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Add box resizing to MD integrators #234

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28696cc
Add volume scaling for Langevin ynamics.
clpetix Feb 7, 2024
1a846ab
Update implementation to match HOOMD required syntax.
clpetix Feb 7, 2024
52a7edb
Update period to prevent triggering repeatedly.
clpetix Feb 7, 2024
b2a16d9
Check if barostat is set before trying to scale box.
clpetix Feb 10, 2024
8576067
Add barostat to LAMMPS and Dilute simulation methods.
clpetix Feb 12, 2024
ac0d4c3
Remove default argument from backend operation.
clpetix Feb 12, 2024
798586d
Set freud version less than 3
clpetix Apr 6, 2024
b87c3c3
Require freud version 2.
clpetix Apr 6, 2024
28f55ce
Revert freud change.
clpetix Apr 6, 2024
4636ea9
Merge branch 'main' into feature/box-resize
clpetix May 3, 2024
4d0567c
Merge branch 'main' into feature/box-resize
clpetix May 3, 2024
d4b929a
Merge branch 'main' into feature/box-resize
mphoward Jun 27, 2024
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3 changes: 2 additions & 1 deletion src/relentless/simulate/dilute.py
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Original file line number Diff line number Diff line change
Expand Up @@ -111,9 +111,10 @@ def _modify_ensemble(self, sim):


class RunLangevinDynamics(_Integrator):
def __init__(self, steps, timestep, T, friction, seed, analyzers):
def __init__(self, steps, timestep, T, friction, seed, analyzers, barostat):
super().__init__(steps, timestep, analyzers)
self.T = T
self.barostat = barostat

_modify_ensemble = RunBrownianDynamics._modify_ensemble

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57 changes: 56 additions & 1 deletion src/relentless/simulate/hoomd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -649,9 +649,10 @@ class RunLangevinDynamics(_Integrator):

"""

def __init__(self, steps, timestep, T, friction, seed, analyzers):
def __init__(self, steps, timestep, T, friction, seed, analyzers, barostat):
super().__init__(steps, timestep, analyzers)
self.T = T
self.barostat = barostat
self.friction = friction
self.seed = seed

Expand Down Expand Up @@ -701,7 +702,61 @@ def _call_v2(self, sim):
# run + analysis
for analyzer in self.analyzers:
analyzer.pre_run(sim, self)
if self.barostat is not None:
if isinstance(self.barostat, extent.Extent):
period = None
if sim.dimension == 2:
Lx, Ly, xy = self.barostat.as_array("HOOMD")
Lz, xz, yz = None, None, None
else:
Lx, Ly, Lz, xy, xz, yz = self.barostat.as_array("HOOMD")
elif len(self.barostat) == 2 and all(
isinstance(n, extent.Extent) for n in self.barostat
):
period = 1
if sim.dimension == 2:
Lx1, Ly1, xy1 = self.barostat[0].as_array("HOOMD")
Lx2, Ly2, xy2 = self.barostat[1].as_array("HOOMD")
Lz, xz, yz = None, None, None
Lx = hoomd.variant.linear_interp(
[(0, Lx1), (self.steps - 1, Lx2)]
)
Ly = hoomd.variant.linear_interp(
[(0, Ly1), (self.steps - 1, Ly2)]
)
xy = hoomd.variant.linear_interp(
[(0, xy1), (self.steps - 1, xy2)]
)
else:
Lx1, Ly1, Lz1, xy1, xz1, yz1 = self.barostat[0].as_array(
"HOOMD"
)
Lx2, Ly2, Lz2, xy2, xz2, yz2 = self.barostat[1].as_array(
"HOOMD"
)

Lx = hoomd.variant.linear_interp(
[(0, Lx1), (self.steps - 1, Lx2)]
)
Ly = hoomd.variant.linear_interp(
[(0, Ly1), (self.steps - 1, Ly2)]
)
Lz = hoomd.variant.linear_interp(
[(0, Lz1), (self.steps - 1, Lz2)]
)
xy = hoomd.variant.linear_interp(
[(0, xy1), (self.steps - 1, xy2)]
)
xz = hoomd.variant.linear_interp(
[(0, xz1), (self.steps - 1, xz2)]
)
yz = hoomd.variant.linear_interp(
[(0, yz1), (self.steps - 1, yz2)]
)

hoomd.update.box_resize(
Lx=Lx, Ly=Ly, Lz=Lz, xy=xy, xz=xz, yz=yz, period=period
)
hoomd.run(self.steps)

for analyzer in self.analyzers:
Expand Down
3 changes: 2 additions & 1 deletion src/relentless/simulate/lammps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -694,9 +694,10 @@ class RunLangevinDynamics(_Integrator):

"""

def __init__(self, steps, timestep, T, friction, seed, analyzers):
def __init__(self, steps, timestep, T, friction, seed, analyzers, barostat):
super().__init__(steps, timestep, analyzers)
self.T = T
self.barostat = barostat
self.friction = friction
self.seed = seed

Expand Down
13 changes: 12 additions & 1 deletion src/relentless/simulate/md.py
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Original file line number Diff line number Diff line change
Expand Up @@ -118,9 +118,19 @@ class RunLangevinDynamics(_Integrator):

"""

def __init__(self, steps, timestep, T, friction, seed, analyzers=None):
def __init__(
self,
steps,
timestep,
T,
friction,
seed,
analyzers=None,
barostat=None,
):
super().__init__(steps, timestep, analyzers)
self.T = T
self.barostat = barostat
self.friction = friction
self.seed = seed

Expand All @@ -133,6 +143,7 @@ def _make_delegate(self, sim):
friction=self.friction,
seed=self.seed,
analyzers=self.analyzers,
barostat=self.barostat,
)


Expand Down
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