Simulation save/restart module about pyelastica HOT 7 OPEN

Comment by armantekinalp
Thursday Dec 30, 2021 at 05:29 GMT

In future implementation of restart I think we should add these functionalities:

• Current implementation allows only loading systems after finalize call. Instead we should call restart functions before finalize.
• Curren implementation only saves systems i.e. rods, rigid bodies. As @skim0119 mentioned above, restart should save a copy of simulator and user can just load & run. However, some users might need more customization and they might want to only save rods but not the simulation. For those cases we should have an option to save/load systems or simulation.
• We could also allow users to save simulator/systems every some steps. This might be useful for debugging purposes.

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is this issue open?
Im a beginner and I'd like to work on it

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@Anika-Roy Thank you for your interest. Yes, this issue is still open.
If you are interested in working, let me know, I can assign you.

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@skim0119 Hello! I'm a beginner looking to make my first contribution to PyElastica, and I'm interested in working on the Simulation save/restart module issue (#33) listed under the good first issue label. I understand that this may involve some challenges, such as handling non-serialisable data and accounting for customised forces/connections, but I'm eager to learn and contribute to the project.
Could you please provide me with some guidance on how to get started with this issue?
Thank you!

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Hi @skim0119 @bhosale2 , I'm interested in contributing to PyElastica and I noticed that issue #33 on simulation save/restart module is still open. Would it be possible to assign this issue to me? I would love to work on it as a beginner.
Thank you!

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I have made changes in "restart.py" and here is the updated code:
doc = """Generate or load restart file implementations."""
all = ["save_state", "load_state"]
import numpy as np
import os
from itertools import groupby

def all_equal(iterable):
"""
Checks if all elements of list are equal.
Parameters
----------
iterable : list
Iterable list
Returns
-------
Boolean
References
----------
https://stackoverflow.com/questions/3844801/check-if-all-elements-in-a-list-are-identical
"""
g = groupby(iterable)
return next(g, True) and not next(g, False)

def save_state(simulator, directory: str = "", time=0.0, verbose: bool = False):
"""
Save state parameters of each rod.
TODO : environment list variable is not uniform at the current stage of development.
It would be nice if we have set list (like env.system) that iterates all the rods.
Parameters
----------
simulator : object
Simulator object.
directory : str
Directory path name. The path must exist.
time : float
Simulation time.
verbose : boolean

"""
os.makedirs(directory, exist_ok=True)
for idx, rod in enumerate(simulator):
    path = os.path.join(directory, "system_{}.npz".format(idx))
    np.savez(path, time=time,
             vertices=rod.vertices,
             edges=rod.edges,
             state_variables=rod.state_variables,
             forces=rod.forces,
             connections=rod.connections,
              **rod.__dict__)

    """
    In the modified version of save_state,
    we are saving the following new pieces of data:

        1. vertices: An array of the rod's vertices.
        2. edges: An array of the rod's edges.
        3. state_variables: A dictionary containing the values of any state variables the rod has.
        4. forces: A dictionary containing information about any forces acting on the rod.
        5. connections: A dictionary containing information about any connections the rod has.
    """

if verbose:
    print("Save complete: {}".format(directory))

def load_state(simulator, directory: str = "", verbose: bool = False):
"""
Load the rod-state. Compatibale with 'save_state' method.
If the save-file does not exist, it returns error.
Call this function after finalize method.

Parameters
----------
simulator : object
    Simulator object.
directory : str
    Directory path name.
verbose : boolean

Returns
------
time : float
    Simulation time of systems when they are saved.
"""
time_list = []  # Simulation time of rods when they are saved.
for idx, rod in enumerate(simulator):
    path = os.path.join(directory, "system_{}.npz".format(idx))
    data = np.load(path, allow_pickle=True)
    for key, value in data.items():
        if key == "time":
            time_list.append(value.item())
            continue

        if key == "vertices":
            rod.vertices[:] = value
        elif key == "edges":
            rod.edges[:] = value
        elif key == "state_variables":
            rod.state_variables.update(value.tolist())
        elif key == "forces":
            rod.forces.update(value.tolist())
        elif key == "connections":
            rod.connections.update(value.tolist())
        elif value.shape != ():
            # Copy data into placeholders
            getattr(rod, key)[:] = value
        else:
            # For single-value data
            setattr(rod, key, value)

if not all_equal(time_list):
    raise ValueError(
        "Restart time of loaded rods are different, check your inputs!"
    )

# Apply boundary conditions, after loading the systems.
simulator.constrain_values(0.0)
simulator.constrain_rates(0.0)

if verbose:
    print("Load complete: {}".format(directory))

return time_list[0]

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@skim0119 @bhosale2 I'm facing some issues while committing the code:

Added the changes by "git add" and it worked perfectly fine.

Next step was to commit the changes, and I tried "git commit -m "Add a code for saving and loading simulation state",
but it showed and error:

Please help me with this!

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