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Clean up and fixes Ions #326

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

Clean up and fixes Ions #326

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2 changes: 2 additions & 0 deletions src/Ion.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,8 @@ unsigned short isqrt(unsigned value)
static unsigned int _nlproj_gid = 0;
static unsigned int _index = 0;

void Ion::resetIndexCount() { _index = 0; }

Ion::Ion(const Species& species, const std::string& name, const double crds[3],
const double velocity[3], const bool lock)
: name_(name), species_(species), index_(_index), nlproj_gid_(_nlproj_gid)
Expand Down
2 changes: 2 additions & 0 deletions src/Ion.h
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Original file line number Diff line number Diff line change
Expand Up @@ -314,6 +314,8 @@ class Ion
void getKBcoeffs(std::vector<double>& coeffs);
double energyDiff(
Ion& ion, const double lattice[3], const short bc[3]) const;

static void resetIndexCount();
};

#endif
109 changes: 40 additions & 69 deletions src/Ions.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@

#include "Ions.h"
#include "Control.h"
#include "HDFrestart.h"
#include "MGmol_MPI.h"
#include "MGmol_blas1.h"
#include "MPIdata.h"
Expand All @@ -20,13 +19,10 @@
#include "mgmol_mpi_tools.h"
#include "tools.h"

#include <mpi.h>

#include <cmath>
#include <iostream>
#include <iterator>
#include <list>
#include <map>
#include <mpi.h>

Timer ions_setupInteractingIons_tm("ions_setupInteractingIons");
Timer ions_setup_tm("ions::setup");
Expand Down Expand Up @@ -187,6 +183,8 @@ void Ions::setup()

ions_setup_tm.start();

Ion::resetIndexCount();

updateListIons();

//#ifndef NDEBUG
Expand Down Expand Up @@ -394,7 +392,7 @@ void Ions::iiforce(const short bc[3])

std::vector<Ion*>::const_iterator ion1 = local_ions_.begin();
int ion1_index = 0;
;

while (ion1 != local_ions_.end())
{
const double z1 = (*ion1)->getZion();
Expand Down Expand Up @@ -1800,7 +1798,7 @@ int Ions::readAtomsFromXYZ(
}

int Ions::setAtoms(
const std::vector<double>& crds, const std::vector<short>& spec)
const std::vector<double>& crds, const std::vector<short>& anum)
{
const int natoms = crds.size() / 3;

Expand All @@ -1813,7 +1811,7 @@ int Ions::setAtoms(
while (it != species_.end())
{
++isp;
if (it->getAtomicNumber() == spec[ia])
if (it->getAtomicNumber() == anum[ia])
{
break;
}
Expand All @@ -1823,7 +1821,7 @@ int Ions::setAtoms(
for (std::map<std::string, short>::iterator itr = map_species_.begin();
itr != map_species_.end(); ++itr)
{
if (itr->second == spec[ia])
if (itr->second == anum[ia])
{
spname = itr->first;
break;
Expand All @@ -1833,7 +1831,7 @@ int Ions::setAtoms(
{
(*MPIdata::serr) << "Ions::setAtoms() --- ERROR: unknown "
"species for atomic number "
<< spec[ia] << std::endl;
<< anum[ia] << std::endl;
return -1;
}

Expand Down Expand Up @@ -2212,6 +2210,7 @@ void Ions::getLocalPositions(std::vector<double>& tau) const

void Ions::getLocalNames(std::vector<std::string>& names) const
{
names.clear();
for (auto& ion : local_ions_)
{
names.push_back(ion->name());
Expand All @@ -2220,6 +2219,7 @@ void Ions::getLocalNames(std::vector<std::string>& names) const

void Ions::getNames(std::vector<std::string>& names) const
{
names.clear();
for (auto& ion : list_ions_)
{
names.push_back(ion->name());
Expand Down Expand Up @@ -2513,7 +2513,6 @@ void Ions::gatherLockedNames(
std::vector<std::string>& names, const int root, const MPI_Comm comm) const
{
std::vector<std::string> local_names;

for (auto& ion : local_ions_)
{
if (ion->locked()) local_names.push_back(ion->name());
Expand All @@ -2533,7 +2532,6 @@ void Ions::gatherIndexes(
std::vector<int>& indexes, const int root, const MPI_Comm comm) const
{
std::vector<int> local_indexes;

for (auto& ion : local_ions_)
{
local_indexes.push_back(ion->index());
Expand All @@ -2553,7 +2551,6 @@ void Ions::gatherNLprojIds(
std::vector<int>& nlprojids, const int root, const MPI_Comm comm) const
{
std::vector<int> local_nlprojids;

for (auto& ion : local_ions_)
{
local_nlprojids.push_back(ion->nlprojid());
Expand All @@ -2573,7 +2570,6 @@ void Ions::gatherAtomicNumbers(
std::vector<int>& atnumbers, const int root, const MPI_Comm comm) const
{
std::vector<int> local_atnumbers;

for (auto& ion : local_ions_)
{
local_atnumbers.push_back(ion->atomic_number());
Expand All @@ -2593,7 +2589,6 @@ void Ions::gatherRandStates(std::vector<unsigned short>& rstates,
const int root, const MPI_Comm comm) const
{
std::vector<unsigned short> local_rstates;

for (auto& ion : local_ions_)
{
local_rstates.push_back(ion->randomState(0));
Expand All @@ -2615,10 +2610,8 @@ void Ions::gatherPositions(
std::vector<double>& positions, const int root, const MPI_Comm comm) const
{
std::vector<double> local_positions;

for (auto& ion : local_ions_)
{
// get position of local ion
double position[3];
ion->getPosition(&position[0]);
local_positions.push_back(position[0]);
Expand All @@ -2640,7 +2633,6 @@ void Ions::gatherPreviousPositions(
std::vector<double>& positions, const int root, const MPI_Comm comm) const
{
std::vector<double> local_positions;

for (auto& ion : local_ions_)
{
local_positions.push_back(ion->getPreviousPosition(0));
Expand All @@ -2662,17 +2654,14 @@ void Ions::gatherForces(
std::vector<double>& forces, const int root, const MPI_Comm comm) const
{
std::vector<double> local_forces;

for (auto& ion : local_ions_)
{
// get position of local ion
double force[3];
ion->getForce(&force[0]);
local_forces.push_back(force[0]);
local_forces.push_back(force[1]);
local_forces.push_back(force[2]);
}

// gather data to PE root
std::vector<double> data;
mgmol_tools::gatherV(local_forces, data, root, comm);
Expand All @@ -2687,7 +2676,6 @@ void Ions::gatherVelocities(
std::vector<double>& velocities, const int root, const MPI_Comm comm) const
{
std::vector<double> local_velocities;

for (auto& ion : local_ions_)
{
local_velocities.push_back(ion->velocity(0));
Expand All @@ -2711,13 +2699,10 @@ void Ions::gatherPositions(std::vector<double>& positions, const int root) const

positions.resize(3 * num_ions_, 0.);

std::vector<Ion*>::const_iterator ion = local_ions_.begin();
while (ion != local_ions().end())
for (auto& ion : local_ions_)
{
// get local positions
const int index = (*ion)->index();
(*ion)->getPosition(&positions[3 * index]);
++ion;
const int index = ion->index();
ion->getPosition(&positions[3 * index]);
}

// gather data to PE root
Expand All @@ -2726,17 +2711,17 @@ void Ions::gatherPositions(std::vector<double>& positions, const int root) const

void Ions::gatherForces(std::vector<double>& forces, const int root) const
{
assert(num_ions_ > 0);

MGmol_MPI& mmpi(*(MGmol_MPI::instance()));

forces.resize(3 * num_ions_, 0.);

std::vector<Ion*>::const_iterator ion = local_ions_.begin();
while (ion != local_ions().end())
for (auto& ion : local_ions_)
{
// get local forces
const int index = (*ion)->index();
(*ion)->getForce(&forces[3 * index]);
ion++;
const int index = ion->index();
assert(forces.size() >= 3 * index);
assert(index < num_ions_);
ion->getForce(&forces[3 * index]);
}

// gather data to PE root
Expand All @@ -2749,15 +2734,10 @@ void Ions::gatherLockedData(std::vector<int>& locked_data, const int root) const
MGmol_MPI& mmpi(*(MGmol_MPI::instance()));

locked_data.resize(num_ions_, 0);

std::vector<Ion*>::const_iterator ion = local_ions_.begin();
while (ion != local_ions().end())
for (auto& ion : local_ions_)
{
// get local ion index
const int index = (*ion)->index();
if ((*ion)->locked()) locked_data[index] = 1;

++ion;
const int index = ion->index();
if (ion->locked()) locked_data[index] = 1;
}

// gather data to PE root
Expand Down Expand Up @@ -3214,11 +3194,9 @@ void Ions::updateTaupInteractingIons()
void Ions::clearLists()
{
local_ions_.clear();
std::vector<Ion*>::iterator ion = list_ions_.begin();
while (ion != list_ions_.end())
for (auto& ion : list_ions_)
{
delete *ion;
ion++;
delete ion;
}
list_ions_.clear();
}
Expand Down Expand Up @@ -3335,24 +3313,21 @@ void Ions::initStepperData()
{
clearStepperData();

std::vector<Ion*>::iterator lion = local_ions_.begin();
while (lion != local_ions_.end())
for (auto& lion : local_ions_)
{
local_names_.push_back((*lion)->name());
atmove_.push_back(!(*lion)->locked());
pmass_.push_back((*lion)->getMass());
gids_.push_back((*lion)->index());
local_names_.push_back(lion->name());
atmove_.push_back(!lion->locked());
pmass_.push_back(lion->getMass());
gids_.push_back(lion->index());

for (short i = 0; i < 3; i++)
{
taum_.push_back((*lion)->getPreviousPosition(i));
tau0_.push_back((*lion)->position(i));
fion_.push_back((*lion)->force(i));
velocity_.push_back((*lion)->velocity(i));
rand_states_.push_back((*lion)->randomState(i));
taum_.push_back(lion->getPreviousPosition(i));
tau0_.push_back(lion->position(i));
fion_.push_back(lion->force(i));
velocity_.push_back(lion->velocity(i));
rand_states_.push_back(lion->randomState(i));
}

lion++;
}
// initialize taup to enable computing velocities
int size_tau = (int)tau0_.size();
Expand Down Expand Up @@ -3399,11 +3374,9 @@ void Ions::updateIons()
void Ions::shiftIons(const Vector3D& shift)
{
// update local_ions data
std::vector<Ion*>::iterator ion = local_ions_.begin();
while (ion != local_ions_.end())
for (auto& ion : local_ions_)
{
(*ion)->shiftPositionXLBOMDTest(shift);
ion++;
ion->shiftPositionXLBOMDTest(shift);
}

// update various list of ions
Expand All @@ -3421,12 +3394,10 @@ void Ions::rescaleVelocities(const double factor)
std::cout << "Ions::rescaleVelocities() with factor " << factor
<< std::endl;
}
std::vector<Ion*>::iterator ion = local_ions_.begin();
while (ion != local_ions_.end())
{
(*ion)->rescaleVelocity(factor);

ion++;
for (auto& ion : local_ions_)
{
ion->rescaleVelocity(factor);
}
}

Expand Down
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