! TRAVIS input file
! Created with TRAVIS version compiled at Jan  8 2025 17:15:42
! Source code version: Jul 29 2022
! Input file written at Sat Nov  8 18:47:27 2025.
! Use the advanced mode until the analysis selection menu (y/n)? [no] 
y
! Use periodic boundary conditions (0=no, x, y, z, xy, xz, xyz)? [xyz]

! Use time-dependent cell vector (NPT ensemble) (y/n)? [no] 

! Is the simulation cell non-orthorhombic (cell angles other than 90 deg) (y/n)? [no] 
y
! Enter three cell vectors (y) or three edge lengths and angles (n)? [no] 
y
! Enter X component of cell vector A in pm:       
880.3479
! Enter Y component of cell vector A in pm: [0.0] 

! Enter Z component of cell vector A in pm: [0.0] 

! Enter X component of cell vector B in pm: [0.0] 
586.8986
! Enter Y component of cell vector B in pm:       
1016.5382
! Enter Z component of cell vector B in pm: [0.0] 

! Enter X component of cell vector C in pm: [0.0] 

! Enter Y component of cell vector C in pm: [0.0] 

! Enter Z component of cell vector C in pm:       
4648.0091
! Should the periodic box be multiplied (y/n)? [no] 

! Exclude Au atoms from bond recognition (y/n)? [yes] 

! Execute molecule recognition for which time step (-1 = disable)? [0] 

! Use spatial domain decomposition for faster mol. rec. (disable if there are problems) (y/n)? [yes] 

! Use refined topological atom ordering (can take very long for large molecules) (y/n)? [yes] 

! Show bond matrices only for first representant of each molecule type (y/n)? [yes] 

! Show only bonds in the bond matrices (y/n)? [yes] 

! Create images of the structural formulas (y/n)? [no] 

! Accept these molecules (y) or change something (n)? [yes] 

! Change the atom ordering in some molecule (y/n)? [no] 

! Define additional virtual atoms (y/n)? [no] 

! Do you want to define pseudo-molecules (y/n)? [no] 

! Which functions to compute (comma separated)?
power
! Use the advanced mode for the main part (y/n)? [no] 

! Enter the physical time distance between successive trajectory frames in fs: [0.5] 
0.75
! Compute global power spectrum of whole system (y/n) [yes] 
no
! Which molecule should be observed (Au=1, C2H3N=2, CN=3)? 
2
! Which atom(s) to observe (e.g. "C1,C3-5,H", "*"=all)? [*]

! Enter the correlation depth of the ACF (in trajectory frames): [4096] 

! Weight autocorrelation functions by atomic mass (y/n)? [yes] 

! Calculate spectrum up to which wave number (cm^-1)? [5000.00 cm^-1] 
3500
! Correct frequency shift of the Verlet integrator (y/n)? [no] 

! Add another power spectrum observation (y/n)? [no] 

! Skip repeated time steps (y/n)? [no] 

! In which trajectory frame to start processing the trajectory? [1] 

! How many trajectory frames to read (from this position on)? [all] 

! Use every n-th read trajectory frame for the analysis: [1] 

