Tinker is a set of small programs for doing general purpose molecular
modeling calculations. Tools are included for energy minimizations,
geometry calculations, simulated annealing, molecular dynamics, and
molecular analysis calculations. Tools for converting coordinate sets
are also provided. Tinker employs several force fields and minimization
techniques.
This port sets the maxatm value to 2500 atoms. This should be
sufficient for most molecular systems. Should you need to work with
larger systems you can set the maxatm parameter in the sizes.i file
located in the tinker/source directory and recompile. Note that if it
is set too large that tinker programs will abort and core dump.
For more information about Tinker see:
WWW: http://dasher.wustl.edu/tinker/
===> The following configuration options are available for tinker-7.1.3_5:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
OPTIMIZED_FFLAGS=off: compilation optimizations
===> Use 'make config' to modify these settings
biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/
Port changes:
* Take maintainership
* Implement the 'benchmarks' target, and stop installing benchmarks
* Add USES=gmake
* Update license
* Change MASTER_SITES and WWW to https
* Silence some commands
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.
This includes ports
- featuring USE_GCC=yes or USE_GCC=any,
- featuring USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and those
- with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.
PR: 222542
Bump PORTREVISION for ports depending on the canonical version of GCC
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 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, c++11-lib, c++11-lang,
c++14-lang, c++0x, c11, or gcc-c++11-lib.
PR: 219275
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using using Mk/bsd.octave.mk which in turn has USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
c++11-lang, c++0x, c11, or gcc-c++11-lib.
PR: 216707
Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms), part II.
The first part covered ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.
This adds ports with USES=fortran and ports using Mk/bsd.octave.mk
which in turn has USES=fortran.
PR: 214965
Reported by: thierry
Convert ports to use the options helpers in categories [abc]*, and minor fixes.
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D3412?
Unbreak by updating from 7.0.1 to 7.1.1. Hopefully, the authors will
stop rerolling releases (and breaking downstream checksums) now.
While here, allow parallel builds (seems to work again now) and stop
extraction of unused subdirectories.
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.
Part II, Bump PORTREVISIONs.
PR: 192025
Tested by: antoine (-exp runs)
Approved by: portmgr (implicit)
- Un-break fetch stage: the name scheme of the source tarballs has changed
- Add LICENSE*
- Remove conflict with hunspell:
- Rename the 'analyze' binary to 'analyze_t'
- put a note in pkg-message.in
- Pet portlint
PR: ports/187569
Submitted by: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
Approved by: thierry (mentor)
MFH: 2014Q2
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3. This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.
Part II, Bump PORTREVISIONs.
PR: 182136
Supported by: Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by: bdrewery (two -exp runs)
Update to libmpc version 1.0.1 which brings the following fixes:
- Switched to automake 1.11.6, see CVE-2012-3386.
- #14669: Fixed extraction of CC from gmp.h.
- Fixed case of intermediate zero real or imaginary part in mpc_fma,
found by hydra with GMP_CHECK_RANDOMIZE=1346362345.
This is on top of the following changes from version 1.0
- Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
invariant sections) for the documentation.
- 100% of all lines are covered by tests
- Renamed functions
. mpc_mul_2exp to mpc_mul_2ui
. mpc_div_2exp to mpc_div_2ui
(Only the first 15 lines of the commit message are shown above )
biology/tinker: Regenerate distinfo to unbreak fetch
Apparently the distfile was rerolled. The sizes of the file are only a few
bytes apart. Since the master site never changed, it's reasonable just to
regenerate the distinfo and bump the PORTREVISION.
PR: 180664
Approved by: bapt/culot (mentors, implicit)
- Unbreak by removing some old and adding some new master sites
- Bump PORTREVISION
PR: ports/151733
Submitted by: Chris Petrik [c.petrik.sosa gmail.com]
- Unbreak by upgrading to 4.2;
- Use DIST_SUBDIR because tarball is not versioned;
- Add sysdate to PORTVERSION to handle minor revisions;
- Do some cleaning.
- Update checksum again, seems author removes .ps version of documentation
from tarball
- Unmark broken, it builds for me just fine
Approved by: adamw (mentor)
Forced commit to add rationale. (Note: this port was previously
broken due to a bad checksum; the initial intent of the update
was to try to fix only that. However, the new revision fails
as well, but this led to my being sloppy with the checkin.
As Maxwell Smart said, "Sorry about that, Chief.")
New distfile 9/13. "Changes from TINKER 4.0 include some new force
field parameter sets, improvements to rigid body dynamics, a
Nose-Hoover thermostat, and numerous minor additions and bug fixes."
However, the compilation fails in sockets.c with an undefined
ref to <jni.h>. This is part of: "an interface between TINKER Fortran
code and FFE Java objects used for socket based communication."
Some interested party is going to have to take up this one, I'm
afraid, as I have no idea what is involved.
Reminded by: kris
Fixes the checksum problem, but doesn't fix the port; adds a BROKEN
line about how it fails. Some other interested person will have
to take it from here.
PR: 56882
a) Some corrupts with Makefile and pkg-plist.
b) forgot to notice that drop maintainership to ports@
Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>
Pointy hat to: myself
a) Forgot to update distinfo 52498
b) added LEGAL. author requests no distribution
except from his FTP site
c) clean-ups for compiler optimization
Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>
Pointy hat to: maho; partially :)
