RE: troublesome unit cell

2004-10-18 Thread alan coelho 
Title: Message



Pam,
 
If the 
other programs are in error at the hkl stage then my suggestion is to send the 
hkls from the apparently working programs to the authors of the apparently not 
working programs. 
 
Or 
better yet those authors should contact you as I for one am always on the look 
out for "apparent" discrepencies.
alan

  
  -Original Message-From: Whitfield, 
  Pamela [mailto:[EMAIL PROTECTED] Sent: Tuesday, 
  October 19, 2004 12:05 AMTo: '[EMAIL PROTECTED]'Subject: 
  RE: troublesome unit cell
  Alan
   
  In the original 
  simulations I used them exactly as you describe :-)
  I modified that file to be able to start refining the TM 
  x and y positions for some data I have.  Topas is still seeing them as 3a 
  and 3b positions, so internally they are still 1/9, 5/9 etc, as they started 
  out.  In any case it doesn't make a massive difference.  
  The problems I refer to in some software are not subtle, they're 
  huge, and seem to reflect a problem in hkl-related 
  multiplicities.
   
  Pam  
   
  Dr Pamela Whitfield CChem MRSCEnergy Materials 
  GroupInstitute for Chemical Process and Environmental TechnologyBuilding 
  M12National Research Council Canada1200 Montreal 
  RoadOttawa ON K1A 0R6CANADATel: (613) 998 8462 Fax: (613) 991 2384Email: 
  <>ICPET 
  WWW:  
  
-Original Message-From: alan coelho 
[mailto:[EMAIL PROTECTED]Sent: October 18, 2004 5:36 
PMTo: [EMAIL PROTECTED]Subject: RE: troublesome unit 
cell
Pam,
 
I 
looked at your INP file and there was a problem in regards to how atomic 
coordinates were defined. As you know TOPAS uses computer algebra with a 
tollerance of 1.0e-15 for checking the equivalence of equivalent positions. 
If I use
 
x 
= 1/9; y = 5/9;  etc,,,
 
then the structures are similar.
 
It 
is not often obvious these equations but it is easy to check using the 
number of equivalent positions or by inspecting the bond 
lengths.
 
My 
guess is that the other programs may have conventions that are also not 
obvious.
 
it 
is always good to do some checking
cheers
alan
 
 

  
  -Original Message-From: Whitfield, 
  Pamela [mailto:[EMAIL PROTECTED] Sent: Monday, 
  October 18, 2004 10:32 PMTo: 
  '[EMAIL PROTECTED]'Subject: RE: troublesome unit 
  cell
  AlanI'm afraid that the cif files weren't overly 
  good ones - I don't normally use them.  For the R-3m the Li 1/2 
  fractional coordinate is for the z, not y.  The structures are 
  related by a Ö3a x Ö3a 
  relationship with Z = 3 for the R-3m and Z = 9 for the P3112.Here are 
  the STR files.  You can refine the 3a and 3b positions for the P3112, 
  but there is a strict relationship that has to be maintained between the x 
  and y coordinates - I have to do it in launch mode to make it work.  
  It's a very picky space group to work with.PamDr 
  Pamela Whitfield CChem MRSCEnergy Materials GroupInstitute for 
  Chemical Process and Environmental TechnologyBuilding M12National 
  Research Council Canada1200 Montreal RoadOttawa  
  ON   K1A 0R6CANADATel: (613) 998 
  8462 Fax: (613) 991 
  2384Email: ICPET 
  WWW: http://icpet-itpce.nrc-cnrc.gc.ca-Original 
  Message-From: alan coelho [mailto:[EMAIL PROTECTED]]Sent: 
  October 18, 2004 4:16 PMTo: [EMAIL PROTECTED]Subject: RE: 
  troublesome unit cellPam,As a developer and someone 
  who uses other software to test against, Ihave been following the 
  discussion with interest. This is a complex areaand it goes to show 
  the importance of having a few programs if only fortesting 
  purposes.I am puzzled by your cif data however as I cant get past 
  verifying theequivalence of the number of equivalent positions for the 
  Li site.In R-3m you have as fractional atomic coordinates for 
  Li1:  x = 0    y = 0.5  and  z = 
  0For P3112 you have three Li sites with x, y, z's 
  as0.77780 0.0 0.833300.0 0.88890 0.833300.0 
  0.55560 0.83330which translates to:0.77780 0.0 
  5/60.0 0.88890 5/60.0 0.55560 5/6Listed below are 
  equivalent positions for a general site.What I dont understand is 
  that for R-3m I get 9 non-overlapping fullyoccupied equivalent 
  positions within the unit cell with a volume of101.2975.For 
  P3112 I get 18 non-overlapping equivalent positions with a volumethree 
  times as large of 303.8968. I was expecting to get 27 if the 
  twostructure were to be equivalent.Thus, from your cif data I 
  am left to conclude that I am generating thewrong number of equivalent 
  positions, or, if I am generating the correctnumber of equivalent 
  positions then the two cif data sets should

RE: troublesome unit cell

2004-10-18 Thread Whitfield, Pamela 
Title: Message



Alan
 
In the original 
simulations I used them exactly as you describe :-)
I modified that file to be able to start refining the TM x 
and y positions for some data I have.  Topas is still seeing them as 3a and 
3b positions, so internally they are still 1/9, 5/9 etc, as they started 
out.  In any case it doesn't make a massive difference.  
The problems I refer to in some software are not subtle, they're huge, 
and seem to reflect a problem in hkl-related 
multiplicities.
 
Pam  
 
Dr Pamela Whitfield CChem MRSCEnergy Materials 
GroupInstitute for Chemical Process and Environmental TechnologyBuilding 
M12National Research Council Canada1200 Montreal 
RoadOttawa ON K1A 0R6CANADATel: (613) 998 8462 Fax: (613) 991 2384Email: <>ICPET 
WWW:  

  -Original Message-From: alan coelho 
  [mailto:[EMAIL PROTECTED]Sent: October 18, 2004 5:36 
  PMTo: [EMAIL PROTECTED]Subject: RE: troublesome unit 
  cell
  Pam,
   
  I 
  looked at your INP file and there was a problem in regards to how atomic 
  coordinates were defined. As you know TOPAS uses computer algebra with a 
  tollerance of 1.0e-15 for checking the equivalence of equivalent positions. If 
  I use
   
  x = 
  1/9; y = 5/9;  etc,,,
   
  then 
  the structures are similar.
   
  It 
  is not often obvious these equations but it is easy to check using the number 
  of equivalent positions or by inspecting the bond lengths.
   
  My 
  guess is that the other programs may have conventions that are also not 
  obvious.
   
  it 
  is always good to do some checking
  cheers
  alan
   
   
  

-Original Message-From: Whitfield, 
Pamela [mailto:[EMAIL PROTECTED] Sent: Monday, 
October 18, 2004 10:32 PMTo: 
'[EMAIL PROTECTED]'Subject: RE: troublesome unit 
cell
AlanI'm afraid that the cif files weren't overly 
good ones - I don't normally use them.  For the R-3m the Li 1/2 
fractional coordinate is for the z, not y.  The structures are related 
by a Ö3a x Ö3a 
relationship with Z = 3 for the R-3m and Z = 9 for the P3112.Here are 
the STR files.  You can refine the 3a and 3b positions for the P3112, 
but there is a strict relationship that has to be maintained between the x 
and y coordinates - I have to do it in launch mode to make it work.  
It's a very picky space group to work with.PamDr 
Pamela Whitfield CChem MRSCEnergy Materials GroupInstitute for 
Chemical Process and Environmental TechnologyBuilding M12National 
Research Council Canada1200 Montreal RoadOttawa  ON   
K1A 0R6CANADATel: (613) 998 
8462 Fax: (613) 991 
2384Email: ICPET 
WWW: http://icpet-itpce.nrc-cnrc.gc.ca-Original 
Message-From: alan coelho [mailto:[EMAIL PROTECTED]]Sent: 
October 18, 2004 4:16 PMTo: [EMAIL PROTECTED]Subject: RE: 
troublesome unit cellPam,As a developer and someone who 
uses other software to test against, Ihave been following the discussion 
with interest. This is a complex areaand it goes to show the importance 
of having a few programs if only fortesting purposes.I am 
puzzled by your cif data however as I cant get past verifying 
theequivalence of the number of equivalent positions for the Li 
site.In R-3m you have as fractional atomic coordinates for 
Li1:  x = 0    y = 0.5  and  z = 
0For P3112 you have three Li sites with x, y, z's as0.77780 
0.0 0.833300.0 0.88890 0.833300.0 0.55560 
0.83330which translates to:0.77780 0.0 5/60.0 
0.88890 5/60.0 0.55560 5/6Listed below are equivalent 
positions for a general site.What I dont understand is that for R-3m 
I get 9 non-overlapping fullyoccupied equivalent positions within the 
unit cell with a volume of101.2975.For P3112 I get 18 
non-overlapping equivalent positions with a volumethree times as large 
of 303.8968. I was expecting to get 27 if the twostructure were to be 
equivalent.Thus, from your cif data I am left to conclude that I am 
generating thewrong number of equivalent positions, or, if I am 
generating the correctnumber of equivalent positions then the two cif 
data sets should indeedgive different powder patterns.Have you 
checked what the number of non-overlapping fully occupiedequivalent 
positions for Li should be for the two 
structures.alanP3112xyzs{    
-x+y, -x, z-1/3    -x+y, y, 
-z+1/3    -y, -x, 
-z-1/3    -y, x-y, 
z+1/3    x, y, 
z    x, x-y, -z} 
6R-3mxyzs{    
-x, -x+y, -z    -x, -y, 
-z    -x+y, -x, 
z    -x+y, y, 
z    -y, -x, 
z    -y, x-y, 
z    y, -x+y, 
-z    y, x, 
-z    x-y, -y, 
-z    x-y, x, 
-z    x, y, 
z    x, x-y, 
z    ' +(-1/3, 1/3, 1/3) 
-    
-x-1

RE: troublesome unit cell

2004-10-18 Thread alan coelho 
Bob and Pam,

Hope others on the list dont consider this topic as spam but the
checking across programs are a critical part of developent.

and a thanks by myself to the both of them for hand checking the
equivalent poistions - no wonder Bob made a goof.
regards
alan



-Original Message-
From: Von Dreele, Robert B. [mailto:[EMAIL PROTECTED] 
Sent: Monday, October 18, 2004 10:39 PM
To: [EMAIL PROTECTED]


Alan,
One of your operators is a typo.
"-x+y, y, -z+1/3" should be " Y-X Y  1/3-Z"
Bob




From: alan coelho [mailto:[EMAIL PROTECTED]
Sent: Mon 10/18/2004 3:16 PM
To: [EMAIL PROTECTED]



Pam,

As a developer and someone who uses other software to test against, I
have been following the discussion with interest. This is a complex area
and it goes to show the importance of having a few programs if only for
testing purposes.

I am puzzled by your cif data however as I cant get past verifying the
equivalence of the number of equivalent positions for the Li site.

In R-3m you have as fractional atomic coordinates for Li1:

  x = 0y = 0.5  and  z = 0

For P3112 you have three Li sites with x, y, z's as

0.77780 0.0 0.83330
0.0 0.88890 0.83330
0.0 0.55560 0.83330

which translates to:

0.77780 0.0 5/6
0.0 0.88890 5/6
0.0 0.55560 5/6

Listed below are equivalent positions for a general site.

What I dont understand is that for R-3m I get 9 non-overlapping fully
occupied equivalent positions within the unit cell with a volume of
101.2975.

For P3112 I get 18 non-overlapping equivalent positions with a volume
three times as large of 303.8968. I was expecting to get 27 if the two
structure were to be equivalent.

Thus, from your cif data I am left to conclude that I am generating the
wrong number of equivalent positions, or, if I am generating the correct
number of equivalent positions then the two cif data sets should indeed
give different powder patterns.

Have you checked what the number of non-overlapping fully occupied
equivalent positions for Li should be for the two structures.

alan





P3112
xyzs
{
-x+y, -x, z-1/3
-x+y, y, -z+1/3
-y, -x, -z-1/3
-y, x-y, z+1/3
x, y, z
x, x-y, -z
} 6


R-3m
xyzs
{
-x, -x+y, -z
-x, -y, -z
-x+y, -x, z
-x+y, y, z
-y, -x, z
-y, x-y, z
y, -x+y, -z
y, x, -z
x-y, -y, -z
x-y, x, -z
x, y, z
x, x-y, z
' +(-1/3, 1/3, 1/3) -
-x-1/3, -x+y+1/3, -z+1/3
-x-1/3, -y+1/3, -z+1/3
-x+y-1/3, -x+1/3, z+1/3
-x+y-1/3, y+1/3, z+1/3
-y-1/3, -x+1/3, z+1/3
-y-1/3, x-y+1/3, z+1/3
y-1/3, -x+y+1/3, -z+1/3
y-1/3, x+1/3, -z+1/3
x-y-1/3, -y+1/3, -z+1/3
x-y-1/3, x+1/3, -z+1/3
x-1/3, y+1/3, z+1/3
x-1/3, x-y+1/3, z+1/3
' +(1/3, -1/3, -1/3) -
-x+1/3, -x+y-1/3, -z-1/3
-x+1/3, -y-1/3, -z-1/3
-x+y+1/3, -x-1/3, z-1/3
-x+y+1/3, y-1/3, z-1/3
-y+1/3, -x-1/3, z-1/3
-y+1/3, x-y-1/3, z-1/3
y+1/3, -x+y-1/3, -z-1/3
y+1/3, x-1/3, -z-1/3
x-y+1/3, -y-1/3, -z-1/3
x-y+1/3, x-1/3, -z-1/3
x+1/3, y-1/3, z-1/3
x+1/3, x-y-1/3, z-1/3
} 36



/* Fractional atomic coordinates for for R-3m
Li1
 0.0  0.5  0.0
 0.5  0.0  0.0
 0.5  0.5  0.0
 0.7  0.8  0.3
 0.16667  0.3  0.3
 0.16667  0.8  0.3
 0.3  0.16667  0.7
 0.8  0.7  0.7
 0.8  0.16667  0.7
*/


/* Fractional atomic coordinates for P3112
Li
 0.0  0.0  0.5
 0.77780  0.0  0.8
 0.77780  0.55560  0.16667
Li
 0.77780  0.88890  0.5
 0.0  0.88890  0.8
 0.0  0.0  0.16667
Li
 0.11120  0.55560  0.5
 0.0  0.55560  0.8
 0.0  0.0  0.16667
*/

RE: troublesome unit cell

2004-10-18 Thread alan coelho 
Title: Message



Pam,
 
I 
looked at your INP file and there was a problem in regards to how atomic 
coordinates were defined. As you know TOPAS uses computer algebra with a 
tollerance of 1.0e-15 for checking the equivalence of equivalent positions. If I 
use
 
x = 
1/9; y = 5/9;  etc,,,
 
then 
the structures are similar.
 
It is 
not often obvious these equations but it is easy to check using the number of 
equivalent positions or by inspecting the bond lengths.
 
My 
guess is that the other programs may have conventions that are also not 
obvious.
 
it is 
always good to do some checking
cheers
alan
 
 

  
  -Original Message-From: Whitfield, 
  Pamela [mailto:[EMAIL PROTECTED] Sent: Monday, 
  October 18, 2004 10:32 PMTo: '[EMAIL PROTECTED]'Subject: 
  RE: troublesome unit cell
  AlanI'm afraid that the cif files weren't overly good 
  ones - I don't normally use them.  For the R-3m the Li 1/2 fractional 
  coordinate is for the z, not y.  The structures are related by a Ö3a x Ö3a relationship with Z = 3 
  for the R-3m and Z = 9 for the P3112.Here are the STR files.  You can 
  refine the 3a and 3b positions for the P3112, but there is a strict 
  relationship that has to be maintained between the x and y coordinates - I 
  have to do it in launch mode to make it work.  It's a very picky space 
  group to work with.PamDr Pamela Whitfield CChem 
  MRSCEnergy Materials GroupInstitute for Chemical Process and 
  Environmental TechnologyBuilding M12National Research Council 
  Canada1200 Montreal RoadOttawa  ON   K1A 
  0R6CANADATel: (613) 998 
  8462 Fax: (613) 991 
  2384Email: ICPET 
  WWW: http://icpet-itpce.nrc-cnrc.gc.ca-Original 
  Message-From: alan coelho [mailto:[EMAIL PROTECTED]]Sent: 
  October 18, 2004 4:16 PMTo: [EMAIL PROTECTED]Subject: RE: troublesome 
  unit cellPam,As a developer and someone who uses other 
  software to test against, Ihave been following the discussion with 
  interest. This is a complex areaand it goes to show the importance of 
  having a few programs if only fortesting purposes.I am puzzled by 
  your cif data however as I cant get past verifying theequivalence of the 
  number of equivalent positions for the Li site.In R-3m you have as 
  fractional atomic coordinates for Li1:  x = 0    y 
  = 0.5  and  z = 0For P3112 you have three Li sites with x, 
  y, z's as0.77780 0.0 0.833300.0 0.88890 0.833300.0 
  0.55560 0.83330which translates to:0.77780 0.0 
  5/60.0 0.88890 5/60.0 0.55560 5/6Listed below are 
  equivalent positions for a general site.What I dont understand is that 
  for R-3m I get 9 non-overlapping fullyoccupied equivalent positions within 
  the unit cell with a volume of101.2975.For P3112 I get 18 
  non-overlapping equivalent positions with a volumethree times as large of 
  303.8968. I was expecting to get 27 if the twostructure were to be 
  equivalent.Thus, from your cif data I am left to conclude that I am 
  generating thewrong number of equivalent positions, or, if I am generating 
  the correctnumber of equivalent positions then the two cif data sets 
  should indeedgive different powder patterns.Have you checked what 
  the number of non-overlapping fully occupiedequivalent positions for Li 
  should be for the two 
  structures.alanP3112xyzs{    
  -x+y, -x, z-1/3    -x+y, y, 
  -z+1/3    -y, -x, 
  -z-1/3    -y, x-y, 
  z+1/3    x, y, 
  z    x, x-y, -z} 
  6R-3mxyzs{    
  -x, -x+y, -z    -x, -y, 
  -z    -x+y, -x, 
  z    -x+y, y, 
  z    -y, -x, 
  z    -y, x-y, 
  z    y, -x+y, 
  -z    y, x, 
  -z    x-y, -y, 
  -z    x-y, x, 
  -z    x, y, 
  z    x, x-y, 
  z    ' +(-1/3, 1/3, 1/3) 
  -    
  -x-1/3, -x+y+1/3, -z+1/3    -x-1/3, 
  -y+1/3, -z+1/3    -x+y-1/3, -x+1/3, 
  z+1/3    -x+y-1/3, y+1/3, 
  z+1/3    -y-1/3, -x+1/3, 
  z+1/3    -y-1/3, x-y+1/3, 
  z+1/3    y-1/3, -x+y+1/3, 
  -z+1/3    y-1/3, x+1/3, 
  -z+1/3    x-y-1/3, -y+1/3, 
  -z+1/3    x-y-1/3, x+1/3, 
  -z+1/3    x-1/3, y+1/3, 
  z+1/3    x-1/3, x-y+1/3, 
  z+1/3    ' +(1/3, -1/3, -1/3) 
  -    
  -x+1/3, -x+y-1/3, -z-1/3    -x+1/3, 
  -y-1/3, -z-1/3    -x+y+1/3, -x-1/3, 
  z-1/3    -x+y+1/3, y-1/3, 
  z-1/3    -y+1/3, -x-1/3, 
  z-1/3    -y+1/3, x-y-1/3, 
  z-1/3    y+1/3, -x+y-1/3, 
  -z-1/3    y+1/3, x-1/3, 
  -z-1/3    x-y+1/3, -y-1/3, 
  -z-1/3    x-y+1/3, x-1/3, 
  -z-1/3    x+1/3, y-1/3, 
  z-1/3    x+1/3, x-y-1/3, z-1/3} 
  36/* Fractional atomic coordinates for for 
  R-3mLi1 0.0  
  0.5  0.0 
  0.5  0.0  
  0.0 0.5  
  0.5  0.0 
  0.7  0.8  
  0.3 0.16667  
  0.3  0.3 
  0.16667  0.8  
  0.3 0.3  
  0.16667  0.7 
  0.8  0.7 

RE: troublesome unit cell

2004-10-18 Thread Von Dreele, Robert B. 
Pam,
Actually you're right! WRT that operator - they are the same. My goof.
Bob



From: Whitfield, Pamela [mailto:[EMAIL PROTECTED]
Sent: Mon 10/18/2004 3:50 PM
To: '[EMAIL PROTECTED]'



Bob

I worked through all of the various operators used in the programs I have
(including Topas) and they are equivalent in each case.  Topas works for
this one just as well as GSAS.

Pam

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Von Dreele, Robert B. [mailto:[EMAIL PROTECTED]
Sent: October 18, 2004 4:39 PM
To: [EMAIL PROTECTED]


Alan,
One of your operators is a typo.
"-x+y, y, -z+1/3" should be " Y-X Y  1/3-Z"
Bob




From: alan coelho [mailto:[EMAIL PROTECTED]
Sent: Mon 10/18/2004 3:16 PM
To: [EMAIL PROTECTED]



Pam,

As a developer and someone who uses other software to test against, I
have been following the discussion with interest. This is a complex area
and it goes to show the importance of having a few programs if only for
testing purposes.

I am puzzled by your cif data however as I cant get past verifying the
equivalence of the number of equivalent positions for the Li site.

In R-3m you have as fractional atomic coordinates for Li1:

  x = 0y = 0.5  and  z = 0

For P3112 you have three Li sites with x, y, z's as

0.77780 0.0 0.83330
0.0 0.88890 0.83330
0.0 0.55560 0.83330

which translates to:

0.77780 0.0 5/6
0.0 0.88890 5/6
0.0 0.55560 5/6

Listed below are equivalent positions for a general site.

What I dont understand is that for R-3m I get 9 non-overlapping fully
occupied equivalent positions within the unit cell with a volume of
101.2975.

For P3112 I get 18 non-overlapping equivalent positions with a volume
three times as large of 303.8968. I was expecting to get 27 if the two
structure were to be equivalent.

Thus, from your cif data I am left to conclude that I am generating the
wrong number of equivalent positions, or, if I am generating the correct
number of equivalent positions then the two cif data sets should indeed
give different powder patterns.

Have you checked what the number of non-overlapping fully occupied
equivalent positions for Li should be for the two structures.

alan





P3112
xyzs
{
-x+y, -x, z-1/3
-x+y, y, -z+1/3
-y, -x, -z-1/3
-y, x-y, z+1/3
x, y, z
x, x-y, -z
} 6


R-3m
xyzs
{
-x, -x+y, -z
-x, -y, -z
-x+y, -x, z
-x+y, y, z
-y, -x, z
-y, x-y, z
y, -x+y, -z
y, x, -z
x-y, -y, -z
x-y, x, -z
x, y, z
x, x-y, z
' +(-1/3, 1/3, 1/3) -
-x-1/3, -x+y+1/3, -z+1/3
-x-1/3, -y+1/3, -z+1/3
-x+y-1/3, -x+1/3, z+1/3
-x+y-1/3, y+1/3, z+1/3
-y-1/3, -x+1/3, z+1/3
-y-1/3, x-y+1/3, z+1/3
y-1/3, -x+y+1/3, -z+1/3
y-1/3, x+1/3, -z+1/3
x-y-1/3, -y+1/3, -z+1/3
x-y-1/3, x+1/3, -z+1/3
x-1/3, y+1/3, z+1/3
x-1/3, x-y+1/3, z+1/3
' +(1/3, -1/3, -1/3) -
-x+1/3, -x+y-1/3, -z-1/3
-x+1/3, -y-1/3, -z-1/3
-x+y+1/3, -x-1/3, z-1/3
-x+y+1/3, y-1/3, z-1/3
-y+1/3, -x-1/3, z-1/3
-y+1/3, x-y-1/3, z-1/3
y+1/3, -x+y-1/3, -z-1/3
y+1/3, x-1/3, -z-1/3
x-y+1/3, -y-1/3, -z-1/3
x-y+1/3, x-1/3, -z-1/3
x+1/3, y-1/3, z-1/3
x+1/3, x-y-1/3, z-1/3
} 36



/* Fractional atomic coordinates for for R-3m
Li1
 0.0  0.5  0.0
 0.5  0.0  0.0
 0.5  0.5  0.0
 0.7  0.8  0.3
 0.16667  0.3  0.3
 0.16667  0.8  0.3
 0.3  0.16667  0.7
 0.8  0.7  0.7
 0.8  0.16667  0.7
*/


/* Fractional atomic coordinates for P3112
Li
 0.0  0.0  0.5
 0.77780  0.0  0.8
 0.77780  0.55560  0.16667
Li
 0.77780  0.88890  0.5
 0.0  0.88890  0.8
 0.0  0.0  0.16667
Li
 0.11120  0.55560  0.5
 0.0  0.55560  0.8
 0.0  0.0  0.16667
*/

RE: troublesome unit cell

2004-10-18 Thread Whitfield, Pamela 
Bob

I worked through all of the various operators used in the programs I have
(including Topas) and they are equivalent in each case.  Topas works for
this one just as well as GSAS.

Pam

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Von Dreele, Robert B. [mailto:[EMAIL PROTECTED]
Sent: October 18, 2004 4:39 PM
To: [EMAIL PROTECTED]


Alan,
One of your operators is a typo.
"-x+y, y, -z+1/3" should be " Y-X Y  1/3-Z"
Bob




From: alan coelho [mailto:[EMAIL PROTECTED]
Sent: Mon 10/18/2004 3:16 PM
To: [EMAIL PROTECTED]



Pam,

As a developer and someone who uses other software to test against, I
have been following the discussion with interest. This is a complex area
and it goes to show the importance of having a few programs if only for
testing purposes.

I am puzzled by your cif data however as I cant get past verifying the
equivalence of the number of equivalent positions for the Li site.

In R-3m you have as fractional atomic coordinates for Li1:

  x = 0y = 0.5  and  z = 0

For P3112 you have three Li sites with x, y, z's as

0.77780 0.0 0.83330
0.0 0.88890 0.83330
0.0 0.55560 0.83330

which translates to:

0.77780 0.0 5/6
0.0 0.88890 5/6
0.0 0.55560 5/6

Listed below are equivalent positions for a general site.

What I dont understand is that for R-3m I get 9 non-overlapping fully
occupied equivalent positions within the unit cell with a volume of
101.2975.

For P3112 I get 18 non-overlapping equivalent positions with a volume
three times as large of 303.8968. I was expecting to get 27 if the two
structure were to be equivalent.

Thus, from your cif data I am left to conclude that I am generating the
wrong number of equivalent positions, or, if I am generating the correct
number of equivalent positions then the two cif data sets should indeed
give different powder patterns.

Have you checked what the number of non-overlapping fully occupied
equivalent positions for Li should be for the two structures.

alan





P3112
xyzs
{
-x+y, -x, z-1/3
-x+y, y, -z+1/3
-y, -x, -z-1/3
-y, x-y, z+1/3
x, y, z
x, x-y, -z
} 6


R-3m
xyzs
{
-x, -x+y, -z
-x, -y, -z
-x+y, -x, z
-x+y, y, z
-y, -x, z
-y, x-y, z
y, -x+y, -z
y, x, -z
x-y, -y, -z
x-y, x, -z
x, y, z
x, x-y, z
' +(-1/3, 1/3, 1/3) -
-x-1/3, -x+y+1/3, -z+1/3
-x-1/3, -y+1/3, -z+1/3
-x+y-1/3, -x+1/3, z+1/3
-x+y-1/3, y+1/3, z+1/3
-y-1/3, -x+1/3, z+1/3
-y-1/3, x-y+1/3, z+1/3
y-1/3, -x+y+1/3, -z+1/3
y-1/3, x+1/3, -z+1/3
x-y-1/3, -y+1/3, -z+1/3
x-y-1/3, x+1/3, -z+1/3
x-1/3, y+1/3, z+1/3
x-1/3, x-y+1/3, z+1/3
' +(1/3, -1/3, -1/3) -
-x+1/3, -x+y-1/3, -z-1/3
-x+1/3, -y-1/3, -z-1/3
-x+y+1/3, -x-1/3, z-1/3
-x+y+1/3, y-1/3, z-1/3
-y+1/3, -x-1/3, z-1/3
-y+1/3, x-y-1/3, z-1/3
y+1/3, -x+y-1/3, -z-1/3
y+1/3, x-1/3, -z-1/3
x-y+1/3, -y-1/3, -z-1/3
x-y+1/3, x-1/3, -z-1/3
x+1/3, y-1/3, z-1/3
x+1/3, x-y-1/3, z-1/3
} 36



/* Fractional atomic coordinates for for R-3m
Li1
 0.0  0.5  0.0
 0.5  0.0  0.0
 0.5  0.5  0.0
 0.7  0.8  0.3
 0.16667  0.3  0.3
 0.16667  0.8  0.3
 0.3  0.16667  0.7
 0.8  0.7  0.7
 0.8  0.16667  0.7
*/


/* Fractional atomic coordinates for P3112
Li
 0.0  0.0  0.5
 0.77780  0.0  0.8
 0.77780  0.55560  0.16667
Li
 0.77780  0.88890  0.5
 0.0  0.88890  0.8
 0.0  0.0  0.16667
Li
 0.11120  0.55560  0.5
 0.0  0.55560  0.8
 0.0  0.0  0.16667
*/

RE: troublesome unit cell

2004-10-18 Thread Von Dreele, Robert B. 
Alan,
One of your operators is a typo.
"-x+y, y, -z+1/3" should be " Y-X Y  1/3-Z"
Bob




From: alan coelho [mailto:[EMAIL PROTECTED]
Sent: Mon 10/18/2004 3:16 PM
To: [EMAIL PROTECTED]



Pam,

As a developer and someone who uses other software to test against, I
have been following the discussion with interest. This is a complex area
and it goes to show the importance of having a few programs if only for
testing purposes.

I am puzzled by your cif data however as I cant get past verifying the
equivalence of the number of equivalent positions for the Li site.

In R-3m you have as fractional atomic coordinates for Li1:

  x = 0y = 0.5  and  z = 0

For P3112 you have three Li sites with x, y, z's as

0.77780 0.0 0.83330
0.0 0.88890 0.83330
0.0 0.55560 0.83330

which translates to:

0.77780 0.0 5/6
0.0 0.88890 5/6
0.0 0.55560 5/6

Listed below are equivalent positions for a general site.

What I dont understand is that for R-3m I get 9 non-overlapping fully
occupied equivalent positions within the unit cell with a volume of
101.2975.

For P3112 I get 18 non-overlapping equivalent positions with a volume
three times as large of 303.8968. I was expecting to get 27 if the two
structure were to be equivalent.

Thus, from your cif data I am left to conclude that I am generating the
wrong number of equivalent positions, or, if I am generating the correct
number of equivalent positions then the two cif data sets should indeed
give different powder patterns.

Have you checked what the number of non-overlapping fully occupied
equivalent positions for Li should be for the two structures.

alan





P3112
xyzs
{
-x+y, -x, z-1/3
-x+y, y, -z+1/3
-y, -x, -z-1/3
-y, x-y, z+1/3
x, y, z
x, x-y, -z
} 6


R-3m
xyzs
{
-x, -x+y, -z
-x, -y, -z
-x+y, -x, z
-x+y, y, z
-y, -x, z
-y, x-y, z
y, -x+y, -z
y, x, -z
x-y, -y, -z
x-y, x, -z
x, y, z
x, x-y, z
' +(-1/3, 1/3, 1/3) -
-x-1/3, -x+y+1/3, -z+1/3
-x-1/3, -y+1/3, -z+1/3
-x+y-1/3, -x+1/3, z+1/3
-x+y-1/3, y+1/3, z+1/3
-y-1/3, -x+1/3, z+1/3
-y-1/3, x-y+1/3, z+1/3
y-1/3, -x+y+1/3, -z+1/3
y-1/3, x+1/3, -z+1/3
x-y-1/3, -y+1/3, -z+1/3
x-y-1/3, x+1/3, -z+1/3
x-1/3, y+1/3, z+1/3
x-1/3, x-y+1/3, z+1/3
' +(1/3, -1/3, -1/3) -
-x+1/3, -x+y-1/3, -z-1/3
-x+1/3, -y-1/3, -z-1/3
-x+y+1/3, -x-1/3, z-1/3
-x+y+1/3, y-1/3, z-1/3
-y+1/3, -x-1/3, z-1/3
-y+1/3, x-y-1/3, z-1/3
y+1/3, -x+y-1/3, -z-1/3
y+1/3, x-1/3, -z-1/3
x-y+1/3, -y-1/3, -z-1/3
x-y+1/3, x-1/3, -z-1/3
x+1/3, y-1/3, z-1/3
x+1/3, x-y-1/3, z-1/3
} 36



/* Fractional atomic coordinates for for R-3m
Li1
 0.0  0.5  0.0
 0.5  0.0  0.0
 0.5  0.5  0.0
 0.7  0.8  0.3
 0.16667  0.3  0.3
 0.16667  0.8  0.3
 0.3  0.16667  0.7
 0.8  0.7  0.7
 0.8  0.16667  0.7
*/


/* Fractional atomic coordinates for P3112
Li
 0.0  0.0  0.5
 0.77780  0.0  0.8
 0.77780  0.55560  0.16667
Li
 0.77780  0.88890  0.5
 0.0  0.88890  0.8
 0.0  0.0  0.16667
Li
 0.11120  0.55560  0.5
 0.0  0.55560  0.8
 0.0  0.0  0.16667
*/

RE: troublesome unit cell

2004-10-18 Thread Whitfield, Pamela 



AlanI'm afraid that the cif files weren't overly good 
ones - I don't normally use them.  For the R-3m the Li 1/2 fractional 
coordinate is for the z, not y.  The structures are related by a Ö3a x Ö3a relationship with Z = 3 
for the R-3m and Z = 9 for the P3112.Here are the STR files.  You can 
refine the 3a and 3b positions for the P3112, but there is a strict relationship 
that has to be maintained between the x and y coordinates - I have to do it in 
launch mode to make it work.  It's a very picky space group to work 
with.PamDr Pamela Whitfield CChem MRSCEnergy 
Materials GroupInstitute for Chemical Process and Environmental 
TechnologyBuilding M12National Research Council Canada1200 Montreal 
RoadOttawa  ON   K1A 0R6CANADATel: (613) 998 
8462 Fax: (613) 991 
2384Email: ICPET 
WWW: http://icpet-itpce.nrc-cnrc.gc.ca-Original 
Message-From: alan coelho [mailto:[EMAIL PROTECTED]]Sent: 
October 18, 2004 4:16 PMTo: [EMAIL PROTECTED]Subject: RE: troublesome 
unit cellPam,As a developer and someone who uses other 
software to test against, Ihave been following the discussion with interest. 
This is a complex areaand it goes to show the importance of having a few 
programs if only fortesting purposes.I am puzzled by your cif data 
however as I cant get past verifying theequivalence of the number of 
equivalent positions for the Li site.In R-3m you have as fractional 
atomic coordinates for Li1:  x = 0    y = 0.5  
and  z = 0For P3112 you have three Li sites with x, y, z's 
as0.77780 0.0 0.833300.0 0.88890 0.833300.0 0.55560 
0.83330which translates to:0.77780 0.0 5/60.0 
0.88890 5/60.0 0.55560 5/6Listed below are equivalent positions 
for a general site.What I dont understand is that for R-3m I get 9 
non-overlapping fullyoccupied equivalent positions within the unit cell with 
a volume of101.2975.For P3112 I get 18 non-overlapping equivalent 
positions with a volumethree times as large of 303.8968. I was expecting to 
get 27 if the twostructure were to be equivalent.Thus, from your cif 
data I am left to conclude that I am generating thewrong number of 
equivalent positions, or, if I am generating the correctnumber of equivalent 
positions then the two cif data sets should indeedgive different powder 
patterns.Have you checked what the number of non-overlapping fully 
occupiedequivalent positions for Li should be for the two 
structures.alanP3112xyzs{    
-x+y, -x, z-1/3    -x+y, y, 
-z+1/3    -y, -x, 
-z-1/3    -y, x-y, 
z+1/3    x, y, 
z    x, x-y, -z} 
6R-3mxyzs{    -x, 
-x+y, -z    -x, -y, 
-z    -x+y, -x, 
z    -x+y, y, 
z    -y, -x, 
z    -y, x-y, 
z    y, -x+y, 
-z    y, x, 
-z    x-y, -y, 
-z    x-y, x, 
-z    x, y, 
z    x, x-y, 
z    ' +(-1/3, 1/3, 1/3) 
-    -x-1/3, 
-x+y+1/3, -z+1/3    -x-1/3, -y+1/3, 
-z+1/3    -x+y-1/3, -x+1/3, 
z+1/3    -x+y-1/3, y+1/3, 
z+1/3    -y-1/3, -x+1/3, 
z+1/3    -y-1/3, x-y+1/3, 
z+1/3    y-1/3, -x+y+1/3, 
-z+1/3    y-1/3, x+1/3, 
-z+1/3    x-y-1/3, -y+1/3, 
-z+1/3    x-y-1/3, x+1/3, 
-z+1/3    x-1/3, y+1/3, 
z+1/3    x-1/3, x-y+1/3, 
z+1/3    ' +(1/3, -1/3, -1/3) 
-    -x+1/3, 
-x+y-1/3, -z-1/3    -x+1/3, -y-1/3, 
-z-1/3    -x+y+1/3, -x-1/3, 
z-1/3    -x+y+1/3, y-1/3, 
z-1/3    -y+1/3, -x-1/3, 
z-1/3    -y+1/3, x-y-1/3, 
z-1/3    y+1/3, -x+y-1/3, 
-z-1/3    y+1/3, x-1/3, 
-z-1/3    x-y+1/3, -y-1/3, 
-z-1/3    x-y+1/3, x-1/3, 
-z-1/3    x+1/3, y-1/3, 
z-1/3    x+1/3, x-y-1/3, z-1/3} 
36/* Fractional atomic coordinates for for 
R-3mLi1 0.0  
0.5  0.0 
0.5  0.0  
0.0 0.5  
0.5  0.0 
0.7  0.8  
0.3 0.16667  
0.3  0.3 
0.16667  0.8  
0.3 0.3  
0.16667  0.7 
0.8  0.7  
0.7 0.8  
0.16667  0.7*//* Fractional atomic coordinates for 
P3112Li 0.0  
0.0  0.5 
0.77780  0.0  
0.8 0.77780  
0.55560  0.16667Li 
0.77780  0.88890  
0.5 0.0  
0.88890  0.8 
0.0  0.0  
0.16667Li 0.11120  
0.55560  0.5 
0.0  0.55560  
0.8 0.0  
0.0  0.16667*/


LiMnNiCoO2 R-3m.str
Description: Binary data


Li3MnCoNiO6.str
Description: Binary data

RE: troublesome unit cell

2004-10-18 Thread alan coelho 
Pam,

As a developer and someone who uses other software to test against, I
have been following the discussion with interest. This is a complex area
and it goes to show the importance of having a few programs if only for
testing purposes.

I am puzzled by your cif data however as I cant get past verifying the
equivalence of the number of equivalent positions for the Li site.

In R-3m you have as fractional atomic coordinates for Li1:

  x = 0y = 0.5  and  z = 0

For P3112 you have three Li sites with x, y, z's as

0.77780 0.0 0.83330 
0.0 0.88890 0.83330 
0.0 0.55560 0.83330 

which translates to:

0.77780 0.0 5/6
0.0 0.88890 5/6
0.0 0.55560 5/6

Listed below are equivalent positions for a general site.

What I dont understand is that for R-3m I get 9 non-overlapping fully
occupied equivalent positions within the unit cell with a volume of
101.2975.

For P3112 I get 18 non-overlapping equivalent positions with a volume
three times as large of 303.8968. I was expecting to get 27 if the two
structure were to be equivalent.

Thus, from your cif data I am left to conclude that I am generating the
wrong number of equivalent positions, or, if I am generating the correct
number of equivalent positions then the two cif data sets should indeed
give different powder patterns.

Have you checked what the number of non-overlapping fully occupied
equivalent positions for Li should be for the two structures.

alan





P3112
xyzs
{
-x+y, -x, z-1/3
-x+y, y, -z+1/3
-y, -x, -z-1/3
-y, x-y, z+1/3
x, y, z
x, x-y, -z
} 6


R-3m
xyzs
{
-x, -x+y, -z
-x, -y, -z
-x+y, -x, z
-x+y, y, z
-y, -x, z
-y, x-y, z
y, -x+y, -z
y, x, -z
x-y, -y, -z
x-y, x, -z
x, y, z
x, x-y, z
' +(-1/3, 1/3, 1/3) -
-x-1/3, -x+y+1/3, -z+1/3
-x-1/3, -y+1/3, -z+1/3
-x+y-1/3, -x+1/3, z+1/3
-x+y-1/3, y+1/3, z+1/3
-y-1/3, -x+1/3, z+1/3
-y-1/3, x-y+1/3, z+1/3
y-1/3, -x+y+1/3, -z+1/3
y-1/3, x+1/3, -z+1/3
x-y-1/3, -y+1/3, -z+1/3
x-y-1/3, x+1/3, -z+1/3
x-1/3, y+1/3, z+1/3
x-1/3, x-y+1/3, z+1/3
' +(1/3, -1/3, -1/3) -
-x+1/3, -x+y-1/3, -z-1/3
-x+1/3, -y-1/3, -z-1/3
-x+y+1/3, -x-1/3, z-1/3
-x+y+1/3, y-1/3, z-1/3
-y+1/3, -x-1/3, z-1/3
-y+1/3, x-y-1/3, z-1/3
y+1/3, -x+y-1/3, -z-1/3
y+1/3, x-1/3, -z-1/3
x-y+1/3, -y-1/3, -z-1/3
x-y+1/3, x-1/3, -z-1/3
x+1/3, y-1/3, z-1/3
x+1/3, x-y-1/3, z-1/3
} 36



/* Fractional atomic coordinates for for R-3m
Li1 
 0.0  0.5  0.0 
 0.5  0.0  0.0 
 0.5  0.5  0.0 
 0.7  0.8  0.3 
 0.16667  0.3  0.3 
 0.16667  0.8  0.3 
 0.3  0.16667  0.7 
 0.8  0.7  0.7 
 0.8  0.16667  0.7 
*/


/* Fractional atomic coordinates for P3112
Li 
 0.0  0.0  0.5 
 0.77780  0.0  0.8 
 0.77780  0.55560  0.16667 
Li 
 0.77780  0.88890  0.5 
 0.0  0.88890  0.8 
 0.0  0.0  0.16667 
Li 
 0.11120  0.55560  0.5 
 0.0  0.55560  0.8 
 0.0  0.0  0.16667 
*/

Re: troublesome unit cell

2004-10-18 Thread Whitfield, Pamela 
Bob
I did indeed - I tried GSAS and it behaves itself.
Pam

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Von Dreele, Robert B. [mailto:[EMAIL PROTECTED]
Sent: October 18, 2004 3:08 PM
To: [EMAIL PROTECTED]


Pam,
I hope that when you used GSAS you entered (as per instructions) "p 31 1
2" and not "p3112".
Bob

R.B. Von Dreele
IPNS Division
Argonne National Laboratory
Argonne, IL 60439-4814



-Original Message-
From: Whitfield, Pamela [mailto:[EMAIL PROTECTED] 
Sent: Monday, October 18, 2004 12:50 PM
To: '[EMAIL PROTECTED]'


Alan

I agree - I found them as well, but this particular P3112/P3212 group is
very rare.  Given that software tends to deal with space group
interpretation on a case-by-case basis it does mean that problems can be
specific to a particular group - especially if it hasn't been tested
before. Some software deals with it OK, others don't. You won't find the
Li material in the database, it's a recent postulated superstructure for
a layered battery material.

Pam

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology Building M12
National Research Council Canada 1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Hewat Alan [mailto:[EMAIL PROTECTED]
Sent: October 18, 2004 2:42 PM
To: [EMAIL PROTECTED]


> The cell is in space group P3112
> There aren't even any structures with this space group in the ICSD 
> (not even the other enantiomorph P3212)

Hmm, I found 24 entries in ICSD for P3122, especially minerals such as
Muscovite 3T but also things like V6C5 and Ag2HPO4 but not Li3MnNiCoO6

Cenzual, K.;Gelato, L.M.;Penzo, M.;Parthe, E.   Inorganic structure
types
with revised space groups.I. (1991) Acta Crystallographica B 47, 433-439
Tordjman, I.;Boudjada, A.;Guitel, J.C.;Masse, R.Structure de
l'Hydrogenophosphate D'Argent (1978) Acta Crystallographica B 34,
3723-3725

Alan.

Re: troublesome unit cell

2004-10-18 Thread Von Dreele, Robert B. 
Pam,
I hope that when you used GSAS you entered (as per instructions) "p 31 1
2" and not "p3112".
Bob

R.B. Von Dreele
IPNS Division
Argonne National Laboratory
Argonne, IL 60439-4814



-Original Message-
From: Whitfield, Pamela [mailto:[EMAIL PROTECTED] 
Sent: Monday, October 18, 2004 12:50 PM
To: '[EMAIL PROTECTED]'


Alan

I agree - I found them as well, but this particular P3112/P3212 group is
very rare.  Given that software tends to deal with space group
interpretation on a case-by-case basis it does mean that problems can be
specific to a particular group - especially if it hasn't been tested
before. Some software deals with it OK, others don't. You won't find the
Li material in the database, it's a recent postulated superstructure for
a layered battery material.

Pam

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology Building M12
National Research Council Canada 1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Hewat Alan [mailto:[EMAIL PROTECTED]
Sent: October 18, 2004 2:42 PM
To: [EMAIL PROTECTED]


> The cell is in space group P3112
> There aren't even any structures with this space group in the ICSD 
> (not even the other enantiomorph P3212)

Hmm, I found 24 entries in ICSD for P3122, especially minerals such as
Muscovite 3T but also things like V6C5 and Ag2HPO4 but not Li3MnNiCoO6

Cenzual, K.;Gelato, L.M.;Penzo, M.;Parthe, E.   Inorganic structure
types
with revised space groups.I. (1991) Acta Crystallographica B 47, 433-439
Tordjman, I.;Boudjada, A.;Guitel, J.C.;Masse, R.Structure de
l'Hydrogenophosphate D'Argent (1978) Acta Crystallographica B 34,
3723-3725

Alan.

Re: troublesome unit cell

2004-10-18 Thread Whitfield, Pamela 
Alan

I agree - I found them as well, but this particular P3112/P3212 group is
very rare.  Given that software tends to deal with space group
interpretation on a case-by-case basis it does mean that problems can be
specific to a particular group - especially if it hasn't been tested before.
Some software deals with it OK, others don't.
You won't find the Li material in the database, it's a recent postulated
superstructure for a layered battery material.

Pam

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Hewat Alan [mailto:[EMAIL PROTECTED]
Sent: October 18, 2004 2:42 PM
To: [EMAIL PROTECTED]


> The cell is in space group P3112
> There aren't even any structures with this space group in the ICSD
> (not even the other enantiomorph P3212)

Hmm, I found 24 entries in ICSD for P3122, especially minerals such as
Muscovite 3T but also things like V6C5 and Ag2HPO4 but not Li3MnNiCoO6

Cenzual, K.;Gelato, L.M.;Penzo, M.;Parthe, E.   Inorganic structure types
with revised space groups.I. (1991) Acta Crystallographica B 47, 433-439
Tordjman, I.;Boudjada, A.;Guitel, J.C.;Masse, R.Structure de
l'Hydrogenophosphate D'Argent (1978) Acta Crystallographica B 34,
3723-3725

Alan.

Re: troublesome unit cell

2004-10-18 Thread Hewat Alan 
> The cell is in space group P3112
> There aren't even any structures with this space group in the ICSD
> (not even the other enantiomorph P3212)

Hmm, I found 24 entries in ICSD for P3122, especially minerals such as
Muscovite 3T but also things like V6C5 and Ag2HPO4 but not Li3MnNiCoO6

Cenzual, K.;Gelato, L.M.;Penzo, M.;Parthe, E.   Inorganic structure types
with revised space groups.I. (1991) Acta Crystallographica B 47, 433-439
Tordjman, I.;Boudjada, A.;Guitel, J.C.;Masse, R.Structure de
l'Hydrogenophosphate D'Argent (1978) Acta Crystallographica B 34,
3723-3725

Alan.

RE: troublesome unit cell

2004-10-18 Thread Whitfield, Pamela 

> - The matrices representing the space-group operators are no longer
> diagonal, and the distinction between R*h and h*R (where R is the
> rotation matrix and h is the reciprocal space vector [h,k,l]) becomes
> important when calculating systematic absences.
This does make sense.  Many of the programs draw the structure properly so
get the symmetry elements right - the trouble is elsewhere.


>And as a third possible source of error, I have noticed that trigonal 
>space groups lead to a rounding error in the translational part that is 
>different from other space groups. Which would make sense if e.g. the 
>program internally defines the translational components of the symmetry 
>operators as 0. instead of 1.0/3.0 (not: 1/3).

This would also crop up in quartz, where the Si z coordinate is 2/3.  If you
shift it the multiplicity goes from 3 to 6.

Pam

Re: troublesome unit cell

2004-10-18 Thread Jacco van de Streek 
Whitfield, Pamela wrote:
The problem also occurred in a program that would take fractional 
coordinates, so that's not the only snag.
I suggested another one:
From: Jacco van de Streek
- The matrices representing the space-group operators are no longer
diagonal, and the distinction between R*h and h*R (where R is the
rotation matrix and h is the reciprocal space vector [h,k,l]) becomes
important when calculating systematic absences.
And as a third possible source of error, I have noticed that trigonal 
space groups lead to a rounding error in the translational part that is 
different from other space groups. Which would make sense if e.g. the 
program internally defines the translational components of the symmetry 
operators as 0. instead of 1.0/3.0 (not: 1/3).

Enough scope for errors. But I'm quite confident I finally got it right 
in Mercury 1.3, and Mercury is free.

Best wishes,
--
Jacco van de Streek
Research Scientist
Cambridge Crystallographic Data Centre
Cambridge, United Kingdom

Re: troublesome unit cell

2004-10-18 Thread Whitfield, Pamela 
Jacco

I didn't actually use these cif files for my simulations, I entered the data
by hand (including fractions where the software would take it).  :-)

The cif data is just there for other people's convenience - different powder
software like different cif file formats anyhow.  In any case, if there is a
significant rounding error in the software, the TM 3a and 3b sites change to
6c.  This space group is very finicky about the positions.  The problem also
occurred in a program that would take fractional coordinates, so that's not
the only snag.

Pam

Dr Pamela Whitfield CChem MRSC
Energy Materials Group
Institute for Chemical Process and Environmental Technology
Building M12
National Research Council Canada
1200 Montreal Road
Ottawa  ON   K1A 0R6
CANADA
Tel: (613) 998 8462 Fax: (613) 991 2384
Email: 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca


-Original Message-
From: Jacco van de Streek [mailto:[EMAIL PROTECTED]
Sent: October 18, 2004 1:32 PM
To: [EMAIL PROTECTED]


Whitfield, Pamela wrote:
> I've come across a unit cell that seems to give alot of software a 
> headache when generating the powder patterns.  I've tested 6 software 
> packages with this (including commercial) and found only a 50% success 
> rate in generating a good pattern with correct relative intensities.  
> Not sure where the problem lies with the 'faulty' software, maybe some 
> of the hkl multiplicities are off.

These two structures (the file needs data_* inserted twice to generate a 
valid cif file, I believe) are in a trigonal or hexagonal space group, 
which has the following consequences:

- There are problems with rounding errors when determining if two atoms 
overlap. Atoms in triclinic through tetragonal space groups do not have 
atoms on special positions with 0.333, but only special positions of the 
type 0.0, 0.25, 0.5 etc. These can be represented exactly in a text 
file, whereas 1/3 cannot. In the first crystal structure, they have even 
been truncated to 0.333, which gives errors of about 0.0003. Most 
computer programs will assume that floating point errors are < 0.1.
- The matrices representing the space-group operators are no longer 
diagonal, and the distinction between R*h and h*R (where R is the 
rotation matrix and h is the reciprocal space vector [h,k,l]) becomes 
important when calculating systematic absences.

The current version of Mercury, the free crystal structure visualiser 
from the CCDC, exhibited both bugs in version 1.2, Mercury 1.2.1 which 
was released several weeks after Mercury 1.2 still contains the first 
bug: because the program that I had used to test Mercury against had the 
same bug... Mercury 1.3, due to be released before the end of this year 
should get the powder diffraction patterns for both crystal structures 
right without any problems (they are the same with version 1.3).

The beta test of Mercury 1.3 is currently in progress. If you would like 
to participate in the beta test for Mercury 1.3, so that you can provide 
us with feedback for the simulated powder diffraction patterns of these 
and similar crystal structures before the final release, please contact 
mailto:[EMAIL PROTECTED]

Best wishes,
-- 
Jacco van de Streek
Research Scientist
Cambridge Crystallographic Data Centre
Cambridge, United Kingdom

Re: troublesome unit cell

2004-10-18 Thread Jacco van de Streek 
Whitfield, Pamela wrote:
I've come across a unit cell that seems to give alot of software a 
headache when generating the powder patterns.  I've tested 6 software 
packages with this (including commercial) and found only a 50% success 
rate in generating a good pattern with correct relative intensities.  
Not sure where the problem lies with the 'faulty' software, maybe some 
of the hkl multiplicities are off.
These two structures (the file needs data_* inserted twice to generate a 
valid cif file, I believe) are in a trigonal or hexagonal space group, 
which has the following consequences:

- There are problems with rounding errors when determining if two atoms 
overlap. Atoms in triclinic through tetragonal space groups do not have 
atoms on special positions with 0.333, but only special positions of the 
type 0.0, 0.25, 0.5 etc. These can be represented exactly in a text 
file, whereas 1/3 cannot. In the first crystal structure, they have even 
been truncated to 0.333, which gives errors of about 0.0003. Most 
computer programs will assume that floating point errors are < 0.1.
- The matrices representing the space-group operators are no longer 
diagonal, and the distinction between R*h and h*R (where R is the 
rotation matrix and h is the reciprocal space vector [h,k,l]) becomes 
important when calculating systematic absences.

The current version of Mercury, the free crystal structure visualiser 
from the CCDC, exhibited both bugs in version 1.2, Mercury 1.2.1 which 
was released several weeks after Mercury 1.2 still contains the first 
bug: because the program that I had used to test Mercury against had the 
same bug... Mercury 1.3, due to be released before the end of this year 
should get the powder diffraction patterns for both crystal structures 
right without any problems (they are the same with version 1.3).

The beta test of Mercury 1.3 is currently in progress. If you would like 
to participate in the beta test for Mercury 1.3, so that you can provide 
us with feedback for the simulated powder diffraction patterns of these 
and similar crystal structures before the final release, please contact 
mailto:[EMAIL PROTECTED]

Best wishes,
--
Jacco van de Streek
Research Scientist
Cambridge Crystallographic Data Centre
Cambridge, United Kingdom

troublesome unit cell

2004-10-18 Thread Whitfield, Pamela 



Hiya 
all
 
I've come across a 
unit cell that seems to give alot of software a headache when generating the 
powder patterns.  I've tested 6 software packages with this (including 
commercial) and found only a 50% success rate in generating a good pattern with 
correct relative intensities.  Not sure where the problem lies with the 
'faulty' software, maybe some of the hkl multiplicities are off.  

 
The cell is in space 
group P3112 and is a Ö3a x Ö3a 
supercell of a nice boring simple R-3m layered structure.  It's quite a 
pretty structure and when the metals are similar in scattering power you'd 
expect a very similar diffraction pattern to the R-3m (identical if all of the 
TMs are the same).  Doesn't always happen though.  If you're curious 
try making these 2 cif files and seeing what your software churns 
out.There aren't even any structures with this space 
group in the ICSD (not even the other enantiomorph P3212), and only a few in the 
PDF2, so it's not exactly a fatal flaw.  Might make it worth checking 
some other trigonal space groups though if your software fails this one.  
BTW I am well aware that quartz has the P3221/P3121 chiral structures, and 
that any software worth its salt gets that one right!
 
Have fun!
 
Pam
 
 
 
 
_chemical_formula_sum 'Li3 Mn Ni Co O6'
_cell_length_a 2.8600
_cell_length_b 2.8600
_cell_length_c 14.3000
_cell_angle_alpha 90.000
_cell_angle_beta 90.000
_cell_angle_gamma 120.000
_symmetry_space_group_name_H-M 'R -3 m'
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_B_iso_or_equiv
Li1 Li 0. 0. 0.5000 1.000 1.0
Mn1 Mn 0. 0. 0. 0.333 1.0
Ni1 Ni 0. 0. 0. 0.333  1.0
Co1 Co 0. 0. 0. 0.333 1.0
O1 O 0. 0. 0.2560 1.000 1.0
 
 
_chemical_formula_sum 'O18 LI9 NI3 CO3 MN3'
_cell_length_a 4.9537
_cell_length_b 4.9537
_cell_length_c 14.3000
_cell_angle_alpha 90.00
_cell_angle_beta 90.00
_cell_angle_gamma 120.00
_symmetry_cell_setting Hexagonal
_symmetry_space_group_name_H-M 'P 31 1 2'
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_B_iso_or_equiv
Li Li 0.77780 0.0 0.83330 1 1
Li Li 0.0 0.88890 0.83330 1 1
Li Li 0.0 0.55560 0.83330 1 1
Ni Ni 0.77780 0.0 0.0 1 1
Co Co 0.0 0.88890 0.0 1 1
Mn Mn 0.0 0.55560 0.0 1 1
O O 0.0 0.0 0.25600 1 1
O O 0.0 0.0 -0.07730 1 1
O O 0.0 0.55560 0.25600 1 1
 
 
 
Dr Pamela Whitfield CChem MRSC Energy Materials Group Institute for Chemical Process and Environmental Technology 
Building M12 National Research Council Canada 1200 
Montreal Road Ottawa  ON   K1A 
0R6 CANADA Tel: (613) 998 8462 Fax: 
(613) 991 2384 Email: 
 
ICPET WWW: http://icpet-itpce.nrc-cnrc.gc.ca