git: 6978db2dccd9 - main - science/gromacs: update 2025.4 → 2026.1

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sun, 19 Apr 2026 07:10:38 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=6978db2dccd902340ac8733dd88b958d1dd09215

commit 6978db2dccd902340ac8733dd88b958d1dd09215
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-04-19 04:46:06 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-04-19 07:10:33 +0000

    science/gromacs: update 2025.4 → 2026.1
---
 science/gromacs/Makefile  |   6 +-
 science/gromacs/distinfo  |   6 +-
 science/gromacs/pkg-plist | 228 +++++++++++++++++++++++++++-------------------
 science/votca/Makefile    |   1 +
 4 files changed, 140 insertions(+), 101 deletions(-)

diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile
index 558eab81f1ba..310a92e93c3f 100644
--- a/science/gromacs/Makefile
+++ b/science/gromacs/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	gromacs
-DISTVERSION=	2025.4
-PORTREVISION=	1
+DISTVERSION=	2026.1
 CATEGORIES=	science
 MASTER_SITES=	https://ftp.gromacs.org/pub/gromacs/
 DISTFILES=	${DISTNAME}${EXTRACT_SUFX} # only for googletest
@@ -126,7 +125,6 @@ post-patch:
 	@${REINPLACE_CMD} -e '/CMAKE_REQUIRED_LIBRARIES/d' \
 		${WRKSRC}/cmake/gmxTestdlopen.cmake
 
-# tests as of 2025.3: 100% tests passed, 0 tests failed out of 92
-# 2025.4: tests fail to compile: https://gitlab.com/gromacs/gromacs/-/issues?show=eyJpaWQiOiI1NTAxIiwiZnVsbF9wYXRoIjoiZ3JvbWFjcy9ncm9tYWNzIiwiaWQiOjE3NzU1MDUzMn0%3D
+# tests as of 2026.1: 100% tests passed, 0 tests failed out of 104
 
 .include <bsd.port.mk>
diff --git a/science/gromacs/distinfo b/science/gromacs/distinfo
index 4cf0d1f50a41..d2944f6d15f0 100644
--- a/science/gromacs/distinfo
+++ b/science/gromacs/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1763922155
-SHA256 (gromacs-2025.4.tar.gz) = ca17720b4a260eb73649211e9f6a940ee7543452129844213c3accb0a927a5c3
-SIZE (gromacs-2025.4.tar.gz) = 44406127
+TIMESTAMP = 1776566754
+SHA256 (gromacs-2026.1.tar.gz) = d95a313f56db7e05ee3a21e50f582fdee5176c2f60b900bab2461fd95c5e81be
+SIZE (gromacs-2026.1.tar.gz) = 45914061
diff --git a/science/gromacs/pkg-plist b/science/gromacs/pkg-plist
index ef617f0ab641..6ba4b46dbb29 100644
--- a/science/gromacs/pkg-plist
+++ b/science/gromacs/pkg-plist
@@ -24,92 +24,92 @@ include/gmxapi/session/resources.h
 include/gmxapi/status.h
 include/gmxapi/system.h
 include/gmxapi/version.h
-%%LEGACY%%include/gromacs/analysisdata/abstractdata.h
-%%LEGACY%%include/gromacs/analysisdata/analysisdata.h
-%%LEGACY%%include/gromacs/analysisdata/arraydata.h
-%%LEGACY%%include/gromacs/analysisdata/dataframe.h
-%%LEGACY%%include/gromacs/analysisdata/datamodule.h
-%%LEGACY%%include/gromacs/analysisdata/modules/average.h
-%%LEGACY%%include/gromacs/analysisdata/modules/displacement.h
-%%LEGACY%%include/gromacs/analysisdata/modules/histogram.h
-%%LEGACY%%include/gromacs/analysisdata/modules/lifetime.h
-%%LEGACY%%include/gromacs/analysisdata/modules/plot.h
-%%LEGACY%%include/gromacs/external/boost/stl_interfaces/fwd.hpp
-%%LEGACY%%include/gromacs/external/boost/stl_interfaces/iterator_interface.hpp
-%%LEGACY%%include/gromacs/fileio/confio.h
-%%LEGACY%%include/gromacs/fileio/filetypes.h
-%%LEGACY%%include/gromacs/fileio/oenv.h
-%%LEGACY%%include/gromacs/fileio/pdbio.h
-%%LEGACY%%include/gromacs/fileio/tpxio.h
-%%LEGACY%%include/gromacs/fileio/trxio.h
-%%LEGACY%%include/gromacs/libgromacs_export.h
-%%LEGACY%%include/gromacs/math/do_fit.h
-%%LEGACY%%include/gromacs/math/functions.h
-%%LEGACY%%include/gromacs/math/units.h
-%%LEGACY%%include/gromacs/math/utilities.h
-%%LEGACY%%include/gromacs/math/vec.h
-%%LEGACY%%include/gromacs/math/vectypes.h
+include/gromacs/analysisdata/abstractdata.h
+include/gromacs/analysisdata/analysisdata.h
+include/gromacs/analysisdata/arraydata.h
+include/gromacs/analysisdata/dataframe.h
+include/gromacs/analysisdata/datamodule.h
+include/gromacs/analysisdata/modules/average.h
+include/gromacs/analysisdata/modules/displacement.h
+include/gromacs/analysisdata/modules/histogram.h
+include/gromacs/analysisdata/modules/lifetime.h
+include/gromacs/analysisdata/modules/plot.h
+include/gromacs/external/boost/stl_interfaces/fwd.hpp
+include/gromacs/external/boost/stl_interfaces/iterator_interface.hpp
+include/gromacs/fileio/confio.h
+include/gromacs/fileio/filetypes.h
+include/gromacs/fileio/oenv.h
+include/gromacs/fileio/pdbio.h
+include/gromacs/fileio/tpxio.h
+include/gromacs/fileio/trxio.h
+include/gromacs/libgromacs_export.h
+include/gromacs/math/do_fit.h
+include/gromacs/math/functions.h
+include/gromacs/math/units.h
+include/gromacs/math/utilities.h
 include/gromacs/mdrun/simulationinputhandle.h
-%%LEGACY%%include/gromacs/mdtypes/inputrec.h
-%%LEGACY%%include/gromacs/mdtypes/md_enums.h
-%%LEGACY%%include/gromacs/options/abstractoption.h
-%%LEGACY%%include/gromacs/options/basicoptions.h
-%%LEGACY%%include/gromacs/options/filenameoption.h
-%%LEGACY%%include/gromacs/options/filenameoptionmanager.h
-%%LEGACY%%include/gromacs/options/ioptionsbehavior.h
-%%LEGACY%%include/gromacs/options/ioptionscontainer.h
-%%LEGACY%%include/gromacs/options/ioptionscontainerwithsections.h
-%%LEGACY%%include/gromacs/options/ivaluestore.h
-%%LEGACY%%include/gromacs/options/optionfiletype.h
-%%LEGACY%%include/gromacs/options/optionflags.h
-%%LEGACY%%include/gromacs/options/options.h
-%%LEGACY%%include/gromacs/options/timeunitmanager.h
-%%LEGACY%%include/gromacs/pbcutil/pbc.h
-%%LEGACY%%include/gromacs/restraint/restraintpotential.h
-%%LEGACY%%include/gromacs/selection/indexutil.h
-%%LEGACY%%include/gromacs/selection/nbsearch.h
-%%LEGACY%%include/gromacs/selection/position.h
-%%LEGACY%%include/gromacs/selection/selection.h
-%%LEGACY%%include/gromacs/selection/selectioncollection.h
-%%LEGACY%%include/gromacs/selection/selectionenums.h
-%%LEGACY%%include/gromacs/selection/selectionoption.h
-%%LEGACY%%include/gromacs/selection/selectionoptionbehavior.h
-%%LEGACY%%include/gromacs/selection/selectionoptionmanager.h
-%%LEGACY%%include/gromacs/topology/atomprop.h
-%%LEGACY%%include/gromacs/topology/atoms.h
-%%LEGACY%%include/gromacs/topology/block.h
-%%LEGACY%%include/gromacs/topology/forcefieldparameters.h
-%%LEGACY%%include/gromacs/topology/idef.h
-%%LEGACY%%include/gromacs/topology/ifunc.h
-%%LEGACY%%include/gromacs/topology/index.h
-%%LEGACY%%include/gromacs/topology/symtab.h
-%%LEGACY%%include/gromacs/topology/topology.h
-%%LEGACY%%include/gromacs/topology/topology_enums.h
-%%LEGACY%%include/gromacs/trajectory/trajectoryframe.h
-%%LEGACY%%include/gromacs/trajectoryanalysis/analysismodule.h
-%%LEGACY%%include/gromacs/trajectoryanalysis/analysissettings.h
-%%LEGACY%%include/gromacs/trajectoryanalysis/cmdlinerunner.h
-%%LEGACY%%include/gromacs/trajectoryanalysis/topologyinformation.h
-%%LEGACY%%include/gromacs/utility/arrayref.h
-%%LEGACY%%include/gromacs/utility/basedefinitions.h
-%%LEGACY%%include/gromacs/utility/baseversion.h
-%%LEGACY%%include/gromacs/utility/classhelpers.h
-%%LEGACY%%include/gromacs/utility/current_function.h
-%%LEGACY%%include/gromacs/utility/enumerationhelpers.h
-%%LEGACY%%include/gromacs/utility/exceptions.h
-%%LEGACY%%include/gromacs/utility/fileptr.h
-%%LEGACY%%include/gromacs/utility/flags.h
-%%LEGACY%%include/gromacs/utility/futil.h
-%%LEGACY%%include/gromacs/utility/gmxassert.h
-%%LEGACY%%include/gromacs/utility/listoflists.h
-%%LEGACY%%include/gromacs/utility/pleasecite.h
-%%LEGACY%%include/gromacs/utility/programcontext.h
-%%LEGACY%%include/gromacs/utility/range.h
-%%LEGACY%%include/gromacs/utility/real.h
-%%LEGACY%%include/gromacs/utility/smalloc.h
-%%LEGACY%%include/gromacs/utility/stringutil.h
-%%LEGACY%%include/gromacs/utility/unique_cptr.h
-%%LEGACY%%include/gromacs/version.h
+include/gromacs/mdtypes/inputrec.h
+include/gromacs/mdtypes/md_enums.h
+include/gromacs/options/abstractoption.h
+include/gromacs/options/basicoptions.h
+include/gromacs/options/filenameoption.h
+include/gromacs/options/filenameoptionmanager.h
+include/gromacs/options/ioptionsbehavior.h
+include/gromacs/options/ioptionscontainer.h
+include/gromacs/options/ioptionscontainerwithsections.h
+include/gromacs/options/ivaluestore.h
+include/gromacs/options/optionfiletype.h
+include/gromacs/options/optionflags.h
+include/gromacs/options/options.h
+include/gromacs/options/timeunitmanager.h
+include/gromacs/pbcutil/pbc.h
+include/gromacs/restraint/restraintpotential.h
+include/gromacs/selection/indexutil.h
+include/gromacs/selection/nbsearch.h
+include/gromacs/selection/position.h
+include/gromacs/selection/selection.h
+include/gromacs/selection/selectioncollection.h
+include/gromacs/selection/selectionenums.h
+include/gromacs/selection/selectionoption.h
+include/gromacs/selection/selectionoptionbehavior.h
+include/gromacs/selection/selectionoptionmanager.h
+include/gromacs/topology/atomprop.h
+include/gromacs/topology/atoms.h
+include/gromacs/topology/block.h
+include/gromacs/topology/forcefieldparameters.h
+include/gromacs/topology/idef.h
+include/gromacs/topology/ifunc.h
+include/gromacs/topology/index.h
+include/gromacs/topology/symtab.h
+include/gromacs/topology/topology.h
+include/gromacs/topology/topology_enums.h
+include/gromacs/trajectory/trajectoryframe.h
+include/gromacs/trajectoryanalysis/analysismodule.h
+include/gromacs/trajectoryanalysis/analysissettings.h
+include/gromacs/trajectoryanalysis/cmdlinerunner.h
+include/gromacs/trajectoryanalysis/topologyinformation.h
+include/gromacs/utility/arrayref.h
+include/gromacs/utility/basedefinitions.h
+include/gromacs/utility/baseversion.h
+include/gromacs/utility/classhelpers.h
+include/gromacs/utility/current_function.h
+include/gromacs/utility/enumerationhelpers.h
+include/gromacs/utility/exceptions.h
+include/gromacs/utility/fileptr.h
+include/gromacs/utility/flags.h
+include/gromacs/utility/futil.h
+include/gromacs/utility/gmxassert.h
+include/gromacs/utility/listoflists.h
+include/gromacs/utility/pleasecite.h
+include/gromacs/utility/programcontext.h
+include/gromacs/utility/range.h
+include/gromacs/utility/real.h
+include/gromacs/utility/smalloc.h
+include/gromacs/utility/stringutil.h
+include/gromacs/utility/unique_cptr.h
+include/gromacs/utility/vec.h
+include/gromacs/utility/vectypes.h
+include/gromacs/version.h
 include/nblib/basicdefinitions.h
 include/nblib/box.h
 include/nblib/exception.h
@@ -136,8 +136,8 @@ lib/libgmxapi%%SUFFIX_D%%.so
 lib/libgmxapi%%SUFFIX_D%%.so.0
 lib/libgmxapi%%SUFFIX_D%%.so.0.4.0
 lib/libgromacs%%SUFFIX_D%%.so
-lib/libgromacs%%SUFFIX_D%%.so.10
-lib/libgromacs%%SUFFIX_D%%.so.10.0.0
+lib/libgromacs%%SUFFIX_D%%.so.11
+lib/libgromacs%%SUFFIX_D%%.so.11.0.0
 lib/libnblib_gmx.so
 lib/libnblib_gmx.so.0
 lib/libnblib_gmx.so.0.1.0
@@ -205,6 +205,53 @@ share/cmake/gromacs%%SUFFIX_D%%/libgromacs.cmake
 %%DATADIR%%/top/amber03.ff/tip5p.itp
 %%DATADIR%%/top/amber03.ff/urea.itp
 %%DATADIR%%/top/amber03.ff/watermodels.dat
+%%DATADIR%%/top/amber14sb.ff/aminoacids.c.tdb
+%%DATADIR%%/top/amber14sb.ff/aminoacids.hdb
+%%DATADIR%%/top/amber14sb.ff/aminoacids.n.tdb
+%%DATADIR%%/top/amber14sb.ff/aminoacids.r2b
+%%DATADIR%%/top/amber14sb.ff/aminoacids.rtp
+%%DATADIR%%/top/amber14sb.ff/atomtypes.atp
+%%DATADIR%%/top/amber14sb.ff/ffbonded.itp
+%%DATADIR%%/top/amber14sb.ff/ffnonbonded.itp
+%%DATADIR%%/top/amber14sb.ff/forcefield.doc
+%%DATADIR%%/top/amber14sb.ff/forcefield.itp
+%%DATADIR%%/top/amber14sb.ff/ions_opc.itp
+%%DATADIR%%/top/amber14sb.ff/ions_opc3.itp
+%%DATADIR%%/top/amber14sb.ff/ions_spc.itp
+%%DATADIR%%/top/amber14sb.ff/ions_spce.itp
+%%DATADIR%%/top/amber14sb.ff/ions_tip3p.itp
+%%DATADIR%%/top/amber14sb.ff/ions_tip4pew.itp
+%%DATADIR%%/top/amber14sb.ff/opc.itp
+%%DATADIR%%/top/amber14sb.ff/opc3.itp
+%%DATADIR%%/top/amber14sb.ff/spc.itp
+%%DATADIR%%/top/amber14sb.ff/spce.itp
+%%DATADIR%%/top/amber14sb.ff/tip3p.itp
+%%DATADIR%%/top/amber14sb.ff/tip4pew.itp
+%%DATADIR%%/top/amber14sb.ff/watermodels.dat
+%%DATADIR%%/top/amber19sb.ff/aminoacids.c.tdb
+%%DATADIR%%/top/amber19sb.ff/aminoacids.hdb
+%%DATADIR%%/top/amber19sb.ff/aminoacids.n.tdb
+%%DATADIR%%/top/amber19sb.ff/aminoacids.r2b
+%%DATADIR%%/top/amber19sb.ff/aminoacids.rtp
+%%DATADIR%%/top/amber19sb.ff/atomtypes.atp
+%%DATADIR%%/top/amber19sb.ff/cmap.itp
+%%DATADIR%%/top/amber19sb.ff/ffbonded.itp
+%%DATADIR%%/top/amber19sb.ff/ffnonbonded.itp
+%%DATADIR%%/top/amber19sb.ff/forcefield.doc
+%%DATADIR%%/top/amber19sb.ff/forcefield.itp
+%%DATADIR%%/top/amber19sb.ff/ions_opc.itp
+%%DATADIR%%/top/amber19sb.ff/ions_opc3.itp
+%%DATADIR%%/top/amber19sb.ff/ions_spc.itp
+%%DATADIR%%/top/amber19sb.ff/ions_spce.itp
+%%DATADIR%%/top/amber19sb.ff/ions_tip3p.itp
+%%DATADIR%%/top/amber19sb.ff/ions_tip4pew.itp
+%%DATADIR%%/top/amber19sb.ff/opc.itp
+%%DATADIR%%/top/amber19sb.ff/opc3.itp
+%%DATADIR%%/top/amber19sb.ff/spc.itp
+%%DATADIR%%/top/amber19sb.ff/spce.itp
+%%DATADIR%%/top/amber19sb.ff/tip3p.itp
+%%DATADIR%%/top/amber19sb.ff/tip4pew.itp
+%%DATADIR%%/top/amber19sb.ff/watermodels.dat
 %%DATADIR%%/top/amber94.ff/aminoacids.arn
 %%DATADIR%%/top/amber94.ff/aminoacids.c.tdb
 %%DATADIR%%/top/amber94.ff/aminoacids.hdb
@@ -421,12 +468,10 @@ share/cmake/gromacs%%SUFFIX_D%%/libgromacs.cmake
 %%DATADIR%%/top/charmm27.ff/tips3p.itp
 %%DATADIR%%/top/charmm27.ff/watermodels.dat
 %%DATADIR%%/top/co-shift.dat
-%%DATADIR%%/top/defselection.dat
 %%DATADIR%%/top/dgsolv.dat
 %%DATADIR%%/top/edissoc.dat
 %%DATADIR%%/top/electroneg.dat
 %%DATADIR%%/top/elements.dat
-%%DATADIR%%/top/export.dlg
 %%DATADIR%%/top/ffG43a1.itp
 %%DATADIR%%/top/ffG43a2.itp
 %%DATADIR%%/top/ffG45a3.itp
@@ -581,9 +626,6 @@ share/cmake/gromacs%%SUFFIX_D%%/libgromacs.cmake
 %%DATADIR%%/top/phbres.dat
 %%DATADIR%%/top/ps.m2p
 %%DATADIR%%/top/random.dat
-%%DATADIR%%/top/refi_aa.dat
-%%DATADIR%%/top/residues.dtd
-%%DATADIR%%/top/residues.xml
 %%DATADIR%%/top/residuetypes.dat
 %%DATADIR%%/top/scatteringfactors.dat
 %%DATADIR%%/top/sfactor.dat
@@ -592,7 +634,6 @@ share/cmake/gromacs%%SUFFIX_D%%/libgromacs.cmake
 %%DATADIR%%/top/spce.itp
 %%DATADIR%%/top/specbond.dat
 %%DATADIR%%/top/ss.map
-%%DATADIR%%/top/surface.dat
 %%DATADIR%%/top/sw.itp
 %%DATADIR%%/top/table6-10.xvg
 %%DATADIR%%/top/table6-11.xvg
@@ -603,7 +644,6 @@ share/cmake/gromacs%%SUFFIX_D%%/libgromacs.cmake
 %%DATADIR%%/top/tip4p.gro
 %%DATADIR%%/top/tip4p.itp
 %%DATADIR%%/top/tip5p.gro
-%%DATADIR%%/top/vdw-msms.dat
 %%DATADIR%%/top/vdwradii.dat
 %%DATADIR%%/top/xlateat.dat
 share/man/man1/gmx-anaeig.1.gz
diff --git a/science/votca/Makefile b/science/votca/Makefile
index b4417e9fffc7..34386f43f3c4 100644
--- a/science/votca/Makefile
+++ b/science/votca/Makefile
@@ -1,6 +1,7 @@
 PORTNAME=	votca
 DISTVERSIONPREFIX=	v
 DISTVERSION=	2026
+PORTREVISION=	1
 CATEGORIES=	science
 
 MAINTAINER=	yuri@FreeBSD.org