glasspy.predict package
Submodules
glasspy.predict.base module
- class glasspy.predict.base.AE(hparams: Dict[str, Any])
Bases:
LightningModule
,Predict
Base class for creating Autoencoders.
- Parameters
hparams –
Dictionary with the hyperparemeters of the network. The possible parameters are: + “n_features”: number of input features (required). Must be a positive
integer. Will be the same as the number of output features.
”num_layers”: number of encoder hidden layers (defaults to 1). Must be a positive integer. NOTE: The decoder will have the same number of hidden layers.
”layer_n_size”: number of neurons in layer n of the encoder (replace n for an integer starting at 1, defaults to 10). Must be a positive integer. NOTE: The decoder architecture will be the same as the encoder, but mirrored.
”layer_n_activation”: activation function of layer n of the encoder (replace n for an integer starting at 1, defaults to Tanh). Available values are [“Tanh”, “Sigmoid”, “ReLU”, “LeakyReLU”, “SELU”, “GELU”, “ELU”, “PReLU”, “SiLU”, “Mish”, “Softplus”, “Linear”].
”layer_n_dropout”: dropout of layer n of the encoder (replace n for an integer starting at 1, defaults to False meaning no dropout). Any value between 0 and 1 (or False) is permitted.
”layer_n_batchnorm”: True will use batch normalization in layer n of the encoder, False will not use batch normalization in layer n (replace n for an integer starting at 1, defaults to False meaning no batch normalization).
”loss”: loss function to use for the backpropagation algorithm (defaults to mse). Use mse for mean squared error loss (L2) or huber for a smooth L1 loss.
”optimizer”: optimizer algorithm to use (defaults SGD). Use SGD for stochastic gradient descend, Adam for Adam, or AdamW for weighted Adam.
”lr”: optimizer learning rate (defaults to 1e-4 if optimizer is SGD or 1e-3 if optimizer is Adam or AdamW).
”momentum”: momentum to use when optmizer is SGD (defaults to 0).
”optimizer_Adam_eps”: eps to use for Adam or AdamW optimizers (defaults to 1e-8).
- Raises
NotImplementedError – When the selected hyperparameters is not one of the permited values.
- configure_optimizers()
Choose what optimizers and learning-rate schedulers to use in your optimization. Normally you’d need one. But in the case of GANs or similar you might have multiple.
- Returns
Any of these 6 options.
Single optimizer.
List or Tuple of optimizers.
Two lists - The first list has multiple optimizers, and the second has multiple LR schedulers (or multiple
lr_scheduler_config
).Dictionary, with an
"optimizer"
key, and (optionally) a"lr_scheduler"
key whose value is a single LR scheduler orlr_scheduler_config
.Tuple of dictionaries as described above, with an optional
"frequency"
key.None - Fit will run without any optimizer.
The
lr_scheduler_config
is a dictionary which contains the scheduler and its associated configuration. The default configuration is shown below.lr_scheduler_config = { # REQUIRED: The scheduler instance "scheduler": lr_scheduler, # The unit of the scheduler's step size, could also be 'step'. # 'epoch' updates the scheduler on epoch end whereas 'step' # updates it after a optimizer update. "interval": "epoch", # How many epochs/steps should pass between calls to # `scheduler.step()`. 1 corresponds to updating the learning # rate after every epoch/step. "frequency": 1, # Metric to to monitor for schedulers like `ReduceLROnPlateau` "monitor": "val_loss", # If set to `True`, will enforce that the value specified 'monitor' # is available when the scheduler is updated, thus stopping # training if not found. If set to `False`, it will only produce a warning "strict": True, # If using the `LearningRateMonitor` callback to monitor the # learning rate progress, this keyword can be used to specify # a custom logged name "name": None, }
When there are schedulers in which the
.step()
method is conditioned on a value, such as thetorch.optim.lr_scheduler.ReduceLROnPlateau
scheduler, Lightning requires that thelr_scheduler_config
contains the keyword"monitor"
set to the metric name that the scheduler should be conditioned on.Metrics can be made available to monitor by simply logging it using
self.log('metric_to_track', metric_val)
in yourLightningModule
.Note
The
frequency
value specified in a dict along with theoptimizer
key is an int corresponding to the number of sequential batches optimized with the specific optimizer. It should be given to none or to all of the optimizers. There is a difference between passing multiple optimizers in a list, and passing multiple optimizers in dictionaries with a frequency of 1:In the former case, all optimizers will operate on the given batch in each optimization step.
In the latter, only one optimizer will operate on the given batch at every step.
This is different from the
frequency
value specified in thelr_scheduler_config
mentioned above.def configure_optimizers(self): optimizer_one = torch.optim.SGD(self.model.parameters(), lr=0.01) optimizer_two = torch.optim.SGD(self.model.parameters(), lr=0.01) return [ {"optimizer": optimizer_one, "frequency": 5}, {"optimizer": optimizer_two, "frequency": 10}, ]
In this example, the first optimizer will be used for the first 5 steps, the second optimizer for the next 10 steps and that cycle will continue. If an LR scheduler is specified for an optimizer using the
lr_scheduler
key in the above dict, the scheduler will only be updated when its optimizer is being used.Examples:
# most cases. no learning rate scheduler def configure_optimizers(self): return Adam(self.parameters(), lr=1e-3) # multiple optimizer case (e.g.: GAN) def configure_optimizers(self): gen_opt = Adam(self.model_gen.parameters(), lr=0.01) dis_opt = Adam(self.model_dis.parameters(), lr=0.02) return gen_opt, dis_opt # example with learning rate schedulers def configure_optimizers(self): gen_opt = Adam(self.model_gen.parameters(), lr=0.01) dis_opt = Adam(self.model_dis.parameters(), lr=0.02) dis_sch = CosineAnnealing(dis_opt, T_max=10) return [gen_opt, dis_opt], [dis_sch] # example with step-based learning rate schedulers # each optimizer has its own scheduler def configure_optimizers(self): gen_opt = Adam(self.model_gen.parameters(), lr=0.01) dis_opt = Adam(self.model_dis.parameters(), lr=0.02) gen_sch = { 'scheduler': ExponentialLR(gen_opt, 0.99), 'interval': 'step' # called after each training step } dis_sch = CosineAnnealing(dis_opt, T_max=10) # called every epoch return [gen_opt, dis_opt], [gen_sch, dis_sch] # example with optimizer frequencies # see training procedure in `Improved Training of Wasserstein GANs`, Algorithm 1 # https://arxiv.org/abs/1704.00028 def configure_optimizers(self): gen_opt = Adam(self.model_gen.parameters(), lr=0.01) dis_opt = Adam(self.model_dis.parameters(), lr=0.02) n_critic = 5 return ( {'optimizer': dis_opt, 'frequency': n_critic}, {'optimizer': gen_opt, 'frequency': 1} )
Note
Some things to know:
Lightning calls
.backward()
and.step()
on each optimizer as needed.If learning rate scheduler is specified in
configure_optimizers()
with key"interval"
(default “epoch”) in the scheduler configuration, Lightning will call the scheduler’s.step()
method automatically in case of automatic optimization.If you use 16-bit precision (
precision=16
), Lightning will automatically handle the optimizers.If you use multiple optimizers,
training_step()
will have an additionaloptimizer_idx
parameter.If you use
torch.optim.LBFGS
, Lightning handles the closure function automatically for you.If you use multiple optimizers, gradients will be calculated only for the parameters of current optimizer at each training step.
If you need to control how often those optimizers step or override the default
.step()
schedule, override theoptimizer_step()
hook.
- distance_from_training()
- forward(x)
Same as
torch.nn.Module.forward()
.- Parameters
*args – Whatever you decide to pass into the forward method.
**kwargs – Keyword arguments are also possible.
- Returns
Your model’s output
- get_test_dataset()
- get_training_dataset()
- get_validation_dataset()
- is_within_domain()
- learning_curve_train = []
- learning_curve_val = []
- load_training(path)
- predict(x)
- save_training(path)
- training_epoch_end(outputs)
Called at the end of the training epoch with the outputs of all training steps. Use this in case you need to do something with all the outputs returned by
training_step()
.# the pseudocode for these calls train_outs = [] for train_batch in train_data: out = training_step(train_batch) train_outs.append(out) training_epoch_end(train_outs)
- Parameters
outputs – List of outputs you defined in
training_step()
. If there are multiple optimizers or when usingtruncated_bptt_steps > 0
, the lists have the dimensions (n_batches, tbptt_steps, n_optimizers). Dimensions of length 1 are squeezed.- Returns
None
Note
If this method is not overridden, this won’t be called.
def training_epoch_end(self, training_step_outputs): # do something with all training_step outputs for out in training_step_outputs: ...
- training_step(batch, batch_idx)
Here you compute and return the training loss and some additional metrics for e.g. the progress bar or logger.
- Parameters
batch (
Tensor
| (Tensor
, …) | [Tensor
, …]) – The output of yourDataLoader
. A tensor, tuple or list.batch_idx (
int
) – Integer displaying index of this batchoptimizer_idx (
int
) – When using multiple optimizers, this argument will also be present.hiddens (
Any
) – Passed in if :paramref:`~pytorch_lightning.core.module.LightningModule.truncated_bptt_steps` > 0.
- Returns
Any of.
Tensor
- The loss tensordict
- A dictionary. Can include any keys, but must include the key'loss'
None
- Training will skip to the next batch. This is only for automatic optimization.This is not supported for multi-GPU, TPU, IPU, or DeepSpeed.
In this step you’d normally do the forward pass and calculate the loss for a batch. You can also do fancier things like multiple forward passes or something model specific.
Example:
def training_step(self, batch, batch_idx): x, y, z = batch out = self.encoder(x) loss = self.loss(out, x) return loss
If you define multiple optimizers, this step will be called with an additional
optimizer_idx
parameter.# Multiple optimizers (e.g.: GANs) def training_step(self, batch, batch_idx, optimizer_idx): if optimizer_idx == 0: # do training_step with encoder ... if optimizer_idx == 1: # do training_step with decoder ...
If you add truncated back propagation through time you will also get an additional argument with the hidden states of the previous step.
# Truncated back-propagation through time def training_step(self, batch, batch_idx, hiddens): # hiddens are the hidden states from the previous truncated backprop step out, hiddens = self.lstm(data, hiddens) loss = ... return {"loss": loss, "hiddens": hiddens}
Note
The loss value shown in the progress bar is smoothed (averaged) over the last values, so it differs from the actual loss returned in train/validation step.
- validation_epoch_end(outputs)
Called at the end of the validation epoch with the outputs of all validation steps.
# the pseudocode for these calls val_outs = [] for val_batch in val_data: out = validation_step(val_batch) val_outs.append(out) validation_epoch_end(val_outs)
- Parameters
outputs – List of outputs you defined in
validation_step()
, or if there are multiple dataloaders, a list containing a list of outputs for each dataloader.- Returns
None
Note
If you didn’t define a
validation_step()
, this won’t be called.Examples
With a single dataloader:
def validation_epoch_end(self, val_step_outputs): for out in val_step_outputs: ...
With multiple dataloaders, outputs will be a list of lists. The outer list contains one entry per dataloader, while the inner list contains the individual outputs of each validation step for that dataloader.
def validation_epoch_end(self, outputs): for dataloader_output_result in outputs: dataloader_outs = dataloader_output_result.dataloader_i_outputs self.log("final_metric", final_value)
- validation_step(batch, batch_idx)
Operates on a single batch of data from the validation set. In this step you’d might generate examples or calculate anything of interest like accuracy.
# the pseudocode for these calls val_outs = [] for val_batch in val_data: out = validation_step(val_batch) val_outs.append(out) validation_epoch_end(val_outs)
- Parameters
batch – The output of your
DataLoader
.batch_idx – The index of this batch.
dataloader_idx – The index of the dataloader that produced this batch. (only if multiple val dataloaders used)
- Returns
Any object or value
None
- Validation will skip to the next batch
# pseudocode of order val_outs = [] for val_batch in val_data: out = validation_step(val_batch) if defined("validation_step_end"): out = validation_step_end(out) val_outs.append(out) val_outs = validation_epoch_end(val_outs)
# if you have one val dataloader: def validation_step(self, batch, batch_idx): ... # if you have multiple val dataloaders: def validation_step(self, batch, batch_idx, dataloader_idx=0): ...
Examples:
# CASE 1: A single validation dataset def validation_step(self, batch, batch_idx): x, y = batch # implement your own out = self(x) loss = self.loss(out, y) # log 6 example images # or generated text... or whatever sample_imgs = x[:6] grid = torchvision.utils.make_grid(sample_imgs) self.logger.experiment.add_image('example_images', grid, 0) # calculate acc labels_hat = torch.argmax(out, dim=1) val_acc = torch.sum(y == labels_hat).item() / (len(y) * 1.0) # log the outputs! self.log_dict({'val_loss': loss, 'val_acc': val_acc})
If you pass in multiple val dataloaders,
validation_step()
will have an additional argument. We recommend setting the default value of 0 so that you can quickly switch between single and multiple dataloaders.# CASE 2: multiple validation dataloaders def validation_step(self, batch, batch_idx, dataloader_idx=0): # dataloader_idx tells you which dataset this is. ...
Note
If you don’t need to validate you don’t need to implement this method.
Note
When the
validation_step()
is called, the model has been put in eval mode and PyTorch gradients have been disabled. At the end of validation, the model goes back to training mode and gradients are enabled.
- class glasspy.predict.base.Domain(element: Optional[Dict[str, float]] = None, compound: Optional[Dict[str, float]] = None)
Bases:
NamedTuple
Simple class to store chemical domain information.
- compound: Dict[str, float]
Alias for field number 1
- element: Dict[str, float]
Alias for field number 0
- class glasspy.predict.base.MLP(hparams: Dict[str, Any])
Bases:
LightningModule
,Predict
Base class for creating Multilayer Perceptrons.
- Parameters
hparams –
Dictionary with the hyperparemeters of the network. The possible parameters are: + “n_features”: number of input features (required). Must be a positive
integer.
”num_layers”: number of hidden layers (defaults to 1). Must be a positive integer.
”layer_n_size”: number of neurons in layer n (replace n for an integer starting at 1, defaults to 10). Must be a positive integer.
”layer_n_activation”: activation function of layer n (replace n for an integer starting at 1, defaults to Tanh). Available values are [“Tanh”, “Sigmoid”, “ReLU”, “LeakyReLU”, “SELU”, “GELU”, “ELU”, “PReLU”, “SiLU”, “Mish”, “Softplus”, “Linear”].
”layer_n_dropout”: dropout of layer n (replace n for an integer starting at 1, defaults to False meaning no dropout). Any value between 0 and 1 (or False) is permitted.
”layer_n_batchnorm”: True will use batch normalization in layer n, False will not use batch normalization in layer n (replace n for an integer starting at 1, defaults to False meaning no batch normalization).
”loss”: loss function to use for the backpropagation algorithm (defaults to mse). Use mse for mean squared error loss (L2) or huber for a smooth L1 loss.
”optimizer”: optimizer algorithm to use (defaults SGD). Use SGD for stochastic gradient descend, Adam for Adam, or AdamW for weighted Adam.
”lr”: optimizer learning rate (defaults to 1e-4 if optimizer is SGD or 1e-3 if optimizer is Adam or AdamW).
”momentum”: momentum to use when optmizer is SGD (defaults to 0).
”optimizer_Adam_eps”: eps to use for Adam or AdamW optimizers (defaults to 1e-8).
- Raises
NotImplementedError – When the selected hyperparameters is not one of the permited values.
- configure_optimizers()
Choose what optimizers and learning-rate schedulers to use in your optimization. Normally you’d need one. But in the case of GANs or similar you might have multiple.
- Returns
Any of these 6 options.
Single optimizer.
List or Tuple of optimizers.
Two lists - The first list has multiple optimizers, and the second has multiple LR schedulers (or multiple
lr_scheduler_config
).Dictionary, with an
"optimizer"
key, and (optionally) a"lr_scheduler"
key whose value is a single LR scheduler orlr_scheduler_config
.Tuple of dictionaries as described above, with an optional
"frequency"
key.None - Fit will run without any optimizer.
The
lr_scheduler_config
is a dictionary which contains the scheduler and its associated configuration. The default configuration is shown below.lr_scheduler_config = { # REQUIRED: The scheduler instance "scheduler": lr_scheduler, # The unit of the scheduler's step size, could also be 'step'. # 'epoch' updates the scheduler on epoch end whereas 'step' # updates it after a optimizer update. "interval": "epoch", # How many epochs/steps should pass between calls to # `scheduler.step()`. 1 corresponds to updating the learning # rate after every epoch/step. "frequency": 1, # Metric to to monitor for schedulers like `ReduceLROnPlateau` "monitor": "val_loss", # If set to `True`, will enforce that the value specified 'monitor' # is available when the scheduler is updated, thus stopping # training if not found. If set to `False`, it will only produce a warning "strict": True, # If using the `LearningRateMonitor` callback to monitor the # learning rate progress, this keyword can be used to specify # a custom logged name "name": None, }
When there are schedulers in which the
.step()
method is conditioned on a value, such as thetorch.optim.lr_scheduler.ReduceLROnPlateau
scheduler, Lightning requires that thelr_scheduler_config
contains the keyword"monitor"
set to the metric name that the scheduler should be conditioned on.Metrics can be made available to monitor by simply logging it using
self.log('metric_to_track', metric_val)
in yourLightningModule
.Note
The
frequency
value specified in a dict along with theoptimizer
key is an int corresponding to the number of sequential batches optimized with the specific optimizer. It should be given to none or to all of the optimizers. There is a difference between passing multiple optimizers in a list, and passing multiple optimizers in dictionaries with a frequency of 1:In the former case, all optimizers will operate on the given batch in each optimization step.
In the latter, only one optimizer will operate on the given batch at every step.
This is different from the
frequency
value specified in thelr_scheduler_config
mentioned above.def configure_optimizers(self): optimizer_one = torch.optim.SGD(self.model.parameters(), lr=0.01) optimizer_two = torch.optim.SGD(self.model.parameters(), lr=0.01) return [ {"optimizer": optimizer_one, "frequency": 5}, {"optimizer": optimizer_two, "frequency": 10}, ]
In this example, the first optimizer will be used for the first 5 steps, the second optimizer for the next 10 steps and that cycle will continue. If an LR scheduler is specified for an optimizer using the
lr_scheduler
key in the above dict, the scheduler will only be updated when its optimizer is being used.Examples:
# most cases. no learning rate scheduler def configure_optimizers(self): return Adam(self.parameters(), lr=1e-3) # multiple optimizer case (e.g.: GAN) def configure_optimizers(self): gen_opt = Adam(self.model_gen.parameters(), lr=0.01) dis_opt = Adam(self.model_dis.parameters(), lr=0.02) return gen_opt, dis_opt # example with learning rate schedulers def configure_optimizers(self): gen_opt = Adam(self.model_gen.parameters(), lr=0.01) dis_opt = Adam(self.model_dis.parameters(), lr=0.02) dis_sch = CosineAnnealing(dis_opt, T_max=10) return [gen_opt, dis_opt], [dis_sch] # example with step-based learning rate schedulers # each optimizer has its own scheduler def configure_optimizers(self): gen_opt = Adam(self.model_gen.parameters(), lr=0.01) dis_opt = Adam(self.model_dis.parameters(), lr=0.02) gen_sch = { 'scheduler': ExponentialLR(gen_opt, 0.99), 'interval': 'step' # called after each training step } dis_sch = CosineAnnealing(dis_opt, T_max=10) # called every epoch return [gen_opt, dis_opt], [gen_sch, dis_sch] # example with optimizer frequencies # see training procedure in `Improved Training of Wasserstein GANs`, Algorithm 1 # https://arxiv.org/abs/1704.00028 def configure_optimizers(self): gen_opt = Adam(self.model_gen.parameters(), lr=0.01) dis_opt = Adam(self.model_dis.parameters(), lr=0.02) n_critic = 5 return ( {'optimizer': dis_opt, 'frequency': n_critic}, {'optimizer': gen_opt, 'frequency': 1} )
Note
Some things to know:
Lightning calls
.backward()
and.step()
on each optimizer as needed.If learning rate scheduler is specified in
configure_optimizers()
with key"interval"
(default “epoch”) in the scheduler configuration, Lightning will call the scheduler’s.step()
method automatically in case of automatic optimization.If you use 16-bit precision (
precision=16
), Lightning will automatically handle the optimizers.If you use multiple optimizers,
training_step()
will have an additionaloptimizer_idx
parameter.If you use
torch.optim.LBFGS
, Lightning handles the closure function automatically for you.If you use multiple optimizers, gradients will be calculated only for the parameters of current optimizer at each training step.
If you need to control how often those optimizers step or override the default
.step()
schedule, override theoptimizer_step()
hook.
- distance_from_training()
- get_test_dataset()
- get_training_dataset()
- is_within_domain()
- learning_curve_train = []
- learning_curve_val = []
- load_training(path)
- save_training(path)
- training_epoch_end(outputs)
Called at the end of the training epoch with the outputs of all training steps. Use this in case you need to do something with all the outputs returned by
training_step()
.# the pseudocode for these calls train_outs = [] for train_batch in train_data: out = training_step(train_batch) train_outs.append(out) training_epoch_end(train_outs)
- Parameters
outputs – List of outputs you defined in
training_step()
. If there are multiple optimizers or when usingtruncated_bptt_steps > 0
, the lists have the dimensions (n_batches, tbptt_steps, n_optimizers). Dimensions of length 1 are squeezed.- Returns
None
Note
If this method is not overridden, this won’t be called.
def training_epoch_end(self, training_step_outputs): # do something with all training_step outputs for out in training_step_outputs: ...
- training_step(batch, batch_idx)
Here you compute and return the training loss and some additional metrics for e.g. the progress bar or logger.
- Parameters
batch (
Tensor
| (Tensor
, …) | [Tensor
, …]) – The output of yourDataLoader
. A tensor, tuple or list.batch_idx (
int
) – Integer displaying index of this batchoptimizer_idx (
int
) – When using multiple optimizers, this argument will also be present.hiddens (
Any
) – Passed in if :paramref:`~pytorch_lightning.core.module.LightningModule.truncated_bptt_steps` > 0.
- Returns
Any of.
Tensor
- The loss tensordict
- A dictionary. Can include any keys, but must include the key'loss'
None
- Training will skip to the next batch. This is only for automatic optimization.This is not supported for multi-GPU, TPU, IPU, or DeepSpeed.
In this step you’d normally do the forward pass and calculate the loss for a batch. You can also do fancier things like multiple forward passes or something model specific.
Example:
def training_step(self, batch, batch_idx): x, y, z = batch out = self.encoder(x) loss = self.loss(out, x) return loss
If you define multiple optimizers, this step will be called with an additional
optimizer_idx
parameter.# Multiple optimizers (e.g.: GANs) def training_step(self, batch, batch_idx, optimizer_idx): if optimizer_idx == 0: # do training_step with encoder ... if optimizer_idx == 1: # do training_step with decoder ...
If you add truncated back propagation through time you will also get an additional argument with the hidden states of the previous step.
# Truncated back-propagation through time def training_step(self, batch, batch_idx, hiddens): # hiddens are the hidden states from the previous truncated backprop step out, hiddens = self.lstm(data, hiddens) loss = ... return {"loss": loss, "hiddens": hiddens}
Note
The loss value shown in the progress bar is smoothed (averaged) over the last values, so it differs from the actual loss returned in train/validation step.
- validation_epoch_end(outputs)
Called at the end of the validation epoch with the outputs of all validation steps.
# the pseudocode for these calls val_outs = [] for val_batch in val_data: out = validation_step(val_batch) val_outs.append(out) validation_epoch_end(val_outs)
- Parameters
outputs – List of outputs you defined in
validation_step()
, or if there are multiple dataloaders, a list containing a list of outputs for each dataloader.- Returns
None
Note
If you didn’t define a
validation_step()
, this won’t be called.Examples
With a single dataloader:
def validation_epoch_end(self, val_step_outputs): for out in val_step_outputs: ...
With multiple dataloaders, outputs will be a list of lists. The outer list contains one entry per dataloader, while the inner list contains the individual outputs of each validation step for that dataloader.
def validation_epoch_end(self, outputs): for dataloader_output_result in outputs: dataloader_outs = dataloader_output_result.dataloader_i_outputs self.log("final_metric", final_value)
- validation_step(batch, batch_idx)
Operates on a single batch of data from the validation set. In this step you’d might generate examples or calculate anything of interest like accuracy.
# the pseudocode for these calls val_outs = [] for val_batch in val_data: out = validation_step(val_batch) val_outs.append(out) validation_epoch_end(val_outs)
- Parameters
batch – The output of your
DataLoader
.batch_idx – The index of this batch.
dataloader_idx – The index of the dataloader that produced this batch. (only if multiple val dataloaders used)
- Returns
Any object or value
None
- Validation will skip to the next batch
# pseudocode of order val_outs = [] for val_batch in val_data: out = validation_step(val_batch) if defined("validation_step_end"): out = validation_step_end(out) val_outs.append(out) val_outs = validation_epoch_end(val_outs)
# if you have one val dataloader: def validation_step(self, batch, batch_idx): ... # if you have multiple val dataloaders: def validation_step(self, batch, batch_idx, dataloader_idx=0): ...
Examples:
# CASE 1: A single validation dataset def validation_step(self, batch, batch_idx): x, y = batch # implement your own out = self(x) loss = self.loss(out, y) # log 6 example images # or generated text... or whatever sample_imgs = x[:6] grid = torchvision.utils.make_grid(sample_imgs) self.logger.experiment.add_image('example_images', grid, 0) # calculate acc labels_hat = torch.argmax(out, dim=1) val_acc = torch.sum(y == labels_hat).item() / (len(y) * 1.0) # log the outputs! self.log_dict({'val_loss': loss, 'val_acc': val_acc})
If you pass in multiple val dataloaders,
validation_step()
will have an additional argument. We recommend setting the default value of 0 so that you can quickly switch between single and multiple dataloaders.# CASE 2: multiple validation dataloaders def validation_step(self, batch, batch_idx, dataloader_idx=0): # dataloader_idx tells you which dataset this is. ...
Note
If you don’t need to validate you don’t need to implement this method.
Note
When the
validation_step()
is called, the model has been put in eval mode and PyTorch gradients have been disabled. At the end of validation, the model goes back to training mode and gradients are enabled.
- class glasspy.predict.base.MTL(hparams: Dict[str, Any])
Bases:
MLP
Base class for creating Multi-task Learning NN.
- Parameters
hparams –
Dictionary with the hyperparemeters of the network. The possible parameters are: + “n_features”: number of input features (required). Must be a positive
integer.
”num_layers”: number of hidden layers (defaults to 1). Must be a positive integer.
”layer_n_size”: number of neurons in layer n (replace n for an integer starting at 1, defaults to 10). Must be a positive integer.
”layer_n_activation”: activation function of layer n (replace n for an integer starting at 1, defaults to Tanh). Available values are [“Tanh”, “Sigmoid”, “ReLU”, “LeakyReLU”, “SELU”, “GELU”, “ELU”, “PReLU”, “SiLU”, “Mish”, “Softplus”, “Linear”].
”layer_n_dropout”: dropout of layer n (replace n for an integer starting at 1, defaults to False meaning no dropout). Any value between 0 and 1 (or False) is permitted.
”layer_n_batchnorm”: True will use batch normalization in layer n, False will not use batch normalization in layer n (replace n for an integer starting at 1, defaults to False meaning no batch normalization).
”loss”: loss function to use for the backpropagation algorithm (defaults to mse). Use mse for mean squared error loss (L2) or huber for a smooth L1 loss.
”optimizer”: optimizer algorithm to use (defaults SGD). Use SGD for stochastic gradient descend, Adam for Adam, or AdamW for weighted Adam.
”lr”: optimizer learning rate (defaults to 1e-4 if optimizer is SGD or 1e-3 if optimizer is Adam or AdamW).
”momentum”: momentum to use when optmizer is SGD (defaults to 0).
”optimizer_Adam_eps”: eps to use for Adam or AdamW optimizers (defaults to 1e-8).
- Raises
NotImplementedError – When the selected hyperparameters is not one of the permited values.
- training_step(batch, batch_idx)
Here you compute and return the training loss and some additional metrics for e.g. the progress bar or logger.
- Parameters
batch (
Tensor
| (Tensor
, …) | [Tensor
, …]) – The output of yourDataLoader
. A tensor, tuple or list.batch_idx (
int
) – Integer displaying index of this batchoptimizer_idx (
int
) – When using multiple optimizers, this argument will also be present.hiddens (
Any
) – Passed in if :paramref:`~pytorch_lightning.core.module.LightningModule.truncated_bptt_steps` > 0.
- Returns
Any of.
Tensor
- The loss tensordict
- A dictionary. Can include any keys, but must include the key'loss'
None
- Training will skip to the next batch. This is only for automatic optimization.This is not supported for multi-GPU, TPU, IPU, or DeepSpeed.
In this step you’d normally do the forward pass and calculate the loss for a batch. You can also do fancier things like multiple forward passes or something model specific.
Example:
def training_step(self, batch, batch_idx): x, y, z = batch out = self.encoder(x) loss = self.loss(out, x) return loss
If you define multiple optimizers, this step will be called with an additional
optimizer_idx
parameter.# Multiple optimizers (e.g.: GANs) def training_step(self, batch, batch_idx, optimizer_idx): if optimizer_idx == 0: # do training_step with encoder ... if optimizer_idx == 1: # do training_step with decoder ...
If you add truncated back propagation through time you will also get an additional argument with the hidden states of the previous step.
# Truncated back-propagation through time def training_step(self, batch, batch_idx, hiddens): # hiddens are the hidden states from the previous truncated backprop step out, hiddens = self.lstm(data, hiddens) loss = ... return {"loss": loss, "hiddens": hiddens}
Note
The loss value shown in the progress bar is smoothed (averaged) over the last values, so it differs from the actual loss returned in train/validation step.
- validation_step(batch, batch_idx)
Operates on a single batch of data from the validation set. In this step you’d might generate examples or calculate anything of interest like accuracy.
# the pseudocode for these calls val_outs = [] for val_batch in val_data: out = validation_step(val_batch) val_outs.append(out) validation_epoch_end(val_outs)
- Parameters
batch – The output of your
DataLoader
.batch_idx – The index of this batch.
dataloader_idx – The index of the dataloader that produced this batch. (only if multiple val dataloaders used)
- Returns
Any object or value
None
- Validation will skip to the next batch
# pseudocode of order val_outs = [] for val_batch in val_data: out = validation_step(val_batch) if defined("validation_step_end"): out = validation_step_end(out) val_outs.append(out) val_outs = validation_epoch_end(val_outs)
# if you have one val dataloader: def validation_step(self, batch, batch_idx): ... # if you have multiple val dataloaders: def validation_step(self, batch, batch_idx, dataloader_idx=0): ...
Examples:
# CASE 1: A single validation dataset def validation_step(self, batch, batch_idx): x, y = batch # implement your own out = self(x) loss = self.loss(out, y) # log 6 example images # or generated text... or whatever sample_imgs = x[:6] grid = torchvision.utils.make_grid(sample_imgs) self.logger.experiment.add_image('example_images', grid, 0) # calculate acc labels_hat = torch.argmax(out, dim=1) val_acc = torch.sum(y == labels_hat).item() / (len(y) * 1.0) # log the outputs! self.log_dict({'val_loss': loss, 'val_acc': val_acc})
If you pass in multiple val dataloaders,
validation_step()
will have an additional argument. We recommend setting the default value of 0 so that you can quickly switch between single and multiple dataloaders.# CASE 2: multiple validation dataloaders def validation_step(self, batch, batch_idx, dataloader_idx=0): # dataloader_idx tells you which dataset this is. ...
Note
If you don’t need to validate you don’t need to implement this method.
Note
When the
validation_step()
is called, the model has been put in eval mode and PyTorch gradients have been disabled. At the end of validation, the model goes back to training mode and gradients are enabled.
- class glasspy.predict.base.Predict(**kwargs)
Bases:
ABC
Base class for GlassPy predictors.
- static MAE(y_true: ndarray, y_pred: ndarray) float
Computes the mean absolute error.
- Parameters
y_true – Array with the true values of y. Can be 1D or 2D.
y_pred – Aray with the predicted values of y. Can be 1D or 2D.
- Returns
The mean absolute error. Will be 1D if the input arrays are 2D. Will be a scalar otherwise.
- static MSE(y_true: ndarray, y_pred: ndarray) float
Computes the mean squared error.
- Parameters
y_true – Array with the true values of y. Can be 1D or 2D.
y_pred – Aray with the predicted values of y. Can be 1D or 2D.
- Returns
The mean squared error. Will be 1D if the input arrays are 2D. Will be a scalar otherwise.
- static MedAE(y_true: ndarray, y_pred: ndarray) float
Computes the median absolute error.
- Parameters
y_true – Array with the true values of y. Can be 1D or 2D.
y_pred – Aray with the predicted values of y. Can be 1D or 2D.
- Returns
The median absolute error. Will be 1D if the input arrays are 2D. Will be a scalar otherwise.
- static PercAE(y_true: ndarray, y_pred: ndarray, q=75) float
Computes the percentile absolute error.
- Parameters
y_true – Array with the true values of y. Can be 1D or 2D.
y_pred – Aray with the predicted values of y. Can be 1D or 2D.
q – Percentile to compute.
- Returns
The percentile absolute error. Will be 1D if the input arrays are 2D. Will be a scalar otherwise.
- static R2(y_true: ndarray, y_pred: ndarray, one_param: bool = True) float
Computes the coefficient of determination.
- Parameters
y_true – 1D array with the true values of y.
y_pred – 1D array with the predicted values of y.
one_param – Determines the relationship between y_true and y_pred. If ´True´ then it is a relationship with one parameter (y_true = y_pred * c_0 + error). If ´False´ then it is a relationship with two parameters (y_true = y_pred * c_0 + c_1 + error). In most of regression problems, the first case is desired.
- Returns
The coefficient of determination.
- static RD(y_true: ndarray, y_pred: ndarray) float
Computes the relative deviation.
- Parameters
y_true – 1D array with the true values of y.
y_pred – 1D array with the predicted values of y.
- Returns
The relative deviation.
- static RMSE(y_true: ndarray, y_pred: ndarray) float
Computes the root mean squared error.
- Parameters
y_true – Array with the true values of y. Can be 1D or 2D.
y_pred – Aray with the predicted values of y. Can be 1D or 2D.
- Returns
The root mean squared error. Will be 1D if the input arrays are 2D. Will be a scalar otherwise.
- static RRMSE(y_true: ndarray, y_pred: ndarray) float
Computes the relative root mean squared error.
- Parameters
y_true – 1D array with the true values of y.
y_pred – 1D array with the predicted values of y.
- Returns
The relative root mean squared error.
- abstract property domain
- abstract get_test_dataset()
- abstract get_training_dataset()
- abstract is_within_domain()
- abstract predict()
glasspy.predict.models module
- class glasspy.predict.models.GlassNet(multihead=True, loadrf=False)
Bases:
MTL
Multi-task neural network for predicting glass properties.
- absolute_features = [('num_oxistates', 'max'), ('NUnfilled', 'min'), ('NdUnfilled', 'max'), ('NdValence', 'max'), ('NfUnfilled', 'sum'), ('NfValence', 'sum'), ('NpUnfilled', 'sum'), ('NpUnfilled', 'max'), ('NpValence', 'max'), ('NsUnfilled', 'sum'), ('NsValence', 'min'), ('nvalence', 'max'), ('vdw_radius_uff', 'max'), ('atomic_radius_rahm', 'max'), ('GSbandgap', 'min'), ('GSestFCClatcnt', 'std1'), ('GSmagmom', 'sum'), ('en_Sanderson', 'max'), ('en_Tardini_Organov', 'min'), ('zeff', 'std1'), ('boiling_point', 'std1'), ('FusionEnthalpy', 'max')]
- static citation(bibtex: bool = False) str
- element_features = ['Ag', 'Al', 'As', 'B', 'Ba', 'Be', 'Bi', 'Br', 'C', 'Ca', 'Cd', 'Ce', 'Cl', 'Co', 'Cr', 'Cs', 'Cu', 'Dy', 'Er', 'Eu', 'Fe', 'Ga', 'Gd', 'Ge', 'H', 'Hf', 'Hg', 'Ho', 'I', 'In', 'K', 'La', 'Li', 'Lu', 'Mg', 'Mn', 'Mo', 'N', 'Na', 'Nb', 'Nd', 'Ni', 'P', 'Pb', 'Pr', 'Rb', 'S', 'Sb', 'Sc', 'Se', 'Sm', 'Sn', 'Sr', 'Ta', 'Tb', 'Te', 'Ti', 'Tl', 'V', 'W', 'Y', 'Yb', 'Zn', 'Zr']
- featurizer(composition: Union[str, List[float], List[List[float]], ndarray, Dict[str, float], Dict[str, List[float]], Dict[str, ndarray], DataFrame, ChemArray], input_cols: List[str] = [], auto_scale: bool = True, return_cols: bool = False) ndarray
Compute the features used for input in GlassNet.
- Parameters
composition – Any composition-like object.
input_cols – List of strings representing the chemical entities related to each column of composition. Necessary only when composition is a list or array, ignored otherwise.
auto_scale – If True, then the features are automatically scaled and ready to use with GlassNet. If False, then the features will not be scaled and should not be used to make predictions with Glassnet. Default value is True.
return_cols – If True, then a list with the name of the feature columns is also returned.
- Returns
Array with the computed features. Optionally, the name of the coulmns can also be returned if return_cols is True.
- forward(x)
Method used for training the neural network.
Consider using the other methods for prediction.
- Parameters
x – Feature tensor.
- Returns
Tensor with the predictions.
- get_test_dataset()
Gets the holdout dataset used in the GlassNet paper.
- Returns
DataFrame containing the holdout dataset used in the GlassNet paper.
- get_training_dataset()
Gets the training dataset used in the GlassNet paper.
- Returns
DataFrame containing the training dataset used in the GlassNet paper.
- hparams = {'batch_size': 256, 'layer_1_activation': 'Softplus', 'layer_1_batchnorm': True, 'layer_1_dropout': 0.08118311665886885, 'layer_1_size': 280, 'layer_2_activation': 'Mish', 'layer_2_batchnorm': True, 'layer_2_dropout': 0.0009472891190852595, 'layer_2_size': 500, 'layer_3_activation': 'LeakyReLU', 'layer_3_batchnorm': False, 'layer_3_dropout': 0.08660291424886811, 'layer_3_size': 390, 'layer_4_activation': 'PReLU', 'layer_4_batchnorm': False, 'layer_4_dropout': 0.16775047518280012, 'layer_4_size': 480, 'loss': 'mse', 'lr': 1.3252600209332101e-05, 'max_epochs': 2000, 'n_features': 98, 'n_targets': 85, 'num_layers': 4, 'optimizer': 'AdamW', 'patience': 27}
- predict(composition: Union[str, List[float], List[List[float]], ndarray, Dict[str, float], Dict[str, List[float]], Dict[str, ndarray], DataFrame, ChemArray], input_cols: List[str] = [], return_dataframe: bool = True)
Makes prediction of properties using GlassNet.
- Parameters
composition – Any composition-like object.
input_cols – List of strings representing the chemical entities related to each column of composition. Necessary only when composition is a list or array, ignored otherwise.
return_dataframe – If True, then returns a pandas DataFrame, else returns an array. Default value is True.
- Returns
Predicted values of properties. Will be a DataFrame if return_dataframe is True, otherwise will be an array.
- predict_log10_viscosity(T: Union[float, List[float], ndarray], composition: Union[str, List[float], List[List[float]], ndarray, Dict[str, float], Dict[str, List[float]], Dict[str, ndarray], DataFrame, ChemArray], input_cols: List[str] = [], log_visc_limit: float = 12, columns: list = ['T1', 'T2', 'T3', 'T4', 'T5', 'T6', 'T7', 'T8', 'T9', 'T10', 'T11', 'T12', 'Viscosity773K', 'Viscosity873K', 'Viscosity973K', 'Viscosity1073K', 'Viscosity1173K', 'Viscosity1273K', 'Viscosity1373K', 'Viscosity1473K', 'Viscosity1573K', 'Viscosity1673K', 'Viscosity1773K', 'Viscosity1873K', 'Viscosity2073K', 'Viscosity2273K', 'Tg', 'TLittletons'], n_points_low: int = 10, return_parameters: bool = False)
Predict the base-10 logarithm of viscosity (viscosity in Pa.s).
This method performs a robust non-linear regression of the MYEGA equation on viscosity data predicted by GlassNet. If the regression cannot be performed, the predicted viscosity will be NaN.
- Parameters
T – Temperature (in Kelvin) to compute the viscosity. If this is a numpy array, it must have only one dimension.
composition – Any composition-like object.
input_cols – List of strings representing the chemical entities related to each column of composition. Necessary only when composition is a list or array, ignored otherwise.
log_visc_limit – Maximum value of log10(viscosity) (viscosity in Pa.s) that is acceptable for the regression. Predictions of values greater than 12 for the log10 of viscosity are prone to higher errors. Default value is 12.
columns – Which targets of GlassNet that will be considered to build the table.
n_points_low – Number of viscosity data points to consider to guess the fragility index. Must be a positive integer. Default value is 10.
return_parameters – If True, also returns the viscosity parameters array.
- Returns
Numpy array of the predicted base-10 logarithm of viscosity :param Numpy array of the viscosity parameters. The first column is the: :param asymptotic viscosity: :type asymptotic viscosity: in base-10 logarithm of Pa.s :param column is the temperature where the viscosity is 10^12 Pa.s; and the: :param third column is the fragility index. Only returned if: :param return_parameters is True.:
- Return type
log_10_viscosity
- predict_viscosity(T: Union[float, List[float], ndarray], composition: Union[str, List[float], List[List[float]], ndarray, Dict[str, float], Dict[str, List[float]], Dict[str, ndarray], DataFrame, ChemArray], input_cols: List[str] = [], log_visc_limit: float = 12, columns: list = ['T1', 'T2', 'T3', 'T4', 'T5', 'T6', 'T7', 'T8', 'T9', 'T10', 'T11', 'T12', 'Viscosity773K', 'Viscosity873K', 'Viscosity973K', 'Viscosity1073K', 'Viscosity1173K', 'Viscosity1273K', 'Viscosity1373K', 'Viscosity1473K', 'Viscosity1573K', 'Viscosity1673K', 'Viscosity1773K', 'Viscosity1873K', 'Viscosity2073K', 'Viscosity2273K', 'Tg', 'TLittletons'], n_points_low: int = 10, return_parameters: bool = False)
Predict the viscosity in Pa.s.
This method performs a robust non-linear regression of the MYEGA equation on viscosity data predicted by GlassNet. If the regression cannot be performed, the predicted viscosity will be NaN.
- Parameters
T – Temperature (in Kelvin) to compute the viscosity. If this is a numpy array, it must have only one dimension.
composition – Any composition-like object.
input_cols – List of strings representing the chemical entities related to each column of composition. Necessary only when composition is a list or array, ignored otherwise.
log_visc_limit – Maximum value of log10(viscosity) (viscosity in Pa.s) that is acceptable for the regression. Predictions of values greater than 12 for the log10 of viscosity are prone to higher errors. Default value is 12.
columns – Which targets of GlassNet that will be considered to perform the regression.
n_points_low – Number of viscosity data points to consider to guess the fragility index for the regression. Must be a positive integer. Default value is 10.
return_parameters – If True, also returns the viscosity parameters array.
- Returns
Numpy array of the predicted viscosity in Pa.s. :param Numpy array of the viscosity parameters. The first column is the: :param asymptotic viscosity: :type asymptotic viscosity: in base-10 logarithm of Pa.s :param column is the temperature where the viscosity is 10^12 Pa.s; and the: :param third column is the fragility index. Only returned if: :param return_parameters is True.:
- Return type
viscosity
- scaler_x_file = PosixPath('/data/Git/Work/glasspy/glasspy/predict/models/GlassNet_scaler_x.joblib')
- scaler_y_file = PosixPath('/data/Git/Work/glasspy/glasspy/predict/models/GlassNet_scaler_y.joblib')
- target_trans = {'AbbeNum': 36, 'CTE328K': 64, 'CTE373K': 65, 'CTE433K': 66, 'CTE483K': 67, 'CTE623K': 68, 'CTEbelowTg': 63, 'Cp1073K': 72, 'Cp1273K': 73, 'Cp1473K': 74, 'Cp1673K': 75, 'Cp293K': 69, 'Cp473K': 70, 'Cp673K': 71, 'CrystallizationOnset': 79, 'CrystallizationPeak': 78, 'Density1073K': 57, 'Density1273K': 58, 'Density1473K': 59, 'Density1673K': 60, 'Density293K': 56, 'MaxGrowthVelocity': 77, 'MeanDispersion': 40, 'Microhardness': 54, 'Permittivity': 41, 'PoissonRatio': 55, 'RefractiveIndex': 37, 'RefractiveIndexHigh': 39, 'RefractiveIndexLow': 38, 'Resistivity1073K': 48, 'Resistivity1273K': 49, 'Resistivity1473K': 50, 'Resistivity1673K': 51, 'Resistivity273K': 44, 'Resistivity373K': 45, 'Resistivity423K': 46, 'Resistivity573K': 47, 'ShearModulus': 53, 'SurfaceTension1173K': 81, 'SurfaceTension1473K': 82, 'SurfaceTension1573K': 83, 'SurfaceTension1673K': 84, 'SurfaceTensionAboveTg': 80, 'T0': 0, 'T1': 1, 'T10': 10, 'T11': 11, 'T12': 12, 'T2': 2, 'T3': 3, 'T4': 4, 'T5': 5, 'T6': 6, 'T7': 7, 'T8': 8, 'T9': 9, 'TAnnealing': 32, 'TLittletons': 31, 'TMaxGrowthVelocity': 76, 'TangentOfLossAngle': 42, 'TdilatometricSoftening': 35, 'Tg': 28, 'ThermalConductivity': 61, 'ThermalShockRes': 62, 'Tliquidus': 30, 'Tmelt': 29, 'TresistivityIs1MOhm.m': 43, 'Tsoft': 34, 'Tstrain': 33, 'Viscosity1073K': 16, 'Viscosity1173K': 17, 'Viscosity1273K': 18, 'Viscosity1373K': 19, 'Viscosity1473K': 20, 'Viscosity1573K': 21, 'Viscosity1673K': 22, 'Viscosity1773K': 23, 'Viscosity1873K': 24, 'Viscosity2073K': 25, 'Viscosity2273K': 26, 'Viscosity2473K': 27, 'Viscosity773K': 13, 'Viscosity873K': 14, 'Viscosity973K': 15, 'YoungModulus': 52}
- targets = ['T0', 'T1', 'T2', 'T3', 'T4', 'T5', 'T6', 'T7', 'T8', 'T9', 'T10', 'T11', 'T12', 'Viscosity773K', 'Viscosity873K', 'Viscosity973K', 'Viscosity1073K', 'Viscosity1173K', 'Viscosity1273K', 'Viscosity1373K', 'Viscosity1473K', 'Viscosity1573K', 'Viscosity1673K', 'Viscosity1773K', 'Viscosity1873K', 'Viscosity2073K', 'Viscosity2273K', 'Viscosity2473K', 'Tg', 'Tmelt', 'Tliquidus', 'TLittletons', 'TAnnealing', 'Tstrain', 'Tsoft', 'TdilatometricSoftening', 'AbbeNum', 'RefractiveIndex', 'RefractiveIndexLow', 'RefractiveIndexHigh', 'MeanDispersion', 'Permittivity', 'TangentOfLossAngle', 'TresistivityIs1MOhm.m', 'Resistivity273K', 'Resistivity373K', 'Resistivity423K', 'Resistivity573K', 'Resistivity1073K', 'Resistivity1273K', 'Resistivity1473K', 'Resistivity1673K', 'YoungModulus', 'ShearModulus', 'Microhardness', 'PoissonRatio', 'Density293K', 'Density1073K', 'Density1273K', 'Density1473K', 'Density1673K', 'ThermalConductivity', 'ThermalShockRes', 'CTEbelowTg', 'CTE328K', 'CTE373K', 'CTE433K', 'CTE483K', 'CTE623K', 'Cp293K', 'Cp473K', 'Cp673K', 'Cp1073K', 'Cp1273K', 'Cp1473K', 'Cp1673K', 'TMaxGrowthVelocity', 'MaxGrowthVelocity', 'CrystallizationPeak', 'CrystallizationOnset', 'SurfaceTensionAboveTg', 'SurfaceTension1173K', 'SurfaceTension1473K', 'SurfaceTension1573K', 'SurfaceTension1673K']
- training_file = PosixPath('/data/Git/Work/glasspy/glasspy/predict/models/GlassNet.p')
- training_file_mh = PosixPath('/data/Git/Work/glasspy/glasspy/predict/models/GlassNetMH.p')
- viscosity_parameters(composition: Union[str, List[float], List[List[float]], ndarray, Dict[str, float], Dict[str, List[float]], Dict[str, ndarray], DataFrame, ChemArray], input_cols: List[str] = [], log_visc_limit: float = 12, columns: list = ['T1', 'T2', 'T3', 'T4', 'T5', 'T6', 'T7', 'T8', 'T9', 'T10', 'T11', 'T12', 'Viscosity773K', 'Viscosity873K', 'Viscosity973K', 'Viscosity1073K', 'Viscosity1173K', 'Viscosity1273K', 'Viscosity1373K', 'Viscosity1473K', 'Viscosity1573K', 'Viscosity1673K', 'Viscosity1773K', 'Viscosity1873K', 'Viscosity2073K', 'Viscosity2273K', 'Tg', 'TLittletons'], n_points_low: int = 10, return_dataframe: bool = True)
Predict the MYEGA viscosity parameters.
This method performs a robust non-linear regression of the MYEGA equation on viscosity data predicted by GlassNet. If the regression cannot be performed, the parameters returned will be NaN.
- Parameters
composition – Any composition-like object.
input_cols – List of strings representing the chemical entities related to each column of composition. Necessary only when composition is a list or array, ignored otherwise.
log_visc_limit – Maximum value of log10(viscosity) (viscosity in Pa.s) that is acceptable. Predictions of values greater than 12 for the log10 of viscosity are prone to higher errors. Default value is 12.
columns – Which targets of GlassNet that will be considered to build the table.
n_points_low – Number of viscosity data points to consider to guess the fragility index. Must be a positive integer. Default value is 10.
return_dataframe – If True, then returns a pandas DataFrame, else returns an array. Default value is True.
- Returns
Numpy array or DataFrame of the viscosity parameters. The first column is the asymptotic viscosity (in base-10 logarithm of Pa.s); the second column is the temperature where the viscosity is 10^12 Pa.s; and the third column is the fragility index.
- Return type
parameters
- weighted_features = [('c6_gb', 'min'), ('ElectronAffinity', 'min'), ('NUnfilled', 'std1'), ('NdValence', 'min'), ('NfValence', 'min'), ('NpUnfilled', 'min'), ('NsUnfilled', 'min'), ('nvalence', 'max'), ('atomic_volume', 'min'), ('GSbandgap', 'min'), ('GSenergy_pa', 'max'), ('FusionEnthalpy', 'min')]
- class glasspy.predict.models.ViscNet
Bases:
_BaseViscNet
ViscNet predictor of viscosity and viscosity parameters.
ViscNet is a physics-informed neural network that has the MYEGA [1] viscosity equation embedded in it. See Ref. [2] for the original publication.
References
- [1] J.C. Mauro, Y. Yue, A.J. Ellison, P.K. Gupta, D.C. Allan, Viscosity of
glass-forming liquids., Proceedings of the National Academy of Sciences of the United States of America. 106 (2009) 19780–19784. https://doi.org/10.1073/pnas.0911705106.
- [2] D.R. Cassar, ViscNet: Neural network for predicting the fragility
index and the temperature-dependency of viscosity, Acta Materialia. 206 (2021) 116602. https://doi.org/10.1016/j.actamat.2020.116602. https://arxiv.org/abs/2007.03719
- absolute_features = [('ElectronAffinity', 'std1'), ('FusionEnthalpy', 'std1'), ('GSenergy_pa', 'std1'), ('GSmagmom', 'std1'), ('NdUnfilled', 'std1'), ('NfValence', 'std1'), ('NpUnfilled', 'std1'), ('atomic_radius_rahm', 'std1'), ('c6_gb', 'std1'), ('lattice_constant', 'std1'), ('mendeleev_number', 'std1'), ('num_oxistates', 'std1'), ('nvalence', 'std1'), ('vdw_radius_alvarez', 'std1'), ('vdw_radius_uff', 'std1'), ('zeff', 'std1')]
- featurizer(composition: Union[str, List[float], List[List[float]], ndarray, Dict[str, float], Dict[str, List[float]], Dict[str, ndarray], DataFrame, ChemArray], input_cols: List[str] = []) ndarray
Compute the chemical features used for viscosity prediction.
- Parameters
composition – Any composition like object.
input_cols – List of strings representing the chemical entities related to each column of composition. Necessary only when composition is a list or array, ignored otherwise.
- Returns
Array with the computed chemical features
- hparams = {'batch_size': 64, 'layer_1_activation': 'ReLU', 'layer_1_batchnorm': False, 'layer_1_dropout': 0.07942161101271952, 'layer_1_size': 192, 'layer_2_activation': 'Tanh', 'layer_2_batchnorm': False, 'layer_2_dropout': 0.05371454289414608, 'layer_2_size': 48, 'loss': 'mse', 'lr': 0.0011695226458761677, 'max_epochs': 500, 'n_features': 35, 'num_layers': 2, 'optimizer': 'AdamW', 'patience': 9}
- log_viscosity_fun(T, log_eta_inf, Tg, m)
Computes the base-10 logarithm of viscosity using the MYEGA equation.
- parameters_range = {'Tg': [400, 1400], 'log_eta_inf': [-18, 5], 'm': [10, 130]}
- state_dict_path = PosixPath('/data/Git/Work/glasspy/glasspy/predict/models/ViscNet_SD.p')
- weighted_features = [('FusionEnthalpy', 'min'), ('GSbandgap', 'max'), ('GSmagmom', 'mean'), ('GSvolume_pa', 'max'), ('MiracleRadius', 'std1'), ('NValence', 'max'), ('NValence', 'min'), ('NdUnfilled', 'max'), ('NdValence', 'max'), ('NsUnfilled', 'max'), ('SpaceGroupNumber', 'max'), ('SpaceGroupNumber', 'min'), ('atomic_radius', 'max'), ('atomic_volume', 'max'), ('c6_gb', 'max'), ('c6_gb', 'min'), ('max_ionenergy', 'min'), ('num_oxistates', 'max'), ('nvalence', 'min')]
- x_mean = tensor([5.7542e+01, 2.2090e+01, 2.0236e+00, 3.6861e-02, 3.2621e-01, 1.4419e+00, 2.0165e+00, 3.4408e+01, 1.2353e+03, 1.4793e+00, 4.2045e+01, 8.4131e-01, 2.3045e+00, 4.7985e+01, 5.6984e+01, 1.1146e+00, 9.2186e-02, 2.1363e-01, 2.2581e-04, 5.8150e+00, 1.2964e+01, 3.7008e+00, 1.3743e-01, 1.8370e-02, 3.2303e-01, 7.1325e-02, 5.0019e+01, 4.3720e+00, 3.6446e+01, 8.4037e+00, 2.0281e+02, 7.5614e+00, 1.2259e+02, 6.7183e-01, 1.0508e-01])
- x_std = tensor([7.6421e+00, 4.7181e+00, 4.5828e-01, 1.6873e-01, 9.7033e-01, 2.7695e+00, 3.3153e-01, 6.4521e+00, 6.3392e+02, 4.0606e-01, 1.1777e+01, 2.8130e-01, 7.9214e-01, 7.5883e+00, 1.1335e+01, 2.8823e-01, 4.4787e-02, 1.1219e-01, 1.2392e-03, 1.1634e+00, 2.9514e+00, 4.7246e-01, 3.1958e-01, 8.8973e-02, 6.7548e-01, 6.2869e-02, 1.0004e+01, 2.7434e+00, 1.9245e+00, 3.4735e-01, 1.2475e+02, 3.2668e+00, 1.5287e+02, 7.3511e-02, 1.6188e-01])
- class glasspy.predict.models.ViscNetHuber
Bases:
ViscNet
ViscNet-Huber predictor of viscosity and viscosity parameters.
ViscNet-Huber is a physics-informed neural network that has the MYEGA [1] viscosity equation embedded in it. The difference between this model and ViscNet is the loss function: this model has a robust smooth-L1 loss function, while ViscNet has a MSE (L2) loss function. See Ref. [2] for the original publication.
References
- [1] J.C. Mauro, Y. Yue, A.J. Ellison, P.K. Gupta, D.C. Allan, Viscosity of
glass-forming liquids., Proceedings of the National Academy of Sciences of the United States of America. 106 (2009) 19780–19784. https://doi.org/10.1073/pnas.0911705106.
- [2] D.R. Cassar, ViscNet: Neural network for predicting the fragility
index and the temperature-dependency of viscosity, Acta Materialia. 206 (2021) 116602. https://doi.org/10.1016/j.actamat.2020.116602. https://arxiv.org/abs/2007.03719
- class glasspy.predict.models.ViscNetVFT
Bases:
ViscNet
ViscNet-VFT predictor of viscosity and viscosity parameters.
ViscNet-VFT is a physics-informed neural network that has the VFT [1-3] viscosity equation embedded in it. See Ref. [4] for the original publication.
References
- [1] H. Vogel, Das Temperatureabhängigketsgesetz der Viskosität von
Flüssigkeiten, Physikalische Zeitschrift. 22 (1921) 645–646.
- [2] G.S. Fulcher, Analysis of recent measurements of the viscosity of
glasses, Journal of the American Ceramic Society. 8 (1925) 339–355. https://doi.org/10.1111/j.1151-2916.1925.tb16731.x.
- [3] G. Tammann, W. Hesse, Die Abhängigkeit der Viscosität von der
Temperatur bie unterkühlten Flüssigkeiten, Z. Anorg. Allg. Chem. 156 (1926) 245–257. https://doi.org/10.1002/zaac.19261560121.
- [4] D.R. Cassar, ViscNet: Neural network for predicting the fragility
index and the temperature-dependency of viscosity, Acta Materialia. 206 (2021) 116602. https://doi.org/10.1016/j.actamat.2020.116602. https://arxiv.org/abs/2007.03719
- log_viscosity_fun(T, log_eta_inf, Tg, m)
Computes the base-10 logarithm of viscosity using the VFT equation.
- Reference:
- [1] H. Vogel, Das Temperatureabhängigketsgesetz der Viskosität von
Flüssigkeiten, Physikalische Zeitschrift. 22 (1921) 645–646.
- [2] G.S. Fulcher, Analysis of recent measurements of the viscosity of
glasses, Journal of the American Ceramic Society. 8 (1925) 339–355. https://doi.org/10.1111/j.1151-2916.1925.tb16731.x.
- [3] G. Tammann, W. Hesse, Die Abhängigkeit der Viscosität von der
Temperatur bie unterkühlten Flüssigkeiten, Z. Anorg. Allg. Chem. 156 (1926) 245–257. https://doi.org/10.1002/zaac.19261560121.