// -------------------------------------------------------------------------- //
//
void Test_Configuration::testMatchLists()
{
// Setup a configuration.
std::vector< std::vector<double> > basis(3, std::vector<double>(3,0.0));
basis[1][0] = 0.25;
basis[1][1] = 0.25;
basis[1][2] = 0.25;
basis[2][0] = 0.75;
basis[2][1] = 0.75;
basis[2][2] = 0.75;
std::vector<int> basis_sites(3);
basis_sites[0] = 0;
basis_sites[1] = 1;
basis_sites[2] = 2;
std::vector<std::string> basis_elements(3);
basis_elements[0] = "A";
basis_elements[1] = "B";
basis_elements[2] = "B";
// Make a 37x18x19 structure.
const int nI = 37;
const int nJ = 18;
const int nK = 19;
const int nB = 3;
// Coordinates and elements.
std::vector<std::vector<double> > coordinates;
std::vector<std::string> elements;
for (int i = 0; i < nI; ++i)
{
for (int j = 0; j < nJ; ++j)
{
for (int k = 0; k < nK; ++k)
{
for (int b = 0; b < nB; ++b)
{
std::vector<double> c(3);
c[0] = i + basis[b][0];
c[1] = j + basis[b][1];
c[2] = k + basis[b][2];
coordinates.push_back(c);
elements.push_back(basis_elements[b]);
}
}
}
}
elements[0] = "V";
elements[216] = "V";
elements[1434] = "V";
elements[2101] = "V";
// Possible types.
std::map<std::string, int> possible_types;
possible_types["*"] = 0;
possible_types["A"] = 1;
possible_types["B"] = 2;
possible_types["V"] = 3;
// Setup the configuration.
Configuration configuration(coordinates, elements, possible_types);
// Setup the lattice map.
std::vector<int> repetitions(3);
repetitions[0] = nI;
repetitions[1] = nJ;
repetitions[2] = nK;
std::vector<bool> periodicity(3, true);
LatticeMap lattice_map(nB, repetitions, periodicity);
// Try to access the match lists before initialization. They should be
// empty.
CPPUNIT_ASSERT( configuration.minimalMatchList(10).empty() );
CPPUNIT_ASSERT( configuration.minimalMatchList(2101).empty() );
CPPUNIT_ASSERT( configuration.minimalMatchList(1434).empty() );
// Init the match lists.
configuration.initMatchLists(lattice_map, 1);
// This did something.
CPPUNIT_ASSERT( !configuration.minimalMatchList(10).empty() );
CPPUNIT_ASSERT( !configuration.minimalMatchList(2101).empty() );
CPPUNIT_ASSERT( !configuration.minimalMatchList(1434).empty() );
// Get the match list the hard way.
const std::vector<MinimalMatchListEntry> ref_1434 = \
configuration.minimalMatchList( 1434,
lattice_map.neighbourIndices(1434),
lattice_map);
// Check the size.
CPPUNIT_ASSERT_EQUAL( static_cast<int>(ref_1434.size()),
static_cast<int>(configuration.minimalMatchList(1434).size()) );
// Check the values.
for (size_t i = 0; i < ref_1434.size(); ++i)
{
CPPUNIT_ASSERT_EQUAL( ref_1434[i].match_type,
configuration.minimalMatchList(1434)[i].match_type );
CPPUNIT_ASSERT_EQUAL( ref_1434[i].update_type,
configuration.minimalMatchList(1434)[i].update_type );
CPPUNIT_ASSERT_EQUAL( ref_1434[i].index,
configuration.minimalMatchList(1434)[i].index );
CPPUNIT_ASSERT_DOUBLES_EQUAL( ref_1434[i].distance,
configuration.minimalMatchList(1434)[i].distance,
1.0e-14 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( ref_1434[i].coordinate.x(),
configuration.minimalMatchList(1434)[i].coordinate.x(),
1.0e-14 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( ref_1434[i].coordinate.y(),
configuration.minimalMatchList(1434)[i].coordinate.y(),
1.0e-14 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( ref_1434[i].coordinate.z(),
configuration.minimalMatchList(1434)[i].coordinate.z(),
1.0e-14 );
}
// Setup a process that changes V to B.
// Get a process that finds a V between two B and turns one of
// the Bs into an A.
std::vector<std::string> process_elements1(3);
process_elements1[0] = "V";
process_elements1[1] = "B";
process_elements1[2] = "B";
std::vector<std::string> process_elements2(3);
process_elements2[0] = "B";
process_elements2[1] = "A";
process_elements2[2] = "B";
std::vector<std::vector<double> > process_coordinates(3, std::vector<double>(3, 0.0));
process_coordinates[1][0] = -0.25;
process_coordinates[1][1] = -0.25;
process_coordinates[1][2] = -0.25;
process_coordinates[2][0] = 0.25;
process_coordinates[2][1] = 0.25;
process_coordinates[2][2] = 0.25;
const double rate = 13.7;
Configuration c1(process_coordinates, process_elements1, possible_types);
Configuration c2(process_coordinates, process_elements2, possible_types);
Process p(c1, c2, rate, basis_sites);
// Now, add index 1434 to the process.
// We know by construction that these match.
p.addSite(1434, 0.0);
// For site 1434
// 350 changes from 1 to 0
// 1434 changes from 2 to 1
// All other must remain unchanged.
CPPUNIT_ASSERT_EQUAL( configuration.types()[1434], 3 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[350], 2 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[1433], 2 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[349], 2 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[351], 1 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[2517], 1 );
// Peform the process.
configuration.performProcess(p, 1434);
// Check that the types were correctly updated.
CPPUNIT_ASSERT_EQUAL( configuration.types()[1434], 2 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[350], 1 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[1433], 2 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[349], 2 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[351], 1 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[2517], 1 );
// Check that updating the matchlist gets us the correct values.
configuration.updateMatchList(1434);
// Reference.
const std::vector<MinimalMatchListEntry> ref2_1434 = \
configuration.minimalMatchList( 1434,
lattice_map.neighbourIndices(1434),
lattice_map);
// Check the size.
CPPUNIT_ASSERT_EQUAL( static_cast<int>(ref2_1434.size()),
static_cast<int>(configuration.minimalMatchList(1434).size()) );
// Check the values.
for (size_t i = 0; i < ref2_1434.size(); ++i)
{
CPPUNIT_ASSERT_EQUAL( ref2_1434[i].match_type,
configuration.minimalMatchList(1434)[i].match_type );
CPPUNIT_ASSERT_EQUAL( ref2_1434[i].update_type,
configuration.minimalMatchList(1434)[i].update_type );
CPPUNIT_ASSERT_EQUAL( ref2_1434[i].index,
configuration.minimalMatchList(1434)[i].index );
CPPUNIT_ASSERT_DOUBLES_EQUAL( ref2_1434[i].distance,
configuration.minimalMatchList(1434)[i].distance,
1.0e-14 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( ref2_1434[i].coordinate.x(),
configuration.minimalMatchList(1434)[i].coordinate.x(),
1.0e-14 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( ref2_1434[i].coordinate.y(),
configuration.minimalMatchList(1434)[i].coordinate.y(),
1.0e-14 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( ref2_1434[i].coordinate.z(),
configuration.minimalMatchList(1434)[i].coordinate.z(),
1.0e-14 );
}
}
// -------------------------------------------------------------------------- //
//
void Test_Configuration::testPerformProcess()
{
// Setup a realistic system.
std::vector< std::vector<double> > basis(3, std::vector<double>(3,0.0));
basis[1][0] = 0.25;
basis[1][1] = 0.25;
basis[1][2] = 0.25;
basis[2][0] = 0.75;
basis[2][1] = 0.75;
basis[2][2] = 0.75;
std::vector<int> basis_sites(3);
basis_sites[0] = 0;
basis_sites[1] = 1;
basis_sites[2] = 2;
std::vector<std::string> basis_elements(3);
basis_elements[0] = "A";
basis_elements[1] = "B";
basis_elements[2] = "B";
// Make a 37x18x19 structure.
const int nI = 37;
const int nJ = 18;
const int nK = 19;
const int nB = 3;
// Coordinates and elements.
std::vector<std::vector<double> > coordinates;
std::vector<std::string> elements;
for (int i = 0; i < nI; ++i)
{
for (int j = 0; j < nJ; ++j)
{
for (int k = 0; k < nK; ++k)
{
for (int b = 0; b < nB; ++b)
{
std::vector<double> c(3);
c[0] = i + basis[b][0];
c[1] = j + basis[b][1];
c[2] = k + basis[b][2];
coordinates.push_back(c);
elements.push_back(basis_elements[b]);
}
}
}
}
elements[0] = "V";
elements[216] = "V"; // These affects process 0,1 and 3
elements[1434] = "V";
elements[2101] = "V"; // This affects process 0,1 and 2
// Possible types.
std::map<std::string, int> possible_types;
possible_types["*"] = 0;
possible_types["A"] = 1;
possible_types["B"] = 2;
possible_types["V"] = 3;
// Setup the configuration.
Configuration configuration(coordinates, elements, possible_types);
// Setup the lattice map.
std::vector<int> repetitions(3);
repetitions[0] = nI;
repetitions[1] = nJ;
repetitions[2] = nK;
std::vector<bool> periodicity(3, true);
LatticeMap lattice_map(nB, repetitions, periodicity);
// Init the match lists.
configuration.initMatchLists(lattice_map, 1);
// Get a process that finds a V between two B and turns one of
// the Bs into an A.
std::vector<std::string> process_elements1(3);
process_elements1[0] = "V";
process_elements1[1] = "B";
process_elements1[2] = "B";
std::vector<std::string> process_elements2(3);
process_elements2[0] = "B";
process_elements2[1] = "A";
process_elements2[2] = "B";
std::vector<std::vector<double> > process_coordinates(3, std::vector<double>(3, 0.0));
process_coordinates[1][0] = -0.25;
process_coordinates[1][1] = -0.25;
process_coordinates[1][2] = -0.25;
process_coordinates[2][0] = 0.25;
process_coordinates[2][1] = 0.25;
process_coordinates[2][2] = 0.25;
const double rate = 13.7;
Configuration c1(process_coordinates, process_elements1, possible_types);
Configuration c2(process_coordinates, process_elements2, possible_types);
Process p(c1, c2, rate, basis_sites);
// Now, add index 1434 to the process.
// We know by construction that these match.
p.addSite(1434, 0.0);
// For site 1434
// 350 changes from 1 to 0
// 1434 changes from 2 to 1
// All other must remain unchanged.
CPPUNIT_ASSERT_EQUAL( configuration.types()[1434], 3 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[350], 2 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[1433], 2 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[349], 2 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[351], 1 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[2517], 1 );
// Peform the process.
configuration.performProcess(p, 1434);
// Check that the types were correctly updated.
CPPUNIT_ASSERT_EQUAL( configuration.types()[1434], 2 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[350], 1 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[1433], 2 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[349], 2 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[351], 1 );
CPPUNIT_ASSERT_EQUAL( configuration.types()[2517], 1 );
// Check that the correct indices were added to the list of affected.
const std::vector<int> affected = p.affectedIndices();
CPPUNIT_ASSERT_EQUAL( affected[0], 1434 );
CPPUNIT_ASSERT_EQUAL( affected[1], 350 );
}
// -------------------------------------------------------------------------- //
//
void Test_Interactions::testUpdateProcessIDMoves()
{
// Setup two valid processes.
std::vector<Process> processes;
std::vector<std::string> process_elements1(3);
process_elements1[0] = "A";
process_elements1[1] = "B";
process_elements1[2] = "V";
std::vector<std::string> process_elements2(3);
process_elements2[0] = "B";
process_elements2[1] = "A";
process_elements2[2] = "A";
std::vector<std::vector<double> > process_coordinates1(3, std::vector<double>(3, 0.0));
process_coordinates1[1][0] = -1.0;
process_coordinates1[1][1] = 0.0;
process_coordinates1[1][2] = 0.0;
process_coordinates1[2][0] = 0.3;
process_coordinates1[2][1] = 0.3;
process_coordinates1[2][2] = 0.3;
std::vector<int> move_origins;
move_origins.push_back(0);
move_origins.push_back(1);
std::vector<Coordinate> move_vectors;
move_vectors.push_back( Coordinate(-1.0, 0.0, 0.0) );
move_vectors.push_back( Coordinate( 1.0, 0.0, 0.0) );
// Possible types.
std::map<std::string, int> possible_types;
possible_types["*"] = 0;
possible_types["A"] = 1;
possible_types["B"] = 2;
possible_types["V"] = 3;
const double rate = 13.7;
const Configuration c1(process_coordinates1, process_elements1, possible_types);
const Configuration c2(process_coordinates1, process_elements2, possible_types);
// Let this process be valid at site 0.
processes.push_back(Process(c1,c2,rate,std::vector<int>(1,0), move_origins, move_vectors));
// Let this process be valid at sites 0 and 2.
std::vector<int> sites_vector(2,0);
sites_vector[1] = 2;
processes.push_back(Process(c1,c2,rate,sites_vector, move_origins, move_vectors));
std::vector<std::vector<double> > process_coordinates2(3, std::vector<double>(3, 0.0));
process_coordinates2[1][0] = 0.7;
process_coordinates2[1][1] = 0.7;
process_coordinates2[1][2] = -0.3;
process_coordinates2[2][0] = 1.0;
process_coordinates2[2][1] = 1.0;
process_coordinates2[2][2] = 1.0;
move_vectors[0] = Coordinate( 0.7, 0.7, -0.3);
move_vectors[1] = Coordinate(-0.7,-0.7, 0.3);
const Configuration c3(process_coordinates2, process_elements1, possible_types);
const Configuration c4(process_coordinates2, process_elements2, possible_types);
// Let the process be valid at site 1.
processes.push_back(Process(c3,c4,rate,std::vector<int>(1,1), move_origins, move_vectors));
Interactions interactions(processes, true);
// Generate a corresponding configuration.
std::vector<std::vector<double> > config_coordinates;
std::vector<std::string> elements;
for (int i = 0; i < 5; ++i)
{
for (int j = 0; j < 5; ++j)
{
for (int k = 0; k < 5; ++k)
{
std::vector<double> coord(3);
coord[0] = 0.0 + i*1.0;
coord[1] = 0.0 + j*1.0;
coord[2] = 0.0 + k*1.0;
config_coordinates.push_back(coord);
elements.push_back("V");
coord[0] = 0.3 + i*1.0;
coord[1] = 0.3 + j*1.0;
coord[2] = 0.3 + k*1.0;
elements.push_back("B");
config_coordinates.push_back(coord);
}
}
}
// Get the config and lattice map.
Configuration config(config_coordinates, elements, possible_types);
const LatticeMap lattice_map(2, std::vector<int>(3,5), std::vector<bool>(3,true));
// Now, setup the matchlists in the configuration.
config.initMatchLists(lattice_map, interactions.maxRange());
// Check the process match lists before we start.
CPPUNIT_ASSERT_EQUAL(static_cast<int>(interactions.processes()[0]->minimalMatchList().size()), 3);
CPPUNIT_ASSERT_EQUAL(static_cast<int>(interactions.processes()[1]->minimalMatchList().size()), 3);
CPPUNIT_ASSERT_EQUAL(static_cast<int>(interactions.processes()[2]->minimalMatchList().size()), 3);
// Check the id moves before update.
{
const std::vector< std::pair<int, int> > & id_moves = interactions.processes()[0]->idMoves();
CPPUNIT_ASSERT_EQUAL( static_cast<int>(id_moves.size()), 2 );
CPPUNIT_ASSERT_EQUAL( id_moves[0].first, 0 );
CPPUNIT_ASSERT_EQUAL( id_moves[0].second, 2 );
CPPUNIT_ASSERT_EQUAL( id_moves[1].first, 2 );
CPPUNIT_ASSERT_EQUAL( id_moves[1].second, 0 );
}
// Update the interactions according to the configuration match lists.
// This also updates the id moves on the processes.
interactions.updateProcessMatchLists(config, lattice_map);
// Check the id moves after update.
{
const std::vector<MinimalMatchListEntry> & match = interactions.processes()[0]->minimalMatchList();
CPPUNIT_ASSERT_EQUAL( static_cast<int>(match.size()), 6 );
const std::vector< std::pair<int, int> > & id_moves = interactions.processes()[0]->idMoves();
CPPUNIT_ASSERT_EQUAL( static_cast<int>(id_moves.size()), 2 );
CPPUNIT_ASSERT_EQUAL( id_moves[0].first, 0 );
CPPUNIT_ASSERT_EQUAL( id_moves[0].second, 5 );
CPPUNIT_ASSERT_EQUAL( id_moves[1].first, 5 );
CPPUNIT_ASSERT_EQUAL( id_moves[1].second, 0 );
// Wildcards are now added.
CPPUNIT_ASSERT_EQUAL( match[0].match_type, 1 );
CPPUNIT_ASSERT_EQUAL( match[1].match_type, 3 );
CPPUNIT_ASSERT_EQUAL( match[2].match_type, 0 );
CPPUNIT_ASSERT_EQUAL( match[3].match_type, 0 );
CPPUNIT_ASSERT_EQUAL( match[4].match_type, 0 );
CPPUNIT_ASSERT_EQUAL( match[5].match_type, 2 );
}
}
// -------------------------------------------------------------------------- //
//
void Test_Interactions::testUpdateProcessMatchLists()
{
// Setup two valid processes.
std::vector<Process> processes;
std::vector<std::string> process_elements1(3);
process_elements1[0] = "A";
process_elements1[1] = "B";
process_elements1[2] = "V";
std::vector<std::string> process_elements2(3);
process_elements2[0] = "B";
process_elements2[1] = "A";
process_elements2[2] = "A";
std::vector<std::vector<double> > process_coordinates1(3, std::vector<double>(3, 0.0));
process_coordinates1[1][0] = -1.0;
process_coordinates1[1][1] = 0.0;
process_coordinates1[1][2] = 0.0;
process_coordinates1[2][0] = 0.3;
process_coordinates1[2][1] = 0.3;
process_coordinates1[2][2] = 0.3;
// Possible types.
std::map<std::string, int> possible_types;
possible_types["*"] = 0;
possible_types["A"] = 1;
possible_types["B"] = 2;
possible_types["V"] = 3;
const double rate = 13.7;
const Configuration c1(process_coordinates1, process_elements1, possible_types);
const Configuration c2(process_coordinates1, process_elements2, possible_types);
// Let this process be valid at site 0.
processes.push_back(Process(c1,c2,rate,std::vector<int>(1,0)));
// Let this process be valid at sites 0 and 2.
std::vector<int> sites_vector(2,0);
sites_vector[1] = 2;
processes.push_back(Process(c1,c2,rate,sites_vector));
std::vector<std::vector<double> > process_coordinates2(3, std::vector<double>(3, 0.0));
process_coordinates2[1][0] = 0.7;
process_coordinates2[1][1] = 0.7;
process_coordinates2[1][2] = -0.3;
process_coordinates2[2][0] = 1.0;
process_coordinates2[2][1] = 1.0;
process_coordinates2[2][2] = 1.0;
const Configuration c3(process_coordinates2, process_elements1, possible_types);
const Configuration c4(process_coordinates2, process_elements2, possible_types);
// Let the process be valid at site 1.
processes.push_back(Process(c3,c4,rate,std::vector<int>(1,1)));
Interactions interactions(processes, true);
// Generate a corresponding configuration.
std::vector<std::vector<double> > config_coordinates;
std::vector<std::string> elements;
for (int i = 0; i < 5; ++i)
{
for (int j = 0; j < 5; ++j)
{
for (int k = 0; k < 5; ++k)
{
std::vector<double> coord(3);
coord[0] = 0.0 + i*1.0;
coord[1] = 0.0 + j*1.0;
coord[2] = 0.0 + k*1.0;
config_coordinates.push_back(coord);
elements.push_back("V");
coord[0] = 0.3 + i*1.0;
coord[1] = 0.3 + j*1.0;
coord[2] = 0.3 + k*1.0;
elements.push_back("B");
config_coordinates.push_back(coord);
}
}
}
// Get the config and lattice map.
Configuration config(config_coordinates, elements, possible_types);
// Make sure we do this on a non-periodic lattice map, to make sure
// the most central cell is choosen for determining wildcard positions.
const LatticeMap lattice_map(2, std::vector<int>(3,5), std::vector<bool>(3,false));
// Now, setup the matchlists in the configuration.
config.initMatchLists(lattice_map, interactions.maxRange());
// Check the process match lists before we start.
CPPUNIT_ASSERT_EQUAL(static_cast<int>(interactions.processes()[0]->minimalMatchList().size()), 3);
CPPUNIT_ASSERT_EQUAL(static_cast<int>(interactions.processes()[1]->minimalMatchList().size()), 3);
CPPUNIT_ASSERT_EQUAL(static_cast<int>(interactions.processes()[2]->minimalMatchList().size()), 3);
// Update the interactions according to the configuration match lists.
interactions.updateProcessMatchLists(config, lattice_map);
// Check a few coordinates and match types.
{
const std::vector<MinimalMatchListEntry> & match = interactions.processes()[0]->minimalMatchList();
CPPUNIT_ASSERT_EQUAL( static_cast<int>(match.size()), 6 );
// Wildcards are now added.
CPPUNIT_ASSERT_EQUAL( match[0].match_type, 1 );
CPPUNIT_ASSERT_EQUAL( match[1].match_type, 3 );
CPPUNIT_ASSERT_EQUAL( match[2].match_type, 0 );
CPPUNIT_ASSERT_EQUAL( match[3].match_type, 0 );
CPPUNIT_ASSERT_EQUAL( match[4].match_type, 0 );
CPPUNIT_ASSERT_EQUAL( match[5].match_type, 2 );
// These are not changed - but sorted.
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[0].coordinate.x(), process_coordinates1[0][0], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[0].coordinate.y(), process_coordinates1[0][1], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[0].coordinate.z(), process_coordinates1[0][2], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[1].coordinate.x(), process_coordinates1[2][0], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[1].coordinate.y(), process_coordinates1[2][1], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[1].coordinate.z(), process_coordinates1[2][2], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[5].coordinate.x(), process_coordinates1[1][0], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[5].coordinate.y(), process_coordinates1[1][1], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[5].coordinate.z(), process_coordinates1[1][2], 1.0e-10 );
// Here are the added wildcards.
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[2].coordinate.x(), -0.7, 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[2].coordinate.y(), 0.3, 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[2].coordinate.z(), 0.3, 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[3].coordinate.x(), 0.3, 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[3].coordinate.y(), -0.7, 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[3].coordinate.z(), 0.3, 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[4].coordinate.x(), 0.3, 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[4].coordinate.y(), 0.3, 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[4].coordinate.z(), -0.7, 1.0e-10 );
}
{
// This one is not changed, since it was applicable to more than one basis site.
const std::vector<MinimalMatchListEntry> & match = interactions.processes()[1]->minimalMatchList();
CPPUNIT_ASSERT_EQUAL( static_cast<int>(match.size()), 3 );
// Not changed - but sorted.
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[0].coordinate.x(), process_coordinates1[0][0], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[0].coordinate.y(), process_coordinates1[0][1], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[0].coordinate.z(), process_coordinates1[0][2], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[1].coordinate.x(), process_coordinates1[2][0], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[1].coordinate.y(), process_coordinates1[2][1], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[1].coordinate.z(), process_coordinates1[2][2], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[2].coordinate.x(), process_coordinates1[1][0], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[2].coordinate.y(), process_coordinates1[1][1], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[2].coordinate.z(), process_coordinates1[1][2], 1.0e-10 );
}
{
const std::vector<MinimalMatchListEntry> & match = interactions.processes()[2]->minimalMatchList();
CPPUNIT_ASSERT_EQUAL( static_cast<int>(match.size()), 47 );
// Not changed.
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[0].coordinate.x(), process_coordinates2[0][0], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[0].coordinate.y(), process_coordinates2[0][1], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[0].coordinate.z(), process_coordinates2[0][2], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[13].coordinate.x(), process_coordinates2[1][0], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[13].coordinate.y(), process_coordinates2[1][1], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[13].coordinate.z(), process_coordinates2[1][2], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[46].coordinate.x(), process_coordinates2[2][0], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[46].coordinate.y(), process_coordinates2[2][1], 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[46].coordinate.z(), process_coordinates2[2][2], 1.0e-10 );
// These are the added wildcards.
for (int i = 0; i < 47; ++i)
{
if (i != 0 && i != 13 && i != 46)
{
CPPUNIT_ASSERT_EQUAL( match[i].match_type, 0 );
}
}
// Check one coordinate.
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[17].coordinate.x(),-0.3, 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[17].coordinate.y(),-0.3, 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[17].coordinate.z(),-1.3, 1.0e-10 );
// Check another one.
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[18].coordinate.x(),-1.0, 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[18].coordinate.y(),-1.0, 1.0e-10 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( match[18].coordinate.z(), 0.0, 1.0e-10 );
}
}
// -------------------------------------------------------------------------- //
//
void Test_Interactions::testMaxRange()
{
// Setup two valid processes.
std::vector<Process> processes;
std::vector<std::string> process_elements1(3);
process_elements1[0] = "A";
process_elements1[1] = "A";
process_elements1[2] = "A";
std::vector<std::string> process_elements2(3);
process_elements2[0] = "B";
process_elements2[1] = "A";
process_elements2[2] = "A";
std::vector<std::vector<double> > process_coordinates(3, std::vector<double>(3, 0.0));
process_coordinates[1][0] = -0.1;
process_coordinates[1][1] = -0.1;
process_coordinates[1][2] = -0.1;
// Possible types.
std::map<std::string, int> possible_types;
possible_types["A"] = 0;
possible_types["B"] = 1;
possible_types["V"] = 2;
const double rate = 13.7;
const Configuration c1(process_coordinates, process_elements1, possible_types);
const Configuration c2(process_coordinates, process_elements2, possible_types);
std::vector<int> sites_vector(0);
processes.push_back(Process(c1,c2,rate,sites_vector));
processes.push_back(Process(c1,c2,rate,sites_vector));
// Setup the interactions object.
const Interactions interactions(processes, true);
// This should have the max range 1.
CPPUNIT_ASSERT_EQUAL( interactions.maxRange(), 1 );
// Adding a process with a -1.1 site should make the max range become 2.
process_coordinates[1][0] = 0.0;
process_coordinates[1][1] = 0.0;
process_coordinates[1][2] = -1.1;
const Configuration c3(process_coordinates, process_elements1, possible_types);
const Configuration c4(process_coordinates, process_elements2, possible_types);
processes.push_back(Process(c3,c4,rate,sites_vector));
// This should have the max range 2.
const Interactions interactions2(processes, true);
CPPUNIT_ASSERT_EQUAL( interactions2.maxRange(), 2 );
// Check the same thing in y.
process_coordinates[1][0] = 0.0;
process_coordinates[1][1] = -2.1;
process_coordinates[1][2] = 0.0;
const Configuration c5(process_coordinates, process_elements1, possible_types);
const Configuration c6(process_coordinates, process_elements2, possible_types);
processes[2] = Process(c5,c6,rate,sites_vector);
// This should have the max range 3.
const Interactions interactions3(processes, true);
CPPUNIT_ASSERT_EQUAL( interactions3.maxRange(), 3 );
// And in x.
process_coordinates[1][0] = -3.1;
process_coordinates[1][1] = 0.0;
process_coordinates[1][2] = 0.0;
const Configuration c7(process_coordinates, process_elements1, possible_types);
const Configuration c8(process_coordinates, process_elements2, possible_types);
processes[2] = Process(c7,c8,rate,sites_vector);
// This should have the max range 4.
const Interactions interactions4(processes, true);
CPPUNIT_ASSERT_EQUAL( interactions4.maxRange(), 4 );
// And in the positive direction.
// Adding a process with a 5.1 site should make the max range become 5.
process_coordinates[1][0] = 0.0;
process_coordinates[1][1] = 0.0;
process_coordinates[1][2] = 5.1;
const Configuration c9(process_coordinates, process_elements1, possible_types);
const Configuration c10(process_coordinates, process_elements2, possible_types);
processes[2] = Process(c9,c10,rate,sites_vector);
// This should have the max range 5.
const Interactions interactions5(processes, true);
CPPUNIT_ASSERT_EQUAL( interactions5.maxRange(), 5 );
// Check the same thing in y.
process_coordinates[1][0] = 0.0;
process_coordinates[1][1] = 2.1;
process_coordinates[1][2] = 0.0;
const Configuration c11(process_coordinates, process_elements1, possible_types);
const Configuration c12(process_coordinates, process_elements2, possible_types);
processes[2] = Process(c11,c12,rate,sites_vector);
// This should have the max range 2.
const Interactions interactions6(processes, true);
CPPUNIT_ASSERT_EQUAL( interactions6.maxRange(), 2 );
// And in x.
process_coordinates[1][0] = 4.1;
process_coordinates[1][1] = 0.0;
process_coordinates[1][2] = 0.0;
const Configuration c13(process_coordinates, process_elements1, possible_types);
const Configuration c14(process_coordinates, process_elements2, possible_types);
processes[2] = Process(c13,c14,rate,sites_vector);
// This should have the max range 4.
const Interactions interactions7(processes, true);
CPPUNIT_ASSERT_EQUAL( interactions7.maxRange(), 4 );
}
// -------------------------------------------------------------------------- //
//
void Test_Interactions::testQuery()
{
// Setup two valid processes.
std::vector<Process> processes;
// Possible types.
std::map<std::string, int> possible_types;
possible_types["A"] = 0;
possible_types["B"] = 1;
possible_types["V"] = 2;
// A process that independent of local environment swaps a "B" to "V"
{
const std::vector<std::string> process_elements1(1,"B");
const std::vector<std::string> process_elements2(1,"V");
const std::vector<std::vector<double> > process_coordinates(1, std::vector<double>(3, 0.0));
const double rate = 1.234;
Configuration c1(process_coordinates, process_elements1, possible_types);
Configuration c2(process_coordinates, process_elements2, possible_types);
Process p(c1, c2, rate, std::vector<int>(1,0));
// Store twize.
processes.push_back(p);
processes.push_back(p);
}
// A process that finds an A between two B's in the 1,1,1 direction
// and swap the A and the first B.
{
std::vector<std::string> process_elements1(3);
process_elements1[0] = "A";
process_elements1[1] = "B";
process_elements1[2] = "B";
std::vector<std::string> process_elements2(3);
process_elements2[0] = "B";
process_elements2[1] = "A";
process_elements2[2] = "B";
std::vector<std::vector<double> > process_coordinates(3, std::vector<double>(3, 0.0));
process_coordinates[1][0] = -0.25;
process_coordinates[1][1] = -0.25;
process_coordinates[1][2] = -0.25;
process_coordinates[2][0] = 0.25;
process_coordinates[2][1] = 0.25;
process_coordinates[2][2] = 0.25;
const double rate = 13.7;
Configuration c1(process_coordinates, process_elements1, possible_types);
Configuration c2(process_coordinates, process_elements2, possible_types);
Process p(c1, c2, rate, std::vector<int>(1,0));
processes.push_back(p);
}
// Setup the interactions object.
Interactions interactions(processes, false);
// Query for the processes.
const std::vector<Process*> & queried_processes = interactions.processes();
// Check the length of the list of processes.
CPPUNIT_ASSERT_EQUAL( static_cast<int>(queried_processes.size()), 3 );
// Get the types in the queried processes and check.
CPPUNIT_ASSERT_EQUAL( queried_processes[0]->minimalMatchList()[0].match_type, 1 );
CPPUNIT_ASSERT_EQUAL( queried_processes[0]->minimalMatchList()[0].update_type, 2 );
CPPUNIT_ASSERT_EQUAL( queried_processes[2]->minimalMatchList()[2].match_type, 1 );
CPPUNIT_ASSERT_EQUAL( queried_processes[2]->minimalMatchList()[2].update_type, 1 );
// Query for the total number of available sites. This is zero since no sites are added to
// the processes.
CPPUNIT_ASSERT_EQUAL( interactions.totalAvailableSites(), 0 );
// Add sites to the processes and see that we get the correct number out.
interactions.processes()[0]->addSite(12);
interactions.processes()[0]->addSite(143);
interactions.processes()[0]->addSite(1654);
interactions.processes()[0]->addSite(177777);
interactions.processes()[1]->addSite(12);
interactions.processes()[1]->addSite(143);
interactions.processes()[2]->addSite(1654);
interactions.processes()[2]->addSite(177777);
interactions.processes()[2]->addSite(177777);
CPPUNIT_ASSERT_EQUAL( interactions.totalAvailableSites(), 9 );
// Query for the rate calculator.
const RateCalculator & rc = interactions.rateCalculator();
CPPUNIT_ASSERT( &rc != NULL );
}
// -------------------------------------------------------------------------- //
//
void Test_Interactions::testUpdateAndPickCustom()
{
// Setup a list of custom rate processes.
std::vector<CustomRateProcess> processes;
// Setup a vector of dummy processes.
std::vector<std::string> process_elements1(1);
process_elements1[0] = "A";
std::vector<std::string> process_elements2(1);
process_elements2[0] = "B";
std::vector<std::vector<double> > process_coordinates(1, std::vector<double>(3, 0.0));
// Possible types.
std::map<std::string, int> possible_types;
possible_types["A"] = 0;
possible_types["B"] = 1;
possible_types["V"] = 2;
const double rate = 1.0/13.7;
Configuration c1(process_coordinates, process_elements1, possible_types);
Configuration c2(process_coordinates, process_elements2, possible_types);
std::vector<int> sites_vector(1,0);
processes.push_back(CustomRateProcess(c1,c2,rate,sites_vector, 1.0));
processes.push_back(CustomRateProcess(c1,c2,rate,sites_vector, 1.0));
processes.push_back(CustomRateProcess(c1,c2,rate/2.0,sites_vector, 1.0));
processes.push_back(CustomRateProcess(c1,c2,rate,sites_vector, 1.0));
processes.push_back(CustomRateProcess(c1,c2,rate,sites_vector, 1.0));
processes.push_back(CustomRateProcess(c1,c2,rate,sites_vector, 1.0));
// Fake a matching by adding sites to the processes.
// First process, 3 sites, total rate 12
processes[0].addSite(12, 4.0);
processes[0].addSite(123, 7.0);
processes[0].addSite(332, 1.0);
// Second process, 2 sites, total rate 4
processes[1].addSite(19, 1.0);
processes[1].addSite(12, 3.0);
// Third process, 4 sites, total rate 3
processes[2].addSite(19, 1.0/4.0);
processes[2].addSite(12, 5.0/4.0);
processes[2].addSite(234, 2.0/4.0);
processes[2].addSite(991, 4.0/4.0);
// The sixth process, one site, total rate 12.
processes[5].addSite(992, 12.0);
// Setup the interactions object.
RateCalculator rc;
Interactions interactions(processes, true, rc);
// Update the probability table.
interactions.updateProbabilityTable();
// Check the values of the probability table.
const std::vector<std::pair<double, int> > & probability_table = \
interactions.probabilityTable();
CPPUNIT_ASSERT_EQUAL( static_cast<int>(probability_table.size()),
static_cast<int>(processes.size()) );
CPPUNIT_ASSERT_DOUBLES_EQUAL( probability_table[0].first, 12.0, 1.0e-14 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( probability_table[1].first, 16.0, 1.0e-14 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( probability_table[2].first, 19.0, 1.0e-14 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( probability_table[3].first, 19.0, 1.0e-14 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( probability_table[4].first, 19.0, 1.0e-14 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( probability_table[5].first, 31.0, 1.0e-14 );
CPPUNIT_ASSERT_EQUAL( probability_table[0].second, 3 );
CPPUNIT_ASSERT_EQUAL( probability_table[1].second, 2 );
CPPUNIT_ASSERT_EQUAL( probability_table[2].second, 4 );
CPPUNIT_ASSERT_EQUAL( probability_table[3].second, 0 );
CPPUNIT_ASSERT_EQUAL( probability_table[4].second, 0 );
CPPUNIT_ASSERT_EQUAL( probability_table[5].second, 1 );
// Make sure to seed the random number generator before we test any
// random dependent stuff.
seedRandom(false, 131);
// Pick processes from this table with enough statistics should give
// the distribution proportional to the number of available sites,
// but with the double rate for the third process should halve
// this entry.
std::vector<int> picked(6,0);
const int n_loop = 1000000;
for (int i = 0; i < n_loop; ++i)
{
const int p = interactions.pickProcessIndex();
// Make sure the picked process is not negative or too large.
CPPUNIT_ASSERT( p >= 0 );
CPPUNIT_ASSERT( p < static_cast<int>(probability_table.size()) );
++picked[p];
}
CPPUNIT_ASSERT_DOUBLES_EQUAL( 1.0*picked[0]/n_loop,
12.0/31.0,
1.0e-2 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( 1.0*picked[1]/n_loop,
4.0/31.0,
1.0e-2 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( 1.0*picked[2]/n_loop,
3.0/31.0,
1.0e-2 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( 1.0*picked[3]/n_loop,
0.0/31.0,
1.0e-2 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( 1.0*picked[4]/n_loop,
0.0/31.0,
1.0e-2 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( 1.0*picked[5]/n_loop,
12.0/31.0,
1.0e-2 );
// Check that picking the process twice with two different access methods and
// a seed reset inbetween gives a reference to the same object.
seedRandom(false, 87);
const int p = interactions.pickProcessIndex();
const Process & proc1 = (*interactions.processes()[p]);
seedRandom(false, 87);
const Process & proc2 = (*interactions.pickProcess());
CPPUNIT_ASSERT_EQUAL( &proc1, &proc2 );
// Alter the total rate in one of the processes and re-run the picking.
interactions.processes()[5]->removeSite(992);
interactions.processes()[5]->addSite(992, 24.0);
// Update the probability table.
interactions.updateProbabilityTable();
std::vector<int> picked2(6,0);
for (int i = 0; i < n_loop; ++i)
{
const int p = interactions.pickProcessIndex();
// Make sure the picked process is not negative or too large.
CPPUNIT_ASSERT( p >= 0 );
CPPUNIT_ASSERT( p < static_cast<int>(probability_table.size()) );
++picked2[p];
}
CPPUNIT_ASSERT_DOUBLES_EQUAL( 1.0*picked2[0]/n_loop,
12.0/43.0,
1.0e-2 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( 1.0*picked2[1]/n_loop,
4.0/43.0,
1.0e-2 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( 1.0*picked2[2]/n_loop,
3.0/43.0,
1.0e-2 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( 1.0*picked2[3]/n_loop,
0.0/43.0,
1.0e-2 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( 1.0*picked2[4]/n_loop,
0.0/43.0,
1.0e-2 );
CPPUNIT_ASSERT_DOUBLES_EQUAL( 1.0*picked2[5]/n_loop,
24.0/43.0,
1.0e-2 );
// DONE
}