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
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