Walktrough: Cross-Compound Analysis#
In this tutorial, we compare the geometrical space explored during photoinduced dynamics for related molecular systems:
the Retinal system (I02)
and the compound I01, methyleneimmonium (\(\mathrm{CH_2NH_2^+}\))
We demonstrate how to select matching substructures across different molecules in order to define comparable, geometry-based descriptors. These descriptors are then processed and analyzed using principal component analysis (PCA) to reduce the dimensionality from six internal coordinates to two, enabling clear and intuitive visualization of the sampled configuration space.
Important: Note, the data of the tutorial is provided as a shnitsel-style NetCDF file for I02 (
./test_data/shnitsel/traj_I02.nc) and imported from SHARC output files for I01 (./test_data/sharc/traj_I01_v3.0_triplets/) to illustrate that we can compare existing datasets to new datasets during analysis.
[1]:
# from IPython.display import display
import matplotlib.pyplot as plt
import shnitsel as st
import shnitsel.xarray
1) Loading and Annotating Molecular Trajectory Data#
In the first step, we load the trajectory data of methyleneimmonium (I01), retinal (I02):
Read the trajectory datasets from disk.
Clean the inputs to eliminate physically unreasonable data.
Merge the data from the different compounds into a common tree that the further analysis will be based on
[2]:
from shnitsel.clean import sanity_check
from shnitsel.data.tree.support_functions import tree_merge
from pathlib import Path
dt_retinal = st.io.read('test_data/shnitsel/traj_I02.nc')
dt_retinal = sanity_check(dt_retinal)
dt_I01 = st.io.read('./test_data/sharc/traj_I01_v3.0_triplets_nacs_socs/', parallel=False).set_compound_info('I01')
dt_I01 = sanity_check(dt_I01)
mc_tree = tree_merge(dt_retinal, dt_I01)
mc_tree
WARNING:root:data does not contain kinetic energy variable ('e_kin')
WARNING:root:data does not contain kinetic energy variable ('e_kin')
WARNING:root:data does not contain kinetic energy variable ('e_kin')
[2]:
<class 'shnitsel.data.tree.tree.ShnitselDBRoot[Trajectory]'> [{'level': 'ShnitselDBRoot', 'children': '2: {\'I02\': \'ABCMeta(_name=\\\'I02\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=None, _children={\\\'0\\\': ABCMeta(_name=\\\'0\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 343kB\\nDimensions: (time: 382, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 189.5 190.0 190.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 384\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 193kB ...\\n atXYZ (time, atom, direction) float32 64kB -4.182 ... 3.616\\n dip_perm (time, state, direction) float32 14kB ...\\n dip_trans (time, statecomb, direction) float32 14kB ...\\n socs (time, full_statecomb) complex128 37kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 3kB 0.0 0.1572 ... 0.0\\n length_filtranda (length_criterion, time) float32 3kB 1.455 ... 1.21\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 384\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00001\\n 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\\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', 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\\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00001\\\', \\\'trajid\\\': 1, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'1\\\': ABCMeta(_name=\\\'1\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 328kB\\nDimensions: (time: 365, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 181.0 181.5 182.0\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 367\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 4kB ...\\n forces (time, state, atom, direction) float32 184kB ...\\n atXYZ (time, atom, direction) float32 61kB -4.215 ... -1.908\\n dip_perm (time, state, direction) float32 13kB ...\\n dip_trans (time, statecomb, direction) float32 13kB ...\\n socs (time, full_statecomb) complex128 35kB ...\\n phases (time, state) float32 4kB ...\\n energy_filtranda (energy_criterion, time) float32 3kB 0.0 0.1167 ... 0.0\\n length_filtranda (length_criterion, time) float32 3kB 1.427 ... 1.223\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 367\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00002\\n trajid: 2\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1802958429\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08f7c270>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 367, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-28912\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 367, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 183.0}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-28912\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00002\\\', \\\'trajid\\\': 2, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'2\\\': ABCMeta(_name=\\\'2\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 397kB\\nDimensions: (time: 442, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 219.5 220.0 220.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 444\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 223kB ...\\n atXYZ (time, atom, direction) float32 74kB -4.284 ... 0.4159\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 42kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 0.106 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.444 ... 1.257\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 444\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00003\\n trajid: 3\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1413818125\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08f7e020>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 444, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-9876\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 444, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 221.5}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-9876\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00003\\\', \\\'trajid\\\': 3, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'3\\\': ABCMeta(_name=\\\'3\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 94kB\\nDimensions: (time: 104, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 832B 0.0 0.5 1.0 1.5 ... 50.5 51.0 51.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 106\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 1kB ...\\n forces (time, state, atom, direction) float32 52kB ...\\n atXYZ (time, atom, direction) float32 17kB -4.143 ... 0.9226\\n dip_perm (time, state, direction) float32 4kB ...\\n dip_trans (time, statecomb, direction) float32 4kB ...\\n socs (time, full_statecomb) complex128 10kB ...\\n phases (time, state) float32 1kB ...\\n energy_filtranda (energy_criterion, time) float32 832B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 832B 1.443 ... 1.278\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 106\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00004\\n trajid: 4\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1157718546\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bbba60>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 106, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', 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\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 85kB\\nDimensions: (time: 94, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 752B 0.0 0.5 1.0 1.5 ... 45.5 46.0 46.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 443\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 1kB ...\\n forces (time, state, atom, direction) float32 47kB ...\\n atXYZ (time, atom, direction) float32 16kB -4.518 ... -1.171\\n dip_perm (time, state, direction) float32 3kB ...\\n dip_trans (time, statecomb, direction) float32 3kB ...\\n socs (time, full_statecomb) complex128 9kB ...\\n phases (time, state) float32 1kB ...\\n energy_filtranda (energy_criterion, time) float32 752B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 752B 1.465 ... 1.149\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 443\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00006\\n trajid: 6\\n DataTree_Level: TrajectoryData\\n trajectory_id: 215286057\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bbb150>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 443, \\\'completed\\\': False, 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\\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 443, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 221.0}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-22669\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00006\\\', \\\'trajid\\\': 6, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'5\\\': ABCMeta(_name=\\\'5\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 402kB\\nDimensions: (time: 448, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 222.5 223.0 223.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 450\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 226kB ...\\n atXYZ (time, atom, direction) float32 75kB -4.122 ... -0.6151\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 43kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.461 ... 1.172\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 450\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00007\\n trajid: 7\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1257393886\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bc3970>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 450, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-26082\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 450, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 224.5}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-26082\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00007\\\', \\\'trajid\\\': 7, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'6\\\': ABCMeta(_name=\\\'6\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 397kB\\nDimensions: (time: 442, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 219.5 220.0 220.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 444\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 223kB ...\\n atXYZ (time, atom, direction) float32 74kB -4.135 ... 1.728\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 42kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 0.2627 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.412 ... 1.233\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 444\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00008\\n trajid: 8\\n DataTree_Level: TrajectoryData\\n trajectory_id: 470449612\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bc35b0>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 444, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 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(length_criterion, time) float32 1kB 1.46 ... 1.224\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 447\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00010\\n trajid: 10\\n DataTree_Level: TrajectoryData\\n trajectory_id: 884240710\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bdf830>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 447, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': 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_level_name=\\\'DataLeaf\\\'), \\\'9\\\': ABCMeta(_name=\\\'9\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 395kB\\nDimensions: (time: 440, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 218.5 219.0 219.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 442\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 222kB ...\\n atXYZ (time, atom, direction) float32 74kB -4.307 ... 3.564\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 42kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.449 ... 1.186\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 442\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00012\\n trajid: 12\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1088618441\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bded40>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 442, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-2750\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': 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_data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 398kB\\nDimensions: (time: 443, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 220.0 220.5 221.0\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 445\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 223kB ...\\n atXYZ (time, atom, direction) float32 74kB -4.153 ... 2.578\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 43kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 0.1743 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.436 ... 1.133\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 445\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00014\\n trajid: 14\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1644969181\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bdffb0>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 445, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', 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\\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 445, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 222.0}, \\\'output.log\\\': {\\\'printlevel\\\': 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delta_t float64 8B 0.5\\n max_ts int64 8B 450\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 217kB ...\\n atXYZ (time, atom, direction) float32 72kB -4.141 ... 1.27\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 41kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 3kB 0.0 0.0874 ... 0.0\\n length_filtranda (length_criterion, time) float32 3kB 1.469 ... 1.181\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 450\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00017\\n trajid: 17\\n DataTree_Level: TrajectoryData\\n trajectory_id: 371103181\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bf2430>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 450, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-29587\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', 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\\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00017\\\', \\\'trajid\\\': 17, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'13\\\': ABCMeta(_name=\\\'13\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 184kB\\nDimensions: (time: 204, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 2kB 0.0 0.5 1.0 ... 100.5 101.0 101.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 449\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 2kB ...\\n forces (time, state, atom, direction) float32 103kB ...\\n atXYZ (time, atom, direction) float32 34kB -4.269 ... -1.398\\n dip_perm (time, state, direction) float32 7kB ...\\n dip_trans (time, statecomb, direction) float32 7kB ...\\n socs (time, full_statecomb) complex128 20kB ...\\n phases (time, state) float32 2kB ...\\n energy_filtranda (energy_criterion, time) float32 2kB 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 2kB 1.502 ... 1.13\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 449\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00018\\n trajid: 18\\n DataTree_Level: TrajectoryData\\n trajectory_id: 2056194826\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bf3c40>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 449, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-15866\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 449, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 224.0}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', 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\\\'retinal_tutorial/I02/TRAJ_00018\\\', \\\'trajid\\\': 18, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'14\\\': ABCMeta(_name=\\\'14\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 5kB\\nDimensions: (time: 5, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 40B 0.0 0.5 1.0 1.5 2.0\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 335\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 60B ...\\n forces (time, state, atom, direction) float32 3kB ...\\n atXYZ (time, atom, direction) float32 840B -4.484 ... 0.5728\\n dip_perm (time, state, direction) float32 180B ...\\n dip_trans (time, statecomb, direction) float32 180B ...\\n socs (time, full_statecomb) complex128 480B ...\\n phases (time, state) float32 60B ...\\n energy_filtranda (energy_criterion, time) float32 40B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 40B 1.44 ... 1.267\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 335\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00019\\n trajid: 19\\n DataTree_Level: TrajectoryData\\n trajectory_id: 36705956\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bf3600>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 335, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'16691\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 335, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 167.0}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'16691\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00019\\\', \\\'trajid\\\': 19, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'15\\\': ABCMeta(_name=\\\'15\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 392kB\\nDimensions: (time: 437, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 217.0 217.5 218.0\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 439\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 220kB ...\\n atXYZ (time, atom, direction) float32 73kB -4.368 ... 1.94\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 42kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 3kB 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 3kB 1.414 ... 1.133\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 439\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00020\\n trajid: 20\\n DataTree_Level: TrajectoryData\\n trajectory_id: 759924551\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08c11f80>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 439, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'15722\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 439, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 219.0}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'15722\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00020\\\', \\\'trajid\\\': 20, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\')}, _attrs={\\\'DataTree_Level\\\': \\\'CompoundGroup\\\', \\\'compound_info\\\': {\\\'compound_name\\\': \\\'I02\\\'}}, _parent=<class \\\'shnitsel.data.tree.tree.ShnitselDBRoot[Trajectory]\\\'> [{\\\'level\\\': \\\'ShnitselDBRoot\\\', \\\'children\\\': \\\'2: {\\\\\\\'I02\\\\\\\': \\\\\\\'...\\\\\\\', \\\\\\\'I01\\\\\\\': \\\\\\\'ABCMeta(_name=\\\\\\\\\\\\\\\'I01\\\\\\\\\\\\\\\', _dtype=<class \\\\\\\\\\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\\\\\\\\\\'>, _data=None, _children={\\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\': ABCMeta(_name=1, _dtype=<class \\\\\\\\\\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\\\\\\\\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 917kB\\\\\\\\nDimensions: (time: 88, state: 13, atom: 6, direction: 3,\\\\\\\\n statecomb: 78, full_statecomb: 156,\\\\\\\\n energy_criterion: 2, length_criterion: 2)\\\\\\\\nCoordinates: (12/27)\\\\\\\\n * time (time) float64 704B 0.0 0.5 1.0 ... 42.5 43.0 43.5\\\\\\\\n * state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13\\\\\\\\n * atom (atom) int64 48B 0 1 2 3 4 5\\\\\\\\n * direction (direction) <U1 12B \\\\\\\\\\\\\\\'x\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'y\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'z\\\\\\\\\\\\\\\'\\\\\\\\n * statecomb (statecomb) object 624B MultiIndex\\\\\\\\n * full_statecomb (full_statecomb) object 1kB MultiIndex\\\\\\\\n ... ...\\\\\\\\n delta_t float64 8B 0.5\\\\\\\\n max_ts int64 8B 90\\\\\\\\n t_max float64 8B 100.0\\\\\\\\n charge float64 8B 1.0\\\\\\\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\\\\\\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\\\\\\\nData variables:\\\\\\\\n energy (time, state) float32 5kB -94.4 -94.06 ... -93.89\\\\\\\\n forces (time, state, atom, direction) float32 82kB -0.06...\\\\\\\\n atXYZ (time, atom, direction) float32 6kB -0.005705 ......\\\\\\\\n nacs (time, statecomb, atom, direction) float32 494kB ...\\\\\\\\n dip_perm (time, state, direction) float32 14kB -0.06869 .....\\\\\\\\n dip_trans (time, statecomb, direction) float32 82kB 0.07728...\\\\\\\\n socs (time, full_statecomb) complex128 220kB 0j ... -4...\\\\\\\\n phases (time, state) float32 5kB -1.0 -1.0 -1.0 ... 1.0 1.0\\\\\\\\n energy_filtranda (energy_criterion, time) float32 704B 0.0 ... 0.0\\\\\\\\n length_filtranda (length_criterion, time) float32 704B 1.324 ... 1...\\\\\\\\nAttributes: (12/15)\\\\\\\\n input_format: sharc\\\\\\\\n _shnitsel_setup_for_cleanup: True\\\\\\\\n completed: False\\\\\\\\n input_type: dynamic\\\\\\\\n input_format_version: 3.0\\\\\\\\n num_singlets: 4\\\\\\\\n ... ...\\\\\\\\n theory_basis_set: cc-pVDZ\\\\\\\\n est_level: CASSCF\\\\\\\\n misc_input_settings: {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'...\\\\\\\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\\\\\\\n trajectory_id: 1\\\\\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0832..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\\\\\\\\\\\\\'DataLeaf\\\\\\\\\\\\\\\'), \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\': ABCMeta(_name=2, _dtype=<class \\\\\\\\\\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\\\\\\\\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 327kB\\\\\\\\nDimensions: (time: 31, state: 13, atom: 6, direction: 3,\\\\\\\\n statecomb: 78, full_statecomb: 156,\\\\\\\\n energy_criterion: 2, length_criterion: 2)\\\\\\\\nCoordinates: (12/27)\\\\\\\\n * time (time) float64 248B 0.0 0.5 1.0 ... 14.0 14.5 15.0\\\\\\\\n * state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13\\\\\\\\n * atom (atom) int64 48B 0 1 2 3 4 5\\\\\\\\n * direction (direction) <U1 12B \\\\\\\\\\\\\\\'x\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'y\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'z\\\\\\\\\\\\\\\'\\\\\\\\n * statecomb (statecomb) object 624B MultiIndex\\\\\\\\n * full_statecomb (full_statecomb) object 1kB MultiIndex\\\\\\\\n ... ...\\\\\\\\n delta_t float64 8B 0.5\\\\\\\\n max_ts int64 8B 108\\\\\\\\n t_max float64 8B 100.0\\\\\\\\n charge float64 8B 1.0\\\\\\\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\\\\\\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\\\\\\\nData variables:\\\\\\\\n energy (time, state) float32 2kB -94.39 -94.06 ... -93.92\\\\\\\\n forces (time, state, atom, direction) float32 29kB 0.058...\\\\\\\\n atXYZ (time, atom, direction) float32 2kB -0.003343 ......\\\\\\\\n nacs (time, statecomb, atom, direction) float32 174kB ...\\\\\\\\n dip_perm (time, state, direction) float32 5kB 0.02128 ... ...\\\\\\\\n dip_trans (time, statecomb, direction) float32 29kB -0.0009...\\\\\\\\n socs (time, full_statecomb) complex128 77kB 0j ... 0.7...\\\\\\\\n phases (time, state) float32 2kB -1.0 -1.0 -1.0 ... 1.0 1.0\\\\\\\\n energy_filtranda (energy_criterion, time) float32 248B 0.0 ... 0.0\\\\\\\\n length_filtranda (length_criterion, time) float32 248B 1.339 ... 1...\\\\\\\\nAttributes: (12/15)\\\\\\\\n input_format: sharc\\\\\\\\n _shnitsel_setup_for_cleanup: True\\\\\\\\n completed: False\\\\\\\\n input_type: dynamic\\\\\\\\n input_format_version: 3.0\\\\\\\\n num_singlets: 4\\\\\\\\n ... ...\\\\\\\\n theory_basis_set: cc-pVDZ\\\\\\\\n est_level: CASSCF\\\\\\\\n misc_input_settings: {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'...\\\\\\\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\\\\\\\n trajectory_id: 2\\\\\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0835..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\\\\\\\\\\\\\'DataLeaf\\\\\\\\\\\\\\\'), \\\\\\\\\\\\\\\'3\\\\\\\\\\\\\\\': ABCMeta(_name=3, _dtype=<class \\\\\\\\\\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\\\\\\\\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 824kB\\\\\\\\nDimensions: (time: 79, state: 13, atom: 6, direction: 3,\\\\\\\\n statecomb: 78, full_statecomb: 156,\\\\\\\\n energy_criterion: 2, length_criterion: 2)\\\\\\\\nCoordinates: (12/27)\\\\\\\\n * time (time) float64 632B 0.0 0.5 1.0 ... 38.0 38.5 39.0\\\\\\\\n * state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13\\\\\\\\n * atom (atom) int64 48B 0 1 2 3 4 5\\\\\\\\n * direction (direction) <U1 12B \\\\\\\\\\\\\\\'x\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'y\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'z\\\\\\\\\\\\\\\'\\\\\\\\n * statecomb (statecomb) object 624B MultiIndex\\\\\\\\n * full_statecomb (full_statecomb) object 1kB MultiIndex\\\\\\\\n ... ...\\\\\\\\n delta_t float64 8B 0.5\\\\\\\\n max_ts int64 8B 179\\\\\\\\n t_max float64 8B 100.0\\\\\\\\n charge float64 8B 1.0\\\\\\\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\\\\\\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\\\\\\\nData variables:\\\\\\\\n energy (time, state) float32 4kB -94.38 -94.07 ... -93.79\\\\\\\\n forces (time, state, atom, direction) float32 74kB 0.054...\\\\\\\\n atXYZ (time, atom, direction) float32 6kB 0.02998 ... -...\\\\\\\\n nacs (time, statecomb, atom, direction) float32 444kB ...\\\\\\\\n dip_perm (time, state, direction) float32 12kB -0.1124 ......\\\\\\\\n dip_trans (time, statecomb, direction) float32 74kB -0.1073...\\\\\\\\n socs (time, full_statecomb) complex128 197kB 0j ... 18...\\\\\\\\n phases (time, state) float32 4kB -1.0 -1.0 -1.0 ... 1.0 1.0\\\\\\\\n energy_filtranda (energy_criterion, time) float32 632B 0.0 ... 0.0\\\\\\\\n length_filtranda (length_criterion, time) float32 632B 1.302 ... 1...\\\\\\\\nAttributes: (12/15)\\\\\\\\n input_format: sharc\\\\\\\\n _shnitsel_setup_for_cleanup: True\\\\\\\\n completed: False\\\\\\\\n input_type: dynamic\\\\\\\\n input_format_version: 3.0\\\\\\\\n num_singlets: 4\\\\\\\\n ... ...\\\\\\\\n theory_basis_set: cc-pVDZ\\\\\\\\n est_level: CASSCF\\\\\\\\n misc_input_settings: {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'...\\\\\\\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\\\\\\\n trajectory_id: 3\\\\\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0834..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\\\\\\\\\\\\\'DataLeaf\\\\\\\\\\\\\\\')}, _attrs={}, _parent=<class \\\\\\\\\\\\\\\'shnitsel.data.tree.tree.ShnitselDBRoot[Trajectory]\\\\\\\\\\\\\\\'> [{\\\\\\\\\\\\\\\'level\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'ShnitselDBRoot\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'children\\\\\\\\\\\\\\\': "2: {\\\\\\\\\\\\\\\'I02\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'...\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'I01\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'...\\\\\\\\\\\\\\\'}"}], _level_name=\\\\\\\\\\\\\\\'CompoundGroup\\\\\\\\\\\\\\\', _group_info=None)\\\\\\\'}\\\'}], _level_name=\\\'CompoundGroup\\\', _group_info=None)\', \'I01\': \'ABCMeta(_name=\\\'I01\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=None, _children={\\\'1\\\': ABCMeta(_name=1, _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 917kB\\nDimensions: (time: 88, state: 13, atom: 6, direction: 3,\\n statecomb: 78, full_statecomb: 156,\\n energy_criterion: 2, length_criterion: 2)\\nCoordinates: (12/27)\\n * time (time) float64 704B 0.0 0.5 1.0 ... 42.5 43.0 43.5\\n * state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * atom (atom) int64 48B 0 1 2 3 4 5\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 624B MultiIndex\\n * full_statecomb (full_statecomb) object 1kB MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 90\\n t_max float64 8B 100.0\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB -94.4 -94.06 ... -93.89\\n forces (time, state, atom, direction) float32 82kB -0.06...\\n atXYZ (time, atom, direction) float32 6kB -0.005705 ......\\n nacs (time, statecomb, atom, direction) float32 494kB ...\\n dip_perm (time, state, direction) float32 14kB -0.06869 .....\\n dip_trans (time, statecomb, direction) float32 82kB 0.07728...\\n socs (time, full_statecomb) complex128 220kB 0j ... -4...\\n phases (time, state) float32 5kB -1.0 -1.0 -1.0 ... 1.0 1.0\\n energy_filtranda (energy_criterion, time) float32 704B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 704B 1.324 ... 1...\\nAttributes: (12/15)\\n input_format: sharc\\n _shnitsel_setup_for_cleanup: True\\n completed: False\\n input_type: dynamic\\n input_format_version: 3.0\\n num_singlets: 4\\n ... ...\\n theory_basis_set: cc-pVDZ\\n est_level: CASSCF\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'...\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\n trajectory_id: 1\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0832..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'2\\\': ABCMeta(_name=2, _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 327kB\\nDimensions: (time: 31, state: 13, atom: 6, direction: 3,\\n statecomb: 78, full_statecomb: 156,\\n energy_criterion: 2, length_criterion: 2)\\nCoordinates: (12/27)\\n * time (time) float64 248B 0.0 0.5 1.0 ... 14.0 14.5 15.0\\n * state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * atom (atom) int64 48B 0 1 2 3 4 5\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 624B MultiIndex\\n * full_statecomb (full_statecomb) object 1kB MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 108\\n t_max float64 8B 100.0\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 2kB -94.39 -94.06 ... -93.92\\n forces (time, state, atom, direction) float32 29kB 0.058...\\n atXYZ (time, atom, direction) float32 2kB -0.003343 ......\\n nacs (time, statecomb, atom, direction) float32 174kB ...\\n dip_perm (time, state, direction) float32 5kB 0.02128 ... ...\\n dip_trans (time, statecomb, direction) float32 29kB -0.0009...\\n socs (time, full_statecomb) complex128 77kB 0j ... 0.7...\\n phases (time, state) float32 2kB -1.0 -1.0 -1.0 ... 1.0 1.0\\n energy_filtranda (energy_criterion, time) float32 248B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 248B 1.339 ... 1...\\nAttributes: (12/15)\\n input_format: sharc\\n _shnitsel_setup_for_cleanup: True\\n completed: False\\n input_type: dynamic\\n input_format_version: 3.0\\n num_singlets: 4\\n ... ...\\n theory_basis_set: cc-pVDZ\\n est_level: CASSCF\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'...\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\n trajectory_id: 2\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0835..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'3\\\': ABCMeta(_name=3, _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 824kB\\nDimensions: (time: 79, state: 13, atom: 6, direction: 3,\\n statecomb: 78, full_statecomb: 156,\\n energy_criterion: 2, length_criterion: 2)\\nCoordinates: (12/27)\\n * time (time) float64 632B 0.0 0.5 1.0 ... 38.0 38.5 39.0\\n * state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * atom (atom) int64 48B 0 1 2 3 4 5\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 624B MultiIndex\\n * full_statecomb (full_statecomb) object 1kB MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 179\\n t_max float64 8B 100.0\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 4kB -94.38 -94.07 ... -93.79\\n forces (time, state, atom, direction) float32 74kB 0.054...\\n atXYZ (time, atom, direction) float32 6kB 0.02998 ... -...\\n nacs (time, statecomb, atom, direction) float32 444kB ...\\n dip_perm (time, state, direction) float32 12kB -0.1124 ......\\n dip_trans (time, statecomb, direction) float32 74kB -0.1073...\\n socs (time, full_statecomb) complex128 197kB 0j ... 18...\\n phases (time, state) float32 4kB -1.0 -1.0 -1.0 ... 1.0 1.0\\n energy_filtranda (energy_criterion, time) float32 632B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 632B 1.302 ... 1...\\nAttributes: (12/15)\\n input_format: sharc\\n _shnitsel_setup_for_cleanup: True\\n completed: False\\n input_type: dynamic\\n input_format_version: 3.0\\n num_singlets: 4\\n ... ...\\n theory_basis_set: cc-pVDZ\\n est_level: CASSCF\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'...\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\n trajectory_id: 3\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0834..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\'DataLeaf\\\')}, _attrs={}, _parent=<class \\\'shnitsel.data.tree.tree.ShnitselDBRoot[Trajectory]\\\'> [{\\\'level\\\': \\\'ShnitselDBRoot\\\', \\\'children\\\': \\\'2: {\\\\\\\'I02\\\\\\\': \\\\\\\'ABCMeta(_name=\\\\\\\\\\\\\\\'I02\\\\\\\\\\\\\\\', _dtype=<class \\\\\\\\\\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\\\\\\\\\\'>, _data=None, _children={\\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\': ABCMeta(_name=\\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', _dtype=<class \\\\\\\\\\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\\\\\\\\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 343kB\\\\\\\\nDimensions: (time: 382, state: 3, atom: 14, direction: 3,\\\\\\\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\\\\\\\n length_criterion: 2)\\\\\\\\nCoordinates: (12/25)\\\\\\\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 189.5 190.0 190.5\\\\\\\\n * state (state) int64 24B 1 2 3\\\\\\\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\\\\\\\n * direction (direction) <U1 12B \\\\\\\\\\\\\\\'x\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'y\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'z\\\\\\\\\\\\\\\'\\\\\\\\n * statecomb (statecomb) object 24B MultiIndex\\\\\\\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\\\\\\\n ... ...\\\\\\\\n delta_t float64 8B 0.5\\\\\\\\n max_ts int64 8B 384\\\\\\\\n t_max float64 8B 1e+03\\\\\\\\n charge float64 8B 1.0\\\\\\\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\\\\\\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\\\\\\\nData variables:\\\\\\\\n energy (time, state) float32 5kB ...\\\\\\\\n forces (time, state, atom, direction) float32 193kB ...\\\\\\\\n atXYZ (time, atom, direction) float32 64kB -4.182 ... 3.616\\\\\\\\n dip_perm (time, state, direction) float32 14kB ...\\\\\\\\n dip_trans (time, statecomb, direction) float32 14kB ...\\\\\\\\n socs (time, full_statecomb) complex128 37kB ...\\\\\\\\n phases (time, state) float32 5kB ...\\\\\\\\n energy_filtranda (energy_criterion, time) float32 3kB 0.0 0.1572 ... 0.0\\\\\\\\n length_filtranda (length_criterion, time) float32 3kB 1.455 ... 1.21\\\\\\\\nAttributes: (12/17)\\\\\\\\n input_format: sharc\\\\\\\\n t_max: 1000.0\\\\\\\\n delta_t: 0.5\\\\\\\\n max_ts: 384\\\\\\\\n completed: False\\\\\\\\n input_type: dynamic\\\\\\\\n ... ...\\\\\\\\n misc_input_settings: {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"geom"...\\\\\\\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00001\\\\\\\\n trajid: 1\\\\\\\\n DataTree_Level: TrajectoryData\\\\\\\\n trajectory_id: 1027217349\\\\\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bba480>, _is_multi_trajectory=False), _children={}, _attrs={\\\\\\\\\\\\\\\'input_format\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'sharc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'t_max\\\\\\\\\\\\\\\': 1000.0, \\\\\\\\\\\\\\\'delta_t\\\\\\\\\\\\\\\': 0.5, \\\\\\\\\\\\\\\'max_ts\\\\\\\\\\\\\\\': 384, \\\\\\\\\\\\\\\'completed\\\\\\\\\\\\\\\': False, \\\\\\\\\\\\\\\'input_type\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'dynamic\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'input_format_version\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3.0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'num_singlets\\\\\\\\\\\\\\\': 3, \\\\\\\\\\\\\\\'num_doublets\\\\\\\\\\\\\\\': 0, \\\\\\\\\\\\\\\'num_triplets\\\\\\\\\\\\\\\': 0, \\\\\\\\\\\\\\\'has_forces\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'misc_input_settings\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"geom"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'veloc\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'external\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'velocfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"veloc"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nstates\\\\\\\\\\\\\\\': [3], \\\\\\\\\\\\\\\'actstates\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'state\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2 mch\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'coeff\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'auto\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'rngseed\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'5199\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'ezero\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'-248.2781283000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'tmax\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1000.000000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'stepsize\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.500000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nsubsteps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'25\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'integrator\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'fvv\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'method\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'tsh\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'surf\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'diagonal\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'coupling\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'overlap\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nogradcorrect\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'ekincorrect\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'parallel_vel\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'reflect_frustrated\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'none\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'decoherence_scheme\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'edc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'decoherence_param\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'hopping_procedure\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'sharc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'grad_all\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'eselect\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.001000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'select_directly\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'nospinorbit\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_grad\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_nacdr\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_overlap\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'output_format\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'ascii\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'output_dat_steps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\'}, \\\\\\\\\\\\\\\'output.dat\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'SHARC_version\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3.0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'method\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'integrator\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'maxmult\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nstates_m\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'natom\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'14\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'dtstep\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'20.670686894780374\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nsteps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nsubsteps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'25\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'ezero\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'-248.27812829999999\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_overlap\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_grad\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_nacdr\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_property1d\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_property2d\\\\\\\\\\\\\\\': 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* direction (direction) <U1 12B \\\\\\\\\\\\\\\'x\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'y\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'z\\\\\\\\\\\\\\\'\\\\\\\\n * statecomb (statecomb) object 24B MultiIndex\\\\\\\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\\\\\\\n ... ...\\\\\\\\n delta_t float64 8B 0.5\\\\\\\\n max_ts int64 8B 335\\\\\\\\n t_max float64 8B 1e+03\\\\\\\\n charge float64 8B 1.0\\\\\\\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\\\\\\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\\\\\\\nData variables:\\\\\\\\n energy (time, state) float32 60B ...\\\\\\\\n forces (time, state, atom, direction) float32 3kB ...\\\\\\\\n atXYZ (time, atom, direction) float32 840B -4.484 ... 0.5728\\\\\\\\n dip_perm (time, state, direction) float32 180B ...\\\\\\\\n dip_trans (time, statecomb, direction) float32 180B ...\\\\\\\\n socs (time, full_statecomb) complex128 480B ...\\\\\\\\n phases (time, state) float32 60B ...\\\\\\\\n energy_filtranda (energy_criterion, time) float32 40B 0.0 ... 0.0\\\\\\\\n length_filtranda (length_criterion, time) float32 40B 1.44 ... 1.267\\\\\\\\nAttributes: (12/17)\\\\\\\\n input_format: sharc\\\\\\\\n t_max: 1000.0\\\\\\\\n delta_t: 0.5\\\\\\\\n max_ts: 335\\\\\\\\n completed: False\\\\\\\\n input_type: dynamic\\\\\\\\n ... ...\\\\\\\\n misc_input_settings: {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"geom"...\\\\\\\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00019\\\\\\\\n trajid: 19\\\\\\\\n DataTree_Level: TrajectoryData\\\\\\\\n trajectory_id: 36705956\\\\\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bf3600>, _is_multi_trajectory=False), _children={}, _attrs={\\\\\\\\\\\\\\\'input_format\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'sharc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'t_max\\\\\\\\\\\\\\\': 1000.0, \\\\\\\\\\\\\\\'delta_t\\\\\\\\\\\\\\\': 0.5, \\\\\\\\\\\\\\\'max_ts\\\\\\\\\\\\\\\': 335, \\\\\\\\\\\\\\\'completed\\\\\\\\\\\\\\\': False, \\\\\\\\\\\\\\\'input_type\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'dynamic\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'input_format_version\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3.0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'num_singlets\\\\\\\\\\\\\\\': 3, \\\\\\\\\\\\\\\'num_doublets\\\\\\\\\\\\\\\': 0, \\\\\\\\\\\\\\\'num_triplets\\\\\\\\\\\\\\\': 0, \\\\\\\\\\\\\\\'has_forces\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'misc_input_settings\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"geom"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'veloc\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'external\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'velocfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"veloc"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nstates\\\\\\\\\\\\\\\': [3], \\\\\\\\\\\\\\\'actstates\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'state\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2 mch\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'coeff\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'auto\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'rngseed\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'16691\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'ezero\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'-248.2781283000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'tmax\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1000.000000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'stepsize\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.500000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nsubsteps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'25\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'integrator\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'fvv\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'method\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'tsh\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'surf\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'diagonal\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'coupling\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'overlap\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nogradcorrect\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'ekincorrect\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'parallel_vel\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'reflect_frustrated\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'none\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'decoherence_scheme\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'edc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'decoherence_param\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'hopping_procedure\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'sharc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'grad_all\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'eselect\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.001000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'select_directly\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'nospinorbit\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_grad\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_nacdr\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_overlap\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'output_format\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'ascii\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'output_dat_steps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\'}, \\\\\\\\\\\\\\\'output.dat\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'SHARC_version\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3.0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'method\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'integrator\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'maxmult\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nstates_m\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'natom\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'14\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'dtstep\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'20.670686894780374\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nsteps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nsubsteps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'25\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'ezero\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'-248.27812829999999\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_overlap\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_grad\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_nacdr\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_property1d\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_property2d\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'n_property1d\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'n_property2d\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'laser\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\'}, \\\\\\\\\\\\\\\'output.lis\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'nsteps\\\\\\\\\\\\\\\': 335, \\\\\\\\\\\\\\\'delta_t\\\\\\\\\\\\\\\': 0.5, \\\\\\\\\\\\\\\'t_max\\\\\\\\\\\\\\\': 167.0}, \\\\\\\\\\\\\\\'output.log\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"geom"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'veloc\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'external\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'velocfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"veloc"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nstates\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'actstates\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'state\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2 mch\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'coeff\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'auto\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'rngseed\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'16691\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'ezero\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'-248.2781283000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'tmax\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1000.000000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'stepsize\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.500000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nsubsteps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'25\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'integrator\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'fvv\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'method\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'tsh\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'surf\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'diagonal\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'coupling\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'overlap\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nogradcorrect\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'ekincorrect\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'parallel_vel\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'reflect_frustrated\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'none\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'decoherence_scheme\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'edc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'decoherence_param\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'hopping_procedure\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'sharc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'grad_all\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'eselect\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.001000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'select_directly\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'nospinorbit\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_grad\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_nacdr\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_overlap\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'output_format\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'ascii\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'output_dat_steps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'version\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3.0\\\\\\\\\\\\\\\'}}, \\\\\\\\\\\\\\\'trajectory_input_path\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'retinal_tutorial/I02/TRAJ_00019\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'trajid\\\\\\\\\\\\\\\': 19, \\\\\\\\\\\\\\\'DataTree_Level\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'TrajectoryData\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'__shnitsel_setup_for_cleanup\\\\\\\\\\\\\\\': True}, _parent=..., _level_name=\\\\\\\\\\\\\\\'DataLeaf\\\\\\\\\\\\\\\'), \\\\\\\\\\\\\\\'15\\\\\\\\\\\\\\\': ABCMeta(_name=\\\\\\\\\\\\\\\'15\\\\\\\\\\\\\\\', _dtype=<class \\\\\\\\\\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\\\\\\\\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 392kB\\\\\\\\nDimensions: (time: 437, state: 3, atom: 14, direction: 3,\\\\\\\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\\\\\\\n length_criterion: 2)\\\\\\\\nCoordinates: (12/25)\\\\\\\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 217.0 217.5 218.0\\\\\\\\n * state (state) int64 24B 1 2 3\\\\\\\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\\\\\\\n * direction (direction) <U1 12B \\\\\\\\\\\\\\\'x\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'y\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'z\\\\\\\\\\\\\\\'\\\\\\\\n * statecomb (statecomb) object 24B MultiIndex\\\\\\\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\\\\\\\n ... ...\\\\\\\\n delta_t float64 8B 0.5\\\\\\\\n max_ts int64 8B 439\\\\\\\\n t_max float64 8B 1e+03\\\\\\\\n charge float64 8B 1.0\\\\\\\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\\\\\\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\\\\\\\nData variables:\\\\\\\\n energy (time, state) float32 5kB ...\\\\\\\\n forces (time, state, atom, direction) float32 220kB ...\\\\\\\\n atXYZ (time, atom, direction) float32 73kB -4.368 ... 1.94\\\\\\\\n dip_perm (time, state, direction) float32 16kB ...\\\\\\\\n dip_trans (time, statecomb, direction) float32 16kB ...\\\\\\\\n socs (time, full_statecomb) complex128 42kB ...\\\\\\\\n phases (time, state) float32 5kB ...\\\\\\\\n energy_filtranda (energy_criterion, time) float32 3kB 0.0 ... 0.0\\\\\\\\n length_filtranda (length_criterion, time) float32 3kB 1.414 ... 1.133\\\\\\\\nAttributes: (12/17)\\\\\\\\n input_format: sharc\\\\\\\\n t_max: 1000.0\\\\\\\\n delta_t: 0.5\\\\\\\\n max_ts: 439\\\\\\\\n completed: False\\\\\\\\n input_type: dynamic\\\\\\\\n ... ...\\\\\\\\n misc_input_settings: {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"geom"...\\\\\\\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00020\\\\\\\\n trajid: 20\\\\\\\\n DataTree_Level: TrajectoryData\\\\\\\\n trajectory_id: 759924551\\\\\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08c11f80>, _is_multi_trajectory=False), _children={}, _attrs={\\\\\\\\\\\\\\\'input_format\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'sharc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'t_max\\\\\\\\\\\\\\\': 1000.0, \\\\\\\\\\\\\\\'delta_t\\\\\\\\\\\\\\\': 0.5, \\\\\\\\\\\\\\\'max_ts\\\\\\\\\\\\\\\': 439, \\\\\\\\\\\\\\\'completed\\\\\\\\\\\\\\\': False, \\\\\\\\\\\\\\\'input_type\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'dynamic\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'input_format_version\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3.0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'num_singlets\\\\\\\\\\\\\\\': 3, \\\\\\\\\\\\\\\'num_doublets\\\\\\\\\\\\\\\': 0, \\\\\\\\\\\\\\\'num_triplets\\\\\\\\\\\\\\\': 0, \\\\\\\\\\\\\\\'has_forces\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'misc_input_settings\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"geom"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'veloc\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'external\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'velocfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"veloc"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nstates\\\\\\\\\\\\\\\': [3], \\\\\\\\\\\\\\\'actstates\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'state\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2 mch\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'coeff\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'auto\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'rngseed\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'15722\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'ezero\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'-248.2781283000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'tmax\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1000.000000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'stepsize\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.500000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nsubsteps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'25\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'integrator\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'fvv\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'method\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'tsh\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'surf\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'diagonal\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'coupling\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'overlap\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nogradcorrect\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'ekincorrect\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'parallel_vel\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'reflect_frustrated\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'none\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'decoherence_scheme\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'edc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'decoherence_param\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'hopping_procedure\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'sharc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'grad_all\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'eselect\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.001000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'select_directly\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'nospinorbit\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_grad\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_nacdr\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_overlap\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'output_format\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'ascii\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'output_dat_steps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\'}, \\\\\\\\\\\\\\\'output.dat\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'SHARC_version\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3.0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'method\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'integrator\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'maxmult\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nstates_m\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'natom\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'14\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'dtstep\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'20.670686894780374\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nsteps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nsubsteps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'25\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'ezero\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'-248.27812829999999\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_overlap\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_grad\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_nacdr\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_property1d\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'write_property2d\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'n_property1d\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'n_property2d\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'laser\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\'}, \\\\\\\\\\\\\\\'output.lis\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'nsteps\\\\\\\\\\\\\\\': 439, \\\\\\\\\\\\\\\'delta_t\\\\\\\\\\\\\\\': 0.5, \\\\\\\\\\\\\\\'t_max\\\\\\\\\\\\\\\': 219.0}, \\\\\\\\\\\\\\\'output.log\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"geom"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'veloc\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'external\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'velocfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"veloc"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nstates\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'actstates\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'state\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2 mch\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'coeff\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'auto\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'rngseed\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'15722\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'ezero\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'-248.2781283000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'tmax\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1000.000000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'stepsize\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.500000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nsubsteps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'25\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'integrator\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'fvv\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'method\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'tsh\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'surf\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'diagonal\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'coupling\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'overlap\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nogradcorrect\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'ekincorrect\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'parallel_vel\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'reflect_frustrated\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'none\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'decoherence_scheme\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'edc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'decoherence_param\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'hopping_procedure\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'sharc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'grad_all\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'eselect\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'0.001000\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'select_directly\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'nospinorbit\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_grad\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_nacdr\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'write_overlap\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'output_format\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'ascii\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'output_dat_steps\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'1\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'version\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3.0\\\\\\\\\\\\\\\'}}, \\\\\\\\\\\\\\\'trajectory_input_path\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'retinal_tutorial/I02/TRAJ_00020\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'trajid\\\\\\\\\\\\\\\': 20, \\\\\\\\\\\\\\\'DataTree_Level\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'TrajectoryData\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'__shnitsel_setup_for_cleanup\\\\\\\\\\\\\\\': True}, _parent=..., _level_name=\\\\\\\\\\\\\\\'DataLeaf\\\\\\\\\\\\\\\')}, _attrs={\\\\\\\\\\\\\\\'DataTree_Level\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'CompoundGroup\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'compound_info\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'compound_name\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'I02\\\\\\\\\\\\\\\'}}, _parent=<class \\\\\\\\\\\\\\\'shnitsel.data.tree.tree.ShnitselDBRoot[Trajectory]\\\\\\\\\\\\\\\'> [{\\\\\\\\\\\\\\\'level\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'ShnitselDBRoot\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'children\\\\\\\\\\\\\\\': "2: {\\\\\\\\\\\\\\\'I02\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'...\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'I01\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'...\\\\\\\\\\\\\\\'}"}], _level_name=\\\\\\\\\\\\\\\'CompoundGroup\\\\\\\\\\\\\\\', _group_info=None)\\\\\\\', \\\\\\\'I01\\\\\\\': \\\\\\\'...\\\\\\\'}\\\'}], _level_name=\\\'CompoundGroup\\\', _group_info=None)\'}'}]If we want to, we can inspect individual compounds in the tree by array-style access:
[3]:
mc_tree['I01']
[3]:
ABCMeta(_name='I01', _dtype=<class 'shnitsel.data.dataset_containers.trajectory.Trajectory'>, _data=None, _children={'1': ABCMeta(_name=1, _dtype=<class 'shnitsel.data.dataset_containers.trajectory.Trajectory'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 917kB
Dimensions: (time: 88, state: 13, atom: 6, direction: 3,
statecomb: 78, full_statecomb: 156,
energy_criterion: 2, length_criterion: 2)
Coordinates: (12/27)
* time (time) float64 704B 0.0 0.5 1.0 ... 42.5 43.0 43.5
* state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13
* atom (atom) int64 48B 0 1 2 3 4 5
* direction (direction) <U1 12B 'x' 'y' 'z'
* statecomb (statecomb) object 624B MultiIndex
* full_statecomb (full_statecomb) object 1kB MultiIndex
... ...
delta_t float64 8B 0.5
max_ts int64 8B 90
t_max float64 8B 100.0
charge float64 8B 1.0
energy_thresholds (energy_criterion) float64 16B 0.7 1.0
length_thresholds (length_criterion) float64 16B 3.0 2.0
Data variables:
energy (time, state) float32 5kB -94.4 -94.06 ... -93.89
forces (time, state, atom, direction) float32 82kB -0.06...
atXYZ (time, atom, direction) float32 6kB -0.005705 ......
nacs (time, statecomb, atom, direction) float32 494kB ...
dip_perm (time, state, direction) float32 14kB -0.06869 .....
dip_trans (time, statecomb, direction) float32 82kB 0.07728...
socs (time, full_statecomb) complex128 220kB 0j ... -4...
phases (time, state) float32 5kB -1.0 -1.0 -1.0 ... 1.0 1.0
energy_filtranda (energy_criterion, time) float32 704B 0.0 ... 0.0
length_filtranda (length_criterion, time) float32 704B 1.324 ... 1...
Attributes: (12/15)
input_format: sharc
_shnitsel_setup_for_cleanup: True
completed: False
input_type: dynamic
input_format_version: 3.0
num_singlets: 4
... ...
theory_basis_set: cc-pVDZ
est_level: CASSCF
misc_input_settings: {'input': {'printlevel': '2', 'geomfile': '...
trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...
trajectory_id: 1
__mol: <rdkit.Chem.rdchem.Mol object at 0x744c0832..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name='DataLeaf'), '2': ABCMeta(_name=2, _dtype=<class 'shnitsel.data.dataset_containers.trajectory.Trajectory'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 327kB
Dimensions: (time: 31, state: 13, atom: 6, direction: 3,
statecomb: 78, full_statecomb: 156,
energy_criterion: 2, length_criterion: 2)
Coordinates: (12/27)
* time (time) float64 248B 0.0 0.5 1.0 ... 14.0 14.5 15.0
* state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13
* atom (atom) int64 48B 0 1 2 3 4 5
* direction (direction) <U1 12B 'x' 'y' 'z'
* statecomb (statecomb) object 624B MultiIndex
* full_statecomb (full_statecomb) object 1kB MultiIndex
... ...
delta_t float64 8B 0.5
max_ts int64 8B 108
t_max float64 8B 100.0
charge float64 8B 1.0
energy_thresholds (energy_criterion) float64 16B 0.7 1.0
length_thresholds (length_criterion) float64 16B 3.0 2.0
Data variables:
energy (time, state) float32 2kB -94.39 -94.06 ... -93.92
forces (time, state, atom, direction) float32 29kB 0.058...
atXYZ (time, atom, direction) float32 2kB -0.003343 ......
nacs (time, statecomb, atom, direction) float32 174kB ...
dip_perm (time, state, direction) float32 5kB 0.02128 ... ...
dip_trans (time, statecomb, direction) float32 29kB -0.0009...
socs (time, full_statecomb) complex128 77kB 0j ... 0.7...
phases (time, state) float32 2kB -1.0 -1.0 -1.0 ... 1.0 1.0
energy_filtranda (energy_criterion, time) float32 248B 0.0 ... 0.0
length_filtranda (length_criterion, time) float32 248B 1.339 ... 1...
Attributes: (12/15)
input_format: sharc
_shnitsel_setup_for_cleanup: True
completed: False
input_type: dynamic
input_format_version: 3.0
num_singlets: 4
... ...
theory_basis_set: cc-pVDZ
est_level: CASSCF
misc_input_settings: {'input': {'printlevel': '2', 'geomfile': '...
trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...
trajectory_id: 2
__mol: <rdkit.Chem.rdchem.Mol object at 0x744c0835..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name='DataLeaf'), '3': ABCMeta(_name=3, _dtype=<class 'shnitsel.data.dataset_containers.trajectory.Trajectory'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 824kB
Dimensions: (time: 79, state: 13, atom: 6, direction: 3,
statecomb: 78, full_statecomb: 156,
energy_criterion: 2, length_criterion: 2)
Coordinates: (12/27)
* time (time) float64 632B 0.0 0.5 1.0 ... 38.0 38.5 39.0
* state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13
* atom (atom) int64 48B 0 1 2 3 4 5
* direction (direction) <U1 12B 'x' 'y' 'z'
* statecomb (statecomb) object 624B MultiIndex
* full_statecomb (full_statecomb) object 1kB MultiIndex
... ...
delta_t float64 8B 0.5
max_ts int64 8B 179
t_max float64 8B 100.0
charge float64 8B 1.0
energy_thresholds (energy_criterion) float64 16B 0.7 1.0
length_thresholds (length_criterion) float64 16B 3.0 2.0
Data variables:
energy (time, state) float32 4kB -94.38 -94.07 ... -93.79
forces (time, state, atom, direction) float32 74kB 0.054...
atXYZ (time, atom, direction) float32 6kB 0.02998 ... -...
nacs (time, statecomb, atom, direction) float32 444kB ...
dip_perm (time, state, direction) float32 12kB -0.1124 ......
dip_trans (time, statecomb, direction) float32 74kB -0.1073...
socs (time, full_statecomb) complex128 197kB 0j ... 18...
phases (time, state) float32 4kB -1.0 -1.0 -1.0 ... 1.0 1.0
energy_filtranda (energy_criterion, time) float32 632B 0.0 ... 0.0
length_filtranda (length_criterion, time) float32 632B 1.302 ... 1...
Attributes: (12/15)
input_format: sharc
_shnitsel_setup_for_cleanup: True
completed: False
input_type: dynamic
input_format_version: 3.0
num_singlets: 4
... ...
theory_basis_set: cc-pVDZ
est_level: CASSCF
misc_input_settings: {'input': {'printlevel': '2', 'geomfile': '...
trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...
trajectory_id: 3
__mol: <rdkit.Chem.rdchem.Mol object at 0x744c0834..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name='DataLeaf')}, _attrs={}, _parent=<class 'shnitsel.data.tree.tree.ShnitselDBRoot[Trajectory]'> [{'level': 'ShnitselDBRoot', 'children': '2: {\'I02\': \'ABCMeta(_name=\\\'I02\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=None, _children={\\\'0\\\': ABCMeta(_name=\\\'0\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 343kB\\nDimensions: (time: 382, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 189.5 190.0 190.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 384\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 193kB ...\\n atXYZ (time, atom, direction) float32 64kB -4.182 ... 3.616\\n dip_perm (time, state, direction) float32 14kB ...\\n dip_trans (time, statecomb, direction) float32 14kB ...\\n socs (time, full_statecomb) complex128 37kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 3kB 0.0 0.1572 ... 0.0\\n length_filtranda (length_criterion, time) float32 3kB 1.455 ... 1.21\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 384\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00001\\n trajid: 1\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1027217349\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bba480>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 384, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'5199\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 384, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 191.5}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'5199\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00001\\\', \\\'trajid\\\': 1, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'1\\\': ABCMeta(_name=\\\'1\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 328kB\\nDimensions: (time: 365, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 181.0 181.5 182.0\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 367\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 4kB ...\\n forces (time, state, atom, direction) float32 184kB ...\\n atXYZ (time, atom, direction) float32 61kB -4.215 ... -1.908\\n dip_perm (time, state, direction) float32 13kB ...\\n dip_trans (time, statecomb, direction) float32 13kB ...\\n socs (time, full_statecomb) complex128 35kB ...\\n phases (time, state) float32 4kB ...\\n energy_filtranda (energy_criterion, time) float32 3kB 0.0 0.1167 ... 0.0\\n length_filtranda (length_criterion, time) float32 3kB 1.427 ... 1.223\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 367\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00002\\n trajid: 2\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1802958429\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08f7c270>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 367, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-28912\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 367, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 183.0}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-28912\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00002\\\', \\\'trajid\\\': 2, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'2\\\': ABCMeta(_name=\\\'2\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 397kB\\nDimensions: (time: 442, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 219.5 220.0 220.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 444\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 223kB ...\\n atXYZ (time, atom, direction) float32 74kB -4.284 ... 0.4159\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 42kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 0.106 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.444 ... 1.257\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 444\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00003\\n trajid: 3\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1413818125\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08f7e020>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 444, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-9876\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 444, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 221.5}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-9876\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00003\\\', \\\'trajid\\\': 3, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'3\\\': ABCMeta(_name=\\\'3\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 94kB\\nDimensions: (time: 104, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 832B 0.0 0.5 1.0 1.5 ... 50.5 51.0 51.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 106\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 1kB ...\\n forces (time, state, atom, direction) float32 52kB ...\\n atXYZ (time, atom, direction) float32 17kB -4.143 ... 0.9226\\n dip_perm (time, state, direction) float32 4kB ...\\n dip_trans (time, statecomb, direction) float32 4kB ...\\n socs (time, full_statecomb) complex128 10kB ...\\n phases (time, state) float32 1kB ...\\n energy_filtranda (energy_criterion, time) float32 832B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 832B 1.443 ... 1.278\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 106\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00004\\n trajid: 4\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1157718546\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bbba60>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 106, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, 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\\\'retinal_tutorial/I02/TRAJ_00004\\\', \\\'trajid\\\': 4, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'4\\\': ABCMeta(_name=\\\'4\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 85kB\\nDimensions: (time: 94, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 752B 0.0 0.5 1.0 1.5 ... 45.5 46.0 46.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 443\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 1kB ...\\n forces (time, state, atom, direction) float32 47kB ...\\n atXYZ (time, atom, direction) float32 16kB -4.518 ... -1.171\\n dip_perm (time, state, direction) float32 3kB ...\\n dip_trans (time, statecomb, direction) float32 3kB ...\\n socs (time, full_statecomb) complex128 9kB ...\\n phases (time, state) float32 1kB ...\\n energy_filtranda (energy_criterion, time) float32 752B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 752B 1.465 ... 1.149\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 443\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00006\\n trajid: 6\\n DataTree_Level: TrajectoryData\\n trajectory_id: 215286057\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bbb150>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 443, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-22669\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', 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\\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00006\\\', \\\'trajid\\\': 6, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'5\\\': ABCMeta(_name=\\\'5\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 402kB\\nDimensions: (time: 448, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 222.5 223.0 223.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 450\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 226kB ...\\n atXYZ (time, atom, direction) float32 75kB -4.122 ... -0.6151\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 43kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.461 ... 1.172\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 450\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00007\\n trajid: 7\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1257393886\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bc3970>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 450, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-26082\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 450, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 224.5}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-26082\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00007\\\', \\\'trajid\\\': 7, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'6\\\': ABCMeta(_name=\\\'6\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 397kB\\nDimensions: (time: 442, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 219.5 220.0 220.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 444\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 223kB ...\\n atXYZ (time, atom, direction) float32 74kB -4.135 ... 1.728\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 42kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 0.2627 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.412 ... 1.233\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 444\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00008\\n trajid: 8\\n DataTree_Level: TrajectoryData\\n trajectory_id: 470449612\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bc35b0>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', 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\\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00008\\\', \\\'trajid\\\': 8, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'7\\\': ABCMeta(_name=\\\'7\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 71kB\\nDimensions: (time: 78, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 624B 0.0 0.5 1.0 1.5 ... 37.5 38.0 38.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 356\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 936B ...\\n forces (time, state, atom, direction) float32 39kB ...\\n atXYZ (time, atom, direction) float32 13kB -4.22 ... -1.146\\n dip_perm (time, state, direction) float32 3kB ...\\n dip_trans (time, statecomb, direction) float32 3kB ...\\n socs (time, full_statecomb) complex128 7kB ...\\n phases (time, state) float32 936B ...\\n energy_filtranda (energy_criterion, time) float32 624B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 624B 1.42 ... 1.22\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 356\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00009\\n trajid: 9\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1337730505\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bc31f0>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 356, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-29045\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', 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_data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 116kB\\nDimensions: (time: 128, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 1kB 0.0 0.5 1.0 1.5 ... 62.5 63.0 63.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 447\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 2kB ...\\n forces (time, state, atom, direction) float32 65kB ...\\n atXYZ (time, atom, direction) float32 22kB -4.286 ... -0.69\\n dip_perm (time, state, direction) float32 5kB ...\\n dip_trans (time, statecomb, direction) float32 5kB ...\\n socs (time, full_statecomb) complex128 12kB ...\\n phases (time, state) float32 2kB ...\\n energy_filtranda (energy_criterion, time) float32 1kB 0.0 0.3184 ... 0.0\\n length_filtranda (length_criterion, time) float32 1kB 1.46 ... 1.224\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 447\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00010\\n trajid: 10\\n DataTree_Level: TrajectoryData\\n trajectory_id: 884240710\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bdf830>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 447, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-17512\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 447, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 223.0}, \\\'output.log\\\': {\\\'printlevel\\\': 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\\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00010\\\', \\\'trajid\\\': 10, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'9\\\': ABCMeta(_name=\\\'9\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 395kB\\nDimensions: (time: 440, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 218.5 219.0 219.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 442\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 222kB ...\\n atXYZ (time, atom, direction) float32 74kB -4.307 ... 3.564\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 42kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.449 ... 1.186\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 442\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00012\\n trajid: 12\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1088618441\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bded40>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 442, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-2750\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', 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\\\'retinal_tutorial/I02/TRAJ_00013\\\', \\\'trajid\\\': 13, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'11\\\': ABCMeta(_name=\\\'11\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 398kB\\nDimensions: (time: 443, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 220.0 220.5 221.0\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 445\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 223kB ...\\n atXYZ (time, atom, direction) float32 74kB -4.153 ... 2.578\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 43kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 0.1743 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.436 ... 1.133\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 445\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00014\\n trajid: 14\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1644969181\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bdffb0>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 445, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-8375\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': 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\\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00014\\\', \\\'trajid\\\': 14, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'12\\\': ABCMeta(_name=\\\'12\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 387kB\\nDimensions: (time: 431, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 3kB 0.0 0.5 1.0 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(length_criterion, time) float32 3kB 1.469 ... 1.181\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 450\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00017\\n trajid: 17\\n DataTree_Level: TrajectoryData\\n trajectory_id: 371103181\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bf2430>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 450, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-29587\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 450, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 224.5}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-29587\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00017\\\', \\\'trajid\\\': 17, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'13\\\': ABCMeta(_name=\\\'13\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 184kB\\nDimensions: (time: 204, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 2kB 0.0 0.5 1.0 ... 100.5 101.0 101.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 449\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 2kB ...\\n forces (time, state, atom, direction) float32 103kB ...\\n atXYZ (time, atom, direction) float32 34kB -4.269 ... -1.398\\n dip_perm (time, state, direction) float32 7kB ...\\n dip_trans (time, statecomb, direction) float32 7kB ...\\n socs (time, full_statecomb) complex128 20kB ...\\n phases (time, state) float32 2kB ...\\n energy_filtranda (energy_criterion, time) float32 2kB 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 2kB 1.502 ... 1.13\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 449\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00018\\n trajid: 18\\n DataTree_Level: TrajectoryData\\n trajectory_id: 2056194826\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bf3c40>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 449, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-15866\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 449, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 224.0}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-15866\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00018\\\', \\\'trajid\\\': 18, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'14\\\': ABCMeta(_name=\\\'14\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 5kB\\nDimensions: (time: 5, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 40B 0.0 0.5 1.0 1.5 2.0\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 335\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 60B ...\\n forces (time, state, atom, direction) float32 3kB ...\\n atXYZ (time, atom, direction) float32 840B -4.484 ... 0.5728\\n dip_perm (time, state, direction) float32 180B ...\\n dip_trans (time, statecomb, direction) float32 180B ...\\n socs (time, full_statecomb) complex128 480B ...\\n phases (time, state) float32 60B ...\\n energy_filtranda (energy_criterion, time) float32 40B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 40B 1.44 ... 1.267\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 335\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00019\\n trajid: 19\\n DataTree_Level: TrajectoryData\\n trajectory_id: 36705956\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08bf3600>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 335, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'16691\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 335, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 167.0}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'16691\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00019\\\', \\\'trajid\\\': 19, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'15\\\': ABCMeta(_name=\\\'15\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 392kB\\nDimensions: (time: 437, state: 3, atom: 14, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/25)\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 217.0 217.5 218.0\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 112B 0 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n delta_t float64 8B 0.5\\n max_ts int64 8B 439\\n t_max float64 8B 1e+03\\n charge float64 8B 1.0\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 220kB ...\\n atXYZ (time, atom, direction) float32 73kB -4.368 ... 1.94\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 42kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 3kB 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 3kB 1.414 ... 1.133\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 439\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00020\\n trajid: 20\\n DataTree_Level: TrajectoryData\\n trajectory_id: 759924551\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08c11f80>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 439, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'15722\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 439, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 219.0}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'15722\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00020\\\', \\\'trajid\\\': 20, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\')}, _attrs={\\\'DataTree_Level\\\': \\\'CompoundGroup\\\', \\\'compound_info\\\': {\\\'compound_name\\\': \\\'I02\\\'}}, _parent=<class \\\'shnitsel.data.tree.tree.ShnitselDBRoot[Trajectory]\\\'> [{\\\'level\\\': \\\'ShnitselDBRoot\\\', \\\'children\\\': "2: {\\\'I02\\\': \\\'...\\\', \\\'I01\\\': \\\'...\\\'}"}], _level_name=\\\'CompoundGroup\\\', _group_info=None)\', \'I01\': \'...\'}'}], _level_name='CompoundGroup', _group_info=None)2) Computing Descriptors for common substructures#
In the next step, we flag a common substructure that all molecules share, namely the central double bond between an N and a C atom and the adjacent H atoms. This flagging identifies which substructure is considered in the subsequent analysis.
2.1) Selecting a substructure#
There are two main strategies to select a substructure of interest for further processing:
provide a SMARTS string that fits the substructure in all compounds
identify the maximum common substructure automatically
The following example will find the maximum common substructure shared between all compounds within the tree:
[4]:
from shnitsel.bridges import to_mol
from shnitsel.geo.analogs import extract_analogs
analogs_tree = extract_analogs(mc_tree)
assert analogs_tree is not None
analogs_tree
[4]:
<class 'shnitsel.data.tree.tree.ShnitselDBRoot[Trajectory]'> [{'level': 'ShnitselDBRoot', 'children': '2: {\'I02\': \'ABCMeta(_name=\\\'I02\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=None, _children={\\\'0\\\': ABCMeta(_name=\\\'0\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 178kB\\nDimensions: (time: 382, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 189.5 190.0 190.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 384\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c081...\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 69kB ...\\n atXYZ (time, atom, direction) float32 23kB 3.795 ... 1.982\\n dip_perm (time, state, direction) float32 14kB ...\\n dip_trans (time, statecomb, direction) float32 14kB ...\\n socs (time, full_statecomb) complex128 37kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 3kB 0.0 0.1572 ... 0.0\\n length_filtranda (length_criterion, time) float32 3kB 1.455 ... 1.21\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 384\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: 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\\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 384, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 191.5}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'5199\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00001\\\', \\\'trajid\\\': 1, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'1\\\': ABCMeta(_name=\\\'1\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 170kB\\nDimensions: (time: 365, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 181.0 181.5 182.0\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 367\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c083...\\nData variables:\\n energy (time, state) float32 4kB ...\\n forces (time, state, atom, direction) float32 66kB ...\\n atXYZ (time, atom, direction) float32 22kB 3.867 ... -2.755\\n dip_perm (time, state, direction) float32 13kB ...\\n dip_trans (time, statecomb, direction) float32 13kB ...\\n socs (time, full_statecomb) complex128 35kB ...\\n phases (time, state) float32 4kB ...\\n energy_filtranda (energy_criterion, time) float32 3kB 0.0 0.1167 ... 0.0\\n length_filtranda (length_criterion, time) float32 3kB 1.427 ... 1.223\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 367\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00002\\n trajid: 2\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1802958429\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0835a7f0>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 367, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': 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True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 367, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 183.0}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-28912\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00002\\\', \\\'trajid\\\': 2, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'2\\\': ABCMeta(_name=\\\'2\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 206kB\\nDimensions: (time: 442, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 219.5 220.0 220.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 444\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c083...\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 80kB ...\\n atXYZ (time, atom, direction) float32 27kB 3.881 ... -1.951\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 42kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 0.106 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.444 ... 1.257\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 444\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00003\\n trajid: 3\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1413818125\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0834c0e0>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 444, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-9876\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 444, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 221.5}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-9876\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00003\\\', \\\'trajid\\\': 3, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'3\\\': ABCMeta(_name=\\\'3\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 49kB\\nDimensions: (time: 104, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 832B 0.0 0.5 1.0 1.5 ... 50.5 51.0 51.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 106\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c081...\\nData variables:\\n energy (time, state) float32 1kB ...\\n forces (time, state, atom, direction) float32 19kB ...\\n atXYZ (time, atom, direction) float32 6kB 3.681 ... -0.2054\\n dip_perm (time, state, direction) float32 4kB ...\\n dip_trans (time, statecomb, direction) float32 4kB ...\\n socs (time, full_statecomb) complex128 10kB ...\\n phases (time, state) float32 1kB ...\\n energy_filtranda (energy_criterion, time) float32 832B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 832B 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full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 1kB 0.0 0.5 1.0 1.5 ... 62.5 63.0 63.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 447\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c081...\\nData variables:\\n energy (time, state) float32 2kB ...\\n forces (time, state, atom, direction) float32 23kB ...\\n atXYZ (time, atom, direction) float32 8kB 3.78 ... 0.413\\n dip_perm (time, state, direction) float32 5kB ...\\n dip_trans (time, statecomb, direction) float32 5kB ...\\n socs (time, full_statecomb) complex128 12kB ...\\n phases (time, state) float32 2kB ...\\n energy_filtranda (energy_criterion, time) float32 1kB 0.0 0.3184 ... 0.0\\n length_filtranda (length_criterion, time) float32 1kB 1.46 ... 1.224\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 447\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00010\\n trajid: 10\\n DataTree_Level: TrajectoryData\\n trajectory_id: 884240710\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c081c28e0>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 447, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-17512\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': 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\\\'retinal_tutorial/I02/TRAJ_00010\\\', \\\'trajid\\\': 10, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'9\\\': ABCMeta(_name=\\\'9\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 205kB\\nDimensions: (time: 440, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 218.5 219.0 219.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 442\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c081...\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 79kB ...\\n atXYZ (time, atom, direction) float32 26kB 3.658 ... -0.1813\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 42kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.449 ... 1.186\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 442\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00012\\n trajid: 12\\n DataTree_Level: 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\\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 442, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 220.5}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-2750\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', 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\\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'11\\\': ABCMeta(_name=\\\'11\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 206kB\\nDimensions: (time: 443, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 220.0 220.5 221.0\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 445\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 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_is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 445, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-8375\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': 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1.181\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 450\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00017\\n trajid: 17\\n DataTree_Level: TrajectoryData\\n trajectory_id: 371103181\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08209f80>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 450, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', 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ABCMeta(_name=\\\'13\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 95kB\\nDimensions: (time: 204, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 2kB 0.0 0.5 1.0 ... 100.5 101.0 101.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 449\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c082...\\nData variables:\\n energy (time, state) float32 2kB ...\\n forces (time, state, atom, direction) 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0x744c...\\\\\\\\nData variables:\\\\\\\\n energy (time, state) float32 5kB -94.4 -94.06 ... -93.89\\\\\\\\n forces (time, state, atom, direction) float32 69kB -0.06...\\\\\\\\n atXYZ (time, atom, direction) float32 5kB -0.005705 ......\\\\\\\\n nacs (time, statecomb, atom, direction) float32 412kB ...\\\\\\\\n dip_perm (time, state, direction) float32 14kB -0.06869 .....\\\\\\\\n dip_trans (time, statecomb, direction) float32 82kB 0.07728...\\\\\\\\n socs (time, full_statecomb) complex128 220kB 0j ... -4...\\\\\\\\n phases (time, state) float32 5kB -1.0 -1.0 -1.0 ... 1.0 1.0\\\\\\\\n energy_filtranda (energy_criterion, time) float32 704B 0.0 ... 0.0\\\\\\\\n length_filtranda (length_criterion, time) float32 704B 1.324 ... 1...\\\\\\\\nAttributes: (12/15)\\\\\\\\n input_format: sharc\\\\\\\\n _shnitsel_setup_for_cleanup: True\\\\\\\\n completed: False\\\\\\\\n input_type: dynamic\\\\\\\\n input_format_version: 3.0\\\\\\\\n num_singlets: 4\\\\\\\\n ... ...\\\\\\\\n theory_basis_set: cc-pVDZ\\\\\\\\n est_level: CASSCF\\\\\\\\n misc_input_settings: {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'...\\\\\\\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\\\\\\\n trajectory_id: 1\\\\\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0823..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\\\\\\\\\\\\\'DataLeaf\\\\\\\\\\\\\\\'), \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\': ABCMeta(_name=2, _dtype=<class \\\\\\\\\\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\\\\\\\\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 293kB\\\\\\\\nDimensions: (time: 31, state: 13, atom: 5, direction: 3,\\\\\\\\n statecomb: 78, full_statecomb: 156,\\\\\\\\n energy_criterion: 2, length_criterion: 2)\\\\\\\\nCoordinates: (12/28)\\\\\\\\n * time (time) float64 248B 0.0 0.5 1.0 ... 14.0 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energy_filtranda (energy_criterion, time) float32 632B 0.0 ... 0.0\\\\\\\\n length_filtranda (length_criterion, time) float32 632B 1.302 ... 1...\\\\\\\\nAttributes: (12/15)\\\\\\\\n input_format: sharc\\\\\\\\n _shnitsel_setup_for_cleanup: True\\\\\\\\n completed: False\\\\\\\\n input_type: dynamic\\\\\\\\n input_format_version: 3.0\\\\\\\\n num_singlets: 4\\\\\\\\n ... ...\\\\\\\\n theory_basis_set: cc-pVDZ\\\\\\\\n est_level: CASSCF\\\\\\\\n misc_input_settings: {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'...\\\\\\\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\\\\\\\n trajectory_id: 3\\\\\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0825..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\\\\\\\\\\\\\'DataLeaf\\\\\\\\\\\\\\\')}, _attrs={}, _parent=<class 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_data=None, _children={\\\'1\\\': ABCMeta(_name=1, _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 820kB\\nDimensions: (time: 88, state: 13, atom: 5, direction: 3,\\n statecomb: 78, full_statecomb: 156,\\n energy_criterion: 2, length_criterion: 2)\\nCoordinates: (12/28)\\n * time (time) float64 704B 0.0 0.5 1.0 ... 42.5 43.0 43.5\\n * state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 624B MultiIndex\\n * full_statecomb (full_statecomb) object 1kB MultiIndex\\n ... ...\\n max_ts int64 8B 90\\n t_max float64 8B 100.0\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c...\\nData variables:\\n energy (time, state) float32 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test_data/sharc/traj_I01_v3.0_triplets_nacs...\\n trajectory_id: 1\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0823..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'2\\\': ABCMeta(_name=2, _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 293kB\\nDimensions: (time: 31, state: 13, atom: 5, direction: 3,\\n statecomb: 78, full_statecomb: 156,\\n energy_criterion: 2, length_criterion: 2)\\nCoordinates: (12/28)\\n * time (time) float64 248B 0.0 0.5 1.0 ... 14.0 14.5 15.0\\n * state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 624B MultiIndex\\n * full_statecomb (full_statecomb) object 1kB MultiIndex\\n ... ...\\n max_ts int64 8B 108\\n t_max float64 8B 100.0\\n charge int64 8B 1\\n energy_thresholds 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... ...\\n theory_basis_set: cc-pVDZ\\n est_level: CASSCF\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'...\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\n trajectory_id: 2\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0823..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'3\\\': ABCMeta(_name=3, _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 737kB\\nDimensions: (time: 79, state: 13, atom: 5, direction: 3,\\n statecomb: 78, full_statecomb: 156,\\n energy_criterion: 2, length_criterion: 2)\\nCoordinates: (12/28)\\n * time (time) float64 632B 0.0 0.5 1.0 ... 38.0 38.5 39.0\\n * state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 624B MultiIndex\\n * full_statecomb (full_statecomb) object 1kB MultiIndex\\n ... ...\\n max_ts int64 8B 179\\n t_max float64 8B 100.0\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c...\\nData variables:\\n energy (time, state) float32 4kB -94.38 -94.07 ... -93.79\\n forces (time, state, atom, direction) float32 62kB 0.054...\\n atXYZ (time, atom, direction) float32 5kB 0.02998 ... -...\\n nacs (time, statecomb, atom, direction) float32 370kB ...\\n dip_perm (time, state, direction) float32 12kB -0.1124 ......\\n dip_trans (time, statecomb, direction) float32 74kB -0.1073...\\n socs (time, full_statecomb) complex128 197kB 0j ... 18...\\n phases (time, state) float32 4kB -1.0 -1.0 -1.0 ... 1.0 1.0\\n energy_filtranda (energy_criterion, time) float32 632B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 632B 1.302 ... 1...\\nAttributes: (12/15)\\n input_format: sharc\\n _shnitsel_setup_for_cleanup: True\\n completed: False\\n input_type: dynamic\\n input_format_version: 3.0\\n num_singlets: 4\\n ... ...\\n theory_basis_set: cc-pVDZ\\n est_level: CASSCF\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'...\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\n trajectory_id: 3\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0825..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\'DataLeaf\\\')}, _attrs={}, _parent=<class \\\'shnitsel.data.tree.tree.ShnitselDBRoot[Trajectory]\\\'> [{\\\'level\\\': \\\'ShnitselDBRoot\\\', \\\'children\\\': \\\'2: {\\\\\\\'I02\\\\\\\': \\\\\\\'ABCMeta(_name=\\\\\\\\\\\\\\\'I02\\\\\\\\\\\\\\\', _dtype=<class \\\\\\\\\\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\\\\\\\\\\'>, _data=None, _children={\\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\': ABCMeta(_name=\\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', _dtype=<class \\\\\\\\\\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\\\\\\\\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 178kB\\\\\\\\nDimensions: (time: 382, state: 3, atom: 5, direction: 3,\\\\\\\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\\\\\\\n length_criterion: 2)\\\\\\\\nCoordinates: (12/26)\\\\\\\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 189.5 190.0 190.5\\\\\\\\n * state (state) int64 24B 1 2 3\\\\\\\\n * atom (atom) int64 40B 0 1 2 3 4\\\\\\\\n * direction (direction) <U1 12B \\\\\\\\\\\\\\\'x\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'y\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'z\\\\\\\\\\\\\\\'\\\\\\\\n * statecomb (statecomb) object 24B MultiIndex\\\\\\\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\\\\\\\n ... ...\\\\\\\\n max_ts int64 8B 384\\\\\\\\n t_max float64 8B 1e+03\\\\\\\\n charge int64 8B 1\\\\\\\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\\\\\\\n 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{\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"geom"...\\\\\\\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00001\\\\\\\\n trajid: 1\\\\\\\\n DataTree_Level: TrajectoryData\\\\\\\\n trajectory_id: 1027217349\\\\\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c081ada30>, _is_multi_trajectory=False), _children={}, _attrs={\\\\\\\\\\\\\\\'input_format\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'sharc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'t_max\\\\\\\\\\\\\\\': 1000.0, \\\\\\\\\\\\\\\'delta_t\\\\\\\\\\\\\\\': 0.5, \\\\\\\\\\\\\\\'max_ts\\\\\\\\\\\\\\\': 384, \\\\\\\\\\\\\\\'completed\\\\\\\\\\\\\\\': False, \\\\\\\\\\\\\\\'input_type\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'dynamic\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'input_format_version\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3.0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'num_singlets\\\\\\\\\\\\\\\': 3, \\\\\\\\\\\\\\\'num_doublets\\\\\\\\\\\\\\\': 0, \\\\\\\\\\\\\\\'num_triplets\\\\\\\\\\\\\\\': 0, \\\\\\\\\\\\\\\'has_forces\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'misc_input_settings\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"geom"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'veloc\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'external\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'velocfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"veloc"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nstates\\\\\\\\\\\\\\\': [3], \\\\\\\\\\\\\\\'actstates\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'state\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2 mch\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'coeff\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'auto\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'rngseed\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'5199\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'ezero\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'-248.2781283000\\\\\\\\\\\\\\\', 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\\\\\\\\\\\\\\\'trajectory_input_path\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'retinal_tutorial/I02/TRAJ_00020\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'trajid\\\\\\\\\\\\\\\': 20, \\\\\\\\\\\\\\\'DataTree_Level\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'TrajectoryData\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'__shnitsel_setup_for_cleanup\\\\\\\\\\\\\\\': True}, _parent=..., _level_name=\\\\\\\\\\\\\\\'DataLeaf\\\\\\\\\\\\\\\')}, _attrs={\\\\\\\\\\\\\\\'DataTree_Level\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'CompoundGroup\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'compound_info\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'compound_name\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'I02\\\\\\\\\\\\\\\'}}, _parent=<class \\\\\\\\\\\\\\\'shnitsel.data.tree.tree.ShnitselDBRoot[Trajectory]\\\\\\\\\\\\\\\'> [{\\\\\\\\\\\\\\\'level\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'ShnitselDBRoot\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'children\\\\\\\\\\\\\\\': "2: {\\\\\\\\\\\\\\\'I02\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'...\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'I01\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'...\\\\\\\\\\\\\\\'}"}], _level_name=\\\\\\\\\\\\\\\'CompoundGroup\\\\\\\\\\\\\\\', _group_info=GroupInfo(group_name="TrajectoryGroupingMetadata(delta_t_in_fs=0.5, input_format_name=\\\\\\\\\\\\\\\'sharc\\\\\\\\\\\\\\\', input_format_version=\\\\\\\\\\\\\\\'3.0\\\\\\\\\\\\\\\', est_level=None, theory_basis_set=None, charge_in_e=1.0, num_states=3)", group_attributes={\\\\\\\\\\\\\\\'delta_t_in_fs\\\\\\\\\\\\\\\': 0.5, \\\\\\\\\\\\\\\'input_format_name\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'sharc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'input_format_version\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3.0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'est_level\\\\\\\\\\\\\\\': None, \\\\\\\\\\\\\\\'theory_basis_set\\\\\\\\\\\\\\\': None, \\\\\\\\\\\\\\\'charge_in_e\\\\\\\\\\\\\\\': 1.0, \\\\\\\\\\\\\\\'num_states\\\\\\\\\\\\\\\': 3}, grouped_properties=None))\\\\\\\', \\\\\\\'I01\\\\\\\': \\\\\\\'...\\\\\\\'}\\\'}], _level_name=\\\'CompoundGroup\\\', _group_info=GroupInfo(group_name="TrajectoryGroupingMetadata(delta_t_in_fs=0.5, input_format_name=\\\'sharc\\\', input_format_version=\\\'3.0\\\', est_level=\\\'CASSCF\\\', theory_basis_set=\\\'cc-pVDZ\\\', charge_in_e=1.0, num_states=13)", group_attributes={\\\'delta_t_in_fs\\\': 0.5, \\\'input_format_name\\\': \\\'sharc\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'est_level\\\': \\\'CASSCF\\\', \\\'theory_basis_set\\\': \\\'cc-pVDZ\\\', \\\'charge_in_e\\\': 1.0, \\\'num_states\\\': 13}, grouped_properties=None))\'}'}]We can also get a more in-detail look at the substructures identified by the analogs function:
[5]:
display(analogs_tree['I02/0/data'].mol)
display(analogs_tree['I01/2/data'].mol)
In fact, the matching has found the greatest possible overlap between the two molecules including the charge center around the nitrogen atom, its double bond to a neighboring C atom and the surrounding H atoms.
In the following, we demonstrate how this selection would also have been possible by providing a SMARTS yourself:
[6]:
from shnitsel.geo.analogs import extract_analogs
smarts_share = '[#6](=[#7](-[#1])-[#1])-[#1]'
tree_smarts_substruct = extract_analogs(mc_tree, smarts=smarts_share)
tree_smarts_substruct
[6]:
<class 'shnitsel.data.tree.tree.ShnitselDBRoot[Trajectory]'> [{'level': 'ShnitselDBRoot', 'children': '2: {\'I02\': \'ABCMeta(_name=\\\'I02\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=None, _children={\\\'0\\\': ABCMeta(_name=\\\'0\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 178kB\\nDimensions: (time: 382, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 189.5 190.0 190.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 384\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds 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length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 181.0 181.5 182.0\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 367\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c083...\\nData variables:\\n energy (time, state) float32 4kB ...\\n forces (time, state, atom, direction) float32 66kB ...\\n atXYZ (time, atom, direction) float32 22kB 3.867 ... -2.755\\n dip_perm (time, state, direction) float32 13kB ...\\n dip_trans (time, statecomb, direction) float32 13kB ...\\n socs (time, full_statecomb) complex128 35kB ...\\n phases (time, state) float32 4kB ...\\n energy_filtranda (energy_criterion, time) float32 3kB 0.0 0.1167 ... 0.0\\n length_filtranda (length_criterion, time) float32 3kB 1.427 ... 1.223\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 367\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00002\\n trajid: 2\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1802958429\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0835afc0>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 367, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': 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True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 367, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 183.0}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-28912\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00002\\\', \\\'trajid\\\': 2, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'2\\\': ABCMeta(_name=\\\'2\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 206kB\\nDimensions: (time: 442, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 219.5 220.0 220.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 444\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744cb72...\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 80kB ...\\n atXYZ (time, atom, direction) float32 27kB 3.881 ... -1.951\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 42kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 0.106 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.444 ... 1.257\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 444\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00003\\n trajid: 3\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1413818125\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744cb72c4090>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 444, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-9876\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 444, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 221.5}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-9876\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00003\\\', \\\'trajid\\\': 3, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'3\\\': ABCMeta(_name=\\\'3\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 49kB\\nDimensions: (time: 104, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 832B 0.0 0.5 1.0 1.5 ... 50.5 51.0 51.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 106\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c081...\\nData variables:\\n energy (time, state) float32 1kB ...\\n forces (time, state, atom, direction) float32 19kB ...\\n atXYZ (time, atom, direction) float32 6kB 3.681 ... -0.2054\\n dip_perm (time, state, direction) float32 4kB ...\\n dip_trans (time, statecomb, direction) float32 4kB ...\\n socs (time, full_statecomb) complex128 10kB ...\\n phases (time, state) float32 1kB ...\\n energy_filtranda (energy_criterion, time) float32 832B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 832B 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\\\'output_dat_steps\\\': \\\'1\\\', \\\'version\\\': \\\'3.0\\\'}}, \\\'trajectory_input_path\\\': \\\'retinal_tutorial/I02/TRAJ_00008\\\', \\\'trajid\\\': 8, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'7\\\': ABCMeta(_name=\\\'7\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 37kB\\nDimensions: (time: 78, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 624B 0.0 0.5 1.0 1.5 ... 37.5 38.0 38.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 356\\n t_max float64 8B 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full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 1kB 0.0 0.5 1.0 1.5 ... 62.5 63.0 63.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 447\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c082...\\nData variables:\\n energy (time, state) float32 2kB ...\\n forces (time, state, atom, direction) float32 23kB ...\\n atXYZ (time, atom, direction) float32 8kB 3.78 ... 0.413\\n dip_perm (time, state, direction) float32 5kB ...\\n dip_trans (time, statecomb, direction) float32 5kB ...\\n socs (time, full_statecomb) complex128 12kB ...\\n phases (time, state) float32 2kB ...\\n energy_filtranda (energy_criterion, time) float32 1kB 0.0 0.3184 ... 0.0\\n length_filtranda (length_criterion, time) float32 1kB 1.46 ... 1.224\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 447\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00010\\n trajid: 10\\n DataTree_Level: TrajectoryData\\n trajectory_id: 884240710\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0828c540>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 447, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-17512\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': 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\\\'retinal_tutorial/I02/TRAJ_00010\\\', \\\'trajid\\\': 10, \\\'DataTree_Level\\\': \\\'TrajectoryData\\\', \\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'9\\\': ABCMeta(_name=\\\'9\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 205kB\\nDimensions: (time: 440, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 218.5 219.0 219.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 442\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c081...\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 79kB ...\\n atXYZ (time, atom, direction) float32 26kB 3.658 ... -0.1813\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 42kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.449 ... 1.186\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 442\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00012\\n trajid: 12\\n DataTree_Level: 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\\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': \\\'0\\\', \\\'n_property1d\\\': \\\'1\\\', \\\'n_property2d\\\': \\\'1\\\', \\\'laser\\\': \\\'0\\\'}, \\\'output.lis\\\': {\\\'nsteps\\\': 442, \\\'delta_t\\\': 0.5, \\\'t_max\\\': 220.5}, \\\'output.log\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': \\\'3\\\', \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-2750\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', 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\\\'__shnitsel_setup_for_cleanup\\\': True}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'11\\\': ABCMeta(_name=\\\'11\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 206kB\\nDimensions: (time: 443, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 220.0 220.5 221.0\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 445\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c082...\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 80kB ...\\n atXYZ (time, atom, direction) float32 27kB 3.79 ... 1.317\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 43kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 4kB 0.0 0.1743 ... 0.0\\n length_filtranda (length_criterion, time) float32 4kB 1.436 ... 1.133\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 445\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00014\\n trajid: 14\\n DataTree_Level: TrajectoryData\\n trajectory_id: 1644969181\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08208720>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 445, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-8375\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': \\\'0\\\', \\\'integrator\\\': \\\'2\\\', \\\'maxmult\\\': \\\'1\\\', \\\'nstates_m\\\': \\\'3\\\', \\\'natom\\\': \\\'14\\\', \\\'dtstep\\\': \\\'20.670686894780374\\\', \\\'nsteps\\\': \\\'2000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'ezero\\\': \\\'-248.27812829999999\\\', \\\'write_overlap\\\': \\\'1\\\', \\\'write_grad\\\': \\\'1\\\', \\\'write_nacdr\\\': \\\'0\\\', \\\'write_property1d\\\': \\\'0\\\', \\\'write_property2d\\\': 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(atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 450\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c037...\\nData variables:\\n energy (time, state) float32 5kB ...\\n forces (time, state, atom, direction) float32 78kB ...\\n atXYZ (time, atom, direction) float32 26kB 3.686 ... 1.709\\n dip_perm (time, state, direction) float32 16kB ...\\n dip_trans (time, statecomb, direction) float32 16kB ...\\n socs (time, full_statecomb) complex128 41kB ...\\n phases (time, state) float32 5kB ...\\n energy_filtranda (energy_criterion, time) float32 3kB 0.0 0.0874 ... 0.0\\n length_filtranda (length_criterion, time) float32 3kB 1.469 ... 1.181\\nAttributes: (12/17)\\n input_format: sharc\\n t_max: 1000.0\\n delta_t: 0.5\\n max_ts: 450\\n completed: False\\n input_type: dynamic\\n ... ...\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"...\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00017\\n trajid: 17\\n DataTree_Level: TrajectoryData\\n trajectory_id: 371103181\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c037104f0>, _is_multi_trajectory=False), _children={}, _attrs={\\\'input_format\\\': \\\'sharc\\\', \\\'t_max\\\': 1000.0, \\\'delta_t\\\': 0.5, \\\'max_ts\\\': 450, \\\'completed\\\': False, \\\'input_type\\\': \\\'dynamic\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'num_singlets\\\': 3, \\\'num_doublets\\\': 0, \\\'num_triplets\\\': 0, \\\'has_forces\\\': True, \\\'misc_input_settings\\\': {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'"geom"\\\', \\\'veloc\\\': \\\'external\\\', \\\'velocfile\\\': \\\'"veloc"\\\', \\\'nstates\\\': [3], \\\'actstates\\\': \\\'3\\\', \\\'state\\\': \\\'2 mch\\\', \\\'coeff\\\': \\\'auto\\\', \\\'rngseed\\\': \\\'-29587\\\', \\\'ezero\\\': \\\'-248.2781283000\\\', \\\'tmax\\\': \\\'1000.000000\\\', \\\'stepsize\\\': \\\'0.500000\\\', \\\'nsubsteps\\\': \\\'25\\\', \\\'integrator\\\': \\\'fvv\\\', \\\'method\\\': \\\'tsh\\\', \\\'surf\\\': \\\'diagonal\\\', \\\'coupling\\\': \\\'overlap\\\', \\\'nogradcorrect\\\': True, \\\'ekincorrect\\\': \\\'parallel_vel\\\', \\\'reflect_frustrated\\\': \\\'none\\\', \\\'decoherence_scheme\\\': \\\'edc\\\', \\\'decoherence_param\\\': \\\'0.1\\\', \\\'hopping_procedure\\\': \\\'sharc\\\', \\\'grad_all\\\': True, \\\'eselect\\\': \\\'0.001000\\\', \\\'select_directly\\\': True, \\\'nospinorbit\\\': True, \\\'write_grad\\\': True, \\\'write_nacdr\\\': True, \\\'write_overlap\\\': True, \\\'output_format\\\': \\\'ascii\\\', \\\'output_dat_steps\\\': \\\'1\\\'}, \\\'output.dat\\\': {\\\'SHARC_version\\\': \\\'3.0\\\', \\\'method\\\': 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ABCMeta(_name=\\\'13\\\', _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 95kB\\nDimensions: (time: 204, state: 3, atom: 5, direction: 3,\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\n length_criterion: 2)\\nCoordinates: (12/26)\\n * time (time) float64 2kB 0.0 0.5 1.0 ... 100.5 101.0 101.5\\n * state (state) int64 24B 1 2 3\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 24B MultiIndex\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\n ... ...\\n max_ts int64 8B 449\\n t_max float64 8B 1e+03\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c082...\\nData variables:\\n energy (time, state) float32 2kB ...\\n forces (time, state, atom, direction) 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0x744c...\\\\\\\\nData variables:\\\\\\\\n energy (time, state) float32 5kB -94.4 -94.06 ... -93.89\\\\\\\\n forces (time, state, atom, direction) float32 69kB -0.06...\\\\\\\\n atXYZ (time, atom, direction) float32 5kB -0.005705 ......\\\\\\\\n nacs (time, statecomb, atom, direction) float32 412kB ...\\\\\\\\n dip_perm (time, state, direction) float32 14kB -0.06869 .....\\\\\\\\n dip_trans (time, statecomb, direction) float32 82kB 0.07728...\\\\\\\\n socs (time, full_statecomb) complex128 220kB 0j ... -4...\\\\\\\\n phases (time, state) float32 5kB -1.0 -1.0 -1.0 ... 1.0 1.0\\\\\\\\n energy_filtranda (energy_criterion, time) float32 704B 0.0 ... 0.0\\\\\\\\n length_filtranda (length_criterion, time) float32 704B 1.324 ... 1...\\\\\\\\nAttributes: (12/15)\\\\\\\\n input_format: sharc\\\\\\\\n _shnitsel_setup_for_cleanup: True\\\\\\\\n completed: False\\\\\\\\n input_type: dynamic\\\\\\\\n input_format_version: 3.0\\\\\\\\n num_singlets: 4\\\\\\\\n ... ...\\\\\\\\n theory_basis_set: cc-pVDZ\\\\\\\\n est_level: CASSCF\\\\\\\\n misc_input_settings: {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'...\\\\\\\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\\\\\\\n trajectory_id: 1\\\\\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0823..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\\\\\\\\\\\\\'DataLeaf\\\\\\\\\\\\\\\'), \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\': ABCMeta(_name=2, _dtype=<class \\\\\\\\\\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\\\\\\\\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 293kB\\\\\\\\nDimensions: (time: 31, state: 13, atom: 5, direction: 3,\\\\\\\\n statecomb: 78, full_statecomb: 156,\\\\\\\\n energy_criterion: 2, length_criterion: 2)\\\\\\\\nCoordinates: (12/28)\\\\\\\\n * time (time) float64 248B 0.0 0.5 1.0 ... 14.0 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energy_filtranda (energy_criterion, time) float32 632B 0.0 ... 0.0\\\\\\\\n length_filtranda (length_criterion, time) float32 632B 1.302 ... 1...\\\\\\\\nAttributes: (12/15)\\\\\\\\n input_format: sharc\\\\\\\\n _shnitsel_setup_for_cleanup: True\\\\\\\\n completed: False\\\\\\\\n input_type: dynamic\\\\\\\\n input_format_version: 3.0\\\\\\\\n num_singlets: 4\\\\\\\\n ... ...\\\\\\\\n theory_basis_set: cc-pVDZ\\\\\\\\n est_level: CASSCF\\\\\\\\n misc_input_settings: {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'...\\\\\\\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\\\\\\\n trajectory_id: 3\\\\\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0378..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\\\\\\\\\\\\\'DataLeaf\\\\\\\\\\\\\\\')}, _attrs={}, _parent=<class 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_data=None, _children={\\\'1\\\': ABCMeta(_name=1, _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 820kB\\nDimensions: (time: 88, state: 13, atom: 5, direction: 3,\\n statecomb: 78, full_statecomb: 156,\\n energy_criterion: 2, length_criterion: 2)\\nCoordinates: (12/28)\\n * time (time) float64 704B 0.0 0.5 1.0 ... 42.5 43.0 43.5\\n * state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 624B MultiIndex\\n * full_statecomb (full_statecomb) object 1kB MultiIndex\\n ... ...\\n max_ts int64 8B 90\\n t_max float64 8B 100.0\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c...\\nData variables:\\n energy (time, state) float32 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test_data/sharc/traj_I01_v3.0_triplets_nacs...\\n trajectory_id: 1\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0823..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'2\\\': ABCMeta(_name=2, _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 293kB\\nDimensions: (time: 31, state: 13, atom: 5, direction: 3,\\n statecomb: 78, full_statecomb: 156,\\n energy_criterion: 2, length_criterion: 2)\\nCoordinates: (12/28)\\n * time (time) float64 248B 0.0 0.5 1.0 ... 14.0 14.5 15.0\\n * state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 624B MultiIndex\\n * full_statecomb (full_statecomb) object 1kB MultiIndex\\n ... ...\\n max_ts int64 8B 108\\n t_max float64 8B 100.0\\n charge int64 8B 1\\n energy_thresholds 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... ...\\n theory_basis_set: cc-pVDZ\\n est_level: CASSCF\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'...\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\n trajectory_id: 2\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0376..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\'DataLeaf\\\'), \\\'3\\\': ABCMeta(_name=3, _dtype=<class \\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 737kB\\nDimensions: (time: 79, state: 13, atom: 5, direction: 3,\\n statecomb: 78, full_statecomb: 156,\\n energy_criterion: 2, length_criterion: 2)\\nCoordinates: (12/28)\\n * time (time) float64 632B 0.0 0.5 1.0 ... 38.0 38.5 39.0\\n * state (state) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13\\n * atom (atom) int64 40B 0 1 2 3 4\\n * direction (direction) <U1 12B \\\'x\\\' \\\'y\\\' \\\'z\\\'\\n * statecomb (statecomb) object 624B MultiIndex\\n * full_statecomb (full_statecomb) object 1kB MultiIndex\\n ... ...\\n max_ts int64 8B 179\\n t_max float64 8B 100.0\\n charge int64 8B 1\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\n length_thresholds (length_criterion) float64 16B 3.0 2.0\\n __mol object 8B <rdkit.Chem.rdchem.Mol object at 0x744c...\\nData variables:\\n energy (time, state) float32 4kB -94.38 -94.07 ... -93.79\\n forces (time, state, atom, direction) float32 62kB 0.054...\\n atXYZ (time, atom, direction) float32 5kB 0.02998 ... -...\\n nacs (time, statecomb, atom, direction) float32 370kB ...\\n dip_perm (time, state, direction) float32 12kB -0.1124 ......\\n dip_trans (time, statecomb, direction) float32 74kB -0.1073...\\n socs (time, full_statecomb) complex128 197kB 0j ... 18...\\n phases (time, state) float32 4kB -1.0 -1.0 -1.0 ... 1.0 1.0\\n energy_filtranda (energy_criterion, time) float32 632B 0.0 ... 0.0\\n length_filtranda (length_criterion, time) float32 632B 1.302 ... 1...\\nAttributes: (12/15)\\n input_format: sharc\\n _shnitsel_setup_for_cleanup: True\\n completed: False\\n input_type: dynamic\\n input_format_version: 3.0\\n num_singlets: 4\\n ... ...\\n theory_basis_set: cc-pVDZ\\n est_level: CASSCF\\n misc_input_settings: {\\\'input\\\': {\\\'printlevel\\\': \\\'2\\\', \\\'geomfile\\\': \\\'...\\n trajectory_input_path: test_data/sharc/traj_I01_v3.0_triplets_nacs...\\n trajectory_id: 3\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c0378..., _is_multi_trajectory=False), _children={}, _attrs={}, _parent=..., _level_name=\\\'DataLeaf\\\')}, _attrs={}, _parent=<class \\\'shnitsel.data.tree.tree.ShnitselDBRoot[Trajectory]\\\'> [{\\\'level\\\': \\\'ShnitselDBRoot\\\', \\\'children\\\': \\\'2: {\\\\\\\'I02\\\\\\\': \\\\\\\'ABCMeta(_name=\\\\\\\\\\\\\\\'I02\\\\\\\\\\\\\\\', _dtype=<class \\\\\\\\\\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\\\\\\\\\\'>, _data=None, _children={\\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\': ABCMeta(_name=\\\\\\\\\\\\\\\'0\\\\\\\\\\\\\\\', _dtype=<class \\\\\\\\\\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\\\\\\\\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 178kB\\\\\\\\nDimensions: (time: 382, state: 3, atom: 5, direction: 3,\\\\\\\\n statecomb: 3, full_statecomb: 6, energy_criterion: 2,\\\\\\\\n length_criterion: 2)\\\\\\\\nCoordinates: (12/26)\\\\\\\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 189.5 190.0 190.5\\\\\\\\n * state (state) int64 24B 1 2 3\\\\\\\\n * atom (atom) int64 40B 0 1 2 3 4\\\\\\\\n * direction (direction) <U1 12B \\\\\\\\\\\\\\\'x\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'y\\\\\\\\\\\\\\\' \\\\\\\\\\\\\\\'z\\\\\\\\\\\\\\\'\\\\\\\\n * statecomb (statecomb) object 24B MultiIndex\\\\\\\\n * full_statecomb (full_statecomb) object 48B MultiIndex\\\\\\\\n ... ...\\\\\\\\n max_ts int64 8B 384\\\\\\\\n t_max float64 8B 1e+03\\\\\\\\n charge int64 8B 1\\\\\\\\n energy_thresholds (energy_criterion) float64 16B 0.7 1.0\\\\\\\\n 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{\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"geom"...\\\\\\\\n trajectory_input_path: retinal_tutorial/I02/TRAJ_00001\\\\\\\\n trajid: 1\\\\\\\\n DataTree_Level: TrajectoryData\\\\\\\\n trajectory_id: 1027217349\\\\\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x744c08282430>, _is_multi_trajectory=False), _children={}, _attrs={\\\\\\\\\\\\\\\'input_format\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'sharc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'t_max\\\\\\\\\\\\\\\': 1000.0, \\\\\\\\\\\\\\\'delta_t\\\\\\\\\\\\\\\': 0.5, \\\\\\\\\\\\\\\'max_ts\\\\\\\\\\\\\\\': 384, \\\\\\\\\\\\\\\'completed\\\\\\\\\\\\\\\': False, \\\\\\\\\\\\\\\'input_type\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'dynamic\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'input_format_version\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3.0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'num_singlets\\\\\\\\\\\\\\\': 3, \\\\\\\\\\\\\\\'num_doublets\\\\\\\\\\\\\\\': 0, \\\\\\\\\\\\\\\'num_triplets\\\\\\\\\\\\\\\': 0, \\\\\\\\\\\\\\\'has_forces\\\\\\\\\\\\\\\': True, \\\\\\\\\\\\\\\'misc_input_settings\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'input\\\\\\\\\\\\\\\': {\\\\\\\\\\\\\\\'printlevel\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'geomfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"geom"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'veloc\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'external\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'velocfile\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'"veloc"\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'nstates\\\\\\\\\\\\\\\': [3], \\\\\\\\\\\\\\\'actstates\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'state\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'2 mch\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'coeff\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'auto\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'rngseed\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'5199\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'ezero\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'-248.2781283000\\\\\\\\\\\\\\\', 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_group_info=GroupInfo(group_name="TrajectoryGroupingMetadata(delta_t_in_fs=0.5, input_format_name=\\\'sharc\\\', input_format_version=\\\'3.0\\\', est_level=\\\'CASSCF\\\', theory_basis_set=\\\'cc-pVDZ\\\', charge_in_e=1.0, num_states=13)", group_attributes={\\\'delta_t_in_fs\\\': 0.5, \\\'input_format_name\\\': \\\'sharc\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'est_level\\\': \\\'CASSCF\\\', \\\'theory_basis_set\\\': \\\'cc-pVDZ\\\', \\\'charge_in_e\\\': 1.0, \\\'num_states\\\': 13}, grouped_properties=None))\'}'}]2.2) Calculate descriptors#
Upon creating the dataset from the matching substructures of all compounds, we can now compute descriptors. Note, the atom numbering was adjusted, so that we can use descriptors that are sensitive to permutation. Since we only searched for 4 atoms in common, the bats, i.e. bonds, angles torsion would only yield 6 descriptors (\(3\cdot 4 - 6 = 6\)). Similarly, there are 6 pairwise distances in the molecule (\(\frac{1}{2}\cdot 4\cdot(4-1) = 6\)).
One could apply the seperate functions subtract_combinations, center, and norm to obtain the pairwise distances, subtract the mean and normalize the features. This is also wrapped in a pipeline within the get_standardized_pairwise_dists function provided in shnitsel.analyze.generic, which we will use in the following. Note, we have to transpose the resulting array, as the PCA requires the data in shape (frames, descriptors).
[7]:
# first we perform PCA over pairwise distances for the whole A03 molecule
from shnitsel.vis.plot import biplot_kde
from shnitsel.analyze.pca import PCA
I02_analog_stacked = analogs_tree["I02"].as_stacked
I02_analog_stacked.mol
/home/tpadmin/git/shnitsel-tools-official/shnitsel/data/traj_combiner_methods.py:491: FutureWarning: In a future version of xarray the default value for compat will change from compat='equals' to compat='override'. This change will result in the following ValueError: Cannot specify both coords='different' and compat='override'. The recommendation is to set compat explicitly for this case.
frames = xr.concat(
[7]:
[8]:
from shnitsel.geo.geocalc import get_bats
selection_keys = ['bonds', 'angles', 'dihedrals', 'pyramids']
# Calculate all BATs for all analogs:
dt_analog_bats_all = get_bats(analogs_tree, selection_keys)
# Get the data for just I02 as one dataset
# I02_analog_bats = dt_analog_bats_all["I02"]#.as_stacked
# print(I02_analog_bats)
# Calculate the PCA for I02
pca_res_I02 = PCA(analogs_tree["I02"], structure_selection=selection_keys)
#Since we provided the inputs as a tree, the result is also a tree:
pca_res_I02
[8]:
ABCMeta(_name='I02', _dtype=<class 'shnitsel.analyze.pca.PCAResult'>, _data=None, _children={'pca': ABCMeta(_name='pca', _dtype=<class 'shnitsel.analyze.pca.PCAResult'>, _data=<shnitsel.analyze.pca.PCAResult object at 0x744c082ff3e0>, _children={}, _attrs={}, _parent=..., _level_name='DataLeaf')}, _attrs={'DataTree_Level': 'CompoundGroup', 'compound_info': {'compound_name': 'I02'}}, _parent=None, _level_name='CompoundGroup', _group_info=GroupInfo(group_name="TrajectoryGroupingMetadata(delta_t_in_fs=0.5, input_format_name='sharc', input_format_version='3.0', est_level=None, theory_basis_set=None, charge_in_e=1.0, num_states=3)", group_attributes={'delta_t_in_fs': 0.5, 'input_format_name': 'sharc', 'input_format_version': '3.0', 'est_level': None, 'theory_basis_set': None, 'charge_in_e': 1.0, 'num_states': 3}, grouped_properties=None))[9]:
# We can obtain the PCA result:
pca_res_I02_unwrapped = pca_res_I02["/pca"].data
# And take a look at the most impactful features identified by PCA:
display(I02_analog_stacked.mol)
print(pca_res_I02_unwrapped.explain_loadings())
Maximum contributing features overall:
dih(2,1,0,4) (weight: 0.3931517004966736) (Idxs: (2, 1, 0, 4))
dih(3,1,0,4) (weight: 0.532825767993927) (Idxs: (3, 1, 0, 4))
dist(0,1) (weight: 0.5414503812789917) (Idxs: (np.int64(0), np.int64(1)))
angle(1,0,4) (weight: 0.5417289733886719) (Idxs: (1, 0, 4))
pyr(1,(0,2,3)) (weight: 0.9353857636451721) (Idxs: (1, (0, 2, 3)))
Maximum contributing features to component 0 :
angle(2,1,3) (weight: -0.12271258980035782) (Idxs: (2, 1, 3))
dist(0,1) (weight: 0.1403753012418747) (Idxs: (np.int64(0), np.int64(1)))
dih(2,1,0,4) (weight: -0.2322123497724533) (Idxs: (2, 1, 0, 4))
dih(3,1,0,4) (weight: 0.347022145986557) (Idxs: (3, 1, 0, 4))
pyr(1,(0,2,3)) (weight: 0.8822901844978333) (Idxs: (1, (0, 2, 3)))
Maximum contributing features to component 1 :
pyr(1,(0,2,3)) (weight: 0.3106614649295807) (Idxs: (1, (0, 2, 3)))
dih(2,1,0,4) (weight: 0.31724703311920166) (Idxs: (2, 1, 0, 4))
dih(3,1,0,4) (weight: -0.4043252766132355) (Idxs: (3, 1, 0, 4))
dist(0,1) (weight: -0.5229371786117554) (Idxs: (np.int64(0), np.int64(1)))
angle(1,0,4) (weight: 0.541694700717926) (Idxs: (1, 0, 4))
[10]:
# We can also take a look at the visualized results:
kde_data = biplot_kde(
analogs_tree["I02"], 1, (0, 2, 3), pca_data=pca_res_I02, num_bins=4, scatter_color_property="geo"
)
3) Compare Compounds#
We have started with different compounds, so it just seems reasonable to try and see, how the PCA of these different compounds compare. For this, we can simply apply the PCA to the combined tree and plot the analysis result, which will be performed on each component separately
[11]:
pca_res = PCA(analogs_tree, structure_selection=selection_keys)
kde_plot = biplot_kde(
analogs_tree, 1, (0, 2, 3), pca_data=pca_res, num_bins=4, scatter_color_property="geo"
)
Let us take a look at the loadings of the different PCA results:
[12]:
for path, pca_data in pca_res.collect_data(with_path = True):
print(f"Results for entry {path}")
print(pca_data.explain_loadings())
Results for entry /I02/pca/
Maximum contributing features overall:
dih(2,1,0,4) (weight: 0.3931517004966736) (Idxs: (2, 1, 0, 4))
dih(3,1,0,4) (weight: 0.532825767993927) (Idxs: (3, 1, 0, 4))
dist(0,1) (weight: 0.5414503812789917) (Idxs: (np.int64(0), np.int64(1)))
angle(1,0,4) (weight: 0.5417289733886719) (Idxs: (1, 0, 4))
pyr(1,(0,2,3)) (weight: 0.9353857636451721) (Idxs: (1, (0, 2, 3)))
Maximum contributing features to component 0 :
angle(2,1,3) (weight: -0.12271258980035782) (Idxs: (2, 1, 3))
dist(0,1) (weight: 0.1403753012418747) (Idxs: (np.int64(0), np.int64(1)))
dih(2,1,0,4) (weight: -0.2322123497724533) (Idxs: (2, 1, 0, 4))
dih(3,1,0,4) (weight: 0.347022145986557) (Idxs: (3, 1, 0, 4))
pyr(1,(0,2,3)) (weight: 0.8822901844978333) (Idxs: (1, (0, 2, 3)))
Maximum contributing features to component 1 :
pyr(1,(0,2,3)) (weight: 0.3106614649295807) (Idxs: (1, (0, 2, 3)))
dih(2,1,0,4) (weight: 0.31724703311920166) (Idxs: (2, 1, 0, 4))
dih(3,1,0,4) (weight: -0.4043252766132355) (Idxs: (3, 1, 0, 4))
dist(0,1) (weight: -0.5229371786117554) (Idxs: (np.int64(0), np.int64(1)))
angle(1,0,4) (weight: 0.541694700717926) (Idxs: (1, 0, 4))
Results for entry /I01/pca/
Maximum contributing features overall:
dist(1,3) (weight: 0.4587743580341339) (Idxs: (np.int64(1), np.int64(3)))
angle(0,1,2) (weight: 0.4637525677680969) (Idxs: (0, 1, 2))
dih(3,1,0,4) (weight: 0.585440993309021) (Idxs: (3, 1, 0, 4))
dist(0,1) (weight: 0.5890254378318787) (Idxs: (np.int64(0), np.int64(1)))
pyr(1,(0,2,3)) (weight: 0.6744986176490784) (Idxs: (1, (0, 2, 3)))
Maximum contributing features to component 0 :
dist(1,2) (weight: -0.1441391408443451) (Idxs: (np.int64(1), np.int64(2)))
dih(3,1,0,4) (weight: 0.38052231073379517) (Idxs: (3, 1, 0, 4))
angle(0,1,2) (weight: -0.4624028205871582) (Idxs: (0, 1, 2))
pyr(1,(0,2,3)) (weight: 0.49887949228286743) (Idxs: (1, (0, 2, 3)))
dist(0,1) (weight: 0.5835738182067871) (Idxs: (np.int64(0), np.int64(1)))
Maximum contributing features to component 1 :
dist(1,2) (weight: 0.270281583070755) (Idxs: (np.int64(1), np.int64(2)))
dih(2,1,0,4) (weight: 0.34814438223838806) (Idxs: (2, 1, 0, 4))
dih(3,1,0,4) (weight: -0.4449089467525482) (Idxs: (3, 1, 0, 4))
dist(1,3) (weight: 0.4497644007205963) (Idxs: (np.int64(1), np.int64(3)))
pyr(1,(0,2,3)) (weight: 0.45394670963287354) (Idxs: (1, (0, 2, 3)))
We see that the pyramidalization around the center N-atom with index 1 is shared between both compounds. But the remaining parameters may look different.
To visually compare the geometrical space exploration of the two compounds, we can now project the features for both components onto the same principal components. Let us use I01 as the basis and then project the results for I02 onto the same subspace.
For this purpose, we can use the tree of BATs for all compounds and use the helper method .project_array() of the PCAResult class:
[13]:
# Retrieve the PCA for I01
pca_res_I01 = pca_res["I01/pca"].data
# Project all features onto the principal components for I01
# The pca result offers the function `.project_array` to project an arbitrary array onto the results of the PCA pipeline
# We
I01_projected_features = dt_analog_bats_all.map_data(pca_res_I01.project_array)
I01_projected_features
ERROR:root:"The 'units' attribute of the DataArray must be set and of type str."
ERROR:root:"The 'units' attribute of the DataArray must be set and of type str."
[13]:
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group_attributes={\\\\\\\\\\\\\\\'delta_t_in_fs\\\\\\\\\\\\\\\': 0.5, \\\\\\\\\\\\\\\'input_format_name\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'sharc\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'input_format_version\\\\\\\\\\\\\\\': \\\\\\\\\\\\\\\'3.0\\\\\\\\\\\\\\\', \\\\\\\\\\\\\\\'est_level\\\\\\\\\\\\\\\': None, \\\\\\\\\\\\\\\'theory_basis_set\\\\\\\\\\\\\\\': None, \\\\\\\\\\\\\\\'charge_in_e\\\\\\\\\\\\\\\': 1.0, \\\\\\\\\\\\\\\'num_states\\\\\\\\\\\\\\\': 3}, grouped_properties=None))\\\\\\\', \\\\\\\'I01\\\\\\\': \\\\\\\'...\\\\\\\'}\\\'}], _level_name=\\\'CompoundGroup\\\', _group_info=GroupInfo(group_name="TrajectoryGroupingMetadata(delta_t_in_fs=0.5, input_format_name=\\\'sharc\\\', input_format_version=\\\'3.0\\\', est_level=\\\'CASSCF\\\', theory_basis_set=\\\'cc-pVDZ\\\', charge_in_e=1.0, num_states=13)", group_attributes={\\\'delta_t_in_fs\\\': 0.5, \\\'input_format_name\\\': \\\'sharc\\\', \\\'input_format_version\\\': \\\'3.0\\\', \\\'est_level\\\': \\\'CASSCF\\\', \\\'theory_basis_set\\\': \\\'cc-pVDZ\\\', \\\'charge_in_e\\\': 1.0, \\\'num_states\\\': 13}, grouped_properties=None))\'}'}]Now we just need to plot the data for the different compounds into a graph:
[14]:
from shnitsel.analyze.hops import filter_data_at_hops
from shnitsel.vis.colormaps import st_grey, st_yellow, st_orange
fig, axs = plt.subplot_mosaic([['I01', 'I02']], layout='constrained')
for ax_name, ax in axs.items():
ax.set_title(ax_name)
for compound_name, data in I01_projected_features.compounds.items():
ax.plot(data.as_stacked.isel(PC=0), data.as_stacked.isel(PC=1), c='#ccc', rasterized=True)
compound_data = I01_projected_features[ax_name].as_stacked
if ax_name == 'I01':
compound_color = st_yellow # if dih_end < 70 else '#2c3e50' if dih_end > 110 else 'gray'
else:
compound_color = st_grey
ax.plot(compound_data.isel(PC=0), compound_data.isel(PC=1), c=compound_color, rasterized=True)
hops_positions_21 = filter_data_at_hops(compound_data, "2->1")
hops_positions_32 = filter_data_at_hops(compound_data, "3->2")
ax.scatter(hops_positions_21.isel(PC=0), hops_positions_21.isel(PC=1), c=st_orange, s=1, zorder=10, rasterized=True)
ax.scatter(hops_positions_32.isel(PC=0), hops_positions_32.isel(PC=1), c='#0D6F71', s=1, zorder=10, rasterized=True)
fig.supxlabel('PC1')
fig.supylabel('PC2')
fig.savefig("./PCA_across_compounds_I01_I02_proj1.pdf", dpi=300)
[15]:
# Retrieve the PCA for I02
pca_res_I02 = pca_res["I02/pca"].data
# Project all features onto the principal components for I02
# The pca result offers the function `.project_array` to project an arbitrary array onto the results of the PCA pipeline
# We
I02_projected_features = dt_analog_bats_all.map_data(pca_res_I02.project_array)
I02_projected_features
ERROR:root:"The 'units' attribute of the DataArray must be set and of type str."
ERROR:root:"The 'units' attribute of the DataArray must be set and of type str."
[15]:
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from shnitsel.analyze.hops import filter_data_at_hops
from shnitsel.vis.colormaps import st_grey, st_yellow, st_orange
fig, axs = plt.subplot_mosaic([['I01', 'I02']], layout='constrained')
for ax_name, ax in axs.items():
ax.set_title(ax_name)
for compound_name, data in I02_projected_features.compounds.items():
ax.plot(data.as_stacked.isel(PC=0), data.as_stacked.isel(PC=1), c="#ccc", rasterized=True)
compound_data = I02_projected_features[ax_name].as_stacked
if ax_name == 'I01':
compound_color = st_yellow # if dih_end < 70 else '#2c3e50' if dih_end > 110 else 'gray'
else:
compound_color = st_grey
ax.plot(compound_data.isel(PC=0), compound_data.isel(PC=1), c=compound_color, rasterized=True)
hops_positions_21 = filter_data_at_hops(compound_data, "2->1")
hops_positions_32 = filter_data_at_hops(compound_data, "3->2")
ax.scatter(hops_positions_21.isel(PC=0), hops_positions_21.isel(PC=1), c=st_orange, s=1, zorder=10, rasterized=True)
ax.scatter(hops_positions_32.isel(PC=0), hops_positions_32.isel(PC=1), c='#0D6F71', s=1, zorder=10, rasterized=True)
fig.supxlabel('PC1')
fig.supylabel('PC2')
fig.savefig("./PCA_across_compounds_I01_I02_proj2.pdf", dpi=300)
In either projection (to the PC of I01 or I02), it becomes apparent that both compounds cover distinct regions of phase space with hops between different states notably happening in entirely different regions of phase space.