Keyword TRAJECTORY

This keyword controls BOMD trajectory operations. It also triggers additional output to the deMon.trj file.
Options: PART=<Integer1>-<Integer2>AA

	RESTART		A BOMD trajectory is restarted.
	READ=$<$Integer$>$		Read specified trajectory step from deMon.trj file.
	PART=$<$Integer1$>$-$<$Integer2$>$		The trajectory part from step $<$Integer1$>$ through $<$Integer2$>$ is loaded from the deMon.trj file.
	CUT> $<$Integer$>$		Trajectory steps above $<$Integer$>$ are cut and removed from the deMon.trj file.
	CUT< $<$Integer$>$		Trajectory steps below $<$Integer$>$ are cut and removed from the deMon.trj file.
	PLOT=$<$Integer1$>$-$<$Integer2$>$		A deMon.mol file for the trajectory part from step $<$Integer1$>$ through $<$Integer2$>$ is created.
	INT=$<$Integer$>$		Interval for trajectory plotting with the PLOT option.
	FORCES		Atomic forces are added to the trajectory file deMon.trj.
	MOS=$<$Integer1$>$-$<$Integer2$>$		MO $<$Integer1$>$ through MO $<$Integer2$>$ energies are added to the trajectory file deMon.trj.

Description:
The data of deMon2k BOMD runs are stored in ASCII format in the file deMon.trj. This permits transferability between different computational architectures. A BOMD run can be restarted with the option RESTART of the TRAJECTORY keyword in combination with the DYNAMICS keyword (see 4.7.1). In this case the old trajectory is read from the deMon.trj file and augmented during the run. As with all deMon2k restarts, a restart input for a BOMD run is written into the deMon.new file. Copying this file to deMon.inp is an easy way to set up a BOMD restart. The restart geometry is read from the input file whereas the restart velocities are read from the corresponding trajectory file deMon.trj. A BOMD restart has the following minimal syntax:

 TRAJECTORY RESTART
 DYNAMICS MAX=10000

This can be augmented by other BOMD relevant keywords such as BATH (see 4.7.6), LPCONSERVE (see 4.7.4), etc. With the READ option of the TRAJECTORY keyword specific trajectory steps can be read from the deMon.trj file. In the following example input, trajectory step 61 is read from deMon.trj and electrostatic moments (see 4.8.3 for the keyword DIPOLE) are calculated for this geometry.

 DIPOLE
 TRAJECTORY READ=61
 #
 GEOMETRY CARTESIAN ANGSTROM
 NA        .000000       .000000      -.666740
 LI        .000000       .000000      2.208355

Please note that the specified input geometry is overwritten by the geometry read from the trajectory file. The corresponding output notes this in the geometry specification.

 *** GEOMETRY ***


 TRAJECTORY STEP 61 ORIENTATION IN ANGSTROM

  NO.  ATOM        X             Y             Z        Z-ATOM   MASS

    1  NA        .000000       .000000      -.701224      11    22.990
    2  LI        .000000       .000000      2.322574       3     6.941

Instead of reading only one step from the trajectory, the option PART for the TRAJECTORY keyword reads step sequences. Typically this option is used in combination with the SIMULATION keyword (see 4.7.3) for a trajectory analysis or the calculation of properties along the BOMD trajectory. With the CUT option trajectory parts, such as equilibration steps, can be removed from the deMon.trj file. The PLOT option has the same syntax as the PART option. However, it does not load trajectory steps but instead generates MOLDEN plot outputs in the file deMon.mol for the specified trajectory part. The step interval between the trajectory snapshots can be defined with the INT option. The following input example will generate 11 MOLDEN snapshots between the trajectory steps 30 and 80 with a 5-step interval.

 TRAJECTORY PLOT=30-80 INT=5

Additional trajectory outputs are triggered by the options FORCES and MOS. The option FORCES causes Cartesian atomic forces for each BOMD step to be written to the trajectory file. With the option MOS, the molecular orbital energies of the specified MO range are written to the deMon.trj file. Please note that trajectory files are usually demanding in terms of storage.

In order to calculate thermodynamic partition functions it is convenient to join together several trajectory files by the multiple histogram method (MHM) [222,223]. This permits the generation of nanosecond statistics with ADFT BOMD simulations, e.g. for the study of melting transitions in finite systems [224]. The input syntax of the external MHM program [225] and its output is described in Appendix C.