Merge pull request #301 from ICB-DCM/fixes_ff

Fixes for incorrectly passing tests
AMICI-dev · May 9, 2018 · 4bc7cd2 · 4bc7cd2
2 parents 6e828d9 + 55e2ae9
commit 4bc7cd2
Show file tree

Hide file tree

Showing 4 changed files with 15 additions and 17 deletions.
diff --git a/src/rdata.cpp b/src/rdata.cpp
@@ -113,24 +113,24 @@ void ReturnData::invalidate(const realtype t) {
 
     for (int it = it_start; it < nt; it++){
         for (int ix = 0; ix < nx; ix++)
-            x.at(ix * nt + it) = getNaN();
+            x.at(ix + nx * it) = getNaN();
         for (int iy = 0; iy < ny; iy++)
-            y.at(iy * nt + it) = getNaN();
+            y.at(iy + ny * it) = getNaN();
     }
 
     if (sx.size()) {
         for (int it = it_start; it < nt; it++){
             for (int ip = 0; ip < nplist; ip++) {
                 for (int ix = 0; ix < nx; ix++)
-                    sx.at((ip*nx + ix) * nt + it) = getNaN();
+                    sx.at(ix + nx*(ip + it*nplist)) = getNaN();
             }
         }
     }
     if(sy.size()) {
         for (int it = it_start; it < nt; it++){
             for (int ip = 0; ip < nplist; ip++) {
                 for (int iy = 0; iy < ny; iy++)
-                    sy.at((ip*ny + iy) * nt + it) = getNaN();
+                    sy.at(iy + ny*(ip + it*nplist)) = getNaN();
             }
         }
     }
@@ -200,23 +200,20 @@ void ReturnData::applyChainRuleFactorToSimulationResults(const Model *model) {
                 for (int ip = 0; ip < nplist; ++ip)
                     for (int ix = 0; ix < nxtrue; ++ix)
                         for (int it = 0; it < nt; ++it)
-                            sx.at((ip * nxtrue + ix) * nt + it) =
-                                x.at((nxtrue + ip * nxtrue + ix) * nt +
-                                  it);
+                            sx.at(ix + nxtrue*(ip + it*nplist)) =
+                                x.at(it * nx + nxtrue + ip * nxtrue + ix);
 
                 for (int ip = 0; ip < nplist; ++ip)
                     for (int iy = 0; iy < nytrue; ++iy)
                         for (int it = 0; it < nt; ++it)
-                            sy.at((ip * nytrue + iy) * nt + it) =
-                                y.at((nytrue + ip * nytrue + iy) * nt +
-                                  it);
+                            sy.at(iy + nytrue*(ip + it*nplist)) =
+                                y.at(it * ny + nytrue + ip * nytrue + iy);
 
                 for (int ip = 0; ip < nplist; ++ip)
                     for (int iz = 0; iz < nztrue; ++iz)
                         for (int it = 0; it < nt; ++it)
-                            sz.at((ip * nztrue + iz) * nt + it) =
-                                z.at((nztrue + ip * nztrue + iz) * nt +
-                                  it);
+                            sz.at(iz + nztrue*(ip + it*nplist)) =
+                                z.at(it * nz + nztrue + ip * nztrue + iz);
             }
         }
 

diff --git a/src/solver.cpp b/src/solver.cpp
@@ -71,9 +71,10 @@ void Solver::setupAMI(ForwardProblem *fwd, Model *model) {
 
             model->fsdx0();
 
-            if (sensi_meth == AMICI_SENSI_FSA) {
+            auto plist = model->getParameterList();
+
+            if (sensi_meth == AMICI_SENSI_FSA && plist.size() > 0) {
                 /* Set sensitivity analysis optional inputs */
-                auto plist = model->getParameterList();
                 auto par = model->getUnscaledParameters();
 
                 /* Activate sensitivity calculations */

diff --git a/tests/cpputest/expectedResults.h5 b/tests/cpputest/expectedResults.h5
diff --git a/tests/cpputest/testfunctions.cpp b/tests/cpputest/testfunctions.cpp
@@ -42,8 +42,7 @@ void simulateVerifyWrite(const std::string hdffileOptions, const std::string hdf
     // simulate & verify
     auto rdata = runAmiciSimulation(*solver, edata.get(), *model);
     std::string resultPath = path + "/results";
-    verifyReturnData(hdffileResults.c_str(), resultPath.c_str(), rdata.get(), model.get(), atol, rtol);
-
+
     // write
     // delete destination group
     H5::H5File in(hdffileOptions, H5F_ACC_RDONLY);
@@ -61,6 +60,7 @@ void simulateVerifyWrite(const std::string hdffileOptions, const std::string hdf
     hdf5::writeReturnData(*rdata, out, writePath);
 
     // verify
+    verifyReturnData(hdffileResults.c_str(), resultPath.c_str(), rdata.get(), model.get(), atol, rtol);
     verifyReturnData(hdffilewrite, writePath, rdata.get(), model.get(), atol, rtol);
     //remove(hdffilewrite.c_str());
 }