Package: release.debian.org
Severity: normal
X-Debbugs-Cc: pack...@packages.debian.org
Control: affects -1 + src:packmol
User: release.debian....@packages.debian.org
Usertags: unblock
Please unblock package packmol
[ Reason ]
Upstream made a minor release shortly before hard freeze.
It would be good for users to include it in trixie.
[ Impact ]
Makes one small bug fix:
- fix type output of iftype molecule in error message by @lmiq in #96
If not allowed in trixie, users will not have this fix.
[ Tests ]
packmol is tested at build time but does not have CI tests,
which is why this unblock request is needed.
[ Risks ]
packmol is a leaf package with no dependent packages.
Risk from the update is negligible.
[ Checklist ]
[. ] all changes are documented in the d/changelog
Identified as new upstream release.
[x ] I reviewed all changes and I approve them
[x ] attach debdiff against the package in testing
unblock packmol/1:21.0.2-1
diff -Nru packmol-21.0.1/app/packmol.f90 packmol-21.0.2/app/packmol.f90
--- packmol-21.0.1/app/packmol.f90 2025-03-31 19:21:30.000000000 +0200
+++ packmol-21.0.2/app/packmol.f90 2025-05-05 22:26:13.000000000 +0200
@@ -64,7 +64,7 @@
double precision :: fimp, fimprov
double precision, parameter :: pi=4.d0*datan(1.d0)
- real :: etime, tarray(2), time0
+ real :: etime, tarray(2), time0, time_writeout
character(len=strl) :: record, restart_from_temp, restart_to_temp
character(len=strl) :: xyzfile
@@ -92,6 +92,7 @@
! Start time computation
time0 = etime(tarray)
+ time_writeout = time0
! Reading input file
@@ -806,7 +807,7 @@
loop = loop + 1
! Moving bad molecules
- if(radscale == 1.d0 .and. fimp.le.10.d0) then
+ if(.not. disable_movebad .and. radscale == 1.d0 .and. fimp.le.10.d0)
then
movebadprint = .true.
call movebad(n,x,fx,movebadprint)
flast = fx
@@ -900,20 +901,22 @@
write(*,dash3_line)
! If this is the best structure so far
- if( mod(loop+1,writeout) == 0 .and. all_type_fx < fprint ) then
- 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
- do i = 1, n
- xprint(i) = x(i)
- end do
-
- ! If the user required printing even bad structures
- else if ( mod(loop+1,writeout) == 0 .and. writebad ) then
- 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))
+ if(etime(tarray) - time_writeout > writeout) then
+ time_writeout = etime(tarray)
+ if(all_type_fx < fprint ) then
+ 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
+ do i = 1, n
+ xprint(i) = x(i)
+ end do
+ ! If the user required printing even bad structures
+ else if (writebad) then
+ 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
end if
! Restore vector for packing this type of molecule, if the case
diff -Nru packmol-21.0.1/debian/changelog packmol-21.0.2/debian/changelog
--- packmol-21.0.1/debian/changelog 2025-04-04 12:15:40.000000000 +0200
+++ packmol-21.0.2/debian/changelog 2025-05-08 22:45:59.000000000 +0200
@@ -1,3 +1,9 @@
+packmol (1:21.0.2-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Drew Parsons <dpars...@debian.org> Thu, 08 May 2025 22:45:59 +0200
+
packmol (1:21.0.1-1) unstable; urgency=medium
* New upstream release
diff -Nru packmol-21.0.1/fpm.toml packmol-21.0.2/fpm.toml
--- packmol-21.0.1/fpm.toml 2025-03-31 19:21:30.000000000 +0200
+++ packmol-21.0.2/fpm.toml 2025-05-05 22:26:13.000000000 +0200
@@ -1,5 +1,5 @@
name = "packmol"
-version = "21.0.1"
+version = "21.0.2"
license = "MIT"
author = "Leandro Martinez, Ernesto Birgin, Jose Mario Martinez"
maintainer = "Leandro Martinez"
diff -Nru packmol-21.0.1/.github/workflows/actions.yml
packmol-21.0.2/.github/workflows/actions.yml
--- packmol-21.0.1/.github/workflows/actions.yml 2025-03-31
19:21:30.000000000 +0200
+++ packmol-21.0.2/.github/workflows/actions.yml 2025-05-05
22:26:13.000000000 +0200
@@ -18,7 +18,7 @@
steps:
- uses: actions/checkout@v3
- - uses: awvwgk/setup-fortran@main
+ - uses: fortran-lang/setup-fortran@main
id: setup-fortran
with:
compiler: gcc
diff -Nru packmol-21.0.1/src/getinp.f90 packmol-21.0.2/src/getinp.f90
--- packmol-21.0.1/src/getinp.f90 2025-03-31 19:21:30.000000000 +0200
+++ packmol-21.0.2/src/getinp.f90 2025-05-05 22:26:13.000000000 +0200
@@ -43,6 +43,7 @@
nloop0 = 0
movefrac = 0.05
movebadrandom = .false.
+ disable_movebad = .false.
precision = 1.d-2
writebad = .false.
add_amber_ter = .false.
@@ -85,6 +86,9 @@
else if(keyword(i,1).eq.'movebadrandom') then
movebadrandom = .true.
write(*,*) ' Will move randomly bad molecues (movebadrandom) '
+ else if(keyword(i,1).eq.'disable_movebad') then
+ disable_movebad = .true.
+ write(*,*) ' Move-bad heursitic is dsabled. '
else if(keyword(i,1).eq.'chkgrad') then
chkgrad = .true.
else if(keyword(i,1).eq.'writeout') then
@@ -220,7 +224,6 @@
keyword(i,1) /= 'chain' .and. &
keyword(i,1) /= 'discale' .and. &
keyword(i,1) /= 'maxit' .and. &
- keyword(i,1) /= 'movebadrandom' .and. &
keyword(i,1) /= 'maxmove' .and. &
keyword(i,1) /= 'add_amber_ter' .and. &
keyword(i,1) /= 'amber_ter_preserve' .and. &
diff -Nru packmol-21.0.1/src/initial.f90 packmol-21.0.2/src/initial.f90
--- packmol-21.0.1/src/initial.f90 2025-03-31 19:21:30.000000000 +0200
+++ packmol-21.0.2/src/initial.f90 2025-05-05 22:26:13.000000000 +0200
@@ -153,7 +153,7 @@
do i = 1, 3
if (xcart(icart, i) < pbc_min(i) .or. xcart(icart, i) >
pbc_max(i)) then
write(*,*) "ERROR: Fixed molecule are outside the PBC
box:"
- write(*,*) " Atom: ", ifatom, " of molecule: ", iftype,
" - coordinate: ", i
+ write(*,*) " Atom: ", ifatom, " of molecule: ",
input_itype(iftype), " - coordinate: ", i
write(*,*) " ", xcart(icart, i), " not in [",
pbc_min(i), ", ", pbc_max(i), "]"
write(*,*) "(after translating/rotation the fixed
molecule with the given orientation)"
stop exit_code_input_error
diff -Nru packmol-21.0.1/src/input.f90 packmol-21.0.2/src/input.f90
--- packmol-21.0.1/src/input.f90 2025-03-31 19:21:30.000000000 +0200
+++ packmol-21.0.2/src/input.f90 2025-05-05 22:26:13.000000000 +0200
@@ -59,6 +59,7 @@
logical :: packall
logical :: use_short_tol
logical :: hexadecimal_indices
+ logical :: disable_movebad
logical, allocatable :: changechains(:) ! (ntype)
logical, allocatable :: fixedoninput(:) ! (ntype)
diff -Nru packmol-21.0.1/src/title.f90 packmol-21.0.2/src/title.f90
--- packmol-21.0.1/src/title.f90 2025-03-31 19:21:30.000000000 +0200
+++ packmol-21.0.2/src/title.f90 2025-05-05 22:26:13.000000000 +0200
@@ -13,7 +13,7 @@
write(*,"(' PACKMOL - Packing optimization for the automated generation
of', /&
&' starting configurations for molecular dynamics simulations.',
/&
&' ',/&
- &t61,' Version 21.0.1 ')")
+ &t61,' Version 21.0.2 ')")
write(*,hash3_line)
end subroutine title
