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Fix a few more issues with class Ions #328

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Merged
jeanlucf22 merged 1 commit into from
Mar 26, 2025
Merged

Fix a few more issues with class Ions #328

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29 changes: 11 additions & 18 deletions src/Ions.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -109,14 +109,12 @@ Ions::Ions(const double lat[3], const std::vector<Species>& sp) : species_(sp)

Ions::Ions(const Ions& ions, const double shift[3]) : species_(ions.species_)
{
std::vector<Ion*>::const_iterator ion = ions.list_ions_.begin();
while (ion != ions.list_ions_.end())
for (const auto& ion : ions.list_ions_)
{
Ion* newion = new Ion(**ion);
Ion* newion = new Ion(*ion);
newion->shiftPosition(shift);
newion->setup();
list_ions_.push_back(newion);
ion++;
}
for (short i = 0; i < 3; ++i)
lattice_[i] = ions.lattice_[i];
Expand Down Expand Up @@ -2211,22 +2209,22 @@ void Ions::getLocalPositions(std::vector<double>& tau) const
void Ions::getLocalNames(std::vector<std::string>& names) const
{
names.clear();
for (auto& ion : local_ions_)
for (const auto& ion : local_ions_)
{
names.push_back(ion->name());
}
}

void Ions::getNames(std::vector<std::string>& names) const
{
names.clear();
for (auto& ion : list_ions_)
{
names.push_back(ion->name());
}
std::vector<std::string> local_names;
getLocalNames(local_names);

MGmol_MPI& mmpi = *(MGmol_MPI::instance());
mmpi.allGatherV(local_names, names);
}

void Ions::getPositions(std::vector<double>& tau)
void Ions::getPositions(std::vector<double>& tau) const
{
std::vector<double> tau_local(3 * local_ions_.size());

Expand All @@ -2236,10 +2234,9 @@ void Ions::getPositions(std::vector<double>& tau)
mmpi.allGatherV(tau_local, tau);
}

void Ions::getAtomicNumbers(std::vector<short>& atnumbers)
void Ions::getAtomicNumbers(std::vector<short>& atnumbers) const
{
std::vector<short> local_atnumbers;

for (auto& ion : local_ions_)
{
local_atnumbers.push_back(ion->atomic_number());
Expand All @@ -2249,15 +2246,11 @@ void Ions::getAtomicNumbers(std::vector<short>& atnumbers)
mmpi.allGatherV(local_atnumbers, atnumbers);
}

void Ions::getForces(std::vector<double>& forces)
void Ions::getForces(std::vector<double>& forces) const
{
std::vector<double> forces_local(3 * local_ions_.size());

getLocalForces(forces_local);

int n = getNumIons();
forces.resize(3 * n);

MGmol_MPI& mmpi = *(MGmol_MPI::instance());
mmpi.allGatherV(forces_local, forces);
}
Expand Down
6 changes: 3 additions & 3 deletions src/Ions.h
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Original file line number Diff line number Diff line change
Expand Up @@ -292,10 +292,10 @@ class Ions
void getLocalPositions(std::vector<double>& tau) const;
void getLocalNames(std::vector<std::string>& names) const;
void getNames(std::vector<std::string>& names) const;
void getPositions(std::vector<double>& tau);
void getAtomicNumbers(std::vector<short>& atnumbers);
void getPositions(std::vector<double>& tau) const;
void getAtomicNumbers(std::vector<short>& atnumbers) const;

void getForces(std::vector<double>& forces);
void getForces(std::vector<double>& forces) const;
void getLocalForces(std::vector<double>& tau) const;

/*!
Expand Down
31 changes: 25 additions & 6 deletions tests/testIons.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -107,6 +107,7 @@ int main(int argc, char** argv)
ions.getAtomicNumbers(anumbers);
if (myrank == 0)
{
std::cout << "Positions:" << std::endl;
int i = 0;
for (auto& position : positions)
{
Expand All @@ -121,7 +122,7 @@ int main(int argc, char** argv)
MPI_Barrier(MPI_COMM_WORLD);

// swap x and z
for (size_t i = 0; i < positions.size() - 2; i++)
for (size_t i = 0; i < positions.size() - 2; i += 3)
{
double x = positions[i];
double z = positions[i + 2];
Expand Down Expand Up @@ -162,11 +163,13 @@ int main(int argc, char** argv)
MPI_Barrier(MPI_COMM_WORLD);

std::vector<double> forces(3 * na);
// arbitrary value
const double fval = 1.12;
// set forces to a different arbitrary value for each component
int i = 0;
for (auto& f : forces)
f = fval;

{
f = (double)i;
i++;
}
ions.getNames(names);
ions.setLocalForces(forces, names);

Expand All @@ -177,13 +180,29 @@ int main(int argc, char** argv)
ions.getLocalForces(lforces);
for (auto& f : lforces)
{
if (std::abs(f - fval) > 1.e-14)
if (std::fmod(f, 1.) > 1.e-14)
{
std::cerr << "f = " << f << std::endl;
MPI_Abort(MPI_COMM_WORLD, EXIT_FAILURE);
}
}

ions.getForces(forces);
if (myrank == 0)
for (auto f0 = forces.begin(); f0 != forces.end(); f0++)
{
std::cout << "f0 = " << *f0 << std::endl;
for (auto f1 = f0 + 1; f1 != forces.end(); f1++)
{
// make sure each force component is different
if (std::abs(*f0 - *f1) < 1.e-14)
{
std::cerr << "f0 = " << *f0 << ", f1 = " << *f1
<< std::endl;
MPI_Abort(MPI_COMM_WORLD, EXIT_FAILURE);
}
}
}
mpirc = MPI_Finalize();
if (mpirc != MPI_SUCCESS)
{
Expand Down