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Contents
Installation
Quick Start
Mathematical Backgrounds
Training Tasks —
colvarsfinder.core
Trajectory Data —
colvarsfinder.utils
Neural Networks —
colvarsfinder.nn
colvars-finder
Index
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Index
A
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B
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C
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D
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E
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F
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G
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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V
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W
A
AutoEncoder (class in colvarsfinder.nn)
AutoEncoderTask (class in colvarsfinder.core)
B
batch_size (colvarsfinder.core.TrainingTask attribute)
C
calc_weights() (in module colvarsfinder.utils)
colvar_model() (colvarsfinder.core.AutoEncoderTask method)
(colvarsfinder.core.EigenFunctionTask method)
(colvarsfinder.core.RegAutoEncoderTask method)
(colvarsfinder.core.TrainingTask method)
colvarsfinder.core
module
colvarsfinder.nn
module
colvarsfinder.utils
module
create_sequential_nn() (in module colvarsfinder.nn)
cvec (colvarsfinder.nn.RegModel attribute)
D
debug_mode (colvarsfinder.core.TrainingTask attribute)
decoder (colvarsfinder.nn.AutoEncoder attribute)
(colvarsfinder.nn.RegAutoEncoder attribute)
device (colvarsfinder.core.TrainingTask attribute)
dt (colvarsfinder.utils.WeightedTrajectory attribute)
E
eigen_funcs (colvarsfinder.nn.EigenFunctions attribute)
EigenFunctions (class in colvarsfinder.nn)
EigenFunctionTask (class in colvarsfinder.core)
encoded_dim (colvarsfinder.nn.AutoEncoder attribute)
(colvarsfinder.nn.RegAutoEncoder attribute)
(colvarsfinder.nn.RegModel attribute)
encoder (colvarsfinder.nn.AutoEncoder attribute)
(colvarsfinder.nn.RegAutoEncoder attribute)
(colvarsfinder.nn.RegModel attribute)
F
forward() (colvarsfinder.nn.AutoEncoder method)
(colvarsfinder.nn.EigenFunctions method)
(colvarsfinder.nn.RegAutoEncoder method)
(colvarsfinder.nn.RegModel method)
forward_ae() (colvarsfinder.nn.RegAutoEncoder method)
forward_reg() (colvarsfinder.nn.RegAutoEncoder method)
G
get_params_of_cv() (colvarsfinder.nn.AutoEncoder method)
(colvarsfinder.nn.EigenFunctions method)
(colvarsfinder.nn.RegAutoEncoder method)
get_reordered_eigenfunctions() (colvarsfinder.core.EigenFunctionTask method)
I
init_model_and_optimizer() (colvarsfinder.core.TrainingTask method)
integrate_md_langevin() (in module colvarsfinder.utils)
integrate_sde_overdamped() (in module colvarsfinder.utils)
K
k (colvarsfinder.core.TrainingTask attribute)
L
learning_rate (colvarsfinder.core.TrainingTask attribute)
load_model_filename (colvarsfinder.core.TrainingTask attribute)
loss_func() (colvarsfinder.core.EigenFunctionTask method)
loss_list (colvarsfinder.core.AutoEncoderTask attribute)
(colvarsfinder.core.EigenFunctionTask attribute)
(colvarsfinder.core.RegAutoEncoderTask attribute)
M
model (colvarsfinder.core.AutoEncoderTask attribute)
(colvarsfinder.core.EigenFunctionTask attribute)
(colvarsfinder.core.RegAutoEncoderTask attribute)
(colvarsfinder.core.TrainingTask attribute)
model_path (colvarsfinder.core.TrainingTask attribute)
module
colvarsfinder.core
colvarsfinder.nn
colvarsfinder.utils
N
n_frames (colvarsfinder.utils.WeightedTrajectory attribute)
num_epochs (colvarsfinder.core.TrainingTask attribute)
num_reg (colvarsfinder.nn.RegAutoEncoder attribute)
(colvarsfinder.nn.RegModel attribute)
O
optimizer (colvarsfinder.core.TrainingTask attribute)
optimizer_name (colvarsfinder.core.TrainingTask attribute)
P
plot_class (colvarsfinder.core.TrainingTask attribute)
plot_frequency (colvarsfinder.core.TrainingTask attribute)
preprocessing_layer (colvarsfinder.core.AutoEncoderTask attribute)
(colvarsfinder.core.EigenFunctionTask attribute)
(colvarsfinder.core.RegAutoEncoderTask attribute)
(colvarsfinder.core.TrainingTask attribute)
R
reg (colvarsfinder.nn.RegAutoEncoder attribute)
(colvarsfinder.nn.RegModel attribute)
reg_eigen_loss() (colvarsfinder.core.RegAutoEncoderTask method)
reg_enc_grad_loss() (colvarsfinder.core.RegAutoEncoderTask method)
reg_enc_norm_loss() (colvarsfinder.core.RegAutoEncoderTask method)
reg_enc_orthognal_loss() (colvarsfinder.core.RegAutoEncoderTask method)
reg_model() (colvarsfinder.core.RegAutoEncoderTask method)
RegAutoEncoder (class in colvarsfinder.nn)
RegAutoEncoderTask (class in colvarsfinder.core)
RegModel (class in colvarsfinder.nn)
S
save_model() (colvarsfinder.core.TrainingTask method)
save_model_every_step (colvarsfinder.core.TrainingTask attribute)
T
test_loss_df (colvarsfinder.core.AutoEncoderTask attribute)
(colvarsfinder.core.EigenFunctionTask attribute)
(colvarsfinder.core.RegAutoEncoderTask attribute)
test_ratio (colvarsfinder.core.TrainingTask attribute)
train() (colvarsfinder.core.AutoEncoderTask method)
(colvarsfinder.core.EigenFunctionTask method)
(colvarsfinder.core.RegAutoEncoderTask method)
(colvarsfinder.core.TrainingTask method)
train_loss_df (colvarsfinder.core.AutoEncoderTask attribute)
(colvarsfinder.core.EigenFunctionTask attribute)
(colvarsfinder.core.RegAutoEncoderTask attribute)
TrainingTask (class in colvarsfinder.core)
traj_obj (colvarsfinder.core.TrainingTask attribute)
trajectory (colvarsfinder.utils.WeightedTrajectory attribute)
V
verbose (colvarsfinder.core.TrainingTask attribute)
W
weighted_MSE_loss() (colvarsfinder.core.AutoEncoderTask method)
(colvarsfinder.core.RegAutoEncoderTask method)
WeightedTrajectory (class in colvarsfinder.utils)
weights (colvarsfinder.utils.WeightedTrajectory attribute)
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