Several changes are involved since they are all interrelated. These
changes affect about 1000 files.
The first major change is rewriting bsd.builtin.mk as well as all of
the builtin.mk files to follow the new example in bsd.builtin.mk.
The loop to include all of the builtin.mk files needed by the package
is moved from bsd.builtin.mk and into bsd.buildlink3.mk. bsd.builtin.mk
is now included by each of the individual builtin.mk files and provides
some common logic for all of the builtin.mk files. Currently, this
includes the computation for whether the native or pkgsrc version of
the package is preferred. This causes USE_BUILTIN.* to be correctly
set when one builtin.mk file includes another.
The second major change is teach the builtin.mk files to consider
files under ${LOCALBASE} to be from pkgsrc-controlled packages. Most
of the builtin.mk files test for the presence of built-in software by
checking for the existence of certain files, e.g. <pthread.h>, and we
now assume that if that file is under ${LOCALBASE}, then it must be
from pkgsrc. This modification is a nod toward LOCALBASE=/usr. The
exceptions to this new check are the X11 distribution packages, which
are handled specially as noted below.
The third major change is providing builtin.mk and version.mk files
for each of the X11 distribution packages in pkgsrc. The builtin.mk
file can detect whether the native X11 distribution is the same as
the one provided by pkgsrc, and the version.mk file computes the
version of the X11 distribution package, whether it's built-in or not.
The fourth major change is that the buildlink3.mk files for X11 packages
that install parts which are part of X11 distribution packages, e.g.
Xpm, Xcursor, etc., now use imake to query the X11 distribution for
whether the software is already provided by the X11 distribution.
This is more accurate than grepping for a symbol name in the imake
config files. Using imake required sprinkling various builtin-imake.mk
helper files into pkgsrc directories. These files are used as input
to imake since imake can't use stdin for that purpose.
The fifth major change is in how packages note that they use X11.
Instead of setting USE_X11, package Makefiles should now include
x11.buildlink3.mk instead. This causes the X11 package buildlink3
and builtin logic to be executed at the correct place for buildlink3.mk
and builtin.mk files that previously set USE_X11, and fixes packages
that relied on buildlink3.mk files to implicitly note that X11 is
needed. Package buildlink3.mk should also include x11.buildlink3.mk
when linking against the package libraries requires also linking
against the X11 libraries. Where it was obvious, redundant inclusions
of x11.buildlink3.mk have been removed.
framework. The list of changes include:
* Modify compiler.mk so that "c" is always prepended to USE_LANGUAGES,
so we no longer need to say it in package Makefiles. Packages
should now append to USE_LANGUAGES instead of setting it.
* Create mk/compiler/f2c.mk which implements another pseudo-compiler
"f2c" that may be used with any C compiler backend, e.g.
PKGSRC_COMPILER= f2c ccache gcc
* Teach the various "real" compiler files, e.g., sunpro.mk, mipspro.mk,
etc., to use f2c if the native Fortran compiler isn't present.
Packages that use Fortran should now simply include the line:
USE_LANGUAGES+= fortran
in the package Makefile.
Changes since 4.0:
- Corrected a few fortran syntax errors, thnx to Gyepes R.
- on some platforms molden would not write a z-matrix, after stating
that it just did. fixed.
- radical changes in the way proteins can be manipulated with the
z-matrix editor
- The zmatrix conversion for proteins containing nucleotides has been
improved, it will now create a zmatrix.
- The windows version of molden now start the opengl helper program
mogl, when you click a *.ogl file in the read file window.
- Now when you apply the tinker amber force, automatically the charges
associated with the atoms belonging to amino acid residues are set.
- Added interactive docking.
- More bug fixes and improvements.
in the process. (More information on tech-pkg.)
Bump PKGREVISION and BUILDLINK_DEPENDS of all packages using libtool and
installing .la files.
Bump PKGREVISION (only) of all packages depending directly on the above
via a buildlink3 include.
master site, and this package has an interactive fetch stage.
Changes between version 3.8 and 4.0:
Many bug fixes
Better support for Mac OS
Molden format files can now be concatenated into one file
Molden now fully supports 5D and 7F orbitals
Added a feature to display an interactive spectrum
Addresses PR pkg/20819 by Robert Elz.
Changes:
- Added the ability to write MDL mol files.
- Added the ability to calculate EEM charges,
a sort of gasteiger charges, by Patrick Bultinck
- The reading of PDB files now handles additional
Hydrogen labels
The oniom stuff had a bug for the linux version, fixed.
Added an update to the ONIOM window.
- Complete update of the Gamess-UK dedicated code by
Huub v. Dam:
- Reading of SCF-convergence for CASSCF and DFT
- Reading of CASSCF orbital occupancies
- Support for HESSIAN jobs added
- and more ...
- Added support for the CPMD program
Distributed with the permission of TEODORO LAINO
NEST Laboratories - INFM - Scuola Normale Superiore
Some work still needs to be done.
- Added makefile entry for Mac OSX, thanks to Eric Brown.
- Molden3.8 has support for tinker3.9, older versions of
tinker are not supported (Molden3.7 support tinker3.6)
(Thanks to Nicolas Ferre)
- Nicolas Ferre added support for ONIOM calculations with
gaussian98.
- In submit gaussian window you can specify
you want to write cartesian coordinates instead of z-matrix.
- You can now run amber from gaussian, in the following way
Read in a pdb file, click the z-matrix button and create
a z-matrix, assign tinker amber atom types (the FF button)
Go to submit job option gaussian, choose method "amber"
"Write XYZ" form the "Gaussian Job" window.
In principle this can be combined with the oniom method
but this is not tested yet.
- When introducing Mopac2000 support a bug was introduced
which interfered with the reading of tinker xyz files, fixed.
MOLDEN is a package for displaying molecular density. It is tuned to
the Ab Initio packages GAMESS* and GAUSSIAN. It can read all the
information it needs from a GAMESS or GAUSSIAN outputfile. In this
form it has been running on a CONVEX C-120, an APOLLO DN10000, an
IRIS 4D/70GT, a DECSTATION 5000 and a SUN, and in slightly adapted
versions on a VAX and a CRAY-YMP. It should run smoothly on most
Unix machines. See section INSTALLATION GUIDE on how to install
MOLDEN. (* The GAMESS version referred to here is the european
version maintaned by M.F. Guest et al not to be confused with the
american version maintained by M.W. Schmidt et al)
This package was provided by Osamu OISHI and modified slightly by me.
