Molecular Dynamics

class quippy.dynamicalsystem.DynamicalSystem(name=dynamicalsystem)[source]

Bases: DynamicalSystem

Defined at DynamicalSystem.fpp lines 195-228

Attributes:

atoms: Element atoms ftype=type(atoms) pytype=Atoms
avg_temp: Element avg_temp ftype=real(dp) pytype=float
avg_time: Element avg_time ftype=real(dp) pytype=float
cur_temp: Element cur_temp ftype=real(dp) pytype=float
dt: Element dt ftype=real(dp) pytype=float
dw: Element dw ftype=real(dp) pytype=float
ekin: Element ekin ftype=real(dp) pytype=float
epot: Element epot ftype=real(dp) pytype=float
ext_energy: Element ext_energy ftype=real(dp) pytype=float
group_lookup: Element group_lookup ftype=integer pytype=int
initialised: Element initialised ftype=logical pytype=bool
n: Element n ftype=integer pytype=int
nconstraints: Element nconstraints ftype=integer pytype=int
ndof: Element ndof ftype=integer pytype=int
nrestraints: Element nrestraints ftype=integer pytype=int
nrigid: Element nrigid ftype=integer pytype=int
nsteps: Element nsteps ftype=integer pytype=int
print_thermostat_temps: Element print_thermostat_temps ftype=logical pytype=bool
random_seed: Element random_seed ftype=integer pytype=int
t: Element t ftype=real(dp) pytype=float
thermostat_dw: Element thermostat_dw ftype=real(dp) pytype=float
thermostat_work: Element thermostat_work ftype=real(dp) pytype=float
wkin: Element wkin ftype=real(dp) pytype=float
work: Element work ftype=real(dp) pytype=float

Methods

`add_atoms`(args, *kwargs)	Defined at DynamicalSystem.fpp lines 235-236
`advance_verlet`(self, dt, f[, virial, e, ...)	Defined at DynamicalSystem.fpp lines 1867-1887
`advance_verlet1`(self, dt[, virial, parallel, ...)	Defined at DynamicalSystem.fpp lines 1547-1714
`advance_verlet2`(self, dt, f[, virial, e, ...)	Defined at DynamicalSystem.fpp lines 1740-1857
`constrain_atom_plane`(self, i, plane_n[, d, ...)	Defined at DynamicalSystem.fpp lines 2225-2248
`constrain_bondanglecos`(self, i, j, k[, c, ...)	Defined at DynamicalSystem.fpp lines 2005-2038
`constrain_bondlength`(self, i, j, d[, di, t0, ...)	Defined at DynamicalSystem.fpp lines 2041-2082
`constrain_bondlength_dev_pow`(self, i, j, p, ...)	Defined at DynamicalSystem.fpp lines 2114-2155
`constrain_bondlength_diff`(self, i, j, k, d[, ...)	Defined at DynamicalSystem.fpp lines 2161-2195
`constrain_bondlength_sq`(self, i, j[, d, ...)	Defined at DynamicalSystem.fpp lines 2085-2111
`constrain_gap_energy`(self, d[, restraint_k, ...)	Defined at DynamicalSystem.fpp lines 2201-2222
`constrain_struct_factor_like_i`(self, z, q, ...)	Defined at DynamicalSystem.fpp lines 2347-2392
`constrain_struct_factor_like_mag`(self, z, q, ...)	Defined at DynamicalSystem.fpp lines 2251-2296
`constrain_struct_factor_like_r`(self, z, q, ...)	Defined at DynamicalSystem.fpp lines 2299-2344
`disable_damping`(self)	Defined at DynamicalSystem.fpp lines 994-996
`ds_add_constraint`(self, atoms, func, data[, ...)	Defined at DynamicalSystem.fpp lines 2396-2468
`ds_add_thermostat`(self, type_bn, t[, gamma, ...)	Defined at DynamicalSystem.fpp lines 842-889
`ds_add_thermostats`(self, type_bn, n[, t, ...)	Defined at DynamicalSystem.fpp lines 896-942
`ds_amend_constraint`(self, constraint, func, ...)	Defined at DynamicalSystem.fpp lines 2474-2479
`ds_angular_momentum`(self[, origin, indices])	Defined at DynamicalSystem.fpp lines 1041-1046
`ds_kinetic_energy`(self[, local_ke, error])	Defined at DynamicalSystem.fpp lines 1135-1143
`ds_kinetic_virial`(self[, error])	Defined at DynamicalSystem.fpp lines 1194-1201
`ds_momentum`(self[, indices])	Defined at DynamicalSystem.fpp lines 1005-1009
`ds_print`(self[, file])	Defined at DynamicalSystem.fpp lines 1970-1994
`ds_print_status`(self[, label, epot, ...)	Defined at DynamicalSystem.fpp lines 1899-1963
`ds_print_thermostats`(self)	Defined at DynamicalSystem.fpp lines 1965-1967
`ds_remove_thermostat`(self, index_bn)	Defined at DynamicalSystem.fpp lines 837-840
`ds_restore_state`(self, from_)	Defined at DynamicalSystem.fpp lines 604-625
`ds_save_state`(self, from_[, error])	Defined at DynamicalSystem.fpp lines 564-596
`ds_set_barostat`(self, type_bn, p_ext, ...)	Defined at DynamicalSystem.fpp lines 814-830
`ds_update_thermostat`(self[, t, p, i])	Defined at DynamicalSystem.fpp lines 949-957
`enable_damping`(self, damp_time)	Defined at DynamicalSystem.fpp lines 988-992
`get_damping_time`(self)	Defined at DynamicalSystem.fpp lines 979-984
`is_damping_enabled`(self)	Defined at DynamicalSystem.fpp lines 970-977
`n_thermostat`(self)	Defined at DynamicalSystem.fpp lines 832-835
`remove_atoms`(args, *kwargs)	Defined at DynamicalSystem.fpp lines 240-241
`rescale_velo`(self, temp[, mass_weighted, zero_l])	Defined at DynamicalSystem.fpp lines 1342-1370
`temperature`(self[, property, value, ...)	Defined at DynamicalSystem.fpp lines 1270-1324
`thermostat_temperatures`(self, temps)	Defined at DynamicalSystem.fpp lines 1246-1258
`zero_momentum`(self[, indices])	Defined at DynamicalSystem.fpp lines 1422-1434

add_atoms(*args, **kwargs)[source]

Defined at DynamicalSystem.fpp lines 235-236

Overloaded interface containing the following procedures:: _ds_add_atom_single _ds_add_atom_multiple

Add one or more atoms to this DynamicalSystem. Equivalent to ‘Atoms%add_atoms’, but also appends the number of degrees of freedom correctly.

advance_verlet(self, dt, f[, virial, e, parallel, store_constraint_force, do_calc_dists, error])[source]

Defined at DynamicalSystem.fpp lines 1867-1887

Parameters:

dsDynamicalsystem
dtfloat
ffloat array
virialfloat array
efloat
parallelbool
store_constraint_forcebool
do_calc_distsbool
errorint
Calls’ advance_verlet2’ followed by ‘advance_verlet1’. Outside this routine the
velocities will be half-stepped. This allows a simpler MD loop:
> for n in range(n_steps):
> pot.calc(ds.atoms, force=True, energy=True)
> ds.advance_verlet(dt, ds.atoms.force)
> ds.print_status(epot=ds.atoms.energy)
> if n % connect_interval == 0:
> ds.atoms.calc_connect()

advance_verlet1(self, dt[, virial, parallel, store_constraint_force, do_calc_dists, error])[source]

Defined at DynamicalSystem.fpp lines 1547-1714

Parameters:

thisDynamicalsystem
dtfloat
virialfloat array
parallelbool
store_constraint_forcebool
do_calc_distsbool
errorint
Advance the velocities by half the time-step ‘dt’ and the
positions by a full time-step. A typical MD loop should
resemble the following code(Python example, Fortran is similar):
> ds.atoms.calc_connect()
> for n in range(n_steps):
> ds.advance_verlet1(dt)
> pot.calc(ds.atoms, force=True, energy=True)
> ds.advance_verlet2(dt, ds.atoms.force)
> ds.print_status(epot=ds.atoms.energy)
> if n % connect_interval == 0:
> ds.atoms.calc_connect()

advance_verlet2(self, dt, f[, virial, e, parallel, store_constraint_force, error])[source]

Defined at DynamicalSystem.fpp lines 1740-1857

Parameters:

thisDynamicalsystem
dtfloat
ffloat array
virialfloat array
efloat
parallelbool
store_constraint_forcebool
errorint
Advances the velocities by the second half time-step

constrain_atom_plane(self, i, plane_n[, d, restraint_k, bound, tol, print_summary])[source]

Defined at DynamicalSystem.fpp lines 2225-2248

Parameters:

thisDynamicalsystem
iint
plane_nfloat array
dfloat
restraint_kfloat
boundint
tolfloat
print_summarybool
Constrain an atom to lie in a particluar plane

constrain_bondanglecos(self, i, j, k[, c, restraint_k, bound, tol, print_summary])[source]

Defined at DynamicalSystem.fpp lines 2005-2038

Parameters:

thisDynamicalsystem
iint
jint
kint
cfloat
restraint_kfloat
boundint
tolfloat
print_summarybool
Constrain the bond angle cosine between atoms i, j, and k

constrain_bondlength(self, i, j, d[, di, t0, tau, restraint_k, bound, tol, print_summary])[source]

Defined at DynamicalSystem.fpp lines 2041-2082

Parameters:

thisDynamicalsystem
iint
jint
dfloat
difloat
t0float
taufloat
restraint_kfloat
boundint
tolfloat
print_summarybool
Constrain the bond between atoms i and j

constrain_bondlength_dev_pow(self, i, j, p, d[, di, t0, tau, restraint_k, bound, tol, print_summary])[source]

Defined at DynamicalSystem.fpp lines 2114-2155

Parameters:

thisDynamicalsystem
iint
jint
pfloat
dfloat
difloat
t0float
taufloat
restraint_kfloat
boundint
tolfloat
print_summarybool
Constrain the bond between atoms i and j

constrain_bondlength_diff(self, i, j, k, d[, di, t0, tau, restraint_k, bound, tol, print_summary])[source]

Defined at DynamicalSystem.fpp lines 2161-2195

Parameters:

thisDynamicalsystem
iint
jint
kint
dfloat
difloat
t0float
taufloat
restraint_kfloat
boundint
tolfloat
print_summarybool
Constrain the difference of bond length between atoms i–j and j–k

constrain_bondlength_sq(self, i, j[, d, restraint_k, bound, tol, print_summary])[source]

Defined at DynamicalSystem.fpp lines 2085-2111

Parameters:

thisDynamicalsystem
iint
jint
dfloat
restraint_kfloat
boundint
tolfloat
print_summarybool
Constrain the bond between atoms i and j

constrain_gap_energy(self, d[, restraint_k, bound, tol, print_summary])[source]

Defined at DynamicalSystem.fpp lines 2201-2222

Parameters:

thisDynamicalsystem
dfloat
restraint_kfloat
boundint
tolfloat
print_summarybool
Constrain the energy gap of two resonance structures

constrain_struct_factor_like_i(self, z, q, sf[, restraint_k, bound, tol, print_summary])[source]

Defined at DynamicalSystem.fpp lines 2347-2392

Parameters:

thisDynamicalsystem
zint
qfloat array
sffloat
restraint_kfloat
boundint
tolfloat
print_summarybool
Constrain an atom to lie in a particluar plane

constrain_struct_factor_like_mag(self, z, q, sf[, restraint_k, bound, tol, print_summary])[source]

Defined at DynamicalSystem.fpp lines 2251-2296

Parameters:

thisDynamicalsystem
zint
qfloat array
sffloat
restraint_kfloat
boundint
tolfloat
print_summarybool
Constrain an atom to lie in a particluar plane

constrain_struct_factor_like_r(self, z, q, sf[, restraint_k, bound, tol, print_summary])[source]

Defined at DynamicalSystem.fpp lines 2299-2344

Parameters:

thisDynamicalsystem
zint
qfloat array
sffloat
restraint_kfloat
boundint
tolfloat
print_summarybool
Constrain an atom to lie in a particluar plane

disable_damping(self)[source]

Defined at DynamicalSystem.fpp lines 994-996

Parameters:

thisDynamicalsystem

ds_add_constraint(self, atoms, func, data[, update_ndof, restraint_k, bound, tol, print_summary])[source]

Defined at DynamicalSystem.fpp lines 2396-2468

Parameters:

thisDynamicalsystem
atomsint array
funcint
datafloat array
update_ndofbool
restraint_kfloat
boundint
tolfloat
print_summarybool
Add a constraint to the DynamicalSystem and reduce the number of degrees of freedom,
unless ‘update_Ndof’ is present and false.

ds_add_thermostat(self, type_bn, t[, gamma, q, tau, tau_cell, p, bulk_modulus_estimate, cell_oscillation_time, nhl_tau, nhl_mu, massive, region_i])[source]

Defined at DynamicalSystem.fpp lines 842-889

Parameters:

thisDynamicalsystem
type_bnint
tfloat
gammafloat
qfloat
taufloat
tau_cellfloat
pfloat
bulk_modulus_estimatefloat
cell_oscillation_timefloat
nhl_taufloat
nhl_mufloat
massivebool
region_iint
Add a new thermostat to this DynamicalSystem. ‘type’ should
be one of the following thermostat types:
* ‘THERMOSTAT_NONE’
* ‘THERMOSTAT_LANGEVIN’
* ‘THERMOSTAT_NOSE_HOOVER’
* ‘THERMOSTAT_NOSE_HOOVER_LANGEVIN’
* ‘THERMOSTAT_LANGEVIN_NPT’
* ‘THERMOSTAT_LANGEVIN_PR’
* ‘THERMOSTAT_NPH_ANDERSEN’
* ‘THERMOSTAT_NPH_PR’
* ‘THERMOSTAT_LANGEVIN_OU’
* ‘THERMOSTAT_LANGEVIN_NPT_NB’
‘T’ is the target temperature. ‘Q’ is the Nose-Hoover coupling constant. Only one
of ‘tau’ or ‘gamma’ should be given. ‘p’ is the external
pressure for the case of Langevin NPT.

ds_add_thermostats(self, type_bn, n[, t, t_a, gamma, gamma_a, q, q_a, tau, tau_a, region_i])[source]

Defined at DynamicalSystem.fpp lines 896-942

Parameters:

thisDynamicalsystem
type_bnint
nint
tfloat
t_afloat array
gammafloat
gamma_afloat array
qfloat
q_afloat array
taufloat
tau_afloat array
region_iint

ds_amend_constraint(self, constraint, func, data[, k])[source]

Defined at DynamicalSystem.fpp lines 2474-2479

Parameters:

thisDynamicalsystem
constraintint
funcint
datafloat array
kfloat
Replace a constraint involving some atoms with a different constraint involving
the same atoms

ds_angular_momentum(self[, origin, indices])[source]

Defined at DynamicalSystem.fpp lines 1041-1046

Parameters:

thisDynamicalsystem
originfloat array
indicesint array

Returns:

lfloat array
Return the angular momentum of all the atoms in this DynamicalSystem, defined by
$mathbf{L} = sum_{i} mathbf{r_i} imes mathbf{v_i}$.

ds_kinetic_energy(self[, local_ke, error])[source]

Defined at DynamicalSystem.fpp lines 1135-1143

Parameters:

thisDynamicalsystem
local_kebool
errorint

Returns:

kefloat: Return the total kinetic energy $E_k = sum_{i}
rac{1}{2} m v^2$

ds_kinetic_virial(self[, error])[source]

Defined at DynamicalSystem.fpp lines 1194-1201

Parameters:

thisDynamicalsystem
errorint

Returns:

kvfloat array: Return the total kinetic virial $w_ij = sum_{k}
rac{1}{2} m v_i v_j$

ds_momentum(self[, indices])[source]

Defined at DynamicalSystem.fpp lines 1005-1009

Parameters:

thisDynamicalsystem
indicesint array

Returns:

pfloat array
Return the total momentum $mathbf{p} = sum_i mathbf{m_i} mathbf{v_i}$.
Optionally only include the contribution of a subset of atoms.

ds_print(self[, file])[source]

Defined at DynamicalSystem.fpp lines 1970-1994

Parameters:

thisDynamicalsystem
fileInoutput
Print lots of information about this DynamicalSystem in text format.

ds_print_status(self[, label, epot, instantaneous, file, error])[source]

Defined at DynamicalSystem.fpp lines 1899-1963

Parameters:

thisDynamicalsystem
labelstr
epotfloat
instantaneousbool
fileInoutput
errorint
Print a status line showing the current time, temperature, the mean temperature
the total energy and the total momentum for this DynamicalSystem. If present, the optional
‘label’ parameter should be a one character label for the log lines and is printed
in the first column of the output. ‘epot’ should be the potential energy
if this is available. ‘instantaneous’ has the same meaning as in ‘temperature’ routine.

ds_print_thermostats(self)[source]

Defined at DynamicalSystem.fpp lines 1965-1967

Parameters:

thisDynamicalsystem

ds_remove_thermostat(self, index_bn)[source]

Defined at DynamicalSystem.fpp lines 837-840

Parameters:

thisDynamicalsystem
index_bnint

ds_restore_state(self, from_)[source]

Defined at DynamicalSystem.fpp lines 604-625

Parameters:

toDynamicalsystem
from_Dynamicalsystem
Restore a DynamicalSystem to a previously saved state.
Only scalar members and ‘ds%atoms’ (minus ‘ds%atoms%connect’)
are copied back; ‘to’ should be a properly initialised
DynamicalSystem object. The saved state of the random
number generator is also restored. ‘calc_dists()’ is
called on the restored atoms object.

ds_save_state(self, from_[, error])[source]

Defined at DynamicalSystem.fpp lines 564-596

Parameters:

toDynamicalsystem
from_Dynamicalsystem
errorint
Save the state of a DynamicalSystem. The output object
cannot be used as an initialised DynamicalSystem since
connectivity and group information is not copied to save
memory. Only scalar members and the ‘ds%atoms’ object
(minus ‘ds%atoms%connect’) are copied. The current
state of the random number generator is also saved.

ds_set_barostat(self, type_bn, p_ext, hydrostatic_strain, diagonal_strain, finite_strain_formulation, tau_epsilon[, w_epsilon, t, w_epsilon_factor, thermalise])[source]

Defined at DynamicalSystem.fpp lines 814-830

Parameters:

thisDynamicalsystem
type_bnint
p_extfloat
hydrostatic_strainbool
diagonal_strainbool
finite_strain_formulationbool
tau_epsilonfloat
w_epsilonfloat
tfloat
w_epsilon_factorfloat
thermalisebool

ds_update_thermostat(self[, t, p, i])[source]

Defined at DynamicalSystem.fpp lines 949-957

Parameters:

thisDynamicalsystem
tfloat
pfloat
iint

enable_damping(self, damp_time)[source]

Defined at DynamicalSystem.fpp lines 988-992

Parameters:

thisDynamicalsystem
damp_timefloat
Enable damping, with damping time set to `damp_time`. Only atoms
flagged in the `damp_mask` property will be affected.

get_damping_time(self)[source]

Defined at DynamicalSystem.fpp lines 979-984

Parameters:

thisDynamicalsystem

Returns:

get_damping_timefloat

is_damping_enabled(self)[source]

Defined at DynamicalSystem.fpp lines 970-977

Parameters:

thisDynamicalsystem

Returns:

is_damping_enabledbool

n_thermostat(self)[source]

Defined at DynamicalSystem.fpp lines 832-835

Parameters:

thisDynamicalsystem

Returns:

n_thermostatint

remove_atoms(*args, **kwargs)[source]

Defined at DynamicalSystem.fpp lines 240-241

Overloaded interface containing the following procedures:: _ds_remove_atom_single _ds_remove_atom_multiple

Remove one or more atoms from this DynamicalSystem. Equivalent of ‘Atoms%remove_atoms’, but also amends the number of degrees of freedom correctly.

rescale_velo(self, temp[, mass_weighted, zero_l])[source]

Defined at DynamicalSystem.fpp lines 1342-1370

Parameters:

thisDynamicalsystem
tempfloat
mass_weightedbool
zero_lbool
Rescale the atomic velocities to temperature ‘temp’. If the
current temperature is zero, we first randomise the velocites.
If ‘mass_weighted’ is true, then the velocites are weighted by
$1/sqrt{m}$. Linear momentum is zeroed automatically. If
‘zero_l’ is true then the angular momentum is also zeroed.

temperature(self[, property, value, include_all, instantaneous, error])[source]

Defined at DynamicalSystem.fpp lines 1270-1324

Parameters:

thisDynamicalsystem
propertystr
valueint
include_allbool
instantaneousbool
errorint

Returns:

temperaturefloat: Return the temperature, assuming each degree of freedom contributes $
rac{1}{2}kT$. By default only moving and thermostatted atoms are: included — this can be overriden by setting ‘include_all’ to true. ‘region’ can be used to restrict the calculation to a particular thermostat region. ‘instantaneous’ controls whether the calculation should be carried out using the current values of the velocities and masses, or whether to return the value at the last Verlet step (the latter is the default).

thermostat_temperatures(self, temps)[source]

Defined at DynamicalSystem.fpp lines 1246-1258

Parameters:

thisDynamicalsystem
tempsfloat array

zero_momentum(self[, indices])[source]

Defined at DynamicalSystem.fpp lines 1422-1434

Parameters:

thisDynamicalsystem
indicesint array
Change velocities to those that the system would have in the zero momentum frame.
Optionalally zero the total momentum of a subset of atoms, specified by ‘indices’.

property atoms

Element atoms ftype=type(atoms) pytype=Atoms

Defined at DynamicalSystem.fpp line 221

property avg_temp

Element avg_temp ftype=real(dp) pytype=float

Defined at DynamicalSystem.fpp line 205

Time-averaged temperature

property avg_time

Element avg_time ftype=real(dp) pytype=float

Defined at DynamicalSystem.fpp line 207

Averaging time, in fs

property cur_temp

Element cur_temp ftype=real(dp) pytype=float

Defined at DynamicalSystem.fpp line 206

Current temperature

property dt

Element dt ftype=real(dp) pytype=float

Defined at DynamicalSystem.fpp line 204

Last time step

property dw

Element dw ftype=real(dp) pytype=float

Defined at DynamicalSystem.fpp line 208

Increment of work done this time step

property ekin

Element ekin ftype=real(dp) pytype=float

Defined at DynamicalSystem.fpp line 211

Current kinetic energy

property epot

Element epot ftype=real(dp) pytype=float

Defined at DynamicalSystem.fpp line 210

Total potential energy

property ext_energy

Element ext_energy ftype=real(dp) pytype=float

Defined at DynamicalSystem.fpp line 213

Extended energy

property group_lookup

Element group_lookup ftype=integer pytype=int

Defined at DynamicalSystem.fpp line 219

Stores which group atom $i$ is in

property initialised

Element initialised ftype=logical pytype=bool

Defined at DynamicalSystem.fpp line 216

property n

Element n ftype=integer pytype=int

Defined at DynamicalSystem.fpp line 197

Number of atoms

property nconstraints

Element nconstraints ftype=integer pytype=int

Defined at DynamicalSystem.fpp line 200

Number of constraints

property ndof

Element ndof ftype=integer pytype=int

Defined at DynamicalSystem.fpp line 202

Number of degrees of freedom

property nrestraints

Element nrestraints ftype=integer pytype=int

Defined at DynamicalSystem.fpp line 201

Number of restraints

property nrigid

Element nrigid ftype=integer pytype=int

Defined at DynamicalSystem.fpp line 199

Number of rigid bodies

property nsteps

Element nsteps ftype=integer pytype=int

Defined at DynamicalSystem.fpp line 198

Number of integration steps

property print_thermostat_temps

Element print_thermostat_temps ftype=logical pytype=bool

Defined at DynamicalSystem.fpp line 228

property random_seed

Element random_seed ftype=integer pytype=int

Defined at DynamicalSystem.fpp line 217

RNG seed, used by ‘ds_save_state’ and ‘ds_restore_state’ only.

property t

Element t ftype=real(dp) pytype=float

Defined at DynamicalSystem.fpp line 203

Time

property thermostat_dw

Element thermostat_dw ftype=real(dp) pytype=float

Defined at DynamicalSystem.fpp line 214

Increment of work done by thermostat

property thermostat_work

Element thermostat_work ftype=real(dp) pytype=float

Defined at DynamicalSystem.fpp line 215

Total work done by thermostat

property wkin

Element wkin ftype=real(dp) pytype=float

Defined at DynamicalSystem.fpp line 212

Current kinetic contribution to the virial

property work

Element work ftype=real(dp) pytype=float

Defined at DynamicalSystem.fpp line 209

Total work done

class quippy.dynamicalsystem.Dynamics(atoms, timestep, trajectory, trajectoryinterval=10, initialtemperature=None, logfile='-', loginterval=1, loglabel='D')[source]

Bases: Dynamics

Wrapper around DynamicalSystem integrator compatible with ASE ase.md.MolecularDynamics interface.

Note

This class uses ASE units for time (and hence velocities and momenta) which differ from the femtoseconds used in QUIP. When using this class, all times should be given in ASE time units.

Parameters:

atoms – quippy or ASE Atoms instance. Note that if atoms is not a quippy Atoms object, a copy will be made.
timestep – in ASE time units (multiply by ase.units.fs to convert from femtoseconds)
trajectory – output file to which to write the trajectory. Can be a string to create a new output object.
trajectoryinterval – interval at which to write frames
initialtemperature – if not None, rescale initial velocities to a specified temperature, given in K.
logfile – filename or open InOutput object to write log lines to. Use special filename "-" for stdout (default).
loginterval – interval at which to write log lines

Attributes:

average_temperature: Average temperature
averaging_time: Averaging time used for average temperature and kinetic energy
damping: Get or set the damping time constant in fs.
number_of_constraints: Get number of constraints
number_of_degrees_of_freedom: Get number of degrees of freedom in system, including QUIP constraints
number_of_restraints: Get number of restraints
number_of_rigid_bodies: Get number of rigid_bodies
state: Save or restore current state of this dynamical system
temperature: Get or set the current temperature
time: Time in ASE units (Note: NOT the same as femtoseconds)
timestep: Set timestep, in ASE time units

Methods

`add_thermostat`(type, T[, gamma, Q, tau, ...])	Add a new thermostat to this Dynamics, and return its index.
`attach`(function[, interval])	Attach callback function.
`converged`()	MD is 'converged' when number of maximum steps is reached.
`get_number_of_thermostats`()	Return the number of active thermostats
`get_thermostat_temperatures`()	Return the current temperatures of all thermostated regions
`insert_observer`(function[, position, interval])	Insert an observer.
`irun`()	Run dynamics algorithm as generator.
`log`(*args)	a dummy function as placeholder for a real logger, e.g.
`print_thermostats`()	Print a table of the current thermostats in this system
`remove_thermostat`(index)	Remove thermostat number index.
`run`([steps])	Run dynamics forwards for steps steps.
`set_barostat`(type, p_ext, ...[, W_epsilon, ...])	Add a barostat to this dynamical system
`set_temperature`(temperature)	Randomise velocities to a target temperature (given in K)
`step`(forces)	Advance dynamics by one time-step.
`update_barostat`(p, T)	Update target pressure p or temperature T for NPT barostat
`update_thermostat`([T, p, index])	Change the target temperature T or presure p for thermostat index.

add_thermostat(type, T, gamma=None, Q=None, tau=None, tau_cell=None, p=None, NHL_tau=None, NHL_mu=None, massive=None)[source]

Add a new thermostat to this Dynamics, and return its index.

By default, all thermostats apply to the whole system. The ‘thermostat_region’ property can be used to control which thermostats affect which atoms. It should be set to the index of the required thermostat for each atom.

Parameters:

type – string or integer giving thermostat type. The following types are supported:: THERMOSTAT_NONE, THERMOSTAT_LANGEVIN, THERMOSTAT_NOSE_HOOVER, THERMOSTAT_NOSE_HOOVER_LANGEVIN, THERMOSTAT_LANGEVIN_NPT, THERMOSTAT_LANGEVIN_PR, THERMOSTAT_NPH_ANDERSEN, THERMOSTAT_NPH_PR, THERMOSTAT_LANGEVIN_OU, THERMOSTAT_LANGEVIN_NPT_NB, THERMOSTAT_ALL_PURPOSE.
T – target temperature for this thermostat, in K.
gamma – decay constant, in units of 1/fs
tau – time constant, in units of fs. tau == 1/gamma, and only one of the two should be specified.
tau_cell – time constant for the cell degrees of freedom (for variable cell thermostats only).
p – target pressure (for variable cell thermostats)
NHL_tau – time constant for Nose-Hoover-Langevein thermostats
NHL_mu – thermostat mass Nose-Hoover-Langevin thermostats
massive – set to True to enable massive Nose-Hoover-Langevin

attach(function, interval=1, *args, **kwargs)[source]

Attach callback function.

At every interval steps, call function with arguments args and keyword arguments kwargs.

converged()[source]: MD is ‘converged’ when number of maximum steps is reached.

get_number_of_thermostats()[source]

Return the number of active thermostats

Excludes thermostat with index zero, which is used for damping.

get_thermostat_temperatures()[source]: Return the current temperatures of all thermostated regions

insert_observer(function, position=0, interval=1, *args, **kwargs)[source]: Insert an observer.

irun()[source]

Run dynamics algorithm as generator. This allows, e.g., to easily run two optimizers or MD thermostats at the same time.

Examples: >>> opt1 = BFGS(atoms) >>> opt2 = BFGS(StrainFilter(atoms)).irun() >>> for _ in opt2: >>> opt1.run()

log(*args)[source]: a dummy function as placeholder for a real logger, e.g. in Optimizer

print_thermostats()[source]: Print a table of the current thermostats in this system

remove_thermostat(index)[source]

Remove thermostat number index.

index should be in range 1 <= index <= dyn.get_number_of_thermostats()

run(steps=50)[source]: Run dynamics forwards for steps steps.

set_barostat(type, p_ext, hydrostatic_strain, diagonal_strain, finite_strain_formulation, tau_epsilon, W_epsilon=None, T=None, W_epsilon_factor=None)[source]

Add a barostat to this dynamical system

Langevin NPT barostat based on fluctuation/dissipation, as originally implemented for hydrostatic strain using EOM from Quigley, D. and Probert, M.I.J., J. Chem. Phys. 120 11432, subsequently rediscretized by Noam Bernstein based on ideas from and discussion with B. Leimkuhler.

Modified for arbitrary strain based on (but not exactly using) formulation in E. Tadmor and R. Miller Modeling Materials: Continuum, Atomistic and Multiscale Techniques (Cambridge University Press, 2011). Chap 9.5. Their definition of stress (factors of F, F^T, J, and F^-T) for finite strain is optionally used, but certain terms in EOM are excluded, and their discretization is entirely ignored.

Parameters:

type – The type of barostat to be used. Currently only BAROSTAT_HOOVER_LANGEVIN is supported.
p_ext – External pressure in QUIP units eV/A^3
hystrostatic_strain – Set to True to constrain a hydrostatic strain tensor
diagonal_strain – Set to True to constrain a diagonal strain tensor
finite_strain_formulation – If True, use finite instead of infinitessimal strain formulation
tau_epsilon – time constant for Langevin part (in fs)
W_epsilon – fictious cell mass used in Langevin NPT
T – target temperature for Langevin part
W_epsilon_factor – Scaling factor for fictious cell mass

set_temperature(temperature)[source]: Randomise velocities to a target temperature (given in K)

step(forces)[source]

Advance dynamics by one time-step.

Returns forces at the end of the time-step, suitable for passing to next step()

update_barostat(p, T)[source]: Update target pressure p or temperature T for NPT barostat

update_thermostat(T=None, p=None, index=1)[source]: Change the target temperature T or presure p for thermostat index.

property average_temperature: Average temperature

property averaging_time: Averaging time used for average temperature and kinetic energy

property damping: Get or set the damping time constant in fs. Set to None to disable damping. By default damping applies to all atoms, but can be selectively enabled with the ‘damp_mask’ property.

property number_of_constraints: Get number of constraints

property number_of_degrees_of_freedom: Get number of degrees of freedom in system, including QUIP constraints

property number_of_restraints: Get number of restraints

property number_of_rigid_bodies: Get number of rigid_bodies

property state: Save or restore current state of this dynamical system

property temperature: Get or set the current temperature

property time: Time in ASE units (Note: NOT the same as femtoseconds)

property timestep: Set timestep, in ASE time units