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espottesmithespottesmith
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All tests now pass for reaction path workflow
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‎atomate/qchem/test_files/reaction_path_wf/block/launcher_backwards/.FW.json.swp‎

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‎atomate/qchem/test_files/reaction_path_wf/block/launcher_backwards/FW.json‎

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{
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"spec": {
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"tags": {
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"class": "autots_testing",
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"set": "20201111_li2o_paths"
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},
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"_tasks": [
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{
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"molecule": {
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"@module": "pymatgen.core.structure",
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"@class": "Molecule",
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"charge": 0,
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"spin_multiplicity": 2,
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"sites": [
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{
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"name": "O",
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"species": [
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{
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"element": "O",
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"occu": 1
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}
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],
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"xyz": [
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],
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"properties": {}
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},
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{
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"name": "C",
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"species": [
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"element": "C",
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"occu": 1
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}
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],
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"xyz": [
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],
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"properties": {}
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},
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{
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"name": "C",
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"species": [
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"element": "C",
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],
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"xyz": [
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],
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"properties": {}
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},
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{
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"name": "O",
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"species": [
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"element": "O",
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"occu": 1
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}
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],
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"xyz": [
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],
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"properties": {}
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},
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{
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"name": "O",
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"element": "O",
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}
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],
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"xyz": [
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"properties": {}
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},
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"name": "C",
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}
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"xyz": [
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"properties": {}
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},
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"name": "H",
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{
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"mode": [
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[
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[
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[
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],
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[
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],
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[
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0.015
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],
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[
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0.009,
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],
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[
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0.03,
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-0.015,
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-0.022
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]
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],
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"scale": -0.6,
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"_fw_name": "{{atomate.qchem.firetasks.geo_transformations.PerturbGeometry}}"
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},
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{
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"molecule": null,
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"qchem_input_set": "OptSet",
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"input_file": "mol.qin",
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"qchem_input_params": {
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"dft_rung": 4,
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"smd_solvent": "custom",
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"custom_smd": "18.5,1.415,0.00,0.735,20.2,0.00,0.00",
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"overwrite_inputs": {
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"rem": {
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"thresh": "14",
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"scf_algorithm": "diis"
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}
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}
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},
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"_fw_name": "{{atomate.qchem.firetasks.write_inputs.WriteInputFromIOSet}}"
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},
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{
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"qchem_cmd": ">>qchem_cmd<<",
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"multimode": ">>multimode<<",
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"input_file": "mol.qin",
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"output_file": "mol.qout",
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"max_cores": ">>max_cores<<",
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"job_type": "opt_with_frequency_flattener",
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"max_iterations": 10,
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"max_molecule_perturb_scale": 0.3,
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"linked": true,
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"freq_before_opt": false,
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"_fw_name": "{{atomate.qchem.firetasks.run_calc.RunQChemCustodian}}"
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},
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{
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"db_file": ">>db_file<<",
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"input_file": "mol.qin",
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"output_file": "mol.qout",
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"additional_fields": {
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"task_label": "C4 H5 O4:perturb_backwardshco__ec___ec_minus_h__formaldehyde",
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"special_run_type": "frequency_flattener",
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"linked": true
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},
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"_fw_name": "{{atomate.qchem.firetasks.parse_outputs.QChemToDb}}"
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}
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]
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},
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"fw_id": 830332,
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"created_on": "2020-11-12T15:30:45.825306",
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"updated_on": "2020-11-12T15:31:06.468693",
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"launches": [
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{
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"fworker": {
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"name": "lr_qchem_dev",
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"category": "",
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"query": "{\"spec.tags.class\": {\"$regex\": \"autots_testing\"}}",
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"env": {
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"db_file": "/global/home/users/ewcspottesmith/config/atomate/sam_db.json",
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"calc_loc": "/tmp",
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"qchem_cmd": "qchem -save",
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"max_cores": 40,
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"multimode": "openmp"
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}
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},
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"fw_id": 830332,
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"launch_dir": "/clusterfs/mp/ewcspottesmith/data/ts_testing/20201111_li2o_paths/block_2020-11-11-16-37-34-113586/launcher_2020-11-12-15-31-02-922842",
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"host": "n0081.lr6",
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"ip": "10.0.41.81",
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"trackers": [],
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"action": null,
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"state": "RUNNING",
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"state_history": [
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{
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"state": "RUNNING",
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"created_on": "2020-11-12T15:31:06.463592",
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"updated_on": "2020-11-12T15:31:06.463597"
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}
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],
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"launch_id": 634109
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}
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],
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"state": "RUNNING",
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"name": "C4 H5 O4:perturb_backwardshco__ec___ec_minus_h__formaldehyde"
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}

‎atomate/qchem/test_files/reaction_path_wf/block/launcher_backwards/FW_submit.script‎

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#!/bin/bash -l
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#SBATCH --nodes=1
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#SBATCH --exclude=n0181.lr6,n0130.lr6,n0249.lr6,n0251.lr6,n0209.lr6,n0171.lr6
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#SBATCH --qos=condo_mp_lr6
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#SBATCH --time=480:00:00
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#SBATCH --partition=lr6
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#SBATCH --account=lr_mp
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#SBATCH --job-name=ts_production
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#SBATCH --output=ts_production-%j.out
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#SBATCH --error=ts_production-%j.error
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conda activate dev && module load qchem/5.2.2
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cd /clusterfs/mp/ewcspottesmith/data/ts_testing/20201111_li2o_paths/block_2020-11-11-16-37-34-113586/launcher_2020-11-12-15-31-02-922842
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rlaunch -l ${FW_CONFIG_FILE%/*}/sam_launchpad.yaml -w ${FW_CONFIG_FILE%/*}/ts_fworker.yaml singleshot
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# CommonAdapter (SLURM) completed writing Template

‎atomate/qchem/test_files/reaction_path_wf/block/launcher_backwards/GRAD.freq_0‎

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$energy
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-456.327435406602
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$gradient
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0.17051477308569E-05 -0.31926916385658E-05 -0.39191085151192E-05
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-0.16185078170333E-05 0.33511684711213E-06 -0.65022870644187E-05
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0.15977781841888E-05 -0.96905270723698E-06 0.27052177340656E-05
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-0.22201709158245E-05 0.42741235056193E-05 -0.10639363777540E-04
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-0.40448234259210E-05 0.44477225522457E-05 -0.16899330204140E-05
9+
-0.41084088015769E-05 0.21078253946879E-05 0.39296465025925E-05
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0.20305494552582E-04 0.54808918335415E-05 0.95819997063028E-05
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0.42638877201292E-05 -0.38074486327019E-05 0.23970647783670E-05
12+
-0.24009098487047E-05 0.43940914258491E-05 0.74662766310256E-05
13+
-0.28339862803081E-05 0.38183303902803E-05 0.25184271656899E-05
14+
-0.17057817609194E-03 0.20244989728709E-05 0.30409231568847E-03
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-0.42709536084227E-04 -0.44583091722531E-05 0.88463813044513E-04
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0.20264221109599E-03 -0.14455098738252E-04 -0.39840406891199E-03
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$end

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