Replace std::copy with simpler direct assignment where possible

src/equil/ChemEquil.cpp

@@ -668,7 +668,7 @@ int ChemEquil::equilibrate(thermo_t& s, const char* XYstr,
             }
         }
 
-        copy(x.begin(), x.end(), oldx.begin());
+        oldx = x;
         oldf = f;
         scale(res_trial.begin(), res_trial.end(), res_trial.begin(), -1.0);
 
@@ -913,12 +913,11 @@ int ChemEquil::estimateEP_Brinkley(thermo_t& s, vector_fp& x,
     vector_fp n_i(m_kk,0.0);
     vector_fp n_i_calc(m_kk,0.0);
     vector_fp actCoeff(m_kk, 1.0);
-    vector_fp Xmol_i_calc(m_kk,0.0);
     double beta = 1.0;
 
     s.getMoleFractions(n_i.data());
     double pressureConst = s.pressure();
-    copy(n_i.begin(), n_i.end(), Xmol_i_calc.begin());
+    vector_fp Xmol_i_calc = n_i;
 
     vector_fp x_old(m_mm+1, 0.0);
     vector_fp resid(m_mm+1, 0.0);

src/equil/MultiPhaseEquil.cpp

@@ -408,7 +408,7 @@ void MultiPhaseEquil::getComponents(const std::vector<size_t>& order)
 
 void MultiPhaseEquil::unsort(vector_fp& x)
 {
-    copy(x.begin(), x.end(), m_work2.begin());
+    m_work2 = x;
     size_t k;
     for (k = 0; k < m_nsp; k++) {
         x[m_order[k]] = m_work2[k];

src/kinetics/AqueousKinetics.cpp

@@ -102,13 +102,13 @@ void AqueousKinetics::updateROP()
     }
 
     // copy rate coefficients into ropf
-    copy(m_rfn.begin(), m_rfn.end(), m_ropf.begin());
+    m_ropf = m_rfn;
 
     // multiply by perturbation factor
     multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());
 
     // copy the forward rates to the reverse rates
-    copy(m_ropf.begin(), m_ropf.end(), m_ropr.begin());
+    m_ropr = m_ropf;
 
     // for reverse rates computed from thermochemistry, multiply the forward
     // rates copied into m_ropr by the reciprocals of the equilibrium constants
@@ -133,7 +133,7 @@ void AqueousKinetics::getFwdRateConstants(doublereal* kfwd)
     _update_rates_C();
 
     // copy rate coefficients into ropf
-    copy(m_rfn.begin(), m_rfn.end(), m_ropf.begin());
+    m_ropf = m_rfn;
 
     // multiply by perturbation factor
     multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());

src/kinetics/GasKinetics.cpp

@@ -168,7 +168,7 @@ void GasKinetics::updateROP()
     }
 
     // copy rate coefficients into ropf
-    copy(m_rfn.begin(), m_rfn.end(), m_ropf.begin());
+    m_ropf = m_rfn;
 
     // multiply ropf by enhanced 3b conc for all 3b rxns
     if (!concm_3b_values.empty()) {
@@ -183,7 +183,7 @@ void GasKinetics::updateROP()
     multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());
 
     // copy the forward rates to the reverse rates
-    copy(m_ropf.begin(), m_ropf.end(), m_ropr.begin());
+    m_ropr = m_ropf;
 
     // for reverse rates computed from thermochemistry, multiply the forward
     // rates copied into m_ropr by the reciprocals of the equilibrium constants
@@ -216,7 +216,7 @@ void GasKinetics::getFwdRateConstants(doublereal* kfwd)
     update_rates_T();
 
     // copy rate coefficients into ropf
-    copy(m_rfn.begin(), m_rfn.end(), m_ropf.begin());
+    m_ropf = m_rfn;
 
     // multiply ropf by enhanced 3b conc for all 3b rxns
     if (!concm_3b_values.empty()) {

src/kinetics/ImplicitSurfChem.cpp

@@ -224,13 +224,13 @@ void ImplicitSurfChem::solvePseudoSteadyStateProblem(int ifuncOverride,
     m_surfSolver->m_ioflag = m_ioFlag;
 
     // Save the current solution
-    copy(m_concSpecies.begin(), m_concSpecies.end(), m_concSpeciesSave.begin());
+    m_concSpeciesSave = m_concSpecies;
 
     int retn = m_surfSolver->solveSurfProb(ifunc, time_scale, TKelvin, PGas,
                                            reltol, atol);
     if (retn != 1) {
         // reset the concentrations
-        copy(m_concSpeciesSave.begin(), m_concSpeciesSave.end(), m_concSpecies.begin());
+        m_concSpecies = m_concSpeciesSave;
         setConcSpecies(m_concSpeciesSave.data());
         ifunc = SFLUX_INITIALIZE;
         retn = m_surfSolver->solveSurfProb(ifunc, time_scale, TKelvin, PGas,

src/kinetics/InterfaceKinetics.cpp

@@ -441,13 +441,13 @@ void InterfaceKinetics::updateROP()
     }
 
     // Copy the reaction rate coefficients, m_rfn, into m_ropf
-    copy(m_rfn.begin(), m_rfn.end(), m_ropf.begin());
+    m_ropf = m_rfn;
 
     // Multiply by the perturbation factor
     multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());
 
     // Copy the forward rate constants to the reverse rate constants
-    copy(m_ropf.begin(), m_ropf.end(), m_ropr.begin());
+    m_ropr = m_ropf;
 
     // For reverse rates computed from thermochemistry, multiply
     // the forward rates copied into m_ropr by the reciprocals of

src/kinetics/solveSP.cpp

@@ -158,7 +158,7 @@ int solveSP::solveSurfProb(int ifunc, doublereal time_scale, doublereal TKelvin,
         }
     }
 
-    std::copy(m_CSolnSP.begin(), m_CSolnSP.end(), m_CSolnSPInit.begin());
+    m_CSolnSPInit = m_CSolnSP;
 
     // Calculate the largest species in each phase
     evalSurfLarge(m_CSolnSP.data());
@@ -177,7 +177,7 @@ int solveSP::solveSurfProb(int ifunc, doublereal time_scale, doublereal TKelvin,
     while (not_converged && iter < iter_max) {
         iter++;
         // Store previous iteration's solution in the old solution vector
-        std::copy(m_CSolnSP.begin(), m_CSolnSP.end(), m_CSolnSPOld.begin());
+        m_CSolnSPOld = m_CSolnSP;
 
         // Evaluate the largest surface species for each surface phase every
         // 5 iterations.

src/numerics/BandMatrix.cpp

@@ -229,7 +229,7 @@ void BandMatrix::leftMult(const doublereal* const b, doublereal* const prod) con
 int BandMatrix::factor()
 {
     int info=0;
-    copy(data.begin(), data.end(), ludata.begin());
+    ludata = data;
     ct_dgbtrf(nRows(), nColumns(), nSubDiagonals(), nSuperDiagonals(),
               ludata.data(), ldim(), ipiv().data(), info);
 

src/oneD/Sim1D.cpp

@@ -194,7 +194,7 @@ int Sim1D::newtonSolve(int loglevel)
 {
     int m = OneDim::solve(m_x.data(), m_xnew.data(), loglevel);
     if (m >= 0) {
-        copy(m_xnew.begin(), m_xnew.end(), m_x.begin());
+        m_x = m_xnew;
         return 0;
     } else if (m > -10) {
         return -1;
@@ -385,8 +385,7 @@ int Sim1D::refine(int loglevel)
     }
 
     // Replace the current solution vector with the new one
-    m_x.resize(xnew.size());
-    copy(xnew.begin(), xnew.end(), m_x.begin());
+    m_x = xnew;
 
     // resize the work array
     m_xnew.resize(xnew.size());
@@ -478,12 +477,10 @@ int Sim1D::setFixedTemperature(doublereal t)
     }
 
     // Replace the current solution vector with the new one
-    m_x.resize(xnew.size());
-    copy(xnew.begin(), xnew.end(), m_x.begin());
+    m_x = xnew;
 
     // resize the work array
-    m_xnew.resize(xnew.size());
-    copy(xnew.begin(), xnew.end(), m_xnew.begin());
+    m_xnew = xnew;
     resize();
     finalize();
     return np;

src/thermo/Phase.cpp

@@ -498,11 +498,7 @@ doublereal Phase::molecularWeight(size_t k) const
 
 void Phase::getMolecularWeights(vector_fp& weights) const
 {
-    const vector_fp& mw = molecularWeights();
-    if (weights.size() < mw.size()) {
-        weights.resize(mw.size());
-    }
-    copy(mw.begin(), mw.end(), weights.begin());
+    weights = molecularWeights();
 }
 
 void Phase::getMolecularWeights(doublereal* weights) const

src/thermo/SpeciesThermoFactory.cpp

@@ -125,8 +125,7 @@ static SpeciesThermoInterpType* newNasaThermoFromXML(vector<XML_Node*> nodes)
             getFloatArray(nodes[1]->child("floatArray"), c1, false);
         } else {
             // if there is no higher range data, then copy c0 to c1.
-            c1.resize(7,0.0);
-            copy(c0.begin(), c0.end(), c1.begin());
+            c1 = c0;
         }
     } else if (fabs(tmax1 - tmin0) < 0.01) {
         // f1 has the lower T data, and f0 the higher T data

src/transport/DustyGasTransport.cpp

@@ -96,8 +96,7 @@ void DustyGasTransport::initialize(ThermoPhase* phase, Transport* gastr)
     }
 
     // make a local copy of the molecular weights
-    m_mw.resize(m_nsp);
-    copy(m_thermo->molecularWeights().begin(), m_thermo->molecularWeights().end(), m_mw.begin());
+    m_mw = m_thermo->molecularWeights();
 
     m_multidiff.resize(m_nsp, m_nsp);
     m_d.resize(m_nsp, m_nsp);

src/transport/GasTransport.cpp

@@ -351,8 +351,7 @@ void GasTransport::init(thermo_t* thermo, int mode, int log_level)
     m_bdiff.resize(m_nsp, m_nsp);
 
     // make a local copy of the molecular weights
-    m_mw.assign(m_thermo->molecularWeights().begin(),
-                m_thermo->molecularWeights().end());
+    m_mw = m_thermo->molecularWeights();
 
     m_wratjk.resize(m_nsp, m_nsp, 0.0);
     m_wratkj1.resize(m_nsp, m_nsp, 0.0);

src/transport/LiquidTransport.cpp

@@ -244,7 +244,7 @@ bool LiquidTransport::initLiquid(LiquidTransportParams& tr)
     m_radiusTempDep_Ns.resize(m_nsp, 0);
 
     //  Make a local copy of the molecular weights
-    copy(m_thermo->molecularWeights().begin(), m_thermo->molecularWeights().end(), m_mw.begin());
+    m_mw = m_thermo->molecularWeights();
 
     // First populate mixing rules and indices (NOTE, we transfer pointers of
     // malloced quantities. We zero out pointers so that we only have one copy

src/transport/MultiTransport.cpp

@@ -156,7 +156,7 @@ void MultiTransport::solveLMatrixEquation()
 
     // Solve it using GMRES or LU decomposition. The last solution in m_a should
     // provide a good starting guess, so convergence should be fast.
-    copy(m_b.begin(), m_b.end(), m_a.begin());
+    m_a = m_b;
     try {
         solve(m_Lmatrix, m_a.data());
     } catch (CanteraError& err) {

src/transport/SimpleTransport.cpp

@@ -170,8 +170,7 @@ bool SimpleTransport::initLiquid(LiquidTransportParams& tr)
     }
 
     // make a local copy of the molecular weights
-    m_mw.resize(m_nsp);
-    copy(m_thermo->molecularWeights().begin(), m_thermo->molecularWeights().end(), m_mw.begin());
+    m_mw = m_thermo->molecularWeights();
 
     // Get the input Viscosities
     m_viscSpecies.resize(m_nsp);