From 1cb809147e1f8f2759660ebbe9ba67846aed9686 Mon Sep 17 00:00:00 2001 From: chrisjonesbsu Date: Tue, 26 Mar 2024 10:25:24 -0600 Subject: [PATCH 1/3] change interface axis to array, fix np.where behavior --- flowermd/modules/welding/welding.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/flowermd/modules/welding/welding.py b/flowermd/modules/welding/welding.py index 36fc4084..656b94b5 100644 --- a/flowermd/modules/welding/welding.py +++ b/flowermd/modules/welding/welding.py @@ -35,7 +35,7 @@ def __init__( remove_void_particles=True, ): self.gsd_files = check_return_iterable(gsd_files) - self.interface_axis = interface_axis + self.interface_axis = np.asarray(interface_axis) self.gap = gap self.wall_sigma = wall_sigma self._remove_void_particles = remove_void_particles @@ -84,6 +84,7 @@ def _build(self): # Set up box. Box edge is doubled along the interface axis direction, # plus the gap axis_index = np.where(self.interface_axis != 0)[0] + print("Axis index:", axis_index) interface.configuration.box = np.copy(snap_L.configuration.box) interface.configuration.box[axis_index] *= 2 interface.configuration.box[axis_index] += self.gap - self.wall_sigma From 3f761ed2bf062d15c0fdef78dd55d2150ff11bc5 Mon Sep 17 00:00:00 2001 From: chrisjonesBSU Date: Tue, 26 Mar 2024 10:38:01 -0600 Subject: [PATCH 2/3] remove print statement --- flowermd/modules/welding/welding.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/flowermd/modules/welding/welding.py b/flowermd/modules/welding/welding.py index 656b94b5..3894b63d 100644 --- a/flowermd/modules/welding/welding.py +++ b/flowermd/modules/welding/welding.py @@ -81,10 +81,8 @@ def _build(self): interface.dihedrals.N = snap_L.dihedrals.N + snap_R.dihedrals.N interface.dihedrals.M = 4 interface.pairs.N = snap_L.pairs.N + snap_R.pairs.N - # Set up box. Box edge is doubled along the interface axis direction, - # plus the gap + # Box edge is doubled along the interface axis plus the gap axis_index = np.where(self.interface_axis != 0)[0] - print("Axis index:", axis_index) interface.configuration.box = np.copy(snap_L.configuration.box) interface.configuration.box[axis_index] *= 2 interface.configuration.box[axis_index] += self.gap - self.wall_sigma From c736dbbc98ecefa9159fea9da142f3a73ccfe09c Mon Sep 17 00:00:00 2001 From: chrisjonesBSU Date: Tue, 26 Mar 2024 10:58:38 -0600 Subject: [PATCH 3/3] update versions for mbuild and python in env files --- environment-dev.yml | 4 ++-- environment.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/environment-dev.yml b/environment-dev.yml index 1f759f69..875718d2 100644 --- a/environment-dev.yml +++ b/environment-dev.yml @@ -8,7 +8,7 @@ dependencies: - gmso >=0.11.2 - gsd >=3.0 - hoomd=4.3 - - mbuild >=0.16.4 + - mbuild >=0.17.0 - numpy - openbabel >=3 - pip @@ -16,7 +16,7 @@ dependencies: - py3Dmol - pytest - pytest-cov - - python >=3.10 + - python >=3.10, <3.12 - fresnel >=0.13.5 - cmeutils >=1.1.1 - grits >=0.3.0 diff --git a/environment.yml b/environment.yml index 7daabc27..166c6bbf 100644 --- a/environment.yml +++ b/environment.yml @@ -8,12 +8,12 @@ dependencies: - gmso >=0.11.2 - gsd >=3.0 - hoomd=4.3 - - mbuild >=0.16.4 + - mbuild >=0.17.0 - numpy - openbabel >=3 - pip - py3Dmol - - python >=3.10 + - python >=3.10, <3.12 - fresnel >=0.13.5 - cmeutils >=1.1.1 - grits >=0.3.0