Frederik Heber

heber@&ins-maildom; &ins-street-address;

13.08.2009 $Id$ 2009University of Bonn 0.1 08/13/09 heber Initial version of documentation $Revision$ $Date$ $Author$ Use CVS keywords as much as possible (do not use $Log$, however); use many DocBook features. The MoleCuilder's man page describes briefly its command synopsis MoleCuilder molecule builder molecular dynamics MoleCuilder 1 molecuilder Manipulate molecular geometries and construct molecular systems. molecuilder sample.conf -e @prefix@bin -aAbBcdDfFhHlmMnoOpPrRsStTuvV ... MoleCuilder is a very powerful package to manipulate nuclear geometries. It works on three different levels: Manipulating of single atoms: adding, removing, translating, changing the element, ... Manipulating of bonds: recognizing, measuring length/angle, scaling, fragmenting, ... Manipulating of single molecules: parsing atoms into a molecule, translating a molecule, calculating surface and volume of a molecule... Manipulating of the domain: changing the domain, specifying a periodic bounding box, centering all atoms, shifting all atoms, ... As it is written for the command-line, it is best suited to use in scripts in order to mass-create many structures at the same time that only differ in a few key parameters. Note that multiple options may be given at the same time, i.e. we may concatenate (-a) an atom, then translate all (-t) by some vector, the center at origin (-O) and so on. -a Z x y z - add atom -a DBOND - create adjacency graph from DBOND file. -b xx xy xz yy yz zz - center atoms in domain. -B xx xy xz yy yz zz - bound atoms by domain. -c x y z - center atoms in rectangular domain with distance to boundary. -d x y z - duplicate domain along each axis by given factor. -D distance - Depth-First-Search Analysis of the system. -fF distance order - fragment the molecule in BOSSANOVA manner -[h|H|?] - print help. -L step0 step1 prefix - linear interpolation between step0 and step1 in config file. -m [0|1] - calculate(0), align in(1) Principal Axis System. -M basis - set basis to store in mpqc config files. -n - don't parse trajectories. -o file - calculate and store convex envelope of molecule in file. -O center atoms in origin. -p file - parse XYZ file into molecule. -P file - Parse given forces file, time integrate and append as subsequent MD step. -s x y z - scale all atom coordinates by the factor per axis. -S file - Store temperatyre from config file in file. -t x y z - translate all atoms by vector. -T x y z - translate all atoms by vector in periodic domain. -u rho- suspend molecular system in watery solution such that average density is rho. -[v|V] - print version information. sample.conf is the config file, which is needed as temporary storage. Must not begin with '-'. -e database_path is the path to the element's database. The files are provided with molecuilder. molecule.xyz is a typical XYZ file containing the geometry for a molecule. Below a typical examples of how to use molecuilder are given. molecuilder sample.conf -e @prefix@ -p molecule.xyz -f 4 2. - creates a number of fragmented output files up to bond order 4 with bonds between atoms at most 2 length units apart. molecuilder sample.conf -e @prefix@ -p molecule.xyz -t -5 0. 0. -a 1 0. 0. 0. - parses the XYZ file molecule.xyz into the molecular system, translates the whole by (-5,0,0) and adds a hydrogen atom at the origin. 0 - success. 1 - failure. 2 - adaptive refinement of fragmentation not finished. 255 - critical failure. Please report any bugs you may encounter to heber@&ins-maildom;.