Fixes suggested by clang-tidy

jhenin · jhenin · commit 9836f6ed229d · 2025-10-13T17:49:02.000+02:00
- fix instances of std::ios::fmtflags(0) which is undefined (apparently)
- use emplace_back() when appropriate to avoid unnecessary copies
diff --git a/src/colvar.cpp b/src/colvar.cpp
@@ -1280,7 +1280,7 @@ int colvar::init_dependencies() {
   // Initialize feature_states for each instance
   feature_states.reserve(f_cv_ntot);
   for (i = feature_states.size(); i < f_cv_ntot; i++) {
-    feature_states.push_back(feature_state(true, false));
+    feature_states.emplace_back(true, false);
     // Most features are available, so we set them so
     // and list exceptions below
    }
@@ -2043,8 +2043,8 @@ void colvar::communicate_forces()
     func_grads.reserve(cvcs.size());
     for (i = 0; i < cvcs.size(); i++) {
       if (!cvcs[i]->is_enabled()) continue;
-      func_grads.push_back(cvm::matrix2d<cvm::real> (x.size(),
-                                                     cvcs[i]->value().size()));
+      func_grads.emplace_back(x.size(),
+                                                     cvcs[i]->value().size());
     }
     int res = cvm::proxy->run_colvar_gradient_callback(scripted_function, sorted_cvc_values, func_grads);
 
@@ -2803,7 +2803,7 @@ int colvar::calc_acf()
     case acf_vel:
       // allocate space for the velocities history
       for (i = 0; i < acf_stride; i++) {
-        acf_v_history.push_back(std::list<colvarvalue>());
+        acf_v_history.emplace_back();
       }
       acf_v_history_p = acf_v_history.begin();
       break;
@@ -2812,7 +2812,7 @@ int colvar::calc_acf()
     case acf_p2coor:
       // allocate space for the coordinates history
       for (i = 0; i < acf_stride; i++) {
-        acf_x_history.push_back(std::list<colvarvalue>());
+        acf_x_history.emplace_back();
       }
       acf_x_history_p = acf_x_history.begin();
       break;
@@ -3003,7 +3003,7 @@ int colvar::calc_runave()
 
     acf_nframes = 0;
 
-    x_history.push_back(std::list<colvarvalue>());
+    x_history.emplace_back();
     x_history_p = x_history.begin();
 
   } else {
diff --git a/src/colvar_neuralnetworkcompute.cpp b/src/colvar_neuralnetworkcompute.cpp
@@ -246,15 +246,15 @@ bool neuralNetworkCompute::addDenseLayer(const denseLayer& layer) {
     if (m_dense_layers.empty()) {
         // add layer to this ann directly if m_dense_layers is empty
         m_dense_layers.push_back(layer);
-        m_layers_output.push_back(std::vector<double>(layer.getOutputSize()));
-        m_grads_tmp.push_back(std::vector<std::vector<double>>(layer.getOutputSize(), std::vector<double>(layer.getInputSize(), 0)));
+        m_layers_output.emplace_back(layer.getOutputSize());
+        m_grads_tmp.emplace_back(layer.getOutputSize(), std::vector<double>(layer.getInputSize(), 0));
         return true;
     } else {
         // otherwise, we need to check if the output of last layer in m_dense_layers matches the input of layer to be added
         if (m_dense_layers.back().getOutputSize() == layer.getInputSize()) {
             m_dense_layers.push_back(layer);
-            m_layers_output.push_back(std::vector<double>(layer.getOutputSize()));
-            m_grads_tmp.push_back(std::vector<std::vector<double>>(layer.getOutputSize(), std::vector<double>(layer.getInputSize(), 0)));
+            m_layers_output.emplace_back(layer.getOutputSize());
+            m_grads_tmp.emplace_back(layer.getOutputSize(), std::vector<double>(layer.getInputSize(), 0));
             return true;
         } else {
             return false;
diff --git a/src/colvaratoms.cpp b/src/colvaratoms.cpp
@@ -213,7 +213,7 @@ int cvm::atom_group::init_dependencies() {
   // default as unavailable, not enabled
   feature_states.reserve(f_ag_ntot);
   for (i = feature_states.size(); i < colvardeps::f_ag_ntot; i++) {
-    feature_states.push_back(feature_state(false, false));
+    feature_states.emplace_back(false, false);
   }
 
   // Features that are implemented (or not) by all atom groups
diff --git a/src/colvarbias.cpp b/src/colvarbias.cpp
@@ -248,7 +248,7 @@ int colvarbias::init_dependencies() {
   // Initialize feature_states for each instance
   feature_states.reserve(f_cvb_ntot);
   for (i = feature_states.size(); i < f_cvb_ntot; i++) {
-    feature_states.push_back(feature_state(true, false));
+    feature_states.emplace_back(true, false);
     // Most features are available, so we set them so
     // and list exceptions below
   }
@@ -352,7 +352,7 @@ int colvarbias::add_colvar(std::string const &cv_name)
     // although possibly not at all timesteps
     add_child(cv);
 
-    colvar_forces.push_back(colvarvalue());
+    colvar_forces.emplace_back();
     colvar_forces.back().type(cv->value()); // make sure each force is initialized to zero
     colvar_forces.back().is_derivative(); // colvar constraints are not applied to the force
     colvar_forces.back().reset();
diff --git a/src/colvarbias_abf.cpp b/src/colvarbias_abf.cpp
@@ -925,7 +925,7 @@ template <typename OST> OST & colvarbias_abf::write_state_data_template_(OST &os
 {
   auto flags = os.flags();
 
-  os.setf(std::ios::fmtflags(std::ios::dec), std::ios::floatfield); // default floating-point format
+  os.unsetf(std::ios::floatfield); // default floating-point format
 
   write_state_data_key(os, "samples");
   samples->write_raw(os, 8);
@@ -941,7 +941,7 @@ template <typename OST> OST & colvarbias_abf::write_state_data_template_(OST &os
   }
 
   if (b_CZAR_estimator) {
-    os.setf(std::ios::fmtflags(std::ios::dec), std::ios::floatfield); // default floating-point format
+    os.unsetf(std::ios::floatfield); // default floating-point format
     write_state_data_key(os, "z_samples");
     z_samples->write_raw(os, 8);
     write_state_data_key(os, "z_gradient");
diff --git a/src/colvarbias_histogram.cpp b/src/colvarbias_histogram.cpp
@@ -216,7 +216,7 @@ cvm::memory_stream & colvarbias_histogram::read_state_data(cvm::memory_stream& i
 std::ostream & colvarbias_histogram::write_state_data(std::ostream& os)
 {
   std::ios::fmtflags flags(os.flags());
-  os.setf(std::ios::fmtflags(std::ios::dec), std::ios::floatfield);
+  os.unsetf(std::ios::floatfield);
   write_state_data_key(os, "grid");
   grid->write_raw(os, 8);
   os.flags(flags);
diff --git a/src/colvarbias_histogram_reweight_amd.cpp b/src/colvarbias_histogram_reweight_amd.cpp
@@ -318,7 +318,7 @@ void colvarbias_reweightaMD::compute_cumulant_expansion_factor(
 template <typename OST> OST & colvarbias_reweightaMD::write_state_data_template_(OST& os)
 {
   std::ios::fmtflags flags(os.flags());
-  os.setf(std::ios::fmtflags(std::ios::dec), std::ios::floatfield);
+  os.unsetf(std::ios::floatfield);
   write_state_data_key(os, "grid");
   grid->write_raw(os, 8);
   write_state_data_key(os, "grid_count");
diff --git a/src/colvarbias_meta.cpp b/src/colvarbias_meta.cpp
@@ -1705,7 +1705,7 @@ template <typename IST> IST &colvarbias_meta::read_hill_template_(IST &is)
   }
 
   hill_iter const hills_end = hills.end();
-  hills.push_back(hill(h_it, h_weight, h_centers, h_sigmas, h_replica));
+  hills.emplace_back(h_it, h_weight, h_centers, h_sigmas, h_replica);
   if (new_hills_begin == hills_end) {
     // if new_hills_begin is unset, set it for the first time
     new_hills_begin = hills.end();
diff --git a/src/colvarcomp.cpp b/src/colvarcomp.cpp
@@ -308,7 +308,7 @@ int colvar::cvc::init_dependencies() {
   feature_states.reserve(f_cvc_ntot);
   for (i = feature_states.size(); i < colvardeps::f_cvc_ntot; i++) {
     bool avail = is_dynamic(i) ? false : true;
-    feature_states.push_back(feature_state(avail, false));
+    feature_states.emplace_back(avail, false);
   }
 
   // Features that are implemented by all cvcs by default
diff --git a/src/colvarcomp_neuralnetwork.cpp b/src/colvarcomp_neuralnetwork.cpp
@@ -77,14 +77,14 @@ int colvar::neuralNetwork::init(std::string const &conf)
                 return cvm::error("Unknown activation function name: \"" + function_name + "\".\n",
                                COLVARS_INPUT_ERROR);
             }
-            activation_functions.push_back(std::make_pair(false, function_name));
+            activation_functions.emplace_back(false, function_name);
             cvm::log(std::string{"The activation function for layer["} + cvm::to_str(num_activation_functions + 1) + std::string{"] is "} + function_name + '\n');
             ++num_activation_functions;
 #ifdef LEPTON
         } else if (key_lookup(conf, lookup_key_custom.c_str())) {
             std::string function_expression;
             get_keyval(conf, lookup_key_custom.c_str(), function_expression, std::string(""));
-            activation_functions.push_back(std::make_pair(true, function_expression));
+            activation_functions.emplace_back(true, function_expression);
             cvm::log(std::string{"The custom activation function for layer["} + cvm::to_str(num_activation_functions + 1) + std::string{"] is "} + function_expression + '\n');
             ++num_activation_functions;
 #endif
diff --git a/src/colvardeps.cpp b/src/colvardeps.cpp
@@ -421,22 +421,22 @@ void colvardeps::require_feature_children(int f, int g) {
 
 
 void colvardeps::require_feature_alt(int f, int g, int h) {
-  features()[f]->requires_alt.push_back(std::vector<int>(2));
+  features()[f]->requires_alt.emplace_back(2);
   features()[f]->requires_alt.back()[0] = g;
   features()[f]->requires_alt.back()[1] = h;
 }
 
 
 void colvardeps::require_feature_alt(int f, int g, int h, int i) {
-  features()[f]->requires_alt.push_back(std::vector<int>(3));
+  features()[f]->requires_alt.emplace_back(3);
   features()[f]->requires_alt.back()[0] = g;
   features()[f]->requires_alt.back()[1] = h;
   features()[f]->requires_alt.back()[2] = i;
 }
 
 
 void colvardeps::require_feature_alt(int f, int g, int h, int i, int j) {
-  features()[f]->requires_alt.push_back(std::vector<int>(4));
+  features()[f]->requires_alt.emplace_back(4);
   features()[f]->requires_alt.back()[0] = g;
   features()[f]->requires_alt.back()[1] = h;
   features()[f]->requires_alt.back()[2] = i;
diff --git a/src/colvargrid_integrate.cpp b/src/colvargrid_integrate.cpp
@@ -49,7 +49,7 @@ colvargrid_integrate::colvargrid_integrate(std::shared_ptr<colvar_grid_gradient>
   for (size_t i = 0; i < nd; i++ ) {
     if (!periodic[i]) nx[i]++;
     // Shift the grid by half the bin width (values at edges instead of center of bins)
-    lower_boundaries.push_back(gradients->lower_boundaries[i].real_value - 0.5 * widths[i]);
+    lower_boundaries.emplace_back(gradients->lower_boundaries[i].real_value - 0.5 * widths[i]);
   }
 
   setup(nx);
diff --git a/src/colvarmodule.cpp b/src/colvarmodule.cpp
@@ -2125,7 +2125,7 @@ int cvm::read_index_file(char const *filename)
   if (!is) {
     return COLVARS_FILE_ERROR;
   } else {
-    index_file_names.push_back(std::string(filename));
+    index_file_names.emplace_back(filename);
   }
 
   while (is.good()) {
diff --git a/src/colvarproxy.cpp b/src/colvarproxy.cpp
@@ -54,9 +54,9 @@ int colvarproxy_atoms::add_atom_slot(int atom_id)
   atoms_refcount.push_back(1);
   atoms_masses.push_back(1.0);
   atoms_charges.push_back(0.0);
-  atoms_positions.push_back(cvm::rvector(0.0, 0.0, 0.0));
-  atoms_total_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
-  atoms_new_colvar_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
+  atoms_positions.emplace_back(0.0, 0.0, 0.0);
+  atoms_total_forces.emplace_back(0.0, 0.0, 0.0);
+  atoms_new_colvar_forces.emplace_back(0.0, 0.0, 0.0);
   modified_atom_list_ = true;
   return (atoms_ids.size() - 1);
 }
@@ -181,9 +181,9 @@ int colvarproxy_atom_groups::add_atom_group_slot(int atom_group_id)
   atom_groups_refcount.push_back(1);
   atom_groups_masses.push_back(1.0);
   atom_groups_charges.push_back(0.0);
-  atom_groups_coms.push_back(cvm::rvector(0.0, 0.0, 0.0));
-  atom_groups_total_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
-  atom_groups_new_colvar_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
+  atom_groups_coms.emplace_back(0.0, 0.0, 0.0);
+  atom_groups_total_forces.emplace_back(0.0, 0.0, 0.0);
+  atom_groups_new_colvar_forces.emplace_back(0.0, 0.0, 0.0);
   return (atom_groups_ids.size() - 1);
 }
 
@@ -503,7 +503,7 @@ int colvarproxy::request_deletion()
 
 void colvarproxy::add_config(std::string const &cmd, std::string const &conf)
 {
-  reinterpret_cast<std::list<std::pair<std::string, std::string> > *>(config_queue_)->push_back(std::make_pair(cmd, conf));
+  reinterpret_cast<std::list<std::pair<std::string, std::string> > *>(config_queue_)->emplace_back(cmd, conf);
 }
 
 
diff --git a/src/colvars_memstream.h b/src/colvars_memstream.h
@@ -106,16 +106,19 @@ class cvm::memory_stream {
   inline memory_stream & seekg(size_t pos) { read_pos_ = pos; return *this; }
 
   /// Ignore formatting operators
-  inline void setf(decltype(std::ios::fmtflags(std::ios::unitbuf)), decltype(std::ios::floatfield)) {}
+  inline void setf(std::ios::fmtflags /* flags */, std::ios::fmtflags /* mask */) {}
 
   /// Ignore formatting operators
-  inline void setf(decltype(std::ios::fmtflags(std::ios::unitbuf))) {}
+  inline void setf(std::ios::fmtflags) {}
 
   /// Ignore formatting operators
-  inline void flags(decltype(std::ios::fmtflags(std::ios::unitbuf))) {}
+  inline void unsetf(std::ios::fmtflags) {}
 
-  /// Get the current formatting flags (throw a useless result because this stream is unformatted)
-  inline decltype(std::ios::fmtflags(std::ios::unitbuf)) flags() const { return std::ios::fmtflags(std::ios::unitbuf); }
+  /// Ignore formatting operators
+  inline void flags(std::ios::fmtflags) {}
+
+  /// Get the current formatting flags (i.e. none because this stream is unformatted)
+  inline std::ios::fmtflags flags() const { return std::ios::fmtflags{}; }
 
   /// Get the error code
   inline std::ios::iostate rdstate() const { return state_; }
diff --git a/src/colvarscript.cpp b/src/colvarscript.cpp
@@ -481,7 +481,7 @@ std::vector<std::string> colvarscript::obj_to_str_vector(unsigned char *obj)
                    str+"\n", COLVARS_INPUT_ERROR);
         break;
       }
-      new_result.push_back(std::string(""));
+      new_result.emplace_back("");
       while (str[i] != '\"') {
         new_result.back().append(1, str[i]);
         if (i >= str.length()) {

Original file line number	Diff line number	Diff line change
`@@ -213,7 +213,7 @@ int cvm::atom_group::init_dependencies() {`
`213`	`213`	`// default as unavailable, not enabled`
`214`	`214`	`feature_states.reserve(f_ag_ntot);`
`215`	`215`	`for (i = feature_states.size(); i < colvardeps::f_ag_ntot; i++) {`
`216`		`- feature_states.push_back(feature_state(false, false));`
	`216`	`+ feature_states.emplace_back(false, false);`
`217`	`217`	`}`
`218`	`218`
`219`	`219`	`// Features that are implemented (or not) by all atom groups`
Original file line number	Diff line number	Diff line change
`@@ -925,7 +925,7 @@ template <typename OST> OST & colvarbias_abf::write_state_data_template_(OST &os`
`925`	`925`	`{`
`926`	`926`	`auto flags = os.flags();`
`927`	`927`
`928`		`- os.setf(std::ios::fmtflags(std::ios::dec), std::ios::floatfield); // default floating-point format`
	`928`	`+ os.unsetf(std::ios::floatfield); // default floating-point format`
`929`	`929`
`930`	`930`	`write_state_data_key(os, "samples");`
`931`	`931`	`samples->write_raw(os, 8);`
`@@ -941,7 +941,7 @@ template <typename OST> OST & colvarbias_abf::write_state_data_template_(OST &os`
`941`	`941`	`}`
`942`	`942`
`943`	`943`	`if (b_CZAR_estimator) {`
`944`		`- os.setf(std::ios::fmtflags(std::ios::dec), std::ios::floatfield); // default floating-point format`
	`944`	`+ os.unsetf(std::ios::floatfield); // default floating-point format`
`945`	`945`	`write_state_data_key(os, "z_samples");`
`946`	`946`	`z_samples->write_raw(os, 8);`
`947`	`947`	`write_state_data_key(os, "z_gradient");`
Original file line number	Diff line number	Diff line change
`@@ -216,7 +216,7 @@ cvm::memory_stream & colvarbias_histogram::read_state_data(cvm::memory_stream& i`
`216`	`216`	`std::ostream & colvarbias_histogram::write_state_data(std::ostream& os)`
`217`	`217`	`{`
`218`	`218`	`std::ios::fmtflags flags(os.flags());`
`219`		`- os.setf(std::ios::fmtflags(std::ios::dec), std::ios::floatfield);`
	`219`	`+ os.unsetf(std::ios::floatfield);`
`220`	`220`	`write_state_data_key(os, "grid");`
`221`	`221`	`grid->write_raw(os, 8);`
`222`	`222`	`os.flags(flags);`
Original file line number	Diff line number	Diff line change
`@@ -318,7 +318,7 @@ void colvarbias_reweightaMD::compute_cumulant_expansion_factor(`
`318`	`318`	`template <typename OST> OST & colvarbias_reweightaMD::write_state_data_template_(OST& os)`
`319`	`319`	`{`
`320`	`320`	`std::ios::fmtflags flags(os.flags());`
`321`		`- os.setf(std::ios::fmtflags(std::ios::dec), std::ios::floatfield);`
	`321`	`+ os.unsetf(std::ios::floatfield);`
`322`	`322`	`write_state_data_key(os, "grid");`
`323`	`323`	`grid->write_raw(os, 8);`
`324`	`324`	`write_state_data_key(os, "grid_count");`
Original file line number	Diff line number	Diff line change
`@@ -1705,7 +1705,7 @@ template <typename IST> IST &colvarbias_meta::read_hill_template_(IST &is)`
`1705`	`1705`	`}`
`1706`	`1706`
`1707`	`1707`	`hill_iter const hills_end = hills.end();`
`1708`		`- hills.push_back(hill(h_it, h_weight, h_centers, h_sigmas, h_replica));`
	`1708`	`+ hills.emplace_back(h_it, h_weight, h_centers, h_sigmas, h_replica);`
`1709`	`1709`	`if (new_hills_begin == hills_end) {`
`1710`	`1710`	`// if new_hills_begin is unset, set it for the first time`
`1711`	`1711`	`new_hills_begin = hills.end();`
Original file line number	Diff line number	Diff line change
`@@ -308,7 +308,7 @@ int colvar::cvc::init_dependencies() {`
`308`	`308`	`feature_states.reserve(f_cvc_ntot);`
`309`	`309`	`for (i = feature_states.size(); i < colvardeps::f_cvc_ntot; i++) {`
`310`	`310`	`bool avail = is_dynamic(i) ? false : true;`
`311`		`- feature_states.push_back(feature_state(avail, false));`
	`311`	`+ feature_states.emplace_back(avail, false);`
`312`	`312`	`}`
`313`	`313`
`314`	`314`	`// Features that are implemented by all cvcs by default`