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Merged
jeanlucf22 merged 1 commit into from
Mar 17, 2025
Merged

Code clean up #320

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1 change: 0 additions & 1 deletion src/HDFrestart.cc
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Expand Up @@ -2104,7 +2104,6 @@ int HDFrestart::readAtomicData(
stripLeadingAndTrailingBlanks(t);
// std::cout<<"stripped name="<<t<<std::endl;

assert(t.size() > 0);
data.push_back(t);
}

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45 changes: 21 additions & 24 deletions src/KBPsiMatrixSparse.cc
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Expand Up @@ -11,16 +11,15 @@

#include "Control.h"
#include "ExtendedGridOrbitals.h"
#include "Ions.h"
#include "LocGridOrbitals.h"
#include "MGmol_MPI.h"
#include "Mesh.h"
#include "ProjectedMatrices.h"
#include "ProjectedMatricesSparse.h"
#include "ReplicatedMatrix.h"
#include "SquareSubMatrix2DistMatrix.h"

#include <limits.h>

#define Ry2Ha 0.5;

Timer KBPsiMatrixSparse::global_sum_tm_("KBPsiMatrixSparse::global_sum");
Expand Down Expand Up @@ -133,7 +132,7 @@ void KBPsiMatrixSparse::globalSumKBpsi()
// Loop over the ions with projectors overlapping with local subdomain
// and evaluate <KB|psi> for some state.
template <class T>
void KBPsiMatrixSparse::computeKBpsi(Ions& ions, T& orbitals,
void KBPsiMatrixSparse::computeKBpsi(const Ions& ions, T& orbitals,
const int first_color, const int nb_colors, const bool flag)
{
assert(first_color >= 0);
Expand Down Expand Up @@ -189,7 +188,7 @@ void KBPsiMatrixSparse::computeKBpsi(Ions& ions, T& orbitals,
// Loop over the ions
if (gid != -1)
{
for (auto ion : ions.overlappingNL_ions())
for (const auto& ion : ions.overlappingNL_ions())
{
computeLocalElement(
*ion, gid, iloc, ppsi + color * ldsize, flag);
Expand All @@ -211,8 +210,8 @@ void KBPsiMatrixSparse::computeKBpsi(Ions& ions, T& orbitals,
compute_kbpsi_tm_.stop();
}

void KBPsiMatrixSparse::computeKBpsi(
Ions& ions, pb::GridFunc<ORBDTYPE>* phi, const int istate, const bool flag)
void KBPsiMatrixSparse::computeKBpsi(const Ions& ions,
pb::GridFunc<ORBDTYPE>* phi, const int istate, const bool flag)
{
assert(lapop_ != nullptr);
compute_kbpsi_tm_.start();
Expand All @@ -238,7 +237,7 @@ void KBPsiMatrixSparse::computeKBpsi(
for (int iloc = 0; iloc < subdivx; iloc++)
{
// Loop over the ions
for (auto ion : ions.overlappingNL_ions())
for (const auto& ion : ions.overlappingNL_ions())
{
computeLocalElement(*ion, istate, iloc, ppsi, flag);
}
Expand All @@ -251,7 +250,7 @@ void KBPsiMatrixSparse::computeKBpsi(

void KBPsiMatrixSparse::scaleWithKBcoeff(const Ions& ions)
{
for (auto ion : ions.overlappingNL_ions())
for (const auto& ion : ions.overlappingNL_ions())
{
std::vector<int> gids;
ion->getGidsNLprojs(gids);
Expand All @@ -266,8 +265,8 @@ void KBPsiMatrixSparse::scaleWithKBcoeff(const Ions& ions)

// loop over states to multiply kbpsi_[st][gid] and kbBpsi_[st][gid]
// by coeff
(*kbpsimat_).scaleRow(gid, coeff);
if (lapop_) (*kbBpsimat_).scaleRow(gid, coeff);
kbpsimat_->scaleRow(gid, coeff);
if (lapop_) kbBpsimat_->scaleRow(gid, coeff);
}
}
}
Expand Down Expand Up @@ -454,7 +453,7 @@ SquareSubMatrix<double> KBPsiMatrixSparse::computeHvnlMatrix(

// Loop over ions centered on current PE only
// (distribution of work AND Hvnlij contributions)
for (auto ion : ions.local_ions())
for (const auto& ion : ions.local_ions())
{
computeHvnlMatrix((KBPsiMatrixSparse*)kbpsi2, *ion, Aij);
}
Expand All @@ -473,7 +472,7 @@ void KBPsiMatrixSparse::computeHvnlMatrix(

// Loop over ions centered on current PE only
// (distribution of work AND Hvnlij contributions)
for (auto ion : ions.local_ions())
for (const auto& ion : ions.local_ions())
{
computeHvnlMatrix((KBPsiMatrixSparse*)kbpsi2, *ion, mat);
}
Expand Down Expand Up @@ -538,14 +537,14 @@ void KBPsiMatrixSparse::getPsiKBPsiSym(
{
// loop over all the ions
// parallelization over ions by including only those centered in subdomain
for (auto& ion : ions.local_ions())
for (const auto& ion : ions.local_ions())
{
getPsiKBPsiSym(*ion, sm);
}
}

template <class T>
void KBPsiMatrixSparse::computeAll(Ions& ions, T& orbitals)
void KBPsiMatrixSparse::computeAll(const Ions& ions, T& orbitals)
{
assert(count_proj_subdomain_ == ions.countProjectorsSubdomain());

Expand Down Expand Up @@ -603,7 +602,7 @@ double KBPsiMatrixSparse::getEvnl(
double trace = 0.0;
// loop over all the ions
// parallelization over ions by including only those centered in subdomain
for (auto& ion : ions.local_ions())
for (const auto& ion : ions.local_ions())
{
std::vector<int> gids;
ion->getGidsNLprojs(gids);
Expand All @@ -618,10 +617,9 @@ double KBPsiMatrixSparse::getEvnl(

/* gather trace result */
MGmol_MPI& mmpi = *(MGmol_MPI::instance());
MPI_Comm comm = mmpi.commSpin();

double evnl = 0.0;
MPI_Allreduce(&trace, &evnl, 1, MPI_DOUBLE, MPI_SUM, comm);
mmpi.allreduce(&trace, &evnl, 1, MPI_SUM);

return evnl * Ry2Ha;
}
Expand All @@ -637,7 +635,7 @@ double KBPsiMatrixSparse::getEvnl(const Ions& ions,
double trace = 0.0;
// loop over all the ions
// parallelization over ions by including only those centered in subdomain
for (auto& ion : ions.local_ions())
for (const auto& ion : ions.local_ions())
{
std::vector<int> gids;
ion->getGidsNLprojs(gids);
Expand All @@ -652,10 +650,9 @@ double KBPsiMatrixSparse::getEvnl(const Ions& ions,

/* gather trace result */
MGmol_MPI& mmpi = *(MGmol_MPI::instance());
MPI_Comm comm = mmpi.commSpin();

double evnl = 0.0;
MPI_Allreduce(&trace, &evnl, 1, MPI_DOUBLE, MPI_SUM, comm);
mmpi.allreduce(&trace, &evnl, 1, MPI_SUM);

return evnl * Ry2Ha;
}
Expand Down Expand Up @@ -736,12 +733,12 @@ double KBPsiMatrixSparse::getTraceDM(
return trace;
}

template void KBPsiMatrixSparse::computeKBpsi(Ions& ions,
template void KBPsiMatrixSparse::computeKBpsi(const Ions& ions,
LocGridOrbitals& orbitals, const int first_color, const int nb_colors,
const bool flag);
template void KBPsiMatrixSparse::computeAll(Ions&, LocGridOrbitals&);
template void KBPsiMatrixSparse::computeAll(const Ions&, LocGridOrbitals&);

template void KBPsiMatrixSparse::computeKBpsi(Ions& ions,
template void KBPsiMatrixSparse::computeKBpsi(const Ions& ions,
ExtendedGridOrbitals& orbitals, const int first_color, const int nb_colors,
const bool flag);
template void KBPsiMatrixSparse::computeAll(Ions&, ExtendedGridOrbitals&);
template void KBPsiMatrixSparse::computeAll(const Ions&, ExtendedGridOrbitals&);
15 changes: 6 additions & 9 deletions src/KBPsiMatrixSparse.h
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Expand Up @@ -12,7 +12,9 @@

#include "DataDistribution.h"
#include "DensityMatrixSparse.h"
#include "Ions.h"
#include "KBPsiMatrixInterface.h"
#include "ProjectedMatricesSparse.h"
#include "SquareSubMatrix.h"
#include "VariableSizeMatrix.h"

Expand All @@ -23,11 +25,6 @@
#include <cassert>
#include <limits.h>

class Ions;
class Ion;
class ProjectedMatricesInterface;
class ProjectedMatricesSparse;

class KBPsiMatrixSparse : public KBPsiMatrixInterface
{
static Timer global_sum_tm_;
Expand Down Expand Up @@ -79,8 +76,8 @@ class KBPsiMatrixSparse : public KBPsiMatrixInterface
void getPsiKBPsiSym(const Ions& ions, VariableSizeMatrix<sparserow>& sm);
void getPsiKBPsiSym(const Ion& ion, VariableSizeMatrix<sparserow>& sm);
template <class OrbitalsType>
void computeKBpsi(Ions& ions, OrbitalsType& orbitals, const int first_color,
const int nb_colors, const bool flag);
void computeKBpsi(const Ions& ions, OrbitalsType& orbitals,
const int first_color, const int nb_colors, const bool flag);
void clearData();

public:
Expand All @@ -105,7 +102,7 @@ class KBPsiMatrixSparse : public KBPsiMatrixInterface
double getEvnl(
const Ions& ions, ProjectedMatrices<MatrixType>* proj_matrices);
void computeKBpsi(
Ions& ions, pb::GridFunc<ORBDTYPE>*, const int, const bool flag);
const Ions& ions, pb::GridFunc<ORBDTYPE>*, const int, const bool flag);
double getValIonState(const int gid, const int st) const
{
return (*kbpsimat_).get_value(gid, st);
Expand All @@ -127,7 +124,7 @@ class KBPsiMatrixSparse : public KBPsiMatrixInterface
const Ions& ions, ProjectedMatricesInterface* proj_matrices) const;

template <class T>
void computeAll(Ions& ions, T& orbitals);
void computeAll(const Ions& ions, T& orbitals);
void setup(const Ions& ions);

double getTraceDM(
Expand Down
18 changes: 9 additions & 9 deletions src/MGmol.cc
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Expand Up @@ -358,8 +358,8 @@ int MGmol<OrbitalsType>::initial()
}

// Initialize the nuclear local potential and the compensating charges
if (ct.verbose > 0) printWithTimeStamp("initNuc()...", os_);
initNuc(*ions_);
if (ct.verbose > 0) printWithTimeStamp("setupPotentials()...", os_);
setupPotentials(*ions_);

// initialize Rho
if (ct.verbose > 0) printWithTimeStamp("Initialize Rho...", os_);
Expand Down Expand Up @@ -415,9 +415,6 @@ int MGmol<OrbitalsType>::initial()
current_orbitals_->checkCond(100000., ct.AtomsMove());
}

if (ct.verbose > 0) printWithTimeStamp("Setup kbpsi...", os_);
g_kbpsi_->setup(*ions_);

if (ct.restart_info == 0)
{
if (ct.verbose > 0) printWithTimeStamp("update_pot...", os_);
Expand Down Expand Up @@ -817,7 +814,7 @@ double get_trilinval(const double xc, const double yc, const double zc,
#endif

template <class OrbitalsType>
void MGmol<OrbitalsType>::initNuc(Ions& ions)
void MGmol<OrbitalsType>::setupPotentials(Ions& ions)
{
init_nuc_tm_.start();

Expand All @@ -829,9 +826,12 @@ void MGmol<OrbitalsType>::initNuc(Ions& ions)
// initialize poentials based on ionic positions and their species
pot.initialize(ions);

if (ct.verbose > 0) printWithTimeStamp("Setup kbpsi...", os_);
g_kbpsi_->setup(*ions_);

electrostat_->setupRhoc(pot.rho_comp());

if (onpe0 && ct.verbose > 3) os_ << " initNuc done" << std::endl;
if (onpe0 && ct.verbose > 3) os_ << " setupPotentials done" << std::endl;

init_nuc_tm_.stop();
}
Expand Down Expand Up @@ -1428,7 +1428,7 @@ double MGmol<OrbitalsType>::evaluateEnergyAndForces(Orbitals* orbitals,

ions_->setPositions(tau, atnumbers);

moveVnuc(*ions_);
setupPotentials(*ions_);

double eks = 0.;
OrbitalsType* dorbitals = dynamic_cast<OrbitalsType*>(orbitals);
Expand All @@ -1450,7 +1450,7 @@ double MGmol<OrbitalsType>::evaluateDMandEnergyAndForces(Orbitals* orbitals,

ions_->setPositions(tau, atnumbers);

moveVnuc(*ions_);
setupPotentials(*ions_);

// initialize electronic density
rho_->update(*dorbitals);
Expand Down
2 changes: 1 addition & 1 deletion src/MGmol.h
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Expand Up @@ -220,7 +220,7 @@ class MGmol : public MGmolInterface

void getAtomicNumbers(std::vector<short>& an);

void initNuc(Ions& ions);
void setupPotentials(Ions& ions);
void initKBR();

void printEigAndOcc();
Expand Down
2 changes: 1 addition & 1 deletion src/md.cc
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Expand Up @@ -59,7 +59,7 @@ void MGmol<OrbitalsType>::moveVnuc(Ions& ions)

// Update items that change when the ionic coordinates change
pot.axpVcompToVh(1.);
initNuc(ions);
setupPotentials(ions);
pot.axpVcompToVh(-1.);

proj_matrices_->setHiterativeIndex(-1, -1);
Expand Down
1 change: 0 additions & 1 deletion src/quench.cc
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Expand Up @@ -545,7 +545,6 @@ int MGmol<OrbitalsType>::quench(OrbitalsType& orbitals, Ions& ions,
// get actual indexes of stored functions
const std::vector<std::vector<int>>& gids(orbitals.getOverlappingGids());

g_kbpsi_->setup(*ions_);
electrostat_->setup(ct.vh_its);
rho_->setup(ct.getOrthoType(), gids);

Expand Down