changed the repo and package name

DESCRIPTION

@@ -1,10 +1,10 @@
-Package: Rcppsbmod
+Package: sundialr
 Type: Package
-Title: Provides a Wrapper Around CVODE from Sundials Library
+Title: Ordinary Differential Equation Solvers (ODE) from Sundials C Library in R
 Version: 0.1.0
-Author: Satya
-Maintainer: Satya <[email protected]>
-Description: Provides a way to call the CVODE function in SUNDIALS C ODE solving library.
+Author: Satyaprakash Nayak
+Maintainer: Satyaprakash Nayak <[email protected]>
+Description: Provides a way to call the functions in SUNDIALS C ODE solving library (developed by Lawrence Livermore National Laboratory) in R. Currently ODE solver, CVODE, and routine to perform sensitivity analysis, CVODES, from the library can be accessed.
 License: MIT + file LICENSE
 LazyData: TRUE
 Imports:

NAMESPACE

@@ -1,3 +1,3 @@
 exportPattern("^[[:alpha:]]+")
 importFrom(Rcpp, evalCpp)
-useDynLib(Rcppsbmod)
+useDynLib(sundialr)

R/RcppExports.R

@@ -10,10 +10,10 @@
 #'@param reltolerance Relative Tolerance (a scalar)
 #'@param abstolerance Absolute Tolerance (a vector with length equal to ydot)
 cvode <- function(time_vec, IC, xpsexp, reltolerance, abstolerance) {
-    .Call('_Rcppsbmod_cvode', PACKAGE = 'Rcppsbmod', time_vec, IC, xpsexp, reltolerance, abstolerance)
+    .Call('_sundialr_cvode', PACKAGE = 'sundialr', time_vec, IC, xpsexp, reltolerance, abstolerance)
 }
 
-#'cvode
+#'cvode_test
 #'
 #' CVODE solver to solve stiff ODEs
 #'@param time_vec time vector
@@ -22,6 +22,6 @@ cvode <- function(time_vec, IC, xpsexp, reltolerance, abstolerance) {
 #'@param reltolerance Relative Tolerance (a scalar)
 #'@param abstolerance Absolute Tolerance (a vector with length equal to ydot)
 cvode_test <- function(time_vec, IC, xpsexp, reltolerance, abstolerance) {
-    .Call('_Rcppsbmod_cvode_test', PACKAGE = 'Rcppsbmod', time_vec, IC, xpsexp, reltolerance, abstolerance)
+    .Call('_sundialr_cvode_test', PACKAGE = 'sundialr', time_vec, IC, xpsexp, reltolerance, abstolerance)
 }
 

README.md

@@ -1,3 +1,3 @@
-# Rcppsbmod
+# sundialr
 
-A wrapper around the SUNDIALS ODE solving library.
+A wrapper around the SUNDIALS ODE solving C library.

src/Makevars

@@ -64,9 +64,15 @@ $(SOURCES_SUNLINSOL_DENSE) $(SOURCES_SUNMAT)
 
 OBJECTS_SUNDIALS_ALL = $(SOURCES_SUNDIALS_ALL:.c=.o)
 
-all: ($SHLIB) ../inst/libsundials_all.a
+all: ($SHLIB)
 
 ($SHLIB): $(OBJECTS) ../inst/libsundials_all.a
 
 ../inst/libsundials_all.a: $(OBJECTS_SUNDIALS_ALL)
-	ar -rvs ../inst/libsundials_all.a $(OBJECTS_SUNDIALS_ALL)
+	$(AR) -crvs ../inst/libsundials_all.a $(OBJECTS_SUNDIALS_ALL)
+
+clean:
+	echo "cleaning .."
+	(rm -f ./sundials/cvode/*.o; rm -f ./sundials/nvec_ser/*.o; rm -f ./sundials/sun*/*.o;)
+	(rm -f *.o *.a)
+	(rm -f ../inst/*.a)

src/Makevars.win

@@ -64,8 +64,10 @@ $(SOURCES_SUNLINSOL_DENSE) $(SOURCES_SUNMAT)
 
 OBJECTS_SUNDIALS_ALL = $(SOURCES_SUNDIALS_ALL:.c=.o)
 
-all: ($SHLIB) ../inst/libsundials_all.a
+all: ($SHLIB)
 
 ($SHLIB): $(OBJECTS) ../inst/libsundials_all.a
 
 ../inst/libsundials_all.a: $(OBJECTS_SUNDIALS_ALL)
+	$(AR) -crvs ../inst/libsundials_all.a $(OBJECTS_SUNDIALS_ALL)
+	$(RANLIB) -v $@

src/RcppExports.cpp

@@ -7,7 +7,7 @@ using namespace Rcpp;
 
 // cvode
 NumericMatrix cvode(NumericVector time_vec, NumericVector IC, SEXP xpsexp, double reltolerance, NumericVector abstolerance);
-RcppExport SEXP _Rcppsbmod_cvode(SEXP time_vecSEXP, SEXP ICSEXP, SEXP xpsexpSEXP, SEXP reltoleranceSEXP, SEXP abstoleranceSEXP) {
+RcppExport SEXP _sundialr_cvode(SEXP time_vecSEXP, SEXP ICSEXP, SEXP xpsexpSEXP, SEXP reltoleranceSEXP, SEXP abstoleranceSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
@@ -22,7 +22,7 @@ END_RCPP
 }
 // cvode_test
 NumericMatrix cvode_test(NumericVector time_vec, NumericVector IC, SEXP xpsexp, double reltolerance, NumericVector abstolerance);
-RcppExport SEXP _Rcppsbmod_cvode_test(SEXP time_vecSEXP, SEXP ICSEXP, SEXP xpsexpSEXP, SEXP reltoleranceSEXP, SEXP abstoleranceSEXP) {
+RcppExport SEXP _sundialr_cvode_test(SEXP time_vecSEXP, SEXP ICSEXP, SEXP xpsexpSEXP, SEXP reltoleranceSEXP, SEXP abstoleranceSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
@@ -37,12 +37,12 @@ END_RCPP
 }
 
 static const R_CallMethodDef CallEntries[] = {
-    {"_Rcppsbmod_cvode", (DL_FUNC) &_Rcppsbmod_cvode, 5},
-    {"_Rcppsbmod_cvode_test", (DL_FUNC) &_Rcppsbmod_cvode_test, 5},
+    {"_sundialr_cvode", (DL_FUNC) &_sundialr_cvode, 5},
+    {"_sundialr_cvode_test", (DL_FUNC) &_sundialr_cvode_test, 5},
     {NULL, NULL, 0}
 };
 
-RcppExport void R_init_Rcppsbmod(DllInfo *dll) {
+RcppExport void R_init_sundialr(DllInfo *dll) {
     R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
     R_useDynamicSymbols(dll, FALSE);
 }

src/cvode.cpp

@@ -20,7 +20,22 @@ using namespace Rcpp;
 // #define NOUT  12
 
 //------------------------------------------------------------------------------
+struct sexp_global {
+  SEXP sexp_g;
+};
+
+// struct sexp_global my_sexp_g = {R_NilValue};
+// struct sexp_global *my_sexp = &my_sexp_g;
+
 typedef int (*funcPtr)(realtype time, N_Vector y, N_Vector ydot, void *user_data);
+typedef NumericVector (*funcPtr_test) (double t, NumericVector y, NumericVector ydot);
+
+struct rhs_data{
+  SEXP rhs_eqn;
+};
+
+struct rhs_data my_rhs = {R_NilValue}; // sets rhs_eqn to NULL
+struct rhs_data *my_rhs_ptr = &my_rhs;
 //------------------------------------------------------------------------------
 
 // function with the definition required
@@ -198,9 +213,9 @@ NumericMatrix cvode (NumericVector time_vec, NumericVector IC, SEXP xpsexp,
 
 
 // cvode - test ----------------------------------------------------------------
-typedef int (*funcPtr_test)(double time, NumericVector y, NumericVector ydot);
+// typedef int (*funcPtr_test)(double time, NumericVector y, NumericVector ydot);
 
-SEXP sexp_g;  // declare a global SEXP
+// SEXP sexp_g = R_NilValue;  // declare a global SEXP
 
 // XPtr<funcPtr_test> xpfun(sexp_g);
 // funcPtr_test fun_test = *xpfun;
@@ -216,8 +231,12 @@ int fun_test1(realtype t, N_Vector y, N_Vector ydot, void* user_data){
      y1[i] = NV_Ith_S(y,i);
    }
 
+  // cast void pointer to struct
+  struct rhs_data *my_rhs_ptr2 = (struct rhs_data*)user_data;
+  SEXP xpsexp = (*my_rhs_ptr2).rhs_eqn;
+
   // use function pointer to get the derivatives
-  XPtr<funcPtr_test> xpfun(sexp_g);
+  XPtr<funcPtr_test> xpfun(xpsexp);
   funcPtr_test fun_test = *xpfun;
 
   NumericVector ydot1(y1.length());
@@ -233,7 +252,49 @@ int fun_test1(realtype t, N_Vector y, N_Vector ydot, void* user_data){
 
   return (0);
 }
-//'cvode
+
+int fun_test2(realtype t, N_Vector y, N_Vector ydot, void* user_data){
+
+  // convert y to NumericVector y1
+  int y_len = NV_LENGTH_S(y);
+
+  NumericVector y1(y_len);    // filled with zeros
+  for (int i = 0; i < y_len; i++){
+    y1[i] = NV_Ith_S(y,i);
+  }
+
+  // convert ydot to NumericVector ydot1
+  int ydot_len = NV_LENGTH_S(ydot);
+
+  NumericVector ydot1(ydot_len);    // filled with zeros
+  for (int i = 0; i < ydot_len; i++){
+    ydot1[i] = NV_Ith_S(ydot,i);
+  }
+
+  // cast void pointer to struct
+  struct rhs_data *my_rhs_ptr2 = (struct rhs_data*)user_data;
+  SEXP xpsexp = (*my_rhs_ptr2).rhs_eqn;
+
+  // use function pointer to get the derivatives
+  XPtr<funcPtr_test> xpfun(xpsexp);
+  funcPtr_test fun = *xpfun;
+
+
+  ydot1 = fun(t, y1, ydot1);
+
+  // convert NumericVector ydot1 to N_Vector ydot
+  // N_Vector ydot; ydot = NULL;
+  // ydot = N_VNew_Serial(ydot1.length());
+  for (int i = 0; i<ydot1.length(); i++){
+    NV_Ith_S(ydot, i) = ydot1[i];
+  }
+
+
+  // return ydot1;
+  return(0);
+}
+
+//'cvode_test
 //'
 //' CVODE solver to solve stiff ODEs
 //'@param time_vec time vector
@@ -315,8 +376,18 @@ NumericMatrix cvode_test (NumericVector time_vec, NumericVector IC,
   //   NV_Ith_S(ydot1, i) = ydot[i];
   // }
 
-  sexp_g = xpsexp;  // assign to glocal sexp
-  flag = CVodeInit(cvode_mem, fun_test1, T0, y0);
+  // (*my_sexp).sexp_g = xpsexp;  // assign to glocal sexp
+
+  (*my_rhs_ptr).rhs_eqn = xpsexp;
+
+  void* my_rhs_ptr1 = (void*)&my_rhs;
+
+  flag = CVodeSetUserData(cvode_mem, (void*)&my_rhs);
+  if (check_flag(&flag, "CVodeSetUserData", 1)) {
+    return (1);
+  }
+
+  flag = CVodeInit(cvode_mem, fun_test2, T0, y0);
 
   // flag = CVodeInit(cvode_mem, fun, T0, y0);
   if (check_flag(&flag, "CVodeInit", 1)) {
@@ -352,7 +423,8 @@ NumericMatrix cvode_test (NumericVector time_vec, NumericVector IC,
 
   // NumericMatrix to store results - filled with 0.0
   // First row for initial conditions, First column is for time
-  NumericMatrix soln = NumericMatrix(time_vec.length()+1, IC.length() + 1);
+  // ASSUMING input time vector (time_vec) has the first element as 0
+  NumericMatrix soln = NumericMatrix(time_vec.length(), IC.length() + 1);
 
   // fill the first row of soln matrix with Initial Conditions
   soln(0,0) = time_vec[0];
@@ -445,4 +517,35 @@ int check_flag(void *flagvalue, const char *funcname, int opt)
 }
 
 
+//------------------------------------------------------------------------------
+
+// // [[Rcpp::export]]
+// NumericVector test_sexp(double t, NumericVector y, NumericVector ydot, SEXP xpsexp){
+//
+//   // convert NumericVector to N_Vector
+//   // Set the initial conditions-------------------------------------------------
+//   N_Vector y0; y0 = NULL;
+//   y0 = N_VNew_Serial(y.length());
+//   for (int i = 0; i<y.length(); i++){
+//     NV_Ith_S(y0, i) = y[i];
+//   }
+//
+//   N_Vector ydot0; ydot0 = NULL;
+//   ydot0 = N_VNew_Serial(ydot.length());
+//   for (int i = 0; i<ydot.length(); i++){
+//     NV_Ith_S(ydot0, i) = ydot[i];
+//   }
+//
+//   (*my_rhs_ptr).rhs_eqn = xpsexp;
+//
+//   // XPtr<funcPtr_test> xpfun(xpsexp);
+//   // funcPtr_test fun = *xpfun;
+//   //
+//   // return fun(t, y, ydot);
+//
+//   return fun_test2(t, y0, ydot0, (void*)&my_rhs);
+//
+// }
+
+
 

vignettes/my-vignette.Rmd

@@ -1,10 +1,10 @@
 ---
-title: "Rcppsbmod - A wrapper around CVODE solver from SUNDIALS"
-author: "Satya"
+title: "sundialr - A wrapper around SUNDIALS ODE solving library"
+author: "Satyaprakash Nayak"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Rcppsbmod - A wrapper around CVODE solver from SUNDIALS}
+  %\VignetteIndexEntry{sundialr - A wrapper around CVODE solver from SUNDIALS}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---

vignettes/my-vignette.html

@@ -10,11 +10,11 @@
 
 <meta name="viewport" content="width=device-width, initial-scale=1">
 
-<meta name="author" content="Satya" />
+<meta name="author" content="Satyaprakash Nayak" />
 
-<meta name="date" content="2018-03-14" />
+<meta name="date" content="2018-05-18" />
 
-<title>Rcppsbmod - A wrapper around CVODE solver from SUNDIALS</title>
+<title>sundialr - A wrapper around SUNDIALS ODE solving library</title>
 
 
 
@@ -30,9 +30,9 @@
 
 
 
-<h1 class="title toc-ignore">Rcppsbmod - A wrapper around CVODE solver from SUNDIALS</h1>
-<h4 class="author"><em>Satya</em></h4>
-<h4 class="date"><em>2018-03-14</em></h4>
+<h1 class="title toc-ignore">sundialr - A wrapper around SUNDIALS ODE solving library</h1>
+<h4 class="author"><em>Satyaprakash Nayak</em></h4>
+<h4 class="date"><em>2018-05-18</em></h4>