md.angle

Overview

md.angle.harmonic Harmonic angle potential.
md.angle.table Tabulated angle potential.

Details

Angle potentials.

Angles add forces between specified triplets of particles and are typically used to model chemical angles between two bonds.

By themselves, angles that have been specified in an initial configuration do nothing. Only when you specify an angle force (i.e. angle.harmonic), are forces actually calculated between the listed particles.

class hoomd.md.angle.coeff

Define angle coefficients.

The coefficients for all angle force are specified using this class. Coefficients are specified per angle type.

There are two ways to set the coefficients for a particular angle potential. The first way is to save the angle potential in a variable and call set() directly. See below for an example of this.

The second method is to build the coeff class first and then assign it to the angle potential. There are some advantages to this method in that you could specify a complicated set of angle potential coefficients in a separate python file and import it into your job script.

Example:

my_coeffs = hoomd.md.angle.coeff();
my_angle_force.angle_coeff.set('polymer', k=330.0, r=0.84)
my_angle_force.angle_coeff.set('backbone', k=330.0, r=0.84)
set(type, **coeffs)

Sets parameters for angle types.

Parameters:
  • type (str) – Type of angle (or a list of type names)
  • coeffs – Named coefficients (see below for examples)

Calling set() results in one or more parameters being set for a angle type. Types are identified by name, and parameters are also added by name. Which parameters you need to specify depends on the angle potential you are setting these coefficients for, see the corresponding documentation.

All possible angle types as defined in the simulation box must be specified before executing run(). You will receive an error if you fail to do so. It is not an error, however, to specify coefficients for angle types that do not exist in the simulation. This can be useful in defining a potential field for many different types of angles even when some simulations only include a subset.

Examples:

my_angle_force.angle_coeff.set('polymer', k=330.0, r0=0.84)
my_angle_force.angle_coeff.set('backbone', k=1000.0, r0=1.0)
my_angle_force.angle_coeff.set(['angleA','angleB'], k=100, r0=0.0)

Note

Single parameters can be updated. If both k and r0 have already been set for a particle type, then executing coeff.set('polymer', r0=1.0) will update the value of r0 and leave the other parameters as they were previously set.

class hoomd.md.angle.harmonic

Harmonic angle potential.

The command angle.harmonic specifies a harmonic potential energy between every triplet of particles with an angle specified between them.

\[V(\theta) = \frac{1}{2} k \left( \theta - \theta_0 \right)^2\]

where \(\theta\) is the angle between the triplet of particles.

Coefficients:

  • \(\theta_0\) - rest angle t0 (in radians)
  • \(k\) - potential constant k (in units of energy/radians^2)

Coefficients \(k\) and \(\theta_0\) must be set for each type of angle in the simulation using the method angle_coeff.set().

Examples:

harmonic = angle.harmonic()
harmonic.angle_coeff.set('polymer', k=3.0, t0=0.7851)
harmonic.angle_coeff.set('backbone', k=100.0, t0=1.0)
disable(log=False)

Disable the force.

Parameters:log (bool) – Set to True if you plan to continue logging the potential energy associated with this force.

Examples:

force.disable()
force.disable(log=True)

Executing the disable command will remove the force from the simulation. Any hoomd.run() command executed after disabling a force will not calculate or use the force during the simulation. A disabled force can be re-enabled with enable().

By setting log to True, the values of the force can be logged even though the forces are not applied in the simulation. For forces that use cutoff radii, setting log=True will cause the correct r_cut values to be used throughout the simulation, and therefore possibly drive the neighbor list size larger than it otherwise would be. If log is left False, the potential energy associated with this force will not be available for logging.

enable()

Enable the force.

Examples:

force.enable()

See disable().

get_energy(group)

Get the energy of a particle group.

Parameters:group (hoomd.group) – The particle group to query the energy for.
Returns:The last computed energy for the members in the group.

Examples:

g = group.all()
energy = force.get_energy(g)
class hoomd.md.angle.table(width, name=None)

Tabulated angle potential.

Parameters:
  • width (int) – Number of points to use to interpolate V and F (see documentation above)
  • name (str) – Name of the force instance

table specifies that a tabulated angle potential should be added to every bonded triple of particles in the simulation.

The torque \(T\) is (in units of force * distance) and the potential \(V(\theta)\) is (in energy units):

\[\begin{split}T(\theta) = & T_{\mathrm{user}}(\theta) \\ V(\theta) = & V_{\mathrm{user}}(\theta)\end{split}\]

where \(\theta\) is the angle from A-B to B-C in the triple.

\(T_{\mathrm{user}}(\theta)\) and \(V_{\mathrm{user}}(\theta)\) are evaluated on width grid points between \(0\) and \(\pi\). Values are interpolated linearly between grid points. For correctness, you must specify: \(T = -\frac{\partial V}{\partial \theta}\)

Parameters:

  • \(T_{\mathrm{user}}(\theta)\) and \(V_{\mathrm{user}}(\theta)\) - evaluated by func (see example)
  • coefficients passed to func - coeff (see example)

The table width is set once when table is specified. There are two ways to specify the other parameters.

Set table from a given function

When you have a functional form for T and F, you can enter that directly into python. table will evaluate the given function over width points between \(0\) and \(\pi\) and use the resulting values in the table:

def harmonic(theta, kappa, theta_0):
    V = 0.5 * kappa * (theta-theta_0)**2;
    T = -kappa*(theta-theta_0);
    return (V, T)

btable = angle.table(width=1000)
btable.angle_coeff.set('angle1', func=harmonic, coeff=dict(kappa=330, theta_0=0))
btable.angle_coeff.set('angle2', func=harmonic,coeff=dict(kappa=30, theta_0=0.1))

Set a table from a file

When you have no function for for T or F, or you otherwise have the data listed in a file, table can use the given values directly. You must first specify the number of rows in your tables when initializing table. Then use set_from_file() to read the file:

btable = angle.table(width=1000)
btable.set_from_file('polymer', 'angle.dat')
disable(log=False)

Disable the force.

Parameters:log (bool) – Set to True if you plan to continue logging the potential energy associated with this force.

Examples:

force.disable()
force.disable(log=True)

Executing the disable command will remove the force from the simulation. Any hoomd.run() command executed after disabling a force will not calculate or use the force during the simulation. A disabled force can be re-enabled with enable().

By setting log to True, the values of the force can be logged even though the forces are not applied in the simulation. For forces that use cutoff radii, setting log=True will cause the correct r_cut values to be used throughout the simulation, and therefore possibly drive the neighbor list size larger than it otherwise would be. If log is left False, the potential energy associated with this force will not be available for logging.

enable()

Enable the force.

Examples:

force.enable()

See disable().

get_energy(group)

Get the energy of a particle group.

Parameters:group (hoomd.group) – The particle group to query the energy for.
Returns:The last computed energy for the members in the group.

Examples:

g = group.all()
energy = force.get_energy(g)
set_from_file(anglename, filename)

Set a angle pair interaction from a file.

Parameters:
  • anglename (str) – Name of angle
  • filename (str) – Name of the file to read

The provided file specifies V and F at equally spaced theta values:

#t  V    T
0.0 2.0 -3.0
1.5707 3.0 -4.0
3.1414 2.0 -3.0

Warning

The theta values are not used by the code. It is assumed that a table that has N rows will start at 0, end at \(\pi\) and that \(\delta \theta = \pi/(N-1)\). The table is read directly into the grid points used to evaluate \(T_{\mathrm{user}}(\theta)\) and \(V_{\mathrm{user}}(\theta)\).