def build_tam_custom(periods,
composition,
bulk_gro,
bulk_top,
displacement=1.1):
"""
Initialize a system that uses a bulk system of TAM to fill the pores
"""
bulk_structure = pmd.load_file(bulk_top, xyz=bulk_gro)
interlayer = mb.Compound()
interlayer.from_parmed(bulk_structure)
interlayer_2 = mb.clone(interlayer)
lopes = get_ff('lopes')
interlayer.translate_to([
interlayer.center[0], interlayer.center[1],
(ti3c2.box[2] / 10 - 2 * displacement) / 2 + 0.15
])
interlayer_2.translate_to([
interlayer_2.center[0], interlayer_2.center[1],
(ti3c2.box[2] / 10 - 2 * displacement) + displacement + 0.15
])
aa1PM = lopes.apply(interlayer,
residues=['alkylam'],
assert_dihedral_params=False)
aa2PM = lopes.apply(interlayer_2,
residues=['alkylam'],
assert_dihedral_params=False)
system = aa1PM + aa2PM + ti3c2
system = aa1PM + aa2PM + ti3c2
system = _apply_nbfixes(system)
system = collapse_atomtypes(system)
change_charge(system, new_charge=0)
system.box = ti3c2.box
for atom in system.atoms:
if atom.name == 'C_E':
atom.name = 'CE'
elif atom.name == 'C_M':
atom.name = 'CM'
elif atom.name == 'C_B1':
atom.name = 'CB1'
elif atom.name == 'C_B2':
atom.name = 'CB2'
system.save('ti3c2.gro', combine='all', overwrite=True)
system.save('ti3c2.top', combine='all', overwrite=True)
write_lammpsdata(system, 'data.mxene')
def build_tam_emim_mxene(n_compounds,
composition,
periods,
chain_length=12,
displacement=1.1):
"""Build a MXene with TAM and EMIM in the interlayer
Parameters
----------
n_compounds : list
List of [TAM, EMIM] compounds
composition : dict
Composition of MXene surface groups
periods : list
Periods of MXene crystal
chain_length : int
Chain length of TAM
displacement : float
Interlayer spacing (nm)
"""
ti3c2 = build_structure(periods=periods,
composition=composition,
displacement=displacement,
lateral_shift=True,
atomtype=True)
n_carbons = 'C' * chain_length
aa = mb.load(f'{n_carbons}[N](C)(C)C', smiles=True)
# Rename some carbons
# CE = end carbon
# CM = middle carbon
# CB = branch carbon
for idx, particle in enumerate(aa.particles()):
if idx == 0:
particle.name = 'C_E'
if idx == chain_length / 2:
particle.name = 'C_M'
# TODO: Find way to get branch carbon index without
# hardcoding
if particle.name == 'N':
n_index = idx
try:
if idx == n_index + 1:
particle.name = 'C_B1'
if idx == n_index + 2:
particle.name = 'C_B2'
except:
continue
emim = mb.load(get_il('emim'))
emim.name = 'emim'
aa.name = 'alkylam'
lopes = get_ff('lopes')
region1 = mb.Box(
mins=[0, 0, (ti3c2.box[2] / 10 - 2 * displacement) / 2 + 0.15],
maxs=[
ti3c2.box[0] / 10, ti3c2.box[1] / 10,
(ti3c2.box[2] / 10 - 2 * displacement) / 2 + displacement
])
region2 = mb.Box(mins=[
0, 0, (ti3c2.box[2] / 10 - 2 * displacement) + displacement + 0.15
],
maxs=[
ti3c2.box[0] / 10, ti3c2.box[1] / 10,
(ti3c2.box[2] / 10 - 2 * displacement) + 2 +
displacement
])
aa_1 = mb.fill_box(compound=[aa, emim],
n_compounds=n_compounds,
box=region1,
fix_orientation=True)
aa_2 = mb.fill_box(compound=[aa, emim],
n_compounds=n_compounds,
box=region2,
fix_orientation=True)
aa1PM = lopes.apply(aa_1,
residues=['alkylam', 'emim'],
assert_dihedral_params=False)
aa2PM = lopes.apply(aa_2,
residues=['alkylam', 'emim'],
assert_dihedral_params=False)
system = aa1PM + aa2PM + ti3c2
system = _apply_nbfixes(system)
system = collapse_atomtypes(system)
change_charge(system, new_charge=0)
system.box = ti3c2.box
for atom in system.atoms:
if atom.name == 'C_E':
atom.name = 'CE'
elif atom.name == 'C_M':
atom.name = 'CM'
elif atom.name == 'C_B1':
atom.name = 'CB1'
elif atom.name == 'C_B2':
atom.name = 'CB2'
system.save('ti3c2.gro', combine='all', overwrite=True)
system.save('ti3c2.top', combine='all', overwrite=True)
write_lammpsdata(system, 'data.mxene')
def build_alkylammonium_mxene(n_compounds,
composition,
periods,
chain_length=12,
displacement=1.1):
ti3c2 = build_structure(periods=periods,
composition=composition,
displacement=displacement,
lateral_shift=True,
atomtype=True)
n_carbons = 'C' * chain_length
aa = mb.load(f'{n_carbons}[N](C)(C)C', smiles=True)
# Rename some carbons
# CE = end carbon
# CM = middle carbon
# CB = branch carbon
for idx, particle in enumerate(aa.particles()):
if idx == 0:
particle.name = 'C_E'
if idx == chain_length / 2:
particle.name = 'C_M'
# TODO: Find way to get branch carbon index without
# hardcoding
if particle.name == 'N':
n_index = idx
try:
if idx == n_index + 1:
particle.name = 'C_B1'
if idx == n_index + 2:
particle.name = 'C_B2'
except:
continue
aa.name = 'alkylam'
lopes = get_ff('lopes')
region1 = mb.Box(
mins=[0, 0, (ti3c2.box[2] / 10 - 2 * displacement) / 2 + 0.15],
maxs=[
ti3c2.box[0] / 10, ti3c2.box[1] / 10,
(ti3c2.box[2] / 10 - 2 * displacement) / 2 + displacement
])
region2 = mb.Box(mins=[
0, 0, (ti3c2.box[2] / 10 - 2 * displacement) + displacement + 0.15
],
maxs=[
ti3c2.box[0] / 10, ti3c2.box[1] / 10,
(ti3c2.box[2] / 10 - 2 * displacement) + 2 +
displacement
])
aa_1 = mb.fill_box(compound=aa,
n_compounds=n_compounds,
box=region1,
fix_orientation=True)
aa_2 = mb.fill_box(compound=aa,
n_compounds=n_compounds,
box=region2,
fix_orientation=True)
aa1PM = lopes.apply(aa_1,
residues=['alkylam'],
assert_dihedral_params=False)
aa2PM = lopes.apply(aa_2,
residues=['alkylam'],
assert_dihedral_params=False)
system = aa1PM + aa2PM + ti3c2
system = _apply_nbfixes(system)
system = collapse_atomtypes(system)
change_charge(system, new_charge=0)
system.box = ti3c2.box
for atom in system.atoms:
if atom.name == 'C_E':
atom.name = 'CE'
elif atom.name == 'C_M':
atom.name = 'CM'
elif atom.name == 'C_B1':
atom.name = 'CB1'
elif atom.name == 'C_B2':
atom.name = 'CB2'
system.save('ti3c2.gro', combine='all', overwrite=True)
system.save('ti3c2.top', combine='all', overwrite=True)
write_lammpsdata(system, 'data.mxene')
def build_two_mxene_pores(
composition,
periods,
bulk_length,
n_il,
n_tam=20,
chain_length=12,
displacement=1.1,
emim_ff="kpl",
tam_ff="seiji",
):
"""Build system with two MXene pores in between a bulk region of EMIM-TF2N
Parameters
----------
composition : dict
Composition of surface groups
periods : list of length 3
Periods in which to build MXene crystal
bulk_legnth : float
length of bulk region between MXene pores
n_il : list, [n_emim, n_tf2n]
Number of IL molecules to add into bulk region.
Half of this value is added to side regions.
If value is odd number, then the number of compounds in the side regions are rounded.
n_tam : int, default=20
Number of TAM molecules to add into pore
chain_length : int, default=12
Chain length of TAM
displacement : float, default=1.1 nm
Displacement of MXene pore
emim_ff : str, default="kpl"
ForceField to apply to EMIM-TF2N
tam_ff : str , default="seiji"
ForceField to apply to TAM
"""
displacement -= 0.08
ti3c2 = build_structure(
periods=periods,
composition=composition,
displacement=displacement,
lateral_shift=True,
atomtype=True,
)
second_ti3c2 = deepcopy(ti3c2)
for atom in second_ti3c2.atoms:
atom.xy += (bulk_length * 10) + ti3c2.box[1] # Convert nm to angstrom
n_carbons = "C" * chain_length
aa = mb.load(f"{n_carbons}[N](C)(C)C", smiles=True)
emim = mb.load(get_il("emim"))
tf2n = mb.load(get_il("tf2n"))
emim.name = "emim"
tf2n.name = "tf2n"
aa.name = "tam"
tam_ff_object = get_ff(tam_ff)
emim_ff_object = get_ff(emim_ff)
# Get mins and maxs for second pore
mins = np.min([i.xy for i in second_ti3c2.atoms])
maxs = np.max([i.xy for i in second_ti3c2.atoms])
bulk_region = mb.Box(
mins=[0, ti3c2.box[1] / 10, 0],
maxs=[
ti3c2.box[0] / 10, ti3c2.box[1] / 10 + bulk_length,
ti3c2.box[2] / 10
],
)
# Fill regions on side of MXene pores
side_region_1 = mb.Box(mins=[0, -bulk_length / 2, 0],
maxs=[ti3c2.box[0] / 10, 0, ti3c2.box[2] / 10])
side_region_2 = mb.Box(
mins=[0, maxs / 10, 0],
maxs=[
ti3c2.box[0] / 10, maxs / 10 + bulk_length / 2, ti3c2.box[2] / 10
],
)
pore1_region1 = mb.Box(
mins=[0, 0, (ti3c2.box[2] / 10 - 2 * displacement) / 2 + 0.15],
maxs=[
ti3c2.box[0] / 10,
ti3c2.box[1] / 10,
(ti3c2.box[2] / 10 - 2 * displacement) / 2 + displacement,
],
)
pore1_region2 = mb.Box(
mins=[0, 0, np.max(ti3c2.coordinates[:, 2]) / 10],
maxs=[
ti3c2.box[0] / 10,
ti3c2.box[1] / 10,
np.max(ti3c2.coordinates[:, 2]) / 10 + displacement + 0.08,
],
)
pore2_region1 = mb.Box(
mins=[0, mins / 10, (ti3c2.box[2] / 10 - 2 * displacement) / 2 + 0.15],
maxs=[
ti3c2.box[0] / 10,
maxs / 10,
(ti3c2.box[2] / 10 - 2 * displacement) / 2 + displacement,
],
)
pore2_region2 = mb.Box(
mins=[0, mins / 10, np.max(ti3c2.coordinates[:, 2]) / 10],
maxs=[
ti3c2.box[0] / 10,
maxs / 10,
np.max(ti3c2.coordinates[:, 2]) / 10 + displacement + 0.08,
],
)
if n_tam != 0:
pore1_aa_1 = mb.fill_box(
compound=aa,
n_compounds=n_tam,
box=pore1_region1,
)
pore1_aa_2 = mb.fill_box(
compound=aa,
n_compounds=n_tam,
box=pore1_region2,
)
pore2_aa_1 = mb.fill_box(
compound=aa,
n_compounds=n_tam,
box=pore2_region1,
)
pore2_aa_2 = mb.fill_box(
compound=aa,
n_compounds=n_tam,
box=pore2_region2,
)
tam_compounds = mb.Compound()
for cmpd in [pore1_aa_1, pore1_aa_2, pore2_aa_1, pore2_aa_2]:
tam_compounds.add(mb.clone(cmpd))
# pore1_aa1PM = tam_ff_object.apply(pore1_aa_1, residues=['tam'],
# assert_dihedral_params=False)
tamPM = tam_ff_object.apply(tam_compounds,
residues=["tam"],
assert_dihedral_params=False)
# pore1_aa2PM = tam_ff_object.apply(pore1_aa_2, residues=['tam'],
# assert_dihedral_params=False)
# pore2_aa1PM = tam_ff_object.apply(pore2_aa_1, residues=['tam'],
# assert_dihedral_params=False)
# pore2_aa2PM = tam_ff_object.apply(pore2_aa_2, residues=['tam'],
# assert_dihedral_params=False)
if n_il[0] != 0 or n_il[1] != 0:
bulk = mb.fill_box(
compound=[emim, tf2n],
n_compounds=[n_il[0], n_il[1]],
box=bulk_region,
fix_orientation=True,
)
side1 = mb.fill_box(
compound=[emim, tf2n],
n_compounds=[round(n_il[0] / 2),
round(n_il[1] / 2)],
box=side_region_1,
fix_orientation=True,
)
side2 = mb.fill_box(
compound=[emim, tf2n],
n_compounds=[round(n_il[0] / 2),
round(n_il[1] / 2)],
box=side_region_2,
fix_orientation=True,
)
cation = mb.Compound()
anion = mb.Compound()
for child in bulk.children:
if child.name == "emim":
cation.add(mb.clone(child))
else:
anion.add(mb.clone(child))
for child in side1.children:
if child.name == "emim":
cation.add(mb.clone(child))
else:
anion.add(mb.clone(child))
for child in side2.children:
if child.name == "emim":
cation.add(mb.clone(child))
else:
anion.add(mb.clone(child))
cationPM = emim_ff_object.apply(cation,
residues="emim",
assert_dihedral_params=False)
anionPM = emim_ff_object.apply(anion,
residues="tf2n",
assert_dihedral_params=False)
if tam_ff == "seiji":
for atom in tamPM.atoms:
if atom.type == "seiji_004":
for bond in atom.bonds:
if "seiji_006" in (bond.atom1.type, bond.atom2.type):
atom.charge = -0.16
continue
if atom.type == "seiji_005":
for bond in atom.bonds:
if "seiji_004" in (bond.atom1.type, bond.atom2.type):
if -0.16 in (bond.atom1.charge, bond.atom2.charge):
atom.charge = 0.18
if n_tam != 0:
ils = tamPM + cationPM + anionPM
elif n_il[0] != 0 or n_il[1] != 0:
ils = cationPM + anionPM
if emim_ff == "lopes":
for atom in ils.atoms:
atom.charge *= 0.8
if n_tam != 0 or n_il[0] != 0 or n_il[1] != 0:
system = ils + ti3c2 + second_ti3c2
else:
system = ti3c2 + second_ti3c2
system = _apply_nbfixes(system)
system = collapse_atomtypes(system)
change_charge(system, new_charge=0)
max_ti3c2 = np.max(ti3c2.coordinates, axis=0)
system.box[0] = max_ti3c2[0]
if n_il[0] != 0 or n_il[1] != 0:
system.box[1] = ti3c2.box[1] * 2 + (bulk_length * 2) * 10
else:
system.box[1] = ti3c2.box[1] * 2 + (bulk_length * 2) * 10
system.box[2] = max_ti3c2[2] + (displacement * 10) + 0.8
# Shift all atoms into box
for atom in system.atoms:
atom.xy += (bulk_length / 2) * 10
system.save("ti3c2.gro", combine="all", overwrite=True)
system.save("ti3c2.top", combine="all", overwrite=True)
def build_emim_in_pore(
n_tam,
composition,
periods,
n_pore_emim,
lattice=Ti3C2Functionalized,
bulk_density=None,
bulk_n_ions=None,
chain_length=12,
displacement=1.1,
emim_ff="kpl",
taa_ff="seiji",
):
"""Function to build MXene exposed to bulk EMIM-TFSI with some EMIM-TFSI in pore
Parameters
----------
n_tam : int
Number of alkylammonium cations to initiialize in pore
composition : dict {"O": composition: "OH": composition, "F": composition}
Composition of surface groups
periods : list of ints
Lattice repeat units for MXene
n_pore_emim : int
Number of EMIM-TFSI ions to place in pore
lattice : class, default=Ti3C2Functionalized
MXene lattice class to use
bulk_density : int or float, default=1420
Density of EMIM-TFSI in bulk
bulk_n_ions : int or float, default=1420
Number of EMIM-TFSI in bulk
chain_length : int, default=12
Chain length of alkylammonium cations
displacement : int or float, default=1.1
Displacement of MXene interlayer
emim_ff : str, default="kpl"
Forcefield to use for EMIM-TFSI atoms
taa_ff : str, default="seiji"
Forcefield to use for TAM atoms
Returns
-------
pmd.Structure : Parameterized ParmEd structure
"""
if bulk_density is None and bulk_n_ions is None:
raise TypeError(
"`bulk_density` and `bulk_n_ions` cannot both be of type None")
if bulk_density and bulk_n_ions:
raise TypeError(
"Either `bulk_density` or `bulk_n_ions` should be of type None")
displacement -= 0.08
ti3c2 = build_structure(
lattice=lattice,
periods=periods,
composition=composition,
displacement=displacement,
lateral_shift=True,
atomtype=True,
)
for bond in ti3c2.bonds:
bond.delete()
for angle in ti3c2.angles:
angle.delete()
ti3c2._prune_empty_bonds()
ti3c2._prune_empty_angles()
n_carbons = "C" * chain_length
aa = mb.load(f"{n_carbons}[N](C)(C)C", smiles=True)
emim = mb.load(get_il("emim"))
tf2n = mb.load(get_il("tf2n"))
emim.name = "emim"
tf2n.name = "tf2n"
aa.name = "tam"
# Rename some carbons
# CE = end carbon
# CM = middle carbon
# CB = branch carbon
for idx, particle in enumerate(aa.particles()):
if idx == 0:
particle.name = "C_E"
if idx == chain_length / 2:
particle.name = "C_M"
# TODO: Find way to get branch carbon index without
# hardcoding
if particle.name == "N":
n_index = idx
try:
if idx == n_index + 1:
particle.name = "C_B1"
if idx == n_index + 2:
particle.name = "C_B2"
except:
continue
taaff = get_ff(taa_ff)
if emim_ff == "kpl":
kpl = get_ff("kpl")
bulk_region = mb.Box(
mins=[0, ti3c2.box[1] / 10, 0],
maxs=[
ti3c2.box[0] / 10, ti3c2.box[1] / 10 + 10, ti3c2.box[2] / 10 - 0.05
],
)
region1 = mb.Box(
mins=[0, 0, (ti3c2.box[2] / 10 - 2 * displacement) / 2 + 0.15],
maxs=[
ti3c2.box[0] / 10,
ti3c2.box[1] / 10,
(ti3c2.box[2] / 10 - 2 * displacement) / 2 + displacement,
],
)
region2 = mb.Box(
mins=[0, 0, np.max(ti3c2.coordinates[:, 2]) / 10],
maxs=[
ti3c2.box[0] / 10,
ti3c2.box[1] / 10,
np.max(ti3c2.coordinates[:, 2]) / 10 + displacement + 0.08,
],
)
aa_1 = mb.fill_box(
compound=[aa, emim, tf2n],
n_compounds=[n_tam, n_pore_emim, n_pore_emim],
box=region1,
)
aa_2 = mb.fill_box(
compound=[aa, emim, tf2n],
n_compounds=[n_tam, n_pore_emim, n_pore_emim],
box=region2,
)
aa_compound = mb.Compound()
for child in aa_1.children:
if child.name == "tam":
aa_compound.add(mb.clone(child))
for child in aa_2.children:
if child.name == "tam":
aa_compound.add(mb.clone(child))
print("Atomtyping TAM")
aaPM = taaff.apply(aa_compound,
residues="tam",
assert_dihedral_params=False)
if bulk_density:
bulk = mb.fill_box(
compound=[emim, tf2n],
density=bulk_density,
compound_ratio=[0.5, 0.5],
box=bulk_region,
fix_orientation=True,
)
elif bulk_n_ions:
bulk = mb.fill_box(
compound=[emim, tf2n],
n_compounds=[bulk_n_ions, bulk_n_ions],
box=bulk_region,
fix_orientation=True,
)
cation = mb.Compound()
anion = mb.Compound()
for child in bulk.children:
if child.name == "emim":
cation.add(mb.clone(child))
else:
anion.add(mb.clone(child))
for child in aa_1.children:
if child.name == "emim":
cation.add(mb.clone(child))
elif child.name == "tf2n":
anion.add(mb.clone(child))
for child in aa_2.children:
if child.name == "emim":
cation.add(mb.clone(child))
elif child.name == "tf2n":
anion.add(mb.clone(child))
print("Atomtyping emim-tf2n")
if emim_ff == "kpl":
cationPM = kpl.apply(cation,
residues="emim",
assert_dihedral_params=False)
anionPM = kpl.apply(anion,
residues="tf2n",
assert_dihedral_params=False)
else:
cationPM = lopes.apply(cation,
residues="emim",
assert_dihedral_params=False)
anionPM = lopes.apply(anion,
residues="tf2n",
assert_dihedral_params=False)
if emim_ff == "lopes":
print("Scaling EMIM-TF2N charges...")
for atom in cationPM.atoms:
atom.charge *= 0.8
for atom in anionPM.atoms:
atom.charge *= 0.8
if taa_ff == "lopes":
print("Scaling TAA charges...")
for atom in aaPM.atoms:
atom.charge *= 0.8
if taa_ff == "seiji":
for atom in aaPM.atoms:
if atom.type == "seiji_004":
for bond in atom.bonds:
if "seiji_006" in (bond.atom1.type, bond.atom2.type):
atom.charge = -0.16
continue
if atom.type == "seiji_005":
for bond in atom.bonds:
if "seiji_004" in (bond.atom1.type, bond.atom2.type):
if -0.16 in (bond.atom1.charge, bond.atom2.charge):
atom.charge = 0.18
ils = aaPM + cationPM + anionPM
system = ils + ti3c2
system = _apply_nbfixes(system)
system = collapse_atomtypes(system)
change_charge(system, new_charge=0)
max_ti3c2 = np.max(ti3c2.coordinates, axis=0)
system.box[0] = max_ti3c2[0]
system.box[1] = bulk.boundingbox.maxs[1] * 10
system.box[2] = max_ti3c2[2] + (displacement * 10) + 0.8
for atom in system.atoms:
if atom.name == "C_E":
atom.name = "CE"
elif atom.name == "C_M":
atom.name = "CM"
elif atom.name == "C_B1":
atom.name = "CB1"
elif atom.name == "C_B2":
atom.name = "CB2"
system.save("ti3c2.gro", combine="all", overwrite=True)
system.save("ti3c2.top", combine="all", overwrite=True)
def build_awh_mxene(n_compounds,
composition,
periods,
chain_length=12,
displacement=1.1):
"""Function to build MXene exposed to bulk EMIM-TFSI for awh simulations
Parameters
----------
n_compounds : int
Number of alkylammonium cations to initiialize in pore
composition : dict {"O": composition: "OH": composition, "F": composition}
Composition of surface groups
periods : list of ints
Lattice repeat units for MXene
density : int or float, default=1420
Density of EMIM-TFSI in bulk
chain_length : int, default=12
Chain length of alkylammonium cations
displacement : int or float, default=1.1
Displacement of MXene interlayer
Returns
-------
pmd.Structure : Parameterized ParmEd structure
"""
displacement -= 0.08
ti3c2 = build_structure(
periods=periods,
composition=composition,
displacement=displacement,
lateral_shift=True,
atomtype=True,
)
n_carbons = "C" * chain_length
aa = mb.load(f"{n_carbons}[N](C)(C)C", smiles=True)
emim = mb.load(get_il("emim"))
tf2n = mb.load(get_il("tf2n"))
emim.name = "emim"
tf2n.name = "tf2n"
aa.name = "alkylam"
emim_awh = mb.clone(emim)
emim_awh.name = "awh"
lopes = get_ff("lopes")
kpl = get_ff("kpl")
bulk_region = mb.Box(
mins=[0, ti3c2.box[1] / 10, 0],
maxs=[ti3c2.box[0] / 10, ti3c2.box[1] / 10 + 10, ti3c2.box[2] / 10],
)
region1 = mb.Box(
mins=[0, 0, (ti3c2.box[2] / 10 - 2 * displacement) / 2 + 0.15],
maxs=[
ti3c2.box[0] / 10,
ti3c2.box[1] / 10,
(ti3c2.box[2] / 10 - 2 * displacement) / 2 + displacement,
],
)
ti3c2_max = np.max(ti3c2.coordinates, axis=0)
region2 = mb.Box(
mins=[0, 0, ti3c2_max[2] / 10],
maxs=[
ti3c2.box[0] / 10,
ti3c2.box[1] / 10,
ti3c2_max[2] / 10 + displacement + 0.08,
],
)
aa_1 = mb.fill_box(
compound=[aa, emim_awh],
n_compounds=[n_compounds, 1],
box=region1,
)
aa_2 = mb.fill_box(
compound=aa,
n_compounds=n_compounds,
box=region2,
)
bulk = mb.fill_box(
compound=[emim, tf2n],
density=1420,
compound_ratio=[0.5, 0.5],
box=bulk_region,
fix_orientation=True,
)
cation = mb.Compound()
anion = mb.Compound()
marker = 0
for child in bulk.children:
if child.name == "emim":
if cation.n_particles == 1:
marker = 1
if marker == 1:
cation.add(mb.clone(child))
else:
anion.add(mb.clone(child))
tam1 = mb.Compound()
new_emim_awh = mb.Compound()
for child in aa_1.children:
if child.name == "awh":
new_emim_awh.add(mb.clone(child))
else:
tam1.add(mb.clone(child))
new_emim_awh.translate_to([(ti3c2_max[0] / 10) / 2, ti3c2_max[1] / 10,
0.937 + (displacement / 2) + 0.08])
aa1PM = lopes.apply(tam1,
residues=["alkylam"],
assert_dihedral_params=False)
aa2PM = lopes.apply(aa_2,
residues=["alkylam"],
assert_dihedral_params=False)
cationPM = kpl.apply(cation, residues="emim", assert_dihedral_params=False)
anionPM = kpl.apply(anion, residues="tf2n", assert_dihedral_params=False)
emim_awhPM = kpl.apply(new_emim_awh,
residues="awh",
assert_dihedral_params=False)
system = aa1PM + aa2PM + ti3c2 + cationPM + anionPM + emim_awhPM
system = _apply_nbfixes(system)
system = collapse_atomtypes(system)
change_charge(system, new_charge=0)
max_ti3c2 = np.max(ti3c2.coordinates, axis=0)
system.box[0] = max_ti3c2[0]
system.box[1] = bulk.boundingbox.maxs[1] * 10
system.box[2] = max_ti3c2[2] + (displacement * 10) + 0.8
system.save("init.gro", combine="all", overwrite=True)
system.save("init.top", combine="all", overwrite=True)
def build_bulk_mxene(
n_compounds,
composition,
periods,
density=1420,
chain_length=12,
displacement=1.1,
emim_ff="kpl",
):
"""Function to build MXene exposed to bulk EMIM-TFSI
Parameters
----------
n_compounds : int
Number of alkylammonium cations to initiialize in pore
periods : list of ints
Lattice repeat units for MXene
density : int or float, default=1420
Density of EMIM-TFSI in bulk
chain_length : int, default=12
Chain length of alkylammonium cations
displacement : int or float, default=1.1
Displacement of MXene interlayer
emim_ff : str, default="kpl"
Forcefield to use for EMIM-TFSI atoms
Returns
-------
pmd.Structure : Parameterized ParmEd structure
"""
displacement -= 0.08
ti3c2 = build_structure(
periods=periods,
composition=composition,
displacement=displacement,
lateral_shift=True,
atomtype=True,
)
for bond in ti3c2.bonds:
bond.delete()
for angle in ti3c2.angles:
angle.delete()
ti3c2._prune_empty_bonds()
ti3c2._prune_empty_angles()
n_carbons = "C" * chain_length
aa = mb.load(f"{n_carbons}[N](C)(C)C", smiles=True)
emim = mb.load(get_il("emim"))
tf2n = mb.load(get_il("tf2n"))
emim.name = "emim"
tf2n.name = "tf2n"
aa.name = "alkylam"
lopes = get_ff("lopes")
if emim_ff == "kpl":
kpl = get_ff("kpl")
bulk_region = mb.Box(
mins=[0, ti3c2.box[1] / 10, 0],
maxs=[ti3c2.box[0] / 10, ti3c2.box[1] / 10 + 10, ti3c2.box[2] / 10],
)
region1 = mb.Box(
mins=[0, 0, (ti3c2.box[2] / 10 - 2 * displacement) / 2 + 0.15],
maxs=[
ti3c2.box[0] / 10,
ti3c2.box[1] / 10,
(ti3c2.box[2] / 10 - 2 * displacement) / 2 + displacement,
],
)
region2 = mb.Box(
mins=[0, 0, np.max(ti3c2.coordinates[:, 2]) / 10],
maxs=[
ti3c2.box[0] / 10,
ti3c2.box[1] / 10,
np.max(ti3c2.coordinates[:, 2]) / 10 + displacement + 0.08,
],
)
if n_compounds != 0:
aa_1 = mb.fill_box(
compound=aa,
n_compounds=n_compounds,
box=region1,
)
aa_2 = mb.fill_box(
compound=aa,
n_compounds=n_compounds,
box=region2,
)
aa1PM = lopes.apply(aa_1,
residues=["alkylam"],
assert_dihedral_params=False)
aa2PM = lopes.apply(aa_2,
residues=["alkylam"],
assert_dihedral_params=False)
if density != 0:
bulk = mb.fill_box(
compound=[emim, tf2n],
density=density,
compound_ratio=[0.5, 0.5],
box=bulk_region,
fix_orientation=True,
)
cation = mb.Compound()
anion = mb.Compound()
for child in bulk.children:
if child.name == "emim":
cation.add(mb.clone(child))
else:
anion.add(mb.clone(child))
if emim_ff == "kpl":
cationPM = kpl.apply(cation,
residues="emim",
assert_dihedral_params=False)
anionPM = kpl.apply(anion,
residues="tf2n",
assert_dihedral_params=False)
else:
cationPM = lopes.apply(cation,
residues="emim",
assert_dihedral_params=False)
anionPM = lopes.apply(anion,
residues="tf2n",
assert_dihedral_params=False)
if n_compounds != 0:
ils = aa1PM + aa2PM + cationPM + anionPM
elif density != 0:
ils = cationPM + anionPM
if emim_ff == "lopes":
for atom in ils.atoms:
atom.charge *= 0.8
if n_compounds != 0 or density != 0:
system = ils + ti3c2
else:
system = ti3c2
system = _apply_nbfixes(system)
system = collapse_atomtypes(system)
change_charge(system, new_charge=0)
max_ti3c2 = np.max(ti3c2.coordinates, axis=0)
system.box[0] = max_ti3c2[0]
if density != 0:
system.box[1] = bulk.boundingbox.maxs[1] * 10
else:
system.box[1] = 20 * 10
system.box[2] = max_ti3c2[2] + (displacement * 10) + 0.8
system.save("ti3c2.gro", combine="all", overwrite=True)
system.save("ti3c2.top", combine="all", overwrite=True)
def build_awh_mxene(n_compounds,
composition,
periods,
chain_length=12,
displacement=1.1):
displacement -= 0.08
ti3c2 = build_structure(
periods=periods,
composition=composition,
displacement=displacement,
lateral_shift=True,
atomtype=True,
)
n_carbons = "C" * chain_length
aa = mb.load(f"{n_carbons}[N](C)(C)C", smiles=True)
emim = mb.load(get_il("emim"))
tf2n = mb.load(get_il("tf2n"))
emim.name = "emim"
tf2n.name = "tf2n"
aa.name = "alkylam"
emim_awh = mb.clone(emim)
emim_awh.name = "awh"
lopes = get_ff("lopes")
kpl = get_ff("kpl")
bulk_region = mb.Box(
mins=[0, ti3c2.box[1] / 10, 0],
maxs=[ti3c2.box[0] / 10, ti3c2.box[1] / 10 + 10, ti3c2.box[2] / 10],
)
region1 = mb.Box(
mins=[0, 0, (ti3c2.box[2] / 10 - 2 * displacement) / 2 + 0.15],
maxs=[
ti3c2.box[0] / 10,
ti3c2.box[1] / 10,
(ti3c2.box[2] / 10 - 2 * displacement) / 2 + displacement,
],
)
ti3c2_max = np.max(ti3c2.coordinates, axis=0)
region2 = mb.Box(
mins=[0, 0, ti3c2_max[2] / 10],
maxs=[
ti3c2.box[0] / 10,
ti3c2.box[1] / 10,
ti3c2_max[2] / 10 + displacement + 0.08,
],
)
aa_1 = mb.fill_box(
compound=[aa, emim_awh],
n_compounds=[n_compounds, 1],
box=region1,
)
aa_2 = mb.fill_box(
compound=aa,
n_compounds=n_compounds,
box=region2,
)
bulk = mb.fill_box(
compound=[emim, tf2n],
density=1420,
compound_ratio=[0.5, 0.5],
box=bulk_region,
fix_orientation=True,
)
cation = mb.Compound()
anion = mb.Compound()
marker = 0
for child in bulk.children:
if child.name == "emim":
if cation.n_particles == 1:
marker = 1
if marker == 1:
cation.add(mb.clone(child))
else:
anion.add(mb.clone(child))
tam1 = mb.Compound()
new_emim_awh = mb.Compound()
for child in aa_1.children:
if child.name == "awh":
new_emim_awh.add(mb.clone(child))
else:
tam1.add(mb.clone(child))
new_emim_awh.translate_to([(ti3c2_max[0] / 10) / 2, ti3c2_max[1] / 10,
0.937 + (displacement / 2) + 0.08])
aa1PM = lopes.apply(tam1,
residues=["alkylam"],
assert_dihedral_params=False)
aa2PM = lopes.apply(aa_2,
residues=["alkylam"],
assert_dihedral_params=False)
cationPM = kpl.apply(cation, residues="emim", assert_dihedral_params=False)
anionPM = kpl.apply(anion, residues="tf2n", assert_dihedral_params=False)
emim_awhPM = kpl.apply(new_emim_awh,
residues="awh",
assert_dihedral_params=False)
system = aa1PM + aa2PM + ti3c2 + cationPM + anionPM + emim_awhPM
system = _apply_nbfixes(system)
system = collapse_atomtypes(system)
change_charge(system, new_charge=0)
max_ti3c2 = np.max(ti3c2.coordinates, axis=0)
system.box[0] = max_ti3c2[0]
system.box[1] = bulk.boundingbox.maxs[1] * 10
system.box[2] = max_ti3c2[2] + (displacement * 10) + 0.8
system.save("init.gro", combine="all", overwrite=True)
system.save("init.top", combine="all", overwrite=True)