From 6821e728841b16cbfe0c283e69b3ada7257531b3 Mon Sep 17 00:00:00 2001
From: Luke Shingles <luke.shingles@gmail.com>
Date: Sun, 8 Sep 2024 23:08:26 +0100
Subject: [PATCH] Renames

---
 atomic.h  |  4 ++--
 globals.h | 14 +++++++-------
 input.cc  | 32 ++++++++++++++++----------------
 3 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/atomic.h b/atomic.h
index 25979c3ad..e6cda880a 100644
--- a/atomic.h
+++ b/atomic.h
@@ -361,7 +361,7 @@ inline auto get_includedlevels() -> int { return includedlevels; }
 }
 
 [[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].downtrans;
+  return globals::alltrans + globals::elements[element].ions[ion].levels[level].alltrans_startdown;
 }
 
 // the number of upward bound-bound transitions from the specified level
@@ -373,7 +373,7 @@ inline auto get_includedlevels() -> int { return includedlevels; }
 }
 
 [[nodiscard]] inline auto get_uptranslist(const int element, const int ion, const int level) -> LevelTransition * {
-  return globals::alltrans + globals::elements[element].ions[ion].levels[level].uptrans;
+  return globals::alltrans + globals::elements[element].ions[ion].levels[level].alltrans_startup;
 }
 
 [[nodiscard]] inline auto get_uptransspan(const int element, const int ion, const int level) {
diff --git a/globals.h b/globals.h
index 9a20ff73e..53ac58a93 100644
--- a/globals.h
+++ b/globals.h
@@ -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;
@@ -80,12 +75,17 @@ 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.
   int nuptrans{0};
-  int uptrans{};  // Allowed upward transitions from this level
+  int alltrans_startup{};  // Allowed upward transitions from this level
   int ndowntrans{0};
-  int downtrans{};                 // Allowed downward transitions from this level
+  int alltrans_startdown{};        // Allowed downward transitions from this level
   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:
diff --git a/input.cc b/input.cc
index 1dce260ad..2d580bd76 100644
--- a/input.cc
+++ b/input.cc
@@ -489,10 +489,10 @@ void add_transitions_to_unsorted_linelist(const int element, const int ion, cons
       int alltransindex = temp_alltranslist.size();
       temp_alltranslist.resize(temp_alltranslist.size() + totupdowntrans);
       for (int level = 0; level < nlevelsmax; level++) {
-        globals::elements[element].ions[ion].levels[level].downtrans = alltransindex;
+        globals::elements[element].ions[ion].levels[level].alltrans_startdown = alltransindex;
         alltransindex += get_ndowntrans(element, ion, level);
 
-        globals::elements[element].ions[ion].levels[level].uptrans = alltransindex;
+        globals::elements[element].ions[ion].levels[level].alltrans_startup = alltransindex;
         alltransindex += get_nuptrans(element, ion, level);
 
         set_ndowntrans(element, ion, level, 0);
@@ -552,20 +552,20 @@ void add_transitions_to_unsorted_linelist(const int element, const int ion, cons
           // the line list has not been sorted yet, so the store the level index for now and
           // the index into the sorted line list will be set later
 
-          temp_alltranslist[globals::elements[element].ions[ion].levels[level].downtrans + nupperdowntrans - 1] = {
-              .lineindex = -1,
-              .targetlevelindex = lowerlevel,
-              .einstein_A = transition.A,
-              .coll_str = transition.coll_str,
-              .osc_strength = f_ul,
-              .forbidden = transition.forbidden};
-          temp_alltranslist[globals::elements[element].ions[ion].levels[lowerlevel].uptrans + nloweruptrans - 1] = {
-              .lineindex = -1,
-              .targetlevelindex = level,
-              .einstein_A = transition.A,
-              .coll_str = transition.coll_str,
-              .osc_strength = f_ul,
-              .forbidden = transition.forbidden};
+          temp_alltranslist[globals::elements[element].ions[ion].levels[level].alltrans_startdown + nupperdowntrans -
+                            1] = {.lineindex = -1,
+                                  .targetlevelindex = lowerlevel,
+                                  .einstein_A = transition.A,
+                                  .coll_str = transition.coll_str,
+                                  .osc_strength = f_ul,
+                                  .forbidden = transition.forbidden};
+          temp_alltranslist[globals::elements[element].ions[ion].levels[lowerlevel].alltrans_startup + nloweruptrans -
+                            1] = {.lineindex = -1,
+                                  .targetlevelindex = level,
+                                  .einstein_A = transition.A,
+                                  .coll_str = transition.coll_str,
+                                  .osc_strength = f_ul,
+                                  .forbidden = transition.forbidden};
         }
 
       } else if (pass == 1 && globals::rank_in_node == 0) {