[Pw_forum] NEB: wild changes in image energies
Layla Martin-Samos
lmartinsamos at gmail.com
Fri Dec 30 17:32:33 CET 2011
Dear Chad, as the energy barrier is very very very small maybe the use of
freezing causes the algorithm to have more instabilities.
bests
Layla
2011/12/29 Chad Junkermeier <junkermeier at yahoo.com>
> Hello,
> I have a problem that I keep encountering when performing NEB
> calculations. I will briefly describe what is happening here, and then
> give a more detailed explanation below. In short, the NEB calculations
> appear to run well for some number of iterations (usually on the order of
> 40 or 50 iterations) and then all of the sudden weird image energies start
> showing up, and the activation energy starts jumping around with each
> iteration.
>
>
>
> More detailed explanation:
>
> Physically what I am trying to do is model the diffusion of a small
> molecule across a graphene surface. This molecule is only weakly absorbed
> (physisorbed) onto the surface, thus, the activation energy is going to be
> rather small. Our relaxation calculations show that van der Waals type
> interactions are important in this system, as should be expected for
> something that is weakly absorbed. In the NEB calculation the molecule is
> going from one lowest energy site to a neighboring lowest energy site that
> is only a few angstroms away, all of which is well within the bounds of the
> supercell.
>
> I am using Quantum Espresso 4.3.2 on a Cray XE6.
>
>
> My input file looks like this:
>
> BEGIN
> BEGIN_PATH_INPUT
> &PATH
> restart_mode = 'from_scratch'
> string_method = 'neb',
> ds = 2.D0,
> opt_scheme = "broyden",
> num_of_images = 45,
> k_max = 0.3D0,
> k_min = 0.2D0,
> CI_scheme = "auto",
> nstep_path=3000,
> use_freezing = .TRUE.
> first_last_opt = .FALSE.
> /
> END_PATH_INPUT
> BEGIN_ENGINE_INPUT
> &CONTROL
> prefix="TW2_u_B3_B4",
> pseudo_dir = "/espresso/pseudo",
> outdir = "/workspace/TW2_u_B3_B4/tmp",
> /
> &SYSTEM
> ibrav = 4,
> celldm(1) = 37.2672889,
> celldm(3) = 0.760623,
> nat = 144,
> ntyp = 4,
> ecutwfc = 50.0,
> ecutrho = 400,
> occupations = "smearing",
> smearing = "methfessel-paxton",
> degauss = 0.01,
> london = .TRUE.
> /
> &ELECTRONS
> conv_thr = 0.0000001,
> mixing_beta = 0.3,
> electron_maxstep = 150,
> /
> ATOMIC_SPECIES
> C 12.0 C.pbe-van_ak.UPF
> H 1.0 H.pbe-van_ak.UPF
> O 18.0 O.pbe-van_ak.UPF
> P 31.0 P.pbe-van_ak.UPF
> BEGIN_POSITIONS
> FIRST_IMAGE
> ATOMIC_POSITIONS angstrom
> C 0.000000000 0.000000000 0.000000000 0 0 0
> C 1.234000000 0.710000000 0.000000000 0 0 0
> C 2.465000000 0.000000000 0.000000000 0 0 0
> C 3.699000000 0.710000000 0.000000000 0 0 0
> C 4.930000000 0.000000000 0.000000000 0 0 0
> .
> .
> .
> LAST_IMAGE
> ATOMIC_POSITIONS angstrom
> .
> .
> .
> H 12.789295543 12.155855132 2.858948537
> H 13.430079977 11.427859045 4.385644094
> H 14.299090315 11.190357788 2.820979411
> END_POSITIONS
> K_POINTS {gamma}
> END_ENGINE_INPUT
> END
>
> While I didn't include all of the atoms in here (since there are a lot,
> and I don't think this is necessarily to the resolution problem), I will
> note that the majority of the atoms will not move appreciably during the
> course of the calculation, and thus to speed up the calculation I tell the
> code to fix the positions of the atoms that aren't moving.
>
> I started off with values that I thought would help the code run quicker:
> conv_thr = 0.00001
> ecutwfc = 30.0,
> ecutrho = 280,
> num_of_images = 15,
> electron_maxstep = 100,
>
> After finding the problem that I am writing here about, and reading
> everything I could find on the QE website, and within pw_forum, I slowly
> made changes trying to work through the problem. Having the number of
> images set to 45 in the above input file has many more images than I think
> I need, but one of the things that I kept reading is that having more
> images will decrease the likelihood of problems arising.
>
>
> After the first few NEB iterations a nice potential barrier curve appears
> and is slowly refined. An example of the standard output for one of the
> well behaved images is given below:
>
> ------------------------------ iteration 44
> ------------------------------
>
> tcpu = 61713.9 self-consistency for image 10
> tcpu = 61932.1 self-consistency for image 21
> tcpu = 62113.6 self-consistency for image 28
> tcpu = 62294.4 self-consistency for image 31
>
> activation energy (->) = 0.043939 eV
> activation energy (<-) = 0.044011 eV
>
> image energy (eV) error (eV/A) frozen
>
> 1 -21959.2382129 0.081337 T
> 2 -21959.2388966 0.020923 T
> 3 -21959.2381194 0.123092 T
> 4 -21959.2363069 0.164123 F
> 5 -21959.2352170 0.044025 T
> 6 -21959.2331629 0.220840 F
> 7 -21959.2301578 0.115291 T
> 8 -21959.2277497 0.199382 F
> 9 -21959.2256241 0.037564 T
> 10 -21959.2216078 0.257680 F
> 11 -21959.2173790 0.220445 F
> 12 -21959.2159181 0.195525 F
> 13 -21959.2122799 0.189871 F
> 14 -21959.2093498 0.070035 T
> 15 -21959.2075466 0.156424 F
> 16 -21959.2037818 0.237338 F
> 17 -21959.2013877 0.059399 T
> 18 -21959.2006768 0.168875 F
> 19 -21959.1986806 0.049577 T
> 20 -21959.1962718 0.054413 T
> 21 -21959.1966851 0.022074 T
> 22 -21959.1954724 0.053047 T
> 23 -21959.1942736 0.054956 T
> 24 -21959.1944583 0.140762 F
> 25 -21959.1964535 0.032502 T
> 26 -21959.1950797 0.210304 F
> 27 -21959.1987196 0.051561 T
> 28 -21959.2008371 0.031058 T
> 29 -21959.2005944 0.183532 F
> 30 -21959.2045923 0.059183 T
> 31 -21959.2074746 0.148483 F
> 32 -21959.2094894 0.139970 F
> 33 -21959.2129334 0.033060 T
> 34 -21959.2156972 0.237590 F
> 35 -21959.2188749 0.065209 T
> 36 -21959.2223341 0.020410 T
> 37 -21959.2256989 0.041502 T
> 38 -21959.2278845 0.206609 F
> 39 -21959.2309458 0.064352 T
> 40 -21959.2333476 0.228702 F
> 41 -21959.2354058 0.034633 T
> 42 -21959.2369634 0.053540 T
> 43 -21959.2383146 0.179708 F
> 44 -21959.2390413 0.052827 T
> 45 -21959.2382847 0.084999 T
>
> climbing image = 23
>
> path length = 18.663 bohr
> inter-image distance = 0.424 bohr
>
>
> If you were to plot the image number versus the energy that is given above
> you would find what appears to be a very well behaved curve.
>
>
> But after a while, all of the sudden, there is a problem with the output.
>
>
>
> ------------------------------ iteration 45
> ------------------------------
>
> tcpu = 62502.4 self-consistency for image 4
> tcpu = 62758.1 self-consistency for image 6
> tcpu = 63006.7 self-consistency for image 8
> tcpu = 63287.9 self-consistency for image 10
> tcpu = 63556.1 self-consistency for image 11
> tcpu = 63876.3 self-consistency for image 12
> tcpu = 64126.9 self-consistency for image 13
> tcpu = 64409.9 self-consistency for image 15
> tcpu = 64661.2 self-consistency for image 16
> tcpu = 64941.7 self-consistency for image 18
> tcpu = 65190.6 self-consistency for image 24
> tcpu = 65480.1 self-consistency for image 26
> tcpu = 65780.1 self-consistency for image 29
> tcpu = 66077.9 self-consistency for image 31
> tcpu = 66317.9 self-consistency for image 32
> tcpu = 66580.4 self-consistency for image 34
> tcpu = 66857.5 self-consistency for image 38
> tcpu = 67137.2 self-consistency for image 40
> tcpu = 67386.9 self-consistency for image 43
>
> activation energy (->) = 0.287582 eV
> activation energy (<-) = 0.287654 eV
>
> image energy (eV) error (eV/A) frozen
>
> 1 -21959.2382129 0.081337 T
> 2 -21959.2388966 0.020929 T
> 3 -21959.2381194 0.128767 T
> 4 -21959.1561960 2.016407 T
> 5 -21959.2352170 0.054181 T
> 6 -21959.1233419 3.440925 F
> 7 -21959.2301578 0.119857 T
> 8 -21959.1295895 3.858443 F
> 9 -21959.2256241 0.031368 T
> 10 -21959.2007906 0.830489 T
> 11 -21958.9506305 4.210877 F
> 12 -21959.1226848 2.774980 F
> 13 -21959.1255613 3.306542 F
> 14 -21959.2093498 0.063904 T
> 15 -21959.1425146 2.576069 F
> 16 -21959.0686534 4.452463 F
> 17 -21959.2013877 0.051986 T
> 18 -21959.1237018 2.915400 F
> 19 -21959.1986806 0.070271 T
> 20 -21959.1962718 0.055066 T
> 21 -21959.1966851 0.022251 T
> 22 -21959.1954724 0.053511 T
> 23 -21959.1942736 0.155528 T
> 24 -21959.0321128 1.669573 T
> 25 -21959.1964535 0.033436 T
> 26 -21958.9641160 2.813188 F
> 27 -21959.1987196 0.170191 T
> 28 -21959.2008371 0.119487 T
> 29 -21959.0410354 2.100854 T
> 30 -21959.2045923 0.217405 T
> 31 -21959.2006761 0.946770 T
> 32 -21959.1091999 2.022318 T
> 33 -21959.2129334 0.033922 T
> 34 -21959.0832736 3.736941 F
> 35 -21959.2188749 0.136602 T
> 36 -21959.2223341 0.033429 T
> 37 -21959.2256989 0.038111 T
> 38 -21959.1226548 4.018138 F
> 39 -21959.2309458 0.068887 T
> 40 -21959.1163356 3.540681 F
> 41 -21959.2354058 0.069677 T
> 42 -21959.2369634 0.053677 T
> 43 -21959.1651795 2.854320 F
> 44 -21959.2390413 0.041340 T
> 45 -21959.2382847 0.084999 T
>
> climbing image = 11
>
> path length = 19.063 bohr
> inter-image distance = 0.433 bohr
>
>
> Where if you plot the image number versus the energy given above you will
> find that many of the points lay on the same curve as in the proceeding
> plot, but now almost half of them are jumping to higher energies. When I
> look at the xyz output in VMD, there doesn't seem to be any change in what
> the images look like pre/post the start of iteration 45.
>
> I will now list some of the activation energies produced towards the end
> of the run (I stopped the code once I saw this happening again).
>
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.046128 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.044786 eV
> activation energy (->) = 0.043951 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.044436 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.043939 eV
> activation energy (->) = 0.287582 eV
> activation energy (->) = 0.206100 eV
> activation energy (->) = 0.601468 eV
> activation energy (->) = 0.231222 eV
> activation energy (->) = 0.216514 eV
> activation energy (->) = 0.252992 eV
> activation energy (->) = 0.289003 eV
> activation energy (->) = 0.107865 eV
> activation energy (->) = 0.154660 eV
> activation energy (->) = 0.302177 eV
> activation energy (->) = 0.154660 eV
> activation energy (->) = 0.290079 eV
>
>
>
> You can see that the activation energy is fairly constant at about 0.04 eV
> for a while and then after a certain point bedlam.
>
>
> Any ideas would be welcome.
>
>
>
> Chad Junkermeier, Ph.D.
> NRC Post-Doctoral Associate
> U. S. Naval Research Laboratory
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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