void test_bondCountWurtzite()
{
StructureAdapterPtr stru =
loadTestPeriodicStructure("ZnS_wurtzite.stru");
BaseBondGeneratorPtr bnds = stru->createBondGenerator();
TS_ASSERT_EQUALS(4, stru->countSites());
bnds->selectAnchorSite(0);
bnds->selectSiteRange(0, 4);
bnds->setRmin(0);
// there should be no bond below the ZnS distance 2.31
bnds->setRmax(2.2);
TS_ASSERT_EQUALS(0, countBonds(*bnds));
// z-neighbor is slightly more distant than 3 in the lower plane
bnds->setRmax(2.35);
TS_ASSERT_EQUALS(3, countBonds(*bnds));
bnds->setRmax(2.5);
TS_ASSERT_EQUALS(4, countBonds(*bnds));
// there are 12 second nearest neighbors at 3.81
bnds->setRmin(3.7);
bnds->setRmax(3.82);
TS_ASSERT_EQUALS(12, countBonds(*bnds));
// and one more at 3.83
bnds->setRmax(3.85);
TS_ASSERT_EQUALS(13, countBonds(*bnds));
// making the total 17
bnds->setRmin(0);
TS_ASSERT_EQUALS(17, countBonds(*bnds));
// and the same happens for all other sites
bnds->selectAnchorSite(1);
TS_ASSERT_EQUALS(17, countBonds(*bnds));
bnds->selectAnchorSite(2);
TS_ASSERT_EQUALS(17, countBonds(*bnds));
bnds->selectAnchorSite(3);
TS_ASSERT_EQUALS(17, countBonds(*bnds));
}
void test_countSites()
{
TS_ASSERT_EQUALS(4, m_ni->countSites());
TS_ASSERT_EQUALS(23, m_kbise->countSites());
TS_ASSERT_EQUALS(20, m_catio3->countSites());
TS_ASSERT_EQUALS(56, m_pswt->countSites());
}
void test_numberDensity()
{
const double eps = 1.0e-7;
TS_ASSERT_DELTA(0.0914114, m_ni->numberDensity(), eps);
TS_ASSERT_DELTA(0.0335565, m_kbise->numberDensity(), eps);
TS_ASSERT_DELTA(0.0894566, m_catio3->numberDensity(), eps);
TS_ASSERT_DELTA(0.0760332, m_pswt->numberDensity(), eps);
}
void test_totalOccupancy()
{
const double eps = 10 * diffpy::mathutils::DOUBLE_EPS;
TS_ASSERT_EQUALS(4.0, m_ni->totalOccupancy());
TS_ASSERT_EQUALS(23.0, m_kbise->totalOccupancy());
TS_ASSERT_EQUALS(20.0, m_catio3->totalOccupancy());
TS_ASSERT_DELTA(40.0, m_pswt->totalOccupancy(), eps);
}
void test_siteAtomType()
{
TS_ASSERT_EQUALS(string("Ni"), m_ni->siteAtomType(0));
TS_ASSERT_EQUALS(string("Ni"), m_ni->siteAtomType(3));
TS_ASSERT_EQUALS(string("K1+"), m_kbise->siteAtomType(0));
TS_ASSERT_EQUALS(string("Bi3+"), m_kbise->siteAtomType(2));
TS_ASSERT_EQUALS(string("Se"), m_kbise->siteAtomType(10));
TS_ASSERT_EQUALS(string("Se"), m_kbise->siteAtomType(22));
}
void test_siteAnisotropy()
{
for (int i = 0; i < m_ni->countSites(); ++i)
{
TS_ASSERT_EQUALS(false, m_ni->siteAnisotropy(i));
}
for (int i = 0; i < m_catio3->countSites(); ++i)
{
TS_ASSERT_EQUALS(true, m_catio3->siteAnisotropy(i));
}
}
void test_serialization()
{
StructureAdapterPtr kbise1 = dumpandload(m_kbise);
TS_ASSERT_DIFFERS(m_kbise.get(), kbise1.get());
const double eps = 1.0e-7;
TS_ASSERT_EQUALS(23, kbise1->countSites());
TS_ASSERT_EQUALS(23.0, kbise1->totalOccupancy());
TS_ASSERT_DELTA(0.0335565, kbise1->numberDensity(), eps);
TS_ASSERT_EQUALS(string("K1+"), kbise1->siteAtomType(0));
TS_ASSERT_EQUALS(string("Bi3+"), kbise1->siteAtomType(2));
TS_ASSERT_EQUALS(string("Se"), kbise1->siteAtomType(10));
TS_ASSERT_EQUALS(string("Se"), kbise1->siteAtomType(22));
PeriodicStructureAdapterPtr pkbise =
boost::dynamic_pointer_cast<PeriodicStructureAdapter>(m_kbise);
PeriodicStructureAdapterPtr pkbise1 =
boost::dynamic_pointer_cast<PeriodicStructureAdapter>(kbise1);
const Lattice& L = pkbise->getLattice();
const Lattice& L1 = pkbise1->getLattice();
TS_ASSERT_EQUALS(L.a(), L1.a());
TS_ASSERT_EQUALS(L.b(), L1.b());
TS_ASSERT_EQUALS(L.c(), L1.c());
TS_ASSERT_EQUALS(L.alpha(), L1.alpha());
TS_ASSERT_EQUALS(L.beta(), L1.beta());
TS_ASSERT_EQUALS(L.gamma(), L1.gamma());
}
void test_NaCl_gradient()
{
using namespace boost;
molc->eval(mnacl);
// default gradients are all zero
std::vector<R3::Vector> g = molc->gradients();
TS_ASSERT_EQUALS(8u, g.size());
for (int i = 0; i < 8; ++i)
{
TS_ASSERT_DELTA(0.0, R3::norm(g[i]), meps);
}
StructureAdapterPtr nacl1 = mnacl->clone();
PeriodicStructureAdapter& nacl1ref =
static_cast<PeriodicStructureAdapter&>(*nacl1);
R3::Vector& xyzc0 = nacl1ref[0].xyz_cartn;
xyzc0 = R3::Vector(0.02, 0.03, 0.07);
molc->eval(nacl1);
double c0 = molc->totalSquareOverlap();
R3::Vector g0 = molc->gradients()[0];
TS_ASSERT(R3::norm(g0) > meps);
R3::Vector g0n;
const double dx = 1e-8;
for (int i = 0; i < R3::Ndim; ++i)
{
xyzc0[i] += dx;
molc->eval(nacl1);
g0n[i] = (molc->totalSquareOverlap() - c0) / dx;
xyzc0[i] -= dx;
}
TS_ASSERT_DELTA(0.0, R3::norm(g0 - g0n), 1e-6);
}
void test_siteCartesianUij()
{
// nickel should have all Uij equal zero.
TS_ASSERT_EQUALS(R3::zeromatrix(), m_ni->siteCartesianUij(0));
// check CaTiO3 values
const R3::Matrix& UO2 = m_catio3->siteCartesianUij(12);
const double eps = 1e-8;
TS_ASSERT_DELTA(0.0065, UO2(0,0), eps);
TS_ASSERT_DELTA(0.0060, UO2(1,1), eps);
TS_ASSERT_DELTA(0.0095, UO2(2,2), eps);
TS_ASSERT_DELTA(0.0020, UO2(0,1), eps);
TS_ASSERT_DELTA(0.0020, UO2(1,0), eps);
TS_ASSERT_DELTA(-0.0008, UO2(0,2), eps);
TS_ASSERT_DELTA(-0.0008, UO2(2,0), eps);
TS_ASSERT_DELTA(-0.0010, UO2(1,2), eps);
TS_ASSERT_DELTA(-0.0010, UO2(2,1), eps);
}
void test_siteCartesianPosition()
{
const double eps = 1.0e-5;
R3::Vector rCa = m_catio3->siteCartesianPosition(4);
TS_ASSERT_DELTA(0.03486, rCa[0], eps);
TS_ASSERT_DELTA(0.19366, rCa[1], eps);
TS_ASSERT_DELTA(1.90975, rCa[2], eps);
}
void test_empty_instance()
{
TS_ASSERT_EQUALS(0, mstru->countSites());
TS_ASSERT_EQUALS(mstru.get(), mstru->clone().get());
TS_ASSERT_EQUALS(mstru, emptyStructureAdapter());
TS_ASSERT_THROWS(mstru->siteAtomType(0), std::out_of_range);
TS_ASSERT_THROWS(mstru->siteCartesianPosition(0),
std::out_of_range);
TS_ASSERT_THROWS(mstru->siteMultiplicity(0), std::out_of_range);
TS_ASSERT_THROWS(mstru->siteOccupancy(0), std::out_of_range);
TS_ASSERT_THROWS(mstru->siteAnisotropy(0), std::out_of_range);
TS_ASSERT_THROWS(mstru->siteCartesianPosition(0),
std::out_of_range);
}
NoMetaStructureAdapter::NoMetaStructureAdapter(
StructureAdapterPtr srcstructure)
{
boost::shared_ptr<NoMetaStructureAdapter> nmptr =
boost::dynamic_pointer_cast<NoMetaStructureAdapter>(srcstructure);
if (nmptr) srcstructure = nmptr->getSourceStructure();
msrcstructure = srcstructure.get() ?
srcstructure : emptyStructureAdapter();
}
void setUp()
{
CxxTest::setAbortTestOnFail(true);
if (!m_ni)
{
m_ni = loadTestPeriodicStructure("Ni.stru");
}
m_nibnds = m_ni->createBondGenerator();
CxxTest::setAbortTestOnFail(false);
}
void test_serialization()
{
StructureAdapterPtr stru1;
stru1 = dumpandload(mstru);
AtomicStructureAdapterPtr astru1 =
boost::dynamic_pointer_cast<AtomicStructureAdapter>(stru1);
TS_ASSERT(!astru1);
TS_ASSERT_EQUALS(0, stru1->countSites());
TS_ASSERT_EQUALS(stru1, stru1->clone());
TS_ASSERT_THROWS(mstru->siteAtomType(0), std::out_of_range);
}
void test_LiTaO3()
{
const string lithium = "Li1+";
const string tantalum = "Ta5+";
const string oxygen = "O2-";
const double epsu = 1e-5;
StructureAdapterPtr stru = loadTestPeriodicStructure("LiTaO3.stru");
TS_ASSERT_EQUALS(30, stru->countSites());
BaseBondGeneratorPtr bnds = stru->createBondGenerator();
bnds->selectAnchorSite(0);
bnds->selectSiteRange(0, 30);
// there are 3 oxygen neighbors at 2.065
bnds->setRmax(2.1);
TS_ASSERT_EQUALS(3, countBonds(*bnds));
// Li at site 0 is isotropic, oxygens have equal msd-s towards Li
for (bnds->rewind(); !bnds->finished(); bnds->next())
{
TS_ASSERT_EQUALS(lithium, stru->siteAtomType(bnds->site0()));
TS_ASSERT_EQUALS(oxygen, stru->siteAtomType(bnds->site1()));
TS_ASSERT_DELTA(0.00265968, testmsd0(stru, bnds), epsu);
TS_ASSERT_DELTA(0.00710945, testmsd1(stru, bnds), epsu);
}
// there are 3 oxygen neighbors at 2.26
bnds->setRmin(2.2);
bnds->setRmax(2.3);
TS_ASSERT_EQUALS(3, countBonds(*bnds));
for (bnds->rewind(); !bnds->finished(); bnds->next())
{
TS_ASSERT_EQUALS(oxygen, stru->siteAtomType(bnds->site1()));
TS_ASSERT_DELTA(0.00265968, testmsd0(stru, bnds), epsu);
TS_ASSERT_DELTA(0.00824319, testmsd1(stru, bnds), epsu);
}
// finally there are 4 Ta neighbors between 2.8 and 3.1
bnds->setRmin(2.8);
bnds->setRmax(3.1);
TS_ASSERT_EQUALS(4, countBonds(*bnds));
for (bnds->rewind(); !bnds->finished(); bnds->next())
{
TS_ASSERT_DELTA(0.00265968, testmsd0(stru, bnds), epsu);
TS_ASSERT_EQUALS(tantalum, stru->siteAtomType(bnds->site1()));
R3::Vector r01xy = bnds->r01();
r01xy[2] = 0.0;
// for the tantalum above Li the msd equals U33
if (R3::norm(r01xy) < 0.1)
{
TS_ASSERT_DELTA(0.00356, testmsd1(stru, bnds), epsu);
}
// other 3 tantalums are related by tripple axis and
// have the same msd towards the central Li
else
{
TS_ASSERT_DELTA(0.00486942, testmsd1(stru, bnds), epsu);
}
}
}
