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Dirac12345

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[交流] PWSCF 提示 problems computing cholesky 已有4人参与

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   task #       98
   from  cdiaghg  : error #    911    problems computing cholesky  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

什么原因呢？是因为原子隔得太近吗，我体系有个原子间隙缺陷，可能会有点近，但是确实结构式这样啊。我用VASP 优化出来没问题怎么用 pwscf 就优花不了呢？

以下是输入文件

&control
calculation = 'relax',
restart_mode='from_scratch',       !do a new calculation, else 'from_start'
prefix='I_i.relax',
pseudo_dir = '/auto/rcf-proj2/op/wl_903/I_int.save',
outdir= './',
! forc_conv_thr = 1.0D-3,  !1.0D-3 is the default
! etot_conv_thr = 1.0D-4, !1.0D-4 is the default
nstep= 1000,
/

&system
ibrav= 0,
celldm(1)=1.8897,
nat= 97,
ntyp= 5,
ecutwfc = 40.D0,
ecutrho = 300.D0, !for norm-conserving pseudo I must use the default value
occupations = 'smearing', !for force/opt/md, 'tetrahedral' is used for DOS, if 'smearing' is chosed, the following two card needs to be set
smearing = 'gauss', !gauss is the default
degauss = 0.02,
input_dft = 'PBE'  !or vdw-DF2
! noncolin = .true. !for soc
! lspinorb = .true. !for soc
/

&electrons
! mixing_mode = 'plain'    !plain is the default
! mixing_beta = 0.1D0       !0.7d0 is the default
conv_thr =  1.0d-8          !1.0d-6 is the default,
electron_maxstep = 100
diagonalization = 'cg'
/

&IONS !use only calculation = relax, md, vc-relax, vc-md
  ion_dynamics = 'bfgs'                                  !case relax, bfgs(default),damp (for constranints), case md, verlet (default) case vc-relax, bfgs (default, cell_dynamics must also be bfgs), damp
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
  trust_radius_max = 0.2D0,
  trust_radius_ini = 0.1D0,
/

!&cell
! cell_dynamics = 'bfgs'
!/

ATOMIC_SPECIES !ATOM mass used only in MD and relax using Damped MD
   H    1.0080000162 H.pbe-rrkjus.UPF
   C    12.0109996796 C.pbe-rrkjus.UPF
   N    14.0069999695 N.pbe-rrkjus.UPF
   I 126.9039993286 I.pbe-n-rrkjus_psl.0.2.UPF
   Pb 207.1999969482 Pb.pbe-dn-rrkjus_psl.0.2.2.UPF

CELL_PARAMETERS (alta)
   12.781200000000002    0.000000000000000    0.000000000000000
   0.000000000000000    12.768300000000002    0.000000000000000
   0.000000000000000    0.000000000000000    12.771799999999999

K_POINTS {automatic}
3 3 3 0 0 0

ATOMIC_POSITIONS (crystal) !if calculation=band or nscf these positions will be ignored
  H 0.4131800000000003 0.0225200000000000 0.4417900000000002
  H 0.0205600000000000 0.4366400000000003 0.4124400000000002
  H 0.4401400000000002 0.4125200000000003 0.0251900000000000
  H 0.0050200000000000 0.0895700000000000 0.0903000000000000
  H 0.0939300000000000 0.0877100000000000 0.4953900000000002
  H 0.0953000000000000 0.4960100000000002 0.0878400000000000
  H 0.9131800000000004 0.0225200000000000 0.4417900000000002
  H 0.5205599999999999 0.4366400000000002 0.4124400000000001
  H 0.9401400000000005 0.4125200000000003 0.0251900000000000
  H 0.5050200000000001 0.0895700000000000 0.0903000000000000
  H 0.5939300000000002 0.0877100000000000 0.4953900000000002
  H 0.5953000000000002 0.4960100000000002 0.0878400000000000
  H 0.4131800000000002 0.5225200000000002 0.4417900000000001
  H 0.0205600000000000 0.9366400000000007 0.4124400000000002
  H 0.4401400000000002 0.9125200000000006 0.0251900000000000
  H 0.0050200000000000 0.5895700000000002 0.0903000000000000
  H 0.0939300000000000 0.5877100000000002 0.4953900000000002
  H 0.0953000000000000 0.9960100000000007 0.0878400000000000
  H 0.9131800000000002 0.5225200000000002 0.4417900000000001
  H 0.5205599999999999 0.9366400000000005 0.4124400000000001
  H 0.9401400000000005 0.9125200000000006 0.0251900000000000
  H 0.5050200000000001 0.5895700000000002 0.0903000000000000
  H 0.5939300000000002 0.5877100000000002 0.4953900000000002
  H 0.5953000000000002 0.9960100000000007 0.0878400000000000
  H 0.4131800000000003 0.0225200000000000 0.9417900000000005
  H 0.0205600000000000 0.4366400000000003 0.9124400000000005
  H 0.4401400000000001 0.4125200000000002 0.5251900000000002
  H 0.0050200000000000 0.0895700000000000 0.5903000000000002
  H 0.0939300000000000 0.0877100000000001 0.9953900000000004
  H 0.0953000000000000 0.4960100000000002 0.5878400000000003
  H 0.9131800000000004 0.0225200000000000 0.9417900000000005
  H 0.5205599999999999 0.4366400000000002 0.9124400000000004
  H 0.9401400000000004 0.4125200000000002 0.5251900000000002
  H 0.5050200000000001 0.0895700000000000 0.5903000000000002
  H 0.5939300000000003 0.0877100000000001 0.9953900000000004
  H 0.5953000000000002 0.4960100000000002 0.5878400000000003
  H 0.4131800000000002 0.5225200000000002 0.9417900000000004
  H 0.0205600000000000 0.9366400000000007 0.9124400000000005
  H 0.4401400000000001 0.9125200000000003 0.5251900000000002
  H 0.0050200000000000 0.5895700000000002 0.5903000000000002
  H 0.0939300000000000 0.5877100000000003 0.9953900000000004
  H 0.0953000000000000 0.9960100000000007 0.5878400000000004
  H 0.9131800000000002 0.5225200000000002 0.9417900000000004
  H 0.5205599999999999 0.9366400000000005 0.9124400000000004
  H 0.9401400000000004 0.9125200000000003 0.5251900000000002
  H 0.5050200000000001 0.5895700000000002 0.5903000000000002
  H 0.5939300000000003 0.5877100000000003 0.9953900000000004
  H 0.5953000000000002 0.9960100000000007 0.5878400000000004
  C 0.4747400000000002 0.4729700000000002 0.4751600000000002
  C 0.9747400000000008 0.4729700000000004 0.4751600000000003
  C 0.4747400000000003 0.9729700000000007 0.4751600000000003
  C 0.9747400000000009 0.9729700000000009 0.4751600000000004
  C 0.4747400000000003 0.4729700000000004 0.9751600000000007
  C 0.9747400000000009 0.4729700000000005 0.9751600000000008
  C 0.4747400000000004 0.9729700000000009 0.9751600000000008
  C 0.9747400000000012 0.9729700000000010 0.9751600000000009
  N 0.0454700000000000 0.0394900000000000 0.0399300000000000
  N 0.5454700000000002 0.0394900000000000 0.0399300000000000
  N 0.0454700000000000 0.5394900000000005 0.0399300000000000
  N 0.5454700000000002 0.5394900000000005 0.0399300000000000
  N 0.0454699999999999 0.0394900000000000 0.5399300000000000
  N 0.5454700000000002 0.0394900000000000 0.5399300000000000
  N 0.0454699999999999 0.5394900000000004 0.5399300000000000
  N 0.5454700000000002 0.5394900000000003 0.5399300000000000
  I 0.2306700000000000 0.4898900000000002 0.2484700000000001
  I 0.2468300000000001 0.2321900000000001 0.4905000000000002
  I 0.4915800000000001 0.2436300000000001 0.2292300000000001
  I 0.7306700000000004 0.4898900000000002 0.2484700000000001
  I 0.7468300000000003 0.2321900000000001 0.4905000000000002
  I 0.9915800000000005 0.2436300000000002 0.2292300000000001
  I 0.2306700000000001 0.9898900000000006 0.2484700000000001
  I 0.2468300000000001 0.7321900000000003 0.4905000000000002
  I 0.4915800000000001 0.7436300000000004 0.2292300000000001
  I 0.7306700000000005 0.9898900000000006 0.2484700000000001
  I 0.7468300000000003 0.7321900000000003 0.4905000000000002
  I 0.9915800000000005 0.7436300000000005 0.2292300000000001
  I 0.2306700000000000 0.4898900000000002 0.7484700000000003
  I 0.2468300000000001 0.2321900000000002 0.9905000000000005
  I 0.4915800000000001 0.2436300000000001 0.7292300000000003
  I 0.7306700000000004 0.4898900000000002 0.7484700000000003
  I 0.7468300000000004 0.2321900000000002 0.9905000000000005
  I 0.9915800000000005 0.2436300000000002 0.7292300000000004
  I 0.2306700000000001 0.9898900000000006 0.7484700000000005
  I 0.2468300000000001 0.7321900000000006 0.9905000000000005
  I 0.4915800000000001 0.7436300000000004 0.7292300000000003
  I 0.7306700000000005 0.9898900000000006 0.7484700000000005
  I 0.7468300000000004 0.7321900000000006 0.9905000000000005
  I 0.9915800000000005 0.7436300000000005 0.7292300000000004
Pb 0.2446700000000002 0.2429400000000003 0.2435800000000002
Pb 0.7446700000000007 0.2429400000000002 0.2435800000000001
Pb 0.2446700000000001 0.7429400000000007 0.2435800000000001
Pb 0.7446700000000006 0.7429400000000006 0.2435800000000001
Pb 0.2446700000000001 0.2429400000000002 0.7435800000000001
Pb 0.7446700000000006 0.2429400000000002 0.7435800000000001
Pb 0.2446700000000001 0.7429400000000006 0.7435800000000001
Pb 0.7446700000000005 0.7429400000000005 0.7435800000000001

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都是斯坦惹的祸

1楼 2015-05-07 11:01:31

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

KalaShayminS

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引用回帖:

9楼: Originally posted by damao4361556 at 2015-05-09 01:10:41
谢谢 liqizuiyang

如果我要将 poscar的分数坐标转换成 alat （笛卡尔坐标）的话这之间是个什么样的转换关系呢？

QE里面的笛卡尔坐标后期可视化结构比较方便，

例如我celldm(1) = 1.889
cell_par ...

这个转换是个简单的矩阵乘法：
笛卡尔坐标  = 晶格矢量点乘分数坐标
[X    [  ax ay az ] [A
Y =  [ bx by bz ] . B
Z]    [ cx cy cz  ]    C]

赞一下

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10楼2015-05-09 09:58:50

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查看全部 14 个回答

KalaShayminS

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★
小木虫: 金币+0.5, 给个红包，谢谢回帖

diagonalization选项可以尝试调一下，

如果不是第一次就出现的问题，那么
pot_extrapolation = "second_order",
wfc_extrapolation = "second_order"
这两个选项也可以改一下

赞一下

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2楼2015-05-07 15:07:40

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damao4361556

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引用回帖:

2楼: Originally posted by KalaShayminS at 2015-05-07 15:07:40
diagonalization选项可以尝试调一下，

如果不是第一次就出现的问题，那么
pot_extrapolation = "second_order",
wfc_extrapolation = "second_order"
这两个选项也可以改一下

你好  非常感谢你的回复。试着调了下还是有问题。提示
task #       76
   from read_cards : error #       97
   end of file reading atomic positions

检查了半天也没查出来到底哪错了。我坐标是MS 里 castep 生成的cell 文件里拷贝过来的，为分数坐标。晶格参数也是拷贝的cell文件里面的  后面单位为 alat celldm（1）设置为 1.8892 请问这样有问题吗？

以下为输入文件，非常感谢

&control
calculation = 'relax',
restart_mode='from_scratch',       !do a new calculation, else 'from_start'
outdir= './',
! forc_conv_thr = 1.0D-3,  !1.0D-3 is the default
! etot_conv_thr = 1.0D-4, !1.0D-4 is the default
nstep= 1000,
/

&system
ibrav= 0,
celldm(1)=1.8897,
nat= 97,
ntyp= 5,
ecutwfc = 40.D0,
ecutrho = 300.D0, !for norm-conserving pseudo I must use the default value
occupations = 'smearing', !for force/opt/md, 'tetrahedral' is used for DOS, if 'smearing' is chosed, the following two card needs to be set
smearing = 'gauss', !gauss is the default
degauss = 0.02,
input_dft = 'PBE'  !or vdw-DF2
! noncolin = .true. !for soc
! lspinorb = .true. !for soc
/

&electrons
! mixing_mode = 'plain'    !plain is the default
! mixing_beta = 0.1D0       !0.7d0 is the default
conv_thr =  1.0d-8          !1.0d-6 is the default,
electron_maxstep = 100
diagonalization = 'cg'
/

&IONS !use only calculation = relax, md, vc-relax, vc-md
! pot_extrapolation = "second_order",
! wfc_extrapolation = "second_order",
  trust_radius_max = 0.2D0,
  trust_radius_ini = 0.1D0,
/

!&cell
! cell_dynamics = 'bfgs'
!/

ATOMIC_SPECIES !ATOM mass used only in MD and relax using Damped MD
   H    1.0080000162 H.pbe-rrkjus.UPF
   C    12.0109996796 C.pbe-rrkjus.UPF
   N    14.0069999695 N.pbe-rrkjus.UPF
   I 126.9039993286 I.pbe-n-rrkjus_psl.0.2.UPF
   Pb 207.1999969482 Pb.pbe-dn-rrkjus_psl.0.2.2.UPF

CELL_PARAMETERS (alta)
   12.781200000000002    0.000000000000000    0.000000000000000
   0.000000000000000    12.768300000000002    0.000000000000000
   0.000000000000000    0.000000000000000    12.771799999999999

K_POINTS {automatic}
3 3 3 0 0 0

ATOMIC_POSITIONS (crystal) !if calculation=band or nscf these positions will be ignored
  H 0.4131800000000003 0.0225200000000000 0.4417900000000002
  H 0.0205600000000000 0.4366400000000003 0.4124400000000002
  H 0.4401400000000002 0.4125200000000003 0.0251900000000000
  H 0.0050200000000000 0.0895700000000000 0.0903000000000000
  H 0.0939300000000000 0.0877100000000000 0.4953900000000002
  H 0.0953000000000000 0.4960100000000002 0.0878400000000000
  H 0.9131800000000004 0.0225200000000000 0.4417900000000002
  H 0.5205599999999999 0.4366400000000002 0.4124400000000001
  H 0.9401400000000005 0.4125200000000003 0.0251900000000000
  H 0.5050200000000001 0.0895700000000000 0.0903000000000000
  H 0.5939300000000002 0.0877100000000000 0.4953900000000002
  H 0.5953000000000002 0.4960100000000002 0.0878400000000000
  H 0.4131800000000002 0.5225200000000002 0.4417900000000001
  H 0.0205600000000000 0.9366400000000007 0.4124400000000002
  H 0.4401400000000002 0.9125200000000006 0.0251900000000000
  H 0.0050200000000000 0.5895700000000002 0.0903000000000000
  H 0.0939300000000000 0.5877100000000002 0.4953900000000002
  H 0.0953000000000000 0.9960100000000007 0.0878400000000000
  H 0.9131800000000002 0.5225200000000002 0.4417900000000001
  H 0.5205599999999999 0.9366400000000005 0.4124400000000001
  H 0.9401400000000005 0.9125200000000006 0.0251900000000000
  H 0.5050200000000001 0.5895700000000002 0.0903000000000000
  H 0.5939300000000002 0.5877100000000002 0.4953900000000002
  H 0.5953000000000002 0.9960100000000007 0.0878400000000000
  H 0.4131800000000003 0.0225200000000000 0.9417900000000005
  H 0.0205600000000000 0.4366400000000003 0.9124400000000005
  H 0.4401400000000001 0.4125200000000002 0.5251900000000002
  H 0.0050200000000000 0.0895700000000000 0.5903000000000002
  H 0.0939300000000000 0.0877100000000001 0.9953900000000004
  H 0.0953000000000000 0.4960100000000002 0.5878400000000003
  H 0.9131800000000004 0.0225200000000000 0.9417900000000005
  H 0.5205599999999999 0.4366400000000002 0.9124400000000004
  H 0.9401400000000004 0.4125200000000002 0.5251900000000002
  H 0.5050200000000001 0.0895700000000000 0.5903000000000002
  H 0.5939300000000003 0.0877100000000001 0.9953900000000004
  H 0.5953000000000002 0.4960100000000002 0.5878400000000003
  H 0.4131800000000002 0.5225200000000002 0.9417900000000004
  H 0.0205600000000000 0.9366400000000007 0.9124400000000005
  H 0.4401400000000001 0.9125200000000003 0.5251900000000002
  H 0.0050200000000000 0.5895700000000002 0.5903000000000002
  H 0.0939300000000000 0.5877100000000003 0.9953900000000004
  H 0.0953000000000000 0.9960100000000007 0.5878400000000004
  H 0.9131800000000002 0.5225200000000002 0.9417900000000004
  H 0.5205599999999999 0.9366400000000005 0.9124400000000004
  H 0.9401400000000004 0.9125200000000003 0.5251900000000002
  H 0.5050200000000001 0.5895700000000002 0.5903000000000002
  H 0.5939300000000003 0.5877100000000003 0.9953900000000004
  H 0.5953000000000002 0.9960100000000007 0.5878400000000004
  C 0.4747400000000002 0.4729700000000002 0.4751600000000002
  C 0.9747400000000008 0.4729700000000004 0.4751600000000003
  C 0.4747400000000003 0.9729700000000007 0.4751600000000003
  C 0.9747400000000009 0.9729700000000009 0.4751600000000004
  C 0.4747400000000003 0.4729700000000004 0.9751600000000007
  C 0.9747400000000009 0.4729700000000005 0.9751600000000008
  C 0.4747400000000004 0.9729700000000009 0.9751600000000008
  C 0.9747400000000012 0.9729700000000010 0.9751600000000009
  N 0.0454700000000000 0.0394900000000000 0.0399300000000000
  N 0.5454700000000002 0.0394900000000000 0.0399300000000000
  N 0.0454700000000000 0.5394900000000005 0.0399300000000000
  N 0.5454700000000002 0.5394900000000005 0.0399300000000000
  N 0.0454699999999999 0.0394900000000000 0.5399300000000000
  N 0.5454700000000002 0.0394900000000000 0.5399300000000000
  N 0.0454699999999999 0.5394900000000004 0.5399300000000000
  N 0.5454700000000002 0.5394900000000003 0.5399300000000000
  I 0.2306700000000000 0.4898900000000002 0.2484700000000001
  I 0.2468300000000001 0.2321900000000001 0.4905000000000002
  I 0.4915800000000001 0.2436300000000001 0.2292300000000001
  I 0.7306700000000004 0.4898900000000002 0.2484700000000001
  I 0.7468300000000003 0.2321900000000001 0.4905000000000002
  I 0.9915800000000005 0.2436300000000002 0.2292300000000001
  I 0.2306700000000001 0.9898900000000006 0.2484700000000001
  I 0.2468300000000001 0.7321900000000003 0.4905000000000002
  I 0.4915800000000001 0.7436300000000004 0.2292300000000001
  I 0.7306700000000005 0.9898900000000006 0.2484700000000001
  I 0.7468300000000003 0.7321900000000003 0.4905000000000002
  I 0.9915800000000005 0.7436300000000005 0.2292300000000001
  I 0.2306700000000000 0.4898900000000002 0.7484700000000003
  I 0.2468300000000001 0.2321900000000002 0.9905000000000005
  I 0.4915800000000001 0.2436300000000001 0.7292300000000003
  I 0.7306700000000004 0.4898900000000002 0.7484700000000003
  I 0.7468300000000004 0.2321900000000002 0.9905000000000005
  I 0.9915800000000005 0.2436300000000002 0.7292300000000004
  I 0.2306700000000001 0.9898900000000006 0.7484700000000005
  I 0.2468300000000001 0.7321900000000006 0.9905000000000005
  I 0.4915800000000001 0.7436300000000004 0.7292300000000003
  I 0.7306700000000005 0.9898900000000006 0.7484700000000005
  I 0.7468300000000004 0.7321900000000006 0.9905000000000005
  I 0.9915800000000005 0.7436300000000005 0.7292300000000004
Pb 0.2446700000000002 0.2429400000000003 0.2435800000000002
Pb 0.7446700000000007 0.2429400000000002 0.2435800000000001
Pb 0.2446700000000001 0.7429400000000007 0.2435800000000001
Pb 0.7446700000000006 0.7429400000000006 0.2435800000000001
Pb 0.2446700000000001 0.2429400000000002 0.7435800000000001
Pb 0.7446700000000006 0.2429400000000002 0.7435800000000001
Pb 0.2446700000000001 0.7429400000000006 0.7435800000000001
Pb 0.7446700000000005 0.7429400000000005 0.7435800000000001

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3楼2015-05-08 02:44:26

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

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KalaShayminS 你好。

关于pwscf 输入结构的构建我现在还是不太明白啊。

我通用的做法是：
celldm(1) = 1.8892
ibrav=0
cell parameter 从 castep cell文件拷过来，单位为 alat
atomic position 也从cell文件拷过来，单位为 crystal

我看到有些同样也是 Ibrav=0 但是atomic position 后的单位却为 alat 呢？我查了说明书说的是原子坐标以alat为单位的话？是以 cell parameter 和 celldm(1) 为单位？这是什么意思呢？到底最后都是以什么味单位呢？有点懵了。

现在的问题是：
1. celldm(1) 这个值到底是怎么得来的
2. 晶格参数的单位到底是什么？
原子坐标的单位为 alat的话具体是怎么个单位换算关系呢？

一直在优化结构也不知道这么做的是不是对的。
还麻烦您的解答

谢谢
祝好

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4楼2015-05-08 06:47:30

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