About OOPSE OOPSE News Features Download CVS Mailing Lists Documentation Authors Funding Results	Coordinate Files The standard format for storage of a systems coordinates is a modified xyz-file syntax, the exact details of which can be seen in Scheme 2.5. As all bonding and molecular information is stored in the meta-data files, the coordinate files contain only the coordinates of the objects which move independently during the simulation. It is important to note that not all atoms are capable of independent motion. Atoms which are part of rigid bodies are not ``integrable objects'' in the equations of motion; the rigid bodies themselves are the integrable objects. Therefore, the coordinate file contains coordinates of all the integrableObjects in the system. For systems without rigid bodies, this is simply the coordinates of all the atoms. It is important to note that although the simulation propagates the complete rotation matrix, directional entities are written out using quaternions to save space in the output files. All objects (atoms, orientational atoms, and rigid bodies) are given quaternions and angular momenta in coordinate files which are output by OOPSE, but it is not necessary for the user to specify the quaternions or angular momenta for atoms without orientational degrees of freedom. The name field for atoms is simply the atom type as specified in the meta-data file. The name field for a rigid body is specified as MOLTYPE_RB_N, to specify that this is rigidBody N in a molecule of type MOLTYPE. In simulations with rigid body models of water, a sample coordinate line might be: TIP3P_RB_0 x y z vx vy vz qw qx qy qz jx jy jz which tells the program that the rigid body representing a TIP3P molecule (rigid body # 0) is listed on that line. There are three files used by OOPSE which are written in the coordinate format. They are: the initial coordinate file (.in), the simulation trajectory file (.dump), and the final coordinates or ``end-of-run'' for the simulation (.eor). The initial coordinate file is necessary for OOPSE to start the simulation with the proper coordinates, and this file must be generated by the user before the simulation run. The trajectory (or ``dump'') file is updated during simulation and is used to store snapshots of the coordinates at regular intervals. The first frame is a duplication of the .in file, and each subsequent frame is appended to the file at an interval specified in the meta-data file with the sampleTime flag. The final coordinate file is the ``end-of-run'' file. The .eor file stores the final configuration of the system for a given simulation. The file is updated at the same time as the .dump file, but it only contains the most recent frame. In this way, an .eor file may be used to initialize a second simulation should it be necessary to recover from a crash or power outage.
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	Updated on January 16, 2006