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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

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liqizuiyang

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描述一个含有N个原子的晶体空间信息，需要3N+9个坐标。其中9个是基矢坐标，其余3N个是原子坐标。

基矢坐标和原子坐标完全独立，理论上可以用两套坐标系，比如说基矢用单位长度为bohr的笛卡尔坐标系而原子坐标用单位长度为angstrom的笛卡尔坐标系。只不过原子坐标多用分数坐标，给人一种原子坐标依赖于基矢坐标的错觉。

了解了这一点，就好理解QE输入文件了。

如果ibrav不等于0，用的是QE自定义的一套基矢坐标，这种情况下celldm(1) - celldm(6)都有确定物理意义。由于程序接管了基矢坐标，需要指定的只有原子坐标。原子坐标可以用crsytal, bohr, angstrom, alat。这里alat的物理意义用个例子说明：

假如celldm(1) = 2.0，ATOMIC_POSITIONS后面接alat，意思就是说后面的原子坐标是笛卡尔坐标，这个笛卡尔坐标单位长度是celldm(1)，也就是2.0 bohr。

这样celldm(1) = 1.8892那种写法也很好理解。1 angstrom = 1.8892 bohr，指定celldm(1) = 1.8892，再指定ATOMIC_POSITIONS {alat}，就是说原子坐标都是以1 angstrom (1.8892 bohr)为单位长度的笛卡尔坐标。至于为什么不直接写成ATOMIC_POSITIONS {angstrom}，是因为这么写XCrysDen不能识别。

CELL_PARAMETERS后面可以接的选项和ATOMIC_POSITIONS一样，除了没有crystal这个选项。因为基矢和原子坐标独立，上面关于原子的讨论也适用于基矢。

你要写转换程序，只需要把celldm(1)设置成1.8892 * POSCAR中缩放系数，CELL_PARAMETERS后面接alat，ATOMIC_POSITIONS后面接crystal，基矢坐标和原子分数坐标可以直接照搬过来。

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8楼2015-05-08 12:03:56

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KalaShayminS

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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

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2楼2015-05-07 15:07:40

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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

damao4361556

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引用回帖:

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

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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