ESTEEM
latest
Contents:
Introduction and Background
Installation
Using ESTEEM
Parallel Execution
Examples of using ESTEEM
Task drivers in ESTEEM
Solutes module
Solvate module
Clusters module
Spectra module
Trajectories module
QMD_Trajectories module
ML_Training module
ML_Testing module
ML_Trajectories module
Wrappers available in ESTEEM
Other Wrappers
ESTEEM
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Index
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Index
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A
add_solvent_box() (esteem.wrappers.amber.AmberWrapper method)
AmberWrapper (class in esteem.wrappers.amber)
AMPWrapper (class in esteem.wrappers.amp)
C
calc_all_excitations() (esteem.tasks.clusters.ClustersTask method)
calc_all_excited_states() (esteem.tasks.solutes.SolutesTask method)
calc_all_vibrations() (esteem.tasks.clusters.ClustersTask method)
calc_vib_freq() (esteem.tasks.solutes.SolutesTask method)
calculate_ir_spectrum() (in module esteem.tasks.ml_trajectories)
carve_spheres() (esteem.tasks.clusters.ClustersTask method)
chdir() (esteem.tasks.solutes.SolutesTask method)
cleanup() (esteem.wrappers.nwchem.NWChemWrapper method)
(esteem.wrappers.orca.ORCAWrapper method)
clusters_driver() (in module esteem.drivers)
ClustersTask (class in esteem.tasks.clusters)
compare_traj_to_traj() (in module esteem.trajectories)
compare_wrapper_to_traj() (in module esteem.tasks.ml_testing)
counterion_charge() (in module esteem.tasks.solvate)
cycle_restarts() (in module esteem.trajectories)
cycle_step_labels_and_restarts() (in module esteem.trajectories)
D
delete_counterions() (in module esteem.tasks.clusters)
delete_distant_molecules() (in module esteem.tasks.clusters)
delete_excess_molecules() (in module esteem.tasks.clusters)
densityequil() (esteem.wrappers.amber.AmberWrapper method)
(esteem.wrappers.lammps.LAMMPSWrapper method)
diff_traj() (in module esteem.trajectories)
dipole() (esteem.wrappers.amber.AmberWrapper method)
E
equil() (esteem.wrappers.amber.AmberWrapper method)
(esteem.wrappers.lammps.LAMMPSWrapper method)
esteem.drivers (module)
esteem.tasks.clusters (module)
esteem.tasks.ml_testing (module)
esteem.tasks.ml_training (module)
esteem.tasks.ml_trajectories (module)
esteem.tasks.qmd_trajectories (module)
esteem.tasks.solutes (module)
esteem.tasks.solvate (module)
esteem.tasks.spectra (module)
esteem.trajectories (module)
esteem.wrappers.amp (module)
esteem.wrappers.lammps (module)
excitations() (esteem.wrappers.nwchem.NWChemWrapper method)
(esteem.wrappers.onetep.OnetepWrapper method)
(esteem.wrappers.orca.ORCAWrapper method)
ezFCFWrapper (class in esteem.wrappers.ezfcf)
F
find_best_rotas() (esteem.tasks.solutes.SolutesTask method)
find_initial_geometry() (in module esteem.trajectories)
find_range_sep() (esteem.tasks.solutes.SolutesTask method)
find_spectral_warp_params() (in module esteem.tasks.spectra)
fix_amber_pdb() (esteem.wrappers.amber.AmberWrapper method)
freq() (esteem.wrappers.amp.AMPWrapper method)
(esteem.wrappers.nwchem.NWChemWrapper method)
(esteem.wrappers.orca.ORCAWrapper method)
(esteem.wrappers.physnet.PhysNetWrapper method)
G
generate_md_trajectory() (in module esteem.trajectories)
geom_opt() (esteem.wrappers.amber.AmberWrapper method)
(esteem.wrappers.amp.AMPWrapper method)
(esteem.wrappers.lammps.LAMMPSWrapper method)
(esteem.wrappers.nwchem.NWChemWrapper method)
(esteem.wrappers.onetep.OnetepWrapper method)
(esteem.wrappers.orca.ORCAWrapper method)
(esteem.wrappers.physnet.PhysNetWrapper method)
geom_opt_all() (esteem.tasks.solutes.SolutesTask method)
get_trajectory_list() (in module esteem.trajectories)
get_xyz_files() (esteem.tasks.solutes.SolutesTask method)
getcwd() (esteem.tasks.solutes.SolutesTask method)
H
heatup() (esteem.wrappers.amber.AmberWrapper method)
(esteem.wrappers.lammps.LAMMPSWrapper method)
L
label_nearby_molecules() (in module esteem.tasks.clusters)
lammps_setup() (esteem.wrappers.lammps.LAMMPSWrapper method)
LAMMPSWrapper (class in esteem.wrappers.lammps)
load() (esteem.wrappers.amp.AMPWrapper method)
(esteem.wrappers.lammps.LAMMPSWrapper method)
(esteem.wrappers.physnet.PhysNetWrapper method)
load_trajectory_dipole() (in module esteem.tasks.ml_trajectories)
M
main() (in module esteem.drivers)
make_parser() (esteem.tasks.ml_trajectories.MLTrajTask method)
makedirs() (esteem.tasks.solutes.SolutesTask method)
merge_traj() (in module esteem.trajectories)
minimise() (esteem.wrappers.lammps.LAMMPSWrapper method)
mltest_driver() (in module esteem.drivers)
MLTestingTask (class in esteem.tasks.ml_testing)
mltrain_driver() (in module esteem.drivers)
MLTrainingTask (class in esteem.tasks.ml_training)
MLTrajTask (class in esteem.tasks.ml_trajectories)
N
np (esteem.tasks.solutes.SolutesTask attribute)
NWChemWrapper (class in esteem.wrappers.nwchem)
O
OnetepWrapper (class in esteem.wrappers.onetep)
ORCAWrapper (class in esteem.wrappers.orca)
P
path (esteem.tasks.solutes.SolutesTask attribute)
(esteem.wrappers.onetep.OnetepWrapper attribute)
PhysNetWrapper (class in esteem.wrappers.physnet)
prepare_input() (esteem.wrappers.amber.AmberWrapper method)
prepare_input_acpype() (esteem.wrappers.amber.AmberWrapper method)
Q
qmd_driver() (in module esteem.drivers)
QMDTrajTask (class in esteem.tasks.qmd_trajectories)
R
read() (esteem.tasks.solutes.SolutesTask method)
read_excitations() (esteem.wrappers.nwchem.NWChemWrapper method)
(esteem.wrappers.orca.ORCAWrapper method)
read_freq() (esteem.wrappers.nwchem.NWChemWrapper method)
(esteem.wrappers.orca.ORCAWrapper method)
recalculate_trajectory() (in module esteem.trajectories)
reimage() (esteem.wrappers.amber.AmberWrapper method)
reimage_cluster() (in module esteem.tasks.clusters)
remove_solute() (esteem.tasks.clusters.ClustersTask method)
reset_loss() (esteem.wrappers.physnet.PhysNetWrapper method)
RGB_colour() (in module esteem.tasks.spectra)
rotate_all_to_xy_plane() (esteem.tasks.solutes.SolutesTask method)
rotate_and_center_solute() (esteem.tasks.solutes.SolutesTask method)
(in module esteem.tasks.clusters)
run() (esteem.tasks.clusters.ClustersTask method)
(esteem.tasks.ml_testing.MLTestingTask method)
(esteem.tasks.ml_training.MLTrainingTask method)
(esteem.tasks.ml_trajectories.MLTrajTask method)
(esteem.tasks.qmd_trajectories.QMDTrajTask method)
(esteem.tasks.solutes.SolutesTask method)
(esteem.tasks.solvate.SolvateTask method)
(esteem.tasks.spectra.SpectraTask method)
run_md() (esteem.wrappers.amp.AMPWrapper method)
(esteem.wrappers.nwchem.NWChemWrapper method)
(esteem.wrappers.orca.ORCAWrapper method)
(esteem.wrappers.physnet.PhysNetWrapper method)
run_mlmd() (esteem.wrappers.lammps.LAMMPSWrapper method)
S
sanity_check() (in module esteem.tasks.clusters)
setup() (esteem.wrappers.nwchem.NWChemWrapper method)
(esteem.wrappers.onetep.OnetepWrapper method)
(esteem.wrappers.orca.ORCAWrapper method)
setup_amber() (esteem.tasks.solvate.SolvateTask method)
setup_lammps() (esteem.tasks.solvate.SolvateTask method)
singlepoint() (esteem.wrappers.amber.AmberWrapper method)
(esteem.wrappers.amp.AMPWrapper method)
(esteem.wrappers.lammps.LAMMPSWrapper method)
(esteem.wrappers.nwchem.NWChemWrapper method)
(esteem.wrappers.onetep.OnetepWrapper method)
(esteem.wrappers.orca.ORCAWrapper method)
(esteem.wrappers.physnet.PhysNetWrapper method)
snapshots() (esteem.wrappers.amber.AmberWrapper method)
(esteem.wrappers.lammps.LAMMPSWrapper method)
solutes_driver() (in module esteem.drivers)
SolutesTask (class in esteem.tasks.solutes)
solvate_driver() (in module esteem.drivers)
SolvateTask (class in esteem.tasks.solvate)
solvents_driver() (in module esteem.drivers)
SpecPyCodeWrapper (class in esteem.wrappers.specpycode)
spectral_warp_driver() (in module esteem.drivers)
SpectraTask (class in esteem.tasks.spectra)
split_traj() (in module esteem.trajectories)
subtract_atom_energies_from_traj() (in module esteem.trajectories)
subtract_reference_energies() (esteem.tasks.ml_testing.MLTestingTask method)
T
train() (esteem.wrappers.amp.AMPWrapper method)
(esteem.wrappers.physnet.PhysNetWrapper method)
W
write() (esteem.tasks.solutes.SolutesTask method)
write_state_xml_file() (esteem.wrappers.ezfcf.ezFCFWrapper method)
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