Keyword Arguments¶
Nearly all options of MoSDeF Cassandra can be controlled through
the use of keyword arguments to the run
/restart
functions.
These arguments can be specified individually or provided to the
run
/restart
functions via a dictionary. The
dictionary-based approach is preferred if there are a large
number of keyword arguments to keep the number of explicit
arguments to the run
/restart
functions manageable.
Usage¶
Below is an example of providing the vdw_cutoff
option
to run
as an extra keyword argument.
mc.run(
system=system,
moveset=moveset,
run_type="equilibration",
run_length=1000,
temperature=300.0 * u.K,
vdw_cutoff=9.0 * u.angstroms
)
or as a dictionary, where the **
operator is used to
expand the dictionary.
custom_args = {
'vdw_cutoff': 9.0 * u.angstroms,
'charge_cutoff': 9.0 * u.angstroms,
}
mc.run(
system=system,
moveset=moveset,
run_type="equilibration",
run_length=1000,
temperature=300.0 * u.K,
**custom_args
)
Valid arguments¶
A list of the valid keyword arguments is provided below with a brief explanation. If more detail is required, please consult the Cassandra user manual. Most arguments below have nearly a one-to-one mapping with options of the Cassandra input file.
run_name
¶
str
"nvt"
, "npt"
, etc.)restart
¶
bool
True
, restart from a Cassandra .chk
fileFalse
restart_name
¶
str
run_name
for the simulation from which you wish to restartrestart=True
verbose_log
¶
bool
True
, print the Cassandra log file with additional verbosityFalse
vdw_style
¶
str
lj
or none
lj
cutoff_style
¶
str
cut_tail
, cut_switch
, cut_shift
cut_tail
vdw_cutoff
¶
unyt_quantity, dimensions=length
, except for cutoff_style="cut_switch"
, which
requires a list of, [inner_cutoff, outer_cutoff]
.12.0 * u.angstroms
vdw_cutoff_box1
and vdw_cutoff_box2
keywords. If provided, these will override the vdw_cutoff
.charge_style
¶
str
none
,
ewald
, or dsf
ewald
charge_cutoff
¶
unyt_quantity, dimensions=length
12.0 * u.angstroms
charge_cutoff_box1
and charge_cutoff_box2
keywords. If provided, these will override the charge_cutoff
. In GEMC simulations
where the vapor box is much larger than the liquid box, it may be necessary to increase
the charge cutoff of the vapor box to maintain the desired ewald_accuracy
without
exceeding the maximum number of k-space vectors.ewald_accuracy
¶
float
1.0e-5
charge_style="ewald"
dsf_damping
¶
float
dsf
charge styleNone
charge_style="dsf"
mixing_rule
¶
str
lb
(Lorentz-Berthelot), geometric
or custom
lb
custom_mixing_dict
¶
dict
opls_140
and opls_141
and the mixed epsilon and sigma are 10.0 * u.Unit('kJ/mol')
and 3.0 * u.angstrom
, then the dict
would be:{ 'opls_140 opls_141': [10.0 * u.Unit('kJ/mol'), 3.0 * u.angstrom] }
None
seeds
¶
list
of two ints
rcut_min
¶
unyt_quantity, dimensions = length
1.0 * u.angstrom
pair_energy
¶
bool
True
max_molecules
¶
list
of ints
, len=n_species
System
for nvt
, npt
,
gemc
, gemc_npt
, and non-insertable species in gcmc
. Number of
molecules in the System
plus 500 for insertable molecules in gcmc
.pressure
¶
unyt_quantity
, valid units of pressureNone
box1
and box2
can be specified
with the pressure_box1
and pressure_box2
. If specified, these values will override
the value in pressure
.chemical_potentials
¶
list
of unyt_array/unyt_quantity
with units of energy/mol
, or "none"
for species that are not insertablegcmc
)None
thermal_stat_freq
¶
int
run_type="equilibration"
),
updating the maximum translation and rotation sizes1000
equilibration
mode, the maximum translation and rotation move sizes
are continuously adjusted to target 50% of moves accepted.vol_stat_freq
¶
int
run_type="equilibration"
),
updating the maximum volume move size100
equilibration
mode, the maximum volume move size
is continuously adjusted to target 50% of moves accepted.units
¶
str
minutes
, steps
, or sweeps
steps
steps_per_sweep
¶
int
None
units="steps"
. A standard choice is one sweep is one attempted move per molecule in the system.prop_freq
¶
int
.prp
fileunits
argumentcoord_freq
¶
int
.xyz
fileunits
argumentblock_avg_freq
¶
int
None
units
argumentproperties
¶
list
of str
.prp
file. Valid options include: energy_total
, energy_intra
, energy_bond
, energy_angle
, energy_diheral
, energy_improper
, energy_intravdw
, energy_intraq
, energy_inter
, energy_intervdw
, energy_lrc
, energy_interq
, energy_recip
, energy_self
, enthalpy
, pressure
, pressure_xx
, pressure_yy
, pressure_zz
, volume
, nmols
, density
, mass_density
.["energy_total", "energy_intra", "energy_inter", "enthalpy", "pressure", "volume", "nmols", "mass_density"]