Merge pull request #57 from m3g/release-20.14.3

Release 20.14.3

.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:
@@ -46,7 +40,8 @@ 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

.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

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

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"

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))

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 
 

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

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

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
+