mirror of https://gitlab.com/QEF/q-e.git
Updated pwi2xsf utility, fully up-to-date with PW2.0.
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@592 c92efa57-630b-4861-b058-cf58834340f0
This commit is contained in:
kokalj
parent
7263de43b8
commit
e9ca78e806
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@ -2,100 +2,426 @@
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! GNU General Public License. See the file `License'
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! in the root directory of the present distribution,
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! or http://www.gnu.org/copyleft/gpl.txt .
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!
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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! Tone: File adapted from pwi2xsf.f file of XCRYSDEN distribution
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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c ------------------------------------------------------------------------
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program pwi2xsf
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c reads preprocessed (with pwi2xsf.sh) PWscf v1.0 input-file
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c Reads pre-procesed (with pwi2xsf.sh) PW-input file
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c and converts to XSF format file
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c
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c This program reads the NEWLY formated preprocessed-PW.X input
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c
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c Usage: pwi2xsf.sh < PW-preprocessed file
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c ------------------------------------------------------------------------
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implicit none
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integer maxtyp
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c maxtyp : maximum number of types of atoms
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c maxatom: maximum number of atoms
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integer
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$ maxtyp,
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$ maxatom,
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$ ALAT_UNIT,
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$ BOHR_UNIT,
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$ ANGSTROM_UNIT,
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$ CRYSTAL_UNIT
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real*8
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$ bohr
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parameter (maxtyp = 100, bohr = 0.529177d0)
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parameter (
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$ maxtyp = 100,
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$ maxatom = 10000,
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$ bohr = 0.529177d0,
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$
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$ ALAT_UNIT = 1,
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$ BOHR_UNIT = 2,
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$ ANGSTROM_UNIT = 3,
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$ CRYSTAL_UNIT = 4 )
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integer
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$ ibrav, ! label for Bravais lattice
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$ nat, ! number of atoms
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$ ntyp ! number of pseudopotentials
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$ ntyp, ! number of pseudopotentials
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$ num_of_images, ! number of NEB images
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$ atomic_posunit ! length-unit of atomic positions
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real*8
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$ celldm(6), ! cell parameters
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$ omega, ! cell volume (not used)
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$ alat ! lattice parameter
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$ alat, ! lattice parameter
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$ a, b, c, cosab, cosac, cosbc ! lattice parameters
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character
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$ dummy*80
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$ calculation*80, ! type of calculation
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$ line*120 ! line of input
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character*3
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$ atm(maxatom) ! atomic symbols
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integer
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$ ityp, ! type of PP
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$ atn(maxtyp), ! nuclear charge
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$ ounit, ! output unit
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$ i, j ! dummies
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$ i, j, ! dummies
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$ inat, iim, m, ! counters
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$ i_trimleft_white_space, ! string whitespace-triming function
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$ len ! length of string
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real*8
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$ tau( 3 ),
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+ p( 3,3 ), ! lattice vectors (PRIMITIVE)
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+ c( 3,3 ) ! lattice vectors (CONVENTIONAL)
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$ x,y,z,w1,w2, ! Cartesian coordinates & weights
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$ tau(3,maxatom), ! atomic coordinates
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$ tau2(3,maxatom), ! atomic coordinates (2nd image)
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+ pv( 3,3 ), ! lattice vectors (PRIMITIVE)
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+ cv( 3,3 ) ! lattice vectors (CONVENTIONAL)
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logical
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$ ltaucry
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namelist/input/ ibrav, nat, celldm, ltaucry
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ltaucry = .false.
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namelist/system/
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$ ibrav, nat, celldm, a, b, c, cosab, cosac, cosbc,
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$ calculation, num_of_images
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ounit=6
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c set default values
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calculation = 'scf'
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num_of_images = 1
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nat = 0
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ibrav = 0
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celldm(1) = 0.0d0
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do i=1,maxtyp
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atn(i) = 0
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enddo
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open(1, file='nuclei.charges', status='old')
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read (1,*) ntyp
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do i=1,ntyp
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read (1,*) j,atn(j)
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enddo
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close(1)
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read (5,input)
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a = 0.0D0
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b = 0.0D0
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c = 0.0D0
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cosab = 0.0D0
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cosac = 0.0D0
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cosbc = 0.0D0
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c
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c read namelist system
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c
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read (5,system)
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if ( nat.eq.0 .or. celldm(1).eq.0.0d0 ) then
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print *,'ERROR reading INPUT. STOPPING !!!'
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print *,'ERROR: while reading INPUT !!!'
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STOP
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endif
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if ( ibrav.eq.0 ) then
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c read custom lattice
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read (5,*) ((p(i,j),i=1,3),j=1,3)
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read (5,*) dummy
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else
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call latgen( ibrav, celldm, p(1,1), p(1,2), p(1,3), omega)
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c was lattice specified in terms of A,B,C,...
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if ( celldm(1) .eq. 0.0D0 .AND. a .ne. 0.0D0 ) THEN
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if ( ibrav .eq. 0 ) ibrav = 14
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celldm(1) = a / bohr
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celldm(2) = b / a
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celldm(3) = c / a
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celldm(4) = cosab
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celldm(5) = cosac
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celldm(6) = cosbc
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else if ( celldm(1) .ne. 0.0D0 .AND. a .ne. 0.0D0 ) THEN
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print *, 'ERROR: do not specify both celldm and a,b,c !!!'
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endif
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c
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c read the rest of the input
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c
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990 continue
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read(5,'(a120)',end=999) line
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len = i_trimleft_white_space(line)
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c
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c CELL_PARAMETERS
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c
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if ( line(1:15) .eq. 'CELL_PARAMETERS' ) then
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read (5,*) ((pv(i,j),i=1,3),j=1,3)
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do j=1,3
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do i=1,3
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p(i,j) = p(i,j)/celldm(1)
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cv(i,j) = pv(i,j)
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end do
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end do
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c
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c ATOMIC_POSITIONS
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c
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elseif ( line(1:16) .eq. 'ATOMIC_POSITIONS' ) then
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c find out the length-unit
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line = line(17:len)
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len = i_trimleft_white_space(line)
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atomic_posunit = ALAT_UNIT
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if (len.gt.0 ) then
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if ( line(1:4) .eq. 'ALAT' ) then
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atomic_posunit = ALAT_UNIT
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elseif ( line(1:4) .eq. 'BOHR' ) then
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atomic_posunit = BOHR_UNIT
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elseif ( line(1:7) .eq. 'CRYSTAL' ) then
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atomic_posunit = CRYSTAL_UNIT
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elseif ( line(1:8) .eq.'ANGSTROM') then
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atomic_posunit = ANGSTROM_UNIT
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endif
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endif
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c
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c read atoms
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c
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if ( calculation(1:3) .ne. 'NEB' ) then
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call read_atoms(nat,atm,tau)
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else
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c
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c NEB: read atoms
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c
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if (num_of_images.lt.2) num_of_images=2
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read (5,'(a120)') line ! line: first_image
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call read_atoms(nat,atm,tau)
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read (5,'(a120)') line ! line: second_image
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call read_atoms(nat,atm,tau2)
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endif
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endif
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goto 990
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999 continue
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if ( ibrav.ne.0 ) then
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call latgen( ibrav, celldm,
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$ pv(1,1), pv(1,2), pv(1,3),
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$ cv(1,1), cv(1,2), cv(1,3), omega )
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do j=1,3
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do i=1,3
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pv(i,j) = pv(i,j)/celldm(1)
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end do
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end do
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call latgen_conventional(ibrav, celldm,
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$ pv(1,1), pv(1,2), pv(1,3),
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$ cv(1,1), cv(1,2), cv(1,3))
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endif
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call latgen_conventional (ibrav, celldm, p(1,1), p(1,2), p(1,3),
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$ c(1,1), c(1,2), c(1,3))
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alat = bohr*celldm(1)
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call write_XSF_header (alat, p, c, nat, ounit)
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call write_XSF_header (num_of_images,alat, pv, cv, nat, ounit)
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do i=1,nat
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read(5,*) tau(1), tau(2), tau(3), ityp
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if (ltaucry) call cryst_to_cart(1, tau, p, 1)
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write(ounit,'(i3,2x,3f15.10)') atn(ityp),
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$ alat*tau(1), alat*tau(2), alat*tau(3)
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do inat=1,nat
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if ( atomic_posunit .eq. BOHR_UNIT ) then
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tau(1,inat) = bohr * tau(1,inat)
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tau(2,inat) = bohr * tau(2,inat)
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tau(3,inat) = bohr * tau(3,inat)
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tau2(1,inat) = bohr * tau2(1,inat)
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tau2(2,inat) = bohr * tau2(2,inat)
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tau2(3,inat) = bohr * tau2(3,inat)
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elseif ( atomic_posunit .eq. ALAT_UNIT ) then
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tau(1,inat) = alat * tau(1,inat)
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tau(2,inat) = alat * tau(2,inat)
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tau(3,inat) = alat * tau(3,inat)
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tau2(1,inat) = alat * tau2(1,inat)
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tau2(2,inat) = alat * tau2(2,inat)
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tau2(3,inat) = alat * tau2(3,inat)
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elseif ( atomic_posunit .eq. CRYSTAL_UNIT ) then
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call cryst_to_cart(1, tau(1,inat), pv, 1)
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call cryst_to_cart(1, tau2(1,inat),pv, 1)
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tau(1,inat) = alat * tau(1,inat)
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tau(2,inat) = alat * tau(2,inat)
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tau(3,inat) = alat * tau(3,inat)
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tau2(1,inat) = alat * tau2(1,inat)
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tau2(2,inat) = alat * tau2(2,inat)
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tau2(3,inat) = alat * tau2(3,inat)
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endif
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if ( num_of_images .lt. 2 ) then
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write(ounit,'(a3,2x,3f15.10)')
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$ atm(inat), tau(1,inat), tau(2,inat), tau(3,inat)
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endif
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enddo
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if ( num_of_images .ge. 2 ) then
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m = num_of_images - 1
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do iim=1,num_of_images
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w1 = dble(m-(iim-1))/dble(m)
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w2 = dble(iim-1)/dble(m)
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write(ounit,'('' PRIMCOORD '',i5)') iim
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write(ounit,*) nat, 1
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do inat=1,nat
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x = w1*tau(1,inat) + w2*tau2(1,inat)
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y = w1*tau(2,inat) + w2*tau2(2,inat)
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z = w1*tau(3,inat) + w2*tau2(3,inat)
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write(ounit,'(a3,2x,3f15.10)') atm(inat), x, y, z
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enddo
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enddo
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endif
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END
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c---------------------------------------------------------------------
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subroutine latgen_conventional
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+ ( ibrav, celldm, p1, p2, p3, c1, c2, c3 )
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c Generate convetional lattice
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c---------------------------------------------------------------------
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c
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c Conventional crystallographic vectors c1, c2, and c3.
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c See "latgen" for the meaning of variables
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c
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implicit none
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c
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c First the input variables
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c
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real*8
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+ celldm( 6 ), ! input : the dimensions of the lattice
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+ p1( 3 ), ! input : first lattice vector (PRIMITIVE)
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+ p2( 3 ), ! input : second lattice vector
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+ p3( 3 ), ! input : third lattice vector
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+ c1( 3 ), ! output: first lattice vector(CONVENTIONAL)
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+ c2( 3 ), ! output: second lattice vector
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+ c3( 3 ) ! output: third lattice vector
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integer
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+ ibrav ! input: the index of the Bravais lattice
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c
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integer i
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c
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c
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do i = 1, 3
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c1(i) =0.d0
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c2(i) =0.d0
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c3(i) =0.d0
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end do
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c
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if ( ibrav .eq. 2 .or. ibrav .eq.3 ) then
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c
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c fcc and bcc lattice
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c
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c1( 1 ) = 1.0d0
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c2( 2 ) = 1.0d0
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c3( 3 ) = 1.0d0
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c
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else if ( ibrav .eq. 7 ) then
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c
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c body centered tetragonal lattice
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c
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if ( celldm( 1 ) .le. 0.d0 .or. celldm( 3 ) .le. 0.d0 )
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+ call errore( 'latgen', 'wrong celldm', 7 )
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c1(1) = 1.0d0
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c2(2) = 1.0d0
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c3(3) = celldm(3)
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c
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else if ( ibrav .eq. 10 ) then
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c
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c All face centered orthorombic lattice
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c
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if ( celldm( 1 ) .le. 0.d0 .or. celldm( 2 ) .le. 0.d0
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+ .or. celldm( 3 ) .le. 0.d0 )
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+ call errore( 'latgen', 'wrong celldm', 10 )
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c1(1) = 1.0d0
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c2(2) = celldm(2)
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c3(3) = celldm(3)
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c
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elseif ( ibrav .eq. 11 ) then
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c
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c Body centered orthorombic lattice
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c
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if ( celldm( 1 ) .le. 0.d0 .or. celldm( 2 ) .le. 0.d0
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+ .or. celldm( 3 ) .le. 0.d0 )
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+ call errore( 'latgen', 'wrong celldm', 11 )
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c1(1) = 1.0d0
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c2(2) = celldm(2)
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c3(3) = celldm(3)
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else
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c **********
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c all other cases : just copy p vectors to c vectors !!!
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c **********
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do i = 1, 3
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c1( i ) = p1( i )
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c2( i ) = p2( i )
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c3( i ) = p3( i )
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enddo
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end if
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c
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return
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end
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c ------------------------------------------------------------------------
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subroutine read_atoms(nat,atm,coor)
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c read atomic coordinates
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c ------------------------------------------------------------------------
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implicit none
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integer
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$ nat, ! number of atoms
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$ ipol,inat,len, ! counters
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$ i_trimleft_white_space ! integer-function
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character
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$ line*120 ! line of input
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character*3
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$ atm(*) ! atomic symbols
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real*8
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$ coor(3,*)
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do inat=1,nat
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10 continue
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read (5,'(a120)') line
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len = i_trimleft_white_space(line)
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if (len.eq.0) then
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c an empty line, read again
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goto 10
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endif
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atm(inat) = line(1:3)
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line = line(3:len)
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read (line,*) (coor(ipol,inat),ipol=1,3)
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enddo
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return
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end
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c ------------------------------------------------------------------------
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subroutine write_XSF_header (num_of_images,alat, p, c, nat, ounit)
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c writes the header for XSF structure file
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c ------------------------------------------------------------------------
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real*8
|
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$ alat, ! lattice parameter
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$ p(3,3), c(3,3), ! lattive vectors (PRIMITIVE & CONVETIONAL)
|
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$ p1(3,3), c1(3,3) ! lattive vectors in ANGSTROMS unit
|
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integer
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$ nat, ! number of atoms
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$ num_of_images, ! number of NEB images
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$ ounit ! output unit
|
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integer
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$ i, j ! dummies
|
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do i=1,3
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do j=1,3
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p1(i,j) = alat*p(i,j)
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c1(i,j) = alat*c(i,j)
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enddo
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enddo
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if (num_of_images .gt. 1)
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$ write(ounit,'('' ANIMSTEPS '',i5)') num_of_images
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write(ounit,'('' CRYSTAL'')')
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write(ounit,'(/,'' PRIMVEC'')')
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write(ounit,'(3(f15.10,2x,f15.10,2x,f15.10,/))')
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$ ((p1(i,j),i=1,3),j=1,3)
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write(ounit,'('' CONVVEC'')')
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write(ounit,'(3(f15.10,2x,f15.10,2x,f15.10,/))')
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$ ((c1(i,j),i=1,3),j=1,3)
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if (num_of_images .eq. 1) then
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write(ounit,'('' PRIMCOORD'')')
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write(ounit,*) nat, 1
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endif
|
||||
return
|
||||
end
|
||||
|
||||
c -------------------------------------------------
|
||||
integer function i_trimleft_white_space(word)
|
||||
c trim left white spaces out of word
|
||||
c -------------------------------------------------
|
||||
character word*(*), auxword*80
|
||||
|
||||
ilen=len(word)
|
||||
auxword=word
|
||||
do i=1,ilen
|
||||
if ( word(i:i) .eq. ' ' ) then
|
||||
auxword=word(i+1:ilen)
|
||||
else
|
||||
goto 1
|
||||
endif
|
||||
enddo
|
||||
1 continue
|
||||
i_trimleft_white_space=len(word)
|
||||
word=auxword(1:i_trimleft_white_space)
|
||||
return
|
||||
END
|
||||
|
|
|
|||
|
|
@ -3,14 +3,8 @@
|
|||
# Author: #
|
||||
# ------ #
|
||||
# Anton Kokalj Email: Tone.Kokalj@ijs.si #
|
||||
# Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 #
|
||||
# Jozef Stefan Institute Fax: x 386 1 477 3811 #
|
||||
# Jamova 39, SI-1000 Ljubljana #
|
||||
# SLOVENIA #
|
||||
# #
|
||||
# Source: $XCRYSDEN_TOPDIR/scripts/pwi2xsf.sh
|
||||
# ------ #
|
||||
# Copyright (c) 1996-2003 by Anton Kokalj #
|
||||
# Copyright (c) 2004 by Anton Kokalj #
|
||||
#############################################################################
|
||||
|
||||
#------------------------------------------------------------------------
|
||||
|
|
@ -20,97 +14,24 @@
|
|||
# or http://www.gnu.org/copyleft/gpl.txt .
|
||||
#------------------------------------------------------------------------
|
||||
|
||||
#------------------------------------------------------------------------
|
||||
# pwi2xsf.sh: PW-input to XSF conversion
|
||||
#
|
||||
# pwi2xsf.sh: PW-input to XSF converison
|
||||
#
|
||||
# Usage: pwi2xsf [-r] pw-input-file
|
||||
#
|
||||
#------------------------------------------------------------------------
|
||||
|
||||
|
||||
|
||||
pwError() {
|
||||
echo "
|
||||
========================================================================
|
||||
$1
|
||||
========================================================================
|
||||
" 1>&2
|
||||
if [ "$2" -ge 0 ]; then
|
||||
exit $2
|
||||
fi
|
||||
}
|
||||
|
||||
# --------------------------------------------------------------------------
|
||||
# FUNCTION: pwNucleiCharges --
|
||||
#
|
||||
# Purpose: ityp->nat conversion data
|
||||
#
|
||||
# Usage: pwNucleiCharges pw_input|pw_output outfile
|
||||
#
|
||||
# Side efect: creates nuclei.charges file
|
||||
# --------------------------------------------------------------------------
|
||||
|
||||
pwNucleiCharges() {
|
||||
#
|
||||
# if file nuclei.charges does not exists prompt for ityp->nat conversion !!
|
||||
#
|
||||
|
||||
if [ \( "$1" = "" \) -o \( "$2" = "" \) ]; then
|
||||
pwError "Usage: pwNucleiCharges pw_input|pw_output outfile" 1
|
||||
fi
|
||||
|
||||
# do we have PW-INPUT or PW-OUTPUT file ???
|
||||
|
||||
if [ "`cat $1 | egrep -i '&input|&system'`" != "" ]; then
|
||||
# it is PW-INPUT
|
||||
ntyp=`cat "$1" | awk '{gsub(",","\n"); print}' | grep ntyp \
|
||||
| awk '{split($0,a,"=|,"); print a[2];}'`
|
||||
else
|
||||
# PW-OUTPUT
|
||||
ntyp=`cat "$1" | grep 'number of atomic types' | \
|
||||
head -1 | awk '{print $NF}'`
|
||||
#echo 'NTYP=$ntyp'
|
||||
if [ "$ntyp" = "" ]; then
|
||||
# some older PWSCF versions didn't have "number of atomic
|
||||
# types" printout -> user will have to make nuclei.charges
|
||||
# file by himself/herself !!!
|
||||
pwError "This is either non PW-output file or is a PW-output file
|
||||
produced with some old PWSCF version" -1
|
||||
echo -n "How many ityp->nat replacements ? " 1>&2
|
||||
read ntyp
|
||||
fi
|
||||
fi
|
||||
|
||||
if [ ! -f nuclei.charges ]; then
|
||||
echo -n "Please enter $ntyp ityp->nat replacements !!! " 1>&2
|
||||
echo $ntyp > nuclei.charges
|
||||
i=0
|
||||
while [ $i -lt "$ntyp" ]
|
||||
do
|
||||
i=`echo "$i + 1"|bc`
|
||||
echo "" 1>&2
|
||||
echo "Replacement #${i}: ityp->nat" 1>&2
|
||||
echo -n "ityp[$i]=$i; nat[$i]=" 1>&2; read nat
|
||||
echo "$i $nat" >> nuclei.charges
|
||||
done
|
||||
fi
|
||||
|
||||
cat nuclei.charges > "$2"
|
||||
}
|
||||
|
||||
|
||||
# ------------------------------------------------------------------------
|
||||
# MAIN
|
||||
# ------------------------------------------------------------------------
|
||||
# Last major rewrite by Tone Kokalj on Mon Feb 9 12:48:10 CET 2004
|
||||
# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
if [ "$#" -lt 1 ]; then
|
||||
echo "
|
||||
Usage: pwi2xsf.sh [-r] pw-input
|
||||
|
||||
-r ... one must specify i.e. ityp->nat conversion, and the corresponding
|
||||
data are written to file nuclei.charges. The -r flag deletes this
|
||||
Option for PWscf version < 1.2:
|
||||
|
||||
-r ... one must spefify i.e. ityp->nat conversion, and the corresponding
|
||||
data are writen to file nuclei.charges. The -r flag deletes this
|
||||
file.
|
||||
" 1>&2
|
||||
"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
|
|
@ -131,23 +52,37 @@ if [ "$new_format1" != "" -a "$new_format2" != "" ]; then
|
|||
#
|
||||
cat $1 | awk 'BEGIN {RS=",";} {print $0}' | awk '
|
||||
BEGIN {
|
||||
end=0;
|
||||
calculation="";
|
||||
num_of_images="";
|
||||
nml_end=0;
|
||||
nml_end_string="";
|
||||
}
|
||||
|
||||
toupper($0) ~ /&SYSTEM/ { sysnml=1; print; }
|
||||
toupper($0) ~ /IBRAV|CELLDM|NAT/ { print; }
|
||||
toupper($0) ~ /&SYSTEM/ { print; }
|
||||
|
||||
/ATOMIC_SPECIES|ATOMIC_POSITIONS|K_POINTS|CELL_PARAMETERS/ {
|
||||
toupper($1) ~ /^IBRAV($|=)|^CELLDM\([1-6]\)($|=)|^NAT($|=)|^A($|=)|^B($|=)|^C($|=)|^COSAB($|=)|^COSAC($|=)|^COSBC($|=)/ { print; }
|
||||
|
||||
toupper($1) ~ /^CALCULATION($|=)/ { calculation=toupper($0); }
|
||||
|
||||
toupper($1) ~ /^NUM_OF_IMAGES($|=)/ { num_of_images=toupper($0); }
|
||||
|
||||
/ATOMIC_POSITIONS|CELL_PARAMETERS/ {
|
||||
if ( !nml_end) {
|
||||
# first finish the namelist
|
||||
nml_end=1;
|
||||
if (calculation != "") print calculation;
|
||||
if (num_of_images != "") print num_of_images;
|
||||
print nml_end_string;
|
||||
}
|
||||
# now print the current record
|
||||
print_line=1;
|
||||
print toupper($0);
|
||||
next;
|
||||
}
|
||||
|
||||
|
||||
toupper($0) ~ /&END|^\/|^ \// {
|
||||
if ( sysnml == 1 ) {
|
||||
print;
|
||||
sysnml=0;
|
||||
}
|
||||
nml_end_string=$0;
|
||||
}
|
||||
|
||||
/a*/ {
|
||||
|
|
@ -155,36 +90,23 @@ toupper($0) ~ /&END|^\/|^ \// {
|
|||
print toupper($0);
|
||||
}
|
||||
}'> pw.$$
|
||||
PWI2XSF=pwi2xsf_new
|
||||
else
|
||||
# we have OLD PW.X input format
|
||||
|
||||
pwNucleiCharges $1 /dev/null
|
||||
|
||||
cat $1 | awk 'BEGIN {RS=",";} {print}' | awk '
|
||||
BEGIN {
|
||||
end=0;
|
||||
}
|
||||
toupper($0) ~ /&INPUT|CELLDM|NAT|LTAUCRY/ { print; }
|
||||
toupper($0) ~ /IBRAV/ {
|
||||
print;
|
||||
split($0,a,"=");
|
||||
split(a[1],b,",");
|
||||
ibrav = b[1];
|
||||
}
|
||||
toupper($0) ~ /&END|^\/|^ \// { end=1; }
|
||||
/a*/ {
|
||||
if ( end == 1 ) print;
|
||||
}' > pw.$$
|
||||
PWI2XSF=pwi2xsf
|
||||
echo "
|
||||
------------------------------------------------------------------------
|
||||
ERROR: This is NOT a PW-input or an input for an older PW version
|
||||
------------------------------------------------------------------------
|
||||
"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
#
|
||||
# execute $PWI2XSF fortran program and print the XSF file
|
||||
#
|
||||
if [ \( "$XCRYSDEN_TOPDIR" != "" \) -a \( -x $XCRYSDEN_TOPDIR/bin/$PWI2XSF \) ]; then
|
||||
$XCRYSDEN_TOPDIR/bin/$PWI2XSF < pw.$$ | tee pwi2xsf.xsf_out
|
||||
if test -f $XCRYSDEN_TOPDIR/bin/$PWI2XSF ; then
|
||||
$XCRYSDEN_TOPDIR/bin/pwi2xsf < pw.$$ | tee pwi2xsf.xsf_out
|
||||
else
|
||||
$PWI2XSF < pw.$$ | tee pwi2xsf.xsf_out
|
||||
pwi2xsf.x < pw.$$ | tee pwi2xsf.xsf_out
|
||||
fi
|
||||
rm -f pw.$$
|
||||
|
||||
|
|
|
|||
|
|
@ -1,188 +0,0 @@
|
|||
! This file is distributed under the terms of the
|
||||
! GNU General Public License. See the file `License'
|
||||
! in the root directory of the present distribution,
|
||||
! or http://www.gnu.org/copyleft/gpl.txt .
|
||||
|
||||
|
||||
c ------------------------------------------------------------------------
|
||||
program pwi2xsf_new
|
||||
c reads preprocessed (with pwi2xsf.sh) PWscf v1.2 input-file
|
||||
c and converts to XSF format file
|
||||
c
|
||||
c This program reads the NEWLY formated preprocessed-PW.X input
|
||||
c
|
||||
c Usage: pwi2xsf.sh < PW-preprocessed file
|
||||
c ------------------------------------------------------------------------
|
||||
|
||||
implicit none
|
||||
|
||||
c maxtyp : maximum number of types of atoms
|
||||
c maxatom: maximum number of atoms
|
||||
|
||||
integer
|
||||
$ maxtyp,
|
||||
$ maxatom,
|
||||
$ ALAT_UNIT,
|
||||
$ BOHR_UNIT,
|
||||
$ ANGSTROM_UNIT,
|
||||
$ CRYSTAL_UNIT
|
||||
|
||||
real*8
|
||||
$ bohr
|
||||
|
||||
parameter (
|
||||
$ maxtyp = 100,
|
||||
$ maxatom = 10000,
|
||||
$ bohr = 0.529177d0,
|
||||
$
|
||||
$ ALAT_UNIT = 1,
|
||||
$ BOHR_UNIT = 2,
|
||||
$ ANGSTROM_UNIT = 3,
|
||||
$ CRYSTAL_UNIT = 4 )
|
||||
|
||||
integer
|
||||
$ ibrav, ! label for Bravais lattice
|
||||
$ nat, ! number of atoms
|
||||
$ ntyp, ! number of pseudopotentials
|
||||
$ atomic_posunit ! length-unit of atomic positions
|
||||
|
||||
real*8
|
||||
$ celldm(6), ! cell parameters
|
||||
$ omega, ! cell volume (not used)
|
||||
$ alat ! lattice parameter
|
||||
|
||||
character
|
||||
$ line*120 ! line of input
|
||||
character*3
|
||||
$ atm(maxatom) ! atomic symbols
|
||||
|
||||
integer
|
||||
$ ityp, ! type of PP
|
||||
$ ounit, ! output unit
|
||||
$ i, j, ! dummies
|
||||
$ ipol,inat, ! counters
|
||||
$ i_trimleft_white_space, ! string whitespace-triming function
|
||||
$ len ! length of string
|
||||
|
||||
real*8
|
||||
$ tau(3,maxatom),
|
||||
+ p( 3,3 ), ! lattice vectors (PRIMITIVE)
|
||||
+ c( 3,3 ) ! lattice vectors (CONVENTIONAL)
|
||||
|
||||
logical
|
||||
$ ltaucry
|
||||
|
||||
namelist/system/ ibrav, nat, celldm
|
||||
|
||||
ounit=6
|
||||
|
||||
c set default values
|
||||
nat = 0
|
||||
ibrav = 0
|
||||
celldm(1) = 0.0d0
|
||||
|
||||
c read namelist system
|
||||
read (5,system)
|
||||
if ( nat.eq.0 .or. celldm(1).eq.0.0d0 ) then
|
||||
print *,'ERROR reading INPUT. STOPING !!!'
|
||||
STOP
|
||||
endif
|
||||
c print *,'DEBUG: namelist read'
|
||||
c print *,'DEBUG: nat = ', nat
|
||||
|
||||
c read the rest of the input
|
||||
990 continue
|
||||
read(5,'(a120)',end=999) line
|
||||
c print *,'DEBUG: read line :', line(1:40)
|
||||
len = i_trimleft_white_space(line)
|
||||
c print *,'DEBUG: read line_trim:', line(1:40)
|
||||
c
|
||||
c CELL_PARAMETERS
|
||||
c
|
||||
if ( line(1:15) .eq. 'CELL_PARAMETERS' ) then
|
||||
read (5,*) ((p(i,j),i=1,3),j=1,3)
|
||||
do j=1,3
|
||||
do i=1,3
|
||||
c(i,j) = p(i,j)
|
||||
end do
|
||||
end do
|
||||
c
|
||||
c ATOMIC_POSITIONS
|
||||
c
|
||||
elseif ( line(1:16) .eq. 'ATOMIC_POSITIONS' ) then
|
||||
c find out the length-unit
|
||||
line = line(17:len)
|
||||
len = i_trimleft_white_space(line)
|
||||
atomic_posunit = ALAT_UNIT
|
||||
if (len.gt.0 ) then
|
||||
if ( line(1:4) .eq. 'ALAT' ) then
|
||||
atomic_posunit = ALAT_UNIT
|
||||
elseif ( line(1:4) .eq. 'BOHR' ) then
|
||||
atomic_posunit = BOHR_UNIT
|
||||
elseif ( line(1:7) .eq. 'CRYSTAL' ) then
|
||||
atomic_posunit = CRYSTAL_UNIT
|
||||
elseif ( line(1:8) .eq.'ANGSTROM') then
|
||||
atomic_posunit = ANGSTROM_UNIT
|
||||
endif
|
||||
endif
|
||||
|
||||
c read atoms
|
||||
do inat=1,nat
|
||||
10 continue
|
||||
read (5,'(a120)') line
|
||||
c print *,'DEBUG: line_len: line:',line(1:40)
|
||||
len = i_trimleft_white_space(line)
|
||||
c print *,'DEBUG: line_len: len: ',len, line
|
||||
|
||||
if (len.eq.0) then
|
||||
c an empty line, read again
|
||||
goto 10
|
||||
endif
|
||||
atm(inat) = line(1:3)
|
||||
c print *,'DEBUG: atm():',atm(inat)
|
||||
line = line(3:len)
|
||||
read (line,*) (tau(ipol,inat),ipol=1,3)
|
||||
enddo
|
||||
endif
|
||||
goto 990
|
||||
|
||||
999 continue
|
||||
|
||||
if ( ibrav.ne.0 ) then
|
||||
call latgen( ibrav, celldm,
|
||||
$ p(1,1), p(1,2), p(1,3), c(1,1), c(1,2), c(1,3), omega )
|
||||
do j=1,3
|
||||
do i=1,3
|
||||
p(i,j) = p(i,j)/celldm(1)
|
||||
end do
|
||||
end do
|
||||
call latgen_conventional(ibrav, celldm, p(1,1), p(1,2), p(1,3),
|
||||
$ c(1,1), c(1,2), c(1,3))
|
||||
endif
|
||||
|
||||
alat = bohr*celldm(1)
|
||||
call write_XSF_header (alat, p, c, nat, ounit)
|
||||
|
||||
do inat=1,nat
|
||||
if ( atomic_posunit .eq. BOHR_UNIT ) then
|
||||
tau(1,inat) = bohr * tau(1,inat)
|
||||
tau(2,inat) = bohr * tau(2,inat)
|
||||
tau(3,inat) = bohr * tau(3,inat)
|
||||
|
||||
elseif ( atomic_posunit .eq. ALAT_UNIT ) then
|
||||
tau(1,inat) = alat * tau(1,inat)
|
||||
tau(2,inat) = alat * tau(2,inat)
|
||||
tau(3,inat) = alat * tau(3,inat)
|
||||
|
||||
elseif ( atomic_posunit .eq. CRYSTAL_UNIT ) then
|
||||
call cryst_to_cart(1, tau(1,inat), p, 1)
|
||||
|
||||
tau(1,inat) = alat * tau(1,inat)
|
||||
tau(2,inat) = alat * tau(2,inat)
|
||||
tau(3,inat) = alat * tau(3,inat)
|
||||
endif
|
||||
|
||||
write(ounit,'(a3,2x,3f15.10)')
|
||||
$ atm(inat), tau(1,inat), tau(2,inat), tau(3,inat)
|
||||
enddo
|
||||
END
|
||||
|
|
@ -1,139 +0,0 @@
|
|||
c
|
||||
c---------------------------------------------------------------------
|
||||
subroutine latgen_conventional
|
||||
+ ( ibrav, celldm, p1, p2, p3, c1, c2, c3 )
|
||||
c---------------------------------------------------------------------
|
||||
c
|
||||
c Conventional crystallographic vectors c1, c2, and c3.
|
||||
c See "latgen" for the meaning of variables
|
||||
c
|
||||
implicit none
|
||||
c
|
||||
c First the input variables
|
||||
c
|
||||
real*8
|
||||
+ celldm( 6 ), ! input : the dimensions of the lattice
|
||||
+ p1( 3 ), ! input : first lattice vector (PRIMITIVE)
|
||||
+ p2( 3 ), ! input : second lattice vector
|
||||
+ p3( 3 ), ! input : third lattice vector
|
||||
+ c1( 3 ), ! output: first lattice vector(CONVENTIONAL)
|
||||
+ c2( 3 ), ! output: second lattice vector
|
||||
+ c3( 3 ) ! output: third lattice vector
|
||||
integer
|
||||
+ ibrav ! input: the index of the Bravais lattice
|
||||
c
|
||||
integer i
|
||||
c
|
||||
c
|
||||
do i = 1, 3
|
||||
c1(i) =0.d0
|
||||
c2(i) =0.d0
|
||||
c3(i) =0.d0
|
||||
end do
|
||||
c
|
||||
if ( ibrav .eq. 2 .or. ibrav .eq.3 ) then
|
||||
c
|
||||
c fcc and bcc lattice
|
||||
c
|
||||
c1( 1 ) = 1.0d0
|
||||
c2( 2 ) = 1.0d0
|
||||
c3( 3 ) = 1.0d0
|
||||
c
|
||||
else if ( ibrav .eq. 7 ) then
|
||||
c
|
||||
c body centered tetragonal lattice
|
||||
c
|
||||
if ( celldm( 1 ) .le. 0.d0 .or. celldm( 3 ) .le. 0.d0 )
|
||||
+ call errore( 'latgen', 'wrong celldm', 7 )
|
||||
c1(1) = 1.0d0
|
||||
c2(2) = 1.0d0
|
||||
c3(3) = celldm(3)
|
||||
c
|
||||
else if ( ibrav .eq. 10 ) then
|
||||
c
|
||||
c All face centered orthorombic lattice
|
||||
c
|
||||
if ( celldm( 1 ) .le. 0.d0 .or. celldm( 2 ) .le. 0.d0
|
||||
+ .or. celldm( 3 ) .le. 0.d0 )
|
||||
+ call errore( 'latgen', 'wrong celldm', 10 )
|
||||
c1(1) = 1.0d0
|
||||
c2(2) = celldm(2)
|
||||
c3(3) = celldm(3)
|
||||
c
|
||||
elseif ( ibrav .eq. 11 ) then
|
||||
c
|
||||
c Body centered orthorombic lattice
|
||||
c
|
||||
if ( celldm( 1 ) .le. 0.d0 .or. celldm( 2 ) .le. 0.d0
|
||||
+ .or. celldm( 3 ) .le. 0.d0 )
|
||||
+ call errore( 'latgen', 'wrong celldm', 11 )
|
||||
c1(1) = 1.0d0
|
||||
c2(2) = celldm(2)
|
||||
c3(3) = celldm(3)
|
||||
else
|
||||
c **********
|
||||
c all other cases : just copy p vectors to c vectors !!!
|
||||
c **********
|
||||
do i = 1, 3
|
||||
c1( i ) = p1( i )
|
||||
c2( i ) = p2( i )
|
||||
c3( i ) = p3( i )
|
||||
enddo
|
||||
end if
|
||||
c
|
||||
return
|
||||
end
|
||||
|
||||
c ------------------------------------------------------------------------
|
||||
subroutine write_XSF_header (alat, p, c, nat, ounit)
|
||||
c writes the header for XSF structure file
|
||||
c ------------------------------------------------------------------------
|
||||
real*8
|
||||
$ alat, ! lattice parameter
|
||||
$ p(3,3), c(3,3), ! lattive vectors (PRIMITIVE & CONVENTIONAL)
|
||||
$ p1(3,3), c1(3,3) ! lattive vectors in ANGSTROMS unit
|
||||
integer
|
||||
$ nat, ! number of atoms
|
||||
$ ounit ! output unit
|
||||
integer
|
||||
$ i, j ! dummies
|
||||
|
||||
do i=1,3
|
||||
do j=1,3
|
||||
p1(i,j) = alat*p(i,j)
|
||||
c1(i,j) = alat*c(i,j)
|
||||
enddo
|
||||
enddo
|
||||
|
||||
write(ounit,'('' CRYSTAL'')')
|
||||
write(ounit,'(/,'' PRIMVEC'')')
|
||||
write(ounit,'(3(f15.10,2x,f15.10,2x,f15.10,/))')
|
||||
$ ((p1(i,j),i=1,3),j=1,3)
|
||||
write(ounit,'('' CONVVEC'')')
|
||||
write(ounit,'(3(f15.10,2x,f15.10,2x,f15.10,/))')
|
||||
$ ((c1(i,j),i=1,3),j=1,3)
|
||||
write(ounit,'('' PRIMCOORD'')')
|
||||
write(ounit,*) nat, 1
|
||||
return
|
||||
end
|
||||
c
|
||||
c -------------------------------------------------
|
||||
integer function i_trimleft_white_space(word)
|
||||
c trim left white spaces out of word
|
||||
c -------------------------------------------------
|
||||
character word*(*), auxword*80
|
||||
|
||||
ilen=len(word)
|
||||
auxword=word
|
||||
do i=1,ilen
|
||||
if ( word(i:i) .eq. ' ' ) then
|
||||
auxword=word(i+1:ilen)
|
||||
else
|
||||
goto 1
|
||||
endif
|
||||
enddo
|
||||
1 continue
|
||||
i_trimleft_white_space=len(word)
|
||||
word=auxword(1:i_trimleft_white_space)
|
||||
return
|
||||
END
|
||||
Loading…
Reference in New Issue