def wide_large_triplelayer():
"""Generate an empty pore with the following:
Three graphene layers
Lateral: 3.0 nm x 3.0 nm
Width: 1.6 nm
Arguments
---------
None
Returns
-------
mbuild.Compound
"""
# Create pore system
pore = recipes.GraphenePore(pore_width=1.6,
pore_length=3.0,
pore_depth=3.0,
n_sheets=3,
slit_pore_dim=2)
# Translate to centered at 0,0,0 and make box larger in z
pore.translate([0, 0, 3.0 - pore.center[2]])
pore.periodicity[2] = 6.0
return pore
def narrow_small_singlelayer():
"""Generate an empty pore with the following:
Single layer graphene
Lateral: 1.0 nm x 1.0 nm
Width: 1.0 nm
Arguments
---------
None
Returns
-------
mbuild.Compound
"""
# Create pore system
pore = recipes.GraphenePore(pore_width=1.0,
pore_length=1.0,
pore_depth=1.1,
n_sheets=1,
slit_pore_dim=2)
# Translate to centered at 0,0,0 and make box larger in z
pore.translate([0, 0, 1.0 - pore.center[2]])
pore.periodicity[2] = 2.0
return pore
# builds water reservoir (end)
#**************************************************************
#**************************************************************
# builds empty graphene slit for 10 Ang or 1nm (start)
#**************************************************************
# Create graphene system
pore_width_nm = 1.0
No_sheets = 3
sheet_spacing = 0.335
#for GOMC, currently we need to add the space at the end of the simulation
# this does not matter as we are using PBC's
graphene =recipes.GraphenePore(
pore_width=sheet_spacing ,
pore_length=3.0,
pore_depth=3.0,
n_sheets=No_sheets,
slit_pore_dim=2
)
# Translate to centered at-graphene.center[0], -graphene.center[1],0 and make box larger in z
graphene.translate([ -graphene.center[0], -graphene.center[1],0])
graphene.periodicity[2] = sheet_spacing*(2*No_sheets-1)+pore_width_nm
mf_charmm.charmm_psf_psb_FF(graphene,
'pore_3x3x1.0nm_3-layer',
structure_1 = box_reservior,
filename_1 = 'GOMC_reservior_box',
# Create graphene system
pore_width_nm = 2
No_sheets = 3
sheet_spacing = 1
water_spacing_from_walls = 0.2
Total_box_z_axis_nm = 6
graphene_sheet_space_nm = 0.335
n_waters = 485
empty_graphene_pore =recipes.GraphenePore( pore_width=pore_width_nm ,
pore_length=3.0,
pore_depth=3.0,
n_sheets=No_sheets,
slit_pore_dim=2 )
z_shift= Total_box_z_axis_nm / 2 - (graphene_sheet_space_nm * (No_sheets - 1) + pore_width_nm/2)
water_between_pores = mb.fill_box(compound=[water], n_compounds= [n_waters] , box=[2.90, 2.90, pore_width_nm - water_spacing_from_walls*1])
water_between_pores.translate([0, 0, water_spacing_from_walls + graphene_sheet_space_nm*(No_sheets-1)])
water_between_pores.translate([ -water_between_pores.center[0], -water_between_pores.center[1], z_shift])
empty_graphene_pore.translate([ -empty_graphene_pore.center[0], -empty_graphene_pore.center[1], z_shift])
filled_pore = empty_graphene_pore
filled_pore.add(water_between_pores, inherit_periodicity=False)
filled_pore.periodicity[2] = Total_box_z_axis_nm