Merge pull request #90 from ICB-DCM/fixes_ff

Various bugfixes

@SBMLode/importSBML.m

@@ -676,7 +676,7 @@ function checkIllegalFunctions(str)
 csym = sym(sanitizeString(strrep(str,'time','__time_internal_amici__')));
 csym = subs(csym,sym('__time_internal_amici__'),sym('time'));
 else
-    csym = sym();
+    csym = sym(0);
 end
 end
 

@amimodel/compileC.m

@@ -405,16 +405,7 @@ function compileC(this)
 
 
     fprintf('amici | ');
-    if(this.nxtrue ~= this.nx)
-        cstr = 'amicio2.cpp';
-    else
-        cstr = 'amici.cpp';
-    end
-    eval(['mex ' DEBUG COPT ...
-        ' -c -outdir ' fullfile(this.wrap_path,'src') ' ' ...
-        fullfile(this.wrap_path,'src',cstr) ' ' ...
-        includesstr]);
-
+
     if(isunix)
         if(~ismac)
             CLIBS = 'CLIBS="-lrt"';
@@ -429,37 +420,37 @@ function compileC(this)
         end
     end
 
-
-    if(this.nxtrue ~= this.nx)
-        cstr = 'amiwrapo2.cpp';
-        o2ext = 'o2';
-    else
-        cstr = 'amiwrap.cpp';
-        o2ext = '';
+    if(this.nxtrue == this.nx)
+        eval(['mex ' DEBUG COPT ...
+            ' -c -outdir ' fullfile(this.wrap_path,'src') ' ' ...
+            fullfile(this.wrap_path,'src','amici.cpp') ' ' ...
+            includesstr]);
     end
-
-    prefix = 'ami';
-
 
-    eval(['mex ' DEBUG ' ' COPT ...
-        ' -c -outdir ' fullfile(this.wrap_path,'src') ' ' ...
-        fullfile(this.wrap_path,'src',cstr) ' ' ...
-        includesstr]);
+    if(this.nxtrue == this.nx)
+        eval(['mex ' DEBUG ' ' COPT ...
+            ' -c -outdir ' fullfile(this.wrap_path,'src') ' ' ...
+            fullfile(this.wrap_path,'src','amiwrap.cpp') ' ' ...
+            includesstr]);
+    end
 
-    eval(['mex ' DEBUG ' ' COPT ...
-        ' -c -outdir ' fullfile(this.wrap_path,'src') ' ' ...
-        fullfile(this.wrap_path,'src','amici_interface_matlab.cpp') ' ' ...
-        includesstr]);
+    if(this.nxtrue == this.nx)
+        eval(['mex ' DEBUG ' ' COPT ...
+            ' -c -outdir ' fullfile(this.wrap_path,'src') ' ' ...
+            fullfile(this.wrap_path,'src','amici_interface_matlab.cpp') ' ' ...
+            includesstr]);
+    end
 
     eval(['mex ' DEBUG ' ' COPT ' ' CLIBS ...
-        ' -output ' fullfile(this.wrap_path,'models',this.modelname,[prefix '_' this.modelname]) ...
-        ' "' fullfile(this.wrap_path,'src',['amiwrap' o2ext o_suffix]) '"' ...
-        ' "' fullfile(this.wrap_path,'src',['amici' o2ext o_suffix]) '"' ...
-        ' "' fullfile(this.wrap_path,'src',['amici_interface_matlab' o2ext o_suffix]) '"' ...
+        ' -output ' fullfile(this.wrap_path,'models',this.modelname,['ami_' this.modelname]) ...
+        ' "' fullfile(this.wrap_path,'src',['amiwrap' o_suffix]) '"' ...
+        ' "' fullfile(this.wrap_path,'src',['amici' o_suffix]) '"' ...
+        ' "' fullfile(this.wrap_path,'src',['amici_interface_matlab' o_suffix]) '"' ...
         ' "' fullfile(this.wrap_path,'models',this.modelname,['wrapfunctions' o_suffix]) '"' ...
         objectsstr ...
         includesstr ...
         ])
+
 
 
 

include/amici.h

@@ -30,6 +30,8 @@
 
 void runAmiciSimulation(UserData *udata, const ExpData *edata, ReturnData *rdata, int *pstatus);
 
+void invalidateReturnData(UserData* udata, ReturnData* rdata);
+
 void *setupAMI(int *status, UserData *udata, TempData *tdata);
 void setupAMIB(int *status, void *ami_mem, UserData *udata, TempData *tdata);
 

src/amici.cpp

@@ -64,9 +64,28 @@ void runAmiciSimulation(UserData *udata, const ExpData *edata, ReturnData *rdata
     applyChainRuleFactorToSimulationResults(udata, rdata, edata);
 
 freturn:
+    if(*pstatus<0){
+        invalidateReturnData(udata, rdata);
+    }
     freeTempDataAmiMem(udata, tdata, ami_mem, setupBdone, *pstatus);
 }
 
+void invalidateReturnData(UserData* udata, ReturnData* rdata) {
+    /**
+     * @brief performs all necessary actions to reset return data upon integration failure
+     * @param[in] udata pointer to the user data struct @type UserData
+     * @param[out] rdata pointer to the return data struct @type ReturnData
+     */
+    if(llhdata)
+        *llhdata = amiGetNaN();
+
+    if(sllhdata)
+        fillArray(sllhdata, nplist, amiGetNaN());
+
+    if(s2llhdata)
+        fillArray(s2llhdata, nplist*(ng-1), amiGetNaN());
+}
+
 void *setupAMI(int *status, UserData *udata, TempData *tdata) {
     /**
      * @brief setupAMIs initialises the ami memory object