{ "cells": [ { "cell_type": "markdown", "id": "e9117ac9-b160-45ef-9d8f-b591b797f2ab", "metadata": {}, "source": [ "# Full tutorial\n", "\n", "In this tutorial, we want to demonstrate the full workflow of shnitsel tools from import to final analysis and output. \n", "Due to size constraints in git, we will use an already compressed shnitsel-file input for Retinal as a basis.\n", "Please refer to the `./0_general_io` tutorial notebook for information on how to read arbitrary input.\n" ] }, { "cell_type": "code", "execution_count": 1, "id": "a00fb44f-5ada-4f14-8829-e9f0ef880470", "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "import seaborn as sns\n", "\n", "import shnitsel as st\n", "import shnitsel.xarray\n" ] }, { "cell_type": "markdown", "id": "2a0f1c9f-0aea-483c-8265-d934940eee64", "metadata": {}, "source": [ "## 1) Import and preparation of data\n", "### 1.1) Loading data\n", "\n", "We use the generic `st.io.read()` function to import an existing shnitsel-tools file. \n", "Here, we could in principle also read from a collection of trajectories produced by one of the supported import formats: `NewtonX`, `SHARC`, `PyRAI2md` or `ASE`." ] }, { "cell_type": "code", "execution_count": 2, "id": "e7117390-21c1-465e-a3e8-10071d728b0d", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 397kB\\\\nDimensions: (time: 451, state: 3, atom: 14, direction: 3,\\\\n statecomb: 3, full_statecomb: 6)\\\\nCoordinates: (12/21)\\\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 224.0 224.5 225.0\\\\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 * full_statecomb_from (full_statecomb) int64 48B 1 1 2 2 3 3\\\\n * full_statecomb_to (full_statecomb) int64 48B 2 3 1 3 1 2\\\\n delta_t float64 8B 0.5\\\\n max_ts int64 8B 451\\\\n t_max float64 8B 1e+03\\\\n charge float64 8B 1.0\\\\nData variables:\\\\n energy (time, state) float32 5kB ...\\\\n forces (time, state, atom, direction) float32 227kB ...\\\\n atXYZ (time, atom, direction) float32 76kB ...\\\\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 ...\\\\nAttributes: (12/17)\\\\n input_format: sharc\\\\n t_max: 1000.0\\\\n delta_t: 0.5\\\\n max_ts: 451\\\\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_00013\\\\n trajid: 13\\\\n DataTree_Level: TrajectoryData\\\\n trajectory_id: 376892732\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x710aca072930>, _is_multi_trajectory=False), _children={}, _attrs={\\\\\\'input_format\\\\\\': \\\\\\'sharc\\\\\\', \\\\\\'t_max\\\\\\': 1000.0, \\\\\\'delta_t\\\\\\': 0.5, \\\\\\'max_ts\\\\\\': 451, \\\\\\'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\\\\\\': \\\\\\'31118\\\\\\', \\\\\\'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\\\\\\': 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\\\\\\'output_format\\\\\\': \\\\\\'ascii\\\\\\', \\\\\\'output_dat_steps\\\\\\': \\\\\\'1\\\\\\', \\\\\\'version\\\\\\': \\\\\\'3.0\\\\\\'}}, \\\\\\'trajectory_input_path\\\\\\': \\\\\\'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: 392kB\\\\nDimensions: (time: 445, state: 3, atom: 14, direction: 3,\\\\n statecomb: 3, full_statecomb: 6)\\\\nCoordinates: (12/21)\\\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 221.0 221.5 222.0\\\\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 * full_statecomb_from (full_statecomb) int64 48B 1 1 2 2 3 3\\\\n * full_statecomb_to (full_statecomb) int64 48B 2 3 1 3 1 2\\\\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\\\\nData variables:\\\\n energy (time, state) float32 5kB ...\\\\n forces (time, state, atom, direction) float32 224kB ...\\\\n atXYZ (time, atom, direction) float32 75kB ...\\\\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 ...\\\\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: 672939289\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x710aca08bec0>, _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, 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\\\\\\'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_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: 397kB\\\\nDimensions: (time: 450, state: 3, atom: 14, direction: 3,\\\\n statecomb: 3, full_statecomb: 6)\\\\nCoordinates: (12/21)\\\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 223.5 224.0 224.5\\\\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 * full_statecomb_from (full_statecomb) int64 48B 1 1 2 2 3 3\\\\n * full_statecomb_to (full_statecomb) int64 48B 2 3 1 3 1 2\\\\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\\\\nData variables:\\\\n energy (time, state) float32 5kB ...\\\\n forces (time, state, atom, direction) float32 227kB ...\\\\n atXYZ 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\\\\\\'shnitsel.data.dataset_containers.trajectory.Trajectory\\\\\\'>, _data=Trajectory(_raw_dataset=<xarray.Dataset> Size: 295kB\\\\nDimensions: (time: 335, state: 3, atom: 14, direction: 3,\\\\n statecomb: 3, full_statecomb: 6)\\\\nCoordinates: (12/21)\\\\n * time (time) float64 3kB 0.0 0.5 1.0 ... 166.0 166.5 167.0\\\\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 * full_statecomb_from (full_statecomb) int64 48B 1 1 2 2 3 3\\\\n * full_statecomb_to (full_statecomb) int64 48B 2 3 1 3 1 2\\\\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\\\\nData variables:\\\\n energy (time, state) float32 4kB ...\\\\n forces (time, state, atom, direction) float32 169kB ...\\\\n atXYZ (time, atom, direction) float32 56kB ...\\\\n dip_perm (time, state, direction) float32 12kB ...\\\\n dip_trans (time, statecomb, direction) float32 12kB ...\\\\n socs (time, full_statecomb) complex128 32kB ...\\\\n phases (time, state) float32 4kB ...\\\\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: 1218685036\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x710aca0890d0>, _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\\\\\\': 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\\\\\\'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: 387kB\\\\nDimensions: (time: 439, state: 3, atom: 14, direction: 3,\\\\n statecomb: 3, full_statecomb: 6)\\\\nCoordinates: (12/21)\\\\n * time (time) float64 4kB 0.0 0.5 1.0 ... 218.0 218.5 219.0\\\\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 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\\\\\\'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, 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\\\\\\'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: 768373212\\\\n __mol: <rdkit.Chem.rdchem.Mol object at 0x710ac9eaa1b0>, _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\\\\\\': "1: {\\\\\\'I02\\\\\\': \\\\\\'...\\\\\\'}"}], _level_name=\\\\\\'CompoundGroup\\\\\\', _group_info=None)\\'}'}]<xarray.DataArray 'HOOP' (frame: 4892)> Size: 20kB\n",
"array([ -1.1290894, -2.127411 , -2.9948273, ..., -46.937065 ,\n",
" -49.536137 , -52.037926 ], shape=(4892,), dtype=float32)\n",
"Coordinates:\n",
" * frame (frame) object 39kB MultiIndex\n",
" astate (frame) int32 20kB 2 2 2 2 2 2 2 2 2 2 ... 1 1 1 1 1 1 1 1 1 1\n",
" sdiag (frame) int32 20kB 2 2 2 2 2 2 2 2 2 2 ... 1 1 1 1 1 1 1 1 1 1\n",
" charge float64 8B 1.0\n",
" * atrajectory (frame) int64 39kB 1 1 1 1 1 1 1 1 ... 20 20 20 20 20 20 20 20\n",
" * time (frame) float64 39kB 0.0 0.5 1.0 1.5 ... 217.0 217.5 218.0\n",
"Attributes:\n",
" units: degrees<xarray.DataArray 'BLA' (descriptor: 1, frame: 4892)> Size: 20kB\n",
"array([[0.10997677, 0.10950518, 0.10680151, ..., 0.12595081, 0.13470912,\n",
" 0.14393115]], shape=(1, 4892), dtype=float32)\n",
"Coordinates:\n",
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" * frame (frame) object 39kB MultiIndex\n",
" astate (frame) int32 20kB 2 2 2 2 2 2 2 2 2 ... 1 1 1 1 1 1 1 1 1\n",
" sdiag (frame) int32 20kB 2 2 2 2 2 2 2 2 2 ... 1 1 1 1 1 1 1 1 1\n",
" charge float64 8B 1.0\n",
" * atrajectory (frame) int64 39kB 1 1 1 1 1 1 1 1 ... 20 20 20 20 20 20 20\n",
" * time (frame) float64 39kB 0.0 0.5 1.0 1.5 ... 217.0 217.5 218.0\n",
" descriptor_tex (descriptor) <U3 12B 'BLA'\n",
" * descriptor_type (descriptor) <U3 12B 'bla'\n",
" * feature_indices (descriptor) object 8B (1, -1)\n",
"Attributes:\n",
" long_name: Bond length alternation (BLA)\n",
" unitdim: length\n",
" units: Bohr<xarray.DataArray 'distances' (descriptor: 28, frame: 4892)> Size: 548kB\n",
"array([[ 1.7274824 , 1.7531409 , 1.8007075 , ..., 2.0762656 ,\n",
" 2.0190077 , 1.9528676 ],\n",
" [ 2.7055476 , 2.6930227 , 2.6798398 , ..., 2.8368409 ,\n",
" 2.8123899 , 2.7849002 ],\n",
" [ 2.7028968 , 2.7058063 , 2.7092056 , ..., 2.910789 ,\n",
" 2.9275563 , 2.942532 ],\n",
" ...,\n",
" [ 0.9976716 , 0.9971196 , 0.99656 , ..., 0.9465555 ,\n",
" 0.9481291 , 0.94996953],\n",
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" 0.13470912, 0.14393115],\n",
" [ -1.1290894 , -2.127411 , -2.9948273 , ..., -46.937065 ,\n",
" -49.536137 , -52.037926 ]], shape=(28, 4892), dtype=float32)\n",
"Coordinates:\n",
" * descriptor (descriptor) <U21 2kB 'dist(11,13)' ... 'hoop(6,5,7,8|3,...\n",
" * frame (frame) object 39kB MultiIndex\n",
" astate (frame) int32 20kB 2 2 2 2 2 2 2 2 2 ... 1 1 1 1 1 1 1 1 1\n",
" sdiag (frame) int32 20kB 2 2 2 2 2 2 2 2 2 ... 1 1 1 1 1 1 1 1 1\n",
" charge float64 8B 1.0\n",
" * atrajectory (frame) int64 39kB 1 1 1 1 1 1 1 1 ... 20 20 20 20 20 20 20\n",
" * time (frame) float64 39kB 0.0 0.5 1.0 1.5 ... 217.0 217.5 218.0\n",
" descriptor_tex (descriptor) <U26 3kB '|\\\\vec{r}_{11,13}|' ... 'hoop(5,7...\n",
" * descriptor_type (descriptor) <U7 784B 'dist' 'dist' 'dist' ... 'bla' 'hoop'\n",
" * feature_indices (descriptor) object 224B (np.int64(11), np.int64(13)) .....\n",
"Attributes:\n",
" long_name: \\|\\mathbf{r}_{11,13}\\|\n",
" unitdim: length\n",
" units: Bohr"
],
"text/plain": [
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