MDynaMix is a general purpose molecular dynamics code for simulations of
mixtures of rigid or flexible molecules, interacting by standard
molecular-mechanics force field including electrostatic and Lennard-Jones
potentials for electrostatic interactions as well as terms describing covalent
bonds, angles and dihedral angles. The program is well suited for simulations of
flexible molecules based on the double time step algorithm. Alternatively, rigid
bonds can be treated by the SHAKE algorithm. Algorithms for NVE, NVT, NPT and
anisotropic NPT ensembles are implemented. The long-range electrostatic
interactions are treated by the Ewald summation method, or alternatively by a
reation field or simple cutoff. The program can be run both in sequential and
parallel execution, in the latter case the MPI parallel environment is required.
From v.5.1 possibility for taking into account quantum motion of nuclei using
Path Integral approach is implemented. Expanded ensemble mode of simulations for
calculation of solvation free energies is added in v.5.2.
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner)
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above )
Add workaround for new failure with Fortran GCC 10 frontend:
Type mismatch between actual argument at (1) and actual argument at (2)
(INTEGER(4)/REAL(4)).
PR: 246700
Approved by: maintainer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.
PR: 238330
Related to revision 499061 bump ports with USES=fortran to have them
benefit from the improved situation where libgcc_s is only used when
absolutely necessary.
Suggested by: tijl
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.
PR: 231590
Change 20 ports from net/mpich2 to net/mpich
mpich2 is the obsolete version 2.x, mpich is at the current version 3.x
Ports:
math/scalapack science/nwchem science/quantum-espresso science/qmcpack
science/madness
science/qbox science/openmx science/jdftx science/fleur science/libgridxc
science/mdynamix science/lm science/dftbplus science/py-gpaw devel/ga
math/elpa net/charm science/gromacs math/pari math/arpack-ng-mpich
