The following describes the version 3 format of the text archive file. The formats of version 1 and version 2 archives can be seen by generating a template using the arc -egn option where n is 1, 2 or 3. Binary formats are not very different from the text formats and are not documented here. Binary formats should not to be manipulated directly.

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Binary format archives are required by the yammp program, while the text format described here is more readable. Archives can be interconverted between the binary and text formats and among the three versions using arc.

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File Header

ARC3

version

numatom

filestat

The string "ARC3" must start on line 1 column 1 of the archive file and must be exact. version (not to be confused with the various archive versions) can be any number, numatom is the number of atoms represented in the archive file and filestat must always be the number 0.

The archive may contain any number of records. Each record may be coordinates or velocities or both for numatom atoms. Each record is identified by a record header line.

Record Header

creator

time

numdimen

recstat

The section header appears at the top of each record. creator is a two digit number code: the first digit is 0, 1 or 2 indicating that the record contains both coordinates and velocities, coordinates only and velocities only respectively; the second digit is 0, 1, 2 or 3 indicating the source of the record as being unknown, output from Molecular Dynamics, output from Energy Minimization and output from Monte Carlo respectively. This is summarized in the following table:

time is the time in picoseconds for the record; useful only in keeping track of molecular dynamics trajectories. numdimen is the number of dimensions; mimesis will only accept three dimensional coordinates. recstat must always be the number 0.

Record

xi	yi	zi	...
...	...	...	...

ui	vi	wi	...
...	...	...	...

Each record is read as a stream of numbers in the following order: the first dimension of the first atom, the second dimension of the first atom,..., the first dimension of the second atom,..., and so on. The formatting of numbers on the line is ignored; if four numbers appear per line and numdimen is 3, then the numbers represent the coordinates of two atoms (one to three dimensions of one atom and one to three dimensions of the other).

If the first digit of creator is 0 (i.e, creator is a number less than 10) then the record contains two sets of numbers. The first set are the coordinates and the second are the velocities.

Comments

# comments

Comments are enclosed by the sharp character # and the end of the line. Comments can appear between records of the archive file but not within records.

Example

ARC3  1  2  0
 
# 1: 5 dimensions, coordinates only, from minimizers
 
12  0.01  5 0
 
   1.1  1.2  1.3  1.4  1.5
   2.1  2.2  2.3  2.4  2.5
 
# 2: 3 dimensions, coordinates+velocities, from dynamics
 
1  0.02  3 0
 
   -10.1  -10.2  -10.3
   -20.1  -20.2  -20.3
 
   1.01    1.02   1.03
   2.01    2.02   2.03

This example is for a system containing only two atoms and the file contains two records. The first record contains coordinates only (first digit of creator is 1), in five dimensions and the coordinates originally came from energy minimization (second digit of creator is 2) although it retained a time of 0.01 ps perhaps from an earlier molecular dynamics simulation. The second record contains both coordinates and velocities (first digit of creator is 0 so creator is a single digit number) in three dimensions originating from molecular dynamics (second digit of creator is 1) at time 0.02 ps. The first set of six numbers (all negative) are the coordinates; the remaining numbers are velocities.