! 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 Tue Oct  1 08:10:33 2024.
! Do you want to assign atom data to them (y/n)? [yes] 

! 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] 
400
! 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] 
0
! Please enter atom mass in u: [1.01] 
350
! 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] 
0
! Please enter atom mass in u: [1.01] 
2
! 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] 
99
! 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] 
11111
! 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] 
7590
! 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] 
29474
! 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: [118.00] 
0
! Please enter atom mass in u: [28.09] 
32323
! 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] 

! 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] 
y
! 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] 
y
! Does your system really contain the chemical element "Hw" (y), or are these "H" atoms (n)? [no] 
y
! Does your system really contain the chemical element "Oh" (y), or are these "O" atoms (n)? [no] 
y
! Does your system really contain the chemical element "OhM" (y), or are these "O" atoms (n)? [no] 
y
! Does your system really contain the chemical element "Om" (y), or are these "O" atoms (n)? [no] 
y
! Does your system really contain the chemical element "Ow" (y), or are these "O" atoms (n)? [no] 
y
! 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] 
y
! 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] 

! Continue with molecule recognition anyways (y/n)? [yes] 

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

! Accept these molecules (y) or change something (n)? [yes] 
n
! Please select: [done] 
2
! Break bonds in which molecule (1-45)? 
1
! Break all bonds within this molecule (y/n)? [no] 
y
! Break another bond (y/n)? [no] 
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] 
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] 
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] 
X
! Please enter new bond radius for X in pm: [115.0] 
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 (SiM=1, Ow=2, OhM=3, Om=4, CaM=5, Hm=6, Oh=7, Ca=8, Cl=9, Si=10, O=11, X=12, Hw=13, H=14)? 
7
! 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] 
y
! Which molecule should be observed (SiM=1, Ow=2, OhM=3, Om=4, CaM=5, Hm=6, Oh=7, Ca=8, Cl=9, Si=10, O=11, X=12, Hw=13, H=14)? 
2
! 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] 
y
! Which molecule should be observed (SiM=1, Ow=2, OhM=3, Om=4, CaM=5, Hm=6, Oh=7, Ca=8, Cl=9, Si=10, O=11, X=12, Hw=13, H=14)? 
13
! 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] 
y
! Which molecule should be observed (SiM=1, Ow=2, OhM=3, Om=4, CaM=5, Hm=6, Oh=7, Ca=8, Cl=9, Si=10, O=11, X=12, Hw=13, H=14)? 
14
! 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] 

