From 14f2d6a58aa0be0deace84cdc31eb700ad002214 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Mon, 13 Jun 2022 10:13:29 +0200
Subject: [PATCH] Code Quality: PVS Studio Finds (#1901)
Fix a number of small issues regarding performance and correctness found by PVS Studio in the quest for a better code base.
---
arbor/backends/event.hpp | 2 +-
.../backends/multicore/multi_event_stream.hpp | 2 +-
arbor/benchmark_cell_group.cpp | 2 +-
arbor/communication/communicator.hpp | 2 +-
arbor/domain_decomposition.cpp | 7 +-
arbor/event_queue.hpp | 2 +-
arbor/fvm_layout.cpp | 88 +++++++++----------
arbor/fvm_layout.hpp | 6 +-
arbor/fvm_lowered_cell_impl.hpp | 15 ++--
arbor/include/arbor/mechanism.hpp | 2 +-
arbor/include/arbor/morph/embed_pwlin.hpp | 12 +--
arbor/include/arbor/morph/mcable_map.hpp | 6 +-
arbor/include/arbor/morph/primitives.hpp | 4 +-
arbor/include/arbor/morph/region.hpp | 2 +-
arbor/include/arbor/s_expr.hpp | 1 +
arbor/include/arbor/simd/simd.hpp | 4 +-
arbor/include/arbor/util/any_ptr.hpp | 2 +-
arbor/include/arbor/util/expected.hpp | 2 +-
arbor/include/arbor/util/scope_exit.hpp | 2 +-
arbor/lif_cell_group.cpp | 4 +-
arbor/mc_cell_group.cpp | 2 +-
arbor/mechcat.cpp | 9 +-
arbor/memory/allocator.hpp | 6 +-
arbor/memory/array_view.hpp | 4 +-
arbor/morph/embed_pwlin.cpp | 12 +--
arbor/morph/locset.cpp | 16 ++--
arbor/morph/place_pwlin.cpp | 6 +-
arbor/morph/region.cpp | 33 ++++---
arbor/partition_load_balance.cpp | 9 +-
arbor/s_expr.cpp | 4 +-
arbor/simulation.cpp | 13 ++-
arbor/thread_private_spike_store.cpp | 17 ++--
arbor/thread_private_spike_store.hpp | 2 +-
arbor/util/padded_alloc.hpp | 2 +-
arbor/util/piecewise.hpp | 2 +-
arbor/util/unwind.cpp | 2 -
arbor/util/unwind.hpp | 2 +-
arborio/cableio.cpp | 30 ++++---
arborio/neurolucida.cpp | 10 +--
sup/include/sup/ioutil.hpp | 2 +-
40 files changed, 167 insertions(+), 183 deletions(-)
diff --git a/arbor/backends/event.hpp b/arbor/backends/event.hpp
index d6656102..d17792ab 100644
--- a/arbor/backends/event.hpp
+++ b/arbor/backends/event.hpp
@@ -15,7 +15,7 @@ struct target_handle {
cell_local_size_type mech_index; // instance of the mechanism
cell_size_type intdom_index; // which integration domain (acts as index into e.g. vec_t)
- target_handle() {}
+ target_handle() = default;
target_handle(cell_local_size_type mech_id, cell_local_size_type mech_index, cell_size_type intdom_index):
mech_id(mech_id), mech_index(mech_index), intdom_index(intdom_index) {}
};
diff --git a/arbor/backends/multicore/multi_event_stream.hpp b/arbor/backends/multicore/multi_event_stream.hpp
index 6fe2a61a..03c2c29d 100644
--- a/arbor/backends/multicore/multi_event_stream.hpp
+++ b/arbor/backends/multicore/multi_event_stream.hpp
@@ -33,7 +33,7 @@ public:
using state = multi_event_stream_state<event_data_type>;
- multi_event_stream() {}
+ multi_event_stream() = default;
explicit multi_event_stream(size_type n_stream):
span_begin_(n_stream), span_end_(n_stream), mark_(n_stream) {}
diff --git a/arbor/benchmark_cell_group.cpp b/arbor/benchmark_cell_group.cpp
index 0069b405..8abe81c2 100644
--- a/arbor/benchmark_cell_group.cpp
+++ b/arbor/benchmark_cell_group.cpp
@@ -39,7 +39,7 @@ benchmark_cell_group::benchmark_cell_group(const std::vector<cell_gid_type>& gid
cg_targets.add_label(c.target, {0, 1});
}
- reset();
+ benchmark_cell_group::reset();
}
void benchmark_cell_group::reset() {
diff --git a/arbor/communication/communicator.hpp b/arbor/communication/communicator.hpp
index fa93adfc..61872c86 100644
--- a/arbor/communication/communicator.hpp
+++ b/arbor/communication/communicator.hpp
@@ -28,7 +28,7 @@ namespace arb {
class ARB_ARBOR_API communicator {
public:
- communicator() {}
+ communicator() = default;
explicit communicator(const recipe& rec,
const domain_decomposition& dom_dec,
diff --git a/arbor/domain_decomposition.cpp b/arbor/domain_decomposition.cpp
index 7a58d804..de443ab3 100644
--- a/arbor/domain_decomposition.cpp
+++ b/arbor/domain_decomposition.cpp
@@ -33,8 +33,9 @@ domain_decomposition::domain_decomposition(
std::unordered_map<cell_gid_type, int> gid_map;
};
- unsigned num_domains = ctx->distributed->size();
- int domain_id = ctx->distributed->id();
+ const auto* dist = ctx->distributed.get();
+ unsigned num_domains = dist->size();
+ int domain_id = dist->id();
cell_size_type num_global_cells = rec.num_cells();
const bool has_gpu = ctx->gpu->has_gpu();
@@ -62,7 +63,7 @@ domain_decomposition::domain_decomposition(
}
cell_size_type num_local_cells = local_gids.size();
- auto global_gids = ctx->distributed->gather_gids(local_gids);
+ auto global_gids = dist->gather_gids(local_gids);
if (global_gids.size() != num_global_cells) {
throw invalid_sum_local_cells(global_gids.size(), num_global_cells);
}
diff --git a/arbor/event_queue.hpp b/arbor/event_queue.hpp
index 59885b43..5e314f8d 100644
--- a/arbor/event_queue.hpp
+++ b/arbor/event_queue.hpp
@@ -27,7 +27,7 @@ public:
using value_type = Event;
using event_time_type = ::arb::event_time_type<Event>;
- event_queue() {}
+ event_queue() = default;
void push(const value_type& e) {
queue_.push(e);
diff --git a/arbor/fvm_layout.cpp b/arbor/fvm_layout.cpp
index 65d0a61a..5f7dd6bc 100644
--- a/arbor/fvm_layout.cpp
+++ b/arbor/fvm_layout.cpp
@@ -105,7 +105,7 @@ cv_geometry::cv_geometry(const cable_cell& cell, const locset& ls):
cell_cv_divs = {0, (fvm_index_type)n_cv};
}
-fvm_size_type cv_geometry::location_cv(size_type cell_idx, mlocation loc, cv_prefer::type prefer) const {
+fvm_size_type cv_geometry::location_cv(size_type cell_idx, const mlocation& loc, cv_prefer::type prefer) const {
auto& pw_cv_offset = branch_cv_map.at(cell_idx).at(loc.branch);
auto zero_extent = [&pw_cv_offset](auto j) {
return pw_cv_offset.extent(j).first==pw_cv_offset.extent(j).second;
@@ -248,18 +248,23 @@ ARB_ARBOR_API fvm_cv_discretization fvm_cv_discretize(const cable_cell& cell, co
double dflt_potential = *(dflt.init_membrane_potential | global_dflt.init_membrane_potential);
double dflt_temperature = *(dflt.temperature_K | global_dflt.temperature_K);
+ const auto& assignments = cell.region_assignments();
+ const auto& resistivity = assignments.get<axial_resistivity>();
+ const auto& capacitance = assignments.get<membrane_capacitance>();
+ const auto& potential = assignments.get<init_membrane_potential>();
+ const auto& temperature = assignments.get<temperature_K>();
+
D.axial_resistivity.resize(1);
msize_t n_branch = D.geometry.n_branch(0);
- D.axial_resistivity[0].reserve(n_branch);
+ auto& ax_res_0 = D.axial_resistivity[0];
+ ax_res_0.reserve(n_branch);
for (msize_t i = 0; i<n_branch; ++i) {
- D.axial_resistivity[0].push_back(pw_over_cable(cell.region_assignments().get<axial_resistivity>(),
- mcable{i, 0., 1.}, dflt_resistivity));
+ ax_res_0.emplace_back(pw_over_cable(resistivity, mcable{i, 0., 1.}, dflt_resistivity));
}
const auto& embedding = cell.embedding();
for (auto i: count_along(D.geometry.cv_parent)) {
auto cv_cables = D.geometry.cables(i);
-
// Computing face_conductance:
//
// Flux between adjacent CVs is computed as if there were no membrane currents, and with the CV voltage
@@ -267,13 +272,10 @@ ARB_ARBOR_API fvm_cv_discretization fvm_cv_discretize(const cable_cell& cell, co
// * If the CV is unbranched, the reference point is taken to be the CV midpoint.
// * If the CV is branched, the reference point is taken to be closest branch point to
// the interface between the two CVs.
-
D.face_conductance[i] = 0;
-
fvm_index_type p = D.geometry.cv_parent[i];
if (p!=-1) {
auto parent_cables = D.geometry.cables(p);
-
msize_t bid = cv_cables.front().branch;
double parent_refpt = 0;
double cv_refpt = 1;
@@ -303,28 +305,19 @@ ARB_ARBOR_API fvm_cv_discretization fvm_cv_discretize(const cable_cell& cell, co
double cv_length = 0;
for (mcable c: cv_cables) {
- D.cv_area[i] += embedding.integrate_area(c);
-
- D.cv_capacitance[i] += embedding.integrate_area(c.branch,
- pw_over_cable(cell.region_assignments().get<membrane_capacitance>(), c, dflt_capacitance));
-
- D.init_membrane_potential[i] += embedding.integrate_area(c.branch,
- pw_over_cable(cell.region_assignments().get<init_membrane_potential>(), c, dflt_potential));
-
- D.temperature_K[i] += embedding.integrate_area(c.branch,
- pw_over_cable(cell.region_assignments().get<temperature_K>(), c, dflt_temperature));
-
+ D.cv_area[i] += embedding.integrate_area(c);
+ D.cv_capacitance[i] += embedding.integrate_area(c.branch, pw_over_cable(capacitance, c, dflt_capacitance));
+ D.init_membrane_potential[i] += embedding.integrate_area(c.branch, pw_over_cable(potential, c, dflt_potential));
+ D.temperature_K[i] += embedding.integrate_area(c.branch, pw_over_cable(temperature, c, dflt_temperature));
cv_length += embedding.integrate_length(c);
}
if (D.cv_area[i]>0) {
D.init_membrane_potential[i] /= D.cv_area[i];
D.temperature_K[i] /= D.cv_area[i];
-
// If parent is trivial, and there is no grandparent, then we can use values from this CV
// to get initial values for the parent. (The other case, when there is a grandparent, is
// caught below.)
-
if (p!=-1 && D.geometry.cv_parent[p]==-1 && D.cv_area[p]==0) {
D.init_membrane_potential[p] = D.init_membrane_potential[i];
D.temperature_K[p] = D.temperature_K[i];
@@ -332,7 +325,6 @@ ARB_ARBOR_API fvm_cv_discretization fvm_cv_discretize(const cable_cell& cell, co
}
else if (p!=-1) {
// Use parent CV to get a sensible initial value for voltage and temp on zero-size CVs.
-
D.init_membrane_potential[i] = D.init_membrane_potential[p];
D.temperature_K[i] = D.temperature_K[p];
}
@@ -341,7 +333,6 @@ ARB_ARBOR_API fvm_cv_discretization fvm_cv_discretize(const cable_cell& cell, co
D.diam_um[i] = D.cv_area[i]/(cv_length*math::pi<double>);
}
}
-
return D;
}
@@ -388,7 +379,7 @@ struct voltage_reference_pair {
};
// Collection of other locations that are coincident under projection.
-std::vector<mlocation> coincident_locations(const morphology& m, mlocation x) {
+std::vector<mlocation> coincident_locations(const morphology& m, const mlocation& x) {
std::vector<mlocation> result;
if (x.pos==0) {
msize_t parent_bid = m.branch_parent(x.branch);
@@ -411,7 +402,7 @@ std::vector<mlocation> coincident_locations(const morphology& m, mlocation x) {
// Test if location intersects (sorted) sequence of cables.
template <typename Seq>
-bool cables_intersect_location(Seq&& cables, mlocation x) {
+bool cables_intersect_location(Seq&& cables, const mlocation& x) {
struct cmp_branch {
bool operator()(const mcable& c, msize_t bid) const { return c.branch<bid; }
bool operator()(msize_t bid, const mcable& c) const { return bid<c.branch; }
@@ -425,7 +416,7 @@ bool cables_intersect_location(Seq&& cables, mlocation x) {
[&x](const mcable& c) { return c.prox_pos<=x.pos && x.pos<=c.dist_pos; });
}
-voltage_reference_pair fvm_voltage_reference_points(const morphology& morph, const cv_geometry& geom, fvm_size_type cell_idx, mlocation site) {
+voltage_reference_pair fvm_voltage_reference_points(const morphology& morph, const cv_geometry& geom, fvm_size_type cell_idx, const mlocation& site) {
voltage_reference site_ref, parent_ref, child_ref;
bool check_parent = true, check_child = true;
msize_t bid = site.branch;
@@ -439,7 +430,7 @@ voltage_reference_pair fvm_voltage_reference_points(const morphology& morph, con
return mlocation{c.branch, (c.prox_pos+c.dist_pos)/2};
};
- auto cv_contains_fork = [&](auto cv, mlocation x) {
+ auto cv_contains_fork = [&](auto cv, const mlocation& x) {
// CV contains fork if it intersects any location coincident with x
// other than x itselfv.
@@ -515,7 +506,7 @@ voltage_reference_pair fvm_voltage_reference_points(const morphology& morph, con
// Interpolate membrane voltage from reference points in adjacent CVs.
-ARB_ARBOR_API fvm_voltage_interpolant fvm_interpolate_voltage(const cable_cell& cell, const fvm_cv_discretization& D, fvm_size_type cell_idx, mlocation site) {
+ARB_ARBOR_API fvm_voltage_interpolant fvm_interpolate_voltage(const cable_cell& cell, const fvm_cv_discretization& D, fvm_size_type cell_idx, const mlocation& site) {
auto& embedding = cell.embedding();
fvm_voltage_interpolant vi;
@@ -556,7 +547,7 @@ ARB_ARBOR_API fvm_voltage_interpolant fvm_interpolate_voltage(const cable_cell&
// Axial current as linear combination of membrane voltages at reference points in adjacent CVs.
-ARB_ARBOR_API fvm_voltage_interpolant fvm_axial_current(const cable_cell& cell, const fvm_cv_discretization& D, fvm_size_type cell_idx, mlocation site) {
+ARB_ARBOR_API fvm_voltage_interpolant fvm_axial_current(const cable_cell& cell, const fvm_cv_discretization& D, fvm_size_type cell_idx, const mlocation& site) {
auto& embedding = cell.embedding();
fvm_voltage_interpolant vi;
@@ -751,6 +742,8 @@ fvm_mechanism_data fvm_build_mechanism_data(
fvm_mechanism_data M;
+ const auto& assignments = cell.region_assignments();
+
// Verify mechanism ion usage, parameter values.
auto verify_mechanism = [&gprop](const mechanism_info& info, const mechanism_desc& desc) {
const auto& global_ions = gprop.ion_species;
@@ -802,8 +795,7 @@ fvm_mechanism_data fvm_build_mechanism_data(
// Density mechanisms:
- for (const auto& entry: cell.region_assignments().get<density>()) {
- const std::string& name = entry.first;
+ for (const auto& [name, cables]: assignments.get<density>()) {
mechanism_info info = catalogue[name];
fvm_mechanism_config config;
@@ -832,7 +824,7 @@ fvm_mechanism_data fvm_build_mechanism_data(
param_maps.resize(n_param);
- for (auto& on_cable: entry.second) {
+ for (auto& on_cable: cables) {
const auto& mech = on_cable.second.mech;
verify_mechanism(info, mech);
mcable cable = on_cable.first;
@@ -1190,10 +1182,9 @@ fvm_mechanism_data fvm_build_mechanism_data(
}
// Ions:
-
- auto initial_iconc_map = cell.region_assignments().get<init_int_concentration>();
- auto initial_econc_map = cell.region_assignments().get<init_ext_concentration>();
- auto initial_rvpot_map = cell.region_assignments().get<init_reversal_potential>();
+ auto initial_iconc_map = assignments.get<init_int_concentration>();
+ auto initial_econc_map = assignments.get<init_ext_concentration>();
+ auto initial_rvpot_map = assignments.get<init_reversal_potential>();
for (const auto& [ion, cvs]: ion_support) {
fvm_ion_config config;
@@ -1212,14 +1203,15 @@ fvm_mechanism_data fvm_build_mechanism_data(
auto dflt_rvpot = global_ion_data.init_reversal_potential.value();
if (auto ion_data = value_by_key(dflt.ion_data, ion)) {
- dflt_iconc = ion_data.value().init_int_concentration.value_or(dflt_iconc);
- dflt_econc = ion_data.value().init_ext_concentration.value_or(dflt_econc);
- dflt_rvpot = ion_data.value().init_reversal_potential.value_or(dflt_rvpot);
+ auto val = ion_data.value();
+ dflt_iconc = val.init_int_concentration.value_or(dflt_iconc);
+ dflt_econc = val.init_ext_concentration.value_or(dflt_econc);
+ dflt_rvpot = val.init_reversal_potential.value_or(dflt_rvpot);
}
- const mcable_map<init_int_concentration>& iconc_on_cable = initial_iconc_map[ion];
- const mcable_map<init_ext_concentration>& econc_on_cable = initial_econc_map[ion];
- const mcable_map<init_reversal_potential>& rvpot_on_cable = initial_rvpot_map[ion];
+ const auto& iconc_on_cable = initial_iconc_map[ion];
+ const auto& econc_on_cable = initial_econc_map[ion];
+ const auto& rvpot_on_cable = initial_rvpot_map[ion];
auto pw_times = [](const pw_elements<double>& pwa, const pw_elements<double>& pwb) {
return pw_zip_with(pwa, pwb, [](std::pair<double, double>, double a, double b) { return a*b; });
@@ -1275,19 +1267,19 @@ fvm_mechanism_data fvm_build_mechanism_data(
revpot_specified.insert(ion);
bool writes_this_revpot = false;
- for (auto& iondep: info.ions) {
- if (iondep.second.write_reversal_potential) {
- if (revpot_tbl.count(iondep.first)) {
- auto& existing_revpot_desc = revpot_tbl.at(iondep.first);
+ for (auto& [name, info]: info.ions) {
+ if (info.write_reversal_potential) {
+ if (revpot_tbl.count(name)) {
+ auto& existing_revpot_desc = revpot_tbl.at(name);
if (existing_revpot_desc.name() != revpot.name() || existing_revpot_desc.values() != revpot.values()) {
throw cable_cell_error("inconsistent revpot ion assignment for mechanism "+revpot.name());
}
}
else {
- revpot_tbl[iondep.first] = revpot;
+ revpot_tbl[name] = revpot;
}
- writes_this_revpot |= iondep.first==ion;
+ writes_this_revpot |= name==ion;
}
}
diff --git a/arbor/fvm_layout.hpp b/arbor/fvm_layout.hpp
index b81debcd..9306c78f 100644
--- a/arbor/fvm_layout.hpp
+++ b/arbor/fvm_layout.hpp
@@ -113,7 +113,7 @@ struct ARB_ARBOR_API cv_geometry: public cell_cv_data_impl {
return branch_cv_map.at(cell_idx).size();
}
- size_type location_cv(size_type cell_idx, mlocation loc, cv_prefer::type prefer) const;
+ size_type location_cv(size_type cell_idx, const mlocation& loc, cv_prefer::type prefer) const;
cv_geometry(const cable_cell& cell, const locset& ls);
};
@@ -180,10 +180,10 @@ struct fvm_voltage_interpolant {
};
// Interpolated membrane voltage.
-ARB_ARBOR_API fvm_voltage_interpolant fvm_interpolate_voltage(const cable_cell& cell, const fvm_cv_discretization& D, fvm_size_type cell_idx, mlocation site);
+ARB_ARBOR_API fvm_voltage_interpolant fvm_interpolate_voltage(const cable_cell& cell, const fvm_cv_discretization& D, fvm_size_type cell_idx, const mlocation& site);
// Axial current as linear combiantion of voltages.
-ARB_ARBOR_API fvm_voltage_interpolant fvm_axial_current(const cable_cell& cell, const fvm_cv_discretization& D, fvm_size_type cell_idx, mlocation site);
+ARB_ARBOR_API fvm_voltage_interpolant fvm_axial_current(const cable_cell& cell, const fvm_cv_discretization& D, fvm_size_type cell_idx, const mlocation& site);
// Post-discretization data for point and density mechanism instantiation.
diff --git a/arbor/fvm_lowered_cell_impl.hpp b/arbor/fvm_lowered_cell_impl.hpp
index fcd7c4ee..400df4d8 100644
--- a/arbor/fvm_lowered_cell_impl.hpp
+++ b/arbor/fvm_lowered_cell_impl.hpp
@@ -207,7 +207,8 @@ fvm_integration_result fvm_lowered_cell_impl<Backend>::integrate(
sample_value_ = array(n_samples);
}
- state_->deliverable_events.init(std::move(staged_events));
+ auto& events = state_->deliverable_events;
+ events.init(std::move(staged_events));
sample_events_.init(std::move(staged_samples));
arb_assert((assert_tmin(), true));
@@ -235,7 +236,7 @@ fvm_integration_result fvm_lowered_cell_impl<Backend>::integrate(
state_->zero_currents();
PL();
for (auto& m: mechanisms_) {
- auto state = state_->deliverable_events.marked_events();
+ auto state = events.marked_events();
arb_deliverable_event_stream events;
events.n_streams = state.n;
events.begin = state.begin_offset;
@@ -246,12 +247,12 @@ fvm_integration_result fvm_lowered_cell_impl<Backend>::integrate(
}
PE(advance:integrate:events);
- state_->deliverable_events.drop_marked_events();
+ events.drop_marked_events();
// Update event list and integration step times.
state_->update_time_to(dt_max, tfinal);
- state_->deliverable_events.event_time_if_before(state_->time_to);
+ events.event_time_if_before(state_->time_to);
state_->set_dt();
PL();
@@ -592,10 +593,10 @@ fvm_initialization_data fvm_lowered_cell_impl<Backend>::initialize(
}
if (config.kind==arb_mechanism_kind_reversal_potential) {
- revpot_mechanisms_.push_back(mechanism_ptr(minst.mech.release()));
+ revpot_mechanisms_.emplace_back(minst.mech.release());
}
else {
- mechanisms_.push_back(mechanism_ptr(minst.mech.release()));
+ mechanisms_.emplace_back(minst.mech.release());
}
}
@@ -616,7 +617,7 @@ fvm_initialization_data fvm_lowered_cell_impl<Backend>::initialize(
std::vector<probe_info> rec_probes = rec.get_probes(gid);
for (cell_lid_type i: count_along(rec_probes)) {
probe_info& pi = rec_probes[i];
- resolve_probe_address(probe_data, cells, cell_idx, std::move(pi.address),
+ resolve_probe_address(probe_data, cells, cell_idx, pi.address,
D, mech_data, fvm_info.target_handles, mechptr_by_name);
if (!probe_data.empty()) {
diff --git a/arbor/include/arbor/mechanism.hpp b/arbor/include/arbor/mechanism.hpp
index d5cc221d..8d30eb35 100644
--- a/arbor/include/arbor/mechanism.hpp
+++ b/arbor/include/arbor/mechanism.hpp
@@ -31,7 +31,7 @@ public:
using index_type = fvm_index_type;
using size_type = fvm_size_type;
- mechanism(const arb_mechanism_type m,
+ mechanism(const arb_mechanism_type& m,
const arb_mechanism_interface& i): mech_{m}, iface_{i}, ppack_{} {
if (mech_.abi_version != ARB_MECH_ABI_VERSION) throw unsupported_abi_error{mech_.abi_version};
state_prof_id = profile::profiler_region_id("advance:integrate:state:"+internal_name());
diff --git a/arbor/include/arbor/morph/embed_pwlin.hpp b/arbor/include/arbor/morph/embed_pwlin.hpp
index 0fe4bf8d..c282cb1f 100644
--- a/arbor/include/arbor/morph/embed_pwlin.hpp
+++ b/arbor/include/arbor/morph/embed_pwlin.hpp
@@ -44,23 +44,23 @@ struct ARB_ARBOR_API embed_pwlin {
mcable_list projection_cmp(msize_t bid, double proj_lim, comp_op op) const;
// Computed length of mcable.
- double integrate_length(mcable c) const;
+ double integrate_length(const mcable& c) const;
double integrate_length(mlocation proxmal, mlocation distal) const;
- double integrate_length(mcable c, const pw_constant_fn&) const;
+ double integrate_length(const mcable& c, const pw_constant_fn&) const;
double integrate_length(msize_t bid, const pw_constant_fn&) const;
// Membrane surface area of given mcable.
- double integrate_area(mcable c) const;
+ double integrate_area(const mcable& c) const;
double integrate_area(mlocation proxmal, mlocation distal) const;
- double integrate_area(mcable c, const pw_constant_fn&) const;
+ double integrate_area(const mcable& c, const pw_constant_fn&) const;
double integrate_area(msize_t bid, const pw_constant_fn&) const;
// Integrated inverse cross-sectional area of given mcable.
- double integrate_ixa(mcable c) const;
+ double integrate_ixa(const mcable& c) const;
- double integrate_ixa(mcable c, const pw_constant_fn&) const;
+ double integrate_ixa(const mcable& c, const pw_constant_fn&) const;
double integrate_ixa(msize_t bid, const pw_constant_fn&) const;
// Length of whole branch.
diff --git a/arbor/include/arbor/morph/mcable_map.hpp b/arbor/include/arbor/morph/mcable_map.hpp
index 76fae779..ce2c270e 100644
--- a/arbor/include/arbor/morph/mcable_map.hpp
+++ b/arbor/include/arbor/morph/mcable_map.hpp
@@ -57,8 +57,7 @@ struct mcable_map {
bool insert(const mcable& c, T value) {
auto opt_it = insertion_point(c);
if (!opt_it) return false;
-
- elements_.insert(*opt_it, value_type{c, std::move(value)});
+ elements_.emplace(*opt_it, c, std::move(value));
assert_invariants();
return true;
}
@@ -67,12 +66,10 @@ struct mcable_map {
bool emplace(const mcable& c, Args&&... args) {
auto opt_it = insertion_point(c);
if (!opt_it) return false;
-
elements_.emplace(*opt_it,
std::piecewise_construct,
std::forward_as_tuple(c),
std::forward_as_tuple(std::forward<Args>(args)...));
-
assert_invariants();
return true;
}
@@ -82,7 +79,6 @@ struct mcable_map {
s.reserve(elements_.size());
std::transform(elements_.begin(), elements_.end(), std::back_inserter(s),
[](const auto& x) { return x.first; });
-
return s;
}
diff --git a/arbor/include/arbor/morph/primitives.hpp b/arbor/include/arbor/morph/primitives.hpp
index 2cfff2ef..6c5d64bf 100644
--- a/arbor/include/arbor/morph/primitives.hpp
+++ b/arbor/include/arbor/morph/primitives.hpp
@@ -59,9 +59,9 @@ struct ARB_SYMBOL_VISIBLE msegment {
// Describe a specific location on a morpholology.
struct ARB_SYMBOL_VISIBLE mlocation {
// The id of the branch.
- msize_t branch;
+ msize_t branch = 0;
// The relative position on the branch ∈ [0,1].
- double pos;
+ double pos = 0.0;
friend std::ostream& operator<<(std::ostream&, const mlocation&);
};
diff --git a/arbor/include/arbor/morph/region.hpp b/arbor/include/arbor/morph/region.hpp
index 0439e23d..a2825abf 100644
--- a/arbor/include/arbor/morph/region.hpp
+++ b/arbor/include/arbor/morph/region.hpp
@@ -101,7 +101,7 @@ private:
explicit wrap(Impl&& impl): wrapped(std::move(impl)) {}
virtual std::unique_ptr<interface> clone() override {
- return std::unique_ptr<interface>(new wrap<Impl>(wrapped));
+ return std::make_unique<wrap<Impl>>(wrapped);
}
virtual mextent thingify(const mprovider& m) override {
diff --git a/arbor/include/arbor/s_expr.hpp b/arbor/include/arbor/s_expr.hpp
index e8ddb218..c5c4f51f 100644
--- a/arbor/include/arbor/s_expr.hpp
+++ b/arbor/include/arbor/s_expr.hpp
@@ -214,6 +214,7 @@ struct ARB_ARBOR_API s_expr {
s_expr(s_expr l, s_expr r):
state(pair_type(std::move(l), std::move(r)))
{}
+ s_expr& operator=(const s_expr& s) { state = s.state; return *this; }
explicit s_expr(std::string s):
s_expr(token{{0,0}, tok::string, std::move(s)}) {}
diff --git a/arbor/include/arbor/simd/simd.hpp b/arbor/include/arbor/simd/simd.hpp
index b0d3b028..d9acc07f 100644
--- a/arbor/include/arbor/simd/simd.hpp
+++ b/arbor/include/arbor/simd/simd.hpp
@@ -104,7 +104,7 @@ detail::simd_mask_impl<T> logical_not(const detail::simd_mask_impl<T>& a) {
}
template <typename T>
-detail::simd_impl<T> fma(const detail::simd_impl<T> a, detail::simd_impl<T> b, detail::simd_impl<T> c) {
+detail::simd_impl<T> fma(const detail::simd_impl<T>& a, detail::simd_impl<T> b, detail::simd_impl<T> c) {
return detail::simd_impl<T>::wrap(T::fma(a.value_, b.value_, c.value_));
}
@@ -684,7 +684,7 @@ namespace detail {
#undef ARB_DECLARE_BINARY_COMPARISON_
template <typename T>
- friend simd_impl<T> arb::simd::fma(const simd_impl<T> a, simd_impl<T> b, simd_impl<T> c);
+ friend simd_impl<T> arb::simd::fma(const simd_impl<T>& a, simd_impl<T> b, simd_impl<T> c);
// Declare Indirect/Indirect indexed/Where Expression copy function as friends
diff --git a/arbor/include/arbor/util/any_ptr.hpp b/arbor/include/arbor/util/any_ptr.hpp
index c6e11b82..80f5273c 100644
--- a/arbor/include/arbor/util/any_ptr.hpp
+++ b/arbor/include/arbor/util/any_ptr.hpp
@@ -37,7 +37,7 @@ namespace arb {
namespace util {
struct ARB_SYMBOL_VISIBLE any_ptr {
- any_ptr() {}
+ any_ptr() = default;
any_ptr(std::nullptr_t) {}
diff --git a/arbor/include/arbor/util/expected.hpp b/arbor/include/arbor/util/expected.hpp
index 45ab99bc..9d860f65 100644
--- a/arbor/include/arbor/util/expected.hpp
+++ b/arbor/include/arbor/util/expected.hpp
@@ -44,7 +44,7 @@ struct bad_expected_access;
template <>
struct bad_expected_access<void>: std::exception {
- bad_expected_access() {}
+ bad_expected_access() = default;
virtual const char* what() const noexcept override { return "bad expected access"; }
};
diff --git a/arbor/include/arbor/util/scope_exit.hpp b/arbor/include/arbor/util/scope_exit.hpp
index f353c1e2..30cdd8b7 100644
--- a/arbor/include/arbor/util/scope_exit.hpp
+++ b/arbor/include/arbor/util/scope_exit.hpp
@@ -50,7 +50,7 @@ namespace impl {
struct wrap_std_function {
std::function<R ()> f;
- wrap_std_function() noexcept {}
+ wrap_std_function() noexcept = default;
wrap_std_function(const std::function<R ()>& f): f(f) {}
wrap_std_function(std::function<R ()>&& f): f(std::move(f)) {}
wrap_std_function(wrap_std_function&& other) noexcept {
diff --git a/arbor/lif_cell_group.cpp b/arbor/lif_cell_group.cpp
index 64ca1c36..e7d24e95 100644
--- a/arbor/lif_cell_group.cpp
+++ b/arbor/lif_cell_group.cpp
@@ -18,7 +18,7 @@ lif_cell_group::lif_cell_group(const std::vector<cell_gid_type>& gids, const rec
}
}
// Default to no binning of events
- set_binning_policy(binning_kind::none, 0);
+ lif_cell_group::set_binning_policy(binning_kind::none, 0);
cells_.reserve(gids_.size());
last_time_updated_.resize(gids_.size());
@@ -119,4 +119,4 @@ void lif_cell_group::advance_cell(time_type tfinal, time_type dt, cell_gid_type
// This is the last time a cell was updated.
last_time_updated_[lid] = t;
-}
\ No newline at end of file
+}
diff --git a/arbor/mc_cell_group.cpp b/arbor/mc_cell_group.cpp
index 8d140e6e..4507afae 100644
--- a/arbor/mc_cell_group.cpp
+++ b/arbor/mc_cell_group.cpp
@@ -38,7 +38,7 @@ mc_cell_group::mc_cell_group(const std::vector<cell_gid_type>& gids,
gids_(gids), lowered_(std::move(lowered))
{
// Default to no binning of events
- set_binning_policy(binning_kind::none, 0);
+ mc_cell_group::set_binning_policy(binning_kind::none, 0);
// Build lookup table for gid to local index.
for (auto i: util::count_along(gids_)) {
diff --git a/arbor/mechcat.cpp b/arbor/mechcat.cpp
index 4fb428d6..06c60ed2 100644
--- a/arbor/mechcat.cpp
+++ b/arbor/mechcat.cpp
@@ -176,7 +176,7 @@ struct catalogue_state {
// Set mechanism info (unchecked).
void bind(const std::string& name, mechanism_info info) {
- info_map_[name] = mechanism_info_ptr(new mechanism_info(std::move(info)));
+ info_map_[name] = std::make_unique<mechanism_info>(std::move(info));
}
// Add derived mechanism (unchecked).
@@ -488,9 +488,12 @@ struct catalogue_state {
}
}
- apply_globals(apply_globals, implicit_deriv? implicit_deriv->parent: name, over);
if (implicit_deriv) {
- apply_deriv(over, implicit_deriv.value());
+ apply_globals(apply_globals, implicit_deriv->parent, over);
+ apply_deriv(over, *implicit_deriv);
+ }
+ else {
+ apply_globals(apply_globals, name, over);
}
return over;
diff --git a/arbor/memory/allocator.hpp b/arbor/memory/allocator.hpp
index 26ca109c..1c2a79f0 100644
--- a/arbor/memory/allocator.hpp
+++ b/arbor/memory/allocator.hpp
@@ -173,9 +173,9 @@ public:
using rebind = allocator<U, Policy>;
public:
- allocator() {}
- ~allocator() {}
- allocator(allocator const&) {}
+ allocator() = default;
+ ~allocator() = default;
+ allocator(allocator const&) = default;
pointer address(reference r) {
return &r;
diff --git a/arbor/memory/array_view.hpp b/arbor/memory/array_view.hpp
index 53a69dfd..0180f6fb 100644
--- a/arbor/memory/array_view.hpp
+++ b/arbor/memory/array_view.hpp
@@ -262,7 +262,7 @@ public:
}
// do nothing for destructor: we don't own the memory in range
- ~array_view() {}
+ ~array_view() = default;
// test whether memory overlaps that referenced by other
template <
@@ -428,7 +428,7 @@ public:
}
// do nothing for destructor: we don't own the memory in range
- ~const_array_view() {}
+ ~const_array_view() = default;
// test whether memory overlaps that referenced by other
template <
diff --git a/arbor/morph/embed_pwlin.cpp b/arbor/morph/embed_pwlin.cpp
index dfe84c73..474cabf9 100644
--- a/arbor/morph/embed_pwlin.cpp
+++ b/arbor/morph/embed_pwlin.cpp
@@ -176,15 +176,15 @@ double embed_pwlin::integrate_ixa(msize_t bid, const pw_constant_fn& g) const {
// Integrate over cable:
-double embed_pwlin::integrate_length(mcable c) const {
+double embed_pwlin::integrate_length(const mcable& c) const {
return integrate_length(c.branch, pw_constant_fn{{c.prox_pos, c.dist_pos}, {1.}});
}
-double embed_pwlin::integrate_area(mcable c) const {
+double embed_pwlin::integrate_area(const mcable& c) const {
return integrate_area(c.branch, pw_constant_fn{{c.prox_pos, c.dist_pos}, {1.}});
}
-double embed_pwlin::integrate_ixa(mcable c) const {
+double embed_pwlin::integrate_ixa(const mcable& c) const {
return integrate_ixa(c.branch, pw_constant_fn{{c.prox_pos, c.dist_pos}, {1.}});
}
@@ -194,15 +194,15 @@ static pw_constant_fn restrict(const pw_constant_fn& g, double left, double righ
return pw_zip_with(g, pw_elements<void>{{left, right}});
}
-double embed_pwlin::integrate_length(mcable c, const pw_constant_fn& g) const {
+double embed_pwlin::integrate_length(const mcable& c, const pw_constant_fn& g) const {
return integrate_length(c.branch, restrict(g, c.prox_pos, c.dist_pos));
}
-double embed_pwlin::integrate_area(mcable c, const pw_constant_fn& g) const {
+double embed_pwlin::integrate_area(const mcable& c, const pw_constant_fn& g) const {
return integrate_area(c.branch, restrict(g, c.prox_pos, c.dist_pos));
}
-double embed_pwlin::integrate_ixa(mcable c, const pw_constant_fn& g) const {
+double embed_pwlin::integrate_ixa(const mcable& c, const pw_constant_fn& g) const {
return integrate_ixa(c.branch, restrict(g, c.prox_pos, c.dist_pos));
}
diff --git a/arbor/morph/locset.cpp b/arbor/morph/locset.cpp
index 3502caa0..dc503510 100644
--- a/arbor/morph/locset.cpp
+++ b/arbor/morph/locset.cpp
@@ -23,7 +23,7 @@ namespace arb {
namespace ls {
// Throw on invalid mlocation.
-void assert_valid(mlocation x) {
+void assert_valid(const mlocation& x) {
if (!test_invariants(x)) {
throw invalid_mlocation(x);
}
@@ -119,7 +119,7 @@ std::ostream& operator<<(std::ostream& o, const terminal_& x) {
// Translate locations in locset distance μm in the proximal direction
struct proximal_translate_: locset_tag {
- proximal_translate_(const locset& ls, double distance): start(ls), distance(distance) {}
+ proximal_translate_(locset ls, double distance): start(std::move(ls)), distance(distance) {}
locset start;
double distance;
};
@@ -163,7 +163,7 @@ mlocation_list thingify_(const proximal_translate_& dt, const mprovider& p) {
}
ARB_ARBOR_API locset proximal_translate(locset ls, double distance) {
- return locset(proximal_translate_{ls, distance});
+ return locset(proximal_translate_{std::move(ls), distance});
}
std::ostream& operator<<(std::ostream& o, const proximal_translate_& l) {
@@ -172,13 +172,13 @@ std::ostream& operator<<(std::ostream& o, const proximal_translate_& l) {
// Translate locations in locset distance μm in the distal direction
struct distal_translate_: locset_tag {
- distal_translate_(const locset& ls, double distance): start(ls), distance(distance) {}
+ distal_translate_(locset ls, double distance): start(std::move(ls)), distance(distance) {}
locset start;
double distance;
};
ARB_ARBOR_API locset distal_translate(locset ls, double distance) {
- return locset(distal_translate_{ls, distance});
+ return locset(distal_translate_{std::move(ls), distance});
}
mlocation_list thingify_(const distal_translate_& dt, const mprovider& p) {
@@ -532,8 +532,8 @@ std::ostream& operator<<(std::ostream& o, const on_components_& x) {
// Uniform locset.
struct uniform_: locset_tag {
- uniform_(const arb::region& reg_, unsigned left_, unsigned right_, uint64_t seed_):
- reg{reg_}, left{left_}, right{right_}, seed{seed_}
+ uniform_(arb::region reg_, unsigned left_, unsigned right_, uint64_t seed_):
+ reg{std::move(reg_)}, left{left_}, right{right_}, seed{seed_}
{}
region reg;
unsigned left;
@@ -542,7 +542,7 @@ struct uniform_: locset_tag {
};
ARB_ARBOR_API locset uniform(arb::region reg, unsigned left, unsigned right, uint64_t seed) {
- return locset(uniform_{reg, left, right, seed});
+ return locset(uniform_{std::move(reg), left, right, seed});
}
mlocation_list thingify_(const uniform_& u, const mprovider& p) {
diff --git a/arbor/morph/place_pwlin.cpp b/arbor/morph/place_pwlin.cpp
index f42475bc..b5492317 100644
--- a/arbor/morph/place_pwlin.cpp
+++ b/arbor/morph/place_pwlin.cpp
@@ -191,7 +191,7 @@ struct p3d {
friend constexpr double dot(const p3d& l, const p3d& r) {
return l.x*r.x + l.y*r.y + l.z*r.z;
}
- friend double norm(const p3d p) {
+ friend double norm(const p3d& p) {
return std::sqrt(dot(p, p));
}
friend std::ostream& operator<<(std::ostream& o, const p3d& p) {
@@ -220,9 +220,7 @@ std::pair<mlocation, double> place_pwlin::closest(double x, double y, double z)
// v and w are the proximal and distal ends of the segment.
const p3d v = seg.prox;
const p3d w = seg.dist;
-
const p3d vw = w-v;
- const p3d vp = p-v;
const double wvs = dot(vw, vw);
if (wvs==0.) { // zero length segment is a special case
const double distance = norm(p-v);
@@ -237,7 +235,7 @@ std::pair<mlocation, double> place_pwlin::closest(double x, double y, double z)
// t=0 -> proximal end of the segment
// t=1 -> distal end of the segment
// values are clamped to the range [0, 1]
- const double t = std::max(0., std::min(1., dot(vw, vp) / wvs));
+ const double t = std::max(0., std::min(1., dot(vw, p-v) / wvs));
const double distance =
t<=0.? norm(p-v):
t>=1.? norm(p-w):
diff --git a/arbor/morph/region.cpp b/arbor/morph/region.cpp
index cf59e6ea..2b84bed7 100644
--- a/arbor/morph/region.cpp
+++ b/arbor/morph/region.cpp
@@ -215,13 +215,13 @@ std::ostream& operator<<(std::ostream& o, const all_& t) {
// Region comprising points up to `distance` distal to a point in `start`.
struct distal_interval_: region_tag {
- distal_interval_(const locset& ls, double d): start{ls}, distance{d} {}
+ distal_interval_(locset ls, double d): start{std::move(ls)}, distance{d} {}
locset start;
double distance; //um
};
ARB_ARBOR_API region distal_interval(locset start, double distance) {
- return region(distal_interval_{start, distance});
+ return region(distal_interval_{std::move(start), distance});
}
mextent thingify_(const distal_interval_& reg, const mprovider& p) {
@@ -290,13 +290,13 @@ std::ostream& operator<<(std::ostream& o, const distal_interval_& d) {
// Region comprising points up to `distance` proximal to a point in `end`.
struct proximal_interval_: region_tag {
- proximal_interval_(const locset& ls, double d): end{ls}, distance{d} {}
+ proximal_interval_(locset ls, double d): end{std::move(ls)}, distance{d} {}
locset end;
double distance; //um
};
ARB_ARBOR_API region proximal_interval(locset end, double distance) {
- return region(proximal_interval_{end, distance});
+ return region(proximal_interval_{std::move(end), distance});
}
mextent thingify_(const proximal_interval_& reg, const mprovider& p) {
@@ -347,29 +347,26 @@ std::ostream& operator<<(std::ostream& o, const proximal_interval_& d) {
mextent radius_cmp(const mprovider& p, region r, double val, comp_op op) {
const auto& e = p.embedding();
auto reg_extent = thingify(r, p);
-
msize_t bid = mnpos;
mcable_list cmp_cables;
-
for (auto c: reg_extent) {
if (bid != c.branch) {
bid = c.branch;
util::append(cmp_cables, e.radius_cmp(bid, val, op));
}
}
-
return intersect(reg_extent, mextent(cmp_cables));
}
// Region with all segments with radius less than r
struct radius_lt_: region_tag {
- radius_lt_(const region& rg, double d): reg{rg}, val{d} {}
+ radius_lt_(region rg, double d): reg{std::move(rg)}, val{d} {}
region reg;
double val; //um
};
ARB_ARBOR_API region radius_lt(region reg, double val) {
- return region(radius_lt_{reg, val});
+ return region(radius_lt_{std::move(reg), val});
}
mextent thingify_(const radius_lt_& r, const mprovider& p) {
@@ -382,13 +379,13 @@ std::ostream& operator<<(std::ostream& o, const radius_lt_& r) {
// Region with all segments with radius less than r
struct radius_le_: region_tag {
- radius_le_(const region& rg, double d): reg{rg}, val{d} {}
+ radius_le_(region rg, double d): reg{std::move(rg)}, val{d} {}
region reg;
double val; //um
};
ARB_ARBOR_API region radius_le(region reg, double val) {
- return region(radius_le_{reg, val});
+ return region(radius_le_{std::move(reg), val});
}
mextent thingify_(const radius_le_& r, const mprovider& p) {
@@ -401,13 +398,13 @@ std::ostream& operator<<(std::ostream& o, const radius_le_& r) {
// Region with all segments with radius greater than r
struct radius_gt_: region_tag {
- radius_gt_(const region& rg, double d): reg{rg}, val{d} {}
+ radius_gt_(region rg, double d): reg{std::move(rg)}, val{d} {}
region reg;
double val; //um
};
ARB_ARBOR_API region radius_gt(region reg, double val) {
- return region(radius_gt_{reg, val});
+ return region(radius_gt_{std::move(reg), val});
}
mextent thingify_(const radius_gt_& r, const mprovider& p) {
@@ -420,13 +417,13 @@ std::ostream& operator<<(std::ostream& o, const radius_gt_& r) {
// Region with all segments with radius greater than or equal to r
struct radius_ge_: region_tag {
- radius_ge_(const region& rg, double d): reg{rg}, val{d} {}
+ radius_ge_(region rg, double d): reg{std::move(rg)}, val{d} {}
region reg;
double val; //um
};
ARB_ARBOR_API region radius_ge(region reg, double val) {
- return region(radius_ge_{reg, val});
+ return region(radius_ge_{std::move(reg), val});
}
mextent thingify_(const radius_ge_& r, const mprovider& p) {
@@ -527,13 +524,13 @@ ARB_ARBOR_API region z_dist_from_root_lt(double r0) {
}
region lt = reg::projection_lt(r0);
region gt = reg::projection_gt(-r0);
- return intersect(std::move(lt), std::move(gt));
+ return intersect(lt, gt);
}
ARB_ARBOR_API region z_dist_from_root_le(double r0) {
region le = reg::projection_le(r0);
region ge = reg::projection_ge(-r0);
- return intersect(std::move(le), std::move(ge));
+ return intersect(le, ge);
}
ARB_ARBOR_API region z_dist_from_root_gt(double r0) {
@@ -720,7 +717,7 @@ struct reg_minus: region_tag {
};
mextent thingify_(const reg_minus& P, const mprovider& p) {
- return thingify(intersect(std::move(P.lhs), complement(std::move(P.rhs))), p);
+ return thingify(intersect(P.lhs, complement(P.rhs)), p);
}
std::ostream& operator<<(std::ostream& o, const reg_minus& x) {
diff --git a/arbor/partition_load_balance.cpp b/arbor/partition_load_balance.cpp
index 254bd53a..19f3ac09 100644
--- a/arbor/partition_load_balance.cpp
+++ b/arbor/partition_load_balance.cpp
@@ -27,8 +27,9 @@ ARB_ARBOR_API domain_decomposition partition_load_balance(
{
using util::make_span;
- unsigned num_domains = ctx->distributed->size();
- unsigned domain_id = ctx->distributed->id();
+ const auto& dist = ctx->distributed;
+ unsigned num_domains = dist->size();
+ unsigned domain_id = dist->id();
const bool gpu_avail = ctx->gpu->has_gpu();
auto num_global_cells = rec.num_cells();
@@ -63,7 +64,7 @@ ARB_ARBOR_API domain_decomposition partition_load_balance(
// Gather the global gj_connection table.
// The global gj_connection table after gathering is indexed by gid.
- auto global_gj_connection_table = ctx->distributed->gather_gj_connections(local_gj_connection_table);
+ auto global_gj_connection_table = dist->gather_gj_connections(local_gj_connection_table);
// Make all gj_connections bidirectional.
std::vector<std::unordered_set<cell_gid_type>> missing_peers(global_gj_connection_table.size());
@@ -224,7 +225,7 @@ ARB_ARBOR_API domain_decomposition partition_load_balance(
// Exchange gid list with all other nodes
// global all-to-all to gather a local copy of the global gid list on each node.
- auto global_gids = ctx->distributed->gather_gids(local_gids);
+ auto global_gids = dist->gather_gids(local_gids);
return domain_decomposition(rec, ctx, groups);
}
diff --git a/arbor/s_expr.cpp b/arbor/s_expr.cpp
index 01e626c3..70da5c7c 100644
--- a/arbor/s_expr.cpp
+++ b/arbor/s_expr.cpp
@@ -281,7 +281,7 @@ private:
}
// test if the symbol matches a keyword
- auto it = keyword_to_tok.find(symbol.c_str());
+ auto it = keyword_to_tok.find(symbol);
if (it!=keyword_to_tok.end()) {
return {start, it->second, std::move(symbol)};
}
@@ -413,7 +413,7 @@ std::ostream& print(std::ostream& o, const s_expr& x, int indent) {
bool first=true;
o << "(";
while (it!=end) {
- if (!first && !it->is_atom() && length(*it)>=0) {
+ if (!first && !it->is_atom()) {
o << "\n" << in;
print(o, *it, indent+1);
++it;
diff --git a/arbor/simulation.cpp b/arbor/simulation.cpp
index 940de4ba..21a07d3c 100644
--- a/arbor/simulation.cpp
+++ b/arbor/simulation.cpp
@@ -189,9 +189,10 @@ simulation_state::simulation_state(
local_spikes_({thread_private_spike_store(ctx.thread_pool), thread_private_spike_store(ctx.thread_pool)})
{
// Generate the cell groups in parallel, with one task per cell group.
- cell_groups_.resize(decomp.num_groups());
- std::vector<cell_labels_and_gids> cg_sources(cell_groups_.size());
- std::vector<cell_labels_and_gids> cg_targets(cell_groups_.size());
+ auto num_groups = decomp.num_groups();
+ cell_groups_.resize(num_groups);
+ std::vector<cell_labels_and_gids> cg_sources(num_groups);
+ std::vector<cell_labels_and_gids> cg_targets(num_groups);
foreach_group_index(
[&](cell_group_ptr& group, int i) {
const auto& group_info = decomp.group(i);
@@ -204,7 +205,7 @@ simulation_state::simulation_state(
});
cell_labels_and_gids local_sources, local_targets;
- for(const auto& i: util::make_span(cell_groups_.size())) {
+ for(const auto& i: util::make_span(num_groups)) {
local_sources.append(cg_sources.at(i));
local_targets.append(cg_targets.at(i));
}
@@ -402,8 +403,6 @@ time_type simulation_state::run(time_type tfinal, time_type dt) {
});
};
- threading::task_group g(task_system_.get());
-
epoch prev = epoch_;
epoch current = next_epoch(prev, t_interval_);
epoch next = next_epoch(current, t_interval_);
@@ -418,7 +417,7 @@ time_type simulation_state::run(time_type tfinal, time_type dt) {
}
else {
enqueue(current);
-
+ threading::task_group g(task_system_.get());
g.run([&]() { enqueue(next); });
g.run([&]() { update(current); });
g.wait();
diff --git a/arbor/thread_private_spike_store.cpp b/arbor/thread_private_spike_store.cpp
index f7805350..e1645f03 100644
--- a/arbor/thread_private_spike_store.cpp
+++ b/arbor/thread_private_spike_store.cpp
@@ -1,4 +1,5 @@
#include <vector>
+#include <numeric>
#include <arbor/common_types.hpp>
#include <arbor/spike.hpp>
@@ -23,20 +24,14 @@ thread_private_spike_store::thread_private_spike_store(const task_system_handle&
impl_(new local_spike_store_type(ts))
{}
-thread_private_spike_store::~thread_private_spike_store() {}
+thread_private_spike_store::~thread_private_spike_store() = default;
std::vector<spike> thread_private_spike_store::gather() const {
+ const auto& bs = impl_->buffers_;
+ auto len = std::accumulate(bs.begin(), bs.end(), 0u, [](auto acc, const auto& b) { return acc + b.size(); });
std::vector<spike> spikes;
- unsigned num_spikes = 0u;
- for (auto& b: impl_->buffers_) {
- num_spikes += b.size();
- }
- spikes.reserve(num_spikes);
-
- for (auto& b: impl_->buffers_) {
- spikes.insert(spikes.begin(), b.begin(), b.end());
- }
-
+ spikes.reserve(len);
+ std::for_each(bs.begin(), bs.end(), [&spikes] (const auto& b) { spikes.insert(spikes.end(), b.begin(), b.end()); });
return spikes;
}
diff --git a/arbor/thread_private_spike_store.hpp b/arbor/thread_private_spike_store.hpp
index ff31f207..d0006ef9 100644
--- a/arbor/thread_private_spike_store.hpp
+++ b/arbor/thread_private_spike_store.hpp
@@ -21,7 +21,7 @@ struct local_spike_store_type;
/// and collate all of the buffers into a single vector respectively.
class ARB_ARBOR_API thread_private_spike_store {
public :
- thread_private_spike_store();
+ thread_private_spike_store() = default;
~thread_private_spike_store();
thread_private_spike_store(thread_private_spike_store&& t);
diff --git a/arbor/util/padded_alloc.hpp b/arbor/util/padded_alloc.hpp
index 9dfe7ea3..d29908f0 100644
--- a/arbor/util/padded_alloc.hpp
+++ b/arbor/util/padded_alloc.hpp
@@ -38,7 +38,7 @@ struct padded_allocator {
using propagate_on_container_swap = std::true_type;
using is_always_equal = std::false_type;
- padded_allocator() noexcept {}
+ padded_allocator() noexcept = default;
template <typename U>
padded_allocator(const padded_allocator<U>& b) noexcept: alignment_(b.alignment()) {}
diff --git a/arbor/util/piecewise.hpp b/arbor/util/piecewise.hpp
index 8f029b4f..1a2a0fae 100644
--- a/arbor/util/piecewise.hpp
+++ b/arbor/util/piecewise.hpp
@@ -742,7 +742,7 @@ struct pw_zip_iterator {
bool is_end = true;
typename pw_elements<A>::const_iterator ai, a_end;
typename pw_elements<B>::const_iterator bi, b_end;
- double left;
+ double left = std::nan("");
pw_zip_iterator() = default;
pw_zip_iterator(const pw_elements<A>& a, const pw_elements<B>& b) {
diff --git a/arbor/util/unwind.cpp b/arbor/util/unwind.cpp
index 4e0e1cb9..28ba9afe 100644
--- a/arbor/util/unwind.cpp
+++ b/arbor/util/unwind.cpp
@@ -111,8 +111,6 @@ void backtrace::print(bool stop_at_main) const {
namespace arb {
namespace util {
-backtrace::backtrace() {}
-
std::ostream& operator<<(std::ostream& out, const backtrace& trace) {
return out;
}
diff --git a/arbor/util/unwind.hpp b/arbor/util/unwind.hpp
index deb8d937..293ecf50 100644
--- a/arbor/util/unwind.hpp
+++ b/arbor/util/unwind.hpp
@@ -19,7 +19,7 @@ struct source_location {
class backtrace {
public:
/// the default constructor will build and store the strack trace.
- backtrace();
+ backtrace() = default;
/// Creates a new file named backtrace_# where # is a number chosen
/// The back trace is printed to the file, and a message printed to
diff --git a/arborio/cableio.cpp b/arborio/cableio.cpp
index 88eefd72..e06d81c1 100644
--- a/arborio/cableio.cpp
+++ b/arborio/cableio.cpp
@@ -68,7 +68,7 @@ s_expr mksexp(const threshold_detector& d) {
}
s_expr mksexp(const mechanism_desc& d) {
std::vector<s_expr> mech;
- mech.push_back(s_expr(d.name()));
+ mech.emplace_back(d.name());
std::transform(d.values().begin(), d.values().end(), std::back_inserter(mech),
[](const auto& x){return slist(s_expr(x.first), x.second);});
return s_expr{"mechanism"_symbol, slist_range(mech)};
@@ -144,7 +144,7 @@ s_expr mksexp(const morphology& morph) {
};
std::vector<s_expr> branches;
for (msize_t i = 0; i < morph.num_branches(); ++i) {
- branches.push_back(make_branch(i));
+ branches.emplace_back(make_branch(i));
}
return s_expr{"morphology"_symbol, slist_range(branches)};
}
@@ -218,7 +218,7 @@ arb::i_clamp make_i_clamp(const std::vector<arb::i_clamp::envelope_point>& envlp
pulse_tuple make_envelope_pulse(double delay, double duration, double amplitude) {
return pulse_tuple{delay, duration, amplitude};
}
-arb::i_clamp make_i_clamp_pulse(pulse_tuple p, double freq, double phase) {
+arb::i_clamp make_i_clamp_pulse(const pulse_tuple& p, double freq, double phase) {
return arb::i_clamp::box(std::get<0>(p), std::get<1>(p), std::get<2>(p), freq, phase);
}
arb::cv_policy make_cv_policy(const cv_policy& p) {
@@ -235,10 +235,10 @@ T make_wrapped_mechanism(const arb::mechanism_desc& mech) {return T(mech);}
// Define makers for placeable pairs, paintable pairs, defaultables and decors
using place_tuple = std::tuple<arb::locset, arb::placeable, std::string>;
using paint_pair = std::pair<arb::region, arb::paintable>;
-place_tuple make_place(locset where, placeable what, std::string name) {
+place_tuple make_place(const locset& where, const placeable& what, const std::string& name) {
return place_tuple{where, what, name};
}
-paint_pair make_paint(region where, paintable what) {
+paint_pair make_paint(const region& where, const paintable& what) {
return paint_pair{where, what};
}
defaultable make_default(defaultable what) {
@@ -259,10 +259,10 @@ decor make_decor(const std::vector<std::variant<place_tuple, paint_pair, default
// Define maker for locset pairs, region pairs and label_dicts
using locset_pair = std::pair<std::string, locset>;
using region_pair = std::pair<std::string, region>;
-locset_pair make_locset_pair(std::string name, locset desc) {
+locset_pair make_locset_pair(const std::string& name, const locset& desc) {
return locset_pair{name, desc};
}
-region_pair make_region_pair(std::string name, region desc) {
+region_pair make_region_pair(const std::string name, const region& desc) {
return region_pair{name, desc};
}
label_dict make_label_dict(const std::vector<std::variant<locset_pair, region_pair>>& args) {
@@ -276,7 +276,7 @@ label_dict make_label_dict(const std::vector<std::variant<locset_pair, region_pa
arb::mpoint make_point(double x, double y, double z, double r) {
return arb::mpoint{x, y, z, r};
}
-arb::msegment make_segment(unsigned id, arb::mpoint prox, arb::mpoint dist, int tag) {
+arb::msegment make_segment(unsigned id, const arb::mpoint& prox, const arb::mpoint& dist, int tag) {
return arb::msegment{id, prox, dist, tag};
}
morphology make_morphology(const std::vector<std::variant<branch_tuple>>& args) {
@@ -328,10 +328,10 @@ cable_cell make_cable_cell(const std::vector<std::variant<morphology, label_dict
}
return cable_cell(morpho, dict, dec);
}
-version_tuple make_version(std::string v) {
+version_tuple make_version(const std::string& v) {
return version_tuple{v};
}
-meta_data make_meta_data(version_tuple v) {
+meta_data make_meta_data(const version_tuple& v) {
return meta_data{std::get<0>(v)};
}
template <typename T>
@@ -502,9 +502,11 @@ parse_hopefully<std::any> eval(const s_expr& e, const eval_map& map, const eval_
return eval_atom<cableio_parse_error>(e);
}
- if (e.head().is_atom()) {
+ auto& hd = e.head();
+ if (hd.is_atom()) {
+ auto& atom = hd.atom();
// If this is not a symbol, parse as a tuple
- if (e.head().atom().kind != tok::symbol) {
+ if (atom.kind != tok::symbol) {
auto args = eval_args(e, map, vec);
if (!args) {
return util::unexpected(args.error());
@@ -535,7 +537,7 @@ parse_hopefully<std::any> eval(const s_expr& e, const eval_map& map, const eval_
}
// Find all candidate functions that match the name of the function.
- auto& name = e.head().atom().spelling;
+ auto& name = atom.spelling;
auto matches = map.equal_range(name);
// Search for a candidate that matches the argument list.
@@ -661,7 +663,7 @@ eval_vec unnamed_evals{
make_call<double, double>(std::make_tuple<double, double>, "tuple<double, double>")
};
-inline parse_hopefully<std::any> parse(const arb::s_expr& s) {
+inline parse_hopefully<std::any> parse(arb::s_expr s) {
return eval(std::move(s), named_evals, unnamed_evals);
}
diff --git a/arborio/neurolucida.cpp b/arborio/neurolucida.cpp
index 2cfc8b16..af033796 100644
--- a/arborio/neurolucida.cpp
+++ b/arborio/neurolucida.cpp
@@ -46,8 +46,8 @@ struct parse_error {
stack.push_back(cpp);
}
- parse_error& append(cpp_info i) {
- stack.push_back(i);
+ parse_error& append(const cpp_info& i) {
+ stack.emplace_back(i);
return *this;
}
@@ -165,9 +165,9 @@ bool is_marker_symbol(const asc::token& t) {
// (Color Red) ; labeled
// (Color RGB (152, 251, 152)) ; RGB literal
struct asc_color {
- uint8_t r;
- uint8_t g;
- uint8_t b;
+ uint8_t r = 0;
+ uint8_t g = 0;
+ uint8_t b = 0;
};
[[maybe_unused]]
diff --git a/sup/include/sup/ioutil.hpp b/sup/include/sup/ioutil.hpp
index c1be394b..af05fa6c 100644
--- a/sup/include/sup/ioutil.hpp
+++ b/sup/include/sup/ioutil.hpp
@@ -32,7 +32,7 @@ public:
typedef typename streambuf_type::off_type off_type;
typedef typename streambuf_type::traits_type traits_type;
- virtual ~basic_null_streambuf() {}
+ virtual ~basic_null_streambuf() = default;
protected:
std::streamsize xsputn(const char_type* s, std::streamsize count) override {
--
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