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Overview

Introduction

Sierra provides a uniform Python API for Entos simulations, such as workflows, energy calculations, and dynamics. The API provides access to low-cost, high-accuracy methods (xTB and OrbNet) as well as more traditional quantum chemistry methods (HF and DFT).

Sierra includes a number of prebuilt workflows for tasks more complicated than simple energy calculations, such as conformer generation, grid optimizations, bond dissociation energies, and many more.

Models

The Entos ecosystem is built up of the idea of Model objects which contain attributes. A Model in Sierra can be created by specifying attributes with the general form model = Model(attribute=data,...). The data in the Model can then be accessed by model.attribute. For example, the Molecule model contains attributes like symbols and geometry that can be called to return the atomic symbols and molecular geometry, respectively.

from sierra.inputs import *

mol = Molecule(pubchem="water")

print(mol.symbols)
#> ['O' 'H' 'H']
print(mol.geometry)
"""
[[ 0.          0.          0.        ]
 [ 0.52421003  1.68733646  0.48074633]
 [ 1.14668581 -0.45032174 -1.35474466]]
"""

Computation

There is a special type of model called Input which provides the input structure for a computation. Each Input object is paired with a corresponding Result object, which contains all information in the Input together with any additional attributes evaluated during the computation. All Input objects can be computed to Result objects with the sierra.run command.

import sierra
from sierra.inputs import *

water = Molecule(pubchem="water")
print(water.measure([0, 1]))  # O-H bond distance
#> 1.8311246594938317

inp = OptimizationInput(initial_molecule=water, method=XTBMethod(model="gfn1"))
result = sierra.run(inp)

print(result.final_molecule.measure([0, 1]))  # Optimized O-H bond distance
#> 1.8104715454450993

Documentation Tree

For further documentation and examples see:

  • Molecule - Details on creating and/or importing a molecular structure.
  • Units - A description of Sierra's unit system.
  • Building Blocks - Energy, gradient, AIMD, etc, which form the basis of Entos workflows.
  • Workflow - Automated technologies which perform commonly used discovery tasks.
  • Energy Methods - Details of DFT, xTB, OrbNet, and other energy methods.