ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
third column the absorbance scaled so that data runs from 1 to 0. Start and end point, and width of the
Gaussian/Lorentzian should be given in cm^-1.
7.21 Molecular dynamics
Typical computer simulations involve moving the atoms around, either to optimize a structure (energy minimization)
or to do molecular dynamics. This chapter discusses molecular dynamics, energy minimization algorithms
will be discussed in the optimize section.
A molecular dynamics object will operate on the atoms by moving them according to their forces - it integrates
Newton’s second law numerically. A typical molecular dynamics simulation will use the Velocity Verlet dynamics.
You create the VelocityVerlet object, giving it the atoms and a time step, and then you perform dynamics
by calling its run() method:
dyn = VelocityVerlet(atoms, 5.0 * units.fs)
dyn.run(1000) # take 1000 steps
A number of different algorithms can be used to perform molecular dynamics, with slightly different results.
7.21.1 Choosing the time step
All the dynamics objects need a time step. Choosing it too small will waste computer time, choosing it too large
will make the dynamics unstable, typically the energy increases dramatically (the system “blows up”). If the time
step is only a little to large, the lack of energy conservation is most obvious in Velocity Verlet dynamics, where
energy should otherwise be conserved.
Experience has shown that 5 femtoseconds is a good choice for most metallic systems. Systems with light atoms
(e.g. hydrogen) and/or with strong bonds (carbon) will need a smaller time step.
All the dynamics objects documented here are sufficiently related to have the same optimal time step.
7.21.2 File output
The time evolution of the system can be saved in a trajectory file, by creating a trajectory object, and attaching it
to the dynamics object. This is documented in the module ase.io.trajectory.
Unlike the geometry optimization classes, the molecular dynamics classes do not support giving a trajectory file
name in the constructor. Instead the trajectory must be attached explicitly to the dynamics, and it is stongly
recommended to use the optional interval argument, so every time step is not written to the file.
7.21.3 Logging
A logging mechanism is provided, printing time; total, potential and kinetic energy; and temperature (calculated
from the kinetic energy). It is enabled by giving the logfile argument when the dynamics object is created,
logfile may be an open file, a filename or the string ‘-‘ meaning standard output. Per default, a line is printed
for each timestep, specifying the loginterval argument will chance this to a more reasonable frequency.
The logging can be customized by explicitly attaching a ase.md.MDLogger object to the dynamics:
from ase.md import MDLogger
dyn = VelocityVerlet(atoms, dt=2*ase.units.fs)
dyn.attach(MDLogger(dyn, atoms, ’md.log’, header=False, stress=False,
peratom=True, mode="a"), interval=1000)
This example will skip the header line and write energies per atom instead of total energies. The parameters are
152 Chapter 7. Documentation for modules in ASE