.. _DumpFileFormats: 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. .. contents:: 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