Installation of Wit!P Source Code Package
Prerequisites:
for
Linux: Fortran 77 and C compilers, OpenGL and X11/Motif
header files and libraries, GNU Readline package (optional).
for Windows: cygwin
package (http://sources.redhat.com/cygwin/), GNU Readline
(optional), Fortran 77 and C compilers (eg. the compilers from the
cygwin package). GLUT library.
for OS-X: gcc and
gfortran, GNU Readline library (optional), X11 server and
libraries
Installation:
A) untar the source package into an
empty directory:
$ mkdir wnpsrc
$ cd wnpsrc
$ tar -zxvf ../wnpexp-yyyymmdd.tgz
B) set up of environment variables for
'make':
$ make newsetup
The makefiles in the Wit!P source
tree use the follwing environment variables:
WNP_MK
:
target system (irix or linux or cygwin)
RELROOT : target directory for
executables (the actual executable will be in $RELROOT/bin)
WNP_FC : compiler to use
to compile Fortran code (g77, gfortran)
WNP_ARCH : target architecture (-m64 for 64 bit, -m32 for 32
bit)
For convenience, it is recommened to
put the definitions of the environment variables into the file
'setup' in 'wnpsrc', and source this file before running make. The
command 'make newsetup' (in 'wnpsrc') generates such a 'setup'
file. If the directory RELROOT does not exist,'make newsetup' will
create an empty release tree (needed in step C).
C) compile the lot, and release to
RELROOT release tree (read the "
Notes"
section for deatils):
$ source setup
$ make install
This will take a while, depending on
the speed of your computer. Most things should compile without
warnings (exception: some routines do not use all arguments of X11
callback routines, which for some compilers may be a reason for
complaint).
D) Configure some shell scripts in the
Wit!P release tree:
CSD Root directory [ ]: /usr/prog/csd (root directory of Cambridge Database, if installed).
Directory with TAFF parameter tables: [ /usr/prog/witnotp/ff_tables_6.1 ] ~widmerar/ff_tables_7.3
E) Running Wit!P:
The (very rudimentay)
tutorial might be helpful to
get you started with Wit!P.
Notes:
The Wit!P source distribution is
divided into several subdirectories:
client:
source code for sw_client.exe, the "core" of Wit!P,
html: (very rudimentary)
documentation in HTML,
minimax: molecular
mechanics program, implements Tripos, Amber, CHARMM force
fields,
misc: a miscellany of
several small helper programs,
ogl: source code for
sw_server.exe, the OpenGL graphics server for Wit!P,
piff: a molecular
mechanics program, combined with a PPP-SCF for delocalized
pi-systems
sodgeom: a simple DG
program, converts 2D MDL SD files to very raw 3D MDL SD files
wnp_configure: scripts,
space group definition files, libraries,... needed by make configure
The source code directories (client,
minimax, misc, ogl, piff, sodgeom) have target platform specific
subdirectories, withe the platform specific Makefiles:
wnpsrc/.../IRIX : for
Silicon Graphics IRIX (IRIX 6.5)
wnpsrc/.../Linux: for Linux systems (RH
7.3, RH 9.0, FC 10,..., SuSE 9.x)
wnpsrc/.../Windows: for MS-Windows (98,
NT, XP) using Cygwin
wnpsrc/.../MinGwin: for MS-Windows with
MinGW (for a Cygwin-free version)
wnpsrc/.../Altix: for SGI Altix/Linux
systems (w/o graphics)
wnpsrc/.../Osx: for Macintosh OS-X
The target platform specific Makefiles work well on the systems on
which the source code was developed. On other systems minor
modifications may be neccessary before the source code can be
compiled. These modifications should be made in the platform
specific Makefile (eg. Linux/Makefile) and typically concern the
definition of the location of libraries to use (LIB macro in the
Makefiles).
The client/
platform/Makefile
files
are configured to use the GNU Readline package. For license
reasons, this package is not included in the Wit!P source code
distribution. If you do not have Readline on you system, and if
you do not want to install this "free" (GPL) package, you can
change the
-DUSEREADLINE
to
-DdontUSEREADLINE in
the definition of the
COMMON
macro of the client/
platform/Makefile
files w/o serious loss of functionality (the readline routine is
only used when witnotp is run w/o graphics).
For scripting it may be useful to compile Wit!P with an
internal XML/RPC server based
on the
xmlrpc-c
library (not part of the Wit!P source package). On Linux and
Cygwin systems, Wit!P will automatically be copiled with the
XML/RPC server if the xmlrpc-c library is installed and properly
configured (c.f. wnpsrc/client/rpcFlags shell script). To disable
the integration of the XML/RPC server set the 'useRPC' flag at the
top of Makefile in client/
platform/
to 'withoutRPC'.
If you want to compute dotted Connolly surfaces through the Wit!P
interface (Wit!P> dots comoute connolly...), you will need the
ms.exe (
QCPE-429) program, or a
program compatible with ms.exe. This program is not part of the
Wit!P distribution. If you do not have ms.exe, you may order it at
http://qcpe.chem.indiana.edu/. Wit!P expects to find ms.exe in its
bin/directory, so you should either make a copy, or set up the
appropriate soft-link.
The molecular program
minimax
is supplied with a Polak-Ribiere conjugate gradient minimizer with
automatic restart in C (a functional equivalent to the well-known
VA14 minimzer [M.J.D. Powell, Harwell Subroutine Library,
1975(?)]. Minimax also has an interface to two minimizers written
by J. Nodecal, Northwestern University: a limited memory BFGS, and
a subroutine implementing Fletcher-Reeves and Polak-Ribiere
conjugate gradient procedures. The Wit!P source code distribution
does not contain the source code for these minimizers. Since the
limited memory BFGS method has significantly better convergence
properties than the the VA14-like minimizer, we highly recommend
to replace the
lbfgs.f,
cgfam.f. and
cgsearch.f 'stubs' in the
wnpsrc/minimax source code
directory by the real subroutines from the LBFGS and CG+ packages
to make these methods available to minimax (simply download, and
copy the files into wnpsrc/minimax before you compile the Wit!P
sources).
A.Widmer,
CPC/CSG-SB