Issue with Pore-Builder when running example

[A-DCA]

Dear Dr Ray Matsumoto,

I came across an error (see below).

It appears the issue is related Pore-Builder. It looks it has not be updated along mbuild. But I am not sure about this. I am aware Pore-Builder (https://github.com/PTC-CMC/Pore-Builder) is a separate module but curious to know which version of mbuild and Pore-Builder on which mosdef_slitpore examples as given your supplementation info (https://aiche.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Faic.17206&file=aic17206-sup-0001-supinfo.pdf) worked.

Look forwards to your reply.

Regards,

Jingsheng

Error:
(slitpore37) D:\mosdef\mosdef_slitpore\simulations\nvt-pore\1x1x1.0nm_1-layer\gromacs>python project.py run -o initialize -n 1
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
D:\3rdps-tools\anaconda3\envs\slitpore37\lib\site-packages\flow\project.py:1803: DeprecatedWarning: root_directory is deprecated as of 1.8 and will be removed in 2.0. Use Project.path instead.
self.root_directory(), self._config.get("template_dir", "templates")
Using environment configuration: StandardEnvironment
D:\3rdps-tools\anaconda3\envs\slitpore37\lib\site-packages\flow\project.py:1030: DeprecatedWarning: root_directory is deprecated as of 1.8 and will be removed in 2.0. Use Project.path instead.
root_directory = project.root_directory()
D:\3rdps-tools\anaconda3\envs\slitpore37\lib\site-packages\mbuild\compound.py:1266: UserWarning: Compound.box.lengths < Compound.boundingbox.lengths. There may be particles outside of the defined simulation box.
warn(
Traceback (most recent call last):
File "D:\3rdps-tools\anaconda3\envs\slitpore37\lib\site-packages\flow\project.py", line 3515, in _execute_operation
self._operationsoperation.name
File "D:\3rdps-tools\anaconda3\envs\slitpore37\lib\site-packages\flow\project.py", line 669, in call
return self._op_func(*jobs)
File "D:\mosdef\mosdef_slitpore\simulations\nvt-pore\1x1x1.0nm_1-layer\gromacs\project.py", line 47, in initialize
pore = mb.recipes.GraphenePoreSolvent(
File "d:\mosdef\pore-builder\porebuilder\porebuilder.py", line 119, in init
pore = GraphenePore(pore_length=pore_length, pore_depth=pore_depth,
File "d:\mosdef\pore-builder\porebuilder\porebuilder.py", line 54, in init
graphene.periodicity[1] = factor # cos(30).246
TypeError: 'tuple' object does not support item assignment