Skip to content

Implement Angle Interactions #282

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
mphoward merged 30 commits into from
Jan 10, 2025
Merged

Implement Angle Interactions #282

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
30 commits
Select commit Hold shift + click to select a range
173bf27
Implement angle potentials and unit test.
clpetix Nov 12, 2024
1f8266b
Update Angle and unit tests.
clpetix Nov 18, 2024
f41d65f
Implement and unittest cosine angle.
clpetix Nov 19, 2024
65ad394
Fix documentation for angle potentials and update examples.
clpetix Nov 20, 2024
ad58150
Keep angles.py consistent with bonds.py.
clpetix Nov 20, 2024
724b686
Update documentation.
clpetix Nov 20, 2024
869a946
Add angle to documentation.
clpetix Dec 10, 2024
875f8ab
Add angle potential tabulator.
clpetix Dec 10, 2024
f7a2a0f
Attach angles to HOOMD
clpetix Dec 10, 2024
ae271e4
Add angle potentials to LAMMPS.
clpetix Dec 10, 2024
d0542bb
Finalize adding angle support to lammps.py.
clpetix Jan 7, 2025
1768f78
Make test_angles conform with test_bonds.
clpetix Jan 7, 2025
7a2509b
Add in tests for HOOMD and LAMMPS.
clpetix Jan 7, 2025
639b4ac
Fix angle derivative test.
clpetix Jan 7, 2025
7882c8c
Make docstring underline appropriate length.
clpetix Jan 7, 2025
5946188
Refactor CosineSquaredAngle to HarmonicCosineAngle.
clpetix Jan 8, 2025
b7f8212
Put in factor of half in HarmonicCosineAngle.
clpetix Jan 8, 2025
f796f50
Fix AnglePotentialTabulator doc string.
clpetix Jan 8, 2025
a6eaf7c
Fix bonded exclusions when None.
clpetix Jan 8, 2025
5f3488f
Use multiple inheritance for BondSpline and AngleSpline.
clpetix Jan 8, 2025
a7513ac
Document AnglePotential to describe how the angle is calculated.
clpetix Jan 8, 2025
e71ae01
Fix documentation.
clpetix Jan 8, 2025
bf89323
Fix documentation order.
clpetix Jan 8, 2025
43a6262
Refactor to use generalized coordinate name in BondedSpline.
clpetix Jan 9, 2025
aab76b7
Fix documentation for BondSpline.
clpetix Jan 9, 2025
1db111b
Add a bound check on angle spline.
clpetix Jan 9, 2025
657b30a
Merge branch 'main' into feature/angle-interactions
clpetix Jan 9, 2025
eb46f04
Apply suggestions from code review
clpetix Jan 9, 2025
a82e867
Ensure bond and angle use r and theta throughout.
clpetix Jan 9, 2025
2188a73
Apply suggestions from code review
mphoward Jan 10, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
25 changes: 24 additions & 1 deletion src/relentless/model/potential/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,18 @@
BondSpline


Angle potentials
================

.. autosummary::
:toctree: generated/

AngleSpline
CosineAngle
HarmonicAngle
HarmonicCosineAngle


Developer classes
=================

Expand All @@ -36,13 +48,24 @@
Potential
Parameters
BondedPotential
BondedSpline
AnglePotential
AngleParameters
BondPotential
BondParameters
PairPotential
PairParameters

"""

from .angle import (
AngleParameters,
AnglePotential,
AngleSpline,
CosineAngle,
HarmonicAngle,
HarmonicCosineAngle,
)
from .bond import FENEWCA, BondParameters, BondPotential, BondSpline, HarmonicBond
from .pair import (
Depletion,
Expand All @@ -52,4 +75,4 @@
PairSpline,
Yukawa,
)
from .potential import BondedPotential, Parameters, Potential
from .potential import BondedPotential, BondedSpline, Parameters, Potential
Loading
Loading