lesson 5 advanced refinements advanced profex...

Lesson 5

Advanced Refinements

Advanced Profex Features

Nicola Döbelin

RMS Foundation, Bettlach, Switzerland

June 13 – 15, 2018, Bettlach, CH

Topics

Advanced Refinements

Bi-modal crystallite sizes

Linked parameters

Chemical substitutions(by Bastien Le Gars Santoni)

Internal standard quantification

Advanced Profex Features

Text blocks

Refinement presets

Base lines

«Scan Math»

FullProf.2k

2

Bi-modal Crystallite Sizes

3

Bi-modal Crystallite Sizes

4

Highly-crystalline hydroxyapatite (HA)

Nano-crystalline hydroxyapatite (HA)

Bi-modal Crystallite Sizes

5

Peak broadening cannot

be described with a

single crystallite size

Bi-modal Crystallite Sizes

6

Two HA phases refined

(= Two independent

crystallite sizes)

Bi-modal Crystallite Sizes

7

Works, but introduces a lot of refined parameters:

- Unit cell dimensions

- Crystallite size

- Micro-strain

- Texture

- Atomic coordinates

- Site occupancies

- …

BGMN Features: Sub-Phases

Allows to refine only certain parameters bi-modal.

Bi-modal Crystallite Sizes

8

Bi-modal Crystallite Sizes

9

RefMult=2

RP=4 k1=0 PARAM=k2=0_0^0.0001

PARAM=B1[1]=0_0^0.01

PARAM=B1[2]=0_0^0.05

PARAM=GEWICHT[1]=0_0

PARAM=GEWICHT[2]=0_0

Activates 2 sub-phases

Instead of refining one crystallite size (B1)

for the hydroxyapatite phase, we can

refine individual B1 for the sub-phases:

B1[1], B1[2]

Bi-modal Crystallite Sizes

10

RefMult=2

RP=4 k1=0 PARAM=k2=0_0^0.0001

PARAM=B1[1]=0_0^0.01

PARAM=B1[2]=0_0^0.05

PARAM=GEWICHT[1]=0_0

PARAM=GEWICHT[2]=0_0

k2 (micro-strain) is not refined

individually for the sub-phases

But two B1 (crystallite size) are

refined for each sub-phase

The weight fraction (GEWICHT)

for both fractions is refined

GOAL:HAp=(GEWICHT[1]+GEWICHT[2])*ifthenelse(ifdef(d),exp(my*d*3/4),1)

The total weight fraction of hydroxyapatite is the

sum of the nano- and micro-crystalline sub-phases

Bi-modal Crystallite Sizes

11

Much better fit

But no anisotropic refinements possible

(B1=ANISO, GEWICHT=SPHARn, etc.)

Limitation by BGMN

Bi-modal Crystallite Sizes

12

Workaround for bimodal crystallite sizes with

anisotropic shape and texture

Bi-modal Crystallite Sizes

13

Workaround for bimodal crystallite sizes with

anisotropic shape and texture

RP=4 k1=0 PARAM=k2=0_0^0.0001 B1=ANISO^0.01 GEWICHT=SPHAR8 //

RefMult=2

PARAM=pB1=5_1^50

B1[1]=B1

B1[2]=pB1*B1

PARAM=pG=0.5_0.05^0.95

GEWICHT[1]=pG*GEWICHT

GEWICHT[2]=(1-pG)*GEWICHT

Refine anisotropic parameters

for the entire phase

(as if no sub-phases were defined)

Bi-modal Crystallite Sizes

14

Workaround for bimodal crystallite sizes with

anisotropic shape and texture

RP=4 k1=0 PARAM=k2=0_0^0.0001 B1=ANISO^0.01 GEWICHT=SPHAR8 //

RefMult=2

PARAM=pB1=5_1^50

B1[1]=B1

B1[2]=pB1*B1

PARAM=pG=0.5_0.05^0.95

GEWICHT[1]=pG*GEWICHT

GEWICHT[2]=(1-pG)*GEWICHT

Define the sub-phase parameters

as multiples of the phase parameters

Refine the multiplicator

Bi-modal Crystallite Sizes

15

Refined with anisotropic B1[1] and B1[2],

and texture for GEWICHT[1] and GEWICHT[2]

Profex Feature: Text Blocks

16

1

2

3

4 Restart Profex

Profex Feature: Text Blocks

17

1 place cursor here

2 3

Profex Feature: Text Blocks

18

Linked Parameters

19

Scenario:

- α-TCP (α-Ca3(PO4)2) sample

- Test for impurities of:

- β-TCP (β-Ca3(PO4)2)

- β-CPP (β-Ca2P2O7)

«Test for impurities» = refining phases that are potentially not present

Linked Parameters

20

α-TCP: 84.36 ± 0.75 %

β-TCP: 12.74 ± 0.70 %

β-CPP: 2.89 ± 0.26 %

Linked Parameters

21

β-TCP refinement

unreliableCrystallite Size = 8.5 nm

after sintering at 1350°C

???

Linked Parameters

22

β-TCP signal too weak (or absent)

to refine crystallite size

Unstable refinement

Best guess for β-TCP crystallite size:

Same as α-TCP

Link B1 of β-TCP to B1 of α-TCP

Linked Parameters

23

PHASE=alphaTCP // 04-010-4348

…

RP=4 k1=0 k2=pk2 B1=pB1 GEWICHT=SPHAR6 //

…

PHASE=betaCaPyrophosphate // 04-009-3876

…

RP=4 k1=0 k2=pk2 B1=pB1 GEWICHT=SPHAR0 //

…

PHASE=betaTCP // 04-008-8714

…

RP=4 k1=0 k2=pk2 B1=pB1 GEWICHT=SPHAR0 //

…

Structure files (*.str)Control file (*.sav)

…

EPS1=0

PARAM[1]=EPS2=0_-0.01^0.01

EPS3=0

PARAM[2]=pB1=0_0^0.01

PARAM[3]=pk2=0_0^0.0001

alpha3ratio=0.020

betaratio=0.005

NTHREADS=8

PROTOKOLL=Y

SAVE=N

…

Linked Parameters

24

α-TCP: 94.93 ± 0.27 %

β-TCP: 2.02 ± 0.19 %

β-CPP: 3.05 ± 0.19 %

Exercise after lunch: further optimize the refinement

Chemical Substitutions

25

X-rays are scattered at the electron shell of atoms/ions (elastic scattering)

More electrons = more scattering

Heavier atoms/ions = more scattered intensity

Structure factor amplitude

|Fhkl| says:

«Scattered intensity

corresponds to 17.937 electrons»

Crystal structure model says:

«at this position we expect

a Ca2+ ion»

Rietveld refinement says:

«Then the site occupancy

is 0.9965»

Chemical Substitutions

26

Structure factor amplitude

|Fhkl| says:

«Scattered intensity

corresponds to 17.937 electrons»

Crystal structure model says:

«at this position we expect

a Sr2+ ion»

Rietveld refinement says:

«Then the site occupancy

is 0.4990»

XRD only sees clouds of electrons

The crystal structure model determines how to

interpret the number of electrons

Chemical Substitutions

27

Goal for refinement of site occupancies:

- Establish a structure model that describes

the number of electrons found…

- … while maintaining charge balance

Chemical Substitutions

28

Presentation by Bastien

Internal Standard Quantification

Only crystalline phases create a distinct diffraction pattern

XRD is «blind» to amorphous phases

Phase quantifications usually report «relative weight-%»

(= relative to all crystalline phases)

Internal standard quantification = spiking with a crystalline phase in

a known quantity

Can be used to normalize relative quantities to absolute values

29

100% − 𝑄𝑎𝑏𝑠𝑜𝑙𝑢𝑡𝑒 = 𝑄𝑎𝑚𝑜𝑟𝑝ℎ𝑜𝑢𝑠

Internal Standard Quantification

30

Partially

amorphous

SiO2

Add 20 wt-%

Al2O3

20.0 %

XRDQtz

40.0 %

20.0 %

Absolute

quantities

normalize

Qtz

66.7 %

Al2O3

33.3 %

Relative

quantities

Amorph∙20.0

33.3

60.0 %

100 - 60

= 40.0 %

Qtz

40.0 %

20.0 %

Absolute

quantities

Amorph

40.0 %

normalize

∙100.0

100.0 − 20.0

Qtz

50.0 %

Amorph

50.0 %

These calculations can be

done in Profex using GOALs

Internal Standard Quantification

31

Sample contains:

- X % Glass

- Y % Hydroxyapatite

20 wt-% Al2O3 (Corundum)

were added as internal standard

Internal Standard Quantification

32

Step 1: Quantify all

crystalline phases

Internal Standard Quantification

33

Step 2: Define Al2O3 as the

internal standard phase

Internal Standard Quantification

34

GOALs section will

be modified

sum=Corundum+HAp

QCorundum=Corundum/sum

QHAp=HAp/sum

GOAL[1]=QCorundum

GOAL[2]=QHAp

ISTD=Corundum

ISTDQ=0.2000

sumabs=ISTD*(1-ISTDQ)/ISTDQ

QabsHAp=HAp/sumabs

QabsAmorph=1-(HAp)/sumabs

GOAL[1]=QabsHAp

GOAL[2]=QabsAmorph

Then repeat the refinement

Internal Standard Quantification

35

Reports absolute phase quantities

without the internal standard

Internal Standard Quantification

36

Exercise for the afternoon:

Improve the fit

Internal Standard Quantification

37

PhasePhase quantity [abs wt-%]

Mixed Internal standard External standard

Hydroxyapatite 50.00 46.56 45.49

MgO - 0.11 0.12

Amorphous 50.00 53.33 54.39

Explanation:

A mixture of 50 wt-% hydroxyapatite + 50 wt-% glass was prepared.

But the hydroxyapatite raw material contained traces

of MgO and 9 wt-% amorphous or undetected phases.

External standard quantification see: …\Handouts\ExternalStandard.pdf

Topics

Advanced Refinements

Bi-modal crystallite sizes

Linked parameters

Chemical substitutions(by Bastien Le Gars Santoni)

Internal standard quantification

Advanced Profex Features

Text blocks

Refinement presets

Base lines

«Scan Math»

FullProf.2k

38

Profex Feature: Refinement Presets

39

Profex Feature: Refinement Presets

40

Refinement Presets:

- Consistent refinement strategies

- Eliminate user influence

- Shared preset repository

Profex Feature: Base Line

41

Warning: DO NOT subtract base lines for Rietveld refinement!

Project Add Base Line…

2 Optimize parameters

1 Select base line algorithm

3 Check for smooth base line

4 Append base line to project

Profex Feature: Base Line

42

Base line is added as a new scan, but not yet saved to disk.

Use right mouse button «Export Scan» to save to disk.

Profex Feature: Scan Math

43

«Tools Scan Math»: Perform mathematical operations

on scans within a project.

Example: Subtract base line from scan

Profex Feature: Scan Math

44

«Tools Scan Math» 1 Enter equation

2 Generate Scan

Profex Feature: Scan Math

45

«Tools Scan Math»

New scan is generated

Profex Feature: Fullprof.2k

46

https://www.ill.eu/sites/fullprof/

Profex Feature: Fullprof.2k

Download and install Fullprof Suite

Select the fullprof executable «fp2k.exe» in the

preferences

47

Set to «Fullprof», restart Profex

«Run Refinement» will call fp2k.exe

Profex Feature: Fullprof.2k

48

Warning: Fullprof only accepts datasets measured with

fixed divergence slit!

When to use Fullprof instead of BGMN:

- When setting up an instrument configuration for BGMN fails

(Fullprof uses empirical profile functions, not fundamental parameters)

- Some features are easier to use in Fullprof

(distance and angle constraints)

- When you like Fullprof better than BGMN