OPTIM version 35025, Copyright (C) David J. Wales
OPTIM comes with ABSOLUTELY NO WARRANTY; for details supply WARRANTY as an input keyword.
This is free software, and you are welcome to redistribute it
under certain conditions; provide keyword COPYRIGHT to see the details.
getparams> Number of atoms (or variables) determined as 97
getparams> Number of optimisation degrees of freedom 291
EOSUNIT,PRINTPTS,MORPHT= 103 T F
fetchz> Hybrid EF/BFGS transition state search, maximum steps= 20000
maximum tangent space steps= 3 or 25 when overlap is better than 0.999900
fetchz> Uphill mode is 0 for initial step and 0 after that
fetchz> No Hessian: Rayleigh-Ritz max steps= 50 RMS < 0.0001 and |% change|< 1.0
fetchz> Hessian eigenvector in Rayleigh-Ritz scheme calculated using method 2
NEWNEBT= T
fetchz> Coordinates of second point read from file finish
SYSTEM 291 Cartesian coordinates will be optimised for 97 SBM sites
fetchz> Point group checked when RMS force < 0.00100000, highest symmetry axis tested for= 6
fetchz> Initial distance and eigenvalue tolerances in symmetry determination= 0.00010000 0.00010000
fetchz> Minimum number of optimization steps= 0
fetchz> Pathways will be calculated saving 100 frames on each side
fetchz> Extra (d)neb steps allowed if the (d)neb energy is > lowest value times 0.0000
fetchz> RMS convergence reset to 0.5000000000E-05 for LBFGS and EF phases for consistency
fetchz> Convergence criterion for LBFGS optimization: RMS force< 0.50000000E-05 maximum steps= 1000000
fetchz> Maximum energy rise in LBFGS minimization= 0.1000000000E-03
fetchz> Number of updates in LBFGS= 200
fetchz> Number of updates in XLBFGS= 4
fetchz> Number of updates in mind= 4
fetchz> Number of updates in neb= 4
fetchz> Initial guess for diagonal elements in LBFGS= 0.1000
fetchz> Initial guess for diagonal elements in XLBFGS= 0.1000
fetchz> Maximum step size in LBFGS energy minimization= 0.2000
fetchz> Maximum step size in XLBFGS= 0.2000
fetchz> Maximum step size in LBFGS neb image minimization= 0.2000
fetchz> Warnings will be issued if atoms become closer than 0.5 units
rotcon> Rotational constants (in cm-1) and principal moments of inertia:
0.00459 0.00489 0.00877 6866.64459 12301.95219 13128.01933
symmetry> The full molecular point group is C1 .
symmetry> The largest Abelian subgroup of the full molecular point group is C1 .
symmetry> Distance tolerance= 0.00010 Inertia tolerance= 0.00010
symmetry> Order of full point group= 1
OPTIM> Using translational/rotational ev shift= 1000000.000
Calculations will use a Structure-Based model
For more information on Structure-Based models, see:
Software: Noel, et al. PLOS Comput Biol 12, e1004794, 2016
Reading the forcefield from SBM.INP
NCswitch,NCcut
8.00000 9.00000
Reading electrostatic parameters
332.00000 80.00000 0.10000 12.00000 15.00000
97 atoms
282 contacts 97 ATOMS
96 bonds
95 angles
94 dihedrals
0 exclusions
0 position restraints
OPTIM> Initial energy= -249.9056167 RMS force= 0.4931914216E-05
OPTIM> Final energy = -246.7902205 RMS force= 0.4943827849E-05
KeyConnect> Maximum cycles = 50, maximum images = 20
KeyConnect> Maximum attempts per pair of minima = 20, with increment image density of 2.00
KeyConnect> Image density = 1.00, iteration density = 50.00
KeyNEB> Initial and final NEB force constants 500.0000000 500.0000000 factor= 1.000000000
KeyNEB> Number of images will vary depending on the separation of the endpoints
KeyGrad> Overall rotation and translation will NOT be removed
KeyGrad> Using doubly nudged elastic band gradient
KeyOutput> Transition state candidates will be optimized
KeyOutput> Concise printing during transition states optimization
KeyOutput> Transition state candidates are maxima along NEB
KeyMin> Maximal number of iterations will vary, depending on the number of images in the band
KeyMin> RMS convergence criterion is set to 0.025
KeyMin> L-BFGS minimization
KeyLBFGS> Maximum step size per image = 0.2000000000
KeyLBFGS> 4 Hessian updates per iteration
KeyLBFGS> Guess for inverse Hessian diagonal elements = 0.1000000000E-02
KeyTau> Using Henkelman and Jonsson's improved tangent
KeyConnect> Using 31 images and 500 iterations in the first NEB run
KeyDecide> Cost function in Dijkstra algorithm is D^20
>>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
decide> Shortest path in Dijkstra has 1 steps with 1 missing connections, weight= 0.15933E+24
decide> The unconnected minima in the chain and their distances are:
2 14.46 1
tryconnect> First DNEB calculation will use parameters from the NEWNEB line in odata
tryconnect> 500-iteration DNEB run for minima 1_S and 2_F using 31 images (DNEB attempt #1) ...
Time to go through NEB: 2.3919999999999999
Double-ended search iterations= 500 RMS= 1.6556 Dev= 3.37% S= 24.06 time= 2.39
Following 3 images are candidates for TS: 3 12 27
Converged to TS (number of iterations): 35
Converged to TS (number of iterations): 47
Converged to TS (number of iterations): 98
DNEB run yielded 3 true transition state(s) time= 1.29
Energies:
-249.80271302785772
-249.77243746000977
-246.37261585917491
>>>>> Path run for ts 1 ...
Plus side of path: 419 steps. Energy= -257.1223560 time= 0.12
Minus side of path: 370 steps. Energy= -249.9056167 time= 0.10
E+ Ets - E+ Ets Ets - E- E- S D gamma ~N
-257.1223560 7.3196 -249.8027130 0.10290 -249.9056167 12.953 5.333 44.651 2.172
*NEW* (Placed in 3) Known (#1)
Unconnected minimum 3 found its way to S set.
>>>>> Path run for ts 2 ...
Plus side of path: 422 steps. Energy= -252.3399330 time= 0.12
Minus side of path: 446 steps. Energy= -257.1223560 time= 0.13
E+ Ets - E+ Ets Ets - E- E- S D gamma ~N
-252.3399330 2.5675 -249.7724375 7.3499 -257.1223560 23.869 11.118 20.384 4.759
*NEW* (Placed in 4) Known (#3)
Unconnected minimum 4 found its way to S set.
>>>>> Path run for ts 3 ...
Plus side of path: 452 steps. Energy= -250.4255983 time= 0.13
Minus side of path: 439 steps. Energy= -258.9506309 time= 0.13
E+ Ets - E+ Ets Ets - E- E- S D gamma ~N
-250.4255983 4.0530 -246.3726159 12.578 -258.9506309 40.217 10.799 17.617 5.506
*NEW* (Placed in 5) *NEW* (Placed in 6)
Connection established between members of the U set.
>>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
decide> Shortest path in Dijkstra has 4 steps with 2 missing connections, weight= 0.10620E+20
decide> The unconnected minima in the chain and their distances are:
2 8.94 6 6 6.78 4
tryconnect> 400-iteration DNEB run for minima 2_F and 6_U using 8 images (DNEB attempt #1) ...
Time to go through NEB: 0.52000000000000046
Double-ended search iterations= 400 RMS= 4.6124 Dev= 0.37% S= 11.55 time= 0.52
Following 1 images are candidates for TS: 4
Converged to TS (number of iterations): 97
DNEB run yielded 1 true transition state(s) time= 0.67
Energies:
-246.37261585974596
isnewts> transition state is the same as number 3 energy= -246.3726158597
tryconnect> Try the path again for ts 1 with pushoff= 0.1000000000E-01
>>>>> Path run for ts 4 ...
tryconnect> Trying this transition state path again with pushoff= 0.1000000000E-01
Plus side of path: 455 steps. Energy= -258.9506309 time= 0.15
Minus side of path: 458 steps. Energy= -250.4255983 time= 0.14
E+ Ets - E+ Ets Ets - E- E- S D gamma ~N
-258.9506309 12.578 -246.3726159 4.0530 -250.4255983 40.675 10.796 17.732 5.470
Known (#6) Known (#5)
Connection established between members of the U set.
tryconnect> 300-iteration DNEB run for minima 4_S and 6_U using 6 images (DNEB attempt #1) ...
Time to go through NEB: 0.18799999999999972
Double-ended search iterations= 300 RMS= 1.6554 Dev= 0.16% S= 7.60 time= 0.19
Following 1 images are candidates for TS: 2
Converged to TS (number of iterations): 28
DNEB run yielded 1 true transition state(s) time= 0.20
Energies:
-251.83729979818906
>>>>> Path run for ts 5 ...
Plus side of path: 356 steps. Energy= -258.9506309 time= 0.10
Minus side of path: 371 steps. Energy= -252.3399330 time= 0.10
E+ Ets - E+ Ets Ets - E- E- S D gamma ~N
-258.9506309 7.1133 -251.8372998 0.50263 -252.3399330 15.198 6.777 26.717 3.631
Known (#6) Known (#4)
Unconnected minimum 6 found its way to S set.
>>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
decide> Shortest path in Dijkstra has 5 steps with 1 missing connections, weight= 0.16702E+20
decide> The unconnected minima in the chain and their distances are:
2 9.14 5
tryconnect> 450-iteration DNEB run for minima 2_F and 5_S using 9 images (DNEB attempt #1) ...
Time to go through NEB: 0.75599999999999934
Double-ended search iterations= 450 RMS= 4.9494 Dev= 0.56% S= 11.30 time= 0.76
Following 1 images are candidates for TS: 3
Converged to TS (number of iterations): 66
DNEB run yielded 1 true transition state(s) time= 0.46
Energies:
-246.54494281842693
>>>>> Path run for ts 6 ...
Plus side of path: 492 steps. Energy= -248.9216023 time= 0.14
Minus side of path: 394 steps. Energy= -246.6367073 time= 0.11
E+ Ets - E+ Ets Ets - E- E- S D gamma ~N
-248.9216023 2.3767 -246.5449428 0.91764E-01 -246.6367073 23.572 10.574 21.271 4.560
*NEW* (Placed in 7) *NEW* (Placed in 8)
Connection established between members of the U set.
>>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
decide> Shortest path in Dijkstra has 5 steps with 2 missing connections, weight= 0.21758E+19
decide> The unconnected minima in the chain and their distances are:
2 4.13 8 8 8.26 6
tryconnect> 200-iteration DNEB run for minima 2_F and 8_U using 4 images (DNEB attempt #1) ...
Time to go through NEB: 7.1999999999999176E-002
Double-ended search iterations= 200 RMS= 0.8186 Dev= 0.01% S= 4.15 time= 0.07
Following 1 images are candidates for TS: 3
Converged to TS (number of iterations): 26
DNEB run yielded 1 true transition state(s) time= 0.19
Energies:
-246.61186815117048
>>>>> Path run for ts 7 ...
Plus side of path: 349 steps. Energy= -246.6367073 time= 0.10
Minus side of path: 363 steps. Energy= -246.7902205 time= 0.10
E+ Ets - E+ Ets Ets - E- E- S D gamma ~N
-246.6367073 0.24839E-01 -246.6118682 0.17835 -246.7902205 8.047 4.126 11.555 8.394
Known (#8) Known (#2)
Unconnected minimum 8 found its way to F set.
tryconnect> 400-iteration DNEB run for minima 6_S and 8_F using 8 images (DNEB attempt #1) ...
Time to go through NEB: 0.36399999999999899
Double-ended search iterations= 400 RMS= 3.9358 Dev= 0.79% S= 10.26 time= 0.36
Following 1 images are candidates for TS: 7
Converged to TS (number of iterations): 169
DNEB run yielded 1 true transition state(s) time= 1.15
Energies:
-248.52903208350401
>>>>> Path run for ts 8 ...
Plus side of path: 366 steps. Energy= -248.9216023 time= 0.10
Minus side of path: 381 steps. Energy= -249.8240591 time= 0.11
E+ Ets - E+ Ets Ets - E- E- S D gamma ~N
-248.9216023 0.39257 -248.5290321 1.2950 -249.8240591 19.167 12.500 21.892 4.431
Known (#7) *NEW* (Placed in 9)
Unconnected minimum 9 found its way to F set.
>>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
decide> Shortest path in Dijkstra has 8 steps with 1 missing connections, weight= 0.99642E+18
decide> The unconnected minima in the chain and their distances are:
9 7.94 5
tryconnect> 350-iteration DNEB run for minima 5_S and 9_F using 7 images (DNEB attempt #1) ...
Time to go through NEB: 0.25200000000000067
Double-ended search iterations= 350 RMS= 2.0259 Dev= 0.19% S= 9.77 time= 0.25
Following 1 images are candidates for TS: 4
Converged to TS (number of iterations): 48
DNEB run yielded 1 true transition state(s) time= 0.32
Energies:
-248.14895098084946
>>>>> Path run for ts 9 ...
Plus side of path: 463 steps. Energy= -249.8240591 time= 0.14
Minus side of path: 405 steps. Energy= -250.4255983 time= 0.12
E+ Ets - E+ Ets Ets - E- E- S D gamma ~N
-249.8240591 1.6751 -248.1489510 2.2766 -250.4255983 24.273 7.948 34.227 2.834
Known (#9) Known (#5)
Connected path found
ts E+ Ets - E+ Ets Ets - E- E- S D gamma ~N
1 -249.9056167 0.10290 -249.8027130 7.3196 -257.1223560 12.953 5.333 44.651 2.172
2 -257.1223560 7.3499 -249.7724375 2.5675 -252.3399330 23.869 11.118 20.384 4.759
5 -252.3399330 0.50263 -251.8372998 7.1133 -258.9506309 15.198 6.777 26.717 3.631
3 -258.9506309 12.578 -246.3726159 4.0530 -250.4255983 40.217 10.799 17.617 5.506
9 -250.4255983 2.2766 -248.1489510 1.6751 -249.8240591 24.273 7.948 34.227 2.834
8 -249.8240591 1.2950 -248.5290321 0.39257 -248.9216023 19.167 12.500 21.892 4.431
6 -248.9216023 2.3767 -246.5449428 0.91764E-01 -246.6367073 23.572 10.574 21.271 4.560
7 -246.6367073 0.24839E-01 -246.6118682 0.17835 -246.7902205 8.047 4.126 11.555 8.394
Number of TS in the path = 8
Number of cycles = 5
Elapsed time= 12.57
OPTIM> # of energy calls= 0 time= 0.00 %= 0.0
OPTIM> # of energy+gradient calls= 157443 time= 7.73 %= 61.5
OPTIM> # of energy+gradient+Hessian calls= 0 time= 0.00 %= 0.0