science/lammps: fix LIB_DEPENDS

science/lammps: Change VTK dependency from VTK-8 to VTK-9; Add option NETCDF

Also correct some other options.

devel/kokkos: Update 3.6.01 -> 3.7.00

Reported by:	portscout

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

science/lammps: Update 23Jun2022 -> 23Jun2022_update1

science/hdf5: bump PORTREVISION of consumers

The SO-version increased in the update to 1.12.2 in
a43418b81530f7e897abfbe18dd59f44265a1a0f .

Reported by:	VVD <vvd@unislabs.com>

science/lammps: Fix MPI option; Change VTK option to use VTK-9.1

science/lammps: patch_2Jun2022 -> stable_23Jun2022

*/*: Replace science/szip with science/libaec

- Bump PORTREVISION of dependent ports for dependency change

szip does not allow redistribution in binary form without proper commercial
license. Its LICENSE_PERMS should be set to no-auto-accept which blocks building
this port, therefore building dependent ports are also blocked. Switch all
dependent ports to science/libaec to avoid conflicts and license issue.

PR:		228743, 246097, 250165

science/lammps: Update 24Mar2022 -> 2Jun2022

devel/cmake: Update to 3.23.0

Update to 3.23.0.
Fix pkg-plist: using the default share/man location

Release Notes:
  https://cmake.org/cmake/help/v3.23/release/3.23.html

PR:		262886
Exp-run by:	antoine

devel/kokkos: Update 3.5.00 -> 3.6.00

Reported by:	portscout

textproc/libxml2: bump all LIB_DEPENDS consumers

This is a separate commit to facilitate easier cherry-picking for
quarterly.

PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)

textproc/libxml2: bump all dependencies

This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd733f67a9fc0dc00ab45268bdc236246

science/lammps: Update patch_7Jan2022 -> patch_24Mar2022

science/lammps: Update 29Sep2021 -> 7Jan2022

science/lammps: Update patch_2Jul2021 -> stable_29Sep2021

Reported by:	upstream notification

science/lammps: Update 14May2021 -> 2Jul2021

Reported by:	GitHub release notification

science/lammps: Update 8Apr2021 -> 14May2021

Reported by:	GitHub release notification

science/plumed: Update 2.7.0 -> 2.7.1

Reported by:	portscout

science/lammps: Update 10Mar2021 -> 8Apr2021

Reported by:	GH release notification

One more small cleanup, forgotten yesterday.
Reported by:	lwhsu

Remove # $FreeBSD$ from Makefiles.

science/lammps: Update 10Feb2021 -> 10Mar2021

Reported by:	GH release notification

science/lammps: Update 24Dec2020 -> 10Feb2021

science/lammps: Update 30Nov2020 -> 24Dec2020

Reported by:	GitHub notification

devel/kokkos: Update 3.2.01 -> 3.3.00

science/lammps: The KIM option isn't broken any more after the latest update of
science/kim-api

- Upgrade math/eigen3 to 3.3.8;

- Add some dependencies which might be detected by Find_Package but not
registered;

- Bump PORTREVISION of consumers.

PR:		250833
Submitted by:	/me
Approved by:	tcberner@ (KDE / maintainer) + exp-run

science/lammps: Update 29Oct2020 -> 30Nov2020

Reported by:	upstream notification

science/lammps: Fix build broken by the latest kim-api update.

science/lammps: Update 22Oct2020 -> 29Oct2020

Reported by:	GitHub notification

science/lammps: Update 18Sep2020 -> 22Oct2020

Reported by:	GitHub notification

science/lammps: Update 24Aug2020 -> 18Sep2020

Reported by:	GitHub notification

science/lammps: Update 21Aug2020 -> 24Aug2020

Reported by:	GitHub notification

science/lammps: Update 21Jul2020 -> 21Aug2020

Reported by:	GitHub notification

science/lammps: Update 30Jun2020 -> 21Jul2020

Reported by:	GitHub release notification

science/lammps: Update 15Jun2020 -> 30Jun2020

Reported by:	GitHub notification

science/lammps: Update 2Jun2020 -> 15Jun2020

Reported by:	GitHub notification

science/lammps: Update 5May2020 -> 2Jun2020

Reported by:	GitHub notification

science/lammps: Enable exceptions

Bump 37 ports depending on math/openblas through USES=blaslapack:openblas
because after the recent math/openblas update the library name changed in
openblas

science/lammps: Update 15Apr2020 -> 5May2020

Reported by:	github release notification

science/lammps: Add the PLUMED option

Also:
* Change USER-LB to be available only for MPI=on
* Sort options alphabetically

science/lammps: Add the science/openkim-models dependency to the KIM option

science/lammps: Add the KIM option to enable the internal KIM package

Also add the C++11 compiler tag.

science/lammps: Add the VTK option enabling the internal VTK package

science/lammps: Remove OPTIONS_DEFINE_clang that doesn't work

According to Mk/bsd.options.mk, only ARCH can be used
(${OPTIONS_DEFINE_${ARCH}}).
OPTIONS_DEFINE_clang caused port options to malfunction.

science/lammps: Enable all packages that don't require dependencies, and
USER-H5MD that does require dependencies

science/lammps: Enable more internal packages; Remove grouped options from the
global context

cience/lammps: Add the option to enable the KOKKOS internal package; Add the
options group PACKAGES

science/lammps: Add internal packages that were off by default; Change to shared
libraries; Add GZIP_DESC

science/lammps: Fix plist when MPI=off; Add to CONFLICTS_BUILD

science/lammps: Update 19Mar2020 -> 15Apr2020

Reported by:	GitHub notification

- Update net/openmpi to 4.0.3 (openmpi 1 is deprecated)
- Remove option for net/openmpi2 from science/pnetcdf (net/openmpi2 is
deprecated and will be removed)
- Fix science/gromacs plist when MPI option is enabled
- Bump PORTREVISION for all the consumers of net/openmpi

science/lammps: don't set -march=native

It breaks compilation on some architectures and runtime on others.

MFH:		2020Q2 (build fix blanket)

science/lammps: Update 3Mar2020 -> 19Mar2020

Reported by:	GitHub notification

Drop dependency on devel/openmp

- Drop if devel/llvm* was used as a substitute

Approved by:	yuri, rene (earlier version)
Differential Revision:	https://reviews.freebsd.org/D23020

science/lammps: Update 27Feb2020 -> 3Mar2020

Reported by:	GitHub notification

science/lammps: Update 18Feb2020 -> 27Feb2020

Reported by:	portscout

science/lammps: Update 4Feb2020 -> 18Feb2020

Reported by:	github notification

science/lammps: Update 24Jan2020 -> 4Feb2020

Reported by:	upstream notification

Fix math/openblas and bump dependent ports

* Fix build on i386 [1]
* Fix science/code_saturne build with new openblas [2]
* Avoid installing private headers [3]
* Prevent build from optimizing for host by correcting build confg [4]
* Bump portrevision of dependent ports [5]

This is correcting issues from r523749 [1][2][4] and r515970 [3]

PR:		231371
Reported by:	build cluster [1]
Reported by:	Dima Pasechnik <dimpase+freebsd@gmail.com> [2]
Reported by:	many [5]
Reviewed by:	mat, bapt
Approved by:	implicit, since this is a build fix

science/lammps: Update 20Nov2019 -> 24Jan2020

Reported by:	upstream notification

science/lammps: Fix the PORTSCOUT tag

science/lammps: fix build on GCC architectures

Don't enable OpenMP everywhere, it causes an error with GCC, reported on
https://github.com/lammps/lammps/pull/1483

This requires some hackery with ports not supporting options for specific
compilers.

OPENMP flag has removed option helpers due to them not being respected
otherwise.

PR:		241156
Approved by:	yuri (maintainer, earlier versior), tcberner (mentor, earlier
version)
Differential Revision:	https://reviews.freebsd.org/D21994

science/lammps: Update patch_30Oct2019 -> patch_20Nov2019

Reported by:	github notification

science/lammps: Update 19Sep2019 -> 30Oct2019

Reported by:	release notification

devel/openmp: update to 9.0.0

- Connect tests to the framework to help QA remaining patches
- Force rebuild all consumers after https://reviews.llvm.org/D59783

Changes:	http://llvm.org/viewvc/llvm-project/openmp/tags/RELEASE_900/final/?view=log
ABI:		https://abi-laboratory.pro/tracker/timeline/llvm_openmp/

science/lammps: Update 7Aug2019 -> 19Sep2019

Reported by:	GitHub release notification

science/lammps: patch_6Aug2019 -> stable_7Aug2019

Reported by:	portscout

science/lammps: Update 2Aug2019 -> 6Aug2019

Reported by:	portscout

multimedia/ffmpeg: update to 4.2

Changes:	https://git.ffmpeg.org/gitweb/ffmpeg.git/blob/n4.2:/Changelog
ABI:		https://abi-laboratory.pro/tracker/timeline/ffmpeg/

science/lammps: Update 19Jul2019 -> 2Aug2019

Reported by:	portscout

Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330

science/lammps: Update patch_5Jun2019 -> patch_19Jul2019

PR fixing folder locations is backported.

Reported by:	GitHub release notification

Clean up LIB_DEPENDS

science/lammps: Add the PORTSCOUT=ignore line

science/lammps: Update 31May2019 -> 5Jun2019

Approved by:	portscout

science/lammps: Update 15May2019 -> 31May2019

Reported by:	GitHub release notification

science/lammps: Update patch_30Apr2019 -> patch_15May2019

Reported by:	github notification

devel/openmp: phase out

- Expire after the last version without /usr/lib/libomp.so
- Drop SOVERSION for seamless transition (i.e., avoid conditionals)

PR:		236907
Approved by:	bapt (maintainer)
Differential Revision:	https://reviews.freebsd.org/D19767

science/lammps: Update patch_29Mar2019 -> patch_30Apr2019

Reported by:	github release notification

Related to revision 499061 bump ports with USES=fortran to have them
benefit from the improved situation where libgcc_s is only used when
absolutely necessary.

Suggested by:	tijl

science/lammps: Update 28Feb2019 -> 29Mar2019

Switch to devel/llvm80 for DEFAULT_VERSIONS

PR:		235215

science/lammps: Update 12Dec2018 -> 28Feb2019

Update math/eigen3 to 3.3.7

- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.6
- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.7

Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine

science/lammps: Update 22Aug2018 -> 12Dec2018

Reported by:	repology

Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590

science/lammps: BROKEN on i386

Fix a few minor problems.

science/lammps: Add port options for additional functionality

multimedia/ffmpeg: update to 4.1

Changes:	https://git.ffmpeg.org/gitweb/ffmpeg.git/blob/n4.1:/Changelog
ABI:		https://abi-laboratory.pro/tracker/timeline/ffmpeg/

New port: science/lammps: Classical molecular dynamics code with a focus on
materials modeling