NEB interpolation: nebmake.pl
Posted: Tue Jan 14, 2014 11:02 am
Dear all
For a NEB calculation, i used the script nebmake.pl. This is a diffusion reaction of O atom from an adsorbed site.
But i think this script didnt give me the right interpolated geometries. Because they are very different from the POSCAR1 and POSCAR2 and possible reaction path.
Here are the POSCAR files. I will be very happy if anyone can tell me whether i have been doing a mistake with the reaction path. Or is there something wrong with the script?
Thank you
POSCAR1
A B
5.500000000000000
0.7070000200000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 1.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 5.6560001400000000
10 22
Selective dynamics
Direct
0.0000000000000000 0.0000000000000000 -0.0030926060068279 T T T
0.5000000000000000 0.5000000000000000 0.0568710979850247 T T T
0.0000000000000000 0.0000000000000000 0.1226159549076618 T T T
0.5000000000000000 0.5000000000000000 0.1853535380403357 T T T
0.0000000000000000 0.0000000000000000 0.2499155384054127 T T T
0.5000000000000000 0.5000000000000000 0.3127996945502868 T T T
0.0000000000000000 0.0000000000000000 0.3763724103711075 T T T
0.5000000000000000 0.5000000000000000 0.4390698402268436 T T T
0.0000000000000000 0.0000000000000000 0.5052263033455902 T T T
0.5000000000000000 0.5000000000000000 0.5628916995542685 T T T
0.5000000000000000 0.2432879951494200 1.0048811627454490 T T T
0.5000000000000000 0.7567120048505946 1.0048811627454490 T T T
0.0000000000000000 0.2593115267986495 0.0613768935267411 T T T
0.0000000000000000 0.7406884732013719 0.0613768935267411 T T T
0.5000000000000000 0.2507540179723185 0.1213788809916193 T T T
0.5000000000000000 0.7492459820277110 0.1213788809916193 T T T
0.0000000000000000 0.2520068022519631 0.1857738854161097 T T T
0.0000000000000000 0.7479931977481027 0.1857738854161097 T T T
0.5000000000000000 0.2505547136222869 0.2497073738181578 T T T
0.5000000000000000 0.7494452863777238 0.2497073738181578 T T T
0.0000000000000000 0.2471771110566951 0.3127115703804629 T T T
0.0000000000000000 0.7528228889432337 0.3127115703804631 T T T
0.5000000000000000 0.2513480081639248 0.3759987967802115 T T T
0.5000000000000000 0.7486519918361039 0.3759987967802115 T T T
0.0000000000000000 0.2485219442737279 0.4399344476561279 T T T
0.0000000000000000 0.7514780557262292 0.4399344476561279 T T T
0.5000000000000000 0.2591367623731777 0.5031941568259526 T T T
0.5000000000000000 0.7408632376268458 0.5031941568259526 T T T
0.0000000000000000 0.2684480899883578 0.5609146785314141 T T T
0.0000000000000000 0.7315519100116273 0.5609146785314141 T T T
0.0000000000000000 0.0000000000000000 0.9378341902223840 T T T
0.5000000000000000 0.5000000000000000 0.6213433787401998 T T T
POSCAR2
A B
5.500000000000000
0.7070000200000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 1.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 5.6560001400000000
10 22
Selective dynamics
Direct
0.0000000000000000 0.0000000000000000 0.0077598071575111 T T T
0.5000000000000000 0.5000000000000000 0.0576738386625394 T T T
0.0000000000000000 0.0000000000000000 0.1218145302801617 T T T
0.5000000000000000 0.5000000000000000 0.1864020691708371 T T T
0.0000000000000000 0.0000000000000000 0.2490937401426081 T T T
0.5000000000000000 0.5000000000000000 0.3134062598573921 T T T
0.0000000000000000 0.0000000000000000 0.3760979308291628 T T T
0.5000000000000000 0.5000000000000000 0.4406854697198384 T T T
0.0000000000000000 0.0000000000000000 0.5048261613374607 T T T
0.5000000000000000 0.5000000000000000 0.5547401928424892 T T T
0.5000000000000000 0.2456354445375899 0.9941396552008275 T T T
0.5000000000000000 0.7543645554624101 0.9941396552008275 T T T
0.0000000000000000 0.2838547423533322 0.0588532889317149 T T T
0.0000000000000000 0.7161452576466675 0.0588532889317149 T T T
0.5000000000000000 0.2667032579847616 0.1235075990649394 T T T
0.5000000000000000 0.7332967420152383 0.1235075990649394 T T T
0.0000000000000000 0.2437679475858568 0.1852811992064954 T T T
0.0000000000000000 0.7562320524141435 0.1852811992064954 T T T
0.5000000000000000 0.2516651694756919 0.2495943104716869 T T T
0.5000000000000000 0.7483348305243076 0.2495943104716869 T T T
0.0000000000000000 0.2483348305243080 0.3129056895283130 T T T
0.0000000000000000 0.7516651694756924 0.3129056895283130 T T T
0.5000000000000000 0.2562320524141430 0.3772188007935047 T T T
0.5000000000000000 0.7437679475858565 0.3772188007935047 T T T
0.0000000000000000 0.2332967420152384 0.4389924009350605 T T T
0.0000000000000000 0.7667032579847617 0.4389924009350605 T T T
0.5000000000000000 0.2161452576466676 0.5036467110682852 T T T
0.5000000000000000 0.7838547423533325 0.5036467110682852 T T T
0.0000000000000000 0.2543645554624099 0.5683603447991725 T T T
0.0000000000000000 0.7456354445375899 0.5683603447991725 T T T
0.0000000000000000 0.5000000000000000 0.5039678062644585 T T T
0.5000000000000000 0.0000000000000000 0.0585321937355415 T T T
For a NEB calculation, i used the script nebmake.pl. This is a diffusion reaction of O atom from an adsorbed site.
But i think this script didnt give me the right interpolated geometries. Because they are very different from the POSCAR1 and POSCAR2 and possible reaction path.
Here are the POSCAR files. I will be very happy if anyone can tell me whether i have been doing a mistake with the reaction path. Or is there something wrong with the script?
Thank you
POSCAR1
A B
5.500000000000000
0.7070000200000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 1.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 5.6560001400000000
10 22
Selective dynamics
Direct
0.0000000000000000 0.0000000000000000 -0.0030926060068279 T T T
0.5000000000000000 0.5000000000000000 0.0568710979850247 T T T
0.0000000000000000 0.0000000000000000 0.1226159549076618 T T T
0.5000000000000000 0.5000000000000000 0.1853535380403357 T T T
0.0000000000000000 0.0000000000000000 0.2499155384054127 T T T
0.5000000000000000 0.5000000000000000 0.3127996945502868 T T T
0.0000000000000000 0.0000000000000000 0.3763724103711075 T T T
0.5000000000000000 0.5000000000000000 0.4390698402268436 T T T
0.0000000000000000 0.0000000000000000 0.5052263033455902 T T T
0.5000000000000000 0.5000000000000000 0.5628916995542685 T T T
0.5000000000000000 0.2432879951494200 1.0048811627454490 T T T
0.5000000000000000 0.7567120048505946 1.0048811627454490 T T T
0.0000000000000000 0.2593115267986495 0.0613768935267411 T T T
0.0000000000000000 0.7406884732013719 0.0613768935267411 T T T
0.5000000000000000 0.2507540179723185 0.1213788809916193 T T T
0.5000000000000000 0.7492459820277110 0.1213788809916193 T T T
0.0000000000000000 0.2520068022519631 0.1857738854161097 T T T
0.0000000000000000 0.7479931977481027 0.1857738854161097 T T T
0.5000000000000000 0.2505547136222869 0.2497073738181578 T T T
0.5000000000000000 0.7494452863777238 0.2497073738181578 T T T
0.0000000000000000 0.2471771110566951 0.3127115703804629 T T T
0.0000000000000000 0.7528228889432337 0.3127115703804631 T T T
0.5000000000000000 0.2513480081639248 0.3759987967802115 T T T
0.5000000000000000 0.7486519918361039 0.3759987967802115 T T T
0.0000000000000000 0.2485219442737279 0.4399344476561279 T T T
0.0000000000000000 0.7514780557262292 0.4399344476561279 T T T
0.5000000000000000 0.2591367623731777 0.5031941568259526 T T T
0.5000000000000000 0.7408632376268458 0.5031941568259526 T T T
0.0000000000000000 0.2684480899883578 0.5609146785314141 T T T
0.0000000000000000 0.7315519100116273 0.5609146785314141 T T T
0.0000000000000000 0.0000000000000000 0.9378341902223840 T T T
0.5000000000000000 0.5000000000000000 0.6213433787401998 T T T
POSCAR2
A B
5.500000000000000
0.7070000200000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 1.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 5.6560001400000000
10 22
Selective dynamics
Direct
0.0000000000000000 0.0000000000000000 0.0077598071575111 T T T
0.5000000000000000 0.5000000000000000 0.0576738386625394 T T T
0.0000000000000000 0.0000000000000000 0.1218145302801617 T T T
0.5000000000000000 0.5000000000000000 0.1864020691708371 T T T
0.0000000000000000 0.0000000000000000 0.2490937401426081 T T T
0.5000000000000000 0.5000000000000000 0.3134062598573921 T T T
0.0000000000000000 0.0000000000000000 0.3760979308291628 T T T
0.5000000000000000 0.5000000000000000 0.4406854697198384 T T T
0.0000000000000000 0.0000000000000000 0.5048261613374607 T T T
0.5000000000000000 0.5000000000000000 0.5547401928424892 T T T
0.5000000000000000 0.2456354445375899 0.9941396552008275 T T T
0.5000000000000000 0.7543645554624101 0.9941396552008275 T T T
0.0000000000000000 0.2838547423533322 0.0588532889317149 T T T
0.0000000000000000 0.7161452576466675 0.0588532889317149 T T T
0.5000000000000000 0.2667032579847616 0.1235075990649394 T T T
0.5000000000000000 0.7332967420152383 0.1235075990649394 T T T
0.0000000000000000 0.2437679475858568 0.1852811992064954 T T T
0.0000000000000000 0.7562320524141435 0.1852811992064954 T T T
0.5000000000000000 0.2516651694756919 0.2495943104716869 T T T
0.5000000000000000 0.7483348305243076 0.2495943104716869 T T T
0.0000000000000000 0.2483348305243080 0.3129056895283130 T T T
0.0000000000000000 0.7516651694756924 0.3129056895283130 T T T
0.5000000000000000 0.2562320524141430 0.3772188007935047 T T T
0.5000000000000000 0.7437679475858565 0.3772188007935047 T T T
0.0000000000000000 0.2332967420152384 0.4389924009350605 T T T
0.0000000000000000 0.7667032579847617 0.4389924009350605 T T T
0.5000000000000000 0.2161452576466676 0.5036467110682852 T T T
0.5000000000000000 0.7838547423533325 0.5036467110682852 T T T
0.0000000000000000 0.2543645554624099 0.5683603447991725 T T T
0.0000000000000000 0.7456354445375899 0.5683603447991725 T T T
0.0000000000000000 0.5000000000000000 0.5039678062644585 T T T
0.5000000000000000 0.0000000000000000 0.0585321937355415 T T T