def initialize(job):
"Initialize the simulation configuration."
from pkg_resources import resource_filename
from mbuild.lib.atoms import H
from atools.fileio import write_monolayer_ndx
from atools.lib.chains import Alkylsilane
from atools.recipes import DualSurface, SilicaInterface, SurfaceMonolayer
from atools.structure import identify_rigid_groups
with job:
chainlength = job.statepoint()['chainlength']
n_chains = job.statepoint()['n']
seed = job.statepoint()['seed']
terminal_group = job.statepoint()['terminal_group']
surface = SilicaInterface(thickness=1.2, seed=seed)
chain_proto = Alkylsilane(chain_length=chainlength,
terminal_group=terminal_group)
monolayer = SurfaceMonolayer(surface=surface,
chains=chain_proto,
n_chains=n_chains,
seed=seed,
backfill=H())
dual_monolayer = DualSurface(monolayer)
box = dual_monolayer.boundingbox
dual_monolayer.periodicity += np.array([0, 0, 5. * box.lengths[2]])
forcefield_dir = resource_filename('atools', 'forcefields')
dual_monolayer.save('init.gro',
forcefield_files=os.path.join(
forcefield_dir, 'oplsaa-silica.xml'),
overwrite=True)
dual_monolayer.save('init.top',
forcefield_files=os.path.join(
forcefield_dir, 'oplsaa-silica.xml'),
overwrite=True)
rigid_groups = identify_rigid_groups(monolayer=dual_monolayer,
terminal_group=terminal_group,
freeze_thickness=0.5)
write_monolayer_ndx(rigid_groups=rigid_groups, filename='init.ndx')
def initialize(job):
"Initialize the simulation configuration."
'''
---------------------------
Read statepoint information
---------------------------
'''
chainlength = job.statepoint()['chainlength']
n_chains = job.statepoint()['n']
seed = job.statepoint()['seed']
terminal_group = job.statepoint()['terminal_group']
'''
-----------------------------------
Generate amorphous silica interface
-----------------------------------
'''
surface = SilicaInterface(thickness=1.2, seed=seed)
'''
------------------------------------------------------
Generate prototype of functionalized alkylsilane chain
------------------------------------------------------
'''
chain_prototype = Alkylsilane(chain_length=chainlength,
terminal_group=terminal_group)
'''
----------------------------------------------------------
Create monolayer on surface, backfilled with hydrogen caps
----------------------------------------------------------
'''
monolayer = SurfaceMonolayer(surface=surface,
chains=chain_prototype,
n_chains=n_chains,
seed=seed,
backfill=H(),
rotate=False)
'''
------------------------------------------
Duplicate to yield two opposing monolayers
------------------------------------------
'''
dual_monolayer = DualSurface(monolayer, separation=2.0)
'''
--------------------------------------------------------
Make sure box is elongated in z to be pseudo-2D periodic
--------------------------------------------------------
'''
box = dual_monolayer.boundingbox
dual_monolayer.periodicity += np.array([0, 0, 5. * box.lengths[2]])
'''
-------------------------------------------------------------------
- Save to .GRO, .TOP, and .LAMMPS formats
- Atom-type the system using Foyer, with parameters from the OPLS
force field obtained from GROMACS. Parameters are located in a
Foyer XML file in the `atools` git repo, with references provided
as well as notes where parameters have been added or altered to
reflect the literature.
-------------------------------------------------------------------
'''
forcefield_dir = resource_filename('atools', 'forcefields')
dual_monolayer.save('init.gro', overwrite=True)
dual_monolayer.save('init.top',
forcefield_files=os.path.join(forcefield_dir,
'oplsaa.xml'),
combining_rule='geometric',
overwrite=True)
dual_monolayer.save('init.lammps',
forcefield_files=os.path.join(forcefield_dir,
'oplsaa.xml'),
combining_rule='geometric',
overwrite=True)
'''
--------------------------------------
Specify index groups and write to file
--------------------------------------
'''
index_groups = generate_index_groups(system=dual_monolayer,
terminal_group=terminal_group,
freeze_thickness=0.5)
write_monolayer_ndx(rigid_groups=index_groups, filename='init.ndx')
def initialize_system(job):
""" Generate the monolayer surfaces, parametrize, save LAMMPS, GRO, TOP.
"""
"""
---------------------------
Read statepoint information
---------------------------
"""
chainlength_a = job.statepoint()["chainlength_a"]
chainlength_b = job.statepoint()["chainlength_b"]
chainlength_c = job.statepoint()["chainlength_c"]
chainlength_d = job.statepoint()["chainlength_d"]
seed = job.statepoint()["seed"]
pattern_type = job.statepoint()["pattern_type"]
terminal_groups = job.statepoint()["terminal_groups"]
a_fraction = job.statepoint()["fraction_a"]
c_fraction = job.statepoint()["fraction_c"]
num_chains = job.statepoint()["n"]
backbone_1 = job.statepoint()["backbone_1"]
backbone_2 = job.statepoint()["backbone_2"]
locations = job.statepoint()["locations"]
"""
-----------------------------------
Generate amorphous silica interface
-----------------------------------
"""
surface_a = SilicaInterface(thickness=1.2, seed=seed)
surface_b = SilicaInterface(thickness=1.2, seed=seed)
"""
------------------------------------------------------
Generate prototype of functionalized alkylsilane chain
------------------------------------------------------
"""
chain_prototype_a = AlkylsilaneInternalplus(
chain_length=chainlength_a, internal_group=backbone_1, locations=locations, terminal_group=terminal_groups[0]
)
chain_prototype_b = AlkylsilaneInternalplus(
chain_length=chainlength_b, internal_group=backbone_2, locations=locations, terminal_group=terminal_groups[1]
)
chain_prototype_c = AlkylsilaneInternalplus(
chain_length=chainlength_c, internal_group=backbone_1, locations=locations, terminal_group=terminal_groups[2]
)
chain_prototype_d = AlkylsilaneInternalplus(
chain_length=chainlength_d, internal_group=backbone_2, locations=locations, terminal_group=terminal_groups[3]
)
"""
----------------------------------------------------------
Create monolayer on surface, backfilled with hydrogen caps
----------------------------------------------------------
"""
# bottom monolayer is backfilled with the other terminal group
# num_chains = num_chains * a_fraction
monolayer_a = SurfaceMonolayer(
surface=surface_a,
chains=[chain_prototype_a, chain_prototype_b],
n_chains=num_chains,
seed=seed,
backfill=H(),
rotate=False,
fractions=[a_fraction, 1.0 - a_fraction],
)
monolayer_a.name = "Bottom"
monolayer_b = SurfaceMonolayer(
surface=surface_b,
chains=[chain_prototype_c, chain_prototype_d],
n_chains=num_chains,
seed=seed,
backfill=H(),
rotate=False,
fractions=[c_fraction, 1.0 - c_fraction],
)
monolayer_b.name = "Top"
"""
------------------------------------------
Duplicate to yield two opposing monolayers
------------------------------------------
"""
dual_monolayer = DualSurface(
bottom=monolayer_a, top=monolayer_b, separation=2.0
)
"""
--------------------------------------------------------
Make sure box is elongated in z to be pseudo-2D periodic
--------------------------------------------------------
"""
box = dual_monolayer.boundingbox
dual_monolayer.periodicity += np.array([0, 0, 5.0 * box.lengths[2]])
"""
-------------------------------------------------------------------
- Save to .GRO, .TOP, and .LAMMPS formats
- Atom-type the system using Foyer, with parameters from the OPLS
force field obtained from GROMACS. Parameters are located in a
Foyer XML file in the `atools` git repo, with references provided
as well as notes where parameters have been added or altered to
reflect the literature.
-------------------------------------------------------------------
"""
# path for project root dir
proj = signac.get_project()
forcefield_filepath = pathlib.Path(
proj.root_directory() + "/src/util/forcefield/oplsaa.xml"
)
# change into job directoryA
_switch_dir(job)
logging.info("at dir: {}".format(job.ws))
for p in dual_monolayer.particles():
if p.name == "OS":
p.name = "O"
dual_monolayer.save("init.gro", residues=["Top", "Bottom"], overwrite=True)
if not (
job.isfile("init.top")
and job.isfile("init.lammps")
and job.isfile("init.gro")
):
structure = dual_monolayer.to_parmed(
box=None, residues=["Top", "Bottom"]
)
ff = Forcefield(forcefield_files=forcefield_filepath.as_posix())
structure = ff.apply(structure)
structure.combining_rule = "geometric"
structure.save("init.top", overwrite=True)
write_lammpsdata(filename="init.lammps", structure=structure, detect_forcefield_style=False)
"""
--------------------------------------
Specify index groups and write to file
--------------------------------------
"""
index_groups = generate_index_groups(
system=dual_monolayer,
terminal_groups=terminal_groups,
freeze_thickness=0.5,
)
write_monolayer_ndx(rigid_groups=index_groups, filename="init.ndx")
def initialize_system(job):
""" Generate the monolayer surfaces, parametrize, save LAMMPS, GRO, TOP.
"""
'''
---------------------------
Read statepoint information
---------------------------
'''
chainlength = job.statepoint()['chainlength']
n_chains = job.statepoint()['n']
seed = job.statepoint()['seed']
terminal_groups = job.statepoint()['terminal_groups']
'''
-----------------------------------
Generate amorphous silica interface
-----------------------------------
'''
surface_a = SilicaInterface(thickness=1.2, seed=seed)
surface_b = SilicaInterface(thickness=1.2, seed=seed)
'''
------------------------------------------------------
Generate prototype of functionalized alkylsilane chain
------------------------------------------------------
'''
chain_prototype_a = Alkylsilane(chain_length=chainlength,
terminal_group=terminal_groups[0])
chain_prototype_b = Alkylsilane(chain_length=chainlength,
terminal_group=terminal_groups[1])
'''
----------------------------------------------------------
Create monolayer on surface, backfilled with hydrogen caps
----------------------------------------------------------
'''
monolayer_a = SurfaceMonolayer(surface=surface_a, chains=chain_prototype_a,
n_chains=n_chains, seed=seed,
backfill=H(), rotate=False)
monolayer_a.name = 'Bottom'
monolayer_b = SurfaceMonolayer(surface=surface_b, chains=chain_prototype_b,
n_chains=n_chains, seed=seed,
backfill=H(), rotate=False)
monolayer_b.name = 'Top'
'''
------------------------------------------
Duplicate to yield two opposing monolayers
------------------------------------------
'''
dual_monolayer = DualSurface(bottom=monolayer_a, top=monolayer_b,
separation=2.0)
'''
--------------------------------------------------------
Make sure box is elongated in z to be pseudo-2D periodic
--------------------------------------------------------
'''
box = dual_monolayer.boundingbox
dual_monolayer.periodicity += np.array([0, 0, 5. * box.lengths[2]])
'''
-------------------------------------------------------------------
- Save to .GRO, .TOP, and .LAMMPS formats
- Atom-type the system using Foyer, with parameters from the OPLS
force field obtained from GROMACS. Parameters are located in a
Foyer XML file in the `atools` git repo, with references provided
as well as notes where parameters have been added or altered to
reflect the literature.
-------------------------------------------------------------------
'''
# path for project root dir
proj = signac.get_project()
forcefield_filepath = pathlib.Path(
proj.root_directory() + "/src/util/forcefield/oplsaa.xml")
# change into job directoryA
_switch_dir(job)
logging.info("at dir: {}".format(job.ws))
dual_monolayer.save('init.gro', residues=['Top', 'Bottom'],
overwrite=True)
if not (job.isfile('init.top') and job.isfile('init.lammps') and
job.isfile('init.gro')):
structure = dual_monolayer.to_parmed(box=None,
residues=['Top', 'Bottom'])
ff = Forcefield(forcefield_files=forcefield_filepath.as_posix())
structure = ff.apply(structure)
structure.combining_rule = 'geometric'
structure.save('init.top', overwrite=True)
write_lammpsdata(filename='init.lammps', structure=structure)
'''
--------------------------------------
Specify index groups and write to file
--------------------------------------
'''
index_groups = generate_index_groups(system=dual_monolayer,
terminal_groups=terminal_groups,
freeze_thickness=0.5)
write_monolayer_ndx(rigid_groups=index_groups, filename='init.ndx')