md.minimize
Overview
Energy Minimizer (FIRE). |
Details
Energy minimizer for molecular dynamics.
- class hoomd.md.minimize.FIRE(dt, force_tol, angmom_tol, energy_tol, integrate_rotational_dof=False, forces=None, constraints=None, methods=None, rigid=None, min_steps_adapt=5, finc_dt=1.1, fdec_dt=0.5, alpha_start=0.1, fdec_alpha=0.99, min_steps_conv=10)
Energy Minimizer (FIRE).
- Parameters
dt (float) – This is the maximum step size the minimizer is permitted to use \([\mathrm{time}]\). Consider the stability of the system when setting.
integrate_rotational_dof (bool) – When True, integrate rotational degrees of freedom.
forces (Sequence[hoomd.md.force.Force]) – Sequence of forces applied to the particles in the system. All the forces are summed together. The default value of
None
initializes an empty list.methods (Sequence[hoomd.md.methods.Method]) – Sequence of integration methods. Each integration method can be applied to only a specific subset of particles. The intersection of the subsets must be null. The default value of
None
initializes an empty list.constraints (Sequence[hoomd.md.constrain.Constraint]) – Sequence of constraint forces applied to the particles in the system. The default value of
None
initializes an empty list. Rigid body objects (i.e.hoomd.md.constrain.Rigid
) are not allowed in the list.rigid (hoomd.md.constrain.Rigid) – A rigid bodies object defining the rigid bodies in the simulation.
min_steps_adapt (int) – Number of steps energy change is negative before allowing \(\alpha\) and \(\delta t\) to adapt.
finc_dt (float) – Factor to increase \(\delta t\) by \([\mathrm{dimensionless}]\).
fdec_dt (float) – Factor to decrease \(\delta t\) by \([\mathrm{dimensionless}]\).
alpha_start (float) – Initial (and maximum) \(\alpha [\mathrm{dimensionless}]\).
fdec_alpha (float) – Factor to decrease \(\alpha t\) by \([\mathrm{dimensionless}]\).
force_tol (float) – Force convergence criteria \([\mathrm{force} / \mathrm{mass}]\).
angmom_tol (float) – Angular momentum convergence criteria \([\mathrm{energy} * \mathrm{time}]\).
energy_tol (float) – Energy convergence criteria \([\mathrm{energy}]\).
min_steps_conv (int) – A minimum number of attempts before convergence criteria are considered.
FIRE
is ahoomd.md.Integrator
that uses the Fast Inertial Relaxation Engine (FIRE) algorithm to minimize the potential energy for a group of particles while keeping all other particles fixed. This method is published in Bitzek, et. al., PRL, 2006. HOOMD-blue’s implementation extends the original formulation to include rotational degrees of freedom.At each time step, \(\delta t\), the algorithm uses the supplied integration methods to generate \(\vec{r}\), \(\vec{v}\), and \(\vec{F}\), and then adjusts \(\vec{v}\) according to
\[\vec{v} = (1-\alpha)\vec{v} + \alpha \hat{F}|\vec{v}|\]where \(\alpha\) and \(\delta t\) are dynamically adaptive quantities. While a current search has been lowering the energy of system for more than \(N_{min}\) steps, \(\alpha\) is decreased by \(\alpha \rightarrow \alpha \cdot \mathrm{fdec}_{\alpha}\) and \(\delta t\) is increased by \(\delta t \rightarrow \max(\delta t \cdot \mathrm{finc}_{dt}, \ \delta t_{max})\). If the energy of the system increases (or stays the same), the velocity of the particles is set to 0, \(\alpha \rightarrow \ \alpha_{start}\) and \(\delta t \rightarrow \delta t \cdot \mathrm{fdec}_{\alpha}\). The method converges when the force per particle is below
force_tol
, the angular momentum is belowangmom_tol
and the change in potential energy from one step to the next is belowenergy_tol
:\[\frac{\sum |F|}{N*\sqrt{N_{dof}}} < \mathrm{\text{force_tol}} \;\;, \;\ \Delta \frac{\sum|E|}{N} < \mathrm{\text{energy_tol}} \;\;, and \;\ \frac{\sum|L|}{N} < \mathrm{\text{angmom_tol}}\]where \(N_{\mathrm{dof}}\) is the number of degrees of freedom the minimization is acting over. Any of the criterion can be effectively disabled by setting the tolerance to a large number.
If the minimization acts on a subset of all the particles in the system, the other particles will be kept frozen but will still interact with the particles being moved.
Examples:
fire = md.minimize.FIRE(dt=0.05, force_tol=1e-2, angmom_tol=1e-2, energy_tol=1e-7) fire.methods.append(md.methods.NVE(hoomd.filter.All())) sim.operations.integrator = fire while not(fire.converged): sim.run(100) fire = md.minimize.FIRE(dt=0.05) fire.methods.append(md.methods.NPH( hoomd.filter.All(), S=1, tauS=1, couple='none')) sim.operations.integrator = fire while not(fire.converged): sim.run(100)
Note
To use
FIRE
, set it as the simulation’s integrator in place of the typicalhoomd.md.Integrator
.Note
The algorithm requires an integration method to update the particle position and velocities. This should either be either
hoomd.md.methods.NVE
(to minimize energy) orhoomd.md.methods.NPH
(to minimize energy and relax the box). The quantity minimized is in any case the potential energy (not the enthalpy or any other quantity).Note
In practice, the default parameters prevents the simulation from making too aggressive a first step, but also from quitting before having found a good search direction. Adjust the parameters as needed for your simulations.
- dt
This is the maximum step size the minimizer is permitted to use \([\mathrm{time}]\). Consider the stability of the system when setting.
- Type
- forces
Sequence of forces applied to the particles in the system. All the forces are summed together. The default value of
None
initializes an empty list.- Type
Sequence[hoomd.md.force.Force]
- methods
Sequence of integration methods. Each integration method can be applied to only a specific subset of particles. The intersection of the subsets must be null. The default value of
None
initializes an empty list.- Type
Sequence[hoomd.md.methods.Method]
- constraints
Sequence of constraint forces applied to the particles in the system. The default value of
None
initializes an empty list. Rigid body objects (i.e.hoomd.md.constrain.Rigid
) are not allowed in the list.- Type
Sequence[hoomd.md.constrain.Constraint]
- rigid
A rigid bodies object defining the rigid bodies in the simulation.
- min_steps_adapt
Number of steps energy change is negative before allowing \(\alpha\) and \(\delta t\) to adapt.
- Type
- property converged
True when the minimizer has converged, else False.
(
Loggable
: category=”scalar”, default=False)- Type
- property energy
Get the energy after the last iteration of the minimizer.
(
Loggable
: category=”scalar”)- Type
- reset()
Reset the minimizer to its initial state.