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Add stress and strain logging to Tensile simulation class. Add flag to turn on particle quantity logging #2

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a148bdd
copy over table pots for pekk cg model
chrisjonesBSU Nov 9, 2023
b43cb23
add pekk cg forcefield class
chrisjonesBSU Nov 9, 2023
dfbe5f8
update file name for angle table pot
chrisjonesBSU Nov 9, 2023
acaa929
fix doc strings, variable name
chrisjonesBSU Nov 9, 2023
1a027d2
Merge branch 'main' of github.com:cmelab/flowerMD into pekk-cg
chrisjonesBSU Nov 15, 2023
bba1326
fix import
chrisjonesBSU Nov 16, 2023
6e47c73
add overlap param to Pack
chrisjonesBSU Nov 16, 2023
6e3036c
fix conflicts
chrisjonesBSU Feb 19, 2024
04edab6
merge and fix conflicts
chrisjonesBSU Apr 22, 2024
232304f
Merge branch 'main' of github.com:cmelab/flowerMD into log-particles
chrisjonesBSU Jul 5, 2024
6131903
add option to log particle data in gsd file
chrisjonesBSU Jul 5, 2024
59f539a
Merge branch 'log-particles' of github.com:chrisjonesBSU/flowerMD int…
chrisjonesBSU Jul 5, 2024
12b0c56
add data logging to tensile test sim class
chrisjonesBSU Jul 5, 2024
800c3cd
go back to original tutorials
chrisjonesBSU Jul 5, 2024
3bd0cbb
add param to set storing of stress and strain data
chrisjonesBSU Jul 5, 2024
b3ec830
Merge branch 'log-particles' of github.com:chrisjonesBSU/flowerMD int…
chrisjonesBSU Jul 5, 2024
047423a
fix attr name
chrisjonesBSU Jul 5, 2024
4ad97ce
fix np.save params
chrisjonesBSU Jul 5, 2024
da1ff5c
fix typo in doc strings
chrisjonesBSU Jul 5, 2024
499f359
add tests
chrisjonesBSU Jul 5, 2024
7afed6a
test logged strain data
chrisjonesBSU Jul 6, 2024
eb40e8b
finish tensile unit tests
chrisjonesBSU Jul 6, 2024
cbb3fff
remove pekk cg forcefield stuff that's on another branch
chrisjonesBSU Jul 6, 2024
d21ae78
remove pekk cg ff import
chrisjonesBSU Jul 6, 2024
cdcfba0
remove code from pekk cg branch
chrisjonesBSU Jul 6, 2024
7f9152c
add conv factor for stress
chrisjonesBSU Jul 7, 2024
ed63007
Merge branch 'main' of github.com:cmelab/flowerMD into log-particles
chrisjonesBSU Jul 12, 2024
162a1b7
Merge branch 'main' of github.com:cmelab/flowerMD into log-particles
chrisjonesBSU Jul 12, 2024
b504029
change gsd buffer size
chrisjonesBSU Sep 4, 2024
76bf5fb
Merge branch 'log-particles' of github.com:chrisjonesBSU/flowerMD int…
chrisjonesBSU Sep 4, 2024
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fix conflicts
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chrisjonesBSU committed Feb 19, 2024
commit 6e3036c96e965d46528ce42f548368a4143f70c7
8 changes: 2 additions & 6 deletions flowermd/base/system.py
Original file line number Diff line number Diff line change
Expand Up @@ -665,11 +665,7 @@ def __init__(
self.packing_expand_factor = packing_expand_factor
self.edge = edge
self.overlap = overlap
super(Pack, self).__init__(
molecules=molecules,
density=density,
base_units=base_units,
)
super(Pack, self).__init__(molecules=molecules, base_units=base_units)

def _build_system(self):
mass_density = u.Unit("kg") / u.Unit("m**3")
Expand All @@ -693,7 +689,7 @@ def _build_system(self):
system = mb.packing.fill_box(
compound=self.all_molecules,
n_compounds=[1 for i in self.all_molecules],
box=list(self._target_box * self.packing_expand_factor),
box=list(target_box * self.packing_expand_factor),
overlap=self.overlap,
edge=self.edge,
)
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