Replace level transition pointers with indicies (#123)

sim2010 classic mode 2-120 days 2e7pkt 960 core JUWELS runtime decreased from 1.18k core hrs (v2024.09) to 1.13k core hours (4.5% faster).

atomic.h

@@ -94,7 +94,9 @@ inline auto get_nphixstargets(const int element, const int ion, const int level)
   assert_testmodeonly(phixstargetindex >= 0);
   assert_testmodeonly(phixstargetindex < get_nphixstargets(element, ion, level));
 
-  return globals::elements[element].ions[ion].levels[level].phixstargets[phixstargetindex].levelindex;
+  return globals::allphixstargets[globals::elements[element].ions[ion].levels[level].phixstargetstart +
+                                  phixstargetindex]
+      .levelindex;
 }
 
 // Return the probability of a target state for photoionization of (element,ion,level).
@@ -106,7 +108,9 @@ inline auto get_nphixstargets(const int element, const int ion, const int level)
   assert_testmodeonly(phixstargetindex >= 0);
   assert_testmodeonly(phixstargetindex < get_nphixstargets(element, ion, level));
 
-  return globals::elements[element].ions[ion].levels[level].phixstargets[phixstargetindex].probability;
+  return globals::allphixstargets[globals::elements[element].ions[ion].levels[level].phixstargetstart +
+                                  phixstargetindex]
+      .probability;
 }
 
 // Return the statistical weight of (element,ion,level).
@@ -360,6 +364,10 @@ inline auto get_includedlevels() -> int { return includedlevels; }
   return globals::elements[element].ions[ion].levels[level].ndowntrans;
 }
 
+[[nodiscard]] inline auto get_downtranslist(const int element, const int ion, const int level) -> LevelTransition * {
+  return globals::alltrans + globals::elements[element].ions[ion].levels[level].alltrans_startdown;
+}
+
 // the number of upward bound-bound transitions from the specified level
 [[nodiscard]] inline auto get_nuptrans(const int element, const int ion, const int level) -> int {
   assert_testmodeonly(element < get_nelements());
@@ -368,6 +376,15 @@ inline auto get_includedlevels() -> int { return includedlevels; }
   return globals::elements[element].ions[ion].levels[level].nuptrans;
 }
 
+[[nodiscard]] inline auto get_uptranslist(const int element, const int ion, const int level) -> LevelTransition * {
+  const auto &levelref = globals::elements[element].ions[ion].levels[level];
+  return globals::alltrans + levelref.alltrans_startdown + levelref.ndowntrans;
+}
+
+[[nodiscard]] inline auto get_uptransspan(const int element, const int ion, const int level) {
+  return std::span(get_uptranslist(element, ion, level), get_nuptrans(element, ion, level));
+}
+
 // the number of downward bound-bound transitions from the specified level
 inline void set_ndowntrans(const int element, const int ion, const int level, const int ndowntrans) {
   assert_testmodeonly(element < get_nelements());
@@ -404,7 +421,7 @@ inline void set_nuptrans(const int element, const int ion, const int level, cons
 [[nodiscard]] inline auto get_emtype_continuum(const int element, const int ion, const int level,
                                                const int upperionlevel) -> int {
   const int phixstargetindex = get_phixtargetindex(element, ion, level, upperionlevel);
-  return globals::elements[element].ions[ion].levels[level].cont_index - phixstargetindex;
+  return -1 - globals::elements[element].ions[ion].levels[level].cont_index - phixstargetindex;
 }
 
 // Returns the energy of (element,ion,level).

globals.h

@@ -54,7 +54,7 @@ struct FullPhotoionTransition {
   int level;
   int phixstargetindex;
   int upperlevel;
-  float *photoion_xs;
+  const float *photoion_xs;
   double probability;
   int index_in_groundphixslist;
   int bfestimindex;
@@ -66,11 +66,6 @@ struct GroundPhotoion {
   int ion;
 };
 
-struct PhotoionTarget {
-  double probability;  // fraction of phixs cross section leading to this final level
-  int levelindex;      // index of upper ion level after photoionisation
-};
-
 struct LevelTransition {
   int lineindex;
   int targetlevelindex;
@@ -80,18 +75,23 @@ struct LevelTransition {
   bool forbidden;
 };
 
+struct PhotoionTarget {
+  double probability;  // fraction of phixs cross section leading to this final level
+  int levelindex;      // index of upper ion level after photoionisation
+};
+
 struct EnergyLevel {
-  double epsilon{-1};            // Excitation energy of this level relative to the neutral ground level.
-  LevelTransition *uptrans{};    // Allowed upward transitions from this level
-  LevelTransition *downtrans{};  // Allowed downward transitions from this level
-  int nuptrans{0};
-  int ndowntrans{0};
-  PhotoionTarget *phixstargets{};  // pointer to table of target states and probabilities
-  int phixsstart{-1};              // index to start of photoionisation cross-sections table in global::allphixs
-  int nphixstargets{0};            // length of phixstargets array:
-  float stat_weight{0.};           // Statistical weight of this level.
-
-  int cont_index{-1};  // Index of the continuum associated to this level. Negative number.
+  double epsilon{-1};        // Excitation energy of this level relative to the neutral ground level.
+  int alltrans_startdown{};  // index into globals::alltrans for first down transition from this level
+  int ndowntrans{0};         // Number of down transitions from this level
+  int nuptrans{0};           // Number of up transitions to this level
+  int phixsstart{-1};        // index to start of photoionisation cross-sections table in global::allphixs
+  int nphixstargets{0};      // number of target levels for photoionisation
+  float stat_weight{0.};     // statistical weight of this level
+  int phixstargetstart{};    // index into globals::allphixstargets
+  int cont_index{-1};        // index of the bound-free continuum (for first target) sorted by
+                             // element/ion/level/phixstargetindex
+                             // (not an index into the nu_edge-sorted allcont list!)
   int closestgroundlevelcont{-1};
 };
 
@@ -109,7 +109,6 @@ struct Ion {
   int uniquelevelindexstart;
   int groundcontindex;
   double ionpot;  // Ionisation threshold to the next ionstage
-  LevelTransition *alltransitions;
 };
 
 struct Element {
@@ -134,7 +133,7 @@ struct TransitionLine {
 struct GSLIntegrationParas {
   double nu_edge;
   float T;
-  float *photoion_xs;
+  const float *photoion_xs;
 };
 
 template <bool separatestimrecomb>
@@ -258,6 +257,8 @@ inline int opacity_case{};  // 0 grey, 1 for Fe-grp dependence.
 inline std::vector<float> ion_alpha_sp;  // alpha_sp for each ion and temperature table value
 
 inline float *allphixs{};
+inline LevelTransition *alltrans;
+inline std::vector<PhotoionTarget> allphixstargets;
 
 inline std::vector<Element> elements;