**************************************************************
parallel and perspective projection of a cluster
in crystals and quasicrystals
In quasicrystals, all atom positions in 3D space
have been given, while in crystals, those for
independent atoms and symmetry operations should
be given
**************************************************************
by A. Yamamoto
Jan. 30, 2004
(0) icase itempf
icase: 0 for qcstrc output format for (9) (no symmetry operators)
1 for iatom output file for (9) (use symmetry operators)
for icase=0, cartesian coordinates with the unit
vectors of 1A are used
for icase=1 unit vectors given in (2) are used
itempf: 1 anisotropic temperature factor
itempf: 0 and icase=0 see (9)
(1) title
****** if icase=0 skip (2) *****
(2) a,b,c,cosa,cosb,cosc
(lattice constants a,b,c in angstrome)
(3) na,ne,ng,ip,iat
na number of independent atoms ( <= 20000)
ne number of elements (1<=ne<=200) (OD number)
ng number of pages (default: 1)
ip 0: atom position is given in this file
1: atom position is read from another file
iat 0: occupation domain number in the second data in (9) for quasicrystals
1: element name 'Na' etc. in the second data in (9) for crystals
****** if icase=0 skip (4)-(6) *****
(4) ns,ig,ic,brv
ns number of symmetry operators or their generators (ns<=1<=48)
ig 0: symmetry operator 1: generator
ic 1:centrocymmetric, 0:noncentrosymmetric
brv bravais lattice ('p', 'a', 'b', 'c', 'i', 'f', 'r')
or non periodic structure (' ')
(5) symmetry operator (header)
(6) symmetry operations in the format of I.T.
for example x,y,z 1/2-x, y, 1/2+z etc.
repeat (6) ns times
(7) ldev,iww,iwb,iwc,iwa,ips,ccol,jmod,iornt
ldev : 1 black and white, 2 color
iww : 1 print out x y z coordinates and bonded pairs
iwb 0: write bonds 1: no bond
iwc 0: write unit cell 1: no unit cell
iwa 0: write atoms joined by bond 1: all atoms
ips 0: parallel projection 1: perspective projection
ccol : unit cell color (color display) or pen number (plotter)
for display
1:blue,2:red,3:purple,4:green,5:sky blue,6:yellow,7:white
(default: white)
jmod : 0 non-shaded atoms without atom number
1 shaded atoms
2 non-shaded atoms with atom number
3 bs-file output for using xbs
4 mld-file output for using vics
c 5 non-shaded atoms with color determined by p1,p2,p3
iornt : orientation 1: portrait 2: landscape
****** if ip=0 skip (8)
(8) flnm
flnm : file name of file including data (9)
(8') flnm1
flnm1 : file name for x,y,z,ui output (jmod=0,1,2,5)
prefix for bs files (nb files are created. see (16).)
(jmod=3)
prefix of the file name for mld file (jmod= 4)
****** bs file ******
prefix of the file name for atom species, x, y, z
spec name radius color
bonds name1 name2 min-length max-length radius color
****** mld file ******
title
na (number of atoms)
atom species x,y,z en (en : element number, repeat na times)
nb (number of bonds)
atom number pair for a bond (repeat nb times)
(en : 1 for H, 2 for He etc.)
****** skip (8") if jmod > 2 *****
(8") flnm2
flnm2 : prefix of the file name for bonds
****** if ip=1 skip (9) but the same date should be given
as a separate file
if icase=0 or iat=0 (for quasicrystals)
(9) atom number, od number, element number,x,y,z, p1, p2, p3 (*)
if itempf=1 u11,u22,u33,u23,u31,u12 should be followed at
the end of each line of (9) else p1,p2,p3 be followed
p1,p2,p3 : partial occupation prb for the 1st, 2nd and 3rd atoms
if iat=1 (for crystals)
(9) atom number, symbol, element number,x,y,z (*)
if itempf=1 u11,u22,u33,u23,u31,u12 should be followed at
the end of each line of (9)
****** repeat (9) na times
(10) rad,acol,symbol
rad: atom radii (in angstrome)
acol: atom color
symbol: 'Al', 'Mn' etc.
repeat (10) ne times
******* repeat (11)-(18) ng times ***********
(11) (S(i,j),j=1,3),T(i) (*)
S :transformation matrix of the coordinate (integer)
T :translation vector
repeat (11) three times (i=1,2,3)
********************************************
(12) atom selection ias(1)-ias(na) (80i1)
ias(i):1 i-th atom is selected, :0 neglected
(13) hp,xp,amgn,xvp
hp(1)-hp(3) : projection axis
hp = hp(1)a* + hp(2)b* + hp(3)c*
xp(1)-xp(3) : y axis
amgn magnification of x,y,radius (cm/angstrome)
(default: 1.0)
xvp distance from visual point to origin (in angstrom)
(default: 20.0)
(14) lxmin,lxmax,lymin,lymax,lzmin,lzmax
from a give atom with the coordinate x,y,z
atoms with the coordinates x+lx, y+ly, z+lz within the ranges
lxmin<=lx<=lxmax,lymin<=ly<=lymax,lzmin<=lz<=lzmax are generated
(for quasicrystals, lxmin=lxmax=lymin=lymax=lzmin=lzmax=0)
(15) fxyz
fxyz(1)-fxyz(3): fixed point for rotation etc.
(origin of the plotter system)
******* data for choosing shells in the cluster *********
we can choose atoms which construct a cluster by rmin,rmax,
zmin,zmax,iaslct,jaslct specified below
(16) nb,nclc
nb : number of shells ( 0 < nb )
nclc: number of cluster centers
(17) hb
hb(1)-hb(3): projection axis
(17') xo,rmin,rmax,jc,zmin,zmax,ns0
hb = hb(1)a* + hb(2)b* + hb(3)c*
xo(1)-xo(3): center of the cluster
xo = xo(1)a + xo(2)b + xo(3)c
rmin minimum radius of the shell in angstrome
rmax maximum radius of the shell in angstrome
jc : 0 place cluster center at the origin
1 place cluster center at average of xo
**** added
ns0 : symmetry operator number which is applied to xo
if centrosymmetric and it is rotoinversion
give nsymo+ns for ns0
ns0=1 means identity operation
********** repeat (17') nclc times ************
(18) shiftx,shifty
sift of origin (in cm) before plot
**************if iwb=1 skip (19,20)************
(19) np,iaslct
np number of element pairs to be joined by bonds(<=20)
iaslct 0,1,2, or 3 for no selection,
select by element No, OD No or serial No.
iaslct=0 means all atoms are selected.
for iaslct>0 give jaslct in (21) for choosing atoms or ODs
(20) ie1,ie2,dmin,dmax,bwdt,bcol
ie1,ie2 element pair to be joined by a line (bond)
dmin min. distance to be joined
dmax max. distance to be joined
bwdt bond width (pen number)
bcol bond color (for color display)
***** if iaslct=0 skip (21)
(21) jaslct (80i1)
(for iaslct=1) 1 for selected element 0 others
(for iaslct=2) 1 for selected OD 0 others
(for iaslct=3) 1 for selected atom (serial No.) 0 others
repeat (20) np times
repeat (16)-(20) nb times
******************limiting conditions******************************
maximum number of atoms in a unit cell namax
maximum number of atoms in each elements namax/ne
*******************************************************************
File translated from
TEX
by
TTH,
version 3.02.
On 16 Aug 2005, 08:50.