From b8047274ed9ddc7c45d8a63142d218cd5da9e7c1 Mon Sep 17 00:00:00 2001
From: Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>
Date: Thu, 26 Nov 2020 09:50:57 +0100
Subject: [PATCH] Fix the 'Below is the bug' bug in Phagen

---
 src/SConstruct                                | 11 ++++++-----
 src/msspec/phagen/fortran/phagen_scf_2.1_dp.f |  9 ++++++---
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/src/SConstruct b/src/SConstruct
index d9d91fd..45dae48 100644
--- a/src/SConstruct
+++ b/src/SConstruct
@@ -20,7 +20,7 @@ def f2py_generator(source, target, env, for_signature):
     modulefile = str(target[0])
     modulename = modulefile.replace(suffix, '').replace('/', '.')
     compiler = env['FORTRAN']
-    
+
     cmd  = f"$F2PY --fcompiler={compiler} "
     cmd += f" $F2PY_OPTS -m {modulename} -c {objects} {main}"
     cmd += f" && cp {'/'.join(modulename.split('.'))}.*.so {modulefile}"
@@ -86,14 +86,15 @@ AddOption('--f2py_path',
 
 # define environments
 gfortran_env = std.Clone(tools=['gfortran'])
-gfortran_env.Replace(FORTRANFLAGS=['-fPIC', '-O2', '-ffast-math'])
+#gfortran_env.Replace(FORTRANFLAGS=['-fPIC', '-O2', '-ffast-math', '-mcmodel=large', '-fdefault-real-8', '-fdefault-double-8'])
+gfortran_env.Replace(FORTRANFLAGS=['-fPIC', '-mcmodel=large'])
 
 ifort_env = std.Clone(tools=['ifort'])
 
 # parse options
 if GetOption('compiler') == 'gfortran':
     env = gfortran_env
-    env.Append(F2PY_OPTS='--opt=-O2')
+    #env.Append(F2PY_OPTS='--opt=-O2')
 elif GetOption('compiler') == 'ifort':
 	env = ifort_env
 
@@ -107,9 +108,9 @@ else:
 if GetOption('dbg'):
     gfortran_env.Append(FORTRANFLAGS = ['-g', '-Wall', '-Wextra', '-Warray-temporaries', 
                                         '-Wconversion', '-fbacktrace', '-ffree-line-length-0', 
-                                        '-fcheck=all', '-ffpe-trap=zero,overflow,underflow', 
+                                        '-fcheck=all', '-ffpe-trap=zero,overflow,underflow,invalid,denormal', 
                                         '-finit-real=nan'],
-                        F2PY_OPTS = ['--debug-capi', '--debug'])
+                        F2PY_OPTS = ['--noopt', '--debug-capi', '--debug'])
 
 if GetOption('verbose'):
     env.Replace(FORTRANCOMSTR = "")
diff --git a/src/msspec/phagen/fortran/phagen_scf_2.1_dp.f b/src/msspec/phagen/fortran/phagen_scf_2.1_dp.f
index deb8bef..9201cec 100644
--- a/src/msspec/phagen/fortran/phagen_scf_2.1_dp.f
+++ b/src/msspec/phagen/fortran/phagen_scf_2.1_dp.f
@@ -14802,13 +14802,16 @@ c      check = .true.
 !
 !   MPI
 !
-      if ( .not. do_r_in ) then
-!      if ( do_r_in ) then
+CST      if ( .not. do_r_in ) then
+CST!      if ( do_r_in ) then
+      if ( do_r_in ) then
 
       i = 1
 !
-      write(6,*) 'Below is the bug!'
+CST      write(6,*) 'Below is the bug!'
+CST      write(6,*) 'r_in=', r_in
       do
+CST        write(6,*) 'r_real(',i,')=', r_real(i)
 !
         if ( r_real ( i ) > r_in ) then