git: ffecb9942256 - main - science/gromacs: Update 2021.5 -> 2022.1

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Thu, 28 Apr 2022 03:39:25 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=ffecb994225660a18261a51e4847606f0973d62d

commit ffecb994225660a18261a51e4847606f0973d62d
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2022-04-28 03:06:20 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2022-04-28 03:39:22 +0000

    science/gromacs: Update 2021.5 -> 2022.1
    
    Reported by:    portscout
---
 science/gromacs/Makefile                           |   7 +-
 science/gromacs/distinfo                           |   6 +-
 .../patch-cmake_gmxManageSharedLibraries.cmake     |  11 -
 science/gromacs/pkg-plist                          | 259 +++++++++++----------
 4 files changed, 145 insertions(+), 138 deletions(-)

diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile
index e0f23553aa1c..28a7df372742 100644
--- a/science/gromacs/Makefile
+++ b/science/gromacs/Makefile
@@ -1,8 +1,7 @@
 # Created by: Stephen Montgomery-Smith <stephen@math.missouri.edu>
 
 PORTNAME=	gromacs
-DISTVERSION=	2021.5
-PORTREVISION=	2
+DISTVERSION=	2022.1
 CATEGORIES=	science
 MASTER_SITES=	ftp://ftp.gromacs.org/pub/gromacs/
 
@@ -12,12 +11,12 @@ COMMENT=	Compute molecular dynamics
 LICENSE=	LGPL21
 LICENSE_FILE=	${WRKSRC}/COPYING
 
-BROKEN_i386=	undefined reference to `__atomic_load' and `__atomic_compare_exchange'
+BROKEN_i386=	undefined reference to `__atomic_load' and `__atomic_compare_exchange' #`
 
 BUILD_DEPENDS=	boost-libs>=1.44:devel/boost-libs
 LIB_DEPENDS=	libhwloc.so:devel/hwloc2
 
-USES=		cmake compiler:c++14-lang fortran gnome perl5 pkgconfig shebangfix xorg
+USES=		cmake compiler:c++17-lang fortran gnome perl5 pkgconfig shebangfix xorg
 SHEBANG_FILES=	admin/*.sh scripts/*.pl scripts/*.sh src/gromacs/selection/*.sh
 bash_CMD=	${SH}
 USE_GNOME=	libxml2
diff --git a/science/gromacs/distinfo b/science/gromacs/distinfo
index 42ab8fafcea0..fadfb2f4ed37 100644
--- a/science/gromacs/distinfo
+++ b/science/gromacs/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1642283496
-SHA256 (gromacs-2021.5.tar.gz) = eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6
-SIZE (gromacs-2021.5.tar.gz) = 38023772
+TIMESTAMP = 1651109042
+SHA256 (gromacs-2022.1.tar.gz) = 85ddab5197d79524a702c4959c2c43be875e0fc471df3a35224939dce8512450
+SIZE (gromacs-2022.1.tar.gz) = 40375423
diff --git a/science/gromacs/files/patch-cmake_gmxManageSharedLibraries.cmake b/science/gromacs/files/patch-cmake_gmxManageSharedLibraries.cmake
deleted file mode 100644
index cb366e776b08..000000000000
--- a/science/gromacs/files/patch-cmake_gmxManageSharedLibraries.cmake
+++ /dev/null
@@ -1,11 +0,0 @@
---- cmake/gmxManageSharedLibraries.cmake.orig	2015-07-27 14:11:45 UTC
-+++ cmake/gmxManageSharedLibraries.cmake
-@@ -39,7 +39,7 @@
- ########################################################################
- # Determine the defaults (this block has no effect if the variables have
- # already been set)
--if((APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD|GNU") AND NOT GMX_BUILD_MDRUN_ONLY)
-+if((APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD|DragonFly") AND NOT GMX_BUILD_MDRUN_ONLY)
-     # Maybe Solaris should be here? Patch this if you know!
-     SET(SHARED_LIBS_DEFAULT ON)
- elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")
diff --git a/science/gromacs/pkg-plist b/science/gromacs/pkg-plist
index 6c35ed2eebf8..38d4889e21b2 100644
--- a/science/gromacs/pkg-plist
+++ b/science/gromacs/pkg-plist
@@ -3,9 +3,9 @@ bin/GMXRC.bash
 bin/GMXRC.csh
 bin/GMXRC.zsh
 bin/demux.pl
-bin/gmx%%SUFFIX_MPI%%%%SUFFIX_D%%
-bin/gmx-completion-gmx%%SUFFIX_MPI%%%%SUFFIX_D%%.bash
+bin/gmx-completion-gmx%%SUFFIX_D%%.bash
 bin/gmx-completion.bash
+bin/gmx%%SUFFIX_D%%
 bin/xplor2gmx.pl
 include/gmxapi/compat/mdparams.h
 include/gmxapi/compat/tpr.h
@@ -94,8 +94,8 @@ include/gromacs/restraint/restraintpotential.h
 %%LEGACY%%include/gromacs/trajectoryanalysis/topologyinformation.h
 %%LEGACY%%include/gromacs/utility/arrayref.h
 include/gromacs/utility/basedefinitions.h
-%%LEGACY%%%%LEGACY%%include/gromacs/utility/baseversion.h
-%%LEGACY%%%%LEGACY%%include/gromacs/utility/classhelpers.h
+%%LEGACY%%include/gromacs/utility/baseversion.h
+%%LEGACY%%include/gromacs/utility/classhelpers.h
 include/gromacs/utility/current_function.h
 %%LEGACY%%include/gromacs/utility/enumerationhelpers.h
 %%LEGACY%%include/gromacs/utility/exceptions.h
@@ -112,10 +112,23 @@ include/gromacs/utility/real.h
 %%LEGACY%%include/gromacs/utility/stringutil.h
 %%LEGACY%%include/gromacs/utility/unique_cptr.h
 %%LEGACY%%include/gromacs/version.h
+include/muParser.h
+include/muParserBase.h
+include/muParserBytecode.h
+include/muParserCallback.h
+include/muParserDLL.h
+include/muParserDef.h
+include/muParserError.h
+include/muParserFixes.h
+include/muParserInt.h
+include/muParserTemplateMagic.h
+include/muParserTest.h
+include/muParserToken.h
+include/muParserTokenReader.h
 include/nblib/basicdefinitions.h
 include/nblib/box.h
 include/nblib/exception.h
-include/nblib/forcecalculator.h
+include/nblib/gmxcalculatorcpu.h
 include/nblib/integrator.h
 include/nblib/interactions.h
 include/nblib/kerneloptions.h
@@ -124,33 +137,139 @@ include/nblib/listed_forces/calculator.h
 include/nblib/listed_forces/definitions.h
 include/nblib/molecules.h
 include/nblib/nblib.h
+include/nblib/nbnxmsetuphelpers.h
 include/nblib/particlesequencer.h
 include/nblib/particletype.h
 include/nblib/simulationstate.h
 include/nblib/topology.h
+include/nblib/tpr.h
 include/nblib/util/setup.h
 include/nblib/util/traits.hpp
 include/nblib/util/util.hpp
 include/nblib/vector.h
-lib/libgmxapi%%SUFFIX_MPI%%%%SUFFIX_D%%.so
-lib/libgmxapi%%SUFFIX_MPI%%%%SUFFIX_D%%.so.0
-lib/libgmxapi%%SUFFIX_MPI%%%%SUFFIX_D%%.so.0.2.1
-lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so
-lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6
-lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6.0.0
-lib/libnblib.so
-lib/libnblib.so.0
-lib/libnblib.so.0.1.0
-libdata/pkgconfig/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
+lib/libgmxapi%%SUFFIX_D%%.so
+lib/libgmxapi%%SUFFIX_D%%.so.0
+lib/libgmxapi%%SUFFIX_D%%.so.0.3.1
+lib/libgromacs%%SUFFIX_D%%.so
+lib/libgromacs%%SUFFIX_D%%.so.7
+lib/libgromacs%%SUFFIX_D%%.so.7.0.0
+lib/libmuparser.so
+lib/libmuparser.so.2
+lib/libmuparser.so.2.3.2
+lib/libnblib_gmx.so
+lib/libnblib_gmx.so.0
+lib/libnblib_gmx.so.0.1.0
+libdata/pkgconfig/libgromacs%%SUFFIX_D%%.pc
+libdata/pkgconfig/muparser.pc
+man/man1/gmx-anaeig.1.gz
+man/man1/gmx-analyze.1.gz
+man/man1/gmx-angle.1.gz
+man/man1/gmx-awh.1.gz
+man/man1/gmx-bar.1.gz
+man/man1/gmx-bundle.1.gz
+man/man1/gmx-check.1.gz
+man/man1/gmx-chi.1.gz
+man/man1/gmx-cluster.1.gz
+man/man1/gmx-clustsize.1.gz
+man/man1/gmx-confrms.1.gz
+man/man1/gmx-convert-tpr.1.gz
+man/man1/gmx-convert-trj.1.gz
+man/man1/gmx-covar.1.gz
+man/man1/gmx-current.1.gz
+man/man1/gmx-density.1.gz
+man/man1/gmx-densmap.1.gz
+man/man1/gmx-densorder.1.gz
+man/man1/gmx-dielectric.1.gz
+man/man1/gmx-dipoles.1.gz
+man/man1/gmx-disre.1.gz
+man/man1/gmx-distance.1.gz
+man/man1/gmx-do%%SUFFIX_D%%ssp.1.gz
+man/man1/gmx-dos.1.gz
+man/man1/gmx-dump.1.gz
+man/man1/gmx-dyecoupl.1.gz
+man/man1/gmx-editconf.1.gz
+man/man1/gmx-eneconv.1.gz
+man/man1/gmx-enemat.1.gz
+man/man1/gmx-energy.1.gz
+man/man1/gmx-extract-cluster.1.gz
+man/man1/gmx-filter.1.gz
+man/man1/gmx-freevolume.1.gz
+man/man1/gmx-gangle.1.gz
+man/man1/gmx-genconf.1.gz
+man/man1/gmx-genion.1.gz
+man/man1/gmx-genrestr.1.gz
+man/man1/gmx-grompp.1.gz
+man/man1/gmx-gyrate.1.gz
+man/man1/gmx-h2order.1.gz
+man/man1/gmx-hbond.1.gz
+man/man1/gmx-helix.1.gz
+man/man1/gmx-helixorient.1.gz
+man/man1/gmx-help.1.gz
+man/man1/gmx-hydorder.1.gz
+man/man1/gmx-insert-molecules.1.gz
+man/man1/gmx-lie.1.gz
+man/man1/gmx-make_edi.1.gz
+man/man1/gmx-make_ndx.1.gz
+man/man1/gmx-mdmat.1.gz
+man/man1/gmx-mdrun.1.gz
+man/man1/gmx-mindist.1.gz
+man/man1/gmx-mk_angndx.1.gz
+man/man1/gmx-msd.1.gz
+man/man1/gmx-nmeig.1.gz
+man/man1/gmx-nmens.1.gz
+man/man1/gmx-nmr.1.gz
+man/man1/gmx-nmtraj.1.gz
+man/man1/gmx-nonbonded-benchmark.1.gz
+man/man1/gmx-order.1.gz
+man/man1/gmx-pairdist.1.gz
+man/man1/gmx-pdb2gmx.1.gz
+man/man1/gmx-pme_error.1.gz
+man/man1/gmx-polystat.1.gz
+man/man1/gmx-potential.1.gz
+man/man1/gmx-principal.1.gz
+man/man1/gmx-rama.1.gz
+man/man1/gmx-rdf.1.gz
+man/man1/gmx-report-methods.1.gz
+man/man1/gmx-rms.1.gz
+man/man1/gmx-rmsdist.1.gz
+man/man1/gmx-rmsf.1.gz
+man/man1/gmx-rotacf.1.gz
+man/man1/gmx-rotmat.1.gz
+man/man1/gmx-saltbr.1.gz
+man/man1/gmx-sans.1.gz
+man/man1/gmx-sasa.1.gz
+man/man1/gmx-saxs.1.gz
+man/man1/gmx-select.1.gz
+man/man1/gmx-sham.1.gz
+man/man1/gmx-sigeps.1.gz
+man/man1/gmx-solvate.1.gz
+man/man1/gmx-sorient.1.gz
+man/man1/gmx-spatial.1.gz
+man/man1/gmx-spol.1.gz
+man/man1/gmx-tcaf.1.gz
+man/man1/gmx-traj.1.gz
+man/man1/gmx-trajectory.1.gz
+man/man1/gmx-trjcat.1.gz
+man/man1/gmx-trjconv.1.gz
+man/man1/gmx-trjorder.1.gz
+man/man1/gmx-tune_pme.1.gz
+man/man1/gmx-vanhove.1.gz
+man/man1/gmx-velacc.1.gz
+man/man1/gmx-view.1.gz
+man/man1/gmx-wham.1.gz
+man/man1/gmx-wheel.1.gz
+man/man1/gmx-x2top.1.gz
+man/man1/gmx-xpm2ps.1.gz
+man/man1/gmx.1.gz
 share/cmake/gmxapi/gmxapi-config-version.cmake
 share/cmake/gmxapi/gmxapi-config.cmake
 share/cmake/gmxapi/gmxapi-%%CMAKE_BUILD_TYPE%%.cmake
 share/cmake/gmxapi/gmxapi.cmake
-share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%-config-version.cmake
-share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%-config.cmake
-share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/gromacs-toolchain%%SUFFIX_MPI%%%%SUFFIX_D%%.cmake
-share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/libgromacs-%%CMAKE_BUILD_TYPE%%.cmake
-share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/libgromacs.cmake
+share/cmake/gromacs%%SUFFIX_D%%/gromacs-hints%%SUFFIX_D%%.cmake
+share/cmake/gromacs%%SUFFIX_D%%/gromacs%%SUFFIX_D%%-config-version.cmake
+share/cmake/gromacs%%SUFFIX_D%%/gromacs%%SUFFIX_D%%-config.cmake
+share/cmake/gromacs%%SUFFIX_D%%/libgromacs-%%CMAKE_BUILD_TYPE%%.cmake
+share/cmake/gromacs%%SUFFIX_D%%/libgromacs.cmake
 %%DATADIR%%/COPYING
 %%DATADIR%%/README.tutor
 %%DATADIR%%/README_FreeEnergyModifications.txt
@@ -599,103 +718,3 @@ share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/libgromacs.cmake
 %%DATADIR%%/top/vdw-msms.dat
 %%DATADIR%%/top/vdwradii.dat
 %%DATADIR%%/top/xlateat.dat
-man/man1/gmx-anaeig.1.gz
-man/man1/gmx-analyze.1.gz
-man/man1/gmx-angle.1.gz
-man/man1/gmx-awh.1.gz
-man/man1/gmx-bar.1.gz
-man/man1/gmx-bundle.1.gz
-man/man1/gmx-check.1.gz
-man/man1/gmx-chi.1.gz
-man/man1/gmx-cluster.1.gz
-man/man1/gmx-clustsize.1.gz
-man/man1/gmx-confrms.1.gz
-man/man1/gmx-convert-tpr.1.gz
-man/man1/gmx-convert-trj.1.gz
-man/man1/gmx-covar.1.gz
-man/man1/gmx-current.1.gz
-man/man1/gmx-density.1.gz
-man/man1/gmx-densmap.1.gz
-man/man1/gmx-densorder.1.gz
-man/man1/gmx-dielectric.1.gz
-man/man1/gmx-dipoles.1.gz
-man/man1/gmx-disre.1.gz
-man/man1/gmx-distance.1.gz
-man/man1/gmx-do_dssp.1.gz
-man/man1/gmx-dos.1.gz
-man/man1/gmx-dump.1.gz
-man/man1/gmx-dyecoupl.1.gz
-man/man1/gmx-editconf.1.gz
-man/man1/gmx-eneconv.1.gz
-man/man1/gmx-enemat.1.gz
-man/man1/gmx-energy.1.gz
-man/man1/gmx-extract-cluster.1.gz
-man/man1/gmx-filter.1.gz
-man/man1/gmx-freevolume.1.gz
-man/man1/gmx-gangle.1.gz
-man/man1/gmx-genconf.1.gz
-man/man1/gmx-genion.1.gz
-man/man1/gmx-genrestr.1.gz
-man/man1/gmx-grompp.1.gz
-man/man1/gmx-gyrate.1.gz
-man/man1/gmx-h2order.1.gz
-man/man1/gmx-hbond.1.gz
-man/man1/gmx-helix.1.gz
-man/man1/gmx-helixorient.1.gz
-man/man1/gmx-help.1.gz
-man/man1/gmx-hydorder.1.gz
-man/man1/gmx-insert-molecules.1.gz
-man/man1/gmx-lie.1.gz
-man/man1/gmx-make_edi.1.gz
-man/man1/gmx-make_ndx.1.gz
-man/man1/gmx-mdmat.1.gz
-man/man1/gmx-mdrun.1.gz
-man/man1/gmx-mindist.1.gz
-man/man1/gmx-mk_angndx.1.gz
-man/man1/gmx-msd.1.gz
-man/man1/gmx-nmeig.1.gz
-man/man1/gmx-nmens.1.gz
-man/man1/gmx-nmr.1.gz
-man/man1/gmx-nmtraj.1.gz
-man/man1/gmx-nonbonded-benchmark.1.gz
-man/man1/gmx-order.1.gz
-man/man1/gmx-pairdist.1.gz
-man/man1/gmx-pdb2gmx.1.gz
-man/man1/gmx-pme_error.1.gz
-man/man1/gmx-polystat.1.gz
-man/man1/gmx-potential.1.gz
-man/man1/gmx-principal.1.gz
-man/man1/gmx-rama.1.gz
-man/man1/gmx-rdf.1.gz
-man/man1/gmx-report-methods.1.gz
-man/man1/gmx-rms.1.gz
-man/man1/gmx-rmsdist.1.gz
-man/man1/gmx-rmsf.1.gz
-man/man1/gmx-rotacf.1.gz
-man/man1/gmx-rotmat.1.gz
-man/man1/gmx-saltbr.1.gz
-man/man1/gmx-sans.1.gz
-man/man1/gmx-sasa.1.gz
-man/man1/gmx-saxs.1.gz
-man/man1/gmx-select.1.gz
-man/man1/gmx-sham.1.gz
-man/man1/gmx-sigeps.1.gz
-man/man1/gmx-solvate.1.gz
-man/man1/gmx-sorient.1.gz
-man/man1/gmx-spatial.1.gz
-man/man1/gmx-spol.1.gz
-man/man1/gmx-tcaf.1.gz
-man/man1/gmx-traj.1.gz
-man/man1/gmx-trajectory.1.gz
-man/man1/gmx-trjcat.1.gz
-man/man1/gmx-trjconv.1.gz
-man/man1/gmx-trjorder.1.gz
-man/man1/gmx-tune_pme.1.gz
-man/man1/gmx-vanhove.1.gz
-man/man1/gmx-velacc.1.gz
-man/man1/gmx-view.1.gz
-man/man1/gmx-wham.1.gz
-man/man1/gmx-wheel.1.gz
-man/man1/gmx-x2top.1.gz
-man/man1/gmx-xpm2ps.1.gz
-man/man1/gmx.1.gz