diff options
Diffstat (limited to 'science')
78 files changed, 618 insertions, 940 deletions
diff --git a/science/Makefile b/science/Makefile index 3e8dbded3d60..f14398a64291 100644 --- a/science/Makefile +++ b/science/Makefile @@ -530,6 +530,5 @@ SUBDIR += xtb SUBDIR += yoda SUBDIR += zotero - SUBDIR += zx .include <bsd.port.subdir.mk> diff --git a/science/afni/Makefile b/science/afni/Makefile index 60a9c6179d87..d9df14c3314c 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -1,6 +1,6 @@ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ -DISTVERSION= 25.2.18 +DISTVERSION= 25.3.00 CATEGORIES= science biology graphics perl5 python MAINTAINER= fernape@FreeBSD.org diff --git a/science/afni/distinfo b/science/afni/distinfo index 86a0070395b4..bbc262bd6adb 100644 --- a/science/afni/distinfo +++ b/science/afni/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1759213947 -SHA256 (afni-afni-AFNI_25.2.18_GH0.tar.gz) = 9f21faf0f8ed66eba8a2c1473a4c5c0421909e0f386fc699ed599bebced96003 -SIZE (afni-afni-AFNI_25.2.18_GH0.tar.gz) = 53390003 +TIMESTAMP = 1763655339 +SHA256 (afni-afni-AFNI_25.3.00_GH0.tar.gz) = 6122a5a48620d84c59ca076967ce53189dd1afb1e31d4cc04b6e4b2ad9598686 +SIZE (afni-afni-AFNI_25.3.00_GH0.tar.gz) = 53396071 diff --git a/science/ascent/Makefile b/science/ascent/Makefile index 700c3175eeba..1687ea96d527 100644 --- a/science/ascent/Makefile +++ b/science/ascent/Makefile @@ -1,6 +1,7 @@ PORTNAME= ascent DISTVERSIONPREFIX= v DISTVERSION= 0.9.5 +PORTREVISION= 1 CATEGORIES= science PKGNAMESUFFIX= -visualizer diff --git a/science/axom/Makefile b/science/axom/Makefile index 25a79bc28304..254bf8397995 100644 --- a/science/axom/Makefile +++ b/science/axom/Makefile @@ -1,7 +1,7 @@ PORTNAME= axom DISTVERSIONPREFIX= v DISTVERSION= 0.10.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/checkmol/Makefile b/science/checkmol/Makefile index 84440a536957..8b92c6ffe802 100644 --- a/science/checkmol/Makefile +++ b/science/checkmol/Makefile @@ -1,6 +1,6 @@ PORTNAME= checkmol PORTVERSION= 0.5 -PORTREVISION= 17 +PORTREVISION= 18 CATEGORIES= science MASTER_SITES= https://homepage.univie.ac.at/norbert.haider/download/chemistry/checkmol/ DISTFILES= ${PORTNAME} diff --git a/science/conduit/Makefile b/science/conduit/Makefile index fe04ba696b7a..5f2c3994456b 100644 --- a/science/conduit/Makefile +++ b/science/conduit/Makefile @@ -1,6 +1,7 @@ PORTNAME= conduit DISTVERSIONPREFIX= v DISTVERSION= 0.9.5 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile index bb661e6ea431..558eab81f1ba 100644 --- a/science/gromacs/Makefile +++ b/science/gromacs/Makefile @@ -1,5 +1,6 @@ PORTNAME= gromacs -DISTVERSION= 2025.3 +DISTVERSION= 2025.4 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://ftp.gromacs.org/pub/gromacs/ DISTFILES= ${DISTNAME}${EXTRACT_SUFX} # only for googletest @@ -126,5 +127,6 @@ post-patch: ${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 .include <bsd.port.mk> diff --git a/science/gromacs/distinfo b/science/gromacs/distinfo index ad696c850693..4cf0d1f50a41 100644 --- a/science/gromacs/distinfo +++ b/science/gromacs/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1760115187 -SHA256 (gromacs-2025.3.tar.gz) = 8bdfca0268f3f10a7ca3c06e59b62f73ea02420c67211c0ff3912f32d7833c65 -SIZE (gromacs-2025.3.tar.gz) = 44407119 +TIMESTAMP = 1763922155 +SHA256 (gromacs-2025.4.tar.gz) = ca17720b4a260eb73649211e9f6a940ee7543452129844213c3accb0a927a5c3 +SIZE (gromacs-2025.4.tar.gz) = 44406127 diff --git a/science/mbdyn/files/patch-libraries_libmbwrap_umfpackwrap.h b/science/mbdyn/files/patch-libraries_libmbwrap_umfpackwrap.h new file mode 100644 index 000000000000..95e7aa4d791a --- /dev/null +++ b/science/mbdyn/files/patch-libraries_libmbwrap_umfpackwrap.h @@ -0,0 +1,19 @@ +-- +-- workaround for https://public.gitlab.polimi.it/DAER/mbdyn/-/issues/431 +-- ... 1.7.3 is very old and it fails to compile: error: templates must have C++ linkage: Please make a release +-- + +--- libraries/libmbwrap/umfpackwrap.h.orig 2025-11-18 16:35:30 UTC ++++ libraries/libmbwrap/umfpackwrap.h +@@ -72,9 +72,9 @@ + #include <iostream> + #include <vector> + +-extern "C" { ++//extern "C" { + #include <umfpack.h> +-} ++//} + + #include "myassert.h" + #include "mynewmem.h" diff --git a/science/mol2ps/Makefile b/science/mol2ps/Makefile index 218698f47061..55e4829e1500 100644 --- a/science/mol2ps/Makefile +++ b/science/mol2ps/Makefile @@ -1,6 +1,6 @@ PORTNAME= mol2ps PORTVERSION= 0.4c -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://homepage.univie.ac.at/norbert.haider/download/chemistry/mol2ps/ DISTNAME= ${PORTNAME} diff --git a/science/mpqc/files/patch-configure b/science/mpqc/files/patch-configure index 692451d6e025..d75a082b072d 100644 --- a/science/mpqc/files/patch-configure +++ b/science/mpqc/files/patch-configure @@ -1,6 +1,6 @@ --- configure.orig 2006-03-22 19:13:52 UTC +++ configure -@@ -2268,14 +2268,12 @@ echo Using FORTRAN runtime libraries: $withval +@@ -2268,14 +2268,12 @@ fi; fi; @@ -15,7 +15,7 @@ echo Using extra library directories: $withval fi; -@@ -2290,7 +2288,7 @@ if test "${with_cca_chem_config+set}" = set; then +@@ -2290,7 +2288,7 @@ else else @@ -24,7 +24,7 @@ # Extract the first word of "cca-chem-config", so it can be a program name with args. set dummy cca-chem-config; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 -@@ -5207,7 +5205,7 @@ case $target_cpu in +@@ -5207,7 +5205,7 @@ esac ;; esac @@ -33,7 +33,7 @@ echo "$as_me:$LINENO: checking for C++ cpu tuning flag" >&5 echo $ECHO_N "checking for C++ cpu tuning flag... $ECHO_C" >&6 -@@ -5265,7 +5263,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu +@@ -5265,7 +5263,7 @@ fi echo "${ECHO_T}$cxx_tuneflag" >&6 fi @@ -42,6 +42,15 @@ echo "$as_me:$LINENO: checking for C cpu tuning flag" >&5 echo $ECHO_N "checking for C cpu tuning flag... $ECHO_C" >&6 CFLAGS_SAV=$CFLAGS +@@ -12444,7 +12442,7 @@ if test -n "$F77" -a "$F77" != no ; then + echo " return" >> ffunc.f + echo " end" >> ffunc.f + $F77 -c ffunc.f 1>/dev/null 2>/dev/null +- echo "main(){ FF(); return 0; }" > flink.c ++ echo "int FF(void); int main(){ FF(); return 0; }" > flink.c + if $CC -o flink -DFF=ffunc flink.c ffunc.o $LDFLAGS $LIBS 1>/dev/null 2>/dev/null; then + echo "$as_me:$LINENO: result: same as C" >&5 + echo "${ECHO_T}same as C" >&6 @@ -28629,10 +28627,10 @@ ENABLESHARED=$enable_shared diff --git a/science/openmodelica/Makefile b/science/openmodelica/Makefile index bfb448159694..eeb9e6e84e73 100644 --- a/science/openmodelica/Makefile +++ b/science/openmodelica/Makefile @@ -1,7 +1,6 @@ PORTNAME= openmodelica DISTVERSIONPREFIX= v -DISTVERSION= 1.25.4 -PORTREVISION= 1 +DISTVERSION= 1.25.7 CATEGORIES= science cad java DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} @@ -38,11 +37,9 @@ RUN_DEPENDS= bash:shells/bash \ gmake:devel/gmake USES= cmake compiler:c++14-lang iconv fortran gettext-runtime gl \ - gnome blaslapack localbase:ldflags qt:5 readline pkgconfig \ + gnome blaslapack localbase:ldflags qt:6 readline pkgconfig \ python:build shebangfix java -USE_QT= concurrent core declarative gui location network opengl \ - printsupport svg webchannel webengine widgets xml xmlpatterns \ - buildtools:build linguisttools:build qmake:build +USE_QT= 5compat base declarative positioning webchannel webengine svg tools:build USE_GL= gl opengl USE_GNOME= libxml2 USE_LDCONFIG= ${PREFIX}/lib/omc ${PREFIX}/lib/omc/OMSimulator ${PREFIX}/lib/omc/cpp ${PREFIX}/lib/omc/ffi # https://github.com/OpenModelica/OpenModelica/issues/9925 @@ -55,28 +52,31 @@ SHEBANG_GLOB= *.sh *.in *.ac GH_TUPLE= \ OpenModelica:OMOptim:d53288b:OpenModelica_OMOptim/OMOptim \ + OpenModelica:OpenModelica-common:08a01802db5ba5edb540383c46718b89ff229ef2:OpenModelica_OpenModelica_common/OMOptim/common \ OpenModelica:OMSimulator:e3a3aeb:OpenModelica_OMSimulator/OMSimulator \ - OpenModelica:OMSimulator-3rdParty:5c10de1648d1134a577d9284b58580a72383d89f:OpenModelica_OMSimulator_3rdParty/OMSimulator/3rdParty \ - OpenModelica:OMCompiler-3rdParty:520663f:OpenModelica_OMCompiler_3rdParty/OMCompiler/3rdParty \ - OpenModelica:OMSens:093ad11:OpenModelica_OMSens/OMSens \ - OpenModelica:OMSens_Qt:bab329a:OpenModelica_OMSens_Qt/OMSens_Qt \ - OpenModelica:OpenModelica-common:08a01802db5ba5edb540383c46718b89ff229ef2:OpenModelica_OpenModelica_common/OMOptim/common \ - OpenModelica:OpenModelica-common:08a01802db5ba5edb540383c46718b89ff229ef2:OpenModelica_OpenModelica_common/OMSens_Qt/common + OpenModelica:OMSimulator-3rdParty:5c10de1648d1134a577d9284b58580a72383d89f:OpenModelica_OMSimulator_3rdParty/OMSimulator/3rdParty \ + OpenModelica:OMCompiler-3rdParty:3d2d50d:OpenModelica_OMCompiler_3rdParty/OMCompiler/3rdParty \ + OpenModelica:OMSens_Qt:9c5dfb2:OpenModelica_OMSens_Qt/OMSens_Qt \ + OpenModelica:OpenModelica-common:6e6d4fd:OpenModelica_OpenModelica_common/OMSens_Qt/common GH_TUPLE+= OpenModelica:OMBootstrapping:04d16f7461e5401321f0f72613daf466ae2f76be:bootstrapping/OMCompiler/Compiler/boot/bomc # downloaded by cmake # this should change make program everywhere, but it doesn't, # hence the patches in OMCompiler/Compiler/runtime/CMakeLists.txt, OMEdit/OMEditLIB/Simulation/SimulationOutputWidget.cpp -CMAKE_ARGS= -DCMAKE_MAKE_PROGRAM=gmake \ +CMAKE_ARGS= -DOM_QT_MAJOR_VERSION=6 \ + -DCMAKE_MAKE_PROGRAM=gmake \ -DPython_EXECUTABLE=${PYTHON_CMD} CMAKE_ARGS+= -DOM_USE_CCACHE:BOOL=${CCACHE_ENABLED:S/yes/ON/:S/no/OFF/} # if refuses to build w/out ccache by default #CMAKE_ARGS+= -DOM_QT_MAJOR_VERSION=6 # broken, see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=287596 CMAKE_ON= OM_OMEDIT_ENABLE_QTWEBENGINE +CMAKE_OFF= OM_OMC_ENABLE_IPOPT # broken: omc::3rd::ipopt isn't found, see https://github.com/OpenModelica/OpenModelica/issues/14702 LDFLAGS+= -lexecinfo -lintl -pthread BINARY_ALIAS= make=${GMAKE} +CONFLICTS_INSTALL= cminpack # see https://github.com/OpenModelica/OpenModelica/issues/14701 + post-extract: # remove stray *.orig files @${FIND} ${WRKSRC} -name "*.orig" -delete diff --git a/science/openmodelica/distinfo b/science/openmodelica/distinfo index 2597c4be9261..2ad0980ff458 100644 --- a/science/openmodelica/distinfo +++ b/science/openmodelica/distinfo @@ -1,19 +1,17 @@ -TIMESTAMP = 1757658835 -SHA256 (openmodelica-1.25.4/OpenModelica-OpenModelica-v1.25.4_GH0.tar.gz) = b9d50f8321f4537735d70368b2ca105e35ad118797d71b0107b24eb660387ad4 -SIZE (openmodelica-1.25.4/OpenModelica-OpenModelica-v1.25.4_GH0.tar.gz) = 148278628 -SHA256 (openmodelica-1.25.4/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = d5012951f43e90dce03d7866d221278ee11ddfbdac4db20fe43d93adbc3748e7 -SIZE (openmodelica-1.25.4/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = 4024177 -SHA256 (openmodelica-1.25.4/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 6192d933c258950fb0171f5d0ddac0353632d17ee99f6974ba53dd654f547e49 -SIZE (openmodelica-1.25.4/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 95557541 -SHA256 (openmodelica-1.25.4/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = ea57e90ea76eca2657e8ddaa6c87301a16661200b3e8a00347a12bfdbb5f973d -SIZE (openmodelica-1.25.4/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = 7637943 -SHA256 (openmodelica-1.25.4/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 37c82357fc1e862eb13d79cf1ff2d143f263502472db9bb2c350c0c551022954 -SIZE (openmodelica-1.25.4/OpenModelica-OMCompiler-3rdParty-520663f_GH0.tar.gz) = 50256095 -SHA256 (openmodelica-1.25.4/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 335512c08f94902bb07e75278cea791370a551336272f7bebef8c707ef5e5e2b -SIZE (openmodelica-1.25.4/OpenModelica-OMSens-093ad11_GH0.tar.gz) = 8871049 -SHA256 (openmodelica-1.25.4/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 2f2dcba4defd7f13e9fd5e0c26bb4951b9f1fcc7da64960a6ad1cee32a628efa -SIZE (openmodelica-1.25.4/OpenModelica-OMSens_Qt-bab329a_GH0.tar.gz) = 211270 -SHA256 (openmodelica-1.25.4/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = fdb5bb442da0375373ef221cf26195114bf149511c1c2be051caad6301c21c9a -SIZE (openmodelica-1.25.4/OpenModelica-OpenModelica-common-08a01802db5ba5edb540383c46718b89ff229ef2_GH0.tar.gz) = 36148 -SHA256 (openmodelica-1.25.4/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 9ac6d28be6a331dfb61a57b033f2bcf984448cd63bc1a4cd140d60c2f5c64a79 -SIZE (openmodelica-1.25.4/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 3346859 +TIMESTAMP = 1764143142 +SHA256 (openmodelica-1.25.7/OpenModelica-OpenModelica-v1.25.7_GH0.tar.gz) = c51a0a3e48c469924469fed14a1d722d15d494673cb20b6f64f38da3540102ae +SIZE (openmodelica-1.25.7/OpenModelica-OpenModelica-v1.25.7_GH0.tar.gz) = 148281929 +SHA256 (openmodelica-1.25.7/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = d5012951f43e90dce03d7866d221278ee11ddfbdac4db20fe43d93adbc3748e7 +SIZE (openmodelica-1.25.7/OpenModelica-OMOptim-d53288b_GH0.tar.gz) = 4024177 +SHA256 (openmodelica-1.25.7/OpenModelica-OpenModelica-common-6e6d4fd_GH0.tar.gz) = bff17b6705ef5fe7c1ebae9ca42c1b29d414d7dec59535e1376499f6a5afac54 +SIZE (openmodelica-1.25.7/OpenModelica-OpenModelica-common-6e6d4fd_GH0.tar.gz) = 36187 +SHA256 (openmodelica-1.25.7/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 6192d933c258950fb0171f5d0ddac0353632d17ee99f6974ba53dd654f547e49 +SIZE (openmodelica-1.25.7/OpenModelica-OMSimulator-e3a3aeb_GH0.tar.gz) = 95557541 +SHA256 (openmodelica-1.25.7/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = ea57e90ea76eca2657e8ddaa6c87301a16661200b3e8a00347a12bfdbb5f973d +SIZE (openmodelica-1.25.7/OpenModelica-OMSimulator-3rdParty-5c10de1648d1134a577d9284b58580a72383d89f_GH0.tar.gz) = 7637943 +SHA256 (openmodelica-1.25.7/OpenModelica-OMCompiler-3rdParty-3d2d50d_GH0.tar.gz) = 5f154453c2018a64e8a8a6e58fea59db7def74b937fafbfbaec73154f00cc96f +SIZE (openmodelica-1.25.7/OpenModelica-OMCompiler-3rdParty-3d2d50d_GH0.tar.gz) = 61466733 +SHA256 (openmodelica-1.25.7/OpenModelica-OMSens_Qt-9c5dfb2_GH0.tar.gz) = 552e96f327678672dfe0d2e9c364deb625651333245613e92e5eea57f50e34c0 +SIZE (openmodelica-1.25.7/OpenModelica-OMSens_Qt-9c5dfb2_GH0.tar.gz) = 210958 +SHA256 (openmodelica-1.25.7/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 9ac6d28be6a331dfb61a57b033f2bcf984448cd63bc1a4cd140d60c2f5c64a79 +SIZE (openmodelica-1.25.7/OpenModelica-OMBootstrapping-04d16f7461e5401321f0f72613daf466ae2f76be_GH0.tar.gz) = 3346859 diff --git a/science/openmodelica/files/patch-OMCompiler_Compiler_runtime_systemimpl.c b/science/openmodelica/files/patch-OMCompiler_Compiler_runtime_systemimpl.c index 9492fab582b3..e76992e3d19e 100644 --- a/science/openmodelica/files/patch-OMCompiler_Compiler_runtime_systemimpl.c +++ b/science/openmodelica/files/patch-OMCompiler_Compiler_runtime_systemimpl.c @@ -1,8 +1,8 @@ - make it single-threaded as a workaround for https://github.com/OpenModelica/OpenModelica/issues/9922 ---- OMCompiler/Compiler/runtime/systemimpl.c.orig 2023-04-14 14:33:28 UTC +--- OMCompiler/Compiler/runtime/systemimpl.c.orig 2025-11-24 16:18:03 UTC +++ OMCompiler/Compiler/runtime/systemimpl.c -@@ -772,6 +772,7 @@ char* System_popen(threadData_t *threadData, const cha +@@ -779,6 +779,7 @@ int System_numProcessors(void) int System_numProcessors(void) { @@ -10,7 +10,7 @@ #if WITH_HWLOC==1 hwloc_topology_t topology; if (0==hwloc_topology_init(&topology) && 0==hwloc_topology_load(topology)) { -@@ -790,6 +791,8 @@ int System_numProcessors(void) +@@ -797,6 +798,8 @@ int System_numProcessors(void) #else return intMax(sysconf(_SC_NPROCESSORS_ONLN), 1); #endif diff --git a/science/openmodelica/files/patch-OMSens__Qt_OMSensPlugin.h b/science/openmodelica/files/patch-OMSens__Qt_OMSensPlugin.h new file mode 100644 index 000000000000..81ab7c6f6374 --- /dev/null +++ b/science/openmodelica/files/patch-OMSens__Qt_OMSensPlugin.h @@ -0,0 +1,13 @@ +--- OMSens_Qt/OMSensPlugin.h.orig 2025-11-26 07:56:10 UTC ++++ OMSens_Qt/OMSensPlugin.h +@@ -24,8 +24,8 @@ class OMSensPlugin: public QObject, public Information + public: + virtual void setOpenModelicaHome(const QString &omhome) override; + virtual void setTempPath(const QString &path) override; +- virtual void setOMSensPath(const QString &path) override; +- virtual void setPython(const QString &path) override; ++ virtual void setOMSensPath(const QString &path); ++ virtual void setPython(const QString &path); + + // ModelInterface interface + public: diff --git a/science/openmodelica/pkg-plist b/science/openmodelica/pkg-plist index 9c08ba4f8e0a..c2d8884127a1 100644 --- a/science/openmodelica/pkg-plist +++ b/science/openmodelica/pkg-plist @@ -7,6 +7,8 @@ bin/OMSimulator bin/OMSimulatorPython3 bin/omc bin/omc-diff +include/cminpack-1/cminpack.h +include/cminpack-1/minpack.h include/omc/FMI/fmi_import_context.h include/omc/FMI/fmi_import_util.h include/omc/FMI/fmi_util.h @@ -42,73 +44,6 @@ include/omc/FMI2/fmi2_import_variable.h include/omc/FMI2/fmi2_import_variable_list.h include/omc/FMI2/fmi2_types.h include/omc/FMI2/fmi2_xml_callbacks.h -include/omc/Ipopt/IpAlgBuilder.hpp -include/omc/Ipopt/IpAlgStrategy.hpp -include/omc/Ipopt/IpAlgTypes.hpp -include/omc/Ipopt/IpAugSystemSolver.hpp -include/omc/Ipopt/IpBlas.hpp -include/omc/Ipopt/IpCachedResults.hpp -include/omc/Ipopt/IpCompoundMatrix.hpp -include/omc/Ipopt/IpCompoundSymMatrix.hpp -include/omc/Ipopt/IpCompoundVector.hpp -include/omc/Ipopt/IpConvCheck.hpp -include/omc/Ipopt/IpDebug.hpp -include/omc/Ipopt/IpDenseVector.hpp -include/omc/Ipopt/IpDiagMatrix.hpp -include/omc/Ipopt/IpEqMultCalculator.hpp -include/omc/Ipopt/IpException.hpp -include/omc/Ipopt/IpExpansionMatrix.hpp -include/omc/Ipopt/IpGenTMatrix.hpp -include/omc/Ipopt/IpHessianUpdater.hpp -include/omc/Ipopt/IpIdentityMatrix.hpp -include/omc/Ipopt/IpIpoptAlg.hpp -include/omc/Ipopt/IpIpoptApplication.hpp -include/omc/Ipopt/IpIpoptCalculatedQuantities.hpp -include/omc/Ipopt/IpIpoptData.hpp -include/omc/Ipopt/IpIpoptNLP.hpp -include/omc/Ipopt/IpIterateInitializer.hpp -include/omc/Ipopt/IpIteratesVector.hpp -include/omc/Ipopt/IpIterationOutput.hpp -include/omc/Ipopt/IpJournalist.hpp -include/omc/Ipopt/IpLapack.hpp -include/omc/Ipopt/IpLineSearch.hpp -include/omc/Ipopt/IpMatrix.hpp -include/omc/Ipopt/IpMuUpdate.hpp -include/omc/Ipopt/IpNLP.hpp -include/omc/Ipopt/IpNLPScaling.hpp -include/omc/Ipopt/IpObserver.hpp -include/omc/Ipopt/IpOptionsList.hpp -include/omc/Ipopt/IpOrigIpoptNLP.hpp -include/omc/Ipopt/IpPDSystemSolver.hpp -include/omc/Ipopt/IpReferenced.hpp -include/omc/Ipopt/IpRegOptions.hpp -include/omc/Ipopt/IpReturnCodes.h -include/omc/Ipopt/IpReturnCodes.hpp -include/omc/Ipopt/IpReturnCodes.inc -include/omc/Ipopt/IpReturnCodes_inc.h -include/omc/Ipopt/IpScaledMatrix.hpp -include/omc/Ipopt/IpSearchDirCalculator.hpp -include/omc/Ipopt/IpSmartPtr.hpp -include/omc/Ipopt/IpSolveStatistics.hpp -include/omc/Ipopt/IpStdCInterface.h -include/omc/Ipopt/IpSumSymMatrix.hpp -include/omc/Ipopt/IpSymLinearSolver.hpp -include/omc/Ipopt/IpSymMatrix.hpp -include/omc/Ipopt/IpSymScaledMatrix.hpp -include/omc/Ipopt/IpSymTMatrix.hpp -include/omc/Ipopt/IpTNLP.hpp -include/omc/Ipopt/IpTNLPAdapter.hpp -include/omc/Ipopt/IpTNLPReducer.hpp -include/omc/Ipopt/IpTaggedObject.hpp -include/omc/Ipopt/IpTimedTask.hpp -include/omc/Ipopt/IpTimingStatistics.hpp -include/omc/Ipopt/IpTripletHelper.hpp -include/omc/Ipopt/IpTypes.hpp -include/omc/Ipopt/IpUtils.hpp -include/omc/Ipopt/IpVector.hpp -include/omc/Ipopt/IpZeroSymMatrix.hpp -include/omc/Ipopt/IpoptConfig.h -include/omc/Ipopt/config_ipopt_default.h include/omc/JM/jm_callbacks.h include/omc/JM/jm_named_ptr.h include/omc/JM/jm_portability.h @@ -117,6 +52,16 @@ include/omc/JM/jm_string_set.h include/omc/JM/jm_types.h include/omc/JM/jm_vector.h include/omc/JM/jm_vector_template.h +include/omc/ModelicaExternalC/ModelicaIO.c +include/omc/ModelicaExternalC/ModelicaIO.h +include/omc/ModelicaExternalC/ModelicaMatIO.c +include/omc/ModelicaExternalC/ModelicaMatIO.h +include/omc/ModelicaExternalC/ModelicaStandardTables.c +include/omc/ModelicaExternalC/ModelicaStandardTables.h +include/omc/ModelicaExternalC/ModelicaStandardTablesDummyUsertab.c +include/omc/ModelicaExternalC/read_data_impl.h +include/omc/ModelicaExternalC/safe-math.h +include/omc/ModelicaExternalC/snprintf.c include/omc/OMSimulator/OMSimulator.h include/omc/OMSimulator/Types.h include/omc/ParModelica/auto/om_pm_interface.hpp @@ -261,8 +206,6 @@ include/omc/c/util/utility.h include/omc/c/util/varinfo.h include/omc/c/util/write_csv.h include/omc/c/util/write_matlab4.h -include/omc/cminpack-1/cminpack.h -include/omc/cminpack-1/minpack.h include/omc/cpp/Core/DataExchange/DefaultContainerManager.h include/omc/cpp/Core/DataExchange/FactoryExport.h include/omc/cpp/Core/DataExchange/FactoryPolicy.h @@ -717,12 +660,12 @@ lib/omc/libamd.a lib/omc/libbtf.a lib/omc/libcdaskr.a lib/omc/libcminpack.a -lib/omc/libcoinmumps.a +lib/omc/libcminpackld.a +lib/omc/libcminpacks.a lib/omc/libcolamd.a lib/omc/libexpat.a lib/omc/libffi.a lib/omc/libfmilib.a -lib/omc/libipopt.a lib/omc/libklu.a lib/omc/liblis.a lib/omc/libmetis.a @@ -761,8 +704,9 @@ lib/omc/libumfpack.a lib/omc/libzlib.a lib/omc/libzmq.a lib/omc/pkgconfig/cminpack.pc +lib/omc/pkgconfig/cminpackld.pc +lib/omc/pkgconfig/cminpacks.pc lib/omc/pkgconfig/expat.pc -lib/omc/pkgconfig/ipopt.pc lib/omc/pkgconfig/libzmq.pc share/OMSimulator/schema/fmi2/fmi2Annotation.xsd share/OMSimulator/schema/fmi2/fmi2AttributeGroups.xsd @@ -793,6 +737,8 @@ share/cmake/ZeroMQ/ZeroMQConfigVersion.cmake share/cmake/ZeroMQ/ZeroMQTargets-%%CMAKE_BUILD_TYPE%%.cmake share/cmake/ZeroMQ/ZeroMQTargets.cmake share/cmake/tbb/TBBConfigVersion.cmake +share/cminpack/CMinpackConfig-%%CMAKE_BUILD_TYPE%%.cmake +share/cminpack/CMinpackConfig.cmake share/omc/runtime/c/fmi/buildproject/CMakeLists.txt.in share/omc/runtime/c/fmi/buildproject/config.guess share/omc/runtime/c/fmi/buildproject/config.sub @@ -808,16 +754,19 @@ share/omc/scripts/replace-startValue.bat share/omc/scripts/replace-startValue.sh share/omc/scripts/replace-startValue.xsl share/omc/scripts/simcodedump.xsl +share/omc/sources/c/external_solvers/F77_aloc.c share/omc/sources/c/external_solvers/blaswrap.h share/omc/sources/c/external_solvers/clapack.h share/omc/sources/c/external_solvers/cminpack.h share/omc/sources/c/external_solvers/dgemm.c +share/omc/sources/c/external_solvers/dgemv.c share/omc/sources/c/external_solvers/dger.c share/omc/sources/c/external_solvers/dgesc2.c share/omc/sources/c/external_solvers/dgesv.c share/omc/sources/c/external_solvers/dgetc2.c share/omc/sources/c/external_solvers/dgetf2.c share/omc/sources/c/external_solvers/dgetrf.c +share/omc/sources/c/external_solvers/dgetri.c share/omc/sources/c/external_solvers/dgetrs.c share/omc/sources/c/external_solvers/dlabad.c share/omc/sources/c/external_solvers/dlamch.c @@ -826,8 +775,13 @@ share/omc/sources/c/external_solvers/dogleg_.c share/omc/sources/c/external_solvers/dpmpar_.c share/omc/sources/c/external_solvers/dscal.c share/omc/sources/c/external_solvers/dswap.c +share/omc/sources/c/external_solvers/dtrmm.c +share/omc/sources/c/external_solvers/dtrmv.c share/omc/sources/c/external_solvers/dtrsm.c +share/omc/sources/c/external_solvers/dtrti2.c +share/omc/sources/c/external_solvers/dtrtri.c share/omc/sources/c/external_solvers/enorm_.c +share/omc/sources/c/external_solvers/exit_.c share/omc/sources/c/external_solvers/f2c.h share/omc/sources/c/external_solvers/hybrj_.c share/omc/sources/c/external_solvers/i_nint.c @@ -837,11 +791,13 @@ share/omc/sources/c/external_solvers/ilaenv.c share/omc/sources/c/external_solvers/iparmq.c share/omc/sources/c/external_solvers/lsame.c share/omc/sources/c/external_solvers/minpack.h +share/omc/sources/c/external_solvers/minpackP.h share/omc/sources/c/external_solvers/pow_di.c share/omc/sources/c/external_solvers/qform_.c share/omc/sources/c/external_solvers/qrfac_.c share/omc/sources/c/external_solvers/r1mpyq_.c share/omc/sources/c/external_solvers/r1updt_.c +share/omc/sources/c/external_solvers/s_cat.c share/omc/sources/c/external_solvers/s_cmp.c share/omc/sources/c/external_solvers/s_copy.c share/omc/sources/c/external_solvers/xerbla.c diff --git a/science/orthanc-dicomweb/Makefile b/science/orthanc-dicomweb/Makefile index cf8110adbcb9..37aadc048c9e 100644 --- a/science/orthanc-dicomweb/Makefile +++ b/science/orthanc-dicomweb/Makefile @@ -1,5 +1,6 @@ PORTNAME= orthanc-dicomweb DISTVERSION= 1.21 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc-dicomweb/:dicomweb \ https://orthanc.uclouvain.be/downloads/third-party-downloads/:thirdparty \ @@ -35,7 +36,6 @@ USES= cmake localbase python:build # FIXME: Should plugins be moved to lib? USE_LDCONFIG= ${DATADIR}/plugins -ORTHANC_VER= 1.12.9 CMAKE_ARGS= -DORTHANC_FRAMEWORK_ROOT=${WRKSRC}/ThirdPartyDownloads/Orthanc-${ORTHANC_VER}/OrthancFramework/Sources \ -DORTHANC_FRAMEWORK_SOURCE=path CMAKE_OFF= USE_SYSTEM_UUID @@ -47,6 +47,8 @@ WRKSRC= ${WRKDIR}/OrthancDicomWeb-${PORTVERSION} PLIST_SUB= DISTVERSION=${DISTVERSION} +.include "${.CURDIR}/../../science/orthanc/version.mk" + post-extract: ${MKDIR} ${WRKSRC}/ThirdPartyDownloads .for f in ${EXTRADISTFILES:C/:[^:]*//} diff --git a/science/orthanc-dicomweb/distinfo b/science/orthanc-dicomweb/distinfo index 97b550726de8..05bf5b856778 100644 --- a/science/orthanc-dicomweb/distinfo +++ b/science/orthanc-dicomweb/distinfo @@ -1,8 +1,8 @@ -TIMESTAMP = 1761569002 +TIMESTAMP = 1764252949 SHA256 (orthanc/OrthancDicomWeb-1.21.tar.gz) = 30b7b1c7e710b78f378fd1e46e09be3ece33111331acb0227f80bfebf7d1417c SIZE (orthanc/OrthancDicomWeb-1.21.tar.gz) = 296207 -SHA256 (orthanc/Orthanc-1.12.9.tar.gz) = 7a7cbc5f3663939fbef31ded021b36fcd52420337911ed43491bb663bcb5a4b2 -SIZE (orthanc/Orthanc-1.12.9.tar.gz) = 2165182 +SHA256 (orthanc/Orthanc-1.12.10.tar.gz) = b5d6934d123182fb2186cd54ef7f203be06b544afb03df67b0c64ad68d6c9286 +SIZE (orthanc/Orthanc-1.12.10.tar.gz) = 2192892 SHA256 (orthanc/e2fsprogs-1.44.5.tar.gz) = 2e211fae27ef74d5af4a4e40b10b8df7f87c655933bd171aab4889bfc4e6d1cc SIZE (orthanc/e2fsprogs-1.44.5.tar.gz) = 7619237 SHA256 (orthanc/bootstrap-5.3.3.zip) = 55d7f1ce795040afb8311df09d29d0d34648400c1eaabb2d0a2ed2216b3db05d diff --git a/science/orthanc-mysql/Makefile b/science/orthanc-mysql/Makefile index 37620e7c7b54..7365fb5e0cc3 100644 --- a/science/orthanc-mysql/Makefile +++ b/science/orthanc-mysql/Makefile @@ -1,5 +1,6 @@ PORTNAME= orthanc-mysql DISTVERSION= 5.2 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc-mysql/:mysql \ https://orthanc.uclouvain.be/downloads/sources/orthanc/:orthanc \ @@ -40,7 +41,7 @@ CXXFLAGS+= -I${LOCALBASE}/include -DNDEBUG PLIST_SUB= DISTVERSION=${DISTVERSION} -ORTHANC_VER= 1.12.9 +.include "${.CURDIR}/../../science/orthanc/version.mk" post-extract: ${MKDIR} ${WRKSRC}/MySQL/ThirdPartyDownloads diff --git a/science/orthanc-mysql/distinfo b/science/orthanc-mysql/distinfo index 7b57fb02015e..facf4c2a58d5 100644 --- a/science/orthanc-mysql/distinfo +++ b/science/orthanc-mysql/distinfo @@ -1,7 +1,7 @@ -TIMESTAMP = 1761521650 +TIMESTAMP = 1764253462 SHA256 (orthanc/OrthancMySQL-5.2.tar.gz) = 0d446b53c3fdaa66d9f2365864f1ac54d133fe3760d7d3bb52c850ca67ce9fbb SIZE (orthanc/OrthancMySQL-5.2.tar.gz) = 603876 -SHA256 (orthanc/Orthanc-1.12.9.tar.gz) = 7a7cbc5f3663939fbef31ded021b36fcd52420337911ed43491bb663bcb5a4b2 -SIZE (orthanc/Orthanc-1.12.9.tar.gz) = 2165182 +SHA256 (orthanc/Orthanc-1.12.10.tar.gz) = b5d6934d123182fb2186cd54ef7f203be06b544afb03df67b0c64ad68d6c9286 +SIZE (orthanc/Orthanc-1.12.10.tar.gz) = 2192892 SHA256 (orthanc/e2fsprogs-1.44.5.tar.gz) = 2e211fae27ef74d5af4a4e40b10b8df7f87c655933bd171aab4889bfc4e6d1cc SIZE (orthanc/e2fsprogs-1.44.5.tar.gz) = 7619237 diff --git a/science/orthanc-mysql/files/patch-OrthancFramework_Resources_CMake_ProtobufConfiguration.cmake b/science/orthanc-mysql/files/patch-OrthancFramework_Resources_CMake_ProtobufConfiguration.cmake index e4826a677166..24de235a27d8 100644 --- a/science/orthanc-mysql/files/patch-OrthancFramework_Resources_CMake_ProtobufConfiguration.cmake +++ b/science/orthanc-mysql/files/patch-OrthancFramework_Resources_CMake_ProtobufConfiguration.cmake @@ -1,5 +1,5 @@ ---- MySQL/ThirdPartyDownloads/Orthanc-1.12.9/OrthancFramework/Resources/CMake/ProtobufConfiguration.cmake.orig 2025-08-11 16:02:50 UTC -+++ MySQL/ThirdPartyDownloads/Orthanc-1.12.9/OrthancFramework/Resources/CMake/ProtobufConfiguration.cmake +--- MySQL/ThirdPartyDownloads/Orthanc-1.12.10/OrthancFramework/Resources/CMake/ProtobufConfiguration.cmake.orig 2025-08-11 16:02:50 UTC ++++ MySQL/ThirdPartyDownloads/Orthanc-1.12.10/OrthancFramework/Resources/CMake/ProtobufConfiguration.cmake @@ -60,27 +60,31 @@ else() add_custom_target(ProtobufCompiler) endif() diff --git a/science/orthanc-postgresql/Makefile b/science/orthanc-postgresql/Makefile index 8b89f3124aee..0c3a2281fe46 100644 --- a/science/orthanc-postgresql/Makefile +++ b/science/orthanc-postgresql/Makefile @@ -1,5 +1,6 @@ PORTNAME= orthanc-postgresql DISTVERSION= 9.0 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc-postgresql/:pgsql \ https://orthanc.uclouvain.be/downloads/sources/orthanc/:orthanc \ @@ -20,9 +21,8 @@ LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= ${LOCALBASE}/include/orthanc/OrthancCDatabasePlugin.h:science/orthanc \ googletest>0:devel/googletest LIB_DEPENDS= libboost_filesystem.so:devel/boost-libs \ - libgdcmCommon.so:devel/gdcm \ libjsoncpp.so:devel/jsoncpp \ - libpugixml.so:textproc/pugixml + libprotobuf.so:devel/protobuf RUN_DEPENDS= Orthanc:science/orthanc USES= cmake localbase pgsql:11+ python:build ssl @@ -40,7 +40,7 @@ CFLAGS+= -DORTHANC_ENABLE_LOGGING_PLUGIN -DNDEBUG PLIST_SUB= DISTVERSION=${DISTVERSION} -ORTHANC_VER= 1.12.9 +.include "${.CURDIR}/../../science/orthanc/version.mk" post-extract: ${MKDIR} ${WRKSRC}/PostgreSQL/ThirdPartyDownloads diff --git a/science/orthanc-postgresql/distinfo b/science/orthanc-postgresql/distinfo index c68e74661ed6..eb471a05a907 100644 --- a/science/orthanc-postgresql/distinfo +++ b/science/orthanc-postgresql/distinfo @@ -1,7 +1,7 @@ -TIMESTAMP = 1761533913 +TIMESTAMP = 1764254021 SHA256 (orthanc/OrthancPostgreSQL-9.0.tar.gz) = 92c3fde9c3baad343a4de7090759274a733ac28af06037538dbf70f0ee50cd75 SIZE (orthanc/OrthancPostgreSQL-9.0.tar.gz) = 790691 -SHA256 (orthanc/Orthanc-1.12.9.tar.gz) = 7a7cbc5f3663939fbef31ded021b36fcd52420337911ed43491bb663bcb5a4b2 -SIZE (orthanc/Orthanc-1.12.9.tar.gz) = 2165182 +SHA256 (orthanc/Orthanc-1.12.10.tar.gz) = b5d6934d123182fb2186cd54ef7f203be06b544afb03df67b0c64ad68d6c9286 +SIZE (orthanc/Orthanc-1.12.10.tar.gz) = 2192892 SHA256 (orthanc/e2fsprogs-1.44.5.tar.gz) = 2e211fae27ef74d5af4a4e40b10b8df7f87c655933bd171aab4889bfc4e6d1cc SIZE (orthanc/e2fsprogs-1.44.5.tar.gz) = 7619237 diff --git a/science/orthanc/Makefile b/science/orthanc/Makefile index 69612bbb386b..e2deb92f1cb0 100644 --- a/science/orthanc/Makefile +++ b/science/orthanc/Makefile @@ -1,5 +1,5 @@ PORTNAME= orthanc -DISTVERSION= 1.12.9 +DISTVERSION= ${ORTHANC_VER} # version.mk CATEGORIES= science MASTER_SITES= https://orthanc.uclouvain.be/downloads/sources/orthanc/ DISTNAME= Orthanc-${PORTVERSION} @@ -54,4 +54,5 @@ post-install: ${REINPLACE_CMD} -e 's|%%PREFIX%%|${PREFIX}|g' ${CMAKE_SOURCE_PATH}/Resources/Configuration.json ${CP} ${CMAKE_SOURCE_PATH}/Resources/Configuration.json ${STAGEDIR}${ETCDIR}/orthanc.json.sample +.include "${.CURDIR}/version.mk" .include <bsd.port.mk> diff --git a/science/orthanc/distinfo b/science/orthanc/distinfo index d57475212b4a..5c616e02b0d7 100644 --- a/science/orthanc/distinfo +++ b/science/orthanc/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1761178767 -SHA256 (Orthanc-1.12.9.tar.gz) = 7a7cbc5f3663939fbef31ded021b36fcd52420337911ed43491bb663bcb5a4b2 -SIZE (Orthanc-1.12.9.tar.gz) = 2165182 +TIMESTAMP = 1764250186 +SHA256 (Orthanc-1.12.10.tar.gz) = b5d6934d123182fb2186cd54ef7f203be06b544afb03df67b0c64ad68d6c9286 +SIZE (Orthanc-1.12.10.tar.gz) = 2192892 diff --git a/science/orthanc/pkg-plist b/science/orthanc/pkg-plist index 293f39bc83d4..0af2331e1a3e 100644 --- a/science/orthanc/pkg-plist +++ b/science/orthanc/pkg-plist @@ -12,6 +12,7 @@ bin/OrthancRecoverCompressedFile include/orthanc/OrthancCDatabasePlugin.h include/orthanc/OrthancCPlugin.h include/orthanc/OrthancDatabasePlugin.proto +include/orthanc/OrthancPluginCodeModel.json sbin/Orthanc %%DATADIR%%/plugins/libDelayedDeletion.so %%DATADIR%%/plugins/libDelayedDeletion.so.%%DISTVERSION%% diff --git a/science/orthanc/version.mk b/science/orthanc/version.mk new file mode 100644 index 000000000000..6069ba9b641c --- /dev/null +++ b/science/orthanc/version.mk @@ -0,0 +1 @@ +ORTHANC_VER= 1.12.10 diff --git a/science/packmol/Makefile b/science/packmol/Makefile index 5f2d5ae0c487..aa9368fabd48 100644 --- a/science/packmol/Makefile +++ b/science/packmol/Makefile @@ -1,6 +1,6 @@ PORTNAME= packmol DISTVERSIONPREFIX= v -DISTVERSION= 21.1.1 +DISTVERSION= 21.1.3 CATEGORIES= science MAINTAINER= eduardo@FreeBSD.org diff --git a/science/packmol/distinfo b/science/packmol/distinfo index a48cfe0d0a3d..04a34d95fab4 100644 --- a/science/packmol/distinfo +++ b/science/packmol/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1759409929 -SHA256 (m3g-packmol-v21.1.1_GH0.tar.gz) = 4bad785e6e1b91d8b80934eeebf91013e940c577693bbecd7ec56eb563f5d97f -SIZE (m3g-packmol-v21.1.1_GH0.tar.gz) = 634943 +TIMESTAMP = 1763590917 +SHA256 (m3g-packmol-v21.1.3_GH0.tar.gz) = 21a22e4e3f183e2c594c2e1d85cd7c16a95a8c609b36fc28d653f6c2c2d54c0c +SIZE (m3g-packmol-v21.1.3_GH0.tar.gz) = 637489 diff --git a/science/paraview/Makefile b/science/paraview/Makefile index 550b2e39fe73..d512d062c0a6 100644 --- a/science/paraview/Makefile +++ b/science/paraview/Makefile @@ -1,6 +1,6 @@ PORTNAME= paraview DISTVERSION= ${PARAVIEW_VER}.3 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= science graphics MASTER_SITES= http://www.paraview.org/files/v${PARAVIEW_VER}/ DISTNAME= ParaView-v${PORTVERSION} diff --git a/science/parthenon/Makefile b/science/parthenon/Makefile index 98f08b45d7b7..b09ecf9ad2ee 100644 --- a/science/parthenon/Makefile +++ b/science/parthenon/Makefile @@ -1,7 +1,7 @@ PORTNAME= parthenon DISTVERSIONPREFIX= v DISTVERSION= 24.08 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/polytope/Makefile b/science/polytope/Makefile index 983c12d09a54..51d29d283c38 100644 --- a/science/polytope/Makefile +++ b/science/polytope/Makefile @@ -1,6 +1,6 @@ PORTNAME= polytope -DISTVERSION= 0.7.3-18 -DISTVERSIONSUFFIX= -gcf83206 +DISTVERSION= 0.7.4 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -32,6 +32,6 @@ SILO_DESC= Use SILO reader/writer SILO_CMAKE_BOOL= USE_SILO SILO_LIB_DEPENDS= libsiloh5.so:science/silo -# tests as of 0.7.3-18: 96% tests passed, 1 tests failed out of 28 +# tests as of 0.7.4: 96% tests passed, 1 tests failed out of 28 .include <bsd.port.mk> diff --git a/science/polytope/distinfo b/science/polytope/distinfo index f53895c10660..f546123336ae 100644 --- a/science/polytope/distinfo +++ b/science/polytope/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1761847798 -SHA256 (LLNL-polytope-0.7.3-18-gcf83206_GH0.tar.gz) = 4800b6f16d33b9c909d7cd39f8507d75584abd93ffab86ad38170e8c41572839 -SIZE (LLNL-polytope-0.7.3-18-gcf83206_GH0.tar.gz) = 6854889 +TIMESTAMP = 1762944488 +SHA256 (LLNL-polytope-0.7.4_GH0.tar.gz) = a1901b0feaf3c4d3660766e8a6c325c0fe1fcaeb236b5ae95c8d139c386147c8 +SIZE (LLNL-polytope-0.7.4_GH0.tar.gz) = 6854579 diff --git a/science/py-hoomd-blue/Makefile b/science/py-hoomd-blue/Makefile index ae4a5b71af2e..5fb3d5f92d35 100644 --- a/science/py-hoomd-blue/Makefile +++ b/science/py-hoomd-blue/Makefile @@ -1,6 +1,6 @@ PORTNAME= hoomd-blue DISTVERSIONPREFIX= v -DISTVERSION= 5.1.0 +DISTVERSION= 6.0.0 CATEGORIES= science # physics PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -20,14 +20,14 @@ USE_GITHUB= yes GH_ACCOUNT= glotzerlab GH_TUPLE= glotzerlab:upp11:0c1fb8dfb4bcdc1c5c4eff9165539b15e70c4360:glotzerlab_upp11/hoomd/extern/upp11 \ - glotzerlab:nano-signal-slot:34223a4a7e97f8e114ef007e5360cf7a71265da3:glotzerlab_nano_signal_slot/hoomd/extern/nano-signal-slot \ + glotzerlab:nano-signal-slot:8d13689:glotzerlab_nano_signal_slot/hoomd/extern/nano-signal-slot \ glotzerlab:quickhull:1ffbc6f884ea1da89e104a5996cf8a726db673d5:glotzerlab_quickhull/hoomd/extern/quickhull \ - glotzerlab:HIP:d211f99eebb3637b6840f310f8797abb25012c18:glotzerlab_HIP/hoomd/extern/HIP \ - glotzerlab:hipCUB:c70e19332a8402049b3359b409e50220a759c42d:glotzerlab_hipCUB/hoomd/extern/hipCUB \ + glotzerlab:HIP:db753e4:glotzerlab_HIP/hoomd/extern/HIP \ + glotzerlab:hipCUB:64d8adf:glotzerlab_hipCUB/hoomd/extern/hipCUB \ mphowardlab:neighbor:ba0f06869b766066a7068852fa3b8c5fa746f71f:mphowardlab_neighbor/hoomd/extern/neighbor \ - mphowardlab:hipper:b6da049a516ada03e4e1b66ca6b4c2c7c9668595:mphowardlab_hipper/hoomd/extern/hipper \ + mphowardlab:hipper:076059b:mphowardlab_hipper/hoomd/extern/hipper \ glotzerlab:hoomd-examples:94a5b52d159bc7c07e2650e31b429cef55384542:glotzerlab_hoomd_examples/sphinx-doc/tutorial \ - glotzerlab:OpenRAND:92dc12a23dff2d0aa3545f749d1c013677b9a87e:glotzerlab_OpenRAND/hoomd/extern/OpenRAND \ + glotzerlab:OpenRAND:92dc12a:glotzerlab_OpenRAND/hoomd/extern/OpenRAND \ mphowardlab:hipper:b6da049a516ada03e4e1b66ca6b4c2c7c9668595:mphowardlab_hipper/hoomd/extern/hipper SHEBANG_GLOB= *.sh @@ -58,7 +58,10 @@ TBB_DESC= Enable support for Threading Building Blocks (TBB) TBB_CMAKE_BOOL= ENABLE_TBB TBB_LIB_DEPENDS= libtbb.so:devel/onetbb -# the test mpi-test_communication requires excessive resources, see https://github.com/glotzerlab/hoomd-blue/issues/1396 +# tests as of 6.0.0: 97% tests passed, 2 tests failed out of 67 +# The following tests FAILED: +# 18 - mpi-test_load_balancer (Failed) +# 35 - mpi-test_communication (Failed) .include <bsd.port.pre.mk> diff --git a/science/py-hoomd-blue/distinfo b/science/py-hoomd-blue/distinfo index 3348d53d200c..6931b40814ac 100644 --- a/science/py-hoomd-blue/distinfo +++ b/science/py-hoomd-blue/distinfo @@ -1,21 +1,21 @@ -TIMESTAMP = 1740212206 -SHA256 (glotzerlab-hoomd-blue-v5.1.0_GH0.tar.gz) = 292d0297c41eeeaf7b7933bffd9dcd1469ca0c009929a257dac396ecd2bad899 -SIZE (glotzerlab-hoomd-blue-v5.1.0_GH0.tar.gz) = 2780980 +TIMESTAMP = 1763921144 +SHA256 (glotzerlab-hoomd-blue-v6.0.0_GH0.tar.gz) = 10e0c681dbd4195aeba66f6873e273b7859e61e647523d2fb2c1fcd1e635b696 +SIZE (glotzerlab-hoomd-blue-v6.0.0_GH0.tar.gz) = 2789144 SHA256 (glotzerlab-upp11-0c1fb8dfb4bcdc1c5c4eff9165539b15e70c4360_GH0.tar.gz) = 759695139bddae1d8a7cd52c967b856d6debf28fb37ea177f78c4434e2b210a8 SIZE (glotzerlab-upp11-0c1fb8dfb4bcdc1c5c4eff9165539b15e70c4360_GH0.tar.gz) = 21058 -SHA256 (glotzerlab-nano-signal-slot-34223a4a7e97f8e114ef007e5360cf7a71265da3_GH0.tar.gz) = d15030482c82d9e4a99c2f67d8ef23b33cc318dd48ac0f8e804c6d4750f27ff4 -SIZE (glotzerlab-nano-signal-slot-34223a4a7e97f8e114ef007e5360cf7a71265da3_GH0.tar.gz) = 4748 +SHA256 (glotzerlab-nano-signal-slot-8d13689_GH0.tar.gz) = 1f29012e0c211fe5c25714fbec858b8f29c3070b75bac893332b65ed46e3cfaa +SIZE (glotzerlab-nano-signal-slot-8d13689_GH0.tar.gz) = 4752 SHA256 (glotzerlab-quickhull-1ffbc6f884ea1da89e104a5996cf8a726db673d5_GH0.tar.gz) = 55c87e78bf990509ff35e3e039213ca6e3890ce988c2891647d65079696ae3a9 SIZE (glotzerlab-quickhull-1ffbc6f884ea1da89e104a5996cf8a726db673d5_GH0.tar.gz) = 16242 -SHA256 (glotzerlab-HIP-d211f99eebb3637b6840f310f8797abb25012c18_GH0.tar.gz) = badcb27eb7d540a668877dd193aba529755d5f69c8e6411ee495668984640e5c -SIZE (glotzerlab-HIP-d211f99eebb3637b6840f310f8797abb25012c18_GH0.tar.gz) = 898870 -SHA256 (glotzerlab-hipCUB-c70e19332a8402049b3359b409e50220a759c42d_GH0.tar.gz) = f3dbd921ea8c5fe9068d6d9e6e9112c11c7e18488169ce48423d9fdb014536c6 -SIZE (glotzerlab-hipCUB-c70e19332a8402049b3359b409e50220a759c42d_GH0.tar.gz) = 110500 +SHA256 (glotzerlab-HIP-db753e4_GH0.tar.gz) = a9cfe87ef06019891506e633d9ac0b8f52414ac1e5e4342d061963cbecdd1d7c +SIZE (glotzerlab-HIP-db753e4_GH0.tar.gz) = 897698 +SHA256 (glotzerlab-hipCUB-64d8adf_GH0.tar.gz) = 0709bc19af69bfed5c711833138bdede78e4e162e3462c7a60985f1555e0d155 +SIZE (glotzerlab-hipCUB-64d8adf_GH0.tar.gz) = 110322 SHA256 (mphowardlab-neighbor-ba0f06869b766066a7068852fa3b8c5fa746f71f_GH0.tar.gz) = 089129a1539d8e993f725017f1aadc60f9e40116e8a65dfbe70b0df9ac2d7cf3 SIZE (mphowardlab-neighbor-ba0f06869b766066a7068852fa3b8c5fa746f71f_GH0.tar.gz) = 49039 SHA256 (mphowardlab-hipper-b6da049a516ada03e4e1b66ca6b4c2c7c9668595_GH0.tar.gz) = c64a484884eaab3eb9fd8f7b27b144a7bfadfeab101e95d82bc2a6f7e4fb7cec SIZE (mphowardlab-hipper-b6da049a516ada03e4e1b66ca6b4c2c7c9668595_GH0.tar.gz) = 20228 SHA256 (glotzerlab-hoomd-examples-94a5b52d159bc7c07e2650e31b429cef55384542_GH0.tar.gz) = f685da65a32566036476a33740b45884bce58798e857d53689d3da20e928436c SIZE (glotzerlab-hoomd-examples-94a5b52d159bc7c07e2650e31b429cef55384542_GH0.tar.gz) = 5969001 -SHA256 (glotzerlab-OpenRAND-92dc12a23dff2d0aa3545f749d1c013677b9a87e_GH0.tar.gz) = a84657d9ac24083c1aef3d883927d5993270697af69a04f616227f9077eb8e19 -SIZE (glotzerlab-OpenRAND-92dc12a23dff2d0aa3545f749d1c013677b9a87e_GH0.tar.gz) = 298040 +SHA256 (glotzerlab-OpenRAND-92dc12a_GH0.tar.gz) = f760eefd9027ee69a5976954a539a28b9ceb581ba089014cec56f6e72c0f6a7d +SIZE (glotzerlab-OpenRAND-92dc12a_GH0.tar.gz) = 298000 diff --git a/science/py-hoomd-blue/files/patch-hoomd_extern_nano-signal-slot_nano__signal__slot.hpp b/science/py-hoomd-blue/files/patch-hoomd_extern_nano-signal-slot_nano__signal__slot.hpp deleted file mode 100644 index cd3fce241f6d..000000000000 --- a/science/py-hoomd-blue/files/patch-hoomd_extern_nano-signal-slot_nano__signal__slot.hpp +++ /dev/null @@ -1,30 +0,0 @@ -Fix build with LLVM 19 - -/wrkdirs/usr/ports/science/py-hoomd-blue/work/hoomd-blue-4.9.0/hoomd/extern/nano-signal-slot/nano_signal_slot.hpp:46:45: -error: a template argument list is expected after a name prefixed by the template keyword [-Wmissing-template-arg-list-after-template-kw] - 46 | Observer::insert(Delegate::template bind (instance), this); - | ^ -/wrkdirs/usr/ports/science/py-hoomd-blue/work/hoomd-blue-4.9.0/hoomd/extern/nano-signal-slot/nano_signal_slot.hpp:87:45: -error: a template argument list is expected after a name prefixed by the template keyword [-Wmissing-template-arg-list-after-template-kw] - 87 | Observer::remove(Delegate::template bind (instance), this); - ---- hoomd/extern/nano-signal-slot/nano_signal_slot.hpp.orig 2016-07-13 20:06:52 UTC -+++ hoomd/extern/nano-signal-slot/nano_signal_slot.hpp -@@ -43,7 +43,7 @@ class Signal<RT(Args...)> : private Observer - template <typename L> - void connect(L* instance) - { -- Observer::insert(Delegate::template bind (instance), this); -+ Observer::insert(Delegate::bind (instance), this); - } - template <typename L> - void connect(L& instance) -@@ -84,7 +84,7 @@ class Signal<RT(Args...)> : private Observer - template <typename L> - void disconnect(L* instance) - { -- Observer::remove(Delegate::template bind (instance), this); -+ Observer::remove(Delegate::bind (instance), this); - } - template <typename L> - void disconnect(L& instance) diff --git a/science/py-hoomd-blue/pkg-plist b/science/py-hoomd-blue/pkg-plist index 004601c86f0c..6f2f97246186 100644 --- a/science/py-hoomd-blue/pkg-plist +++ b/science/py-hoomd-blue/pkg-plist @@ -57,6 +57,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/pair.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/step.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/union.py +%%PYTHON_SITELIBDIR%%/hoomd/hpmc/pair/zetterling.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/conftest.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_boxmc.py @@ -77,6 +78,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_opp.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_step.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_union.py +%%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_pair_zetterling.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_quick_compress.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_scale.py %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_shape.py @@ -315,7 +317,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/dfft_cuda.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/dfft_cuda.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/dfft_host.h -%%NO_NOMPI%%%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/dfft_lib_config.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/dfft_lib_config.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/dfft_local_fft_config.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/dfftlib/src/mkl_single_interface.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/extern/gsd.h @@ -461,6 +463,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/PairPotentialOPP.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/PairPotentialStep.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/PairPotentialUnion.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/PairPotentialZetterling.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/ShapeConvexPolygon.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/ShapeConvexPolyhedron.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/ShapeEllipsoid.h @@ -517,9 +520,11 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ComputeThermoHMATypes.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ComputeThermoTypes.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ConstantForceCompute.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ConstantForceComputeGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ConstantForceComputeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/CosineSqAngleForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/CosineSqAngleForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/CosineSqAngleForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/CustomForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorBondFENE.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorBondHarmonic.h @@ -539,6 +544,8 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairExpandedMie.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairForceShiftedLJ.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairFourier.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairFrictionLJBase.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairFrictionLJVariants.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairGB.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairGauss.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairLJ.h @@ -552,25 +559,37 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairTWF.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairTable.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairWangFrenkel.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairYLZ.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairYukawa.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairZBL.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairZetterling.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorSpecialPairCoulomb.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorSpecialPairLJ.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorTersoff.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorWalls.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/FIREEnergyMinimizer.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/FIREEnergyMinimizerGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/FIREEnergyMinimizerGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ForceComposite.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ForceCompositeGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ForceCompositeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ForceDistanceConstraint.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ForceDistanceConstraintGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ForceDistanceConstraintGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/FrictionPair.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/FrictionPairGPU.cuh +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/FrictionPairGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicAngleForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicAngleForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicAngleForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicDihedralForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicDihedralForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicDihedralForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicImproperForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicImproperForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HarmonicImproperForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HelfrichMeshForceCompute.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HelfrichMeshForceComputeGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/HelfrichMeshForceComputeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/IntegrationMethodTwoStep.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/IntegratorTwoStep.h @@ -581,28 +600,37 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ManifoldSphere.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ManifoldXYPlane.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ManifoldZCylinder.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MeshDynamicBondUpdater.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MeshForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MolecularForceCompute.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MolecularForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MuellerPlatheFlow.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MuellerPlatheFlowEnum.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MuellerPlatheFlowGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/MuellerPlatheFlowGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborList.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListBinned.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPUBinned.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPUStencil.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPUStencil.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPUTree.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListGPUTree.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListStencil.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/NeighborListTree.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/OPLSDihedralForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/OPLSDihedralForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/OPLSDihedralForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PPPMForceCompute.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PPPMForceComputeGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PPPMForceComputeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PairModulator.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PatchEnvelope.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PeriodicImproper.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PeriodicImproperForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PeriodicImproperForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PeriodicImproperForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialBond.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialBondGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialBondGPU.h @@ -623,6 +651,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialTersoffGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TableAngleForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TableAngleForceComputeGPU.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TableAngleForceGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TableDihedralForceCompute.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TableDihedralForceComputeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TriangleAreaConservationMeshForceCompute.h @@ -632,10 +661,14 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepBD.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepBDGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepConstantPressure.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepConstantPressureGPU.cuh +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepConstantPressureGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepConstantVolume.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepConstantVolumeGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepConstantVolumeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepLangevin.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepLangevinBase.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepLangevinGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepLangevinGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepNVTAlchemy.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepRATTLEBD.h @@ -648,6 +681,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepRATTLENVEGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepRATTLENVEGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/VolumeConservationMeshForceCompute.h +%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/VolumeConservationMeshForceComputeGPU.cuh %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/VolumeConservationMeshForceComputeGPU.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/VolumeConservationMeshParameters.h %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/WallData.h @@ -728,6 +762,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/md/nlist.py %%PYTHON_SITELIBDIR%%/hoomd/md/pair/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/md/pair/aniso.py +%%PYTHON_SITELIBDIR%%/hoomd/md/pair/friction.py %%PYTHON_SITELIBDIR%%/hoomd/md/pair/pair.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/__init__.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/aniso_forces_and_energies.json @@ -756,6 +791,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_kernel_parameters.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_manifolds.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_meshpotential.py +%%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_meshupdater.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_meta_wall_list.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_methods.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_minimize_fire.py @@ -773,6 +809,7 @@ lib/cmake/hoomd/hoomd-targets.cmake %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_update_group_dof.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_wall_data.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_wall_potential.py +%%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_ylz.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_zero_momentum.py %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/true_pair_list.json %%PYTHON_SITELIBDIR%%/hoomd/md/special_pair.py diff --git a/science/py-mne/Makefile b/science/py-mne/Makefile index 3f15411d9c98..bf89de5d9db3 100644 --- a/science/py-mne/Makefile +++ b/science/py-mne/Makefile @@ -1,5 +1,5 @@ PORTNAME= mne -PORTVERSION= 1.10.1 +PORTVERSION= 1.11.0 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -10,14 +10,13 @@ WWW= https://mne.tools/stable/ \ https://github.com/mne-tools/mne-python LICENSE= BSD3CLAUSE -LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}hatchling>0:devel/py-hatchling@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}hatch-vcs>0:devel/py-hatch-vcs@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}decorator>0:devel/py-decorator@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Jinja2>0:devel/py-Jinja2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}lazy_loader>=0.3:devel/py-lazy_loader@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.7:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.8:math/py-matplotlib@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}packaging>0:devel/py-packaging@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pooch>=1.5:devel/py-pooch@${PY_FLAVOR} \ diff --git a/science/py-mne/distinfo b/science/py-mne/distinfo index f63a12725683..c24c3f5eff30 100644 --- a/science/py-mne/distinfo +++ b/science/py-mne/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1759525649 -SHA256 (mne-1.10.1.tar.gz) = a93e3d772d551e43ec5ddcd3495fffe0f98e3e384045bcd96497636e86a32a0b -SIZE (mne-1.10.1.tar.gz) = 7123187 +TIMESTAMP = 1763923010 +SHA256 (mne-1.11.0.tar.gz) = 0a89b8fc44133b81218a35cdcba74ad0f8ae2e265136249b365b9ce04864c688 +SIZE (mne-1.11.0.tar.gz) = 7152794 diff --git a/science/py-qiskit/Makefile b/science/py-qiskit/Makefile index 579d27ae333b..26690ce9ba2e 100644 --- a/science/py-qiskit/Makefile +++ b/science/py-qiskit/Makefile @@ -1,5 +1,6 @@ PORTNAME= qiskit DISTVERSION= 2.2.1 +PORTREVISION= 1 CATEGORIES= science python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-segregation/Makefile b/science/py-segregation/Makefile index 88bd0223be01..45c0e6a206cf 100644 --- a/science/py-segregation/Makefile +++ b/science/py-segregation/Makefile @@ -1,6 +1,5 @@ PORTNAME= segregation -PORTVERSION= 2.5 -PORTREVISION= 2 +PORTVERSION= 2.5.2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/py-segregation/distinfo b/science/py-segregation/distinfo index 15fdc5337c67..562ab0b0feab 100644 --- a/science/py-segregation/distinfo +++ b/science/py-segregation/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1722711247 -SHA256 (segregation-2.5.tar.gz) = 0329668682fe3e7c114ebe586619d7702af05d978b124efda0a5fce08b4afe8d -SIZE (segregation-2.5.tar.gz) = 15929712 +TIMESTAMP = 1748831254 +SHA256 (segregation-2.5.2.tar.gz) = e2a2e580818032f7924b871ee43257cfc684572305df3a9f27ff6e1d647643c6 +SIZE (segregation-2.5.2.tar.gz) = 15930587 diff --git a/science/quantum-espresso/Makefile b/science/quantum-espresso/Makefile index 9557826c3c85..90d7bb73b6ca 100644 --- a/science/quantum-espresso/Makefile +++ b/science/quantum-espresso/Makefile @@ -1,7 +1,6 @@ PORTNAME= quantum-espresso DISTVERSIONPREFIX= qe- -DISTVERSION= 7.4 -PORTREVISION= 1 +DISTVERSION= 7.5 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -13,24 +12,26 @@ WWW= https://www.quantum-espresso.org \ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/License -BROKEN_aarch64= compilation fails: cannot find an intrinsic module named 'ieee_arithmetic', see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=278942 -BROKEN_armv6= fails to build: gfortran8: error: iotk_base_tmp.f90: No such file or directory -BROKEN_armv7= fails to build: gfortran8: error: iotk_base_tmp.f90: No such file or directory +ONLY_FOR_ARCHS= amd64 i386 +ONLY_FOR_ARCHS_REASON= requires the intrinsic module 'ieee_arithmetic' which is not available on other architectures +#BROKEN_aarch64= compilation fails: cannot find an intrinsic module named 'ieee_arithmetic', see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=278942 +#BROKEN_armv6= fails to build: gfortran8: error: iotk_base_tmp.f90: No such file or directory +#BROKEN_armv7= fails to build: gfortran8: error: iotk_base_tmp.f90: No such file or directory -BUILD_DEPENDS= fox-xml>0:textproc/fox-xml \ +#BUILD_DEPENDS= fox-xml>0:textproc/fox-xml \ bash:shells/bash LIB_DEPENDS= libblas.so:math/blas \ libfftw3.so:math/fftw3 \ liblapack.so:math/lapack \ libopenblas.so:math/openblas -USES= cmake fortran python shebangfix +USES= cmake fortran localbase:ldflags python shebangfix GNU_CONFIGURE= yes USE_GITHUB= yes GH_ACCOUNT= QEF GH_PROJECT= q-e -GH_TUPLE= anharmonic:d3q:de47183:anharmonic_d3q/external/d3q \ +GH_TUPLE= anharmonic:d3q:6e5f978:anharmonic_d3q/external/d3q \ pietrodelugas:fox:3453648e6837658b747b895bb7bef4b1ed2eac40:pietrodelugas_fox/external/fox \ Reference-LAPACK:lapack:12d825396fcef1e0a1b27be9f119f9e554621e55:Reference_LAPACK_lapack/external/lapack \ libmbd:libmbd:89a3cc1:libmbd_libmbd/external/mbd \ @@ -57,7 +58,7 @@ OPTIONS_DEFAULT= OPENMPI MPICH_USES= mpi:mpich -OPENMPI_USES= mpi:openmpi +OPENMPI_USES= mpi:mpich # SEGV with openmpi4 .include <bsd.port.pre.mk> @@ -80,13 +81,18 @@ post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.x do-test: - @cd ${WRKSRC}/test-suite && ${GMAKE} run-tests + @cd ${WRKSRC}/test-suite && \ + ${GMAKE} ESPRESSO_BUILD=${BUILD_WRKSRC} ESPRESSO_PSEUDO=${WRKSRC}/pseudo run-tests run-examples: build .for c in PP PW PWCOND PHonon - @cd ${WRKSRC}/$c/examples && PREFIX=${STAGEDIR}${PREFIX} ./run_all_examples + @cd ${WRKSRC}/$c/examples && PREFIX=${STAGEDIR}${PREFIX} PSEUDO_DIR=/usr/local/share/quantum-espresso ./run_all_examples .endfor -# all tests fail, possibly due to wrong pseudo-potentials, see https://gitlab.com/QEF/q-e/-/issues/745 +# tests as of QE 7.5: 243 out of 247 tests passed (5 skipped, 4 unknown) + +# many pseudopotentials that can be used with QE are listed in https://pseudopotentials.quantum-espresso.org/ +# QE became so popular that many other parties develop and distribute pseudopotentials compatible with QE +# ESPRESSO_PSEUDO is an env variable that can be set to point to a directory with pseudopotentials .include <bsd.port.post.mk> diff --git a/science/quantum-espresso/distinfo b/science/quantum-espresso/distinfo index 835b6e262ce3..bbe9a16b0148 100644 --- a/science/quantum-espresso/distinfo +++ b/science/quantum-espresso/distinfo @@ -1,8 +1,8 @@ -TIMESTAMP = 1737938704 -SHA256 (QEF-q-e-qe-7.4_GH0.tar.gz) = b15dcfe25f4fbf15ccd34c1194021e90996393478226e601d876f7dea481d104 -SIZE (QEF-q-e-qe-7.4_GH0.tar.gz) = 71424988 -SHA256 (anharmonic-d3q-de47183_GH0.tar.gz) = 36477748aa9a445d465974e7ba8e3e2e09c9fac7b2114c24cc768fa72510e807 -SIZE (anharmonic-d3q-de47183_GH0.tar.gz) = 24080083 +TIMESTAMP = 1762823217 +SHA256 (QEF-q-e-qe-7.5_GH0.tar.gz) = 7e1f7a9a21b63192f5135218bee20a5321b66582e4756536681b76e9c59b3cc8 +SIZE (QEF-q-e-qe-7.5_GH0.tar.gz) = 72479566 +SHA256 (anharmonic-d3q-6e5f978_GH0.tar.gz) = f49158ed25709e82fcd793f9f56a1534b1130833937ec9e2236b7670b8d6eda6 +SIZE (anharmonic-d3q-6e5f978_GH0.tar.gz) = 24095924 SHA256 (pietrodelugas-fox-3453648e6837658b747b895bb7bef4b1ed2eac40_GH0.tar.gz) = 107b1d58eb6a0a730c98520a8f99a6459b2a0e06b06f4b037abf358b29d50df1 SIZE (pietrodelugas-fox-3453648e6837658b747b895bb7bef4b1ed2eac40_GH0.tar.gz) = 988789 SHA256 (Reference-LAPACK-lapack-12d825396fcef1e0a1b27be9f119f9e554621e55_GH0.tar.gz) = 2ae8b6eb09e9c1d3b5d66bb778a5a5119af13575bb7fd8016f5cabb319253257 diff --git a/science/quantum-espresso/files/patch-CMakeLists.txt b/science/quantum-espresso/files/patch-CMakeLists.txt index d315d0c9420b..40e483c19d13 100644 --- a/science/quantum-espresso/files/patch-CMakeLists.txt +++ b/science/quantum-espresso/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2024-03-16 03:53:23 UTC +--- CMakeLists.txt.orig 2025-08-19 09:57:12 UTC +++ CMakeLists.txt -@@ -395,14 +395,14 @@ endif(QE_ENABLE_MPI) +@@ -415,14 +415,14 @@ endif(QE_ENABLE_MPI) ########################################################### # Git ########################################################### diff --git a/science/quantum-espresso/files/patch-environment__variables b/science/quantum-espresso/files/patch-environment__variables index afa3ad0d0e6d..e241b507051a 100644 --- a/science/quantum-espresso/files/patch-environment__variables +++ b/science/quantum-espresso/files/patch-environment__variables @@ -1,4 +1,4 @@ ---- environment_variables.orig 2024-02-29 10:18:05 UTC +--- environment_variables.orig 2025-08-19 09:57:12 UTC +++ environment_variables @@ -66,12 +66,16 @@ # For this reason, a plain "diff" of your results against the reference @@ -12,7 +12,7 @@ # $PREFIX is the root of the Quantum ESPRESSO source tree. BIN_DIR=$PREFIX/bin -PSEUDO_DIR=$PREFIX/pseudo -+PSEUDO_DIR=$PREFIX/share/quantum-espresso/pseudo ++PSEUDO_DIR=$PREFIX/share/quantum-espresso +ESPRESSO_PSEUDO=/tmp # Beware: everything in $TMP_DIR will be destroyed ! -TMP_DIR=$PREFIX/tempdir diff --git a/science/quantum-espresso/pkg-plist b/science/quantum-espresso/pkg-plist index 00abbc0f54cb..8842a50352e7 100644 --- a/science/quantum-espresso/pkg-plist +++ b/science/quantum-espresso/pkg-plist @@ -53,11 +53,13 @@ bin/merge_wann.x bin/molecularnexafs.x bin/molecularpdos.x bin/neb.x +bin/nscf2supercond.x bin/open_grid.x bin/path_interpolation.x bin/pawplot.x bin/ph.x bin/phcg.x +bin/pioud.x bin/plan_avg.x bin/plotband.x bin/plotproj.x @@ -126,8 +128,8 @@ include/qe/qe_atomic/kli.mod include/qe/qe_atomic/ld1_parameters.mod include/qe/qe_atomic/ld1inc.mod include/qe/qe_atomic/paw_type.mod +include/qe/qe_couple/libqecouple.h include/qe/qe_cpv/betax.mod -include/qe/qe_cpv/cell_nose.mod include/qe/qe_cpv/cg_module.mod include/qe/qe_cpv/cg_sub.mod include/qe/qe_cpv/core.mod @@ -136,6 +138,7 @@ include/qe/qe_cpv/cp_electronic_mass.mod include/qe/qe_cpv/cp_interfaces.mod include/qe/qe_cpv/cp_main_variables.mod include/qe/qe_cpv/cp_restart_new.mod +include/qe/qe_cpv/cp_wavefunctions.mod include/qe/qe_cpv/dener.mod include/qe/qe_cpv/efcalc.mod include/qe/qe_cpv/efield_module.mod @@ -147,7 +150,6 @@ include/qe/qe_cpv/ensemble_dft.mod include/qe/qe_cpv/environ_cp_module.mod include/qe/qe_cpv/exx_module.mod include/qe/qe_cpv/input.mod -include/qe/qe_cpv/ions_nose.mod include/qe/qe_cpv/ions_positions.mod include/qe/qe_cpv/kohn_sham_states.mod include/qe/qe_cpv/ldau_cp.mod @@ -196,6 +198,8 @@ include/qe/qe_epw/cumulant.mod include/qe/qe_epw/dvqpsi.mod include/qe/qe_epw/ep_coarse.mod include/qe/qe_epw/ep_constants.mod +include/qe/qe_epw/exphonon.mod +include/qe/qe_epw/expolaron.mod include/qe/qe_epw/global_var.mod include/qe/qe_epw/ifconstants.mod include/qe/qe_epw/indabs.mod @@ -212,6 +216,7 @@ include/qe/qe_epw/kfold.mod include/qe/qe_epw/longrange.mod include/qe/qe_epw/low_lvl.mod include/qe/qe_epw/parallelism.mod +include/qe/qe_epw/phph.mod include/qe/qe_epw/polaron.mod include/qe/qe_epw/printing.mod include/qe/qe_epw/pw2wan.mod @@ -227,7 +232,13 @@ include/qe/qe_epw/supercond_common.mod include/qe/qe_epw/supercond_coul.mod include/qe/qe_epw/supercond_driver.mod include/qe/qe_epw/supercond_iso.mod +include/qe/qe_epw/supercond_vertex.mod include/qe/qe_epw/symmetry.mod +include/qe/qe_epw/tdbe_common.mod +include/qe/qe_epw/tdbe_driver.mod +include/qe/qe_epw/tdbe_eph_common.mod +include/qe/qe_epw/tdbe_mod.mod +include/qe/qe_epw/tdbe_phph_common.mod include/qe/qe_epw/transport.mod include/qe/qe_epw/transport_legacy.mod include/qe/qe_epw/transport_mag.mod @@ -342,6 +353,7 @@ include/qe/qe_modules/bfgs_module.mod include/qe/qe_modules/bspline.mod include/qe/qe_modules/bz_form.mod include/qe/qe_modules/cell_base.mod +include/qe/qe_modules/cell_nose.mod include/qe/qe_modules/check_stop.mod include/qe/qe_modules/command_line_options.mod include/qe/qe_modules/constants.mod @@ -373,6 +385,7 @@ include/qe/qe_modules/io_files.mod include/qe/qe_modules/io_global.mod include/qe/qe_modules/io_rism_xml.mod include/qe/qe_modules/ions_base.mod +include/qe/qe_modules/ions_nose.mod include/qe/qe_modules/kinds.mod include/qe/qe_modules/lauefft.mod include/qe/qe_modules/libmbd_interface.mod @@ -470,6 +483,7 @@ include/qe/qe_phonon_ph/cryst_ph.mod include/qe/qe_phonon_ph/d2nsq_bare_module.mod include/qe/qe_phonon_ph/dfile_autoname.mod include/qe/qe_phonon_ph/dfile_star.mod +include/qe/qe_phonon_ph/dfpt_kernels.mod include/qe/qe_phonon_ph/dielectric.mod include/qe/qe_phonon_ph/diffs.mod include/qe/qe_phonon_ph/disp.mod @@ -502,7 +516,6 @@ include/qe/qe_phonon_ph/ramanm.mod include/qe/qe_phonon_ph/recover_mod.mod include/qe/qe_phonon_ph/rigid.mod include/qe/qe_phonon_ph/save_ph.mod -include/qe/qe_phonon_ph/sym_def_module.mod include/qe/qe_phonon_ph/symmetry.mod include/qe/qe_phonon_ph/term_one_1_module.mod include/qe/qe_phonon_ph/term_one_module.mod @@ -511,6 +524,16 @@ include/qe/qe_phonon_ph/term_three_module.mod include/qe/qe_phonon_ph/units_ph.mod include/qe/qe_phonon_ph/write_hub.mod include/qe/qe_phonon_ph/yambo.mod +include/qe/qe_pioud/fcp_opt_routines.mod +include/qe/qe_pioud/fcp_variables.mod +include/qe/qe_pioud/pimd_variables.mod +include/qe/qe_pioud/random_pioud.mod +include/qe/qe_pioud/ring_formats.mod +include/qe/qe_pioud/ring_input_parameters_module.mod +include/qe/qe_pioud/ring_io_units_module.mod +include/qe/qe_pioud/ring_variables.mod +include/qe/qe_pioud/trpmd_base.mod +include/qe/qe_pioud/trpmd_io_routines.mod include/qe/qe_pp/adduscore.mod include/qe/qe_pp/atproj.mod include/qe/qe_pp/chdens_module.mod @@ -543,7 +566,6 @@ include/qe/qe_pw/cellmd.mod include/qe/qe_pw/coul_cut_2d.mod include/qe/qe_pw/d3hess_mod.mod include/qe/qe_pw/dfunct.mod -include/qe/qe_pw/dfunct_gpum.mod include/qe/qe_pw/dynamics_module.mod include/qe/qe_pw/ener.mod include/qe/qe_pw/environ_pw_module.mod @@ -565,7 +587,6 @@ include/qe/qe_pw/fcp_relaxation.mod include/qe/qe_pw/fixed_occ.mod include/qe/qe_pw/force_mod.mod include/qe/qe_pw/g_psi_mod.mod -include/qe/qe_pw/g_psi_mod_gpum.mod include/qe/qe_pw/gcscf_module.mod include/qe/qe_pw/io_rho_xml.mod include/qe/qe_pw/klist.mod @@ -615,7 +636,6 @@ include/qe/qe_pwcond_exe/scattnl_cond.mod include/qe/qe_tddfpt/charg_resp.mod include/qe/qe_tddfpt/environ_td_module.mod include/qe/qe_tddfpt/linear_solvers.mod -include/qe/qe_tddfpt/lr_dav_debug.mod include/qe/qe_tddfpt/lr_dav_routines.mod include/qe/qe_tddfpt/lr_dav_variables.mod include/qe/qe_tddfpt/lr_exx_kernel.mod @@ -759,7 +779,6 @@ lib/libqe_kssolver_davidson.a lib/libqe_kssolver_davidsonrci.a lib/libqe_kssolver_dense.a lib/libqe_kssolver_paro.a -lib/libqe_kssolver_ppcg.a lib/libqe_kssolver_rmmdiis.a lib/libqe_lax.a lib/libqe_libbeef.a @@ -771,6 +790,7 @@ lib/libqe_phonon_fd.a lib/libqe_phonon_gamma.a lib/libqe_phonon_ph.a lib/libqe_phonon_phaux.a +lib/libqe_pioud.a lib/libqe_pp.a lib/libqe_pw.a lib/libqe_tddfpt.a @@ -1065,6 +1085,5 @@ share/GUI/QE-modes/qe-modes/qe-funcs.el share/GUI/QE-modes/qe-modes/qe-mode.el share/GUI/QE-modes/qe-modes/qe-modes.el share/GUI/README -@dir include/qe/qe_couple @dir include/qe/qe_device_lapack @dir include/qe/qe_qeheat_exe diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile index 9b740c002de8..f02115771af1 100644 --- a/science/rdkit/Makefile +++ b/science/rdkit/Makefile @@ -1,6 +1,6 @@ PORTNAME= rdkit DISTVERSIONPREFIX= Release_ -DISTVERSION= 2025_09_1 +DISTVERSION= 2025_09_2 CATEGORIES= science MASTER_SITES= https://github.com/schrodinger/maeparser/archive/:maeparser \ https://github.com/schrodinger/coordgenlibs/archive/:coordgen \ @@ -41,7 +41,7 @@ GH_TUPLE+= ncbi:pubchem-align3d:daefab3:align3d/External/pubchem_shape/pubchem-a MAEPARSER_VERSION= 1.3.3 COORDGEN_VERSION= 3.0.2 -CHEMDRAW_VERSION= 1.0.10 +CHEMDRAW_VERSION= 1.0.11 RAPIDJSON_VERSION= 1.1.0 CMAKE_ON= RDK_BUILD_CAIRO_SUPPORT @@ -121,10 +121,14 @@ pre-build: -e 's|const SizeType length;|SizeType length;|g' \ ${WRKSRC}/External/rapidjson/rapidjson-1.1.0/include/rapidjson/document.h +post-install: + @${RM} -f ${STAGEDIR}${PREFIX}/lib/libexpat.a + post-install-PGSQL-on: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/postgresql/rdkit.so # many tests fail, see https://github.com/rdkit/rdkit/issues/7779 # tests as of 2025_09_1: 65% tests passed, 24 tests failed out of 68 +# tests as of 2025_09_2: 63% tests passed, 26 tests failed out of 70 .include <bsd.port.mk> diff --git a/science/rdkit/distinfo b/science/rdkit/distinfo index e84d47fcbb7e..2dd40d607202 100644 --- a/science/rdkit/distinfo +++ b/science/rdkit/distinfo @@ -1,19 +1,19 @@ -TIMESTAMP = 1761887207 -SHA256 (rdkit-2025.09.1/v1.3.3.tar.gz) = 78e7571a779ea4952e752ecef57c62fb26463947e29ef7f4b31b11988d88ca07 -SIZE (rdkit-2025.09.1/v1.3.3.tar.gz) = 39896 -SHA256 (rdkit-2025.09.1/v3.0.2.tar.gz) = f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3 -SIZE (rdkit-2025.09.1/v3.0.2.tar.gz) = 166817 -SHA256 (rdkit-2025.09.1/v1.0.10) = 300680457c92a61ba49b678405906054ab64d3635c49309e37ea2a96c513fa8d -SIZE (rdkit-2025.09.1/v1.0.10) = 1043718 -SHA256 (rdkit-2025.09.1/v1.1.0.tar.gz) = bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e -SIZE (rdkit-2025.09.1/v1.1.0.tar.gz) = 1019402 -SHA256 (rdkit-2025.09.1/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6 -SIZE (rdkit-2025.09.1/ComicNeue-Regular.ttf) = 21915 -SHA256 (rdkit-2025.09.1/rdkit-rdkit-Release_2025_09_1_GH0.tar.gz) = 7fb3510b69af358009e2d0763c1d9665ac34f4c2cd3314cf5210ee3d5a33d501 -SIZE (rdkit-2025.09.1/rdkit-rdkit-Release_2025_09_1_GH0.tar.gz) = 82885226 -SHA256 (rdkit-2025.09.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715 -SIZE (rdkit-2025.09.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931 -SHA256 (rdkit-2025.09.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0 -SIZE (rdkit-2025.09.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = 112376 -SHA256 (rdkit-2025.09.1/aantron-better-enums-520d8ee_GH0.tar.gz) = 29ef26e79eb489b3ef71f85f904f3f1173ffefc6c853219bee7520188805eca5 -SIZE (rdkit-2025.09.1/aantron-better-enums-520d8ee_GH0.tar.gz) = 136592 +TIMESTAMP = 1762809861 +SHA256 (rdkit-2025.09.2/v1.3.3.tar.gz) = 78e7571a779ea4952e752ecef57c62fb26463947e29ef7f4b31b11988d88ca07 +SIZE (rdkit-2025.09.2/v1.3.3.tar.gz) = 39896 +SHA256 (rdkit-2025.09.2/v3.0.2.tar.gz) = f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3 +SIZE (rdkit-2025.09.2/v3.0.2.tar.gz) = 166817 +SHA256 (rdkit-2025.09.2/v1.0.11) = 405869fc8b3f73395047bc7c54e1da62ef66c08d48bd71af66e47ec9cbe86814 +SIZE (rdkit-2025.09.2/v1.0.11) = 1043261 +SHA256 (rdkit-2025.09.2/v1.1.0.tar.gz) = bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e +SIZE (rdkit-2025.09.2/v1.1.0.tar.gz) = 1019402 +SHA256 (rdkit-2025.09.2/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6 +SIZE (rdkit-2025.09.2/ComicNeue-Regular.ttf) = 21915 +SHA256 (rdkit-2025.09.2/rdkit-rdkit-Release_2025_09_2_GH0.tar.gz) = db3254e88ef17cac7bb8480e6da9d1e69dfe180c21774b11637d8a17b5a98fb9 +SIZE (rdkit-2025.09.2/rdkit-rdkit-Release_2025_09_2_GH0.tar.gz) = 82911180 +SHA256 (rdkit-2025.09.2/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715 +SIZE (rdkit-2025.09.2/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931 +SHA256 (rdkit-2025.09.2/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0 +SIZE (rdkit-2025.09.2/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = 112376 +SHA256 (rdkit-2025.09.2/aantron-better-enums-520d8ee_GH0.tar.gz) = 29ef26e79eb489b3ef71f85f904f3f1173ffefc6c853219bee7520188805eca5 +SIZE (rdkit-2025.09.2/aantron-better-enums-520d8ee_GH0.tar.gz) = 136592 diff --git a/science/rdkit/pkg-plist b/science/rdkit/pkg-plist index c4c3acd8b3c9..3cd23f7e900b 100644 --- a/science/rdkit/pkg-plist +++ b/science/rdkit/pkg-plist @@ -1200,6 +1200,7 @@ lib/libRDKitmaeparser.so.1.%%SHLIB_VER%% %%PYTHON%%%%DATADIR%%/Scripts/create_deb_packages.sh %%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/__init__.py %%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/__main__.py +%%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/patch/rdkit/Chem/inchi.pyi.diff %%PYTHON%%%%DATADIR%%/Scripts/gen_rdkit_stubs/worker.py %%PYTHON%%%%DATADIR%%/Scripts/patch_rdkit_docstrings/__init__.py %%PYTHON%%%%DATADIR%%/Scripts/patch_rdkit_docstrings/__main__.py diff --git a/science/serac/Makefile b/science/serac/Makefile index 79535619d3e5..9ced914a7e86 100644 --- a/science/serac/Makefile +++ b/science/serac/Makefile @@ -1,6 +1,6 @@ PORTNAME= serac PORTVERSION= g20220823 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/silo/Makefile b/science/silo/Makefile index 9759d1b7565c..dac1c6649952 100644 --- a/science/silo/Makefile +++ b/science/silo/Makefile @@ -1,7 +1,5 @@ PORTNAME= silo -DISTVERSION= 4.11-68 -PORTREVISION= 1 -DISTVERSIONSUFFIX= -g819658e +DISTVERSION= 4.12.0 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -19,6 +17,7 @@ USE_GITHUB= yes GH_ACCOUNT= LLNL GH_PROJECT= Silo +CMAKE_ON= SILO_ENABLE_INSTALL_LITE_HEADERS CMAKE_TESTING_ON= SILO_ENABLE_TESTS # 3 tests fail, see https://github.com/LLNL/Silo/issues/289 CMAKE_TESTING_TARGET= check diff --git a/science/silo/distinfo b/science/silo/distinfo index a3cf26715bd2..2fe4efe79810 100644 --- a/science/silo/distinfo +++ b/science/silo/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1670041617 -SHA256 (LLNL-Silo-4.11-68-g819658e_GH0.tar.gz) = 3a7a75e196c9e39922998054378efa02b2d24dc57ab126ab15a631e2645bd0ce -SIZE (LLNL-Silo-4.11-68-g819658e_GH0.tar.gz) = 14028123 +TIMESTAMP = 1763923185 +SHA256 (LLNL-Silo-4.12.0_GH0.tar.gz) = 5251816e43b08c19c925480b2daf85cc9b75e494b91df37df0eacc092279cfd0 +SIZE (LLNL-Silo-4.12.0_GH0.tar.gz) = 99198889 diff --git a/science/silo/files/patch-CMakeLists.txt b/science/silo/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..1d76b4832b67 --- /dev/null +++ b/science/silo/files/patch-CMakeLists.txt @@ -0,0 +1,13 @@ +- workaround for https://github.com/LLNL/Silo/issues/501 + +--- CMakeLists.txt.orig 2025-11-23 19:03:43 UTC ++++ CMakeLists.txt +@@ -700,7 +700,7 @@ install(FILES ${silo_public_headers} DESTINATION ${CMA + WORLD_READ) + + # Symlink old style silo_f77.inc +-if(SILO_ENABLE_FORTRAN AND CMAKE_Fortran_COMPILER) ++if(FALSE AND SILO_ENABLE_FORTRAN AND CMAKE_Fortran_COMPILER) + install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink silo.inc silo_f77.inc + WORKING_DIRECTORY ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR})") + endif() diff --git a/science/silo/files/patch-git-commit-be29ddf b/science/silo/files/patch-git-commit-be29ddf deleted file mode 100644 index fba494b0b956..000000000000 --- a/science/silo/files/patch-git-commit-be29ddf +++ /dev/null @@ -1,44 +0,0 @@ -commit be29ddf0352bc8e5a7eecc8772a3acb64dfde18c -Author: miller86 <miller86@llnl.gov> -Date: Fri Dec 2 19:00:20 2022 -0800 - - fix obj-case-macro - -diff --git src/hdf5_drv/silo_hdf5.c src/hdf5_drv/silo_hdf5.c -index 17af250..c45d689 100644 ---- src/hdf5_drv/silo_hdf5.c -+++ src/hdf5_drv/silo_hdf5.c -@@ -1809,7 +1809,7 @@ db_hdf5_cwg(DBfile *_dbfile) - *dscount = m.MEMCNT; \ - *dsnames = (char **) calloc(*dscount, sizeof(char**)); \ - for (i = 0; i < *dscount; i++) \ -- (*dsnames)[i] = strdup(m.MEMNAME[i]); \ -+ (*dsnames)[i] = strdup(m.MEMNAME); \ - break; \ - } - -@@ -1857,15 +1857,15 @@ db_hdf5_get_obj_dsnames(DBfile *_dbfile, char const *name, int *dscount, char ** - - switch(_objtype) - { -- DB_OBJ_CASE(DB_QUADVAR, DBquadvar_mt, nvals, value) -- /*DB_OBJ_CASE(DB_QUAD_RECT, DBquadmesh_mt, nspace, coord) wont work for rect case */ -- DB_OBJ_CASE(DB_QUAD_CURV, DBquadmesh_mt, nspace, coord) -- DB_OBJ_CASE(DB_QUADMESH, DBquadmesh_mt, nspace, coord) -- DB_OBJ_CASE(DB_UCDVAR, DBucdvar_mt, nvals, value) -- DB_OBJ_CASE(DB_UCDMESH, DBucdmesh_mt, ndims, coord) -- DB_OBJ_CASE(DB_POINTVAR, DBpointvar_mt, nvals, data) -- DB_OBJ_CASE(DB_POINTMESH, DBpointmesh_mt, ndims, coord) -- DB_OBJ_CASE(DB_CSGVAR, DBcsgvar_mt, nvals, vals) -+ DB_OBJ_CASE(DB_QUADVAR, DBquadvar_mt, nvals, value[i]) -+ /*DB_OBJ_CASE(DB_QUAD_RECT, DBquadmesh_mt, nspace, coord[i]) wont work for rect case */ -+ DB_OBJ_CASE(DB_QUAD_CURV, DBquadmesh_mt, nspace, coord[i]) -+ DB_OBJ_CASE(DB_QUADMESH, DBquadmesh_mt, nspace, coord[i]) -+ DB_OBJ_CASE(DB_UCDVAR, DBucdvar_mt, nvals, value[i]) -+ DB_OBJ_CASE(DB_UCDMESH, DBucdmesh_mt, ndims, coord[i]) -+ DB_OBJ_CASE(DB_POINTVAR, DBpointvar_mt, nvals, data[i]) -+ DB_OBJ_CASE(DB_POINTMESH, DBpointmesh_mt, ndims, coord[i]) -+ DB_OBJ_CASE(DB_CSGVAR, DBcsgvar_mt, nvals, vals[i]) - DB_OBJ_CASE(DB_CURVE, DBcurve_mt, npts?1:1, yvarname) - } - H5Tclose(o); diff --git a/science/silo/files/patch-src_silo_silo.c b/science/silo/files/patch-src_silo_silo.c deleted file mode 100644 index d20855c5ca9b..000000000000 --- a/science/silo/files/patch-src_silo_silo.c +++ /dev/null @@ -1,39 +0,0 @@ ---- src/silo/silo.c.orig 2022-12-03 02:30:10 UTC -+++ src/silo/silo.c -@@ -238,12 +238,8 @@ typedef struct db_silo_stat_t { - #ifndef SIZEOF_OFF64_T - #error missing definition for SIZEOF_OFF64_T in silo_private.h - #else --#if SIZEOF_OFF64_T > 4 -- struct stat64 s; --#else - struct stat s; - #endif --#endif - #ifdef _WIN32 - DWORD fileindexlo; - DWORD fileindexhi; -@@ -2121,11 +2117,7 @@ db_silo_stat_one_file(const char *name, db_silo_stat_t - errno = 0; - memset(&(statbuf->s), 0, sizeof(statbuf->s)); - --#if SIZEOF_OFF64_T > 4 -- retval = stat64(name, &(statbuf->s)); --#else - retval = stat(name, &(statbuf->s)); --#endif /* #if SIZEOF_OFF64_T > 4 */ - - #ifdef _WIN32 - if (retval == 0) -@@ -4136,11 +4128,7 @@ DBOpenReal(const char *name, int type, int mode) - /********************************/ - /* System level error occured. */ - /********************************/ --#if SIZEOF_OFF64_T > 4 -- printf("stat64() failed with error: "); --#else - printf("stat() failed with error: "); --#endif - switch (errno) - { - case EACCES: printf("EACCES\n"); break; diff --git a/science/silo/files/patch-src_silo_silo__json.c b/science/silo/files/patch-src_silo_silo__json.c index 576f7eea757f..331a87c8890e 100644 --- a/science/silo/files/patch-src_silo_silo__json.c +++ b/science/silo/files/patch-src_silo_silo__json.c @@ -1,6 +1,6 @@ ---- src/silo/silo_json.c.orig 2022-12-03 02:30:10 UTC +--- src/silo/silo_json.c.orig 2025-11-21 05:30:59 UTC +++ src/silo/silo_json.c -@@ -441,11 +441,7 @@ json_object_from_binary_file(char const *filename) +@@ -446,11 +446,7 @@ json_object_from_binary_file(char const *filename) #ifndef SIZEOF_OFF64_T #error missing definition for SIZEOF_OFF64_T in silo_private.h #else diff --git a/science/silo/files/patch-tests_CMake_SiloMakeCheckRunner.cmake b/science/silo/files/patch-tests_CMake_SiloMakeCheckRunner.cmake deleted file mode 100644 index c25272a9a103..000000000000 --- a/science/silo/files/patch-tests_CMake_SiloMakeCheckRunner.cmake +++ /dev/null @@ -1,13 +0,0 @@ -- workaround for https://github.com/LLNL/Silo/issues/288 - ---- tests/CMake/SiloMakeCheckRunner.cmake.orig 2022-12-03 06:53:38 UTC -+++ tests/CMake/SiloMakeCheckRunner.cmake -@@ -72,7 +72,7 @@ function(silo_add_make_check_runner) - message(WARNING "silo_add_make_check_runner: NAME argument is required.") - return() - endif() -- set(test_cmd ${samcr_NAME}) -+ set(test_cmd "./${samcr_NAME}") - if("ARGS" IN_LIST samcr_KEYWORDS_MISSING_VALUES) - message(WARNING "silo_add_make_check_runner: ARGS argument provided without a value.") - return() diff --git a/science/silo/pkg-plist b/science/silo/pkg-plist index c55c7a873580..fc056e66313d 100644 --- a/science/silo/pkg-plist +++ b/science/silo/pkg-plist @@ -3,18 +3,19 @@ %%SILOCK%%bin/silock %%BROWSER%%bin/silodiff %%BROWSER%%bin/silofile -cmake/SiloConfig.cmake -cmake/SiloConfigVersion.cmake -cmake/SiloTargets-%%CMAKE_BUILD_TYPE%%.cmake -cmake/SiloTargets.cmake include/lite_pdb.h include/lite_score.h -include/pdform.h include/pmpio.h include/silo.h -include/silo.inc +%%FORTRAN%%include/silo.inc %%FORTRAN%%include/silo_FC.h include/silo_exports.h include/silo_f9x.inc %%PYTHON%%lib/Silo.so +lib/cmake/Silo/SiloConfig.cmake +lib/cmake/Silo/SiloConfigVersion.cmake +lib/cmake/Silo/SiloTargets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/Silo/SiloTargets.cmake lib/libsilo%%SUFX_HDF5%%.so +lib/libsilo%%SUFX_HDF5%%.so.4.12.0 +lib/libsilo%%SUFX_HDF5%%.so.412 diff --git a/science/spheral/Makefile b/science/spheral/Makefile index ca4af45f614b..d35d06393bf2 100644 --- a/science/spheral/Makefile +++ b/science/spheral/Makefile @@ -1,7 +1,7 @@ PORTNAME= spheral DISTVERSIONPREFIX= v DISTVERSION= 2025.06.1 -PORTREVISION= 2 +PORTREVISION= 4 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org diff --git a/science/tinker/Makefile b/science/tinker/Makefile index 3a5cb18b0c75..f66cb43850b0 100644 --- a/science/tinker/Makefile +++ b/science/tinker/Makefile @@ -1,6 +1,6 @@ PORTNAME= tinker DISTVERSIONPREFIX= v -DISTVERSION= 25.5.2 +DISTVERSION= 25.5.4 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/tinker/distinfo b/science/tinker/distinfo index da2498d5f92a..c80318510948 100644 --- a/science/tinker/distinfo +++ b/science/tinker/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1760108472 -SHA256 (TinkerTools-tinker-v25.5.2_GH0.tar.gz) = 3a474a892892ab0b77a86599dd57c17731c64c363af7e48cfe6915a6d4276df6 -SIZE (TinkerTools-tinker-v25.5.2_GH0.tar.gz) = 34670489 +TIMESTAMP = 1763921430 +SHA256 (TinkerTools-tinker-v25.5.4_GH0.tar.gz) = 410d02d3fe7b42b124cc38cef8cf3c077037a099465c799259f60bdae4e367b2 +SIZE (TinkerTools-tinker-v25.5.4_GH0.tar.gz) = 34197683 diff --git a/science/tinker/files/patch-make_Makefile b/science/tinker/files/patch-make_Makefile index 7e1f679a86a0..b92cb6e976c7 100644 --- a/science/tinker/files/patch-make_Makefile +++ b/science/tinker/files/patch-make_Makefile @@ -1,6 +1,6 @@ ---- make/Makefile.orig 2025-09-30 16:25:57 UTC +--- make/Makefile.orig 2025-11-21 04:02:18 UTC +++ make/Makefile -@@ -813,138 +813,138 @@ rename_bin: +@@ -818,72 +818,72 @@ rename_bin: cat *.f *.c > tinker.txt rename_bin: @@ -20,6 +20,7 @@ - mv gda.x $(BINDIR)/gda - mv intedit.x $(BINDIR)/intedit - mv intxyz.x $(BINDIR)/intxyz +- mv mdavg.x $(BINDIR)/mdavg - mv minimize.x $(BINDIR)/minimize - mv minirot.x $(BINDIR)/minirot - mv minrigid.x $(BINDIR)/minrigid @@ -85,6 +86,7 @@ + ${BSD_INSTALL_PROGRAM} gda.x $(BINDIR)/gda + ${BSD_INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit + ${BSD_INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz ++ ${BSD_INSTALL_PROGRAM} mdavg.x $(BINDIR)/mdavg + ${BSD_INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize + ${BSD_INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot + ${BSD_INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid @@ -136,136 +138,4 @@ + ${BSD_INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb rename_exe: -- mv alchemy.x $(BINDIR)/alchemy.exe -- mv analyze.x $(BINDIR)/analyze.exe -- mv anneal.x $(BINDIR)/anneal.exe -- mv arcedit.x $(BINDIR)/arcedit.exe -- mv bar.x $(BINDIR)/bar.exe -- mv correlate.x $(BINDIR)/correlate.exe -- mv critical.x $(BINDIR)/critical.exe -- mv crystal.x $(BINDIR)/crystal.exe -- mv diffuse.x $(BINDIR)/diffuse.exe -- mv distgeom.x $(BINDIR)/distgeom.exe -- mv document.x $(BINDIR)/document.exe -- mv dynamic.x $(BINDIR)/dynamic.exe -- mv freefix.x $(BINDIR)/freefix.exe -- mv gda.x $(BINDIR)/gda.exe -- mv intedit.x $(BINDIR)/intedit.exe -- mv intxyz.x $(BINDIR)/intxyz.exe -- mv minimize.x $(BINDIR)/minimize.exe -- mv minirot.x $(BINDIR)/minirot.exe -- mv minrigid.x $(BINDIR)/minrigid.exe -- mv mol2xyz.x $(BINDIR)/mol2xyz.exe -- mv molxyz.x $(BINDIR)/molxyz.exe -- mv monte.x $(BINDIR)/monte.exe -- mv newton.x $(BINDIR)/newton.exe -- mv newtrot.x $(BINDIR)/newtrot.exe -- mv nucleic.x $(BINDIR)/nucleic.exe -- mv optimize.x $(BINDIR)/optimize.exe -- mv optirot.x $(BINDIR)/optirot.exe -- mv optrigid.x $(BINDIR)/optrigid.exe -- mv path.x $(BINDIR)/path.exe -- mv pdbxyz.x $(BINDIR)/pdbxyz.exe -- mv polarize.x $(BINDIR)/polarize.exe -- mv poledit.x $(BINDIR)/poledit.exe -- mv potential.x $(BINDIR)/potential.exe -- mv prmedit.x $(BINDIR)/prmedit.exe -- mv protein.x $(BINDIR)/protein.exe -- mv pss.x $(BINDIR)/pss.exe -- mv pssrigid.x $(BINDIR)/pssrigid.exe -- mv pssrot.x $(BINDIR)/pssrot.exe -- mv radial.x $(BINDIR)/radial.exe -- mv saddle.x $(BINDIR)/saddle.exe -- mv scan.x $(BINDIR)/scan.exe -- mv sniffer.x $(BINDIR)/sniffer.exe -- mv spacefill.x $(BINDIR)/spacefill.exe -- mv spectrum.x $(BINDIR)/spectrum.exe -- mv superpose.x $(BINDIR)/superpose.exe -- mv testgrad.x $(BINDIR)/testgrad.exe -- mv testhess.x $(BINDIR)/testhess.exe -- mv testpair.x $(BINDIR)/testpair.exe -- mv testpol.x $(BINDIR)/testpol.exe -- mv testrot.x $(BINDIR)/testrot.exe -- mv testsurf.x $(BINDIR)/testsurf.exe -- mv testvir.x $(BINDIR)/testvir.exe -- mv timer.x $(BINDIR)/timer.exe -- mv timerot.x $(BINDIR)/timerot.exe -- mv torsfit.x $(BINDIR)/torsfit.exe -- mv valence.x $(BINDIR)/valence.exe -- mv vibbig.x $(BINDIR)/vibbig.exe -- mv vibrate.x $(BINDIR)/vibrate.exe -- mv vibrot.x $(BINDIR)/vibrot.exe -- mv xtalfit.x $(BINDIR)/xtalfit.exe -- mv xtalmin.x $(BINDIR)/xtalmin.exe -- mv xyzedit.x $(BINDIR)/xyzedit.exe -- mv xyzint.x $(BINDIR)/xyzint.exe -- mv xyzmol2.x $(BINDIR)/xyzmol2.exe -- mv xyzpdb.x $(BINDIR)/xyzpdb.exe -+ ${BSD_INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy.exe -+ ${BSD_INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze.exe -+ ${BSD_INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal.exe -+ ${BSD_INSTALL_PROGRAM} arcedit.x $(BINDIR)/arcedit.exe -+ ${BSD_INSTALL_PROGRAM} bar.x $(BINDIR)/bar.exe -+ ${BSD_INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate.exe -+ ${BSD_INSTALL_PROGRAM} critical.x $(BINDIR)/critical.exe -+ ${BSD_INSTALL_PROGRAM} crystal.x $(BINDIR)/crystal.exe -+ ${BSD_INSTALL_PROGRAM} diffuse.x $(BINDIR)/diffuse.exe -+ ${BSD_INSTALL_PROGRAM} distgeom.x $(BINDIR)/distgeom.exe -+ ${BSD_INSTALL_PROGRAM} document.x $(BINDIR)/document.exe -+ ${BSD_INSTALL_PROGRAM} dynamic.x $(BINDIR)/dynamic.exe -+ ${BSD_INSTALL_PROGRAM} freefix.x $(BINDIR)/freefix.exe -+ ${BSD_INSTALL_PROGRAM} gda.x $(BINDIR)/gda.exe -+ ${BSD_INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit.exe -+ ${BSD_INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz.exe -+ ${BSD_INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize.exe -+ ${BSD_INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot.exe -+ ${BSD_INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid.exe -+ ${BSD_INSTALL_PROGRAM} mol2xyz.x $(BINDIR)/mol2xyz.exe -+ ${BSD_INSTALL_PROGRAM} molxyz.x $(BINDIR)/molxyz.exe -+ ${BSD_INSTALL_PROGRAM} monte.x $(BINDIR)/monte.exe -+ ${BSD_INSTALL_PROGRAM} newton.x $(BINDIR)/newton.exe -+ ${BSD_INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot.exe -+ ${BSD_INSTALL_PROGRAM} nucleic.x $(BINDIR)/nucleic.exe -+ ${BSD_INSTALL_PROGRAM} optimize.x $(BINDIR)/optimize.exe -+ ${BSD_INSTALL_PROGRAM} optirot.x $(BINDIR)/optirot.exe -+ ${BSD_INSTALL_PROGRAM} optrigid.x $(BINDIR)/optrigid.exe -+ ${BSD_INSTALL_PROGRAM} path.x $(BINDIR)/path.exe -+ ${BSD_INSTALL_PROGRAM} pdbxyz.x $(BINDIR)/pdbxyz.exe -+ ${BSD_INSTALL_PROGRAM} polarize.x $(BINDIR)/polarize.exe -+ ${BSD_INSTALL_PROGRAM} poledit.x $(BINDIR)/poledit.exe -+ ${BSD_INSTALL_PROGRAM} potential.x $(BINDIR)/potential.exe -+ ${BSD_INSTALL_PROGRAM} prmedit.x $(BINDIR)/prmedit.exe -+ ${BSD_INSTALL_PROGRAM} protein.x $(BINDIR)/protein.exe -+ ${BSD_INSTALL_PROGRAM} pss.x $(BINDIR)/pss.exe -+ ${BSD_INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid.exe -+ ${BSD_INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot.exe -+ ${BSD_INSTALL_PROGRAM} radial.x $(BINDIR)/radial.exe -+ ${BSD_INSTALL_PROGRAM} saddle.x $(BINDIR)/saddle.exe -+ ${BSD_INSTALL_PROGRAM} scan.x $(BINDIR)/scan.exe -+ ${BSD_INSTALL_PROGRAM} sniffer.x $(BINDIR)/sniffer.exe -+ ${BSD_INSTALL_PROGRAM} spacefill.x $(BINDIR)/spacefill.exe -+ ${BSD_INSTALL_PROGRAM} spectrum.x $(BINDIR)/spectrum.exe -+ ${BSD_INSTALL_PROGRAM} superpose.x $(BINDIR)/superpose.exe -+ ${BSD_INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad.exe -+ ${BSD_INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess.exe -+ ${BSD_INSTALL_PROGRAM} testpair.x $(BINDIR)/testpair.exe -+ ${BSD_INSTALL_PROGRAM} testpol.x $(BINDIR)/testpol.exe -+ ${BSD_INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot.exe -+ ${BSD_INSTALL_PROGRAM} testsurf.x $(BINDIR)/testsurf.exe -+ ${BSD_INSTALL_PROGRAM} testvir.x $(BINDIR)/testvir.exe -+ ${BSD_INSTALL_PROGRAM} timer.x $(BINDIR)/timer.exe -+ ${BSD_INSTALL_PROGRAM} timerot.x $(BINDIR)/timerot.exe -+ ${BSD_INSTALL_PROGRAM} torsfit.x $(BINDIR)/torsfit.exe -+ ${BSD_INSTALL_PROGRAM} valence.x $(BINDIR)/valence.exe -+ ${BSD_INSTALL_PROGRAM} vibbig.x $(BINDIR)/vibbig.exe -+ ${BSD_INSTALL_PROGRAM} vibrate.x $(BINDIR)/vibrate.exe -+ ${BSD_INSTALL_PROGRAM} vibrot.x $(BINDIR)/vibrot.exe -+ ${BSD_INSTALL_PROGRAM} xtalfit.x $(BINDIR)/xtalfit.exe -+ ${BSD_INSTALL_PROGRAM} xtalmin.x $(BINDIR)/xtalmin.exe -+ ${BSD_INSTALL_PROGRAM} xyzedit.x $(BINDIR)/xyzedit.exe -+ ${BSD_INSTALL_PROGRAM} xyzint.x $(BINDIR)/xyzint.exe -+ ${BSD_INSTALL_PROGRAM} xyzmol2.x $(BINDIR)/xyzmol2.exe -+ ${BSD_INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb.exe - - remove_links: - rm -f $(LINKDIR)/alchemy + mv alchemy.x $(BINDIR)/alchemy.exe diff --git a/science/tinker/pkg-plist b/science/tinker/pkg-plist index b0f9367ade44..cf05ef8ea37c 100644 --- a/science/tinker/pkg-plist +++ b/science/tinker/pkg-plist @@ -14,6 +14,7 @@ bin/freefix bin/gda bin/intedit bin/intxyz +bin/mdavg bin/minimize bin/minirot bin/minrigid @@ -85,7 +86,7 @@ bin/xyzpdb %%DATADIR%%/params/charmm19.prm %%DATADIR%%/params/charmm22.prm %%DATADIR%%/params/charmm27.prm -%%DATADIR%%/params/charmm36.prm +%%DATADIR%%/params/charmm36m.prm %%DATADIR%%/params/dang.prm %%DATADIR%%/params/hippo19.prm %%DATADIR%%/params/hoch.prm diff --git a/science/trilinos/Makefile b/science/trilinos/Makefile index d2c8f9e9253c..bf02f46f6ed9 100644 --- a/science/trilinos/Makefile +++ b/science/trilinos/Makefile @@ -1,17 +1,15 @@ PORTNAME= trilinos -DISTVERSIONPREFIX= trilinos-release- -DISTVERSION= 16-1-0 -PORTREVISION= 1 +DISTVERSION= 16.2.0 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org COMMENT= Solver for multi-physics engineering and scientific problems -WWW= https://trilinos.github.io/ +WWW= https://trilinos.github.io/ \ + https://github.com/trilinos/trilinos LICENSE= BSD3CLAUSE LGPL20 # Trilinos is licensed on a per-package basis. Most packages are under a BSD license, some are published under the (L)GPL. LICENSE_COMB= multi -BROKEN_FreeBSD_15= compilation fails with clang-19, see https://github.com/trilinos/Trilinos/issues/13570 BROKEN_armv6= kokkos assumes a 64-bit build; i.e., 8-byte pointers, but found 4-byte BROKEN_armv7= kokkos assumes a 64-bit build; i.e., 8-byte pointers, but found 4-byte BROKEN_i386= kokkos assumes a 64-bit build; i.e., 8-byte pointers, but found 4-byte @@ -95,4 +93,6 @@ post-install: # remove MPI headers that it installs @${RM} ${STAGEDIR}${PREFIX}/include/mpi*.h +# Tests fail to compile, see https://github.com/trilinos/Trilinos/issues/14748 + .include <bsd.port.mk> diff --git a/science/trilinos/distinfo b/science/trilinos/distinfo index d9e1b7f1a849..09f91c91366b 100644 --- a/science/trilinos/distinfo +++ b/science/trilinos/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1743061355 -SHA256 (trilinos-Trilinos-trilinos-release-16-1-0_GH0.tar.gz) = e9651c88f581049457036cfc01b527a9d3903c257338eeeab942befd7452f23a -SIZE (trilinos-Trilinos-trilinos-release-16-1-0_GH0.tar.gz) = 197260161 +TIMESTAMP = 1764144792 +SHA256 (trilinos-Trilinos-16.2.0_GH0.tar.gz) = a5dd61e7752b6c0c53e89495aa68e099a5f68b6b775fff49e324c3b177174488 +SIZE (trilinos-Trilinos-16.2.0_GH0.tar.gz) = 198602159 diff --git a/science/trilinos/files/patch-packages_zoltan_src_driver_dr__random__io.c b/science/trilinos/files/patch-packages_zoltan_src_driver_dr__random__io.c new file mode 100644 index 000000000000..42037d4236a8 --- /dev/null +++ b/science/trilinos/files/patch-packages_zoltan_src_driver_dr__random__io.c @@ -0,0 +1,13 @@ +--- packages/zoltan/src/driver/dr_random_io.c.orig 2025-11-26 08:50:26 UTC ++++ packages/zoltan/src/driver/dr_random_io.c +@@ -42,10 +42,6 @@ extern "C" { + #define MAX_STR_LENGTH 80 + #endif + +-#ifdef M_PIl +-#error "HAVE M_PI1" +-#endif +- + /****************************************************************************/ + /****************************************************************************/ + /****************************************************************************/ diff --git a/science/trilinos/pkg-plist b/science/trilinos/pkg-plist index 4c08fb328b63..32e53c10a615 100644 --- a/science/trilinos/pkg-plist +++ b/science/trilinos/pkg-plist @@ -62,7 +62,6 @@ include/Amesos2_SolverCore_decl.hpp include/Amesos2_SolverCore_def.hpp include/Amesos2_SolverTraits.hpp include/Amesos2_Solver_MP_Vector.hpp -include/Amesos2_Solver_UQ_PCE.hpp include/Amesos2_Solver_decl.hpp include/Amesos2_Status.hpp include/Amesos2_Tacho.hpp @@ -180,6 +179,7 @@ include/Anasazi_LOCA_Sort.H include/Anasazi_config.h include/Anasaziepetra_DLLExportMacro.h include/Anasaziepetra_ModeLaplace_DLLExportMacro.h +include/Anasazitpetra_ModeLaplace_DLLExportMacro.h include/AssemblyUtils.hpp include/Aztec2Petra.h include/AztecOO.h @@ -312,7 +312,6 @@ include/Belos_SolverManager_MP_Vector.hpp include/Belos_StatusTest_GenResNorm_MP_Vector.hpp include/Belos_StatusTest_ImpResNorm_MP_Vector.hpp include/Belos_TpetraAdapter_MP_Vector.hpp -include/Belos_TpetraAdapter_UQ_PCE.hpp include/Belos_Tpetra_Cg.hpp include/Belos_Tpetra_CgPipeline.hpp include/Belos_Tpetra_CgSingleReduce.hpp @@ -504,6 +503,8 @@ include/Galeri_FileGrid.h include/Galeri_FiniteElements.h include/Galeri_GalerkinVariational.h include/Galeri_Hanowa.h +include/Galeri_HelmholtzFEM2DProblem.hpp +include/Galeri_HelmholtzFEM3DProblem.hpp include/Galeri_HexCubeGrid.h include/Galeri_HexQuadrature.h include/Galeri_Hilbert.h @@ -525,6 +526,7 @@ include/Galeri_Ones.h include/Galeri_Parter.h include/Galeri_Pei.h include/Galeri_Problem.hpp +include/Galeri_Problem_Helmholtz.hpp include/Galeri_QuadQuadrature.h include/Galeri_QuadRectangleGrid.h include/Galeri_Random.h @@ -547,6 +549,7 @@ include/Galeri_Utils.h include/Galeri_Vander.h include/Galeri_VbrMatrices.h include/Galeri_VectorTraits.hpp +include/Galeri_VelocityModel.hpp include/Galeri_Version.h include/Galeri_Workspace.h include/Galeri_XpetraCartesian.hpp @@ -566,6 +569,7 @@ include/Ifpack2_AdditiveSchwarz_def.hpp include/Ifpack2_BandedContainer.hpp include/Ifpack2_BandedContainer_decl.hpp include/Ifpack2_BandedContainer_def.hpp +include/Ifpack2_BlockComputeResidualAndSolve.hpp include/Ifpack2_BlockComputeResidualVector.hpp include/Ifpack2_BlockHelper.hpp include/Ifpack2_BlockHelper_Timers.hpp @@ -674,7 +678,6 @@ include/Ifpack2_Diagonal_def.hpp include/Ifpack2_DropFilter.hpp include/Ifpack2_DropFilter_decl.hpp include/Ifpack2_DropFilter_def.hpp -include/Ifpack2_ETIHelperMacros.h include/Ifpack2_Experimental_RBILUK.hpp include/Ifpack2_Experimental_RBILUK_decl.hpp include/Ifpack2_Experimental_RBILUK_def.hpp @@ -1099,6 +1102,12 @@ include/KokkosBatched_GMRES.hpp include/KokkosBatched_GMRES_Serial_Impl.hpp include/KokkosBatched_GMRES_TeamVector_Impl.hpp include/KokkosBatched_GMRES_Team_Impl.hpp +include/KokkosBatched_Gbtrf.hpp +include/KokkosBatched_Gbtrf_Serial_Impl.hpp +include/KokkosBatched_Gbtrf_Serial_Internal.hpp +include/KokkosBatched_Gbtrs.hpp +include/KokkosBatched_Gbtrs_Serial_Impl.hpp +include/KokkosBatched_Gbtrs_Serial_Internal.hpp include/KokkosBatched_Gemm_Decl.hpp include/KokkosBatched_Gemm_Serial_Impl.hpp include/KokkosBatched_Gemm_Serial_Internal.hpp @@ -1111,8 +1120,17 @@ include/KokkosBatched_Gemv_TeamVector_Impl.hpp include/KokkosBatched_Gemv_TeamVector_Internal.hpp include/KokkosBatched_Gemv_Team_Impl.hpp include/KokkosBatched_Gemv_Team_Internal.hpp +include/KokkosBatched_Ger.hpp +include/KokkosBatched_Ger_Serial_Impl.hpp +include/KokkosBatched_Ger_Serial_Internal.hpp include/KokkosBatched_Gesv.hpp include/KokkosBatched_Gesv_Impl.hpp +include/KokkosBatched_Getrf.hpp +include/KokkosBatched_Getrf_Serial_Impl.hpp +include/KokkosBatched_Getrf_Serial_Internal.hpp +include/KokkosBatched_Getrs.hpp +include/KokkosBatched_Getrs_Serial_Impl.hpp +include/KokkosBatched_Getrs_Serial_Internal.hpp include/KokkosBatched_Givens_Serial_Internal.hpp include/KokkosBatched_HadamardProduct.hpp include/KokkosBatched_HadamardProduct_Impl.hpp @@ -1147,7 +1165,6 @@ include/KokkosBatched_InnerLU_Serial_Impl.hpp include/KokkosBatched_InnerTrsm_Decl.hpp include/KokkosBatched_InnerTrsm_Serial_Impl.hpp include/KokkosBatched_InverseLU_Decl.hpp -include/KokkosBatched_InverseLU_Serial_Impl.hpp include/KokkosBatched_JacobiPrec.hpp include/KokkosBatched_Kernel_Handle.hpp include/KokkosBatched_Krylov_Handle.hpp @@ -1157,6 +1174,9 @@ include/KokkosBatched_LU_Serial_Impl.hpp include/KokkosBatched_LU_Serial_Internal.hpp include/KokkosBatched_LU_Team_Impl.hpp include/KokkosBatched_LU_Team_Internal.hpp +include/KokkosBatched_Lacgv.hpp +include/KokkosBatched_Lacgv_Serial_Impl.hpp +include/KokkosBatched_Lacgv_Serial_Internal.hpp include/KokkosBatched_Laswp.hpp include/KokkosBatched_Laswp_Serial_Impl.hpp include/KokkosBatched_Laswp_Serial_Internal.hpp @@ -1205,6 +1225,9 @@ include/KokkosBatched_Spmv.hpp include/KokkosBatched_Spmv_Serial_Impl.hpp include/KokkosBatched_Spmv_TeamVector_Impl.hpp include/KokkosBatched_Spmv_Team_Impl.hpp +include/KokkosBatched_Syr.hpp +include/KokkosBatched_Syr_Serial_Impl.hpp +include/KokkosBatched_Syr_Serial_Internal.hpp include/KokkosBatched_Tbsv.hpp include/KokkosBatched_Tbsv_Serial_Impl.hpp include/KokkosBatched_Tbsv_Serial_Internal.hpp @@ -1435,7 +1458,6 @@ include/KokkosCompat_config.h include/KokkosExp_View_Fad.hpp include/KokkosExp_View_Fad_Contiguous.hpp include/KokkosExp_View_MP_Vector_Contiguous.hpp -include/KokkosExp_View_UQ_PCE_Contiguous.hpp include/KokkosGraph_BFS_impl.hpp include/KokkosGraph_CoarsenConstruct.hpp include/KokkosGraph_CoarsenHeuristics.hpp @@ -1450,6 +1472,8 @@ include/KokkosGraph_ExplicitCoarsening.hpp include/KokkosGraph_ExplicitCoarsening_impl.hpp include/KokkosGraph_GraphColorHandle.hpp include/KokkosGraph_MIS2.hpp +include/KokkosGraph_RCB.hpp +include/KokkosGraph_RCB_impl.hpp include/KokkosGraph_RCM.hpp include/KokkosGraph_Triangle.hpp include/KokkosGraph_color_d1_spec.hpp @@ -1474,6 +1498,7 @@ include/KokkosKernels_PrintConfiguration.hpp include/KokkosKernels_PrintUtils.hpp include/KokkosKernels_SafeCompare.hpp include/KokkosKernels_SimpleUtils.hpp +include/KokkosKernels_Singleton.hpp include/KokkosKernels_Sorting.hpp include/KokkosKernels_TplsVersion.hpp include/KokkosKernels_Uniform_Initialized_MemoryPool.hpp @@ -1525,6 +1550,8 @@ include/KokkosSparse_MatrixPrec.hpp include/KokkosSparse_OrdinalTraits.hpp include/KokkosSparse_Preconditioner.hpp include/KokkosSparse_SortCrs.hpp +include/KokkosSparse_StaticCcsGraph.hpp +include/KokkosSparse_StaticCrsGraph.hpp include/KokkosSparse_Utils.hpp include/KokkosSparse_Utils_cusparse.hpp include/KokkosSparse_Utils_mkl.hpp @@ -1673,31 +1700,22 @@ include/KokkosSparse_twostage_gauss_seidel_impl.hpp include/Kokkos_AnalyzeStokhosShape.hpp include/Kokkos_ArithTraits.hpp include/Kokkos_ArithTraits_MP_Vector.hpp -include/Kokkos_ArithTraits_UQ_PCE.hpp include/Kokkos_Atomic_MP_Vector.hpp -include/Kokkos_Atomic_UQ_PCE.hpp include/Kokkos_Blas1_MP_Vector.hpp -include/Kokkos_Blas1_UQ_PCE.hpp include/Kokkos_CrsMatrix_MP_Vector.hpp include/Kokkos_CrsMatrix_MP_Vector_Cuda.hpp -include/Kokkos_CrsMatrix_UQ_PCE.hpp -include/Kokkos_CrsMatrix_UQ_PCE_Cuda.hpp include/Kokkos_DynRankView_Fad.hpp include/Kokkos_DynRankView_Fad_Contiguous.hpp include/Kokkos_InnerProductSpaceTraits.hpp include/Kokkos_InnerProductSpaceTraits_MP_Vector.hpp -include/Kokkos_InnerProductSpaceTraits_UQ_PCE.hpp include/Kokkos_LayoutContiguous.hpp include/Kokkos_LayoutNatural.hpp include/Kokkos_MV_MP_Vector.hpp -include/Kokkos_MV_UQ_PCE.hpp include/Kokkos_MpiTypeTraits.hpp include/Kokkos_Parallel_MP_Vector.hpp include/Kokkos_Random_MP_Vector.hpp -include/Kokkos_Random_UQ_PCE.hpp include/Kokkos_TeuchosCommAdapters.hpp include/Kokkos_TeuchosCommAdapters_MP_Vector.hpp -include/Kokkos_TeuchosCommAdapters_UQ_PCE.hpp include/Kokkos_ViewFactory.hpp include/Kokkos_View_Fad.hpp include/Kokkos_View_Fad_Fwd.hpp @@ -1705,9 +1723,6 @@ include/Kokkos_View_MP_Vector.hpp include/Kokkos_View_MP_Vector_Fwd.hpp include/Kokkos_View_MP_Vector_Interlaced.hpp include/Kokkos_View_MP_Vector_Utils.hpp -include/Kokkos_View_UQ_PCE.hpp -include/Kokkos_View_UQ_PCE_Fwd.hpp -include/Kokkos_View_UQ_PCE_Utils.hpp include/Kokkos_View_Utils.hpp include/Kokkos_View_Utils_Def.hpp include/LOCA.H @@ -1882,7 +1897,7 @@ include/LOCA_TurningPoint_MooreSpence_PhippsBordering.H include/LOCA_TurningPoint_MooreSpence_SalingerBordering.H include/LOCA_TurningPoint_MooreSpence_SolverFactory.H include/LOCA_TurningPoint_MooreSpence_SolverStrategy.H -include/ML_Linker.hpp +include/Legendre.hpp include/MatrixMarket_Tpetra.hpp include/MatrixMarket_TpetraNew.hpp include/MiniTensor.h @@ -1926,6 +1941,7 @@ include/MiniTensor_version.h include/ModalProblem.h include/ModeLaplace.h include/ModeLaplace1DQ1.h +include/ModeLaplace1DQ1.hpp include/ModeLaplace1DQ2.h include/ModeLaplace2DQ1.h include/ModeLaplace2DQ2.h @@ -2093,6 +2109,7 @@ include/MueLu_CoupledRBMFactory_def.hpp include/MueLu_CoupledRBMFactory_fwd.hpp include/MueLu_CreateTpetraPreconditioner.hpp include/MueLu_CreateXpetraPreconditioner.hpp +include/MueLu_CrsMatrixUtils.hpp include/MueLu_CutDrop.hpp include/MueLu_DemoFactory.hpp include/MueLu_DemoFactory_decl.hpp @@ -2214,6 +2231,7 @@ include/MueLu_Ifpack2Smoother_def.hpp include/MueLu_Ifpack2Smoother_fwd.hpp include/MueLu_IfpackSmoother.hpp include/MueLu_IfpackSmoother_fwd.hpp +include/MueLu_ImportUtils.hpp include/MueLu_IndefBlockedDiagonalSmoother.hpp include/MueLu_IndefBlockedDiagonalSmoother_decl.hpp include/MueLu_IndefBlockedDiagonalSmoother_def.hpp @@ -2254,7 +2272,9 @@ include/MueLu_IsorropiaInterface.hpp include/MueLu_IsorropiaInterface_decl.hpp include/MueLu_IsorropiaInterface_def.hpp include/MueLu_IsorropiaInterface_fwd.hpp +include/MueLu_IteratorOps.hpp include/MueLu_KeepType.hpp +include/MueLu_KokkosTuningInterface.hpp include/MueLu_LWGraph.hpp include/MueLu_LWGraphBase.hpp include/MueLu_LWGraphBase_fwd.hpp @@ -2339,7 +2359,6 @@ include/MueLu_MultiVectorTransferFactory.hpp include/MueLu_MultiVectorTransferFactory_decl.hpp include/MueLu_MultiVectorTransferFactory_def.hpp include/MueLu_MultiVectorTransferFactory_fwd.hpp -include/MueLu_MutuallyExclusiveTime.hpp include/MueLu_NoFactory.hpp include/MueLu_NodePartitionInterface.hpp include/MueLu_NodePartitionInterface_decl.hpp @@ -2488,6 +2507,10 @@ include/MueLu_RepartitionInterface.hpp include/MueLu_RepartitionInterface_decl.hpp include/MueLu_RepartitionInterface_def.hpp include/MueLu_RepartitionInterface_fwd.hpp +include/MueLu_RepartitionUtilities.hpp +include/MueLu_RepartitionUtilities_decl.hpp +include/MueLu_RepartitionUtilities_def.hpp +include/MueLu_RepartitionUtilities_fwd.hpp include/MueLu_ReplicatePFactory.hpp include/MueLu_ReplicatePFactory_decl.hpp include/MueLu_ReplicatePFactory_def.hpp @@ -2508,6 +2531,13 @@ include/MueLu_SaPFactory_kokkos.hpp include/MueLu_SaPFactory_kokkos_decl.hpp include/MueLu_SaPFactory_kokkos_def.hpp include/MueLu_SaPFactory_kokkos_fwd.hpp +include/MueLu_ScalarDroppingBase.hpp +include/MueLu_ScalarDroppingClassical.hpp +include/MueLu_ScalarDroppingClassical_decl.hpp +include/MueLu_ScalarDroppingClassical_def.hpp +include/MueLu_ScalarDroppingDistanceLaplacian.hpp +include/MueLu_ScalarDroppingDistanceLaplacian_decl.hpp +include/MueLu_ScalarDroppingDistanceLaplacian_def.hpp include/MueLu_ScaledNullspaceFactory.hpp include/MueLu_ScaledNullspaceFactory_decl.hpp include/MueLu_ScaledNullspaceFactory_def.hpp @@ -2530,7 +2560,11 @@ include/MueLu_SemiCoarsenPFactory_kokkos_def.hpp include/MueLu_SemiCoarsenPFactory_kokkos_fwd.hpp include/MueLu_ShiftedLaplacian.hpp include/MueLu_ShiftedLaplacianOperator.hpp +include/MueLu_ShiftedLaplacianOperator_decl.hpp +include/MueLu_ShiftedLaplacianOperator_def.hpp include/MueLu_ShiftedLaplacianOperator_fwd.hpp +include/MueLu_ShiftedLaplacian_decl.hpp +include/MueLu_ShiftedLaplacian_def.hpp include/MueLu_ShiftedLaplacian_fwd.hpp include/MueLu_SimpleSmoother.hpp include/MueLu_SimpleSmoother_decl.hpp @@ -2676,6 +2710,13 @@ include/MueLu_VariableDofLaplacianFactory.hpp include/MueLu_VariableDofLaplacianFactory_decl.hpp include/MueLu_VariableDofLaplacianFactory_def.hpp include/MueLu_VariableDofLaplacianFactory_fwd.hpp +include/MueLu_VectorDroppingBase.hpp +include/MueLu_VectorDroppingClassical.hpp +include/MueLu_VectorDroppingClassical_decl.hpp +include/MueLu_VectorDroppingClassical_def.hpp +include/MueLu_VectorDroppingDistanceLaplacian.hpp +include/MueLu_VectorDroppingDistanceLaplacian_decl.hpp +include/MueLu_VectorDroppingDistanceLaplacian_def.hpp include/MueLu_VerboseObject.hpp include/MueLu_VerbosityLevel.hpp include/MueLu_Version.hpp @@ -2821,8 +2862,13 @@ include/NOX_Thyra_MatrixFreeJacobianOperator_impl.hpp include/NOX_Thyra_MultiVector.H include/NOX_Thyra_Vector.H include/NOX_TpetraTypedefs.hpp +include/NOX_Tpetra_MultiVector.hpp +include/NOX_Tpetra_MultiVector_def.hpp +include/NOX_Tpetra_Vector.hpp +include/NOX_Tpetra_Vector_def.hpp include/NOX_Utils.H include/OED_SplitComm.hpp +include/ObjectLifetimeSpy.hpp include/PamgenStrLoopLimits.h include/Pamgen_config.h include/PanzerCore_config.hpp @@ -2883,12 +2929,12 @@ include/Phalanx_KokkosViewOfViews.hpp include/Phalanx_KokkosView_AllocationSize.hpp include/Phalanx_KokkosView_CreateView.hpp include/Phalanx_KokkosView_HiddenDimensionForSFINAE.hpp -include/Phalanx_Kokkos_PrintViewValues.hpp include/Phalanx_Kokkos_Tools_CheckStreams.hpp include/Phalanx_MDField.hpp include/Phalanx_MDField_UnmanagedAllocator.hpp include/Phalanx_MemoryManager.hpp include/Phalanx_Print.hpp +include/Phalanx_PrintValues.hpp include/Phalanx_Scratch_Utilities.hpp include/Phalanx_TemplateIterator.hpp include/Phalanx_TemplateManager.hpp @@ -2901,8 +2947,6 @@ include/Piro_CustomLBFGSSecant.hpp include/Piro_Helpers.hpp include/Piro_InvertMassMatrixDecorator.hpp include/Piro_InvertMassMatrixDecorator_Def.hpp -include/Piro_LOCAAdaptiveSolver.hpp -include/Piro_LOCAAdaptiveSolver_Def.hpp include/Piro_LOCASolver.hpp include/Piro_LOCASolver_Def.hpp include/Piro_MatrixFreeDecorator.hpp @@ -2943,8 +2987,6 @@ include/Piro_TransientSolver_Def.hpp include/Piro_TrapezoidRuleSolver.hpp include/Piro_TrapezoidRuleSolver_Def.hpp include/Piro_ValidPiroParameters.hpp -include/Piro_VelocityVerletSolver.hpp -include/Piro_VelocityVerletSolver_Def.hpp include/Piro_Version.hpp include/Piro_config.hpp include/ProblemLOCAPrototype.H @@ -3134,6 +3176,7 @@ include/ROL_GenMoreauYosidaCVaR.hpp include/ROL_GenericFunction.hpp include/ROL_GenericUnaryFunction.hpp include/ROL_GetTestProblems.hpp +include/ROL_GlobalMPISession.hpp include/ROL_GoldenSection.hpp include/ROL_GoldenSectionScalarMinimization.hpp include/ROL_GradientStep.hpp @@ -3800,6 +3843,10 @@ include/Sacado_Fad_GeneralFad.hpp include/Sacado_Fad_GeneralFadExpr.hpp include/Sacado_Fad_GeneralFadTestingHelpers.hpp include/Sacado_Fad_GeneralFad_MP_Vector.hpp +include/Sacado_Fad_Kokkos_Specialization.hpp +include/Sacado_Fad_Kokkos_TeuchosComm.hpp +include/Sacado_Fad_Kokkos_ThreadLocalScalar.hpp +include/Sacado_Fad_Kokkos_View_Support.hpp include/Sacado_Fad_LAPACK.hpp include/Sacado_Fad_LAPACKImp.hpp include/Sacado_Fad_MP_Vector.hpp @@ -3881,10 +3928,6 @@ include/Sacado_TemplateIterator.hpp include/Sacado_TemplateManager.hpp include/Sacado_TemplateManagerImp.hpp include/Sacado_Traits.hpp -include/Sacado_UQ_PCE.hpp -include/Sacado_UQ_PCE_Imp.hpp -include/Sacado_UQ_PCE_ScalarTraitsImp.hpp -include/Sacado_UQ_PCE_Traits.hpp include/Sacado_Version.hpp include/Sacado_cmath.hpp include/Sacado_config.h @@ -3941,6 +3984,7 @@ include/Shards_config.h include/ShyLU_NodeFastILU_config.h include/SideGeometry.hpp include/Simd.hpp +include/SimdAVX512Specializations.hpp include/SimdBool.hpp include/SimdBoolF.hpp include/SimdDouble.hpp @@ -3951,6 +3995,7 @@ include/SimdFloat.hpp include/SimdFloatLoadStore.hpp include/SimdFloatMath.hpp include/SimdFloatOperators.hpp +include/SimdLoadStoreImpl.hpp include/SortingTools.h include/StkMath.hpp include/StkPlane.hpp @@ -3963,7 +4008,6 @@ include/Stokhos_AdaptivityUtils.hpp include/Stokhos_AlgebraicOrthogPolyExpansion.hpp include/Stokhos_AlgebraicOrthogPolyExpansionImp.hpp include/Stokhos_Amesos2_MP_Vector.hpp -include/Stokhos_Amesos2_UQ_PCE.hpp include/Stokhos_AnisoSparseGridQuadrature.hpp include/Stokhos_AnisoSparseGridQuadratureImp.hpp include/Stokhos_ApproxGaussSeidelPreconditioner.hpp @@ -4032,7 +4076,6 @@ include/Stokhos_GrowthRules.hpp include/Stokhos_HermiteBasis.hpp include/Stokhos_HermiteBasisImp.hpp include/Stokhos_Ifpack2_MP_Vector.hpp -include/Stokhos_Ifpack2_UQ_PCE.hpp include/Stokhos_IfpackPreconditionerFactory.hpp include/Stokhos_InterlacedOperator.hpp include/Stokhos_InversePreconditioner.hpp @@ -4085,7 +4128,6 @@ include/Stokhos_MonomialProjGramSchmidtPCEBasis2.hpp include/Stokhos_MonomialProjGramSchmidtPCEBasis2Imp.hpp include/Stokhos_MonomialProjGramSchmidtPCEBasisImp.hpp include/Stokhos_MueLu_MP_Vector.hpp -include/Stokhos_MueLu_UQ_PCE.hpp include/Stokhos_Multiply.hpp include/Stokhos_OneDOrthogPolyBasis.hpp include/Stokhos_Operator.hpp @@ -4151,7 +4193,6 @@ include/Stokhos_Sacado.hpp include/Stokhos_Sacado_Kokkos.hpp include/Stokhos_Sacado_Kokkos_MP_Vector.hpp include/Stokhos_Sacado_Kokkos_MathFunctions.hpp -include/Stokhos_Sacado_Kokkos_UQ_PCE.hpp include/Stokhos_Sacado_MathFunctions.hpp include/Stokhos_SchurPreconditioner.hpp include/Stokhos_SchurPreconditionerImp.hpp @@ -4197,13 +4238,9 @@ include/Stokhos_TotalOrderBasisImp.hpp include/Stokhos_Tpetra_CG.hpp include/Stokhos_Tpetra_ETI_Helpers_MP_Vector.hpp include/Stokhos_Tpetra_ETI_Helpers_MP_Vector_ENSEMBLE_SIZE_DEVICE.hpp -include/Stokhos_Tpetra_ETI_Helpers_UQ_PCE.hpp -include/Stokhos_Tpetra_ETI_Helpers_UQ_PCE_DEVICE.hpp include/Stokhos_Tpetra_MP_Vector.hpp -include/Stokhos_Tpetra_UQ_PCE.hpp include/Stokhos_Tpetra_Utilities.hpp include/Stokhos_Tpetra_Utilities_MP_Vector.hpp -include/Stokhos_Tpetra_Utilities_UQ_PCE.hpp include/Stokhos_Update.hpp include/Stokhos_UserDefinedQuadrature.hpp include/Stokhos_UserDefinedQuadratureImp.hpp @@ -4213,7 +4250,6 @@ include/Stokhos_VectorOrthogPolyTraitsEpetra.hpp include/Stokhos_Version.hpp include/Stokhos_ViewStorage.hpp include/Stokhos_Xpetra_MP_Vector.hpp -include/Stokhos_Xpetra_UQ_PCE.hpp include/Stokhos_config.h include/Stokhos_gaussq.h include/Stokhos_mpl_for_each.hpp @@ -4299,6 +4335,7 @@ include/Tacho_MatrixMarket.hpp include/Tacho_ModifyDiagonals.hpp include/Tacho_ModifyDiagonals_Internal.hpp include/Tacho_ModifyDiagonals_OnDevice.hpp +include/Tacho_NonPivLDL_OnDevice.hpp include/Tacho_NumericTools_Base.hpp include/Tacho_NumericTools_Factory.hpp include/Tacho_NumericTools_LevelSet.hpp @@ -4328,6 +4365,10 @@ include/Tacho_TeamFunctor_SolveLowerLU.hpp include/Tacho_TeamFunctor_SolveUpperChol.hpp include/Tacho_TeamFunctor_SolveUpperLDL.hpp include/Tacho_TeamFunctor_SolveUpperLU.hpp +include/Tacho_Trmv.hpp +include/Tacho_Trmv_External.hpp +include/Tacho_Trmv_Internal.hpp +include/Tacho_Trmv_OnDevice.hpp include/Tacho_Trsm.hpp include/Tacho_Trsm_External.hpp include/Tacho_Trsm_Internal.hpp @@ -4340,6 +4381,7 @@ include/Tacho_Trsv_OnDevice.hpp include/Tacho_Trsv_Serial.hpp include/Tacho_Util.hpp include/Tacho_config.h +include/Teko_AdaptivePreconditionerFactory.hpp include/Teko_AddPreconditionerFactory.hpp include/Teko_BlockDiagonalInverseOp.hpp include/Teko_BlockImplicitLinearOp.hpp @@ -4688,148 +4730,6 @@ include/Tempus_WrapperModelEvaluatorSecondOrder.hpp include/Tempus_WrapperModelEvaluatorSecondOrder_decl.hpp include/Tempus_WrapperModelEvaluatorSecondOrder_impl.hpp include/Tempus_config.hpp -include/Test_Batched_BatchedGemm.hpp -include/Test_Batched_BatchedGemm_Complex.hpp -include/Test_Batched_BatchedGemm_Real.hpp -include/Test_Batched_Dense.hpp -include/Test_Batched_DenseUtils.hpp -include/Test_Batched_Dense_GEMM.hpp -include/Test_Batched_SerialAxpy.hpp -include/Test_Batched_SerialAxpy_Complex.hpp -include/Test_Batched_SerialAxpy_Real.hpp -include/Test_Batched_SerialEigendecomposition.hpp -include/Test_Batched_SerialEigendecomposition_Real.hpp -include/Test_Batched_SerialGMRES.hpp -include/Test_Batched_SerialGMRES_Real.hpp -include/Test_Batched_SerialGemm.hpp -include/Test_Batched_SerialGemm_Complex.hpp -include/Test_Batched_SerialGemm_Real.hpp -include/Test_Batched_SerialGesv.hpp -include/Test_Batched_SerialGesv_Real.hpp -include/Test_Batched_SerialIamax.hpp -include/Test_Batched_SerialInverseLU.hpp -include/Test_Batched_SerialInverseLU_Complex.hpp -include/Test_Batched_SerialInverseLU_Real.hpp -include/Test_Batched_SerialLU.hpp -include/Test_Batched_SerialLU_Complex.hpp -include/Test_Batched_SerialLU_Real.hpp -include/Test_Batched_SerialLaswp.hpp -include/Test_Batched_SerialPbtrf.hpp -include/Test_Batched_SerialPbtrf_Complex.hpp -include/Test_Batched_SerialPbtrf_Real.hpp -include/Test_Batched_SerialPbtrs.hpp -include/Test_Batched_SerialPbtrs_Complex.hpp -include/Test_Batched_SerialPbtrs_Real.hpp -include/Test_Batched_SerialPttrf.hpp -include/Test_Batched_SerialPttrf_Complex.hpp -include/Test_Batched_SerialPttrf_Real.hpp -include/Test_Batched_SerialPttrs.hpp -include/Test_Batched_SerialPttrs_Complex.hpp -include/Test_Batched_SerialPttrs_Real.hpp -include/Test_Batched_SerialSVD.hpp -include/Test_Batched_SerialSolveLU.hpp -include/Test_Batched_SerialSolveLU_Complex.hpp -include/Test_Batched_SerialSolveLU_Real.hpp -include/Test_Batched_SerialSpmv.hpp -include/Test_Batched_SerialSpmv_Real.hpp -include/Test_Batched_SerialTbsv.hpp -include/Test_Batched_SerialTbsv_Complex.hpp -include/Test_Batched_SerialTbsv_Real.hpp -include/Test_Batched_SerialTrmm.hpp -include/Test_Batched_SerialTrmm_Complex.hpp -include/Test_Batched_SerialTrmm_Real.hpp -include/Test_Batched_SerialTrsm.hpp -include/Test_Batched_SerialTrsm_Complex.hpp -include/Test_Batched_SerialTrsm_Real.hpp -include/Test_Batched_SerialTrsv.hpp -include/Test_Batched_SerialTrsv_Complex.hpp -include/Test_Batched_SerialTrsv_Real.hpp -include/Test_Batched_SerialTrtri.hpp -include/Test_Batched_SerialTrtri_Complex.hpp -include/Test_Batched_SerialTrtri_Real.hpp -include/Test_Batched_Sparse.hpp -include/Test_Batched_SparseUtils.hpp -include/Test_Batched_TeamAxpy.hpp -include/Test_Batched_TeamAxpy_Complex.hpp -include/Test_Batched_TeamAxpy_Real.hpp -include/Test_Batched_TeamCG.hpp -include/Test_Batched_TeamCG_Real.hpp -include/Test_Batched_TeamGMRES.hpp -include/Test_Batched_TeamGMRES_Real.hpp -include/Test_Batched_TeamGemm.hpp -include/Test_Batched_TeamGemm_Complex.hpp -include/Test_Batched_TeamGemm_Real.hpp -include/Test_Batched_TeamGesv.hpp -include/Test_Batched_TeamGesv_Real.hpp -include/Test_Batched_TeamInverseLU.hpp -include/Test_Batched_TeamInverseLU_Complex.hpp -include/Test_Batched_TeamInverseLU_Real.hpp -include/Test_Batched_TeamLU.hpp -include/Test_Batched_TeamLU_Complex.hpp -include/Test_Batched_TeamLU_Real.hpp -include/Test_Batched_TeamSolveLU.hpp -include/Test_Batched_TeamSolveLU_Complex.hpp -include/Test_Batched_TeamSolveLU_Real.hpp -include/Test_Batched_TeamSpmv.hpp -include/Test_Batched_TeamSpmv_Real.hpp -include/Test_Batched_TeamTrsm.hpp -include/Test_Batched_TeamTrsm_Complex.hpp -include/Test_Batched_TeamTrsm_Real.hpp -include/Test_Batched_TeamTrsv.hpp -include/Test_Batched_TeamTrsv_Complex.hpp -include/Test_Batched_TeamTrsv_Real.hpp -include/Test_Batched_TeamVectorAxpy.hpp -include/Test_Batched_TeamVectorAxpy_Complex.hpp -include/Test_Batched_TeamVectorAxpy_Real.hpp -include/Test_Batched_TeamVectorCG.hpp -include/Test_Batched_TeamVectorCG_Real.hpp -include/Test_Batched_TeamVectorEigendecomposition.hpp -include/Test_Batched_TeamVectorEigendecomposition_Real.hpp -include/Test_Batched_TeamVectorGMRES.hpp -include/Test_Batched_TeamVectorGMRES_Real.hpp -include/Test_Batched_TeamVectorGemm.hpp -include/Test_Batched_TeamVectorGemm_Complex.hpp -include/Test_Batched_TeamVectorGemm_Real.hpp -include/Test_Batched_TeamVectorGesv.hpp -include/Test_Batched_TeamVectorGesv_Real.hpp -include/Test_Batched_TeamVectorQR.hpp -include/Test_Batched_TeamVectorQR_Real.hpp -include/Test_Batched_TeamVectorQR_WithColumnPivoting.hpp -include/Test_Batched_TeamVectorQR_WithColumnPivoting_Real.hpp -include/Test_Batched_TeamVectorSolveUTV.hpp -include/Test_Batched_TeamVectorSolveUTV2.hpp -include/Test_Batched_TeamVectorSolveUTV2_Real.hpp -include/Test_Batched_TeamVectorSolveUTV_Real.hpp -include/Test_Batched_TeamVectorSpmv.hpp -include/Test_Batched_TeamVectorSpmv_Real.hpp -include/Test_Batched_TeamVectorUTV.hpp -include/Test_Batched_TeamVectorUTV_Real.hpp -include/Test_Batched_VectorArithmatic.hpp -include/Test_Batched_VectorLogical.hpp -include/Test_Batched_VectorMath.hpp -include/Test_Batched_VectorMisc.hpp -include/Test_Batched_VectorRelation.hpp -include/Test_Batched_VectorView.hpp -include/Test_Common.hpp -include/Test_Common_AlignPtrTo.hpp -include/Test_Common_ArithTraits.hpp -include/Test_Common_Error.hpp -include/Test_Common_IOUtils.hpp -include/Test_Common_Iota.hpp -include/Test_Common_LowerBound.hpp -include/Test_Common_PrintConfiguration.hpp -include/Test_Common_Sorting.hpp -include/Test_Common_UpperBound.hpp -include/Test_Common_Version.hpp -include/Test_Common_float128.hpp -include/Test_Common_set_bit_count.hpp -include/Test_ODE.hpp -include/Test_ODE_BDF.hpp -include/Test_ODE_Newton.hpp -include/Test_ODE_RK.hpp -include/Test_ODE_RK_chem.hpp -include/Test_ODE_RK_counts.hpp -include/Test_ODE_TestProblems.hpp include/TeuchosCore_ConfigDefs.hpp include/TeuchosCore_config.h include/TeuchosKokkosComm_config.h @@ -4847,9 +4747,9 @@ include/Teuchos_ArrayViewDecl.hpp include/Teuchos_Assert.hpp include/Teuchos_BLAS.hpp include/Teuchos_BLAS_MP_Vector.hpp -include/Teuchos_BLAS_UQ_PCE.hpp include/Teuchos_BLAS_types.hpp include/Teuchos_BLAS_wrappers.hpp +include/Teuchos_Behavior.hpp include/Teuchos_BigUInt.hpp include/Teuchos_BigUIntDecl.hpp include/Teuchos_CTimeMonitor.h @@ -4883,6 +4783,7 @@ include/Teuchos_Details_MpiTypeTraits.hpp include/Teuchos_DummyObjectGetter.hpp include/Teuchos_ENull.hpp include/Teuchos_EReductionType.hpp +include/Teuchos_EnvVariables.hpp include/Teuchos_Exceptions.hpp include/Teuchos_ExpandScalarTypeMacros.hpp include/Teuchos_ExpatHandlerAdapter.hpp @@ -4911,7 +4812,6 @@ include/Teuchos_InvalidConditionException.hpp include/Teuchos_InvalidDependencyException.hpp include/Teuchos_LAPACK.hpp include/Teuchos_LAPACK_MP_Vector.hpp -include/Teuchos_LAPACK_UQ_PCE.hpp include/Teuchos_LAPACK_wrappers.hpp include/Teuchos_LabeledObject.hpp include/Teuchos_Language.hpp @@ -4981,7 +4881,6 @@ include/Teuchos_SerialDenseSolver.hpp include/Teuchos_SerialDenseVector.hpp include/Teuchos_SerialQRDenseSolver.hpp include/Teuchos_SerialQRDenseSolver_MP_Vector.hpp -include/Teuchos_SerialQRDenseSolver_UQ_PCE.hpp include/Teuchos_SerialSpdDenseSolver.hpp include/Teuchos_SerialSymDenseMatrix.hpp include/Teuchos_SerialTriDiMatrix.hpp @@ -5011,6 +4910,7 @@ include/Teuchos_StringIndexedOrderedValueObjectContainer.hpp include/Teuchos_StringInputSource.hpp include/Teuchos_StringInputStream.hpp include/Teuchos_StringToIntMap.hpp +include/Teuchos_SystemInformation.hpp include/Teuchos_TableColumn.hpp include/Teuchos_TableDecl.hpp include/Teuchos_TableEntry.hpp @@ -5420,6 +5320,7 @@ include/Thyra_apply_op_helper_def.hpp include/Thyra_describeLinearOp.hpp include/Thyra_describeLinearOp_decl.hpp include/Thyra_describeLinearOp_def.hpp +include/TpetraCheckingTools.hpp include/TpetraCore_ETIHelperMacros.h include/TpetraCore_config.h include/TpetraExt_MMHelpers.hpp @@ -5439,6 +5340,7 @@ include/TpetraExt_MatrixMatrix_fwd.hpp include/TpetraExt_TripleMatrixMultiply.hpp include/TpetraExt_TripleMatrixMultiply_decl.hpp include/TpetraExt_TripleMatrixMultiply_def.hpp +include/TpetraSortingTools.hpp include/TpetraTSQR_config.h include/Tpetra_Access.hpp include/Tpetra_ApplyOp.hpp @@ -5475,11 +5377,12 @@ include/Tpetra_CrsGraph_fwd.hpp include/Tpetra_CrsMatrix.hpp include/Tpetra_CrsMatrixMultiplyOp.hpp include/Tpetra_CrsMatrixMultiplyOp_fwd.hpp -include/Tpetra_CrsMatrix_UQ_PCE.hpp -include/Tpetra_CrsMatrix_UQ_PCE_def.hpp include/Tpetra_CrsMatrix_decl.hpp include/Tpetra_CrsMatrix_def.hpp include/Tpetra_CrsMatrix_fwd.hpp +include/Tpetra_CrsSingletonFilter_LinearProblem.hpp +include/Tpetra_CrsSingletonFilter_LinearProblem_decl.hpp +include/Tpetra_CrsSingletonFilter_LinearProblem_def.hpp include/Tpetra_Details_Behavior.hpp include/Tpetra_Details_Blas.hpp include/Tpetra_Details_CooMatrix.hpp @@ -5509,6 +5412,8 @@ include/Tpetra_Details_PackTraits.hpp include/Tpetra_Details_PackTriples.hpp include/Tpetra_Details_Profiling.hpp include/Tpetra_Details_Random.hpp +include/Tpetra_Details_Random_decl.hpp +include/Tpetra_Details_Random_def.hpp include/Tpetra_Details_ReadTriples.hpp include/Tpetra_Details_ScalarViewTraits.hpp include/Tpetra_Details_StaticView.hpp @@ -5533,7 +5438,6 @@ include/Tpetra_Details_extractBlockDiagonal.hpp include/Tpetra_Details_extractMpiCommFromTeuchos.hpp include/Tpetra_Details_fill.hpp include/Tpetra_Details_fill_MP_Vector.hpp -include/Tpetra_Details_fill_UQ_PCE.hpp include/Tpetra_Details_gathervPrint.hpp include/Tpetra_Details_get1DConstView.hpp include/Tpetra_Details_getDiagCopyWithoutOffsets.hpp @@ -5617,6 +5521,7 @@ include/Tpetra_FEMultiVector.hpp include/Tpetra_FEMultiVector_decl.hpp include/Tpetra_FEMultiVector_def.hpp include/Tpetra_FEMultiVector_fwd.hpp +include/Tpetra_Filter.hpp include/Tpetra_HashTable.hpp include/Tpetra_HashTable_decl.hpp include/Tpetra_HashTable_def.hpp @@ -5635,10 +5540,8 @@ include/Tpetra_KokkosCompat_ClassicNodeAPI_Wrapper.hpp include/Tpetra_KokkosCompat_DefaultNode.hpp include/Tpetra_KokkosRefactor_Details_MultiVectorDistObjectKernels.hpp include/Tpetra_KokkosRefactor_Details_MultiVectorDistObjectKernels_MP_Vector.hpp -include/Tpetra_KokkosRefactor_Details_MultiVectorDistObjectKernels_UQ_PCE.hpp include/Tpetra_KokkosRefactor_Details_MultiVectorLocalDeepCopy.hpp include/Tpetra_KokkosRefactor_Details_MultiVectorLocalDeepCopy_MP_Vector.hpp -include/Tpetra_KokkosRefactor_Details_MultiVectorLocalDeepCopy_UQ_PCE.hpp include/Tpetra_LinearProblem.hpp include/Tpetra_LinearProblem_decl.hpp include/Tpetra_LinearProblem_def.hpp @@ -5665,6 +5568,15 @@ include/Tpetra_Operator.hpp include/Tpetra_Operator_fwd.hpp include/Tpetra_Packable.hpp include/Tpetra_Packable_fwd.hpp +include/Tpetra_Reindex_CrsMatrix.hpp +include/Tpetra_Reindex_CrsMatrix_decl.hpp +include/Tpetra_Reindex_CrsMatrix_def.hpp +include/Tpetra_Reindex_LinearProblem.hpp +include/Tpetra_Reindex_LinearProblem_decl.hpp +include/Tpetra_Reindex_LinearProblem_def.hpp +include/Tpetra_Reindex_MultiVector.hpp +include/Tpetra_Reindex_MultiVector_decl.hpp +include/Tpetra_Reindex_MultiVector_def.hpp include/Tpetra_RowGraph.hpp include/Tpetra_RowGraph_decl.hpp include/Tpetra_RowGraph_def.hpp @@ -5677,13 +5589,20 @@ include/Tpetra_RowMatrixTransposer_fwd.hpp include/Tpetra_RowMatrix_decl.hpp include/Tpetra_RowMatrix_def.hpp include/Tpetra_RowMatrix_fwd.hpp +include/Tpetra_SolverMap_CrsMatrix.hpp +include/Tpetra_SolverMap_CrsMatrix_decl.hpp +include/Tpetra_SolverMap_CrsMatrix_def.hpp +include/Tpetra_SolverMap_LinearProblem.hpp +include/Tpetra_SolverMap_LinearProblem_decl.hpp +include/Tpetra_SolverMap_LinearProblem_def.hpp include/Tpetra_SrcDistObject.hpp include/Tpetra_TieBreak.hpp include/Tpetra_TieBreak_fwd.hpp +include/Tpetra_Transform.hpp include/Tpetra_TsqrAdaptor.hpp include/Tpetra_TsqrAdaptor_MP_Vector.hpp -include/Tpetra_TsqrAdaptor_UQ_PCE.hpp include/Tpetra_Util.hpp +include/Tpetra_Util_iohb.h include/Tpetra_Vector.hpp include/Tpetra_Vector_decl.hpp include/Tpetra_Vector_def.hpp @@ -5703,6 +5622,8 @@ include/Tpetra_replaceDiagonalCrsMatrix_decl.hpp include/Tpetra_replaceDiagonalCrsMatrix_def.hpp include/Traits.hpp include/TrilinosConfig.cmake +include/TrilinosCouplings_Rebalance_LinearProblem_decl.hpp +include/TrilinosCouplings_Rebalance_LinearProblem_def.hpp include/TrilinosCouplings_Version.h include/TrilinosCouplings_config.h include/TrilinosSS_config.h @@ -5784,7 +5705,6 @@ include/Tsqr_generateStack.hpp include/Tsqr_nodeTestProblem.hpp include/Tsqr_printGlobalMatrix.hpp include/Tsqr_verifyTimerConcept.hpp -include/Xpetra_Access.hpp include/Xpetra_BlockReorderManager.hpp include/Xpetra_BlockedCrsMatrix.hpp include/Xpetra_BlockedCrsMatrix_decl.hpp @@ -5810,7 +5730,6 @@ include/Xpetra_CrsGraph_fwd.hpp include/Xpetra_CrsMatrix.hpp include/Xpetra_CrsMatrixFactory.hpp include/Xpetra_CrsMatrixFactory_fwd.hpp -include/Xpetra_CrsMatrixUtils.hpp include/Xpetra_CrsMatrixUtils_fwd.hpp include/Xpetra_CrsMatrixWrap.hpp include/Xpetra_CrsMatrixWrap_decl.hpp @@ -5860,9 +5779,7 @@ include/Xpetra_IO_def.hpp include/Xpetra_Import.hpp include/Xpetra_ImportFactory.hpp include/Xpetra_ImportFactory_fwd.hpp -include/Xpetra_ImportUtils.hpp include/Xpetra_Import_fwd.hpp -include/Xpetra_IteratorOps.hpp include/Xpetra_Map.hpp include/Xpetra_MapExtractor.hpp include/Xpetra_MapExtractorFactory.hpp @@ -6315,6 +6232,7 @@ include/kokkos/Cuda/Kokkos_Cuda_GraphNode_Impl.hpp include/kokkos/Cuda/Kokkos_Cuda_Graph_Impl.hpp include/kokkos/Cuda/Kokkos_Cuda_Half_Conversion.hpp include/kokkos/Cuda/Kokkos_Cuda_Half_Impl_Type.hpp +include/kokkos/Cuda/Kokkos_Cuda_Half_MathematicalFunctions.hpp include/kokkos/Cuda/Kokkos_Cuda_Instance.hpp include/kokkos/Cuda/Kokkos_Cuda_KernelLaunch.hpp include/kokkos/Cuda/Kokkos_Cuda_MDRangePolicy.hpp @@ -6341,6 +6259,7 @@ include/kokkos/HIP/Kokkos_HIP_Graph_Impl.hpp include/kokkos/HIP/Kokkos_HIP_Half_Conversion.hpp include/kokkos/HIP/Kokkos_HIP_Half_Impl_Type.hpp include/kokkos/HIP/Kokkos_HIP_Instance.hpp +include/kokkos/HIP/Kokkos_HIP_IsXnack.hpp include/kokkos/HIP/Kokkos_HIP_KernelLaunch.hpp include/kokkos/HIP/Kokkos_HIP_MDRangePolicy.hpp include/kokkos/HIP/Kokkos_HIP_ParallelFor_MDRange.hpp @@ -6427,6 +6346,7 @@ include/kokkos/Kokkos_SIMD_AVX512.hpp include/kokkos/Kokkos_SIMD_Common.hpp include/kokkos/Kokkos_SIMD_Common_Math.hpp include/kokkos/Kokkos_SIMD_NEON.hpp +include/kokkos/Kokkos_SIMD_SVE.hpp include/kokkos/Kokkos_SIMD_Scalar.hpp include/kokkos/Kokkos_ScatterView.hpp include/kokkos/Kokkos_ScratchSpace.hpp @@ -6503,6 +6423,7 @@ include/kokkos/SYCL/Kokkos_SYCL_GraphNode_Impl.hpp include/kokkos/SYCL/Kokkos_SYCL_Graph_Impl.hpp include/kokkos/SYCL/Kokkos_SYCL_Half_Conversion.hpp include/kokkos/SYCL/Kokkos_SYCL_Half_Impl_Type.hpp +include/kokkos/SYCL/Kokkos_SYCL_Half_MathematicalFunctions.hpp include/kokkos/SYCL/Kokkos_SYCL_Instance.hpp include/kokkos/SYCL/Kokkos_SYCL_MDRangePolicy.hpp include/kokkos/SYCL/Kokkos_SYCL_ParallelFor_MDRange.hpp @@ -6544,8 +6465,10 @@ include/kokkos/Threads/Kokkos_Threads_UniqueToken.hpp include/kokkos/Threads/Kokkos_Threads_WorkGraphPolicy.hpp include/kokkos/View/Hooks/Kokkos_ViewHooks.hpp include/kokkos/View/Kokkos_BasicView.hpp +include/kokkos/View/Kokkos_ViewAccessPreconditionsCheck.hpp include/kokkos/View/Kokkos_ViewAlloc.hpp include/kokkos/View/Kokkos_ViewAtomic.hpp +include/kokkos/View/Kokkos_ViewCommonType.hpp include/kokkos/View/Kokkos_ViewCtor.hpp include/kokkos/View/Kokkos_ViewDataAnalysis.hpp include/kokkos/View/Kokkos_ViewLegacy.hpp @@ -6665,7 +6588,6 @@ include/kokkos/fwd/Kokkos_Fwd_THREADS.hpp include/kokkos/impl/KokkosExp_Host_IterateTile.hpp include/kokkos/impl/KokkosExp_IterateTileGPU.hpp include/kokkos/impl/Kokkos_AnalyzePolicy.hpp -include/kokkos/impl/Kokkos_BitOps.hpp include/kokkos/impl/Kokkos_Bitset_impl.hpp include/kokkos/impl/Kokkos_CPUDiscovery.hpp include/kokkos/impl/Kokkos_ChaseLev.hpp @@ -6690,6 +6612,7 @@ include/kokkos/impl/Kokkos_GraphImpl_Utilities.hpp include/kokkos/impl/Kokkos_GraphImpl_fwd.hpp include/kokkos/impl/Kokkos_GraphNodeCustomization.hpp include/kokkos/impl/Kokkos_GraphNodeImpl.hpp +include/kokkos/impl/Kokkos_GraphNodeThenImpl.hpp include/kokkos/impl/Kokkos_Half_FloatingPointWrapper.hpp include/kokkos/impl/Kokkos_Half_MathematicalFunctions.hpp include/kokkos/impl/Kokkos_Half_NumericTraits.hpp @@ -6702,6 +6625,7 @@ include/kokkos/impl/Kokkos_InitializationSettings.hpp include/kokkos/impl/Kokkos_LIFO.hpp include/kokkos/impl/Kokkos_LinkedListNode.hpp include/kokkos/impl/Kokkos_MultipleTaskQueue.hpp +include/kokkos/impl/Kokkos_Neon_SVE_bridge.hpp include/kokkos/impl/Kokkos_NvidiaGpuArchitectures.hpp include/kokkos/impl/Kokkos_OptionalRef.hpp include/kokkos/impl/Kokkos_ParseCommandLineArgumentsAndEnvironmentVariables.hpp @@ -6927,6 +6851,7 @@ include/stk_ngp_test/NgpTestDeviceMacros.hpp include/stk_ngp_test/Reporter.hpp include/stk_ngp_test/ngp_test.hpp include/stk_simd/Simd.hpp +include/stk_simd/SimdAVX512Specializations.hpp include/stk_simd/SimdBool.hpp include/stk_simd/SimdBoolF.hpp include/stk_simd/SimdDouble.hpp @@ -6937,6 +6862,7 @@ include/stk_simd/SimdFloat.hpp include/stk_simd/SimdFloatLoadStore.hpp include/stk_simd/SimdFloatMath.hpp include/stk_simd/SimdFloatOperators.hpp +include/stk_simd/SimdLoadStoreImpl.hpp include/stk_simd/Traits.hpp include/stk_simd/kokkos_simd/avx.hpp include/stk_simd/kokkos_simd/avx512.hpp @@ -6967,11 +6893,14 @@ include/stk_topology/topology_utils.hpp include/stk_topology/types.hpp include/stk_unit_test_utils/AssemblyUtils.hpp include/stk_unit_test_utils/CommandLineArgs.hpp +include/stk_unit_test_utils/Legendre.hpp +include/stk_unit_test_utils/ObjectLifetimeSpy.hpp include/stk_unit_test_utils/StkReportRedirector.hpp include/stk_unit_test_utils/algorithmTimer.hpp include/stk_unit_test_utils/getOption.h include/stk_unit_test_utils/stringAndNumberComparisons.hpp -include/stk_util/STK_Trilinos_config.h +include/stk_unit_test_utils/timer.hpp +include/stk_util/STK_cmake_config.h include/stk_util/Version.hpp include/stk_util/command_line/CommandLineParser.hpp include/stk_util/command_line/CommandLineParserParallel.hpp @@ -6979,13 +6908,10 @@ include/stk_util/command_line/CommandLineParserUtils.hpp include/stk_util/diag/FArrayPrint.hpp include/stk_util/diag/Option.hpp include/stk_util/diag/ParallelTimerImpl.hpp -include/stk_util/diag/ParserVarUtil.hpp include/stk_util/diag/Platform.hpp include/stk_util/diag/PrintTable.hpp include/stk_util/diag/PrintTimer.hpp -include/stk_util/diag/Resource2.h include/stk_util/diag/SlibDiagWriter.hpp -include/stk_util/diag/String.hpp include/stk_util/diag/StringUtil.hpp include/stk_util/diag/Timer.hpp include/stk_util/diag/TimerImpl.hpp @@ -7037,6 +6963,7 @@ include/stk_util/util/AlignedAllocator.hpp include/stk_util/util/AllocatorMemoryUsage.hpp include/stk_util/util/AnyData.hpp include/stk_util/util/Array.hpp +include/stk_util/util/Blas.hpp include/stk_util/util/BlasLapack.hpp include/stk_util/util/Bootstrap.hpp include/stk_util/util/CSet.hpp @@ -7051,6 +6978,7 @@ include/stk_util/util/Fortran.hpp include/stk_util/util/GetEnv.hpp include/stk_util/util/GraphCycleDetector.hpp include/stk_util/util/IndentStreambuf.hpp +include/stk_util/util/Lapack.hpp include/stk_util/util/MCSR.hpp include/stk_util/util/MallocUsed.h include/stk_util/util/Marshal.hpp @@ -7059,7 +6987,6 @@ include/stk_util/util/NamedPair.hpp include/stk_util/util/Null_Streambuf.hpp include/stk_util/util/PairIter.hpp include/stk_util/util/ParameterList.hpp -include/stk_util/util/Pool.hpp include/stk_util/util/RadixSort.hpp include/stk_util/util/RemoveIntersection.hpp include/stk_util/util/ReportHandler.hpp @@ -7092,6 +7019,7 @@ include/stk_util/util/string_utils.hpp include/stk_util/util/tokenize.hpp include/stk_util/util/vectorization.hpp include/stringAndNumberComparisons.hpp +include/timer.hpp include/topology_enum.h include/trilinos_UFconfig.h include/trilinos_amd.h @@ -7358,6 +7286,7 @@ lib/cmake/tribits/ci_support/get-tribits-packages-from-files-list.py lib/cmake/tribits/ci_support/get-tribits-packages-from-last-tests-failed.py lib/cmake/tribits/ci_support/get-tribits-packages.py lib/cmake/tribits/ci_support/is_checkin_tested_commit.py +lib/cmake/tribits/common_tpls/FindTPLADIOS2.cmake lib/cmake/tribits/common_tpls/FindTPLBLAS.cmake lib/cmake/tribits/common_tpls/FindTPLBinUtils.cmake lib/cmake/tribits/common_tpls/FindTPLBoost.cmake @@ -8041,316 +7970,304 @@ lib/external_packages/UMFPACK/UMFPACKConfig.cmake lib/external_packages/UMFPACK/UMFPACKConfigVersion.cmake lib/libModeLaplace.so lib/libModeLaplace.so.16 -lib/libModeLaplace.so.16.1.0 +lib/libModeLaplace.so.16.2.0 +lib/libTpetraModeLaplace.so +lib/libTpetraModeLaplace.so.16 +lib/libTpetraModeLaplace.so.16.2.0 lib/libamesos.so lib/libamesos.so.16 -lib/libamesos.so.16.1.0 +lib/libamesos.so.16.2.0 lib/libamesos2.so lib/libamesos2.so.16 -lib/libamesos2.so.16.1.0 +lib/libamesos2.so.16.2.0 lib/libanasazi.so lib/libanasazi.so.16 -lib/libanasazi.so.16.1.0 +lib/libanasazi.so.16.2.0 lib/libanasaziepetra.so lib/libanasaziepetra.so.16 -lib/libanasaziepetra.so.16.1.0 +lib/libanasaziepetra.so.16.2.0 lib/libanasazitpetra.so lib/libanasazitpetra.so.16 -lib/libanasazitpetra.so.16.1.0 +lib/libanasazitpetra.so.16.2.0 lib/libaztecoo.so lib/libaztecoo.so.16 -lib/libaztecoo.so.16.1.0 +lib/libaztecoo.so.16.2.0 lib/libbelos.so lib/libbelos.so.16 -lib/libbelos.so.16.1.0 +lib/libbelos.so.16.2.0 lib/libbelosepetra.so lib/libbelosepetra.so.16 -lib/libbelosepetra.so.16.1.0 +lib/libbelosepetra.so.16.2.0 lib/libbelostpetra.so lib/libbelostpetra.so.16 -lib/libbelostpetra.so.16.1.0 +lib/libbelostpetra.so.16.2.0 lib/libbelosxpetra.so lib/libbelosxpetra.so.16 -lib/libbelosxpetra.so.16.1.0 +lib/libbelosxpetra.so.16.2.0 lib/libepetra.so lib/libepetra.so.16 -lib/libepetra.so.16.1.0 +lib/libepetra.so.16.2.0 lib/libepetraext.so lib/libepetraext.so.16 -lib/libepetraext.so.16.1.0 +lib/libepetraext.so.16.2.0 lib/libgaleri-epetra.so lib/libgaleri-epetra.so.16 -lib/libgaleri-epetra.so.16.1.0 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-lib/libstokhos_amesos2.so.16.1.0 +lib/libstokhos_amesos2.so.16.2.0 lib/libstokhos_ifpack2.so lib/libstokhos_ifpack2.so.16 -lib/libstokhos_ifpack2.so.16.1.0 +lib/libstokhos_ifpack2.so.16.2.0 lib/libstokhos_ifpack2_mp_16_serial.so lib/libstokhos_ifpack2_mp_16_serial.so.16 -lib/libstokhos_ifpack2_mp_16_serial.so.16.1.0 -lib/libstokhos_ifpack2_pce_serial.so -lib/libstokhos_ifpack2_pce_serial.so.16 -lib/libstokhos_ifpack2_pce_serial.so.16.1.0 +lib/libstokhos_ifpack2_mp_16_serial.so.16.2.0 lib/libstokhos_muelu.so lib/libstokhos_muelu.so.16 -lib/libstokhos_muelu.so.16.1.0 +lib/libstokhos_muelu.so.16.2.0 lib/libstokhos_muelu_mp_16_serial.so lib/libstokhos_muelu_mp_16_serial.so.16 -lib/libstokhos_muelu_mp_16_serial.so.16.1.0 -lib/libstokhos_muelu_pce_serial.so -lib/libstokhos_muelu_pce_serial.so.16 -lib/libstokhos_muelu_pce_serial.so.16.1.0 +lib/libstokhos_muelu_mp_16_serial.so.16.2.0 lib/libstokhos_sacado.so lib/libstokhos_sacado.so.16 -lib/libstokhos_sacado.so.16.1.0 +lib/libstokhos_sacado.so.16.2.0 lib/libstokhos_tpetra.so lib/libstokhos_tpetra.so.16 -lib/libstokhos_tpetra.so.16.1.0 +lib/libstokhos_tpetra.so.16.2.0 lib/libstokhos_tpetra_mp_16_serial.so lib/libstokhos_tpetra_mp_16_serial.so.16 -lib/libstokhos_tpetra_mp_16_serial.so.16.1.0 -lib/libstokhos_tpetra_pce_serial.so -lib/libstokhos_tpetra_pce_serial.so.16 -lib/libstokhos_tpetra_pce_serial.so.16.1.0 +lib/libstokhos_tpetra_mp_16_serial.so.16.2.0 lib/libstokhos_tpetra_sd_mp_16_serial.so lib/libstokhos_tpetra_sd_mp_16_serial.so.16 -lib/libstokhos_tpetra_sd_mp_16_serial.so.16.1.0 -lib/libstokhos_tpetra_sd_pce_serial.so -lib/libstokhos_tpetra_sd_pce_serial.so.16 -lib/libstokhos_tpetra_sd_pce_serial.so.16.1.0 +lib/libstokhos_tpetra_sd_mp_16_serial.so.16.2.0 lib/libstokhos_tpetraext_mp_16_serial.so lib/libstokhos_tpetraext_mp_16_serial.so.16 -lib/libstokhos_tpetraext_mp_16_serial.so.16.1.0 -lib/libstokhos_tpetraext_pce_serial.so -lib/libstokhos_tpetraext_pce_serial.so.16 -lib/libstokhos_tpetraext_pce_serial.so.16.1.0 +lib/libstokhos_tpetraext_mp_16_serial.so.16.2.0 lib/libstokhos_xpetra.so lib/libstokhos_xpetra.so.16 -lib/libstokhos_xpetra.so.16.1.0 +lib/libstokhos_xpetra.so.16.2.0 lib/libstokhos_xpetra_mp_16_serial.so lib/libstokhos_xpetra_mp_16_serial.so.16 -lib/libstokhos_xpetra_mp_16_serial.so.16.1.0 -lib/libstokhos_xpetra_pce_serial.so -lib/libstokhos_xpetra_pce_serial.so.16 -lib/libstokhos_xpetra_pce_serial.so.16.1.0 +lib/libstokhos_xpetra_mp_16_serial.so.16.2.0 lib/libstratimikos.so lib/libstratimikos.so.16 -lib/libstratimikos.so.16.1.0 +lib/libstratimikos.so.16.2.0 lib/libstratimikosamesos2.so lib/libstratimikosamesos2.so.16 -lib/libstratimikosamesos2.so.16.1.0 +lib/libstratimikosamesos2.so.16.2.0 lib/libstratimikosbelos.so lib/libstratimikosbelos.so.16 -lib/libstratimikosbelos.so.16.1.0 +lib/libstratimikosbelos.so.16.2.0 lib/libtacho.so lib/libtacho.so.16 -lib/libtacho.so.16.1.0 +lib/libtacho.so.16.2.0 lib/libteko.so lib/libteko.so.16 -lib/libteko.so.16.1.0 +lib/libteko.so.16.2.0 lib/libtempus.so lib/libtempus.so.16 -lib/libtempus.so.16.1.0 +lib/libtempus.so.16.2.0 lib/libteuchoscomm.so lib/libteuchoscomm.so.16 -lib/libteuchoscomm.so.16.1.0 +lib/libteuchoscomm.so.16.2.0 lib/libteuchoscore.so lib/libteuchoscore.so.16 -lib/libteuchoscore.so.16.1.0 +lib/libteuchoscore.so.16.2.0 lib/libteuchoskokkoscomm.so lib/libteuchoskokkoscomm.so.16 -lib/libteuchoskokkoscomm.so.16.1.0 +lib/libteuchoskokkoscomm.so.16.2.0 lib/libteuchoskokkoscompat.so lib/libteuchoskokkoscompat.so.16 -lib/libteuchoskokkoscompat.so.16.1.0 +lib/libteuchoskokkoscompat.so.16.2.0 lib/libteuchosnumerics.so lib/libteuchosnumerics.so.16 -lib/libteuchosnumerics.so.16.1.0 +lib/libteuchosnumerics.so.16.2.0 lib/libteuchosparameterlist.so lib/libteuchosparameterlist.so.16 -lib/libteuchosparameterlist.so.16.1.0 +lib/libteuchosparameterlist.so.16.2.0 lib/libteuchosparser.so lib/libteuchosparser.so.16 -lib/libteuchosparser.so.16.1.0 +lib/libteuchosparser.so.16.2.0 lib/libteuchosremainder.so lib/libteuchosremainder.so.16 -lib/libteuchosremainder.so.16.1.0 +lib/libteuchosremainder.so.16.2.0 lib/libthyracore.so lib/libthyracore.so.16 -lib/libthyracore.so.16.1.0 +lib/libthyracore.so.16.2.0 lib/libthyratpetra.so lib/libthyratpetra.so.16 -lib/libthyratpetra.so.16.1.0 +lib/libthyratpetra.so.16.2.0 lib/libtpetra.so lib/libtpetra.so.16 -lib/libtpetra.so.16.1.0 +lib/libtpetra.so.16.2.0 lib/libtpetraclassic.so lib/libtpetraclassic.so.16 -lib/libtpetraclassic.so.16.1.0 +lib/libtpetraclassic.so.16.2.0 lib/libtpetraext.so lib/libtpetraext.so.16 -lib/libtpetraext.so.16.1.0 +lib/libtpetraext.so.16.2.0 lib/libtpetrainout.so lib/libtpetrainout.so.16 -lib/libtpetrainout.so.16.1.0 +lib/libtpetrainout.so.16.2.0 lib/libtrilinoscouplings.so lib/libtrilinoscouplings.so.16 -lib/libtrilinoscouplings.so.16.1.0 +lib/libtrilinoscouplings.so.16.2.0 lib/libtrilinosss.so lib/libtrilinosss.so.16 -lib/libtrilinosss.so.16.1.0 +lib/libtrilinosss.so.16.2.0 lib/libtriutils.so lib/libtriutils.so.16 -lib/libtriutils.so.16.1.0 +lib/libtriutils.so.16.2.0 lib/libxpetra.so lib/libxpetra.so.16 -lib/libxpetra.so.16.1.0 +lib/libxpetra.so.16.2.0 lib/libzadelus.so lib/libzadelus.so.16 -lib/libzadelus.so.16.1.0 +lib/libzadelus.so.16.2.0 lib/libzoltan.so lib/libzoltan.so.16 -lib/libzoltan.so.16.1.0 +lib/libzoltan.so.16.2.0 lib/libzoltan2.so lib/libzoltan2.so.16 -lib/libzoltan2.so.16.1.0 +lib/libzoltan2.so.16.2.0 lib/libzoltan2sphynx.so lib/libzoltan2sphynx.so.16 -lib/libzoltan2sphynx.so.16.1.0 +lib/libzoltan2sphynx.so.16.2.0 diff --git a/science/wwplot/Makefile b/science/wwplot/Makefile index ab33bcd5f63e..616d7305b5ff 100644 --- a/science/wwplot/Makefile +++ b/science/wwplot/Makefile @@ -1,7 +1,6 @@ PORTNAME= wwplot DISTVERSIONPREFIX= v -DISTVERSION= 1.0.0 -PORTREVISION= 1 +DISTVERSION= 1.0.1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/wwplot/distinfo b/science/wwplot/distinfo index d13afa21537a..e99d77ecb996 100644 --- a/science/wwplot/distinfo +++ b/science/wwplot/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1713505502 -SHA256 (wwmm-wwplot-v1.0.0_GH0.tar.gz) = e2c04731dcd2c4c9ba37510504aef777adba0744ff7b3b8ddcf963dcc9bb6de8 -SIZE (wwmm-wwplot-v1.0.0_GH0.tar.gz) = 438404 +TIMESTAMP = 1762894379 +SHA256 (wwmm-wwplot-v1.0.1_GH0.tar.gz) = 913d264798bd5b807bcb5e385d0a1a91b78e26a476bcd089164045ca4f2cba2e +SIZE (wwmm-wwplot-v1.0.1_GH0.tar.gz) = 439519 diff --git a/science/xdrawchem/Makefile b/science/xdrawchem/Makefile index 0d25d06e5bdd..1107c82018c2 100644 --- a/science/xdrawchem/Makefile +++ b/science/xdrawchem/Makefile @@ -1,25 +1,25 @@ PORTNAME= xdrawchem -DISTVERSION= 1.11.0-2 -PORTREVISION= 2 +DISTVERSION= 1.11.1-2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Two-dimensional molecule drawing program -WWW= https://www.woodsidelabs.com/chemistry/xdrawchem.php +WWW= https://sourceforge.net/projects/xdrawchem/ \ + https://github.com/bryanherger/xdrawchem LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libopenbabel.so:science/openbabel -USES= compiler:c++11-lang gl qmake qt:5 +USES= compiler:c++11-lang gl pkgconfig qmake qt:5 USE_QT= core gui network printsupport svg widgets xml buildtools:build USE_GL= gl USE_GITLAB= yes GL_SITE= https://salsa.debian.org GL_ACCOUNT= georgesk -GL_TAGNAME= a3f74c34eb09fa72ee16848ec6901049ca5309d5 +GL_TAGNAME= 48f2e4817be451550a2cd80263344642a8611b15 pre-configure: ${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|' \ diff --git a/science/xdrawchem/distinfo b/science/xdrawchem/distinfo index c7880162be1b..c421a4325d93 100644 --- a/science/xdrawchem/distinfo +++ b/science/xdrawchem/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1617891979 -SHA256 (georgesk-xdrawchem-a3f74c34eb09fa72ee16848ec6901049ca5309d5_GL0.tar.gz) = f1b843ebeca09e8f242e927740a6668c2ceaaf4ff47816bd7a7510f33723ebab -SIZE (georgesk-xdrawchem-a3f74c34eb09fa72ee16848ec6901049ca5309d5_GL0.tar.gz) = 720241 +TIMESTAMP = 1762920603 +SHA256 (georgesk-xdrawchem-48f2e4817be451550a2cd80263344642a8611b15_GL0.tar.gz) = ffb94399cebdcdcb9d2011476d4094ec34ee95fe684d8a000b80da4c686f97be +SIZE (georgesk-xdrawchem-48f2e4817be451550a2cd80263344642a8611b15_GL0.tar.gz) = 719899 diff --git a/science/xdrawchem/files/patch-xdrawchem.pro b/science/xdrawchem/files/patch-xdrawchem.pro index f5121eaf6e9b..829d8ac9920c 100644 --- a/science/xdrawchem/files/patch-xdrawchem.pro +++ b/science/xdrawchem/files/patch-xdrawchem.pro @@ -1,38 +1,7 @@ ---- xdrawchem.pro.orig 2021-01-06 18:45:48 UTC +--- xdrawchem.pro.orig 2024-11-15 16:56:22 UTC +++ xdrawchem.pro -@@ -2,17 +2,17 @@ TEMPLATE = app - TARGET = xdrawchem +@@ -3,7 +3,7 @@ isEmpty(PREFIX) { - # edit to match your OB install --exists(/usr/include/openbabel3/openbabel/mol.h) { --INCLUDEPATH += /usr/include/openbabel3 -+exists(%%LOCALBASE%%/include/openbabel3/openbabel/mol.h) { -+INCLUDEPATH += %%LOCALBASE%%/include/openbabel3 - LIBS += -lopenbabel - } --exists(/usr/local/include/openbabel-3.0/openbabel/mol.h) { --INCLUDEPATH += /usr/local/include/openbabel-3.0 -+exists(%%LOCALBASE%%/include/openbabel3/openbabel/mol.h) { -+INCLUDEPATH += %%LOCALBASE%%/include/openbabel3 - LIBS += -lopenbabel - } --exists(/Developer/openbabel-3.0/include/openbabel/mol.h) { --INCLUDEPATH += /Developer/openbabel-3.0/include --LIBS += -L/Developer/openbabel-3.0/lib/Debug -lopenbabel -+exists(%%LOCALBASE%%/openbabel3/include/openbabel/mol.h) { -+INCLUDEPATH += /Developer/openbabel3/include -+LIBS += -L/Developer/openbabel3/lib/Debug -lopenbabel - } - # exit if openbabel wasn't found - contains( LIBS, -lopenbabel ) { -@@ -20,12 +20,12 @@ contains( LIBS, -lopenbabel ) { - error(OpenBabel was not found. Edit xdrawchem.pro and add valid include and lib values) - # if you get this error, comment the above with #, uncomment the variables below, and set - # the paths to match your OpenBabel install --#INCLUDEPATH += /usr/local/include/openbabel-3.0 -+#INCLUDEPATH += %%LOCALBASE%%/include/openbabel-3.0 - #LIBS += -lopenbabel - } # set PREFIX if not set (it is set when building RPM) isEmpty(PREFIX) { -PREFIX = /usr/local diff --git a/science/zx/Makefile b/science/zx/Makefile deleted file mode 100644 index 0061dee5a10e..000000000000 --- a/science/zx/Makefile +++ /dev/null @@ -1,31 +0,0 @@ -PORTNAME= zx -PORTVERSION= g20221101 -CATEGORIES= science # quantum-computing - -MAINTAINER= yuri@FreeBSD.org -COMMENT= MQT ZX: A library for working with ZX-diagrams -WWW= https://www.cda.cit.tum.de/research/quantum/ - -LICENSE= MIT -LICENSE_FILE= ${WRKSRC}/LICENSE - -LIB_DEPENDS= libgmp.so:math/gmp - -USES= cmake:testing compiler:c++17-lang python:test - -USE_GITHUB= yes -GH_ACCOUNT= cda-tum -GH_TAGNAME= b01ba5e -GH_TUPLE= boostorg:config:2543ff1:boostorg_config/extern/boost/config \ - boostorg:multiprecision:be4b8e8:boostorg_multiprecision/extern/boost/multiprecision \ - google:googletest:3026483:googletest/extern/googletest - -CMAKE_ON= BUILD_SHARED_LIBS -CMAKE_OFF= BUILD_ZX_TESTS -CMAKE_TESTING_ON= BUILD_ZX_TESTS - -do-install: # workaround for https://github.com/cda-tum/dd_package/issues/115 - cd ${WRKSRC}/include && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include - ${INSTALL_LIB} ${BUILD_WRKSRC}/src/libzx.so ${STAGEDIR}${PREFIX}/lib - -.include <bsd.port.mk> diff --git a/science/zx/distinfo b/science/zx/distinfo deleted file mode 100644 index 21d52858dc74..000000000000 --- a/science/zx/distinfo +++ /dev/null @@ -1,9 +0,0 @@ -TIMESTAMP = 1667348044 -SHA256 (cda-tum-zx-g20221101-b01ba5e_GH0.tar.gz) = 4f106f5bb3f8651e91e25fd15c353f7d08c77bb34b5bb61c138a11cca3a7a50f -SIZE (cda-tum-zx-g20221101-b01ba5e_GH0.tar.gz) = 26179 -SHA256 (boostorg-config-2543ff1_GH0.tar.gz) = aed1996926016faee81de7219a74f9fd41c9c3a4bb292f8936b54245b57ad3c2 -SIZE (boostorg-config-2543ff1_GH0.tar.gz) = 379371 -SHA256 (boostorg-multiprecision-be4b8e8_GH0.tar.gz) = 78b681530deb9c911f485f70d438099b9a7f7e63f61dba572ed68f32306e35c2 -SIZE (boostorg-multiprecision-be4b8e8_GH0.tar.gz) = 4144005 -SHA256 (google-googletest-3026483_GH0.tar.gz) = 1790cf41d6b9b023e1751888155b4fe1a20cd5b9842c3aa67633aac4b2610ba2 -SIZE (google-googletest-3026483_GH0.tar.gz) = 859168 diff --git a/science/zx/pkg-descr b/science/zx/pkg-descr deleted file mode 100644 index 51d87020ae3a..000000000000 --- a/science/zx/pkg-descr +++ /dev/null @@ -1,3 +0,0 @@ -zx is a library for working with ZX-diagrams developed by the Chair for Design -Automation at the Technical University of Munich as part of the Munich Quantum -Toolkit (MQT). diff --git a/science/zx/pkg-plist b/science/zx/pkg-plist deleted file mode 100644 index e8e6b0491112..000000000000 --- a/science/zx/pkg-plist +++ /dev/null @@ -1,8 +0,0 @@ -include/Definitions.hpp -include/Expression.hpp -include/Rational.hpp -include/Rules.hpp -include/Simplify.hpp -include/Utils.hpp -include/ZXDiagram.hpp -lib/libzx.so |