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Add ability to use number density when calculating target box lenghts for shrinking and NVT. #112

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merged 35 commits into from
Jan 22, 2024
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9fd764f
add support for number density
chrisjonesBSU Jan 10, 2024
fe53c61
clean up a few lines
chrisjonesBSU Jan 10, 2024
b51c873
fix n density variable
chrisjonesBSU Jan 10, 2024
9f5d382
Merge branch 'main' of github.com:cmelab/flowerMD into number-density
chrisjonesBSU Jan 11, 2024
9d68d38
fix f strings, start adding unit tests
chrisjonesBSU Jan 11, 2024
366758b
fix unit tests
chrisjonesBSU Jan 11, 2024
89feaa2
fix param names to match new ones
chrisjonesBSU Jan 11, 2024
5946794
fix param names
chrisjonesBSU Jan 11, 2024
dc80e48
remove set target_box from Lattice system, fix tests
chrisjonesBSU Jan 11, 2024
410b5e3
Fix tests
chrisjonesBSU Jan 11, 2024
2d8801f
remove N_beads property for now
chrisjonesBSU Jan 11, 2024
084a8b1
implement new design choices for getting target boxes
chrisjonesBSU Jan 12, 2024
c61d2b2
remove target box attr from System, fix unit test
chrisjonesBSU Jan 12, 2024
a934902
update tests
chrisjonesBSU Jan 16, 2024
790c06a
make sure target box array has units, convert to nm in Pack
chrisjonesBSU Jan 16, 2024
762626b
add warning message if units not given for density
chrisjonesBSU Jan 16, 2024
3132e0d
fix tests, convert box in run update vol
chrisjonesBSU Jan 16, 2024
fa0dd65
fix density in droplet module
chrisjonesBSU Jan 16, 2024
7de8652
fix test
chrisjonesBSU Jan 16, 2024
e11e6b5
fix tests
chrisjonesBSU Jan 17, 2024
340f0c7
add units check, remove debug line
chrisjonesBSU Jan 17, 2024
97e406d
update basics tutorial
chrisjonesBSU Jan 18, 2024
9fb2744
use amu units in System.mass property
chrisjonesBSU Jan 18, 2024
2d712e8
finish checking the rest of the tutorials
chrisjonesBSU Jan 18, 2024
4344d84
fix unit tests
chrisjonesBSU Jan 18, 2024
732670b
add doc strings for target box funcs
chrisjonesBSU Jan 19, 2024
15e0581
add unit test for no refs, add example to doc strings
chrisjonesBSU Jan 19, 2024
6146a4d
create internal module, add doc for utils
chrisjonesBSU Jan 19, 2024
3e8d8fd
delete swp files, fix imports in tests
chrisjonesBSU Jan 22, 2024
893a4ed
remove swp file
chrisjonesBSU Jan 22, 2024
2ec25b3
add swp files to git ignore
chrisjonesBSU Jan 22, 2024
d2cb45e
fix utils rst file
marjanalbooyeh Jan 22, 2024
746b85f
add docstrings
marjanalbooyeh Jan 22, 2024
f76a5c0
finish default density behavior in surface wetting
chrisjonesBSU Jan 22, 2024
a919fed
Merge branch 'number-density' of github.com:chrisjonesBSU/flowerMD in…
chrisjonesBSU Jan 22, 2024
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delete swp files, fix imports in tests
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chrisjonesBSU committed Jan 22, 2024
commit 3e8d8fd1d4d3cc2462821d67fc63df7cbe7aec8a
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2 changes: 1 addition & 1 deletion flowermd/tests/utils/test_ff_utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@
import pytest
from gmso.core.forcefield import ForceField

from flowermd.internal.ff_utils import find_xml_ff, xml_to_gmso_ff
from flowermd.tests import BaseTest
from flowermd.utils.ff_utils import find_xml_ff, xml_to_gmso_ff


class TestFFUtils(BaseTest):
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5 changes: 2 additions & 3 deletions flowermd/tests/utils/test_utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,14 +2,13 @@
import pytest
import unyt as u

from flowermd.internal import check_return_iterable, validate_ref_value
from flowermd.internal.exceptions import ReferenceUnitError
from flowermd.utils import (
_calculate_box_length,
check_return_iterable,
get_target_box_mass_density,
get_target_box_number_density,
validate_ref_value,
)
from flowermd.utils.exceptions import ReferenceUnitError


class TestUtils:
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6 changes: 5 additions & 1 deletion flowermd/utils/__init__.py
Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
from .actions import *
from .base_types import HOOMDThermostats
from .utils import get_target_box_mass_density, get_target_box_number_density
from .utils import (
_calculate_box_length,
get_target_box_mass_density,
get_target_box_number_density,
)
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