GPR for ideal gas (ig_active)

Generates ideal gas (1D in external potential) data to test GP models and active learning strategies.

Classes:

IG_DataWrapper(beta[, rng])	Data object for gpr with ideal gas.
SimulateIG([sim_func])	Simulation object for ideal gas.

class thermoextrap.gpr_active.ig_active.IG_DataWrapper(beta, rng=None)

Bases: DataWrapper

Data object for gpr with ideal gas.

Methods:

load_U_info()	Loads potential energies from a list of files.
load_CV_info()	Loads data from a file specifying CV coordinate and added bias at each frame.
load_x_info()	Loads observable data.
get_data([n_conf, n_part])	Loads data from files needed to generate data classes for thermoextrap.
build_state([all_data, max_order])	Builds a thermoextrap data object for the data described by this wrapper class.

load_U_info()

Loads potential energies from a list of files.

load_CV_info()

Loads data from a file specifying CV coordinate and added bias at each frame. Assumes that the first value in col_ind is the index of the CV coordinate column and the second is the index for the bias.

load_x_info()

Loads observable data.

get_data(n_conf=10000, n_part=1000)

Loads data from files needed to generate data classes for thermoextrap. Will change significantly if using MBAR on trajectories with different biases.

build_state(all_data=None, max_order=6)

Builds a thermoextrap data object for the data described by this wrapper class. If all_data is provided, should be list or tuple of (potential energies, X) to be used, where X should be appropriately weighted if the simulation is biased.

class thermoextrap.gpr_active.ig_active.SimulateIG(sim_func=None)

Bases: object

Simulation object for ideal gas.