Fix variables that hide class members

As noted by MSVC; to improve clarity

include/teqp/models/CPA.hpp

@@ -318,7 +318,7 @@ inline auto CPAfactory(const nlohmann::json &j){
             }
         }
         else{
-            kmat.resize(N); for (auto i = 0U; i < N; ++i){ kmat[i].resize(N); for (auto j = 0U; j < N; ++j){kmat[i][j] = 0.0;} }
+            kmat.resize(N); for (auto i = 0U; i < N; ++i){ kmat[i].resize(N); for (auto k = 0U; k < N; ++k){kmat[i][k] = 0.0;} }
         }
 
         std::size_t i = 0;

include/teqp/models/activity/COSMOSAC.hpp

@@ -91,11 +91,11 @@ class COSMO3 {
         Eigen::Index min_ileft = 51, max_iright = 0;
         for (auto i = 0U; i < profiles.size(); ++i) {
             const Eigen::ArrayXd psigma = profiles[i].nhb.psigma(A_COSMO_A2[i]);
-            Eigen::Index ileft = 0, iright = psigma.size();
-            for (auto ii = 0; ii < psigma.size(); ++ii) { if (std::abs(psigma(ii)) > 1e-16) { ileft = ii; break; } }
-            for (auto ii = psigma.size() - 1; ii > ileft; --ii) { if (std::abs(psigma(ii)) > 1e-16) { iright = ii; break; } }
-            if (ileft < min_ileft) { min_ileft = ileft; }
-            if (iright > max_iright) { max_iright = iright; }
+            Eigen::Index ileft_ = 0, iright_ = psigma.size();
+            for (auto ii = 0; ii < psigma.size(); ++ii) { if (std::abs(psigma(ii)) > 1e-16) { ileft_ = ii; break; } }
+            for (auto ii = psigma.size() - 1; ii > ileft_; --ii) { if (std::abs(psigma(ii)) > 1e-16) { iright_ = ii; break; } }
+            if (ileft_ < min_ileft) { min_ileft = ileft_; }
+            if (iright_ > max_iright) { max_iright = iright_; }
         }
         return std::make_tuple(min_ileft, max_iright);
     }

include/teqp/models/association/association.hpp

@@ -72,7 +72,7 @@ class Association{
         std::vector<std::vector<std::string>> molecule_sites;
     };
 private:
-    IndexMapper make_mapper(const std::vector<std::vector<std::string>>& molecule_sites, const AssociationOptions& options) const {
+    IndexMapper make_mapper(const std::vector<std::vector<std::string>>& molecule_sites, const AssociationOptions& options_in) const {
         IndexMapper ind;
         ind.counts.resize(1000);
         ind.comp_index.resize(1000);
@@ -90,7 +90,7 @@ class Association{
                 ++site_counts[site];
             }
             auto unique_sites_on_molecule = std::set(molecule.begin(), molecule.end());
-            if (!options.site_order.empty()){
+            if (!options_in.site_order.empty()){
                 // TODO: enforce sites to appear in the order matching the specification
                 // TODO: this would be required to for instance check the D matrix of Langenbach and Enders
             }
@@ -118,9 +118,9 @@ class Association{
     /***
     Construct the counting matrix \f$ D_{IJ} \f$ as given by Langenbach and Enders
     */
-    auto make_D(const IndexMapper& ind, const AssociationOptions& options ) const{
+    auto make_D(const IndexMapper& ind, const AssociationOptions& options_in ) const{
 
-        auto get_DIJ = [&ind, &options](std::size_t I, std::size_t J) -> int {
+        auto get_DIJ = [&ind, &options_in](std::size_t I, std::size_t J) -> int {
             /** Return the value of an entry in the D_{IJ} matrix
             
             For a given unique site, look at all other sites on all other molecules
@@ -129,17 +129,17 @@ class Association{
             auto [ph2, typej] = ind.to_CompSite.at(J);
 
             // If self-association is disabled for this site, then return zero for the D matrix
-            if (!options.self_association_mask.empty() && ph1 == ph2 && !options.self_association_mask[ph1]){
+            if (!options_in.self_association_mask.empty() && ph1 == ph2 && !options_in.self_association_mask[ph1]){
                 return 0;
             }
             auto contains = [](auto& container, const auto& val){ return std::find(container.begin(), container.end(), val) != container.end(); };
             /// If interaction parameters are not provided, assume conservatively that all sites can interact with all other sites
-            if (options.interaction_partners.empty() || (contains(options.interaction_partners.at(typei), typej))){
+            if (options_in.interaction_partners.empty() || (contains(options_in.interaction_partners.at(typei), typej))){
                 return ind.counts[J];
             }
             return 0;
         };
-        if (!options.self_association_mask.empty() && options.self_association_mask.size() != static_cast<std::size_t>(ind.N_sites.size())){
+        if (!options_in.self_association_mask.empty() && options_in.self_association_mask.size() != static_cast<std::size_t>(ind.N_sites.size())){
             throw teqp::InvalidArgument("self_association_mask is of the wrong size");
         }
         int Ngroups = static_cast<int>(ind.to_siteid.size());