This package is designed with three goals in mind:
- Enable rapid prototyping of potential functions and automatic generation of gradients of arbitrary order.
- Generate performant code using a jax/xla backend that can be run on CPUs, GPUs, and TPUs.
- Meta-optimization of optimizers and integrators, allowing one to generate analytic derivatives of a trajectory.
The code is implemented against OpenMM for numerical accuracy.
import functools
import numpy as np
import jax
from timemachine.potentials import bonded
x0 = np.array([
[1.0, 0.2, 3.3], # H
[-0.5,-1.1,-0.9], # C
[3.4, 5.5, 0.2], # H
], dtype=np.float64)
params = np.array([10.0, 3.0, 5.5], dtype=np.float64)
param_idxs = np.array([
[0,1],
[1,2],
], dtype=np.int32)
bond_idxs = np.array([
[0,1],
[1,2]
], dtype=np.int32)
# wrap the energy function for convenience
energy_fn = functools.partial(
bonded.harmonic_bond,
param_idxs=param_idxs,
bond_idxs=bond_idxs)
# dE/dx, shape [N,3]:
dedx_fn = jax.grad(energy_fn, argnums=(0,))
dedx_fn(x0, params, box=None)
# dE/dparams, shape [3,]:
dedp_fn = jax.grad(energy_fn, argnums=(1,))
dedp_fn(x0, params, box=None)
# d^2E/dx^2, shape [N,3,N,3]:
d2edx2_fn = jax.hessian(energy_fn, argnums=(0,))
d2edx2_fn(x0, params, box=None)
# d^2E/dxde, shape [N,3,3]:
d2edxde_fn = jax.jacfwd(jax.jacrev(energy_fn, argnums=(0,)), argnums=(1,))
d2edxde_fn(x0, params, box=None)This code is under heavy development. APIs for potential energies are fairly stable now.
We currently support the following functional forms:
- (Periodic) Harmonic Bond
- (Periodic) Harmonic Angle
- (Periodic) Periodic Torsion
- (Periodic) Electrostatic
- (Periodic) Lennard-Jones
- GBSA OBC
See requirements.txt
Copyright 2019 Yutong Zhao
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.