Updated sundials to ver 7.2.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: sundialr
 Type: Package
 Title: An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE) Solvers
-Version: 0.1.5
+Version: 0.1.6
 Authors@R: c(
     person("Satyaprakash", "Nayak", "", "[email protected]", c("aut", "cre","cph"), comment = c(ORCID = "0000-0001-7225-1317")),
     person("Lawrence Livermore National Security", role =  c("cph")),

LICENSE

@@ -1,4 +1,3 @@
-YEAR: 2020
+YEAR: 2024
 COPYRIGHT HOLDER: Satyaprakash Nayak
 ORGANIZATION: Satyaprakash Nayak
-

README.md

@@ -17,16 +17,23 @@ information about `SUNDIALS` can be found [here](https://computing.llnl.gov/proj
 Currently `sundialr` provides an interface to the `serial` versions of `cvode` (for solving ODES), `cvodes` (for solving ODE with sensitivity equations) and `ida` (for solving differential-algebraic equations) using the Linear Solver (dense version).
 
 A convenience function `cvsolve` is provided which allows solving a system of equations with
-multiple discontinutities in solution. An application of such a system of equations would be 
+multiple discontinuities in solution. An application of such a system of equations would be 
 to simulate the effect of multiple bolus doses of a drug in clinical pharmacokinetics. See the 
 vignette for more details.
 
 ## What's new?
 
-### Release 0.1.5
+## Comments for version 0.1.6
++ Updated the upstream `SUNDIALS` to version 7.2.0
++ Complete overall of the build system to use `cmake` based installation
+
+### Comments for version 0.1.5
 + Updated the upstream `SUNDIALS` to version 7.1.1. 
 + Fixed the `pkgdown` website
-+ There was a bug is assigning absolute tolerance in equations. Fixed now.
++ There was a bug in assigning absolute tolerance in equations. Fixed now.
+
+## Comments for version 0.1.4.1.2
+* Fixed the issue with forwarded email address.
 
 ### Release 0.1.4.1
 + Fixed the linking bug due to multiple defined symbols. No other change.

cran-comments.md

@@ -1,3 +1,12 @@
+## Comments for version 0.1.6
++ Updated the upstream `SUNDIALS` to version 7.2.0
++ Complete overall of the build system to use `cmake` based installation
+
+## Comments for 0.1.5
++ Updated the upstream `SUNDIALS` to version 7.1.1. 
++ Fixed the `pkgdown` website
++ There was a bug in assigning absolute tolerance in equations. Fixed now.
+
 ## Comments for version 0.1.4.1.2
 * Fixed the issue with forwarded email address.
 
@@ -19,10 +28,3 @@ There were no ERRORs or WARNINGs or NOTEs.
 ## Downstream dependencies
 There are currently one downstream dependency for this package (CausalKinetiX) 
 which should be unaffected.
-
-
-
-
-
-
-

inst/include/arkode/arkode.h

@@ -31,6 +31,7 @@
 #include <arkode/arkode_butcher.h>
 #include <stdio.h>
 #include <sundials/sundials_core.h>
+#include <sundials/sundials_stepper.h>
 
 #ifdef __cplusplus /* wrapper to enable C++ usage */
 extern "C" {
@@ -140,6 +141,13 @@ extern "C" {
 
 #define ARK_STEPPER_UNSUPPORTED -48
 
+#define ARK_DOMEIG_FAIL          -49
+#define ARK_MAX_STAGE_LIMIT_FAIL -50
+
+#define ARK_SUNSTEPPER_ERR -51
+
+#define ARK_STEP_DIRECTION_ERR -52
+
 #define ARK_UNRECOGNIZED_ERROR -99
 
 /* ------------------------------
@@ -190,6 +198,18 @@ typedef enum
   ARK_RELAX_NEWTON
 } ARKRelaxSolver;
 
+/* --------------------------
+ * Error Accumulation Options
+ * -------------------------- */
+
+typedef enum
+{
+  ARK_ACCUMERROR_NONE,
+  ARK_ACCUMERROR_MAX,
+  ARK_ACCUMERROR_SUM,
+  ARK_ACCUMERROR_AVG
+} ARKAccumError;
+
 /* --------------------------
  * Shared API routines
  * -------------------------- */
@@ -200,6 +220,10 @@ SUNDIALS_EXPORT int ARKodeResize(void* arkode_mem, N_Vector ynew,
                                  ARKVecResizeFn resize, void* resize_data);
 SUNDIALS_EXPORT int ARKodeReset(void* arkode_mem, sunrealtype tR, N_Vector yR);
 
+/* Utility to wrap ARKODE as an MRIStepInnerStepper */
+SUNDIALS_EXPORT int ARKodeCreateMRIStepInnerStepper(void* arkode_mem,
+                                                    MRIStepInnerStepper* stepper);
+
 /* Tolerance input functions */
 SUNDIALS_EXPORT int ARKodeSStolerances(void* arkode_mem, sunrealtype reltol,
                                        sunrealtype abstol);
@@ -228,6 +252,7 @@ SUNDIALS_EXPORT int ARKodeSetInterpolateStopTime(void* arkode_mem,
 SUNDIALS_EXPORT int ARKodeSetStopTime(void* arkode_mem, sunrealtype tstop);
 SUNDIALS_EXPORT int ARKodeClearStopTime(void* arkode_mem);
 SUNDIALS_EXPORT int ARKodeSetFixedStep(void* arkode_mem, sunrealtype hfixed);
+SUNDIALS_EXPORT int ARKodeSetStepDirection(void* arkode_mem, sunrealtype stepdir);
 SUNDIALS_EXPORT int ARKodeSetUserData(void* arkode_mem, void* user_data);
 SUNDIALS_EXPORT int ARKodeSetPostprocessStepFn(void* arkode_mem,
                                                ARKPostProcessFn ProcessStep);
@@ -280,6 +305,9 @@ SUNDIALS_EXPORT int ARKodeSetInitStep(void* arkode_mem, sunrealtype hin);
 SUNDIALS_EXPORT int ARKodeSetMinStep(void* arkode_mem, sunrealtype hmin);
 SUNDIALS_EXPORT int ARKodeSetMaxStep(void* arkode_mem, sunrealtype hmax);
 SUNDIALS_EXPORT int ARKodeSetMaxNumConstrFails(void* arkode_mem, int maxfails);
+SUNDIALS_EXPORT int ARKodeSetAccumulatedErrorType(void* arkode_mem,
+                                                  ARKAccumError accum_type);
+SUNDIALS_EXPORT int ARKodeResetAccumulatedError(void* arkode_mem);
 
 /* Integrate the ODE over an interval in t */
 SUNDIALS_EXPORT int ARKodeEvolve(void* arkode_mem, sunrealtype tout,
@@ -294,13 +322,17 @@ SUNDIALS_EXPORT int ARKodeComputeState(void* arkode_mem, N_Vector zcor,
                                        N_Vector z);
 
 /* Optional output functions (general) */
+SUNDIALS_EXPORT int ARKodeGetNumRhsEvals(void* arkode_mem, int partition_index,
+                                         long int* num_rhs_evals);
 SUNDIALS_EXPORT int ARKodeGetNumStepAttempts(void* arkode_mem,
                                              long int* step_attempts);
 SUNDIALS_EXPORT int ARKodeGetWorkSpace(void* arkode_mem, long int* lenrw,
                                        long int* leniw);
 SUNDIALS_EXPORT int ARKodeGetNumSteps(void* arkode_mem, long int* nsteps);
 SUNDIALS_EXPORT int ARKodeGetLastStep(void* arkode_mem, sunrealtype* hlast);
 SUNDIALS_EXPORT int ARKodeGetCurrentStep(void* arkode_mem, sunrealtype* hcur);
+SUNDIALS_EXPORT int ARKodeGetStepDirection(void* arkode_mem,
+                                           sunrealtype* stepdir);
 SUNDIALS_EXPORT int ARKodeGetErrWeights(void* arkode_mem, N_Vector eweight);
 SUNDIALS_EXPORT int ARKodeGetNumGEvals(void* arkode_mem, long int* ngevals);
 SUNDIALS_EXPORT int ARKodeGetRootInfo(void* arkode_mem, int* rootsfound);
@@ -325,6 +357,8 @@ SUNDIALS_EXPORT int ARKodeGetNumConstrFails(void* arkode_mem,
 SUNDIALS_EXPORT int ARKodeGetStepStats(void* arkode_mem, long int* nsteps,
                                        sunrealtype* hinused, sunrealtype* hlast,
                                        sunrealtype* hcur, sunrealtype* tcur);
+SUNDIALS_EXPORT int ARKodeGetAccumulatedError(void* arkode_mem,
+                                              sunrealtype* accum_error);
 
 /* Optional output functions (implicit solver) */
 SUNDIALS_EXPORT int ARKodeGetNumLinSolvSetups(void* arkode_mem,
@@ -412,6 +446,9 @@ SUNDIALS_EXPORT int ARKodeGetNumRelaxSolveFails(void* arkode_mem,
 SUNDIALS_EXPORT int ARKodeGetNumRelaxSolveIters(void* arkode_mem,
                                                 long int* iters);
 
+/* SUNStepper functions */
+SUNDIALS_EXPORT int ARKodeCreateSUNStepper(void* arkode_mem, SUNStepper* stepper);
+
 #ifdef __cplusplus
 }
 #endif

inst/include/arkode/arkode_arkstep.h

@@ -86,8 +86,6 @@ SUNDIALS_EXPORT int ARKStepSetTableName(void* arkode_mem, const char* itable,
                                         const char* etable);
 
 /* Optional output functions */
-SUNDIALS_EXPORT int ARKStepGetNumRhsEvals(void* arkode_mem, long int* nfe_evals,
-                                          long int* nfi_evals);
 SUNDIALS_EXPORT int ARKStepGetCurrentButcherTables(void* arkode_mem,
                                                    ARKodeButcherTable* Bi,
                                                    ARKodeButcherTable* Be);
@@ -96,14 +94,13 @@ SUNDIALS_EXPORT int ARKStepGetTimestepperStats(
   long int* step_attempts, long int* nfe_evals, long int* nfi_evals,
   long int* nlinsetups, long int* netfails);
 
-/* MRIStep interface functions */
-SUNDIALS_EXPORT int ARKStepCreateMRIStepInnerStepper(void* arkode_mem,
-                                                     MRIStepInnerStepper* stepper);
-
 /* --------------------------------------------------------------------------
  * Deprecated Functions -- all are superseded by shared ARKODE-level routines
  * -------------------------------------------------------------------------- */
 
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeCreateMRIStepInnerStepper instead")
+int ARKStepCreateMRIStepInnerStepper(void* arkode_mem,
+                                     MRIStepInnerStepper* stepper);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeResize instead")
 int ARKStepResize(void* arkode_mem, N_Vector ynew, sunrealtype hscale,
                   sunrealtype t0, ARKVecResizeFn resize, void* resize_data);
@@ -430,7 +427,9 @@ SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetNumRelaxSolveFails instead")
 int ARKStepGetNumRelaxSolveFails(void* arkode_mem, long int* fails);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetNumRelaxSolveIters instead")
 int ARKStepGetNumRelaxSolveIters(void* arkode_mem, long int* iters);
-
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetNumRhsEvals instead")
+int ARKStepGetNumRhsEvals(void* arkode_mem, long int* nfe_evals,
+                          long int* nfi_evals);
 #ifdef __cplusplus
 }
 #endif

inst/include/arkode/arkode_bandpre.h

@@ -24,7 +24,7 @@
 extern "C" {
 #endif
 
-/* BandPrec inititialization function */
+/* BandPrec initialization function */
 
 SUNDIALS_EXPORT int ARKBandPrecInit(void* arkode_mem, sunindextype N,
                                     sunindextype mu, sunindextype ml);

inst/include/arkode/arkode_erkstep.h

@@ -59,7 +59,6 @@ SUNDIALS_EXPORT int ERKStepSetTableNum(void* arkode_mem,
 SUNDIALS_EXPORT int ERKStepSetTableName(void* arkode_mem, const char* etable);
 
 /* Optional output functions */
-SUNDIALS_EXPORT int ERKStepGetNumRhsEvals(void* arkode_mem, long int* nfevals);
 SUNDIALS_EXPORT int ERKStepGetCurrentButcherTable(void* arkode_mem,
                                                   ARKodeButcherTable* B);
 
@@ -109,7 +108,7 @@ SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetMaxGrowth instead")
 int ERKStepSetMaxGrowth(void* arkode_mem, sunrealtype mx_growth);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetMinReduction instead")
 int ERKStepSetMinReduction(void* arkode_mem, sunrealtype eta_min);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepSetFiARKodeBounds instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetFixedStepBounds instead")
 int ERKStepSetFixedStepBounds(void* arkode_mem, sunrealtype lb, sunrealtype ub);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use SUNAdaptController instead")
 int ERKStepSetAdaptivityMethod(void* arkode_mem, int imethod, int idefault,
@@ -128,23 +127,23 @@ SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetMaxErrTestFails instead")
 int ERKStepSetMaxErrTestFails(void* arkode_mem, int maxnef);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetConstraints instead")
 int ERKStepSetConstraints(void* arkode_mem, N_Vector constraints);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepSetMaxARKodes instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetMaxNumSteps instead")
 int ERKStepSetMaxNumSteps(void* arkode_mem, long int mxsteps);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetMaxHnilWarns instead")
 int ERKStepSetMaxHnilWarns(void* arkode_mem, int mxhnil);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepSetIARKode instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetInitStep instead")
 int ERKStepSetInitStep(void* arkode_mem, sunrealtype hin);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepSetARKode instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetMinStep instead")
 int ERKStepSetMinStep(void* arkode_mem, sunrealtype hmin);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepSetARKode instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetMaxStep instead")
 int ERKStepSetMaxStep(void* arkode_mem, sunrealtype hmax);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetInterpolateStopTime instead")
 int ERKStepSetInterpolateStopTime(void* arkode_mem, sunbooleantype interp);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetStopTime instead")
 int ERKStepSetStopTime(void* arkode_mem, sunrealtype tstop);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeClearStopTime instead")
 int ERKStepClearStopTime(void* arkode_mem);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepSetFiARKode instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetFixedStep instead")
 int ERKStepSetFixedStep(void* arkode_mem, sunrealtype hfixed);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetMaxNumConstrFails instead")
 int ERKStepSetMaxNumConstrFails(void* arkode_mem, int maxfails);
@@ -154,7 +153,7 @@ SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetNoInactiveRootWarn instead")
 int ERKStepSetNoInactiveRootWarn(void* arkode_mem);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetUserData instead")
 int ERKStepSetUserData(void* arkode_mem, void* user_data);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepSetPostprocARKodeFn instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetPostprocessStepFn instead")
 int ERKStepSetPostprocessStepFn(void* arkode_mem, ARKPostProcessFn ProcessStep);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeSetPostprocessStageFn instead")
 int ERKStepSetPostprocessStageFn(void* arkode_mem, ARKPostProcessFn ProcessStage);
@@ -163,25 +162,25 @@ int ERKStepEvolve(void* arkode_mem, sunrealtype tout, N_Vector yout,
                   sunrealtype* tret, int itask);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetDky instead")
 int ERKStepGetDky(void* arkode_mem, sunrealtype t, int k, N_Vector dky);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepGetNumARKodes instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetNumExpSteps instead")
 int ERKStepGetNumExpSteps(void* arkode_mem, long int* expsteps);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepGetNumARKodes instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetNumAccSteps instead")
 int ERKStepGetNumAccSteps(void* arkode_mem, long int* accsteps);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepGetARKodeAttempts instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetNumStepAttempts instead")
 int ERKStepGetNumStepAttempts(void* arkode_mem, long int* step_attempts);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetNumErrTestFails instead")
 int ERKStepGetNumErrTestFails(void* arkode_mem, long int* netfails);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetEstLocalErrors instead")
 int ERKStepGetEstLocalErrors(void* arkode_mem, N_Vector ele);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetWorkSpace instead")
 int ERKStepGetWorkSpace(void* arkode_mem, long int* lenrw, long int* leniw);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepGetARKodes instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetNumSteps instead")
 int ERKStepGetNumSteps(void* arkode_mem, long int* nsteps);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepGetActualIARKode instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetActualInitStep instead")
 int ERKStepGetActualInitStep(void* arkode_mem, sunrealtype* hinused);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepGetLARKode instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetLastStep instead")
 int ERKStepGetLastStep(void* arkode_mem, sunrealtype* hlast);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepGetCurrARKode instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetCurrentStep instead")
 int ERKStepGetCurrentStep(void* arkode_mem, sunrealtype* hcur);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetCurrentTime instead")
 int ERKStepGetCurrentTime(void* arkode_mem, sunrealtype* tcur);
@@ -206,7 +205,7 @@ int ERKStepWriteParameters(void* arkode_mem, FILE* fp);
 SUNDIALS_DEPRECATED_EXPORT_MSG(
   "use ERKStepGetCurrentButcherTable and ARKodeButcherTable_Write instead")
 int ERKStepWriteButcher(void* arkode_mem, FILE* fp);
-SUNDIALS_DEPRECATED_EXPORT_MSG("use ERKStepARKodeStats instead")
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetStepStats instead")
 int ERKStepGetStepStats(void* arkode_mem, long int* nsteps, sunrealtype* hinused,
                         sunrealtype* hlast, sunrealtype* hcur, sunrealtype* tcur);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeFree instead")
@@ -244,6 +243,8 @@ SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetNumRelaxSolveFails instead")
 int ERKStepGetNumRelaxSolveFails(void* arkode_mem, long int* fails);
 SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetNumRelaxSolveIters instead")
 int ERKStepGetNumRelaxSolveIters(void* arkode_mem, long int* iters);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use ARKodeGetNumRhsEvals instead")
+int ERKStepGetNumRhsEvals(void* arkode_mem, long int* nfevals);
 
 #ifdef __cplusplus
 }

inst/include/arkode/arkode_forcingstep.h

@@ -0,0 +1,43 @@
+/*---------------------------------------------------------------
+ * Programmer(s): Steven B. Roberts @ LLNL
+ *---------------------------------------------------------------
+ * SUNDIALS Copyright Start
+ * Copyright (c) 2002-2024, Lawrence Livermore National Security
+ * and Southern Methodist University.
+ * All rights reserved.
+ *
+ * See the top-level LICENSE and NOTICE files for details.
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ * SUNDIALS Copyright End
+ *---------------------------------------------------------------
+ * This is the header file for the ARKODE ForcingStep module.
+ *--------------------------------------------------------------*/
+
+#ifndef ARKODE_FORCINGINGSTEP_H_
+#define ARKODE_FORCINGINGSTEP_H_
+
+#include <sundials/sundials_nvector.h>
+#include <sundials/sundials_stepper.h>
+#include <sundials/sundials_types.h>
+
+#ifdef __cplusplus /* wrapper to enable C++ usage */
+extern "C" {
+#endif
+
+SUNDIALS_EXPORT void* ForcingStepCreate(SUNStepper stepper1,
+                                        SUNStepper stepper2, sunrealtype t0,
+                                        N_Vector y0, SUNContext sunctx);
+
+SUNDIALS_EXPORT int ForcingStepReInit(void* arkode_mem, SUNStepper stepper1,
+                                      SUNStepper stepper2, sunrealtype t0,
+                                      N_Vector y0);
+
+SUNDIALS_EXPORT int ForcingStepGetNumEvolves(void* arkode_mem, int partition,
+                                             long int* evolves);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif