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vels file — MD restart file (positions, velocities, accelerations)

The vels file stores atomic positions, velocities, and accelerations and is used to restart ReaxFF MD simulations.

During an MD run, ReaxFF periodically writes restart files based on the control keywords iout2 and iout6. These files can be reused to continue a simulation seamlessly.

Purpose of the vels file

  • Restart an interrupted MD simulation
  • Continue dynamics with the latest positions and velocities
  • Override the geometry provided in the geo file (positions only)

Important: The geo file is still required. ReaxFF checks that geo and vels contain the same number of atoms before restarting.

File handling and naming

  • During MD, ReaxFF generates:
  • moldyn.vel — most recent restart snapshot
  • molsav.xxxx — periodic restart snapshots
  • To restart:
  • Copy a restart file to vels
  • Re-run the exe script
  • The exe script then copies vels to moldyn.vel
  • ReaxFF reads moldyn.vel and overwrites it at intervals set by iout2

This naming can be confusing, but the flow is consistent once understood.

What the vels file contains

In order, the file includes:

  1. Lattice parameters
  2. Atom coordinates
  3. Atom velocities
  4. Atom accelerations
  5. Previous atom accelerations
  6. Instantaneous MD temperature

Acceleration history is included for completeness but does not influence restarted runs if outdated.

Example 2.16: vels restart file

The following example shows a restart file generated for an MD simulation of an ethyl radical.

Lattice parameters:

80.00000000 80.00000000 80.00000000
90.00000000 90.00000000 90.00000000

7 Atom coordinates (Angstrom):

0.392027787892917E+02 0.400902383055691E+02 0.396569719222545E+02 C
0.408076194536754E+02 0.407017914536647E+02 0.409641189620557E+02 H
0.406156358473423E+02 0.399085739070730E+02 0.402446784332288E+02 C
0.389320157142440E+02 0.409742263417328E+02 0.391261065022365E+02 H
0.384743625215192E+02 0.392966529997087E+02 0.397356676283833E+02 H
0.413546771765171E+02 0.399886339278518E+02 0.394389532581619E+02 H
0.407016447482017E+02 0.389398236842467E+02 0.407560383741949E+02 H

Atom velocities (Angstrom/s):

-0.639976248783438E+12  0.451200007339684E+11 -0.216754312886992E+12
-0.703141792567835E+11  0.421377644135005E+13  0.824472191800807E+13
 0.447898432906652E+12 -0.105077751499844E+13 -0.658290512224369E+11
 0.195067105934229E+13  0.289176812368303E+13 -0.140045800761676E+14
 0.476126532155786E+13 -0.152785617001799E+13  0.169491694508477E+14
 0.456467329116016E+13  0.118352257917078E+14 -0.396100285863348E+12
-0.891965482760371E+13 -0.544080092166964E+13 -0.742912333885548E+13

Atom accelerations (Angstrom/s**2):

-0.810436027147472E+27 -0.981147717871880E+27 -0.313616213868668E+27
 0.116753745428499E+29  0.109570643908876E+29  0.135954922986376E+29
-0.244853315374905E+27 -0.599286401168541E+27 -0.831858387309253E+27
 0.105361267406127E+28  0.134697085751095E+28 -0.115819691864393E+27
 0.208416152961380E+28  0.364332842399750E+28 -0.673228416751219E+27
-0.149559883359616E+28 -0.125042567119739E+28  0.468080992010752E+28
-0.754581549567212E+27  0.411775389213967E+28 -0.385065171515426E+28

Previous atom accelerations:

0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00
0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00
0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00
0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00
0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00
0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00
0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00

MD-temperature (K):

0.550040311117348E+02

Notes and best practices

  • Geometry precedence: positions in vels override those in geo
  • Atom count must match between vels and geo
  • Acceleration history is generally not critical for restarts
  • Restart files are essential for:
  • Long simulations
  • Queue-limited HPC jobs
  • Crash recovery

Summary

  • vels enables robust MD restarts
  • Generated automatically during MD
  • Copied to moldyn.vel and refreshed during the run
  • Central to production-scale ReaxFF workflows