21:33 yuri 

New port: science/py-chempy: Package useful useful for solving problems in
chemistry

 

07:44 yuri 

New port: science/luscus: Molecular editor and viewer

 

05:37 yuri 

New port: science/py-phono3py: Software to calculate phonon-phonon interaction
and related properties

 

05:01 yuri 

New port: science/py-phonopy: Package for phonon calculations at harmonic and
quasi-harmonic levels

 

03:10 yuri 

New port: science/py-molmod: Collection of molecular modelling tools for python

 

22:25 yuri 

New port: science/dftbplus: Package for performing fast atomistic simulations

 

03:00 yuri 

New port: science/openmx: Nanoscale material simulations using density
functional theories (DFT)

 

05:53 yuri 

New port: science/msms: Program to efficiently compute molecular surfaces

 

20:57 yuri 

New port: science/lm: Software for sampling trajectories of the
reaction-diffusion equations

 

23:28 yuri 

New port: science/namd: Computer software for molecular dynamics simulation

 

06:31 yuri 

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

 

05:14 yuri 

New port: science/mdynamix: General purpose molecular dynamics code

 

21:28 yuri 

New port: science/cp2k: Quantum chemistry and solid state physics software
package

 

15:05 yuri 

New port: science/atom: Program for DFT calculations in atoms

 

15:03 yuri 

New port: science/libgridxc: Library to compute the exchange and correlation
energy and potentials

 

06:07 yuri 

Remove science/mpqc-mpich: Enable MPI option in science/mpqc by default

* MPICH option in science/mpqc is renamed to MPI, because MPI exists in many
other
  ports and there's MPI_DESC predefined for it.
* MPI option in science/mpqc is made default.

 

17:51 yuri 

New port: science/siesta: Program to perform efficient electronic structure
calculations

 

04:09 yuri 

New port: science/wannier90: Maximally-localized Wannier functions (MLWFs) and
Wannier90

 

21:10 yuri 

New port: science/fleur: FLAPW code for atomic computations in quantum chemistry
and physics

 

07:49 yuri 

New port: science/dalton: Powerful molecular electronic structure program for
quantum chemistry

 

06:43 yuri 

New port: science/teem: Libraries for representing, processing and visualizing
scientific data

 

18:31 yuri 

New port: science/py-gpaw:  DFT and beyond within the projector-augmented wave
method in chemistry

 

18:17 yuri 

New port: science/py-ase: Atomic simulation environment

 

06:30 yuri 

New port: science/jdftx: Software for joint density functional theory in
chemistry

 

06:45 yuri 

New port: science/qbox: First-principles molecular dynamics code

 

00:57 yuri 

New port: science/libint2: Evaluate the integrals in modern atomic and molecular
theory

Repocopy of science/libint.
science/libint is at version 1.X, is incompatible, and is used by several other
packages.

 

07:56 yuri 

New port: science/madness: Multiresolution adaptive numeric environment for
scientific simulation

 

06:15 yuri 

New port: science/datawarrior: Chemistry-aware multi-purpose data visualization
and analysis program

 

19:04 yuri 

New port: science/multiwfn: Multifunctional wavefunction analysis for quantum
chemistry

 

18:08 yuri 

New port: science/gabedit: Graphical user interface for several chemistry
software packages

 

17:54 yuri 

New port: science/octopus: Scientific program aimed at the ab initio virtual
experimentation

 

22:00 yuri 

New port: science/nwchem: High-performance computational chemistry sotware

 

04:31 yuri 

New port: science/qwalk: Quantum Monte Carlo package for quantum chemistry
computations

 

07:44 yuri 

New port: science/qmcpack: Many-body ab initio Quantum Monte Carlo code for
quantum chemstry

 

23:16 yuri 

New port: science/chrono: C++ library for multi-physics simulation

 

08:13 yuri 

Re-add port: science/xdrawchem: Two-dimensional molecule drawing program

 

19:09 brooks 

Remove broken and expired port which also depends on clang38 (on 10).

 

19:19 yuri 

New port: science/xcrysden: Crystalline and molecular structure visualisation
program

 

21:47 yuri 

New port: science/quantum-espresso: Package for research in electronic
structure, simulation, optimization

 

04:41 yuri 

New port: science/openstructure: Molecular modelling and visualization
environment

 

04:45 yuri 

New port: science/coot: Crystallographic Object-Oriented Toolkit

 

01:27 yuri 

New port: science/clipper: Libraries for the organisation of crystallographic
data

 

00:39 yuri 

New port: science/libssm: C++ toolkit for superposition of macromolecules

 

00:24 yuri 

New port: science/libccp4: Protein X-ray crystallography toolkit

 

23:32 yuri 

New port: science/mmdb2: C++ toolkit for working with macromolecular coordinate
files

 

05:22 yuri 

New port: science/py-rmf: Library to support reading and writing of Rich
Molecular Format files

 

09:04 yuri 

New port: science/rmf: Library to support reading and writing of Rich Molecular
Format files

 

08:34 yuri 

New port: science/py-ScientificPython: Various Python modules for scientific
computing

 

21:18 sunpoet 

Add eccodes 2.8.0

ecCodes is a package developed by ECMWF which provides an application
programming interface and a set of tools for decoding and encoding messages in
the following formats:
- WMO FM-92 GRIB edition 1 and edition 2
- WMO FM-94 BUFR edition 3 and edition 4
- WMO GTS abbreviated header (only decoding).

A useful set of command line tools provide quick access to the messages. C,
Fortran 90 and Python interfaces provide access to the main ecCodes
functionality.

ecCodes is an evolution of GRIB-API. It is designed to provide the user with a
simple set of functions to access data from several formats with a key/value
approach.

For GRIB encoding and decoding, the GRIB-API functionality is provided fully in
ecCodes with only minor interface and behaviour changes. Interfaces for C,
Fortran 90 and Python are all maintained as in GRIB-API. However, the GRIB-API
Fortran 77 interface is no longer available.

WWW: https://software.ecmwf.int/wiki/display/ECC

 

20:05 sunpoet 

Add py-kinematics 0.0.7

kinematics is Python package to perform attitude kinematics. It is written
completely in Python and only requires numpy as a runtime dependency.

WWW: https://github.com/skulumani/kinematics

 

02:34 yuri 

New port: science/py-SimpleSpectral: Simplified scipy.signal.spectral module
with only pyFFTW support

 

21:25 yuri 

science/Makefile: Fix sortedness

 

21:24 yuri 

New port: science/py-PyQuante: Quantum chemistry in Python

 

02:42 yuri 

New port: science/dft_tools: Interface to DFT codes in TRIQS

 

23:24 yuri 

New port: science/triqs: Toolbox for Research on Interacting Quantum Systems

 

00:37 yuri 

New port: science/py-abipy: Library for analyzing the results produced by ABINIT

 

23:49 yuri 

New port: science/py-pymatgen: Python Materials Genomics is a robust materials
analysis code

 

22:28 yuri 

New port: science/py-spglib: Library for finding and handling crystal symmetries

 

17:42 yuri 

New port: science/spglib: C library for finding and handling crystal symmetries

 

05:52 yuri 

New port: science/atompaw: Tool for projector augmented wave functions for
molecular simulations

 

05:49 yuri 

Re-add port: science/abinit: Full-featured atomic-scale first-principles
simulation software

I couldn't make MPI work, created a bug report.
Will add DOCS and EXAMPLES options later.

PR:		219025

 

00:40 rene 

Remove science/orthanc and dependent ports, it has expired

 

21:44 tcberner 

Update lang/ghc 8.4.2 and the hs-* ports the newer versions

* Update lang/ghc to 8.4.2
* Update the boostrap compiler to 8.4.1
* Update the many hs-* ports
* Bump the rest

Thanks a lot to arrowd for doing all the heavy lifting :)

PR:		227968
Exp-run by:	antoine
Submitted by:	arrowd
Differential Revision:	https://reviews.freebsd.org/D15005

 

00:16 yuri 

New port: science/py-MDAnalysisTests: Test code and the trajectory data for test
cases of MDAnalysis

 

00:15 yuri 

New port: science/py-MDAnalysis: Python library to analyze molecular dynamics
trajectories

 

20:32 yuri 

New port: science/py-gsd: GSD (General Simulation Data) file format for Python

 

17:14 yuri 

New port: science/py-mmtf-python: MMTF (Macromolecular Transmission Format)
Python API

 

19:36 pi 

New port: science/mcxtrace-comps

McXtrace - Monte Carlo ray tracing simulations of X-ray experiments.

McXtrace is a tool for simulating X-ray instrumentation and experiments
using a ray-tracing formalism. Currently the main use of McXtrace
is in the field of synchrotron beamline instrumentation design, but
various other uses have been found, for instance for designing X-ray
telescopes or for laboratory sources.

This port contains the McXtrace component library.

WWW: http://www.mcxtrace.org

PR:		206506
Submitted by:	Erik B. Knudsen <erkn@fysik.dtu.dk>

 

20:39 adridg 

New ports science/dlib-cpp and science/py-dlib (Python bindings for the former)

Changed from the reviewed form:
 - fixed typo's
 - added support for suffixed Boost::Python
 - removed commented-out lines from patch

Submitted by:	arrowsvc (6yearold@gmail.com, new maintainer)
Reviewed by:	tcberner, adridg
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D14798

 

06:51 yuri 

New port: science/antioch: C++ Chemical Kinetics, Thermodynaimics, and Transport
Library

 

04:59 yuri 

New port: science/metaphysicl: Metaprogramming, operator-overloaded classes for
numerical simulations

 

18:15 jwb 

fsom: Tiny C library for managing SOM (Self-Organizing Maps) neural networks

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15103

 

18:32 tcberner 

New port: science/step, science/kalzium

This is the current version of KDE Applications <foo>.
Note that users of KDE SC4 should stick with <foo>-kde4.

 

16:33 sunpoet 

Add rubygem-rgeo-shapefile 1.0.0

RGeo::Shapefile is an optional module for RGeo for reading geospatial data from
ESRI shapefiles.

WWW: https://github.com/rgeo/rgeo-shapefile

 

16:33 sunpoet 

Add rubygem-rgeo-proj4 1.0.0

RGeo::Proj4 contains proj.4 extensions to the RGeo gem.

WWW: https://github.com/rgeo/rgeo-proj4

 

16:32 sunpoet 

Add rubygem-rgeo-geojson 2.0.0

RGeo::GeoJSON is an extension to the RGeo gem that provides GeoJSON encoding and
decoding.

WWW: https://github.com/rgeo/rgeo-geojson

 

16:32 sunpoet 

Add rubygem-rgeo 1.0.0

RGeo is a geospatial data library for Ruby.

RGeo is a key component for writing location-aware applications in the Ruby
programming language. At its core is an implementation of the industry standard
OGC Simple Features Specification, which provides data representations of
geometric objects such as points, lines, and polygons, along with a set of
geometric analysis operations. This makes it ideal for modeling geolocation
data. It also supports a suite of optional add-on modules that provide various
geolocation-related services.

Use the core rgeo gem to:
- Represent spatial and geolocation data objects such as points, lines, and
  polygons in your Ruby application.
- Perform standard spatial analysis operations such as finding intersections,
  creating buffers, and computing lengths and areas.
- Correctly handle spherical geometry, and compute geographic projections for
  map display and data analysis.
- Read and write location data in the WKT and WKB representations used by
  spatial databases.

WWW: https://github.com/rgeo/rgeo

 

08:43 makc 

Add new port science/py-openpiv:

Python module for Particle Image Velocimetry (PIV) image analysis
and post-processing.

WWW: http://www.openpiv.net/

 

20:37 yuri 

New port: science/py-quantities: Support for physical quantities with units,
based on numpy

 

23:13 yuri 

New port: science/libcint: General GTO integrals for quantum chemistry

 

09:39 yuri 

New port: science/py-OpenFermion: Electronic structure package for quantum
computers

 

09:04 yuri 

science/siril: Move to astro/siril; Mark broken on i386; Add OPENMP category

 

06:38 yuri 

New port: science/py-pyosf: Python lib for synching with OpenScienceFramework
projects

 

08:23 yuri 

New port: science/rdkit: Collection of cheminformatics and machine-learning
software

 

11:29 yuri 

science/veusz: Unbroke; Renamed to science/py-veusz.

It was breaking because of wrong python shebang.

This port is a python port, renamed per section 6.17.

Unbroke:
* Added USES=shebangfix and SHEBANG_FILES
* Added stripping (post-install)

Additional changes:
* Added USE_QT4
* Added USE_PYTHON=concurrent

Approved by:	tcberner (mentor, implicit)
Approved by:	portmgr (port compliance, infrastructure)

 

19:03 tcberner 

Give the KDE SC4 applications ports a -kde4 suffix

In order to make room for the up-to-date version of the KDE Desktop and its
applications move the KDE Application ports based on Qt4.

PR:		225992
Exp-run by:	antoine
Reviewed by:	rakuco, adridg
Differential Revision:	https://reviews.freebsd.org/D14413

 

19:00 yuri 

New port: science/siril: Astronomical image processing software

See details here: https://free-astro.org/index.php/Siril

Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D14190

 

19:49 yuri 

Re-added port: science/py-pymol: OpenGL based molecular visualization system
(existed 2002/08/13-2014/09/01, deleted in r366862)

Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D12902

 

16:04 yuri 

New port: science/MOOSE-neural-simulator: Multiphysics Object Oriented
Simulation Environment

Multiphysics Object Oriented Simulation Environment

MOOSE-neural-simulator allows to simulate
- chemical and biochemical reactions
- networks of neurons
- neural networks

This project is commonly referred to as MOOSE, in the capitalized form.
There is another science project called MOOSE, completely unrelated to this one,
which will also be ported.
MOOSE-neural-simulator is a candidate for the future 'chemistry' category in
case it will be approved.

Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13539

 

00:03 yuri 

New port: science/PETSc: Suite of data structures and routines from Argonne
National Laboratory

Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13527

 

12:31 dbn 

science/R-cran-fastICA: FastICA Algorithms to Perform ICA and Projection Pursuit

Generated by:	portcran (0.1.7)

 

19:15 yuri 

New port: science/mcxtrace: Monte Carlo X-ray tracing package

PR:		206505
Submitted by:	Erik B Knudsen <erkn@fysik.dtu.dk>
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13216

 

21:26 rodrigo 

Add new port science/aircraft-datcom
aircraft-datcom is a modified version of USAF Aircraft DATCOM
The goal of the project is to update the code and make it more usable by the end
users

PR:		207928
Submitted by:	Michael Danilov <mike.d.ft402@gmail.com>

 

19:29 yuri 

New port: science/ALPSCore: Generic algorithms and utilities for condensed
matter physics

PR:		223850
Submitted by:	Michael Danilov <mike.d.ft402@gmail.com>
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13237

 

05:58 yuri 

New port: science/chemps2: Spin-adapted implementation of DMRG for ab initio
quantum chemistry

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13100

 

05:12 yuri 

New port: science/gdma: Anthony Stone's Gaussian Distributed Multipole Analysis

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13110

 

18:27 yuri 

New port: science/py-scoria: Lightweight molecule manipulation codebase

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13119

 

18:44 yuri 

New port: science/erd: AcesIII electron repulsion integrals

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13080

 

18:05 yuri 

New port: science/pcmsolver: API for the Polarizable Continuum Model

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13069

 

04:31 yuri 

New port: science/libefp: Effective fragment potential method in quantum
chemistry

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13072