Trajectory and structure file formats

Frames can have different number of atoms and lattice parameters – no problem.

Important

lionanalysis only supports orthorhombic cells. Some file formats require you to specify the full lattice. Off-diagonal elements are either ignored or nonzero values will give an error.

lionanalysis always assumes periodic boundary conditions. For non-periodic systems, specify large lattice vectors.

XYZ files

mattixyz

The comment line should read: “XYZ cellx celly cellz”, where it is assumed that the cell is orthorhombic with lattice parameters cellx celly and cellz (for the periodic boundary conditions). For nonperiodic systems, set these numbers to large values.

3
XYZ 10 10 10
O 0 0 0
H 1 1 1
H -1 1 1
3
XYZ 12 13 14
O 0.1 0.1 0.1
H 1 -1 1
H -1 1 1

Read this format with lionanalysis:

DumpFileFormat mattixyz

Write this format with lionanalysis:

PrintGroup All XYZ my_xyz_file.xyz

asexyz

Important

All components of the lattice vectors are specified, but all off-diagonal components must be 0! lionanalysis does not support non-orthorhobic cells.

3
Lattice="10.0 0.0 0.0 0.0 10.0 0.0 0.0 0.0 10.0"
O 0 0 0
H 1 1 1
H -1 1 1

Read this format with lionanalysis:

DumpFileFormat asexyz

Write this format with lionanalysis:

PrintGroup All ASEXYZ my_xyz_file.xyz

ceriottixyz

As output from i-PI, with a lattice line in angstrom, atomic coordinates in angstroms

7
# CELL(abcABC):   13.38377    13.38377    13.38377    90.00000    90.00000    90.00000  Step:           4  Bead:       1 positions{angstrom}  cell{angstrom}
       O  5.40520e-01 -9.74800e-01 -2.16618e-01
       O  2.92479e+00 -8.39306e-01  1.52342e-01
       H  1.85094e-01 -1.25718e+00 -1.07674e+00
       H  1.74325e+00 -9.09271e-01 -1.00174e-01
       H  3.29578e+00 -1.59156e+00  6.45803e-01
       H  3.52853e+00 -6.08880e-01 -5.74492e-01
       H  4.39795e-02 -1.96614e-01  9.14013e-02

Read this format with lionanalysis:

DumpFileFormat ceriottixyz

ceriotticellbohrxyz

As output from i-PI, with a lattice line in bohr (atomic units), atomic coordinates in angstrom

LAMMPS “custom” output

In the LAMMPS input file, make SURE you have set “dump_modify sort id”, so that the atoms are printed in ascending order with respect to their “id”.

lammpsrdx

LAMMPS input:

dump 1 all custom 200 dump.cfg id type x y z q
dump_modify 1 sort id

Trajectory file:

ITEM: TIMESTEP
1000
ITEM: NUMBER OF ATOMS
2
ITEM: BOX BOUNDS pp pp pp
0.0 11.0
0.0 12.0
0.0 13.0
ITEM: ATOMS id type x y z q
1 1 0 0 0 -1.0
2 2 1 1 1 1.0

Read this format with lionanalysis:

DumpFileFormat lammpsrdx

Write this format with lionanalysis:

PrintGroup All LAMMPSRDX output.cfg

lammpsrdxnoq

LAMMPS input:

dump 1 all custom 200 dump.cfg id type x y z
dump_modify 1 sort id

Trajectory file looks like this:

ITEM: TIMESTEP
1000
ITEM: NUMBER OF ATOMS
2
ITEM: BOX BOUNDS pp pp pp
0.0 11.0
0.0 12.0
0.0 13.0
ITEM: ATOMS id type x y z
1 1 0 0 0
2 2 1 1 1

Read this format with lionanalysis:

DumpFileFormat lammpsrdxnoq

lammpsrdxvelnoq

id type x y z vx vy vz

RuNNer files

runnerdata

The program can read the RuNNer input.data format. Only orthogonal lattices can be read correctly.

Example:

begin
lattice 20.787 0.0 0.0
lattice 0.0 22.6767 0.0
lattice 0.0 0.0 24.5664
atom 0 0 0 H 0 0 0 0 0
atom 1.88973 1.88973 1.88973 He 0 0 0 0 0
energy 0.000000
end

Read this format with lionanalysis:

DumpFileFormat runnerdata

Write this format with lionanalysis:

PrintGroup All RUNNERDATA runner_input.data