pyretis.tools package¶
Tools which can help with setting up simulations.
This package defines some simple tools which may be useful for creating simulations.
Package structure¶
Modules¶
- lattice.py (
pyretis.tools.lattice
) - Defines tools for setting up and generating lattice points.
- recalculate_order.py (
pyretis.tools.recalculate_order
) - Methods for recalculating order parameters on external paths.
Important methods defined in this package¶
- generate_lattice (
generate_lattice()
) - Generates points on a lattice.
- recalculate_order (
recalculate_order()
) - Recalculate order parameter(s).
List of submodules¶
pyretis.tools.lattice module¶
Some methods for generating initial lattice structures.
Important methods defined here¶
- generate_lattice (
generate_lattice()
) - Generate points on a simple lattice.
Examples
>>> from pyretis.tools.lattice import generate_lattice
>>> xyz, size = generate_lattice('diamond', [1, 1, 1], lcon=1)
-
pyretis.tools.lattice.
generate_lattice
(lattice, repeat=None, lcon=None, density=None)[source]¶ Generate points on a simple lattice.
The lattice is one of the defined keys in the global variable UNIT_CELL. This lattice will be repeated a number of times. The lattice spacing can be given explicitly, or it can be given implicitly by the number density.
Parameters: lattice (string) – Select the kind of lattice. The following options are currently defined in UNIT_CELL:
- 1d : 1D lattice
- sc : Simple cubic lattice.
- sq : Square lattice (2D) with one atom in the unit cell.
- sq2 : Square lattice with two atoms in the unit cell.
- bcc : Body-centred cubic lattice.
- fcc : Face-centred cubic lattice.
- hcp : Hexagonal close-packed lattice.
- diamond : Diamond structure.
repeat (list of integers, optional.) – How many time the cell is replicated.
lcon (float, optional) – The lattice constant.
density (float, optional) – The desired density. If this is given, lcon is calculated. Note that density will be interpreted as given in internal units.
Returns: - positions (numpy.array) – The lattice positions.
- size (list of floats) – The corresponding size(s), can be used to define a simulation box.
pyretis.tools.recalculate_order module¶
Method to re-calculate order parameters for external trajectories.
Important methods defined here¶
- recalculate_order (
recalculate_order()
) - Generic method for recalculating order parameters.
- recalculate_from_trj (
recalculate_from_trj()
) - Recalculate order parameters using a GROMACS .trr file.
- recalculate_from_xyz (
recalculate_from_xyz()
) - Recalculate order parameters using a .xyz file.
- recalculate_from_frame (
recalculate_from_frame()
) - Recalculate order parameters using a .gro or .g96 file.
-
pyretis.tools.recalculate_order.
recalculate_from_frame
(order_parameter, frame_file, options)[source]¶ Re-calculate order parameters from a .g96/.gro file.
Here we assume that there is ONE frame in the
frame_file
.Parameters: - order_parameter (object like
OrderParameter
) – The order parameter to use. - frame_file (string) – The path to the frame file we should read.
- options (dict) – It contains:
- ext: string
File extension for the
frame_file
. - reverse: boolean, optional If True, we reverse the velocities.
- ext: string
File extension for the
Returns: out (list of lists of floats) – The order parameters for the current frame.
- order_parameter (object like
-
pyretis.tools.recalculate_order.
recalculate_from_trj
(order_parameter, trr_file, options)[source]¶ Re-calculate order parameters from a .trr file.
Parameters: - order_parameter (object like
OrderParameter
) – The order parameter to use. - trr_file (string) – The path to the trr file we should read.
- options (dict) – It contains:
- reverse: boolean, optional If True, we reverse the velocities.
- maxidx: integer, optional This is the maximum frame we will read. Can be used in case the .trr file contains extra frames not needed by us.
- minidx: integer, optional This is the first frame we will read. Can be used in case we want to skip some frames from the .trr file.
- idx: integer, optional This allows the selection of a single frame to recompute.
Yields: out (list of lists of floats) – The order parameters, calculated per frame.
- order_parameter (object like
-
pyretis.tools.recalculate_order.
recalculate_from_xyz
(order_parameter, traj_file, options)[source]¶ Re-calculate order parameters from a .xyz file.
Parameters: - order_parameter (object like
OrderParameter
) – The order parameter to use. - traj_file (string) – The path to the trajectory file we should read.
- options (dict) – It contains:
- reverse: boolean, optional If True, we reverse the velocities.
- maxidx: integer, optional This is the maximum frame we will read. Can be used in case the .trr file contains extra frames not needed by us.
- minidx: integer, optional This is the first frame we will read. Can be used in case we want to skip some frames from the .trr file.
- box: list of floats It contains the box vector lenght. It is required in the case that .xyz do not normally contains the simulation box dimension.
Yields: out (list of lists of floats) – The order parameters as a list.
- order_parameter (object like
-
pyretis.tools.recalculate_order.
recalculate_order
(order_parameter, traj_file, options)[source]¶ Re-calculate order parameters.
Parameters: - order_parameter (object like
OrderParameter
) – The order parameter to use. - traj_file (string) – Path to the trajectory file to recalculate for.
- options (dict) – It contains:
- reverse: boolean, optional If True, we reverse the velocities.
- maxidx: integer, optional This is the maximum frame we will read. Can be used in case the .trr file contains extra frames not needed by us.
- minidx: integer, optional This is the first frame we will read. Can be used in case we want to skip some frames from the .trr file.
- order_parameter (object like