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fort.7 / fort.8 files — Connectivity and charge output

The fort.7 and fort.8 files contain ReaxFF‑generated connectivity tables and partial charge information.
They describe which atoms are bonded, the corresponding bond orders, molecular membership, and atomic charges.

These files are central for: - Bond analysis - Molecule identification - Charge tracking - Graph‑based post‑processing (e.g. fragmentation, reactions)

Difference between fort.7 and fort.8

File Contents
fort.8 All bonds and bond orders
fort.7 Only bonds with bond order > cutof2 (from control file)

fort.7 is therefore a filtered version of fort.8, typically used for molecular graphs.

Output frequency

Both files are updated at the same frequency as xmolout:

  • MD simulations: every iout2 iterations
  • MM runs: every iout4 iterations

By default, these files are overwritten with the most recent data.

Setting the control keyword:

iappen = 1

causes both fort.7 and fort.8 to be appended instead.

File structure

Header line

The first line contains:

<number_of_atoms> <structure_identifier>

Example:

7 Ethyl_radical

Atom records

Each subsequent line corresponds to one atom and contains:

  1. Atom number
  2. Atom type number (as defined in ffield)
  3. Connectivity list (bonded atom indices)
  4. Molecule number
  5. Bond orders (one per bonded neighbor)
  6. Sum of bond orders
  7. Number of lone pairs
  8. Partial charge

Example 3.2: fort.7 connection table

7 Ethyl_radical

1 1 2 3 4 5 0 1 0.985 1.024 0.986 0.986 0.000 3.981 0.000 -0.289
2 2 1 0 0 0 0 1 0.985 0.000 0.000 0.000 0.000 0.985 0.000 0.103
3 1 1 6 7 0 0 1 1.024 0.987 0.987 0.000 0.000 2.999 0.000 -0.233
4 2 1 0 0 0 0 1 0.986 0.000 0.000 0.000 0.000 0.986 0.000 0.105
5 2 1 0 0 0 0 1 0.986 0.000 0.000 0.000 0.000 0.986 0.000 0.105
6 2 3 0 0 0 0 1 0.987 0.000 0.000 0.000 0.000 0.987 0.000 0.105
7 2 3 0 0 0 0 1 0.987 0.000 0.000 0.000 0.000 0.987 0.000 0.105

Column interpretation (conceptual)

Field Meaning
Atom number Index of atom
Atom type Force‑field atom type
Connectivity Indices of bonded atoms
Molecule number Molecular fragment ID
Bond orders Bond order per connection
Σ bond orders Total bond order
Lone pairs Number of lone pairs
Partial charge Atomic charge

The number of connectivity entries and bond orders varies depending on how many neighbors an atom has.

Practical notes

  • fort.7 is commonly used for molecule detection and reaction tracking
  • fort.8 is useful for detailed bond‑order analysis
  • Both files are tightly coupled to cutof2, iout2, iout4, and iappen
  • They are ideal inputs for graph‑based post‑processing tools

Summary

  • fort.7 / fort.8 store ReaxFF connectivity and charge data
  • Updated synchronously with xmolout
  • fort.7 is a bond‑order‑filtered subset of fort.8
  • Essential for bonding, molecule, and charge analysis workflows