fixed bug when using -m and -p option simultaneously

.github/workflows/build.yml

@@ -51,8 +51,9 @@ jobs:
       PYTHON_V: 3.8
 
     steps:
-    - name: Checkout code
+    - name: Checkout code 
       uses: actions/checkout@v4
+
 
     - uses: actions/setup-python@v4
       with:

src/entries.f90

@@ -5,7 +5,7 @@ module count_entries
   contains
 
     subroutine check_entries(index_mass, isotope_masses, exact_intensity, &
-        list_masses,  intensity,  count_mass, chrg)
+        list_masses,  intensity,  count_mass, chrg, int_masses)
 
       integer :: loop, loop2, index_mass
       integer :: count_mass
@@ -31,6 +31,7 @@ subroutine check_entries(index_mass, isotope_masses, exact_intensity, &
       !real (wp) :: save_list(1000)
 
       logical :: there = .true.
+      logical :: int_masses
 
       xmass = 0
       loop = 0
@@ -47,11 +48,13 @@ subroutine check_entries(index_mass, isotope_masses, exact_intensity, &
       !> loop over the list from the isotope subroutine
 outer: do loop2 = 1, index_mass 
         loop = 0
-
+        if (int_masses) isotope_masses(loop2) = int(isotope_masses(loop2))
         !> loop over all entries of new (check) list 
 inner:  do 
           loop = loop + 1
+          if (int_masses) list_masses(loop) = int(list_masses(loop))
           mass_diff = abs(list_masses(loop) - isotope_masses(loop2))
+
 
           if ( list_masses(loop) == 0.0_wp ) then
             there = .false.

src/entries.i90

@@ -0,0 +1,95 @@
+# 1 "/tmp1/coding/PlotMS/src/entries.f90"
+module count_entries
+  use xtb_mctc_accuracy, only: wp
+  implicit none
+
+  contains
+
+    subroutine check_entries(index_mass, isotope_masses, exact_intensity, &
+        list_masses,  intensity,  count_mass, chrg, int_masses)
+
+      integer :: loop, loop2, index_mass
+      integer :: count_mass
+      integer :: sum_index, i
+      integer :: check
+
+!real(wp) :: intensity(index_mass)
+      real(wp) :: xmass
+      real(wp) :: isotope_masses(index_mass)
+      real(wp) :: exact_intensity(index_mass)
+      real(wp) :: chrg
+
+      real(wp) :: list_masses(10000)
+      real(wp) :: intensity(10000)
+
+      real(wp) :: mass_diff
+
+!real(wp), allocatable :: list_masses(:)
+!real(wp), allocatable :: save_list(:)
+!real(wp), allocatable :: save_int(:)
+!real(wp), allocatable :: intensity(:)
+!real (wp) :: save_list(1000)
+!real (wp) :: save_list(1000)
+
+      logical :: there = .true.
+      logical :: int_masses
+
+      xmass = 0
+      loop = 0
+      loop2 = 0
+      check = 0
+!count_mass = count_mass + index_mass
+      if(count_mass == 0)then
+        sum_index =  index_mass
+      else
+        sum_index = count_mass + index_mass
+      endif
+
+
+!> loop over the list from the isotope subroutine
+outer: do loop2 = 1, index_mass 
+        loop = 0
+        if (int_masses) isotope_masses(loop2) = int(isotope_masses(loop2))
+!> loop over all entries of new (check) list
+inner:  do 
+          loop = loop + 1
+          if (int_masses) list_masses(loop) = int(list_masses(loop))
+          mass_diff = abs(list_masses(loop) - isotope_masses(loop2))
+
+
+          if ( list_masses(loop) == 0.0_wp ) then
+            there = .false.
+!write(*,*) 'NULL'
+            exit inner
+
+!elseif  ( list_masses(loop) == isotope_masses(loop2) ) then
+          elseif  ( mass_diff < 1.0d0-10 .or. mass_diff == 0.0_wp) then
+            there = .true.
+            intensity(loop) = intensity(loop) +  1 * exact_intensity(loop2) &
+              * abs(chrg)
+            if (loop2 < index_mass ) cycle outer 
+            if (loop2 == index_mass ) exit inner
+
+
+!>> false if not in list, store
+!elseif ( list_masses(loop) /= isotope_masses(loop2) ) then
+          elseif  ( mass_diff > 1.0d0-10 ) then
+            there = .false.
+            if (loop == sum_index ) exit inner
+          endif
+        enddo inner
+
+
+        if ( .not. there ) then
+          count_mass = count_mass + 1
+          list_masses(count_mass) = isotope_masses(loop2)
+          intensity(count_mass) = intensity(count_mass) + 1 * exact_intensity(loop2) &
+            * abs(chrg)
+        endif
+
+      enddo outer
+
+
+    end subroutine check_entries
+
+end module count_entries 

src/isotopes.f90

@@ -26,7 +26,7 @@ subroutine isotope(counter, mzmin, ntot, iat_save, maxatm, rnd, &
   integer :: loop, index_mass
 !  integer :: tmp_intensity
   integer :: store_int(1000)
-  integer :: mzmin
+  real(wp) :: mzmin
   integer :: z_chrg
 
   real(wp) :: rnd(nrnd,maxatm)
@@ -984,9 +984,9 @@ subroutine isotope(counter, mzmin, ntot, iat_save, maxatm, rnd, &
       endif
 
 
-    enddo
-
 
+    enddo
+
   allocate(exact_intensity(index_mass))
   allocate(isotope_masses(index_mass))
 
@@ -1003,7 +1003,7 @@ subroutine isotope(counter, mzmin, ntot, iat_save, maxatm, rnd, &
 
 
   ! if no isotopes we take here the peak of the isotope pattern with the highest intensity
-  if ( no_isotopes ) then 
+  if ( no_isotopes .and. index_mass .gt. 0 ) then 
   iipmax = maxval(exact_intensity)
   indexipmax = maxloc(exact_intensity, dim = 1)
   mipmax = isotope_masses(indexipmax)