From 4c8c2698a551cdedd1fae2f4f3ecc9275b3e10e2 Mon Sep 17 00:00:00 2001
From: Luke Shingles <luke.shingles@gmail.com>
Date: Mon, 9 Sep 2024 10:36:57 +0100
Subject: [PATCH] Make cont_index positive

---
 atomic.h | 2 +-
 input.cc | 7 +++----
 sn3d.h   | 2 +-
 3 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/atomic.h b/atomic.h
index b48497e97..8e0483fe2 100644
--- a/atomic.h
+++ b/atomic.h
@@ -417,7 +417,7 @@ 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 globals::elements[element].ions[ion].levels[level].cont_index + phixstargetindex;
 }
 
 // Returns the energy of (element,ion,level).
diff --git a/input.cc b/input.cc
index dcc5a4967..78aba3e23 100644
--- a/input.cc
+++ b/input.cc
@@ -866,7 +866,7 @@ void read_phixs_data() {
     read_phixs_file(1, tmpallphixs);
   }
 
-  int cont_index = -1;
+  int cont_index = 0;
   ptrdiff_t nbftables = 0;
   for (int element = 0; element < get_nelements(); element++) {
     const int nions = get_nions(element);
@@ -874,9 +874,8 @@ void read_phixs_data() {
       const int nlevels = get_nlevels(element, ion);
       for (int level = 0; level < nlevels; level++) {
         const int nphixstargets = get_nphixstargets(element, ion, level);
-        globals::elements[element].ions[ion].levels[level].cont_index =
-            (nphixstargets > 0) ? cont_index : std::numeric_limits<int>::max();
-        cont_index -= nphixstargets;
+        globals::elements[element].ions[ion].levels[level].cont_index = (nphixstargets > 0) ? cont_index : -1;
+        cont_index += nphixstargets;
         if (nphixstargets > 0) {
           nbftables++;
         }
diff --git a/sn3d.h b/sn3d.h
index 6dfb7cce6..458e501c9 100644
--- a/sn3d.h
+++ b/sn3d.h
@@ -216,7 +216,7 @@ inline void gsl_error_handler_printout(const char *reason, const char *file, int
 
 [[nodiscard]] inline auto get_bflutindex(const int tempindex, const int element, const int ion, const int level,
                                          const int phixstargetindex) -> int {
-  const int contindex = -1 - globals::elements[element].ions[ion].levels[level].cont_index + phixstargetindex;
+  const int contindex = globals::elements[element].ions[ion].levels[level].cont_index + phixstargetindex;
 
   const int bflutindex = (tempindex * globals::nbfcontinua) + contindex;
   assert_testmodeonly(bflutindex >= 0);