Python Interface

class ndsimulator.bias.Gaussian(w=None, sigma=None, dep_freq=10, biasf=1.0, adapsig=False, adapsig_geo=False, run=None)

The gaussian_bias object implements gaussian shape bias.

This object does not directly modify atom energy and forces. It only computes them and return them in the force() function.

Example

fix = Gaussian_Bias() … … pointer = all_data(run=self) pointer.atoms = atoms pointer.fix = fix … … fix.initialize(pointer)

compute(x0=None, col0=None)

compute the energy and force from gaussian function the energy equation will be called as well

dump_data()

sum up the gaussian hills and return a NXN matrix for the computed free energy landscape input X, Y matrix for each point the X and Y are taken along the colvar1 and colvar2 directions only add the new hills that weren’t added before

force(x0=None, col0=None)

compute the force from gaussian function the energy equation will be called as well

projection(X, Y)

sum up the gaussian hills and return a NXN matrix for the computed free energy landscape input X, Y matrix for each point the X and Y are taken along the colvar1 and colvar2 directions only add the new hills that weren’t added before

update(step, time)

gaussian function will be deposited when the time step is a multiple of the _dep_freq