summaryrefslogtreecommitdiff
path: root/science
diff options
context:
space:
mode:
Diffstat (limited to 'science')
-rw-r--r--science/ALPSCore/Makefile2
-rw-r--r--science/agrum/Makefile8
-rw-r--r--science/agrum/distinfo6
-rw-r--r--science/agrum/pkg-plist1
-rw-r--r--science/cdf/Makefile2
-rw-r--r--science/chemical-mime-data/Makefile23
-rw-r--r--science/chemical-mime-data/distinfo5
-rw-r--r--science/chemical-mime-data/pkg-plist37
-rw-r--r--science/cp2k-data/Makefile2
-rw-r--r--science/cp2k-data/distinfo6
-rw-r--r--science/cp2k-data/pkg-plist15
-rw-r--r--science/cp2k/Makefile4
-rw-r--r--science/cp2k/distinfo6
-rw-r--r--science/cp2k/files/patch-cmake_CompilerConfiguration.cmake46
-rw-r--r--science/cp2k/pkg-plist50
-rw-r--r--science/csvtk/Makefile3
-rw-r--r--science/csvtk/distinfo14
-rw-r--r--science/tinker/Makefile3
-rw-r--r--science/tinker/distinfo6
-rw-r--r--science/tinker/pkg-plist14
20 files changed, 166 insertions, 87 deletions
diff --git a/science/ALPSCore/Makefile b/science/ALPSCore/Makefile
index cf74402f2eed..b2dcc2d64830 100644
--- a/science/ALPSCore/Makefile
+++ b/science/ALPSCore/Makefile
@@ -3,7 +3,7 @@ DISTVERSIONPREFIX= v
DISTVERSION= 2.3.2
CATEGORIES= science
-MAINTAINER= alster@vinterdalen.se
+MAINTAINER= alven@FreeBSD.org
COMMENT= Generic algorithms and utilities for condensed matter physics
WWW= https://alpscore.org/ \
https://github.com/ALPSCore/ALPSCore/
diff --git a/science/agrum/Makefile b/science/agrum/Makefile
index 5046ef8d6bc2..ff6dce0acfc3 100644
--- a/science/agrum/Makefile
+++ b/science/agrum/Makefile
@@ -1,5 +1,5 @@
PORTNAME= agrum
-DISTVERSION= 2.1.1
+DISTVERSION= 2.2.0
CATEGORIES= science math
MAINTAINER= yuri@FreeBSD.org
@@ -20,7 +20,7 @@ LLD_UNSAFE= yes
USE_GITLAB= yes
GL_ACCOUNT= agrumery
GL_PROJECT= aGrUM
-GL_TAGNAME= d15a377b0f745a6afd15139d780b23056305a851
+GL_TAGNAME= cf1283f783aa6803bafbd9a3fb4991316c1b52d9
SHEBANG_FILES= act
@@ -58,8 +58,10 @@ PYTHON_RUN_DEPENDS= ${PYNUMPY} \
BINARY_ALIAS= gcc=${CC} g++=${CXX} # only for tests, see https://gitlab.com/agrumery/aGrUM/-/issues/100
-do-test: # tests fail to compile, see https://gitlab.com/agrumery/aGrUM/-/issues/148
+do-test:
@cd ${WRKSRC} && \
${SETENV} ${MAKE_ENV} ./act test release agrum -t all
+# tests as of 2.2.0: Failed 0 of 1483 tests
+
.include <bsd.port.mk>
diff --git a/science/agrum/distinfo b/science/agrum/distinfo
index 13627e87a707..62c51836a6d8 100644
--- a/science/agrum/distinfo
+++ b/science/agrum/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1750005327
-SHA256 (agrumery-aGrUM-d15a377b0f745a6afd15139d780b23056305a851_GL0.tar.gz) = 21f6ad004e8ff15d4b41fb6e30f8c60db3631a84d756bd91d3972432710f8048
-SIZE (agrumery-aGrUM-d15a377b0f745a6afd15139d780b23056305a851_GL0.tar.gz) = 28781050
+TIMESTAMP = 1753632410
+SHA256 (agrumery-aGrUM-cf1283f783aa6803bafbd9a3fb4991316c1b52d9_GL0.tar.gz) = 57f7274925f64129c2f3bfcd178f75edd4cb6eaff1d06c30f20c85c41e6ca3d9
+SIZE (agrumery-aGrUM-cf1283f783aa6803bafbd9a3fb4991316c1b52d9_GL0.tar.gz) = 29175753
diff --git a/science/agrum/pkg-plist b/science/agrum/pkg-plist
index 123d787ba5bd..9fe1f9999703 100644
--- a/science/agrum/pkg-plist
+++ b/science/agrum/pkg-plist
@@ -180,6 +180,7 @@ include/agrum/BN/learning/localSearchWithTabuList_tpl.h
include/agrum/BN/learning/paramUtils/DAG2BNLearner.h
include/agrum/BN/learning/paramUtils/DAG2BNLearner_inl.h
include/agrum/BN/learning/paramUtils/DAG2BNLearner_tpl.h
+include/agrum/BN/learning/paramUtils/EMApproximationScheme.h
include/agrum/BN/learning/paramUtils/paramEstimator.h
include/agrum/BN/learning/paramUtils/paramEstimatorML.h
include/agrum/BN/learning/paramUtils/paramEstimatorML_inl.h
diff --git a/science/cdf/Makefile b/science/cdf/Makefile
index 803a95f11b0d..edc94cf929c9 100644
--- a/science/cdf/Makefile
+++ b/science/cdf/Makefile
@@ -5,7 +5,7 @@ MASTER_SITES= https://spdf.gsfc.nasa.gov/pub/software/cdf/dist/cdf39_1/
DISTNAME= cdf${VER}-dist-cdf
DIST_SUBDIR= ${PORTNAME}-${PORTVERSION}
-MAINTAINER= alster@vinterdalen.se
+MAINTAINER= alven@FreeBSD.org
COMMENT= Device independent view of the CDF data model
WWW= https://cdf.gsfc.nasa.gov/
diff --git a/science/chemical-mime-data/Makefile b/science/chemical-mime-data/Makefile
index 064fad3e2128..f2cf0d3ea3dd 100644
--- a/science/chemical-mime-data/Makefile
+++ b/science/chemical-mime-data/Makefile
@@ -1,21 +1,28 @@
PORTNAME= chemical-mime-data
PORTVERSION= 0.1.94
-PORTREVISION= 11
+PORTREVISION= 12
CATEGORIES= science
-MASTER_SITES= SF/chemical-mime/${PORTNAME}/${PORTVERSION}
-
MAINTAINER= ports@FreeBSD.org
COMMENT= Collection of chemical MIME types for UNIX desktops
-WWW= http://chemical-mime.sourceforge.net/
+WWW= https://github.com/dleidert/chemical-mime
+
+LICENSE= LGPL21
+LICENSE_FILE= ${WRKSRC}/COPYING
-USES= gettext-tools gmake gnome localbase:ldflags pathfix pkgconfig \
+USES= autoreconf gettext-tools gmake gnome localbase:ldflags pathfix pkgconfig \
shared-mime-info tar:bzip2
USE_GNOME= gnomemimedata intlhack librsvg2:build libxslt:build
GNU_CONFIGURE= yes
-CONFIGURE_ARGS= --disable-update-database
+CONFIGURE_ARGS= --disable-update-database \
+ --without-kde-magic
+
+USE_GITHUB= yes
+GH_ACCOUNT= dleidert
+GH_PROJECT= chemical-mime
+GH_TAGNAME= 4fd66e3b3b7d922555d1e25587908b036805c45b
post-patch:
- @${REINPLACE_CMD} -e 's|*-*-solaris*|*| ; s|rsvg|rsvg-convert|g' ${WRKSRC}/configure
- @${REINPLACE_CMD} -e 's|-f png $$< |-f png $$< > |' ${WRKSRC}/icons/hicolor/Makefile.in
+ @${REINPLACE_CMD} -e 's:acronym|alias|comment|:acronym|alias|comment|generic-icon|:' \
+ ${WRKSRC}/xsl/cmd_freedesktop_org.xsl
.include <bsd.port.mk>
diff --git a/science/chemical-mime-data/distinfo b/science/chemical-mime-data/distinfo
index d00a171cc183..efec878a86be 100644
--- a/science/chemical-mime-data/distinfo
+++ b/science/chemical-mime-data/distinfo
@@ -1,2 +1,3 @@
-SHA256 (chemical-mime-data-0.1.94.tar.bz2) = 4907cdf60e9edca0a453f6f24e9179ae9da085b67168e932ba44a4280316bff1
-SIZE (chemical-mime-data-0.1.94.tar.bz2) = 146077
+TIMESTAMP = 1753696974
+SHA256 (dleidert-chemical-mime-0.1.94-4fd66e3b3b7d922555d1e25587908b036805c45b_GH0.tar.gz) = f40fdf56ef14c67ab59b6ebb2e6d513ddf5070929695b62e04d9f40a2baccfff
+SIZE (dleidert-chemical-mime-0.1.94-4fd66e3b3b7d922555d1e25587908b036805c45b_GH0.tar.gz) = 84515
diff --git a/science/chemical-mime-data/pkg-plist b/science/chemical-mime-data/pkg-plist
index c22391dc17c7..aaf1cf38383d 100644
--- a/science/chemical-mime-data/pkg-plist
+++ b/science/chemical-mime-data/pkg-plist
@@ -1,26 +1,14 @@
libdata/pkgconfig/chemical-mime-data.pc
-share/doc/chemical-mime-data/chemical-mime-data.html
-share/doc/chemical-mime-data/cmd.css
-share/doc/chemical-mime-data/index.html
-share/icons/hicolor/16x16/mimetypes/gnome-mime-chemical.png
-share/icons/hicolor/22x22/mimetypes/gnome-mime-chemical.png
-share/icons/hicolor/24x24/mimetypes/gnome-mime-chemical.png
-share/icons/hicolor/32x32/mimetypes/gnome-mime-chemical.png
-share/icons/hicolor/36x36/mimetypes/gnome-mime-chemical.png
-share/icons/hicolor/48x48/mimetypes/gnome-mime-chemical.png
-share/icons/hicolor/64x64/mimetypes/gnome-mime-chemical.png
-share/icons/hicolor/72x72/mimetypes/gnome-mime-chemical.png
-share/icons/hicolor/96x96/mimetypes/gnome-mime-chemical.png
-share/icons/hicolor/128x128/mimetypes/gnome-mime-chemical.png
-share/icons/hicolor/192x192/mimetypes/gnome-mime-chemical.png
-share/icons/hicolor/scalable/mimetypes/gnome-mime-chemical.svgz
+%%DATADIR%%/file/magic.mime
+%%DATADIR%%/mime.types
share/locale/de/LC_MESSAGES/chemical-mime-data.mo
share/locale/fr/LC_MESSAGES/chemical-mime-data.mo
-share/pixmaps/chemistry.png
-share/pixmaps/gnome-mime-chemical.png
-share/mime/packages/chemical-mime-data.xml
share/mime-info/chemical-mime-data.keys
share/mime-info/chemical-mime-data.mime
+share/mime/packages/chemical-mime-data.xml
+share/mimelnk/chemical/cml.desktop
+share/mimelnk/chemical/pdb.desktop
+share/mimelnk/chemical/seq-na-genbank.desktop
share/mimelnk/chemical/x-alchemy.desktop
share/mimelnk/chemical/x-cache.desktop
share/mimelnk/chemical/x-cactvs-ascii.desktop
@@ -31,11 +19,18 @@ share/mimelnk/chemical/x-cdxml.desktop
share/mimelnk/chemical/x-chem3d.desktop
share/mimelnk/chemical/x-cif.desktop
share/mimelnk/chemical/x-cml.desktop
+share/mimelnk/chemical/x-daylight-smiles.desktop
share/mimelnk/chemical/x-dmol.desktop
share/mimelnk/chemical/x-gamess-input.desktop
share/mimelnk/chemical/x-gamess-output.desktop
share/mimelnk/chemical/x-gaussian-input.desktop
share/mimelnk/chemical/x-gaussian-log.desktop
+share/mimelnk/chemical/x-gaussian-output.desktop
+share/mimelnk/chemical/x-gaussian.desktop
+share/mimelnk/chemical/x-gaussian03-output.desktop
+share/mimelnk/chemical/x-gaussian92-output.desktop
+share/mimelnk/chemical/x-gaussian94-output.desktop
+share/mimelnk/chemical/x-gaussian98-output.desktop
share/mimelnk/chemical/x-genbank.desktop
share/mimelnk/chemical/x-gulp.desktop
share/mimelnk/chemical/x-hin.desktop
@@ -46,18 +41,24 @@ share/mimelnk/chemical/x-macromodel-input.desktop
share/mimelnk/chemical/x-mdl-molfile.desktop
share/mimelnk/chemical/x-mdl-rdfile.desktop
share/mimelnk/chemical/x-mdl-rxnfile.desktop
+share/mimelnk/chemical/x-mdl-sdfile.desktop
share/mimelnk/chemical/x-mdl-tgf.desktop
share/mimelnk/chemical/x-mmcif.desktop
share/mimelnk/chemical/x-mol2.desktop
share/mimelnk/chemical/x-mopac-graph.desktop
+share/mimelnk/chemical/x-mopac-input.desktop
share/mimelnk/chemical/x-mopac-out.desktop
+share/mimelnk/chemical/x-mopac.desktop
share/mimelnk/chemical/x-msi-car.desktop
share/mimelnk/chemical/x-msi-hessian.desktop
share/mimelnk/chemical/x-msi-mdf.desktop
share/mimelnk/chemical/x-msi-msi.desktop
+share/mimelnk/chemical/x-ncbi-asn1-ascii.desktop
share/mimelnk/chemical/x-ncbi-asn1-binary.desktop
share/mimelnk/chemical/x-ncbi-asn1-xml.desktop
share/mimelnk/chemical/x-ncbi-asn1.desktop
+share/mimelnk/chemical/x-pdb.desktop
share/mimelnk/chemical/x-shelx.desktop
share/mimelnk/chemical/x-vmd.desktop
share/mimelnk/chemical/x-xyz.desktop
+share/mimelnk/chemical/xyz.desktop
diff --git a/science/cp2k-data/Makefile b/science/cp2k-data/Makefile
index 8bc9337cd7b9..bc2ad72bb356 100644
--- a/science/cp2k-data/Makefile
+++ b/science/cp2k-data/Makefile
@@ -1,6 +1,6 @@
PORTNAME= cp2k-data
DISTVERSIONPREFIX= v
-DISTVERSION= 2025.1
+DISTVERSION= 2025.2
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
diff --git a/science/cp2k-data/distinfo b/science/cp2k-data/distinfo
index 004194f14912..264eccf26d02 100644
--- a/science/cp2k-data/distinfo
+++ b/science/cp2k-data/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1735891303
-SHA256 (cp2k-cp2k-v2025.1_GH0.tar.gz) = 9b58062b9aed51de06cb1248f5dbeab2741962f03eb72c4025b9d0533af1805e
-SIZE (cp2k-cp2k-v2025.1_GH0.tar.gz) = 87315415
+TIMESTAMP = 1753646804
+SHA256 (cp2k-cp2k-v2025.2_GH0.tar.gz) = 02432be1f6b56bab1d4b43e86e28ba495405d6f4015f2610f3376d56495ef74b
+SIZE (cp2k-cp2k-v2025.2_GH0.tar.gz) = 88095973
diff --git a/science/cp2k-data/pkg-plist b/science/cp2k-data/pkg-plist
index 3e641bb9296c..27d24338488a 100644
--- a/science/cp2k-data/pkg-plist
+++ b/science/cp2k-data/pkg-plist
@@ -1,6 +1,7 @@
%%DATADIR%%/ALL_BASIS_SETS
%%DATADIR%%/ALL_POTENTIALS
%%DATADIR%%/AcPP1_POTENTIALS
+%%DATADIR%%/AcPP2_POTENTIALS
%%DATADIR%%/Allegro/gra-water-deployed-neq060sp.pth
%%DATADIR%%/Allegro/si-deployed-neq060dp.pth
%%DATADIR%%/BASIS_ADMM
@@ -12,6 +13,7 @@
%%DATADIR%%/BASIS_MINIX
%%DATADIR%%/BASIS_MOLOPT
%%DATADIR%%/BASIS_MOLOPT_AcPP1
+%%DATADIR%%/BASIS_MOLOPT_AcPP2
%%DATADIR%%/BASIS_MOLOPT_LnPP1
%%DATADIR%%/BASIS_MOLOPT_LnPP2
%%DATADIR%%/BASIS_MOLOPT_PSI
@@ -139,7 +141,7 @@
%%DATADIR%%/DFTB/scc/zns.spl
%%DATADIR%%/DFTB/scc/znzn.spl
%%DATADIR%%/DFTB/uff_table
-%%DATADIR%%/DeePMD/W.pb
+%%DATADIR%%/DeePMD/water_dpa2.pth
%%DATADIR%%/ECP_POTENTIALS
%%DATADIR%%/ECP_POTENTIALS_pob-TZVP-rev2
%%DATADIR%%/EMSL_BASIS_SETS
@@ -185,6 +187,17 @@
%%DATADIR%%/NNP/bulkH2O-jcp2020-cnnp/nnp-8/scaling.data
%%DATADIR%%/NNP/bulkH2O-jcp2020-cnnp/nnp-8/weights.001.data
%%DATADIR%%/NNP/bulkH2O-jcp2020-cnnp/nnp-8/weights.008.data
+%%DATADIR%%/NNP/protH2OHelium-interaction-nnp/input.nn
+%%DATADIR%%/NNP/protH2OHelium-interaction-nnp/readme.md
+%%DATADIR%%/NNP/protH2OHelium-interaction-nnp/scaling.data
+%%DATADIR%%/NNP/protH2OHelium-interaction-nnp/weights.001.data
+%%DATADIR%%/NNP/protH2OHelium-interaction-nnp/weights.002.data
+%%DATADIR%%/NNP/protH2OHelium-interaction-nnp/weights.008.data
+%%DATADIR%%/NNP/protH2Ocluster-jctc2020-nnp/input.nn
+%%DATADIR%%/NNP/protH2Ocluster-jctc2020-nnp/readme.md
+%%DATADIR%%/NNP/protH2Ocluster-jctc2020-nnp/scaling.data
+%%DATADIR%%/NNP/protH2Ocluster-jctc2020-nnp/weights.001.data
+%%DATADIR%%/NNP/protH2Ocluster-jctc2020-nnp/weights.008.data
%%DATADIR%%/NequIP/water-deployed-neq060dp.pth
%%DATADIR%%/NequIP/water-deployed-neq060sp.pth
%%DATADIR%%/POTENTIAL
diff --git a/science/cp2k/Makefile b/science/cp2k/Makefile
index f6b05741f098..46e7081d3302 100644
--- a/science/cp2k/Makefile
+++ b/science/cp2k/Makefile
@@ -1,7 +1,6 @@
PORTNAME= cp2k
DISTVERSIONPREFIX= v
-DISTVERSION= 2025.1
-PORTREVISION= 2
+DISTVERSION= 2025.2
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
@@ -61,5 +60,6 @@ do-test: install
./tests/do_regtest.py ${BUILD_WRKSRC}/bin ${EXE_VERSION}
# build instructions: https://github.com/cp2k/cp2k/blob/master/INSTALL.md
+# tests as of 2025.2: Summary: correct: 3009 / 3012; failed: 3; 141min
.include <bsd.port.mk>
diff --git a/science/cp2k/distinfo b/science/cp2k/distinfo
index e6c365e0e377..aee1bed85e63 100644
--- a/science/cp2k/distinfo
+++ b/science/cp2k/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1735886722
-SHA256 (cp2k-cp2k-v2025.1_GH0.tar.gz) = 9b58062b9aed51de06cb1248f5dbeab2741962f03eb72c4025b9d0533af1805e
-SIZE (cp2k-cp2k-v2025.1_GH0.tar.gz) = 87315415
+TIMESTAMP = 1753641251
+SHA256 (cp2k-cp2k-v2025.2_GH0.tar.gz) = 02432be1f6b56bab1d4b43e86e28ba495405d6f4015f2610f3376d56495ef74b
+SIZE (cp2k-cp2k-v2025.2_GH0.tar.gz) = 88095973
diff --git a/science/cp2k/files/patch-cmake_CompilerConfiguration.cmake b/science/cp2k/files/patch-cmake_CompilerConfiguration.cmake
index 1ec302774635..3b5407d20736 100644
--- a/science/cp2k/files/patch-cmake_CompilerConfiguration.cmake
+++ b/science/cp2k/files/patch-cmake_CompilerConfiguration.cmake
@@ -1,11 +1,37 @@
---- cmake/CompilerConfiguration.cmake.orig 2024-09-04 05:25:49 UTC
+--- cmake/CompilerConfiguration.cmake.orig 2025-07-23 08:02:03 UTC
+++ cmake/CompilerConfiguration.cmake
-@@ -35,7 +35,7 @@ add_compile_options(
- # https://github.com/cp2k/dbcsr/issues/261 eventually check compiler version
- # (similar to -h system_alloc)
- add_compile_options(
-- "$<$<COMPILE_LANG_AND_ID:Fortran,GNU>:-mtune=native;-ffree-line-length-512;-ffree-form;-std=f2008;-fimplicit-none;-Werror=aliasing;-Werror=ampersand;-Werror=c-binding-type;-Werror=conversion;-Werror=intrinsic-shadow;-Werror=intrinsics-std;-Werror=line-truncation;-Werror=tabs;-Werror=target-lifetime;-Werror=underflow;-Werror=unused-but-set-variable;-Werror=unused-variable>"
-+ "$<$<COMPILE_LANG_AND_ID:Fortran,GNU>:-ffree-line-length-512;-ffree-form;-std=f2008;-fimplicit-none;-Werror=aliasing;-Werror=ampersand;-Werror=c-binding-type;-Werror=conversion;-Werror=intrinsic-shadow;-Werror=intrinsics-std;-Werror=line-truncation;-Werror=tabs;-Werror=target-lifetime;-Werror=underflow;-Werror=unused-but-set-variable;-Werror=unused-variable>"
- "$<$<AND:$<COMPILE_LANG_AND_ID:Fortran,GNU>,$<VERSION_GREATER_EQUAL:${CMAKE_Fortran_COMPILER_VERSION},11>>:-fallow-argument-mismatch>"
- "$<$<COMPILE_LANG_AND_ID:Fortran,Intel>:-free -stand=f18 -fpp -heap-arrays>"
- "$<$<COMPILE_LANG_AND_ID:Fortran,PGI>:-Mfreeform -Mextend -Mallocatable=03>"
+@@ -53,9 +53,9 @@ add_compile_options(
+
+ # Release
+ add_compile_options(
+- "$<$<AND:$<CONFIG:RELEASE>,$<COMPILE_LANG_AND_ID:Fortran,GNU>>:-O3;-march=native;-mtune=native;-funroll-loops>"
+- "$<$<AND:$<CONFIG:RELEASE>,$<COMPILE_LANG_AND_ID:CXX,GNU>>:-O3;-march=native;-mtune=native;-funroll-loops>"
+- "$<$<AND:$<CONFIG:RELEASE>,$<COMPILE_LANG_AND_ID:C,GNU>>:-O3;-march=native;-mtune=native;-funroll-loops>"
++ "$<$<AND:$<CONFIG:RELEASE>,$<COMPILE_LANG_AND_ID:Fortran,GNU>>:-O3;-funroll-loops>"
++ "$<$<AND:$<CONFIG:RELEASE>,$<COMPILE_LANG_AND_ID:CXX,GNU>>:-O3;-funroll-loops>"
++ "$<$<AND:$<CONFIG:RELEASE>,$<COMPILE_LANG_AND_ID:C,GNU>>:-O3;-funroll-loops>"
+ )
+
+ # Generic
+@@ -67,9 +67,9 @@ add_compile_options(
+
+ # Debug
+ add_compile_options(
+- "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:Fortran,GNU>>:-O1;-march=native;-mtune=native>"
+- "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:CXX,GNU>>:-O1;-march=native;-mtune=native>"
+- "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:C,GNU>>:-O1;-march=native;-mtune=native>"
++ "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:Fortran,GNU>>:-O1>"
++ "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:CXX,GNU>>:-O1>"
++ "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:C,GNU>>:-O1>"
+ )
+ add_compile_options(
+ "$<$<AND:$<CONFIG:DEBUG>,$<COMPILE_LANG_AND_ID:Fortran,GNU>>:-fsanitize=leak;-Werror=realloc-lhs>"
+@@ -100,7 +100,7 @@ add_compile_options(
+
+ # Address Sanitizer
+ add_compile_options(
+- "$<$<CONFIG:ASAN>:-fsanitize=address;-no-pie;-O3;-march=native;-mtune=native;-funroll-loops>"
++ "$<$<CONFIG:ASAN>:-fsanitize=address;-no-pie;-O3;-funroll-loops>"
+ )
+ add_link_options("$<$<CONFIG:ASAN>:-fsanitize=address>")
+
diff --git a/science/cp2k/pkg-plist b/science/cp2k/pkg-plist
index b502f43f6bfb..bc47f0049444 100644
--- a/science/cp2k/pkg-plist
+++ b/science/cp2k/pkg-plist
@@ -6,12 +6,15 @@ bin/dumpdcd%%SUFFIX%%
bin/graph%%SUFFIX%%
bin/grid_miniapp%%SUFFIX%%
bin/grid_unittest%%SUFFIX%%
+bin/gx_ac_unittest%%SUFFIX%%
bin/libcp2k_unittest%%SUFFIX%%
bin/memory_utilities_unittest%%SUFFIX%%
bin/nequip_unittest%%SUFFIX%%
bin/parallel_rng_types_unittest%%SUFFIX%%
bin/xyz2dcd%%SUFFIX%%
include/cp2k/libcp2k.h
+include/cp2k/mod_files/ace_nlist.mod
+include/cp2k/mod_files/ace_wrapper.mod
include/cp2k/mod_files/admm_dm_methods.mod
include/cp2k/mod_files/admm_dm_types.mod
include/cp2k/mod_files/admm_methods.mod
@@ -59,6 +62,7 @@ include/cp2k/mod_files/arnoldi_data_methods.mod
include/cp2k/mod_files/arnoldi_geev.mod
include/cp2k/mod_files/arnoldi_methods.mod
include/cp2k/mod_files/arnoldi_types.mod
+include/cp2k/mod_files/arnoldi_vector.mod
include/cp2k/mod_files/atom.mod
include/cp2k/mod_files/atom_admm_methods.mod
include/cp2k/mod_files/atom_basis.mod
@@ -146,6 +150,7 @@ include/cp2k/mod_files/cp_control_types.mod
include/cp2k/mod_files/cp_control_utils.mod
include/cp2k/mod_files/cp_dbcsr_api.mod
include/cp2k/mod_files/cp_dbcsr_cholesky.mod
+include/cp2k/mod_files/cp_dbcsr_contrib.mod
include/cp2k/mod_files/cp_dbcsr_cp2k_link.mod
include/cp2k/mod_files/cp_dbcsr_diag.mod
include/cp2k/mod_files/cp_dbcsr_operations.mod
@@ -209,7 +214,6 @@ include/cp2k/mod_files/ct_types.mod
include/cp2k/mod_files/cube_utils.mod
include/cp2k/mod_files/d3_poly.mod
include/cp2k/mod_files/damping_dipole_types.mod
-include/cp2k/mod_files/dbcsr_vector.mod
include/cp2k/mod_files/dbm_api.mod
include/cp2k/mod_files/dbm_tests.mod
include/cp2k/mod_files/dbt_allocate_wrap.mod
@@ -354,6 +358,7 @@ include/cp2k/mod_files/generic_os_integrals.mod
include/cp2k/mod_files/generic_shg_integrals.mod
include/cp2k/mod_files/generic_shg_integrals_init.mod
include/cp2k/mod_files/geo_opt.mod
+include/cp2k/mod_files/gfun.mod
include/cp2k/mod_files/glbopt_callback.mod
include/cp2k/mod_files/glbopt_history.mod
include/cp2k/mod_files/glbopt_input.mod
@@ -370,6 +375,7 @@ include/cp2k/mod_files/gopt_param_types.mod
include/cp2k/mod_files/graph_methods.mod
include/cp2k/mod_files/graph_utils.mod
include/cp2k/mod_files/graphcon.mod
+include/cp2k/mod_files/greenx_interface.mod
include/cp2k/mod_files/grid_api.mod
include/cp2k/mod_files/group_dist_types.mod
include/cp2k/mod_files/grrm_utils.mod
@@ -380,6 +386,7 @@ include/cp2k/mod_files/gw_large_cell_gamma.mod
include/cp2k/mod_files/gw_main.mod
include/cp2k/mod_files/gw_small_cell_full_kp.mod
include/cp2k/mod_files/gw_utils.mod
+include/cp2k/mod_files/hairy_probes.mod
include/cp2k/mod_files/hartree_local_methods.mod
include/cp2k/mod_files/hartree_local_types.mod
include/cp2k/mod_files/hdf5_wrapper.mod
@@ -505,7 +512,6 @@ include/cp2k/mod_files/kpoint_methods.mod
include/cp2k/mod_files/kpoint_transitional.mod
include/cp2k/mod_files/kpoint_types.mod
include/cp2k/mod_files/kpsym.mod
-include/cp2k/mod_files/lapack.mod
include/cp2k/mod_files/lazy.mod
include/cp2k/mod_files/lebedev.mod
include/cp2k/mod_files/libcp2k.mod
@@ -533,6 +539,7 @@ include/cp2k/mod_files/lri_optimize_ri_basis.mod
include/cp2k/mod_files/lri_optimize_ri_basis_types.mod
include/cp2k/mod_files/ls_matrix_exp.mod
include/cp2k/mod_files/machine.mod
+include/cp2k/mod_files/manybody_ace.mod
include/cp2k/mod_files/manybody_allegro.mod
include/cp2k/mod_files/manybody_deepmd.mod
include/cp2k/mod_files/manybody_eam.mod
@@ -790,6 +797,8 @@ include/cp2k/mod_files/qs_2nd_kernel_ao.mod
include/cp2k/mod_files/qs_active_space_methods.mod
include/cp2k/mod_files/qs_active_space_types.mod
include/cp2k/mod_files/qs_active_space_utils.mod
+include/cp2k/mod_files/qs_apt_fdiff_methods.mod
+include/cp2k/mod_files/qs_apt_fdiff_types.mod
include/cp2k/mod_files/qs_atomic_block.mod
include/cp2k/mod_files/qs_band_structure.mod
include/cp2k/mod_files/qs_basis_gradient.mod
@@ -1001,10 +1010,6 @@ include/cp2k/mod_files/qs_tddfpt2_stda_utils.mod
include/cp2k/mod_files/qs_tddfpt2_subgroups.mod
include/cp2k/mod_files/qs_tddfpt2_types.mod
include/cp2k/mod_files/qs_tddfpt2_utils.mod
-include/cp2k/mod_files/qs_tddfpt_eigensolver.mod
-include/cp2k/mod_files/qs_tddfpt_module.mod
-include/cp2k/mod_files/qs_tddfpt_types.mod
-include/cp2k/mod_files/qs_tddfpt_utils.mod
include/cp2k/mod_files/qs_tensors.mod
include/cp2k/mod_files/qs_tensors_types.mod
include/cp2k/mod_files/qs_update_s_mstruct.mod
@@ -1027,6 +1032,8 @@ include/cp2k/mod_files/replica_types.mod
include/cp2k/mod_files/response_solver.mod
include/cp2k/mod_files/restraint.mod
include/cp2k/mod_files/ri_environment_methods.mod
+include/cp2k/mod_files/rixs_methods.mod
+include/cp2k/mod_files/rixs_types.mod
include/cp2k/mod_files/rmsd.mod
include/cp2k/mod_files/routine_map.mod
include/cp2k/mod_files/rpa_communication.mod
@@ -1135,6 +1142,9 @@ include/cp2k/mod_files/tamc_run.mod
include/cp2k/mod_files/taper_types.mod
include/cp2k/mod_files/task_list_methods.mod
include/cp2k/mod_files/task_list_types.mod
+include/cp2k/mod_files/tblite_interface.mod
+include/cp2k/mod_files/tblite_ks_matrix.mod
+include/cp2k/mod_files/tblite_types.mod
include/cp2k/mod_files/thermal_region_types.mod
include/cp2k/mod_files/thermal_region_utils.mod
include/cp2k/mod_files/thermostat_mapping.mod
@@ -1259,6 +1269,7 @@ include/cp2k/mod_files/xc_xbr_pbe_lda_hole_t_c_lr.mod
include/cp2k/mod_files/xc_xlda_hole_t_c_lr.mod
include/cp2k/mod_files/xc_xpbe_hole_t_c_lr.mod
include/cp2k/mod_files/xc_xwpbe.mod
+include/cp2k/mod_files/xmgrace.mod
include/cp2k/mod_files/xray_diffraction.mod
include/cp2k/mod_files/xtb_coulomb.mod
include/cp2k/mod_files/xtb_eeq.mod
@@ -1270,11 +1281,13 @@ include/cp2k/mod_files/xtb_ks_matrix.mod
include/cp2k/mod_files/xtb_matrices.mod
include/cp2k/mod_files/xtb_parameters.mod
include/cp2k/mod_files/xtb_potentials.mod
+include/cp2k/mod_files/xtb_qresp.mod
include/cp2k/mod_files/xtb_types.mod
lib/cmake/cp2k/cp2kConfig.cmake
lib/cmake/cp2k/cp2kConfigVersion.cmake
lib/cmake/cp2k/cp2kTargets-%%CMAKE_BUILD_TYPE%%.cmake
lib/cmake/cp2k/cp2kTargets.cmake
+lib/cmake/cp2k/modules/FindACE.cmake
lib/cmake/cp2k/modules/FindArmpl.cmake
lib/cmake/cp2k/modules/FindAtlas.cmake
lib/cmake/cp2k/modules/FindBlas.cmake
@@ -1288,28 +1301,25 @@ lib/cmake/cp2k/modules/FindGenericBLAS.cmake
lib/cmake/cp2k/modules/FindLapack.cmake
lib/cmake/cp2k/modules/FindLibVDWXC.cmake
lib/cmake/cp2k/modules/FindLibVORI.cmake
-lib/cmake/cp2k/modules/FindLibXC.cmake
lib/cmake/cp2k/modules/FindLibXSMM.cmake
lib/cmake/cp2k/modules/FindLibint2.cmake
lib/cmake/cp2k/modules/FindMKL.cmake
-lib/cmake/cp2k/modules/FindMetis.cmake
lib/cmake/cp2k/modules/FindNVHPCBlas.cmake
lib/cmake/cp2k/modules/FindOpenBLAS.cmake
-lib/cmake/cp2k/modules/FindPEXSI.cmake
lib/cmake/cp2k/modules/FindPlumed.cmake
-lib/cmake/cp2k/modules/FindPtscotch.cmake
-lib/cmake/cp2k/modules/FindQuip.cmake
lib/cmake/cp2k/modules/FindSCALAPACK.cmake
lib/cmake/cp2k/modules/FindSCI.cmake
-lib/cmake/cp2k/modules/FindSuperLU.cmake
+lib/cmake/cp2k/modules/FindTrexIO.cmake
+lib/cmake/cp2k/modules/Findlibsmeagol.cmake
lib/cmake/cp2k/modules/Finducc.cmake
lib/cmake/cp2k/modules/cp2k_utils.cmake
lib/libcp2k.so
-lib/libcp2k.so.2025.1
+lib/libcp2k.so.2025.2
libdata/pkgconfig/libcp2k.pc
%%DATADIR%%/data/ALL_BASIS_SETS
%%DATADIR%%/data/ALL_POTENTIALS
%%DATADIR%%/data/AcPP1_POTENTIALS
+%%DATADIR%%/data/AcPP2_POTENTIALS
%%DATADIR%%/data/Allegro/gra-water-deployed-neq060sp.pth
%%DATADIR%%/data/Allegro/si-deployed-neq060dp.pth
%%DATADIR%%/data/BASIS_ADMM
@@ -1321,6 +1331,7 @@ libdata/pkgconfig/libcp2k.pc
%%DATADIR%%/data/BASIS_MINIX
%%DATADIR%%/data/BASIS_MOLOPT
%%DATADIR%%/data/BASIS_MOLOPT_AcPP1
+%%DATADIR%%/data/BASIS_MOLOPT_AcPP2
%%DATADIR%%/data/BASIS_MOLOPT_LnPP1
%%DATADIR%%/data/BASIS_MOLOPT_LnPP2
%%DATADIR%%/data/BASIS_MOLOPT_PSI
@@ -1448,7 +1459,7 @@ libdata/pkgconfig/libcp2k.pc
%%DATADIR%%/data/DFTB/scc/zns.spl
%%DATADIR%%/data/DFTB/scc/znzn.spl
%%DATADIR%%/data/DFTB/uff_table
-%%DATADIR%%/data/DeePMD/W.pb
+%%DATADIR%%/data/DeePMD/water_dpa2.pth
%%DATADIR%%/data/ECP_POTENTIALS
%%DATADIR%%/data/ECP_POTENTIALS_pob-TZVP-rev2
%%DATADIR%%/data/EMSL_BASIS_SETS
@@ -1494,6 +1505,17 @@ libdata/pkgconfig/libcp2k.pc
%%DATADIR%%/data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/scaling.data
%%DATADIR%%/data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/weights.001.data
%%DATADIR%%/data/NNP/bulkH2O-jcp2020-cnnp/nnp-8/weights.008.data
+%%DATADIR%%/data/NNP/protH2OHelium-interaction-nnp/input.nn
+%%DATADIR%%/data/NNP/protH2OHelium-interaction-nnp/readme.md
+%%DATADIR%%/data/NNP/protH2OHelium-interaction-nnp/scaling.data
+%%DATADIR%%/data/NNP/protH2OHelium-interaction-nnp/weights.001.data
+%%DATADIR%%/data/NNP/protH2OHelium-interaction-nnp/weights.002.data
+%%DATADIR%%/data/NNP/protH2OHelium-interaction-nnp/weights.008.data
+%%DATADIR%%/data/NNP/protH2Ocluster-jctc2020-nnp/input.nn
+%%DATADIR%%/data/NNP/protH2Ocluster-jctc2020-nnp/readme.md
+%%DATADIR%%/data/NNP/protH2Ocluster-jctc2020-nnp/scaling.data
+%%DATADIR%%/data/NNP/protH2Ocluster-jctc2020-nnp/weights.001.data
+%%DATADIR%%/data/NNP/protH2Ocluster-jctc2020-nnp/weights.008.data
%%DATADIR%%/data/NequIP/water-deployed-neq060dp.pth
%%DATADIR%%/data/NequIP/water-deployed-neq060sp.pth
%%DATADIR%%/data/POTENTIAL
diff --git a/science/csvtk/Makefile b/science/csvtk/Makefile
index 707410f4fa7a..a9105577fa35 100644
--- a/science/csvtk/Makefile
+++ b/science/csvtk/Makefile
@@ -1,7 +1,6 @@
PORTNAME= csvtk
DISTVERSIONPREFIX= v
-DISTVERSION= 0.33.0
-PORTREVISION= 4
+DISTVERSION= 0.34.0
CATEGORIES= science
MAINTAINER= jwb@FreeBSD.org
diff --git a/science/csvtk/distinfo b/science/csvtk/distinfo
index 2baa84299593..0dfce56d9fa9 100644
--- a/science/csvtk/distinfo
+++ b/science/csvtk/distinfo
@@ -1,7 +1,7 @@
-TIMESTAMP = 1741868386
-SHA256 (go/science_csvtk/csvtk-v0.33.0/v0.33.0.mod) = b5fff90dd2b700db63cca9340ed60790096bd3f0e6650b0e159d9fa860fcc121
-SIZE (go/science_csvtk/csvtk-v0.33.0/v0.33.0.mod) = 2688
-SHA256 (go/science_csvtk/csvtk-v0.33.0/v0.33.0.zip) = 54d692d43c8c6dbd578355c7e810a658b52f68513e6a6246df192e139d6c1f3b
-SIZE (go/science_csvtk/csvtk-v0.33.0/v0.33.0.zip) = 2617821
-SHA256 (go/science_csvtk/csvtk-v0.33.0/golang-sys-v0.6.0_GH0.tar.gz) = b4f6d17c7a128f76169964b437cb66b3f2dbf9a33361928ec19dfecf7b03fc54
-SIZE (go/science_csvtk/csvtk-v0.33.0/golang-sys-v0.6.0_GH0.tar.gz) = 1434234
+TIMESTAMP = 1753550609
+SHA256 (go/science_csvtk/csvtk-v0.34.0/v0.34.0.mod) = 485d911da4192efc1aaf72df722990fb897f03cdac18aff77fee199a3dab507f
+SIZE (go/science_csvtk/csvtk-v0.34.0/v0.34.0.mod) = 2607
+SHA256 (go/science_csvtk/csvtk-v0.34.0/v0.34.0.zip) = aa1a8825b1c69e507717b825c270d9849234ee21da04f0b58d9f064056f1c971
+SIZE (go/science_csvtk/csvtk-v0.34.0/v0.34.0.zip) = 2656260
+SHA256 (go/science_csvtk/csvtk-v0.34.0/golang-sys-v0.6.0_GH0.tar.gz) = b4f6d17c7a128f76169964b437cb66b3f2dbf9a33361928ec19dfecf7b03fc54
+SIZE (go/science_csvtk/csvtk-v0.34.0/golang-sys-v0.6.0_GH0.tar.gz) = 1434234
diff --git a/science/tinker/Makefile b/science/tinker/Makefile
index c5b9b72ff278..a62f2268609b 100644
--- a/science/tinker/Makefile
+++ b/science/tinker/Makefile
@@ -1,6 +1,5 @@
PORTNAME= tinker
-DISTVERSION= 8.11.3
-PORTREVISION= 1
+DISTVERSION= 25.3
CATEGORIES= science
MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/
diff --git a/science/tinker/distinfo b/science/tinker/distinfo
index 6c20209908c4..7ca60014bed4 100644
--- a/science/tinker/distinfo
+++ b/science/tinker/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1719188902
-SHA256 (tinker-8.11.3.tar.gz) = 8dfbc9fb8f26742d91139187657e2c905744b0243538f81b75bc04cdc2606ff7
-SIZE (tinker-8.11.3.tar.gz) = 73256260
+TIMESTAMP = 1753634645
+SHA256 (tinker-25.3.tar.gz) = d536f1d4d0d7d4394b3b3d88a52cf12ed3489312ac2ad9c6ce4d198bd681e36c
+SIZE (tinker-25.3.tar.gz) = 80772142
diff --git a/science/tinker/pkg-plist b/science/tinker/pkg-plist
index 286fc0abcadd..b0f9367ade44 100644
--- a/science/tinker/pkg-plist
+++ b/science/tinker/pkg-plist
@@ -64,6 +64,8 @@ bin/xyzint
bin/xyzmol2
bin/xyzpdb
%%DATADIR%%/params/0README
+%%DATADIR%%/params/amber14sb.prm
+%%DATADIR%%/params/amber19sb.prm
%%DATADIR%%/params/amber94.prm
%%DATADIR%%/params/amber96.prm
%%DATADIR%%/params/amber98.prm
@@ -82,7 +84,8 @@ bin/xyzpdb
%%DATADIR%%/params/basic.prm
%%DATADIR%%/params/charmm19.prm
%%DATADIR%%/params/charmm22.prm
-%%DATADIR%%/params/charmm22cmap.prm
+%%DATADIR%%/params/charmm27.prm
+%%DATADIR%%/params/charmm36.prm
%%DATADIR%%/params/dang.prm
%%DATADIR%%/params/hippo19.prm
%%DATADIR%%/params/hoch.prm
@@ -90,8 +93,9 @@ bin/xyzpdb
%%DATADIR%%/params/mm2.prm
%%DATADIR%%/params/mm3.prm
%%DATADIR%%/params/mm3pro.prm
-%%DATADIR%%/params/mmff.prm
-%%DATADIR%%/params/oplsaa.prm
+%%DATADIR%%/params/mmff94.prm
+%%DATADIR%%/params/mmff94s.prm
+%%DATADIR%%/params/oplsaa08.prm
%%DATADIR%%/params/oplsaal.prm
%%DATADIR%%/params/oplsua.prm
%%DATADIR%%/params/smoothaa.prm
@@ -206,6 +210,10 @@ bin/xyzpdb
%%DATADIR%%/test/polyala.key
%%DATADIR%%/test/polyala.log
%%DATADIR%%/test/polyala.run
+%%DATADIR%%/test/pyridine.dat
+%%DATADIR%%/test/pyridine.log
+%%DATADIR%%/test/pyridine.run
+%%DATADIR%%/test/pyridine.xyz
%%DATADIR%%/test/salt.cell
%%DATADIR%%/test/salt.key
%%DATADIR%%/test/salt.log
generated by cgit v1.2.3 (git 2.25.1) at 2025-08-01 16:21:14 +0000