RE: correlation matrix interpretation
As the matter of fact there is "print options" button in "LS control: tab.
Click the button and select what information you want to see in the listing
file.
Dr. Peter Y. Zavalij
Director, X-ray Crystallographic Center
Department of Chemistry and Biochemistry
091 Chemistry Building
University of Maryland
College Park, MD 20742-4454
Phone: (301)405-1861
Lab: (301)405-1861
Fax: (301)314-9121
E-mail: [EMAIL PROTECTED]
http://www.chem.umd.edu/facility/xray/
_
From: Santosh Babu [mailto:[EMAIL PROTECTED]
Sent: Tuesday, April 08, 2008 11:49 PM
Cc: rietveld_l@ill.fr
Subject: Re: correlation matrix interpretation
Dear all,
How to obtain correlation matrix (using GSAS)? Is there any option with
EXPGUI?
regards,
Santosh Babu
On Tue, Apr 8, 2008 at 8:33 PM, Brian H. Toby <[EMAIL PROTECTED]> wrote:
The sign of the numbers indicates correlation vs. anticorrelation. For
example, Uiso's correlate between atom 1 and 2 in phase "1 1 1UISO" & "1
2UISO" so that Uiso increasing on one atom has a similar impact as an
increase on the other. In the case of the reciprocal cell tensor (related to
cell parameters) an increase on one of the diagonal terms has a similar
effect as a decrease on the zero correction ("1 RM11" & "ZERO 1").
Brian
On Apr 8, 2008, at 8:55 AM, Leopoldo Suescun wrote:
Dear Gerard,
Here is how to read it:
The correlation matrix terms greater than 0.50 are
1 1UISO-1 2UISO 5011 3UISO 687 1HSCL 801
1 2UISO- 1HSCL 650
1 3UISO- 1HSCL 852
1 RM11-ZERO 1 -642
1 RM22-ZERO 1 -640
1 RM33-ZERO 1 -692
1ABS1- 1ABS2 1000
1 1PF 2-1 1PF 3 -727
v-cov distribution 0...1 by 0.05
430 125 77 347 107201102
3101101
1st column (8 characters wide): Variable 1, 2nd column: (also 8
characters wide) Variable 2, with "-" separating both columns, 3rd
column (6 characters wide) the correlation value multiplied by 1000.
Following collumns are show if more paramters have correlations greater
than 0.5 with the parameters in the first collumn. So in this case, 4th
collumn (8 characters wide with no separation from 3rd): Variable 2',
5th collumn (6 char wide): correlation between Var1 and Var2', etc for
var 2''...
So you can read the first column this way:
1 1UISO (Iso thermal param. for atom 1 in phase 1) shows a correlation
of 0.501 with 1 2UISO (iso param for atom 2 in phase 1) so thermal
parameters for atoms 1 and 2 inphase one have 50% correlation.
1 1UISO shows .687 corelation with 1 3UISO, or atom's 1 and 3 Uisos
are correlated 68.7%
1 1UISO is correlated with histogram scale factor by 80.1 %
ABS = absorption correction if my memory is good but you can check in
the GSAS manual that accompanies GSAS distribution. You have a problem
with the setup of the refinement because you have 2 absorption
corrections and both parameters are correlated by 100% so they are not
refining independently. I don't remember what the numbers before and
after ABS mean (histogram, phase, model applied) but check in the manual
and you'll find it.
The last line, v-cov distribution 0...1 by 0.05 shows the values in a
histogram with range of covariances from 0 to 1 divided in classes 0.05
wide. First value means that 430 pairs of parameters show absolute value
of correlation between 0.0 and 0.025, 2nd value means 127 parameters
show absolute value of correlation between 0.025 and 0.075 and so forth.
The top list only gives those higher than 0.5 in absolute value so you
expect 10 counting the last 10 entries in the bottom line, as shown.
Hope this helps.
Leo
Dr. Leopoldo Suescun
Argonne National Laboratory
Materials Science Division Bldg 223
9700 S. Cass Ave. Argonne IL 60439
Phone: 1 (630) 252-9760
Fax: 1 (630) 252-
- Original Message -
From: "Gerard, Garcia S" <[EMAIL PROTECTED]>
Date: Tuesday, April 8, 2008 7:37 am
Subject: correlation matrix interpretation
Dear all,
Could you please help me to translate this chunk of the correlation
matrix?HSCL is the histogram scale factor
PF profile coefficients
RMii lattice parameters
ABS?
UISo thermal parameters
how do i interpret the numbers? and the signs? how strongly
correlated these variables are?
regards
--
Heriot-Watt University is a Scottish charity
registered under charity number SC000278.
Brian H. Toby, Ph.D.office: 630-252-5488
Materials Characterization Group Leader, Advanced Photon Source
9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426
Argonne National Laboratory secretary (Marija): 630-252-5453
Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: correlation matrix interpretation
Dear all,
How to obtain correlation matrix (using GSAS)? Is there any option with
EXPGUI?
regards,
Santosh Babu
On Tue, Apr 8, 2008 at 8:33 PM, Brian H. Toby <[EMAIL PROTECTED]> wrote:
> The sign of the numbers indicates correlation vs. anticorrelation. For
> example, Uiso's correlate between atom 1 and 2 in phase "1 1 1UISO" &
> "1 2UISO" so that Uiso increasing on one atom has a similar impact as an
> increase on the other. In the case of the reciprocal cell tensor (related to
> cell parameters) an increase on one of the diagonal terms has a similar
> effect as a decrease on the zero correction ("1 RM11" & "ZERO 1").
>
> Brian
>
>
> On Apr 8, 2008, at 8:55 AM, Leopoldo Suescun wrote:
>
> Dear Gerard,
> Here is how to read it:
>
> The correlation matrix terms greater than 0.50 are
> 1 1UISO-1 2UISO 5011 3UISO 687 1HSCL 801
> 1 2UISO- 1HSCL 650
> 1 3UISO- 1HSCL 852
> 1 RM11-ZERO 1 -642
> 1 RM22-ZERO 1 -640
> 1 RM33-ZERO 1 -692
>1ABS1- 1ABS2 1000
> 1 1PF 2-1 1PF 3 -727
> v-cov distribution 0...1 by 0.05
>430 125 77 347 107201102
> 3101101
>
>
> 1st column (8 characters wide): Variable 1, 2nd column: (also 8
> characters wide) Variable 2, with "-" separating both columns, 3rd
> column (6 characters wide) the correlation value multiplied by 1000.
> Following collumns are show if more paramters have correlations greater
> than 0.5 with the parameters in the first collumn. So in this case, 4th
> collumn (8 characters wide with no separation from 3rd): Variable 2',
> 5th collumn (6 char wide): correlation between Var1 and Var2', etc for
> var 2''...
>
> So you can read the first column this way:
> 1 1UISO (Iso thermal param. for atom 1 in phase 1) shows a correlation
> of 0.501 with 1 2UISO (iso param for atom 2 in phase 1) so thermal
> parameters for atoms 1 and 2 inphase one have 50% correlation.
> 1 1UISO shows .687 corelation with 1 3UISO, or atom's 1 and 3 Uisos
> are correlated 68.7%
> 1 1UISO is correlated with histogram scale factor by 80.1 %
>
> ABS = absorption correction if my memory is good but you can check in
> the GSAS manual that accompanies GSAS distribution. You have a problem
> with the setup of the refinement because you have 2 absorption
> corrections and both parameters are correlated by 100% so they are not
> refining independently. I don't remember what the numbers before and
> after ABS mean (histogram, phase, model applied) but check in the manual
> and you'll find it.
>
> The last line, v-cov distribution 0...1 by 0.05 shows the values in a
> histogram with range of covariances from 0 to 1 divided in classes 0.05
> wide. First value means that 430 pairs of parameters show absolute value
> of correlation between 0.0 and 0.025, 2nd value means 127 parameters
> show absolute value of correlation between 0.025 and 0.075 and so forth.
>
> The top list only gives those higher than 0.5 in absolute value so you
> expect 10 counting the last 10 entries in the bottom line, as shown.
>
> Hope this helps.
> Leo
>
> Dr. Leopoldo Suescun
> Argonne National Laboratory
> Materials Science Division Bldg 223
> 9700 S. Cass Ave. Argonne IL 60439
> Phone: 1 (630) 252-9760
> Fax: 1 (630) 252-
>
> - Original Message -
> From: "Gerard, Garcia S" <[EMAIL PROTECTED]>
> Date: Tuesday, April 8, 2008 7:37 am
> Subject: correlation matrix interpretation
>
> Dear all,
>
> Could you please help me to translate this chunk of the correlation
> matrix?HSCL is the histogram scale factor
> PF profile coefficients
> RMii lattice parameters
> ABS?
> UISo thermal parameters
>
> how do i interpret the numbers? and the signs? how strongly
> correlated these variables are?
>
> regards
>
>
>
>
> --
> Heriot-Watt University is a Scottish charity
> registered under charity number SC000278.
>
>
>
>
>
> Brian
> H. Toby, Ph.D.office: 630-252-5488
> Materials Characterization Group Leader, Advanced Photon Source
> 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426
> Argonne National Laboratory secretary (Marija): 630-252-5453
> Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
>
>
>
>
Re: correlation matrix interpretation
The sign of the numbers indicates correlation vs. anticorrelation.
For example, Uiso's correlate between atom 1 and 2 in phase "1 1
1UISO" & "1 2UISO" so that Uiso increasing on one atom has a
similar impact as an increase on the other. In the case of the
reciprocal cell tensor (related to cell parameters) an increase on
one of the diagonal terms has a similar effect as a decrease on the
zero correction ("1 RM11" & "ZERO 1").
Brian
On Apr 8, 2008, at 8:55 AM, Leopoldo Suescun wrote:
Dear Gerard,
Here is how to read it:
The correlation matrix terms greater than 0.50 are
1 1UISO-1 2UISO 5011 3UISO 687 1HSCL 801
1 2UISO- 1HSCL 650
1 3UISO- 1HSCL 852
1 RM11-ZERO 1 -642
1 RM22-ZERO 1 -640
1 RM33-ZERO 1 -692
1ABS1- 1ABS2 1000
1 1PF 2-1 1PF 3 -727
v-cov distribution 0...1 by 0.05
430 125 77 347 107201102
3101101
1st column (8 characters wide): Variable 1, 2nd column: (also 8
characters wide) Variable 2, with "-" separating both columns, 3rd
column (6 characters wide) the correlation value multiplied by 1000.
Following collumns are show if more paramters have correlations
greater
than 0.5 with the parameters in the first collumn. So in this case,
4th
collumn (8 characters wide with no separation from 3rd): Variable 2',
5th collumn (6 char wide): correlation between Var1 and Var2', etc for
var 2''...
So you can read the first column this way:
1 1UISO (Iso thermal param. for atom 1 in phase 1) shows a
correlation
of 0.501 with 1 2UISO (iso param for atom 2 in phase 1) so thermal
parameters for atoms 1 and 2 inphase one have 50% correlation.
1 1UISO shows .687 corelation with 1 3UISO, or atom's 1 and 3 Uisos
are correlated 68.7%
1 1UISO is correlated with histogram scale factor by 80.1 %
ABS = absorption correction if my memory is good but you can check in
the GSAS manual that accompanies GSAS distribution. You have a problem
with the setup of the refinement because you have 2 absorption
corrections and both parameters are correlated by 100% so they are not
refining independently. I don't remember what the numbers before and
after ABS mean (histogram, phase, model applied) but check in the
manual
and you'll find it.
The last line, v-cov distribution 0...1 by 0.05 shows the values in a
histogram with range of covariances from 0 to 1 divided in classes
0.05
wide. First value means that 430 pairs of parameters show absolute
value
of correlation between 0.0 and 0.025, 2nd value means 127 parameters
show absolute value of correlation between 0.025 and 0.075 and so
forth.
The top list only gives those higher than 0.5 in absolute value so you
expect 10 counting the last 10 entries in the bottom line, as shown.
Hope this helps.
Leo
Dr. Leopoldo Suescun
Argonne National Laboratory
Materials Science Division Bldg 223
9700 S. Cass Ave. Argonne IL 60439
Phone: 1 (630) 252-9760
Fax: 1 (630) 252-
- Original Message -
From: "Gerard, Garcia S" <[EMAIL PROTECTED]>
Date: Tuesday, April 8, 2008 7:37 am
Subject: correlation matrix interpretation
Dear all,
Could you please help me to translate this chunk of the correlation
matrix?HSCL is the histogram scale factor
PF profile coefficients
RMii lattice parameters
ABS?
UISo thermal parameters
how do i interpret the numbers? and the signs? how strongly
correlated these variables are?
regards
--
Heriot-Watt University is a Scottish charity
registered under charity number SC000278.
Brian H. Toby, Ph.D.office: 630-252-5488
Materials Characterization Group Leader, Advanced Photon Source
9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426
Argonne National Laboratory secretary (Marija): 630-252-5453
Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: correlation matrix interpretation
Dear Gerard, Here is how to read it: > The correlation matrix terms greater than 0.50 are > 1 1UISO-1 2UISO 5011 3UISO 687 1HSCL 801 > 1 2UISO- 1HSCL 650 > 1 3UISO- 1HSCL 852 > 1 RM11-ZERO 1 -642 > 1 RM22-ZERO 1 -640 > 1 RM33-ZERO 1 -692 >1ABS1- 1ABS2 1000 > 1 1PF 2-1 1PF 3 -727 > v-cov distribution 0...1 by 0.05 >430 125 77 347 107201102 > 3101101 1st column (8 characters wide): Variable 1, 2nd column: (also 8 characters wide) Variable 2, with "-" separating both columns, 3rd column (6 characters wide) the correlation value multiplied by 1000. Following collumns are show if more paramters have correlations greater than 0.5 with the parameters in the first collumn. So in this case, 4th collumn (8 characters wide with no separation from 3rd): Variable 2', 5th collumn (6 char wide): correlation between Var1 and Var2', etc for var 2''... So you can read the first column this way: 1 1UISO (Iso thermal param. for atom 1 in phase 1) shows a correlation of 0.501 with 1 2UISO (iso param for atom 2 in phase 1) so thermal parameters for atoms 1 and 2 inphase one have 50% correlation. 1 1UISO shows .687 corelation with 1 3UISO, or atom's 1 and 3 Uisos are correlated 68.7% 1 1UISO is correlated with histogram scale factor by 80.1 % ABS = absorption correction if my memory is good but you can check in the GSAS manual that accompanies GSAS distribution. You have a problem with the setup of the refinement because you have 2 absorption corrections and both parameters are correlated by 100% so they are not refining independently. I don't remember what the numbers before and after ABS mean (histogram, phase, model applied) but check in the manual and you'll find it. The last line, v-cov distribution 0...1 by 0.05 shows the values in a histogram with range of covariances from 0 to 1 divided in classes 0.05 wide. First value means that 430 pairs of parameters show absolute value of correlation between 0.0 and 0.025, 2nd value means 127 parameters show absolute value of correlation between 0.025 and 0.075 and so forth. The top list only gives those higher than 0.5 in absolute value so you expect 10 counting the last 10 entries in the bottom line, as shown. Hope this helps. Leo Dr. Leopoldo Suescun Argonne National Laboratory Materials Science Division Bldg 223 9700 S. Cass Ave. Argonne IL 60439 Phone: 1 (630) 252-9760 Fax: 1 (630) 252- - Original Message - From: "Gerard, Garcia S" <[EMAIL PROTECTED]> Date: Tuesday, April 8, 2008 7:37 am Subject: correlation matrix interpretation > Dear all, > > Could you please help me to translate this chunk of the correlation > matrix?HSCL is the histogram scale factor > PF profile coefficients > RMii lattice parameters > ABS? > UISo thermal parameters > > how do i interpret the numbers? and the signs? how strongly > correlated these variables are? > > regards > > > > > -- > Heriot-Watt University is a Scottish charity > registered under charity number SC000278. > > begin:vcard n:Suescun;Leopoldo fn:Leopoldo Suescun tel;fax:1 (630) 252- tel;work:1 (630) 252-9760 org:Argonne National Laboratory;Materials Science Division adr:;;9700 S. Cass Avenue;Argonne;IL;60439;USA version:2.1 email;internet:[EMAIL PROTECTED] title:Dr. end:vcard
RE: correlation matrix
Title: Message Gerard, In GSAS there is a GENLES "print" option that will give the covariance terms larger than +/- 0.5 in the list file. There aren't as many large ones as you might think apart from the various background terms. Bob Von Dreele R.B. Von Dreele IPNS Division Argonne National Laboratory Argonne, IL 60439-4814 -Original Message-From: Gerard, Garcia S [mailto:[EMAIL PROTECTED] Sent: Thursday, May 05, 2005 8:56 AMTo: [EMAIL PROTECTED]Cc: rietveld_l@ill.frSubject: correlation matrix Dear all, I suspect that in my rietveld refinements i have severe correlation problems. Is there any way of having a look at the matrix where this correlations are stood out? Thanks Gerard
