| Port details |
- mdynamix General purpose molecular dynamics code
- 5.3.0 science
 =0      5.3.0Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2018-09-06 05:14:10
- Last Update: 2023-12-14 20:34:17
- Commit Hash: b4fb7db
- License: GPLv2+
- WWW:
- http://www.fos.su.se/~sasha/mdynamix/
- Description:
- 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.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- mdynamix>0:science/mdynamix
- To install the port:
- cd /usr/ports/science/mdynamix/ && make install clean
- To add the package, run one of these commands:
- pkg install science/mdynamix
- pkg install mdynamix
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: mdynamix
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1702575904
SHA256 (md530.tar.gz) = 5d427ea4ca7dcdc07c503c1e93c17803d70c73971b19809726e223127cc3582f
SIZE (md530.tar.gz) = 16744902
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gfortran12 : lang/gcc12
- gmake>=4.3 : devel/gmake
- as : devel/binutils
- Runtime dependencies:
-
- gfortran12 : lang/gcc12
- Library dependencies:
-
- libmpich.so : net/mpich
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- science_mdynamix
- USES:
- fortran gmake
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
5.3.0
14 Dec 2023 20:34:17
 |
Yuri Victorovich (yuri) |
science/mdynamix: update 5.2.8 → 5.3.0 |
5.2.8_6
10 Dec 2023 10:23:11
|
Thierry Thomas (thierry) |
*/*: bump PORTREVISION after the upgrade of MPICH to 4.1.2 |
5.2.8_5
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
5.2.8_4
18 Feb 2023 22:37:20
|
Jan Beich (jbeich) |
science/mdynamix: drop BROKEN after 68552883830e
Only builds Fortran files, so the actual error was:
mpif77 -O -Wl,-rpath=/usr/local/lib/gcc11 -fallow-argument-mismatch -ffast-math
-c -o util.o util.f
gfortran -O -Wl,-rpath=/usr/local/lib/gcc11 -fallow-argument-mismatch
-ffast-math -c -o util.o util.f
[...]
gfortran -Wl,-rpath=/usr/local/lib/gcc11 -L/usr/local/lib/gcc11
-B/usr/local/bin -fstack-protector-strong -o md aver.o cpu_intel.o input.o
forces.o main.o mdee.o mdstep.o restart.o scalar.o service.o setup.o util.o
util.o: file not recognized: file format not recognized
collect2: error: ld returned 1 exit status
https://lists.freebsd.org/archives/freebsd-pkg-fallout/2022-December/294928.html
This reverts commit 5a6b6b37458fa3b3678d95247fb90772ae3a64e9. |
5.2.8_4
04 Dec 2022 21:17:44
|
Yuri Victorovich (yuri) |
science/mdynamix: Broken on 12
Reported by: fallout |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
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) |
5.2.8_4
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
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  ) |
5.2.8_4
01 Apr 2022 15:09:49
|
Dmitry Marakasov (amdmi3) |
*/*: fix trailing whitespace in pkg-descr's
Approved by: portmgr blanket |
5.2.8_4
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
5.2.8_4
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
5.2.8_4
01 Feb 2021 19:54:12
 |
antoine |
Do not include bsd.port.mk twice |
5.2.8_4
17 Nov 2020 22:37:32
|
linimon |
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 |
5.2.8_4
26 Jul 2019 20:46:57
|
gerald |
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 |
5.2.8_3
22 Apr 2019 13:16:34
|
gerald |
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 |
5.2.8_2
12 Dec 2018 01:35:36
|
gerald |
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 |
5.2.8_1
22 Sep 2018 16:36:38
|
yuri |
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 |
5.2.8
06 Sep 2018 05:14:01
|
yuri |
New port: science/mdynamix: General purpose molecular dynamics code |
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