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Map forces onto beads #80

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Map forces onto beads #80

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5766156
adding comments for things to do
StephMcCallum Jun 22, 2024
00a4681
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 22, 2024
365d643
Adding force list
StephMcCallum Jun 22, 2024
1a63d1e
Adding force list
StephMcCallum Jun 22, 2024
8b51bdd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 22, 2024
83c887a
Adding test velocity calculation
StephMcCallum Jun 25, 2024
eb743e7
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 26, 2024
b0f80dc
Adding force calculation and test file. Need to update method of addi…
StephMcCallum Aug 8, 2024
2a4194f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 8, 2024
6d35f1a
Changing axis of reduce function and adding squeeze function for a te…
StephMcCallum Aug 12, 2024
03a04b4
changing axis for reduce function and adding squeeze
StephMcCallum Aug 12, 2024
660bf1c
Updating net force calculation
StephMcCallum Aug 13, 2024
13eda05
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 13, 2024
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5 changes: 5 additions & 0 deletions grits/coarsegrain.py
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I think the additons so far look good. Now, you'll have to add the coarse-grained velocities to the new gsd frame that GRiTS is making.

You can see what is done for other properties around lines 780:

                new_snap.particles.N = len(typeid)
                new_snap.particles.position = position
                new_snap.particles.image = images
                new_snap.particles.typeid = typeid.astype(int)
                new_snap.particles.types = types
                new_snap.particles.mass = mass

So, you can define the new_snap.particles.velocity property with the velocity list being populated.

Original file line number Diff line number Diff line change
Expand Up @@ -727,6 +727,8 @@ def save(self, cg_gsdfile, start=0, stop=None, stride=1):
new_snap = gsd.hoomd.Frame()
position = []
mass = []
# make an empty list for forces here
forces = []
orientation = [] if self.aniso_beads else None
f_box = freud.Box.from_box(s.configuration.box)
unwrap_pos = f_box.unwrap(
Expand All @@ -738,6 +740,9 @@ def save(self, cg_gsdfile, start=0, stop=None, stride=1):
mass += [
sum(s.particles.mass[x]) * self.mass_scale for x in inds
]

# do the force calculation here

if self.aniso_beads:
for x in inds:
masses = s.particles.mass[x] * self.mass_scale
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