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* New port: science/opensim-core: Software for modeling of musculoskeletal stru...yuri2018-11-168-0/+470
* New port: science/simbody: Multibody dynamics library for (bio)mechanical sys...yuri2018-11-155-0/+287
* math/libxsmm: Update 1.9 -> 1.10yuri2018-11-151-0/+1
* science/libgridxc: Update 0.8.0 -> 0.8.3yuri2018-11-153-12/+9
* science/gromacs: Update 2018.3 -> 2018.4yuri2018-11-153-7/+6
* science/metaphysicl: Update 0.3.1 -> 0.3.2yuri2018-11-153-5/+5
* Change to my FreeBSD mailing address for two remaining ports.jmd2018-11-151-1/+1
* science/spglib: Update 1.10.4 -> 1.11.1yuri2018-11-152-4/+4
* science/py-ase: Update 3.16.2 -> 3.17.0yuri2018-11-153-5/+6
* Survival analysis in Python, including Kaplan Meier, Nelson Aalen and regressionrm2018-11-144-0/+30
* - Take maintainership of devel/gdcm.stephen2018-11-131-1/+1
* science/lammps: BROKEN on i386yuri2018-11-121-3/+2
* New port: science/sparta: Gas simulator: SPARTA DSMC software packageyuri2018-11-125-0/+76
* science/py-scikit-sparse: Update 0.4.3 -> 0.4.4yuri2018-11-123-6/+5
* science/py-MDAnalysisTests/: Update 0.19.0 -> 0.19.2yuri2018-11-122-4/+4
* science/py-MDAnalysis: Update 0.19.0 -> 0.19.2yuri2018-11-122-6/+7
* - Update math/armadillo to 9.200.4danilo2018-11-111-0/+1
* Update ImageMagick to 6.9.10.14 [1]kwm2018-11-111-2/+2
* Install texinfo files (GNU info) into ${PREFIX}/share/infobapt2018-11-111-1/+1
* science/nwchem: Fix build on 32-bit systemsyuri2018-11-101-3/+3
* science/kalzium: switch to depend on science/avogadrolibstcberner2018-11-102-5/+9
* Update KDE Applications to 18.09.3tcberner2018-11-102-6/+6
* science/avogadrolibs: Update 1.91.0-107 -> 1.92.0yuri2018-11-093-13/+20
* science/nwchem: Unbreak on i386: use NWCHEM_TARGET=LINUX on 32-bit architecturesyuri2018-11-091-3/+2
* Upgrade science/hdf5-18 to 1.8.21.thierry2018-11-093-15/+17
* On i386, OpenMP seems incompatible with libatomic.thierry2018-11-091-0/+7
* science/nwchem: Update to the latest revision: 6.8.1-release-144 -> 6.8.1.201...yuri2018-11-083-5/+6
* science/lammps: Add port options for additional functionalityyuri2018-11-072-9/+48
* multimedia/ffmpeg: update to 4.1jbeich2018-11-061-0/+1
* Add compiler:c++11-lang to USES to fix build on gcc-based archs.linimon2018-11-061-1/+1
* Drop remaining BROKEN_FreeBSD_10 per EOL after r483807jbeich2018-11-051-1/+0
* New port: science/esys-particle: Particle-based numerical modelling softwareyuri2018-11-059-0/+112
* Merge lang/qt5-qml and x11-toolkits/qt5-quick into x11-toolkits/qt5-declarativetcberner2018-11-052-2/+4
* science/dalton: Fix build with GCC8yuri2018-11-052-3/+7
* science/xcrysden: Fix GCC 8 build failure (update patch)yuri2018-11-052-11/+15
* science/xcrysden: Fix GCC 8 build failureyuri2018-11-052-2/+15
* bft, ecs, fvm, mei and ncs have been merged to code_saturne.thierry2018-11-051-5/+1
* bft, ecs, fvm, mei and ncs have been merged to code_saturne.thierry2018-11-0535-1474/+1518
* science/voro++: Add shared libraryjwb2018-11-046-17/+164
* science/liggghts: Set VTK_DIR to prevent conflicts with other vtk versionsyuri2018-11-041-1/+2
* science/liggghts: Move headers to the dedicated subdirectoryyuri2018-11-043-448/+454
* New port: science/liggghts: Discrete element method particle simulation softwareyuri2018-11-0410-0/+667
* science/pulseview: Update to version 0.4.1bsam2018-11-032-6/+6
* science/sigrok-cli: Update to version 0.7.1bsam2018-11-032-6/+11
* Remove compatibility code for FreeBSD < 11.2 from all ports.rene2018-11-026-9/+1
* New port: science/latte: Quantum chemistry: Density functional tight binding ...yuri2018-11-014-0/+60
* - Add LICENSEamdmi32018-10-301-0/+3
* science/chemps2: Update 1.8.8 -> 1.8.9yuri2018-10-302-4/+4
* science/py-gpaw: Add pkg-message; Add LICENSE_FILE; Change /usr/local to LOCA...yuri2018-10-302-1/+12
* New port: science/gpaw-setups: Setups (data files) for py-gpaw, the DFT quant...yuri2018-10-304-0/+38
* Fix typo in previous commit.linimon2018-10-291-1/+1
* science/py-chempy: Update 0.7.5 -> 0.7.6yuri2018-10-292-7/+10
* science/bagel: Update 1.1.2-21 -> 1.2.0yuri2018-10-292-6/+4
* Fix build with GCC-based architectures.linimon2018-10-281-1/+1
* science/kalzium-kde4: Fix buildyuri2018-10-284-5/+71
* Fix build with GCC-based architectures for various kde@ ports.tcberner2018-10-271-1/+6
* New port: science/coordgenlibs: Schrodinger-developed 2D coordinate generationyuri2018-10-255-0/+53
* New port: science/maeparser: Parser for Schrodinger Maestro filesyuri2018-10-255-0/+40
* science/rdkit: Update 2018_03_4 -> 2018_09_1yuri2018-10-255-16/+90
* - Update to 3.0.3.stephen2018-10-242-4/+4
* science/avogadro: Add CONFLICTS statementyuri2018-10-241-0/+2
* New port: science/molsketch: 2D molecule editoryuri2018-10-249-0/+191
* New port: science/erkale: Quantum chemistry program to solve the electronic s...yuri2018-10-226-0/+156
* New port: science/py-avogadrolibs: Python bindings for Avogadro2 chemistry li...yuri2018-10-225-0/+55
* science/libxc: Update 3.0.0 -> 4.2.3yuri2018-10-2112-30/+37
* science/avogadro: Update 1.1.1 -> 1.2.0yuri2018-10-2110-92/+157
* science/chemtool: fix build with GCC-based architecturesyuri2018-10-211-1/+1
* science/PETSc: Update 3.10.1 -> 3.10.2yuri2018-10-212-4/+4
* science/py-chempy: Update 0.7.4 -> 0.7.5yuri2018-10-202-4/+4
* science/hypre: Update 2.15.0 -> 2.15.1yuri2018-10-202-5/+5
* science/simlib: Update 3.02 -> 3.06yuri2018-10-193-18/+8
* science/py-chempy: Update 0.7.3 -> 0.7.4yuri2018-10-192-4/+4
* science/py-scikit-fuzzy: Update 0.3.1 -> 0.4.0yuri2018-10-192-5/+4
* science/avogadrolibs: Update 1.91.0 -> 1.91.0-107yuri2018-10-199-51/+11
* science/metaphysicl: Update 0.3.0.1 -> 0.3.1yuri2018-10-192-4/+4
* New port: science/mmtf: C++ implementation of the MMTF API, decoder and encoderyuri2018-10-195-0/+72
* Sscience/luscus: Update 0.8.5 -> 0.8.6yuri2018-10-183-5/+4
* science/cgnslib: Update to 3.3.1 and modernizejrm2018-10-1810-86/+58
* science/py-PyFR: Update 1.7.6 -> 1.8.0yuri2018-10-172-5/+4
* science/py-phonopy: Fix testsyuri2018-10-171-2/+2
* science/avogadrolibs: Add optionsyuri2018-10-172-142/+182
* New port: science/avogadro2: Chemical editor and visualization applicationyuri2018-10-174-0/+58
* New port: science/avogadrolibs: Avogadro2 libraries for chemical editor and v...yuri2018-10-1712-0/+351
* New port: science/libmsym: Molecular point group symmetry libraryyuri2018-10-175-0/+49
* science/gamess-us: Cosmetic change: internal version number change to 00 for ...yuri2018-10-152-3/+8
* New port: science/wxmacmolplt: Graphical user interface principally for the G...yuri2018-10-155-0/+84
* science/gamess-us: Add math library selection optionsyuri2018-10-152-2/+48
* Re-add port: science/gamess-us: General Atomic and Molecular Electronic Struc...yuri2018-10-1414-0/+729
* - Update pkg-descrwen2018-10-131-8/+2
* Fix packaging with python 3.xantoine2018-10-121-105/+105
* science/py-MDAnalysisTests: Update 0.18.0 -> 0.19.0yuri2018-10-122-4/+4
* science/py-MDAnalysis: Update 0.18.0 -> 0.19.0yuri2018-10-122-4/+4
* Update to 1.1.2sunpoet2018-10-122-5/+5
* Update KDE Applications to 18.08.2tcberner2018-10-122-6/+6
* Update devel/tbb to version 2019.1 and bump dependent ports' revisionsmartymac2018-10-111-1/+1
* science/simint: Update 0.7 -> 0.8yuri2018-10-113-5/+17
* - Update to 0.110wen2018-10-102-4/+4
* Update to 4.4.0cs2018-10-103-834/+109
* - Add LICENSEamdmi32018-10-091-0/+4
* science/nwchem: Update 6.8.1-release-94 -> 6.8.1-release-144yuri2018-10-094-13/+6
* science/hypre: Update 2.11.2 -> 2.15.0yuri2018-10-094-31/+24
* science/hypre: Take maintainershipyuri2018-10-091-1/+1
* - Update to 1.2.0wen2018-10-082-4/+4
* New port: science/simint: Obara-Saika (OS) method of calculating electron rep...yuri2018-10-085-0/+94
* - Update to 3.23wen2018-10-082-5/+5
* New port: science/molgif: Tool to create GIF animations of moleculesyuri2018-10-084-0/+38
* Deprecate some GNOME 2 applicationsantoine2018-10-081-0/+3
* biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/yuri2018-10-078-0/+565
* Mark BROKEN: conflicting dependenciesantoine2018-10-071-0/+2
* Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, exceptdes2018-10-066-12/+12
* Update MASTER_SITESsunpoet2018-10-061-1/+1
* science/nwchem: Remove the wrapper script with LD_PRELOAD, achieve the same b...yuri2018-10-063-9/+14
* science/py-gsd: Update 1.5.3 -> 1.5.4yuri2018-10-062-4/+4
* - Add LICENSEamdmi32018-10-051-0/+3
* science/dftbplus science/mbdyn science/octopus: Change from math/arpack to ma...yuri2018-10-053-5/+6
* Update devel/tbb to version 2019 and bump dependent port's revisionsmartymac2018-10-041-1/+1
* science/PETSc: Update 3.9.4->3.10.1; math/py-petsc4py: Update 3.9.1->3.10.0; ...yuri2018-10-033-6/+24
* science/gnudatalanguage: Change from net/mpich2 to net/mpichyuri2018-10-031-6/+7
* science/fvm: Change from net/mpich2 to net/mpichyuri2018-10-031-4/+4
* science/bagel: Mark BROKEN on 10yuri2018-10-031-0/+1
* Cleanup plistsantoine2018-10-011-62/+62
* Cleanup plistantoine2018-10-011-297/+297
* science/fsom: Fix build on GCC-based architecturesjwb2018-10-011-0/+1
* science/bagel: Fix build on 10yuri2018-10-011-1/+2
* science/chemps2: Update 1.8.7 -> 1.8.8yuri2018-09-282-5/+4
* textproc/py-pygments and science/paraview conflict each otheryuri2018-09-281-0/+2
* Mark BROKEN: wrong LIB_DEPENDSantoine2018-09-272-0/+3
* science/clipper: Update 2.1.20180526 -> 2.1.20180802yuri2018-09-273-6/+5
* Update Objective-C LLVM version to 6.0.brooks2018-09-263-3/+3
* science/bagel: Correctionyuri2018-09-261-3/+3
* science/bagel: Remove the unnecessary line.yuri2018-09-261-1/+0
* New port: science/bagel: Brilliantly Advanced General Electronic-structure Li...yuri2018-09-266-0/+137
* Change from MPICH2 to MPICH optionsunpoet2018-09-241-4/+4
* science/hypre: Change from net/mpich2 to net/mpichyuri2018-09-241-7/+8
* New port: science/elk: All-electron full-potential linearised augmented-plane...yuri2018-09-237-0/+102
* science/cp2k: Change from net/mpich2 -> net/mpichyuri2018-09-231-2/+4
* Change 10 ports from net/mpich2 to net/mpichyuri2018-09-232-4/+7
* Change 20 ports from net/mpich2 to net/mpichyuri2018-09-2315-29/+40
* Update ilmbase and openexr to 2.3.0, rename OpenEXR to openexr.mandree2018-09-221-1/+2
* science/py-PyFR: Update dependencies: move one under the option option, add a...yuri2018-09-221-5/+6
* Fix build on gcc-based archs by updating USES.linimon2018-09-221-2/+1
* science/py-PyFR: Fix the OpenMP computation mode by adding -I and -L flags to...yuri2018-09-222-5/+20
* science/py-chempy: python2 is deprecated for this version of chempy.yuri2018-09-221-2/+1
* science/py-chempy: Update 0.7.2 -> 0.7.3yuri2018-09-212-4/+18
* New port: science/py-PyFR: Framework for solving advection-diffusion type pro...yuri2018-09-214-0/+65
* Update to 1.4.0sunpoet2018-09-212-6/+7
* Update to 1.4.0sunpoet2018-09-212-6/+7
* science/atompaw: Update 4.1.0.3 -> 4.1.0.4yuri2018-09-202-5/+4
* science/py-chempy: Fix typosyuri2018-09-202-2/+2
* New port: science/py-chempy: Package useful useful for solving problems in ch...yuri2018-09-204-0/+53
* science/py-spglib: Update 1.10.4.1 -> 1.10.4.11yuri2018-09-202-4/+4
* Upgrade these ports to USES=compiler:c++11-lang to fix build on gcc-basedlinimon2018-09-181-1/+1
* Previous commit unbroke on powerpc64.linimon2018-09-181-2/+1
* - Update to 0.4-3tota2018-09-182-5/+4
* science/py-pymol: Update 2.1.0 -> 2.2.0yuri2018-09-186-39/+52
* science/py-pymatgen: Update 2018.8.10 -> 2018.9.1yuri2018-09-182-4/+4
* science/openmx: BROKEN on i386 pending the llvm bug resolutionyuri2018-09-151-0/+2
* Never use ${FLAVOR} directly in dependencies, FLAVOR is not transitive.mat2018-09-141-1/+1
* science/cp2k: Require the option OPENMP=on in fftw3 for options OPENMP and OP...yuri2018-09-141-2/+11
* New port: science/luscus: Molecular editor and vieweryuri2018-09-146-0/+178
* New port: science/py-phono3py: Software to calculate phonon-phonon interactio...yuri2018-09-144-0/+45
* New port: science/py-phonopy: Package for phonon calculations at harmonic and...yuri2018-09-144-0/+56
* New port: science/py-molmod: Collection of molecular modelling tools for pythonyuri2018-09-144-0/+36
* science/dftbplus: Correct license; Correct patchesyuri2018-09-145-26/+4
* science/dftbplus: Update license; Add the 'test' target; etc.yuri2018-09-144-37/+29
* science/qbox: Update 1.66.1 -> 1.66.2yuri2018-09-132-4/+4
* science/dftbplus: Fix ARPACK handling; Link with clang; etcyuri2018-09-133-13/+82
* New port: science/dftbplus: Package for performing fast atomistic simulationsyuri2018-09-138-0/+194
* - Make NLS support optionaldanfe2018-09-122-14/+16
* - Update `science/gwyddion' to version 2.51danfe2018-09-123-278/+95
* science/qbox: Update 1.65.0 -> 1.66.1yuri2018-09-122-4/+4
* science/PETSc: Update 3.9.3 -> 3.9.4yuri2018-09-122-5/+4
* New port: science/openmx: Nanoscale material simulations using density functi...yuri2018-09-1215-0/+599
* Change x11/xorgproto to become a build depzeising2018-09-126-5/+6
* - Update to 3.0.2.stephen2018-09-112-4/+4
* Remove MASTER_SITE_SUBDIRsunpoet2018-09-111-1/+0
* Add EXAMPLES options to ports that should have one.mat2018-09-101-1/+1
* Add DOCS options to ports that should have one.mat2018-09-107-3/+15
* After an include, PLIST_SUB must be appended to, not overwritten.mat2018-09-101-4/+4
* Remove ONLY_FOR_ARCHS_REASON_<arch> that are not architecture dependant.mat2018-09-101-1/+0
* science/msms: Add back NO_WRKSUBDIRyuri2018-09-101-4/+5
* science/vmd: Remove RESTRICTED: not requiredyuri2018-09-101-2/+0
* science/msms: Remove RESTRICTED, change LICENSE_PERMS to noneyuri2018-09-101-3/+1
* science/namd: Remove RESTRICTED because LICENSE_PERMS is restrictiveyuri2018-09-101-3/+1
* science/msms: Simplifyyuri2018-09-101-6/+4
* New port: science/msms: Program to efficiently compute molecular surfacesyuri2018-09-106-0/+77
* - Update to 3.0.1.stephen2018-09-102-4/+4
* science/lm: USES=python only when PYTHON=ONyuri2018-09-101-1/+2
* science/vmd: License auto-accept -> no-auto-acceptyuri2018-09-101-1/+1
* New port: science/lm: Software for sampling trajectories of the reaction-diff...yuri2018-09-1011-0/+254
* science/vmd: Add RESTRICTED clause.yuri2018-09-101-1/+3
* science/namd: Add IGNORE clause instead of the custom do-fetch clause for the...yuri2018-09-101-14/+7
* Take maintainershipsunpoet2018-09-101-2/+3
* science/namd: Downgrade 2-12-211 -> 2.12yuri2018-09-094-25/+22
* science/namd: Change LICENSE_PERMS: no redistribution is allowed.yuri2018-09-091-1/+1
* New port: science/namd: Computer software for molecular dynamics simulationyuri2018-09-096-0/+115
* science/metaphysicl: Update 0.3.0 -> 0.3.0.1yuri2018-09-082-4/+4
* science/metaphysicl: Update 0.2.0-23 -> 0.3.0yuri2018-09-083-5/+7
* science/mpqc: Add -lmpich to LDFLAGS: this fixes science/libghemical buildyuri2018-09-071-1/+2
* Update the current KDE Applications to 18.08.1, the latest release.adridg2018-09-072-6/+6
* Update to 1.27.0sunpoet2018-09-073-6/+6
* Update MASTER_SITES and WWWsunpoet2018-09-072-2/+2
* New port: science/lammps: Classical molecular dynamics code with a focus on m...yuri2018-09-065-0/+199
* New port: science/mdynamix: General purpose molecular dynamics codeyuri2018-09-064-0/+48
* science/cp2k: Add multiprocessing options MPI and OPENMP_MPIyuri2018-09-062-5/+22
* Update science/hdf5 to 1.10.2sunpoet2018-09-0627-39/+36
* New port: science/cp2k: Quantum chemistry and solid state physics software pa...yuri2018-09-055-0/+167
* science/atom: Correctionsyuri2018-09-052-9/+10
* New port: science/atom: Program for DFT calculations in atomsyuri2018-09-045-0/+60
* New port: science/libgridxc: Library to compute the exchange and correlation ...yuri2018-09-049-0/+228
* Remove science/mpqc-mpich: Enable MPI option in science/mpqc by defaultyuri2018-09-043-19/+6
* New port: science/siesta: Program to perform efficient electronic structure c...yuri2018-09-044-0/+48
* Fix build with Qt 5.11jhale2018-09-032-1/+6
* science/fleur: Add the forgotten patches.yuri2018-09-035-0/+116
* science/fleur: Add WANNIER option to use Wannier libraryyuri2018-09-031-3/+9
* New port: science/wannier90: Maximally-localized Wannier functions (MLWFs) an...yuri2018-09-035-0/+65
* science/fleur: Add port options for libraries: mpi, scalapack, elpa, hdf5yuri2018-09-031-0/+32
* New port: science/fleur: FLAPW code for atomic computations in quantum chemis...yuri2018-09-034-0/+36
* science/dalton: Fix license.yuri2018-09-021-2/+1
* New port: science/dalton: Powerful molecular electronic structure program for...yuri2018-09-029-0/+438
* New port: science/teem: Libraries for representing, processing and visualizin...yuri2018-09-025-0/+75
* science/jdftxL Update 1.4.2-73 -> 1.4.2-74yuri2018-09-023-15/+486
* science/nwchem: Add build-time python dependencyyuri2018-09-021-1/+3
* New port: science/py-gpaw: DFT and beyond within the projector-augmented wav...yuri2018-09-024-0/+40
* New port: science/py-ase: Atomic simulation environmentyuri2018-09-024-0/+33
* science/crf++: Fix build with Clang 6tobik2018-09-011-0/+21
* New port: science/jdftx: Software for joint density functional theory in chem...yuri2018-09-017-0/+554
* devel/google{test,mock}: update to 1.8.1jbeich2018-09-011-1/+1
* devel/boehm-gc: update to 7.6.8fernape2018-09-011-1/+1
* science/qbox: Correct LICENSE, etcyuri2018-09-012-3/+3
* Remove LICENSE_FILE from PORTDOCSsunpoet2018-08-312-1/+4
* Fix build with Qt 5.11jhale2018-08-313-1/+18
* New port: science/qbox: First-principles molecular dynamics codeyuri2018-08-315-0/+96
* science/chrono: Update 2.0.0-9063 -> 2.0.0-9070yuri2018-08-313-8/+29
* Deprecate KDE4 software in categories graphics-textproc.adridg2018-08-312-0/+6
* science/gabedit: Add BROKEN_i386yuri2018-08-311-3/+5
* science/qwalk: Add PORTSCOUT=limityuri2018-08-311-0/+2
* science/py-rmf: Correct versionyuri2018-08-312-4/+4
* science/rmf: Correct versionyuri2018-08-312-11/+4
* science/libint: PORTSCOUT=limityuri2018-08-311-0/+2
* Update to 1.1.1sunpoet2018-08-302-4/+4
* Update to 2.8.2sunpoet2018-08-303-5/+5
* science/libint2: Add configure options needed for depending ports; Add STATIC...yuri2018-08-292-2/+9
* science/libint: Add STATIC option that keeps static libsyuri2018-08-292-1/+9
* science/py-gsd: Update 1.5.2 -> 1.5.3yuri2018-08-282-5/+6
* science/libint2: Use PKGNAMESUFFIXyuri2018-08-281-4/+2
* New port: science/libint2: Evaluate the integrals in modern atomic and molecu...yuri2018-08-286-0/+411
* science/libint: Update 1.1.6 -> 1.2.1yuri2018-08-287-30/+20
* science/mpqc: Fix portlint warnings about non-ASCII characters; Change WWW to...yuri2018-08-281-4/+4
* science/ghemical: Fix build error on CURRENT; Add missing dependencesyuri2018-08-281-7/+13
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