Used std::vector in Heterogeneous map in gate merge procedure

There is some potential compatibility issues with external linkage.
Signed-off-by: Thien Nguyen <nguyentm@ornl.gov>

quantum/plugins/circuits/kak/kak.cpp

@@ -1296,6 +1296,22 @@ bool ZYZ::expand(const xacc::HeterogeneousMap& runtimeOptions)
   {
     unitary = runtimeOptions.get<Eigen::Matrix2cd>("unitary");
   }
+  else if (runtimeOptions.keyExists<std::vector<std::complex<double>>>("unitary"))
+  {
+    auto matAsVec = runtimeOptions.get<std::vector<std::complex<double>>>("unitary");
+    // Correct size: 2 x 2
+    if (matAsVec.size() == 4)
+    {
+      for (int row = 0; row < 2; ++row)
+      {
+        for (int col = 0; col < 2; ++col)
+        {
+          // Expect row-by-row layout
+          unitary(row, col) = matAsVec[2*row + col];
+        }
+      }
+    }
+  }
   else
   {
     xacc::error("unitary matrix is required.");

quantum/plugins/optimizers/gate_merge/GateMergeOptimizer.cpp

@@ -72,10 +72,16 @@ void MergeSingleQubitGatesOptimizer::apply(std::shared_ptr<CompositeInstruction>
 
             auto fuser = xacc::getService<xacc::quantum::GateFuser>("default");
             fuser->initialize(tmpKernel);
-            const Eigen::Matrix2cd uMat = fuser->calcFusedGate(1);
+            Eigen::Matrix2cd uMat = fuser->calcFusedGate(1);
+            uMat.transposeInPlace();
+            Eigen::Vector4cd matAsVec(Eigen::Map<Eigen::Vector4cd>(uMat.data(), uMat.cols()*uMat.rows()));
+            std::vector<std::complex<double>> flattenedUnitary;
+            flattenedUnitary.resize(matAsVec.size());
+            Eigen::Vector4cd::Map(&flattenedUnitary[0], flattenedUnitary.size()) = matAsVec;
+
             auto zyz = std::dynamic_pointer_cast<quantum::Circuit>(xacc::getService<Instruction>("z-y-z"));
             const bool expandOk = zyz->expand({ 
-                std::make_pair("unitary", uMat)
+                std::make_pair("unitary", flattenedUnitary)
             });
             assert(expandOk);
             // Optimized decomposed sequence:
@@ -235,10 +241,15 @@ void MergeTwoQubitBlockOptimizer::apply(std::shared_ptr<CompositeInstruction> pr
             }
             auto fuser = xacc::getService<xacc::quantum::GateFuser>("default");
             fuser->initialize(tmpKernel);
-            const Eigen::Matrix4cd uMat = fuser->calcFusedGate(2);
+            Eigen::Matrix4cd uMat = fuser->calcFusedGate(2);
+            uMat.transposeInPlace();
+            Eigen::VectorXcd matAsVec(Eigen::Map<Eigen::VectorXcd>(uMat.data(), uMat.cols()*uMat.rows()));
+            std::vector<std::complex<double>> flattenedUnitary;
+            flattenedUnitary.resize(matAsVec.size());
+            Eigen::VectorXcd::Map(&flattenedUnitary[0], flattenedUnitary.size()) = matAsVec;
             auto kak = std::dynamic_pointer_cast<quantum::Circuit>(xacc::getService<Instruction>("kak"));
             const bool expandOk = kak->expand({ 
-                std::make_pair("unitary", uMat)
+                std::make_pair("unitary", flattenedUnitary)
             });
             assert(expandOk);