.. _qcxms2_example: -------------- Example Usage -------------- ``QCxMS2`` is usually invoked via command line, and requires only a coordinate input file in xyz file format. .. code:: qcxms2 [INPUT] [OPTIONS] .. note:: Especially for larger molecules, the conformation of the input molecule can have a significan impact on the generated reaction network. It is recommended to use a conformational search tool to generate a set of conformers at the respective charge of the QCxMS2 calculation and use the most stable one as input for QCxMS2. Using `crest `_ is recommended for this. The default settings provided in QCxMS2 are a good starting point for the calculations. The default setting is performing an `EI`_ calculation. To change the behavior of the program, keywords have to be provided via command line flags. .. note:: The default values are **not always** giving the best results, but are set to cover the majority of systems. Molecules have different characteristics that can significantely influence the outcome. Changing the input settings can improve upon the final result, e.g. decreasing the molecular ion peak abundance or producing more low *m/z* fragments. For more details on the different settings that can be set in a QCxMS2 calculation, see section :ref:`qcxms2_run`. EI - positive Ion Electron Ionization ------------------------------------- .. _EI: Calculation of the electron ionization mass spectrum (EI-MS) is the default setting of QCxMS2. In this example, we compute the EI-MS at 70 eV for 2-pentanone. We use 16 CPU cores (``-T 16``) to speed up the calculation. Geometries, reaction barriers and energies and Ionizaion potentials are calculated at the GFN2-xTB level of theory. First we generate the input molecule in xyz format and search for the most stable conformer at the charge of the calculation. .. code:: crest in.xyz -T 16 --chrg 1 cp crest_best.xyz in.xyz The QCxMS2 calculation is then started with the following command: .. tab-set:: .. tab-item:: command .. code:: bash qcxms2 in.xyz -T 16 .. tab-item:: input .. code:: text 16 energy: -19.369243382271 gnorm: 0.000059854204 xtb: 6.7.1 (c3cfd38) C -2.29405560010000 -0.27259858260000 -0.04531328360000 C -0.85954151760000 0.13277118300000 0.03148097580000 H 2.24425572750000 0.53480936730000 1.23713232400000 H 2.96327249650000 0.83035531710000 -0.38177427930000 H 1.31387583970000 1.35087511890000 -0.01066709370000 H -2.93292965850000 0.59208722380000 0.12637019020000 H -2.48111111390000 -0.64731393490000 -1.05423159230000 H -2.52058929890000 -1.07062880960000 0.65758710200000 C 0.10120807380000 -1.03484257470000 0.26200375960000 H 1.40410160480000 -0.72810178930000 -1.43884752540000 O -0.47850220350000 1.26211030440000 -0.06582215180000 C 1.45928778880000 -0.72962759280000 -0.34614099520000 H 0.16276621020000 -1.12030023870000 1.35329069430000 H -0.32390361780000 -1.95834270590000 -0.12964936090000 C 2.06708660020000 0.54100991220000 0.16232423460000 H 2.11763590860000 -1.57227915380000 -0.08124961590000 .. tab-item:: output .. code:: text ----------------------------------------------------------- | ===================== | | = QCxMS2 = | | ===================== | | J. Gorges | | S. Grimme | | Mulliken Center for Theoretical Chemistry | | University of Bonn | ----------------------------------------------------------- * QCxMS2 version 1.0.0 (24729a4) compiled by 'gorges@joey' on 2025-01-20 QCxMS2 is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. QCxMS2 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. Command line input: > qcxms2 in.xyz -T 16 input file given: in.xyz Settings: ************************************************************ + Positive Ion mode + IEE distribution: poisson width of IEE distribution (eimpw) is: 0.10 energy per atom (ieeatm) is: 0.80 eV eimp0 is: 70.00 eV spectral mode: EI-MS QM methods used: Level for geometry optimizations and path searches: gfn2 Level for reaction energy and barrier calculations: gfn2 Level for IP prescreening: gfn2 Runtime settings used: Number of cores used: 16 Number of allowed subsequent fragmentations: 6 Intensity threshold for further fragmentation: 1.00% ************************************************************ External programs used: /home/mctc/software/xtb_qcxms2/6.7.1_dev/bin/xtb /home/mctc/software/crest_qcxms2/3.0.2_dev/bin/crest /home/mctc/software/orca/6.0.1/orca xtb path set for orca: /home/mctc/software/xtb_qcxms2/6.7.1_dev/bin/xtb /home/mctc/software/mambaforge3/23.11.0/envs/qcxms2/bin/molbar /home/mctc/software/mambaforge3/23.11.0/envs/qcxms2/bin/geodesic_interpolate Optimizing starting structure at the gfn2 level Compute IP at level gfn2 1 2 IP of input molecule is 13.057 eV Average temperature set to 3536 K Generate energy distribution for IEE Poisson distribution to approximate IEE -------------------------------- | Starting first fragmentation | -------------------------------- Generate new fragments with CREST within energy window of 885.53 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 1 --T 16 --gfn2 --ewin 885.52508 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 26 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 26 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 35.1s Generated fragments were read from msreact.out Number of generated fragments and isomers is 24 14 starting 14 GFN-FF optimizations in parallel before topology check 1 2 3 4 5 6 7 8 9 10 11 12 13 14 starting 14 topo calculations in parallel: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Check product topology after optimization 1 2 3 4 5 6 7 8 9 10 11 12 13 14 p16 is a duplicate of p15 16 is a duplicate of 15 remaining number of products is: 25 starting 40 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 starting 0 gfn2restarted optimizations in parallel remaining number of products is: 25 Computing statistical charges via Delta SCF procedure starting 48 gfn2 calculations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 starting 0 gfn2restart IP calculations in parallel remaining number of products is: 25 Time spent for IP calculation: 0.6s Optimizing products at assigned charge starting 13 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization 1 2 3 4 5 6 7 8 9 10 11 12 13 9 is a duplicate of 0 remaining number of products is: 24 Computing reaction energy of fragmentation Starting 12 fragment pair calculations in parallel at gfn2 level 1 2 3 4 5 6 7 8 9 10 11 12 Starting 0 restart product calculations in parallel at gfn2 level Starting 36 SPH calculations in parallel at gfn2 level 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy Internal energy of H-diss to fragpair p11 scaled with 0.50 Internal energy of H-diss to fragpair p20 scaled with 0.50 Internal energy of H-diss to fragpair p22 scaled with 0.50 Internal energy of H-diss to fragpair p24 scaled with 0.50 remaining number of products is: 24 from 24 fragment pairs 24 are left after sorting step Remaining Pairs: 24 Search for transition states for 24 pairs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Starting 24 neb transition state searches 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Time spent for path search and barrier calculation: 313.5s Retry NEB searches for 1 pairs 1 WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one remaining number of products is: 24 Number of succesfull ts searches is 24 Starting 24 gfn2 First Hessian calculations 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Identifying IRC mode IRC MODE found! mode 1 with -866.777500000000 Identifying IRC mode IRC MODE found! mode 1 with -1902.34670000000 Identifying IRC mode IRC MODE found! mode 1 with -1759.99720000000 Identifying IRC mode IRC MODE found! mode 1 with -558.713100000000 Identifying IRC mode IRC MODE found! mode 1 with -1023.87980000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -182.698800000000 Identifying IRC mode IRC MODE found! mode 1 with -1107.70280000000 Identifying IRC mode IRC MODE found! mode 1 with -1154.44550000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -121.474800000000 Identifying IRC mode IRC MODE found! mode 1 with -970.919900000000 Identifying IRC mode IRC MODE found! mode 1 with -198.722800000000 Identifying IRC mode IRC MODE found! mode 1 with -142.899000000000 Identifying IRC mode IRC MODE found! mode 1 with -823.333400000000 Identifying IRC mode IRC MODE found! mode 1 with -879.723200000000 Identifying IRC mode IRC MODE found! mode 1 with -943.845600000000 Identifying IRC mode IRC MODE found! mode 1 with -161.584500000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -58.9807000000000 Identifying IRC mode IRC MODE found! mode 1 with -114.434500000000 Identifying IRC mode IRC MODE found! mode 1 with -483.636100000000 Identifying IRC mode IRC MODE found! mode 1 with -324.575400000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -137.692900000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -81.1523000000000 Identifying IRC mode IRC MODE found! mode 1 with -841.678000000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -493.165900000000 Starting 24 gfn2 TS optimizations 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p6/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p12/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p13/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p19/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p20/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p21/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p22/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p23/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p24/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Starting 15 gfn2 Hessian calculations 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Identifying IRC mode IRC MODE found! mode 1 with -987.927800000000 Identifying IRC mode IRC MODE found! mode 1 with -1522.46650000000 Identifying IRC mode IRC MODE found! mode 1 with -1836.45200000000 Identifying IRC mode IRC MODE found! mode 1 with -687.254000000000 Identifying IRC mode no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p5/ts/hess2 No imaginary mode found, we just take highest point on reaction path as transi tion state Identifying IRC mode IRC MODE found! mode 1 with -659.967900000000 Identifying IRC mode IRC MODE found! mode 1 with -965.347300000000 Identifying IRC mode IRC MODE found! mode 1 with -75.7530000000000 Identifying IRC mode IRC MODE found! mode 1 with -987.788300000000 Identifying IRC mode IRC MODE found! mode 1 with -892.303800000000 Identifying IRC mode IRC MODE found! mode 1 with -592.919800000000 Identifying IRC mode have to continue search no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p17/ts/hess2 No imaginary mode found, we just take highest point on reaction path as transi tion state Identifying IRC mode IRC MODE found! mode 1 with -75.0823000000000 Identifying IRC mode IRC MODE found! mode 1 with -996.699600000000 Identifying IRC mode IRC MODE found! mode 1 with -444.997900000000 Starting 24 gfn2 Singlepoint calculations on TS 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Starting 24 bhess calculations on TS structures 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 npairs are 24 ---------------------------------------------------------------------- |Initializing the Monte Carlo Simulation to calculate all intensities| ---------------------------------------------------------------------- Eyring equation is used to compute rate constants, with mRRHO-cutoff: 0.00 cm-1 sum of half lifes of prior reactions is: 0.00E+00 s Scaling of IEE for H-dissociation is0.50 time of flight is 0.50E-04 s Reading barriers and frequencies reaction | barrier/kcal/mol | barrier/eV | irc mode /cm -1 p1 41.2 1.79 -987.9 p2 41.7 1.81 -1522.5 p3 51.4 2.23 -1836.5 p4 58.5 2.54 -687.3 p5 22.8 0.99 -493.2 p6 43.3 1.88 0.0 p7 56.4 2.45 -660.0 p8 33.7 1.46 -965.3 p10 54.2 2.35 -75.8 p11 41.2 1.79 -987.8 p12 41.6 1.80 0.0 p13 44.4 1.92 0.0 p14 29.2 1.27 -892.3 p15 49.4 2.14 -592.9 p17 68.7 2.98 0.0 p18 54.1 2.35 -75.1 p19 69.2 3.00 0.0 p20 95.2 4.13 0.0 p21 136.9 5.94 0.0 p22 67.4 2.92 0.0 p23 80.0 3.47 0.0 p24 116.8 5.06 0.0 p25 83.9 3.64 -996.7 p26 120.4 5.22 -445.0 Internal energy of H-diss to fragpair p11 scaled with 0.50 Internal energy of H-diss to fragpair p20 scaled with 0.50 Internal energy of H-diss to fragpair p22 scaled with 0.50 Internal energy of H-diss to fragpair p24 scaled with 0.50 Compute Isomer equilibrium Intensity of initial peak was 100.0% Intensity of initial peak is now 96.3% Compute fragmentation branching ratios Intensity of initial peak was 96.3% Intensity of initial peak is now 7.8% --------------------------------- |Monte Carlo simulation finished| --------------------------------- Writing fragments and isomers to file fragments Important fragments are: dir | mass | sumformula | rel. I / % p5 86.132 H10C5O1 3.3 p12f1 58.079 H6C3O1 23.7 p13f1 43.045 H3C2O1 20.7 p18f2 71.098 H7C4O1 9.5 p23f1 71.098 H7C4O1 1.3 p25f1 59.087 H7C3O1 31.5 -------------------------------------------------- |Starting fragmentation 2 for 36 fragments -------------------------------------------------- Fragment p1 is not fragmented further due to too low propability (0.0) Fragment p2 is not fragmented further due to too low propability (0.2) Fragment p3 is not fragmented further due to too low propability (0.0) Fragment p4 is not fragmented further due to too low propability (0.1) ------------------------------------ | Starting fragmentation of: p5 ------------------------------------ Average temperature set to 3536 K Generate new fragments with CREST within energy window of 873.17 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 1 --T 16 --gfn2 --ewin 873.16902 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 24 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 24 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 7.2s Generated fragments were read from msreact.out Number of generated fragments and isomers is 26 11 starting 11 GFN-FF optimizations in parallel before topology check 1 2 3 4 5 6 7 8 9 10 11 starting 11 topo calculations in parallel: 1 2 3 4 5 6 7 8 9 10 11 Check product topology after optimization 1 2 3 4 5 6 7 8 9 10 11 p5 is a duplicate of p3 5 is a duplicate of 3 p7 is a duplicate of p6 7 is a duplicate of 6 remaining number of products is: 22 starting 42 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 starting 0 gfn2restarted optimizations in parallel fragment p13f2 dissociated upon charged optimization, take neutrally charged geometry instead remaining number of products is: 22 Computing statistical charges via Delta SCF procedure starting 52 gfn2 calculations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 starting 0 gfn2restart IP calculations in parallel remaining number of products is: 22 Time spent for IP calculation: 0.6s Optimizing products at assigned charge starting 9 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 9 starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization 1 2 3 4 5 6 7 8 9 21 is a duplicate of 0 remaining number of products is: 21 Computing reaction energy of fragmentation Starting 8 fragment pair calculations in parallel at gfn2 level 1 2 3 4 5 6 7 8 Starting 0 restart product calculations in parallel at gfn2 level Starting 34 SPH calculations in parallel at gfn2 level 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy Internal energy of H-diss to fragpair p11 scaled with 0.50 Internal energy of H-diss to fragpair p13 scaled with 0.50 Internal energy of H-diss to fragpair p15 scaled with 0.50 Internal energy of H-diss to fragpair p17 scaled with 0.50 Internal energy of H-diss to fragpair p20 scaled with 0.50 Internal energy of H-diss to fragpair p22 scaled with 0.50 remaining number of products is: 21 from 21 fragment pairs 21 are left after sorting step Remaining Pairs: 21 Search for transition states for 21 pairs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 Starting 21 neb transition state searches 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 Time spent for path search and barrier calculation: 96.5s Retry NEB searches for 0 pairs WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one remaining number of products is: 21 Number of succesfull ts searches is 21 Starting 21 gfn2 First Hessian calculations 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 Identifying IRC mode IRC MODE found! mode 1 with -1210.20580000000 Identifying IRC mode IRC MODE found! mode 1 with -1460.26880000000 Identifying IRC mode IRC MODE found! mode 1 with -940.511100000000 Identifying IRC mode IRC MODE found! mode 1 with -347.891600000000 Identifying IRC mode IRC MODE found! mode 1 with -580.295200000000 Identifying IRC mode IRC MODE found! mode 1 with -1014.34130000000 Identifying IRC mode IRC MODE found! mode 1 with -482.207800000000 Identifying IRC mode IRC MODE found! mode 1 with -1275.54930000000 Identifying IRC mode IRC MODE found! mode 1 with -646.413300000000 Identifying IRC mode IRC MODE found! mode 1 with -605.868600000000 Identifying IRC mode have to continue search have to continue search have to continue search have to continue search no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p5/p13/ts/hess No imaginary mode found, we have to take end as ts ircmode set to 0 Identifying IRC mode have to continue search have to continue search have to continue search no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p5/p14/ts/hess No imaginary mode found, we have to take end as ts ircmode set to 0 Identifying IRC mode IRC MODE found! mode 1 with -834.547100000000 Identifying IRC mode IRC MODE found! mode 1 with -94.2849000000000 Identifying IRC mode IRC MODE found! mode 1 with -370.390300000000 Identifying IRC mode IRC MODE found! mode 1 with -695.121500000000 Identifying IRC mode IRC MODE found! mode 1 with -269.517600000000 Identifying IRC mode IRC MODE found! mode 1 with -372.566200000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -108.673800000000 Identifying IRC mode IRC MODE found! mode 1 with -714.465200000000 Identifying IRC mode IRC MODE found! mode 1 with -152.468700000000 Starting 19 gfn2 TS optimizations 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5/p16/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5/p17/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5/p19/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5/p20/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5/p22/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5/p24/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Starting 13 gfn2 Hessian calculations 1 2 3 4 5 6 7 8 9 10 11 12 13 Identifying IRC mode IRC MODE found! mode 1 with -1026.72200000000 Identifying IRC mode IRC MODE found! mode 1 with -1776.93200000000 Identifying IRC mode IRC MODE found! mode 1 with -1002.78810000000 Identifying IRC mode have to continue search no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p5/p4/ts/hess2 No imaginary mode found, we just take highest point on reaction path as transi tion state Identifying IRC mode IRC MODE found! mode 1 with -813.291800000000 Identifying IRC mode have to continue search no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p5/p8/ts/hess2 No imaginary mode found, we just take highest point on reaction path as transi tion state Identifying IRC mode IRC MODE found! mode 1 with -570.226800000000 Identifying IRC mode IRC MODE found! mode 1 with -1191.59080000000 Identifying IRC mode have to continue search no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p5/p11/ts/hess2 No imaginary mode found, we just take highest point on reaction path as transi tion state Identifying IRC mode have to continue search no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p5/p12/ts/hess2 No imaginary mode found, we just take highest point on reaction path as transi tion state Identifying IRC mode IRC MODE found! mode 1 with -247.232700000000 Identifying IRC mode have to continue search have to continue search no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p5/p18/ts/hess2 No imaginary mode found, we just take highest point on reaction path as transi tion state Identifying IRC mode IRC MODE found! mode 1 with -56.4974000000000 Starting 21 gfn2 Singlepoint calculations on TS 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 Starting 21 bhess calculations on TS structures 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 npairs are 21 ---------------------------------------------------------------------- |Initializing the Monte Carlo Simulation to calculate all intensities| ---------------------------------------------------------------------- Eyring equation is used to compute rate constants, with mRRHO-cutoff: 0.00 cm-1 sum of half lifes of prior reactions is: 0.15E-12 s Scaling of IEE for H-dissociation is0.50 time of flight is 0.50E-04 s Reading barriers and frequencies reaction | barrier/kcal/mol | barrier/eV | irc mode /cm -1 p1 10.2 0.44 -1026.7 p2 39.0 1.69 -1776.9 p3 13.0 0.56 -1002.8 p4 41.3 1.79 -152.5 p6 19.6 0.85 -813.3 p8 50.1 2.17 -152.5 p9 35.1 1.52 -570.2 p10 39.3 1.70 -1191.6 p11 44.2 1.92 -152.5 p12 14.9 0.65 -152.5 p13 41.8 1.81 0.0 p14 55.7 2.42 0.0 p15 45.2 1.96 -247.2 p16 51.5 2.23 0.0 p17 61.0 2.64 0.0 p18 94.5 4.10 0.0 p19 106.8 4.63 0.0 p20 68.8 2.98 0.0 p21 72.0 3.12 -56.5 p22 109.6 4.75 0.0 p24 98.7 4.28 0.0 Internal energy of H-diss to fragpair p11 scaled with 0.50 Internal energy of H-diss to fragpair p13 scaled with 0.50 Internal energy of H-diss to fragpair p15 scaled with 0.50 Internal energy of H-diss to fragpair p17 scaled with 0.50 Internal energy of H-diss to fragpair p20 scaled with 0.50 Internal energy of H-diss to fragpair p22 scaled with 0.50 Compute Isomer equilibrium Intensity of initial peak was 3.3% Intensity of initial peak is now 0.7% Compute fragmentation branching ratios Intensity of initial peak was 0.7% Intensity of initial peak is now 0.1% --------------------------------- |Monte Carlo simulation finished| --------------------------------- Writing fragments and isomers to file fragments Important fragments are: dir | mass | sumformula | rel. I / % p5p12 86.132 H10C5O1 1.6 newly generated products: 34 total number of products is now: 70 Fragment p6 is not fragmented further due to too low propability (0.0) Fragment p7 is not fragmented further due to too low propability (0.0) Fragment p8 is not fragmented further due to too low propability (0.1) Fragment p10 is not fragmented further due to too low propability (0.1) Fragment p11f1 is not fragmented further due to too low propability (0.0) Fragment p11f2 is not fragmented further due to too low propability (0.0) ------------------------------------ | Starting fragmentation of: p12f1 ------------------------------------ Average temperature set to 3868 K Generate new fragments with CREST within energy window of 836.51 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 1 --T 16 --gfn2 --ewin 836.50872 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 15 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 15 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 5.0s Generated fragments were read from msreact.out Number of generated fragments and isomers is 20 5 starting 5 GFN-FF optimizations in parallel before topology check 1 2 3 4 5 starting 5 topo calculations in parallel: 1 2 3 4 5 Check product topology after optimization 1 2 3 4 5 remaining number of products is: 15 starting 32 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 starting 0 gfn2restarted optimizations in parallel remaining number of products is: 15 Computing statistical charges via Delta SCF procedure starting 40 gfn2 calculations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 starting 0 gfn2restart IP calculations in parallel remaining number of products is: 15 Time spent for IP calculation: 0.5s Optimizing products at assigned charge starting 5 gfn2 optimizations in parallel 1 2 3 4 5 starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization 1 2 3 4 5 8 is a duplicate of 0 p9 is a duplicate of p2 9 is a duplicate of 2 remaining number of products is: 13 Computing reaction energy of fragmentation Starting 3 fragment pair calculations in parallel at gfn2 level 1 2 3 Starting 0 restart product calculations in parallel at gfn2 level Starting 23 SPH calculations in parallel at gfn2 level 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy Internal energy of H-diss to fragpair p11 scaled with 0.50 Internal energy of H-diss to fragpair p12 scaled with 0.50 Internal energy of H-diss to fragpair p13 scaled with 0.50 Internal energy of H-diss to fragpair p14 scaled with 0.50 remaining number of products is: 13 from 13 fragment pairs 13 are left after sorting step Remaining Pairs: 13 Search for transition states for 13 pairs 1 2 3 4 5 6 7 8 9 10 11 12 13 Starting 13 neb transition state searches 1 2 3 4 5 6 7 8 9 10 11 12 13 Time spent for path search and barrier calculation: 195.4s Retry NEB searches for 4 pairs 1 2 3 4 WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p12f1/p6 WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p12f1/p6 calculation failed, retrying with different settings WARNING: more than one maximum in path, but we take highest one Retry transition state searches for 1 pairs 1 WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one remaining number of products is: 13 Number of succesfull ts searches is 13 Starting 13 gfn2 First Hessian calculations 1 2 3 4 5 6 7 8 9 10 11 12 13 Identifying IRC mode IRC MODE found! mode 1 with -1260.09740000000 Identifying IRC mode IRC MODE found! mode 1 with -1773.60280000000 Identifying IRC mode IRC MODE found! mode 1 with -1595.62160000000 Identifying IRC mode IRC MODE found! mode 1 with -1607.50760000000 Identifying IRC mode IRC MODE found! mode 1 with -247.037700000000 Identifying IRC mode IRC MODE found! mode 1 with -741.141000000000 Identifying IRC mode IRC MODE found! mode 1 with -189.193300000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -163.366300000000 Identifying IRC mode IRC MODE found! mode 1 with -425.412200000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -422.755100000000 Identifying IRC mode have to continue search no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p12f1/p13/ts/hess No imaginary mode found, we have to take end as ts ircmode set to 0 Identifying IRC mode IRC MODE found! mode 1 with -578.035900000000 Identifying IRC mode have to continue search have to continue search have to continue search IRC MODE found! mode 4 with -32.3568000000000 Starting 12 gfn2 TS optimizations 1 2 3 4 5 6 7 8 9 10 11 12 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p12f1/p12/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p12f1/p14/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p12f1/p15/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Starting 9 gfn2 Hessian calculations 1 2 3 4 5 6 7 8 9 Warning! Zero point energy ... not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p12f1/p7/ts/hess2 Warning! Zero point energy ... not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p12f1/p7/ts/hess2 calculation failed, retrying with different settings 1 Identifying IRC mode IRC MODE found! mode 1 with -1179.98630000000 Identifying IRC mode IRC MODE found! mode 1 with -1584.34520000000 Identifying IRC mode IRC MODE found! mode 1 with -1517.52200000000 Identifying IRC mode IRC MODE found! mode 1 with -1509.58200000000 Identifying IRC mode IRC MODE found! mode 1 with -87.2040000000000 Identifying IRC mode IRC MODE found! mode 1 with -1515.64170000000 file orca.g98.out does not exist! ERROR: Could not find orca.g98.out, Hessian calculation failed current working directory is/tmp1/gorges/7867629/default/p12f1/p7/ts/hess2 No imaginary mode found, we just take highest point on reaction path as transi tion state Identifying IRC mode IRC MODE found! mode 1 with -105.332700000000 Identifying IRC mode IRC MODE found! mode 1 with -288.967500000000 Starting 13 gfn2 Singlepoint calculations on TS 1 2 3 4 5 6 7 8 9 10 11 12 13 Starting 13 bhess calculations on TS structures 1 2 3 4 5 6 7 8 9 10 11 12 13 npairs are 13 ---------------------------------------------------------------------- |Initializing the Monte Carlo Simulation to calculate all intensities| ---------------------------------------------------------------------- Eyring equation is used to compute rate constants, with mRRHO-cutoff: 0.00 cm-1 sum of half lifes of prior reactions is: 0.40E-12 s Scaling of IEE for H-dissociation is0.50 time of flight is 0.50E-04 s Reading barriers and frequencies reaction | barrier/kcal/mol | barrier/eV | irc mode /cm -1 p1 43.2 1.87 -1180.0 p2 40.0 1.74 -1584.3 p3 46.6 2.02 -1517.5 p4 60.3 2.62 -1509.6 p5 61.6 2.67 -87.2 p6 46.4 2.01 -1515.6 p7 44.0 1.91 -32.4 p10 61.6 2.67 -105.3 p11 77.5 3.36 -289.0 p12 95.9 4.16 0.0 p13 101.5 4.40 0.0 p14 99.9 4.33 0.0 p15 142.5 6.18 0.0 Internal energy of H-diss to fragpair p11 scaled with 0.50 Internal energy of H-diss to fragpair p12 scaled with 0.50 Internal energy of H-diss to fragpair p13 scaled with 0.50 Internal energy of H-diss to fragpair p14 scaled with 0.50 energy is scaled according to proportion of atom with other fragment with0.62 Compute Isomer equilibrium Intensity of initial peak was 23.7% Intensity of initial peak is now 23.7% Compute fragmentation branching ratios Intensity of initial peak was 23.7% Intensity of initial peak is now 7.1% --------------------------------- |Monte Carlo simulation finished| --------------------------------- Writing fragments and isomers to file fragments Important fragments are: dir | mass | sumformula | rel. I / % p12f1p7f1 43.045 H3C2O1 15.5 newly generated products: 23 total number of products is now: 93 Fragment p12f2 is not fragmented further due to too low propability (0.3) ------------------------------------ | Starting fragmentation of: p13f1 ------------------------------------ Average temperature set to 4641 K Generate new fragments with CREST within energy window of 825.06 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 0 --T 16 --gfn2 --ewin 825.05704 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 4 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 4 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 4.0s Generated fragments were read from msreact.out Number of generated fragments and isomers is 6 1 starting 1 GFN-FF optimizations in parallel before topology check 1 starting 1 topo calculations in parallel: 1 Check product topology after optimization 1 remaining number of products is: 4 starting 8 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 starting 0 gfn2restarted optimizations in parallel remaining number of products is: 4 Computing statistical charges via Delta SCF procedure starting 12 gfn2 calculations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 starting 0 gfn2restart IP calculations in parallel remaining number of products is: 4 Time spent for IP calculation: 0.2s Optimizing products at assigned charge starting 1 gfn2 optimizations in parallel 1 starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization 1 remaining number of products is: 4 Computing reaction energy of fragmentation Starting 1 fragment pair calculations in parallel at gfn2 level 1 Starting 0 restart product calculations in parallel at gfn2 level Starting 7 SPH calculations in parallel at gfn2 level 1 2 3 4 5 6 7 Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy Internal energy of H-diss to fragpair p2 scaled with 0.50 fragment pair p4 is sorted out with an reaction energy of 304.2 kcal/mol ( 13.2 eV) remaining number of products is: 3 from 4 fragment pairs 3 are left after sorting step Remaining Pairs: 3 Search for transition states for 3 pairs 1 2 3 Starting 3 neb transition state searches 1 2 3 Time spent for path search and barrier calculation: 8.2s Retry NEB searches for 1 pairs 1 calculation failed, retrying with different settings Retry NEB again at 5000 K searches for 1 pairs 1 remaining number of products is: 3 Number of succesfull ts searches is 3 Starting 3 gfn2 First Hessian calculations 1 2 3 Identifying IRC mode IRC MODE found! mode 1 with -1749.71680000000 Identifying IRC mode IRC MODE found! mode 1 with -443.793500000000 Identifying IRC mode IRC MODE found! mode 1 with -204.775200000000 Starting 3 gfn2 TS optimizations 1 2 3 Starting 3 gfn2 Hessian calculations 1 2 3 Warning! Zero point energy ... not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p13f1/p3/ts/hess2 Warning! Zero point energy ... not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p13f1/p3/ts/hess2 calculation failed, retrying with different settings 1 Identifying IRC mode IRC MODE found! mode 1 with -1668.21630000000 Identifying IRC mode IRC MODE found! mode 1 with -396.390700000000 file orca.g98.out does not exist! ERROR: Could not find orca.g98.out, Hessian calculation failed current working directory is/tmp1/gorges/7867629/default/p13f1/p3/ts/hess2 No imaginary mode found, we just take highest point on reaction path as transi tion state Starting 3 gfn2 Singlepoint calculations on TS 1 2 3 Starting 3 bhess calculations on TS structures 1 2 3 npairs are 3 ---------------------------------------------------------------------- |Initializing the Monte Carlo Simulation to calculate all intensities| ---------------------------------------------------------------------- Eyring equation is used to compute rate constants, with mRRHO-cutoff: 0.00 cm-1 sum of half lifes of prior reactions is: 0.43E-12 s Scaling of IEE for H-dissociation is0.50 time of flight is 0.50E-04 s Reading barriers and frequencies reaction | barrier/kcal/mol | barrier/eV | irc mode /cm -1 p1 81.4 3.53 -1668.2 p2 96.5 4.19 -396.4 p3 114.9 4.98 -204.8 Internal energy of H-diss to fragpair p2 scaled with 0.50 energy is scaled according to proportion of atom with other fragment with0.38 Compute Isomer equilibrium Intensity of initial peak was 20.7% Intensity of initial peak is now 18.0% Compute fragmentation branching ratios Intensity of initial peak was 18.0% Intensity of initial peak is now 16.9% --------------------------------- |Monte Carlo simulation finished| --------------------------------- Writing fragments and isomers to file fragments Important fragments are: dir | mass | sumformula | rel. I / % p13f1p1 43.045 H3C2O1 2.7 p13f1p3f1 15.035 H3C1 1.2 newly generated products: 5 total number of products is now: 98 Fragment p13f2 is not fragmented further due to too low propability (0.7) Fragment p14 is not fragmented further due to too low propability (0.0) Fragment p15 is not fragmented further due to too low propability (0.0) Fragment p17 is not fragmented further due to too low propability (0.0) Fragment p18f1 is not fragmented further due to too low propability (0.0) ------------------------------------ | Starting fragmentation of: p18f2 ------------------------------------ Average temperature set to 3713 K Generate new fragments with CREST within energy window of 826.09 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 0 --T 16 --gfn2 --ewin 826.08991 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 13 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 13 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 5.1s Generated fragments were read from msreact.out Number of generated fragments and isomers is 12 7 starting 7 GFN-FF optimizations in parallel before topology check 1 2 3 4 5 6 7 starting 7 topo calculations in parallel: 1 2 3 4 5 6 7 Check product topology after optimization 1 2 3 4 5 6 7 remaining number of products is: 13 starting 18 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 starting 0 gfn2restarted optimizations in parallel fragment p13f1 dissociated upon neutrally charged optimization, take charged geometry instead remaining number of products is: 13 Computing statistical charges via Delta SCF procedure starting 24 gfn2 calculations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 starting 0 gfn2restart IP calculations in parallel remaining number of products is: 13 Time spent for IP calculation: 0.3s Optimizing products at assigned charge starting 7 gfn2 optimizations in parallel 1 2 3 4 5 6 7 starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization 1 2 3 4 5 6 7 6 is a duplicate of 0 remaining number of products is: 12 Computing reaction energy of fragmentation Starting 6 fragment pair calculations in parallel at gfn2 level 1 2 3 4 5 6 Starting 0 restart product calculations in parallel at gfn2 level Starting 18 SPH calculations in parallel at gfn2 level 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy Internal energy of H-diss to fragpair p8 scaled with 0.50 Internal energy of H-diss to fragpair p11 scaled with 0.50 Internal energy of H-diss to fragpair p13 scaled with 0.50 remaining number of products is: 12 from 12 fragment pairs 12 are left after sorting step Remaining Pairs: 12 Search for transition states for 12 pairs 1 2 3 4 5 6 7 8 9 10 11 12 Starting 12 neb transition state searches 1 2 3 4 5 6 7 8 9 10 11 12 Time spent for path search and barrier calculation: 157.7s Retry NEB searches for 1 pairs 1 WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one remaining number of products is: 12 Number of succesfull ts searches is 12 Starting 12 gfn2 First Hessian calculations 1 2 3 4 5 6 7 8 9 10 11 12 Identifying IRC mode IRC MODE found! mode 1 with -1175.41170000000 Identifying IRC mode IRC MODE found! mode 1 with -705.872500000000 Identifying IRC mode IRC MODE found! mode 1 with -549.624500000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -82.6147000000000 Identifying IRC mode IRC MODE found! mode 1 with -324.533300000000 Identifying IRC mode IRC MODE found! mode 1 with -397.404900000000 Identifying IRC mode IRC MODE found! mode 1 with -303.929100000000 Identifying IRC mode IRC MODE found! mode 1 with -1071.84980000000 Identifying IRC mode have to continue search have to continue search have to continue search IRC MODE found! mode 4 with -34.6903000000000 Identifying IRC mode IRC MODE found! mode 1 with -466.400900000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -70.2625000000000 Identifying IRC mode IRC MODE found! mode 1 with -328.903100000000 Starting 12 gfn2 TS optimizations 1 2 3 4 5 6 7 8 9 10 11 12 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p18f2/p4/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p18f2/p5/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p18f2/p10/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p18f2/p11/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p18f2/p12/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Starting 7 gfn2 Hessian calculations 1 2 3 4 5 6 7 Identifying IRC mode IRC MODE found! mode 1 with -1907.00130000000 Identifying IRC mode IRC MODE found! mode 1 with -637.614700000000 Identifying IRC mode have to continue search no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p18f2/p3/ts/hess2 No imaginary mode found, we just take highest point on reaction path as transi tion state Identifying IRC mode IRC MODE found! mode 1 with -970.551900000000 Identifying IRC mode IRC MODE found! mode 1 with -289.619500000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -9.49530000000000 Identifying IRC mode IRC MODE found! mode 1 with -236.381200000000 Starting 12 gfn2 Singlepoint calculations on TS 1 2 3 4 5 6 7 8 9 10 11 12 Starting 12 bhess calculations on TS structures 1 2 3 4 5 6 7 8 9 10 11 12 npairs are 12 ---------------------------------------------------------------------- |Initializing the Monte Carlo Simulation to calculate all intensities| ---------------------------------------------------------------------- Eyring equation is used to compute rate constants, with mRRHO-cutoff: 0.00 cm-1 sum of half lifes of prior reactions is: 0.69E-12 s Scaling of IEE for H-dissociation is0.50 time of flight is 0.50E-04 s Reading barriers and frequencies reaction | barrier/kcal/mol | barrier/eV | irc mode /cm -1 p1 73.0 3.16 -1907.0 p2 41.7 1.81 -637.6 p3 44.3 1.92 -328.9 p4 50.9 2.21 0.0 p5 53.1 2.30 0.0 p7 64.7 2.81 -970.6 p8 82.0 3.56 -289.6 p9 95.5 4.14 -9.5 p10 73.2 3.18 0.0 p11 109.9 4.76 0.0 p12 112.0 4.86 0.0 p13 112.9 4.90 -236.4 Internal energy of H-diss to fragpair p8 scaled with 0.50 Internal energy of H-diss to fragpair p11 scaled with 0.50 Internal energy of H-diss to fragpair p13 scaled with 0.50 energy is scaled according to proportion of atom with other fragment with0.75 Compute Isomer equilibrium Intensity of initial peak was 9.5% Intensity of initial peak is now 9.5% Compute fragmentation branching ratios Intensity of initial peak was 9.5% Intensity of initial peak is now 2.9% --------------------------------- |Monte Carlo simulation finished| --------------------------------- Writing fragments and isomers to file fragments Important fragments are: dir | mass | sumformula | rel. I / % p18f2p4f2 29.061 H5C2 6.5 newly generated products: 18 total number of products is now: 116 Fragment p19f1 is not fragmented further due to too low propability (0.5) Fragment p19f2 is not fragmented further due to too low propability (0.0) Fragment p20f1 is not fragmented further due to too low propability (0.0) Fragment p20f2 is not fragmented further due to too low propability (0.0) Fragment p21f1 is not fragmented further due to too low propability (0.0) Fragment p21f2 is not fragmented further due to too low propability (0.2) Fragment p22f1 is not fragmented further due to too low propability (0.0) Fragment p22f2 is not fragmented further due to too low propability (0.0) ------------------------------------ | Starting fragmentation of: p23f1 ------------------------------------ Average temperature set to 3713 K Generate new fragments with CREST within energy window of 800.68 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 0 --T 16 --gfn2 --ewin 800.68292 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 14 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 14 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 5.2s Generated fragments were read from msreact.out Number of generated fragments and isomers is 12 8 starting 8 GFN-FF optimizations in parallel before topology check 1 2 3 4 5 6 7 8 starting 8 topo calculations in parallel: 1 2 3 4 5 6 7 8 Check product topology after optimization 1 2 3 4 5 6 7 8 remaining number of products is: 14 starting 20 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 starting 0 gfn2restarted optimizations in parallel remaining number of products is: 14 Computing statistical charges via Delta SCF procedure starting 24 gfn2 calculations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 starting 0 gfn2restart IP calculations in parallel remaining number of products is: 14 Time spent for IP calculation: 0.3s Optimizing products at assigned charge starting 8 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization 1 2 3 4 5 6 7 8 remaining number of products is: 14 Computing reaction energy of fragmentation Starting 8 fragment pair calculations in parallel at gfn2 level 1 2 3 4 5 6 7 8 Starting 0 restart product calculations in parallel at gfn2 level Starting 20 SPH calculations in parallel at gfn2 level 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy Internal energy of H-diss to fragpair p13 scaled with 0.50 Internal energy of H-diss to fragpair p14 scaled with 0.50 remaining number of products is: 14 from 14 fragment pairs 14 are left after sorting step Remaining Pairs: 14 Search for transition states for 14 pairs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Starting 14 neb transition state searches 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Time spent for path search and barrier calculation: 101.9s Retry NEB searches for 3 pairs 1 2 3 WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p23f1/p10 WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p23f1/p12 WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p23f1/p10 calculation failed, retrying with different settings WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p23f1/p12 calculation failed, retrying with different settings Retry transition state searches for 2 pairs 1 2 WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one WARNING: more than one maximum in path, but we take highest one remaining number of products is: 14 Number of succesfull ts searches is 14 Starting 14 gfn2 First Hessian calculations 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Warning! Zero point energy ... not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p23f1/p12/ts/hess Warning! Zero point energy ... not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p23f1/p12/ts/hess calculation failed, retrying with different settings 1 Identifying IRC mode IRC MODE found! mode 1 with -1818.05050000000 Identifying IRC mode IRC MODE found! mode 1 with -1040.12920000000 Identifying IRC mode IRC MODE found! mode 1 with -871.481800000000 Identifying IRC mode IRC MODE found! mode 1 with -850.702200000000 Identifying IRC mode IRC MODE found! mode 1 with -2114.81270000000 Identifying IRC mode IRC MODE found! mode 1 with -931.858000000000 Identifying IRC mode IRC MODE found! mode 1 with -1850.36200000000 Identifying IRC mode IRC MODE found! mode 1 with -677.431300000000 Identifying IRC mode IRC MODE found! mode 1 with -1794.67650000000 Identifying IRC mode IRC MODE found! mode 1 with -638.250200000000 Identifying IRC mode have to continue search have to continue search have to continue search IRC MODE found! mode 4 with -64.2539000000000 Warning! Zero point energy ... not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p23f1/p12/ts/hess TS Hessian calculation failed, we have to take end as ts ircmode set to 0 Identifying IRC mode IRC MODE found! mode 1 with -316.867200000000 Identifying IRC mode IRC MODE found! mode 1 with -440.174200000000 Starting 13 gfn2 TS optimizations 1 2 3 4 5 6 7 8 9 10 11 12 13 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p23f1/p1/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p23f1/p8/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p23f1/p11/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p23f1/p13/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Starting 9 gfn2 Hessian calculations 1 2 3 4 5 6 7 8 9 Identifying IRC mode IRC MODE found! mode 1 with -908.820700000000 Identifying IRC mode IRC MODE found! mode 1 with -1307.70680000000 Identifying IRC mode IRC MODE found! mode 1 with -719.745100000000 Identifying IRC mode IRC MODE found! mode 1 with -2048.21270000000 Identifying IRC mode IRC MODE found! mode 1 with -721.599700000000 Identifying IRC mode IRC MODE found! mode 1 with -857.423300000000 Identifying IRC mode IRC MODE found! mode 1 with -1451.18170000000 Identifying IRC mode IRC MODE found! mode 1 with -148.280000000000 Identifying IRC mode IRC MODE found! mode 1 with -287.183600000000 Starting 14 gfn2 Singlepoint calculations on TS 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Warning! | TOTAL ENERGY not found in xtb.outcalculations failed in: current working directory is/tmp1/gorges/7867629/default/p23f1/p12/ts Warning! | TOTAL ENERGY not found in xtb.outcalculations failed in: current working directory is/tmp1/gorges/7867629/default/p23f1/p12/ts calculation failed, retrying with different settings Restarting 1 gfn2 singlepoint calculations on TS 1 Starting 14 bhess calculations on TS structures 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Warning! zero point energy not found in xtb.outcalculations failed in: current working directory is/tmp1/gorges/7867629/default/p23f1/p12/ts/bhess calculation failed, retrying with different settings Restarting 1 failed bhess calculations on TS structures 1 npairs are 14 ---------------------------------------------------------------------- |Initializing the Monte Carlo Simulation to calculate all intensities| ---------------------------------------------------------------------- Eyring equation is used to compute rate constants, with mRRHO-cutoff: 0.00 cm-1 sum of half lifes of prior reactions is: 0.20E-10 s Scaling of IEE for H-dissociation is0.50 time of flight is 0.50E-04 s Reading barriers and frequencies reaction | barrier/kcal/mol | barrier/eV | irc mode /cm -1 p1 40.6 1.76 0.0 p2 56.6 2.46 -908.8 p3 16.0 0.69 -1307.7 p4 15.4 0.67 -719.7 p5 64.0 2.78 -2048.2 p6 12.2 0.53 -721.6 p7 32.5 1.41 -857.4 p8 92.0 3.99 0.0 p9 65.2 2.83 -1451.2 p10 60.5 2.62 -148.3 p11 68.9 2.99 0.0 p12 40.9 1.77 0.0 p13 72.4 3.14 0.0 p14 120.8 5.24 -287.2 Internal energy of H-diss to fragpair p13 scaled with 0.50 Internal energy of H-diss to fragpair p14 scaled with 0.50 energy is scaled according to proportion of atom with other fragment with0.75 Compute Isomer equilibrium Intensity of initial peak was 1.3% Intensity of initial peak is now 0.9% Compute fragmentation branching ratios Intensity of initial peak was 0.9% Intensity of initial peak is now 0.4% --------------------------------- |Monte Carlo simulation finished| --------------------------------- Writing fragments and isomers to file fragments Important fragments are: dir | mass | sumformula | rel. I / % newly generated products: 20 total number of products is now: 136 Fragment p23f2 is not fragmented further due to too low propability (0.0) Fragment p24f1 is not fragmented further due to too low propability (0.0) Fragment p24f2 is not fragmented further due to too low propability (0.0) ------------------------------------ | Starting fragmentation of: p25f1 ------------------------------------ Average temperature set to 3782 K Generate new fragments with CREST within energy window of 821.79 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 0 --T 16 --gfn2 --ewin 821.78844 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 7 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 7 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 5.1s Generated fragments were read from msreact.out Number of generated fragments and isomers is 10 2 starting 2 GFN-FF optimizations in parallel before topology check 1 2 starting 2 topo calculations in parallel: 1 2 Check product topology after optimization 1 2 remaining number of products is: 7 starting 16 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 starting 0 gfn2restarted optimizations in parallel remaining number of products is: 7 Computing statistical charges via Delta SCF procedure starting 20 gfn2 calculations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 starting 0 gfn2restart IP calculations in parallel remaining number of products is: 7 Time spent for IP calculation: 0.3s Optimizing products at assigned charge starting 2 gfn2 optimizations in parallel 1 2 starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization 1 2 remaining number of products is: 7 Computing reaction energy of fragmentation Starting 2 fragment pair calculations in parallel at gfn2 level 1 2 Starting 0 restart product calculations in parallel at gfn2 level Starting 12 SPH calculations in parallel at gfn2 level 1 2 3 4 5 6 7 8 9 10 11 12 Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy Internal energy of H-diss to fragpair p5 scaled with 0.50 Internal energy of H-diss to fragpair p6 scaled with 0.50 remaining number of products is: 7 from 7 fragment pairs 7 are left after sorting step Remaining Pairs: 7 Search for transition states for 7 pairs 1 2 3 4 5 6 7 Starting 7 neb transition state searches 1 2 3 4 5 6 7 Time spent for path search and barrier calculation: 20.1s Retry NEB searches for 2 pairs 1 2 remaining number of products is: 7 Number of succesfull ts searches is 7 Starting 7 gfn2 First Hessian calculations 1 2 3 4 5 6 7 Identifying IRC mode IRC MODE found! mode 1 with -432.694200000000 Identifying IRC mode IRC MODE found! mode 1 with -452.880600000000 Identifying IRC mode IRC MODE found! mode 1 with -1493.14100000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -33.6673000000000 Identifying IRC mode IRC MODE found! mode 1 with -107.004100000000 Identifying IRC mode IRC MODE found! mode 1 with -674.697700000000 Identifying IRC mode IRC MODE found! mode 1 with -179.644600000000 Starting 7 gfn2 TS optimizations 1 2 3 4 5 6 7 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p25f1/p4/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p25f1/p5/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Starting 5 gfn2 Hessian calculations 1 2 3 4 5 Identifying IRC mode have to continue search no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p25f1/p1/ts/hess2 No imaginary mode found, we just take highest point on reaction path as transi tion state Identifying IRC mode IRC MODE found! mode 1 with -1067.56080000000 Identifying IRC mode IRC MODE found! mode 1 with -1462.86260000000 Identifying IRC mode IRC MODE found! mode 1 with -1084.19550000000 Identifying IRC mode IRC MODE found! mode 1 with -89.2705000000000 Starting 7 gfn2 Singlepoint calculations on TS 1 2 3 4 5 6 7 Starting 7 bhess calculations on TS structures 1 2 3 4 5 6 7 npairs are 7 ---------------------------------------------------------------------- |Initializing the Monte Carlo Simulation to calculate all intensities| ---------------------------------------------------------------------- Eyring equation is used to compute rate constants, with mRRHO-cutoff: 0.00 cm-1 sum of half lifes of prior reactions is: 0.12E-12 s Scaling of IEE for H-dissociation is0.50 time of flight is 0.50E-04 s Reading barriers and frequencies reaction | barrier/kcal/mol | barrier/eV | irc mode /cm -1 p1 56.7 2.46 -179.6 p2 59.4 2.58 -1067.6 p3 55.5 2.41 -1462.9 p4 54.1 2.35 0.0 p5 103.5 4.49 0.0 p6 59.4 2.58 -1084.2 p7 116.2 5.04 -89.3 Internal energy of H-diss to fragpair p5 scaled with 0.50 Internal energy of H-diss to fragpair p6 scaled with 0.50 energy is scaled according to proportion of atom with other fragment with0.69 Compute Isomer equilibrium Intensity of initial peak was 31.5% Intensity of initial peak is now 31.5% Compute fragmentation branching ratios Intensity of initial peak was 31.5% Intensity of initial peak is now 11.5% --------------------------------- |Monte Carlo simulation finished| --------------------------------- Writing fragments and isomers to file fragments Important fragments are: dir | mass | sumformula | rel. I / % p25f1p4f1 41.072 H5C3 20.0 newly generated products: 12 total number of products is now: 148 Fragment p25f2 is not fragmented further due to too low propability (0.0) Fragment p26f1 is not fragmented further due to too low propability (0.1) Fragment p26f2 is not fragmented further due to too low propability (0.0) -------------------------------------------------- |Starting fragmentation 3 for 112 fragments -------------------------------------------------- Fragment p5p1 is not fragmented further due to too low propability (0.9) Fragment p5p2 is not fragmented further due to too low propability (0.0) Fragment p5p3 is not fragmented further due to too low propability (0.1) Fragment p5p4 is not fragmented further due to too low propability (0.0) Fragment p5p6 is not fragmented further due to too low propability (0.0) Fragment p5p8f1 is not fragmented further due to too low propability (0.1) Fragment p5p8f2 is not fragmented further due to too low propability (0.0) Fragment p5p9 is not fragmented further due to too low propability (0.0) Fragment p5p10 is not fragmented further due to too low propability (0.0) Fragment p5p11f1 is not fragmented further due to too low propability (0.0) Fragment p5p11f2 is not fragmented further due to too low propability (0.0) ------------------------------------ | Starting fragmentation of: p5p12 ------------------------------------ Average temperature set to 3536 K Generate new fragments with CREST within energy window of 885.53 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 1 --T 16 --gfn2 --ewin 885.52508 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 19 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 19 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 7.2s Generated fragments were read from msreact.out Number of generated fragments and isomers is 26 6 starting 6 GFN-FF optimizations in parallel before topology check 1 2 3 4 5 6 starting 6 topo calculations in parallel: 1 2 3 4 5 6 Check product topology after optimization 1 2 3 4 5 6 2 is a duplicate of its pre-precursor is a duplicate of its pre-precursor remaining number of products is: 18 starting 42 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 starting 0 gfn2restarted optimizations in parallel remaining number of products is: 18 Computing statistical charges via Delta SCF procedure starting 52 gfn2 calculations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 starting 0 gfn2restart IP calculations in parallel remaining number of products is: 18 Time spent for IP calculation: 0.7s Optimizing products at assigned charge starting 5 gfn2 optimizations in parallel 1 2 3 4 5 starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization 1 2 3 4 5 8 is a duplicate of 0 remaining number of products is: 17 Computing reaction energy of fragmentation Starting 4 fragment pair calculations in parallel at gfn2 level 1 2 3 4 Starting 0 restart product calculations in parallel at gfn2 level Starting 30 SPH calculations in parallel at gfn2 level 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy Internal energy of H-diss to fragpair p10 scaled with 0.50 Internal energy of H-diss to fragpair p13 scaled with 0.50 Internal energy of H-diss to fragpair p14 scaled with 0.50 Internal energy of H-diss to fragpair p16 scaled with 0.50 Internal energy of H-diss to fragpair p18 scaled with 0.50 remaining number of products is: 17 from 17 fragment pairs 17 are left after sorting step Remaining Pairs: 17 Search for transition states for 17 pairs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Starting 17 neb transition state searches 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Time spent for path search and barrier calculation: 70.0s Retry NEB searches for 1 pairs 1 WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p5p12/p18 WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p5p12/p18 calculation failed, retrying with different settings Retry transition state searches for 1 pairs 1 remaining number of products is: 17 Number of succesfull ts searches is 17 Starting 17 gfn2 First Hessian calculations 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Warning! Zero point energy ... not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5p12/p18/ts/hess Warning! Zero point energy ... not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5p12/p18/ts/hess calculation failed, retrying with different settings 1 Identifying IRC mode IRC MODE found! mode 1 with -209.147700000000 Identifying IRC mode IRC MODE found! mode 1 with -345.006200000000 Identifying IRC mode IRC MODE found! mode 1 with -139.042100000000 Identifying IRC mode no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p5p12/p5/ts/hess No imaginary mode found, we have to take end as ts ircmode set to 0 Identifying IRC mode IRC MODE found! mode 1 with -363.306200000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -322.459300000000 Identifying IRC mode IRC MODE found! mode 1 with -328.786600000000 Identifying IRC mode IRC MODE found! mode 1 with -673.778300000000 Identifying IRC mode IRC MODE found! mode 1 with -297.600400000000 Identifying IRC mode IRC MODE found! mode 1 with -108.689600000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -37.4567000000000 Identifying IRC mode IRC MODE found! mode 1 with -336.101600000000 Identifying IRC mode IRC MODE found! mode 1 with -119.387500000000 Identifying IRC mode no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p5p12/p16/ts/hess No imaginary mode found, we have to take end as ts ircmode set to 0 Identifying IRC mode IRC MODE found! mode 1 with -122.901700000000 Warning! Zero point energy ... not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5p12/p18/ts/hess TS Hessian calculation failed, we have to take end as ts ircmode set to 0 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -113.988200000000 Starting 14 gfn2 TS optimizations 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5p12/p6/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5p12/p7/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5p12/p10/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5p12/p14/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p5p12/p19/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Starting 9 gfn2 Hessian calculations 1 2 3 4 5 6 7 8 9 Identifying IRC mode IRC MODE found! mode 1 with -266.167200000000 Identifying IRC mode have to continue search no suitable IRC mode found within first 9 frequencies for current working directory is/tmp1/gorges/7867629/default/p5p12/p3/ts/hess2 No imaginary mode found, we just take highest point on reaction path as transi tion state Identifying IRC mode IRC MODE found! mode 1 with -510.631800000000 Identifying IRC mode IRC MODE found! mode 1 with -685.323500000000 Identifying IRC mode IRC MODE found! mode 1 with -357.970300000000 Identifying IRC mode IRC MODE found! mode 1 with -53.5531000000000 Identifying IRC mode IRC MODE found! mode 1 with -121.952500000000 Identifying IRC mode IRC MODE found! mode 1 with -80.0307000000000 Identifying IRC mode IRC MODE found! mode 1 with -32.7223000000000 Starting 17 gfn2 Singlepoint calculations on TS 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Warning! | TOTAL ENERGY not found in xtb.outcalculations failed in: current working directory is/tmp1/gorges/7867629/default/p5p12/p18/ts Warning! | TOTAL ENERGY not found in xtb.outcalculations failed in: current working directory is/tmp1/gorges/7867629/default/p5p12/p18/ts calculation failed, retrying with different settings Restarting 1 gfn2 singlepoint calculations on TS 1 Starting 17 bhess calculations on TS structures 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Warning! zero point energy not found in xtb.outcalculations failed in: current working directory is/tmp1/gorges/7867629/default/p5p12/p18/ts/bhess calculation failed, retrying with different settings Restarting 1 failed bhess calculations on TS structures 1 npairs are 17 ---------------------------------------------------------------------- |Initializing the Monte Carlo Simulation to calculate all intensities| ---------------------------------------------------------------------- Eyring equation is used to compute rate constants, with mRRHO-cutoff: 0.00 cm-1 sum of half lifes of prior reactions is: 0.22E-12 s Scaling of IEE for H-dissociation is0.50 time of flight is 0.50E-04 s Reading barriers and frequencies reaction | barrier/kcal/mol | barrier/eV | irc mode /cm -1 p1 50.4 2.19 -266.2 p3 57.5 2.49 -114.0 p4 25.1 1.09 -510.6 p5 52.0 2.25 0.0 p6 82.3 3.57 0.0 p7 65.9 2.86 0.0 p8 49.2 2.14 -685.3 p10 65.6 2.84 0.0 p11 60.0 2.60 -358.0 p12 59.6 2.58 -53.6 p13 59.3 2.57 -122.0 p14 66.3 2.87 0.0 p15 70.0 3.04 -80.0 p16 74.8 3.24 0.0 p17 84.1 3.65 -32.7 p18 71.0 3.08 0.0 p19 97.6 4.23 0.0 Internal energy of H-diss to fragpair p10 scaled with 0.50 Internal energy of H-diss to fragpair p13 scaled with 0.50 Internal energy of H-diss to fragpair p14 scaled with 0.50 Internal energy of H-diss to fragpair p16 scaled with 0.50 Internal energy of H-diss to fragpair p18 scaled with 0.50 Compute Isomer equilibrium Intensity of initial peak was 1.6% Intensity of initial peak is now 1.6% Compute fragmentation branching ratios Intensity of initial peak was 1.6% Intensity of initial peak is now 0.2% --------------------------------- |Monte Carlo simulation finished| --------------------------------- Writing fragments and isomers to file fragments Important fragments are: dir | mass | sumformula | rel. I / % newly generated products: 30 total number of products is now: 178 Fragment p5p13f1 is not fragmented further due to too low propability (0.0) Fragment p5p13f2 is not fragmented further due to too low propability (0.0) Fragment p5p14f1 is not fragmented further due to too low propability (0.2) Fragment p5p14f2 is not fragmented further due to too low propability (0.0) Fragment p5p15f1 is not fragmented further due to too low propability (0.0) Fragment p5p15f2 is not fragmented further due to too low propability (0.0) Fragment p5p16f1 is not fragmented further due to too low propability (0.1) Fragment p5p16f2 is not fragmented further due to too low propability (0.0) Fragment p5p17f1 is not fragmented further due to too low propability (0.0) Fragment p5p17f2 is not fragmented further due to too low propability (0.0) Fragment p5p18f1 is not fragmented further due to too low propability (0.0) Fragment p5p18f2 is not fragmented further due to too low propability (0.0) Fragment p5p19f1 is not fragmented further due to too low propability (0.0) Fragment p5p19f2 is not fragmented further due to too low propability (0.0) Fragment p5p20f1 is not fragmented further due to too low propability (0.0) Fragment p5p20f2 is not fragmented further due to too low propability (0.0) Fragment p5p21f1 is not fragmented further due to too low propability (0.0) Fragment p5p21f2 is not fragmented further due to too low propability (0.0) Fragment p5p22f1 is not fragmented further due to too low propability (0.0) Fragment p5p22f2 is not fragmented further due to too low propability (0.0) Fragment p5p24f1 is not fragmented further due to too low propability (0.0) Fragment p5p24f2 is not fragmented further due to too low propability (0.0) Fragment p12f1p1 is not fragmented further due to too low propability (0.0) Fragment p12f1p2 is not fragmented further due to too low propability (0.0) Fragment p12f1p3 is not fragmented further due to too low propability (0.0) Fragment p12f1p4f1 is not fragmented further due to too low propability (0.0) Fragment p12f1p4f2 is not fragmented further due to too low propability (0.0) Fragment p12f1p5f1 is not fragmented further due to too low propability (0.0) Fragment p12f1p5f2 is not fragmented further due to too low propability (0.9) Fragment p12f1p6f1 is not fragmented further due to too low propability (0.0) Fragment p12f1p6f2 is not fragmented further due to too low propability (0.0) ------------------------------------ | Starting fragmentation of: p12f1p7f1 ------------------------------------ Average temperature set to 4641 K Generate new fragments with CREST within energy window of 788.75 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 0 --T 16 --gfn2 --ewin 788.74865 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 4 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 4 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 4.2s Generated fragments were read from msreact.out Number of generated fragments and isomers is 6 1 starting 1 GFN-FF optimizations in parallel before topology check 1 starting 1 topo calculations in parallel: 1 Check product topology after optimization 1 remaining number of products is: 4 starting 8 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 starting 0 gfn2restarted optimizations in parallel remaining number of products is: 4 Computing statistical charges via Delta SCF procedure starting 12 gfn2 calculations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 starting 0 gfn2restart IP calculations in parallel remaining number of products is: 4 Time spent for IP calculation: 0.2s Optimizing products at assigned charge starting 1 gfn2 optimizations in parallel 1 starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization 1 remaining number of products is: 4 Computing reaction energy of fragmentation Starting 1 fragment pair calculations in parallel at gfn2 level 1 Starting 0 restart product calculations in parallel at gfn2 level Starting 7 SPH calculations in parallel at gfn2 level 1 2 3 4 5 6 7 Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy Internal energy of H-diss to fragpair p2 scaled with 0.50 fragment pair p4 is sorted out with an reaction energy of 304.2 kcal/mol ( 13.2 eV) remaining number of products is: 3 from 4 fragment pairs 3 are left after sorting step Remaining Pairs: 3 Search for transition states for 3 pairs 1 2 3 Starting 3 neb transition state searches 1 2 3 Time spent for path search and barrier calculation: 6.1s Retry NEB searches for 2 pairs 1 2 WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p12f1p7f1/p3 WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p12f1p7f1/p3 calculation failed, retrying with different settings Retry transition state searches for 1 pairs 1 remaining number of products is: 3 Number of succesfull ts searches is 3 Starting 3 gfn2 First Hessian calculations 1 2 3 Identifying IRC mode IRC MODE found! mode 1 with -1763.32530000000 Identifying IRC mode IRC MODE found! mode 1 with -454.834000000000 Identifying IRC mode IRC MODE found! mode 1 with -214.434600000000 Starting 3 gfn2 TS optimizations 1 2 3 Starting 3 gfn2 Hessian calculations 1 2 3 Warning! Zero point energy ... not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p12f1p7f1/p3/ts/hess2 Warning! Zero point energy ... not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p12f1p7f1/p3/ts/hess2 calculation failed, retrying with different settings 1 Identifying IRC mode IRC MODE found! mode 1 with -1668.07740000000 Identifying IRC mode IRC MODE found! mode 1 with -398.750600000000 file orca.g98.out does not exist! ERROR: Could not find orca.g98.out, Hessian calculation failed current working directory is/tmp1/gorges/7867629/default/p12f1p7f1/p3/ts/hess2 No imaginary mode found, we just take highest point on reaction path as transi tion state Starting 3 gfn2 Singlepoint calculations on TS 1 2 3 Starting 3 bhess calculations on TS structures 1 2 3 npairs are 3 ---------------------------------------------------------------------- |Initializing the Monte Carlo Simulation to calculate all intensities| ---------------------------------------------------------------------- Eyring equation is used to compute rate constants, with mRRHO-cutoff: 0.00 cm-1 sum of half lifes of prior reactions is: 0.66E-09 s Scaling of IEE for H-dissociation is0.50 time of flight is 0.50E-04 s Reading barriers and frequencies reaction | barrier/kcal/mol | barrier/eV | irc mode /cm -1 p1 81.4 3.53 -1668.1 p2 96.5 4.19 -398.8 p3 114.2 4.95 -214.4 Internal energy of H-diss to fragpair p2 scaled with 0.50 energy is scaled according to proportion of atom with other fragment with0.38 Compute Isomer equilibrium Intensity of initial peak was 15.5% Intensity of initial peak is now 14.3% Compute fragmentation branching ratios Intensity of initial peak was 14.3% Intensity of initial peak is now 13.8% --------------------------------- |Monte Carlo simulation finished| --------------------------------- Writing fragments and isomers to file fragments Important fragments are: dir | mass | sumformula | rel. I / % p12f1p7f1p1 43.045 H3C2O1 1.2 newly generated products: 5 total number of products is now: 183 Fragment p12f1p7f2 is not fragmented further due to too low propability (0.0) Fragment p12f1p10f1 is not fragmented further due to too low propability (0.0) Fragment p12f1p10f2 is not fragmented further due to too low propability (0.3) Fragment p12f1p11f1 is not fragmented further due to too low propability (0.0) Fragment p12f1p11f2 is not fragmented further due to too low propability (0.0) Fragment p12f1p12f1 is not fragmented further due to too low propability (0.0) Fragment p12f1p12f2 is not fragmented further due to too low propability (0.0) Fragment p12f1p13f1 is not fragmented further due to too low propability (0.0) Fragment p12f1p13f2 is not fragmented further due to too low propability (0.0) Fragment p12f1p14f1 is not fragmented further due to too low propability (0.0) Fragment p12f1p14f2 is not fragmented further due to too low propability (0.0) Fragment p12f1p15f1 is not fragmented further due to too low propability (0.0) Fragment p12f1p15f2 is not fragmented further due to too low propability (0.0) ------------------------------------ | Starting fragmentation of: p13f1p1 ------------------------------------ Average temperature set to 4641 K Generate new fragments with CREST within energy window of 804.82 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 0 --T 16 --gfn2 --ewin 804.82056 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 7 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 7 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 3.8s Generated fragments were read from msreact.out Number of generated fragments and isomers is 8 3 starting 3 GFN-FF optimizations in parallel before topology check 1 2 3 starting 3 topo calculations in parallel: 1 2 3 Check product topology after optimization 1 2 3 1 is a duplicate of its pre-precursor is a duplicate of its pre-precursor remaining number of products is: 6 starting 12 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 starting 0 gfn2restarted optimizations in parallel remaining number of products is: 6 Computing statistical charges via Delta SCF procedure starting 16 gfn2 calculations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 starting 0 gfn2restart IP calculations in parallel remaining number of products is: 6 Time spent for IP calculation: 0.2s Optimizing products at assigned charge starting 2 gfn2 optimizations in parallel 1 2 starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization 1 2 2 is a duplicate of 0 remaining number of products is: 5 Computing reaction energy of fragmentation Starting 1 fragment pair calculations in parallel at gfn2 level 1 Starting 0 restart product calculations in parallel at gfn2 level Starting 9 SPH calculations in parallel at gfn2 level 1 2 3 4 5 6 7 8 9 Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy Internal energy of H-diss to fragpair p4 scaled with 0.50 Internal energy of H-diss to fragpair p5 scaled with 0.50 fragment pair p7 is sorted out with an reaction energy of 219.3 kcal/mol ( 9.5 eV) remaining number of products is: 4 from 5 fragment pairs 4 are left after sorting step Remaining Pairs: 4 Search for transition states for 4 pairs 1 2 3 4 Starting 4 neb transition state searches 1 2 3 4 Time spent for path search and barrier calculation: 12.0s Retry NEB searches for 1 pairs 1 WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p13f1p1/p6 WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p13f1p1/p6 calculation failed, retrying with different settings Retry transition state searches for 1 pairs 1 remaining number of products is: 4 Number of succesfull ts searches is 4 Starting 4 gfn2 First Hessian calculations 1 2 3 4 Identifying IRC mode IRC MODE found! mode 1 with -1204.35570000000 Identifying IRC mode IRC MODE found! mode 1 with -399.192000000000 Identifying IRC mode IRC MODE found! mode 1 with -441.425700000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -174.361100000000 Starting 4 gfn2 TS optimizations 1 2 3 4 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p13f1p1/p6/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Starting 3 gfn2 Hessian calculations 1 2 3 Identifying IRC mode IRC MODE found! mode 1 with -1407.53330000000 Identifying IRC mode IRC MODE found! mode 1 with -299.874200000000 Identifying IRC mode IRC MODE found! mode 1 with -384.356800000000 Starting 4 gfn2 Singlepoint calculations on TS 1 2 3 4 Starting 4 bhess calculations on TS structures 1 2 3 4 npairs are 4 ---------------------------------------------------------------------- |Initializing the Monte Carlo Simulation to calculate all intensities| ---------------------------------------------------------------------- Eyring equation is used to compute rate constants, with mRRHO-cutoff: 0.00 cm-1 sum of half lifes of prior reactions is: 0.38E-08 s Scaling of IEE for H-dissociation is0.50 time of flight is 0.50E-04 s Reading barriers and frequencies reaction | barrier/kcal/mol | barrier/eV | irc mode /cm -1 p2 63.9 2.77 -1407.5 p4 71.3 3.09 -299.9 p5 97.1 4.21 -384.4 p6 173.9 7.54 0.0 Internal energy of H-diss to fragpair p4 scaled with 0.50 Internal energy of H-diss to fragpair p5 scaled with 0.50 Compute Isomer equilibrium Intensity of initial peak was 2.7% Intensity of initial peak is now 2.5% Compute fragmentation branching ratios Intensity of initial peak was 2.5% Intensity of initial peak is now 0.7% --------------------------------- |Monte Carlo simulation finished| --------------------------------- Writing fragments and isomers to file fragments Important fragments are: dir | mass | sumformula | rel. I / % newly generated products: 7 total number of products is now: 190 Fragment p13f1p2f1 is not fragmented further due to too low propability (0.0) Fragment p13f1p2f2 is not fragmented further due to too low propability (0.0) ------------------------------------ | Starting fragmentation of: p13f1p3f1 ------------------------------------ Average temperature set to 6189 K Generate new fragments with CREST within energy window of 689.64 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 0 --T 16 --gfn2 --ewin 689.63522 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 0 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 0 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 3.3s Generated fragments were read from msreact.out Number of generated fragments and isomers is 0 0 starting 0 GFN-FF optimizations in parallel before topology check starting 0 topo calculations in parallel: Check product topology after optimization no products left starting 0 gfn2 optimizations in parallel starting 0 gfn2restarted optimizations in parallel no products left Computing statistical charges via Delta SCF procedure starting 0 gfn2 calculations in parallel starting 0 gfn2restart IP calculations in parallel no products left Time spent for IP calculation: 0.0s Optimizing products at assigned charge starting 0 gfn2 optimizations in parallel starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization no products left Computing reaction energy of fragmentation Starting 0 fragment pair calculations in parallel at gfn2 level Starting 0 restart product calculations in parallel at gfn2 level Starting 0 SPH calculations in parallel at gfn2 level Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy tav is much to large, something went wrong, set it to 0 no products left from 0 fragment pairs 0 are left after sorting step Remaining Pairs: 0 No fragments left newly generated products: 0 total number of products is now: 190 Fragment p13f1p3f2 is not fragmented further due to too low propability (0.0) Fragment p18f2p1 is not fragmented further due to too low propability (0.0) Fragment p18f2p2 is not fragmented further due to too low propability (0.0) Fragment p18f2p3 is not fragmented further due to too low propability (0.0) Fragment p18f2p4f1 is not fragmented further due to too low propability (0.0) ------------------------------------ | Starting fragmentation of: p18f2p4f2 ------------------------------------ Average temperature set to 4332 K Generate new fragments with CREST within energy window of 764.63 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 0 --T 16 --gfn2 --ewin 764.63086 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 4 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 4 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 4.0s Generated fragments were read from msreact.out Number of generated fragments and isomers is 6 1 starting 1 GFN-FF optimizations in parallel before topology check 1 starting 1 topo calculations in parallel: 1 Check product topology after optimization 1 remaining number of products is: 4 starting 8 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 starting 0 gfn2restarted optimizations in parallel remaining number of products is: 4 Computing statistical charges via Delta SCF procedure starting 12 gfn2 calculations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 starting 0 gfn2restart IP calculations in parallel remaining number of products is: 4 Time spent for IP calculation: 0.2s Optimizing products at assigned charge starting 1 gfn2 optimizations in parallel 1 starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization 1 2 is a duplicate of 0 remaining number of products is: 3 Computing reaction energy of fragmentation Starting 0 fragment pair calculations in parallel at gfn2 level Starting 0 restart product calculations in parallel at gfn2 level Starting 6 SPH calculations in parallel at gfn2 level 1 2 3 4 5 6 Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy Internal energy of H-diss to fragpair p1 scaled with 0.50 Internal energy of H-diss to fragpair p3 scaled with 0.50 fragment pair p4 is sorted out with an reaction energy of 173.8 kcal/mol ( 7.5 eV) remaining number of products is: 2 from 3 fragment pairs 2 are left after sorting step Remaining Pairs: 2 Search for transition states for 2 pairs 1 2 Starting 2 neb transition state searches 1 2 Time spent for path search and barrier calculation: 3.0s Retry NEB searches for 1 pairs 1 remaining number of products is: 2 Number of succesfull ts searches is 2 Starting 2 gfn2 First Hessian calculations 1 2 Identifying IRC mode IRC MODE found! mode 1 with -446.877800000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -35.3065000000000 Starting 2 gfn2 TS optimizations 1 2 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p18f2p4f2/p3/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Starting 1 gfn2 Hessian calculations 1 Identifying IRC mode IRC MODE found! mode 1 with -355.178100000000 Starting 2 gfn2 Singlepoint calculations on TS 1 2 Starting 2 bhess calculations on TS structures 1 2 npairs are 2 ---------------------------------------------------------------------- |Initializing the Monte Carlo Simulation to calculate all intensities| ---------------------------------------------------------------------- Eyring equation is used to compute rate constants, with mRRHO-cutoff: 0.00 cm-1 sum of half lifes of prior reactions is: 0.29E-09 s Scaling of IEE for H-dissociation is0.50 time of flight is 0.50E-04 s Reading barriers and frequencies reaction | barrier/kcal/mol | barrier/eV | irc mode /cm -1 p1 75.0 3.25 -355.2 p3 116.9 5.07 0.0 Internal energy of H-diss to fragpair p1 scaled with 0.50 Internal energy of H-diss to fragpair p3 scaled with 0.50 energy is scaled according to proportion of atom with other fragment with0.44 Compute Isomer equilibrium Intensity of initial peak was 6.5% Intensity of initial peak is now 6.5% Compute fragmentation branching ratios Intensity of initial peak was 6.5% Intensity of initial peak is now 6.5% --------------------------------- |Monte Carlo simulation finished| --------------------------------- Writing fragments and isomers to file fragments Important fragments are: dir | mass | sumformula | rel. I / % newly generated products: 4 total number of products is now: 194 Fragment p18f2p5 is not fragmented further due to too low propability (0.0) Fragment p18f2p7 is not fragmented further due to too low propability (0.0) Fragment p18f2p8f1 is not fragmented further due to too low propability (0.0) Fragment p18f2p8f2 is not fragmented further due to too low propability (0.0) Fragment p18f2p9 is not fragmented further due to too low propability (0.0) Fragment p18f2p10f1 is not fragmented further due to too low propability (0.0) Fragment p18f2p10f2 is not fragmented further due to too low propability (0.1) Fragment p18f2p11f1 is not fragmented further due to too low propability (0.0) Fragment p18f2p11f2 is not fragmented further due to too low propability (0.0) Fragment p18f2p12f1 is not fragmented further due to too low propability (0.0) Fragment p18f2p12f2 is not fragmented further due to too low propability (0.0) Fragment p18f2p13f1 is not fragmented further due to too low propability (0.0) Fragment p18f2p13f2 is not fragmented further due to too low propability (0.0) Fragment p23f1p1 is not fragmented further due to too low propability (0.0) Fragment p23f1p2 is not fragmented further due to too low propability (0.0) Fragment p23f1p3 is not fragmented further due to too low propability (0.1) Fragment p23f1p4 is not fragmented further due to too low propability (0.0) Fragment p23f1p5 is not fragmented further due to too low propability (0.0) Fragment p23f1p6 is not fragmented further due to too low propability (0.2) Fragment p23f1p7 is not fragmented further due to too low propability (0.0) Fragment p23f1p8 is not fragmented further due to too low propability (0.0) Fragment p23f1p9f1 is not fragmented further due to too low propability (0.0) Fragment p23f1p9f2 is not fragmented further due to too low propability (0.0) Fragment p23f1p10f1 is not fragmented further due to too low propability (0.0) Fragment p23f1p10f2 is not fragmented further due to too low propability (0.0) Fragment p23f1p11f1 is not fragmented further due to too low propability (0.0) Fragment p23f1p11f2 is not fragmented further due to too low propability (0.0) Fragment p23f1p12f1 is not fragmented further due to too low propability (0.5) Fragment p23f1p12f2 is not fragmented further due to too low propability (0.0) Fragment p23f1p13f1 is not fragmented further due to too low propability (0.0) Fragment p23f1p13f2 is not fragmented further due to too low propability (0.0) Fragment p23f1p14f1 is not fragmented further due to too low propability (0.0) Fragment p23f1p14f2 is not fragmented further due to too low propability (0.0) Fragment p25f1p1 is not fragmented further due to too low propability (0.0) Fragment p25f1p2f1 is not fragmented further due to too low propability (0.0) Fragment p25f1p2f2 is not fragmented further due to too low propability (0.0) Fragment p25f1p3 is not fragmented further due to too low propability (0.0) ------------------------------------ | Starting fragmentation of: p25f1p4f1 ------------------------------------ Average temperature set to 4126 K Generate new fragments with CREST within energy window of 764.41 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 0 --T 16 --gfn2 --ewin 764.40995 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 7 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 7 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 4.2s Generated fragments were read from msreact.out Number of generated fragments and isomers is 8 3 starting 3 GFN-FF optimizations in parallel before topology check 1 2 3 starting 3 topo calculations in parallel: 1 2 3 Check product topology after optimization 1 2 3 remaining number of products is: 7 starting 12 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 starting 0 gfn2restarted optimizations in parallel remaining number of products is: 7 Computing statistical charges via Delta SCF procedure starting 16 gfn2 calculations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 starting 0 gfn2restart IP calculations in parallel remaining number of products is: 7 Time spent for IP calculation: 0.2s Optimizing products at assigned charge starting 3 gfn2 optimizations in parallel 1 2 3 starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization 1 2 3 2 is a duplicate of 0 remaining number of products is: 6 Computing reaction energy of fragmentation Starting 2 fragment pair calculations in parallel at gfn2 level 1 2 Starting 0 restart product calculations in parallel at gfn2 level Starting 10 SPH calculations in parallel at gfn2 level 1 2 3 4 5 6 7 8 9 10 Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy Internal energy of H-diss to fragpair p4 scaled with 0.50 Internal energy of H-diss to fragpair p5 scaled with 0.50 fragment pair p6 is sorted out with an reaction energy of 172.0 kcal/mol ( 7.5 eV) fragment pair p7 is sorted out with an reaction energy of 214.3 kcal/mol ( 9.3 eV) remaining number of products is: 4 from 6 fragment pairs 4 are left after sorting step Remaining Pairs: 4 Search for transition states for 4 pairs 1 2 3 4 Starting 4 neb transition state searches 1 2 3 4 Time spent for path search and barrier calculation: 9.5s Retry NEB searches for 2 pairs 1 2 WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p25f1p4f1/p4 WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p25f1p4f1/p5 WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p25f1p4f1/p4 calculation failed, retrying with different settings WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p25f1p4f1/p5 calculation failed, retrying with different settings Retry transition state searches for 2 pairs 1 2 remaining number of products is: 4 Number of succesfull ts searches is 4 Starting 4 gfn2 First Hessian calculations 1 2 3 4 Identifying IRC mode IRC MODE found! mode 1 with -793.674000000000 Identifying IRC mode IRC MODE found! mode 1 with -766.325900000000 Identifying IRC mode IRC MODE found! mode 1 with -698.907000000000 Identifying IRC mode IRC MODE found! mode 1 with -699.415300000000 Starting 4 gfn2 TS optimizations 1 2 3 4 Starting 4 gfn2 Hessian calculations 1 2 3 4 Identifying IRC mode IRC MODE found! mode 1 with -704.460300000000 Identifying IRC mode IRC MODE found! mode 1 with -720.480800000000 Identifying IRC mode IRC MODE found! mode 1 with -350.278500000000 Identifying IRC mode IRC MODE found! mode 1 with -336.502100000000 Starting 4 gfn2 Singlepoint calculations on TS 1 2 3 4 Starting 4 bhess calculations on TS structures 1 2 3 4 npairs are 4 ---------------------------------------------------------------------- |Initializing the Monte Carlo Simulation to calculate all intensities| ---------------------------------------------------------------------- Eyring equation is used to compute rate constants, with mRRHO-cutoff: 0.00 cm-1 sum of half lifes of prior reactions is: 0.15E-08 s Scaling of IEE for H-dissociation is0.50 time of flight is 0.50E-04 s Reading barriers and frequencies reaction | barrier/kcal/mol | barrier/eV | irc mode /cm -1 p1 24.7 1.07 -704.5 p3 41.4 1.80 -720.5 p4 90.5 3.93 -350.3 p5 87.6 3.80 -336.5 Internal energy of H-diss to fragpair p4 scaled with 0.50 Internal energy of H-diss to fragpair p5 scaled with 0.50 energy is scaled according to proportion of atom with other fragment with0.50 Compute Isomer equilibrium Intensity of initial peak was 20.0% Intensity of initial peak is now 20.0% Compute fragmentation branching ratios Intensity of initial peak was 20.0% Intensity of initial peak is now 19.9% --------------------------------- |Monte Carlo simulation finished| --------------------------------- Writing fragments and isomers to file fragments Important fragments are: dir | mass | sumformula | rel. I / % newly generated products: 6 total number of products is now: 200 Fragment p25f1p4f2 is not fragmented further due to too low propability (0.0) Fragment p25f1p5f1 is not fragmented further due to too low propability (0.0) Fragment p25f1p5f2 is not fragmented further due to too low propability (0.0) Fragment p25f1p6f1 is not fragmented further due to too low propability (0.0) Fragment p25f1p6f2 is not fragmented further due to too low propability (0.0) Fragment p25f1p7f1 is not fragmented further due to too low propability (0.0) Fragment p25f1p7f2 is not fragmented further due to too low propability (0.0) -------------------------------------------------- |Starting fragmentation 4 for 52 fragments -------------------------------------------------- Fragment p5p12p1 is not fragmented further due to too low propability (0.0) Fragment p5p12p3 is not fragmented further due to too low propability (0.0) Fragment p5p12p4 is not fragmented further due to too low propability (0.0) Fragment p5p12p5f1 is not fragmented further due to too low propability (0.1) Fragment p5p12p5f2 is not fragmented further due to too low propability (0.0) Fragment p5p12p6f1 is not fragmented further due to too low propability (0.1) Fragment p5p12p6f2 is not fragmented further due to too low propability (0.0) Fragment p5p12p7f1 is not fragmented further due to too low propability (0.0) Fragment p5p12p7f2 is not fragmented further due to too low propability (0.0) Fragment p5p12p8 is not fragmented further due to too low propability (0.0) Fragment p5p12p10f1 is not fragmented further due to too low propability (0.0) Fragment p5p12p10f2 is not fragmented further due to too low propability (0.0) Fragment p5p12p11f1 is not fragmented further due to too low propability (0.9) Fragment p5p12p11f2 is not fragmented further due to too low propability (0.0) Fragment p5p12p12f1 is not fragmented further due to too low propability (0.3) Fragment p5p12p12f2 is not fragmented further due to too low propability (0.0) Fragment p5p12p13f1 is not fragmented further due to too low propability (0.0) Fragment p5p12p13f2 is not fragmented further due to too low propability (0.0) Fragment p5p12p14f1 is not fragmented further due to too low propability (0.0) Fragment p5p12p14f2 is not fragmented further due to too low propability (0.0) Fragment p5p12p15f1 is not fragmented further due to too low propability (0.0) Fragment p5p12p15f2 is not fragmented further due to too low propability (0.0) Fragment p5p12p16f1 is not fragmented further due to too low propability (0.0) Fragment p5p12p16f2 is not fragmented further due to too low propability (0.0) Fragment p5p12p17f1 is not fragmented further due to too low propability (0.0) Fragment p5p12p17f2 is not fragmented further due to too low propability (0.0) Fragment p5p12p18f1 is not fragmented further due to too low propability (0.0) Fragment p5p12p18f2 is not fragmented further due to too low propability (0.0) Fragment p5p12p19f1 is not fragmented further due to too low propability (0.0) Fragment p5p12p19f2 is not fragmented further due to too low propability (0.0) ------------------------------------ | Starting fragmentation of: p12f1p7f1p1 ------------------------------------ Average temperature set to 4641 K Generate new fragments with CREST within energy window of 768.51 kcal/mol crestcall is: crest infrag.xyz --msreact --mslargeprint --msnbonds 3 --chrg 1 --uhf 0 --T 16 --gfn2 --ewin 768.51356 --msnshifts 0 --msnshifts2 0 --msattrh --msmolbar --ms input crestms.inp > msreact.out 2>cresterror.out 7 new fragment pairs 'pairs.xyz' and 'isomers.xyz' were generated and written to pXX directories 7 fragment structures fragment.xyz were written to pXXfX directories Time spent for MSREACT calculation: 4.0s Generated fragments were read from msreact.out Number of generated fragments and isomers is 8 3 starting 3 GFN-FF optimizations in parallel before topology check 1 2 3 starting 3 topo calculations in parallel: 1 2 3 Check product topology after optimization 1 2 3 1 is a duplicate of its pre-precursor is a duplicate of its pre-precursor remaining number of products is: 6 starting 12 gfn2 optimizations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 starting 0 gfn2restarted optimizations in parallel remaining number of products is: 6 Computing statistical charges via Delta SCF procedure starting 16 gfn2 calculations in parallel 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 starting 0 gfn2restart IP calculations in parallel remaining number of products is: 6 Time spent for IP calculation: 0.2s Optimizing products at assigned charge starting 2 gfn2 optimizations in parallel 1 2 starting 0 gfn2 restarted optimizations in parallel Check product topology after optimization 1 2 2 is a duplicate of 0 remaining number of products is: 5 Computing reaction energy of fragmentation Starting 1 fragment pair calculations in parallel at gfn2 level 1 Starting 0 restart product calculations in parallel at gfn2 level Starting 9 SPH calculations in parallel at gfn2 level 1 2 3 4 5 6 7 8 9 Starting 0 restart SPH calculations in parallel at gfn2 level Sorting out fragmentpairs which are too high in energy Internal energy of H-diss to fragpair p4 scaled with 0.50 Internal energy of H-diss to fragpair p5 scaled with 0.50 fragment pair p7 is sorted out with an reaction energy of 219.3 kcal/mol ( 9.5 eV) remaining number of products is: 4 from 5 fragment pairs 4 are left after sorting step Remaining Pairs: 4 Search for transition states for 4 pairs 1 2 3 4 Starting 4 neb transition state searches 1 2 3 4 Time spent for path search and barrier calculation: 7.8s Retry NEB searches for 1 pairs 1 WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p12f1p7f1p1/p6 WARNING: no stringfile found, search was not succesfull current working directory is/tmp1/gorges/7867629/default/p12f1p7f1p1/p6 calculation failed, retrying with different settings Retry transition state searches for 1 pairs 1 remaining number of products is: 4 Number of succesfull ts searches is 4 Starting 4 gfn2 First Hessian calculations 1 2 3 4 Identifying IRC mode IRC MODE found! mode 1 with -1177.05010000000 Identifying IRC mode IRC MODE found! mode 1 with -464.814500000000 Identifying IRC mode IRC MODE found! mode 1 with -419.740100000000 Identifying IRC mode have to continue search IRC MODE found! mode 2 with -171.108600000000 Starting 4 gfn2 TS optimizations 1 2 3 4 Warning! THE OPTIMIZATION HAS CONVERGED not found in orca.out calculations failed in: current working directory is/tmp1/gorges/7867629/default/p12f1p7f1p1/p6/ts TS Optimization not converged we have to take last point of path as ts and ircm odeis set to 0 Starting 3 gfn2 Hessian calculations 1 2 3 Identifying IRC mode IRC MODE found! mode 1 with -1406.91760000000 Identifying IRC mode IRC MODE found! mode 1 with -299.377500000000 Identifying IRC mode IRC MODE found! mode 1 with -384.575900000000 Starting 4 gfn2 Singlepoint calculations on TS 1 2 3 4 Starting 4 bhess calculations on TS structures 1 2 3 4 npairs are 4 ---------------------------------------------------------------------- |Initializing the Monte Carlo Simulation to calculate all intensities| ---------------------------------------------------------------------- Eyring equation is used to compute rate constants, with mRRHO-cutoff: 0.00 cm-1 sum of half lifes of prior reactions is: 0.54E-06 s Scaling of IEE for H-dissociation is0.50 time of flight is 0.49E-04 s Reading barriers and frequencies reaction | barrier/kcal/mol | barrier/eV | irc mode /cm -1 p2 63.9 2.77 -1406.9 p4 71.3 3.09 -299.4 p5 97.1 4.21 -384.6 p6 173.6 7.53 0.0 Internal energy of H-diss to fragpair p4 scaled with 0.50 Internal energy of H-diss to fragpair p5 scaled with 0.50 Compute Isomer equilibrium Intensity of initial peak was 1.2% Intensity of initial peak is now 1.2% Compute fragmentation branching ratios Intensity of initial peak was 1.2% Intensity of initial peak is now 0.4% --------------------------------- |Monte Carlo simulation finished| --------------------------------- Writing fragments and isomers to file fragments Important fragments are: dir | mass | sumformula | rel. I / % newly generated products: 7 total number of products is now: 207 Fragment p12f1p7f1p2f1 is not fragmented further due to too low propability (0.0) Fragment p12f1p7f1p2f2 is not fragmented further due to too low propability (0.0) Fragment p12f1p7f1p3f1 is not fragmented further due to too low propability (0.4) Fragment p12f1p7f1p3f2 is not fragmented further due to too low propability (0.0) Fragment p13f1p1p2 is not fragmented further due to too low propability (0.1) Fragment p13f1p1p4f1 is not fragmented further due to too low propability (0.9) Fragment p13f1p1p4f2 is not fragmented further due to too low propability (0.0) Fragment p13f1p1p5f1 is not fragmented further due to too low propability (0.2) Fragment p13f1p1p5f2 is not fragmented further due to too low propability (0.0) Fragment p13f1p1p6f1 is not fragmented further due to too low propability (0.0) Fragment p13f1p1p6f2 is not fragmented further due to too low propability (0.7) Fragment p18f2p4f2p1f1 is not fragmented further due to too low propability (0.0) Fragment p18f2p4f2p1f2 is not fragmented further due to too low propability (0.0) Fragment p18f2p4f2p3f1 is not fragmented further due to too low propability (0.0) Fragment p18f2p4f2p3f2 is not fragmented further due to too low propability (0.0) Fragment p25f1p4f1p1 is not fragmented further due to too low propability (0.0) Fragment p25f1p4f1p3 is not fragmented further due to too low propability (0.0) Fragment p25f1p4f1p4f1 is not fragmented further due to too low propability (0.1) Fragment p25f1p4f1p4f2 is not fragmented further due to too low propability (0.0) Fragment p25f1p4f1p5f1 is not fragmented further due to too low propability (0.0) Fragment p25f1p4f1p5f2 is not fragmented further due to too low propability (0.0) -------------------------------------------------- |Starting fragmentation 5 for 7 fragments -------------------------------------------------- Fragment p12f1p7f1p1p2 is not fragmented further due to too low propability (0.0) Fragment p12f1p7f1p1p4f1 is not fragmented further due to too low propability (0.4) Fragment p12f1p7f1p1p4f2 is not fragmented further due to too low propability (0.0) Fragment p12f1p7f1p1p5f1 is not fragmented further due to too low propability (0.1) Fragment p12f1p7f1p1p5f2 is not fragmented further due to too low propability (0.0) Fragment p12f1p7f1p1p6f1 is not fragmented further due to too low propability (0.0) Fragment p12f1p7f1p1p6f2 is not fragmented further due to too low propability (0.2) No new fragments were generated ------------------------------------- |Reaction network generation finished| ------------------------------------- Normalize Intensities for all fragments Number of fragments is: 207 Computed spectrum is written to peaks.dat and peaks.csv Important peaks (above 10 %) are: (m/z | intensity - normalized to 10000) 29.039125 1975.4 41.039125 5990.5 43.018389 10000.0 58.041864 2129.1 59.049689 3447.3 71.049689 1083.7 86.073164 2801.8 Writing all fragment intensities without isotope pattern to allpeaks.dat Important fragments (above 10 %) are: (fragment | m/z | intensity - normalized to 10000) input structure 86.073164 3837.3 p12f1 58.041864 3538.3 p13f1 43.018389 8549.4 p18f2 71.049689 1436.6 p25f1 59.049689 5754.6 p12f1p7f1 43.018389 7001.3 p18f2p4f2 29.039125 3294.4 p25f1p4f1 41.039125 10000.0 ----------------- Wall Time Summary ----------------- first fragmentation wall time : 0h : 6m :51s Fragmentation level 2 wall time : 0h :15m :47s Fragmentation level 3 wall time : 0h : 4m :31s Fragmentation level 4 wall time : 0h : 0m :32s Fragmentation level 5 wall time : 0h : 0m : 0s -------------------- Overall wall time : 0h :27m :43s QCxMS2 terminated normally. .. tab-item:: spectrum (peaks.csv) .. code:: text 1.00782500000000 , 3.54023986610509 2.01410100000000 , 2.124271368758087E-004 2.01565000000000 , 1.510101236010183E-006 3.02192600000000 , 3.322953797477602E-010 14.0156500000000 , 4.262834922092613E-002 15.0190040000000 , 4.479386520840423E-004 15.0219260000000 , 1.065631589381359E-005 15.0234750000000 , 491.944784934372 16.0268290000000 , 5.26263436198465 16.0297510000000 , 0.208839582262939 16.0313000000000 , 0.619900387216992 17.0346540000000 , 6.607089228131758E-003 17.0375760000000 , 3.259664473285532E-004 18.0105640000000 , 3.833000081928205E-004 18.0409300000000 , 2.507434140050467E-005 19.0147810000000 , 1.245516298288313E-007 19.0168400000000 , 7.897147639302775E-008 20.0148090000000 , 7.526114641805165E-007 27.0234750000000 , 1.23563167358444 27.9949140000000 , 5.063150314414833E-002 28.0268290000000 , 2.594952813073624E-002 28.0297510000000 , 4.038836943088412E-004 28.0313000000000 , 121.558367824746 28.9982680000000 , 5.406959333184353E-004 28.9991310000000 , 2.051976892966003E-005 29.0027390000000 , 276.699019658113 29.0301830000000 , 1.514563853658155E-004 29.0346540000000 , 2.55305944632487 29.0375760000000 , 5.216993384382967E-002 29.0391250000000 , 1975.37595188737 29.9991590000000 , 1.046508207947613E-004 30.0060930000000 , 2.96024722174827 30.0069560000000 , 8.409793317771892E-002 30.0090150000000 , 4.485223211592659E-002 30.0380080000000 , 1.490740455485626E-002 30.0409300000000 , 5.983002773145308E-006 30.0424790000000 , 42.1993973792333 30.0454010000000 , 1.17108374647432 31.0025130000000 , 2.051976892966003E-006 31.0069840000000 , 0.532620246178411 31.0458330000000 , 0.363439793520277 32.0103380000000 , 5.606529014490824E-003 40.0313000000000 , 37.6506121538535 41.0346540000000 , 1.22591388529463 41.0375760000000 , 1.752967510601747E-002 41.0391250000000 , 5990.52556966287 42.0105640000000 , 759.021617052873 42.0380080000000 , 1.277630663587563E-002 42.0409300000000 , 1.103925609094813E-003 42.0424790000000 , 196.575142815631 42.0454010000000 , 3.59211047197095 42.0469500000000 , 75.2245327403721 43.0139180000000 , 16.2571574066349 43.0147810000000 , 0.247208297296425 43.0168400000000 , 0.202097467291991 43.0183890000000 , 10000.0000000000 43.0458330000000 , 2.22958587234355 43.0487550000000 , 0.371597630369876 43.0503040000000 , 2.40271233685203 43.0532260000000 , 4.804832751150426E-002 43.0547750000000 , 255.333999402968 44.0148090000000 , 1.46995235306703 44.0172720000000 , 8.393853174297256E-002 44.0181350000000 , 4.581150232289419E-002 44.0201940000000 , 1.092364719436842E-002 44.0217430000000 , 218.421772722849 44.0226060000000 , 4.71779061178641 44.0246650000000 , 3.48650640316288 44.0262140000000 , 126.954874359568 44.0536580000000 , 1.893149634474956E-002 44.0581290000000 , 8.30298657401460 44.0610510000000 , 0.211137617356099 45.0181630000000 , 2.179849326863942E-002 45.0226340000000 , 21.0922546024020 45.0250970000000 , 0.826571934097455 45.0259600000000 , 0.204951969142402 45.0280190000000 , 0.613322852591194 45.0295680000000 , 2.77385568683869 45.0304310000000 , 4.432803451288241E-002 45.0324900000000 , 5.467714145018298E-002 45.0614830000000 , 7.389816223406352E-002 46.0259880000000 , 0.210025012288287 46.0304590000000 , 0.280905984671875 46.0329220000000 , 1.045189174452091E-002 46.0337850000000 , 1.027848146989182E-005 46.0358440000000 , 7.797804882511111E-003 46.0367070000000 , 2.592415973190442E-003 47.0338130000000 , 5.225945872260453E-003 53.0391250000000 , 4.230125314567164E-003 54.0424790000000 , 1.834727609466497E-004 54.0454010000000 , 2.209450270875211E-006 55.0458330000000 , 2.916474388420945E-006 55.0487550000000 , 1.767560293864334E-007 56.0262140000000 , 1.12596710553260 57.0295680000000 , 3.647574647749247E-002 57.0304310000000 , 5.830521777540366E-004 57.0324900000000 , 5.130859557917549E-004 57.0340390000000 , 146.384512643486 58.0304590000000 , 2.192276334967795E-003 58.0329220000000 , 3.498313473781489E-004 58.0337850000000 , 2.332208812830464E-005 58.0373930000000 , 4.80959062943232 58.0382560000000 , 5.158551468336160E-002 58.0403150000000 , 7.586104476987085E-002 58.0418640000000 , 2129.13572893409 59.0382840000000 , 0.327719721360788 59.0407470000000 , 5.461995667930854E-002 59.0416100000000 , 1.753813225719751E-010 59.0436690000000 , 9.103326183696903E-003 59.0445320000000 , 3.034441768930097E-003 59.0452180000000 , 70.1521862053974 59.0460810000000 , 0.882433230482965 59.0481400000000 , 1.19164446244334 59.0496890000000 , 3447.26012880927 60.0416380000000 , 6.068883888622838E-003 60.0461090000000 , 3.70604066053434 60.0485720000000 , 0.662364221715470 60.0494350000000 , 4.412164378836200E-002 60.0514940000000 , 0.220248811429450 60.0523570000000 , 2.086563041390361E-008 60.0530430000000 , 113.594119667704 60.0539060000000 , 1.42885689889754 60.0559650000000 , 2.21472827126346 61.0494630000000 , 8.842306436261037E-002 61.0539340000000 , 6.00119907933270 61.0563970000000 , 1.07164264818240 61.0572600000000 , 7.144284494487708E-002 61.0593190000000 , 0.357214224724385 62.0572880000000 , 0.142885689889754 68.0626000000000 , 374.006340710268 69.0659540000000 , 20.0945918563419 69.0688760000000 , 0.349531314725522 70.0418640000000 , 3.165564501633224E-004 70.0693080000000 , 0.473954782556728 70.0722300000000 , 3.159648035629131E-002 71.0452180000000 , 1.363184462909165E-005 71.0460810000000 , 1.241881155500218E-007 71.0481400000000 , 2.057211574281398E-007 71.0496890000000 , 1083.74730892848 72.0461090000000 , 6.572673171157613E-007 72.0485720000000 , 2.436414280104883E-007 72.0494350000000 , 2.673112635827508E-009 72.0514940000000 , 6.755196130280508E-009 72.0523570000000 , 3.956109698463257E-009 72.0530430000000 , 46.3005266257240 72.0539060000000 , 0.381264416345657 72.0559650000000 , 0.975845973224385 72.0575140000000 , 18.1692221593976 73.0494630000000 , 2.862441145111278E-008 73.0539340000000 , 2.31023488527455 73.0563970000000 , 0.839681434181100 73.0572600000000 , 2.269409259256856E-002 73.0593190000000 , 3.177356002484847E-002 73.0601820000000 , 1.815435887642862E-002 73.0608680000000 , 0.791605138959847 73.0617310000000 , 6.472961820297413E-003 73.0637900000000 , 1.979964805128204E-002 74.0572880000000 , 7.716174520998559E-002 74.0617590000000 , 3.464938408974357E-002 74.0642220000000 , 1.370744882137443E-002 74.0650850000000 , 3.807624518692257E-004 74.0671440000000 , 1.903812259346129E-003 75.0651130000000 , 3.807624518692257E-004 84.0575140000000 , 3.41065081887935 85.0608680000000 , 0.183329519991580 85.0617310000000 , 1.082654605095669E-003 85.0637900000000 , 3.392317923681128E-003 85.0653390000000 , 3.47799486933606 86.0617590000000 , 6.062866040610927E-003 86.0642220000000 , 3.392317923681128E-003 86.0671440000000 , 2.887079016942668E-004 86.0686930000000 , 0.187166886980034 86.0695560000000 , 1.249233262150080E-003 86.0716150000000 , 4.390172460056265E-003 86.0731640000000 , 2801.83751704970 87.0651130000000 , 5.774158033885335E-004 87.0675760000000 , 7.217697542356669E-005 87.0695840000000 , 6.109762228592492E-003 87.0720470000000 , 3.685195461842396E-003 87.0729100000000 , 1.447447791506992E-004 87.0749690000000 , 3.669026448097248E-004 87.0765180000000 , 147.362219593464 87.0773810000000 , 0.888795046525780 87.0794400000000 , 3.61443329842251 88.0729380000000 , 5.196888054008154E-004 88.0754010000000 , 8.254507931819439E-007 88.0774090000000 , 5.15501145954337 88.0798720000000 , 3.19966220198260 88.0827940000000 , 0.296265022693966 89.0807630000000 , 0.296265022693966 The ``peaks.csv`` file can be visualized using any suitable plotting tools. The spectrum shown here is plotted together with the experimental spectrum taken from the `NIST `_ database. .. figure:: ../../figures/qcxms2/2pentanone_gfn2.png :scale: 100 % :alt: 2pentanone_gfn2.png Computed EI-MS spectrum of 2-pentanone using GFN2-xTB level of theory and inverted experimental spectrum. For more details on visualization of spectra, see section :ref:`qcxms2_plot`.