This program generates a mem map, fourier map or patterson map
for crystals including modulated and composite crystals
input format as follows
key=value where key is key work shown below
for character value it should be enclosed by '
as flnm1='filename'
for numerical value it is like ndm=1 or f000=123.4
(01) iwflag :
(02) flnm1 : file name of hkl,Fobs,Fcal,phase,sig for MEM
file name of hkl,Fobs,Fcal,phase for Fourier
(03) flnm2 : file name for nD density file (iplot=0)
file name for 2D density file (iplot>0)
file name for 3D density file (iplot<0) (.win file)
(1) title
(2) a,b,c,cosa,cosb,cosc
a,b,c in angstrome
(2') nsub, zmtrx
nsub : number of subsystems
zmtrx: z matrix (permutation matrix for nsub >=2)
(3) ndm,nsymo,icent,ige,nctr
ndm: order of modulations 1 for one-dimensional modulation etc
(or extra dimension)
nsymo: number of symmetry operators
icent: 1 for centrosymmetric 0 for noncentrosymmetric
ige: 1 when generating elements are given else 0
nctr: number of centering translation (excluding 0,0,0,0,0,0)
********if ndm=0 skip (4)********
(4) a*,b*,c* components of the wave vector icorc, ilm (*)
if incommensurate icorc=1, commensurate icorc=0
ilm number of divisions of gauss integrals in structure
factor formula in incommensurate cases 3<=ilm<=100
******caution: satellite with order greater than****
*******ilm/5 is not calculated. This means that ****
*******if second order satellite intensity must be***
*******necessary ilm >= 10 is necessary *************
=========== repeat (4) ndm times ============
if nctr > 0 then (5)
(5) 'centering translation'
in the format of I.T. 1/2,1/2,1/2,0,0,0 etc
(6) 'symmetry operator'
in the format of I.T. x,y,z,t,u,v etc
(7) f000, sg00, sg0, sg1, fmag
f000: fc at the origin
(number of electrons in the unit cell of the first substructure)
sg00: sigma for f000
sg0: average sigma
sg1: sigma for strongest (Fcal) reflection
fmag: f000,sg00,sg0,sg1,fobs,fcal are
magnifiled by this factor
(fmag is the scale factor for the given structure factor)
if observed structure factor includes f000, this is replaced
(8) lgr: laue group: m3m,m3,4/mmm,4/m,mmm,2/m,-1,6/mmm,6/m,-3m,-31
laue group (number of equivalent positions)
m3m(48),m3(24),4/mmm(16),4/m(8),mmm(8),2/m(4),-1(2)
6/mmm(24),6/m(12),-3m(12),-31(6)
when lgr=2/m,(h2>=0 or h2<=0) and (h3>=0 or h3<=0) are assumed
when lgr=-1, h3>=0 or h3<=0 is assumed
(9) jbc
jbc: kind of map 1 : no axis transformation
-1: see (10)
-2: see (10')
(this program only write a plane normal to a*, b* or c*.
to write arbitrary plane, give jbc < 0 and
specify transformation matrix (10) which defines
new a*,b*,c* from old ones.)
**if jbc !=-1 skip (10_1) (10_2)**
(10_1) transformation matrix for miller index itr(6,6)
(for superstructures)
itr(i,j),j=1,6 (*)
repeat 6 times
which is equal to transformation matrix for
unit vectors in direct space
(10_2) s1, s2, s3, s4 : orthogonal transformation matrix for q1-q6
((s1(i,j),j=1,3),i=1,3) etc.
s1, s2 etc. should be in different lines
total 6x6 matrix is given by
s1,s3
s4,s2
**if jbc !=-2 skip (10'_1)-(10'_3)**
(10'_1) isetting
isetting : 1 c axis unique, 2 b axis unique, 3 a axis unique
(10'_2) v
v : matrix ((v(i,j),j=1,3),i=1,6)
6x3 U matrix, which gives the a1-a3 coefficient of
6 unit vectors in reciprocal space, is calculated from
iseging and a*,b*,c*,cosa*,cosb*,cosc* and k1,k2,k3
6x3 V matrix, which gives the a4-a6 coefficient of
6 unit vectors in reciprocal space, should be given
here
first 6x3 part of 6x6 R matrix is U while
second 6x3 part is V
in the standard setting for modulated structure
first 3x3 part of V is zero matrix while second 3x3
part is unit matrix for many cases, but may be
different for triclinic,monoclinic,hexagonal system
in idm=5
for example, k1 and k2 are in the a*-b* plane in hexagonal system,
we may take v(4,1)=a*, v(4,2)=0, v(4,3)=0
v(5,1)=-a*/2, v(5,2)=sqrt(3)a*/2, v(5,3)=0
v(6,1)=v(6,2)=v(6,3)=0
the best v(1,1)-v(3,3) are sample-dependent for which
the modulation wave should be parallel to the internal space
v(1,1)=v(1,2)=...=v(3,3)=0 gives the standard setting for
modulated structure but this is not appropriate for
semi-quasicrystals
(10'_3) s1, s2, s3, s4 : orthogonal transformation matrix for q1-q6
((s1(i,j),j=1,3),i=1,3) etc.
s1, s2 etc. should be in different lines
total 6x6 matrix is given by
s1,s3
s4,s2
(11) iplot,hmax,pkmin,rwmin (for iplot=5)
iplot=1, -1: Patterson map
=2, -2: Fourier map
=3, -3: difference Fourier map
=4, -4: MEM map (starting flat electronndensity)
=5, -5: MEM and LDEM starting from the result of LDEM
=6, -6: MEM and LDEM starting from the result of LDEM
f000 should be includel in observed structure factor
calculated f is not normalized by f000
*****************new***************
for negative iplot, 3D density function is saved in a file flnm2
hmax(1-6): number of grid points along principal axes
(these sould be the multiple of the power of prime numbers
up to 21)
hmax(1)*hmax(2)*..*hmax(6) <=256*256*256
*****hmax(i) >= 1 (for i=1,2,..,6)******
pkmin : minimum peak height fraction to be printed in Fourier
or Difference Fourier map
(real minimum peak hekgit is given by pkmax*pkmin
where pkmax is the maximum peak density)
abs(peak density) > pkmax*pkmin is printed
rwmin : rw factor below which LEM method works
*******(pkmin > 0)*******
***** if abs(iplot)=1,2,3 skip (12)
(12) ex1,ex2,nex1,nex2,icont
ex1,ex2: constants needed for smooth convergence
nex1: number of iterations in imode=1 (Yamamoto)
nex2: number of iterations in imode=2 (Sakata)
icont : 1 continue from former results
***** imode=1 mode is dangerous for accurate electron density map
***** imode=2 mode should be used for MEM
data for plotter
(12') frmt
frmt: file format for hkl, fobs, fcal, phs, sig(f)
phs : phase in degree
sig(f) is necessary only for MEM
(13) ldev,iwhkl
ldev : 1: B&W Postscript printer 2: color Postscript printer
iwhkl : 0 no output, 1: output of hkl fo fc
obtained from MEM or Fourier map
write strongest positive peak positions
for difference fourier (abs(iplot)=3)
(14) nsh: number of sheets for electron density map output
*********if nsh=0 skip (15)-(23)*******
(15) ng ismth
ng : number of graphs in a sheet
ismth : 0=no smoothing
1=3 point average
2=5 point average
(16) xs: origin coordinate in each map (xs(1)-xs(6))
(coordinates of the map origin in the new coordinate system
specified at (10))
(17) iax: selection of axes (iax(1)-iax(6))
write (electron) density in iax(1)-iax(2) plane
if iplot > 0
(18) ax,bx,coscx (length of axes in cm and cos angles)
default ax,bx: a,b,c for iax=1,2,3, d=5 for iax=4
coscx,: cosc,cosa,cosb for ax,bx=1,2;2,3;3,1
coscx: calculated from k1,k2,k3 for ax=a,b,c and bx=d
to use default falues, give ax=bx=0
(19) xmin,xmax,ymin,ymax,hscl,xdiv,ydiv
xmin,..,ymax:coordinate reanges along x and y axes
hscl : scale for F
xdiv, ydiv : intervals of the scale in x and y axes
if iplot < 0
(18) ax,bx,cx,cosax,cosbx,coscx (length of axes in cm and cos angles)
default ax,bx,cx: a,b,c for iax=1,2,3, d=5 for iax=4
cosax,cosbx,coscx,: cosc,cosa,cosb for ax,bx=1,2;2,3;3,1
cosax,cosbx,coscx: calculated from k1,k2,k3 for ax=a,b,c and bx=d
to use default falues, give ax=bx=0
(19) xmin,xmax,ymin,ymax,zmin,zmax,hscl,xdiv,ydiv,zdiv
xmin,..,zmax:coordinate reanges along x,y and z axes
hscl : scale for F
xdiv, ydiv, zdiv : intervals of the scale in x and y axes
if iplot < 0 skip (20)-(23)
(20) hmin,div,lf
hmin: minimum hight (density) in the division
div : interval of hight
lf : number of contour lines
(21) amagx,amagy,shftxb,shftyb,shftxa,shftya
amagx: magnification for x
amagy: magnification for y
shftxb,shftyb: shifts before each copy
shftxa,shftya: shifts after each copy
(22) iwtitl,wx,wy,ws,angl
if iwtitl=1, title is written
wx,wy: coordinates for the title
ws size of letter in cm, angle is the angle
from the x axis in degree
(23) wtitle : title for the figure
****************repeat (16)-(23) ng times****************
****************repeat (15)-(24) nsh times***************
File translated from
TEX
by
TTH,
version 3.02.
On 15 Mar 2005, 15:34.