Example Usage
QCxMS2 is usually invoked via command line, and requires only a coordinate input file in xyz file format.
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 Settings for QCxMS2.
EI - positive Ion Electron Ionization
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.
crest in.xyz -T 16 --chrg 1 cp crest_best.xyz in.xyz
The QCxMS2 calculation is then started with the following command:
qcxms2 in.xyz -T 16
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
-----------------------------------------------------------
| ===================== |
| = 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.
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.
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 Visualization.