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gynan2008

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应助: 3 (幼儿园)
金币: 1621.4
散金: 100
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帖子: 367
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注册: 2011-09-28
性别: MM
专业: 凝聚态物性 II ：电子结构

[求助] 关于晶体优化问题

有两个问题：
①in文件中晶体的晶格参数为
ngkpt  3  3  4 # Number of k-points
chksymbreak 0
acell  7.885  7.885  6.727  Angstroms
angdeg  90  90  120
chkprim 0
spgroup 160
brvltt -1
natrd    5
xred    0.796740  0.203260  0.744830
      0.000000  0.000000  0.000000
      0.000000  0.000000  0.234010
      0.540530  0.459470  0.849360
      0.560330  0.439670  0.272960
而out文件输出的结果却默认为1.0000000000 1.0000000000  1.0000000000Bohr
......
outvars: echo values of preprocessed input variables --------
acell 1.0000000000E+00  1.0000000000E+00  1.0000000000E+00 Bohr
            amu 6.97230000E+01  3.09737620E+01  1.59994000E+01
   chksymbreak       0
         diemac 9.00000000E+00
         ecut 3.70000000E+01 Hartree
         enunit       2
         jdtset    1 2 3 4 5 6 7 8 9 10
                  11 12 13 14 15
            kpt 1.66666667E-01  1.66666667E-01  1.25000000E-01
                  5.00000000E-01  1.66666667E-01  1.25000000E-01
                  -1.66666667E-01  1.66666667E-01  1.25000000E-01
                  5.00000000E-01  5.00000000E-01  1.25000000E-01
                  -1.66666667E-01  5.00000000E-01  1.25000000E-01
                  -1.66666667E-01 -1.66666667E-01  1.25000000E-01
                  1.66666667E-01  1.66666667E-01  3.75000000E-01
                  5.00000000E-01  1.66666667E-01  3.75000000E-01
                  -1.66666667E-01  1.66666667E-01  3.75000000E-01
                  5.00000000E-01  5.00000000E-01  3.75000000E-01
                  -1.66666667E-01  5.00000000E-01  3.75000000E-01
                  -1.66666667E-01 -1.66666667E-01  3.75000000E-01
      kptrlen1 2.87631709E+01
      kptrlen2 2.87651665E+01
      kptrlen3 2.87671621E+01
......
②计算另外一个晶体时，用的同样的方式，但是out文件的acell没有变成上面的情况，但是根据文献输入晶体的原子位置
计算过程中说是第1个原子和第17个原子的位置重合，在MS中建模利用CAstep模块refine crystal以后，是23个原子，但这23个原子的位置写入abinit的in文件中显然是不对的，难道要根据MS中的原子位置写进in文件中么，可并不是标准的24个原子，这种情况应该怎么办？

求高手指点不胜感激！

[ Last edited by gynan2008 on 2013-3-13 at 18:13 ]

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苔花如米小，也学牡丹开！

1楼 2013-03-13 18:12:11

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

gynan2008

金虫 (正式写手)

应助: 3 (幼儿园)
金币: 1621.4
散金: 100
红花: 4
帖子: 367
在线: 94.4小时
虫号: 1421581
注册: 2011-09-28
性别: MM
专业: 凝聚态物性 II ：电子结构

???????:

2?: Originally posted by tangosnow at 2013-03-14 01:04:54
????????? ??rprim????
??????????????????????????????

?????????in???????????
#Common input data
chksymbreak 0
#Definition of the unit cell
#**********************************
acell 2*4.90251 11.052620  Angstroms #设置晶常?? angdeg 90  90  120
chkprim  0
#Definition of the atoms
#*********************
spgroup 152
ntypat 3                            #原胞的原????类数?? znucl 31 15 8
natom 24                         #原胞中总的原??数目
brvltt -1
natrd 4                               #读入的原??数目，就是晶?
typat 1 2 3 3
xred 0.4563320  0.0000000  0.3333300
         0.4565550  0.0000000  0.8333300
         0.4086518  0.3182717  0.3922150
         0.4093416  0.2732817  0.8718840
kptopt 1    # Kpoint option ( default 0.0 )
ngkpt 2  2  4    # Number of k-points
nshiftk 1
shiftk 0.0 0.0 0.5 # These shifts will be the same for all grids

out????????????
-outvars: echo values of preprocessed input variables --------
         acell 9.4110251144E+00  9.4110251144E+00  2.0883363495E+01 Bohr
            amu 6.97230000E+01  3.09737620E+01  1.59994000E+01
   chksymbreak       0
         diemac 1.20000000E+01
         ecut1 8.00000000E+00 Hartree
         ecut2 1.10000000E+01 Hartree
         ecut3 1.40000000E+01 Hartree
         ecut4 1.70000000E+01 Hartree
         ecut5 2.00000000E+01 Hartree
         ecut6 2.30000000E+01 Hartree
         ecut7 2.60000000E+01 Hartree
         ecut8 2.90000000E+01 Hartree
         enunit       2
         jdtset    1 2 3 4 5 6 7 8
            kpt 0.00000000E+00  0.00000000E+00  1.25000000E-01
                  5.00000000E-01  0.00000000E+00  1.25000000E-01
                  0.00000000E+00  0.00000000E+00  3.75000000E-01
                  5.00000000E-01  0.00000000E+00  3.75000000E-01
      kptrlen 1.88220502E+01
      kptrlatt 2  0  0 0  2  0 0  0  4
P          mkmem       4
         natom       24
         nband       63
         ndtset       8
         ngfft1    24    24    54
         ngfft2    30    30    64
         ngfft3    32    32    72
         ngfft4    36    36    80
         ngfft5    40    40    90
         ngfft6    45    45    96
         ngfft7    45    45    96
         ngfft8    48    48    108
         nkpt       4
         nstep    200
         nsym       6
         ntypat       3
            occ 2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                  2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                  2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                  2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                  2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                  2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                  2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                  2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                  2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                  2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
                  0.000000  0.000000  0.000000
         rprim 1.0000000000E+00  0.0000000000E+00  0.0000000000E+00
                  -5.0000000000E-01  8.6602540378E-01  0.0000000000E+00
                  0.0000000000E+00  0.0000000000E+00  1.0000000000E+00
         shiftk 0.00000000E+00  0.00000000E+00  5.00000000E-01
      spgroup    152
         symrel 1  0  0 0  1  0 0  0  1    -1 -1  0 1  0  0 0  0  1
                  0  1  0 1  0  0 0  0 -1    0  1  0  -1 -1  0 0  0  1
                  1  0  0  -1 -1  0 0  0 -1    -1 -1  0 0  1  0 0  0 -1
         tnons 0.0000000  0.0000000  0.0000000    0.0000000  0.0000000 -0.3333333
                  0.0000000  0.0000000  0.0000000    0.0000000  0.0000000  0.3333333
                  0.0000000  0.0000000 -0.3333333    0.0000000  0.0000000  0.3333333
         toldfe 1.00000000E-09 Hartree
         typat 1  2  3  3  1  2  3  3  1  2  3  3  1  2  3  3  1  2  3  3
                  1  2  3  3
            wtk    0.12500 0.37500 0.12500 0.37500
         xangst 2.2725789932E+00  3.9068017476E-16  3.6836629830E+00
                  2.2736895555E+00  9.7670102292E-16  9.2091629830E+00
                  1.2426143826E+00  1.3726718231E+00  4.3343679650E+00
                  1.3580770051E+00  1.1786347619E+00  9.6351900840E+00
                  1.3537605034E+00  2.3447819732E+00  1.1050996316E+01
                  1.3532052223E+00  2.3438201980E+00  5.5254963163E+00
                  3.0575114786E+00  2.5504215794E+00  6.5070129833E-01
                  2.8317391431E+00  2.5474465457E+00  5.9515234173E+00
                  -1.1362894966E+00  1.9681111402E+00  7.3673370170E+00
                  -1.1368447777E+00  1.9690729154E+00  1.8418370170E+00
                  5.6746147858E-01  1.7624715340E+00  6.7166320350E+00
                  3.4168914309E-01  1.7654465677E+00  1.4158099160E+00
                  -1.1362894966E+00  1.9681111402E+00  7.3673296497E+00
                  -1.1368447777E+00  1.9690729154E+00  1.8418296497E+00
                  3.1700241388E+00  3.8979971088E-01  8.0180346317E+00
                  3.2803338518E+00  5.8681180572E-01  2.2678567507E+00
                  2.2725789932E+00  3.9068095612E-16  3.6836703503E+00
                  2.2736895555E+00  9.7670180428E-16  9.2091703503E+00
                  -1.2474356174E+00  2.9402212903E+00  3.0329653683E+00
                  -1.1319729949E+00  3.1342583514E+00  8.7831432493E+00
                  1.3537605034E+00  2.3447819732E+00  3.6836666666E-06
                  1.3532052223E+00  2.3438201980E+00  5.5255036837E+00
                  6.7997413883E-01  3.9230934025E+00  1.0400298702E+01
                  7.9028385184E-01  3.7260813077E+00  5.0994765827E+00
         xcart 4.2945519125E+00  7.3827853584E-16  6.9611142037E+00
                  4.2966505711E+00  1.8456974470E-15  1.7402795951E+01
                  2.3482008719E+00  2.5939738160E+00  8.1907684130E+00
                  2.5663936070E+00  2.2272969108E+00  1.8207870497E+01
                  2.5582366009E+00  4.4309957706E+00  2.0883356533E+01
                  2.5571872716E+00  4.4291782790E+00  1.0441674786E+01
                  5.7778593427E+00  4.8195983085E+00  1.2296472482E+00
                  5.3512114602E+00  4.8139763096E+00  1.1246749332E+01
                  -2.1472759562E+00  3.7191910541E+00  1.3922249291E+01
                  -2.1483252855E+00  3.7210085458E+00  3.4805675435E+00
                  1.0723467855E+00  3.3305885163E+00  1.2692595082E+01
                  6.4569890302E-01  3.3362105151E+00  2.6754929975E+00
                  -2.1472759562E+00  3.7191910541E+00  1.3922235369E+01
                  -2.1483252855E+00  3.7210085458E+00  3.4805536213E+00
                  5.9904774570E+00  7.3661470024E-01  1.5151889578E+01
                  6.1989326044E+00  1.1089136044E+00  4.2856281674E+00
                  4.2945519125E+00  7.3828001240E-16  6.9611281260E+00
                  4.2966505711E+00  1.8456989236E-15  1.7402809873E+01
                  -2.3573116853E+00  5.5562130087E+00  5.7314739167E+00
                  -2.1391189502E+00  5.9228899139E+00  1.6597735327E+01
                  2.5582366009E+00  4.4309957706E+00  6.9611211647E-06
                  2.5571872716E+00  4.4291782790E+00  1.0441688708E+01
                  1.2849648998E+00  7.4135721245E+00  1.9653716246E+01
                  1.4934200472E+00  7.0412732204E+00  9.6366141623E+00
         xred 4.5633200000E-01  0.0000000000E+00  3.3333300000E-01
                  4.5655500000E-01 -4.9303806576E-32  8.3333300000E-01
                  4.0865180000E-01  3.1827170000E-01  3.9221500000E-01
                  4.0934160000E-01  2.7328170000E-01  8.7188400000E-01
                  5.4366800000E-01  5.4366800000E-01  9.9999966667E-01
                  5.4344500000E-01  5.4344500000E-01  4.9999966667E-01
                  9.0961990000E-01  5.9134820000E-01  5.8881666667E-02
                  8.6394010000E-01  5.9065840000E-01  5.3855066667E-01
                  0.0000000000E+00  4.5633200000E-01  6.6666700000E-01
                  -4.9303806576E-32  4.5655500000E-01  1.6666700000E-01
                  3.1827170000E-01  4.0865180000E-01  6.0778500000E-01
                  2.7328170000E-01  4.0934160000E-01  1.2811600000E-01
                  0.0000000000E+00  4.5633200000E-01  6.6666633333E-01
                  4.9303806576E-32  4.5655500000E-01  1.6666633333E-01
                  6.8172830000E-01  9.0380100000E-02  7.2554833333E-01
                  7.2671830000E-01  1.3605990000E-01  2.0521733333E-01
                  4.5633200000E-01  0.0000000000E+00  3.3333366667E-01
                  4.5655500000E-01  4.9303806576E-32  8.3333366667E-01
                  9.0380100000E-02  6.8172830000E-01  2.7445166667E-01
                  1.3605990000E-01  7.2671830000E-01  7.9478266667E-01
                  5.4366800000E-01  5.4366800000E-01  3.3333333332E-07
                  5.4344500000E-01  5.4344500000E-01  5.0000033333E-01
                  5.9134820000E-01  9.0961990000E-01  9.4111833333E-01
                  5.9065840000E-01  8.6394010000E-01  4.6144933333E-01
         znucl    31.00000 15.00000 8.00000

================================================================================

chkinp: Checking input parameters for consistency, jdtset= 1.

chkinp: ERROR -
  Atoms number 1 and  17 are located at the same point of the unit cell
  (periodic images are taken into account).
  Action: change the coordinate of one of these atoms in the input file.

MS??Redefine Lattice??????????????Щ???????λ??д??in??????????????????????лл

δ????.jpg