matscipy.pressurecoupling

Classes to be used with ASE in order to perform pressure relaxation and/or sliding simulations under pressure.

A usage example can be found in docs/applications/tribology.ipynb.

Some parts are based on L. Pastewka, S. Moser, and M. Moseler, Tribol. Lett. 39, 49 (2010) as indicated again below.

Classes

`AutoDamping`(C11[, p_c])	Automatic damping.
`FixedDamping`(gamma[, M_factor])	Damping with fixed damping constant and fixed mass.
`FixedMassCriticalDamping`(C11[, M_factor])	Damping with fixed mass and critical damping constant.
`SlideLog`(handle)	Reader for logs written with SlideLogger instance.
`SlideLogger`(handle, atoms, slider, integrator)	Logger to be attached to an ASE integrator.
`SlideWithNormalPressureCuboidCell`(top_mask, ...)	ASE constraint used for sliding with pressure coupling.

class matscipy.pressurecoupling.AutoDamping(C11, p_c=0.01)

Bases: object

Automatic damping.

Following L. Pastewka, S. Moser, and M. Moseler, Tribol. Lett. 39, 49 (2010).

Parameters:

C11 (float) – Elastic material constant.
p_c (float) – Empirical cut-off parameter.

Methods

get_M_gamma(slider, atoms)

Calculate mass M and dissipation constant gamma.

__init__(C11, p_c=0.01)

get_M_gamma(slider, atoms)

Calculate mass M and dissipation constant gamma.

Parameters:

slider (matscipy.pressurecoupling.SlideWithNormalPressureCuboidCell) – ASE constraint used for sliding with pressure coupling.
atoms (ase.Atoms) – Atomic configuration.

Returns:

M (float) – Mass parameter.
gamma (float) – Dissipation constant parameter.

class matscipy.pressurecoupling.FixedDamping(gamma, M_factor=1.0)

Bases: object

Damping with fixed damping constant and fixed mass.

Parameters:

gamma (float) – Damping constant.
M_factor (float) – Multiplicative factor to increase actual mass of upper rigid atoms.

Methods

get_M_gamma(slider, atoms)

Calculate mass M and damping constant gamma.

__init__(gamma, M_factor=1.0)

get_M_gamma(slider, atoms)

Calculate mass M and damping constant gamma.

Parameters:

slider (matscipy.pressurecoupling.SlideWithNormalPressureCuboidCell) – ASE constraint used for sliding with pressure coupling.
atoms (ase.Atoms) – Atomic configuration.

Returns:

M (float) – Mass parameter.
gamma (float) – Damping parameter.

class matscipy.pressurecoupling.FixedMassCriticalDamping(C11, M_factor=1.0)

Bases: object

Damping with fixed mass and critical damping constant.

Useful for fast pressure equilibration with small lid mass.

Parameters:

C11 (float) – Elastic material constant.
M_factor (float) – Multiplicative factor to increase actual mass of upper rigid atoms.

Methods

get_M_gamma(slider, atoms)

Calculate mass M and damping constant gamma.

__init__(C11, M_factor=1.0)

get_M_gamma(slider, atoms)

Calculate mass M and damping constant gamma.

Parameters:

slider (matscipy.pressurecoupling.SlideWithNormalPressureCuboidCell) – ASE constraint used for sliding with pressure coupling.
atoms (ase.Atoms) – Atomic configuration.

Returns:

M (float) – Mass parameter.
gamma (float) – Damping parameter.

class matscipy.pressurecoupling.SlideWithNormalPressureCuboidCell(top_mask, bottom_mask, Pdir, P, vdir, v, damping)

Bases: object

ASE constraint used for sliding with pressure coupling.

Following L. Pastewka, S. Moser, and M. Moseler, Tribol. Lett. 39, 49 (2010).

Parameters:

top_mask (boolean numpy array) – Array a with a[i] == True for each index i of the constraint top atoms (the atoms which slide with constant speed).
bottom_mask (boolean numpy array) – same as top_mask but for completely fixed bottom atoms.
Pdir (int) – Index of cell axis (0, 1, 2) along which normal pressure is applied.
P (int) – Normal pressure in ASE units (e.g. 10.0 * ase.units.GPa).
vdir (int) – Index of cell axis (0, 1, 2) along which to slide.
v (float) – Constant sliding speed in ASE units (e.g. 100.0 * ase.units.m / ase.units.s).
damping – Damping object (e.g. matscipy.pressurecoupling.AutoDamping instance).

Attributes:

Tdir: Direction used for thermostatting.
middle_mask: Mask of free atoms.

Methods

`adjust_forces`(atoms, forces)	Adjust forces of upper and lower rigid atoms.
`adjust_momenta`(atoms, momenta)	Adjust momenta of upper and lower rigid atoms.
`adjust_positions`(atoms, positions)	Do not adjust positions.
`adjust_potential_energy`(atoms)	Do not adjust energy.
`get_A`(atoms)	Calculate cell area normal to applied load.

__init__(top_mask, bottom_mask, Pdir, P, vdir, v, damping)

property Tdir

Direction used for thermostatting.

Thermostat direction is normal to the sliding direction and the direction of the applied load direction.

Returns:: Direction used for thermostatting.
Return type:: int

property middle_mask

Mask of free atoms.

Returns:: Array a with a[i] == True for each index i of the atoms not being part of lower or upper rigid group.
Return type:: numpy boolean array

adjust_positions(atoms, positions): Do not adjust positions.

get_A(atoms)

Calculate cell area normal to applied load.

Returns:: Cell area normal to applied load.
Return type:: float
Raises:: NotImplementedError – If atoms.get_cell() is non-orthogonal, SlideWithNormalPressureCuboidCell only works for orthogonal cells.

adjust_forces(atoms, forces)

Adjust forces of upper and lower rigid atoms.

Raises:: NotImplementedError – If atoms.get_cell() is non-orthogonal, SlideWithNormalPressureCuboidCell only works for orthogonal cells.

adjust_momenta(atoms, momenta)

Adjust momenta of upper and lower rigid atoms.

Raises:: NotImplementedError – If atoms.get_cell() is non-orthogonal, SlideWithNormalPressureCuboidCell only works for orthogonal cells.

adjust_potential_energy(atoms): Do not adjust energy.

class matscipy.pressurecoupling.SlideLogger(handle, atoms, slider, integrator, step_offset=0)

Bases: object

Logger to be attached to an ASE integrator.

For new files (not restart jobs), the write_header method should be called once in order to write the header to the file.

Parameters:

handle (filehandle) – Filehandle e.g. pointing to a file opened in w or a mode.
atoms (ase.Atoms) – Atomic configuration.
slider (slider object) – Instance of SlideWithNormalPressureCuboidCell.
integrator (ASE integrator object,) – Instance of ASE integrator e.g. ase.md.langevin.Langevin.
step_offset (int) – Last step already written to log file, useful for restarts.

Examples

For new runs:
log_handle = open(logfn, ‘w’, 1) # line buffered

logger = SlideLogger(log_handle, …)

logger.write_header()

integrator.attach(logger)

integrator.run(steps_integrate)

log_handle.close()
For restarts:
with open(logfn, ‘r’) as log_handle:

step_offset = SlideLog(log_handle).step[-1]

log_handle = open(logfn, ‘a’, 1) # line buffered append

logger = SlideLogger(log_handle, …, step_offset=step_offset)

integrator.attach(logger)

integrator.run(steps_integrate)

log_handle.close()

Methods

`__call__`()	Write current status (time, T, P, ...) to log-file.
`write_header`()	Write header of log-file.

__init__(handle, atoms, slider, integrator, step_offset=0)

write_header(): Write header of log-file.

class matscipy.pressurecoupling.SlideLog(handle)

Bases: object

Reader for logs written with SlideLogger instance.

Parameters:: instance (handle matscipy.pressurecoupling.SlideLogger) – Handle or filename pointing to log file.

step

Step indices 0, 1, 2, ….

Type:: ndarray

time

Simulation time in fs at step.

Type:: ndarray

T_thermostat

Instantantaneous temperature in K from thermostat-region only from degrees of freedom along thermalized direction.

Type:: ndarray

P_top

Normal pressure on lid in GPa.

Type:: ndarray

P_bottom

Normal pressure on base in GPa.

Type:: ndarray

h

Separation of lid and base in Ang.

Type:: ndarray

v

Normal speed of lid in Ang / fs.

Type:: ndarray

a

Normal acceleration of lid in Ang / fs ** 2.

Type:: ndarray

tau_top

Shear stress on lid in GPa.

Type:: ndarray

tau_bottom

Shear stress on base in GPa.

Type:: ndarray

rows

All data in a 2d array with axis 0 step and axis 1 the values ordered as above.

Type:: ndarray

__init__(handle)