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Merged
mphoward merged 55 commits into from
Jan 7, 2025
Merged

Implement bond interactions #272

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526d84c
Add bond potential module. Add Harmonic and FENE.
clpetix Sep 3, 2024
946ea3a
Merge branch 'main' of https://github.com/mphowardlab/relentless into…
clpetix Sep 3, 2024
0056c42
Add bond potentials to HOOMD.
clpetix Sep 9, 2024
44b41bc
Merge branch 'main' into feature/bonded-interactions
clpetix Sep 9, 2024
6547fc8
Merge branch 'main' of https://github.com/mphowardlab/relentless into…
clpetix Sep 9, 2024
5422657
Update BondParameters and BondPotential to be for typechecking only.
clpetix Sep 9, 2024
00b8852
Merge branch 'main' of https://github.com/mphowardlab/relentless into…
clpetix Oct 2, 2024
4418122
Add in bond exclusions to HOOMD.
clpetix Oct 7, 2024
1108d28
Simplifiy BondPotential init.
clpetix Oct 7, 2024
10458e5
Ensure bonds are only called when they exist.
clpetix Oct 7, 2024
8344a48
Remove _potentials_rmax as it is vestigial
clpetix Oct 9, 2024
e81f873
Change hoomd exclusions to be optional in g(r) calculation.
clpetix Oct 10, 2024
c443276
Add spline potential to bond.py
clpetix Oct 10, 2024
e4ccee0
Fix exclusions on neighborlist in HOOMD.
clpetix Oct 10, 2024
b9e662d
Rough implementation of LAMMPS when coming from HOOMD GSD.
clpetix Oct 11, 2024
334809b
Fix LAMMPS support from data file.
clpetix Oct 15, 2024
8e33f36
Only write potential if has_bonds().
clpetix Oct 15, 2024
aae3b66
Process exclusions to neighborlist in LAMMPS.
clpetix Oct 16, 2024
e3a47fe
add option to specify atom_style.
clpetix Oct 17, 2024
4abd1f5
Add cantor pairing as private method to reduce duplication.
clpetix Nov 6, 2024
830e06d
Clean up implementation of bond potentials.
clpetix Nov 7, 2024
579bdbd
Clean up hoomd.py file.
clpetix Nov 7, 2024
ace9ae3
Merge remote-tracking branch 'origin' into feature/bonded-interactions
clpetix Nov 7, 2024
119cac1
Fix exclusion implementation in HOOMD.
clpetix Nov 7, 2024
114f42b
Fix MPI issue in LAMMPS.
clpetix Nov 7, 2024
f02ad2a
Add default exclusions in HOOMD.
clpetix Nov 7, 2024
f075591
Add bond unit tests.
clpetix Nov 12, 2024
d0e8b53
Add BondedPotential class, fix derivative method, update tests.
clpetix Nov 14, 2024
3eda5d5
Add bonds to documentation.
clpetix Nov 20, 2024
55dbac2
Check that exclusions are of allowed type.
clpetix Nov 20, 2024
a1c54d9
Clean up exlcusion and remove r_bond from HOOMD.
clpetix Nov 20, 2024
3e5ebdc
Merge branch 'main' of https://github.com/mphowardlab/relentless into…
clpetix Nov 20, 2024
d589580
Update documentation.
clpetix Nov 20, 2024
1305c36
Implement reviewer suggestions in bond.py.
clpetix Nov 20, 2024
97cd2ad
Update documentation.
clpetix Nov 20, 2024
0613020
Update the allowed exclusions.
clpetix Nov 20, 2024
fd37ded
Update BondedPotential documentation.
clpetix Nov 20, 2024
a431bb0
Fix docs failing on bonded potential.
clpetix Nov 20, 2024
89e448e
Update HOOMD handing bonds.
clpetix Nov 20, 2024
5bc1900
Remove broadcasting entire snapshot in lammps.py.
clpetix Nov 20, 2024
9e04d45
Update exclusions documentation.
clpetix Nov 20, 2024
08edbb7
Add bond potential tabulator to documentation.
clpetix Nov 20, 2024
5b0e461
Clean up bond potentials and documentation.
clpetix Nov 21, 2024
e08dc02
Add bond property to Potentials.
clpetix Nov 21, 2024
ae6f433
Update bonds testing for HOOMD and LAMMPS.
clpetix Nov 22, 2024
cc2ec6b
Use broadcasted bond type for MPI compatability.
clpetix Nov 22, 2024
176f105
Bump lammpsio version.
clpetix Dec 10, 2024
2bb48e4
Merge branch 'main' into feature/bonded-interactions
clpetix Dec 11, 2024
2d78e78
Bump lammpsio in setup.cfg
clpetix Dec 11, 2024
bf4e820
Remove 3.8 testing.
clpetix Dec 11, 2024
5642ed6
Remove Python 3.8.
clpetix Jan 6, 2025
039c8f2
Cleanup implementation as requested in review.
clpetix Jan 6, 2025
e1f6f5c
Fix or when checking atom style.
clpetix Jan 6, 2025
da2ed46
Bump readthedocs python version.
clpetix Jan 6, 2025
4909cb9
Merge branch 'main' into feature/bonded-interactions
mphoward Jan 7, 2025
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6 changes: 3 additions & 3 deletions .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
python-version: ["3.9", "3.10", "3.11", "3.12"]
mpi: ["nompi", "mpich", "openmpi"]
steps:
- name: Checkout code
Expand Down Expand Up @@ -68,7 +68,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ["3.8", "3.9", "3.10", "3.11"]
python-version: ["3.9", "3.10", "3.11"]
hoomd-version: ["2.9.7", "3.11.0", "4.7.0"]
include:
- python-version: "3.12"
Expand Down Expand Up @@ -113,7 +113,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ["3.8", "3.9", "3.10", "3.11"]
python-version: ["3.9", "3.10", "3.11"]
lammps-version: ["2022.06.23", "2023.08.02"]
mpi: ["mpich", "openmpi"]
steps:
Expand Down
2 changes: 1 addition & 1 deletion .readthedocs.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ version: 2
build:
os: ubuntu-22.04
tools:
python: "3.8"
python: "3.9"

sphinx:
configuration: doc/source/conf.py
Expand Down
5 changes: 2 additions & 3 deletions requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
freud-analysis>=2
gsd<3.3.0; python_version < '3.9'
gsd; python_version >= '3.9'
lammpsio>=0.6.1
gsd
lammpsio>=0.7.0
networkx>=2.5
numpy
packaging
Expand Down
8 changes: 3 additions & 5 deletions setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,6 @@ classifiers =
License :: OSI Approved :: BSD License
Topic :: Scientific/Engineering :: Chemistry
Topic :: Scientific/Engineering :: Physics
Programming Language :: Python :: 3.8
Programming Language :: Python :: 3.9
Programming Language :: Python :: 3.10
Programming Language :: Python :: 3.11
Expand All @@ -42,12 +41,11 @@ packages = find:
package_dir =
= src
include_package_data = True
python_requires = >=3.8
python_requires = >=3.9
install_requires =
freud-analysis>=2
gsd<3.3.0; python_version < '3.9'
gsd; python_version >= '3.9'
lammpsio>=0.6.1
gsd
lammpsio>=0.7.0
networkx>=2.5
numpy
packaging
Expand Down
17 changes: 16 additions & 1 deletion src/relentless/model/potential/__init__.py
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Expand Up @@ -16,6 +16,17 @@
PairSpline
Yukawa

Bond potentials
===============

.. autosummary::
:toctree: generated/

HarmonicBond
FENEWCA
BondSpline


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

Expand All @@ -24,11 +35,15 @@

Potential
Parameters
BondedPotential
BondPotential
BondParameters
PairPotential
PairParameters

"""

from .bond import FENEWCA, BondParameters, BondPotential, BondSpline, HarmonicBond
from .pair import (
Depletion,
LennardJones,
Expand All @@ -37,4 +52,4 @@
PairSpline,
Yukawa,
)
from .potential import Parameters, Potential
from .potential import BondedPotential, Parameters, Potential
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