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sponge.core.AnalysisCell

class sponge.core.AnalysisCell(system: Molecule, potential: PotentialCell, neighbour_list: NeighbourList = None)

Cell for analysis.

Parameters

• system (sponge.system.Molecule) – Simulation system.

• potential (sponge.potential.PotentialCell) – Potential energy.

• neighbour_list (sponge.partition.NeighbourList, optional) – Neighbour list. Default: None.

Inputs:

• coordinate (Tensor) - Coordinate. Tensor of shape $(B,A,D)$. Data type is float. Here $B$ is the number of walkers in simulation, $A$ is the number of atoms, and $D$ is the spatial dimension of the simulation system, which is usually 3.

• pbc_box (Tensor) - Periodic boundary condition box. Tensor of shape $(B,D)$. Data type is float.

• energy (Tensor) - Energy. Tensor of shape $(B,1)$. Data type is float.

• force (Tensor) - Force. Tensor of shape $(B,A,D)$. Data type is float.

• potentials (Tensor, optional) - Original potential energies from force field. Tensor of shape $(B,U)$. Here $U$ is the number of potential energies. Data type is float. Default: 0.

• total_bias (Tensor, optional) - Total bias energy for reweighting. Tensor of shape $(B,1)$. Data type is float. Default: 0.

• biases (Tensor, optional) - Original bias potential energies from bias functions. Tensor of shape $(B,V)$. Here V is the number of bias potential energies. Data type is float. Default: 0.

Outputs:

• coordinate (Tensor) - with shape of $(B,A,D)$. Coordinate. Data type is float.

• pbc_box (Tensor) - with shape of $(B,D)$, PBC box. Data type is float.

• energy (Tensor) - with shape of $(B,1)$, Total potential energy of the simulation system. Data type is float.

• force (Tensor) - with shape of $(B,A,D)$. Force on each atom of the simulation system. Data type is float.

• potentials (Tensor) - with shape of $(B,U)$. Original potential energies from force field. Data type is float.

• total_bias (Tensor) - with shape of $(B,1)$. Total bias energy for reweighting. Data type is float.

• biases (Tensor) - with shape of $(B,V)$. Bias potential energies from bias functions. Data type is float.

Supported Platforms:

Ascend GPU

Examples

>>> from sponge.system import Molecule
>>> from sponge.potential.forcefield import ForceField
>>> from sponge.core.sponge import Sponge
>>> from sponge.core.analysis import AnalysisCell
>>> system = Molecule(template='water.tip3p.yaml')
>>> potential = ForceField(system, parameters='SPCE')
>>> analysis = AnalysisCell(system, potential)