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REQUIREMENTS:
-------------
You will probably need the following software to compile and run this
program (or at least this is the configuration I've used myself):
g++ gcc version 2.95.4 (release) or 3.2
f2c f2c version 19991025-1
make GNU Make version 3.76.1
glut glut 3.6 (TARGET2 + bitmap text drawing???)
GNOME gnome 1.0.55 (for TARGET3)
gtkglarea gtkglarea 1.2.2 (for TARGET3)
MPQC + SC toolkit MPQC 1.2.5 or later (for ab initio QM)
In short, any up-to-date Linux installation like Redhat 8.0, Mandrake 9.0
or Debian 3.0 should work, if the necessary development packages (that
contain the header files) are also present, in addition to the standard
packages (that contain the libraries).
INSTALLATION:
-------------
To perform ab initio quantum mechanical calculations, this program links
directly to the quantum chemistry program MPQC and it's Scientific Computing
toolkit (SC toolkit). So, in order to enable these features you must first
compile and install both the MPQC program and the SC toolkit to your computer.
Furthermore, these features are disabled by default in makefiles, to make it
easier for newcomers to compile this program and start working with it.
Advanced users can easily enable those features and compile/link to the MPQC
program.
In the following I suggest a way how to compile the MPQC program in a way that
makes working with Ghemical as easy as possible (no parallel processing):
tar -zxvvf mpqc-1.2.5.tgz
mkdir mpqc-target
cd mpqc-target
/home/youracct/mpqc-1.2.5/configure --disable-parallel --disable-threads
make
make install [run as root user; installs the MPQC program]
make install_devel [run as root user; installs the SC toolkit]
You can check the status of SC toolkit using the program sc-config; if the
toolkit is properly installed the sc-config program will list the header files
(using option --cppflags) and library files (using option --libs) that the
toolkit contains.
When you want to compile Ghemical, with or without MPQC features, you should do
the following. First extract all files from your gzipped tar-archive:
tar -zxvvf ghemical-X.YZ.tgz
or equivalently
gunzip -c ghemical-X.YZ.tgz | tar -xvvf
This will create a new directory tree under "ghemical-X.YZ". You can now
choose between easy installation of the GNOME target (recommended), and
not-so-easy installation of any of the targets using the old makefiles. If
you choose the harder way of old makefiles, jump to Appendix I now...
For easy installation, just give the following commmands:
cd ghemical-X.YZ
./configure
make
make install [run as root user]
The above procedure should create the and install the GNOME application
"ghemical". If you want to compile MPQC-enabled version of Ghemical, you will
need to supply some extra flags to the configure script; use ./configure --help
to get information on this; your configure-command in this case is
./configure --enable-mpqc
After the first "make" command the executable should exist in the "bin"
directory, and you should be able to test it:
xterm [this will open a new terminal; use it!!!]
cd bin
export GHEMICAL_DIR=../openbabel/
./ghemical
exit [this will close the terminal used in test]
You are adviced to use the above procedure, where you open a new terminal
and run the testing there. The environment variable GHEMICAL_DIR will work
correctly only in the "bin" directory, and in the above procedure it will
not cause problems later when running the installed program.
The "make install"-command will copy the executable and some extra files to
their proper places so that the program can be run anywhere. After you have
installed the program you can click the item "Help/Help" from the main menu
to read the User's Manual (highly recommended).
In the "bin/examples"-directory there are some useful example molecules, and
in the "small-utilities"-directory there are... well, some small utilities.
Enjoy!!!
APPENDIX I: INSTALLATION USING THE OLD MAKEFILES
------------------------------------------------
The old way of installation will not detect any features of your system, so
be prepared to manually modify the makefiles if needed. The following example
shows how to compile the GNOME version (TARGET3); you can also work with other
targets in a similar way. Currently the GLUT version (TARGET2) is intended as a
development tool only, so it will not necessarily contain any new features, and
it's use is therefore not recommended...
cd ghemical-X.Y.Z
cd openbabel
make
rm main.o
cd ..
cd miniMOPAC
cp Makefile.OLD Makefile
make
cd ..
cd src
cp Makefile.OLD Makefile
make config-target3
cd common
make
cd ..
cd graphics
make
cd ..
cd target3/glade
make
cd ..
make
The above procedure should create the TARGET3-executable in the path
"bin/ghemical". There is no "install" option in the old makefiles. On SGI-
machines you may want use gmake instead of make, and configure OpenBabel
using command "./configure gcc" to force the script to use GNU compilers.
The GNOME target is pretty easy to use, but the GLUT target is more tricky.
Appendix II contains some advice on how to deal with that...
APPENDIX II: SOME INSTRUCTIONS ON HOW TO USE THE GLUT TARGET
------------------------------------------------------------
The TARGET2-executable will start an "all-atoms" molecular mechanics model
by default. You can check other possible options with command-line arguments
"-h" or "--help". You can start a QM model with arguments "-m q1" or
"--model q1".
To run the program just type
cd ../../bin
export GHEMICAL_DIR=../openbabel/
./gt2
Now some text should appear to the console window, and a black graphics
window should also appear. You should give your keyboard and mouse commands
to the black graphics window; check that correct window has the input focus
before you give commands. If some text input (filenames etc) is needed, it
is asked in the console window; just give focus to the console window and
type the input.
Once the program is running, set focus to the black window (by clicking the
window title bar, for example) and press the 'h'-key for help. The function
keys F1-F9 are used to select the mouse tool. Try selecting the drawing tool
with F1 and drawing something with the mouse, then select the rotating tool
with F7 and try to view it. Try adding the hydrogens and optimizing then...
Using the "draw" tool (key F1) you can add atoms and bonds (using left mouse
button), and using the "erase" tool (key F2) you can remove them. You can make
modifications just by drawing the structure again using different element or
bond type. You can also modify the 3D-arrangement of atoms using the following
procedure. First select a set of atoms using the "select" tool (key F3). The
selected atoms will appear in different color. Then select a translation (keys
F5/F6) or a rotation (keys F7-F8) tool, hold down the SHIFT key, and use the
tool in the usual way. The result is that the modification is done to the
selected set of atoms only. You can apply the same technique to any other
selected object (that is, to lights and colored planes and surfaces).
In the "bin/examples"-directory there are some useful example molecules.
Enjoy!!!
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