[Pw_forum] Relaxation of hydrogenated amorphous carbon

Alan J. R. Ambrozio ambrozio at mit.edu
Wed Nov 25 02:49:37 CET 2015


Hi,

I'm trying to make a 'vc-relax' for an amorphous carbon structure (216
atoms 5% of H) obtained running a Quench from 6000K to 300K on LAMMPS. I'm
using gipaw pseudopotentials because I'll make some NMR calculations. To
have good results for NMR I need to have very good relaxed structures, but
to be honest, this is the first time that I'm running amorphous relaxation
on QE. I ran the vc-relax and scf normally, but when a try to run gipaw I
have an error message like this

    "Error in routine cdiaghg (989):
     S matrix not positive definite"

I think this problem is because my structure isn't well relaxed... I
had this problem before with graphene... The think this problem can be
the numbers of atoms...


Could anyone give me some tricks to do good relaxation?

this is the input:

&CONTROL
  calculation='vc-relax'
  nstep=150
  tstress= .true.
  tprnfor= .true.
  prefix='50K'
  etot_conv_thr = 1.0D-4
  forc_conv_thr = 1.0D-3
  pseudo_dir ='/home/ambrozio/qe-gipaw-5.1/pseudo'
  outdir='./data/'

/
&SYSTEM
  ibrav     = 0
  celldm(1)=  24.465150
  nat       = 216
  ntyp      = 2
  ecutwfc   = 100
  ecutrho   = 1200
  occupations ='smearing'  (I don't know if the system is metalic)
  spline_ps=.true.
  degauss=0.01
  london=.true.
  london_s6 = 0.75            (use or not?  The structure has some parts
like graphite..)
/
&ELECTRONS
  electron_maxstep=5000
  conv_thr = 1.0D-6
  diagonalization='david'
  diago_thr_init = 1e-4
  mixing_mode = 'plain'
  mixing_beta = 0.7
/
&ions
upscale =100    #this is default
/
&cell
Press = 0.0    #this is default
/
ATOMIC_SPECIES
C  12.000  C.pbe-tm-gipaw.UPF
H   1.000   H.pbe-tm-gipaw.UPF

ATOMIC_POSITIONS {angstrom}

 C     0.7882546   0.6065626   0.7211832
 C     0.2881642  -0.0123605   0.2760093
 C     0.0228301   0.1905951   0.7547355
 C     0.2101520   0.4086151   0.1766798
 C     0.4457151   0.5643135   0.6661727
 C     0.7067007   0.7879631   0.4144110
 C     0.6855365   0.2258298   0.8198372
 C     0.1355208   0.0621604   0.8276883
 C     0.4363931   0.5141174   0.2279694
 C     0.5936407   0.7793334   0.4207085
 C     0.5859244   0.8848937   0.5767109
 C     0.5283677   0.3653187   0.3869548
 C     0.8312999   0.6246249   0.4091983
 C     0.9102840   0.1264440   0.3886683
 C     0.5469423   0.8867824   0.7639739
 C     0.2558971   0.4344034   0.4441222
 C     0.6662662   0.8590280   0.0741248
 C     0.6664248   0.5830016   0.8693308
 C     0.5466290   0.5737425   0.6999028
 H     0.4707029   0.2232765   0.6511726
 H     0.0072009   0.3950743   0.6588494
 C     0.8611044   0.4493360   0.3356426
 C     0.6113547   0.5271664   0.4131907
 C     0.1964175   0.7970353   0.8351151
 C     0.2675415   0.5302418   0.4948854
 C     0.7605494   0.7040310   0.6668560
 C     0.1249042   0.8634550   0.6759987
 C     0.7977951   0.2084323   0.2152986
 C     0.7664191   0.1562074   0.8031255
 C     0.6870201   0.1912958   0.3798247
 C     0.7330213   0.2870536   0.3933979
 H     0.7352675   0.6415087   0.0335573
 C     0.4422958   0.6995388   0.3650615
 C     0.5615385   0.5503336   0.5185775
 C     0.1080644   0.0077391   0.0778919
 C     0.0137435   0.4257022   0.9510966
 C     0.4321943   0.8571357   0.4714686
 C     0.4236154   0.0912046   0.8144852
 C     0.1254605   0.6280411   0.8449147
 C     0.0726748   0.4434211   0.4621965
 C     0.8205852   0.1096019   0.4662541
 C     0.3039631   0.1120866   0.6416651
 C     0.4248404   0.2169526   0.3711035
 C     0.4480209   0.1353904   0.2180935
 C     0.7788020   0.2023157   0.6274172
 C     0.6988667   0.3412404   0.0080584
 C     0.0707365   0.2193770   0.4688107
 C     0.5201701   0.2634695   0.3564601
 C     0.1846393   0.4134481   0.0784198
 C     0.4773098   0.6538072   0.9542338
 C     0.1421370   0.6011298   0.7244798
 C     0.4816710   0.8609266   0.9401489
 C     0.1243995   0.4561090   0.9586360
 C     0.6979409   0.3656521   0.5866604
 C     0.5678397   0.5603686   0.8130475
 C     0.7817233   0.4107388   0.0294312
 C     0.7626229   0.5919446   0.8315008
 H     0.1012895   0.7976846   0.2087955
 C     0.5516746   0.7019484   0.3614000
 C     0.1340584   0.0528037   0.7209917
 C     0.3689985   0.5777822   0.4903572
 C     0.4901815   0.3781462   0.8693084
 C     0.8851079   0.4363028   0.0200746
 C     0.1846087   0.5720996   0.5447761
 C     0.8238119   0.1755254   0.1111199
 C     0.0380825   0.0904789   0.0564483
 C     0.1225714   0.7981857   0.5002325
 C     0.4431491   0.4194498   0.9662942
 C     0.3424259   0.2698411   0.4176993
 C     0.6320468   0.4064309   0.0657004
 C     0.4744210   0.6037999   0.8630263
 C    -0.0645495   0.0378500   0.5134204
 C    -0.0251843   0.4104928   0.4205102
 C     0.3722911   0.7383781   0.0915926
 C     0.2422193   0.7343280   0.6339831
 C     0.1143970   0.1530761   0.6753776
 C     0.5932143   0.8382484   0.9562124
 C     0.0641976   0.6583118   0.0934076
 C     0.4117867   0.8358148   0.0525381
 C     0.4514283   0.5697306   0.5537673
 C     0.0411872   0.6205243   0.6718877
 C     0.0000914   0.6215519   0.2622158
 C     0.5317304   0.5156047   0.1737630
 C     0.5576306   0.1218793   0.2495774
 C     0.0759395  -0.0070872   0.3550120
 C     0.6349202   0.5730947   0.2269157
 C     0.7835882   0.3925515   0.5318163
 C     0.9049173   0.5546661   0.0245965
 C     0.7980700   0.7112016   0.5682304
 C     0.1641652   0.3509395   0.6456624
 C     0.2434832   0.5137931   0.2107852
 C     0.6600724   0.5941172   0.9816287
 C     0.7018533   0.3650399   0.3088071
 C     0.0838401   0.5405435   0.5108023
 C     0.7764151   0.4428771   0.2710543
 C     0.6068100   0.2101666   0.3015694
 H    -0.0506552   0.7811249   0.3042182
 C     0.7134427   0.4874436   0.0839294
 C     0.4366368   0.4212076   0.3943046
 C     0.1739573   0.7111789   0.9019941
 C     0.4699783   0.9053046   0.8432698
 C     0.9036835   0.0832656   0.9077267
 C     0.7726827   0.1707331   0.0152917
 C     0.3851938   0.1375097   0.3050462
 C     0.1492703   0.5156237   0.8682568
 C     0.7540634   0.8056340   0.5196295
 C     0.0041723   0.3488196   0.8779497
 C     0.4375410   0.2870831   0.6949490
 C     0.5390704   0.8501125   0.4828984
 C     0.9156090   0.1116298   0.1146791
 H     0.8249506   0.7724338   0.8341527
 C     0.3134065   0.4291290   0.7048480
 C     0.0762430   0.1514537   0.5684462
 C     0.3980968   0.6475938   0.0446690
 C     0.8147691   0.7402851   0.0354438
 C     0.9421864   0.0960119   0.2168788
 C     0.5839119   0.6345546   0.0503136
 C     0.0137844   0.6507228   0.8410578
 C     0.6802291   0.8407512   0.5985764
 H     0.6552802   0.2888353   0.1555128
 C     0.2504631   0.2831754   0.6300173
 C     0.3930018   0.6012036   0.3826009
 C     0.6959098   0.8944698   0.3552692
 C     0.1382247   0.7270917   0.0296495
 C     0.8331251   0.2093819   0.5296311
 C    -0.0266525   0.5918541   0.3652134
 C     0.6348080   0.6174475   0.3396926
 C     0.1913162   0.6012450   0.2335006
 C     0.3881938   0.0860474   0.7014981
 C     0.7996022   0.7133449   0.2599920
 C     0.8176381   0.3102349   0.4606942
 C     0.3723826   0.5180863   0.7387808
 C     0.4387738   0.1140663   0.1137675
 C     0.5318530   0.4333308   0.0836886
 C     0.6039791   0.0977102   0.1502132
 C     0.1074246   0.8464461   0.9878132
 C     0.0442993   0.1192479   0.8424408
 C     0.0784481   0.8577879   0.5760579
 C     0.1566402   0.4965989   0.7673763
 C     0.7717450   0.5091943   0.6620732
 C     0.2990407   0.7542217   0.1752115
 C     0.3598945   0.4905058   0.9445020
 C     0.6570272   0.2899750   0.7404002
 C     0.6680658   0.8084990   0.8791393
 C     0.6866329   0.2717096   0.2314402
 C     0.1585305   0.2744493   0.4298868
 C     0.0734377   0.8742127   0.1903041
 C     0.5417163   0.1349444   0.0672818
 C     0.4278478   0.5153555   0.3373616
 C     0.7718081   0.7782094   0.8991499
 C     0.8323849   0.4791026   0.5810236
 C     0.4577465   0.0411276   0.6282220
 C     0.0607799   0.3387863   0.6261699
 C    -0.0024383   0.5863706   0.5727849
 C     0.2970536   0.8626989   0.1917701
 C     0.2088608   0.7833409   0.3348125
 H     0.3572173   0.0749275   0.8660937
 C     0.0713730   0.0405329   0.2562863
 C     0.6956670   0.7915151   0.6918282
 C     0.1072486   0.8105197   0.3918937
 C     0.2479373   0.2188146   0.4315399
 C     0.6062909   0.5347139   0.6148817
 C     0.0184417   0.2549948   0.5638276
 C     0.3038566   0.0761873   0.3367842
 C     0.3451266   0.3762998   0.4226916
 C     0.6728021   0.4503975   0.6575528
 C     0.0302557   0.2916346   0.8053658
 C     0.6162650   0.4260009   0.3699910
 C     0.8295286   0.6205234   0.1920241
 C     0.8074738   0.1315538   0.9015089
 C     0.2382046   0.7026588   0.2476332
 C     0.7446111   0.6849712   0.3585024
 C     0.8717991   0.6510481   0.0864770
 C     0.3166116   0.0751988   0.5329103
 C     0.6360759   0.8237912   0.7775608
 H     0.2417428   0.3406335   0.2163995
 C     0.1609508   0.3839813   0.4389177
 C     0.3869047   0.7776696   0.4138502
 C     0.2067845   0.6356980   0.6376352
 C     0.9388744   0.0117565   0.4070905
 C    -0.0241899   0.6554334   0.7418886
 C     0.4756463   0.1952079   0.8559425
 C     0.0846771   0.6181581   0.2033143
 C     0.6628681   0.2420290   0.9331942
 C     0.6879514   0.8739749   0.2492518
 C     0.3492499   0.5214079   0.1726193
 C     0.8608550   0.5924798   0.8864503
 C     0.2681385   0.1068859   0.4418196
 C     0.5220454   0.9102976   0.6610222
 C     0.5647047   0.4393735   0.8186854
 C     0.8256976   0.1529240   0.7112944
 C     0.4140015   0.0236115   0.5323472
 C     0.2077059   0.4250932   0.7085360
 C     0.8548290   0.6368232   0.5093393
 C     0.0434195   0.0462168   0.5401138
 C     0.7530644   0.7992852   0.1012346
 C     0.3562089   0.5476559   0.0606882
 C     0.6364431   0.9169238   0.1613395
 C     0.1473451   0.8794749   0.8913063
 C     0.1991903   0.7971216   0.7203825
 C     0.7483087   0.7950211   0.2078045
 C     0.2780106   0.7625802   0.4299914
 C     0.2258245   0.7654766   0.5217513
 C     0.4627690   0.2887726   0.8059750
 C     0.6948250   0.2688580   0.6407361
 C     0.5695497   0.6308869   0.1567187
 H     0.5563181   0.0535121   0.3011196
 C     0.6278136   0.3956849   0.7478082
 C     0.8790859   0.1586894   0.2806473
 C     0.7279496   0.0937319   0.4025826
 C     0.3933563   0.0161949   0.0995037
 C     0.7415341   0.5272286   0.1943218
 C     0.3494643   0.3359090   0.6588465
 C     0.3811770   0.5461123   0.8407482
 C     0.2257054   0.1875406   0.6617942
 C     0.5477204   0.1963896   0.9447466

CELL_PARAMETERS  {alat}
  0.925200  -0.036749  -0.017857
 -0.036597   0.895520   0.010785
 -0.017919   0.010902   0.966447


K_POINTS automatic
2 2 2  0 0 0

-- 
Alan J. R. Ambrozio
Visitant PhD student
Room E19-722
Massachusetts Institute of Technology
857 316-8562
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