="X">42.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">-10.000000</Real>
+ </Vector>
+ </Position>
+ </Positions>
+ </EvaluatedPositions>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <InitializedPositions>
+ <Positions>
+ <Int Name="Count">1</Int>
+ <String Name="Type">single</String>
+ <Sequence Name="Block">
+ <Int Name="Length">2</Int>
+ <Int>0</Int>
+ <Int>9</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">9</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ </Position>
+ </Positions>
+ </InitializedPositions>
+ <EvaluatedPositions Name="Frame0">
+ <Positions>
+ <Int Name="Count">1</Int>
+ <String Name="Type">single</String>
+ <Sequence Name="Block">
+ <Int Name="Length">2</Int>
+ <Int>0</Int>
+ <Int>9</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">9</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">3.750000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ <Vector Name="Velocity">
+ <Real Name="X">3.750000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">1.000000</Real>
+ </Vector>
+ <Vector Name="Force">
+ <Real Name="X">36.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">-9.000000</Real>
+ </Vector>
+ </Position>
+ </Positions>
+ </EvaluatedPositions>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <InitializedPositions>
+ <Positions>
+ <Int Name="Count">6</Int>
+ <String Name="Type">atoms</String>
+ <Sequence Name="Block">
+ <Int Name="Length">7</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>0</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>1</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>2</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>3</Int>
+ </Sequence>
+ <Int Name="RefId">3</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Int Name="RefId">4</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Int Name="RefId">5</Int>
+ </Position>
+ </Positions>
+ </InitializedPositions>
+ <EvaluatedPositions Name="Frame0">
+ <Positions>
+ <Int Name="Count">6</Int>
+ <String Name="Type">atoms</String>
+ <Sequence Name="Block">
+ <Int Name="Length">7</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>0</Int>
+ </Sequence>
+ <Int Name="RefId">-1</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">0.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>1</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">1.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>2</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">2.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>3</Int>
+ </Sequence>
+ <Int Name="RefId">-1</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">3.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Int Name="RefId">4</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">4.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Int Name="RefId">-1</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">5.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ </Positions>
+ </EvaluatedPositions>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <InitializedPositions>
+ <Positions>
+ <Int Name="Count">3</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">4</Int>
+ <Int>0</Int>
+ <Int>2</Int>
+ <Int>4</Int>
+ <Int>6</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>6</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ </Position>
+ </Positions>
+ </InitializedPositions>
+ <EvaluatedPositions Name="Frame0">
+ <Positions>
+ <Int Name="Count">3</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">4</Int>
+ <Int>0</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">0.500000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">4.500000</Real>
+ <Real Name="Y">1.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>6</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">7.000000</Real>
+ <Real Name="Y">2.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ </Positions>
+ </EvaluatedPositions>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <InitializedPositions>
+ <Positions>
+ <Int Name="Count">3</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">4</Int>
+ <Int>0</Int>
+ <Int>3</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">3</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ </Position>
+ </Positions>
+ </InitializedPositions>
+ <EvaluatedPositions Name="Frame0">
+ <Positions>
+ <Int Name="Count">3</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">4</Int>
+ <Int>0</Int>
+ <Int>3</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">3</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">1.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">4.000000</Real>
+ <Real Name="Y">1.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">7.000000</Real>
+ <Real Name="Y">2.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ </Positions>
+ </EvaluatedPositions>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <InitializedPositions>
+ <Positions>
+ <Int Name="Count">3</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">4</Int>
+ <Int>0</Int>
+ <Int>3</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">3</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ </Position>
+ </Positions>
+ </InitializedPositions>
+ <EvaluatedPositions Name="Frame0">
+ <Positions>
+ <Int Name="Count">3</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">4</Int>
+ <Int>0</Int>
+ <Int>3</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">3</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">1.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ <Vector Name="Velocity">
+ <Real Name="X">1.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">1.000000</Real>
+ </Vector>
+ <Vector Name="Force">
+ <Real Name="X">4.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">-3.333333</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">3.500000</Real>
+ <Real Name="Y">1.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ <Vector Name="Velocity">
+ <Real Name="X">3.500000</Real>
+ <Real Name="Y">1.000000</Real>
+ <Real Name="Z">1.000000</Real>
+ </Vector>
+ <Vector Name="Force">
+ <Real Name="X">8.250000</Real>
+ <Real Name="Y">2.250000</Real>
+ <Real Name="Z">-2.250000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">8.000000</Real>
+ <Real Name="Y">2.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ <Vector Name="Velocity">
+ <Real Name="X">8.000000</Real>
+ <Real Name="Y">2.000000</Real>
+ <Real Name="Z">1.000000</Real>
+ </Vector>
+ <Vector Name="Force">
+ <Real Name="X">8.000000</Real>
+ <Real Name="Y">2.000000</Real>
+ <Real Name="Z">-1.000000</Real>
+ </Vector>
+ </Position>
+ </Positions>
+ </EvaluatedPositions>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <InitializedPositions>
+ <Positions>
+ <Int Name="Count">3</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">4</Int>
+ <Int>0</Int>
+ <Int>3</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">3</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ </Position>
+ </Positions>
+ </InitializedPositions>
+ <EvaluatedPositions Name="Frame0">
+ <Positions>
+ <Int Name="Count">3</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">4</Int>
+ <Int>0</Int>
+ <Int>3</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">3</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">0.750000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ <Vector Name="Velocity">
+ <Real Name="X">0.750000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">1.000000</Real>
+ </Vector>
+ <Vector Name="Force">
+ <Real Name="X">3.000000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">-3.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">3.333333</Real>
+ <Real Name="Y">1.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ <Vector Name="Velocity">
+ <Real Name="X">3.333333</Real>
+ <Real Name="Y">1.000000</Real>
+ <Real Name="Z">1.000000</Real>
+ </Vector>
+ <Vector Name="Force">
+ <Real Name="X">7.000000</Real>
+ <Real Name="Y">2.000000</Real>
+ <Real Name="Z">-2.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">8.000000</Real>
+ <Real Name="Y">2.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ <Vector Name="Velocity">
+ <Real Name="X">8.000000</Real>
+ <Real Name="Y">2.000000</Real>
+ <Real Name="Z">1.000000</Real>
+ </Vector>
+ <Vector Name="Force">
+ <Real Name="X">8.000000</Real>
+ <Real Name="Y">2.000000</Real>
+ <Real Name="Z">-1.000000</Real>
+ </Vector>
+ </Position>
+ </Positions>
+ </EvaluatedPositions>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <InitializedPositions>
+ <Positions Name="Positions">
+ <Int Name="Count">3</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">4</Int>
+ <Int>0</Int>
+ <Int>2</Int>
+ <Int>4</Int>
+ <Int>6</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ </Position>
+ </Positions>
+ </InitializedPositions>
+ <EvaluatedPositions Name="Frame0">
+ <Positions Name="Positions">
+ <Int Name="Count">3</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">4</Int>
+ <Int>0</Int>
+ <Int>2</Int>
+ <Int>4</Int>
+ <Int>6</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">0.500000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">4.500000</Real>
+ <Real Name="Y">1.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">6.500000</Real>
+ <Real Name="Y">2.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ </Positions>
+ </EvaluatedPositions>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <InitializedPositions>
+ <Positions Name="P1">
+ <Int Name="Count">2</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">3</Int>
+ <Int>0</Int>
+ <Int>2</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ </Position>
+ </Positions>
+ <Positions Name="P2">
+ <Int Name="Count">2</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">3</Int>
+ <Int>0</Int>
+ <Int>2</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ </Position>
+ </Positions>
+ </InitializedPositions>
+ <EvaluatedPositions Name="Frame0">
+ <Positions Name="P1">
+ <Int Name="Count">2</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">3</Int>
+ <Int>0</Int>
+ <Int>2</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">0.500000</Real>
+ <Real Name="Y">0.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">4.500000</Real>
+ <Real Name="Y">1.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ </Positions>
+ <Positions Name="P2">
+ <Int Name="Count">2</Int>
+ <String Name="Type">residues</String>
+ <Sequence Name="Block">
+ <Int Name="Length">3</Int>
+ <Int>0</Int>
+ <Int>2</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">4.500000</Real>
+ <Real Name="Y">1.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ <Position>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ <Vector Name="Coordinates">
+ <Real Name="X">7.500000</Real>
+ <Real Name="Y">2.000000</Real>
+ <Real Name="Z">0.000000</Real>
+ </Vector>
+ </Position>
+ </Positions>
+ </EvaluatedPositions>
+</ReferenceData>
</table>
</xsl:template>
+<!-- Position calculation reference data -->
+
+<xsl:template match="InitializedPositions">
+ <h2>Initialized Positions</h2>
+ <xsl:apply-templates />
+</xsl:template>
+
+<xsl:template match="EvaluatedPositions">
+ <h2>Evaluated for <xsl:value-of select="@Name"/></h2>
+ <xsl:apply-templates />
+</xsl:template>
+
+<xsl:template match="Positions">
+ <xsl:if test="@Name">
+ <h3><xsl:value-of select="@Name"/></h3>
+ </xsl:if>
+ <table>
+ <tr>
+ <td>Count:</td>
+ <td>
+ <xsl:value-of select="Int[@Name='Count']"/>
+ (type: <xsl:value-of select="String[@Name='Type']"/>)
+ </td>
+ </tr>
+ <tr>
+ <td>Blocks:</td>
+ <td>
+ <xsl:call-template name="SequenceAsCSV">
+ <xsl:with-param name="root" select="Sequence[@Name='Block']"/>
+ </xsl:call-template>
+ </td>
+ </tr>
+ </table>
+ <table border="1">
+ <tr>
+ <th>RefId</th>
+ <th>Atom count</th>
+ <th>Atoms</th>
+ <xsl:if test="Position/Vector[@Name='Coordinates']">
+ <th>Coordinates</th>
+ </xsl:if>
+ <xsl:if test="Position/Vector[@Name='Velocity']">
+ <th>Velocity</th>
+ </xsl:if>
+ <xsl:if test="Position/Vector[@Name='Force']">
+ <th>Force</th>
+ </xsl:if>
+ </tr>
+ <xsl:for-each select="Position">
+ <tr>
+ <td><xsl:value-of select="Int[@Name='RefId']"/></td>
+ <td><xsl:value-of select="Sequence[@Name='Atoms']/Int[@Name='Length']"/></td>
+ <td>
+ <xsl:call-template name="SequenceAsCSV">
+ <xsl:with-param name="root" select="Sequence[@Name='Atoms']"/>
+ </xsl:call-template>
+ </td>
+ <xsl:if test="Vector[@Name='Coordinates']">
+ <td>
+ <xsl:apply-templates select="Vector[@Name='Coordinates']"/>
+ </td>
+ </xsl:if>
+ <xsl:if test="Vector[@Name='Velocity']">
+ <td>
+ <xsl:apply-templates select="Vector[@Name='Velocity']"/>
+ </td>
+ </xsl:if>
+ <xsl:if test="Vector[@Name='Force']">
+ <td>
+ <xsl:apply-templates select="Vector[@Name='Force']"/>
+ </td>
+ </xsl:if>
+ </tr>
+ </xsl:for-each>
+ </table>
+</xsl:template>
+
<!-- Selection reference data -->
<xsl:key name="SelectionName" match="ParsedSelections/ParsedSelection" use="@Name"/>
if (frame_ != NULL)
{
sfree(frame_->x);
+ sfree(frame_->v);
+ sfree(frame_->f);
sfree(frame_);
}
}
}
}
+void TopologyManager::requestVelocities()
+{
+ GMX_RELEASE_ASSERT(frame_ != NULL,
+ "Velocities requested before requesting a frame");
+ frame_->bV = TRUE;
+ if (frame_->natoms > 0)
+ {
+ snew(frame_->v, frame_->natoms);
+ }
+}
+
+void TopologyManager::requestForces()
+{
+ GMX_RELEASE_ASSERT(frame_ != NULL,
+ "Forces requested before requesting a frame");
+ frame_->bF = TRUE;
+ if (frame_->natoms > 0)
+ {
+ snew(frame_->f, frame_->natoms);
+ }
+}
+
void TopologyManager::loadTopology(const char *filename)
{
char title[STRLEN];
frame_->natoms = count;
frame_->bX = TRUE;
snew(frame_->x, count);
+ if (frame_->bV)
+ {
+ snew(frame_->v, count);
+ }
+ if (frame_->bF)
+ {
+ snew(frame_->f, count);
+ }
}
}
~TopologyManager();
void requestFrame();
+ void requestVelocities();
+ void requestForces();
void loadTopology(const char *filename);
void initAtoms(int count);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff