Merge pull request #34 from afonari/exit_codes

Return non-zero exit codes on packmol failure
m3g · Nov 1, 2022 · 65daf5f · 65daf5f
2 parents 1838438 + f15c913
commit 65daf5f
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Showing 8 changed files with 97 additions and 57 deletions.
diff --git a/Makefile b/Makefile
@@ -50,6 +50,7 @@ oall = cenmass.o \
        initial.o \
        title.o \
        setsizes.o \
+       exit_codes.o \
        getinp.o \
        strlength.o \
        output.o \
@@ -111,7 +112,10 @@ devel : $(oall)
 #
 # Modules
 #
-modules = sizes.o compute_data.o usegencan.o input.o flashmod.o swaptypemod.o ahestetic.o
+modules = exit_codes.o sizes.o compute_data.o usegencan.o input.o flashmod.o \
+          swaptypemod.o ahestetic.o
+exit_codes.o : exit_codes.f90
+	@$(FORTRAN) $(FLAGS) -c exit_codes.f90
 sizes.o : sizes.f90 
 	@$(FORTRAN) $(FLAGS) -c sizes.f90
 compute_data.o : compute_data.f90 sizes.o

diff --git a/exit_codes.f90 b/exit_codes.f90
@@ -0,0 +1,18 @@
+!
+!  Written by Alexandr Fonari, 2022.
+!  Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez,
+!  Ernesto G. Birgin.
+!  
+
+module exit_codes
+
+  IMPLICIT NONE
+
+  ! Codes 1, 2, 126 – 165 and 255 have special meaning
+  integer, parameter :: exit_code_success = 0
+  integer, parameter :: exit_code_general_error = 170
+  integer, parameter :: exit_code_input_error = 171
+  integer, parameter :: exit_code_open_file = 172
+  integer, parameter :: exit_code_failed_to_converge = 173
+
+end module exit_codes
diff --git a/getinp.f90 b/getinp.f90
@@ -8,6 +8,7 @@
 
 subroutine getinp()
 
+  use exit_codes
   use sizes
   use compute_data, only : ntype, natoms, idfirst, nmols, ityperest, coor, restpars
   use input
@@ -199,12 +200,12 @@ subroutine getinp()
              keyword(i,1) /= 'segid' .and. &
              keyword(i,1) /= 'chkgrad' ) then
       write(*,*) ' ERROR: Keyword not recognized: ', trim(keyword(i,1))
-      stop
+      stop exit_code_input_error
     end if
   end do
   if ( ioerr /= 0 ) then
     write(*,*) ' ERROR: Some optional keyword was not used correctly: ', trim(keyword(i,1))
-    stop
+    stop exit_code_input_error
   end if
   write(*,*) ' Seed for random number generator: ', seed
   call init_random_number(seed)
@@ -220,7 +221,7 @@ subroutine getinp()
   end do
   if(xyzout(1:4) == '####') then
     write(*,*)' ERROR: Output file not (correctly?) specified. '
-    stop
+    stop exit_code_input_error
   end if
   write(*,*)' Output file: ', trim(adjustl(xyzout))
 
@@ -271,7 +272,7 @@ subroutine getinp()
               write(*,*) ' Standard PDB format specifications', &
                          ' can be found at: '
               write(*,*) ' www.rcsb.org/pdb '
-              stop
+              stop exit_code_input_error
             end if
 
             ! This only tests if residue numbers can be read, they are used 
@@ -288,7 +289,7 @@ subroutine getinp()
               write(*,*) ' Standard PDB format specifications',&
                          ' can be found at: '
               write(*,*) ' www.rcsb.org/pdb '
-              stop
+              stop exit_code_input_error
             end if   
           end if
           read(10,str_format,iostat=ioerr) record
@@ -306,14 +307,14 @@ subroutine getinp()
             if(ioerr /= 0) then
               write(*,*) " ERROR: Could not read atom index from CONECT line: "
               write(*,*) trim(adjustl(record))
-              stop
+              stop exit_code_input_error
             end if
             iread = iread + 5
             read(record(iread:iread+4),*,iostat=ioerr) nconnect(idatom,1)
             if(ioerr /= 0) then
               write(*,*) " ERROR: Could not read any connection index from CONECT line: "
               write(*,*) trim(adjustl(record))
-              stop
+              stop exit_code_input_error
             end if
             nconnect(idatom,1) = nconnect(idatom,1) - idfirstatom + 1
             maxcon(idatom) = 1
@@ -680,7 +681,7 @@ subroutine getinp()
 
     if ( ioerr /= 0 ) then
       write(*,*) ' ERROR: Some restriction is not set correctly. '
-      stop
+      stop exit_code_input_error
     end if
 
   end do
@@ -696,14 +697,14 @@ subroutine getinp()
       read(keyword(iline,2),*,iostat=ioerr) dism
       if ( ioerr /= 0 ) then
         write(*,*) ' ERROR: Failed reading tolerance. '
-        stop
+        stop exit_code_input_error
       end if
       exit
     end if
   end do
   if ( ioerr /= 0 ) then
     write(*,*) ' ERROR: Overall tolerance not set. Use, for example: tolerance 2.0 '
-    stop
+    stop exit_code_input_error
   end if
   write(*,*) ' Distance tolerance: ', dism
 
@@ -717,11 +718,11 @@ subroutine getinp()
       read(keyword(iline,2),*,iostat=ioerr) short_tol_dist
       if ( ioerr /= 0 ) then
         write(*,*) ' ERROR: Failed reading short_tol_dist. '
-        stop
+        stop exit_code_input_error
       end if
       if ( short_tol_dist > dism ) then 
         write(*,*) ' ERROR: The short_tol_dist parameter must be smaller than the tolerance. '
-        stop
+        stop exit_code_input_error
       end if
       write(*,*) ' User defined short tolerance distance: ', short_tol_dist
       short_tol_dist = short_tol_dist**2
@@ -735,11 +736,11 @@ subroutine getinp()
       read(keyword(iline,2),*,iostat=ioerr) short_tol_scale
       if ( ioerr /= 0 ) then
         write(*,*) ' ERROR: Failed reading short_tol_scale. '
-        stop
+        stop exit_code_input_error
       end if
       if ( short_tol_dist <= 0.d0 ) then 
         write(*,*) ' ERROR: The short_tol_scale parameter must be positive. '
-        stop
+        stop exit_code_input_error
       end if
       write(*,*) ' User defined short tolerance scale: ', short_tol_scale
       exit
@@ -761,7 +762,7 @@ subroutine getinp()
         if(keyword(iline,1) == 'structure'.or.&
            iline == nlines) then
           write(*,*) ' ERROR: Structure specification not ending with "end structure"'
-          stop
+          stop exit_code_input_error
         end if
         iline = iline + 1
       end do
@@ -830,7 +831,7 @@ subroutine getinp()
       if ( chain(itype) /= "#" .and. changechains(itype) ) then
         write(*,*) " ERROR: 'changechains' and 'chain' input parameters are not compatible "
         write(*,*) "        for a single structure. "
-        stop
+        stop exit_code_input_error
       end if
     end do
   end if
@@ -874,7 +875,7 @@ subroutine getinp()
         restart_from(0) = keyword(iline,2)
       else
         write(*,*) ' ERROR: More than one definition of restart_from file for all system. '
-        stop
+        stop exit_code_input_error
       end if
     end if
     if ( keyword(iline,1) == 'restart_to' ) then
@@ -889,7 +890,7 @@ subroutine getinp()
         restart_to(0) = keyword(iline,2)
       else
         write(*,*) ' ERROR: More than one definition of restart_to file for all system. '
-        stop
+        stop exit_code_input_error
       end if
     end if
   end do lines
@@ -902,6 +903,7 @@ end subroutine getinp
 !
 
 subroutine failopen(record)
+  use exit_codes
   use sizes
   character(len=strl) :: record
   write(*,*) 
@@ -911,7 +913,7 @@ subroutine failopen(record)
   write(*,*) '        files are in the current directory or if the' 
   write(*,*) '        correct paths are provided.'
   write(*,*) 
-  stop 
+  stop exit_code_open_file
 end subroutine failopen
 
 !

diff --git a/initial.f90 b/initial.f90
@@ -9,6 +9,7 @@
 
 subroutine initial(n,x)
 
+  use exit_codes
   use sizes
   use compute_data
   use input, only : randini, ntfix, fix, moldy, chkgrad, avoidoverlap,&
@@ -238,7 +239,7 @@ subroutine initial(n,x)
       end if
         write(*,*) ' >The maximum number of cycles (',nloop0_type(itype),') was achieved.' 
         write(*,*) '  You may try increasing it with the',' nloop0 keyword, as in: nloop0 1000 '
-      stop
+      stop exit_code_failed_to_converge
     end if
   end do
   init1 = .false.
@@ -364,7 +365,7 @@ subroutine initial(n,x)
                               x(ilugan+1), x(ilugan+2), x(ilugan+3)
       if ( ioerr /= 0 ) then
         write(*,*) ' ERROR: Could not read restart file: ', trim(adjustl(record))
-        stop
+        stop exit_code_open_file
       end if
       ilubar = ilubar + 3
       ilugan = ilugan + 3
@@ -516,14 +517,14 @@ subroutine initial(n,x)
       open(10,file=record,status='old',action='read',iostat=ioerr)
       if ( ioerr /= 0 ) then
         write(*,*) ' ERROR: Could not open restart file: ', trim(adjustl(record))
-        stop
+        stop exit_code_open_file
       end if
       do i = 1, nmols(itype)
         read(10,*,iostat=ioerr) x(ilubar+1), x(ilubar+2), x(ilubar+3), &
                                 x(ilugan+1), x(ilugan+2), x(ilugan+3)
         if ( ioerr /= 0 ) then
           write(*,*) ' ERROR: Could not read restart file: ', trim(adjustl(record))
-          stop
+          stop exit_code_open_file
         end if
         ilubar = ilubar + 3
         ilugan = ilugan + 3

diff --git a/output.f90 b/output.f90
@@ -8,6 +8,7 @@
 
 subroutine output(n,x)
 
+  use exit_codes
   use sizes
   use compute_data
   use input
@@ -52,7 +53,7 @@ subroutine output(n,x)
     open(10,file=restart_to(0),iostat=ioerr)
     if ( ioerr /= 0 ) then
       write(*,*) ' ERROR: Could not open restart_to file: ', trim(adjustl(record))
-      stop
+      stop exit_code_open_file
     end if
     ilubar = 0
     ilugan = ntotmol*3
@@ -76,7 +77,7 @@ subroutine output(n,x)
       open(10,file=record,iostat=ioerr)
       if ( ioerr /= 0 ) then
         write(*,*) ' ERROR: Could not open restart_to file: ', trim(adjustl(record))
-        stop
+        stop exit_code_open_file
       end if
       do i = 1, nmols(itype)
         write(10,"(6(tr1,es23.16))") x(ilubar+1), x(ilubar+2), x(ilubar+3), &
@@ -412,7 +413,7 @@ subroutine output(n,x)
               write(*,*) ' Standard PDB format specifications can',&
                          ' be found at: '
               write(*,*) ' www.rcsb.org/pdb '
-              stop
+              stop exit_code_input_error
             end if
             if ( ifres .eq. 0 ) ifres = imark
             ilres = imark
@@ -558,7 +559,7 @@ subroutine output(n,x)
               write(*,*) ' Standard PDB format specifications can',&
                          ' be found at: '
               write(*,*) ' www.rcsb.org/pdb '
-              stop
+              stop exit_code_input_error
             end if
             if ( ifres .eq. 0 ) ifres = imark
             ilres = imark