! TRAVIS input file
! Created with TRAVIS version compiled at Feb 28 2024 12:48:47
! Source code version: Jul 29 2022
! Input file written at Mon Sep 30 16:04:44 2024.
! Do you want to assign atom data to them (y/n)? [yes] 
y
! Automatically rename all atoms to corresponding elements (recommended) (y/n)? [yes] 
n
! Do you want to rename this element (y/n)? [yes] 
n
! Do you want to copy the atom parameters from another element (y/n)? [yes] 
n
! Please enter covalent radius in pm: [174.00] 
0
! Please enter atom mass in u: [40.08] 

! Do you want to rename this element (y/n)? [yes] 
n
! Do you want to copy the atom parameters from another element (y/n)? [yes] 
n
! Please enter covalent radius in pm: [37.00] 

! Please enter atom mass in u: [1.01] 

! Do you want to rename this element (y/n)? [yes] 

! Enter new name for "Hw": [H] 
H
! Element H is known. Merge Hw atoms into H (y/n)? [yes] 

! Do you want to rename this element (y/n)? [yes] 

! Enter new name for "Oh": [O] 

! Element O is known. Merge Oh atoms into O (y/n)? [yes] 

! Do you want to rename this element (y/n)? [yes] 
n
! Do you want to copy the atom parameters from another element (y/n)? [yes] 
n
! Please enter covalent radius in pm: [75.00] 
0
! Please enter atom mass in u: [16.00] 

! Do you want to rename this element (y/n)? [yes] 
n
! Do you want to copy the atom parameters from another element (y/n)? [yes] 
n
! Please enter covalent radius in pm: [75.00] 

! Please enter atom mass in u: [16.00] 

! Do you want to rename this element (y/n)? [yes] 

! Enter new name for "Ow": [O] 

! Element O is known. Merge Ow atoms into O (y/n)? [yes] 

! Do you want to rename this element (y/n)? [yes] 
n
! Do you want to copy the atom parameters from another element (y/n)? [yes] 

! Copy atom parameters from which element? [Si] 

! Please enter covalent radius in pm: [118.00] 
0
! Please enter atom mass in u: [28.09] 

! Do you want to rename this element (y/n)? [yes] 
n
! Do you want to copy the atom parameters from another element (y/n)? [yes] 
n
! Please enter covalent radius in pm: [100] 
0
! Please enter atom mass in u: [10] 

! Does your system really contain the chemical element "Ca" (y), or are these "C" atoms (n)? [no] 
y
! Does your system really contain the chemical element "CaM" (y), or are these "C" atoms (n)? [no] 
n
! Does your system really contain the chemical element "Cl" (y), or are these "C" atoms (n)? [no] 
y
! Does your system really contain the chemical element "Hm" (y), or are these "H" atoms (n)? [no] 
n
! Does your system really contain the chemical element "OhM" (y), or are these "O" atoms (n)? [no] 
n
! Does your system really contain the chemical element "Om" (y), or are these "O" atoms (n)? [no] 
n
! Does your system really contain the chemical element "Si" (y), or are these "S" atoms (n)? [no] 
y
! Does your system really contain the chemical element "SiM" (y), or are these "S" atoms (n)? [no] 
n
! Use the advanced mode until the analysis selection menu (y/n)? [no] 

! Use these values (y) or enter different values (n)? [yes] 

! Update cell geometry in every time step (i.e., NPT ensemble) (y) or use fixed cell (n)? [yes] 
n
! Exclude Ca atoms from bond recognition (y/n)? [yes] 

! Create images of the structural formulas (y/n)? [no] 
n
! Accept these molecules (y) or change something (n)? [yes] 
n
! Please select: [done] 
1
! The radius of which element do you want to change (enter element label)? [done] 
Cl
! Please enter new bond radius for Cl in pm: [117.3] 
0
! Also remove this atom type from the system (y/n)? [no] 

! The radius of which element do you want to change (enter element label)? [done] 
H
! Please enter new bond radius for H in pm: [42.5] 
0
! Also remove this atom type from the system (y/n)? [no] 

! The radius of which element do you want to change (enter element label)? [done] 
Hm
! Please enter new bond radius for Hm in pm: [42.5] 
0
! Also remove this atom type from the system (y/n)? [no] 

! The radius of which element do you want to change (enter element label)? [done] 

! Please select: [done] 
Om
! Invalid input. Enter an integer number between 1 and 5.
! Please select: [done] 
1
! The radius of which element do you want to change (enter element label)? [done] 
O
! Please enter new bond radius for O in pm: [86.2] 
0
! Also remove this atom type from the system (y/n)? [no] 

! The radius of which element do you want to change (enter element label)? [done] 
Om
! Please enter new bond radius for Om in pm: [86.2] 
0
! Also remove this atom type from the system (y/n)? [no] 

! The radius of which element do you want to change (enter element label)? [done] 
Si
! Please enter new bond radius for Si in pm: [135.7] 
0
! Also remove this atom type from the system (y/n)? [no] 

! The radius of which element do you want to change (enter element label)? [done] 
C
! Please enter new bond radius for C in pm: [94.3] 
0
! Also remove this atom type from the system (y/n)? [no] 

! The radius of which element do you want to change (enter element label)? [done] 

! Please select: [done] 

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

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

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

! x component [0.0] 

! y component [0.0] 

! z component [1.0] 

! Use a specified atom (y) or absolute coordinates (n) as origin? [no] 

! x component [0.0] 

! y component [0.0] 

! z component [0.0] 

! Which molecule should be observed (Ca=1, Cl=2, S=3, Si=4, O=5, C=6, X=7, H=8)? 
8
! Enter the minimal distance of this density profile in pm: [-1300.0] 
-4000
! Enter the maximal distance of this density profile in pm: [1300.0] 
4000
! Enter the resolution (bin count) for this density profile: [300] 
600
! Scale to uniform density (y) or to nm^(-1) (n)? [no] 

! Enforce mirror symmetry of this profile (y/n)? [no] 

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

! Remove center of mass movement of the box (y/n)? [yes] 

! 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] 

