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The Symmetric Molecular Geometry Generating Program MOLLY
=========================================================
The Fortran 77 program MOLLY generates atomic positions in a molecule from
those of a small number of prototype atoms, using the molecule's point symmetry
and the associated transformation operations. It is intended as a time-saving
aid in preparing input data for computational physics (or chemistry) software.
The primary scenario envisaged for a potential user is something like the
following: for the purpose of providing input to some major computational
package in physics or quantum chemistry, say, one needs to generate a molecular
geometry file, with (x,y,z) coordinates for all atoms, for a molecule with a
certain point symmetry, perhaps repetitively with different bond-length or
bond-angle parameters, or as part of an automated workflow. If one has to
rely on doing this by hand, then plainly the higher the symmetry of the
molecule the larger, more complicated (and error prone) and more tedious the
task becomes. Even for molecules with lower symmetries frequent repetition
may be similarly problematic. An automatic method of generating a full
geometry from prototype atomic positions for a wide range of molecular
symmetries is provided by Molly.
The Molly package itself consists of the MOLLY program (as source code) as
well as a library of data files for a large selection of symmetry point groups,
along with the GROUPY program (new in this release) which performs mathematical
checks on individual symmetry data files. There are also shell scripts for the
compilation and running of the programs. The package is command-line oriented
and intended for use under Unix or Linux. The code is as near ANSI standard
Fortran 77 as could be contrived. A compiler is of course required.
The Molly source code, data files and executables may be copied
and/or modified freely as long as the copyright messages are left intact.
Downloads, Copyright, Bug Reports, etc
--------------------------------------
The latest release may be found at the project's development page at
SourceForge:
http://sourceforge.net/projects/molly-cool/
Any queries, comments or bug reports (please!) may be communicated via the
appropriate sections of this page.
Once unpacked see the copyright conditions in the file:
... molly/v1.1/doc/COPYING
and the log of changes and possible future developments in the file:
... molly/v1.1/doc/changes_and_to_do_list.txt
Installation and Usage
----------------------
Molly does not require any installation. One need only unpack the archive
to some desired location, compile the programs in situ, create an input file
for some molecule of interest, and run MOLLY to generate an output file with
the complete geometry of the molecule.
The unpacked material should contain the following sub-directories:
bin : executable files resulting from compilation script
data1 : user created input data
data2 : program produced output data
doc : detailed documentation with further information about
the programs (including precise input file specs);
and other text files
scripts : shell scripts to compile and run programs
src : program Fortran 77 sources
store : miscellaneous files of incidental interest
sym-data : input symmetry information
While the full instructions for using Molly may be found in the documentation,
it is easier from a practical point of view just to try to modify one of the
pre-existing molecular input files in the "data1" directory. Some of them
have "template" in their names and have been exhaustively commented. It will
be apparent from a brief perusal that a minimal input file consists of only
three types of input line: a title, prototype atom positions (one atom per
line), and a line specifying which point symmetry the molecule possesses.
(In practice it is usually unnecessary to use any other apart from the
unit conversion and the informational inter-atom distance output options.)
Note that input is not free format (unfortunately) and input fields must
correspond precisely.
Thus for a particular molecule a user needs to know which of the atoms can
be considered prototypes. (In the fullerene molecule, C60, for example, there
is only one, from which all the rest may be generated by symmetry operations of
the icosahedral group, I.) It is also necessary to know where the prototypes
should be placed relative to the origin of coordinates (= centre of symmetry).
This in turn depends on the way the symmetry operations are implemented and
may be seen directly from the relevant symmetry input file in "sym-data".
(For the icosahedral group, I, see the file "molly-4-sym-new_i.dat".) Symmetry
files exist in old and new formats. The old format is for consistency with
some older software outside the Molly package. The new format should be the
only one used: these input files are commented to help interpret the
orientation of the point group in space. The orientation is usually fairly
intuitive: the cubic and related groups (T, Td, Th, O, Oh, I and Ih), for
example, are in the obvious relationship to the X, Y and Z axes, and to each
other. Lower symmetry groups have their main rotation axis along the Z axis,
but are otherwise not always consistent from one group to another. It is worth
experimenting with test prototype geometries to see if the results are as
expected. Finally the molecular input file must have a name:
molly-1-ctrl_pro-my_molecule.dat
where the string "my_molecule" may be any desired label for the particular
molecule under consideration.
Once a molecular input file is created, check that the appropriate
symmetry file is available. Then compile MOLLY by going to the "scripts"
directory and entering the command:
$ ./molly-compile.sh molly
Run MOLLY by:
$ ./molly-run molly my_molecule new_my_symmetry
where "my_symmetry" is the label of the desired symmetry (and the file
"molly-4-sym-new_my_symmetry.dat" must exist in "sym-data"). (In the case of
benzene, for example, which has D6h symmetry, the command would be
$ ./molly-run.sh molly benzene_v1 new_d6h
the relevant files having been provided in the package.) The result of a
successful run will appear in the commonly used XYZ chemical file format
in the directory "data2" with the name
molly-7-my_molecule.xyz
and may be viewed using whatever molecular viewer is to hand.
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I hope that Molly proves useful, at least in some small way, and I am
always open to comments and suggestions.
David Foulis
(16 December 2010)
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