Changeset 1708 for branches/newmole/source

Timestamp:

12/21/07 12:00:45 (11 months ago)

Author:

rjrw

Message:

Note some implementation oddities in grain surface reactions -- mostly
not in presently active code.

Files:

• branches/newmole/source/mole_reactions.cpp (modified) (8 diffs)

branches/newmole/source/mole_reactions.cpp

@@ -932 +932 @@
          * activ_barrier provides information on how well two atoms on the surface of a grain 
          * can actually interact to form a new molecule. The formalism below is taken from
-         * the Hasegawa, Herbst, and Leune paper from 1992 (referenced above)*/
+         * the Hasegawa, Herbst, and Leung paper from 1992 (referenced above)*/
 
         double E_i, E_j, quant_barrier, 
-        vib_freq_i, vib_freq_j, surface_density_of_sites, activ_barrier,
-        diff_i, diff_j, Exp_i, Exp_j,dust_density,total_sites;
+                vib_freq_i, vib_freq_j, surface_density_of_sites, activ_barrier,
+                diff_i, diff_j, Exp_i, Exp_j,dust_density, scale, total_sites;
         
         int nd;
@@ -945 +945 @@
         surface_density_of_sites = 1.5e15; /* number of sites available for adsorption */
         total_sites = 1.0e6; /* total number of sites */
+        fixit(); // rate->a is _always_ overall scaling factor
         E_i = rate->a; /* adsorption energy barrier (w/ grain) for first reactant */
         E_j = rate->b; /* adsorption energy barrier (w/ grain)for second reactant */
@@ -950 +951 @@
 
         /* Each species has a vibrational frequency, dependent on its adsorption energy barrier */
-        fixit(); /* Ordering of reactants may have switched, is rate->reduced_mass better?? */
+        fixit(); /* Ordering of reactants may have switched */
         vib_freq_i = sqrt(2*surface_density_of_sites*(0.3*BOLTZMANN)*E_i/(PI*PI*rate->reactants[0]->mole_mass));
-        vib_freq_j = sqrt(2*surface_density_of_sites*(0.3*BOLTZMANN)*E_j/(PI*PI*rate->reactants[0]->mole_mass));
+        vib_freq_j = sqrt(2*surface_density_of_sites*(0.3*BOLTZMANN)*E_j/(PI*PI*rate->reactants[1]->mole_mass));
  
         Exp_i = 0.0;
@@ -959 +960 @@
 
         /* Compute thermal evaporation terms along with total dust number density */
+        fixit(); // should there be an area weighting to exponential terms?
         if( conv.nTotalIoniz > 1 || iteration > 1 )
         {
@@ -975 +977 @@
         /* Exponential term models the likelyhood that two species, once they meet on the surface, will interact.  Larger the barrier, the smaller
          * the chance of a new molecule */
-        activ_barrier = exp(-2*(quant_barrier/(HBAReV*EN1EV))*sqrt(2*rate->reduced_mass*0.3*BOLTZMANN*activ_barrier));
+        scale = exp(-2*(quant_barrier/(HBAReV*EN1EV))*sqrt(2*rate->reduced_mass*0.3*BOLTZMANN*activ_barrier));
 
         /* Total Rate */
-        return activ_barrier*(diff_i + diff_j)/SDIV(dust_density);
+        return scale*(diff_i + diff_j)/SDIV(dust_density);
 }
 
@@ -988 +990 @@
          * The following treatment uses their equation 3 */
 
-        double yield, grain_area;
+        double grain_area;
         int nd;
 
@@ -995 +997 @@
         grain_area = 0.;
         for( nd=0; nd < gv.nBin; nd++ )
-                {
-                        grain_area += gv.bin[nd]->AvArea;
-                }
+        {
+                grain_area += gv.bin[nd]->AvArea;
+        }
 
         /* This is the number of molecules removed from the grain per incident photon
          * use same value of 1e-4 as used in Bergin */
 
-        yield = rate->a;
-
-        return yield*grain_area* hmi.UV_Cont_rel2_Draine_DB96_depth;
+        return grain_area* hmi.UV_Cont_rel2_Draine_DB96_depth;
 }
 
@@ -1923 +1923 @@
         {
                 rate = p->second;
-                if(rate->fun != NULL) {
-                        rate->rk = rate->a*rate->fun(rate);
-                }
+                ASSERT(rate->fun != NULL);
+                rate->rk = rate->a*rate->fun(rate);
         }       
 }