From fdd4d332599d8ee20d8af437d808bc8e0b71aaa8 Mon Sep 17 00:00:00 2001
From: Leandro Martinez <lmartine@unicamp.br>
Date: Thu, 23 Nov 2023 13:48:54 -0300
Subject: [PATCH 1/4] output receives file name as parameter

---
 app/packmol.f90    | 14 +++++++-------
 src/checkpoint.f90 |  4 ++--
 src/output.f90     | 11 ++++++-----
 3 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/app/packmol.f90 b/app/packmol.f90
index f1d8558..2a2f56e 100644
--- a/app/packmol.f90
+++ b/app/packmol.f90
@@ -668,7 +668,7 @@ program packmol
   ! If there are no variables (only fixed molecules, stop)
 
   if(n.eq.0) then
-    call output(n,x)
+    call output(n,x, xyzout)
     write(*,dash1_line)
     write(*,*) ' There are only fixed molecules, therefore there is nothing to do. '
     write(*,*) ' The output file contains the fixed molecules in the desired positions. '
@@ -701,7 +701,7 @@ program packmol
   ! Stop if only checking the initial approximation
 
   if(check) then
-    call output(n,x)
+    call output(n,x,xyzout)
     write(*,*) ' Wrote initial point to output file: ', trim(adjustl(xyzout)) 
     if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile))
     stop
@@ -753,7 +753,7 @@ program packmol
       write(*,*) ' Initial approximation is a solution. Nothing to do. '
       write(*,*)
       call swaptype(n,x,itype,3) ! Restore all-molecule vectors
-      call output(n,x)
+      call output(n,x,xyzout)
       if( itype == ntype + 1 ) then
         write(*,*) ' Solution written to file: ', trim(adjustl(xyzout))
         if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile))
@@ -849,7 +849,7 @@ program packmol
           ! If the solution was found for this type
           if( fdist < precision .and. frest < precision ) then
             call swaptype(n,x,itype,3) ! Restore all molecule vectors
-            call output(n,x)
+            call output(n,x,xyzout)
             write(*,*) ' Current structure written to file: ', trim(adjustl(xyzout))
             if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile))
             call writesuccess(itype,fdist,frest,fx)
@@ -869,7 +869,7 @@ program packmol
           if ( fx < bestf ) bestf = fx
           ! If solution was found for all system
           if ( fdist < precision .and. frest < precision ) then
-            call output(n,x)
+            call output(n,x,xyzout)
             call writesuccess(itype,fdist,frest,fx)
             write(*,*) ' Solution written to file: ', trim(adjustl(xyzout))
             if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile))
@@ -882,7 +882,7 @@ program packmol
 
         ! If this is the best structure so far
         if( mod(loop+1,writeout) == 0 .and. all_type_fx < fprint ) then
-          call output(n,x)
+          call output(n,x,xyzout)
           write(*,*) ' Current solution written to file: ', trim(adjustl(xyzout))
           if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile))
           fprint = all_type_fx
@@ -892,7 +892,7 @@ program packmol
 
         ! If the user required printing even bad structures
         else if ( mod(loop+1,writeout) == 0 .and. writebad ) then
-          call output(n,x)
+          call output(n,x,xyzout)
           write(*,*) ' Writing current (perhaps bad) structure to file: ', trim(adjustl(xyzout))
           if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile))
         end if
diff --git a/src/checkpoint.f90 b/src/checkpoint.f90
index a40b625..d4dc8bf 100644
--- a/src/checkpoint.f90
+++ b/src/checkpoint.f90
@@ -59,7 +59,7 @@ subroutine checkpoint(n,x)
             &)") fx
   write(*,dash3_line)
 
-  call output(n,x)
+  call output(n,x,xyzout)
 
   write(*,*) ' The solution with the best function value was '
   write(*,*) ' written to the output file: ', trim(adjustl(xyzout))
@@ -82,7 +82,7 @@ subroutine checkpoint(n,x)
   write(*,*)
   write(*,dash1_line)
   xyzout_forced = trim(adjustl(xyzout))//'_FORCED'
-  call output(n,x)
+  call output(n,x,xyzout_forced)
 
   write(*,*) ' The forced point was writen to the '
   write(*,*) ' output file: ', trim(adjustl(xyzout_forced))
diff --git a/src/output.f90 b/src/output.f90
index b970748..15e1d55 100644
--- a/src/output.f90
+++ b/src/output.f90
@@ -6,7 +6,7 @@
 ! Subroutine output: Subroutine that writes the output file
 !
 
-subroutine output(n,x)
+subroutine output(n, x, output_file_name)
 
   use exit_codes
   use sizes
@@ -36,6 +36,7 @@ subroutine output(n,x)
   character(len=strl) :: pdb_atom_line, tinker_atom_line, crd_format
   character(len=8) :: crdires,crdresn,crdsegi,atmname
   character(len=strl) :: record
+  character(len=strl) :: output_file_name
   character(len=5) :: i5hex, tmp_i5hex
 
   ! Job title
@@ -96,7 +97,7 @@ subroutine output(n,x)
   ! Write the output (xyz file)
 
   if(xyz) then
-    open(30,file=xyzout,status='unknown') 
+    open(30,file=output_file_name,status='unknown') 
     write(30,*) ntotat
     write(30,*) title 
     ilubar = 0 
@@ -143,7 +144,7 @@ subroutine output(n,x)
   ! write the output as a MOLDY file
 
   if(moldy) then
-    open(30,file=xyzout,status='unknown') 
+    open(30,file=output_file_name,status='unknown') 
     ! For square moldy boxes, this must be the side dimensions of the box 
     sxmin = 1.d30
     symin = 1.d30
@@ -351,7 +352,7 @@ subroutine output(n,x)
                       &f8.3,t55,a26 )"
     crd_format='(2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10)'
 
-    open(30,file=xyzout,status='unknown') 
+    open(30,file=output_file_name,status='unknown') 
     if ( crd ) then
       open(40,file=crdfile,status='unknown')
       write(40,'("* TITLE ", a64,/&
@@ -696,7 +697,7 @@ subroutine output(n,x)
 
     tinker_atom_line = "( i7,tr2,a3,3(tr2,f10.6),9(tr2,i7) )"
 
-    open(30, file = xyzout,status='unknown') 
+    open(30, file = output_file_name,status='unknown') 
  
     write(30,"( i6,tr2,a64 )") ntotat, title 
 

From 32721eb90a3e168191fa84cfa9a84d6e1bd91330 Mon Sep 17 00:00:00 2001
From: Leandro Martinez <lmartine@unicamp.br>
Date: Thu, 23 Nov 2023 13:49:22 -0300
Subject: [PATCH 2/4] add failing forced tests, improve testing script

---
 .github/workflows/actions.yml |  5 +++--
 .gitignore                    |  2 ++
 testing/test.sh               | 25 +++++++++++++++++++++++++
 testing/water_box_failed.inp  | 16 ++++++++++++++++
 4 files changed, 46 insertions(+), 2 deletions(-)
 create mode 100755 testing/test.sh
 create mode 100644 testing/water_box_failed.inp

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index ec05215..f0114fd 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -46,7 +46,8 @@ jobs:
     - name: Run
       run: |
           cd testing
-          ../packmol < water_box.inp
-          ../packmol < ieee_signaling.inp
+          ./test.sh "water_box.inp" "packmol.log" "Success!"
+          ./test.sh "ieee_signaling.inp" "packmol.log" "Success!"
+          ./test.sh "water_box_failed.inp" "packmol.log" "FORCED"
           cd ..
       shell: bash
diff --git a/.gitignore b/.gitignore
index a654385..8b45a66 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,5 @@ cmake_install.cmake
 tmpfile.txt
 testing/ieee_signaling_box.pdb
 testing/water_box.pdb
+testing/water_box.pdb_FORCED
+testing/packmol.log
diff --git a/testing/test.sh b/testing/test.sh
new file mode 100755
index 0000000..ad9ff54
--- /dev/null
+++ b/testing/test.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+#
+# First argument: input file name
+# Second argument: log file name
+#
+# Third argument: string to be searched in the log file, to declare that
+# the test passed
+#
+# Example: ./test.sh "water_box.inp" "packmol.log" "Success!"
+#
+if ! [ -f $1 ]; then
+    echo "Error: input file not found: $1"
+    exit 1
+fi
+../packmol < $1 > $2
+if ! [ -f $2 ]; then
+    echo "Error: Log file not generated: $2"
+    exit 1
+fi
+if ! grep -q $3 $2; then
+    echo "Error: could not find $3 in $2"
+    exit 1
+fi
+echo "Test passed."
+exit 0
diff --git a/testing/water_box_failed.inp b/testing/water_box_failed.inp
new file mode 100644
index 0000000..d315e57
--- /dev/null
+++ b/testing/water_box_failed.inp
@@ -0,0 +1,16 @@
+#
+# A box with water for which the packing will fail
+#
+
+tolerance 2.0
+filetype pdb
+output water_box.pdb
+
+maxit 2
+nloop 1
+
+structure water.pdb
+  number 2
+  inside box 0. 0. 0. 3.0 3.0 1.0
+end structure
+

From d4c9ad4da6e845c4bd91b2705fd66d548eda7990 Mon Sep 17 00:00:00 2001
From: Leandro Martinez <lmartine@unicamp.br>
Date: Thu, 23 Nov 2023 13:49:59 -0300
Subject: [PATCH 3/4] set version to 20.14.3

---
 fpm.toml      | 2 +-
 src/title.f90 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/fpm.toml b/fpm.toml
index 8253d04..1eaeec2 100644
--- a/fpm.toml
+++ b/fpm.toml
@@ -1,5 +1,5 @@
 name = "packmol"
-version = "20.14.2"
+version = "20.14.3"
 license = "MIT"
 author = "Leandro Martinez, Ernesto Birgin, Jose Mario Martinez"
 maintainer = "Leandro Martinez"
diff --git a/src/title.f90 b/src/title.f90
index 6cd6af9..3968cac 100644
--- a/src/title.f90
+++ b/src/title.f90
@@ -13,7 +13,7 @@ subroutine title()
   write(*,"(' PACKMOL - Packing optimization for the automated generation of', /&
            &' starting configurations for molecular dynamics simulations.', /&
            &' ',/&
-           &t62,' Version 20.14.2 ')")
+           &t62,' Version 20.14.3 ')")
   write(*,hash3_line)
 
 end subroutine title

From 6a50d6a5cab70a79dd0f5a8eea5a0a08b21afcfe Mon Sep 17 00:00:00 2001
From: Leandro Martinez <lmartine@unicamp.br>
Date: Thu, 23 Nov 2023 13:54:24 -0300
Subject: [PATCH 4/4] run CI on all push and pull requests

---
 .github/workflows/actions.yml | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index f0114fd..ff165c8 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -1,14 +1,8 @@
 name: actions
 
 on:
-  push:
-    branches:
-      - master
-  pull_request:
-    branches:
-      - master
-  schedule:
-    - cron: '0 6 * * *'
+  - push
+  - pull_request
 
 jobs:
   test: