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[求助]
R.I.N.G.S. code运行报错
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用VASP跑完AIMD后，想用RINGS(http://rings-code.sourceforge.net/)处理下数据，按照官网的example写好输入input（重命名为my-input）和options文件，也吧XDATCAR放在了data文件夹里，在终端中运行 rings my-input 出现报错“At line 230 of file input.f90 (unit = 10, file = 'options') Fortran runtime error: Bad logical value while reading item 2”，不知道问题出在哪里，怎么解决？ |
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2楼2021-07-28 11:45:54
get-it
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3楼2021-07-28 16:43:58
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options文件没有230行，是input.f90文件的第230行，但是我不知道是什么问题，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: ! "http://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 |
4楼2021-07-29 20:11:26
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官网有人问了同样的问题，不过似乎没有回答。 |
5楼2021-07-29 21:10:50
6楼2021-07-30 10:10:52
7楼2021-12-30 15:11:19
8楼2022-03-07 20:20:11
jackwangee
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9楼2022-08-22 16:26:49
10楼2024-01-29 10:46:22
5