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Rietveld Refinement with GSAS. Recent Quote seen in Rietveld e-mail:. “Rietveld refinement is one of those few fields of intellectual endeavor wherein the more one does it, the less one understands.” (Sue Kesson). Stephens’ Law – “A Rietveld refinement is never perfected, merely abandoned”.

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Rietveld refinement with gsas

Rietveld Refinement with GSAS

Recent Quote seen in Rietveld e-mail:

“Rietveld refinement is one of those few fields of intellectual endeavor wherein the more one does it, the less one understands.” (Sue Kesson)

Stephens’ Law –

“A Rietveld refinement is never perfected,

merely abandoned”

Demonstration – refinement of fluroapatite

R.B. Von Dreele, Advanced Photon Source

Argonne National Laboratory


Rietveld refinement is multiparameter curve fitting
Rietveld refinement is multiparameter curve fitting

  • Result from fluoroapatite refinement – powder profile is curve with counting noise & fit is smooth curve

  • NB: big plot is sqrt(I)

(lab CuKa B-B data)

)

Iobs+

Icalc|

Io-Ic|

Refl. positions


So how do we get there
So how do we get there?

  • Beginning – model errors  misfits to pattern

  • Can’t just let go all parameters – too far from best model (minimum c2)

False minimum

Least-squares cycles

c2

True minimum – “global” minimum

parameter

c2 surface shape depends on parameter suite


Fluoroapatite start add model 1 st choose lattice sp grp
Fluoroapatite start – add model (1st choose lattice/sp. grp.)

  • important – reflection marks match peaks

  • Bad start otherwise – adjust lattice parameters (wrong space group?)


2 nd add atoms do default initial refinement scale background
2nd add atoms & do default initial refinement – scale & background

  • Notice shape of difference curve – position/shape/intensity errors


Errors parameters
Errors & parameters?

  • position – lattice parameters, zero point (not common)

    - other systematic effects – sample shift/offset

  • shape – profile coefficients (GU, GV, GW, LX, LY, etc. in GSAS)

  • intensity – crystal structure (atom positions & thermal parameters)

    - other systematic effects (absorption/extinction/preferred orientation)

NB – get linear combination of all the above

NB2 – trend with 2Q (or TOF) important

peak shift

wrong intensity

too sharp

LX - too small

a – too small

Ca2(x) – too small


Difference curve what to do next
Difference curve – what to do next?

  • Dominant error – peak shapes? Too sharp?

  • Refine profile parameters next (maybe include lattice parameters)

  • NB - EACH CASE IS DIFFERENT

  • Characteristic “up-down-up”

  • profile error

    NB – can be “down-up-down” for too “fat” profile


Result much improved
Result – much improved!

  • maybe intensity differences left – refine coordinates & thermal parms.


Result essentially unchanged
Result – essentially unchanged

Ca

F

PO4

  • Thus, major error in this initial model – peak shapes


So how does Rietveld refinement work?

Rietveld Minimize

Exact overlaps

- symmetry

Residuals:

Io

Incomplete overlaps

SIc

Ic

Extract structure factors:

Apportion Io by ratio of Ic to Sic & apply corrections


Rietveld refinement - Least Squares Theory

Given a set of observations Gobs

and a function

then the best estimate of the values pi is found by

minimizing

This is done by setting the derivative to zero

Results in n “normal” equations (one for each variable) - solve for pi


Least Squares Theory - continued

Problem - g(pi) is nonlinear & transcendental (sin, cos, etc.)

so can’t solve directly

Expand g(pi) as Taylor series & toss high order terms

ai - initial values of pi

Dpi = pi - ai (shift)

Substitute above

Normal equations - one for each Dpi; outer sum over observations

Solve for Dpi - shifts of parameters, NOT values


Least Squares Theory - continued

Rearrange

.

.

.

Matrix form: Ax=v


Least Squares Theory - continued

Matrix equation Ax=v

Solve x = A-1v = Bv; B = A-1

This gives set of Dpi to apply to “old” set of ai

repeat until all xi~0 (i.e. no more shifts)

Quality of fit – “c2” = M/(N-P)  1 if weights “correct” & model without systematic errors (very rarely achieved)

Bii = s2i – “standard uncertainty” (“variance”) in Dpi

(usually scaled by c2)

Bij/(Bii*Bjj) – “covariance” between Dpi & Dpj

Rietveld refinement - this process applied to powder profiles

Gcalc - model function for the powder profile (Y elsewhere)


Rietveld Model: Yc = Io{SkhF2hmhLhP(Dh) + Ib}

Least-squares: minimize M=Sw(Yo-Yc)2

Io - incident intensity - variable for fixed 2Q

kh - scale factor for particular phase

F2h - structure factor for particular reflection

mh - reflection multiplicity

Lh - correction factors on intensity - texture, etc.

P(Dh) - peak shape function - strain & microstrain, etc.

Ib - background contribution


Peak shape functions – can get exotic!

Convolution of contributing functions

Instrumental effects

Source

Geometric aberrations

Sample effects

Particle size - crystallite size

Microstrain - nonidentical unit cell

sizes


Gaussian usual instrument contribution is mostly gaussian

2

1

2

2

)

=

=

L

P

(

D

[

-

4

l

n

2

D

/

H

]

4

l

n

2

2

p

H

2

k

P

(

D

)

=

e

=

G

k

k

/

H

1

+

4

D

k

H

p

k

k

k

k

CW Peak Shape Functions – basically 2 parts:

Gaussian – usual instrument contribution is “mostly” Gaussian

Lorentzian – usual sample broadening contribution

  • H - full width at half maximum - expression

  • from soller slit sizes and monochromator

  • angle

  • - displacement from peak position

Convolution – Voigt; linear combination - pseudoVoigt


CW Profile Function in GSAS

Thompson, Cox & Hastings (with modifications)

Pseudo-Voigt

Mixing coefficient

FWHM parameter


CW Axial Broadening Function

Finger, Cox & Jephcoat based on van Laar & Yelon

Debye-Scherrer

cone

2Q Scan

H

Slit

2QBragg

2Qmin

2Qi

Depend on slit & sample “heights” wrt diffr. radius

H/L & S/L - parameters in function

(typically 0.002 - 0.020)

Ä Pseudo-Voigt (TCH)

= profile function


How good is this function?

Protein Rietveld refinement - Very low angle fit

1.0-4.0° peaks - strong asymmetry “perfect” fit to shape


Bragg-Brentano Diffractometer – “parafocusing”

Focusing circle

X-ray source

Diffractometer

circle

Receiving slit

Incident beam

slit

Sample

displaced

Sample

transparency

Beam footprint

Divergent beam optics


CW Function Coefficients - GSAS

Shifted difference

Sample shift

Sample transparency

Gaussian profile

Lorentzian profile

(plus anisotropic broadening terms) Intrepretation?


b*

a*

Crystallite Size Broadening

Dd*=constant

Lorentzian term - usual

K - Scherrer const.

Gaussian term - rare

particles same size?


b*

a*

Microstrain Broadening

Lorentzian term - usual effect

Gaussian term - theory?

Remove instrumental part


Microstrain broadening – physical model

Model – elastic deformation of crystallites

Stephens, P.W. (1999). J. Appl. Cryst. 32, 281-289.

Also see Popa, N. (1998). J. Appl. Cryst. 31, 176-180.

d-spacing expression

Broadening – variance in Mhkl


Microstrain broadening - continued

Terms in variance

Substitute – note similar terms in matrix – collect terms


Microstrain broadening - continued

Broadening – as variance

3 collected terms

General expression – triclinic – 15 terms

Symmetry effects – e.g. monoclinic (b unique) – 9 terms

Cubic – m3m – 2 terms


Example - unusual line broadening effects

in Na parahydroxybenzoate

Sharp lines

Broad lines

Directional dependence -

Lattice defects?

Seeming inconsistency in line broadening

- hkl dependent


H-atom location in Na parahydroxybenzoate

Good DF map allowed by better fit to pattern

DF contour map

H-atom location

from x-ray powder data


Macroscopic strain
Macroscopic Strain

Part of peak shape function #5 – TOF & CW

d-spacing expression; aij from recip. metric tensor

Elastic strain – symmetry restricted lattice distortion

TOF:

ΔT = (d11h2+d22k2+d33l2+d12hk+d13hl+d23kl)d3

CW:

ΔT = (d11h2+d22k2+d33l2+d12hk+d13hl+d23kl)d2tanQ

Why? Multiple data sets under different conditions (T,P, x, etc.)


Symmetry macrostrain
Symmetry & macrostrain

dij – restricted by symmetry

e.g. for cubic

DT = d11h2d3 for TOF

Result: change in lattice parameters via change in metric coeff.

aij’ = aij-2dij/C for TOF

aij’ = aij-(p/9000)dij for CW

Use new aij’ to get lattice parameters

e.g. for cubic


L

h

Nonstructural Features

Affect the integrated peak intensity and not peak shape

Bragg Intensity Corrections:

Extinction

Preferred Orientation

Absorption & Surface Roughness

Other Geometric Factors


1

E

=

1

+

x

b

2

3

x

x

5

x

E

=

1

-

+

-

.

.

.

x

<

1

2

4

4

8

l

2

1

3

é

ù

E

=

1

-

-

.

.

.

x

>

1

p

x

ê

ú

8

x

2

l

1

2

8

x

ë

û

2

2

E

=

E

s

i

n

Q

+

E

c

o

s

Q

h

b

l

Extinction

Sabine model - Darwin, Zachariasen & Hamilton

Bragg component - reflection

Laue component - transmission

Combination of two parts


80%

E

x

60%

40%

20%

0%

0.0

25.0

50.0

75.0

100.0

125.0

150.0

Sabine Extinction Coefficient

Crystallite grain size =

Increasing

wavelength

(1-5 Å)

Eh

2Q


What is texture? Nonrandom crystallite grain orientations

Random powder - all crystallite orientations equally probable - flat pole figure

Pole figure - stereographic projection of a crystal axis down some sample direction

Loose powder

(100) random texture

(100) wire texture

Crystallites oriented along wire axis - pole figure peaked in center and at the rim (100’s are 90º apart)

Orientation Distribution Function - probability function for texture

Metal wire


Texture - measurement by diffraction

(220)

Non-random crystallite orientations in sample

(200)

Incident beam

x-rays or neutrons

Sample

(111)

  • Debye-Scherrer cones

  • uneven intensity due to texture

  • also different pattern of unevenness for different hkl’s

  • Intensity pattern changes as sample is turned


Preferred Orientation - March/Dollase Model

Uniaxial packing

Ellipsoidal Distribution -

assumed cylindrical

Ro - ratio of ellipsoid

axes = 1.0 for no

preferred orientation

Ellipsoidal particles

Spherical Distribution

Integral about distribution

- modify multiplicity


l

l

¥

m

n

m

n

å

å

å

f

(

g

)

=

C

T

(

g

)

l

l

l=0

m=-l

n=-l

F1

F2

Y

Texture - Orientation Distribution Function - GSAS

Probability distribution of crystallite orientations - f(g)

f(g) = f(F1,Y,F2)

Tlmn = Associated Legendre functions or generalized spherical harmonics

F1,Y,F2 - Euler angles


Texture effect on reflection intensity - Rietveld model

  • Projection of orientation distribution function for chosen reflection (h) and sample direction (y)

  • K - symmetrized spherical harmonics - account for sample & crystal symmetry

  • “Pole figure” - variation of single reflection intensity as fxn. of sample orientation - fixed h

  • “Inverse pole figure” - modification of all reflection intensities by sample texture - fixed y - Ideally suited for neutron TOF diffraction

  • Rietveld refinement of coefficients, Clmn, and 3 orientation angles - sample alignment


Absorption

X-rays - independent of 2Q

- flat sample – surface roughness effect

- microabsorption effects

- but can change peak shape and shift

their positions if small (thick sample)

Neutrons - depend on 2Q and l but much

smaller effect

- includes multiple scattering

much bigger effect

- assume cylindrical sample

Debye-Scherrer geometry


Model - A.W. Hewat

For cylinders and weak absorption only

i.e. neutrons - most needed for TOF data

not for CW data – fails for mR>1

GSAS – New more elaborate model by

Lobanov & alte de Viega – works to mR>10

Other corrections - simple transmission & flat plate


Surface Roughness – Bragg-Brentano only

Low angle – less penetration (scatter in less dense material) - less intensity

High angle – more penetration (go thru surface roughness) - more dense material; more intensity

Nonuniform sample density with depth from surface

Most prevalent with strong sample absorption

If uncorrected - atom temperature factors too small

Suortti model Pitschke, et al. model

(a bit more stable)


2

1

+

M

c

o

s

2

Q

L

=

2

p

2

s

i

n

Q

c

o

s

Q

1

L

=

2

p

2

s

i

n

Q

c

o

s

Q

4

L

=

d

s

i

n

Q

p

Other Geometric Corrections

Lorentz correction - both X-rays and neutrons

Polarization correction - only X-rays

X-rays

Neutrons - CW

Neutrons - TOF


Carbon scattering factor

uncorrected

6

4

fC

Solvent

corrected

2

0

0 5 10 15 20

2Q

Solvent scattering – proteins & zeolites?

Contrast effect between structure & “disordered” solvent region

f = fo-Aexp(-8pBsin2Q/l2)

Babinet’s Principle:

Atoms not in vacuum –

change form factors


Background scattering

Manual subtraction – not recommended - distorts the weighting scheme for the observations& puts a bias in the observationsFit to a function - many possibilities:

Fourier series - empirical

Chebyschev power series - ditto

Exponential expansions - air scatter & TDS

Fixed interval points - brute force

Debye equation - amorphous background

(separate diffuse scattering in GSAS)


Real space correlation function especially good for tof terms with

Debye Equation - Amorphous Scattering

real space correlation functionespecially good for TOFterms with

vibration

amplitude

distance



Rietveld Refinement with Debye Function

O

1.60Å

4.13Å

Si

2.63Å

3.12Å

5.11Å

6.1Å

a-quartz distances

7 terms Ri –interatomic distances in SiO2 glass

1.587(1), 2.648(1), 4.133(3), 4.998(2), 6.201(7), 7.411(7) & 8.837(21)

Same as found in a-quartz


Non-Structural Features in Powder Patterns

Summary

1. Large crystallite size - extinction

2. Preferred orientation

3. Small crystallite size - peak shape

4. Microstrain (defect concentration)

5. Amorphous scattering - background


Time to quit
Time to quit?

Stephens’ Law –

“A Rietveld refinement is never perfected,

merely abandoned”

Also – “stop when you’ve run out of things to vary”

What if problem is more complex?

Apply constraints & restraints 

“What to do when you have

too many parameters

& not enough data”


Complex structures (even proteins)

Too many parameters – “free” refinement fails

Known stereochemistry:

Bond distances

Bond angles

Torsion angles (less definite)

Group planarity (e.g. phenyl groups)

Chiral centers – handedness

Etc.

Choice:

rigid body description – fixed geometry/fewer parameters

stereochemical restraints – more data


Constraints vs restraints

Constraints – reduce no. of parameters

Derivative vector

Before constraints

(longer)

Derivative vector

After constraints

(shorter)

Rigid body

User

Symmetry

Rectangular matrices

Restraints – additional information (data) that model must fit

Ex. Bond lengths, angles, etc.


Space group symmetry constraints

Special positions – on symmetry elements

Axes, mirrors & inversion centers (not glides & screws)

Restrictions on refineable parameters

Simple example: atom on inversion center – fixed x,y,z

What about Uij’s?

– no restriction

– ellipsoid has inversion center

Mirrors & axes ? – depends on orientation

Example: P 2/m – 2 || b-axis, m ^ 2-fold

on 2-fold: x,z – fixed & U11,U22,U33, & U13 variable

on m: y fixed & U11,U22, U33, & U13 variable

Rietveld programs – GSAS automatic, others not


Multi-atom site fractions

“site fraction” – fraction of site occupied by atom

“site multiplicity”- no. times site occurs in cell

“occupancy” – site fraction * site multiplicity

may be normalized by max multiplicity

GSAS uses fraction & multiplicity derived from sp. gp.

Others use occupancy

If two atoms in site – Ex. Fe/Mg in olivine

Then (if site full) FMg = 1-FFe


Multi-atom site fractions - continued

If 3 atoms A,B,C on site – problem

Diffraction experiment – relative scattering power of site

“1-equation & 2-unknowns” unsolvable problem

Need extra information to solve problem –

2nd diffraction experiment – different scattering power

“2-equations & 2-unknowns” problem

Constraint: solution of J.-M. Joubert

Add an atom – site has 4 atoms A, B, C, C’

so that FA+FB+FC+FC’=1

Then constrain so DFA = -DFC and DFB = -D FC’


Multi-phase mixtures & multiple data sets

Neutron TOF – multiple detectors

Multi- wavelength synchrotron

X-ray/neutron experiments

How constrain scales, etc.?

Histogram scale

Phase scale

Ex. 2 phases & 2 histograms – 2 Sh & 4 Sph – 6 scales

Only 4 refinable – remove 2 by constraints

Ex. DS11 = -DS21 & DS12 = -DS22


Rigid body problem – 88 atoms – [FeCl2{OP(C6H5)3}4][FeCl4]

P21/c

a=14.00Å

b=27.71Å

c=18.31Å

b=104.53

V=6879Å3

264 parameters – no constraints

Just one x-ray pattern – not enough data!

Use rigid bodies – reduce parameters

V. Jorik, I. Ondrejkovicova, R.B. Von Dreele & H. Eherenberg, Cryst. Res. Technol., 38, 174-181 (2003)


Rigid body description – 3 rigid bodies

FeCl4 – tetrahedron, origin at Fe

1 translation, 5 vectors

Fe [ 0, 0, 0 ]

Cl1 [ sin(54.75), 0, cos(54.75)]

Cl2 [ -sin(54,75), 0, cos(54.75)]

Cl3 [ 0, sin(54.75), -cos(54.75)]

Cl4 [ 0, -sin(54.75), -cos(54.75)]

D=2.1Å; Fe-Cl bond

z

Fe - origin

Cl2

Cl1

y

Cl4

x

Cl3


Rigid body description – continued

PO – linear, origin at P

C6 – ring, origin at P(!)

x

C4

C2

(ties them together)

D2

C1

D1

D

z

C6

P

O

C1-C6 [ 0, 0, -1 ]

D1=1.6Å; P-C bond

C1 [ 0, 0, 0 ]

C2 [ sin(60), 0, -1/2 ]

C3 [-sin(60), 0, -1/2 ]

C4 [ sin(60), 0, -3/2 ]

C5 [-sin(60), 0, -3/2 ]

C6 [ 0, 0, -2 ]

D2=1.38Å; C-C aromatic bond

C5

C3

P [ 0, 0, 0 ]

O [ 0, 0 1 ]

D=1.4Å


Rigid body description – continued

C

C

x

R5(z)

R4(x)

P

C

R1(x)

C

R3(z)

y

R2(y)

z

Fe

C

C

O

Rigid body rotations – about P atom origin

For PO group – R1(x) & R2(y) – 4 sets

For C6 group – R1(x), R2(y),R3(z),R4(x),R5(z)

3 for each PO; R3(z)=+0, +120, & +240; R4(x)=70.55

Transform: X’=R1(x)R2(y)R3(z)R4(x)R5(z)X

47 structural variables


Refinement - results

Rwp=4.49%

Rp =3.29%

RF2 =9.98%

Nrb =47

Ntot =69


Refinement – RB distances & angles

OP(C6)3 1 2 3 4

R1(x) 122.5(13) -76.6(4) 69.3(3) -158.8(9)

R2(y) -71.7(3) -15.4(3) 12.8(3) 69.2(4)

R3(z)a 27.5(12) 51.7(3) -10.4(3) -53.8(9)

R3(z)b 147.5(12) 171.7(3) 109.6(3) 66.2(9)

R3(z)c 267.5(12) 291.7(3) 229.6(3) 186.2(9)

R4(x) 68.7(2) 68.7(2) 68.7(2) 68.7(2)

R5(z)a 99.8(15) 193.0(14) 139.2(16) 64.6(14)

R5(z)b 81.7(14) 88.3(17) 135.7(17) -133.3(16)

R5(z)c 155.3(16) 63.8(16) 156.2(15) 224.0(16)

P-O = 1.482(19)Å, P-C = 1.747(7)Å, C-C = 1.357(4)Å,

Fe-Cl = 2.209(9)Å

}

PO orientation

}

C3PO torsion

(+0,+120,+240)

p − C-P-O angle

}

Phenyl twist

x

R5(z)

R4(x)

R1(x - PO)

R3(z)

R2(y- PO)

Fe

z



Stereochemical restraints – additional “data”

Powder profile (Rietveld)*

Bond angles*

Bond distances*

Torsion angle pseudopotentials

Plane RMS displacements*

van der Waals distances (if voi<vci)Hydrogen bonds

Chiral volumes**

“f/y” pseudopotential

wi = 1/s2 weighting factor

fx - weight multipliers (typically 0.1-3)


For [FeCl2{OP(C6H5)3}4][FeCl4] - restraints

Bond distances:

Fe-Cl = 2.21(1)Å, P-O = 1.48(2)Å, P-C = 1.75(1)Å, C-C = 1.36(1)Å

Number = 4 + 4 + 12 + 72 = 92

Bond angles:

O-P-C, C-P-C & Cl-Fe-Cl = 109.5(10) – assume tetrahedral

C-C-C & P-C-C = 120(1) – assume hexagon

Number = 12 + 12 + 6 + 72 + 24 = 126

Planes: C6 to 0.01 – flat phenyl

Number = 72

Total = 92 + 126 + 72 = 290 restraints

A lot easier to setup than RB!!


Refinement - results

Rwp=3.94%

Rp =2.89%

RF2 =7.70%

Ntot =277


Stereochemical restraints – superimpose on RB results

Nearly identical with RB refinement

Different assumptions – different results


New rigid bodies for proteins actually more general
New rigid bodies for proteins (actually more general)

  • Proteins have too many parameters

  • Poor data/parameter ratio - especially for powder data

  • Very well known amino acid bonding –

    e.g. Engh & Huber

  • Reduce “free” variables – fixed bond lengths & angles

  • Define new objects for protein structure –

    flexible rigid bodies for amino acid residues

  • Focus on the “real” variables –

    location/orientation & torsion angles of each residue

  • Parameter reduction ~1/3 of original protein xyz set


Residue rigid body model for phenylalanine

Qijk

c2

txyz

c1

y

3txyz+3Qijk+y+c1+c2 = 9 variables

vs 33 unconstrained xyz coordinates


Q ijk quaternion to represent rotations
Qijk – Quaternion to represent rotations

In GSAS defined as: Qijk = r+ai+bj+ck – 4D complex number – 1 real + 3 imaginary components

Normalization: r2+a2+b2+c2 = 1

Rotation vector: v = ax+by+cz; u = (ax+by+cz)/sin(a/2)

Rotation angle: r2 = cos2(a/2); a2+b2+c2 = sin2(a/2)

Quaternion product: Qab = Qa * Qb≠ Qb * Qa

Quaternion vector transformation: v’ = QvQ-1


How effective pdb 194l hewl from a space crystallization single xtal data 1 40 resolution
How effective? PDB 194L – HEWL from a space crystallization; single xtal data,1.40Å resolution

21542 observations; 1148 atoms (1001 HEWL)

X-Plor 3.1 – RF = 25.8% ~4600 variables

GSAS RB refinement – RF=20.9% ~2700 variables

RMS difference -

0.10Å main chain & 0.21Å all protein atoms

RB refinement reduces effect of “over refinement”


194l rigid body model essentially identical
194L & rigid body model – essentially identical crystallization; single xtal data,1.40


Conclusions – constraints vs. restraints crystallization; single xtal data,1.40

Constraints required

space group restrictions

multiatom site occupancy

Rigid body constraints

reduce number of parameters

molecular geometry assumptions

Restraints

add data

molecular geometry assumptions (again)


GSAS - A bit of history crystallization; single xtal data,1.40

  • GSAS – conceived in 1982-1983 (A.C. Larson & R.B. Von Dreele)

  • 1st version released in Dec. 1985

    • Only TOF neutrons (& buggy)

    • Only for VAX

    • Designed for multiple data (histograms) & multiple phases from the start

    • Did single crystal from start

  • Later – add CW neutrons & CW x-rays (powder data)

  • SGI unix version & then PC (MS-DOS) version

  • also Linux version (briefly HP unix version)

  • 2001 – EXPGUI developed by B.H. Toby

  • Recent – spherical harmonics texture & proteins

  • New Windows, MacOSX, Fedora & RedHat linux versions

  • All identical code – g77 Fortran; 50 pgms. & 800 subroutines

  • GrWin & X graphics via pgplot

  • EXPGUI – all Tcl/Tk – user additions welcome

  • Basic structure is essentially unchanged


Structure of GSAS crystallization; single xtal data,1.40

1. Multiple programs - each with specific purpose

editing, powder preparation, least squares, etc.

2. User interface - EXPEDT

edit control data & problem parameters for

calculations - multilevel menus & help listings

text interface (no mouse!)

visualize “tree” structure for menus

3. Common file structure – all named as “experiment.ext”

experiment name used throughout, extension

differs by type of file

4. Graphics - both screen & hardcopy

5. EXPGUI – graphical interface (windows, buttons, edit boxes, etc.); incomplete overlap with EXPEDT but with useful extra features – by B. H. Toby


Pc gsas gui only for access to gsas programs
PC-GSAS – GUI only for access to GSAS programs crystallization; single xtal data,1.40

pull down menus for GSAS programs

(not linux)


Gsas expgui interfaces
GSAS & EXPGUI interfaces crystallization; single xtal data,1.40

GSAS – EXPEDT (and everything else):

On console screen

Keyboard input – text & numbers

1 letter commands – menu help

Layers of menus – tree structure

Type ahead thru layers of menus

Macros (@M, @R & @X commands)

EXPEDT data setup option (<?>,D,F,K,L,P,R,S,X) >EXPEDT data setup options: <?> - Type this help listing D - Distance/angle calculation set up F - Fourier calculation set up K n - Delete all but the last n history records L - Least squares refinement set up P - Powder data preparation R - Review data in the experiment file S - Single crystal data preparation X - Exit from EXPEDT

Numbers – real: ‘0.25’, or ‘1/3’, or ‘2.5e-5’ all allowed

Drag & drop for e.g. file names


Gsas expgui interfaces1
GSAS & EXPGUI interfaces crystallization; single xtal data,1.40

EXPGUI:

Access to GSAS

Typical GUI – edit boxes,

buttons, pull downs etc.

Liveplot – powder pattern


Unique expgui features not in gsas
Unique EXPGUI crystallization; single xtal data,1.40features (not in GSAS)

  • CIF input – read CIF files (not mmCIF)

  • widplt/absplt

  • coordinate export – various formats

  • instrument parameter file creation/edit

widplt

Sum

Lorentz FWHM

(sample)

Gauss FWHM

(instrument)


Powder pattern display liveplot
Powder pattern display - liveplot crystallization; single xtal data,1.40

Zoom

(new plot)

cum. c2 on

updates at end of genles run – check if OK!


Powder pattern display powplot
Powder pattern display - powplot crystallization; single xtal data,1.40

Io

Ic

Refl. pos.

Io-Ic

“publication style” plot – works OK for many journals; save as “emf”

can be “dressed up”; also ascii output of x,y table


Powplot options x y axes improved plot
Powplot options – x & y axes – “improved” plot? crystallization; single xtal data,1.40

Sqrt(I)

Refl. pos.

rescale y by 4x

Q-scale (from Q=pl/sinq)


Citations
Citations: crystallization; single xtal data,1.40

  • GSAS:

    A.C. Larson and R.B. Von Dreele, General Structure Analysis System (GSAS), Los Alamos National Laboratory Report LAUR 86-748 (2004).

  • EXPGUI:

    B. H. Toby, EXPGUI, a graphical user interface for GSAS, J. Appl. Cryst. 34, 210-213 (2001).


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