pyiron.yaff.yaff module¶
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class
pyiron.yaff.yaff.Yaff(project, job_name)[source]¶ Bases:
pyiron.atomistics.job.atomistic.AtomisticGenericJob-
calc_md(temperature=None, pressure=None, nsteps=1000, time_step=41.341373336646825, n_print=5, timecon_thermo=4134.137333664683, timecon_baro=41341.37333664682)[source]¶ Set an MD calculation within Yaff. Nosé Hoover chain is used by default.
Arguments
- temperature (None/float): Target temperature. If set to None, an NVE calculation is performed.
It is required when the pressure is set
pressure (None/float): Target pressure. If set to None, an NVE or an NVT calculation is performed. nsteps (int): Number of md steps time_step (float): Step size between two steps. n_print (int): Print frequency timecon_thermo (float): The time associated with the thermostat adjusting the temperature. timecon_baro (float): The time associated with the barostat adjusting the temperature.
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calc_minimize(cell=False, gpos_tol=1e-08, dpos_tol=1e-06, grvecs_tol=1e-08, drvecs_tol=1e-06, max_iter=1000, n_print=5)[source]¶ Set up an optimization calculation.
Arguments
cell (bool): Set True if the cell also has to be optimized gpos_tol (float): Convergence criterion for RMS of gradients towards atomic coordinates dpos_tol (float): Convergence criterion for RMS of differences of atomic coordinates grvecs_tol (float): Convergence criterion for RMS of gradients towards cell parameters drvecs_tol (float): Convergence criterion for RMS of differences of cell parameters max_iter (int): Maximum number of optimization steps n_print (int): Print frequency
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collect_output()[source]¶ Collect the output files of the external executable and store the information in the HDF5 file. This method has to be implemented in the individual hamiltonians.
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detect_ffatypes(ffatypes=None, ffatype_rules=None, ffatype_level=None)[source]¶ Define atom types by explicitely giving them through the ffatypes keyword, defining atype rules using the ATSELECT language implemented in Yaff (see the Yaff documentation at http://molmod.github.io/yaff/ug_atselect.html) or by specifying the ffatype_level employing the built-in routine in QuickFF.
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from_hdf(hdf=None, group_name=None)[source]¶ Recreates instance from the hdf5 file :param hdf: Path to the hdf5 file :type hdf: str :param group_name: Name of the group which contains the object :type group_name: str
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get_structure(iteration_step=- 1, wrap_atoms=True)[source]¶ Overwrite the get_structure routine from AtomisticGenericJob because we want to avoid defining a unit cell when one does not exist
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load_chk(fn)[source]¶ Load the atom types, atom type ids and structure by reading a .chk file.
Arguments
fn the path to the chk file
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mtd_sum_hills_1d(fn=None)[source]¶ Creates a fes.dat file for plotting the free energy surface after a mtd simulation.
Arguments
fn path to the hills file or hills files (comma separated)
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plot(ykey, xkey='generic/steps', xunit='au', yunit='au', ref=None, linestyle='-', rolling_average=False)[source]¶
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plot_multi(ykeys, xkey='generic/steps', xunit='au', yunit='au', ref=None, linestyle='-', rolling_average=False)[source]¶
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set_mtd(ics, height, sigma, pace, fn='HILLS', fn_colvar='COLVAR', stride=10, temp=300)[source]¶ Setup a Metadynamics run using PLUMED along the internal coordinates defined in the ICs argument.
Arguments
- ics a list of entries defining each internal coordinate. Each
of these entries should be of the form (kind, [i, j, …])
Herein, kind defines the kind of IC as implemented in PLUMED:
i.e. distance, angle, torsion, volume, cell, … see https://www.plumed.org/doc-v2.5/user-doc/html/_colvar.html for more information).
and [i, j, …] is a list of atom indices, starting from 0, involved in this IC. If no atom indices are required for e.g. volume, provide an empty list.
An example for a 1D metadynamica using the distance between atoms 2 and 4:
ics = [(‘distance’, [2,4])]
- height the height of the Gaussian hills, can be a single value
(the gaussian hills for each IC have identical height) or a list of values, one for each IC defined.
- sigmas the sigma of the Gaussian hills, can be a single value
(the gaussian hills for each IC have identical height) or a list of values, one for each IC defined.
- pace the number of steps after which the gaussian hills are
updated.
fn the PLUMED output file for the gaussian hills
- fn_colvar
the PLUMED output file for logging of collective variables
- stride the number of steps after which the internal coordinate
values and bias are printed to the COLVAR output file.
temp the system temperature
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set_us(ics, kappa, loc, fn_colvar='COLVAR', stride=10, temp=300)[source]¶ Setup an Umbrella sampling run using PLUMED along the internal coordinates defined in the ICs argument.
Arguments
- ics a list of entries defining each an internal coordinate. Each
of these entries should be of the form (kind, [i, j, …])
Herein, kind defines the kind of IC as implemented in PLUMED:
i.e. distance, angle, torsion, volume, cell, … see https://www.plumed.org/doc-v2.5/user-doc/html/_colvar.html for more information).
and [i, j, …] is a list of atom indices, starting from 0, involved in this IC. If no atom indices are required for e.g. volume, provide an empty list.
An example for a 1D metadynamica using the distance between atoms 2 and 4:
ics = [(‘distance’, [2,4])]
- kappa the value of the force constant of the harmonic bias potential,
can be a single value (the harmonic bias potential for each IC has identical kappa) or a list of values, one for each IC defined.
- loc the location of the umbrella
(should have a length equal to the number of ICs)
- fn_colvar
the PLUMED output file for logging of collective variables
- stride the number of steps after which the internal coordinate
values and bias are printed to the COLVAR output file.
temp the system temperature
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to_hdf(hdf=None, group_name=None)[source]¶ Store the GenericJob in an HDF5 file
- Parameters
hdf (ProjectHDFio) – HDF5 group object - optional
group_name (str) – HDF5 subgroup name - optional
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