def wrongbox(self):
box = mbuild.Compound()
box.box = mbuild.Box([5.0, 5.0, 5.0])
return box
def test_init_with_subcompounds1(self, ethane):
compound = mb.Compound(ethane)
assert compound.n_particles == 8
assert compound.n_bonds == 7
def test_init_with_subcompounds3(self, ethane, h2o):
compound = mb.Compound([ethane, [h2o, mb.clone(h2o)]])
assert compound.n_particles == 8 + 2 * 3
assert compound.n_bonds == 7 + 2 * 2
def test_clone_outside_containment(self, ch2, ch3):
compound = mb.Compound()
compound.add(ch2)
mb.force_overlap(ch3, ch3['up'], ch2['up'])
with pytest.raises(MBuildError):
ch3_clone = mb.clone(ch3)
def __init__(self,
lipids,
ref_atoms,
n_lipids_x=10,
n_lipids_y=10,
area_per_lipid=1.0,
solvent=None,
lipid_box=None,
spacing_z=0.5,
solvent_per_lipid=None,
n_solvent=None,
random_seed=12345,
mirror=True):
super(Bilayer, self).__init__()
# Santitize inputs.
if sum([lipid[1] for lipid in lipids]) != 1.0:
raise ValueError('Lipid fractions do not add up to 1.')
assert len(ref_atoms) == len(lipids)
self.lipids = lipids
self.ref_atoms = ref_atoms
self._lipid_box = lipid_box
# 2D Lipid locations.
self.n_lipids_x = n_lipids_x
self.n_lipids_y = n_lipids_y
self.apl = area_per_lipid
self.n_lipids_per_layer = self.n_lipids_x * self.n_lipids_y
self.pattern = mb.Grid2DPattern(n_lipids_x, n_lipids_y)
self.pattern.scale(np.sqrt(self.apl * self.n_lipids_per_layer))
# Solvent info.
self.solvent = solvent
self.n_solvent = n_solvent
self.solvent_per_lipid = solvent_per_lipid
# Other inputs.
self.spacing = np.array([0, 0, spacing_z])
self.random_seed = random_seed
self.mirror = mirror
self._number_of_each_lipid_per_layer = []
self._solvent_per_layer = None
# Containers for lipids and solvent.
self.lipid_components = mb.Compound()
self.solvent_components = mb.Compound()
# Assemble the lipid layers
seed(self.random_seed)
top_layer, top_lipid_labels = self.create_layer()
self.lipid_components.add(top_layer)
if self.mirror == True:
bottom_layer, bottom_lipid_labels = self.create_layer(
lipid_indices=top_lipid_labels, flip_orientation=True)
else:
bottom_layer, bottom_lipid_labels = self.create_layer(
flip_orientation=True)
self.lipid_components.add(bottom_layer)
# solvate the lipids
#self.solvate_bilayer() # TODO: needs fixing
# add everything to the big list
self.add(self.lipid_components)
self.add(self.solvent_components)
print(self.number_of_each_lipid_per_layer)
def test_batch_add(self, ethane, h2o):
compound = mb.Compound()
compound.add([ethane, h2o])
assert compound.n_particles == 8 + 3
assert compound.n_bonds == 7 + 2
def test_parmed_box(self, h2o):
compound = mb.Compound()
compound.add(h2o)
tilted_box = mb.Box(lengths=[2.0, 2.0, 2.0], angles=[60.0, 80.0, 100.0])
structure = compound.to_parmed(box=tilted_box)
assert all(structure.box == [20.0, 20.0, 20.0, 60.0, 80.0, 100.0])
def main():
# Create a CG methane, load and apply ff
methane = mbuild.Compound(name="_CH4")
ff_path = resource_filename(
"mc_examples",
"realistic_workflows/zeolite_adsorption/resources/ffxml/adsorbates.xml",
)
ff_ads = foyer.Forcefield(ff_path)
methane_ff = ff_ads.apply(methane)
# Define a few keyword args that will be the
# same for all fluid phase simulations
custom_args = {
"charge_style": "none",
"vdw_cutoff": 14.0 * u.angstrom,
"prop_freq": 10,
}
# Define temperatures and chemical potential values
# for the single phase GCMC simulations
temperatures = [298 * u.K, 309 * u.K, 350 * u.K]
mus = np.arange(-49, -30, 3) * u.Unit("kJ/mol")
# Loop over temperatures and mus and run simulations
for temperature in temperatures:
for mu in mus:
# For each simulation -- first estimate
# the box volume to target ~40 molecules
n_methane_target = 40
beta = 1.0 / (u.kb * temperature)
mass = 16.04 * u.amu
debroglie = np.sqrt(2 * np.pi * u.hbar**2 * beta / mass)
vol = n_methane_target * debroglie**3 * np.exp(
-beta.to("mol/kJ") * mu)
boxl = (vol**(1.0 / 3.0)).to_value("nm")
if boxl < 2.0 * custom_args["vdw_cutoff"].to_value("nm"):
boxl = 2.0 * custom_args["vdw_cutoff"].to_value("nm")
# Define the species list, box list, system, moveset
# We start with an empty box
species_list = [methane_ff]
box_list = [mbuild.Box([boxl, boxl, boxl])]
system = mc.System(box_list, species_list)
moveset = mc.MoveSet("gcmc", species_list)
# Create a new directory, temporary cd, and run
# the equilibration and production simulations!
print(f"\nRun simulation: T = {temperature}, mu = {mu}\n")
dirname = f"fluid_T_{temperature:0.1f}_mu_{mu:.1f}".replace(
" ", "_").replace("/", "-")
if not os.path.isdir(dirname):
os.mkdir(dirname)
else:
pass
with temporary_cd(dirname):
mc.run(
system=system,
moveset=moveset,
run_type="equil",
run_length=50000,
temperature=temperature,
run_name="equil",
chemical_potentials=[mu],
**custom_args,
)
mc.restart(
restart_from="equil",
run_name="prod",
run_type="prod",
total_run_length=400000,
)
def __init__(self,
radius=2,
angle=90.0,
fluid=None,
density=None,
lattice=None,
lattice_compound=None,
x=None,
y=None):
super(Droplet, self).__init__()
if fluid is None:
raise ValueError('Fluid droplet compounds must be specified')
if density is None:
raise ValueError('Fluid density must be specified (units kg/m^3)')
if x:
if x < radius * 4:
raise ValueError(
'Dimension x of sheet must be at least radius * 4')
elif x > 100:
raise ValueError(
'Dimension x of sheet must be less than 100 nm')
else:
x = radius * 4
if y:
if y < radius * 4:
raise ValueError(
'Dimension y of sheet must be at least radius * 4')
elif y > 100:
raise ValueError(
'Dimension y of sheet must be less than 100 nm')
else:
y = radius * 4
# Default to graphene lattice
if lattice is None:
if lattice_compound is not None:
raise ValueError(
'If Lattice is None, defaults to a Graphene surface. ' +
'In this case, do not specify lattice_compound.')
lattice_compound = mbuild.Compound(name='C')
lattice_spacing = [0.2456, 0.2456, 0.335]
angles = [90.0, 90.0, 120.0]
carbon_locations = [[0, 0, 0], [2 / 3, 1 / 3, 0]]
basis = {lattice_compound.name: carbon_locations}
lattice = mbuild.Lattice(lattice_spacing=lattice_spacing,
angles=angles,
lattice_points=basis)
compound_dict = {lattice_compound.name: lattice_compound}
factor = np.cos(np.pi / 6) # fixes non-cubic lattice
# Estimate the number of lattice repeat units
replicate = [int(x / 0.2456), int(y / 0.2456) * (1 / factor)]
lat = lattice.populate(compound_dict=compound_dict,
x=replicate[0],
y=replicate[1],
z=3)
for particle in lat.particles():
if particle.xyz[0][0] < 0:
particle.xyz[0][0] += lat.periodicity[0]
lat.periodicity[1] *= factor
else:
if lattice_compound is None:
raise ValueError('Lattice compounds must be specified')
if not np.all(lattice.angles == 90.0):
raise ValueError(
'Currently, only cubic lattices are supported. ' +
'If using Graphene, do not pass in a Lattice.')
compound_dict = {lattice_compound.name: lattice_compound}
lat = lattice.populate(compound_dict=compound_dict,
x=int(x / lattice.lattice_spacing[0]),
y=int(y / lattice.lattice_spacing[1]),
z=int(1.5 / lattice.lattice_spacing[2]))
sheet = mbuild.clone(lat)
self.surface_height = np.max(sheet.xyz, axis=0)[2]
coords = list(sheet.periodicity)
height = get_height(radius, angle)
sphere_coords = [coords[0] / 2, coords[1] / 2, radius, radius]
sphere = mbuild.fill_sphere(compound=fluid,
sphere=sphere_coords,
density=density)
to_remove = []
for child in sphere.children:
for atom_coords in child.xyz:
if height > radius:
if atom_coords[2] < height - radius:
to_remove += child
break
else:
if atom_coords[2] < height:
to_remove += child
break
sphere.remove(to_remove)
sheet.name = 'LAT'
sphere.name = 'FLD'
sphere.xyz -= [0, 0, np.min(sphere.xyz, axis=0)[2]]
sphere.xyz += [0, 0, self.surface_height + 0.3]
self.add(sheet)
self.add(sphere)
self.periodicity[0] = sheet.periodicity[0]
self.periodicity[1] = sheet.periodicity[1]
self.periodicity[2] = radius * 5
from dropletbuilder.dropletbuilder import GrapheneDroplet
import mbuild
from mbuild.examples.alkane.alkane import Alkane
from dropletbuilder.utils.io_tools import get_fn
from foyer import Forcefield
# build the lattice
lattice_compound = mbuild.Compound(name='Au')
lattice_spacing = [0.40788, 0.40788, 0.40788]
lattice_vector = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
gold_locations = [[0., 0., 0.], [.5, .5, 0.], [.5, 0., .5], [0, .5, .5]]
basis = {lattice_compound.name: gold_locations}
gold_lattice = mbuild.Lattice(lattice_spacing=lattice_spacing,
lattice_vectors=lattice_vector,
lattice_points=basis)
# hexane compound
hexane = Alkane(n=6)
hexane.name = 'HEX'
# build the system
system = GrapheneDroplet(radius=3,
angle=90,
fluid=hexane,
density=655,
lattice=gold_lattice,
lattice_compound=lattice_compound)
# get and apply forcefields
AU = Forcefield(get_fn('heinz2008.xml'))
OPLSAA = Forcefield(name='oplsaa')
index = 0
# Loop through each type of molecule (DSPC, DPPC, etc.)
for i, lipid_type in enumerate(lipid_system_info):
# Loop through the quantity of that particular molecule
for n in range(int(lipid_type[1])):
lipid_molecule = lipid_type[0]
lipid_offset = lipid_type[2]
top_lipids.append([lipid_molecule, lipid_offset])
bot_lipids.append([lipid_molecule, lipid_offset])
index += 1
if len(bot_lipids) != n_lipid:
sys.exit('Error setting up system components')
# Generate bottom layer randomly
bot_layer = mb.Compound()
for i in range(n_x):
for j in range(n_y):
# Randomly select a lipid that has not yet been selected
random_lipid = np.random.randint(0, len(bot_lipids))
# Create the mbuild Molecule for this lipid
molecule_i = bot_lipids.pop(random_lipid)
molecule_to_add = mb.clone(molecule_i[0])
# Apply tilt angle
mb.spin_y(molecule_to_add, tilt_angle)
# Apply z_offset
z_offset = molecule_i[1]
#z_offset = 0
# Apply APL and z_offset to identify the position for the molecule in the grid
position = [i * spacing, j * spacing, z_offset]
mb.translate(molecule_to_add, position)
def make_leaflet(leaflet_info,
n_x=8,
n_y=8,
tilt_angle=0,
spacing=0,
random_z_displacement=0):
""" Generate a leaflet by laying down molecules in a 2D grid at random grid points
Parameters
---------
n_x : int
Number of lipids in x direction
n_y : int
Number of lipids in y direction
leaflet_info : n x 3 array
Each row corresponds to a molecule
First column is the mB.compound
Second column is the number of that molecule
Third column is a z-offset specific to molecules of that type (positive means closer to the solvent,
negative means deeper inside the bilayer)
tilt_angle : float (rad)
tilt angle (spun around y-axis)
spacing : float (nm)
spacing between leaflets, based on area per lipid
random_z_displacement : float (nm)
Randomly offset molecules by a small amount
Returns
-------
leaflet : mb.Compound()
Leaflet of molecules
"""
_validate_leaflet_info(leaflet_info, n_x, n_y)
leaflet = mb.Compound()
# Create ordered pairs
ordered_pairs = []
for i, j in product(range(n_x), range(n_y)):
ordered_pairs.append((i, j))
# Randomly assign ordered pairs to each lipid
# based on the way lipids is set, all of one molecule is listed first
# before getting to the next one
# Loop through each type of molecule (DSPC, DPPC, etc.)
for i, lipid_type in enumerate(leaflet_info):
# Loop through the system's quantity of that particular molecule
for n in range(lipid_type[1]):
random_index = np.random.randint(0, len(ordered_pairs))
(i, j) = ordered_pairs.pop(random_index)
# Do geometry transformations
molecule_to_add = mb.clone(lipid_type[0])
# Apply tilt angle
molecule_to_add.spin(tilt_angle, [0, 1, 0])
# Apply z_offset
z_offset = lipid_type[2]
# Apply APL and z_offset to identify the position for the
# molecule in the grid
position = [
i * spacing, j * spacing,
z_offset + (-1 * np.random.random() * random_z_displacement)
]
molecule_to_add.translate(position)
# Add the new molecule to the leaflet
leaflet.add(molecule_to_add)
return leaflet
self.add_bond([n, c5])
self.add_bond([c5, c6])
self.add(mb.Port(anchor=c5), 'up')
self.add(mb.Port(anchor=c6), 'down')
# Implicit hydrogens
# XYZ doesn't matter, we just need bonds and particle names
# So we can upload to charmm-gui
cap_with = 'H'
pvp = mb.Polymer(mvp(), n=2)
if cap_with == 'C':
c_top = mb.Particle(name='C')
cap_top = mb.Compound()
cap_top.add(c_top)
cap_top.add(mb.Port(anchor=c_top), 'down')
mb.force_overlap(cap_top, cap_top['down'], pvp['up'])
c_bot = mb.Particle(name='C')
cap_bot = mb.Compound()
cap_bot.add(c_bot)
cap_bot.add(mb.Port(anchor=c_bot), 'up')
mb.force_overlap(cap_bot, cap_bot['up'], pvp['down'])
pvp.add(cap_top)
pvp.add(cap_bot)
elif cap_with == 'H':
pass
import mbuild
import foyer
import unyt as u
import mosdef_cassandra as mc
# Load the force field from foyer
ff = foyer.forcefields.load_TRAPPE_UA()
# Create a single site methane molecule
methane = mbuild.Compound(name="_CH4")
# Apply the force field
methane_ff = ff.apply(methane)
# Create an empty 3x3x3 nm^3 simulation box
box = mbuild.Box([3., 3., 3.])
# Define the box/species lists
box_list = [box]
species_list = [methane_ff]
# Tell Cassandra to add 100 methane at the start
mols_to_add = [[100]]
# Create the System and MoveSet
system = mc.System(box_list, species_list, mols_to_add=mols_to_add)
moveset = mc.MoveSet("npt", species_list)
# Run the Monte Carlo simulation
mc.run(
system=system,
def populate(self, compound_dict=None, x=1, y=1, z=1):
"""Expand lattice and create compound from lattice.
Expands lattice based on user input. The user must also
pass in a dictionary that contains the keys that exist in the
basis_dict. The corresponding Compound will be the full lattice
returned to the user.
If no dictionary is passed to the user, Dummy Compounds will be used.
Parameters
----------
x : int, optional, default=1
How many iterations in the x direction.
y : int, optional, default=1
How many iterations in the y direction.
z : int, optional, default=1
How many iterations in the z direction.
compound_dict : dictionary, optional, default=None
Link between basis_dict and Compounds.
Exceptions Raised
-----------------
ValueError : incorrect x,y, or z values.
TypeError : incorrect type for basis vector
Call Restrictions
-----------------
Called after constructor by user.
"""
x, y, z = self._sanitize_populate_args(x=x, y=y, z=z)
if ((isinstance(compound_dict, dict)) or (compound_dict is None)):
pass
else:
raise TypeError('Compound dictionary is not of type dict. '
'{} was passed.'.format(type(compound_dict)))
cell = defaultdict(list)
[a, b, c] = self.lattice_spacing
transform_mat = self.lattice_vectors
# Unit vectors
transform_mat = np.asarray(transform_mat, dtype=np.float64)
transform_mat = np.reshape(transform_mat, newshape=(3,3))
norms = np.linalg.norm(transform_mat, axis=1)
# Normalized vectors for change of basis
unit_vecs = np.divide(transform_mat.transpose(), norms)
# Generate new coordinates
for key, locations in self.lattice_points.items():
for coords in locations:
for replication in it.product(range(x), range(y), range(z)):
new_coords = np.asarray(coords, dtype=np.float64)
new_coords = np.reshape(new_coords, (1, 3), order='C')
new_coords[0][0] = new_coords[0][0] + replication[0]
new_coords[0][1] = new_coords[0][1] + replication[1]
new_coords[0][2] = new_coords[0][2] + replication[2]
# Change of basis to cartesian
new_coords = np.dot(unit_vecs, new_coords.transpose())
new_coords[0] = new_coords[0] * a
new_coords[1] = new_coords[1] * b
new_coords[2] = new_coords[2] * c
new_coords = np.reshape(new_coords, (1, 3), order='C')
tuple_of_coords = tuple(new_coords.flatten())
cell[key].append(tuple_of_coords)
ret_lattice = mb.Compound()
# Create (clone) a mb.Compound for the newly generate positions
if compound_dict is None:
for key_id, all_pos in cell.items():
particle = mb.Compound(name=key_id, pos=[0, 0, 0])
for pos in all_pos:
particle_to_add = mb.clone(particle)
particle_to_add.translate_to(list(pos))
ret_lattice.add(particle_to_add)
else:
for key_id, all_pos in cell.items():
if isinstance(compound_dict[key_id], mb.Compound):
compound_to_move = compound_dict[key_id]
for pos in all_pos:
tmp_comp = mb.clone(compound_to_move)
tmp_comp.translate_to(list(pos))
ret_lattice.add(tmp_comp)
else:
err_type = type(compound_dict.get(key_id))
raise TypeError('Invalid type in provided Compound '
'dictionary. For key {}, type: {} was '
'provided, not mbuild.Compound.'
.format(key_id, err_type))
# set periodicity, currently assuming rectangular system
if not np.all(np.allclose(self.angles, [90.0, 90.0, 90.0])):
warn('Periodicity of non-rectangular lattices are not valid with '
'default boxes. Only rectangular lattices are valid '
'at this time.')
ret_lattice.periodicity = np.asarray([a * x, b * y, c * z], dtype=np.float64)
# if coordinates are below a certain threshold, set to 0
tolerance = 1e-12
ret_lattice.xyz_with_ports[ret_lattice.xyz_with_ports <= tolerance] = 0.
return ret_lattice
"""
def __init__(self,
lattice_spacing=None,
compound_to_add=None,
x=1,
y=1,
z=1):
super(FCC, self).__init__()
lattice_points = {
'A': [[0, 0, 0], [0, 0.5, 0.5], [0.5, 0.5, 0], [0.5, 0, 0.5]]
}
angles = [90, 90, 90]
fcc_lattice = mbuild.Lattice(lattice_spacing=lattice_spacing,
angles=angles,
lattice_points=lattice_points)
self.add(
fcc_lattice.populate(x=x,
y=y,
z=z,
compound_dict={'A': compound_to_add}))
if __name__ == "__main__":
au_fcc_lattice = FCC(lattice_spacing=0.40782,
compound_to_add=mbuild.Compound(name="Au"),
x=5,
y=5,
z=1)
print(au_fcc_lattice)
def test_incorrect_populate_inputs(self, x, y, z):
with pytest.raises(ValueError):
test_lattice = mb.Lattice(lattice_spacing=[1, 1, 1])
test_lattice.populate(
compound_dict={"id": mb.Compound()}, x=x, y=y, z=z
)
def create_system(
pore_width,
n_ion_pairs,
n_water,
pve_ion=mbuild.Compound(name="Na"),
nve_ion=mbuild.Compound(name="Cl"),
engine="cassandra",
):
"""Create a system with a graphene pore filled with n_ion_pairs,
(na, cl), and n_water spce water molecules.
Parameters
----------
pore_width : u.unyt_quantity (length)
width of pore for restricted insertions
n_ion_pairs : int
number of na, cl ion pairs
n_water : int
number of water molecules
pve_ion : mbuild.Compound, optional, default=Na
positive ion
nve_ion : mbuild.Compound, optional, default=Cl
negative ion
engine : str, optional, default="cassandra"
engine system is being initialized for, determines how box is created
Returns
-------
filled_pore : mbuild.Compound
"""
if n_ion_pairs == 0:
filled_pore = mbuild.recipes.GraphenePoreSolvent(
pore_length=2.3,
pore_depth=2.2,
pore_width=pore_width.to_value("nm"),
n_sheets=3,
slit_pore_dim=2,
x_bulk=0,
solvent=spce_water,
n_solvent=n_water,
)
else:
# Create pore system
filled_pore = mbuild.recipes.GraphenePoreSolvent(
pore_length=2.3,
pore_depth=2.2,
pore_width=pore_width.to_value("nm"),
n_sheets=3,
slit_pore_dim=2,
x_bulk=0,
solvent=[pve_ion, nve_ion, spce_water],
n_solvent=[n_ion_pairs, n_ion_pairs, n_water],
)
# Translate to centered at 0,0,0 and make box larger in z
if engine == 'cassandra':
box_center = filled_pore.periodicity / 2.0
filled_pore.translate(-box_center)
return filled_pore
def test_remove_no_bond_graph(self):
compound = mb.Compound()
particle = mb.Compound(name='C', pos=[0, 0, 0])
compound.add(particle, 'test-particle')
compound.remove(particle)
assert particle not in compound.particles()
import mbuild as mb
from mbuild.formats.lammpsdata import write_lammpsdata
import scripts.bilayer as bilayer
# Import statements for molecule prototypes
import atomistic.dppc.DPPC as DPPC
import atomistic.c24ffa.ffa24 as ffa24
import atomistic.tip3p.SOL as SOL
###################
## Sample script to convert a GROMACS structure to a
## fully-parameterized LAMMPS system
####################
system = mb.Compound()
for i in range(72):
system.add(DPPC.DPPC(use_atom_name=False))
for i in range(2160):
system.add(SOL.SOL(use_atom_name=False))
system.update_coordinates('wrapped.gro')
# In order to avoid using smarts, define custom elements in parmed
# by adding underscores to mb particle names
for num, i in enumerate(system.particles()):
i.name = "_{}".format(i.name)
structure = system.to_parmed(box=system.boundingbox,
residues=set(
[p.parent.name for p in system.particles()]))
def test_min_periodic_dist(self, ethane):
compound = mb.Compound(ethane)
C_pos = np.array([atom.pos for atom in list(compound.particles_by_name('C'))])
assert round(compound.min_periodic_distance(C_pos[0], C_pos[1]), 2) == 0.14
compound.periodicity = np.array([0.2, 0.2, 0.2])
assert round(compound.min_periodic_distance(C_pos[0], C_pos[1]), 2) == 0.06
def methane_trappe(self):
trappe = foyer.forcefields.load_TRAPPE_UA()
methane = mbuild.Compound(pos=[0.0, 0.0, 0.0], name="_CH4")
methane = trappe.apply(methane)
return methane
def test_save_resnames_single(self, c3, n4):
system = mb.Compound([c3, n4])
system.save('resnames_single.gro', residues=['C3', 'N4'])
struct = pmd.load_file('resnames_single.gro')
assert struct.residues[0].number == 1
assert struct.residues[1].number == 2
def wrongbox(self):
box = mbuild.Compound()
box.boundingbox.lengths = [5.0, 5.0, 5.0]
return box
def methane_ua_gomc(self):
methane_ua_gomc = mb.Compound(name="_CH4")
return methane_ua_gomc
def from_mbuild(compound, box=None, search_method=element_by_symbol):
"""Convert an mbuild.Compound to a gmso.Topology.
This conversion makes the following assumptions about the inputted `Compound`:
* All positional and box dimension values in compound are in nanometers.
* If the `Compound` has 4 or more levels of hierarchy, these are\
compressed to 3 levels of hierarchy in the resulting `Topology`. The\
top level `Compound` becomes the `Topology`, the second level\
Compounds become `SubTopologies`, and each particle becomes a `Site`,\
which are added to their corresponding `SubTopologies`.
* Furthermore, `Sites` that do not belong to a sub-`Compound` are\
added to a single-`Site` `SubTopology`.
* The box dimension are extracted from `compound.periodicity`. If\
the `compound.periodicity` is `None`, the box lengths are the lengths of\
the bounding box + a 0.5 nm buffer.
* Only `Bonds` are added for each bond in the `Compound`. If `Angles`\
and `Dihedrals` are desired in the resulting `Topology`, they must be\
added separately from this function.
Parameters
----------
compound : mbuild.Compound
mbuild.Compound instance that need to be converted
box : mbuild.Box, optional, default=None
Box information to be loaded to a gmso.Topology
search_method : function, optional, default=element_by_symbol
Searching method used to assign element from periodic table to
particle site.
The information specified in the `search_method` argument is extracted
from each `Particle`'s `name` attribute.
Valid functions are element_by_symbol, element_by_name,
element_by_atomic_number, and element_by_mass, which can be imported
from `gmso.core.element'
Returns
-------
top : gmso.Topology
"""
msg = "Argument compound is not an mbuild.Compound"
assert isinstance(compound, mb.Compound), msg
top = Topology()
top.typed = False
# Keep the name if it is not the default mBuild Compound name
if compound.name != mb.Compound().name:
top.name = compound.name
site_map = dict()
for child in compound.children:
if len(child.children) == 0:
continue
else:
subtop = SubTopology(name=child.name)
top.add_subtopology(subtop, update=False)
for particle in child.particles():
pos = particle.xyz[0] * u.nanometer
ele = search_method(particle.name)
site = Atom(name=particle.name, position=pos, element=ele)
site_map[particle] = site
subtop.add_site(site, update_types=False)
for particle in compound.particles():
already_added_site = site_map.get(particle, None)
if already_added_site:
continue
pos = particle.xyz[0] * u.nanometer
ele = search_method(particle.name)
site = Atom(name=particle.name, position=pos, element=ele)
site_map[particle] = site
# If the top has subtopologies, then place this particle into
# a single-site subtopology -- ensures that all sites are in the
# same level of hierarchy.
if len(top.subtops) > 0:
subtop = SubTopology(name=particle.name)
top.add_subtopology(subtop)
subtop.add_site(site, update_types=False)
else:
top.add_site(site, update_types=False)
for b1, b2 in compound.bonds():
new_bond = Bond(connection_members=[site_map[b1], site_map[b2]],
bond_type=None)
top.add_connection(new_bond, update_types=False)
top.update_topology()
if box:
top.box = from_mbuild_box(box)
# Assumes 2-D systems are not supported in mBuild
# if compound.periodicity is None and not box:
else:
if compound.box:
top.box = from_mbuild_box(compound.box)
else:
top.box = from_mbuild_box(compound.get_boundingbox())
top.periodicity = compound.periodicity
return top
def test_init_with_subcompounds2(self, ethane, h2o):
compound = mb.Compound([ethane, h2o])
assert compound.n_particles == 8 + 3
assert compound.n_bonds == 7 + 2
def run_gemc(**custom_args):
# Use mbuild to create molecules
methane = mbuild.Compound(name="_CH4")
# Create two empty mbuild.Box
# (vapor = larger, liquid = smaller)
liquid_box = mbuild.Box(lengths=[3.0, 3.0, 3.0])
vapor_box = mbuild.Box(lengths=[4.0, 4.0, 4.0])
# Load forcefields
trappe = foyer.forcefields.load_TRAPPE_UA()
# Use foyer to apply forcefields
typed_methane = trappe.apply(methane)
# Create box and species list
box_list = [liquid_box, vapor_box]
species_list = [typed_methane]
mols_to_add = [[350], [100]]
system = mc.System(box_list, species_list, mols_to_add=mols_to_add)
moveset = mc.MoveSet("gemc", species_list)
moveset.prob_volume = 0.010
moveset.prob_swap = 0.11
thermo_props = [
"energy_total",
"energy_intervdw",
"pressure",
"volume",
"nmols",
"mass_density",
]
default_args = {
"run_name": "equil",
"charge_style": "none",
"rcut_min": 2.0 * u.angstrom,
"vdw_cutoff": 14.0 * u.angstrom,
"units": "sweeps",
"steps_per_sweep": 450,
"coord_freq": 50,
"prop_freq": 10,
"properties": thermo_props,
}
# Combine default/custom args and override default
custom_args = {**default_args, **custom_args}
mc.run(
system=system,
moveset=moveset,
run_type="equilibration",
run_length=250,
temperature=151.0 * u.K,
**custom_args,
)
# Update run_name and restart_name
custom_args["run_name"] = "prod"
custom_args["restart_name"] = "equil"
mc.restart(
system=system,
moveset=moveset,
run_type="production",
run_length=750,
temperature=151.0 * u.K,
**custom_args,
)
def test_init_with_bad_name(self):
with pytest.raises(ValueError):
mb.Compound(name=1)
def construct_system(dist_from_sheet=0.7,
box_thickness=0.5,
n_load_per_side=10,
bilayer_center=[5.387, 5.347, 3.26]):
""" Build graphene + sds + bilayer + ions
The idea is to pack a box below the sheet and below the sheet.
The density of SDS is 1.01 g/cm$^3$, which equates to 2.109 molecules/nm$^3$
The box we are filling is about 5nm x 5nm x 0.635nm.
At max SDS density, this is 33.5 molecules of SDS
Parameters
---------
dist_from_sheet : float, default 0.7 nm
When defining the box above/below the sheet, specify how far above/below
box_thickness : float: default 0.5nm
When defining the box to fill, the X and Y dimensions take from
the graphene sheet, but the Z dimensions (thickness) is defined
in box_thickneess
n_load_per_side : int, default 10
Important for packing the boxes and specifying number of SDS (and Na ions)
to add to the system
"""
header = """; Include forcefield parameters
#include "/raid6/homes/ahy3nz/Programs/graphene_build/force-field/ffmix.itp"
#include "/raid6/homes/ahy3nz/Programs/graphene_build/force-field/molecules.itp"
#include "/raid6/homes/ahy3nz/Programs/graphene_build/force-field/ions.itp
"""
gra = mb.load(os.path.join(PATH_TO_MOLECULES, 'sheet.gro'))
gra.name = 'GRA_5'
sds = mb.load(os.path.join(PATH_TO_MOLECULES, 'SDS.gro'))
sds.name = 'SDS'
# The SDS molecules are initially aligned with the Z-axis, so do a rotation
sds.spin(np.pi / 2, [1, 0, 0])
na_part = mb.Particle(name="NA")
na = mb.Compound()
na.name = "NA"
na.add(na_part)
above_box = mb.Box(mins=np.min(gra.xyz, axis=0) + [0, 0, dist_from_sheet],
maxs=np.max(gra.xyz, axis=0) +
[0, 0, dist_from_sheet + box_thickness])
fill_above = fill_box([sds, na],
n_compounds=[n_load_per_side, n_load_per_side],
box=above_box,
edge=0.1,
overlap=0.1)
below_box = mb.Box(mins=np.min(gra.xyz, axis=0) -
[0, 0, dist_from_sheet + box_thickness],
maxs=np.max(gra.xyz, axis=0) - [0, 0, dist_from_sheet])
fill_below = fill_box([sds, na],
n_compounds=[n_load_per_side, n_load_per_side],
box=below_box,
edge=0.1,
overlap=0.1)
sys = mb.Compound()
sys.add([gra, fill_above, fill_below])
sys.spin(np.pi / 2, [1, 0, 0]) # Do some rotations to get it corner first
sys.spin(np.pi / 4, [0, 1, 0])
sys.translate_to(bilayer_center) # This is the bilayer center
sys.translate([0, 0, 6]) # Shift the loaded GNF up to be above the bialyer
# For the sake of writing, we will be using a lot of mdtraj functionality
traj = sys.to_trajectory(residues=['GRA_5', 'SDS', 'NA'])
bilayer = mdtraj.load(os.path.join(PATH_TO_MOLECULES, 'bilayer.gro'))
composite_traj = traj.stack(bilayer)
composite_traj.unitcell_lengths = bilayer.unitcell_lengths
composite_traj.unitcell_lengths[0, 2] = 13
composite_traj[0].save('composite.gro')
write_gmx_topology('topol.top', composite_traj, header=header)
# Use external module to perform rotations and write pulling MDP
graphene_rotations.rotate_gnf_write_mdp(gro_file='composite.gro',
angle_of_attack=0,
force_constant=50,
outgro='composite_rotated.gro')