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Coordinate folding change #388

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merged 3 commits into from
Mar 25, 2024
Merged

Coordinate folding change #388

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b59b0ae
change fold setting to false for all converters. added fold setting t…
ChiCheng45 Mar 21, 2024
d55503a
adjusted fold coordinates method so that the fractional coordinates o…
ChiCheng45 Mar 21, 2024
bbdc4f6
fixed unit tests
ChiCheng45 Mar 21, 2024
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12 changes: 6 additions & 6 deletions MDANSE/Extensions/fold_coordinates.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -76,22 +76,22 @@ def fold_coordinates(
by = box_coords[i,j,1]
bz = box_coords[i,j,2]

while bx < -0.5:
while bx < 0.0:
bx += 1.0

while by < -0.5:
while by < 0.0:
by += 1.0

while bz < -0.5:
while bz < 0.0:
bz += 1.0

while bx > 0.5:
while bx >= 1.0:
bx -= 1.0

while by > 0.5:
while by >= 1.0:
by -= 1.0

while bz > 0.5:
while bz >= 1.0:
bz -= 1.0

box_coords[i,j,0] = bx
Expand Down
6 changes: 6 additions & 0 deletions MDANSE/Src/MDANSE/Framework/Converters/ASE.py
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Expand Up @@ -79,6 +79,10 @@ class ASE(Converter):
"mini": 0,
},
)
settings["fold"] = (
"BooleanConfigurator",
{"default": False, "label": "Fold coordinates into box"},
)
settings["output_file"] = (
"OutputTrajectoryConfigurator",
{
Expand Down Expand Up @@ -156,6 +160,8 @@ def run_step(self, index):
realConf = PeriodicRealConfiguration(
self._trajectory.chemical_system, coords, unitCell
)
if self._configuration["fold"]["value"]:
realConf.fold_coordinates()
else:
realConf = RealConfiguration(
self._trajectory.chemical_system,
Expand Down
7 changes: 6 additions & 1 deletion MDANSE/Src/MDANSE/Framework/Converters/CP2K.py
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Expand Up @@ -140,6 +140,10 @@ class CP2K(Converter):
"dependencies": {"input_file": "pos_file"},
},
)
settings["fold"] = (
"BooleanConfigurator",
{"default": False, "label": "Fold coordinates into box"},
)
settings["output_file"] = (
"OutputTrajectoryConfigurator",
{
Expand Down Expand Up @@ -232,7 +236,8 @@ def run_step(self, index):
self._trajectory.chemical_system, coords, unitcell, **variables
)

realConf.fold_coordinates()
if self._configuration["fold"]["value"]:
realConf.fold_coordinates()

self._trajectory.chemical_system.configuration = realConf

Expand Down
2 changes: 1 addition & 1 deletion MDANSE/Src/MDANSE/Framework/Converters/DFTB.py
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Expand Up @@ -54,7 +54,7 @@ class DFTB(Forcite):
)
settings["fold"] = (
"BooleanConfigurator",
{"default": True, "label": "Fold coordinates in to box"},
{"default": False, "label": "Fold coordinates into box"},
)
settings["output_file"] = (
"OutputTrajectoryConfigurator",
Expand Down
2 changes: 1 addition & 1 deletion MDANSE/Src/MDANSE/Framework/Converters/Discover.py
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Expand Up @@ -275,7 +275,7 @@ class Discover(Converter):
)
settings["fold"] = (
"BooleanConfigurator",
{"default": True, "label": "Fold coordinates into box"},
{"default": False, "label": "Fold coordinates into box"},
)
settings["output_file"] = (
"OutputTrajectoryConfigurator",
Expand Down
6 changes: 3 additions & 3 deletions MDANSE/Tests/UnitTests/test_configuration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -449,9 +449,9 @@ def test_fold_coordinates(self):
np.allclose(
conf["coordinates"],
[
[-0.65955991, 1.40648987, -1.9977125],
[1.04665145, -1.06488218, -0.1532281],
[-0.27479577, -0.08878546, 1.93534948],
[1.34044009, 2.40648987, -1.9977125],
[0.04665145, 1.93511782, -0.1532281],
[1.72520423, 0.91121454, -2.06465052],
[-0.22366532, 1.38389029, -0.29560999],
],
rtol=1.0e-6,
Expand Down
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