Skip to content

Commit

Permalink
Partial migration from range-v3 to std::ranges (#452)
Browse files Browse the repository at this point in the history
  • Loading branch information
@mlund
mlund authored Jul 4, 2024
1 parent 4abb330 commit 15c1f28
Show file tree
Hide file tree
Showing 35 changed files with 318 additions and 344 deletions.
10 changes: 0 additions & 10 deletions .idea/inspectionProfiles/Project_Default.xml
View file

This file was deleted.

11 changes: 6 additions & 5 deletions src/actions.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
#include "io.h"
#include "aux/arange.h"
#include <progress_tracker.h>
#include <ranges>
#include <range/v3/view/concat.hpp>

namespace Faunus {
Expand Down Expand Up @@ -49,7 +50,7 @@ AngularScan::AngularScan(const json& j, const Space& spc)
*/
void AngularScan::Molecule::initialize(const Space::GroupVector& groups, int molecule_index)
{
namespace rv = ranges::cpp20::views;
namespace rv = std::views;
index = molecule_index;
const auto& group = groups.at(index);
if (group.isAtomic()) {
Expand All @@ -66,7 +67,7 @@ void AngularScan::Molecule::initialize(const Space::GroupVector& groups, int mol
ParticleVector AngularScan::Molecule::getRotatedReference(const Space::GroupVector& groups,
const Eigen::Quaterniond& q)
{
namespace rv = ranges::cpp20::views;
namespace rv = std::views;
const auto& group = groups.at(index);
auto particles = ParticleVector(group.begin(), group.end()); // copy particles from Space
auto positions =
Expand Down Expand Up @@ -94,8 +95,8 @@ void AngularScan::report(const Group& group1, const Group& group2, const Eigen::
*stream << format(q1) << format(q2)
<< fmt::format("{:8.4f} {:>10.3E}\n", group2.mass_center.z(), energy / 1.0_kJmol);
if (trajectory) {
auto positions = ranges::views::concat(group1, group2) |
ranges::cpp20::views::transform(&Particle::pos);
auto positions =
ranges::views::concat(group1, group2) | std::views::transform(&Particle::pos);
trajectory->writeNext({500, 500, 500}, positions.begin(), positions.end());
}
}
Expand Down Expand Up @@ -127,7 +128,7 @@ void AngularScan::operator()(Space& spc, Energy::Hamiltonian& hamiltonian)
const auto q2 =
q_dihedral * q_body2; // simultaneous rotations (non-commutative)
auto particles2 = molecules.second.getRotatedReference(spc.groups, q2);
ranges::cpp20::for_each(particles2, translate);
std::ranges::for_each(particles2, translate);
auto group2 = Group(0, particles2.begin(), particles2.end());
group2.mass_center = {0.0, 0.0, z_pos};
report(group1, group2, q1, q2, *nonbonded);
Expand Down
101 changes: 52 additions & 49 deletions src/analysis.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -385,7 +385,7 @@ void SystemEnergy::createOutputStream()
*output_stream << "#";
}
*output_stream << fmt::format("{:>9}{}{:12}", "step", separator, "total");
ranges::for_each(hamiltonian, [&](auto& energy) {
std::ranges::for_each(hamiltonian, [&](auto& energy) {
*output_stream << fmt::format("{}{:12}", separator, energy->name);
});
*output_stream << "\n";
Expand All @@ -405,7 +405,7 @@ std::vector<double> SystemEnergy::calculateEnergies() const
{
Change change;
change.everything = true; // trigger full energy calculation
return hamiltonian | ranges::views::transform([&](auto& i) { return i->energy(change); }) |
return hamiltonian | std::views::transform([&](auto& i) { return i->energy(change); }) |
ranges::to_vector;
}

Expand Down Expand Up @@ -540,7 +540,7 @@ GroupMatrixAnalysis::GroupMatrixAnalysis(const json& j, const Space& spc,
Energy::Hamiltonian& hamiltonian)
: PairMatrixAnalysis(j, spc)
{
namespace rv = ranges::cpp20::views;
namespace rv = std::views;
// finds the molecule ids and store their indices
auto molids = Faunus::parseMolecules(j.at("molecules"));
auto is_selected = [&](const auto& group) {
Expand All @@ -562,8 +562,7 @@ GroupMatrixAnalysis::GroupMatrixAnalysis(const json& j, const Space& spc,
void GroupMatrixAnalysis::setPairMatrix()
{
auto is_active = [&](auto index) { return !spc.groups.at(index).empty(); };
const auto indices =
group_indices | ranges::cpp20::views::filter(is_active) | ranges::to_vector;
const auto indices = group_indices | std::views::filter(is_active) | ranges::to_vector;

// zero matrix, then fill it
pair_matrix.setZero();
Expand Down Expand Up @@ -1090,7 +1089,7 @@ AtomicDisplacement::AtomicDisplacement(const json& j, const Space& spc, std::str
molid = molecule_data.id();

auto positions = getPositions();
const auto num_positions = ranges::cpp20::distance(positions.begin(), positions.end());
const auto num_positions = std::ranges::distance(positions.begin(), positions.end());
reference_positions = positions | ranges::to_vector;
cell_indices.resize(num_positions, {0, 0, 0});
mean_squared_displacement.resize(num_positions);
Expand Down Expand Up @@ -1191,7 +1190,7 @@ void AtomicDisplacement::_to_disk()
PointVector AtomicDisplacement::getPositions() const
{
auto active_and_inactive = [&](const Group& group) {
return ranges::make_subrange(group.begin(), group.trueend());
return std::ranges::subrange(group.begin(), group.trueend());
};
namespace rv = ranges::cpp20::views;
return spc.findMolecules(molid, Space::Selection::ALL) | rv::transform(active_and_inactive) |
Expand All @@ -1211,7 +1210,7 @@ MassCenterDisplacement::MassCenterDisplacement(const json& j, const Space& spc,

PointVector MassCenterDisplacement::getPositions() const
{
namespace rv = ranges::cpp20::views;
namespace rv = std::views;
return spc.findMolecules(molid, Space::Selection::ACTIVE) | rv::transform(&Group::mass_center) |
ranges::to<PointVector>;
}
Expand All @@ -1227,7 +1226,7 @@ void WidomInsertion::selectGhostGroup()
{
change.clear();
auto inactive_groups = spc.findMolecules(molid, Space::Selection::INACTIVE);
if (!ranges::cpp20::empty(inactive_groups)) {
if (!std::ranges::empty(inactive_groups)) {
const auto& group = *inactive_groups.begin(); // select first group
if (group.empty() && group.capacity() > 0) {
// must be inactive and have a non-zero capacity
Expand Down Expand Up @@ -1384,7 +1383,7 @@ void AtomDensity::_sample()
const auto& atomic_ids = reaction.participatingAtomsAndMolecules().first;
unique_reactive_atoms.insert(atomic_ids.begin(), atomic_ids.end());
}
ranges::cpp20::for_each(unique_reactive_atoms, [&](auto id) {
std::ranges::for_each(unique_reactive_atoms, [&](auto id) {
const auto count = spc.countAtoms(id);
atomswap_probability_density[id](count)++;
});
Expand All @@ -1395,21 +1394,23 @@ void AtomDensity::_sample()
*/
std::map<Density::id_type, int> AtomDensity::count() const
{
namespace rv = ranges::cpp20::views;
using ranges::cpp20::views::filter;
using ranges::cpp20::views::join;
using ranges::cpp20::views::transform;

// All ids incl. inactive are counted; std::vector ensures constant lookup (index = id)
std::vector<int> atom_count(names.size(), 0);

// Count number of active atoms in atomic groups
auto particle_ids_in_atomic_groups =
spc.groups | rv::filter(&Group::isAtomic) | rv::join | rv::transform(&Particle::id);
ranges::cpp20::for_each(particle_ids_in_atomic_groups, [&](auto id) { atom_count.at(id)++; });
spc.groups | filter(&Group::isAtomic) | join | transform(&Particle::id);
std::ranges::for_each(particle_ids_in_atomic_groups, [&](auto id) { atom_count.at(id)++; });

// Copy vector --> map
id_type id = 0U;
std::map<id_type, int> map;
ranges::cpp20::for_each(atom_count,
[&id, &map](auto count) { map.emplace_hint(map.end(), id++, count); });
std::ranges::for_each(atom_count,
[&id, &map](auto count) { map.emplace_hint(map.end(), id++, count); });
return map;
}

Expand Down Expand Up @@ -1442,20 +1443,20 @@ void AtomDensity::_to_disk()
*/
std::map<Density::id_type, int> MoleculeDensity::count() const
{
using namespace ranges::cpp20;
using std::views::transform;
using std::views::filter;
std::map<id_type, int> molecular_group_count;

// ensure that also inactive groups are registered (as zero)
for_each(Faunus::molecules | views::filter(&MoleculeData::isMolecular),
[&](auto& moldata) { molecular_group_count[moldata.id()] = 0; });
std::ranges::for_each(Faunus::molecules | filter(&MoleculeData::isMolecular),
[&](auto& moldata) { molecular_group_count[moldata.id()] = 0; });

auto non_empty_molecular = [](const Group& group) {
return group.isMolecular() && !group.empty();
};
auto molecular_group_ids =
spc.groups | views::filter(non_empty_molecular) | views::transform(&Group::id);
auto molecular_group_ids = spc.groups | filter(non_empty_molecular) | transform(&Group::id);

for_each(molecular_group_ids, [&](auto id) { molecular_group_count[id]++; });
std::ranges::for_each(molecular_group_ids, [&](auto id) { molecular_group_count[id]++; });
return molecular_group_count;
}

Expand Down Expand Up @@ -1506,7 +1507,7 @@ void SanityCheck::checkGroupsCoverParticles()
void SanityCheck::checkWithinContainer(const Space::GroupType& group)
{
bool outside_simulation_cell = false;
auto outside_particles = group | ranges::cpp20::views::filter([&](const Particle& particle) {
auto outside_particles = group | std::views::filter([&](const Particle& particle) {
return spc.geometry.collision(particle.pos);
});

Expand Down Expand Up @@ -1703,15 +1704,19 @@ XTCtraj::XTCtraj(const Space& spc, const std::string& filename,
const std::vector<std::string>& molecule_names)
: Analysis(spc, "xtcfile")
{
namespace rv = ranges::cpp20::views;
using ranges::cpp20::views::filter;
using ranges::cpp20::views::join;
using ranges::cpp20::views::transform;
using ranges::views::cache1;

writer = std::make_unique<XTCWriter>(filename);
if (!molecule_names.empty()) {
group_ids = Faunus::names2ids(Faunus::molecules, molecule_names); // molecule types to save
group_indices =
group_ids |
rv::transform([&](auto id) { return spc.findMolecules(id, Space::Selection::ALL); }) |
ranges::views::cache1 | rv::join |
rv::transform([&](const Group& group) { return spc.getGroupIndex(group); }) |
transform([&](auto id) { return spc.findMolecules(id, Space::Selection::ALL); }) |
cache1 | join |
transform([&](const Group& group) { return spc.getGroupIndex(group); }) |
ranges::to_vector;
if (group_indices.empty()) {
throw ConfigurationError("xtc selection is empty - nothing to sample");
Expand All @@ -1732,7 +1737,7 @@ void XTCtraj::_to_json(json& j) const
if (!group_ids.empty()) {
j["molecules"] =
group_ids |
ranges::cpp20::views::transform([](auto id) { return Faunus::molecules.at(id).name; }) |
std::views::transform([](auto id) { return Faunus::molecules.at(id).name; }) |
ranges::to_vector;
}
}
Expand All @@ -1744,7 +1749,7 @@ void XTCtraj::_sample()
{
namespace rv = ranges::cpp20::views;
if (group_ids.empty()) {
auto positions = spc.particles | rv::transform(&Particle::pos);
auto positions = spc.particles | std::views::transform(&Particle::pos);
writer->writeNext(spc.geometry.getLength(), positions.begin(), positions.end());
}
else {
Expand Down Expand Up @@ -1895,7 +1900,7 @@ void InertiaTensor::_to_json(json& j) const
std::pair<Point, Point> InertiaTensor::compute() const
{
const auto& group = spc.groups.at(group_index);
auto subgroup = ranges::make_subrange(group.begin() + particle_range.at(0),
auto subgroup = std::ranges::subrange(group.begin() + particle_range.at(0),
group.begin() + particle_range.at(1) + 1);

auto I = Geometry::inertia(subgroup.begin(), subgroup.end(), group.mass_center,
Expand Down Expand Up @@ -2323,11 +2328,11 @@ void AtomsInMoleculePolicy::sample(const Space& spc, SASAAnalysis& analysis)
{

auto molecules = spc.findMolecules(molecule_id);
ranges::for_each(molecules, [&](const auto& molecule) {
std::ranges::for_each(molecules, [&](const auto& molecule) {
auto is_selected = [&](const Particle& particle) {
return selected_indices.count(molecule.getParticleIndex(particle)) > 0;
};
auto selected_atoms = molecule | ranges::cpp20::views::filter(is_selected);
auto selected_atoms = molecule | std::views::filter(is_selected);
sampleTotalSASA(selected_atoms.begin(), selected_atoms.end(), analysis);
});
}
Expand Down Expand Up @@ -2396,7 +2401,7 @@ void AtomProfile::_sample()
}

auto selected_particles =
spc.activeParticles() | ranges::cpp20::views::filter([&](const Particle& particle) {
spc.activeParticles() | std::views::filter([&](const Particle& particle) {
return atom_id_selection.count(particle.id) > 0;
});

Expand Down Expand Up @@ -2485,7 +2490,7 @@ void SlicedDensity::_sample()
}

auto filtered_particles =
spc.activeParticles() | ranges::cpp20::views::filter([&](const auto& particle) {
spc.activeParticles() | std::views::filter([&](const auto& particle) {
return std::find(atom_ids.begin(), atom_ids.end(), particle.id) != atom_ids.end();
});

Expand Down Expand Up @@ -2553,29 +2558,28 @@ std::vector<std::string> ChargeFluctuations::getPredominantParticleNames() const
return Faunus::atoms[atomid].name;
}; // in a histogram, find the atom name with most counts

auto atom_names = atom_histograms | ranges::cpp20::views::transform(most_frequent_name);
return std::vector<std::string>(ranges::cpp20::begin(atom_names),
ranges::cpp20::end(atom_names));
auto atom_names = atom_histograms | std::views::transform(most_frequent_name);
return std::vector<std::string>(std::ranges::begin(atom_names), std::ranges::end(atom_names));
}

std::vector<double> ChargeFluctuations::getChargeStandardDeviation() const
{
auto stdev =
atom_mean_charges | ranges::cpp20::views::transform([](auto& i) { return i.stdev(); });
return std::vector<double>(ranges::cpp20::begin(stdev), ranges::cpp20::end(stdev));
using namespace std::ranges;
auto stdev = atom_mean_charges | views::transform([](auto& i) { return i.stdev(); });
return std::vector<double>(begin(stdev), end(stdev));
}

std::vector<double> ChargeFluctuations::getMeanCharges() const
{
return std::vector<double>(ranges::cpp20::begin(atom_mean_charges),
ranges::cpp20::end(atom_mean_charges));
return std::vector<double>(std::ranges::begin(atom_mean_charges),
std::ranges::end(atom_mean_charges));
}

void ChargeFluctuations::_to_disk()
{
if (not filename.empty()) {
auto molecules = spc.findMolecules(mol_iter->id(), Space::Selection::ALL);
if (not ranges::cpp20::empty(molecules)) {
if (not std::ranges::empty(molecules)) {
const auto particles_with_avg_charges = averageChargeParticles(*molecules.begin());
PQRWriter().save(MPI::prefix + filename, particles_with_avg_charges.begin(),
particles_with_avg_charges.end(), spc.geometry.getLength());
Expand Down Expand Up @@ -2667,7 +2671,8 @@ void ScatteringFunction::_sample()
scatter_positions.clear();
auto groups =
molecule_ids | rv::transform([&](auto id) { return spc.findMolecules(id); }) | rv::join;
ranges::cpp20::for_each(groups, [&](auto& group) {

std::ranges::for_each(groups, [&](auto& group) {
if (mass_center_scattering && group.isMolecular()) {
scatter_positions.push_back(group.mass_center);
}
Expand Down Expand Up @@ -2809,8 +2814,8 @@ void VirtualTranslate::_sample()
return;
}
if (auto mollist = mutable_space.findMolecules(molid, Space::Selection::ACTIVE);
!ranges::cpp20::empty(mollist)) {
if (ranges::distance(mollist.begin(), mollist.end()) > 1) {
!std::ranges::empty(mollist)) {
if (std::ranges::distance(mollist.begin(), mollist.end()) > 1) {
throw std::runtime_error("exactly ONE active molecule expected");
}
if (auto group_it = random.sample(mollist.begin(), mollist.end()); not group_it->empty()) {
Expand Down Expand Up @@ -3004,8 +3009,7 @@ void ElectricPotential::getTargets(const json& j)
if (structure->is_string()) {
// load positions from chemical structure file
auto particles = loadStructure(structure->get<std::string>(), false);
positions =
particles | ranges::cpp20::views::transform(&Particle::pos) | ranges::to_vector;
positions = particles | std::views::transform(&Particle::pos) | ranges::to_vector;
}
else if (structure->is_array()) {
// list of positions
Expand Down Expand Up @@ -3049,8 +3053,7 @@ double ElectricPotential::calcPotentialOnTarget(const ElectricPotential::Target&
std::sqrt(spc.geometry.sqdist(particle.pos, target.position));
return coulomb->getCoulombGalore().ion_potential(particle.charge, distance_to_target);
};
auto potentials =
spc.activeParticles() | ranges::cpp20::views::transform(potential_from_particle);
auto potentials = spc.activeParticles() | std::views::transform(potential_from_particle);
return std::accumulate(potentials.begin(), potentials.end(), 0.0);
}

Expand Down
Loading

0 comments on commit 15c1f28

Please sign in to comment.