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Merged
avishart merged 3 commits into from
Sep 30, 2025
Merged

Activelearning #11

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39e46e8
Reintroduce last structure(s) trajectory file
avishart Sep 24, 2025
4eec9af
Change in README
avishart Sep 30, 2025
922ede1
Merge branch 'master' into activelearning
avishart Sep 30, 2025
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14 changes: 7 additions & 7 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,18 +14,18 @@ CalLearn uses ASE to handle atomic systems and the calculator interface to calcu

You can install CatLearn by downloading it from GitHub as:
```shell
$ git clone https://github.com/avishart/CatLearn
$ pip install -e CatLearn/.
git clone --single-branch --branch activelearning https://github.com/avishart/CatLearn
pip install -e CatLearn/.
```

You can also install CatLearn directly from GitHub:
```shell
$ pip install git@github.com:avishart/CatLearn.git
pip install git+https://github.com/avishart/CatLearn.git@activelearning
```

However, it is recommended to install a specific tag to ensure it is a stable version:
```shell
$ pip install git+https://github.com/avishart/CatLearn.git@v.x.x.x
pip install git+https://github.com/avishart/CatLearn.git@v.x.x.x
```

The dependency of ASE has only been thoroughly tested up to version 3.26.0.
Expand Down Expand Up @@ -74,7 +74,7 @@ dyn.run(
fmax=0.05,
max_unc=0.30,
steps=100,
ml_steps=1000,
ml_steps=500,
)

```
Expand Down Expand Up @@ -117,7 +117,7 @@ mlneb = MLNEB(
start_without_ci=True,
reuse_ci_path=True,
save_memory=False,
parallel_run=False,
parallel_run=True,
local_opt=FIRE,
local_opt_kwargs={},
use_restart=True,
Expand All @@ -129,7 +129,7 @@ mlneb.run(
fmax=0.05,
max_unc=0.30,
steps=100,
ml_steps=1000,
ml_steps=500,
)

```
Expand Down
2 changes: 1 addition & 1 deletion catlearn/_version.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
__version__ = "7.2.0"
__version__ = "7.2.1"

__all__ = ["__version__"]
24 changes: 20 additions & 4 deletions catlearn/activelearning/activelearning.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,7 @@ def __init__(
pred_evaluated="predicted_evaluated.traj",
converged_trajectory="converged.traj",
initial_traj="initial_struc.traj",
last_traj=None,
tabletxt="ml_summary.txt",
timetxt="ml_time.txt",
prev_calculations=None,
Expand Down Expand Up @@ -187,14 +188,18 @@ def __init__(
training data with predicted properties.
If pred_evaluated is None, then the predicted data is
not saved.
converged_trajectory: str or TrajectoryWriter instance
converged_trajectory: str or TrajectoryWriter instance (optional)
Trajectory filename to store the converged structure(s).
Or the TrajectoryWriter instance to store the converged
structure(s).
initial_traj: str or TrajectoryWriter instance
initial_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the initial structure(s).
Or the TrajectoryWriter instance to store the initial
structure(s).
last_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the last structure(s).
Or the TrajectoryWriter instance to store the last
structure(s).
tabletxt: str (optional)
Name of the .txt file where the summary table is printed.
It is not saved to the file if tabletxt=None.
Expand Down Expand Up @@ -267,6 +272,7 @@ def __init__(
pred_evaluated=pred_evaluated,
converged_trajectory=converged_trajectory,
initial_traj=initial_traj,
last_traj=last_traj,
tabletxt=tabletxt,
timetxt=timetxt,
seed=seed,
Expand Down Expand Up @@ -856,6 +862,7 @@ def update_arguments(
pred_evaluated=None,
converged_trajectory=None,
initial_traj=None,
last_traj=None,
tabletxt=None,
timetxt=None,
seed=None,
Expand Down Expand Up @@ -978,14 +985,18 @@ def update_arguments(
training data with predicted properties.
If pred_evaluated is None, then the predicted data is
not saved.
converged_trajectory: str or TrajectoryWriter instance
converged_trajectory: str or TrajectoryWriter instance (optional)
Trajectory filename to store the converged structure(s).
Or the TrajectoryWriter instance to store the converged
structure(s).
initial_traj: str or TrajectoryWriter instance
initial_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the initial structure(s).
Or the TrajectoryWriter instance to store the initial
structure(s).
last_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the last structure(s).
Or the TrajectoryWriter instance to store the last
structure(s).
tabletxt: str (optional)
Name of the .txt file where the summary table is printed.
It is not saved to the file if tabletxt=None.
Expand Down Expand Up @@ -1101,6 +1112,8 @@ def update_arguments(
self.converged_trajectory = converged_trajectory
if initial_traj is not None or not hasattr(self, "initial_traj"):
self.initial_traj = initial_traj
if last_traj is not None or not hasattr(self, "last_traj"):
self.last_traj = last_traj
if tabletxt is not None:
self.tabletxt = str(tabletxt)
elif not hasattr(self, "tabletxt"):
Expand Down Expand Up @@ -1198,6 +1211,8 @@ def run_method(
self.structures = self.get_structures()
# Write atoms to trajectory
self.save_trajectory(self.trajectory, self.structures, mode=self.mode)
# Write atoms to last_traj trajectory
self.save_trajectory(self.last_traj, self.structures, mode="w")
return method_converged

def initiate_structure(self, step=1, **kwargs):
Expand Down Expand Up @@ -2118,6 +2133,7 @@ def get_arguments(self):
pred_evaluated=self.pred_evaluated,
converged_trajectory=self.converged_trajectory,
initial_traj=self.initial_traj,
last_traj=self.last_traj,
tabletxt=self.tabletxt,
timetxt=self.timetxt,
seed=self.seed,
Expand Down
11 changes: 9 additions & 2 deletions catlearn/activelearning/adsorption.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@ def __init__(
pred_evaluated="predicted_evaluated.traj",
converged_trajectory="converged.traj",
initial_traj="initial_struc.traj",
last_traj=None,
tabletxt="ml_summary.txt",
timetxt="ml_time.txt",
prev_calculations=None,
Expand Down Expand Up @@ -193,14 +194,18 @@ def __init__(
training data with predicted properties.
If pred_evaluated is None, then the predicted data is
not saved.
converged_trajectory: str or TrajectoryWriter instance
converged_trajectory: str or TrajectoryWriter instance (optional)
Trajectory filename to store the converged structure(s).
Or the TrajectoryWriter instance to store the converged
structure(s).
initial_traj: str or TrajectoryWriter instance
initial_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the initial structure(s).
Or the TrajectoryWriter instance to store the initial
structure(s).
last_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the last structure(s).
Or the TrajectoryWriter instance to store the last
structure(s).
tabletxt: str
Name of the .txt file where the summary table is printed.
It is not saved to the file if tabletxt=None.
Expand Down Expand Up @@ -272,6 +277,7 @@ def __init__(
pred_evaluated=pred_evaluated,
converged_trajectory=converged_trajectory,
initial_traj=initial_traj,
last_traj=last_traj,
tabletxt=tabletxt,
timetxt=timetxt,
prev_calculations=prev_calculations,
Expand Down Expand Up @@ -458,6 +464,7 @@ def get_arguments(self):
pred_evaluated=self.pred_evaluated,
converged_trajectory=self.converged_trajectory,
initial_traj=self.initial_traj,
last_traj=self.last_traj,
tabletxt=self.tabletxt,
timetxt=self.timetxt,
seed=self.seed,
Expand Down
11 changes: 9 additions & 2 deletions catlearn/activelearning/local.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,7 @@ def __init__(
pred_evaluated="predicted_evaluated.traj",
converged_trajectory="converged.traj",
initial_traj="initial_struc.traj",
last_traj=None,
tabletxt="ml_summary.txt",
timetxt="ml_time.txt",
prev_calculations=None,
Expand Down Expand Up @@ -177,14 +178,18 @@ def __init__(
training data with predicted properties.
If pred_evaluated is None, then the predicted data is
not saved.
converged_trajectory: str or TrajectoryWriter instance
converged_trajectory: str or TrajectoryWriter instance (optional)
Trajectory filename to store the converged structure(s).
Or the TrajectoryWriter instance to store the converged
structure(s).
initial_traj: str or TrajectoryWriter instance
initial_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the initial structure(s).
Or the TrajectoryWriter instance to store the initial
structure(s).
last_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the last structure(s).
Or the TrajectoryWriter instance to store the last
structure(s).
tabletxt: str
Name of the .txt file where the summary table is printed.
It is not saved to the file if tabletxt=None.
Expand Down Expand Up @@ -252,6 +257,7 @@ def __init__(
pred_evaluated=pred_evaluated,
converged_trajectory=converged_trajectory,
initial_traj=initial_traj,
last_traj=last_traj,
tabletxt=tabletxt,
timetxt=timetxt,
prev_calculations=prev_calculations,
Expand Down Expand Up @@ -361,6 +367,7 @@ def get_arguments(self):
pred_evaluated=self.pred_evaluated,
converged_trajectory=self.converged_trajectory,
initial_traj=self.initial_traj,
last_traj=self.last_traj,
tabletxt=self.tabletxt,
timetxt=self.timetxt,
seed=self.seed,
Expand Down
11 changes: 9 additions & 2 deletions catlearn/activelearning/mlgo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,7 @@ def __init__(
pred_evaluated="predicted_evaluated.traj",
converged_trajectory="converged.traj",
initial_traj="initial_struc.traj",
last_traj=None,
tabletxt="ml_summary.txt",
timetxt="ml_time.txt",
prev_calculations=None,
Expand Down Expand Up @@ -231,14 +232,18 @@ def __init__(
training data with predicted properties.
If pred_evaluated is None, then the predicted data is
not saved.
converged_trajectory: str or TrajectoryWriter instance
converged_trajectory: str or TrajectoryWriter instance (optional)
Trajectory filename to store the converged structure(s).
Or the TrajectoryWriter instance to store the converged
structure(s).
initial_traj: str or TrajectoryWriter instance
initial_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the initial structure(s).
Or the TrajectoryWriter instance to store the initial
structure(s).
last_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the last structure(s).
Or the TrajectoryWriter instance to store the last
structure(s).
tabletxt: str
Name of the .txt file where the summary table is printed.
It is not saved to the file if tabletxt=None.
Expand Down Expand Up @@ -307,6 +312,7 @@ def __init__(
pred_evaluated=pred_evaluated,
converged_trajectory=converged_trajectory,
initial_traj=initial_traj,
last_traj=last_traj,
tabletxt=tabletxt,
timetxt=timetxt,
prev_calculations=None,
Expand Down Expand Up @@ -592,6 +598,7 @@ def get_arguments(self):
pred_evaluated=self.pred_evaluated,
converged_trajectory=self.converged_trajectory,
initial_traj=self.initial_traj,
last_traj=self.last_traj,
tabletxt=self.tabletxt,
timetxt=self.timetxt,
seed=self.seed,
Expand Down
11 changes: 9 additions & 2 deletions catlearn/activelearning/mlneb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@ def __init__(
pred_evaluated="predicted_evaluated.traj",
converged_trajectory="converged.traj",
initial_traj="initial_struc.traj",
last_traj=None,
tabletxt="ml_summary.txt",
timetxt="ml_time.txt",
prev_calculations=None,
Expand Down Expand Up @@ -229,14 +230,18 @@ def __init__(
training data with predicted properties.
If pred_evaluated is None, then the predicted data is
not saved.
converged_trajectory: str or TrajectoryWriter instance
converged_trajectory: str or TrajectoryWriter instance (optional)
Trajectory filename to store the converged structure(s).
Or the TrajectoryWriter instance to store the converged
structure(s).
initial_traj: str or TrajectoryWriter instance
initial_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the initial structure(s).
Or the TrajectoryWriter instance to store the initial
structure(s).
last_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the last structure(s).
Or the TrajectoryWriter instance to store the last
structure(s).
tabletxt: str
Name of the .txt file where the summary table is printed.
It is not saved to the file if tabletxt=None.
Expand Down Expand Up @@ -315,6 +320,7 @@ def __init__(
pred_evaluated=pred_evaluated,
converged_trajectory=converged_trajectory,
initial_traj=initial_traj,
last_traj=last_traj,
tabletxt=tabletxt,
timetxt=timetxt,
prev_calculations=self.prev_calculations,
Expand Down Expand Up @@ -528,6 +534,7 @@ def get_arguments(self):
pred_evaluated=self.pred_evaluated,
converged_trajectory=self.converged_trajectory,
initial_traj=self.initial_traj,
last_traj=self.last_traj,
tabletxt=self.tabletxt,
timetxt=self.timetxt,
seed=self.seed,
Expand Down
11 changes: 9 additions & 2 deletions catlearn/activelearning/randomadsorption.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,7 @@ def __init__(
pred_evaluated="predicted_evaluated.traj",
converged_trajectory="converged.traj",
initial_traj="initial_struc.traj",
last_traj=None,
tabletxt="ml_summary.txt",
timetxt="ml_time.txt",
prev_calculations=None,
Expand Down Expand Up @@ -228,14 +229,18 @@ def __init__(
training data with predicted properties.
If pred_evaluated is None, then the predicted data is
not saved.
converged_trajectory: str or TrajectoryWriter instance
converged_trajectory: str or TrajectoryWriter instance (optional)
Trajectory filename to store the converged structure(s).
Or the TrajectoryWriter instance to store the converged
structure(s).
initial_traj: str or TrajectoryWriter instance
initial_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the initial structure(s).
Or the TrajectoryWriter instance to store the initial
structure(s).
last_traj: str or TrajectoryWriter instance (optional)
Trajectory filename to store the last structure(s).
Or the TrajectoryWriter instance to store the last
structure(s).
tabletxt: str
Name of the .txt file where the summary table is printed.
It is not saved to the file if tabletxt=None.
Expand Down Expand Up @@ -316,6 +321,7 @@ def __init__(
pred_evaluated=pred_evaluated,
converged_trajectory=converged_trajectory,
initial_traj=initial_traj,
last_traj=last_traj,
tabletxt=tabletxt,
timetxt=timetxt,
prev_calculations=prev_calculations,
Expand Down Expand Up @@ -496,6 +502,7 @@ def get_arguments(self):
pred_evaluated=self.pred_evaluated,
converged_trajectory=self.converged_trajectory,
initial_traj=self.initial_traj,
last_traj=self.last_traj,
tabletxt=self.tabletxt,
timetxt=self.timetxt,
seed=self.seed,
Expand Down