ULaMDyn
0+untagged.27.g14c3b49.dirty
Getting Started:
Installation
Wrapper program
Tutorial:
Data curation
Source documentation:
ulamdyn package
ULaMDyn
»
Index
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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H
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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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U
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V
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X
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Z
A
aggregate_data() (in module ulamdyn.statistics)
align_geoms (ulamdyn.data_loader.GetCoords property)
all_grads (ulamdyn.data_loader.GetGradients attribute)
all_nacs (ulamdyn.data_loader.GetCouplings attribute)
angleconnectivity (ulamdyn.descriptors.ZMatrix attribute)
atom_labels (ulamdyn.kinetics.KineticEnergy attribute)
atom_mass (ulamdyn.kinetics.KineticEnergy attribute)
B
bootstrap() (in module ulamdyn.statistics)
build_dataframe() (ulamdyn.data_loader.GetCoords method)
(ulamdyn.data_loader.GetCouplings method)
(ulamdyn.data_loader.GetGradients method)
(ulamdyn.kinetics.KineticEnergy method)
(ulamdyn.kinetics.VibrationalSpectra method)
build_descriptor() (in module ulamdyn.interface)
(ulamdyn.descriptors.R2 method)
(ulamdyn.descriptors.ZMatrix method)
C
calc_all_trajs() (ulamdyn.kinetics.VibrationalSpectra method)
calc_avg_occupations() (in module ulamdyn.statistics)
calc_pdos() (ulamdyn.kinetics.VibrationalSpectra static method)
calc_per_atom() (ulamdyn.kinetics.KineticEnergy method)
calc_per_molecule() (ulamdyn.kinetics.KineticEnergy method)
Clustering (class in ulamdyn.unsup_models)
connectivity (ulamdyn.descriptors.ZMatrix attribute)
create_bootstrap_stats() (in module ulamdyn.statistics)
create_stats() (in module ulamdyn.statistics)
D
dataset (ulamdyn.data_loader.GetCoords attribute)
(ulamdyn.data_loader.GetProperties attribute)
datasets (ulamdyn.data_loader.GetCouplings attribute)
(ulamdyn.data_loader.GetGradients attribute)
dihedralconnectivity (ulamdyn.descriptors.ZMatrix attribute)
DimensionalityReduction (class in ulamdyn.unsup_models)
distancematrix (ulamdyn.descriptors.ZMatrix attribute)
E
energies (ulamdyn.kinetics.KineticEnergy attribute)
energies() (ulamdyn.data_loader.GetProperties method)
eq_xyz (ulamdyn.data_loader.GetCoords attribute)
export() (in module ulamdyn)
F
from_all_trajs() (ulamdyn.kinetics.GetVelocities class method)
from_dyn() (ulamdyn.data_loader.GetCoords method)
(ulamdyn.kinetics.GetVelocities method)
from_h5() (ulamdyn.data_loader.GetCoords static method)
(ulamdyn.data_loader.GetCouplings static method)
(ulamdyn.data_loader.GetGradients static method)
(ulamdyn.kinetics.GetVelocities method)
from_nxlog() (ulamdyn.data_loader.GetCouplings static method)
(ulamdyn.data_loader.GetGradients static method)
from_xyz() (ulamdyn.data_loader.GetCoords static method)
G
Geometries (class in ulamdyn.data_writer)
get_angle() (ulamdyn.descriptors.ZMatrix static method)
get_bending() (ulamdyn.descriptors.ZMatrix static method)
get_dihedral() (ulamdyn.descriptors.ZMatrix static method)
get_distance() (ulamdyn.descriptors.ZMatrix static method)
get_kinetic_energies() (in module ulamdyn.interface)
get_labels_masses() (in module ulamdyn.utilities)
get_num_atoms() (in module ulamdyn.utilities)
get_nx_version() (in module ulamdyn.utilities)
get_properties_data() (in module ulamdyn.interface)
get_traj_dirs() (in module ulamdyn.utilities)
GetCoords (class in ulamdyn.data_loader)
GetCouplings (class in ulamdyn.data_loader)
GetGradients (class in ulamdyn.data_loader)
GetProperties (class in ulamdyn.data_loader)
GetVelocities (class in ulamdyn.kinetics)
H
hierarchical() (ulamdyn.unsup_models.Clustering method)
I
isomap() (ulamdyn.unsup_models.DimensionalityReduction method)
K
KineticEnergy (class in ulamdyn.kinetics)
kmeans() (ulamdyn.unsup_models.Clustering method)
kpca() (ulamdyn.unsup_models.DimensionalityReduction method)
L
labels (ulamdyn.data_loader.GetCoords attribute)
M
main() (in module ulamdyn.run_analysis)
mcscf_coefs() (ulamdyn.data_loader.GetProperties method)
module
ulamdyn.data_loader
ulamdyn.data_writer
ulamdyn.descriptors
ulamdyn.interface
ulamdyn.kinetics
ulamdyn.run_analysis
ulamdyn.statistics
ulamdyn.unsup_models
ulamdyn.utilities
N
n_atoms (ulamdyn.kinetics.GetVelocities attribute)
(ulamdyn.kinetics.KineticEnergy attribute)
(ulamdyn.kinetics.VibrationalSpectra attribute)
nac_norm() (ulamdyn.data_loader.GetProperties method)
num_states (ulamdyn.data_loader.GetProperties attribute)
nx_version (ulamdyn.data_loader.GetProperties attribute)
O
oscillator_strength() (ulamdyn.data_loader.GetProperties method)
P
pca() (ulamdyn.unsup_models.DimensionalityReduction method)
populations() (ulamdyn.data_loader.GetProperties method)
R
R2 (class in ulamdyn.descriptors)
r2_descriptor (ulamdyn.descriptors.R2 attribute)
r2_ref_geom (ulamdyn.descriptors.R2 attribute)
read_all_trajs() (ulamdyn.data_loader.GetCoords method)
(ulamdyn.data_loader.GetCouplings method)
(ulamdyn.data_loader.GetGradients method)
(ulamdyn.kinetics.GetVelocities method)
read_eq_geom() (ulamdyn.data_loader.GetCoords method)
read_h5_nx() (in module ulamdyn.utilities)
read_nx_control() (in module ulamdyn.utilities)
rmsd (ulamdyn.data_loader.GetCoords attribute)
run_bootstrap() (in module ulamdyn.interface)
run_clustering() (in module ulamdyn.interface)
run_dim_reduction() (in module ulamdyn.interface)
S
save_csv (ulamdyn.data_loader.GetCoords property)
(ulamdyn.data_loader.GetProperties property)
save_data() (in module ulamdyn.interface)
save_xyz() (ulamdyn.data_writer.Geometries method)
save_xyz_hoppings() (in module ulamdyn.interface)
spectral() (ulamdyn.unsup_models.Clustering method)
stats_hopping() (in module ulamdyn.statistics)
T
trajectories (ulamdyn.data_loader.GetCoords attribute)
(ulamdyn.data_loader.GetCouplings attribute)
(ulamdyn.data_loader.GetGradients attribute)
(ulamdyn.data_loader.GetProperties attribute)
(ulamdyn.kinetics.GetVelocities attribute)
(ulamdyn.kinetics.KineticEnergy attribute)
(ulamdyn.kinetics.VibrationalSpectra attribute)
tsne() (ulamdyn.unsup_models.DimensionalityReduction method)
U
ulamdyn.data_loader
module
ulamdyn.data_writer
module
ulamdyn.descriptors
module
ulamdyn.interface
module
ulamdyn.kinetics
module
ulamdyn.run_analysis
module
ulamdyn.statistics
module
ulamdyn.unsup_models
module
ulamdyn.utilities
module
V
veloc (ulamdyn.kinetics.GetVelocities attribute)
(ulamdyn.kinetics.VibrationalSpectra attribute)
VibrationalSpectra (class in ulamdyn.kinetics)
X
xyz (ulamdyn.data_loader.GetCoords attribute)
xyz_to_distances() (ulamdyn.descriptors.R2 static method)
Z
zmat_ref_geom (ulamdyn.descriptors.ZMatrix attribute)
ZMatrix (class in ulamdyn.descriptors)