Single molecule: access results¶

#!/usr/bin/env amspython
# coding: utf-8

# ## Load a SimpleActiveLearningJob from disk
#
# Use ``load_external`` to load the job from the previous Jupyter Notebook tutorial. Make sure to provide the correct path!

from scm.simple_active_learning import SimpleActiveLearningJob
import scm.plams as plams
import matplotlib.pyplot as plt
import os


# replace the path with your own path !
previous_sal_job_path = os.path.expandvars("$AMSHOME/examples/SAL/Output/SingleMolecule/plams_workdir/sal")
job = SimpleActiveLearningJob.load_external(previous_sal_job_path)


# ## Access the log file
#
# The results of the active learning are printed in a human-friendly format in the log file. For example, let's print the last few lines:

n_lines = 40
end_of_logfile = "\n".join(job.results.read_file("simple_active_learning.log").split("\n")[-n_lines:])
print(end_of_logfile)


# Above we can easily see that there were 5 active learning steps, and the engine settings for the final trained ML potential.
#
# Tip: You can copy-paste the lines from ``Engine MLPotential`` to ``EndEngine`` into AMSinput to use those engine settings for other production simulations in the GUI.

# ## Access the MD trajectories
#
# By default, the ``ActiveLearning%AtEnd%RerunSimulation`` option is enabled. This means that after the active learning loop has finished, the entire simulation is rerun from scratch with the final set of parameters.
#
# There are thus two trajectories:
#
# * A trajectory run only with the final parameters, and that is just a normal AMS job. This trajectory is located in the directory ``final_production_simulation`` if it exists.
#
# * A trajectory where the parameters have been updated on-the-fly, and which may also have an inconsistent MD sampling frequency. This trajectory is located in one of the ``stepX_attemptY_simulation`` directories.
#
# Use the ``get_simulation_directory`` method to get the corresponding directories.
#
# Let's start with the **final production simulation**:

final_production_simulation_dir = job.results.get_simulation_directory(allow_final=True)
print(final_production_simulation_dir)


# View the trajectory in AMSmovie:

final_job = plams.AMSJob.load_external(final_production_simulation_dir)
final_rkf = final_job.results.rkfpath()


# Let's then get the **other (with on-the-fly-updated-engine) trajectory**:

onthefly_simulation_dir = job.results.get_simulation_directory(allow_final=False)
print(onthefly_simulation_dir)


onthefly_job = plams.AMSJob.load_external(onthefly_simulation_dir)
onthefly_rkf = onthefly_job.results.rkfpath()


# Let's compare energy-vs-frame for the two trajectories:

plt.plot(
    final_job.results.get_history_property("Time", "MDHistory"),
    final_job.results.get_history_property("EngineEnergy"),
)
plt.plot(
    onthefly_job.results.get_history_property("Time", "MDHistory"),
    onthefly_job.results.get_history_property("EngineEnergy"),
)
plt.legend(["Final", "On-the-fly"])
plt.xlabel("Time (fs)")
plt.ylabel("Engine energy (hartree)")


# The energy profiles look quite similar. For the on-the-fly trajectory, there are more datapoints for short times since the Simple Active Learning tool samples more frequently in the beginning of the simulation when there are only a few MD steps per active learning step.

# ## Access the ParAMS training results
#
# Similarly to the final production trajectory, there is an input option ``ActiveLearning%AtEnd%RetrainModel`` which will retrain the model at the end, guaranteeing that all the generated reference data is used during the training or validation. However, this option is off by default.
#
# The method ``get_params_results_directory()`` returns the ParAMS results directory, which can be
# * used as the value for ``MachineLearning%LoadModel`` to continue with another active learning run, or
# * opened in the ParAMS GUI to view all results, including loss function minimization and predicted-vs-reference scatter plots
#
# The method ``get_params_job()`` returns a ``ParAMSJob`` whose results can directly be accessed using the normal ``ParAMSJob`` and ``ParAMSResults`` python APIs.

params_results_dir = job.results.get_params_results_directory(allow_final=True)
print(params_results_dir)


# **Open it in the ParAMS GUI**:


# The ParAMS GUI is the best way to quickly get an overview of the data sets and results.
#
# However, it can also be useful to **access results from Python**.
#
# The details of the ParAMSJob and ParAMSResults classes are shown in the ParAMS Python examples, here we just provide a quick example:

params_job = job.results.get_params_job()
params_job.results.plot_simple_correlation("forces", source="best")


# If you want to access individual data entries or the MAE in Python, you can use the ``params_job.results.get_data_set_evaluator()`` method. See the ParAMS DataSetEvaluator documentation for details.

# ## Access the production engine settings
#
# The engine settings used for production simulation can be accessed from the ParAMS job:

engine_settings = params_job.results.get_production_engine_settings()
print(plams.AMSJob(settings=engine_settings).get_input())


# ## Access the reference data

# The ``stepX_attemptY_reference_data`` directories can be accessed using ``get_reference_data_directory()``:

ref_dir = job.results.get_reference_data_directory()
print(ref_dir)