Changeset 1683 for branches/newmole/source

Timestamp:

12/16/07 11:29:33 (11 months ago)

Author:

rjrw

Message:

Eliminate coreactions list in favour of iterator on reaction table.

Location:

branches/newmole/source

Files:

• mole_co_etc.cpp (modified) (16 diffs)
• mole_eval_balance.cpp (modified) (2 diffs)
• mole_priv.h (modified) (1 diff)
• mole_reactions.cpp (modified) (8 diffs)

branches/newmole/source/mole_co_etc.cpp

@@ -278 +278 @@
         /* ...first active species */
         i = 0;
-        for (map<string,struct molecule *>::iterator p
+        for (molecule_i p
                                  =mole_priv.spectab.begin(); p != mole_priv.spectab.end(); p++) 
         {
@@ -290 +290 @@
                                 mole_cmp);
 
-        for (map<string,struct molecule *>::iterator p
+        for (molecule_i p
                                  =mole_priv.spectab.begin(); p != mole_priv.spectab.end(); p++) 
         {
@@ -531 +531 @@
 struct molecule *findspecies(const char buf[])
 {
-        map<string,struct molecule *>::iterator p;
+        molecule_i p;
 
         DEBUG_ENTRY("findspecies()");
@@ -545 +545 @@
 STATIC struct chem_element_s *findelement(const char buf[])
 {
-        map<string,struct chem_element_s *>::iterator p;
+        chem_element_i p;
 
         DEBUG_ENTRY("findelement()");
@@ -559 +559 @@
 struct mole_reaction_s *mole_findrate_s(const char buf[])
 {
-        map<string,struct mole_reaction_s *>::iterator p;
+        mole_reaction_i p;
 
         DEBUG_ENTRY("mole_findrate_s()");
@@ -672 +672 @@
 double mole_sink_rate(const char chSpecies[7])
 {
-        int ipthis, i, n, nt;
+        int ipthis, i;
         double ratev, ratevi;
         struct mole_reaction_s *rate;
@@ -681 +681 @@
         sp = findspecies(chSpecies);
         ratev = 0;
-        nt = coreactions.n;
-
-        for(n=0;n<nt;n++) 
-        {
-                rate = coreactions.list[n];
+
+        for(mole_reaction_i p=mole_priv.reactab.begin(); 
+                        p != mole_priv.reactab.end(); p++) 
+        {
+                rate = p->second;
                 ipthis = -1;
                 for(i=0;i<rate->nreactants && ipthis == -1;i++)
@@ -729 +729 @@
 void mole_update_rks(void)
 {
-        int n, nt;
         struct mole_reaction_s *rate;
 
@@ -740 +739 @@
         hmole_reactions();
         
-        nt = coreactions.n;
-
-        for(n=0;n<nt;n++) 
-        {
-                rate = coreactions.list[n];
+        for (mole_reaction_i p
+                                 =mole_priv.reactab.begin(); p != mole_priv.reactab.end(); p++) 
+        {
+                rate = p->second;
                 if(rate->fun != NULL) {
                         rate->rk = rate->a*rate->fun(rate);
@@ -753 +751 @@
 double mole_dissoc_rate(const char chSpecies[7])
 {
-        int ipsp, ipph, i, n, nt;
+        int ipsp, ipph, i;
         double ratev, ratevi;
         struct mole_reaction_s *rate;
@@ -763 +761 @@
         ph = findspecies("PHOTON");
         ratev = 0;
-        nt = coreactions.n;
-
-        for(n=0;n<nt;n++) 
-        {
-                rate = coreactions.list[n];
+
+        for (mole_reaction_i p
+                                 =mole_priv.reactab.begin(); p != mole_priv.reactab.end(); p++) 
+        {
+                rate = p->second;
                 
                 ipph = 0;
@@ -807 +805 @@
 double mole_source_rate(const char chSpecies[7])
 {
-        int ipthis, i, n, nt;
+        int ipthis, i;
         double ratev, ratevi;
         struct mole_reaction_s *rate;
@@ -816 +814 @@
         sp = findspecies(chSpecies);
         ratev = 0;
-        nt = coreactions.n;
-
-        for(n=0;n<nt;n++) 
-        {
-                rate = coreactions.list[n];
+
+        for (mole_reaction_i p
+                                 =mole_priv.reactab.begin(); p != mole_priv.reactab.end(); p++) 
+        {
+                rate = p->second;
                 ipthis = 0;
                 for(i=0;i<rate->nproducts;i++)
@@ -855 +853 @@
          */
 
-        long int  nt, n, i;
+        long int  i;
         struct mole_reaction_s *rate;
         double rate_tot, heating;
         realnum reaction_enthalpy;
         
-        nt = coreactions.n;
-        
         heating = 0;
         /* loop over all reactions */
-        for(n=0;n<nt;n++) 
-        {               
-                rate = coreactions.list[n];
+        for (mole_reaction_i p
+                                 =mole_priv.reactab.begin(); p != mole_priv.reactab.end(); p++) 
+        {
+                rate = p->second;
                 /* This loop calculates the product of the rate constant times the densities*/
                 rate_tot = rate->rk;
@@ -904 +901 @@
                                                                         bool lgData, double depth)
 {
-        int n, nt, i, ipthis;
+        int i, ipthis;
         double ratevi;
         struct mole_reaction_s *rate;
@@ -922 +919 @@
         }
                 
-        nt = coreactions.n;
-        for(n=0;n<nt;n++) {
-                rate = coreactions.list[n];
+        for (mole_reaction_i p
+                                 =mole_priv.reactab.begin(); p != mole_priv.reactab.end(); p++) 
+        {
+                rate = p->second;
                 ipthis = 0;
                 for (i=0;i<rate->nreactants;i++)

branches/newmole/source/mole_eval_balance.cpp

@@ -32 +32 @@
 void mole_eval_balance(long int num_total, double *b, double **c)
 {
-        long int i, j, n, nt, nelem, ratei, ratej, ion, ion2;
+        long int i, j, nelem, ratei, ratej, ion, ion2;
         struct mole_reaction_s *rate, *ratesnk=NULL, *ratesrc=NULL;
         double rate_tot, rate_deriv[MAXREACTANTS], rated, rk;
@@ -77 +77 @@
         /* Fills matrix elements for passive species -- these can be used to
                  derive sources & sinks resulting from this part of the network */
-        nt = coreactions.n;
-        for(n=0;n<nt;n++) 
-        {
-                rate = coreactions.list[n];
+        for(mole_reaction_i p=mole_priv.reactab.begin(); 
+                        p != mole_priv.reactab.end(); p++) 
+        {
+                rate = p->second;
                 rk = rate->rk;
                 

branches/newmole/source/mole_priv.h

@@ -13 +13 @@
         map <string,double (*)(struct mole_reaction_s *rate)> functab;
 } mole_priv;
+typedef map<string,struct mole_reaction_s *>::iterator mole_reaction_i;
+typedef map<string,struct molecule *>::iterator molecule_i;
+typedef map<string,struct chem_element_s *>::iterator chem_element_i;
 
 extern struct molecule **groupspecies;
 
 extern struct molecule *null_mole;
-
-EXTERN struct t_coreactions {
-        struct mole_reaction_s **list;
-        long int n;
-} coreactions;
 
 #define MAXREACTANTS 3

branches/newmole/source/mole_reactions.cpp

@@ -40 +40 @@
 
 enum {UDFA = 0}; /* UDFA = 1 for: make UDFA comparison and stop */
-
-/* Structures containing reaction data */
-struct t_coreactions coreactions;
 
 STATIC void newreact(const char label[], 
@@ -146 +143 @@
 
         long int i;
-        /* Initialize number of reactions added to list in coreactions of reactions
-           treated by new methodology, incremented by newreact() */
 
         DEBUG_ENTRY("mole_create_react()");
@@ -153 +148 @@
         if (UDFA)
                 read_data("rate05_feb17.csv",parse_udfa);
-
-        coreactions.n = 0; 
 
         /* Set up registry of rate functions -- could do something intelligent about
@@ -415 +408 @@
         }
 
-        /* Create linear list of reactions ... */
-        if (coreactions.n != 0)
-        {
-                coreactions.list =  (struct mole_reaction_s **)
-                        MALLOC((size_t)coreactions.n*sizeof(struct mole_reaction_s *));
-        }
-        else
-        {
-                coreactions.list = NULL;
-        }
-
-        /* ...and populate it */
-        i = 0;
-        for (map<string,struct mole_reaction_s *>::iterator p
-                                 =mole_priv.reactab.begin(); p != mole_priv.reactab.end(); p++) 
-        {
-                coreactions.list[i++] = p->second;
-        }
-        ASSERT (i == coreactions.n); 
-
         if (0) 
                 plot_sparsity();
@@ -462 +435 @@
         struct molecule    *sp;
         ratefunc func;
-        map <string,struct mole_reaction_s *>::iterator p;
+        mole_reaction_i p;
         int i,j,k,exists;
         char buf[NBUF];
@@ -653 +626 @@
                 free(p->second);
         }
-        else
-        {
-                coreactions.n++;
-        }
         mole_priv.reactab[label] = rate;
         rate->label = label;
@@ -1487 +1456 @@
         FILE *sparsefp;
         int i, j, nb, ch;
-        long int ratej, nt, n;
+        long int ratej;
         struct mole_reaction_s *rate;
         double **c;
@@ -1508 +1477 @@
         }
 
-        nt = coreactions.n;
-        
-        for (n=0;n<nt;n++) 
-        {
-                rate = coreactions.list[n];
+        for(mole_reaction_i p=mole_priv.reactab.begin(); 
+                        p != mole_priv.reactab.end(); p++) 
+        {
+                rate = p->second;
                 
                 for (j=0;j<rate->nreactants;j++)