Next: Combine Command, Previous: Averaging Data Structures, Up: Dynamics Analysis
{ IC }
ACCUM [COMPARE] [ADD] {COOR} FIRSTU unit-number [NUNIT integer]
{VEL }
[BEGIN integer] [STOP integer] [SKIP integer]
The function of the ACCUM command is to accumulate averaging information for the internal coordinates, positions, or velocities. The ACCUM command can add to existing accumulations or initiate a new set of accumulations. It will also perform the principal axis transformation on positional or velocity moments automatically once the accumulation is complete.
The data used by ACCUM is produced during the dynamics calculations. Two sets of data are produced, the coordinates and velocities of all the atoms at periodic intervals during the runs. One specifies a set of these files by specifying the first unit number of the first file and specifying how many unit numbers after that should also be read. These files should be arranged in time order.
To use the ACCUM command, two operands must always be specified — the first unit from which the coordinate or velocity sets will be read and which data structures the accumulations should go into. FIRSTU specifies the unit number of the first unit. IC specifies that the internal coordinate averages are to be accumulated; the files which are read must be dynamical coordinates. COOR specifies that the coordinates averages are to be accumulated; the files must dynamical coordinates. VEL specifies that velocity averages are to be accumulated; the files must be dynamical velocities. If the files do not have what they are expected to have, the analysis facility will stop execution of CONGEN. The files themselves may be read repeatedly.
The NUNIT option specifies how many units are to be read for the accumulation. If not specified, it defaults to 1.
The COMPARE option specifies that the accumulation should be done using the comparison structure's averages. This allows comparisons between dynamical calculations. If not specified, the accumulation is done with respect to the main structure.
The ADD option allows one to add to a preexisting accumulation. If not specified, the accumulation is started from scratch. When it is specified, the data in the files is added to what is already present in the accumulation. Some important conditions must be satisfied for this to be done. First, the sampling interval for the pre-existing accumulation and the added data must be the same. The sampling interval is determined by the SKIP option (see below). Next, the range of the dynamics steps covered by the pre-existing accumulation and the files to be read must be adjacent in time. In other words, the stopping step of one set plus the sampling interval must equal the beginning step of the other set. These conditions ensure that the averages will be meaningful.
The BEGIN option specifies the first step in the files to be accumulated. All records which have a step number greater than or equal to BEGIN will be accumulated. If not specified, it defaults to 1 so that the range of steps to be accepted is not bounded from below.
The STOP option specifies the last step in the files to be accumulated. All records which have a step number less than or equal to STOP will be accumulated. If not specified, it defaults to infinity so that the range of steps to be accepted is not bounded from above.
The SKIP option indirectly specifies the sampling interval. As the coordinates or velocities are read in, the step number modulo SKIP is computed. If this number is zero, the step is used in the accumulation. If the step number modulo SKIP is not zero, the step is ignored. If not specified, SKIP defaults to 1. One must careful when using this option. If coordinates were written every 5 steps of dynamics and one specifies SKIP to be 7, the sampling interval will be 35 steps.
Reorienting a coordinate trajectory is possible using the COMPARE command. For details see Reorienting a Coordinate Trajectory.