Molecule H2()
{
int nAtoms = 2;
Eigen::Vector3d H1( 0.735000, 0.000000, 0.000000);
Eigen::Vector3d H2(-0.735000, 0.000000, 0.000000);
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = H1.transpose();
geom.col(1) = H2.transpose();
Eigen::Vector2d charges, masses;
charges << 1.0, 1.0;
masses << 1.0078250, 1.0078250;
std::vector<Atom> atoms;
double radiusH = 1.20;
atoms.push_back( Atom("Hydrogen", "H", charges(0), masses(0), radiusH, H1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(1), masses(1), radiusH, H2, 1.0) );
std::vector<Sphere> spheres;
Sphere sph2(H1, radiusH);
Sphere sph3(H2, radiusH);
spheres.push_back(sph2);
spheres.push_back(sph3);
Symmetry pGroup = buildGroup(0, 0, 0, 0);
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
int main() {
typedef TempKernel kernel_type;
typedef kernel_type::source_type source_type;
typedef kernel_type::charge_type charge_type;
typedef kernel_type::target_type target_type;
typedef kernel_type::result_type result_type;
kernel_type K;
// init source
std::vector<source_type> sources(2);
// init charge
std::vector<charge_type> charges(sources.size());
// init target
std::vector<target_type> targets(2);
// init results vectors for exact
std::vector<result_type> exact(targets.size());
// test direct
fmmtl::direct(K, sources, charges, targets, exact);
std::cout << exact[0] << "\n";
fmmtl::direct(K, sources, charges, exact);
std::cout << exact[0] << "\n";
}
int main(int argc, char **argv)
{
int numBodies = 1000;
bool checkErrors = true;
// Parse custom command line args
for (int i = 1; i < argc; ++i) {
if (strcmp(argv[i],"-N") == 0) {
i++;
numBodies = atoi(argv[i]);
} else if (strcmp(argv[i],"-nocheck") == 0) {
checkErrors = false;
}
}
// Init the FMM Kernel and options
FMMOptions opts = get_options(argc, argv);
typedef UnitKernel kernel_type;
kernel_type K;
typedef kernel_type::point_type point_type;
typedef kernel_type::source_type source_type;
typedef kernel_type::target_type target_type;
typedef kernel_type::charge_type charge_type;
typedef kernel_type::result_type result_type;
// Init points and charges
std::vector<source_type> points(numBodies);
for (int k = 0; k < numBodies; ++k)
points[k] = source_type(drand(), drand(), drand());
std::vector<charge_type> charges(numBodies);
for (int k = 0; k < numBodies; ++k)
charges[k] = drand();
// Build the FMM
//fmm_plan plan = fmm_plan(K, bodies, opts);
FMM_plan<kernel_type> plan = FMM_plan<kernel_type>(K, points, opts);
// Execute the FMM
//fmm_execute(plan, charges, target_points);
std::vector<result_type> result = plan.execute(charges);
// Check the result
if (checkErrors) {
std::vector<result_type> exact(numBodies);
// Compute the result with a direct matrix-vector multiplication
Direct::matvec(K, points, charges, exact);
int wrong_results = 0;
for (unsigned k = 0; k < result.size(); ++k) {
printf("[%03d] exact: %lg, FMM: %lg\n", k, exact[k], result[k]);
if ((exact[k] - result[k]) / exact[k] > 1e-13)
++wrong_results;
}
printf("Wrong counts: %d\n", wrong_results);
}
}
Molecule H3()
{
int nAtoms = 3;
Eigen::Vector3d H1( 0.735000, 0.000000, -1.333333);
Eigen::Vector3d H2(-0.735000, 0.000000, -1.333333);
Eigen::Vector3d H3( 0.000000, 0.000000, 2.666667);
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = H1.transpose();
geom.col(1) = H2.transpose();
geom.col(2) = H3.transpose();
Eigen::Vector3d charges, masses;
charges << 1.0, 1.0, 1.0;
masses << 1.0078250, 1.0078250, 1.0078250;
std::vector<Atom> atoms;
double radiusH = (1.20 * 1.20) / convertBohrToAngstrom;
atoms.push_back( Atom("Hydrogen", "H", charges(0), masses(0), radiusH, H1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(1), masses(1), radiusH, H2, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(2), masses(2), radiusH, H3, 1.0) );
std::vector<Sphere> spheres;
Sphere sph2(H1, radiusH);
Sphere sph3(H2, radiusH);
Sphere sph4(H3, radiusH);
spheres.push_back(sph2);
spheres.push_back(sph3);
spheres.push_back(sph4);
enum pointGroup { pgC1, pgC2, pgCs, pgCi, pgD2, pgC2v, pgC2h, pgD2h };
Symmetry pGroup;
switch(group) {
case(pgC1):
pGroup = buildGroup(0, 0, 0, 0);
break;
case(pgC2v):
// C2v as generated by Oyz and Oxz
pGroup = buildGroup(2, 1, 2, 0);
break;
default:
pGroup = buildGroup(0, 0, 0, 0);
break;
}
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
int Stick::Worth() const
{
int worth = Category()->worth();
worth += 20 * charges();
if (!is_known())
worth /= 2;
return worth;
}
Molecule NH3()
{
int nAtoms = 4;
Eigen::Vector3d N( -0.000000000, -0.104038047, 0.000000000);
Eigen::Vector3d H1(-0.901584415, 0.481847022, -1.561590016);
Eigen::Vector3d H2(-0.901584415, 0.481847022, 1.561590016);
Eigen::Vector3d H3( 1.803168833, 0.481847022, 0.000000000);
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = N.transpose();
geom.col(1) = H1.transpose();
geom.col(2) = H2.transpose();
geom.col(3) = H3.transpose();
Eigen::Vector4d charges, masses;
charges << 7.0, 1.0, 1.0, 1.0;
masses << 14.0030740, 1.0078250, 1.0078250, 1.0078250;
std::vector<Atom> atoms;
atoms.push_back( Atom("Nitrogen", "N", charges(0), masses(0), 2.929075493, N,
1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(1), masses(1), 2.267671349, H1,
1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(2), masses(2), 2.267671349, H2,
1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(3), masses(3), 2.267671349, H3,
1.0) );
std::vector<Sphere> spheres;
Sphere sph1(N, 2.929075493);
Sphere sph2(H1, 2.267671349);
Sphere sph3(H2, 2.267671349);
Sphere sph4(H3, 2.267671349);
spheres.push_back(sph1);
spheres.push_back(sph2);
spheres.push_back(sph3);
spheres.push_back(sph4);
// C1
Symmetry pGroup = buildGroup(0, 0, 0, 0);
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
void execute(const Kernel& K,
ChargeIter cfirst, ChargeIter clast,
ResultIter rfirst, ResultIter rlast) {
// TODO: Ugh, iterator type hiding via copy
std::vector<charge_type> charges(cfirst, clast);
std::vector<result_type> results(rfirst, rlast);
execute(K, charges, results);
std::copy(results.begin(), results.end(), rfirst);
}
int main()
{
typedef LaplaceSpherical kernel_type;
kernel_type K(5);
typedef kernel_type::point_type point_type;
typedef kernel_type::charge_type charge_type;
typedef kernel_type::result_type result_type;
FMMOptions opts;
opts.set_mac_theta(.5);
opts.set_max_per_box(125); // optimal ncrit
std::vector<std::pair<unsigned,double>> times;
double tic, toc;
int numBodies = 1000000;
// initialize points
std::vector<point_type> points(numBodies);
for (int k=0; k<numBodies; ++k){
points[k] = point_type(drand(), drand(), drand());
}
// initialize charges
std::vector<charge_type> charges(numBodies);
for (int k=0; k<numBodies; ++k){
charges[k] = drand();
}
// loop in ncrit
for (int ncrit=50; ncrit<=400; ncrit+=50){
opts.set_max_per_box(ncrit);
// create FMM plan
FMM_plan<kernel_type> plan = FMM_plan<kernel_type>(K, points, opts);
// execute FMM
// run 3 times and make an average
int nt = 3; // number of identical runs for timing
std::vector<double> timings(nt);
std::vector<result_type> result(numBodies);
for (int i=0; i<nt; i++){
tic = get_time();
result = plan.execute(charges);
toc = get_time();
timings[i] = toc-tic;
}
double FMM_time = std::accumulate(timings.begin(), timings.end(), 0.0) / timings.size();
std::cout << ncrit << " " << FMM_time << std::endl;
}
return 0;
}
Molecule CH3()
{
int nAtoms = 4;
Eigen::Vector3d C1( 0.0006122714, 0.0000000000, 0.0000000000);
Eigen::Vector3d H1( 1.5162556382, -1.3708721537, 0.0000000000);
Eigen::Vector3d H2(-0.7584339548, 0.6854360769, 1.7695110698);
Eigen::Vector3d H3(-0.7584339548, 0.6854360769, -1.7695110698);
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = C1.transpose();
geom.col(1) = H1.transpose();
geom.col(2) = H2.transpose();
geom.col(3) = H3.transpose();
Eigen::Vector4d charges, masses;
charges << 6.0, 1.0, 1.0, 1.0;
masses << 12.00, 1.0078250, 1.0078250, 1.0078250;
double radiusC = (1.70 * 1.20) / convertBohrToAngstrom;
double radiusH = (1.20 * 1.20) / convertBohrToAngstrom;
std::vector<Atom> atoms;
atoms.push_back( Atom("Carbon", "C", charges(0), masses(0), radiusC, C1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(1), masses(1), radiusH, H1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(2), masses(2), radiusH, H2, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(3), masses(3), radiusH, H3, 1.0) );
std::vector<Sphere> spheres;
Sphere sph1(C1, radiusC);
Sphere sph2(H1, radiusH);
Sphere sph3(H2, radiusH);
Sphere sph4(H3, radiusH);
spheres.push_back(sph1);
spheres.push_back(sph2);
spheres.push_back(sph3);
spheres.push_back(sph4);
// Cs as generated by Oxy
Symmetry pGroup = buildGroup(1, 4, 0, 0);
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
bool ExternalCharges::parse(TextStream& textStream)
{
int max(INT_MAX);
bool allOk(true), isDouble;
bool maxSet(false), invalidFormat(false);
double x, y, z, q;
QStringList tokens;
Data::PointChargeList* charges(new Data::PointChargeList);
while (!textStream.atEnd() && charges->size() < max) {
tokens = textStream.nextLineAsTokens();
if (tokens.size() >= 4) {
x = tokens[0].toDouble(&isDouble); allOk = allOk && isDouble;
y = tokens[1].toDouble(&isDouble); allOk = allOk && isDouble;
z = tokens[2].toDouble(&isDouble); allOk = allOk && isDouble;
q = tokens[3].toDouble(&isDouble); allOk = allOk && isDouble;
if (allOk) {
charges->append(new Data::PointCharge(q, qglviewer::Vec(x,y,z)));
}else {
invalidFormat = true;
break;
}
}else if (tokens.size() >= 1) {
if (tokens.first().contains("$end", Qt::CaseInsensitive) || maxSet) {
break;
}else {
max = tokens[0].toInt(&maxSet);
}
}
}
if (maxSet && charges->size() != max) {
if (invalidFormat) {
QString msg("Invalid format on line ");
m_errors.append(msg += QString::number(textStream.lineNumber()));
}else {
m_errors.append("End of stream encountered");
}
delete charges;
}else if (charges->isEmpty()) {
m_errors.append("No charges found");
delete charges;
}else {
m_dataBank.append(charges);
}
return m_errors.isEmpty();
}
Molecule C2H4()
{
int nAtoms = 6;
Eigen::Vector3d C1(0.0000000000, 0.0000000000, 1.2578920000);
Eigen::Vector3d H1(0.0000000000, 1.7454620000, 2.3427160000);
Eigen::Vector3d H2(0.0000000000, -1.7454620000, 2.3427160000);
Eigen::Vector3d C2(0.0000000000, 0.0000000000, -1.2578920000);
Eigen::Vector3d H3(0.0000000000, 1.7454620000, -2.3427160000);
Eigen::Vector3d H4(0.0000000000, -1.7454620000, -2.3427160000);
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = C1.transpose();
geom.col(1) = H1.transpose();
geom.col(2) = H2.transpose();
geom.col(3) = C2.transpose();
geom.col(4) = H3.transpose();
geom.col(5) = H4.transpose();
Eigen::VectorXd charges(6), masses(6);
charges << 6.0, 1.0, 1.0, 6.0, 1.0, 1.0;
masses << 12.00, 1.0078250, 1.0078250, 12.0, 1.0078250, 1.0078250;
double radiusC = (1.70 * 1.20) / convertBohrToAngstrom;
double radiusH = (1.20 * 1.20) / convertBohrToAngstrom;
std::vector<Atom> atoms;
atoms.push_back( Atom("Carbon", "C", charges(0), masses(0), radiusC, C1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(1), masses(1), radiusH, H1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(2), masses(2), radiusH, H2, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(3), masses(3), radiusC, C2, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(4), masses(4), radiusH, H3, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(5), masses(5), radiusH, H4, 1.0) );
std::vector<Sphere> spheres;
Sphere sph1(C1, radiusC);
Sphere sph2(H1, radiusH);
Sphere sph3(H2, radiusH);
Sphere sph4(C2, radiusC);
Sphere sph5(H3, radiusH);
Sphere sph6(H4, radiusH);
spheres.push_back(sph1);
spheres.push_back(sph2);
spheres.push_back(sph3);
spheres.push_back(sph4);
spheres.push_back(sph5);
spheres.push_back(sph6);
// D2h as generated by Oxy, Oxz, Oyz
Symmetry pGroup = buildGroup(3, 4, 2, 1);
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
void QChemInput::readExternalChargesSection(TextStream& textStream)
{
ExternalCharges parser;
if (parser.parse(textStream)) {
Data::Bank& bank(parser.data());
if (!bank.isEmpty()) {
Data::Base* base(bank.takeFirst());
Data::PointChargeList* charges(dynamic_cast<Data::PointChargeList*>(base));
if (charges) m_dataBank.append(charges);
}
}else {
m_errors << parser.errors();
}
}
List Factory::convert(Data::PointChargeList& pointCharges)
{
Charges* charges(new Charges());
unsigned nCharges(pointCharges.size());
for (unsigned i = 0; i < nCharges; ++i) {
double q(pointCharges[i]->value());
qglviewer::Vec position(pointCharges[i]->position());
Charge* charge(new Charge(q,position));
charges->appendLayer(charge);
}
List list;
list.append(charges);
return list;
}
void test_kernel(const Kernel& K) {
typedef typename Kernel::source_type source_type;
typedef typename Kernel::charge_type charge_type;
typedef typename Kernel::target_type target_type;
typedef typename Kernel::result_type result_type;
std::vector<source_type> sources(1);
std::vector<charge_type> charges(1);
std::vector<target_type> targets(1);
std::vector<result_type> results(1);
Direct::matvec(K, sources, charges, targets, results);
std::cout << results[0] << std::endl;
std::cout << KernelTraits<Kernel>() << std::endl;
std::cout << typeid(Kernel).name() << " OK." << std::endl;
}
int task1_main (void)
{
FILE* infile = NULL, *outfile = NULL;
int month = 0, year = 0,
customer_number = 0, hours_used = 0;
double charge = 0.0, average_cost = 0.0;
printf ("\nOpening files...");
infile = fopen ("task1_input.dat", "r");
outfile = fopen ("task1_output.dat", "w");
fscanf (infile, " %d", &month);
fscanf (infile, " %d", &year);
fprintf (outfile, "InternetLite Charges for %d/%d\n\nCustomer # --|-- Hours Used --|-- Total Charge --|-- Average Cost\n", month, year);
printf ("Calculating Costs...");
while (!feof (infile))
{
fscanf (infile, " %d", &customer_number);
fscanf (infile, " %d", &hours_used);
charges (hours_used, &charge, &average_cost);
fprintf (outfile, "%d\t\t --|-- %d\t\t\t--|-- $%.2lf\t\t --|-- $%.2lf\n", customer_number, hours_used, charge, average_cost);
}
printf ("Closing files...");
fclose (infile);
fclose (outfile);
printf ("Charges complete!\n");
system ("pause");
return 0;
}
int main(int argc, char **argv)
{
int numPanels= 1000, recursions = 4, p = 5, k = 3, max_iterations = 500;
FMMOptions opts = get_options(argc,argv);
opts.sparse_local = true;
SolverOptions solver_options;
bool second_kind = false;
char *mesh_name;
bool mesh = false;
// solve / PC settings
SOLVERS solver = SOLVE_GMRES;
PRECONDITIONERS pc = IDENTITY;
// use lazy evaluator by default
// opts.lazy_evaluation = true;
// parse command line args
// check if no arguments given
printf("\nLaplaceBEM on a sphere\n");
if (argc == 1) printHelpAndExit();
printf("parameters : \n");
printf("============ \n");
for (int i = 1; i < argc; ++i) {
if (strcmp(argv[i],"-theta") == 0) {
i++;
printf("theta = %s\n", argv[i]);
} else if (strcmp(argv[i],"-recursions") == 0) {
i++;
recursions = atoi(argv[i]);
// print out problem size based on the # of recursions
printf("N = %i\n", 2* (int) pow(4, recursions));
} else if (strcmp(argv[i],"-eval") == 0) {
i++;
} else if (strcmp(argv[i], "-ncrit") == 0) {
i++;
printf("ncrit = %s\n", argv[i]);
} else if (strcmp(argv[i], "-printtree") == 0) {
} else if (strcmp(argv[i],"-p") == 0) {
i++;
p = atoi(argv[i]);
solver_options.max_p = p;
printf("max-p = %i\n", p);
} else if (strcmp(argv[i],"-k") == 0) {
i++;
k = atoi(argv[i]);
} else if (strcmp(argv[i],"-second_kind") == 0) {
second_kind = true;
printf("second-kind = True\n");
} else if (strcmp(argv[i],"-fixed_p") == 0) {
solver_options.variable_p = false;
printf("relaxed = False\n");
} else if (strcmp(argv[i],"-solver_tol") == 0) {
i++;
solver_options.residual = (double)atof(argv[i]);
printf("solver_tol = %.2e\n", solver_options.residual);
} else if (strcmp(argv[i],"-max_iters") == 0) {
i++;
max_iterations = atoi(argv[i]);
} else if (strcmp(argv[i],"-gmres") == 0) {
solver = SOLVE_GMRES;
} else if (strcmp(argv[i],"-fgmres") == 0) {
solver = SOLVE_FGMRES;
} else if (strcmp(argv[i],"-local") == 0) {
solver = SOLVE_FGMRES;
pc = LOCAL;
} else if (strcmp(argv[i],"-diagonal") == 0) {
pc = DIAGONAL;
} else if (strcmp(argv[i],"-help") == 0) {
printHelpAndExit();
} else if (strcmp(argv[i],"-mesh") == 0) {
i++;
mesh_name = argv[i];
mesh = true;
}
else {
printf("[W]: Unknown command line arg: \"%s\"\n",argv[i]);
printHelpAndExit();
}
}
printf("============\n");
solver_options.max_iters = max_iterations;
solver_options.restart = max_iterations;
// opts.sparse_local = true;
double tic, toc;
// Init the FMM Kernel
typedef LaplaceSphericalBEM kernel_type;
kernel_type K(p,k);
// useful typedefs
typedef kernel_type::point_type point_type;
typedef kernel_type::source_type source_type;
typedef kernel_type::target_type target_type;
typedef kernel_type::charge_type charge_type;
typedef kernel_type::result_type result_type;
// Init points and charges
std::vector<source_type> panels(numPanels);
std::vector<charge_type> charges(numPanels);
if (mesh) {
printf("reading mesh from: %s\n",mesh_name);
MeshIO::readMsh<point_type,source_type>(mesh_name, panels); // , panels);
} else {
Triangulation::UnitSphere(panels, recursions);
// initialiseSphere(panels, charges, recursions); //, ProblemOptions());
}
// run case solving for Phi (instead of dPhi/dn)
if (second_kind)
for (auto& it : panels) it.switch_BC();
// set constant Phi || dPhi/dn for each panel
charges.resize(panels.size());
// set up a more complicated charge, from BEM++
for (unsigned i=0; i<panels.size(); i++) {
#if BEMCPP_TEST
auto center = panels[i].center;
double x = center[0], y = center[1], z = center[2];
double r = norm(center);
charges[i] = 2*x*z/(r*r*r*r*r) - y/(r*r*r);
#else
charges[i] = 1.;
#endif
}
// charges = std::vector<charge_type>(panels.size(),1.);
// Build the FMM structure
FMM_plan<kernel_type> plan = FMM_plan<kernel_type>(K, panels, opts);
// generate the RHS and initial condition
std::vector<charge_type> x(panels.size(),0.);
tic = get_time();
std::vector<result_type> b(panels.size(),0.);
double tic2, toc2;
// generate RHS using temporary FMM plan
{
tic2 = get_time();
for (auto& it : panels) it.switch_BC();
toc2 = get_time();
printf("Flipping BC: %g\n",toc2-tic2);
tic2 = get_time();
FMM_plan<kernel_type> rhs_plan = FMM_plan<kernel_type>(K,panels,opts);
toc2 = get_time();
printf("Creating plan: %g\n",toc2-tic2);
tic2 = get_time();
b = rhs_plan.execute(charges);
toc2 = get_time();
printf("Executing plan: %g\n",toc2-tic2);
for (auto& it : panels) it.switch_BC();
}
toc = get_time();
double setup_time = toc-tic;
// Solve the system using GMRES
// generate the Preconditioner
tic = get_time();
Preconditioners::Diagonal<charge_type> M(K,
plan.source_begin(),
plan.source_end()
);
// M.print();
SolverOptions inner_options(1e-2,1,2);
inner_options.variable_p = true;
/*
// Preconditioners::FMGMRES<FMM_plan<kernel_type>,Preconditioners::Diagonal<charge_type>> inner(plan, b, inner_options, M);
// Local preconditioner
Preconditioners::LocalInnerSolver<FMM_plan<kernel_type>, Preconditioners::Diagonal<result_type>> local(K, panels, b);
// block diagonal preconditioner
Preconditioners::BlockDiagonal<FMM_plan<kernel_type>> block_diag(K,panels);
*/
// Initial low accuracy solve
//
/*
double tic2, toc2;
tic2 = get_time();
{
printf("Initial solve starting..\n");
// initial solve to 1e-2 accuracy, 5 iterations, P = 2
SolverOptions initial_solve(5e-3,50,3);
// fmm_gmres(plan, x, b, solver_options, M);
GMRES(plan, x, b, initial_solve, M);
printf("Initial solve finished..\n");
}
toc2 = get_time();
printf("Initial solve took: %.4es\n",toc2-tic2);
*/
// Outer GMRES solve with diagonal preconditioner & relaxation
FGMRESContext<result_type> context(x.size(), solver_options.restart);
if (second_kind) printf("2nd-kind equation being solved\n");
else printf("1st-kind equation being solved\n");
#if 1
if (solver == SOLVE_GMRES && pc == IDENTITY){
printf("Solver: GMRES\nPreconditioner: Identity\n");
// straight GMRES, no preconditioner
// DirectMV<kernel_type> MV(K, panels, panels);
GMRES(plan,x,b,solver_options);
}
else if (solver == SOLVE_GMRES && pc == DIAGONAL) {
printf("Solver: GMRES\nPreconditioner: Diagonal\n");
// GMRES, diagonal preconditioner
GMRES(plan, x, b, solver_options, M, context);
}
#else
else if (solver == SOLVE_GMRES && pc == DIAGONAL) {
printf("Solver: GMRES\nPreconditioner: Diagonal\n");
// GMRES, diagonal preconditioner
GMRES(plan,x,b,solver_options, M, context);
}
else if (solver == SOLVE_FGMRES && pc == IDENTITY) {
printf("Solver: FMRES\nPreconditioner: Identity\n");
// GMRES, diagonal preconditioner
FGMRES(plan,x,b,solver_options);
}
else if (solver == SOLVE_FGMRES && pc == DIAGONAL) {
printf("Solver: FGMRES\nPreconditioner: Block Diagonal\n");
// GMRES, diagonal preconditioner
FGMRES(plan,x,b,solver_options, block_diag, context);
}
else if (solver == SOLVE_FGMRES && pc == LOCAL) {
printf("Solver: FGMRES\nPreconditioner: Local solve\n");
// FGMRES, Local inner solver
FGMRES(plan,x,b,solver_options, local, context);
}
else {
printf("[E] no valid solver / preconditioner option chosen\n");
exit(0);
}
#endif
// GMRES(MV,x,b,solver_options, M, context);
// FGMRES(plan,x,b,solver_options, inner, context); // , context);
// Outer/Inner FGMRES / GMRES (Diagonal)
toc = get_time();
double solve_time = toc-tic;
printf("\nTIMING:\n");
printf("\tsetup : %.4es\n",setup_time);
printf("\tsolve : %.4es\n",solve_time);
// check errors -- analytical solution for dPhi/dn = 1.
double e = 0.;
double e2 = 0.;
#if BEMCPP_TEST
std::vector<result_type> analytical(panels.size());
for (unsigned i=0; i<panels.size(); i++) {
auto center = panels[i].center;
double x = center[0], y = center[1], z = center[2];
double r = norm(center);
analytical[i] = -(-6 * x * z / (r*r*r*r*r*r) + 2 * y / (r*r*r*r));
}
auto ai = analytical.begin();
for (auto xi : x) {
// printf("approx: %.4g, analytical: %.4g\n",xi,*ai);
e += (xi-*ai)*(xi-*ai);
e2 += (*ai)*(*ai);
++ai;
}
#else
double an = 1.;
for (auto xi : x) { e += (xi-an)*(xi-an); e2 += an*an; }
#endif
#define EXTERNAL_ERROR
#ifdef EXTERNAL_ERROR
std::vector<target_type> outside_point(1);
outside_point[0] = target_type(point_type(3.,3.,3.),point_type(3.,3.,3.),point_type(3.,3.,3.));
outside_point[0].center = point_type(3.,3.,3.);
std::vector<result_type> outside_result_1(1);
std::vector<result_type> outside_result_2(1);
outside_result_1[0] = 0.;
outside_result_2[0] = 0.;
// first layer
Direct::matvec(K, panels.begin(), panels.end(), x.begin(), outside_point.begin(), outside_point.end(), outside_result_2.begin());
// for (auto& pi : panels) pi.switch_BC();
for (auto& op : outside_point) op.switch_BC();
Direct::matvec(K, panels.begin(), panels.end(), charges.begin(), outside_point.begin(), outside_point.end(), outside_result_1.begin());
double exact = 1. / norm(static_cast<point_type>(outside_point[0])) * 1;
double outside_result = (outside_result_2[0]-outside_result_1[0])/4/M_PI;
double outside_error = fabs(outside_result-exact)/fabs(exact);
printf("external phi: %.5g, exact: %.5g, error: %.4e\n",outside_result,exact, outside_error);
#endif
printf("relative error: %.3e\n",sqrt(e/e2));
}
int main(int argc, char **argv)
{
int N = 1 << 20;
// Parse custom command line args
for (int i = 1; i < argc; ++i) {
if (strcmp(argv[i],"-N") == 0) {
N = atoi(argv[++i]);
}
}
// Round up to the nearest square number
int n_side = int(std::ceil(std::sqrt(N)));
N = n_side * n_side;
// Init the FMM Kernel and options
FMMOptions opts = get_options(argc, argv);
//typedef UnitExpansion kernel_type;
//typedef ExpExpansion kernel_type;
typedef LaplaceSpherical kernel_type;
//typedef YukawaCartesian kernel_type;
// Init kernel
kernel_type K;
typedef kernel_type::point_type point_type;
typedef kernel_type::source_type source_type;
typedef kernel_type::target_type target_type;
typedef kernel_type::charge_type charge_type;
typedef kernel_type::result_type result_type;
std::cout << "Initializing source and N = " << N << " targets..." << std::endl;
// Init a square targets
double xmin = -1;
double xmax = 1;
double ymin = -1;
double ymax = 1;
std::vector<target_type> targets;
targets.reserve(N);
for (int n = 0; n < n_side; ++n) {
for (int m = 0; m < n_side; ++m) {
targets.push_back(target_type(xmin + n * (xmax-xmin) / (n_side-1),
ymin + m * (ymax-ymin) / (n_side-1)));
}
}
//int middle = n_side/2 * n_side + n_side/2;
int middle = fmmtl::random<unsigned>::get(0, N);
// Init charges, only the middle source has a charge
std::vector<charge_type> charges(N);
charges[middle] = charge_type(1);
std::cout << "Building the kernel matrix..." << std::endl;
// Build the FMM
fmmtl::kernel_matrix<kernel_type> A = K(targets, targets);
A.set_options(opts);
std::cout << "Performing the kernel matrix-vector mult..." << std::endl;
// Execute the FMM
std::vector<result_type> result = A * charges;
// Check the result
std::cout << "Computing direct kernel matrix-vector mult..." << std::endl;
// Compute the result with a direct matrix-vector multiplication
std::vector<result_type> exact(N);
fmmtl::direct(K,
targets.begin()+middle, targets.begin()+middle+1,
charges.begin()+middle,
targets.begin(), targets.end(),
exact.begin());
std::cout << "Computing the errors..." << std::endl;
std::vector<double> log_error(result.size());
double min_error = std::numeric_limits<double>::max();
double max_error = std::numeric_limits<double>::lowest();
for (unsigned k = 0; k < result.size(); ++k) {
double error = norm_2(exact[k] - result[k]) / norm_2(exact[k]);
if (error > 1e-15)
log_error[k] = std::log10(error);
else
log_error[k] = -16;
min_error = std::min(min_error, log_error[k]);
max_error = std::max(max_error, log_error[k]);
}
std::cout << "Min log error: " << min_error << std::endl;
std::cout << "Max log error: " << max_error << std::endl;
// Fill the image with the errors computed above
gil::rgb8_image_t img(n_side, n_side);
auto img_view = gil::view(img);
for (int n = 0; n < n_side; ++n) {
for (int m = 0; m < n_side; ++m) {
img_view(n,m) = make_heat((log_error[n*n_side+m] - min_error) / (max_error - min_error));
}
}
gil::png_write_view("fmmtl_errors.png", const_view(img));
}
Layer::List Factory::toLayers(Data::Base& data)
{
Layer::List layers;
//qDebug() << "Layer::Factory converting" << Data::Type::toString(data.typeID());
try {
switch (data.typeID()) {
case Data::Type::Bank: {
Data::Bank& bank(dynamic_cast<Data::Bank&>(data));
layers << convert(bank);
} break;
case Data::Type::GeometryList: {
Data::GeometryList& list(dynamic_cast<Data::GeometryList&>(data));
layers << convert(list);
} break;
case Data::Type::Geometry: {
Data::Geometry& geometry(dynamic_cast<Data::Geometry&>(data));
layers << convert(geometry);
} break;
case Data::Type::PointChargeList: {
Data::PointChargeList& charges(dynamic_cast<Data::PointChargeList&>(data));
layers << convert(charges);
} break;
case Data::Type::MolecularOrbitalsList: {
Data::MolecularOrbitalsList& list(dynamic_cast<Data::MolecularOrbitalsList&>(data));
layers << convert(list);
} break;
case Data::Type::MolecularOrbitals: {
Data::MolecularOrbitals&
molecularOrbitals(dynamic_cast<Data::MolecularOrbitals&>(data));
layers.append(new MolecularOrbitals(molecularOrbitals));
} break;
case Data::Type::ExcitedStates: {
Data::ExcitedStates&
states(dynamic_cast<Data::ExcitedStates&>(data));
layers.append(new ExcitedStates(states));
} break;
case Data::Type::Frequencies: {
Data::Frequencies&
frequencies(dynamic_cast<Data::Frequencies&>(data));
layers.append(new Frequencies(frequencies));
} break;
case Data::Type::FileList: {
Data::FileList& fileList(dynamic_cast<Data::FileList&>(data));
layers << convert(fileList);
} break;
case Data::Type::GridData: {
QLOG_WARN() << "Data::GridData passed to LayerFactory";
//Data::GridData& grid(dynamic_cast<Data::GridData&>(data));
//layers.append(new CubeData(grid));
} break;
case Data::Type::CubeData: {
Data::CubeData& cube(dynamic_cast<Data::CubeData&>(data));
layers.append(new CubeData(cube));
} break;
case Data::Type::EfpFragment: {
Data::EfpFragment& efp(dynamic_cast<Data::EfpFragment&>(data));
layers.append(new EfpFragment(efp));
} break;
case Data::Type::EfpFragmentList: {
Data::EfpFragmentList&
efpList(dynamic_cast<Data::EfpFragmentList&>(data));
layers << convert(efpList);
} break;
case Data::Type::Mesh: {
Data::Mesh& meshData(dynamic_cast<Data::Mesh&>(data));
Data::Surface surface(meshData);
Layer::Surface* surfaceLayer(new Surface(surface));
surfaceLayer->setCheckState(Qt::Checked);
layers.append(surfaceLayer);
} break;
case Data::Type::Surface: {
Data::Surface& surfaceData(dynamic_cast<Data::Surface&>(data));
Layer::Surface* surfaceLayer(new Surface(surfaceData));
surfaceLayer->setCheckState(surfaceData.isVisible() ? Qt::Checked : Qt::Unchecked);
layers.append(surfaceLayer);
} break;
case Data::Type::Nmr: {
Data::Nmr& nmrData(dynamic_cast<Data::Nmr&>(data));
Layer::Nmr* nmrLayer(new Nmr(nmrData));
layers.append(nmrLayer);
} break;
default:
QLOG_WARN() << "Unimplemented data type in Layer::Factory"
<< Data::Type::toString(data.typeID());
break;
}
} catch (const std::bad_cast& e) {
QLOG_ERROR() << "Data cast in Layer::Factory failed"
<< Data::Type::toString(data.typeID());
}
return layers;
}
int main(int argc, const char * argv[]) {
int numParticles = 24;
double charges_arr[] = {0.131300, 0.147300, 0.139400, 0.157400, 0.117000, 0.067800, 0.091200, 0.424900, 0.425600, 0.483500, 0.423600, -0.109800, -0.094800, -0.207900, -0.146800, -0.151000, 0.126300, 0.936500, -0.045900, -0.074300, -0.833000, -0.711000, -0.801600, -0.495800};
double atomicRadii_arr[] = {0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.170000, 0.170000, 0.170000, 0.170000, 0.170000, 0.170000, 0.170000, 0.170000, 0.170000, 0.155000, 0.150000, 0.150000, 0.150000};
double scaleFactors_arr[] = {0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.720000, 0.720000, 0.720000, 0.720000, 0.720000, 0.720000, 0.720000, 0.720000, 0.720000, 0.790000, 0.850000, 0.850000, 0.850000};
std::vector<double> charges(charges_arr, charges_arr + sizeof(charges_arr) / sizeof(double));
std::vector<double> atomicRadii(atomicRadii_arr, atomicRadii_arr + sizeof(atomicRadii_arr) / sizeof(double));
std::vector<double> scaleFactors(scaleFactors_arr, scaleFactors_arr + sizeof(scaleFactors_arr) / sizeof(double));
vector3 atomCoordinates[numParticles];
atomCoordinates[0][0] = 2.805550;
atomCoordinates[0][1] = 0.089450;
atomCoordinates[0][2] = 1.683500;
atomCoordinates[1][0] = 2.713690;
atomCoordinates[1][1] = 0.503260;
atomCoordinates[1][2] = 1.735420;
atomCoordinates[2][0] = 2.580450;
atomCoordinates[2][1] = 0.033700;
atomCoordinates[2][2] = 1.759150;
atomCoordinates[3][0] = 2.487860;
atomCoordinates[3][1] = 0.447340;
atomCoordinates[3][2] = 1.816930;
atomCoordinates[4][0] = 2.946940;
atomCoordinates[4][1] = 0.422240;
atomCoordinates[4][2] = 1.714860;
atomCoordinates[5][0] = 2.984070;
atomCoordinates[5][1] = 0.255700;
atomCoordinates[5][2] = 1.683920;
atomCoordinates[6][0] = 2.861380;
atomCoordinates[6][1] = 0.300150;
atomCoordinates[6][2] = 1.449780;
atomCoordinates[7][0] = 3.095920;
atomCoordinates[7][1] = 0.243650;
atomCoordinates[7][2] = 1.485840;
atomCoordinates[8][0] = 3.085850;
atomCoordinates[8][1] = 0.363430;
atomCoordinates[8][2] = 1.370570;
atomCoordinates[9][0] = 3.130310;
atomCoordinates[9][1] = 0.402180;
atomCoordinates[9][2] = 1.526820;
atomCoordinates[10][0] = 2.352870;
atomCoordinates[10][1] = 0.278670;
atomCoordinates[10][2] = 1.858320;
atomCoordinates[11][0] = 2.737170;
atomCoordinates[11][1] = 0.168810;
atomCoordinates[11][2] = 1.712970;
atomCoordinates[12][0] = 2.683540;
atomCoordinates[12][1] = 0.398830;
atomCoordinates[12][2] = 1.742020;
atomCoordinates[13][0] = 2.610740;
atomCoordinates[13][1] = 0.137850;
atomCoordinates[13][2] = 1.754950;
atomCoordinates[14][0] = 2.556960;
atomCoordinates[14][1] = 0.368490;
atomCoordinates[14][2] = 1.788380;
atomCoordinates[15][0] = 2.774370;
atomCoordinates[15][1] = 0.299610;
atomCoordinates[15][2] = 1.706940;
atomCoordinates[16][0] = 2.522120;
atomCoordinates[16][1] = 0.234120;
atomCoordinates[16][2] = 1.795440;
atomCoordinates[17][0] = 2.884280;
atomCoordinates[17][1] = 0.507750;
atomCoordinates[17][2] = 1.481190;
atomCoordinates[18][0] = 2.913600;
atomCoordinates[18][1] = 0.335030;
atomCoordinates[18][2] = 1.658250;
atomCoordinates[19][0] = 2.926150;
atomCoordinates[19][1] = 0.365170;
atomCoordinates[19][2] = 1.508870;
atomCoordinates[20][0] = 3.065150;
atomCoordinates[20][1] = 0.341270;
atomCoordinates[20][2] = 1.470230;
atomCoordinates[21][0] = 2.912950;
atomCoordinates[21][1] = 0.548670;
atomCoordinates[21][2] = 1.368890;
atomCoordinates[22][0] = 2.827210;
atomCoordinates[22][1] = 0.581440;
atomCoordinates[22][2] = 1.566630;
atomCoordinates[23][0] = 2.405610;
atomCoordinates[23][1] = 0.197730;
atomCoordinates[23][2] = 1.831700;
ObcParameters* obcParameters = new ObcParameters(numParticles,
ObcParameters::ObcTypeII);
obcParameters->setAtomicRadii(atomicRadii);
obcParameters->setScaledRadiusFactors(scaleFactors);
obcParameters->setSolventDielectric(static_cast<double>(78.5));
obcParameters->setSoluteDielectric(static_cast<double>(1.0));
obcParameters->setPi4Asolv(4*M_PI*2.25936);
obcParameters->setUseCutoff(static_cast<double>(1.5));
ReferenceObc *obc = new ReferenceObc(obcParameters);
obc->setIncludeAceApproximation(true);
vector3 inputForces[numParticles];
double obcEnergy;
obcEnergy = obc->computeBornEnergyForces(atomCoordinates, charges, inputForces);
// Energy is inconsistent with MMTK version
std::cout << "Obc energy: " << obcEnergy << std::endl;
for (int i = 0; i < numParticles; ++i)
std::cout << inputForces[i][0] << ' ' << inputForces[i][1] << ' ' << inputForces[i][2] << std::endl;
delete obcParameters;
return 0;
}
int main(int argc, char **argv)
{
int N = 10000;
bool checkErrors = true;
// Parse custom command line args
for (int i = 1; i < argc; ++i) {
if (strcmp(argv[i],"-N") == 0) {
N = atoi(argv[++i]);
} else if (strcmp(argv[i],"-nocheck") == 0) {
checkErrors = false;
}
}
// Init the FMM Kernel and options
FMMOptions opts = get_options(argc, argv);
// Init kernel
typedef LaplaceSpherical kernel_type;
kernel_type K;
typedef kernel_type::point_type point_type;
typedef kernel_type::source_type source_type;
typedef kernel_type::target_type target_type;
typedef kernel_type::charge_type charge_type;
typedef kernel_type::result_type result_type;
// Init points and charges
std::vector<source_type> points(N);
for (unsigned k = 0; k < points.size(); ++k)
points[k] = fmmtl::random<source_type>::get();
std::vector<charge_type> charges(N);
for (unsigned k = 0; k < charges.size(); ++k)
charges[k] = fmmtl::random<charge_type>::get();
// Build the FMM
fmmtl::kernel_matrix<kernel_type> A = K(points, points);
A.set_options(opts);
// Execute the FMM
Clock t1;
std::vector<result_type> result = A * charges;
double time1 = t1.seconds();
std::cout << "FMM in " << time1 << " secs" << std::endl;
// Execute the FMM
Clock t2;
result = A * charges;
double time2 = t2.seconds();
std::cout << "FMM in " << time2 << " secs" << std::endl;
// Execute the FMM
Clock t3;
result = A * charges;
double time3 = t3.seconds();
std::cout << "FMM in " << time3 << " secs" << std::endl;
// Check the result
if (checkErrors) {
std::cout << "Computing direct matvec..." << std::endl;
std::vector<result_type> exact(N);
// Compute the result with a direct matrix-vector multiplication
Direct::matvec(K, points, charges, exact);
double tot_error_sq = 0;
double tot_norm_sq = 0;
double tot_ind_rel_err = 0;
double max_ind_rel_err = 0;
for (unsigned k = 0; k < result.size(); ++k) {
// Individual relative error
double rel_error = norm(exact[k] - result[k]) / norm(exact[k]);
tot_ind_rel_err += rel_error;
// Maximum relative error
max_ind_rel_err = std::max(max_ind_rel_err, rel_error);
// Total relative error
tot_error_sq += normSq(exact[k] - result[k]);
tot_norm_sq += normSq(exact[k]);
}
double tot_rel_err = sqrt(tot_error_sq/tot_norm_sq);
std::cout << "Vector relative error: " << tot_rel_err << std::endl;
double ave_rel_err = tot_ind_rel_err / result.size();
std::cout << "Average relative error: " << ave_rel_err << std::endl;
std::cout << "Maximum relative error: " << max_ind_rel_err << std::endl;
}
}
int main(int argc, char **argv)
{
int numBodies = 1000, p=5;
bool checkErrors = true;
double beta = 0.125;
FMMOptions opts = get_options(argc, argv);
// parse custom command line args
for (int i = 1; i < argc; ++i) {
if (strcmp(argv[i],"-N") == 0) {
i++;
numBodies = atoi(argv[i]);
} else if (strcmp(argv[i],"-p") == 0) {
i++;
p = atoi(argv[i]);
} else if (strcmp(argv[i],"-beta") == 0) {
i++;
beta = atof(argv[i]);
} else if (strcmp(argv[i],"-nocheck") == 0) {
checkErrors = false;
}
}
// Init the FMM Kernel
#ifdef SKELETON_KERNEL
typedef KernelSkeleton kernel_type;
kernel_type K;
#endif
#ifdef SPH_KERNEL
typedef LaplaceSpherical kernel_type;
kernel_type K(p);
#endif
#ifdef CART_KERNEL
typedef LaplaceCartesian<5> kernel_type;
kernel_type K;
#endif
#ifdef YUKAWA_KERNEL
typedef YukawaCartesian kernel_type;
kernel_type K(p,beta);
#endif
#ifdef YUKAWA_SPH
typedef YukawaSpherical kernel_type;
kernel_type K(p,beta);
#endif
#ifdef UNIT_KERNEL
typedef UnitKernel kernel_type;
kernel_type K;
#endif
#ifdef STOKES_SPH
typedef StokesSpherical kernel_type;
kernel_type K(p);
#endif
// if not using a Yukawa kernel, quiet warnings
#if !defined(YUKAWA_KERNEL) && !defined(YUKAWA_SPH)
(void) beta;
#endif
typedef kernel_type::point_type point_type;
typedef kernel_type::source_type source_type;
typedef kernel_type::target_type target_type;
typedef kernel_type::charge_type charge_type;
typedef kernel_type::result_type result_type;
// Init points and charges
std::vector<source_type> points(numBodies);
for (int k = 0; k < numBodies; ++k)
points[k] = source_type(drand(), drand(), drand());
//std::vector<point_type> target_points = points;
std::vector<charge_type> charges(numBodies);
for (int k = 0; k < numBodies; ++k) {
#if defined(STOKES_SPH)
#if defined(STRESSLET)
charges[k][0] = drand();
charges[k][1] = drand();
charges[k][2] = drand();
charges[k][3] = 1.;
charges[k][4] = 0.;
charges[k][5] = 0.;
#else
charges[k] = charge_type(1,1,1); // charge_type(drand(),drand(),drand());
#endif
#else
charges[k] = drand();
#endif
}
// Build the FMM
//fmm_plan plan = fmm_plan(K, bodies, opts);
FMM_plan<kernel_type> plan = FMM_plan<kernel_type>(K, points, opts);
// Execute the FMM
//fmm_execute(plan, charges, target_points);
std::vector<result_type> result = plan.execute(charges);
// Check the result
// TODO: More elegant
if (checkErrors) {
// choose a number of samples to use
int numSamples = std::min(numBodies, 1000);
std::vector<int> sample_map(numSamples);
std::vector<point_type> sample_targets(numSamples);
std::vector<result_type> exact(numSamples);
// sample the space (needs to be done better)
for (int i=0; i<numSamples; i++) {
int sample = i >> 15 % numBodies;
sample_map[i] = sample;
sample_targets[i] = points[sample];
}
// Compute the result with a direct matrix-vector multiplication
Direct::matvec(K, points.begin(), points.end(), charges.begin(),
sample_targets.begin(), sample_targets.end(), exact.begin());
#if defined(SPH_KERNEL) || defined(CART_KERNEL) || defined(YUKAWA_KERNEL)
result_type rdiff, rnorm;
for (unsigned k = 0; k < exact.size(); ++k) {
auto exact_val = exact[k];
auto fmm_val = result[sample_map[k]];
// printf("[%03d] exact: %lg, FMM: %lg\n", k, exact_val[0], fmm_val[0]);
rdiff += (fmm_val - exact_val) * (fmm_val - exact_val);
rnorm += exact_val * exact_val;
}
printf("Error (pot) : %.4e\n", sqrt(rdiff[0] / rnorm[0]));
printf("Error (acc) : %.4e\n", sqrt((rdiff[1]+rdiff[2]+rdiff[3]) /
(rnorm[1]+rnorm[2]+rnorm[3])));
#endif
#if defined(YUKAWA_SPH)
result_type rdiff = 0., rnorm = 0.;
for (unsigned k = 0; k < exact.size(); ++k) {
// printf("[%03d] exact: %lg, FMM: %lg\n", k, exact[k], result[k]);
auto exact_val = exact[k];
auto fmm_val = result[sample_map[k]];
rdiff = (fmm_val - exact_val) * (fmm_val - exact_val);
rnorm = exact_val * exact_val;
}
printf("Error (pot) : %.4e\n", sqrt(rdiff / rnorm));
#endif
#if defined(STOKES_SPH)
result_type rdiff = result_type(0.), rnorm = result_type(0.);
for (unsigned k = 0; k < exact.size(); ++k) {
auto exact_val = exact[k];
auto fmm_val = result[sample_map[k]];
// std::cout << exact_val << " : " << fmm_val << std::endl;
for (unsigned i=0; i < 3; i++) {
rdiff[i] += (fmm_val[i]-exact_val[i])*(fmm_val[i]-exact_val[i]);
rnorm[i] += exact_val[i]*exact_val[i];
}
}
auto div = rdiff/rnorm;
printf("Error (u) : %.4e, (v) : %.4e, (w) : %.4e\n",sqrt(div[0]),sqrt(div[1]),sqrt(div[2]));
#endif
#ifdef UNIT_KERNEL
int wrong_results = 0;
for (unsigned k = 0; k < exact.size(); ++k) {
auto exact_val = exact[k];
auto fmm_val = result[sample_map[k]];
// printf("[%03d] exact: %lg, FMM: %lg\n", k, exact[k], result[k]);
if ((exact_val - fmm_val) / exact_val > 1e-13)
++wrong_results;
}
printf("Wrong counts: %d\n", wrong_results);
#endif
}
}
Molecule C6H6()
{
int nAtoms = 12;
// These are in Angstrom
Eigen::Vector3d C1(5.274, 1.999, -8.568);
Eigen::Vector3d C2(6.627, 2.018, -8.209);
Eigen::Vector3d C3(7.366, 0.829, -8.202);
Eigen::Vector3d C4(6.752, -0.379, -8.554);
Eigen::Vector3d C5(5.399, -0.398, -8.912);
Eigen::Vector3d C6(4.660, 0.791, -8.919);
Eigen::Vector3d H1(4.704, 2.916, -8.573);
Eigen::Vector3d H2(7.101, 2.950, -7.938);
Eigen::Vector3d H3(8.410, 0.844, -7.926);
Eigen::Vector3d H4(7.322, -1.296, -8.548);
Eigen::Vector3d H5(4.925, -1.330, -9.183);
Eigen::Vector3d H6(3.616, 0.776, -9.196);
// Scale
C1 /= convertBohrToAngstrom;
C2 /= convertBohrToAngstrom;
C3 /= convertBohrToAngstrom;
C4 /= convertBohrToAngstrom;
C5 /= convertBohrToAngstrom;
C6 /= convertBohrToAngstrom;
H1 /= convertBohrToAngstrom;
H2 /= convertBohrToAngstrom;
H3 /= convertBohrToAngstrom;
H4 /= convertBohrToAngstrom;
H5 /= convertBohrToAngstrom;
H6 /= convertBohrToAngstrom;
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = C1.transpose();
geom.col(1) = C2.transpose();
geom.col(2) = C3.transpose();
geom.col(3) = C4.transpose();
geom.col(4) = C5.transpose();
geom.col(5) = C6.transpose();
geom.col(6) = H1.transpose();
geom.col(7) = H2.transpose();
geom.col(8) = H3.transpose();
geom.col(9) = H4.transpose();
geom.col(10) = H5.transpose();
geom.col(11) = H6.transpose();
Eigen::VectorXd charges(12), masses(12);
charges << 6.0, 6.0, 6.0, 6.0, 6.0, 6.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0;
masses << 12.00, 12.0, 12.0, 12.0, 12.0, 12.0, 1.0078250, 1.0078250, 1.0078250,
1.0078250, 1.0078250, 1.0078250;
double radiusC = 1.70 / convertBohrToAngstrom;
double radiusH = 1.20 / convertBohrToAngstrom;
std::vector<Atom> atoms;
atoms.push_back( Atom("Carbon", "C", charges(0), masses(0), radiusC, C1, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(1), masses(1), radiusC, C2, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(2), masses(2), radiusC, C3, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(3), masses(3), radiusC, C4, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(4), masses(4), radiusC, C5, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(5), masses(5), radiusC, C6, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(6), masses(6), radiusH, H1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(7), masses(7), radiusH, H2, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(8), masses(8), radiusH, H3, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(9), masses(9), radiusH, H4, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(10), masses(10), radiusH, H5, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(11), masses(11), radiusH, H6, 1.0) );
std::vector<Sphere> spheres;
Sphere sph1(C1, radiusC);
Sphere sph2(C2, radiusC);
Sphere sph3(C3, radiusC);
Sphere sph4(C4, radiusC);
Sphere sph5(C5, radiusC);
Sphere sph6(C6, radiusC);
Sphere sph7(H1, radiusH);
Sphere sph8(H2, radiusH);
Sphere sph9(H3, radiusH);
Sphere sph10(H4, radiusH);
Sphere sph11(H5, radiusH);
Sphere sph12(H6, radiusH);
spheres.push_back(sph1);
spheres.push_back(sph2);
spheres.push_back(sph3);
spheres.push_back(sph4);
spheres.push_back(sph5);
spheres.push_back(sph6);
spheres.push_back(sph7);
spheres.push_back(sph8);
spheres.push_back(sph9);
spheres.push_back(sph10);
spheres.push_back(sph11);
spheres.push_back(sph12);
// D2h as generated by Oxy, Oxz, Oyz
Symmetry pGroup = buildGroup(0, 0, 0, 0);
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
Molecule CO2()
{
int nAtoms = 3;
Eigen::Vector3d C1( 0.0000000000, 0.0000000000, 0.0000000000);
Eigen::Vector3d O1( 2.1316110791, 0.0000000000, 0.0000000000);
Eigen::Vector3d O2(-2.1316110791, 0.0000000000, 0.0000000000);
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = C1.transpose();
geom.col(1) = O1.transpose();
geom.col(2) = O2.transpose();
Eigen::Vector3d charges, masses;
charges << 6.0, 8.0, 8.0;
masses << 12.00, 15.9949150, 15.9949150;
std::vector<Atom> atoms;
double radiusC = (1.70 * 1.20) / convertBohrToAngstrom;
double radiusO = (1.52 * 1.20) / convertBohrToAngstrom;
atoms.push_back( Atom("Carbon", "C", charges(0), masses(0), radiusC, C1, 1.0) );
atoms.push_back( Atom("Oxygen", "O", charges(1), masses(1), radiusO, O1, 1.0) );
atoms.push_back( Atom("Oxygen", "O", charges(2), masses(2), radiusO, O2, 1.0) );
std::vector<Sphere> spheres;
Sphere sph1(C1, radiusC);
Sphere sph2(O1, radiusO);
Sphere sph3(O2, radiusO);
spheres.push_back(sph1);
spheres.push_back(sph2);
spheres.push_back(sph3);
enum pointGroup { pgC1, pgC2, pgCs, pgCi, pgD2, pgC2v, pgC2h, pgD2h };
Symmetry pGroup;
switch(group) {
case(pgC1):
pGroup = buildGroup(0, 0, 0, 0);
break;
case(pgC2):
// C2 as generated by C2z
pGroup = buildGroup(1, 3, 0, 0);
break;
case(pgCs):
// Cs as generated by Oyz
pGroup = buildGroup(1, 1, 0, 0);
break;
case(pgCi):
// Ci as generated by i
pGroup = buildGroup(1, 7, 0, 0);
break;
case(pgD2):
// D2 as generated by C2z and C2x
pGroup = buildGroup(2, 3, 6, 0);
break;
case(pgC2v):
// C2v as generated by Oyz and Oxz
pGroup = buildGroup(2, 1, 2, 0);
break;
case(pgC2h):
// C2h as generated by Oxy and i
pGroup = buildGroup(2, 4, 7, 0);
break;
case(pgD2h):
// D2h as generated by Oxy, Oxz and Oyz
pGroup = buildGroup(3, 4, 2, 1);
break;
default:
pGroup = buildGroup(0, 0, 0, 0);
break;
}
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
