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[求助] R.I.N.G.S. code運(yùn)行報(bào)錯(cuò)

用VASP跑完AIMD后，想用RINGS(https://rings-code.sourceforge.net/)處理下數(shù)據(jù)，按照官網(wǎng)的example寫(xiě)好輸入input（重命名為my-input）和options文件，也吧XDATCAR放在了data文件夾里，在終端中運(yùn)行 rings my-input 出現(xiàn)報(bào)錯(cuò)“At line 230 of file input.f90 (unit = 10, file = 'options')
Fortran runtime error: Bad logical value while reading item 2”，不知道問(wèn)題出在哪里，怎么解決？

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At line 230 of file input.f90 (unit = 10, file = 'options')
它叫你檢查options 230行

贊一下

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3樓2021-07-28 16:43:58

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引用回帖:

3樓: Originally posted by get-it at 2021-07-28 16:43:58
At line 230 of file input.f90 (unit = 10, file = 'options')
它叫你檢查options 230行

options文件沒(méi)有230行，是input.f90文件的第230行，但是我不知道是什么問(wèn)題，以下是input.f90文件。

! Copyright

! The University Montpellier 2, a scientific, cultural and professional
! public establishment whose registered office is at
! Place Eugène Bataillon - 34095 Montpellier CEDEX 05 - France.
! N° SIREN 193 410 883, APE Code 803Z
! represented by its President, Danièle HERIN.

! Authors : Dr. Sébastien Le Roux (sebastien.leroux@ipcms.unistra.fr)
!          Pr. Philippe Jund (pjund@univ-montp2.fr)

! This software is a computer program whose purpose is to analyse
! the results of molecular dynamics simulations.
! This code is named R.I.N.G.S “Rigorous Investigation of Networks
! Generated using Simulations” and its main feature is the analysis of
! the connectivity using ring statistics.

! This software is governed by the CeCILL-B license under French law and
! abiding by the rules of distribution of free software.
! You can  use, modify and/ or redistribute the software under the terms
! of the [CeCILL|CeCILL-B|CeCILL-C] license as circulated by CEA, CNRS
! and INRIA at the following URL:
! "https://www.cecill.info".

! As a counterpart to the access to the source code and  rights to copy,
! modify and redistribute granted by the license, users are provided only
! with a limited warranty  and the software's author, the holder of the
! economic rights,  and the successive licensors have only limited
! liability.

! In this respect, the user's attention is drawn to the risks associated
! with loading,  using,  modifying and/or developing or reproducing the
! software by the user in light of its specific status of free software,
! that may mean  that it is complicated to manipulate,  and  that  also
! therefore means  that it is reserved for developers  and  experienced
! professionals having in-depth computer knowledge. Users are therefore
! encouraged to load and test the software's suitability as regards their
! requirements in conditions enabling the security of their systems and/or
! data to be ensured and,  more generally, to use and operate it in the
! same conditions as regards security.

! The fact that you are presently reading this means that you have had
! knowledge of the CeCILL-B license and that you accept its terms.

SUBROUTINE READ_INPUT

!
! Read the user input file and the 'options' file
!

USE PARAMETERS
USE EXTRA

LOGICAL :: CALC_R=.false.

open (unit=9, file=NOM_FILE, action='read', status='old')

  read (9, *)
  read (9, *)
  read (9, *)
  read (9, *) SYSTLABEL
  if (DEBUGINP) write (6, *) SYSTLABEL
  read (9, *) NA
  if (DEBUGINP) write (6, *) NA
  read (9, *) NSP
  if (DEBUGINP) write (6, *) NSP
!allocate (S_LENGTH(NSP), STAT=ERR)
!if (ERR .ne. 0) then
! write (6, 001) t_p, "S_LENGTH"
!  STOP
!endif
allocate (LABEL(NSP), STAT=ERR)
if (ERR .ne. 0) then
write (6, 001) t_p, "LABEL"
  STOP
endif
!allocate (M_SS(NSP), STAT=ERR)
!if (ERR .ne. 0) then
! write (6, 001) t_p, "M_SS"
!endif
!allocate (R_DW(NSP), STAT=ERR)
!if (ERR .ne. 0) then
! write (6, 001) t_p, "R_DW"
!endif

  do i=1, NSP
LABEL(i)=""
  enddo
! S_LENGTH(i)=0.0d0
! M_SS(i)=0.0d0
! R_DW(i)=0.0d0
  read (9, *) LABEL!, S_LENGTH(i), M_SS(i), R_DW(i)
  if (DEBUGINP) then
do i=1, NSP
   write (6, *) LABEL(i)!, S_LENGTH(i), M_SS(i), R_DW(i)
enddo
  endif
  read (9, *) NS
  if (DEBUGINP) write (6, *) NS
  do i=1,3
  do j=1, 3
lvect(i,j)=0.0d0
  enddo
  enddo
  read (9, *) LATTYPE
  if (LATTYPE .eq. 1) then
read (9, *) lvect(1,1), lvect(1,2), lvect(1,3)
if (DEBUGINP) write (6, *) lvect(1,1), lvect(1,2), lvect(1,3)
read (9, *) lvect(2,1), lvect(2,2), lvect(2,3)
if (DEBUGINP) write (6, *) lvect(2,1), lvect(2,2), lvect(2,3)
read (9, *) lvect(3,1), lvect(3,2), lvect(3,3)
if (DEBUGINP) write (6, *) lvect(3,1), lvect(3,2), lvect(3,3)
  else
read (9, *) modv(1), modv(2), modv(3)
if (DEBUGINP) write (6, *) modv(1), modv(2), modv(3)
ALPHA=0.0d0
BETA=0.0d0
GAMA=0.0d0
read (9, *) ALPHA, BETA, GAMA
if (DEBUGINP) write (6, *) ALPHA, BETA, GAMA
  endif
  DELTA_T=0.0d0
  read (9, *) DELTA_T
  if (DEBUGINP) write (6, *) DELTA_T
  read (9, *) DATA_FORM
  if (DEBUGINP) write (6, *) DATA_FORM
  if (DATA_FORM .eq. "MSF") then
read (9, 106) MSF_ROOT
if (DEBUGINP) write (6, 106) MSF_ROOT
read (9, *) FIRST_INDEX
if (DEBUGINP) write (6, *) FIRST_INDEX
read (9, *) LAST_INDEX
if (DEBUGINP) write (6, *) LAST_INDEX
read (9, *) NSBG
if (NSBG .eq. 0) NSBG=1
if (DEBUGINP) write (6, *) NSBG
  else
read (9, *) NOM_FILE
if (DEBUGINP) write (6, *) NOM_FILE
if (DATA_FORM.eq."VAS" .or. DATA_FORM.eq."TRJ") then
   allocate (NBSPBS(NSP), STAT=ERR)
   if (ERR .ne. 0) then
      write (6, 001) t_p, "NBSPBS"
      STOP
   endif
   do i=1, NSP
      read (9, *) LABEL(i), NBSPBS(i)
      if (DEBUGINP) write (6, *) LABEL(i), NBSPBS(i)
   enddo
else if (DATA_FORM.eq."PDB" .and. NS.gt.1) then
   write (6, '("Error: for PDB files the number of steps, NS, must be 1")')
   STOP
endif
  endif
  read (9, *) NUMBER_OF_DELTA_R
  NUMBER_OF_DELTA_R=2*NUMBER_OF_DELTA_R
  if (DEBUGINP) write (6, *) NUMBER_OF_DELTA_R
  read (9, *) NUMBER_OF_Q_POINTS
  if (DEBUGINP) write (6, *) NUMBER_OF_Q_POINTS
  QMAX=0.0d0
  read (9, *) QMAX
  if (DEBUGINP) write (6, *) QMAX
  SIGMA_LISS=0.0d0
  read (9, *) SIGMA_LISS
  if (DEBUGINP) write (6, *) SIGMA_LISS
  read (9, *) NUMBER_OF_DELTA_ANG
  if (DEBUGINP) write (6, *) NUMBER_OF_DELTA_ANG
  read (9, *) NDV
  if (DEBUGINP) write (6, *) NDV
  read (9, *) TAILLE_REF
  TAILLD=2*TAILLE_REF
  if (TAILLD .lt. 3) then
write (6, '(" Changing option =>  Max. ring size must be >= 3")')
TAILLD=4
TAILLE_REF=2
  endif
  if (DEBUGINP) write (6, *) TAILLE_REF
  read (9, *) TAILLC
  if (TAILLC .lt. 2) then
write (6, '(" Changing option =>  Max. chain length must be >= 2")')
TAILLC=2
  endif
  if (DEBUGINP) write (6, *) TAILLC

  read (9, *)
  NL=NSP*(NSP+1)/2
  allocate (GCUT(NSP,NSP), STAT=ERR)
  if (ERR .ne. 0) then
   write (6, 001) t_p, "GCUT"
STOP
  endif

  do i=1, NL

read (9, *) A1, A2, DC
if (DEBUGINP) write (6, *) A1, " ", A2, DC
j=1
do while (LABEL(j) .ne. A1)

   j=j+1

enddo
l=1
do while (LABEL(l) .ne. A2)

   l=l+1

enddo

GCUT(j,l)=0.0d0
GCUT(l,j)=0.0d0
GCUT(j,l)=DC
GCUT(l,j)=DC

  enddo

  Gr_cutoff=0.0d0
  read (9, *) ATOT, Gr_cutoff
  if (DEBUGINP) write (6, *) ATOT, Gr_cutoff

close (9)

! Now read 'options' file

  open (unit=10, file="options", action="read", status='old')
  if(t_p .eq. 0) write (6, '(/,"==========    Options    ==========",/)')
  read (10, *)
  read (10, *)
  read (10, *)
  read (10, *) Nom1, PBC
  if (PBC) then
if(t_p .eq. 0) write (6, '("  =>  Periodic Boundary Conditions applied")')
  else
if(t_p .eq. 0) write (6, '("  =>  No Periodic Boundary Conditions applied")')
  endif
  read (10, *) Nom1, FRAC
  if (FRAC) then
if(t_p .eq. 0) write (6, '("  =>  Atomic positions in fractional coordinates")')
  else
if(t_p .eq. 0) write (6, '("  =>  Atomic positions in real coordinates")')
  endif
  read (10, *) Nom1, CALC_GR
  if(t_p .eq. 0) then
if (CALC_GR) write (6, '("  =>  Calculate g(r) radial distribution functions")')
  endif
  read (10, *) Nom1, CALC_SQ
  if (CALC_SQ .and. .not.(CALC_GR)) then
if(t_p .eq. 0) write (6, '(" Changing option =>  Calculate g(r) is needed to compute S(q)")')
CALC_GR=.true.
  endif
  if(t_p .eq. 0) then
if (CALC_SQ) write (6, '("  =>  Calculate S(q) structure factor from FFT[g(r)]")')
  endif
  read (10, *) Nom1, CALC_SK
  if(t_p .eq. 0) then
if (CALC_SK) write (6, '("  =>  Calculate S(k) structure factor from Debye equation")')
  endif
  read (10, *) Nom1, CALC_GK
  if (CALC_GK .and. .not.(CALC_SK)) then
if(t_p .eq. 0) write (6, '(" Changing option =>  Calculate S(k) Debye is needed to compute g(r) from FFT[S(k) Debye]")')
CALC_SK=.true.
  endif
  if(t_p .eq. 0) then
if (CALC_GK) write (6, '("  =>  Calculate g(r) from FFT[S(k) Debye]")')
  endif
  read (10, *) Nom1, CALC_MSD
  if(t_p .eq. 0) then
if (CALC_MSD) write (6, '("  =>  Calculate Mean Square Displacement MSD")')
  endif
  read (10, *) Nom1, MSDEA
  if(t_p .eq. 0) then
if (MSDEA) write (6, '("  =>  Calculate single atom MSDs")')
  endif
  read (10, *) Nom1, CALC_BONDS
  if(t_p .eq. 0) then
if (CALC_BONDS) write (6, '("  =>  Calculate bond properties")')
  endif
  read (10, *) Nom1, CALC_ANG
  if(t_p .eq. 0) then
if (CALC_ANG) write (6, '("  =>  Calculate angles distribution")')
  endif
! Chains statistics:
  read (10, *) Nom1, CALC_CHAINS
  read (10, *)
  read (10, *) Nom1, CTLT
  read (10, *) Nom1, AAAA
  read (10, *) Nom1, ACAC
  read (10, *) Nom1, ISOLATED
  if(t_p .eq. 0) then
if (CALC_CHAINS) write (6, '("  =>  Calculate chains statistics")')
if (CALC_CHAINS .and. CTLT .eq. 0)then
   write (6, '(3x," =>  Using all atoms as nodes")')
elseif (CALC_CHAINS .and. (CTLT.le.NSP .and. CTLT.gt.0)) then
   write (6, '(3x," =>  Using species ",I2," as nodes")') CTLT
elseif (CALC_CHAINS) then
   write (6, '(" Problem in ''options'' file => check chains statistics options")')
   STOP
endif
if (CALC_CHAINS .and. AAAA .and. ACAC) then
   write (6, '(" Problem in ''options'' file => check chains statistics options")')
   write (6, '(" Problem in ''options'' file => AAAA, ABAB or none, not both !")')
   STOP
endif
if (CALC_CHAINS .and. AAAA) write (6, '(3x," =>  Pure AAAA chains")')
if (CALC_CHAINS .and. ACAC) write (6, '(3x," =>  Pure ABAB chains")')
if (CALC_CHAINS .and. ISOLATED) write (6, '(3x," =>  Only 1-(2)n-1 coordinations chains")')
if (CALC_CHAINS .and. .not.(CALC_BONDS)) then
   if(t_p .eq. 0) then
      write (6, '(" Changing option =>  Bond properties are needed to compute chains statistics")')
   endif
   CALC_BONDS=.true.
endif
  endif
  read (10, *)
! Rings statistics:
  read (10, *) Nom1, CALC_R
  read (10, *)
  read (10, *) Nom1, LTLT
  read (10, *) Nom1, ABAB
  read (10, *) Nom1, CALC_R0
  read (10, *) Nom1, CALC_R1
  read (10, *) Nom1, CALC_R2
  read (10, *) Nom1, CALC_R3
  read (10, *) Nom1, CALC_R4
  read (10, *) Nom1, CALC_PRINGS
  read (10, *) Nom1, CALC_STRINGS
  read (10, *) Nom1, BARYCROUT
  read (10, *) Nom1, RING_P1
  read (10, *) Nom1, RING_P2
  read (10, *) Nom1, RING_P3
  read (10, *) Nom1, RING_P4
  read (10, *) Nom1, RING_P5
  if (CALC_R .and. (CALC_R0.or.CALC_R1.or.CALC_R2.or.CALC_R3.or.CALC_R4.or.CALC_PRINGS.or.CALC_STRINGS)) then
CALC_RINGS=.true.
if (CALC_R1.or.CALC_R2.or.CALC_R3.or.CALC_R4) DOAMPAT=.true.
  else
CALC_RINGS=.false.
ABAB=.false.
  endif
  if (RING_P1 .or. RING_P2 .or. RING_P3 .or. RING_P4 .or. RING_P5) then
CALC_RPROP=.true.
  else
CALC_RPROP=.false.
  endif
  if(t_p .eq. 0) then
if (CALC_RINGS) write (6, '("  =>  Calculate rings statistics")')
if (CALC_RINGS .and. LTLT .eq. 0)then
   write (6, '(3x," =>  Using all atoms as nodes")')
elseif (CALC_RINGS .and. (LTLT.le.NSP .and. LTLT.gt.0)) then
   write (6, '(3x," =>  Using species ",I2," as nodes")') LTLT
elseif (CALC_RINGS) then
   write (6, '(" Problem in ''options'' file => check rings statistics options")')
   STOP
endif
if (CALC_RINGS .and. ABAB) write (6, '(3x," =>  Pure ABAB rings")')
if (CALC_RINGS .and. CALC_R0) write (6, '(3x," =>  Find all rings in the simulation box")')
if (CALC_RINGS .and. CALC_R1) write (6, '(3x," =>  King''s rings statistics")')
if (CALC_RINGS .and. CALC_R2) write (6, '(3x," =>  Guttman''s rings statistics")')
if (CALC_RINGS .and. CALC_R3) write (6, '(3x," =>  King''s + homopolar bonds rings statistics")')
if (CALC_RINGS .and. CALC_R4) write (6, '(3x," =>  Guttman''s + homopolar bonds rings statistics")')
if (CALC_RINGS .and. CALC_PRINGS) write (6, '(3x," =>  Primitive rings statistics")')
if (CALC_RINGS .and. CALC_STRINGS) write (6, '(3x," =>  Strong rings statistics")')
if (CALC_RINGS .and. BARYCROUT) write (6, '(3x," =>  Output OpenDX rings barycenters positions")')
if (CALC_RINGS .and. CALC_RPROP) write (6, '(3x," =>  Compute detailed rings properties")')
if (CALC_RINGS .and. .not.CALC_BONDS) then
   write (6, '(" Changing option =>  Bond properties are needed to compute rings statistics")')
   CALC_BONDS=.true.
endif
  endif
  read (10, *)
  read (10, *) Nom1, CALC_VAC
  if(t_p .eq. 0) then
if (CALC_VAC) write (6, '("  =>  Calculate voids distribution")')
  endif
  if (CALC_VAC .and. .not.(CALC_BONDS)) then
if(t_p .eq. 0) then
   write (6, '(" Changing option =>  Bond properties are needed to evaluate void distribution")')
endif
CALC_BONDS=.true.
  endif
  read (10, *)
  read (10, *)
  read (10, *)
  read (10, *) Nom1, EVOLOUT
  if(t_p .eq. 0) then
if (EVOLOUT) write (6, '("  =>  Ouptut calculations results for each MD steps")')
  endif
  read (10, *) Nom1, DXOUT
  if(t_p .eq. 0) then
if (DXOUT) then
   write (6, '("  =>  Ouptut OpenDX .dx file(s)")')
   write (6, '("    Main file = ''SYSTEM.dx''")')
endif
  endif
  read (10, *)
  read (10, *) Nom1, RADOUT
  if (DXOUT .and. RADOUT) then
if(t_p .eq. 0) write (6, '(3x," =>  Using atomic radius as color map")')
IDOUT=.false.
  endif
  read (10, *) Nom1, RNGOUT
  if (DXOUT .and. RNGOUT) then
if (LTLT .ne. 0) then
   if(t_p .eq. 0) then
      write (6, '(3x," =>  Atomic ring factor can''t be used as color map")')
      write (6, '(3x,"    if rings search options are not changed")')
      write (6, '(3x,"    Uing atomic mass as color map instead")')
   endif
else
   if(t_p .eq. 0) write (6, '(3x," =>  Using atomic ring factor as color map")')
   IDOUT=.false.
   FACTATPNA=.true.
endif
  endif
  read (10, *) Nom1, DRNGOUT
  if (DXOUT .and. DRNGOUT) then
if (LTLT .ne. 0) then
   if(t_p .eq. 0) then
      write (6, '(3x," =>  Delta ring factor can''t be used as color map")')
      write (6, '(3x,"    if rings search options are not changed")')
      write (6, '(3x,"    Uing atomic mass as color map instead")')
   endif
else
   if(t_p .eq. 0) write (6, '(3x," =>  Using Delta ring factor as color map")')
   IDOUT=.false.
   FACTATPNA=.true.
endif
  endif
  if (DXOUT .and. IDOUT) then
if(t_p .eq. 0) write (6, '(3x," =>  Using atomic mass as color map")')
  endif
  read (10, *) Nom1, VACOUT
  if (DXOUT .and. VACOUT) then
if(t_p .eq. 0) write (6, '(3x," =>  Voids visualization using OpenDX")')
if (.not.(CALC_VAC)) then
   if(t_p .eq. 0) write (6, '(" Changing option =>  Evaluate voids distribution is needed to visualize voids")')
   CALC_VAC=.true.
   if (.not.(CALC_BONDS)) then
      if(t_p .eq. 0) then
      write (6, '(" Changing option =>  Bond properties are needed to evaluate voids distribution")')
      endif
      CALC_BONDS=.true.
   endif
endif
  endif
  read (10, *) Nom1, DXTETRA
  if (DXOUT .and. DXTETRA) then
if(t_p .eq. 0) write (6, '(3x," =>  Tetrahedra visualization using OpenDX")')
   if (.not.(CALC_BONDS)) then
      if(t_p .eq. 0) then
      write (6, '(" Changing option =>  Bond properties are needed to visualize tetrahedra")')
      endif
      CALC_BONDS=.true.
   endif
  endif
  read (10, *) Nom1, PATHDX
  if (PATHDX) then
if(t_p .eq. 0) write (6, '(3x," =>  Trajectories of the ",I4," particles of highest MSD")') NVALT
if (.not.CALC_MSD) then
   if (t_p .eq. 0) write (6, '(" Changing option =>  MSD has to be computed to output trajectories")')
   CALC_MSD=.true.
endif
if (.not.MSDEA) then
   if (t_p .eq. 0) write (6, '(" Changing option =>  MSD for single atoms have to be computed to output trajectories")')
   MSDEA=.true.
endif
  endif
  read (10, *)
  read (10, *) Nom1, NOM_OUT
  if(t_p .eq. 0) write (6, '(/,"========    End Options    ========",//)')

  close (10)

!101 FORMAT (I4)
!102 FORMAT (I2)
!103 FORMAT (I5)
!104 FORMAT (f15.10)
!105 FORMAT (A3)
106 FORMAT (A13)
!107 FORMAT (I10)
!109 FORMAT (A17)
!111 FORMAT (A2,2x,f9.6)
!113 FORMAT (A15)
!114 FORMAT (f7.5)
001 FORMAT (/," Allocation Problem -> No space left ?! :: node ",i3," READ_INPUT allocation of ",A15)

END SUBROUTINE READ_INPUT

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4樓2021-07-29 20:11:26

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get-it

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抱歉了，我也不太熟。
https://sourceforge.net/p/rings- ... il.com/#msg33203770

我看到rings官網(wǎng)有人問(wèn)了同樣的問(wèn)題，不過(guò)似乎沒(méi)有回答。

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5樓2021-07-29 21:10:50

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量子海洋

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引用回帖:

5樓: Originally posted by get-it at 2021-07-29 21:10:50
抱歉了，我也不太熟。
https://sourceforge.net/p/rings-code/mailman/rings-code-news/thread/CALA6MD8rEa-3tYqJR7Xqz5NCtmSZaXnPP%2BNyYUx1W%3DUFuB-4yw%40mail.gmail.com/#msg33203770

我看到rings官網(wǎng)有人問(wèn) ...

好的，謝謝你。

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6樓2021-07-30 10:10:52

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我是Alun

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引用回帖:

6樓: Originally posted by 量子海洋 at 2021-07-30 10:10:52
好的，謝謝你。...

您好，我運(yùn)行時(shí)候報(bào)錯(cuò) Number of species in step 1 has changed, see input file line 3
請(qǐng)問(wèn)您有遇到這種情況嗎？該如何解決？

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7樓2021-12-30 15:11:19

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風(fēng)卷木葉

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RINGS 怎么用呀？

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問(wèn)菩薩為何倒坐，嘆眾生不肯回頭。

8樓2022-03-07 20:20:11

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jackwangee

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大家怎么解決的？我現(xiàn)在遇到這個(gè)問(wèn)題
Error in XDATCAR file format :: node 0, Please check file:data/XDATCAR
Exiting ...

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9樓2022-08-22 16:26:49

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luoxin558

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樓主能加個(gè)QQ交流一下嗎？

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10樓2024-01-29 10:46:22

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