diff --git a/_modules/hippynn/databases/database.html b/_modules/hippynn/databases/database.html
index 7fe0528b..d3a8c80e 100644
--- a/_modules/hippynn/databases/database.html
+++ b/_modules/hippynn/databases/database.html
@@ -79,6 +79,8 @@
"""
Base database functionality from dictionary of numpy arrays
"""
+
+from typing import Union
import warnings
import numpy as np
import torch
@@ -102,17 +104,18 @@ Source code for hippynn.databases.database
[docs]
def __init__ (
self ,
- arr_dict ,
- inputs ,
- targets ,
- seed ,
- test_size = None ,
- valid_size = None ,
- num_workers = 0 ,
- pin_memory = True ,
- allow_unfound = False ,
- auto_split = False ,
- device = None ,
+ arr_dict : dict [ str , torch . Tensor ],
+ inputs : list [ str ],
+ targets : list [ str ],
+ seed : [ int , np . random . RandomState , tuple ],
+ test_size : Union [ float , int ] = None ,
+ valid_size : Union [ float , int ] = None ,
+ num_workers : int = 0 ,
+ pin_memory : bool = True ,
+ allow_unfound : bool = False ,
+ auto_split : bool = False ,
+ device : torch . device = None ,
+ dataloader_kwargs : dict [ str , object ] = None ,
quiet = False ,
):
"""
@@ -129,6 +132,9 @@ Source code for hippynn.databases.database
:param allow_unfound: If true, skip checking if the needed inputs and targets are found.
This allows setting inputs=None and/or targets=None.
:param auto_split: If true, look for keys like "split_*" to make initial splits from. See write_npz() method.
+ :param device: if set, move the dataset to this device after splitting.
+ :param dataloader_kwargs: dictionary, passed to pytorch dataloaders in addition to num_workers, pin_memory.
+ Refer to pytorch documentation for details.
:param quiet: If True, print little or nothing while loading.
"""
@@ -203,7 +209,9 @@ Source code for hippynn.databases.database
if not self . splitting_completed :
raise ValueError ( "Device cannot be set in constructor unless automatic split provided." )
else :
- self . send_to_device ( device ) self . send_to_device ( device )
+
+ self . dataloader_kwargs = dataloader_kwargs . copy () if dataloader_kwargs else {} def __len__ ( self ):
@@ -534,6 +542,7 @@ Source code for hippynn.databases.database
shuffle = shuffle ,
pin_memory = self . pin_memory ,
num_workers = self . num_workers ,
+ ** self . dataloader_kwargs ,
)
return generator Source code for hippynn.databases.database
[docs]
-
def write_npz ( self , file : str , record_split_masks : bool = True , overwrite : bool = False , split_prefix = None , return_only = False ):
+
def write_npz ( self , file : str , record_split_masks : bool = True , compressed : bool = True , overwrite : bool = False , split_prefix = None , return_only = False ):
"""
:param file: str, Path, or file object compatible with np.save
:param record_split_masks:
@@ -679,7 +688,10 @@
Source code for hippynn.databases.database
if file . exists () and not overwrite :
raise FileExistsError ( f "File exists: { file } " )
- np . savez_compressed ( file , ** arr_dict )
+ if compressed :
+ np . savez_compressed ( file , ** arr_dict )
+ else :
+ np . savez ( file , ** arr_dict )
return arr_dict
diff --git a/_modules/hippynn/experiment/controllers.html b/_modules/hippynn/experiment/controllers.html
index a724cc3e..336bd205 100644
--- a/_modules/hippynn/experiment/controllers.html
+++ b/_modules/hippynn/experiment/controllers.html
@@ -84,7 +84,6 @@
Source code for hippynn.experiment.controllers from torch.optim.lr_scheduler import ReduceLROnPlateau
-
[docs]
class Controller :
@@ -133,12 +132,10 @@
Source code for hippynn.experiment.controllers fraction_train_eval= 0.1 ,
quiet = False ,
):
+ super () . __init__ ()
self . optimizer = optimizer
- self . scheduler = scheduler
-
self . stopping_key = stopping_key
-
self . batch_size = batch_size
self . eval_batch_size = eval_batch_size or batch_size
if max_epochs is None :
@@ -170,7 +167,8 @@
Source code for hippynn.experiment.controllers [docs]
def state_dict ( self ):
state_dict = { k : getattr ( self , k ) for k in self . _state_vars }
- state_dict [ "optimizer" ] = self . optimizer . state_dict ()
+ if self . optimizer is not None :
+ state_dict [ "optimizer" ] = self . optimizer . state_dict ()
state_dict [ "scheduler" ] = [ sch . state_dict () for sch in self . scheduler_list ]
return state_dict
@@ -182,7 +180,8 @@
Source code for hippynn.experiment.controllers for sch , sdict in zip ( self . scheduler_list , state_dict [ "scheduler" ]):
sch . load_state_dict ( sdict )
- self . optimizer . load_state_dict ( state_dict [ "optimizer" ])
+ if self . optimizer is not None :
+ self . optimizer . load_state_dict ( state_dict [ "optimizer" ])
for k in self . _state_vars :
setattr ( self , k , state_dict [ k ])
@@ -194,7 +193,7 @@
Source code for hippynn.experiment.controllers
[docs]
- def push_epoch ( self , epoch , better_model , metric ):
+ def push_epoch ( self , epoch , better_model , metric , _print = print ):
self . current_epoch += 1
if better_model :
@@ -209,8 +208,9 @@
Source code for hippynn.experiment.controllers sch. step ()
if not self . quiet :
- print ( "Epochs since last best:" , self . boredom )
- print ( "Current max epochs:" , self . max_epochs )
+ _print ( "Epochs since last best:" , self . boredom )
+ _print ( "Current max epochs:" , self . max_epochs )
+
return self . current_epoch < self . max_epochs
@@ -239,27 +239,31 @@
Source code for hippynn.experiment.controllers
[docs]
- def push_epoch ( self , epoch , better_model , metric ):
+ def push_epoch ( self , epoch , better_model , metric , _print = print ):
if better_model :
if self . boredom > 0 and not self . quiet :
- print ( "Patience for training restored." )
+ _print ( "Patience for training restored." )
self . boredom = 0
self . last_best = epoch
- return super () . push_epoch ( epoch , better_model , metric )
+
return super () . push_epoch ( epoch , better_model , metric , _print = _print ) @property
def max_epochs ( self ):
-
return min ( self . last_best + self . patience , self . _max_epochs )
+
return min ( self . last_best + self . patience + 1 , self . _max_epochs )
+
# Developer note: The inheritance here is only so that pytorch lightning
+
# readily identifies this as a scheduler.
[docs]
-
class RaiseBatchSizeOnPlateau :
+
class RaiseBatchSizeOnPlateau ( ReduceLROnPlateau ):
"""
Learning rate scheduler compatible with pytorch schedulers.
+
Note: The "VERBOSE" Parameter has been deprecated and no longer does anything.
+
This roughly implements the scheme outlined in the following paper:
.. code-block:: none
@@ -288,9 +292,20 @@
Source code for hippynn.experiment.controllers patience= 10 ,
threshold = 0.0001 ,
threshold_mode = "rel" ,
- verbose = True ,
+ verbose = None , # DEPRECATED
controller = None ,
):
+ """
+
+ :param optimizer:
+ :param max_batch_size:
+ :param factor:
+ :param patience:
+ :param threshold:
+ :param threshold_mode:
+ :param verbose:
+ :param controller:
+ """
if threshold_mode not in ( "abs" , "rel" ):
raise ValueError ( "Mode must be 'abs' or 'rel'" )
@@ -301,14 +316,18 @@
Source code for hippynn.experiment.controllers factor= factor ,
threshold = threshold ,
threshold_mode = threshold_mode ,
- verbose = verbose ,
)
self . controller = controller
self . max_batch_size = max_batch_size
self . best_metric = float ( "inf" )
self . boredom = 0
- self . last_epoch = 0
+
self . last_epoch = 0
+
warnings . warn ( "Parameter verbose no longer supported for schedulers. It will be ignored." )
+
+
@property
+
def optimizer ( self ):
+
return self . inner . optimizer
[docs]
@@ -368,12 +387,9 @@
Source code for hippynn.experiment.controllers new_batch_size = min ( new_batch_size , self . max_batch_size )
self . controller . batch_size = new_batch_size
self . boredom = 0
- if self . inner . verbose :
- print ( "Raising batch size to" , new_batch_size )
+
if new_batch_size >= self . max_batch_size :
self . inner . last_epoch = self . last_epoch - 1
- if self . inner . verbose :
- print ( "Max batch size reached, Lowering learning rate from here." )
return
diff --git a/_modules/hippynn/experiment/lightning_trainer.html b/_modules/hippynn/experiment/lightning_trainer.html
new file mode 100644
index 00000000..ad7282ee
--- /dev/null
+++ b/_modules/hippynn/experiment/lightning_trainer.html
@@ -0,0 +1,543 @@
+
+
+
+
+
+
hippynn.experiment.lightning_trainer — hippynn 0+unknown documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ hippynn
+
+
+
+
+
+
+ Module code hippynn.experiment.lightning_trainer
+
+
+
+
+
+
+
+
+
Source code for hippynn.experiment.lightning_trainer
+"""
+Pytorch Lightning training interface.
+
+This module is somewhat experimental. Using pytorch lightning
+successfully in a distributed context may require understanding
+and adjusting the various settings related to parallelism, e.g.
+multiprocessing context, torch ddp backend, and how they interact
+with your HPC environment.
+
+Some features of hippynn experiments may not be implemented yet.
+ - The plotmaker is currently not supported.
+
+"""
+import warnings
+import copy
+from pathlib import Path
+
+import torch
+
+import pytorch_lightning as pl
+
+from .routines import TrainingModules
+from ..databases import Database
+from .routines import SetupParams , setup_training
+from ..graphs import GraphModule
+from .controllers import Controller
+from .metric_tracker import MetricTracker
+from .step_functions import get_step_function , StandardStep
+from ..tools import print_lr
+from . import serialization
+
+
+
+
[docs]
+
class HippynnLightningModule ( pl . LightningModule ):
+
+
[docs]
+
def __init__ (
+
self ,
+
model : GraphModule ,
+
loss : GraphModule ,
+
eval_loss : GraphModule ,
+
eval_names : list [ str ],
+
stopping_key : str ,
+
optimizer_list : list [ torch . optim . Optimizer ],
+
scheduler_list : list [ torch . optim . lr_scheduler ],
+
controller : Controller ,
+
metric_tracker : MetricTracker ,
+
inputs : list [ str ],
+
targets : list [ str ],
+
n_outputs : int ,
+
* args ,
+
** kwargs ,
+
): # forwards args and kwargs to where?
+
super () . __init__ ()
+
+
self . save_hyperparameters ( ignore = [ "loss" , "model" , "eval_loss" , "controller" , "optimizer_list" , "scheduler_list" ])
+
+
self . model = model
+
self . loss = loss
+
self . eval_loss = eval_loss
+
self . eval_names = eval_names
+
self . stopping_key = stopping_key
+
self . controller = controller
+
self . metric_tracker = metric_tracker
+
self . optimizer_list = optimizer_list
+
self . scheduler_list = scheduler_list
+
self . inputs = inputs
+
self . targets = targets
+
self . n_inputs = len ( self . inputs )
+
self . n_targets = len ( self . targets )
+
self . n_outputs = n_outputs
+
+
self . structure_file = None
+
+
self . _last_reload_dlene = None # storage for whether batch size should be changed.
+
+
# Storage for predictions across batches for eval mode.
+
self . eval_step_outputs = []
+
self . controller . optimizer = None
+
+
for optimizer in self . optimizer_list :
+
if not isinstance ( step_fn := get_step_function ( optimizer ), StandardStep ): # :=
+
raise NotImplementedError ( f "Optimzers with non-standard steps are not yet supported. { optimizer , step_fn } " )
+
+
if args or kwargs :
+
raise NotImplementedError ( "Generic args and kwargs not supported." )
+
+
+
+
[docs]
+
@classmethod
+
def from_experiment_setup ( cls , training_modules : TrainingModules , database : Database , setup_params : SetupParams , ** kwargs ):
+
training_modules , controller , metric_tracker = setup_training ( training_modules , setup_params )
+
return cls . from_train_setup ( training_modules , database , controller , metric_tracker , ** kwargs )
+
+
+
+
[docs]
+
@classmethod
+
def from_train_setup (
+
cls ,
+
training_modules : TrainingModules ,
+
database : Database ,
+
controller : Controller ,
+
metric_tracker : MetricTracker ,
+
callbacks = None ,
+
batch_callbacks = None ,
+
** kwargs ,
+
):
+
+
model , loss , evaluator = training_modules
+
+
warnings . warn ( "PytorchLightning hippynn trainer is still experimental." )
+
+
if evaluator . plot_maker is not None :
+
warnings . warn ( "plot_maker is not currently supported in pytorch lightning. The current plot_maker will be ignored." )
+
+
trainer = cls (
+
model = model ,
+
loss = loss ,
+
eval_loss = evaluator . loss ,
+
eval_names = evaluator . loss_names ,
+
optimizer_list = [ controller . optimizer ],
+
scheduler_list = controller . scheduler_list ,
+
stopping_key = controller . stopping_key ,
+
controller = controller ,
+
metric_tracker = metric_tracker ,
+
inputs = database . inputs ,
+
targets = database . targets ,
+
n_outputs = evaluator . n_outputs ,
+
** kwargs ,
+
)
+
+
# pytorch lightning is now in charge of stepping the scheduler.
+
controller . scheduler_list = []
+
+
if callbacks is not None or batch_callbacks is not None :
+
return NotImplemented ( "arbitrary callbacks are not yet supported with pytorch lightning." )
+
+
return trainer , HippynnDataModule ( database , controller . batch_size )
+
+
+
+
[docs]
+
def on_save_checkpoint ( self , checkpoint ) -> None :
+
+
# Note to future developers:
+
# trainer.log_dir property needs to be called on all ranks! This is weird but important;
+
# do not move trainer.log_dir inside of a rank zero operation!
+
# see https://github.com/Lightning-AI/pytorch-lightning/discussions/8321
+
# Thank you to https://github.com/semaphore-egg .
+
log_dir = self . trainer . log_dir
+
+
if not self . structure_file :
+
# Perform change on all ranks.
+
sf = serialization . DEFAULT_STRUCTURE_FNAME
+
self . structure_file = sf
+
+
if self . global_rank == 0 and not self . structure_file :
+
self . print ( "creating structure file." )
+
structure = dict (
+
model = self . model ,
+
loss = self . loss ,
+
eval_loss = self . eval_loss ,
+
controller = self . controller ,
+
optimizer_list = self . optimizer_list ,
+
scheduler_list = self . scheduler_list ,
+
)
+
path : Path = Path ( log_dir ) . joinpath ( sf )
+
self . print ( "Saving structure file at" , path )
+
torch . save ( obj = structure , f = path )
+
+
checkpoint [ "controller_state" ] = self . controller . state_dict ()
+
return
+
+
+
+
[docs]
+
@classmethod
+
def load_from_checkpoint ( cls , checkpoint_path , map_location = None , structure_file = None , hparams_file = None , strict = True , ** kwargs ):
+
+
if structure_file is None :
+
# Assume checkpoint_path is like <model_name>/version_<n>/checkpoints/<something>.chkpt
+
# and that experiment file is stored at <model_name>/version_<n>/experiment_structure.pt
+
structure_file = Path ( checkpoint_path )
+
structure_file = structure_file . parent . parent
+
structure_file = structure_file . joinpath ( serialization . DEFAULT_STRUCTURE_FNAME )
+
+
structure_args = torch . load ( structure_file )
+
+
return super () . load_from_checkpoint (
+
checkpoint_path , map_location = map_location , hparams_file = hparams_file , strict = strict , ** structure_args , ** kwargs
+
)
+
+
+
+
[docs]
+
def on_load_checkpoint ( self , checkpoint ) -> None :
+
cstate = checkpoint . pop ( "controller_state" )
+
self . controller . load_state_dict ( cstate )
+
return
+
+
+
+
+
+
+
[docs]
+
def on_train_epoch_start ( self ):
+
for optimizer in self . optimizer_list :
+
print_lr ( optimizer , print_ = self . print )
+
self . print ( "Batch size:" , self . trainer . train_dataloader . batch_size )
+
+
+
+
[docs]
+
def training_step ( self , batch , batch_idx ):
+
+
batch_inputs = batch [: self . n_inputs ]
+
batch_targets = batch [ - self . n_targets :]
+
+
batch_model_outputs = self . model ( * batch_inputs )
+
batch_train_loss = self . loss ( * batch_model_outputs , * batch_targets )[ 0 ]
+
+
self . log ( "train_loss" , batch_train_loss )
+
return batch_train_loss
+
+
+
def _eval_step ( self , batch , batch_idx ):
+
+
batch_inputs = batch [: self . n_inputs ]
+
batch_targets = batch [ - self . n_targets :]
+
+
# It is very, very common to fit to derivatives, e.g. force, in hippynn. Override lightning default.
+
with torch . autograd . set_grad_enabled ( True ):
+
batch_predictions = self . model ( * batch_inputs )
+
+
batch_predictions = [ bp . detach () for bp in batch_predictions ]
+
+
outputs = ( batch_predictions , batch_targets )
+
self . eval_step_outputs . append ( outputs )
+
return batch_predictions
+
+
+
[docs]
+
def validation_step ( self , batch , batch_idx ):
+
return self . _eval_step ( batch , batch_idx )
+
+
+
+
[docs]
+
def test_step ( self , batch , batch_idx ):
+
return self . _eval_step ( batch , batch_idx )
+
+
+
def _eval_epoch_end ( self , prefix ):
+
+
all_batch_predictions , all_batch_targets = zip ( * self . eval_step_outputs )
+
# now 'shape' (n_batch, n_outputs) -> need to transpose.
+
all_batch_predictions = [[ bpred [ i ] for bpred in all_batch_predictions ] for i in range ( self . n_outputs )]
+
# now 'shape' (n_batch, n_targets) -> need to transpose.
+
all_batch_targets = [[ bpred [ i ] for bpred in all_batch_targets ] for i in range ( self . n_targets )]
+
+
# now cat each prediction and target across the batch index.
+
all_predictions = [ torch . cat ( x , dim = 0 ) if x [ 0 ] . shape != () else x [ 0 ] for x in all_batch_predictions ]
+
all_targets = [ torch . cat ( x , dim = 0 ) for x in all_batch_targets ]
+
+
all_losses = [ x . item () for x in self . eval_loss ( * all_predictions , * all_targets )]
+
self . eval_step_outputs . clear () # free memory
+
+
loss_dict = { name : value for name , value in zip ( self . eval_names , all_losses )}
+
+
self . log_dict ({ prefix + k : v for k , v in loss_dict . items ()}, sync_dist = True )
+
+
return
+
+
+
[docs]
+
def on_validation_epoch_end ( self ):
+
self . _eval_epoch_end ( prefix = "valid_" )
+
return
+
+
+
+
[docs]
+
def on_test_epoch_end ( self ):
+
self . _eval_epoch_end ( prefix = "test_" )
+
return
+
+
+
def _eval_end ( self , prefix , when = None ) -> None :
+
if when is None :
+
if self . trainer . sanity_checking :
+
when = "Sanity Check"
+
else :
+
when = self . current_epoch
+
+
# Step 1: get metrics reduced from all ranks.
+
# Copied pattern from pytorch_lightning.
+
metrics = copy . deepcopy ( self . trainer . callback_metrics )
+
+
pre_len = len ( prefix )
+
loss_dict = { k [ pre_len :]: v . item () for k , v in metrics . items () if k . startswith ( prefix )}
+
+
loss_dict = { prefix [: - 1 ]: loss_dict } # strip underscore from prefix and wrap.
+
+
if self . trainer . sanity_checking :
+
self . print ( "Sanity check metric values:" )
+
self . metric_tracker . evaluation_print ( loss_dict , _print = self . print )
+
return
+
+
# Step 2: register metrics
+
out_ = self . metric_tracker . register_metrics ( loss_dict , when = when )
+
better_metrics , better_model , stopping_metric = out_
+
self . metric_tracker . evaluation_print_better ( loss_dict , better_metrics , _print = self . print )
+
+
continue_training = self . controller . push_epoch ( self . current_epoch , better_model , stopping_metric , _print = self . print )
+
+
if not continue_training :
+
self . print ( "Controller is terminating training." )
+
self . trainer . should_stop = True
+
+
# Step 3: Logic for changing the batch size without always requiring new dataloaders.
+
# Step 3a: don't do this when not testing.
+
if not self . trainer . training :
+
return
+
+
controller_batch_size = self . controller . batch_size
+
trainer_batch_size = self . trainer . train_dataloader . batch_size
+
if controller_batch_size != trainer_batch_size :
+
# Need to trigger a batch size change.
+
if self . _last_reload_dlene is None :
+
# save the original value of this variable to the pl module
+
self . _last_reload_dlene = self . trainer . reload_dataloaders_every_n_epochs
+
+
# TODO: Make this run even if there isn't an explicit datamodule?
+
self . trainer . datamodule . batch_size = controller_batch_size
+
# Tell PL lightning to reload the dataloaders now.
+
self . trainer . reload_dataloaders_every_n_epochs = 1
+
+
elif self . _last_reload_dlene is not None :
+
# Restore the last saved value from the pl module.
+
self . trainer . reload_dataloaders_every_n_epochs = self . _last_reload_dlene
+
self . _last_reload_dlene = None
+
else :
+
# Batch sizes match, and there's no variable to restore.
+
pass
+
return
+
+
+
[docs]
+
def on_validation_end ( self ):
+
self . _eval_end ( prefix = "valid_" )
+
return
+
+
+
+
[docs]
+
def on_test_end ( self ):
+
self . _eval_end ( prefix = "test_" , when = "test" )
+
return
+
+
[docs]
+
class LightingPrintStagesCallback ( pl . Callback ):
+
"""
+
This callback is for debugging only.
+
It prints whenever a callback stage is entered in pytorch lightning.
+
"""
+
+
for k in dir ( pl . Callback ):
+
if k . startswith ( "on_" ):
+
+
def some_method ( self , * args , _k = k , ** kwargs ):
+
all_args = kwargs . copy ()
+
all_args . update ({ i : a for i , a in enumerate ( args )})
+
int_args = { k : v for k , v in all_args . items () if isinstance ( v , int )}
+
print ( "Callback stage:" , _k , "with integer arguments:" , int_args )
+
+
exec ( f " { k } = some_method" )
+
del some_method
+
[docs]
+
class HippynnDataModule ( pl . LightningDataModule ):
+
+
[docs]
+
def __init__ ( self , database : Database , batch_size ):
+
super () . __init__ ()
+
self . database = database
+
self . batch_size = batch_size
+
+
+
+
[docs]
+
def train_dataloader ( self ):
+
return self . database . make_generator ( "train" , "train" , self . batch_size )
+
+
+
+
[docs]
+
def val_dataloader ( self ):
+
return self . database . make_generator ( "valid" , "eval" , self . batch_size )
+
+
+
+
[docs]
+
def test_dataloader ( self ):
+
return self . database . make_generator ( "test" , "eval" , self . batch_size )
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/_modules/hippynn/experiment/metric_tracker.html b/_modules/hippynn/experiment/metric_tracker.html
index 3b738653..2ec760a2 100644
--- a/_modules/hippynn/experiment/metric_tracker.html
+++ b/_modules/hippynn/experiment/metric_tracker.html
@@ -173,7 +173,6 @@
Source code for hippynn.experiment.metric_tracker except
KeyError :
if split_type not in self . best_metric_values :
# Haven't seen this split before!
-
print ( "ADDING " , split_type )
self . best_metric_values [ split_type ] = {}
better_metrics [ split_type ] = {}
better = True # old best was not found!
@@ -187,7 +186,7 @@
Source code for hippynn.experiment.metric_tracker else
:
self . other_metric_values [ when ] = metric_info
-
if self . stopping_key :
+
if self . stopping_key and "valid" in metric_info :
better_model = better_metrics . get ( "valid" , {}) . get ( self . stopping_key , False )
stopping_key_metric = metric_info [ "valid" ][ self . stopping_key ]
else :
@@ -199,24 +198,24 @@
Source code for hippynn.experiment.metric_tracker
[docs]
-
def evaluation_print ( self , evaluation_dict , quiet = None ):
+
def evaluation_print ( self , evaluation_dict , quiet = None , _print = print ):
if quiet is None :
quiet = self . quiet
if quiet :
return
-
table_evaluation_print ( evaluation_dict , self . metric_names , self . name_column_width )
+
table_evaluation_print ( evaluation_dict , self . metric_names , self . name_column_width , _print = _print )
[docs]
-
def evaluation_print_better ( self , evaluation_dict , better_dict , quiet = None ):
+
def evaluation_print_better ( self , evaluation_dict , better_dict , quiet = None , _print = print ):
if quiet is None :
quiet = self . quiet
if quiet :
return
-
table_evaluation_print_better ( evaluation_dict , better_dict , self . metric_names , self . name_column_width )
+
table_evaluation_print_better ( evaluation_dict , better_dict , self . metric_names , self . name_column_width , _print = print )
if self . stopping_key :
-
print (
+
_print (
"Best {} so far: {:>8.5g} " . format (
self . stopping_key , self . best_metric_values [ "valid" ][ self . stopping_key ]
)
@@ -235,7 +234,7 @@
Source code for hippynn.experiment.metric_tracker # Decoupled from the estate in case we want to more easily change print formatting.
[docs]
-
def table_evaluation_print_better ( evaluation_dict , better_dict , metric_names , n_columns ):
+
def table_evaluation_print_better ( evaluation_dict , better_dict , metric_names , n_columns , _print = print ):
"""
Print metric results as a table, add a '*' character for metrics in better_dict.
@@ -258,11 +257,11 @@
Source code for hippynn.experiment.metric_tracker header = " " * ( n_columns + 2 ) + "" . join ( " {:>14} " . format ( tn ) for tn in type_names )
rowstring = "{:<" + str ( n_columns ) + "}: " + " {}{:>10.5g} " * n_types
- print ( header )
- print ( "-" * len ( header ))
+ _print ( header )
+ _print ( "-" * len ( header ))
for n , valsbet in zip ( metric_names , transposed_values_better ):
rowoutput = [ k for bv in valsbet for k in bv ]
- print ( rowstring . format ( n , * rowoutput ))
+
_print ( rowstring . format ( n , * rowoutput ))
@@ -270,7 +269,7 @@
Source code for hippynn.experiment.metric_tracker # Decoupled from the estate in case we want to more easily change print formatting.
[docs]
-
def table_evaluation_print ( evaluation_dict , metric_names , n_columns ):
+
def table_evaluation_print ( evaluation_dict , metric_names , n_columns , _print = print ):
"""
Print metric results as a table.
@@ -288,11 +287,11 @@
Source code for hippynn.experiment.metric_tracker header = " " * ( n_columns + 2 ) + "" . join ( " {:>14} " . format ( tn ) for tn in type_names )
rowstring = "{:<" + str ( n_columns ) + "}: " + " {:>10.5g} " * n_types
- print ( header )
- print ( "-" * len ( header ))
+ _print ( header )
+ _print ( "-" * len ( header ))
for n , vals in zip ( metric_names , transposed_values ):
- print ( rowstring . format ( n , * vals ))
- print ( "-" * len ( header ))
+
_print ( rowstring . format ( n , * vals ))
+
_print ( "-" * len ( header ))
diff --git a/_modules/hippynn/experiment/routines.html b/_modules/hippynn/experiment/routines.html
index 8787754e..457fc1e7 100644
--- a/_modules/hippynn/experiment/routines.html
+++ b/_modules/hippynn/experiment/routines.html
@@ -395,9 +395,7 @@
Source code for hippynn.experiment.routines
print ( "Finishing up..." )
print ( "Training phase ended." )
- if store_metrics :
- with open ( "training_metrics.pkl" , "wb" ) as pfile :
- pickle . dump ( metric_tracker , pfile )
+ torch . save ( metric_tracker , "training_metrics.pt" )
best_model = metric_tracker . best_model
if best_model :
@@ -543,6 +541,7 @@ Source code for hippynn.experiment.routines
qprint ( "_" * 50 )
qprint ( "Epoch {} :" . format ( epoch ))
tools . print_lr ( optimizer )
+ qprint ( "Batch Size:" , controller . batch_size )
qprint ( flush = True , end = "" )
diff --git a/_modules/hippynn/experiment/serialization.html b/_modules/hippynn/experiment/serialization.html
index e428f4db..3d523e12 100644
--- a/_modules/hippynn/experiment/serialization.html
+++ b/_modules/hippynn/experiment/serialization.html
@@ -77,7 +77,9 @@
Source code for hippynn.experiment.serialization
"""
-checkpoint and state generation
+Checkpoint and state generation.
+
+As a user, in most cases you will only need the `load` functions here.
"""
from typing import Tuple , Union
@@ -90,7 +92,7 @@ Source code for hippynn.experiment.serialization
from ..graphs import GraphModule
from ..tools import device_fallback
from .assembly import TrainingModules
-
from .controllers import PatienceController
+
from .controllers import Controller
from .device import set_devices
from .metric_tracker import MetricTracker
@@ -101,13 +103,13 @@
Source code for hippynn.experiment.serialization
[docs]
def create_state (
model : GraphModule ,
-
controller : PatienceController ,
+
controller : Controller ,
metric_tracker : MetricTracker ,
) -> dict :
"""Create an experiment state dictionary.
:param model: current model
-
:param controller: patience controller
+
:param controller: controller
:param metric_tracker: current metrics
:return: dictionary containing experiment state.
:rtype: dict
@@ -126,7 +128,7 @@
Source code for hippynn.experiment.serialization
def create_structure_file (
training_modules : TrainingModules ,
database : Database ,
-
controller : PatienceController ,
+
controller : Controller ,
fname = DEFAULT_STRUCTURE_FNAME ,
) -> None :
"""
@@ -134,7 +136,7 @@
Source code for hippynn.experiment.serialization
:param training_modules: contains model, controller, and loss
:param database: database for training
-
:param controller: patience controller
+
:param controller: controller
:param fname: filename to save the checkpoint
:return: None
diff --git a/_modules/hippynn/graphs/gops.html b/_modules/hippynn/graphs/gops.html
index a8aedce0..2b28fe68 100644
--- a/_modules/hippynn/graphs/gops.html
+++ b/_modules/hippynn/graphs/gops.html
@@ -133,7 +133,8 @@
Source code for hippynn.graphs.gops
evaluation_inputs_list = []
evaluation_outputs_list = []
- unsatisfied_nodes = all_nodes . copy ()
+ # need to sort to get stable results between runs/processes.
+ unsatisfied_nodes = list ( sorted ( all_nodes , key = lambda node : node . name ))
satisfied_nodes = set ()
n = - 1
while len ( unsatisfied_nodes ) > 0 :
diff --git a/_modules/hippynn/interfaces/ase_interface/ase_database.html b/_modules/hippynn/interfaces/ase_interface/ase_database.html
index 5355c7a2..a77d015a 100644
--- a/_modules/hippynn/interfaces/ase_interface/ase_database.html
+++ b/_modules/hippynn/interfaces/ase_interface/ase_database.html
@@ -102,14 +102,14 @@ Source code for hippynn.interfaces.ase_interface.ase_database import
os
import numpy as np
-
from ase.io import read
+
from ase.io import read , iread
-
from ...tools import np_of_torchdefaultdtype
+
from ...tools import np_of_torchdefaultdtype , progress_bar
from ...databases.database import Database
from ...databases.restarter import Restartable
from typing import Union
from typing import List
-
+
import hippynn.tools
[docs]
@@ -169,11 +169,11 @@
Source code for hippynn.interfaces.ase_interface.ase_database var_list
= inputs + targets
try :
if isinstance ( filename , str ):
-
db = read ( directory + filename , index = ":" )
+
db = list ( progress_bar ( iread ( directory + filename , index = ":" ), desc = 'configs' )) #read(directory + filename, index=":")
elif isinstance ( filename , ( list , np . ndarray )):
db = []
-
for name in filename :
-
temp_db = read ( directory + name , index = ":" )
+
for name in progress_bar ( filename , desc = 'files' ):
+
temp_db = list ( progress_bar ( iread ( directory + name , index = ":" ), desc = 'configs' ))
db += temp_db
except FileNotFoundError as fee :
raise FileNotFoundError (
diff --git a/_modules/hippynn/layers/hiplayers.html b/_modules/hippynn/layers/hiplayers.html
index 5167421c..6f8adc85 100644
--- a/_modules/hippynn/layers/hiplayers.html
+++ b/_modules/hippynn/layers/hiplayers.html
@@ -426,16 +426,26 @@
Source code for hippynn.layers.hiplayers
n_atoms_real = in_features . shape [ 0 ]
sense_vals = self . sensitivity ( dist_pairs )
+ # Sensitivity stacking
+ sense_vec = sense_vals . unsqueeze ( 1 ) * ( coord_pairs / dist_pairs . unsqueeze ( 1 )) . unsqueeze ( 2 )
+ sense_vec = sense_vec . reshape ( - 1 , self . n_dist * 3 )
+ sense_stacked = torch . concatenate ([ sense_vals , sense_vec ], dim = 1 )
+
+ # Message passing, stack sensitivities to coalesce custom kernel call.
+ # shape (n_atoms, n_nu + 3*n_nu, n_feat)
+ env_features_stacked = custom_kernels . envsum ( sense_stacked , in_features , pair_first , pair_second )
+ # shape (n_atoms, 4, n_nu, n_feat)
+ env_features_stacked = env_features_stacked . reshape ( - 1 , 4 , self . n_dist , self . nf_in )
+
+ # separate to tensor components
+ env_features , env_features_vec = torch . split ( env_features_stacked , [ 1 , 3 ], dim = 1 )
+
# Scalar part
- env_features = custom_kernels . envsum ( sense_vals , in_features , pair_first , pair_second )
env_features = torch . reshape ( env_features , ( n_atoms_real , self . n_dist * self . nf_in ))
weights_rs = torch . reshape ( self . int_weights . permute ( 0 , 2 , 1 ), ( self . n_dist * self . nf_in , self . nf_out ))
features_out = torch . mm ( env_features , weights_rs )
# Vector part
- sense_vec = sense_vals . unsqueeze ( 1 ) * ( coord_pairs / dist_pairs . unsqueeze ( 1 )) . unsqueeze ( 2 )
- sense_vec = sense_vec . reshape ( - 1 , self . n_dist * 3 )
- env_features_vec = custom_kernels . envsum ( sense_vec , in_features , pair_first , pair_second )
env_features_vec = env_features_vec . reshape ( n_atoms_real * 3 , self . n_dist * self . nf_in )
features_out_vec = torch . mm ( env_features_vec , weights_rs )
features_out_vec = features_out_vec . reshape ( n_atoms_real , 3 , self . nf_out )
@@ -475,19 +485,41 @@ Source code for hippynn.layers.hiplayers
n_atoms_real = in_features . shape [ 0 ]
sense_vals = self . sensitivity ( dist_pairs )
- # Scalar part
- env_features = custom_kernels . envsum ( sense_vals , in_features , pair_first , pair_second )
+ ####
+ # Sensitivity calculations
+ # scalar: sense_vals
+ # vector: sense_vec
+ # quadrupole: sense_quad
+ rhats = coord_pairs / dist_pairs . unsqueeze ( 1 )
+ sense_vec = sense_vals . unsqueeze ( 1 ) * rhats . unsqueeze ( 2 )
+ sense_vec = sense_vec . reshape ( - 1 , self . n_dist * 3 )
+ rhatsquad = rhats . unsqueeze ( 1 ) * rhats . unsqueeze ( 2 )
+ rhatsquad = ( rhatsquad + rhatsquad . transpose ( 1 , 2 )) / 2
+ tr = torch . diagonal ( rhatsquad , dim1 = 1 , dim2 = 2 ) . sum ( dim = 1 ) / 3.0 # Add divide by 3 early to save flops
+ tr = tr . unsqueeze ( 1 ) . unsqueeze ( 2 ) * torch . eye ( 3 , dtype = tr . dtype , device = tr . device ) . unsqueeze ( 0 )
+ rhatsquad = rhatsquad - tr
+ rhatsqflat = rhatsquad . reshape ( - 1 , 9 )[:, self . upper_ind ] # Upper-diagonal part
+ sense_quad = sense_vals . unsqueeze ( 1 ) * rhatsqflat . unsqueeze ( 2 )
+ sense_quad = sense_quad . reshape ( - 1 , self . n_dist * 5 )
+ sense_stacked = torch . concatenate ([ sense_vals , sense_vec , sense_quad ], dim = 1 )
+
+ # Message passing, stack sensitivities to coalesce custom kernel call.
+ # shape (n_atoms, n_nu + 3*n_nu + 5*n_nu, n_feat)
+ env_features_stacked = custom_kernels . envsum ( sense_stacked , in_features , pair_first , pair_second )
+ # shape (n_atoms, 9, n_nu, n_feat)
+ env_features_stacked = env_features_stacked . reshape ( - 1 , 9 , self . n_dist , self . nf_in )
+
+ # separate to tensor components
+ env_features , env_features_vec , env_features_quad = torch . split ( env_features_stacked , [ 1 , 3 , 5 ], dim = 1 )
+
+ # Scalar stuff.
env_features = torch . reshape ( env_features , ( n_atoms_real , self . n_dist * self . nf_in ))
weights_rs = torch . reshape ( self . int_weights . permute ( 0 , 2 , 1 ), ( self . n_dist * self . nf_in , self . nf_out ))
features_out = torch . mm ( env_features , weights_rs )
# Vector part
# Sensitivity
- rhats = coord_pairs / dist_pairs . unsqueeze ( 1 )
- sense_vec = sense_vals . unsqueeze ( 1 ) * rhats . unsqueeze ( 2 )
- sense_vec = sense_vec . reshape ( - 1 , self . n_dist * 3 )
# Weights
- env_features_vec = custom_kernels . envsum ( sense_vec , in_features , pair_first , pair_second )
env_features_vec = env_features_vec . reshape ( n_atoms_real * 3 , self . n_dist * self . nf_in )
features_out_vec = torch . mm ( env_features_vec , weights_rs )
# Norm and scale
@@ -498,16 +530,7 @@ Source code for hippynn.layers.hiplayers
# Quadrupole part
# Sensitivity
- rhatsquad = rhats . unsqueeze ( 1 ) * rhats . unsqueeze ( 2 )
- rhatsquad = ( rhatsquad + rhatsquad . transpose ( 1 , 2 )) / 2
- tr = torch . diagonal ( rhatsquad , dim1 = 1 , dim2 = 2 ) . sum ( dim = 1 ) / 3.0 # Add divide by 3 early to save flops
- tr = tr . unsqueeze ( 1 ) . unsqueeze ( 2 ) * torch . eye ( 3 , dtype = tr . dtype , device = tr . device ) . unsqueeze ( 0 )
- rhatsquad = rhatsquad - tr
- rhatsqflat = rhatsquad . reshape ( - 1 , 9 )[:, self . upper_ind ] # Upper-diagonal part
- sense_quad = sense_vals . unsqueeze ( 1 ) * rhatsqflat . unsqueeze ( 2 )
- sense_quad = sense_quad . reshape ( - 1 , self . n_dist * 5 )
# Weights
- env_features_quad = custom_kernels . envsum ( sense_quad , in_features , pair_first , pair_second )
env_features_quad = env_features_quad . reshape ( n_atoms_real * 5 , self . n_dist * self . nf_in )
features_out_quad = torch . mm ( env_features_quad , weights_rs ) ##sum v b
features_out_quad = features_out_quad . reshape ( n_atoms_real , 5 , self . nf_out )
@@ -519,6 +542,7 @@ Source code for hippynn.layers.hiplayers
# Scales
features_out_quad = features_out_quad * self . quadscales . unsqueeze ( 0 )
+ # Combine
features_out_selfpart = self . selfint ( in_features )
features_out_total = features_out + features_out_vec + features_out_quad + features_out_selfpart
diff --git a/_modules/hippynn/pretraining.html b/_modules/hippynn/pretraining.html
index 97d8e47c..c8a5d9b4 100644
--- a/_modules/hippynn/pretraining.html
+++ b/_modules/hippynn/pretraining.html
@@ -150,7 +150,7 @@ Source code for hippynn.pretraining
if not eo_layer . weight . data . shape [ - 1 ] == eovals . shape [ - 1 ]:
raise ValueError ( "The shape of the computed E0 values does not match the shape expected by the model." )
- eo_layer . weight . data = eovals . reshape ( 1 , - 1 )
+ eo_layer . weight . data = eovals . reshape ( 1 , - 1 )
print ( "Computed E0 energies:" , eovals )
eo_layer . weight . data = eovals . expand_as ( eo_layer . weight . data )
eo_layer . weight . requires_grad_ ( trainable_after )
diff --git a/_modules/hippynn/tools.html b/_modules/hippynn/tools.html
index 76315e82..8b253050 100644
--- a/_modules/hippynn/tools.html
+++ b/_modules/hippynn/tools.html
@@ -243,9 +243,9 @@ Source code for hippynn.tools
[docs]
-
def print_lr ( optimizer ):
+
def print_lr ( optimizer , print_ = print ):
for i , param_group in enumerate ( optimizer . param_groups ):
-
print ( "Learning rate: {:>10.5g} " . format ( param_group [ "lr" ]))
+ print_ ( "Learning rate: {:>10.5g} " . format ( param_group [ "lr" ])) Source code for hippynn.tools
+
+
[docs]
+
def recursive_param_count ( state_dict , n = 0 ):
+
for k , v in state_dict . items ():
+
if isinstance ( v , torch . Tensor ):
+
n += v . numel ()
+
elif isinstance ( v , dict ):
+
n += recursive_param_count ( v )
+
elif isinstance ( v , ( list , tuple )):
+
n += recursive_param_count ({ i : x for i , x in enumerate ( v )})
+
elif isinstance ( v , ( float , int )):
+
n += 1
+
elif v is None :
+
pass
+
else :
+
raise TypeError ( f 'Unknown type { type ( v ) =} , value= { v } ' )
+
return n All modules for which code is available
hippynn.custom_kernels.env_cupy hippynn.custom_kernels.env_numba hippynn.custom_kernels.env_pytorch
+
hippynn.custom_kernels.env_triton hippynn.custom_kernels.tensor_wrapper hippynn.custom_kernels.test_env_numba hippynn.custom_kernels.utils
@@ -91,6 +92,7 @@
All modules for which code is available
hippynn.experiment.controllers hippynn.experiment.device hippynn.experiment.evaluator
+
hippynn.experiment.lightning_trainer hippynn.experiment.metric_tracker hippynn.experiment.routines hippynn.experiment.serialization
diff --git a/_sources/api_documentation/hippynn.experiment.lightning_trainer.rst.txt b/_sources/api_documentation/hippynn.experiment.lightning_trainer.rst.txt
new file mode 100644
index 00000000..0ec1714c
--- /dev/null
+++ b/_sources/api_documentation/hippynn.experiment.lightning_trainer.rst.txt
@@ -0,0 +1,7 @@
+hippynn.experiment.lightning\_trainer module
+============================================
+
+.. automodule:: hippynn.experiment.lightning_trainer
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/_sources/api_documentation/hippynn.experiment.rst.txt b/_sources/api_documentation/hippynn.experiment.rst.txt
index 3758f813..73ed4b81 100644
--- a/_sources/api_documentation/hippynn.experiment.rst.txt
+++ b/_sources/api_documentation/hippynn.experiment.rst.txt
@@ -16,6 +16,7 @@ Submodules
hippynn.experiment.controllers
hippynn.experiment.device
hippynn.experiment.evaluator
+ hippynn.experiment.lightning_trainer
hippynn.experiment.metric_tracker
hippynn.experiment.routines
hippynn.experiment.serialization
diff --git a/_sources/installation.rst.txt b/_sources/installation.rst.txt
index 54384e44..4064fea9 100644
--- a/_sources/installation.rst.txt
+++ b/_sources/installation.rst.txt
@@ -10,16 +10,18 @@ Requirements:
* Python_ >= 3.9
* pytorch_ >= 1.9
* numpy_
+
Optional Dependencies:
* triton_ (recommended, for improved GPU performance)
* numba_ (recommended for improved CPU performance)
- * cupy_ (Alternative for accelerating GPU performance)
- * ASE_ (for usage with ase)
+ * cupy_ (alternative for accelerating GPU performance)
+ * ASE_ (for usage with ase and other misc. features)
* matplotlib_ (for plotting)
* tqdm_ (for progress bars)
- * graphviz_ (for viewing model graphs as figures)
+ * graphviz_ (for visualizing model graphs)
* h5py_ (for loading ani-h5 datasets)
* pyanitools_ (for loading ani-h5 datasets)
+ * pytorch-lightning_ (for distributed training)
Interfacing codes:
* ASE_
@@ -40,7 +42,7 @@ Interfacing codes:
.. _ASE: https://wiki.fysik.dtu.dk/ase/
.. _LAMMPS: https://www.lammps.org/
.. _PYSEQM: https://github.com/lanl/PYSEQM
-
+.. _pytorch-lightning: https://github.com/Lightning-AI/pytorch-lightning
Installation Instructions
^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -67,9 +69,6 @@ Clone the hippynn_ repository and navigate into it, e.g.::
.. _hippynn: https://github.com/lanl/hippynn/
-.. note::
- If you wish to do a cpu-only install, you may need to comment
- out ``cupy`` from the conda_requirements.txt file.
Dependencies using conda
........................
@@ -78,6 +77,10 @@ Install dependencies from conda using recommended channels::
$ conda install -c pytorch -c conda-forge --file conda_requirements.txt
+.. note::
+ If you wish to do a cpu-only install, you may need to comment
+ out ``cupy`` from the conda_requirements.txt file.
+
Dependencies using pip
.......................
diff --git a/_sources/user_guide/settings.rst.txt b/_sources/user_guide/settings.rst.txt
index d8657de4..c6764206 100644
--- a/_sources/user_guide/settings.rst.txt
+++ b/_sources/user_guide/settings.rst.txt
@@ -31,7 +31,7 @@ The following settings are available:
- Dynamic
* - PROGRESS
- Progress bars function during training, evaluation, and prediction
- - tqdm, none
+ - tqdm, none, or floating point string specifying default update rate in seconds (default 1).
- tqdm
- Yes, but assign this to a generator-wrapper such as ``tqdm.tqdm``, or with a python ``None`` to disable. The wrapper must accept ``tqdm`` arguments, although it technically doesn't have to do anything with them.
* - DEFAULT_PLOT_FILETYPE
diff --git a/api_documentation/hippynn.custom_kernels.env_triton.html b/api_documentation/hippynn.custom_kernels.env_triton.html
index 44efd06c..1e11e09f 100644
--- a/api_documentation/hippynn.custom_kernels.env_triton.html
+++ b/api_documentation/hippynn.custom_kernels.env_triton.html
@@ -59,7 +59,16 @@
hippynn.custom_kernels.env_cupy module hippynn.custom_kernels.env_numba module hippynn.custom_kernels.env_pytorch module
-
hippynn.custom_kernels.env_triton module
+
hippynn.custom_kernels.env_triton module
+hippynn.custom_kernels.fast_convert module hippynn.custom_kernels.tensor_wrapper module hippynn.custom_kernels.test_env_cupy module
@@ -116,8 +125,47 @@
-
-hippynn.custom_kernels.env_triton module
+
+hippynn.custom_kernels.env_triton module
+
+
+config_pruner ( configs nargs ** kwargs ) [source]
+Trims the unnecessary config options based on the sens. and feat. sizes
+
+
+
+
+envsum ( sense features pfirst psecond ) [source]
+
+
+
+
+envsum_triton ( sensitivities features pair_first pair_second atom_ids atom_starts out_env = None ) [source]
+
+
+
+
+featsum ( env sense pfirst psecond ) [source]
+
+
+
+
+featsum_triton ( env sense pair_first pair_second atom2_ids atom2_starts out_feat = None ) [source]
+
+
+
+
+get_autotune_config ( ) [source]
+Create a list of config options for the kernels
+TODO: Need to spend time actually figuring out more reasonable options
+targeted for modern GPUs
+
+
+
+
+sensesum ( env features pair_first pair_second out_sense = None ) [source]
+
+
diff --git a/api_documentation/hippynn.custom_kernels.html b/api_documentation/hippynn.custom_kernels.html
index 9f8c3800..221d25a4 100644
--- a/api_documentation/hippynn.custom_kernels.html
+++ b/api_documentation/hippynn.custom_kernels.html
@@ -186,7 +186,16 @@ hippynn.custom_kernels.env_triton module hippynn.custom_kernels.env_triton module
+hippynn.custom_kernels.fast_convert module
diff --git a/api_documentation/hippynn.custom_kernels.test_env_triton.html b/api_documentation/hippynn.custom_kernels.test_env_triton.html
index a4076a9c..33c34c9b 100644
--- a/api_documentation/hippynn.custom_kernels.test_env_triton.html
+++ b/api_documentation/hippynn.custom_kernels.test_env_triton.html
@@ -116,8 +116,8 @@
-
-hippynn.custom_kernels.test_env_triton module
+
+hippynn.custom_kernels.test_env_triton module
diff --git a/api_documentation/hippynn.databases.SNAPJson.html b/api_documentation/hippynn.databases.SNAPJson.html
index 6b2bb4c2..025c5d4f 100644
--- a/api_documentation/hippynn.databases.SNAPJson.html
+++ b/api_documentation/hippynn.databases.SNAPJson.html
@@ -149,6 +149,9 @@
allow_unfound – If true, skip checking if the needed inputs and targets are found.
This allows setting inputs=None and/or targets=None.
auto_split – If true, look for keys like “split_*” to make initial splits from. See write_npz() method.
device – if set, move the dataset to this device after splitting.
dataloader_kwargs – dictionary, passed to pytorch dataloaders in addition to num_workers, pin_memory.
+Refer to pytorch documentation for details.
quiet – If True, print little or nothing while loading.
Base database functionality from dictionary of numpy arrays
-class Database ( arr_dict inputs targets seed test_size = None valid_size = None num_workers = 0 pin_memory = True allow_unfound = False auto_split = False device = None quiet = False ) [source]
+class Database ( arr_dict: dict[str, ~torch.Tensor], inputs: list[str], targets: list[str], seed: [<class 'int'>, <class 'numpy.random.mtrand.RandomState'>, <class 'tuple'>], test_size: float | int | None = None, valid_size: float | int | None = None, num_workers: int = 0, pin_memory: bool = True, allow_unfound: bool = False, auto_split: bool = False, device: ~torch.device | None = None, dataloader_kwargs: dict[str, object] | None = None, quiet=False ) [source] Bases: object
Class for holding a pytorch dataset, splitting it, generating dataloaders, etc.”
-__init__ ( arr_dict inputs targets seed test_size = None valid_size = None num_workers = 0 pin_memory = True allow_unfound = False auto_split = False device = None quiet = False ) [source]
+__init__ ( arr_dict: dict[str, ~torch.Tensor], inputs: list[str], targets: list[str], seed: [<class 'int'>, <class 'numpy.random.mtrand.RandomState'>, <class 'tuple'>], test_size: float | int | None = None, valid_size: float | int | None = None, num_workers: int = 0, pin_memory: bool = True, allow_unfound: bool = False, auto_split: bool = False, device: ~torch.device | None = None, dataloader_kwargs: dict[str, object] | None = None, quiet=False ) [source]
Parameters:
@@ -169,6 +169,9 @@
allow_unfound – If true, skip checking if the needed inputs and targets are found.
This allows setting inputs=None and/or targets=None.
auto_split – If true, look for keys like “split_*” to make initial splits from. See write_npz() method.
device – if set, move the dataset to this device after splitting.
dataloader_kwargs – dictionary, passed to pytorch dataloaders in addition to num_workers, pin_memory.
+Refer to pytorch documentation for details.
quiet – If True, print little or nothing while loading.
-write_npz ( file : str record_split_masks : bool = True overwrite : bool = False split_prefix = None return_only = False ) [source]
+write_npz ( file : str record_split_masks : bool = True compressed : bool = True overwrite : bool = False split_prefix = None return_only = False ) [source]
Parameters:
diff --git a/api_documentation/hippynn.databases.html b/api_documentation/hippynn.databases.html
index ad2946bd..2fd00500 100644
--- a/api_documentation/hippynn.databases.html
+++ b/api_documentation/hippynn.databases.html
@@ -195,6 +195,9 @@
allow_unfound – If true, skip checking if the needed inputs and targets are found.
This allows setting inputs=None and/or targets=None.
auto_split – If true, look for keys like “split_*” to make initial splits from. See write_npz() method.
device – if set, move the dataset to this device after splitting.
dataloader_kwargs – dictionary, passed to pytorch dataloaders in addition to num_workers, pin_memory.
+Refer to pytorch documentation for details.
quiet – If True, print little or nothing while loading.
-class Database ( arr_dict inputs targets seed test_size = None valid_size = None num_workers = 0 pin_memory = True allow_unfound = False auto_split = False device = None quiet = False ) [source]
+class Database ( arr_dict: dict[str, ~torch.Tensor], inputs: list[str], targets: list[str], seed: [<class 'int'>, <class 'numpy.random.mtrand.RandomState'>, <class 'tuple'>], test_size: float | int | None = None, valid_size: float | int | None = None, num_workers: int = 0, pin_memory: bool = True, allow_unfound: bool = False, auto_split: bool = False, device: ~torch.device | None = None, dataloader_kwargs: dict[str, object] | None = None, quiet=False ) [source] Bases: object
Class for holding a pytorch dataset, splitting it, generating dataloaders, etc.”
-__init__ ( arr_dict inputs targets seed test_size = None valid_size = None num_workers = 0 pin_memory = True allow_unfound = False auto_split = False device = None quiet = False ) [source]
+__init__ ( arr_dict: dict[str, ~torch.Tensor], inputs: list[str], targets: list[str], seed: [<class 'int'>, <class 'numpy.random.mtrand.RandomState'>, <class 'tuple'>], test_size: float | int | None = None, valid_size: float | int | None = None, num_workers: int = 0, pin_memory: bool = True, allow_unfound: bool = False, auto_split: bool = False, device: ~torch.device | None = None, dataloader_kwargs: dict[str, object] | None = None, quiet=False ) [source]
Parameters:
@@ -248,6 +251,9 @@
allow_unfound – If true, skip checking if the needed inputs and targets are found.
This allows setting inputs=None and/or targets=None.
auto_split – If true, look for keys like “split_*” to make initial splits from. See write_npz() method.
device – if set, move the dataset to this device after splitting.
dataloader_kwargs – dictionary, passed to pytorch dataloaders in addition to num_workers, pin_memory.
+Refer to pytorch documentation for details.
quiet – If True, print little or nothing while loading.
-write_npz ( file : str record_split_masks : bool = True overwrite : bool = False split_prefix = None return_only = False ) [source]
+write_npz ( file : str record_split_masks : bool = True compressed : bool = True overwrite : bool = False split_prefix = None return_only = False ) [source]
Parameters:
@@ -516,6 +522,9 @@
allow_unfound – If true, skip checking if the needed inputs and targets are found.
This allows setting inputs=None and/or targets=None.
auto_split – If true, look for keys like “split_*” to make initial splits from. See write_npz() method.
device – if set, move the dataset to this device after splitting.
dataloader_kwargs – dictionary, passed to pytorch dataloaders in addition to num_workers, pin_memory.
+Refer to pytorch documentation for details.
quiet – If True, print little or nothing while loading.
allow_unfound – If true, skip checking if the needed inputs and targets are found.
This allows setting inputs=None and/or targets=None.
auto_split – If true, look for keys like “split_*” to make initial splits from. See write_npz() method.
device – if set, move the dataset to this device after splitting.
dataloader_kwargs – dictionary, passed to pytorch dataloaders in addition to num_workers, pin_memory.
+Refer to pytorch documentation for details.
quiet – If True, print little or nothing while loading.
allow_unfound – If true, skip checking if the needed inputs and targets are found.
This allows setting inputs=None and/or targets=None.
auto_split – If true, look for keys like “split_*” to make initial splits from. See write_npz() method.
device – if set, move the dataset to this device after splitting.
dataloader_kwargs – dictionary, passed to pytorch dataloaders in addition to num_workers, pin_memory.
+Refer to pytorch documentation for details.
quiet – If True, print little or nothing while loading.
allow_unfound – If true, skip checking if the needed inputs and targets are found.
This allows setting inputs=None and/or targets=None.
auto_split – If true, look for keys like “split_*” to make initial splits from. See write_npz() method.
device – if set, move the dataset to this device after splitting.
dataloader_kwargs – dictionary, passed to pytorch dataloaders in addition to num_workers, pin_memory.
+Refer to pytorch documentation for details.
quiet – If True, print little or nothing while loading.
hippynn.experiment.controllers module hippynn.experiment.device module hippynn.experiment.evaluator module hippynn.experiment.lightning_trainer module hippynn.experiment.metric_tracker module hippynn.experiment.routines module hippynn.experiment.serialization module RaiseBatchSizeOnPlateau hippynn.experiment.device module hippynn.experiment.evaluator module hippynn.experiment.lightning_trainer module hippynn.experiment.metric_tracker module hippynn.experiment.routines module hippynn.experiment.serialization module
-push_epoch ( epoch better_model metric ) [source]
+push_epoch ( epoch better_model metric _print=<built-in function print> ) [source]
@@ -226,16 +228,17 @@
-push_epoch ( epoch better_model metric ) [source]
+push_epoch ( epoch better_model metric _print=<built-in function print> ) [source]
-class RaiseBatchSizeOnPlateau ( optimizer max_batch_size factor = 0.5 patience = 10 threshold = 0.0001 threshold_mode = 'rel' verbose = True controller = None ) [source]
-Bases: object
+class RaiseBatchSizeOnPlateau ( optimizer max_batch_size factor = 0.5 patience = 10 threshold = 0.0001 threshold_mode = 'rel' verbose = None controller = None ) [source] Bases: ReduceLROnPlateau
Learning rate scheduler compatible with pytorch schedulers.
+Note: The “VERBOSE” Parameter has been deprecated and no longer does anything.
This roughly implements the scheme outlined in the following paper:
-__init__ ( optimizer max_batch_size factor = 0.5 patience = 10 threshold = 0.0001 threshold_mode = 'rel' verbose = True controller = None ) [source]
-
+
__init__ ( optimizer ,
max_batch_size ,
factor = 0.5 ,
patience = 10 ,
threshold = 0.0001 ,
threshold_mode = 'rel' ,
verbose = None ,
controller = None ) [source]
+
+Parameters:
+
+optimizer
max_batch_size
factor
patience
threshold
threshold_mode
verbose
controller
+
+
load_state_dict ( state_dict ) [source]
+Loads the schedulers state.
+
+Args:
+state_dict (dict): scheduler state. Should be an object returned from a call to state_dict()
+
+
+
+
+
+
+property optimizer
@@ -269,7 +299,10 @@
state_dict ( ) [source]
-
+Returns the state of the scheduler as a dict
+It contains an entry for every variable in self.__dict__ which
+is not the optimizer.
+
diff --git a/api_documentation/hippynn.experiment.device.html b/api_documentation/hippynn.experiment.device.html
index a8c128ce..f2d90aec 100644
--- a/api_documentation/hippynn.experiment.device.html
+++ b/api_documentation/hippynn.experiment.device.html
@@ -69,6 +69,7 @@
hippynn.experiment.evaluator module hippynn.experiment.lightning_trainer module hippynn.experiment.metric_tracker module hippynn.experiment.routines module hippynn.experiment.serialization module hippynn.experiment.lightning_trainer module hippynn.experiment.metric_tracker module hippynn.experiment.routines module hippynn.experiment.serialization module
hippynn.experiment.controllers module hippynn.experiment.device module hippynn.experiment.evaluator module hippynn.experiment.lightning_trainer module hippynn.experiment.metric_tracker module hippynn.experiment.routines module hippynn.experiment.serialization module SubmodulesRaiseBatchSizeOnPlateau
RaiseBatchSizeOnPlateau.__init__() RaiseBatchSizeOnPlateau.load_state_dict() RaiseBatchSizeOnPlateau.optimizer RaiseBatchSizeOnPlateau.set_controller() RaiseBatchSizeOnPlateau.state_dict() RaiseBatchSizeOnPlateau.step() hippynn.experiment.metric_tracker module
MetricTracker
MetricTracker.__init__() hippynn.experiment.lightning_trainer module — hippynn 0+unknown documentation
+
+
+
+
+
+
+ hippynn
+
+
+
+
+
+
+
+
+
+hippynn.experiment.lightning_trainer module
+Pytorch Lightning training interface.
+This module is somewhat experimental. Using pytorch lightning
+successfully in a distributed context may require understanding
+and adjusting the various settings related to parallelism, e.g.
+multiprocessing context, torch ddp backend, and how they interact
+with your HPC environment.
+
+Some features of hippynn experiments may not be implemented yet.
+
+
+
+
+class HippynnDataModule ( * args : Any ** kwargs : Any ) [source]
+Bases: LightningDataModule
+
+
+__init__ ( database : Database batch_size ) [source]
+
+
+
+
+test_dataloader ( ) [source]
+
+
+
+
+train_dataloader ( ) [source]
+
+
+
+
+val_dataloader ( ) [source]
+
+
+
+
+
+
+class HippynnLightningModule ( * args : Any ** kwargs : Any ) [source]
+Bases: LightningModule
+
+
+__init__ ( model: ~hippynn.graphs.graph.GraphModule, loss: ~hippynn.graphs.graph.GraphModule, eval_loss: ~hippynn.graphs.graph.GraphModule, eval_names: list[str], stopping_key: str, optimizer_list: list[~torch.optim.optimizer.Optimizer], scheduler_list: list[<module 'torch.optim.lr_scheduler' from '/opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/torch/optim/lr_scheduler.py'>], controller: ~hippynn.experiment.controllers.Controller, metric_tracker: ~hippynn.experiment.metric_tracker.MetricTracker, inputs: list[str], targets: list[str], n_outputs: int, *args, **kwargs ) [source]
+
+
+
+
+configure_optimizers ( ) [source]
+
+
+
+
+classmethod from_experiment_setup ( training_modules : TrainingModules database : Database setup_params : SetupParams ** kwargs ) [source]
+
+
+
+
+classmethod from_train_setup ( training_modules : TrainingModules database : Database controller : Controller metric_tracker : MetricTracker callbacks = None batch_callbacks = None ** kwargs ) [source]
+
+
+
+
+classmethod load_from_checkpoint ( checkpoint_path map_location = None structure_file = None hparams_file = None strict = True ** kwargs ) [source]
+
+
+
+
+on_load_checkpoint ( checkpoint ) → None [source]
+
+
+
+
+on_save_checkpoint ( checkpoint ) → None [source]
+
+
+
+
+on_test_end ( ) [source]
+
+
+
+
+on_test_epoch_end ( ) [source]
+
+
+
+
+on_train_epoch_start ( ) [source]
+
+
+
+
+on_validation_end ( ) [source]
+
+
+
+
+on_validation_epoch_end ( ) [source]
+
+
+
+
+test_step ( batch batch_idx ) [source]
+
+
+
+
+training_step ( batch batch_idx ) [source]
+
+
+
+
+validation_step ( batch batch_idx ) [source]
+
+
+
+
+
+
+class LightingPrintStagesCallback ( * args : Any ** kwargs : Any ) [source]
+Bases: Callback
+This callback is for debugging only.
+It prints whenever a callback stage is entered in pytorch lightning.
+
+
+k = '__weakref__'
+
+
+
+
+
+
+
+
+
+
+
+
+
hippynn.experiment.controllers module hippynn.experiment.device module hippynn.experiment.evaluator module hippynn.experiment.lightning_trainer module hippynn.experiment.metric_tracker module
-evaluation_print ( evaluation_dict quiet = None ) [source]
+evaluation_print ( evaluation_dict quiet=None _print=<built-in function print> ) [source]
-evaluation_print_better ( evaluation_dict better_dict quiet = None ) [source]
+evaluation_print_better ( evaluation_dict better_dict quiet=None _print=<built-in function print> ) [source]
@@ -217,7 +218,7 @@
-table_evaluation_print ( evaluation_dict metric_names n_columns ) [source]
+table_evaluation_print ( evaluation_dict metric_names n_columns _print=<built-in function print> ) [source] Print metric results as a table.
Parameters:
@@ -235,7 +236,7 @@
-table_evaluation_print_better ( evaluation_dict better_dict metric_names n_columns ) [source]
+table_evaluation_print_better ( evaluation_dict better_dict metric_names n_columns _print=<built-in function print> ) [source] Print metric results as a table, add a ‘*’ character for metrics in better_dict.
Parameters:
@@ -258,7 +259,7 @@
diff --git a/api_documentation/hippynn.experiment.routines.html b/api_documentation/hippynn.experiment.routines.html
index 854ebfb3..7211e7b0 100644
--- a/api_documentation/hippynn.experiment.routines.html
+++ b/api_documentation/hippynn.experiment.routines.html
@@ -66,6 +66,7 @@
hippynn.experiment.controllers module hippynn.experiment.device module hippynn.experiment.evaluator module hippynn.experiment.lightning_trainer module hippynn.experiment.metric_tracker module hippynn.experiment.routines module
SetupParams
diff --git a/api_documentation/hippynn.experiment.serialization.html b/api_documentation/hippynn.experiment.serialization.html
index 7d878ee6..2582389e 100644
--- a/api_documentation/hippynn.experiment.serialization.html
+++ b/api_documentation/hippynn.experiment.serialization.html
@@ -66,6 +66,7 @@
hippynn.experiment.controllers module hippynn.experiment.device module hippynn.experiment.evaluator module hippynn.experiment.lightning_trainer module hippynn.experiment.metric_tracker module hippynn.experiment.routines module hippynn.experiment.serialization module
@@ -130,7 +131,8 @@
hippynn.experiment.serialization module
-checkpoint and state generation
+Checkpoint and state generation.
+As a user, in most cases you will only need the load functions here.
check_mapping_devices ( map_location model_device ) [source]
@@ -153,13 +155,13 @@
-create_state ( model : GraphModule controller : PatienceController metric_tracker : MetricTracker ) → dict [source]
+create_state ( model : GraphModule controller : Controller metric_tracker : MetricTracker ) → dict [source] Create an experiment state dictionary.
Parameters:
@@ -174,14 +176,14 @@
-create_structure_file ( training_modules : TrainingModules database : Database controller : PatienceController fname = 'experiment_structure.pt' ) → None [source]
+create_structure_file ( training_modules : TrainingModules database : Database controller : Controller fname = 'experiment_structure.pt' ) → None [source] Save an experiment structure. (i.e. full model, not just state_dict).
Parameters:
training_modules – contains model, controller, and loss
database – database for training
controller – patience controller
controller – controller
fname – filename to save the checkpoint
hippynn.experiment.controllers module hippynn.experiment.device module hippynn.experiment.evaluator module hippynn.experiment.lightning_trainer module hippynn.experiment.metric_tracker module hippynn.experiment.routines module hippynn.experiment.serialization module
hippynn.custom_kernels.env_triton module hippynn.custom_kernels.env_triton module
+hippynn.custom_kernels.fast_convert module
@@ -387,6 +396,7 @@ hippynn.experiment.metric_tracker module
MetricTracker print_lr() progress_bar() recursive_param_count() teed_file_output
teed_file_output.__init__() teed_file_output.flush() allow_unfound – If true, skip checking if the needed inputs and targets are found.
This allows setting inputs=None and/or targets=None.
auto_split – If true, look for keys like “split_*” to make initial splits from. See write_npz() method.
device – if set, move the dataset to this device after splitting.
dataloader_kwargs – dictionary, passed to pytorch dataloaders in addition to num_workers, pin_memory.
+Refer to pytorch documentation for details.
quiet – If True, print little or nothing while loading.
diff --git a/api_documentation/hippynn.interfaces.ase_interface.html b/api_documentation/hippynn.interfaces.ase_interface.html
index 8e3c4284..506fa505 100644
--- a/api_documentation/hippynn.interfaces.ase_interface.html
+++ b/api_documentation/hippynn.interfaces.ase_interface.html
@@ -189,6 +189,9 @@
allow_unfound – If true, skip checking if the needed inputs and targets are found.
This allows setting inputs=None and/or targets=None.
auto_split – If true, look for keys like “split_*” to make initial splits from. See write_npz() method.
device – if set, move the dataset to this device after splitting.
dataloader_kwargs – dictionary, passed to pytorch dataloaders in addition to num_workers, pin_memory.
+Refer to pytorch documentation for details.
quiet – If True, print little or nothing while loading.
diff --git a/api_documentation/hippynn.tools.html b/api_documentation/hippynn.tools.html
index 00a9e3fe..c40e4995 100644
--- a/api_documentation/hippynn.tools.html
+++ b/api_documentation/hippynn.tools.html
@@ -66,6 +66,7 @@
param_print() print_lr() progress_bar() recursive_param_count() teed_file_output
teed_file_output.__init__() teed_file_output.flush()
-print_lr ( optimizer ) [source]
+print_lr ( optimizer print_=<built-in function print> ) [source]
@@ -222,6 +223,11 @@
progress_bar ( iterable * args ** kwargs ) [source]
+
+
+recursive_param_count ( state_dict n = 0 ) [source]
+
+
class teed_file_output ( * streams ) [source]
diff --git a/api_documentation/modules.html b/api_documentation/modules.html
index fe9ed750..f0117af8 100644
--- a/api_documentation/modules.html
+++ b/api_documentation/modules.html
@@ -173,6 +173,7 @@ hippynn
-
+ config_pruner() (in module hippynn.custom_kernels.env_triton)
+configure_optimizers() (HippynnLightningModule method)
+construct_outputs() (in module hippynn.graphs.ensemble)
Controller (class in hippynn.experiment.controllers)
@@ -903,6 +911,12 @@ E
Envops_tester (class in hippynn.custom_kernels.test_env_numba)
envsum() (in module hippynn.custom_kernels.env_pytorch)
+
+ envsum_triton() (in module hippynn.custom_kernels.env_triton)
eval_batch_size (SetupParams attribute) , [1]
F
featsum() (in module hippynn.custom_kernels.env_pytorch)
+
+ featsum_triton() (in module hippynn.custom_kernels.env_triton)
filter_arrays() (SNAPDirectoryDatabase method)
F
fraction_train_eval (SetupParams attribute) , [1]
from_evaluator() (MetricTracker class method)
+from_experiment_setup() (HippynnLightningModule class method)
from_graph() (Predictor class method) , [1]
+from_train_setup() (HippynnLightningModule class method)
FuzzyHistogram (class in hippynn.layers.indexers)
G
generate_database_info() (in module hippynn.experiment.assembly)
GeometryOptimizer (class in hippynn.optimizer.algorithms)
+get_autotune_config() (in module hippynn.custom_kernels.env_triton)
get_charges() (HippynnCalculator method) , [1]
G
get_free_energy() (HippynnCalculator method) , [1]
get_graphs() (in module hippynn.graphs.ensemble)
-get_magmom() (HippynnCalculator method) , [1]
+ get_magmom() (HippynnCalculator method) , [1]
+get_magmoms() (HippynnCalculator method) , [1]
get_main_outputs() (ParentExpander method)
@@ -1490,6 +1516,13 @@ H
+ hippynn.custom_kernels.env_triton
+
+
@@ -1518,6 +1551,13 @@ H
+
+ hippynn.custom_kernels.test_env_triton
+
+
@@ -1595,6 +1635,13 @@ H
+
+ hippynn.experiment.lightning_trainer
+
+
@@ -1786,6 +1833,8 @@ H
module
+
hippynn.graphs.nodes.misc
@@ -1793,8 +1842,6 @@ H
module
-
+ HippynnDataModule (class in hippynn.experiment.lightning_trainer)
+HippynnLightningModule (class in hippynn.experiment.lightning_trainer)
+Hist1D (class in hippynn.plotting.plotters)
Hist1DComp (class in hippynn.plotting.plotters)
@@ -2287,12 +2338,14 @@ I
K
learning_rate (SetupParams attribute) , [1]
+LightingPrintStagesCallback (class in hippynn.experiment.lightning_trainer)
ListMod (class in hippynn.layers.algebra)
L
load_checkpoint() (in module hippynn.experiment.serialization)
load_checkpoint_from_cwd() (in module hippynn.experiment.serialization)
+load_from_checkpoint() (HippynnLightningModule class method)
load_model_from_cwd() (in module hippynn.experiment.serialization)
load_saved_tensors() (in module hippynn.experiment.serialization)
+
LocalAtomEnergyNode (class in hippynn.interfaces.lammps_interface.mliap_interface)
LocalAtomsEnergy (class in hippynn.interfaces.lammps_interface.mliap_interface)
@@ -2532,6 +2589,8 @@ M
hippynn.custom_kernels.env_numba
hippynn.custom_kernels.env_pytorch
+hippynn.custom_kernels.env_triton
hippynn.custom_kernels.fast_convert
M
hippynn.custom_kernels.test_env_cupy
hippynn.custom_kernels.test_env_numba
+hippynn.custom_kernels.test_env_triton
hippynn.custom_kernels.utils
M
hippynn.experiment.device
hippynn.experiment.evaluator
+hippynn.experiment.lightning_trainer
hippynn.experiment.metric_tracker
O
- optimizer (SetupParams attribute) , [1]
+ optimizer (RaiseBatchSizeOnPlateau property)
+
+ out_shape() (NumbaCompatibleTensorFunction method)
@@ -3079,6 +3160,8 @@ R
rebuild_neighbors() (HippynnCalculator method) , [1]
recalculation_needed() (PairMemory method)
+recursive_param_count() (in module hippynn.tools)
ReduceSingleNode (class in hippynn.graphs.nodes.loss)
S
send_to_device() (Database method) , [1]
sensesum() (in module hippynn.custom_kernels.env_pytorch)
+
+ sensitivity_layers (Hipnn property)
SensitivityBottleneck (class in hippynn.layers.hiplayers)
@@ -3401,6 +3488,8 @@ T
teed_file_output (class in hippynn.tools)
temporary_parents() (in module hippynn.graphs.nodes.base.definition_helpers)
+test_dataloader() (HippynnDataModule method)
test_model() (in module hippynn.experiment)
@@ -3408,6 +3497,8 @@ T
(in module hippynn.experiment.routines)
test_step() (HippynnLightningModule method)
+TimedSnippet (class in hippynn.custom_kernels.test_env_numba)
TimerHolder (class in hippynn.custom_kernels.test_env_numba)
@@ -3465,6 +3556,8 @@ T
training_loop() (in module hippynn.experiment.routines)
+training_step() (HippynnLightningModule method)
TrainingModules (class in hippynn.experiment.assembly)
U
V
Interfacing codes:
@@ -149,17 +150,17 @@ Install from source:
+
+
+ hippynn.custom_kernels.env_triton
+
@@ -139,6 +144,11 @@ Python Module Index
hippynn.custom_kernels.test_env_numba
+
+
+ hippynn.custom_kernels.test_env_triton
+
@@ -194,6 +204,11 @@ Python Module Index
hippynn.experiment.evaluator
+
+
+ hippynn.experiment.lightning_trainer
+
diff --git a/searchindex.js b/searchindex.js
index 8937c008..82b0b17e 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"A MultiNode": [[125, "a-multinode"]], "ASE Calculators": [[107, null]], "ASE Objects Database handling": [[126, "ase-objects-database-handling"]], "Adding constraints to possible parents": [[125, "adding-constraints-to-possible-parents"]], "Advanced Details": [[118, "advanced-details"]], "Bottom line up front": [[123, "bottom-line-up-front"]], "Caching Pre-computed Pairs": [[115, "caching-pre-computed-pairs"]], "Conda": [[121, "conda"]], "Contents:": [[120, null], [128, null]], "Controller": [[108, null]], "Creating Custom Node Types": [[125, null]], "Cross-device restart": [[118, "cross-device-restart"]], "Custom Kernels": [[123, null]], "Custom Kernels for fast execution": [[127, "custom-kernels-for-fast-execution"]], "Databases": [[126, null]], "Dependencies using conda": [[121, "dependencies-using-conda"]], "Dependencies using pip": [[121, "dependencies-using-pip"]], "Detailed Explanation": [[123, "detailed-explanation"]], "Dynamic Pair Finder": [[115, "dynamic-pair-finder"]], "Ensembling Models": [[109, null]], "Examples": [[112, null]], "Experiment": [[124, "experiment"]], "Force Training": [[111, null]], "Graph level API for simple and flexible construction of models from pytorch components.": [[127, "graph-level-api-for-simple-and-flexible-construction-of-models-from-pytorch-components"]], "Graphs": [[124, "graphs"]], "Hippynn Settings Summary": [[130, "id1"]], "Indices and tables": [[120, "indices-and-tables"]], "Install from source:": [[121, "install-from-source"]], "Installation": [[121, null]], "Installation Instructions": [[121, "installation-instructions"]], "Interfaces": [[127, "interfaces"]], "LAMMPS interface": [[114, null]], "Layers/Networks": [[124, "layers-networks"]], "Library Settings": [[130, null]], "License": [[122, null]], "Minimal Workflow": [[113, null]], "Model and Loss Graphs": [[129, null]], "Modular set of pytorch layers for atomistic operations": [[127, "modular-set-of-pytorch-layers-for-atomistic-operations"]], "Nodes": [[124, "nodes"]], "Non-Adiabiatic Excited States": [[110, null]], "Notes": [[121, "notes"]], "Pair Finder Memory": [[115, "pair-finder-memory"]], "Parent expansion": [[125, "parent-expansion"]], "Periodic Boundary Conditions": [[115, null]], "Pip": [[121, "pip"]], "Plot level API for tracking your training.": [[127, "plot-level-api-for-tracking-your-training"]], "Plotting": [[116, null]], "Predictor": [[117, null]], "Requirements": [[121, "requirements"]], "Restarting training": [[118, null]], "Simple restart": [[118, "simple-restart"]], "Submodules": [[0, "submodules"], [1, "submodules"], [13, "submodules"], [19, "submodules"], [28, "submodules"], [32, "submodules"], [36, "submodules"], [40, "submodules"], [41, "submodules"], [60, "submodules"], [65, "submodules"], [67, "submodules"], [76, "submodules"], [81, "submodules"], [92, "submodules"], [94, "submodules"], [96, "submodules"], [100, "submodules"]], "Subpackages": [[0, "subpackages"], [28, "subpackages"], [40, "subpackages"], [59, "subpackages"], [76, "subpackages"]], "The very basics": [[125, "the-very-basics"]], "Training & Experiment API": [[127, "training-experiment-api"]], "Units in hippynn": [[131, null]], "User Guide": [[128, null]], "Weighted/Masked Loss Functions": [[119, null]], "Welcome to hippynn\u2019s documentation!": [[120, null]], "What is hippynn?": [[120, "what-is-hippynn"]], "What\u2019s not yet supported": [[115, "what-s-not-yet-supported"]], "hippynn": [[106, null]], "hippynn Concepts": [[124, null]], "hippynn Features": [[127, null]], "hippynn package": [[0, null]], "hippynn.custom_kernels package": [[1, null]], "hippynn.custom_kernels.autograd_wrapper module": [[2, null]], "hippynn.custom_kernels.env_cupy module": [[3, null]], "hippynn.custom_kernels.env_numba module": [[4, null]], "hippynn.custom_kernels.env_pytorch module": [[5, null]], "hippynn.custom_kernels.env_triton module": [[6, null]], "hippynn.custom_kernels.fast_convert module": [[7, null]], "hippynn.custom_kernels.tensor_wrapper module": [[8, null]], "hippynn.custom_kernels.test_env_cupy module": [[9, null]], "hippynn.custom_kernels.test_env_numba module": [[10, null]], "hippynn.custom_kernels.test_env_triton module": [[11, null]], "hippynn.custom_kernels.utils module": [[12, null]], "hippynn.databases package": [[13, null]], "hippynn.databases.SNAPJson module": [[14, null]], "hippynn.databases.database module": [[15, null]], "hippynn.databases.h5_pyanitools module": [[16, null]], "hippynn.databases.ondisk module": [[17, null]], "hippynn.databases.restarter module": [[18, null]], "hippynn.experiment package": [[19, null]], "hippynn.experiment.assembly module": [[20, null]], "hippynn.experiment.controllers module": [[21, null]], "hippynn.experiment.device module": [[22, null]], "hippynn.experiment.evaluator module": [[23, null]], "hippynn.experiment.metric_tracker module": [[24, null]], "hippynn.experiment.routines module": [[25, null]], "hippynn.experiment.serialization module": [[26, null]], "hippynn.experiment.step_functions module": [[27, null]], "hippynn.graphs package": [[28, null]], "hippynn.graphs.ensemble module": [[29, null]], "hippynn.graphs.gops module": [[30, null]], "hippynn.graphs.graph module": [[31, null]], "hippynn.graphs.indextransformers package": [[32, null]], "hippynn.graphs.indextransformers.atoms module": [[33, null]], "hippynn.graphs.indextransformers.pairs module": [[34, null]], "hippynn.graphs.indextransformers.tensors module": [[35, null]], "hippynn.graphs.indextypes package": [[36, null]], "hippynn.graphs.indextypes.reduce_funcs module": [[37, null]], "hippynn.graphs.indextypes.registry module": [[38, null]], "hippynn.graphs.indextypes.type_def module": [[39, null]], "hippynn.graphs.nodes package": [[40, null]], "hippynn.graphs.nodes.base package": [[41, null]], "hippynn.graphs.nodes.base.algebra module": [[42, null]], "hippynn.graphs.nodes.base.base module": [[43, null]], "hippynn.graphs.nodes.base.definition_helpers module": [[44, null]], "hippynn.graphs.nodes.base.multi module": [[45, null]], "hippynn.graphs.nodes.base.node_functions module": [[46, null]], "hippynn.graphs.nodes.excited module": [[47, null]], "hippynn.graphs.nodes.indexers module": [[48, null]], "hippynn.graphs.nodes.inputs module": [[49, null]], "hippynn.graphs.nodes.loss module": [[50, null]], "hippynn.graphs.nodes.misc module": [[51, null]], "hippynn.graphs.nodes.networks module": [[52, null]], "hippynn.graphs.nodes.pairs module": [[53, null]], "hippynn.graphs.nodes.physics module": [[54, null]], "hippynn.graphs.nodes.tags module": [[55, null]], "hippynn.graphs.nodes.targets module": [[56, null]], "hippynn.graphs.predictor module": [[57, null]], "hippynn.graphs.viz module": [[58, null]], "hippynn.interfaces package": [[59, null]], "hippynn.interfaces.ase_interface package": [[60, null]], "hippynn.interfaces.ase_interface.ase_database module": [[61, null]], "hippynn.interfaces.ase_interface.ase_unittests module": [[62, null]], "hippynn.interfaces.ase_interface.calculator module": [[63, null]], "hippynn.interfaces.ase_interface.pairfinder module": [[64, null]], "hippynn.interfaces.lammps_interface package": [[65, null]], "hippynn.interfaces.lammps_interface.mliap_interface module": [[66, null]], "hippynn.interfaces.pyseqm_interface package": [[67, null]], "hippynn.interfaces.pyseqm_interface.callback module": [[68, null]], "hippynn.interfaces.pyseqm_interface.check module": [[69, null]], "hippynn.interfaces.pyseqm_interface.gen_par module": [[70, null]], "hippynn.interfaces.pyseqm_interface.mlseqm module": [[71, null]], "hippynn.interfaces.pyseqm_interface.seqm_modules module": [[72, null]], "hippynn.interfaces.pyseqm_interface.seqm_nodes module": [[73, null]], "hippynn.interfaces.pyseqm_interface.seqm_one module": [[74, null]], "hippynn.interfaces.schnetpack_interface package": [[75, null]], "hippynn.layers package": [[76, null]], "hippynn.layers.algebra module": [[77, null]], "hippynn.layers.excited module": [[78, null]], "hippynn.layers.hiplayers module": [[79, null]], "hippynn.layers.indexers module": [[80, null]], "hippynn.layers.pairs package": [[81, null]], "hippynn.layers.pairs.analysis module": [[82, null]], "hippynn.layers.pairs.dispatch module": [[83, null]], "hippynn.layers.pairs.filters module": [[84, null]], "hippynn.layers.pairs.indexing module": [[85, null]], "hippynn.layers.pairs.open module": [[86, null]], "hippynn.layers.pairs.periodic module": [[87, null]], "hippynn.layers.physics module": [[88, null]], "hippynn.layers.regularization module": [[89, null]], "hippynn.layers.targets module": [[90, null]], "hippynn.layers.transform module": [[91, null]], "hippynn.molecular_dynamics package": [[92, null]], "hippynn.molecular_dynamics.md module": [[93, null]], "hippynn.networks package": [[94, null]], "hippynn.networks.hipnn module": [[95, null]], "hippynn.optimizer package": [[96, null]], "hippynn.optimizer.algorithms module": [[97, null]], "hippynn.optimizer.batch_optimizer module": [[98, null]], "hippynn.optimizer.utils module": [[99, null]], "hippynn.plotting package": [[100, null]], "hippynn.plotting.plotmaker module": [[101, null]], "hippynn.plotting.plotters module": [[102, null]], "hippynn.plotting.timeplots module": [[103, null]], "hippynn.pretraining module": [[104, null]], "hippynn.tools module": [[105, null]]}, "docnames": ["api_documentation/hippynn", "api_documentation/hippynn.custom_kernels", "api_documentation/hippynn.custom_kernels.autograd_wrapper", "api_documentation/hippynn.custom_kernels.env_cupy", "api_documentation/hippynn.custom_kernels.env_numba", "api_documentation/hippynn.custom_kernels.env_pytorch", "api_documentation/hippynn.custom_kernels.env_triton", "api_documentation/hippynn.custom_kernels.fast_convert", "api_documentation/hippynn.custom_kernels.tensor_wrapper", "api_documentation/hippynn.custom_kernels.test_env_cupy", 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"hippynn.graphs.nodes.indexers.SysMaxOfAtomsNode.__init__", false]], "__init__() (teed_file_output method)": [[105, "hippynn.tools.teed_file_output.__init__", false]], "__init__() (timedsnippet method)": [[10, "hippynn.custom_kernels.test_env_numba.TimedSnippet.__init__", false]], "__init__() (timerholder method)": [[10, "hippynn.custom_kernels.test_env_numba.TimerHolder.__init__", false]], "__init__() (unarynode method)": [[42, "hippynn.graphs.nodes.base.algebra.UnaryNode.__init__", false]], "__init__() (valuemod method)": [[77, "hippynn.layers.algebra.ValueMod.__init__", false]], "__init__() (valuenode method)": [[42, "hippynn.graphs.nodes.base.algebra.ValueNode.__init__", false]], "__init__() (variable method)": [[93, "hippynn.molecular_dynamics.md.Variable.__init__", false]], "__init__() (variableupdater method)": [[93, "hippynn.molecular_dynamics.md.VariableUpdater.__init__", false]], "__init__() (vecmag method)": [[54, "hippynn.graphs.nodes.physics.VecMag.__init__", false]], "__init__() (velocityverlet method)": [[93, "hippynn.molecular_dynamics.md.VelocityVerlet.__init__", false]], "__init__() (wolfscreening method)": [[88, "hippynn.layers.physics.WolfScreening.__init__", false]], "absolute_errors() (in module hippynn.graphs.nodes.loss)": [[50, "hippynn.graphs.nodes.loss.absolute_errors", false]], "acquire_encoding_padding() (in module hippynn.graphs.nodes.indexers)": [[48, "hippynn.graphs.nodes.indexers.acquire_encoding_padding", false]], "active_directory() (in module hippynn.tools)": [[105, "hippynn.tools.active_directory", false]], "add() (timerholder method)": [[10, "hippynn.custom_kernels.test_env_numba.TimerHolder.add", false]], "add_class_doc() (compatibleidxtypetransformer method)": [[44, "hippynn.graphs.nodes.base.definition_helpers.CompatibleIdxTypeTransformer.add_class_doc", false]], "add_class_doc() (formassertion method)": [[44, "hippynn.graphs.nodes.base.definition_helpers.FormAssertion.add_class_doc", false]], "add_class_doc() 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"hippynn.plotting.plotters.as_numpy", false]], "as_tensor() (mliapinterface method)": [[66, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.as_tensor", false]], "ase_compute_neighbors() (in module hippynn.interfaces.ase_interface.pairfinder)": [[64, "hippynn.interfaces.ase_interface.pairfinder.ASE_compute_neighbors", false]], "ase_filterpair_coulomb_construct() (in module hippynn.interfaces.ase_interface.ase_unittests)": [[62, "hippynn.interfaces.ase_interface.ase_unittests.ASE_FilterPair_Coulomb_Construct", false]], "asedatabase (class in hippynn.databases)": [[13, "hippynn.databases.AseDatabase", false]], "asedatabase (class in hippynn.interfaces.ase_interface)": [[60, "hippynn.interfaces.ase_interface.AseDatabase", false]], "asedatabase (class in hippynn.interfaces.ase_interface.ase_database)": [[61, "hippynn.interfaces.ase_interface.ase_database.AseDatabase", false]], "aseneighbors (class in hippynn.interfaces.ase_interface.pairfinder)": [[64, "hippynn.interfaces.ase_interface.pairfinder.ASENeighbors", false]], "asepairnode (class in hippynn.interfaces.ase_interface.pairfinder)": [[64, "hippynn.interfaces.ase_interface.pairfinder.ASEPairNode", false]], "assemble_for_training() (in module hippynn.experiment)": [[19, "hippynn.experiment.assemble_for_training", false]], "assemble_for_training() (in module hippynn.experiment.assembly)": [[20, "hippynn.experiment.assembly.assemble_for_training", false]], "assemble_module() (plotmaker method)": [[101, "hippynn.plotting.plotmaker.PlotMaker.assemble_module", false]], "assertion() (parentexpander method)": [[44, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.assertion", false]], "assertlen() (parentexpander method)": [[44, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.assertlen", false]], "assign_index_aliases() (in module hippynn.graphs.indextypes.registry)": [[38, "hippynn.graphs.indextypes.registry.assign_index_aliases", false]], "atleast2d (class in hippynn.graphs.nodes.base.algebra)": [[42, "hippynn.graphs.nodes.base.algebra.AtLeast2D", false]], "atleast2d (class in hippynn.layers.algebra)": [[77, "hippynn.layers.algebra.AtLeast2D", false]], "atomdeindexer (class in hippynn.graphs.nodes.indexers)": [[48, "hippynn.graphs.nodes.indexers.AtomDeIndexer", false]], "atomdeindexer (class in hippynn.layers.indexers)": [[80, "hippynn.layers.indexers.AtomDeIndexer", false]], "atomindexer (class in hippynn.graphs.nodes.tags)": [[55, "hippynn.graphs.nodes.tags.AtomIndexer", false]], "atommask (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_modules.AtomMask", false]], "atommasknode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_nodes.AtomMaskNode", false]], "atomreindexer (class in hippynn.graphs.nodes.indexers)": [[48, "hippynn.graphs.nodes.indexers.AtomReIndexer", false]], "atomreindexer (class in hippynn.layers.indexers)": [[80, "hippynn.layers.indexers.AtomReIndexer", false]], "atoms (idxtype attribute)": [[28, "hippynn.graphs.IdxType.Atoms", false], [36, "hippynn.graphs.indextypes.IdxType.Atoms", false], [39, "hippynn.graphs.indextypes.type_def.IdxType.Atoms", false]], "atomtomolsummer (class in hippynn.graphs.nodes.physics)": [[54, "hippynn.graphs.nodes.physics.AtomToMolSummer", false]], "attempt_restart() (norestart method)": [[18, "hippynn.databases.restarter.NoRestart.attempt_restart", false]], "attempt_restart() (restartdb method)": [[18, "hippynn.databases.restarter.RestartDB.attempt_restart", false]], "attempt_restart() (restarter method)": [[18, "hippynn.databases.restarter.Restarter.attempt_restart", false]], "auto_module() (autokw method)": [[44, "hippynn.graphs.nodes.base.definition_helpers.AutoKw.auto_module", false]], "auto_module() (autonokw method)": [[44, "hippynn.graphs.nodes.base.definition_helpers.AutoNoKw.auto_module", false]], "auto_module() (localenergynode method)": [[47, "hippynn.graphs.nodes.excited.LocalEnergyNode.auto_module", false]], "auto_module() (onehotencoder method)": [[48, "hippynn.graphs.nodes.indexers.OneHotEncoder.auto_module", false]], "auto_module() (openpairindexer method)": [[53, "hippynn.graphs.nodes.pairs.OpenPairIndexer.auto_module", false]], "auto_module() (valuenode method)": [[42, "hippynn.graphs.nodes.base.algebra.ValueNode.auto_module", false]], "autokw (class in hippynn.graphs.nodes.base.definition_helpers)": [[44, "hippynn.graphs.nodes.base.definition_helpers.AutoKw", false]], "autonokw (class in hippynn.graphs.nodes.base.definition_helpers)": [[44, "hippynn.graphs.nodes.base.definition_helpers.AutoNoKw", false]], "batch_convert_torch_to_numba() (in module hippynn.custom_kernels.fast_convert)": [[7, "hippynn.custom_kernels.fast_convert.batch_convert_torch_to_numba", false]], "batch_size (setupparams attribute)": [[19, "hippynn.experiment.SetupParams.batch_size", false], [25, "hippynn.experiment.routines.SetupParams.batch_size", false]], "bfgsv1 (class in hippynn.optimizer.algorithms)": [[97, "hippynn.optimizer.algorithms.BFGSv1", false]], "bfgsv2 (class in hippynn.optimizer.algorithms)": [[97, "hippynn.optimizer.algorithms.BFGSv2", false]], "bfgsv3 (class in hippynn.optimizer.algorithms)": [[97, "hippynn.optimizer.algorithms.BFGSv3", false]], "bin_info() (rdfbins method)": [[82, "hippynn.layers.pairs.analysis.RDFBins.bin_info", false]], "binnode (class in hippynn.graphs.nodes.base.algebra)": [[42, "hippynn.graphs.nodes.base.algebra.BinNode", false]], "bondtomolsummmer (class in hippynn.graphs.nodes.physics)": [[54, "hippynn.graphs.nodes.physics.BondToMolSummmer", false]], "build_loss_modules() (in module hippynn.experiment.assembly)": [[20, "hippynn.experiment.assembly.build_loss_modules", false]], "calculate() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.calculate", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.calculate", false]], "calculate_max_system_force() (in module hippynn.pretraining)": [[104, "hippynn.pretraining.calculate_max_system_force", false]], "calculate_min_dists() (in module hippynn.pretraining)": [[104, "hippynn.pretraining.calculate_min_dists", false]], "calculation_required() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.calculation_required", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.calculation_required", false]], "calculator_from_model() (in module hippynn.interfaces.ase_interface)": [[60, "hippynn.interfaces.ase_interface.calculator_from_model", false]], "calculator_from_model() (in module hippynn.interfaces.ase_interface.calculator)": [[63, "hippynn.interfaces.ase_interface.calculator.calculator_from_model", false]], "cellnode (class in hippynn.graphs.nodes.inputs)": [[49, "hippynn.graphs.nodes.inputs.CellNode", false]], 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"check_allclose_once() (envops_tester method)": [[10, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_allclose_once", false]], "check_correctness() (envops_tester method)": [[10, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_correctness", false]], "check_dist() (in module hippynn.interfaces.pyseqm_interface.check)": [[69, "hippynn.interfaces.pyseqm_interface.check.check_dist", false]], "check_empty() (envops_tester method)": [[10, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_empty", false]], "check_evaluation_order() (in module hippynn.graphs.gops)": [[30, "hippynn.graphs.gops.check_evaluation_order", false]], "check_grad_and_gradgrad() (envops_tester method)": [[10, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_grad_and_gradgrad", false]], "check_gradient() (in module hippynn.interfaces.pyseqm_interface.check)": [[69, "hippynn.interfaces.pyseqm_interface.check.check_gradient", false]], "check_link_consistency() (in module 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"coerces_values_to_nodes() (in module hippynn.graphs.nodes.base.algebra)": [[42, "hippynn.graphs.nodes.base.algebra.coerces_values_to_nodes", false]], "collate_inputs() (in module hippynn.graphs.ensemble)": [[29, "hippynn.graphs.ensemble.collate_inputs", false]], "collate_targets() (in module hippynn.graphs.ensemble)": [[29, "hippynn.graphs.ensemble.collate_targets", false]], "combineenergy (class in hippynn.layers.physics)": [[88, "hippynn.layers.physics.CombineEnergy", false]], "combineenergynode (class in hippynn.graphs.nodes.physics)": [[54, "hippynn.graphs.nodes.physics.CombineEnergyNode", false]], "combinescreenings (class in hippynn.layers.physics)": [[88, "hippynn.layers.physics.CombineScreenings", false]], "compatibility_hook() (interactlayervec static method)": [[79, "hippynn.layers.hiplayers.InteractLayerVec.compatibility_hook", false]], "compatibleidxtypetransformer (class in hippynn.graphs.nodes.base.definition_helpers)": [[44, "hippynn.graphs.nodes.base.definition_helpers.CompatibleIdxTypeTransformer", false]], "composedplotter (class in hippynn.plotting.plotters)": [[102, "hippynn.plotting.plotters.ComposedPlotter", false]], "compute_descriptors() (mliapinterface method)": [[66, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_descriptors", false]], "compute_evaluation_order() (in module hippynn.graphs)": [[28, "hippynn.graphs.compute_evaluation_order", false]], "compute_evaluation_order() (in module hippynn.graphs.gops)": [[30, "hippynn.graphs.gops.compute_evaluation_order", false]], "compute_forces() (mliapinterface method)": [[66, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_forces", false]], "compute_gradients() (mliapinterface method)": [[66, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_gradients", false]], "compute_hipnn_e0() (in module hippynn.networks.hipnn)": [[95, "hippynn.networks.hipnn.compute_hipnn_e0", false]], "compute_index_mask() (in module hippynn.databases.database)": [[15, "hippynn.databases.database.compute_index_mask", false]], "compute_one() (aseneighbors method)": [[64, "hippynn.interfaces.ase_interface.pairfinder.ASENeighbors.compute_one", false]], "compute_one() (kdtreeneighbors method)": [[83, "hippynn.layers.pairs.dispatch.KDTreeNeighbors.compute_one", false]], "compute_one() (npneighbors method)": [[83, "hippynn.layers.pairs.dispatch.NPNeighbors.compute_one", false]], "compute_one() (torchneighbors method)": [[83, "hippynn.layers.pairs.dispatch.TorchNeighbors.compute_one", false]], "construct_outputs() (in module hippynn.graphs.ensemble)": [[29, "hippynn.graphs.ensemble.construct_outputs", false]], "controller (class in hippynn.experiment.controllers)": [[21, "hippynn.experiment.controllers.Controller", false]], "controller (setupparams attribute)": [[19, "hippynn.experiment.SetupParams.controller", false], [25, "hippynn.experiment.routines.SetupParams.controller", false]], "copy_subgraph() (in module hippynn.graphs)": [[28, "hippynn.graphs.copy_subgraph", false]], "copy_subgraph() (in module hippynn.graphs.gops)": [[30, "hippynn.graphs.gops.copy_subgraph", false]], "coscutoff (class in hippynn.layers.hiplayers)": [[79, "hippynn.layers.hiplayers.CosCutoff", false]], "coulombenergy (class in hippynn.layers.physics)": [[88, "hippynn.layers.physics.CoulombEnergy", false]], "coulombenergynode (class in hippynn.graphs.nodes.physics)": [[54, "hippynn.graphs.nodes.physics.CoulombEnergyNode", false]], "cpu_kernel() (numbacompatibletensorfunction method)": [[8, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction.cpu_kernel", false]], "cpu_kernel() (wrappedenvsum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedEnvsum.cpu_kernel", false]], "cpu_kernel() (wrappedfeatsum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedFeatsum.cpu_kernel", false]], "cpu_kernel() (wrappedsensesum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedSensesum.cpu_kernel", false]], "create_schnetpack_inputs() (in module hippynn.interfaces.schnetpack_interface)": [[75, "hippynn.interfaces.schnetpack_interface.create_schnetpack_inputs", false]], "create_state() (in module hippynn.experiment.serialization)": [[26, "hippynn.experiment.serialization.create_state", false]], "create_structure_file() (in module hippynn.experiment.serialization)": [[26, "hippynn.experiment.serialization.create_structure_file", false]], "cupyenvsum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyEnvsum", false]], "cupyfeatsum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyFeatsum", false]], "cupygpukernel (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyGPUKernel", false]], "cupysensesum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupySensesum", false]], "current_epoch (metrictracker property)": [[24, "hippynn.experiment.metric_tracker.MetricTracker.current_epoch", false]], "data (variable property)": [[93, "hippynn.molecular_dynamics.md.Variable.data", false]], "database (class in hippynn.databases)": [[13, "hippynn.databases.Database", false]], "database (class in hippynn.databases.database)": [[15, "hippynn.databases.database.Database", false]], "db_form() (in module hippynn.graphs.indextypes)": [[36, "hippynn.graphs.indextypes.db_form", false]], "db_form() (in module hippynn.graphs.indextypes.reduce_funcs)": [[37, "hippynn.graphs.indextypes.reduce_funcs.db_form", false]], "db_state_of() (in module hippynn.graphs.indextypes.reduce_funcs)": [[37, "hippynn.graphs.indextypes.reduce_funcs.db_state_of", false]], "debatch() (in module hippynn.optimizer.utils)": [[99, "hippynn.optimizer.utils.debatch", false]], "debatch_coords() (in module hippynn.optimizer.utils)": [[99, "hippynn.optimizer.utils.debatch_coords", false]], 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"hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_OrbitalMask.forward", false]], "forward() (staticimageperiodicpairindexer method)": [[87, "hippynn.layers.pairs.periodic.StaticImagePeriodicPairIndexer.forward", false]], "forward() (stressforce method)": [[88, "hippynn.layers.physics.StressForce.forward", false]], "forward() (sysmaxofatoms method)": [[80, "hippynn.layers.indexers.SysMaxOfAtoms.forward", false]], "forward() (valuemod method)": [[77, "hippynn.layers.algebra.ValueMod.forward", false]], "forward() (vecmag method)": [[88, "hippynn.layers.physics.VecMag.forward", false]], "forward() (wolfscreening method)": [[88, "hippynn.layers.physics.WolfScreening.forward", false]], "fraction_train_eval (setupparams attribute)": [[19, "hippynn.experiment.SetupParams.fraction_train_eval", false], [25, "hippynn.experiment.routines.SetupParams.fraction_train_eval", false]], "from_evaluator() (metrictracker class method)": [[24, "hippynn.experiment.metric_tracker.MetricTracker.from_evaluator", false]], "from_graph() (predictor class method)": [[28, "hippynn.graphs.Predictor.from_graph", false], [57, "hippynn.graphs.predictor.Predictor.from_graph", false]], "fuzzyhistogram (class in hippynn.layers.indexers)": [[80, "hippynn.layers.indexers.FuzzyHistogram", false]], "fuzzyhistogrammer (class in hippynn.graphs.nodes.indexers)": [[48, "hippynn.graphs.nodes.indexers.FuzzyHistogrammer", false]], "gaussiansensitivitymodule (class in hippynn.layers.hiplayers)": [[79, "hippynn.layers.hiplayers.GaussianSensitivityModule", false]], "gen_par (class in hippynn.interfaces.pyseqm_interface.gen_par)": [[70, "hippynn.interfaces.pyseqm_interface.gen_par.gen_par", false]], "generate_database_info() (in module hippynn.experiment.assembly)": [[20, "hippynn.experiment.assembly.generate_database_info", false]], "geometryoptimizer (class in hippynn.optimizer.algorithms)": [[97, "hippynn.optimizer.algorithms.GeometryOptimizer", false]], "get_charges() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_charges", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_charges", false]], "get_connected_nodes() (in module hippynn.graphs)": [[28, "hippynn.graphs.get_connected_nodes", false]], "get_connected_nodes() (in module hippynn.graphs.nodes.base.node_functions)": [[46, "hippynn.graphs.nodes.base.node_functions.get_connected_nodes", false]], "get_data() (moleculardynamics method)": [[93, "hippynn.molecular_dynamics.md.MolecularDynamics.get_data", false]], "get_device() (database method)": [[13, "hippynn.databases.Database.get_device", false], [15, "hippynn.databases.database.Database.get_device", false]], "get_dipole() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_dipole", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_dipole", false]], "get_dipole_moment() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_dipole_moment", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_dipole_moment", false]], "get_energies() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_energies", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_energies", false]], "get_energy() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_energy", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_energy", false]], "get_extra_state() (interactlayervec method)": [[79, "hippynn.layers.hiplayers.InteractLayerVec.get_extra_state", false]], "get_file_dict() (directorydatabase method)": [[13, "hippynn.databases.DirectoryDatabase.get_file_dict", false], [17, "hippynn.databases.ondisk.DirectoryDatabase.get_file_dict", false]], "get_forces() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_forces", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_forces", false]], "get_free_energy() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_free_energy", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_free_energy", false]], "get_graphs() (in module hippynn.graphs.ensemble)": [[29, "hippynn.graphs.ensemble.get_graphs", false]], "get_magmom() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_magmom", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_magmom", false]], "get_magmoms() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_magmoms", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_magmoms", false]], "get_main_outputs() (parentexpander method)": [[44, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.get_main_outputs", false]], "get_module() (graphmodule method)": [[28, "hippynn.graphs.GraphModule.get_module", false], [31, "hippynn.graphs.graph.GraphModule.get_module", false]], "get_potential_energies() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_potential_energies", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_potential_energies", false]], "get_potential_energy() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_potential_energy", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_potential_energy", false]], "get_property() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_property", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_property", false]], "get_reduced_index_state() (in module hippynn.graphs.indextypes)": [[36, "hippynn.graphs.indextypes.get_reduced_index_state", false]], "get_reduced_index_state() (in module hippynn.graphs.indextypes.reduce_funcs)": [[37, "hippynn.graphs.indextypes.reduce_funcs.get_reduced_index_state", false]], "get_simulated_data() (in module hippynn.custom_kernels.test_env_numba)": [[10, "hippynn.custom_kernels.test_env_numba.get_simulated_data", false]], "get_step_function() (in module hippynn.experiment.step_functions)": [[27, "hippynn.experiment.step_functions.get_step_function", false]], "get_stress() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_stress", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_stress", false]], "get_stresses() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.get_stresses", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_stresses", false]], "get_subgraph() (in module hippynn.graphs)": [[28, "hippynn.graphs.get_subgraph", false]], "get_subgraph() (in module hippynn.graphs.gops)": [[30, "hippynn.graphs.gops.get_subgraph", false]], "gradient (class in hippynn.layers.physics)": [[88, "hippynn.layers.physics.Gradient", false]], "gradientnode (class in hippynn.graphs.nodes.physics)": [[54, "hippynn.graphs.nodes.physics.GradientNode", false]], "graphinconsistency": [[30, "hippynn.graphs.gops.GraphInconsistency", false]], "graphmodule (class in hippynn.graphs)": [[28, "hippynn.graphs.GraphModule", false]], "graphmodule (class in hippynn.graphs.graph)": [[31, "hippynn.graphs.graph.GraphModule", false]], "hamiltonian_one (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[74, "hippynn.interfaces.pyseqm_interface.seqm_one.Hamiltonian_One", false]], "hatomregressor (class in hippynn.graphs.nodes.tags)": [[55, "hippynn.graphs.nodes.tags.HAtomRegressor", false]], "hbondnode (class in hippynn.graphs.nodes.targets)": [[56, "hippynn.graphs.nodes.targets.HBondNode", false]], "hbondsymmetric (class in hippynn.layers.targets)": [[90, "hippynn.layers.targets.HBondSymmetric", false]], "hcharge (class in hippynn.layers.targets)": [[90, "hippynn.layers.targets.HCharge", false]], "hchargenode (class in hippynn.graphs.nodes.targets)": [[56, "hippynn.graphs.nodes.targets.HChargeNode", false]], "henergy (class in hippynn.layers.targets)": [[90, "hippynn.layers.targets.HEnergy", false]], "henergynode (class in hippynn.graphs.nodes.targets)": [[56, "hippynn.graphs.nodes.targets.HEnergyNode", false]], "hierarchical_energy_initialization() (in module hippynn.pretraining)": [[104, "hippynn.pretraining.hierarchical_energy_initialization", false]], "hierarchicalityplot (class in hippynn.plotting.plotters)": [[102, "hippynn.plotting.plotters.HierarchicalityPlot", false]], "hipnn (class in hippynn.graphs.nodes.networks)": [[52, "hippynn.graphs.nodes.networks.Hipnn", false]], "hipnn (class in hippynn.networks.hipnn)": [[95, "hippynn.networks.hipnn.Hipnn", false]], "hipnnquad (class in hippynn.graphs.nodes.networks)": [[52, "hippynn.graphs.nodes.networks.HipnnQuad", false]], "hipnnquad (class in hippynn.networks.hipnn)": [[95, "hippynn.networks.hipnn.HipnnQuad", false]], "hipnnvec (class in hippynn.graphs.nodes.networks)": [[52, "hippynn.graphs.nodes.networks.HipnnVec", false]], "hipnnvec (class in hippynn.networks.hipnn)": [[95, "hippynn.networks.hipnn.HipnnVec", false]], "hippynn": [[0, "module-hippynn", false]], "hippynn.custom_kernels": [[1, "module-hippynn.custom_kernels", false]], "hippynn.custom_kernels.autograd_wrapper": [[2, "module-hippynn.custom_kernels.autograd_wrapper", false]], "hippynn.custom_kernels.env_cupy": [[3, "module-hippynn.custom_kernels.env_cupy", false]], "hippynn.custom_kernels.env_numba": [[4, "module-hippynn.custom_kernels.env_numba", false]], "hippynn.custom_kernels.env_pytorch": [[5, "module-hippynn.custom_kernels.env_pytorch", false]], "hippynn.custom_kernels.fast_convert": [[7, "module-hippynn.custom_kernels.fast_convert", false]], "hippynn.custom_kernels.tensor_wrapper": [[8, "module-hippynn.custom_kernels.tensor_wrapper", false]], "hippynn.custom_kernels.test_env_cupy": [[9, "module-hippynn.custom_kernels.test_env_cupy", false]], "hippynn.custom_kernels.test_env_numba": [[10, "module-hippynn.custom_kernels.test_env_numba", false]], "hippynn.custom_kernels.utils": [[12, "module-hippynn.custom_kernels.utils", false]], "hippynn.databases": [[13, "module-hippynn.databases", false]], "hippynn.databases.database": [[15, "module-hippynn.databases.database", false]], "hippynn.databases.ondisk": [[17, "module-hippynn.databases.ondisk", false]], "hippynn.databases.restarter": [[18, "module-hippynn.databases.restarter", false]], "hippynn.databases.snapjson": [[14, "module-hippynn.databases.SNAPJson", false]], "hippynn.experiment": [[19, "module-hippynn.experiment", false]], "hippynn.experiment.assembly": [[20, "module-hippynn.experiment.assembly", false]], "hippynn.experiment.controllers": [[21, "module-hippynn.experiment.controllers", false]], "hippynn.experiment.device": [[22, "module-hippynn.experiment.device", false]], "hippynn.experiment.evaluator": [[23, "module-hippynn.experiment.evaluator", false]], "hippynn.experiment.metric_tracker": [[24, "module-hippynn.experiment.metric_tracker", false]], "hippynn.experiment.routines": [[25, "module-hippynn.experiment.routines", false]], "hippynn.experiment.serialization": [[26, "module-hippynn.experiment.serialization", false]], "hippynn.experiment.step_functions": [[27, "module-hippynn.experiment.step_functions", false]], "hippynn.graphs": [[28, "module-hippynn.graphs", false]], "hippynn.graphs.ensemble": [[29, "module-hippynn.graphs.ensemble", false]], "hippynn.graphs.gops": [[30, "module-hippynn.graphs.gops", false]], "hippynn.graphs.graph": [[31, "module-hippynn.graphs.graph", false]], "hippynn.graphs.indextransformers": [[32, "module-hippynn.graphs.indextransformers", false]], "hippynn.graphs.indextransformers.atoms": [[33, "module-hippynn.graphs.indextransformers.atoms", false]], "hippynn.graphs.indextransformers.pairs": [[34, "module-hippynn.graphs.indextransformers.pairs", false]], "hippynn.graphs.indextransformers.tensors": [[35, "module-hippynn.graphs.indextransformers.tensors", false]], "hippynn.graphs.indextypes": [[36, "module-hippynn.graphs.indextypes", false]], "hippynn.graphs.indextypes.reduce_funcs": [[37, "module-hippynn.graphs.indextypes.reduce_funcs", false]], "hippynn.graphs.indextypes.registry": [[38, "module-hippynn.graphs.indextypes.registry", false]], "hippynn.graphs.indextypes.type_def": [[39, "module-hippynn.graphs.indextypes.type_def", false]], "hippynn.graphs.nodes": [[40, "module-hippynn.graphs.nodes", false]], "hippynn.graphs.nodes.base": [[41, "module-hippynn.graphs.nodes.base", false]], "hippynn.graphs.nodes.base.algebra": [[42, "module-hippynn.graphs.nodes.base.algebra", false]], "hippynn.graphs.nodes.base.base": [[43, "module-hippynn.graphs.nodes.base.base", false]], "hippynn.graphs.nodes.base.definition_helpers": [[44, "module-hippynn.graphs.nodes.base.definition_helpers", false]], "hippynn.graphs.nodes.base.multi": [[45, "module-hippynn.graphs.nodes.base.multi", false]], "hippynn.graphs.nodes.base.node_functions": [[46, "module-hippynn.graphs.nodes.base.node_functions", false]], "hippynn.graphs.nodes.excited": [[47, "module-hippynn.graphs.nodes.excited", false]], "hippynn.graphs.nodes.indexers": [[48, "module-hippynn.graphs.nodes.indexers", false]], "hippynn.graphs.nodes.inputs": [[49, "module-hippynn.graphs.nodes.inputs", false]], "hippynn.graphs.nodes.loss": [[50, "module-hippynn.graphs.nodes.loss", false]], "hippynn.graphs.nodes.misc": [[51, "module-hippynn.graphs.nodes.misc", false]], "hippynn.graphs.nodes.networks": [[52, "module-hippynn.graphs.nodes.networks", false]], "hippynn.graphs.nodes.pairs": [[53, "module-hippynn.graphs.nodes.pairs", false]], "hippynn.graphs.nodes.physics": [[54, "module-hippynn.graphs.nodes.physics", false]], "hippynn.graphs.nodes.tags": [[55, "module-hippynn.graphs.nodes.tags", false]], "hippynn.graphs.nodes.targets": [[56, "module-hippynn.graphs.nodes.targets", false]], "hippynn.graphs.predictor": [[57, "module-hippynn.graphs.predictor", false]], "hippynn.graphs.viz": [[58, "module-hippynn.graphs.viz", false]], "hippynn.interfaces": [[59, "module-hippynn.interfaces", false]], "hippynn.interfaces.ase_interface": [[60, "module-hippynn.interfaces.ase_interface", false]], "hippynn.interfaces.ase_interface.ase_database": [[61, "module-hippynn.interfaces.ase_interface.ase_database", false]], "hippynn.interfaces.ase_interface.ase_unittests": [[62, "module-hippynn.interfaces.ase_interface.ase_unittests", false]], "hippynn.interfaces.ase_interface.calculator": [[63, "module-hippynn.interfaces.ase_interface.calculator", false]], "hippynn.interfaces.ase_interface.pairfinder": [[64, "module-hippynn.interfaces.ase_interface.pairfinder", false]], "hippynn.interfaces.lammps_interface": [[65, "module-hippynn.interfaces.lammps_interface", false]], "hippynn.interfaces.lammps_interface.mliap_interface": [[66, "module-hippynn.interfaces.lammps_interface.mliap_interface", false]], "hippynn.interfaces.pyseqm_interface": [[67, "module-hippynn.interfaces.pyseqm_interface", false]], "hippynn.interfaces.pyseqm_interface.callback": [[68, "module-hippynn.interfaces.pyseqm_interface.callback", false]], "hippynn.interfaces.pyseqm_interface.check": [[69, "module-hippynn.interfaces.pyseqm_interface.check", false]], "hippynn.interfaces.pyseqm_interface.gen_par": [[70, "module-hippynn.interfaces.pyseqm_interface.gen_par", false]], "hippynn.interfaces.pyseqm_interface.mlseqm": [[71, "module-hippynn.interfaces.pyseqm_interface.mlseqm", false]], "hippynn.interfaces.pyseqm_interface.seqm_modules": [[72, "module-hippynn.interfaces.pyseqm_interface.seqm_modules", false]], "hippynn.interfaces.pyseqm_interface.seqm_nodes": [[73, "module-hippynn.interfaces.pyseqm_interface.seqm_nodes", false]], "hippynn.interfaces.pyseqm_interface.seqm_one": [[74, "module-hippynn.interfaces.pyseqm_interface.seqm_one", false]], "hippynn.interfaces.schnetpack_interface": [[75, "module-hippynn.interfaces.schnetpack_interface", false]], "hippynn.layers": [[76, "module-hippynn.layers", false]], "hippynn.layers.algebra": [[77, "module-hippynn.layers.algebra", false]], "hippynn.layers.excited": [[78, "module-hippynn.layers.excited", false]], "hippynn.layers.hiplayers": [[79, "module-hippynn.layers.hiplayers", false]], "hippynn.layers.indexers": [[80, "module-hippynn.layers.indexers", false]], "hippynn.layers.pairs": [[81, "module-hippynn.layers.pairs", false]], "hippynn.layers.pairs.analysis": [[82, "module-hippynn.layers.pairs.analysis", false]], "hippynn.layers.pairs.dispatch": [[83, "module-hippynn.layers.pairs.dispatch", false]], "hippynn.layers.pairs.filters": [[84, "module-hippynn.layers.pairs.filters", false]], "hippynn.layers.pairs.indexing": [[85, "module-hippynn.layers.pairs.indexing", false]], "hippynn.layers.pairs.open": [[86, "module-hippynn.layers.pairs.open", false]], "hippynn.layers.pairs.periodic": [[87, "module-hippynn.layers.pairs.periodic", false]], "hippynn.layers.physics": [[88, "module-hippynn.layers.physics", false]], "hippynn.layers.regularization": [[89, "module-hippynn.layers.regularization", false]], "hippynn.layers.targets": [[90, "module-hippynn.layers.targets", false]], "hippynn.layers.transform": [[91, "module-hippynn.layers.transform", false]], "hippynn.molecular_dynamics": [[92, "module-hippynn.molecular_dynamics", false]], "hippynn.molecular_dynamics.md": [[93, "module-hippynn.molecular_dynamics.md", false]], "hippynn.networks": [[94, "module-hippynn.networks", false]], "hippynn.networks.hipnn": [[95, "module-hippynn.networks.hipnn", false]], "hippynn.optimizer": [[96, "module-hippynn.optimizer", false]], "hippynn.optimizer.algorithms": [[97, "module-hippynn.optimizer.algorithms", false]], "hippynn.optimizer.batch_optimizer": [[98, "module-hippynn.optimizer.batch_optimizer", false]], "hippynn.optimizer.utils": [[99, "module-hippynn.optimizer.utils", false]], "hippynn.plotting": [[100, "module-hippynn.plotting", false]], "hippynn.plotting.plotmaker": [[101, "module-hippynn.plotting.plotmaker", false]], "hippynn.plotting.plotters": [[102, "module-hippynn.plotting.plotters", false]], "hippynn.plotting.timeplots": [[103, "module-hippynn.plotting.timeplots", false]], "hippynn.pretraining": [[104, "module-hippynn.pretraining", false]], "hippynn.tools": [[105, "module-hippynn.tools", false]], "hippynncalculator (class in hippynn.interfaces.ase_interface)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator", false]], "hippynncalculator (class in hippynn.interfaces.ase_interface.calculator)": [[63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator", false]], "hist1d (class in hippynn.plotting.plotters)": [[102, "hippynn.plotting.plotters.Hist1D", false]], "hist1dcomp (class in hippynn.plotting.plotters)": [[102, "hippynn.plotting.plotters.Hist1DComp", false]], "hist2d (class in hippynn.plotting.plotters)": [[102, "hippynn.plotting.plotters.Hist2D", false]], "identify_inputs() (in module hippynn.graphs.ensemble)": [[29, "hippynn.graphs.ensemble.identify_inputs", false]], "identify_targets() (in module hippynn.graphs.ensemble)": [[29, "hippynn.graphs.ensemble.identify_targets", false]], "idx (class in hippynn.layers.algebra)": [[77, "hippynn.layers.algebra.Idx", false]], "idx_atom_molatom() (in module hippynn.graphs.indextransformers.atoms)": [[33, "hippynn.graphs.indextransformers.atoms.idx_atom_molatom", false]], "idx_molatom_atom() (in module hippynn.graphs.indextransformers.atoms)": [[33, "hippynn.graphs.indextransformers.atoms.idx_molatom_atom", false]], "idx_molatomatom_pair() (in module hippynn.graphs.indextransformers.pairs)": [[34, "hippynn.graphs.indextransformers.pairs.idx_molatomatom_pair", false]], "idx_pair_molatomatom() (in module hippynn.graphs.indextransformers.pairs)": [[34, "hippynn.graphs.indextransformers.pairs.idx_pair_molatomatom", false]], "idx_quadtrimol() (in module hippynn.graphs.indextransformers.tensors)": [[35, "hippynn.graphs.indextransformers.tensors.idx_QuadTriMol", false]], "idxtype (class in hippynn.graphs)": [[28, "hippynn.graphs.IdxType", false]], "idxtype (class in hippynn.graphs.indextypes)": [[36, "hippynn.graphs.indextypes.IdxType", false]], "idxtype (class in hippynn.graphs.indextypes.type_def)": [[39, "hippynn.graphs.indextypes.type_def.IdxType", false]], "index_type_coercion() (in module hippynn.graphs.indextypes)": [[36, "hippynn.graphs.indextypes.index_type_coercion", false]], "index_type_coercion() (in module hippynn.graphs.indextypes.reduce_funcs)": [[37, "hippynn.graphs.indextypes.reduce_funcs.index_type_coercion", false]], "indexformtransformer (class in 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"module-hippynn.plotting.plotters", false], [103, "module-hippynn.plotting.timeplots", false], [104, "module-hippynn.pretraining", false], [105, "module-hippynn.tools", false]], "molatom (idxtype attribute)": [[28, "hippynn.graphs.IdxType.MolAtom", false], [36, "hippynn.graphs.indextypes.IdxType.MolAtom", false], [39, "hippynn.graphs.indextypes.type_def.IdxType.MolAtom", false]], "molatomatom (idxtype attribute)": [[28, "hippynn.graphs.IdxType.MolAtomAtom", false], [36, "hippynn.graphs.indextypes.IdxType.MolAtomAtom", false], [39, "hippynn.graphs.indextypes.type_def.IdxType.MolAtomAtom", false]], "moleculardynamics (class in hippynn.molecular_dynamics.md)": [[93, "hippynn.molecular_dynamics.md.MolecularDynamics", false]], "molecules (idxtype attribute)": [[28, "hippynn.graphs.IdxType.Molecules", false], [36, "hippynn.graphs.indextypes.IdxType.Molecules", false], [39, "hippynn.graphs.indextypes.type_def.IdxType.Molecules", false]], "molpairsummer (class in hippynn.layers.pairs.indexing)": [[85, "hippynn.layers.pairs.indexing.MolPairSummer", false]], "molsummer (class in hippynn.layers.indexers)": [[80, "hippynn.layers.indexers.MolSummer", false]], "mseloss (class in hippynn.graphs.nodes.loss)": [[50, "hippynn.graphs.nodes.loss.MSELoss", false]], "msephaseloss (class in hippynn.graphs.nodes.excited)": [[47, "hippynn.graphs.nodes.excited.MSEPhaseLoss", false]], "mulnode (class in hippynn.graphs.nodes.base.algebra)": [[42, "hippynn.graphs.nodes.base.algebra.MulNode", false]], "multigradient (class in hippynn.layers.physics)": [[88, "hippynn.layers.physics.MultiGradient", false]], "multigradientnode (class in hippynn.graphs.nodes.physics)": [[54, "hippynn.graphs.nodes.physics.MultiGradientNode", false]], "multinode (class in hippynn.graphs.nodes.base.multi)": [[45, "hippynn.graphs.nodes.base.multi.MultiNode", false]], "nacr (class in hippynn.layers.excited)": [[78, "hippynn.layers.excited.NACR", false]], "nacrmultistate (class in hippynn.layers.excited)": [[78, "hippynn.layers.excited.NACRMultiState", false]], "nacrmultistatenode (class in hippynn.graphs.nodes.excited)": [[47, "hippynn.graphs.nodes.excited.NACRMultiStateNode", false]], "nacrnode (class in hippynn.graphs.nodes.excited)": [[47, "hippynn.graphs.nodes.excited.NACRNode", false]], "namedtensordataset (class in hippynn.databases.database)": [[15, "hippynn.databases.database.NamedTensorDataset", false]], "negnode (class in hippynn.graphs.nodes.base.algebra)": [[42, "hippynn.graphs.nodes.base.algebra.NegNode", false]], "neighbor_list_kdtree() (in module hippynn.layers.pairs.dispatch)": [[83, "hippynn.layers.pairs.dispatch.neighbor_list_kdtree", false]], "neighbor_list_np() (in module hippynn.layers.pairs.dispatch)": [[83, "hippynn.layers.pairs.dispatch.neighbor_list_np", false]], "network (class in hippynn.graphs.nodes.tags)": [[55, "hippynn.graphs.nodes.tags.Network", false]], "newtonraphson (class in hippynn.optimizer.algorithms)": [[97, "hippynn.optimizer.algorithms.NewtonRaphson", false]], "node (class in hippynn.graphs.nodes.base.base)": [[43, "hippynn.graphs.nodes.base.base.Node", false]], "node_from_name() (graphmodule method)": [[28, "hippynn.graphs.GraphModule.node_from_name", false], [31, "hippynn.graphs.graph.GraphModule.node_from_name", false]], "nodeambiguityerror": [[46, "hippynn.graphs.nodes.base.node_functions.NodeAmbiguityError", false]], "nodenotfound": [[46, "hippynn.graphs.nodes.base.node_functions.NodeNotFound", false]], "nodeoperationerror": [[46, "hippynn.graphs.nodes.base.node_functions.NodeOperationError", false]], "norestart (class in hippynn.databases.restarter)": [[18, "hippynn.databases.restarter.NoRestart", false]], "norm (hist2d property)": [[102, "hippynn.plotting.plotters.Hist2D.norm", false]], "notconvergednode (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[74, "hippynn.interfaces.pyseqm_interface.seqm_one.NotConvergedNode", false]], "notfound (idxtype attribute)": [[28, "hippynn.graphs.IdxType.NotFound", false], [36, "hippynn.graphs.indextypes.IdxType.NotFound", false], [39, "hippynn.graphs.indextypes.type_def.IdxType.NotFound", false]], "np_of_torchdefaultdtype() (in module hippynn.tools)": [[105, "hippynn.tools.np_of_torchdefaultdtype", false]], "npneighbors (class in hippynn.layers.pairs.dispatch)": [[83, "hippynn.layers.pairs.dispatch.NPNeighbors", false]], "npzdatabase (class in hippynn.databases)": [[13, "hippynn.databases.NPZDatabase", false]], "npzdatabase (class in hippynn.databases.ondisk)": [[17, "hippynn.databases.ondisk.NPZDatabase", false]], "nullupdater (class in hippynn.molecular_dynamics.md)": [[93, "hippynn.molecular_dynamics.md.NullUpdater", false]], "num_orb() (in module hippynn.interfaces.pyseqm_interface.seqm_modules)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_modules.num_orb", false]], "numbacompatibletensorfunction (class in hippynn.custom_kernels.tensor_wrapper)": [[8, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction", false]], "numpydynamicpairs (class in hippynn.graphs.nodes.pairs)": [[53, "hippynn.graphs.nodes.pairs.NumpyDynamicPairs", false]], "of_node() (reducesinglenode class method)": [[50, "hippynn.graphs.nodes.loss.ReduceSingleNode.of_node", false]], "onehotencoder (class in hippynn.graphs.nodes.indexers)": [[48, "hippynn.graphs.nodes.indexers.OneHotEncoder", false]], "onehotspecies (class in hippynn.layers.indexers)": [[80, "hippynn.layers.indexers.OneHotSpecies", false]], "openpairindexer (class in hippynn.graphs.nodes.pairs)": [[53, "hippynn.graphs.nodes.pairs.OpenPairIndexer", false]], "openpairindexer (class in hippynn.layers.pairs.open)": [[86, "hippynn.layers.pairs.open.OpenPairIndexer", false]], "optimizer (class in hippynn.optimizer.batch_optimizer)": [[98, "hippynn.optimizer.batch_optimizer.Optimizer", false]], "optimizer (setupparams attribute)": [[19, "hippynn.experiment.SetupParams.optimizer", false], [25, "hippynn.experiment.routines.SetupParams.optimizer", false]], "out_shape() (numbacompatibletensorfunction method)": [[8, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction.out_shape", false]], "out_shape() (wrappedenvsum method)": [[4, "hippynn.custom_kernels.env_numba.WrappedEnvsum.out_shape", false]], "out_shape() (wrappedfeatsum method)": [[4, "hippynn.custom_kernels.env_numba.WrappedFeatsum.out_shape", false]], "out_shape() (wrappedsensesum method)": [[4, "hippynn.custom_kernels.env_numba.WrappedSensesum.out_shape", false]], "outputs (predictor property)": [[28, "hippynn.graphs.Predictor.outputs", false], [57, "hippynn.graphs.predictor.Predictor.outputs", false]], "p_value (qscreening property)": [[88, "hippynn.layers.physics.QScreening.p_value", false]], "pack_par() (in module hippynn.interfaces.pyseqm_interface.seqm_modules)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_modules.pack_par", false]], "pad_np_array_to_length_with_zeros() (in module hippynn.tools)": [[105, "hippynn.tools.pad_np_array_to_length_with_zeros", false]], "padded_neighlist() (in module hippynn.layers.pairs.indexing)": [[85, "hippynn.layers.pairs.indexing.padded_neighlist", false]], "paddedneighbornode (class in hippynn.graphs.nodes.pairs)": [[53, "hippynn.graphs.nodes.pairs.PaddedNeighborNode", false]], "paddedneighmodule (class in hippynn.layers.pairs.indexing)": [[85, "hippynn.layers.pairs.indexing.PaddedNeighModule", false]], "paddingindexer (class in hippynn.graphs.nodes.indexers)": [[48, "hippynn.graphs.nodes.indexers.PaddingIndexer", false]], "paddingindexer (class in hippynn.layers.indexers)": [[80, "hippynn.layers.indexers.PaddingIndexer", false]], "pair (idxtype attribute)": [[28, "hippynn.graphs.IdxType.Pair", false], [36, "hippynn.graphs.indextypes.IdxType.Pair", false], [39, "hippynn.graphs.indextypes.type_def.IdxType.Pair", false]], "paircache (class in hippynn.graphs.nodes.tags)": [[55, "hippynn.graphs.nodes.tags.PairCache", false]], "paircacher (class in hippynn.graphs.nodes.pairs)": [[53, "hippynn.graphs.nodes.pairs.PairCacher", false]], "paircacher (class in hippynn.layers.pairs.indexing)": [[85, "hippynn.layers.pairs.indexing.PairCacher", false]], "pairdeindexer (class in hippynn.graphs.nodes.pairs)": [[53, "hippynn.graphs.nodes.pairs.PairDeIndexer", false]], "pairdeindexer (class in hippynn.layers.pairs.indexing)": [[85, "hippynn.layers.pairs.indexing.PairDeIndexer", false]], "pairfilter (class in hippynn.graphs.nodes.pairs)": [[53, "hippynn.graphs.nodes.pairs.PairFilter", false]], "pairindexer (class in hippynn.graphs.nodes.tags)": [[55, "hippynn.graphs.nodes.tags.PairIndexer", false]], "pairindices (class in hippynn.graphs.nodes.inputs)": [[49, "hippynn.graphs.nodes.inputs.PairIndices", false]], "pairmemory (class in hippynn.layers.pairs.open)": [[86, "hippynn.layers.pairs.open.PairMemory", false]], "pairreindexer (class in hippynn.graphs.nodes.pairs)": [[53, "hippynn.graphs.nodes.pairs.PairReIndexer", false]], "pairreindexer (class in hippynn.layers.pairs.indexing)": [[85, "hippynn.layers.pairs.indexing.PairReIndexer", false]], "pairuncacher (class in hippynn.graphs.nodes.pairs)": [[53, "hippynn.graphs.nodes.pairs.PairUncacher", false]], "pairuncacher (class in hippynn.layers.pairs.indexing)": [[85, "hippynn.layers.pairs.indexing.PairUncacher", false]], "param_print() (in module hippynn.tools)": [[105, "hippynn.tools.param_print", false]], "parentexpander (class in hippynn.graphs.nodes.base.definition_helpers)": [[44, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander", false]], "parse_args() (in module hippynn.custom_kernels.test_env_numba)": [[10, "hippynn.custom_kernels.test_env_numba.parse_args", false]], "pass_to_pytorch() (in module hippynn.interfaces.ase_interface.calculator)": [[63, "hippynn.interfaces.ase_interface.calculator.pass_to_pytorch", false]], "patiencecontroller (class in hippynn.experiment.controllers)": [[21, 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false]], "post_step() (variableupdater method)": [[93, "hippynn.molecular_dynamics.md.VariableUpdater.post_step", false]], "post_step() (velocityverlet method)": [[93, "hippynn.molecular_dynamics.md.VelocityVerlet.post_step", false]], "pownode (class in hippynn.graphs.nodes.base.algebra)": [[42, "hippynn.graphs.nodes.base.algebra.PowNode", false]], "pre_step() (langevindynamics method)": [[93, "hippynn.molecular_dynamics.md.LangevinDynamics.pre_step", false]], "pre_step() (nullupdater method)": [[93, "hippynn.molecular_dynamics.md.NullUpdater.pre_step", false]], "pre_step() (variableupdater method)": [[93, "hippynn.molecular_dynamics.md.VariableUpdater.pre_step", false]], "pre_step() (velocityverlet method)": [[93, "hippynn.molecular_dynamics.md.VelocityVerlet.pre_step", false]], "precompute_pairs() (in module hippynn.experiment.assembly)": [[20, "hippynn.experiment.assembly.precompute_pairs", false]], "pred (lossinputnode property)": [[43, 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false]], "quadrupole (class in hippynn.layers.physics)": [[88, "hippynn.layers.physics.Quadrupole", false]], "quadrupolenode (class in hippynn.graphs.nodes.physics)": [[54, "hippynn.graphs.nodes.physics.QuadrupoleNode", false]], "quadunpack (class in hippynn.layers.indexers)": [[80, "hippynn.layers.indexers.QuadUnpack", false]], "quadunpacknode (class in hippynn.graphs.nodes.indexers)": [[48, "hippynn.graphs.nodes.indexers.QuadUnpackNode", false]], "raisebatchsizeonplateau (class in hippynn.experiment.controllers)": [[21, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau", false]], "rdfbins (class in hippynn.graphs.nodes.pairs)": [[53, "hippynn.graphs.nodes.pairs.RDFBins", false]], "rdfbins (class in hippynn.layers.pairs.analysis)": [[82, "hippynn.layers.pairs.analysis.RDFBins", false]], "rebuild_neighbors() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.rebuild_neighbors", false], [63, 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"regularization_params() (resnetwrapper method)": [[91, "hippynn.layers.transform.ResNetWrapper.regularization_params", false]], "reindexatommod (class in hippynn.interfaces.lammps_interface.mliap_interface)": [[66, "hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomMod", false]], "reindexatomnode (class in hippynn.interfaces.lammps_interface.mliap_interface)": [[66, "hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomNode", false]], "remove_high_property() (database method)": [[13, "hippynn.databases.Database.remove_high_property", false], [15, "hippynn.databases.database.Database.remove_high_property", false]], "replace_inputs() (in module hippynn.graphs.ensemble)": [[29, "hippynn.graphs.ensemble.replace_inputs", false]], "replace_node() (in module hippynn.graphs)": [[28, "hippynn.graphs.replace_node", false]], "replace_node() (in module hippynn.graphs.gops)": [[30, "hippynn.graphs.gops.replace_node", false]], "replace_node_with_constant() (in module 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"hippynn.graphs.nodes.base.base.InputNode.requires_grad", false]], "reset() (bfgsv1 method)": [[97, "hippynn.optimizer.algorithms.BFGSv1.reset", false]], "reset() (bfgsv2 method)": [[97, "hippynn.optimizer.algorithms.BFGSv2.reset", false]], "reset() (bfgsv3 method)": [[97, "hippynn.optimizer.algorithms.BFGSv3.reset", false]], "reset() (fire method)": [[97, "hippynn.optimizer.algorithms.FIRE.reset", false]], "reset() (newtonraphson method)": [[97, "hippynn.optimizer.algorithms.NewtonRaphson.reset", false]], "reset_data() (moleculardynamics method)": [[93, "hippynn.molecular_dynamics.md.MolecularDynamics.reset_data", false]], "reset_reuse_percentage() (memory method)": [[53, "hippynn.graphs.nodes.pairs.Memory.reset_reuse_percentage", false]], "reset_reuse_percentage() (pairmemory method)": [[86, "hippynn.layers.pairs.open.PairMemory.reset_reuse_percentage", false]], "resnetwrapper (class in hippynn.layers.transform)": [[91, "hippynn.layers.transform.ResNetWrapper", false]], 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"hippynn.interfaces.pyseqm_interface.seqm_nodes.ScaleNode", false]], "scheduler (setupparams attribute)": [[19, "hippynn.experiment.SetupParams.scheduler", false], [25, "hippynn.experiment.routines.SetupParams.scheduler", false]], "schnetnode (class in hippynn.interfaces.schnetpack_interface)": [[75, "hippynn.interfaces.schnetpack_interface.SchNetNode", false]], "schnetwrapper (class in hippynn.interfaces.schnetpack_interface)": [[75, "hippynn.interfaces.schnetpack_interface.SchNetWrapper", false]], "screenedcoulombenergy (class in hippynn.layers.physics)": [[88, "hippynn.layers.physics.ScreenedCoulombEnergy", false]], "screenedcoulombenergynode (class in hippynn.graphs.nodes.physics)": [[54, "hippynn.graphs.nodes.physics.ScreenedCoulombEnergyNode", false]], "search_by_name() (in module hippynn.graphs.gops)": [[30, "hippynn.graphs.gops.search_by_name", false]], "send_to_device() (database method)": [[13, "hippynn.databases.Database.send_to_device", false], [15, "hippynn.databases.database.Database.send_to_device", false]], "sensesum() (in module hippynn.custom_kernels.env_pytorch)": [[5, "hippynn.custom_kernels.env_pytorch.sensesum", false]], "sensitivity_layers (hipnn property)": [[95, "hippynn.networks.hipnn.Hipnn.sensitivity_layers", false]], "sensitivitybottleneck (class in hippynn.layers.hiplayers)": [[79, "hippynn.layers.hiplayers.SensitivityBottleneck", false]], "sensitivitymodule (class in hippynn.layers.hiplayers)": [[79, "hippynn.layers.hiplayers.SensitivityModule", false]], "sensitivityplot (class in hippynn.plotting.plotters)": [[102, "hippynn.plotting.plotters.SensitivityPlot", false]], "seqm_all (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_All", false]], "seqm_allnode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_AllNode", false]], "seqm_energy (class in 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hippynn.interfaces.pyseqm_interface.seqm_modules)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolOrbital", false]], "seqm_maskonmolorbitalatom (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolOrbitalAtom", false]], "seqm_maskonmolorbitalatomnode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_MaskOnMolOrbitalAtomNode", false]], "seqm_maskonmolorbitalnode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_MaskOnMolOrbitalNode", false]], "seqm_molmask (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MolMask", false]], "seqm_molmasknode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_MolMaskNode", false]], "seqm_one_all (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[74, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_All", false]], "seqm_one_allnode (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[74, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_AllNode", false]], "seqm_one_energy (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[74, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_Energy", false]], "seqm_one_energynode (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[74, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_EnergyNode", false]], "seqm_orbitalmask (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_OrbitalMask", false]], "seqm_orbitalmasknode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_OrbitalMaskNode", false]], "set() (pbchandle method)": [[63, "hippynn.interfaces.ase_interface.calculator.PBCHandle.set", false]], "set_atoms() (hippynncalculator method)": [[60, "hippynn.interfaces.ase_interface.HippynnCalculator.set_atoms", false], [63, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.set_atoms", false]], "set_controller() (raisebatchsizeonplateau method)": [[21, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau.set_controller", false]], "set_custom_kernels() (in module hippynn.custom_kernels)": [[1, "hippynn.custom_kernels.set_custom_kernels", false]], "set_dbname() (multinode method)": [[45, "hippynn.graphs.nodes.base.multi.MultiNode.set_dbname", false]], "set_devices() (in module hippynn.experiment.device)": [[22, "hippynn.experiment.device.set_devices", false]], "set_e0_values() (in module hippynn.pretraining)": [[104, "hippynn.pretraining.set_e0_values", false]], "set_extra_state() (interactlayervec method)": [[79, "hippynn.layers.hiplayers.InteractLayerVec.set_extra_state", false]], "set_images() (paircacher method)": [[85, "hippynn.layers.pairs.indexing.PairCacher.set_images", false]], "set_images() (pairuncacher method)": [[85, "hippynn.layers.pairs.indexing.PairUncacher.set_images", false]], "set_skin() (pairmemory method)": [[86, "hippynn.layers.pairs.open.PairMemory.set_skin", false]], "setup_and_train() (in module hippynn.experiment)": [[19, "hippynn.experiment.setup_and_train", false]], "setup_and_train() (in module hippynn.experiment.routines)": [[25, "hippynn.experiment.routines.setup_and_train", false]], "setup_ase_graph() (in module hippynn.interfaces.ase_interface.calculator)": [[63, "hippynn.interfaces.ase_interface.calculator.setup_ASE_graph", false]], "setup_lammps_graph() (in module hippynn.interfaces.lammps_interface.mliap_interface)": [[66, "hippynn.interfaces.lammps_interface.mliap_interface.setup_LAMMPS_graph", false]], "setup_training() (in module hippynn.experiment)": [[19, "hippynn.experiment.setup_training", false]], "setup_training() (in module 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"hippynn.graphs.indextypes.reduce_funcs.soft_index_type_coercion", false]], "sort_by_index() (database method)": [[13, "hippynn.databases.Database.sort_by_index", false], [15, "hippynn.databases.database.Database.sort_by_index", false]], "species (class in hippynn.graphs.nodes.tags)": [[55, "hippynn.graphs.nodes.tags.Species", false]], "species_set (encoder attribute)": [[55, "hippynn.graphs.nodes.tags.Encoder.species_set", false]], "speciesnode (class in hippynn.graphs.nodes.inputs)": [[49, "hippynn.graphs.nodes.inputs.SpeciesNode", false]], "split_the_rest() (database method)": [[13, "hippynn.databases.Database.split_the_rest", false], [15, "hippynn.databases.database.Database.split_the_rest", false]], "splitindices (class in hippynn.graphs.nodes.inputs)": [[49, "hippynn.graphs.nodes.inputs.SplitIndices", false]], "standard_step_fn() (in module hippynn.experiment.step_functions)": [[27, "hippynn.experiment.step_functions.standard_step_fn", false]], "standardstep (class in 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"hippynn.graphs.predictor.Predictor.to", false]], "to() (variable method)": [[93, "hippynn.molecular_dynamics.md.Variable.to", false]], "torch_module (addnode attribute)": [[42, "hippynn.graphs.nodes.base.algebra.AddNode.torch_module", false]], "torch_module (atleast2d attribute)": [[42, "hippynn.graphs.nodes.base.algebra.AtLeast2D.torch_module", false]], "torch_module (divnode attribute)": [[42, "hippynn.graphs.nodes.base.algebra.DivNode.torch_module", false]], "torch_module (invnode attribute)": [[42, "hippynn.graphs.nodes.base.algebra.InvNode.torch_module", false]], "torch_module (maeloss attribute)": [[50, "hippynn.graphs.nodes.loss.MAELoss.torch_module", false]], "torch_module (maephaseloss attribute)": [[47, "hippynn.graphs.nodes.excited.MAEPhaseLoss.torch_module", false]], "torch_module (mean attribute)": [[50, "hippynn.graphs.nodes.loss.Mean.torch_module", false]], "torch_module (meansq attribute)": [[50, "hippynn.graphs.nodes.loss.MeanSq.torch_module", false]], "torch_module 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"hippynn.graphs.nodes.base.definition_helpers.AutoKw", false]], "autonokw (class in hippynn.graphs.nodes.base.definition_helpers)": [[45, "hippynn.graphs.nodes.base.definition_helpers.AutoNoKw", false]], "batch_convert_torch_to_numba() (in module hippynn.custom_kernels.fast_convert)": [[7, "hippynn.custom_kernels.fast_convert.batch_convert_torch_to_numba", false]], "batch_size (setupparams attribute)": [[19, "hippynn.experiment.SetupParams.batch_size", false], [26, "hippynn.experiment.routines.SetupParams.batch_size", false]], "bfgsv1 (class in hippynn.optimizer.algorithms)": [[98, "hippynn.optimizer.algorithms.BFGSv1", false]], "bfgsv2 (class in hippynn.optimizer.algorithms)": [[98, "hippynn.optimizer.algorithms.BFGSv2", false]], "bfgsv3 (class in hippynn.optimizer.algorithms)": [[98, "hippynn.optimizer.algorithms.BFGSv3", false]], "bin_info() (rdfbins method)": [[83, "hippynn.layers.pairs.analysis.RDFBins.bin_info", false]], "binnode (class in hippynn.graphs.nodes.base.algebra)": [[43, "hippynn.graphs.nodes.base.algebra.BinNode", false]], "bondtomolsummmer (class in hippynn.graphs.nodes.physics)": [[55, "hippynn.graphs.nodes.physics.BondToMolSummmer", false]], "build_loss_modules() (in module hippynn.experiment.assembly)": [[20, "hippynn.experiment.assembly.build_loss_modules", false]], "calculate() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.calculate", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.calculate", false]], "calculate_max_system_force() (in module hippynn.pretraining)": [[105, "hippynn.pretraining.calculate_max_system_force", false]], "calculate_min_dists() (in module hippynn.pretraining)": [[105, "hippynn.pretraining.calculate_min_dists", false]], "calculation_required() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.calculation_required", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.calculation_required", false]], "calculator_from_model() (in module hippynn.interfaces.ase_interface)": [[61, "hippynn.interfaces.ase_interface.calculator_from_model", false]], "calculator_from_model() (in module hippynn.interfaces.ase_interface.calculator)": [[64, "hippynn.interfaces.ase_interface.calculator.calculator_from_model", false]], "cellnode (class in hippynn.graphs.nodes.inputs)": [[50, "hippynn.graphs.nodes.inputs.CellNode", false]], "cellscaleinducer (class in hippynn.layers.indexers)": [[81, "hippynn.layers.indexers.CellScaleInducer", false]], "chargemomentnode (class in hippynn.graphs.nodes.physics)": [[55, "hippynn.graphs.nodes.physics.ChargeMomentNode", false]], "chargepairsetup (class in hippynn.graphs.nodes.physics)": [[55, "hippynn.graphs.nodes.physics.ChargePairSetup", false]], "charges (class in hippynn.graphs.nodes.tags)": [[56, "hippynn.graphs.nodes.tags.Charges", false]], "check() (in module hippynn.interfaces.pyseqm_interface.check)": [[70, "hippynn.interfaces.pyseqm_interface.check.check", false]], "check_all_grad() (envops_tester method)": [[10, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_all_grad", false]], "check_all_grad_once() (envops_tester method)": [[10, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_all_grad_once", false]], "check_allclose() (envops_tester method)": [[10, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_allclose", false]], "check_allclose_once() (envops_tester method)": [[10, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_allclose_once", false]], "check_correctness() (envops_tester method)": [[10, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_correctness", false]], "check_dist() (in module hippynn.interfaces.pyseqm_interface.check)": [[70, "hippynn.interfaces.pyseqm_interface.check.check_dist", false]], "check_empty() (envops_tester method)": [[10, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_empty", false]], "check_evaluation_order() (in module hippynn.graphs.gops)": [[31, "hippynn.graphs.gops.check_evaluation_order", false]], "check_grad_and_gradgrad() (envops_tester method)": [[10, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_grad_and_gradgrad", false]], "check_gradient() (in module hippynn.interfaces.pyseqm_interface.check)": [[70, "hippynn.interfaces.pyseqm_interface.check.check_gradient", false]], "check_link_consistency() (in module hippynn.graphs.gops)": [[31, "hippynn.graphs.gops.check_link_consistency", false]], "check_mapping_devices() (in module hippynn.experiment.serialization)": [[27, "hippynn.experiment.serialization.check_mapping_devices", false]], "check_speed() (envops_tester method)": [[10, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_speed", false]], "clear_index_cache() (in module hippynn.graphs.indextypes)": [[37, "hippynn.graphs.indextypes.clear_index_cache", false]], "clear_index_cache() (in module hippynn.graphs.indextypes.registry)": [[39, "hippynn.graphs.indextypes.registry.clear_index_cache", false]], "clear_pair_cache() (in module hippynn.custom_kernels.utils)": [[12, "hippynn.custom_kernels.utils.clear_pair_cache", false]], "closure_step_fn() (in module hippynn.experiment.step_functions)": [[28, "hippynn.experiment.step_functions.closure_step_fn", false]], "closurestep (class in hippynn.experiment.step_functions)": [[28, "hippynn.experiment.step_functions.ClosureStep", false]], "coerces_values_to_nodes() (in module hippynn.graphs.nodes.base.algebra)": [[43, "hippynn.graphs.nodes.base.algebra.coerces_values_to_nodes", false]], "collate_inputs() (in module hippynn.graphs.ensemble)": [[30, "hippynn.graphs.ensemble.collate_inputs", false]], "collate_targets() (in module hippynn.graphs.ensemble)": [[30, "hippynn.graphs.ensemble.collate_targets", false]], "combineenergy (class in hippynn.layers.physics)": [[89, "hippynn.layers.physics.CombineEnergy", false]], "combineenergynode (class in hippynn.graphs.nodes.physics)": [[55, "hippynn.graphs.nodes.physics.CombineEnergyNode", false]], "combinescreenings (class in hippynn.layers.physics)": [[89, "hippynn.layers.physics.CombineScreenings", false]], "compatibility_hook() (interactlayervec static method)": [[80, "hippynn.layers.hiplayers.InteractLayerVec.compatibility_hook", false]], "compatibleidxtypetransformer (class in hippynn.graphs.nodes.base.definition_helpers)": [[45, "hippynn.graphs.nodes.base.definition_helpers.CompatibleIdxTypeTransformer", false]], "composedplotter (class in hippynn.plotting.plotters)": [[103, "hippynn.plotting.plotters.ComposedPlotter", false]], "compute_descriptors() (mliapinterface method)": [[67, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_descriptors", false]], "compute_evaluation_order() (in module hippynn.graphs)": [[29, "hippynn.graphs.compute_evaluation_order", false]], "compute_evaluation_order() (in module hippynn.graphs.gops)": [[31, "hippynn.graphs.gops.compute_evaluation_order", false]], "compute_forces() (mliapinterface method)": [[67, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_forces", false]], "compute_gradients() (mliapinterface method)": [[67, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_gradients", false]], "compute_hipnn_e0() (in module hippynn.networks.hipnn)": [[96, "hippynn.networks.hipnn.compute_hipnn_e0", false]], "compute_index_mask() (in module hippynn.databases.database)": [[15, "hippynn.databases.database.compute_index_mask", false]], "compute_one() (aseneighbors method)": [[65, "hippynn.interfaces.ase_interface.pairfinder.ASENeighbors.compute_one", false]], "compute_one() (kdtreeneighbors method)": [[84, "hippynn.layers.pairs.dispatch.KDTreeNeighbors.compute_one", false]], "compute_one() (npneighbors method)": [[84, "hippynn.layers.pairs.dispatch.NPNeighbors.compute_one", false]], "compute_one() (torchneighbors method)": [[84, "hippynn.layers.pairs.dispatch.TorchNeighbors.compute_one", false]], "config_pruner() (in module hippynn.custom_kernels.env_triton)": [[6, "hippynn.custom_kernels.env_triton.config_pruner", false]], "configure_optimizers() (hippynnlightningmodule method)": [[24, "hippynn.experiment.lightning_trainer.HippynnLightningModule.configure_optimizers", false]], "construct_outputs() (in module hippynn.graphs.ensemble)": [[30, "hippynn.graphs.ensemble.construct_outputs", false]], "controller (class in hippynn.experiment.controllers)": [[21, "hippynn.experiment.controllers.Controller", false]], "controller (setupparams attribute)": [[19, "hippynn.experiment.SetupParams.controller", false], [26, "hippynn.experiment.routines.SetupParams.controller", false]], "copy_subgraph() (in module hippynn.graphs)": [[29, "hippynn.graphs.copy_subgraph", false]], "copy_subgraph() (in module hippynn.graphs.gops)": [[31, "hippynn.graphs.gops.copy_subgraph", false]], "coscutoff (class in hippynn.layers.hiplayers)": [[80, "hippynn.layers.hiplayers.CosCutoff", false]], "coulombenergy (class in hippynn.layers.physics)": [[89, "hippynn.layers.physics.CoulombEnergy", false]], "coulombenergynode (class in hippynn.graphs.nodes.physics)": [[55, "hippynn.graphs.nodes.physics.CoulombEnergyNode", false]], "cpu_kernel() (numbacompatibletensorfunction method)": [[8, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction.cpu_kernel", false]], "cpu_kernel() (wrappedenvsum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedEnvsum.cpu_kernel", false]], "cpu_kernel() (wrappedfeatsum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedFeatsum.cpu_kernel", false]], "cpu_kernel() (wrappedsensesum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedSensesum.cpu_kernel", false]], "create_schnetpack_inputs() (in module hippynn.interfaces.schnetpack_interface)": [[76, "hippynn.interfaces.schnetpack_interface.create_schnetpack_inputs", false]], "create_state() (in module hippynn.experiment.serialization)": [[27, "hippynn.experiment.serialization.create_state", false]], "create_structure_file() (in module hippynn.experiment.serialization)": [[27, "hippynn.experiment.serialization.create_structure_file", false]], "cupyenvsum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyEnvsum", false]], "cupyfeatsum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyFeatsum", false]], "cupygpukernel (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyGPUKernel", false]], "cupysensesum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupySensesum", false]], "current_epoch (metrictracker property)": [[25, "hippynn.experiment.metric_tracker.MetricTracker.current_epoch", false]], "data (variable property)": [[94, "hippynn.molecular_dynamics.md.Variable.data", false]], "database (class in hippynn.databases)": [[13, "hippynn.databases.Database", false]], "database (class in hippynn.databases.database)": [[15, "hippynn.databases.database.Database", false]], "db_form() (in module hippynn.graphs.indextypes)": [[37, "hippynn.graphs.indextypes.db_form", false]], "db_form() (in module hippynn.graphs.indextypes.reduce_funcs)": [[38, "hippynn.graphs.indextypes.reduce_funcs.db_form", false]], "db_state_of() (in module hippynn.graphs.indextypes.reduce_funcs)": [[38, "hippynn.graphs.indextypes.reduce_funcs.db_state_of", false]], "debatch() (in module hippynn.optimizer.utils)": [[100, "hippynn.optimizer.utils.debatch", false]], "debatch_coords() (in module hippynn.optimizer.utils)": [[100, "hippynn.optimizer.utils.debatch_coords", false]], "debatch_numbers() (in module hippynn.optimizer.utils)": [[100, "hippynn.optimizer.utils.debatch_numbers", false]], "defaultnetworkexpansion (class in hippynn.graphs.nodes.networks)": [[53, "hippynn.graphs.nodes.networks.DefaultNetworkExpansion", false]], "densitymatrixnode (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[75, "hippynn.interfaces.pyseqm_interface.seqm_one.DensityMatrixNode", false]], "determine_out_in_targ() (in module hippynn.experiment.assembly)": [[20, "hippynn.experiment.assembly.determine_out_in_targ", false]], "device (moleculardynamics property)": [[94, "hippynn.molecular_dynamics.md.MolecularDynamics.device", false]], "device (setupparams attribute)": [[19, "hippynn.experiment.SetupParams.device", false], [26, "hippynn.experiment.routines.SetupParams.device", false]], "device (variable property)": [[94, "hippynn.molecular_dynamics.md.Variable.device", false]], "device_fallback() (in module hippynn.tools)": [[106, "hippynn.tools.device_fallback", false]], "dipole (class in hippynn.layers.physics)": [[89, "hippynn.layers.physics.Dipole", false]], "dipolenode (class in hippynn.graphs.nodes.physics)": [[55, "hippynn.graphs.nodes.physics.DipoleNode", false]], "directorydatabase (class in hippynn.databases)": [[13, "hippynn.databases.DirectoryDatabase", false]], "directorydatabase (class in hippynn.databases.ondisk)": [[17, "hippynn.databases.ondisk.DirectoryDatabase", false]], "dispatch_indexing() (in module hippynn.graphs.indextypes.reduce_funcs)": [[38, "hippynn.graphs.indextypes.reduce_funcs.dispatch_indexing", false]], "divnode (class in hippynn.graphs.nodes.base.algebra)": [[43, "hippynn.graphs.nodes.base.algebra.DivNode", false]], "dtype (moleculardynamics property)": [[94, "hippynn.molecular_dynamics.md.MolecularDynamics.dtype", false]], "dtype (variable property)": [[94, "hippynn.molecular_dynamics.md.Variable.dtype", false]], "dump_a_step() (optimizer method)": [[99, "hippynn.optimizer.batch_optimizer.Optimizer.dump_a_step", false]], "duq() (geometryoptimizer static method)": [[98, "hippynn.optimizer.algorithms.GeometryOptimizer.duq", false]], "dynamicperiodicpairs (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.DynamicPeriodicPairs", false]], "elapsed (timedsnippet property)": [[10, "hippynn.custom_kernels.test_env_numba.TimedSnippet.elapsed", false]], "elapsed (timerholder property)": [[10, "hippynn.custom_kernels.test_env_numba.TimerHolder.elapsed", false]], "elementwise_compare_reduce() (in module hippynn.graphs.indextypes)": [[37, "hippynn.graphs.indextypes.elementwise_compare_reduce", false]], "elementwise_compare_reduce() (in module hippynn.graphs.indextypes.reduce_funcs)": [[38, "hippynn.graphs.indextypes.reduce_funcs.elementwise_compare_reduce", false]], "emax_criteria() (newtonraphson method)": [[98, "hippynn.optimizer.algorithms.NewtonRaphson.emax_criteria", false]], "empty_tensor() (mliapinterface method)": [[67, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.empty_tensor", false]], "encoder (class in hippynn.graphs.nodes.tags)": [[56, "hippynn.graphs.nodes.tags.Encoder", false]], "energies (class in hippynn.graphs.nodes.tags)": [[56, "hippynn.graphs.nodes.tags.Energies", false]], "energy_one (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[75, "hippynn.interfaces.pyseqm_interface.seqm_one.Energy_One", false]], "ensembletarget (class in hippynn.graphs.nodes.misc)": [[52, "hippynn.graphs.nodes.misc.EnsembleTarget", false]], "ensembletarget (class in hippynn.layers.algebra)": [[78, "hippynn.layers.algebra.EnsembleTarget", false]], "envops_tester (class in hippynn.custom_kernels.test_env_numba)": [[10, "hippynn.custom_kernels.test_env_numba.Envops_tester", false]], "envsum() (in module hippynn.custom_kernels.env_pytorch)": [[5, "hippynn.custom_kernels.env_pytorch.envsum", false]], "envsum() (in module hippynn.custom_kernels.env_triton)": [[6, "hippynn.custom_kernels.env_triton.envsum", false]], "envsum_triton() (in module hippynn.custom_kernels.env_triton)": [[6, "hippynn.custom_kernels.env_triton.envsum_triton", false]], "eval_batch_size (setupparams attribute)": [[19, "hippynn.experiment.SetupParams.eval_batch_size", false], [26, "hippynn.experiment.routines.SetupParams.eval_batch_size", false]], "evaluate() (evaluator method)": [[23, "hippynn.experiment.evaluator.Evaluator.evaluate", false]], "evaluation_print() (metrictracker method)": [[25, "hippynn.experiment.metric_tracker.MetricTracker.evaluation_print", false]], "evaluation_print_better() (metrictracker method)": [[25, "hippynn.experiment.metric_tracker.MetricTracker.evaluation_print_better", false]], "evaluator (class in hippynn.experiment.evaluator)": [[23, "hippynn.experiment.evaluator.Evaluator", false]], "evaluator (trainingmodules attribute)": [[20, "hippynn.experiment.assembly.TrainingModules.evaluator", false]], "ewaldrealspacescreening (class in hippynn.layers.physics)": [[89, "hippynn.layers.physics.EwaldRealSpaceScreening", false]], "expand0() (atomdeindexer method)": [[49, "hippynn.graphs.nodes.indexers.AtomDeIndexer.expand0", false]], "expand0() (atomreindexer method)": [[49, "hippynn.graphs.nodes.indexers.AtomReIndexer.expand0", false]], "expand0() (hbondnode method)": [[57, "hippynn.graphs.nodes.targets.HBondNode.expand0", false]], "expand0() (mindistnode method)": [[54, "hippynn.graphs.nodes.pairs.MinDistNode.expand0", false]], "expand0() (openpairindexer method)": [[54, "hippynn.graphs.nodes.pairs.OpenPairIndexer.expand0", false]], "expand0() (paddedneighbornode method)": [[54, "hippynn.graphs.nodes.pairs.PaddedNeighborNode.expand0", false]], "expand0() (paddingindexer method)": [[49, "hippynn.graphs.nodes.indexers.PaddingIndexer.expand0", false]], "expand0() (paircacher method)": [[54, "hippynn.graphs.nodes.pairs.PairCacher.expand0", false]], "expand0() (pairdeindexer method)": [[54, "hippynn.graphs.nodes.pairs.PairDeIndexer.expand0", false]], "expand0() (pairfilter method)": [[54, "hippynn.graphs.nodes.pairs.PairFilter.expand0", false]], "expand0() (pairreindexer method)": [[54, "hippynn.graphs.nodes.pairs.PairReIndexer.expand0", false]], "expand0() (pairuncacher method)": [[54, "hippynn.graphs.nodes.pairs.PairUncacher.expand0", false]], "expand0() (periodicpairindexer method)": [[54, "hippynn.graphs.nodes.pairs.PeriodicPairIndexer.expand0", false]], "expand0() (rdfbins method)": [[54, "hippynn.graphs.nodes.pairs.RDFBins.expand0", false]], "expand0() (seqm_energynode method)": [[74, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_EnergyNode.expand0", false]], "expand0() (seqm_one_energynode method)": [[75, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_EnergyNode.expand0", false]], "expand1() (atomreindexer method)": [[49, "hippynn.graphs.nodes.indexers.AtomReIndexer.expand1", false]], "expand1() (hbondnode method)": [[57, "hippynn.graphs.nodes.targets.HBondNode.expand1", false]], "expand1() (mindistnode method)": [[54, "hippynn.graphs.nodes.pairs.MinDistNode.expand1", false]], "expand1() (paircacher method)": [[54, "hippynn.graphs.nodes.pairs.PairCacher.expand1", false]], "expand1() (pairdeindexer method)": [[54, "hippynn.graphs.nodes.pairs.PairDeIndexer.expand1", false]], "expand1() (pairreindexer method)": [[54, "hippynn.graphs.nodes.pairs.PairReIndexer.expand1", false]], "expand1() (pairuncacher method)": [[54, "hippynn.graphs.nodes.pairs.PairUncacher.expand1", false]], "expand1() (periodicpairindexer method)": [[54, "hippynn.graphs.nodes.pairs.PeriodicPairIndexer.expand1", false]], "expand1() (rdfbins method)": [[54, "hippynn.graphs.nodes.pairs.RDFBins.expand1", false]], "expand2() (mindistnode method)": [[54, "hippynn.graphs.nodes.pairs.MinDistNode.expand2", false]], "expand2() (rdfbins method)": [[54, "hippynn.graphs.nodes.pairs.RDFBins.expand2", false]], "expand3() (rdfbins method)": [[54, "hippynn.graphs.nodes.pairs.RDFBins.expand3", false]], "expand_parents() (expandparents method)": [[45, "hippynn.graphs.nodes.base.definition_helpers.ExpandParents.expand_parents", false]], "expandparentmeta (class in hippynn.graphs.nodes.base.definition_helpers)": [[45, "hippynn.graphs.nodes.base.definition_helpers.ExpandParentMeta", false]], "expandparents (class in hippynn.graphs.nodes.base.definition_helpers)": [[45, "hippynn.graphs.nodes.base.definition_helpers.ExpandParents", false]], "expansion0() (atomtomolsummer method)": [[55, "hippynn.graphs.nodes.physics.AtomToMolSummer.expansion0", false]], "expansion0() (bondtomolsummmer method)": [[55, "hippynn.graphs.nodes.physics.BondToMolSummmer.expansion0", false]], "expansion0() (chargemomentnode method)": [[55, "hippynn.graphs.nodes.physics.ChargeMomentNode.expansion0", false]], "expansion0() (chargepairsetup method)": [[55, "hippynn.graphs.nodes.physics.ChargePairSetup.expansion0", false]], "expansion0() (combineenergynode method)": [[55, "hippynn.graphs.nodes.physics.CombineEnergyNode.expansion0", false]], "expansion0() (defaultnetworkexpansion method)": [[53, "hippynn.graphs.nodes.networks.DefaultNetworkExpansion.expansion0", false]], "expansion0() (hchargenode method)": [[57, "hippynn.graphs.nodes.targets.HChargeNode.expansion0", false]], "expansion0() (henergynode method)": [[57, "hippynn.graphs.nodes.targets.HEnergyNode.expansion0", false]], "expansion0() (localchargeenergy method)": [[57, "hippynn.graphs.nodes.targets.LocalChargeEnergy.expansion0", false]], "expansion0() (localenergynode method)": [[48, "hippynn.graphs.nodes.excited.LocalEnergyNode.expansion0", false]], "expansion0() (peratom method)": [[55, "hippynn.graphs.nodes.physics.PerAtom.expansion0", false]], "expansion0() (sysmaxofatomsnode method)": [[49, "hippynn.graphs.nodes.indexers.SysMaxOfAtomsNode.expansion0", false]], "expansion1() (atomtomolsummer method)": [[55, "hippynn.graphs.nodes.physics.AtomToMolSummer.expansion1", false]], "expansion1() (bondtomolsummmer method)": [[55, "hippynn.graphs.nodes.physics.BondToMolSummmer.expansion1", false]], "expansion1() (chargemomentnode method)": [[55, "hippynn.graphs.nodes.physics.ChargeMomentNode.expansion1", false]], "expansion1() 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"hippynn.graphs.nodes.physics.ChargePairSetup.expansion2", false]], "expansion2() (combineenergynode method)": [[55, "hippynn.graphs.nodes.physics.CombineEnergyNode.expansion2", false]], "expansion2() (hipnn method)": [[53, "hippynn.graphs.nodes.networks.Hipnn.expansion2", false]], "expansion2() (hipnnvec method)": [[53, "hippynn.graphs.nodes.networks.HipnnVec.expansion2", false]], "expansion2() (vecmag method)": [[55, "hippynn.graphs.nodes.physics.VecMag.expansion2", false]], "expansion3() (chargepairsetup method)": [[55, "hippynn.graphs.nodes.physics.ChargePairSetup.expansion3", false]], "expansion4() (chargepairsetup method)": [[55, "hippynn.graphs.nodes.physics.ChargePairSetup.expansion4", false]], "externalneighborindexer (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.ExternalNeighborIndexer", false]], "externalneighbors (class in hippynn.layers.pairs.indexing)": [[86, "hippynn.layers.pairs.indexing.ExternalNeighbors", false]], "extra_repr() (graphmodule method)": [[29, "hippynn.graphs.GraphModule.extra_repr", false], [32, "hippynn.graphs.graph.GraphModule.extra_repr", false]], "extra_repr() (idx method)": [[78, "hippynn.layers.algebra.Idx.extra_repr", false]], "extra_repr() (lambdamodule method)": [[78, "hippynn.layers.algebra.LambdaModule.extra_repr", false]], "extra_repr() (valuemod method)": [[78, "hippynn.layers.algebra.ValueMod.extra_repr", false]], "extract_snap_file() (snapdirectorydatabase method)": [[14, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.extract_snap_file", false]], "featsum() (in module hippynn.custom_kernels.env_pytorch)": [[5, "hippynn.custom_kernels.env_pytorch.featsum", false]], "featsum() (in module hippynn.custom_kernels.env_triton)": [[6, "hippynn.custom_kernels.env_triton.featsum", false]], "featsum_triton() (in module hippynn.custom_kernels.env_triton)": [[6, "hippynn.custom_kernels.env_triton.featsum_triton", false]], "filter_arrays() (snapdirectorydatabase method)": [[14, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.filter_arrays", false]], "filter_pairs() (in module hippynn.layers.pairs.periodic)": [[88, "hippynn.layers.pairs.periodic.filter_pairs", false]], "filterbondsoneway (class in hippynn.graphs.nodes.indexers)": [[49, "hippynn.graphs.nodes.indexers.FilterBondsOneway", false]], "filterbondsoneway (class in hippynn.layers.indexers)": [[81, "hippynn.layers.indexers.FilterBondsOneway", false]], "filterdistance (class in hippynn.layers.pairs.filters)": [[85, "hippynn.layers.pairs.filters.FilterDistance", false]], "find_relatives() (in module hippynn.graphs)": [[29, "hippynn.graphs.find_relatives", false]], "find_relatives() (in module hippynn.graphs.nodes.base.node_functions)": [[47, "hippynn.graphs.nodes.base.node_functions.find_relatives", false]], "find_unique_relative() (in module hippynn.graphs)": [[29, "hippynn.graphs.find_unique_relative", false]], "find_unique_relative() (in module hippynn.graphs.nodes.base.node_functions)": [[47, "hippynn.graphs.nodes.base.node_functions.find_unique_relative", false]], "fire (class in hippynn.optimizer.algorithms)": [[98, "hippynn.optimizer.algorithms.FIRE", false]], "flush() (teed_file_output method)": [[106, "hippynn.tools.teed_file_output.flush", false]], "fmax_criteria() (geometryoptimizer static method)": [[98, "hippynn.optimizer.algorithms.GeometryOptimizer.fmax_criteria", false]], "fn() (compatibleidxtypetransformer static method)": [[45, "hippynn.graphs.nodes.base.definition_helpers.CompatibleIdxTypeTransformer.fn", false]], "fn() (indexformtransformer method)": [[45, "hippynn.graphs.nodes.base.definition_helpers.IndexFormTransformer.fn", false]], "fn() (mainoutputtransformer static method)": [[45, "hippynn.graphs.nodes.base.definition_helpers.MainOutputTransformer.fn", false]], "forcenode (class in hippynn.graphs.nodes.inputs)": [[50, "hippynn.graphs.nodes.inputs.ForceNode", false]], "formassertion (class in hippynn.graphs.nodes.base.definition_helpers)": [[45, "hippynn.graphs.nodes.base.definition_helpers.FormAssertion", false]], "formassertlength (class in hippynn.graphs.nodes.base.definition_helpers)": [[45, "hippynn.graphs.nodes.base.definition_helpers.FormAssertLength", false]], "format_form_name() (in module hippynn.graphs.nodes.base.definition_helpers)": [[45, "hippynn.graphs.nodes.base.definition_helpers.format_form_name", false]], "formhandler (class in hippynn.graphs.nodes.base.definition_helpers)": [[45, "hippynn.graphs.nodes.base.definition_helpers.FormHandler", false]], "formtransformer (class in hippynn.graphs.nodes.base.definition_helpers)": [[45, "hippynn.graphs.nodes.base.definition_helpers.FormTransformer", false]], "forward() (atleast2d method)": [[78, "hippynn.layers.algebra.AtLeast2D.forward", false]], "forward() (atomdeindexer method)": [[81, "hippynn.layers.indexers.AtomDeIndexer.forward", false]], "forward() (atommask method)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_modules.AtomMask.forward", false]], 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"hippynn.layers.pairs.indexing.ExternalNeighbors.forward", false]], "forward() (filterbondsoneway method)": [[81, "hippynn.layers.indexers.FilterBondsOneway.forward", false]], "forward() (filterdistance method)": [[85, "hippynn.layers.pairs.filters.FilterDistance.forward", false]], "forward() (fuzzyhistogram method)": [[81, "hippynn.layers.indexers.FuzzyHistogram.forward", false]], "forward() (gaussiansensitivitymodule method)": [[80, "hippynn.layers.hiplayers.GaussianSensitivityModule.forward", false]], "forward() (gen_par method)": [[71, "hippynn.interfaces.pyseqm_interface.gen_par.gen_par.forward", false]], "forward() (gradient method)": [[89, "hippynn.layers.physics.Gradient.forward", false]], "forward() (graphmodule method)": [[29, "hippynn.graphs.GraphModule.forward", false], [32, "hippynn.graphs.graph.GraphModule.forward", false]], "forward() (hamiltonian_one method)": [[75, "hippynn.interfaces.pyseqm_interface.seqm_one.Hamiltonian_One.forward", false]], "forward() (hbondsymmetric method)": [[91, "hippynn.layers.targets.HBondSymmetric.forward", false]], "forward() (hcharge method)": [[91, "hippynn.layers.targets.HCharge.forward", false]], "forward() (henergy method)": [[91, "hippynn.layers.targets.HEnergy.forward", false]], "forward() (hipnn method)": [[96, "hippynn.networks.hipnn.Hipnn.forward", false]], "forward() (hipnnvec method)": [[96, "hippynn.networks.hipnn.HipnnVec.forward", false]], "forward() (idx method)": [[78, "hippynn.layers.algebra.Idx.forward", false]], "forward() (interactlayer method)": [[80, "hippynn.layers.hiplayers.InteractLayer.forward", false]], "forward() (interactlayerquad method)": [[80, "hippynn.layers.hiplayers.InteractLayerQuad.forward", false]], "forward() (interactlayervec method)": [[80, "hippynn.layers.hiplayers.InteractLayerVec.forward", false]], "forward() (inversesensitivitymodule method)": [[80, "hippynn.layers.hiplayers.InverseSensitivityModule.forward", false]], "forward() (kdtreepairsmemory method)": [[84, "hippynn.layers.pairs.dispatch.KDTreePairsMemory.forward", false]], "forward() (lambdamodule method)": [[78, "hippynn.layers.algebra.LambdaModule.forward", false]], "forward() (listmod method)": [[78, "hippynn.layers.algebra.ListMod.forward", false]], "forward() (localatomsenergy method)": [[67, "hippynn.interfaces.lammps_interface.mliap_interface.LocalAtomsEnergy.forward", false]], "forward() (localchargeenergy method)": [[91, "hippynn.layers.targets.LocalChargeEnergy.forward", false]], "forward() (localdampingcosine method)": [[89, "hippynn.layers.physics.LocalDampingCosine.forward", false]], "forward() (localenergy method)": [[79, "hippynn.layers.excited.LocalEnergy.forward", false]], "forward() (lpreg method)": [[90, "hippynn.layers.regularization.LPReg.forward", false]], "forward() (mindistmodule method)": [[83, "hippynn.layers.pairs.analysis.MinDistModule.forward", false]], "forward() (mlseqm method)": [[72, "hippynn.interfaces.pyseqm_interface.mlseqm.MLSEQM.forward", false]], "forward() (molpairsummer method)": [[86, "hippynn.layers.pairs.indexing.MolPairSummer.forward", false]], "forward() (molsummer method)": [[81, "hippynn.layers.indexers.MolSummer.forward", false]], "forward() (multigradient method)": [[89, "hippynn.layers.physics.MultiGradient.forward", false]], "forward() (nacr method)": [[79, "hippynn.layers.excited.NACR.forward", false]], "forward() (nacrmultistate method)": [[79, "hippynn.layers.excited.NACRMultiState.forward", false]], "forward() (onehotspecies method)": [[81, "hippynn.layers.indexers.OneHotSpecies.forward", false]], "forward() (openpairindexer method)": [[87, "hippynn.layers.pairs.open.OpenPairIndexer.forward", false]], "forward() (paddedneighmodule method)": [[86, "hippynn.layers.pairs.indexing.PaddedNeighModule.forward", false]], "forward() (paddingindexer method)": [[81, "hippynn.layers.indexers.PaddingIndexer.forward", false]], "forward() (paircacher method)": [[86, "hippynn.layers.pairs.indexing.PairCacher.forward", false]], "forward() (pairdeindexer method)": [[86, "hippynn.layers.pairs.indexing.PairDeIndexer.forward", false]], "forward() (pairmemory method)": [[87, "hippynn.layers.pairs.open.PairMemory.forward", false]], "forward() (pairreindexer method)": [[86, "hippynn.layers.pairs.indexing.PairReIndexer.forward", false]], "forward() (pairuncacher method)": [[86, "hippynn.layers.pairs.indexing.PairUncacher.forward", false]], "forward() (peratom method)": [[89, "hippynn.layers.physics.PerAtom.forward", false]], "forward() (periodicpairindexer method)": [[88, "hippynn.layers.pairs.periodic.PeriodicPairIndexer.forward", false]], "forward() (periodicpairindexermemory method)": [[88, "hippynn.layers.pairs.periodic.PeriodicPairIndexerMemory.forward", false]], "forward() (qscreening method)": [[89, "hippynn.layers.physics.QScreening.forward", false]], "forward() (quadpack method)": [[81, "hippynn.layers.indexers.QuadPack.forward", false]], "forward() (quadrupole method)": [[89, "hippynn.layers.physics.Quadrupole.forward", false]], "forward() (quadunpack method)": [[81, "hippynn.layers.indexers.QuadUnpack.forward", false]], "forward() (rdfbins method)": [[83, "hippynn.layers.pairs.analysis.RDFBins.forward", false]], "forward() (reindexatommod method)": [[67, "hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomMod.forward", false]], "forward() (resnetwrapper method)": [[92, "hippynn.layers.transform.ResNetWrapper.forward", false]], "forward() (rsqmod method)": [[51, "hippynn.graphs.nodes.loss.RsqMod.forward", false]], "forward() (scale method)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_modules.Scale.forward", false]], "forward() (schnetwrapper method)": [[76, "hippynn.interfaces.schnetpack_interface.SchNetWrapper.forward", false]], "forward() (screenedcoulombenergy method)": [[89, "hippynn.layers.physics.ScreenedCoulombEnergy.forward", false]], "forward() (sensitivitybottleneck method)": [[80, "hippynn.layers.hiplayers.SensitivityBottleneck.forward", false]], "forward() (seqm_all method)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_All.forward", false]], "forward() (seqm_energy method)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_Energy.forward", false]], "forward() (seqm_maskonmol method)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMol.forward", false]], "forward() (seqm_maskonmolatom method)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolAtom.forward", false]], "forward() (seqm_maskonmolorbital method)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolOrbital.forward", false]], "forward() (seqm_maskonmolorbitalatom method)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolOrbitalAtom.forward", false]], "forward() (seqm_molmask method)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MolMask.forward", false]], "forward() (seqm_one_all method)": [[75, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_All.forward", false]], "forward() (seqm_one_energy method)": [[75, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_Energy.forward", false]], "forward() (seqm_orbitalmask method)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_OrbitalMask.forward", false]], "forward() (staticimageperiodicpairindexer method)": [[88, "hippynn.layers.pairs.periodic.StaticImagePeriodicPairIndexer.forward", false]], "forward() (stressforce method)": [[89, "hippynn.layers.physics.StressForce.forward", false]], "forward() (sysmaxofatoms method)": [[81, "hippynn.layers.indexers.SysMaxOfAtoms.forward", false]], "forward() (valuemod method)": [[78, "hippynn.layers.algebra.ValueMod.forward", false]], "forward() (vecmag method)": [[89, "hippynn.layers.physics.VecMag.forward", false]], "forward() (wolfscreening method)": [[89, "hippynn.layers.physics.WolfScreening.forward", false]], "fraction_train_eval (setupparams attribute)": [[19, "hippynn.experiment.SetupParams.fraction_train_eval", false], [26, "hippynn.experiment.routines.SetupParams.fraction_train_eval", false]], "from_evaluator() (metrictracker class method)": [[25, "hippynn.experiment.metric_tracker.MetricTracker.from_evaluator", false]], "from_experiment_setup() (hippynnlightningmodule class method)": [[24, "hippynn.experiment.lightning_trainer.HippynnLightningModule.from_experiment_setup", false]], "from_graph() (predictor class method)": [[29, "hippynn.graphs.Predictor.from_graph", false], [58, "hippynn.graphs.predictor.Predictor.from_graph", false]], "from_train_setup() (hippynnlightningmodule class method)": [[24, "hippynn.experiment.lightning_trainer.HippynnLightningModule.from_train_setup", false]], "fuzzyhistogram (class in hippynn.layers.indexers)": [[81, "hippynn.layers.indexers.FuzzyHistogram", false]], "fuzzyhistogrammer (class in hippynn.graphs.nodes.indexers)": [[49, "hippynn.graphs.nodes.indexers.FuzzyHistogrammer", false]], "gaussiansensitivitymodule (class in hippynn.layers.hiplayers)": [[80, "hippynn.layers.hiplayers.GaussianSensitivityModule", false]], "gen_par (class in hippynn.interfaces.pyseqm_interface.gen_par)": [[71, "hippynn.interfaces.pyseqm_interface.gen_par.gen_par", false]], "generate_database_info() (in module hippynn.experiment.assembly)": [[20, "hippynn.experiment.assembly.generate_database_info", false]], "geometryoptimizer (class in hippynn.optimizer.algorithms)": [[98, "hippynn.optimizer.algorithms.GeometryOptimizer", false]], "get_autotune_config() (in module hippynn.custom_kernels.env_triton)": [[6, "hippynn.custom_kernels.env_triton.get_autotune_config", false]], "get_charges() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_charges", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_charges", false]], "get_connected_nodes() (in module hippynn.graphs)": [[29, "hippynn.graphs.get_connected_nodes", false]], "get_connected_nodes() (in module hippynn.graphs.nodes.base.node_functions)": [[47, "hippynn.graphs.nodes.base.node_functions.get_connected_nodes", false]], "get_data() (moleculardynamics method)": [[94, "hippynn.molecular_dynamics.md.MolecularDynamics.get_data", false]], "get_device() (database method)": [[13, "hippynn.databases.Database.get_device", false], [15, "hippynn.databases.database.Database.get_device", false]], "get_dipole() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_dipole", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_dipole", false]], "get_dipole_moment() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_dipole_moment", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_dipole_moment", false]], "get_energies() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_energies", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_energies", false]], "get_energy() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_energy", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_energy", false]], "get_extra_state() (interactlayervec method)": [[80, "hippynn.layers.hiplayers.InteractLayerVec.get_extra_state", false]], "get_file_dict() (directorydatabase method)": [[13, "hippynn.databases.DirectoryDatabase.get_file_dict", false], [17, "hippynn.databases.ondisk.DirectoryDatabase.get_file_dict", false]], "get_forces() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_forces", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_forces", false]], "get_free_energy() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_free_energy", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_free_energy", false]], "get_graphs() (in module hippynn.graphs.ensemble)": [[30, "hippynn.graphs.ensemble.get_graphs", false]], "get_magmom() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_magmom", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_magmom", false]], "get_magmoms() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_magmoms", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_magmoms", false]], "get_main_outputs() (parentexpander method)": [[45, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.get_main_outputs", false]], "get_module() (graphmodule method)": [[29, "hippynn.graphs.GraphModule.get_module", false], [32, "hippynn.graphs.graph.GraphModule.get_module", false]], "get_potential_energies() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_potential_energies", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_potential_energies", false]], "get_potential_energy() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_potential_energy", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_potential_energy", false]], "get_property() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_property", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_property", false]], "get_reduced_index_state() (in module hippynn.graphs.indextypes)": [[37, "hippynn.graphs.indextypes.get_reduced_index_state", false]], "get_reduced_index_state() (in module hippynn.graphs.indextypes.reduce_funcs)": [[38, "hippynn.graphs.indextypes.reduce_funcs.get_reduced_index_state", false]], "get_simulated_data() (in module hippynn.custom_kernels.test_env_numba)": [[10, "hippynn.custom_kernels.test_env_numba.get_simulated_data", false]], "get_step_function() (in module hippynn.experiment.step_functions)": [[28, "hippynn.experiment.step_functions.get_step_function", false]], "get_stress() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_stress", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_stress", false]], "get_stresses() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.get_stresses", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_stresses", false]], "get_subgraph() (in module hippynn.graphs)": [[29, "hippynn.graphs.get_subgraph", false]], "get_subgraph() (in module hippynn.graphs.gops)": [[31, "hippynn.graphs.gops.get_subgraph", false]], "gradient (class in hippynn.layers.physics)": [[89, "hippynn.layers.physics.Gradient", false]], "gradientnode (class in hippynn.graphs.nodes.physics)": [[55, "hippynn.graphs.nodes.physics.GradientNode", false]], "graphinconsistency": [[31, "hippynn.graphs.gops.GraphInconsistency", false]], "graphmodule (class in hippynn.graphs)": [[29, "hippynn.graphs.GraphModule", false]], "graphmodule (class in hippynn.graphs.graph)": [[32, "hippynn.graphs.graph.GraphModule", false]], "hamiltonian_one (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[75, "hippynn.interfaces.pyseqm_interface.seqm_one.Hamiltonian_One", false]], "hatomregressor (class in hippynn.graphs.nodes.tags)": [[56, "hippynn.graphs.nodes.tags.HAtomRegressor", false]], "hbondnode (class in hippynn.graphs.nodes.targets)": [[57, "hippynn.graphs.nodes.targets.HBondNode", false]], "hbondsymmetric (class in hippynn.layers.targets)": [[91, "hippynn.layers.targets.HBondSymmetric", false]], "hcharge (class in hippynn.layers.targets)": [[91, "hippynn.layers.targets.HCharge", false]], "hchargenode (class in hippynn.graphs.nodes.targets)": [[57, "hippynn.graphs.nodes.targets.HChargeNode", false]], "henergy (class in hippynn.layers.targets)": [[91, "hippynn.layers.targets.HEnergy", false]], "henergynode (class in hippynn.graphs.nodes.targets)": [[57, "hippynn.graphs.nodes.targets.HEnergyNode", false]], "hierarchical_energy_initialization() (in module hippynn.pretraining)": [[105, "hippynn.pretraining.hierarchical_energy_initialization", false]], "hierarchicalityplot (class in hippynn.plotting.plotters)": [[103, "hippynn.plotting.plotters.HierarchicalityPlot", false]], "hipnn (class in hippynn.graphs.nodes.networks)": [[53, "hippynn.graphs.nodes.networks.Hipnn", false]], "hipnn (class in hippynn.networks.hipnn)": [[96, "hippynn.networks.hipnn.Hipnn", false]], "hipnnquad (class in hippynn.graphs.nodes.networks)": [[53, "hippynn.graphs.nodes.networks.HipnnQuad", false]], "hipnnquad (class in hippynn.networks.hipnn)": [[96, "hippynn.networks.hipnn.HipnnQuad", false]], "hipnnvec (class in hippynn.graphs.nodes.networks)": [[53, "hippynn.graphs.nodes.networks.HipnnVec", false]], "hipnnvec (class in hippynn.networks.hipnn)": [[96, "hippynn.networks.hipnn.HipnnVec", false]], "hippynn": [[0, "module-hippynn", false]], "hippynn.custom_kernels": [[1, "module-hippynn.custom_kernels", false]], "hippynn.custom_kernels.autograd_wrapper": [[2, "module-hippynn.custom_kernels.autograd_wrapper", false]], "hippynn.custom_kernels.env_cupy": [[3, "module-hippynn.custom_kernels.env_cupy", false]], "hippynn.custom_kernels.env_numba": [[4, "module-hippynn.custom_kernels.env_numba", false]], "hippynn.custom_kernels.env_pytorch": [[5, "module-hippynn.custom_kernels.env_pytorch", false]], "hippynn.custom_kernels.env_triton": [[6, "module-hippynn.custom_kernels.env_triton", false]], "hippynn.custom_kernels.fast_convert": [[7, "module-hippynn.custom_kernels.fast_convert", false]], "hippynn.custom_kernels.tensor_wrapper": [[8, "module-hippynn.custom_kernels.tensor_wrapper", false]], "hippynn.custom_kernels.test_env_cupy": [[9, "module-hippynn.custom_kernels.test_env_cupy", false]], "hippynn.custom_kernels.test_env_numba": [[10, "module-hippynn.custom_kernels.test_env_numba", false]], "hippynn.custom_kernels.test_env_triton": [[11, "module-hippynn.custom_kernels.test_env_triton", false]], "hippynn.custom_kernels.utils": [[12, "module-hippynn.custom_kernels.utils", false]], "hippynn.databases": [[13, "module-hippynn.databases", false]], "hippynn.databases.database": [[15, "module-hippynn.databases.database", false]], "hippynn.databases.ondisk": [[17, "module-hippynn.databases.ondisk", false]], "hippynn.databases.restarter": [[18, "module-hippynn.databases.restarter", false]], "hippynn.databases.snapjson": [[14, "module-hippynn.databases.SNAPJson", false]], "hippynn.experiment": [[19, "module-hippynn.experiment", false]], "hippynn.experiment.assembly": [[20, "module-hippynn.experiment.assembly", false]], "hippynn.experiment.controllers": [[21, "module-hippynn.experiment.controllers", false]], "hippynn.experiment.device": [[22, "module-hippynn.experiment.device", false]], "hippynn.experiment.evaluator": [[23, "module-hippynn.experiment.evaluator", false]], "hippynn.experiment.lightning_trainer": [[24, "module-hippynn.experiment.lightning_trainer", false]], "hippynn.experiment.metric_tracker": [[25, "module-hippynn.experiment.metric_tracker", false]], "hippynn.experiment.routines": [[26, "module-hippynn.experiment.routines", false]], "hippynn.experiment.serialization": [[27, "module-hippynn.experiment.serialization", false]], "hippynn.experiment.step_functions": [[28, "module-hippynn.experiment.step_functions", false]], "hippynn.graphs": [[29, "module-hippynn.graphs", false]], "hippynn.graphs.ensemble": [[30, "module-hippynn.graphs.ensemble", false]], "hippynn.graphs.gops": [[31, "module-hippynn.graphs.gops", false]], "hippynn.graphs.graph": [[32, "module-hippynn.graphs.graph", false]], "hippynn.graphs.indextransformers": [[33, "module-hippynn.graphs.indextransformers", false]], "hippynn.graphs.indextransformers.atoms": [[34, "module-hippynn.graphs.indextransformers.atoms", false]], "hippynn.graphs.indextransformers.pairs": [[35, "module-hippynn.graphs.indextransformers.pairs", false]], "hippynn.graphs.indextransformers.tensors": [[36, "module-hippynn.graphs.indextransformers.tensors", false]], "hippynn.graphs.indextypes": [[37, "module-hippynn.graphs.indextypes", false]], "hippynn.graphs.indextypes.reduce_funcs": [[38, "module-hippynn.graphs.indextypes.reduce_funcs", false]], "hippynn.graphs.indextypes.registry": [[39, "module-hippynn.graphs.indextypes.registry", false]], "hippynn.graphs.indextypes.type_def": [[40, "module-hippynn.graphs.indextypes.type_def", false]], "hippynn.graphs.nodes": [[41, "module-hippynn.graphs.nodes", false]], "hippynn.graphs.nodes.base": [[42, "module-hippynn.graphs.nodes.base", false]], "hippynn.graphs.nodes.base.algebra": [[43, "module-hippynn.graphs.nodes.base.algebra", false]], "hippynn.graphs.nodes.base.base": [[44, "module-hippynn.graphs.nodes.base.base", false]], "hippynn.graphs.nodes.base.definition_helpers": [[45, "module-hippynn.graphs.nodes.base.definition_helpers", false]], "hippynn.graphs.nodes.base.multi": [[46, "module-hippynn.graphs.nodes.base.multi", false]], "hippynn.graphs.nodes.base.node_functions": [[47, "module-hippynn.graphs.nodes.base.node_functions", false]], "hippynn.graphs.nodes.excited": [[48, "module-hippynn.graphs.nodes.excited", false]], "hippynn.graphs.nodes.indexers": [[49, "module-hippynn.graphs.nodes.indexers", false]], "hippynn.graphs.nodes.inputs": [[50, "module-hippynn.graphs.nodes.inputs", false]], "hippynn.graphs.nodes.loss": [[51, "module-hippynn.graphs.nodes.loss", false]], "hippynn.graphs.nodes.misc": [[52, "module-hippynn.graphs.nodes.misc", false]], "hippynn.graphs.nodes.networks": [[53, "module-hippynn.graphs.nodes.networks", false]], "hippynn.graphs.nodes.pairs": [[54, "module-hippynn.graphs.nodes.pairs", false]], "hippynn.graphs.nodes.physics": [[55, "module-hippynn.graphs.nodes.physics", false]], "hippynn.graphs.nodes.tags": [[56, "module-hippynn.graphs.nodes.tags", false]], "hippynn.graphs.nodes.targets": [[57, "module-hippynn.graphs.nodes.targets", false]], "hippynn.graphs.predictor": [[58, "module-hippynn.graphs.predictor", false]], "hippynn.graphs.viz": [[59, "module-hippynn.graphs.viz", false]], "hippynn.interfaces": [[60, "module-hippynn.interfaces", false]], "hippynn.interfaces.ase_interface": [[61, "module-hippynn.interfaces.ase_interface", false]], "hippynn.interfaces.ase_interface.ase_database": [[62, "module-hippynn.interfaces.ase_interface.ase_database", false]], "hippynn.interfaces.ase_interface.ase_unittests": [[63, "module-hippynn.interfaces.ase_interface.ase_unittests", false]], "hippynn.interfaces.ase_interface.calculator": [[64, "module-hippynn.interfaces.ase_interface.calculator", false]], "hippynn.interfaces.ase_interface.pairfinder": [[65, "module-hippynn.interfaces.ase_interface.pairfinder", false]], "hippynn.interfaces.lammps_interface": [[66, "module-hippynn.interfaces.lammps_interface", false]], "hippynn.interfaces.lammps_interface.mliap_interface": [[67, "module-hippynn.interfaces.lammps_interface.mliap_interface", false]], "hippynn.interfaces.pyseqm_interface": [[68, "module-hippynn.interfaces.pyseqm_interface", false]], "hippynn.interfaces.pyseqm_interface.callback": [[69, "module-hippynn.interfaces.pyseqm_interface.callback", false]], "hippynn.interfaces.pyseqm_interface.check": [[70, "module-hippynn.interfaces.pyseqm_interface.check", false]], "hippynn.interfaces.pyseqm_interface.gen_par": [[71, "module-hippynn.interfaces.pyseqm_interface.gen_par", false]], "hippynn.interfaces.pyseqm_interface.mlseqm": [[72, "module-hippynn.interfaces.pyseqm_interface.mlseqm", false]], "hippynn.interfaces.pyseqm_interface.seqm_modules": [[73, "module-hippynn.interfaces.pyseqm_interface.seqm_modules", false]], "hippynn.interfaces.pyseqm_interface.seqm_nodes": [[74, "module-hippynn.interfaces.pyseqm_interface.seqm_nodes", false]], "hippynn.interfaces.pyseqm_interface.seqm_one": [[75, "module-hippynn.interfaces.pyseqm_interface.seqm_one", false]], "hippynn.interfaces.schnetpack_interface": [[76, "module-hippynn.interfaces.schnetpack_interface", false]], "hippynn.layers": [[77, "module-hippynn.layers", false]], "hippynn.layers.algebra": [[78, "module-hippynn.layers.algebra", false]], "hippynn.layers.excited": [[79, "module-hippynn.layers.excited", false]], "hippynn.layers.hiplayers": [[80, "module-hippynn.layers.hiplayers", false]], "hippynn.layers.indexers": [[81, "module-hippynn.layers.indexers", false]], "hippynn.layers.pairs": [[82, "module-hippynn.layers.pairs", false]], "hippynn.layers.pairs.analysis": [[83, "module-hippynn.layers.pairs.analysis", false]], "hippynn.layers.pairs.dispatch": [[84, "module-hippynn.layers.pairs.dispatch", false]], "hippynn.layers.pairs.filters": [[85, "module-hippynn.layers.pairs.filters", false]], "hippynn.layers.pairs.indexing": [[86, "module-hippynn.layers.pairs.indexing", false]], "hippynn.layers.pairs.open": [[87, "module-hippynn.layers.pairs.open", false]], "hippynn.layers.pairs.periodic": [[88, "module-hippynn.layers.pairs.periodic", false]], "hippynn.layers.physics": [[89, "module-hippynn.layers.physics", false]], "hippynn.layers.regularization": [[90, "module-hippynn.layers.regularization", false]], "hippynn.layers.targets": [[91, "module-hippynn.layers.targets", false]], "hippynn.layers.transform": [[92, "module-hippynn.layers.transform", false]], "hippynn.molecular_dynamics": [[93, "module-hippynn.molecular_dynamics", false]], "hippynn.molecular_dynamics.md": [[94, "module-hippynn.molecular_dynamics.md", false]], "hippynn.networks": [[95, "module-hippynn.networks", false]], "hippynn.networks.hipnn": [[96, "module-hippynn.networks.hipnn", false]], "hippynn.optimizer": [[97, "module-hippynn.optimizer", false]], "hippynn.optimizer.algorithms": [[98, "module-hippynn.optimizer.algorithms", false]], "hippynn.optimizer.batch_optimizer": [[99, "module-hippynn.optimizer.batch_optimizer", false]], "hippynn.optimizer.utils": [[100, "module-hippynn.optimizer.utils", false]], "hippynn.plotting": [[101, "module-hippynn.plotting", false]], "hippynn.plotting.plotmaker": [[102, "module-hippynn.plotting.plotmaker", false]], "hippynn.plotting.plotters": [[103, "module-hippynn.plotting.plotters", false]], "hippynn.plotting.timeplots": [[104, "module-hippynn.plotting.timeplots", false]], "hippynn.pretraining": [[105, "module-hippynn.pretraining", false]], "hippynn.tools": [[106, "module-hippynn.tools", false]], "hippynncalculator (class in hippynn.interfaces.ase_interface)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator", false]], "hippynncalculator (class in hippynn.interfaces.ase_interface.calculator)": [[64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator", false]], "hippynndatamodule (class in hippynn.experiment.lightning_trainer)": [[24, "hippynn.experiment.lightning_trainer.HippynnDataModule", false]], "hippynnlightningmodule (class in hippynn.experiment.lightning_trainer)": [[24, "hippynn.experiment.lightning_trainer.HippynnLightningModule", false]], "hist1d (class in hippynn.plotting.plotters)": [[103, "hippynn.plotting.plotters.Hist1D", false]], "hist1dcomp (class in hippynn.plotting.plotters)": [[103, "hippynn.plotting.plotters.Hist1DComp", false]], "hist2d (class in hippynn.plotting.plotters)": [[103, "hippynn.plotting.plotters.Hist2D", false]], "identify_inputs() (in module hippynn.graphs.ensemble)": [[30, "hippynn.graphs.ensemble.identify_inputs", false]], "identify_targets() (in module hippynn.graphs.ensemble)": [[30, "hippynn.graphs.ensemble.identify_targets", false]], "idx (class in hippynn.layers.algebra)": [[78, "hippynn.layers.algebra.Idx", false]], "idx_atom_molatom() (in module hippynn.graphs.indextransformers.atoms)": [[34, "hippynn.graphs.indextransformers.atoms.idx_atom_molatom", false]], "idx_molatom_atom() (in module hippynn.graphs.indextransformers.atoms)": [[34, "hippynn.graphs.indextransformers.atoms.idx_molatom_atom", false]], "idx_molatomatom_pair() (in module hippynn.graphs.indextransformers.pairs)": [[35, "hippynn.graphs.indextransformers.pairs.idx_molatomatom_pair", false]], "idx_pair_molatomatom() (in module hippynn.graphs.indextransformers.pairs)": [[35, "hippynn.graphs.indextransformers.pairs.idx_pair_molatomatom", false]], "idx_quadtrimol() (in module hippynn.graphs.indextransformers.tensors)": [[36, "hippynn.graphs.indextransformers.tensors.idx_QuadTriMol", false]], "idxtype (class in hippynn.graphs)": [[29, "hippynn.graphs.IdxType", false]], "idxtype (class in hippynn.graphs.indextypes)": [[37, "hippynn.graphs.indextypes.IdxType", false]], "idxtype (class in hippynn.graphs.indextypes.type_def)": [[40, "hippynn.graphs.indextypes.type_def.IdxType", false]], "index_type_coercion() (in module hippynn.graphs.indextypes)": [[37, "hippynn.graphs.indextypes.index_type_coercion", false]], "index_type_coercion() (in module hippynn.graphs.indextypes.reduce_funcs)": [[38, "hippynn.graphs.indextypes.reduce_funcs.index_type_coercion", false]], "indexformtransformer (class in hippynn.graphs.nodes.base.definition_helpers)": [[45, "hippynn.graphs.nodes.base.definition_helpers.IndexFormTransformer", false]], "indexnode (class in hippynn.graphs.nodes.base.multi)": [[46, "hippynn.graphs.nodes.base.multi.IndexNode", false]], "indices (class in hippynn.graphs.nodes.inputs)": [[50, "hippynn.graphs.nodes.inputs.Indices", false]], "initialize_buffers() (pairmemory method)": [[87, "hippynn.layers.pairs.open.PairMemory.initialize_buffers", false]], "input_type_str (cellnode attribute)": [[50, "hippynn.graphs.nodes.inputs.CellNode.input_type_str", false]], "input_type_str (densitymatrixnode attribute)": [[75, "hippynn.interfaces.pyseqm_interface.seqm_one.DensityMatrixNode.input_type_str", false]], "input_type_str (forcenode attribute)": [[50, "hippynn.graphs.nodes.inputs.ForceNode.input_type_str", false]], "input_type_str (indices attribute)": [[50, "hippynn.graphs.nodes.inputs.Indices.input_type_str", false]], "input_type_str (inputcharges attribute)": [[50, "hippynn.graphs.nodes.inputs.InputCharges.input_type_str", false]], "input_type_str (inputnode attribute)": [[44, "hippynn.graphs.nodes.base.base.InputNode.input_type_str", false]], "input_type_str (notconvergednode attribute)": [[75, "hippynn.interfaces.pyseqm_interface.seqm_one.NotConvergedNode.input_type_str", false]], "input_type_str (pairindices attribute)": [[50, "hippynn.graphs.nodes.inputs.PairIndices.input_type_str", false]], "input_type_str (positionsnode attribute)": [[50, "hippynn.graphs.nodes.inputs.PositionsNode.input_type_str", false]], "input_type_str (speciesnode attribute)": [[50, "hippynn.graphs.nodes.inputs.SpeciesNode.input_type_str", false]], "input_type_str (splitindices attribute)": [[50, "hippynn.graphs.nodes.inputs.SplitIndices.input_type_str", false]], "inputcharges (class in hippynn.graphs.nodes.inputs)": [[50, "hippynn.graphs.nodes.inputs.InputCharges", false]], "inputnode (class in hippynn.graphs.nodes.base.base)": [[44, "hippynn.graphs.nodes.base.base.InputNode", false]], "inputs (predictor property)": [[29, "hippynn.graphs.Predictor.inputs", false], [58, "hippynn.graphs.predictor.Predictor.inputs", false]], "interaction_layers (hipnn property)": [[96, "hippynn.networks.hipnn.Hipnn.interaction_layers", false]], "interactionplot (class in hippynn.plotting.plotters)": [[103, "hippynn.plotting.plotters.InteractionPlot", false]], "interactlayer (class in hippynn.layers.hiplayers)": [[80, "hippynn.layers.hiplayers.InteractLayer", false]], "interactlayerquad (class in hippynn.layers.hiplayers)": [[80, "hippynn.layers.hiplayers.InteractLayerQuad", false]], "interactlayervec (class in hippynn.layers.hiplayers)": [[80, "hippynn.layers.hiplayers.InteractLayerVec", false]], "inversesensitivitymodule (class in hippynn.layers.hiplayers)": [[80, "hippynn.layers.hiplayers.InverseSensitivityModule", false]], "invnode (class in hippynn.graphs.nodes.base.algebra)": [[43, "hippynn.graphs.nodes.base.algebra.InvNode", false]], "is_equal_state_dict() (in module hippynn.tools)": [[106, "hippynn.tools.is_equal_state_dict", false]], "is_scheduler_like() (in module hippynn.experiment.controllers)": [[21, "hippynn.experiment.controllers.is_scheduler_like", false]], "isiterable() (in module hippynn.tools)": [[106, "hippynn.tools.isiterable", false]], "k (lightingprintstagescallback attribute)": [[24, "hippynn.experiment.lightning_trainer.LightingPrintStagesCallback.k", false]], "kdtreeneighbors (class in hippynn.layers.pairs.dispatch)": [[84, "hippynn.layers.pairs.dispatch.KDTreeNeighbors", false]], "kdtreepairs (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.KDTreePairs", false]], "kdtreepairsmemory (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.KDTreePairsMemory", false]], "kdtreepairsmemory (class in hippynn.layers.pairs.dispatch)": [[84, "hippynn.layers.pairs.dispatch.KDTreePairsMemory", false]], "l1reg() (in module hippynn.graphs.nodes.loss)": [[51, "hippynn.graphs.nodes.loss.l1reg", false]], "l2reg() (in module hippynn.graphs.nodes.loss)": [[51, "hippynn.graphs.nodes.loss.l2reg", false]], "lambdamodule (class in hippynn.layers.algebra)": [[78, "hippynn.layers.algebra.LambdaModule", false]], "langevindynamics (class in hippynn.molecular_dynamics.md)": [[94, "hippynn.molecular_dynamics.md.LangevinDynamics", false]], "launch_bounds() (numbacompatibletensorfunction method)": [[8, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction.launch_bounds", false]], "launch_bounds() (wrappedenvsum method)": [[4, 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"on_train_epoch_start() (hippynnlightningmodule method)": [[24, "hippynn.experiment.lightning_trainer.HippynnLightningModule.on_train_epoch_start", false]], "on_validation_end() (hippynnlightningmodule method)": [[24, "hippynn.experiment.lightning_trainer.HippynnLightningModule.on_validation_end", false]], "on_validation_epoch_end() (hippynnlightningmodule method)": [[24, "hippynn.experiment.lightning_trainer.HippynnLightningModule.on_validation_epoch_end", false]], "onehotencoder (class in hippynn.graphs.nodes.indexers)": [[49, "hippynn.graphs.nodes.indexers.OneHotEncoder", false]], "onehotspecies (class in hippynn.layers.indexers)": [[81, "hippynn.layers.indexers.OneHotSpecies", false]], "openpairindexer (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.OpenPairIndexer", false]], "openpairindexer (class in hippynn.layers.pairs.open)": [[87, "hippynn.layers.pairs.open.OpenPairIndexer", false]], "optimizer (class in hippynn.optimizer.batch_optimizer)": [[99, "hippynn.optimizer.batch_optimizer.Optimizer", false]], "optimizer (raisebatchsizeonplateau property)": [[21, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau.optimizer", false]], "optimizer (setupparams attribute)": [[19, "hippynn.experiment.SetupParams.optimizer", false], [26, "hippynn.experiment.routines.SetupParams.optimizer", false]], "out_shape() (numbacompatibletensorfunction method)": [[8, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction.out_shape", false]], "out_shape() (wrappedenvsum method)": [[4, "hippynn.custom_kernels.env_numba.WrappedEnvsum.out_shape", false]], "out_shape() (wrappedfeatsum method)": [[4, "hippynn.custom_kernels.env_numba.WrappedFeatsum.out_shape", false]], "out_shape() (wrappedsensesum method)": [[4, "hippynn.custom_kernels.env_numba.WrappedSensesum.out_shape", false]], "outputs (predictor property)": [[29, "hippynn.graphs.Predictor.outputs", false], [58, "hippynn.graphs.predictor.Predictor.outputs", false]], "p_value (qscreening property)": [[89, "hippynn.layers.physics.QScreening.p_value", false]], "pack_par() (in module hippynn.interfaces.pyseqm_interface.seqm_modules)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_modules.pack_par", false]], "pad_np_array_to_length_with_zeros() (in module hippynn.tools)": [[106, "hippynn.tools.pad_np_array_to_length_with_zeros", false]], "padded_neighlist() (in module hippynn.layers.pairs.indexing)": [[86, "hippynn.layers.pairs.indexing.padded_neighlist", false]], "paddedneighbornode (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.PaddedNeighborNode", false]], "paddedneighmodule (class in hippynn.layers.pairs.indexing)": [[86, "hippynn.layers.pairs.indexing.PaddedNeighModule", false]], "paddingindexer (class in hippynn.graphs.nodes.indexers)": [[49, "hippynn.graphs.nodes.indexers.PaddingIndexer", false]], "paddingindexer (class in hippynn.layers.indexers)": [[81, "hippynn.layers.indexers.PaddingIndexer", false]], "pair (idxtype attribute)": [[29, "hippynn.graphs.IdxType.Pair", false], [37, "hippynn.graphs.indextypes.IdxType.Pair", false], [40, "hippynn.graphs.indextypes.type_def.IdxType.Pair", false]], "paircache (class in hippynn.graphs.nodes.tags)": [[56, "hippynn.graphs.nodes.tags.PairCache", false]], "paircacher (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.PairCacher", false]], "paircacher (class in hippynn.layers.pairs.indexing)": [[86, "hippynn.layers.pairs.indexing.PairCacher", false]], "pairdeindexer (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.PairDeIndexer", false]], "pairdeindexer (class in hippynn.layers.pairs.indexing)": [[86, "hippynn.layers.pairs.indexing.PairDeIndexer", false]], "pairfilter (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.PairFilter", false]], "pairindexer (class in hippynn.graphs.nodes.tags)": [[56, "hippynn.graphs.nodes.tags.PairIndexer", false]], "pairindices (class in hippynn.graphs.nodes.inputs)": [[50, "hippynn.graphs.nodes.inputs.PairIndices", false]], "pairmemory (class in hippynn.layers.pairs.open)": [[87, "hippynn.layers.pairs.open.PairMemory", false]], "pairreindexer (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.PairReIndexer", false]], "pairreindexer (class in hippynn.layers.pairs.indexing)": [[86, "hippynn.layers.pairs.indexing.PairReIndexer", false]], "pairuncacher (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.PairUncacher", false]], "pairuncacher (class in hippynn.layers.pairs.indexing)": [[86, "hippynn.layers.pairs.indexing.PairUncacher", false]], "param_print() (in module hippynn.tools)": [[106, "hippynn.tools.param_print", false]], "parentexpander (class in hippynn.graphs.nodes.base.definition_helpers)": [[45, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander", false]], "parse_args() (in module hippynn.custom_kernels.test_env_numba)": [[10, "hippynn.custom_kernels.test_env_numba.parse_args", false]], "pass_to_pytorch() (in module hippynn.interfaces.ase_interface.calculator)": [[64, "hippynn.interfaces.ase_interface.calculator.pass_to_pytorch", false]], "patiencecontroller (class in hippynn.experiment.controllers)": [[21, "hippynn.experiment.controllers.PatienceController", false]], "pbchandle (class in hippynn.interfaces.ase_interface.calculator)": [[64, "hippynn.interfaces.ase_interface.calculator.PBCHandle", false]], "peratom (class in hippynn.graphs.nodes.physics)": [[55, "hippynn.graphs.nodes.physics.PerAtom", false]], "peratom (class in hippynn.layers.physics)": [[89, "hippynn.layers.physics.PerAtom", false]], "periodicpairindexer (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.PeriodicPairIndexer", false]], "periodicpairindexer (class in hippynn.layers.pairs.periodic)": [[88, "hippynn.layers.pairs.periodic.PeriodicPairIndexer", false]], "periodicpairindexermemory (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.PeriodicPairIndexerMemory", false]], "periodicpairindexermemory (class in hippynn.layers.pairs.periodic)": [[88, "hippynn.layers.pairs.periodic.PeriodicPairIndexerMemory", false]], "periodicpairoutputs (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.PeriodicPairOutputs", false]], "plot_all_over_time() (in module hippynn.plotting.timeplots)": [[104, "hippynn.plotting.timeplots.plot_all_over_time", false]], "plot_over_time() (in module hippynn.plotting.timeplots)": [[104, "hippynn.plotting.timeplots.plot_over_time", false]], "plot_over_time() (metrictracker method)": [[25, "hippynn.experiment.metric_tracker.MetricTracker.plot_over_time", false]], "plot_phase() (plotmaker method)": [[102, "hippynn.plotting.plotmaker.PlotMaker.plot_phase", false]], "plotmaker (class in hippynn.plotting.plotmaker)": [[102, "hippynn.plotting.plotmaker.PlotMaker", false]], "plotter (class in hippynn.plotting.plotters)": 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[[50, "hippynn.graphs.nodes.inputs.PositionsNode", false]], "post_step() (langevindynamics method)": [[94, "hippynn.molecular_dynamics.md.LangevinDynamics.post_step", false]], "post_step() (nullupdater method)": [[94, "hippynn.molecular_dynamics.md.NullUpdater.post_step", false]], "post_step() (variableupdater method)": [[94, "hippynn.molecular_dynamics.md.VariableUpdater.post_step", false]], "post_step() (velocityverlet method)": [[94, "hippynn.molecular_dynamics.md.VelocityVerlet.post_step", false]], "pownode (class in hippynn.graphs.nodes.base.algebra)": [[43, "hippynn.graphs.nodes.base.algebra.PowNode", false]], "pre_step() (langevindynamics method)": [[94, "hippynn.molecular_dynamics.md.LangevinDynamics.pre_step", false]], "pre_step() (nullupdater method)": [[94, "hippynn.molecular_dynamics.md.NullUpdater.pre_step", false]], "pre_step() (variableupdater method)": [[94, "hippynn.molecular_dynamics.md.VariableUpdater.pre_step", false]], "pre_step() (velocityverlet method)": [[94, "hippynn.molecular_dynamics.md.VelocityVerlet.pre_step", false]], "precompute_pairs() (in module hippynn.experiment.assembly)": [[20, "hippynn.experiment.assembly.precompute_pairs", false]], "pred (lossinputnode property)": [[44, "hippynn.graphs.nodes.base.base.LossInputNode.pred", false]], "predict_all() (predictor method)": [[29, "hippynn.graphs.Predictor.predict_all", false], [58, "hippynn.graphs.predictor.Predictor.predict_all", false]], "predict_batched() (predictor method)": [[29, "hippynn.graphs.Predictor.predict_batched", false], [58, "hippynn.graphs.predictor.Predictor.predict_batched", false]], "predictor (class in hippynn.graphs)": [[29, "hippynn.graphs.Predictor", false]], "predictor (class in hippynn.graphs.predictor)": [[58, "hippynn.graphs.predictor.Predictor", false]], "prettyprint_arrays() (in module hippynn.databases.database)": [[15, "hippynn.databases.database.prettyprint_arrays", false]], "print_lr() (in module hippynn.tools)": [[106, "hippynn.tools.print_lr", false]], "print_structure() (graphmodule method)": [[29, "hippynn.graphs.GraphModule.print_structure", false], [32, "hippynn.graphs.graph.GraphModule.print_structure", false]], "process_configs() (snapdirectorydatabase method)": [[14, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.process_configs", false]], "progress_bar() (in module hippynn.tools)": [[106, "hippynn.tools.progress_bar", false]], "push_epoch() (controller method)": [[21, "hippynn.experiment.controllers.Controller.push_epoch", false]], "push_epoch() (patiencecontroller method)": [[21, "hippynn.experiment.controllers.PatienceController.push_epoch", false]], "qscreening (class in hippynn.layers.physics)": [[89, "hippynn.layers.physics.QScreening", false]], "quadmol (idxtype attribute)": [[29, "hippynn.graphs.IdxType.QuadMol", false], [37, "hippynn.graphs.indextypes.IdxType.QuadMol", false], [40, "hippynn.graphs.indextypes.type_def.IdxType.QuadMol", false]], "quadpack (class in hippynn.layers.indexers)": [[81, "hippynn.layers.indexers.QuadPack", false]], "quadpack (idxtype attribute)": [[29, "hippynn.graphs.IdxType.QuadPack", false], [37, "hippynn.graphs.indextypes.IdxType.QuadPack", false], [40, "hippynn.graphs.indextypes.type_def.IdxType.QuadPack", false]], "quadrupole (class in hippynn.layers.physics)": [[89, "hippynn.layers.physics.Quadrupole", false]], "quadrupolenode (class in hippynn.graphs.nodes.physics)": [[55, "hippynn.graphs.nodes.physics.QuadrupoleNode", false]], "quadunpack (class in hippynn.layers.indexers)": [[81, "hippynn.layers.indexers.QuadUnpack", false]], "quadunpacknode (class in hippynn.graphs.nodes.indexers)": [[49, "hippynn.graphs.nodes.indexers.QuadUnpackNode", false]], "raisebatchsizeonplateau (class in hippynn.experiment.controllers)": [[21, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau", false]], "rdfbins (class in hippynn.graphs.nodes.pairs)": [[54, "hippynn.graphs.nodes.pairs.RDFBins", false]], "rdfbins (class in hippynn.layers.pairs.analysis)": [[83, "hippynn.layers.pairs.analysis.RDFBins", false]], "rebuild_neighbors() (hippynncalculator method)": [[61, "hippynn.interfaces.ase_interface.HippynnCalculator.rebuild_neighbors", false], [64, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.rebuild_neighbors", false]], "recalculation_needed() (pairmemory method)": [[87, "hippynn.layers.pairs.open.PairMemory.recalculation_needed", false]], "recursive_param_count() (in module hippynn.tools)": [[106, "hippynn.tools.recursive_param_count", false]], "reducesinglenode (class in hippynn.graphs.nodes.loss)": [[51, "hippynn.graphs.nodes.loss.ReduceSingleNode", false]], "register_index_transformer() (in module hippynn.graphs.indextypes)": [[37, "hippynn.graphs.indextypes.register_index_transformer", false]], "register_index_transformer() (in module hippynn.graphs.indextypes.registry)": [[39, "hippynn.graphs.indextypes.registry.register_index_transformer", false]], "register_metrics() (metrictracker method)": [[25, "hippynn.experiment.metric_tracker.MetricTracker.register_metrics", false]], "regularization_params() (hipnn method)": [[96, "hippynn.networks.hipnn.Hipnn.regularization_params", false]], "regularization_params() (interactlayer method)": [[80, "hippynn.layers.hiplayers.InteractLayer.regularization_params", false]], "regularization_params() (resnetwrapper method)": [[92, "hippynn.layers.transform.ResNetWrapper.regularization_params", false]], "reindexatommod (class in hippynn.interfaces.lammps_interface.mliap_interface)": [[67, "hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomMod", false]], "reindexatomnode (class in hippynn.interfaces.lammps_interface.mliap_interface)": [[67, "hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomNode", false]], "remove_high_property() (database method)": [[13, "hippynn.databases.Database.remove_high_property", false], [15, "hippynn.databases.database.Database.remove_high_property", false]], "replace_inputs() (in module hippynn.graphs.ensemble)": [[30, "hippynn.graphs.ensemble.replace_inputs", false]], "replace_node() (in module hippynn.graphs)": [[29, "hippynn.graphs.replace_node", false]], "replace_node() (in module hippynn.graphs.gops)": [[31, "hippynn.graphs.gops.replace_node", false]], "replace_node_with_constant() (in module hippynn.graphs.gops)": [[31, "hippynn.graphs.gops.replace_node_with_constant", false]], "require_compatible_idx_states() (parentexpander method)": [[45, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.require_compatible_idx_states", false]], "require_idx_states() (parentexpander method)": [[45, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.require_idx_states", false]], "required_nodes (plotmaker property)": [[102, "hippynn.plotting.plotmaker.PlotMaker.required_nodes", false]], "required_variable_data (langevindynamics attribute)": [[94, "hippynn.molecular_dynamics.md.LangevinDynamics.required_variable_data", false]], "required_variable_data (variableupdater attribute)": [[94, "hippynn.molecular_dynamics.md.VariableUpdater.required_variable_data", false]], "required_variable_data (velocityverlet attribute)": [[94, "hippynn.molecular_dynamics.md.VelocityVerlet.required_variable_data", false]], "requires_grad (inputnode attribute)": [[44, "hippynn.graphs.nodes.base.base.InputNode.requires_grad", false]], "reset() (bfgsv1 method)": [[98, "hippynn.optimizer.algorithms.BFGSv1.reset", false]], "reset() (bfgsv2 method)": [[98, "hippynn.optimizer.algorithms.BFGSv2.reset", false]], "reset() (bfgsv3 method)": [[98, "hippynn.optimizer.algorithms.BFGSv3.reset", false]], "reset() (fire method)": [[98, "hippynn.optimizer.algorithms.FIRE.reset", false]], "reset() (newtonraphson method)": [[98, "hippynn.optimizer.algorithms.NewtonRaphson.reset", false]], "reset_data() (moleculardynamics method)": [[94, "hippynn.molecular_dynamics.md.MolecularDynamics.reset_data", false]], "reset_reuse_percentage() (memory method)": [[54, "hippynn.graphs.nodes.pairs.Memory.reset_reuse_percentage", false]], "reset_reuse_percentage() (pairmemory method)": [[87, "hippynn.layers.pairs.open.PairMemory.reset_reuse_percentage", false]], "resnetwrapper (class in hippynn.layers.transform)": [[92, "hippynn.layers.transform.ResNetWrapper", false]], "resort_pairs_cached() (in module hippynn.custom_kernels.utils)": [[12, "hippynn.custom_kernels.utils.resort_pairs_cached", false]], "restartable (class in hippynn.databases.restarter)": [[18, "hippynn.databases.restarter.Restartable", false]], "restartdb (class in hippynn.databases.restarter)": [[18, "hippynn.databases.restarter.RestartDB", false]], "restarter (class in hippynn.databases.restarter)": [[18, "hippynn.databases.restarter.Restarter", false]], "restore_checkpoint() (in module hippynn.experiment.serialization)": [[27, "hippynn.experiment.serialization.restore_checkpoint", false]], "reuse_percentage (memory property)": [[54, "hippynn.graphs.nodes.pairs.Memory.reuse_percentage", false]], "reuse_percentage (pairmemory property)": [[87, "hippynn.layers.pairs.open.PairMemory.reuse_percentage", false]], "rsq (class in hippynn.graphs.nodes.loss)": [[51, "hippynn.graphs.nodes.loss.Rsq", false]], "rsqmod (class in hippynn.graphs.nodes.loss)": [[51, "hippynn.graphs.nodes.loss.RsqMod", false]], "run() (moleculardynamics method)": [[94, "hippynn.molecular_dynamics.md.MolecularDynamics.run", false]], "save() (in module hippynn.interfaces.pyseqm_interface.check)": [[70, "hippynn.interfaces.pyseqm_interface.check.save", false]], "save() (mlseqm method)": [[72, "hippynn.interfaces.pyseqm_interface.mlseqm.MLSEQM.save", false]], "save_and_stop_after() (in module hippynn.interfaces.pyseqm_interface.callback)": [[69, "hippynn.interfaces.pyseqm_interface.callback.save_and_stop_after", false]], "scalar (idxtype attribute)": [[29, "hippynn.graphs.IdxType.Scalar", false], [37, "hippynn.graphs.indextypes.IdxType.Scalar", false], [40, "hippynn.graphs.indextypes.type_def.IdxType.Scalar", false]], "scale (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[73, "hippynn.interfaces.pyseqm_interface.seqm_modules.Scale", false]], "scalenode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[74, "hippynn.interfaces.pyseqm_interface.seqm_nodes.ScaleNode", false]], "scheduler (setupparams attribute)": [[19, "hippynn.experiment.SetupParams.scheduler", false], [26, "hippynn.experiment.routines.SetupParams.scheduler", false]], "schnetnode (class in hippynn.interfaces.schnetpack_interface)": [[76, "hippynn.interfaces.schnetpack_interface.SchNetNode", false]], "schnetwrapper (class in hippynn.interfaces.schnetpack_interface)": [[76, "hippynn.interfaces.schnetpack_interface.SchNetWrapper", false]], "screenedcoulombenergy (class in hippynn.layers.physics)": [[89, "hippynn.layers.physics.ScreenedCoulombEnergy", false]], "screenedcoulombenergynode (class in hippynn.graphs.nodes.physics)": [[55, 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"hippynn.custom_kernels.utils module", "hippynn.databases package", "hippynn.databases.SNAPJson module", "hippynn.databases.database module", "hippynn.databases.h5_pyanitools module", "hippynn.databases.ondisk module", "hippynn.databases.restarter module", "hippynn.experiment package", "hippynn.experiment.assembly module", "hippynn.experiment.controllers module", "hippynn.experiment.device module", "hippynn.experiment.evaluator module", "hippynn.experiment.lightning_trainer module", "hippynn.experiment.metric_tracker module", "hippynn.experiment.routines module", "hippynn.experiment.serialization module", "hippynn.experiment.step_functions module", "hippynn.graphs package", "hippynn.graphs.ensemble module", "hippynn.graphs.gops module", "hippynn.graphs.graph module", "hippynn.graphs.indextransformers package", "hippynn.graphs.indextransformers.atoms module", "hippynn.graphs.indextransformers.pairs module", "hippynn.graphs.indextransformers.tensors module", "hippynn.graphs.indextypes package", "hippynn.graphs.indextypes.reduce_funcs module", "hippynn.graphs.indextypes.registry module", "hippynn.graphs.indextypes.type_def module", "hippynn.graphs.nodes package", "hippynn.graphs.nodes.base package", "hippynn.graphs.nodes.base.algebra module", "hippynn.graphs.nodes.base.base module", "hippynn.graphs.nodes.base.definition_helpers module", "hippynn.graphs.nodes.base.multi module", "hippynn.graphs.nodes.base.node_functions module", "hippynn.graphs.nodes.excited module", "hippynn.graphs.nodes.indexers module", "hippynn.graphs.nodes.inputs module", "hippynn.graphs.nodes.loss module", "hippynn.graphs.nodes.misc module", "hippynn.graphs.nodes.networks module", "hippynn.graphs.nodes.pairs module", "hippynn.graphs.nodes.physics module", "hippynn.graphs.nodes.tags module", "hippynn.graphs.nodes.targets module", "hippynn.graphs.predictor module", "hippynn.graphs.viz module", "hippynn.interfaces package", "hippynn.interfaces.ase_interface package", "hippynn.interfaces.ase_interface.ase_database module", "hippynn.interfaces.ase_interface.ase_unittests module", "hippynn.interfaces.ase_interface.calculator module", "hippynn.interfaces.ase_interface.pairfinder module", "hippynn.interfaces.lammps_interface package", "hippynn.interfaces.lammps_interface.mliap_interface module", "hippynn.interfaces.pyseqm_interface package", "hippynn.interfaces.pyseqm_interface.callback module", "hippynn.interfaces.pyseqm_interface.check module", "hippynn.interfaces.pyseqm_interface.gen_par module", "hippynn.interfaces.pyseqm_interface.mlseqm module", "hippynn.interfaces.pyseqm_interface.seqm_modules module", "hippynn.interfaces.pyseqm_interface.seqm_nodes module", "hippynn.interfaces.pyseqm_interface.seqm_one module", "hippynn.interfaces.schnetpack_interface package", "hippynn.layers package", "hippynn.layers.algebra module", "hippynn.layers.excited module", "hippynn.layers.hiplayers module", "hippynn.layers.indexers module", "hippynn.layers.pairs package", "hippynn.layers.pairs.analysis module", "hippynn.layers.pairs.dispatch module", "hippynn.layers.pairs.filters module", "hippynn.layers.pairs.indexing module", "hippynn.layers.pairs.open module", "hippynn.layers.pairs.periodic module", "hippynn.layers.physics module", "hippynn.layers.regularization module", "hippynn.layers.targets module", "hippynn.layers.transform module", "hippynn.molecular_dynamics package", "hippynn.molecular_dynamics.md module", "hippynn.networks package", "hippynn.networks.hipnn module", "hippynn.optimizer package", "hippynn.optimizer.algorithms module", "hippynn.optimizer.batch_optimizer module", "hippynn.optimizer.utils module", "hippynn.plotting package", "hippynn.plotting.plotmaker module", "hippynn.plotting.plotters module", "hippynn.plotting.timeplots module", "hippynn.pretraining module", "hippynn.tools module", "hippynn", "ASE Calculators", "Controller", "Ensembling Models", "Non-Adiabiatic Excited States", "Force Training", "Examples", "Minimal Workflow", "LAMMPS interface", "Periodic Boundary Conditions", "Plotting", "Predictor", "Restarting training", "Weighted/Masked Loss Functions", "Welcome to hippynn\u2019s documentation!", "Installation", "License", "Custom Kernels", "hippynn Concepts", "Creating Custom Node Types", "Databases", "hippynn Features", "User Guide", "Model and Loss Graphs", "Library Settings", "Units in hippynn"], "titleterms": {"": [116, 121], "A": 126, "ASE": [108, 127], "The": 126, "ad": 126, "adiabiat": 111, "advanc": 119, "algebra": [43, 78], "algorithm": 98, "analysi": 83, "api": 128, "ase_databas": 62, "ase_interfac": [61, 62, 63, 64, 65], "ase_unittest": 63, "assembli": 20, "atom": 34, "atomist": 128, "autograd_wrapp": 2, "base": [42, 43, 44, 45, 46, 47], "basic": 126, "batch_optim": 99, "bottom": 124, "boundari": 116, "cach": 116, "calcul": [64, 108], "callback": 69, "check": 70, "compon": 128, "comput": 116, "concept": 125, "conda": 122, "condit": 116, "constraint": 126, "construct": 128, 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\ No newline at end of file
diff --git a/user_guide/settings.html b/user_guide/settings.html
index c30d3020..edc101c3 100644
--- a/user_guide/settings.html
+++ b/user_guide/settings.html
@@ -129,7 +129,7 @@ Library SettingsPROGRESS
Progress bars function during training, evaluation, and prediction
tqdm, none
tqdm, none, or floating point string specifying default update rate in seconds (default 1).
tqdm
Yes, but assign this to a generator-wrapper such as tqdm.tqdm None tqdm