[iss-255]

Squashed commit of the following:

commit 1a5504b
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 21:04:38 2024 -0300

    Updated/fixed advection x test.

commit be1106c
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 21:04:19 2024 -0300

    Fix sym diff in virus replication test model.

commit 9d7550d
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 21:03:47 2024 -0300

    Update/fix virus replication test.

commit 2202618
Merge: 215152f 757f4e1
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 20:35:12 2024 -0300

    Merge branch 'qss-solver-dev' into engine/iss-255-allow-output-state-variables

commit 215152f
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 19:42:52 2024 -0300

    Update vs code settings file.

commit 807b5dd
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 19:42:30 2024 -0300

    Added system test.

commit 88b816e
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 19:31:43 2024 -0300

    Update sample interface.

commit e95480e
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 19:31:15 2024 -0300

    Upfate file interface for x output.

commit 4ef139c
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 19:28:17 2024 -0300

    Update qss log interface.

commit 63ad39f
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 19:27:41 2024 -0300

    Updated qss output interface.

commit 7bf9a25
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 19:26:53 2024 -0300

    Updated qss step inferface.

commit 41e539e
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 19:24:54 2024 -0300

    Added gui vs code config file.

commit 2f3f002
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 19:24:28 2024 -0300

    Updated qss data settings and parameters, code improvement.

commit 6058edf
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 19:23:34 2024 -0300

    Added checkedFree method to utils.

commit 48f7319
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 19:23:03 2024 -0300

    Update parameters struct.

commit 5aa67a7
Author: joaquin.f.fernandez <[email protected]>
Date:   Tue Aug 27 19:22:00 2024 -0300

    Added x output option to settings.

src/engine/classic/classic_data.c

@@ -85,7 +85,7 @@ CLC_data CLC_Data(int states, int discretes, int events, int inputs, int algebra
   p->event = SD_EventData(events);
   p->params = SD_Parameters(settings->derdelta, settings->zchyst, settings->minstep, settings->symdiff, settings->lps, settings->nodesize,
                             settings->pm, settings->dt, settings->dtSynch, settings->partitionerOptions, settings->jacobian,
-                            settings->CVODE_max_order);
+                            settings->CVODE_max_order, settings->x_output);
   p->scalarEvaluations = 0;
   p->zeroCrossings = 0;
   p->funEvaluations = 0;

src/engine/common/data.c

@@ -171,7 +171,8 @@ void SD_cleanEventData(SD_eventData events, int size)
 }
 
 SD_parameters SD_Parameters(double derDelta, double zcHyst, double minStep, int symDiff, int lps, int nodeSize, SD_PartitionMethod pm,
-                            double dt, SD_DtSynch synch, SD_partitionerOptions partitionerOptions, int jacobian, int CVODE_max_order)
+                            double dt, SD_DtSynch synch, SD_partitionerOptions partitionerOptions, int jacobian, int CVODE_max_order,
+                            int x_output)
 {
   SD_parameters p = checkedMalloc(sizeof(*p));
   p->derDelta = derDelta;
@@ -186,10 +187,11 @@ SD_parameters SD_Parameters(double derDelta, double zcHyst, double minStep, int
   p->partitionerOptions = partitionerOptions;
   p->jacobian = jacobian;
   p->CVODE_max_order = CVODE_max_order;
+  p->x_output = x_output;
   return p;
 }
 
-SD_parameters SD_copyParameters(SD_parameters parameters)
+SD_parameters SD_copyParameters(const_SD_parameters parameters)
 {
   SD_parameters p = checkedMalloc(sizeof(*p));
   p->derDelta = parameters->derDelta;
@@ -200,6 +202,7 @@ SD_parameters SD_copyParameters(SD_parameters parameters)
   p->nodeSize = parameters->nodeSize;
   p->pm = parameters->pm;
   p->dt = parameters->dt;
+  p->x_output = parameters->x_output;
   return p;
 }
 
@@ -437,8 +440,8 @@ SD_jacMatrix SD_JacMatrix(int variables)
 
 void SD_allocJacMatrix(SD_jacMatrix jac_matrix)
 {
-  int i, variables = jac_matrix->variables;
-  for (i = 0; i < variables; i++) {
+  int variables = jac_matrix->variables;
+  for (int i = 0; i < variables; i++) {
     int size = jac_matrix->size[i];
     if (size > 0) {
       jac_matrix->index[i] = (int *)malloc(size * sizeof(int));
@@ -453,8 +456,8 @@ void SD_allocJacMatrix(SD_jacMatrix jac_matrix)
 
 void SD_cleanJacMatrix(SD_jacMatrix jac_matrix)
 {
-  int i, variables = jac_matrix->variables;
-  for (i = 0; i < variables; i++) {
+  int variables = jac_matrix->variables;
+  for (int i = 0; i < variables; i++) {
     if (jac_matrix->size[i] > 0) {
       cleanDoubleVector(jac_matrix->value[i], 0, jac_matrix->size[i]);
     }
@@ -463,13 +466,13 @@ void SD_cleanJacMatrix(SD_jacMatrix jac_matrix)
 
 void SD_freeJacMatrix(SD_jacMatrix jac_matrix)
 {
-  int i, variables = jac_matrix->variables;
+  int variables = jac_matrix->variables;
   free(jac_matrix->size);
-  for (i = 0; i < variables; i++) {
+  for (int i = 0; i < variables; i++) {
     free(jac_matrix->index[i]);
   }
   free(jac_matrix->index);
-  for (i = 0; i < variables; i++) {
+  for (int i = 0; i < variables; i++) {
     free(jac_matrix->value[i]);
   }
   free(jac_matrix->value);

src/engine/common/data.h

@@ -21,6 +21,7 @@
 
 #include <stdio.h>
 
+#include <common/macros.h>
 #include "utils.h"
 
 typedef void (*SD_eq)(int, double *, double *, double *, double, double *);
@@ -158,7 +159,7 @@ void SD_freeEventData(SD_eventData events, int size);
 
 void SD_cleanEventData(SD_eventData events, int size);
 
-typedef struct SD_parameters_ *SD_parameters;
+TYPE_DEF(SD_parameters)
 
 struct SD_parameters_ {
   double derDelta;
@@ -173,12 +174,14 @@ struct SD_parameters_ {
   SD_PartitionMethod pm;  //!< Partition method used to obtain a model partition for parallel simulations.
   SD_DtSynch dtSynch;     //!< \f $ \delta t $ \f synchronization policy.
   SD_partitionerOptions partitionerOptions;
+  int x_output;
 };
 
 SD_parameters SD_Parameters(double derDelta, double zcHyst, double minStep, int symDiff, int lps, int nodeSize, SD_PartitionMethod pm,
-                            double dt, SD_DtSynch synch, SD_partitionerOptions partitionerOptions, int jacobian, int CVODE_max_order);
+                            double dt, SD_DtSynch synch, SD_partitionerOptions partitionerOptions, int jacobian, int CVODE_max_order,
+                            int x_output);
 
-SD_parameters SD_copyParameters(SD_parameters parameters);
+SD_parameters SD_copyParameters(const_SD_parameters parameters);
 
 void SD_freeParameters(SD_parameters params);
 
@@ -205,7 +208,7 @@ SD_outputVariable SD_OutputVariable(int outputs);
 
 void SD_freeOutputVariable(SD_outputVariable variable);
 
-typedef struct SD_output_ *SD_output;
+TYPE_DEF(SD_output)
 
 struct SD_output_ {
   char *name;

src/engine/common/settings.c

@@ -158,6 +158,7 @@ SET_settings SET_Settings(char *fname)
   p->BDFPartitionDepth = 1;
   p->CVODE_max_order = 0;
   p->BDFMaxStep = 0;
+  p->x_output = 0;
   if (config_lookup_float(cf, "minstep", &dres)) {
     if (dres == 0) {
       p->minstep = MIN_STEP;
@@ -278,6 +279,9 @@ SET_settings SET_Settings(char *fname)
     }
     p->partitionerOptions.nMetis = option;
   }
+  if (config_lookup_int(cf, "XOutput", &ires)) {
+    p->x_output = ires;
+  }
   config_destroy(cf);
   return p;
 }

src/engine/common/settings.h

@@ -16,13 +16,12 @@
  along with QSS Solver.  If not, see <http://www.gnu.org/licenses/>.
 
  ******************************************************************************/
+#pragma once
 
-#ifndef SETTINGS_H_
-#define SETTINGS_H_
-
+#include <common/macros.h>
 #include "data.h"
 
-typedef struct SET_settings_ *SET_settings;
+TYPE_DEF(SET_settings)
 
 struct SET_settings_ {
   double minstep;
@@ -48,10 +47,9 @@ struct SET_settings_ {
   SD_DtSynch dtSynch;
   SD_partitionerOptions partitionerOptions;
   int BDFPart;
+  int x_output;
 };
 
 SET_settings SET_Settings(char *fname);
 
 void freeSettings(SET_settings settings);
-
-#endif /* SETTINGS_H_ */

src/engine/common/utils.c

@@ -30,6 +30,13 @@
 
 #include <common/utils.h>
 
+void checkedFree(void *ptr)
+{
+  if (ptr != NULL) {
+    free(ptr);
+  }
+}
+
 void *checkedMalloc(unsigned long long len)
 {
   void *p = malloc(len);
@@ -158,7 +165,7 @@ double minPosRoot(double *coeff, int order)
       mpr = INF;
     } else {
       mpr = -coeff[0] / coeff[1];
-    };
+    }
     if (mpr < 0) {
       mpr = INF;
     }
@@ -169,7 +176,7 @@ double minPosRoot(double *coeff, int order)
         mpr = INF;
       } else {
         mpr = -coeff[0] / coeff[1];
-      };
+      }
       if (mpr < 0) {
         mpr = INF;
       }
@@ -187,13 +194,13 @@ double minPosRoot(double *coeff, int order)
           mpr = r1;
         } else {
           mpr = INF;
-        };
+        }
         r1 = (-coeff[1] - sd) / 2 / coeff[2];
         if ((r1 > 0) && (r1 < mpr)) {
           mpr = r1;
         }
-      };
-    };
+      }
+    }
     break;
   case 3:
     if ((coeff[3] == 0) || (1000 * fabs(coeff[3]) < fabs(coeff[2]))) {
@@ -234,7 +241,14 @@ double minPosRoot(double *coeff, int order)
         }
       } else {
         // three real roots
-        double rho, th, rho13, costh3, sinth3, spt, smti32, r1;
+        double rho;
+        double th;
+        double rho13;
+        double costh3;
+        double sinth3;
+        double spt;
+        double smti32;
+        double r1;
         rho = sqrt(-q * q * q);
         th = acos(r / rho);
         rho13 = pow(rho, 1.0 / 3);

src/engine/common/utils.h

@@ -17,8 +17,7 @@
 
  ******************************************************************************/
 
-#ifndef UTILS_H_
-#define UTILS_H_
+#pragma once
 
 #ifdef _WIN32
 #include <sys/time.h>
@@ -67,6 +66,8 @@ typedef char bool;
 
 typedef char *string;
 
+void checkedFree(void *ptr);
+
 void *checkedMalloc(unsigned long long len);
 
 double minPosRoot(double *coeff, int order) __attribute__((hot));
@@ -413,5 +414,3 @@ void waitUntil(double until);
 void setInitRealTime();
 
 #endif
-
-#endif /* UTILS_H_ */

src/engine/qss/qss_data.c

@@ -37,8 +37,7 @@ QSS_reinit QSS_Reinit()
     return NULL;
   }
   QSS_reinit p = checkedMalloc(sizeof(*p));
-  int i;
-  for (i = 0; i < QSS_REINIT_BUFFER; i++) {
+  for (int i = 0; i < QSS_REINIT_BUFFER; i++) {
     p->variable[i] = NOT_ASSIGNED;
   }
   p->time = INF;
@@ -230,8 +229,8 @@ QSS_LP_dataArray QSS_LP_DataArray(int size)
 void QSS_LP_freeDataArray(QSS_LP_dataArray array)
 {
   if (!QSS_hardCopyStruct) {
-    int i, size = array->size;
-    for (i = 0; i < size; i++) {
+    int size = array->size;
+    for (int i = 0; i < size; i++) {
       if (array->lp[i] != NULL) {
         QSS_LP_freeData(array->lp[i]);
       }
@@ -253,36 +252,16 @@ void QSS_LP_freeData(QSS_LP_data data)
   if (data == NULL) {
     return;
   }
-  if (data->nLPS != NULL) {
-    free(data->nLPS);
-  }
-  if (data->lps != NULL) {
-    free(data->lps);
-  }
-  if (data->qOutMap != NULL) {
-    free(data->qOutMap);
-  }
-  if (data->eOutMap != NULL) {
-    free(data->eOutMap);
-  }
-  if (data->qMap != NULL) {
-    free(data->qMap);
-  }
-  if (data->qInMap != NULL) {
-    free(data->qInMap);
-  }
-  if (data->eMap != NULL) {
-    free(data->eMap);
-  }
-  if (data->eInMap != NULL) {
-    free(data->eInMap);
-  }
-  if (data->iMap != NULL) {
-    free(data->iMap);
-  }
-  if (data->dscMap != NULL) {
-    free(data->dscMap);
-  }
+  checkedFree(data->nLPS);
+  checkedFree(data->lps);
+  checkedFree(data->qOutMap);
+  checkedFree(data->eOutMap);
+  checkedFree(data->qMap);
+  checkedFree(data->qInMap);
+  checkedFree(data->eMap);
+  checkedFree(data->eInMap);
+  checkedFree(data->iMap);
+  checkedFree(data->dscMap);
   free(data);
 }
 
@@ -440,7 +419,7 @@ QSS_data QSS_Data(int states, int discretes, int events, int inputs, int algs, i
   }
   p->params = SD_Parameters(settings->derdelta, settings->zchyst, settings->minstep, settings->symdiff, settings->lps, settings->nodesize,
                             settings->pm, settings->dt, settings->dtSynch, settings->partitionerOptions, settings->jacobian,
-                            settings->CVODE_max_order);
+                            settings->CVODE_max_order, settings->x_output);
   p->lp = NULL;
   if (settings->lps > 0) {
     QSS_setReinitBuffer(TRUE);

src/engine/qss/qss_data.h

@@ -29,6 +29,7 @@
 #pragma once
 
 #include <common/data.h>
+#include <common/macros.h>
 #include <common/utils.h>
 
 #define QSS_REINIT_BUFFER 10000
@@ -168,7 +169,7 @@ QSS_event SD_Event(QSS_zc zeroCrossing, QSS_hnd handlerPos, QSS_hnd handlerNeg);
 
 void QSS_freeEvent(QSS_event events);
 
-typedef struct QSS_data_ *QSS_data;
+TYPE_DEF(QSS_data)
 
 struct QSS_data_ {
   double *dQMin;
@@ -245,7 +246,7 @@ void QSS_cleanData(QSS_data data);
 
 void QSS_allocDataMatrix(QSS_data data);
 
-typedef struct QSS_time_ *QSS_time;
+TYPE_DEF(QSS_time)
 
 /**
  * @struct QSS_time_

src/engine/qss/qss_file.c

@@ -37,6 +37,10 @@ void F_init(LG_log log, QSS_data sim_data, SD_output sim_output)
   int i, j, size;
   log->state->data = sim_data;
   log->state->output = sim_output;
+  int output_coeffs = sim_data->order;
+  if (sim_data->params->x_output == 1) {
+    output_coeffs++;
+  }
 #ifdef QSS_PARALLEL
   QSS_LP_data lp = sim_data->lp;
   log->state->size = lp->outputs;
@@ -64,7 +68,7 @@ void F_init(LG_log log, QSS_data sim_data, SD_output sim_output)
         sprintf(log->state->fileName, "%s%s.dat", sim_output->variable[i].name, ext);
         log->state->files[j] = fopen(log->state->fileName, "w+");
         if (sim_output->commInterval == CI_Dense || sim_output->commInterval == CI_Sampled) {
-          log->state->values[j] = sim_output->nOS[i] * sim_data->order + sim_output->nOD[i];
+          log->state->values[j] = sim_output->nOS[i] * output_coeffs + sim_output->nOD[i];
         }
         j++;
 #ifdef QSS_PARALLEL