Small Angle X-Ray Scattering System (SAXS) · Simon Fraser University 8888 University Drive, Burnaby, B.C. V5A 1S6 E [email protected] T 778.782.8158 F 778.782.3765 1 Purpose This document

1

Simon Fraser University 8888 University Drive, Burnaby, B.C. V5A 1S6

E [email protected] T 778.782.8158 F 778.782.3765 www.4dlabs.ca

Small Angle X-Ray Scattering

System (SAXS)

Standard Operating Procedure

Revision: 0.2 — Last Updated: September 8, 2015

Revision History

# Revised by: Date Modification

1 Philip Kubik Initial Release

2

3

4

5

2



Table of Contents

1 Purpose ........................................................................................................................................... 5

2 Definitions ....................................................................................................................................... 5

3 Conventions .................................................................................................................................... 6

4 References ....................................................................................................................................... 6

5 Contact ........................................................................................................................................... 7

6 Overview ......................................................................................................................................... 7

6.1 Transmission and Grazing Incidence Modes ............................................................................... 7

6.2 X-Ray Scattering Measurements ............................................................................................... 8

6.3 Sample Preparation ................................................................................................................. 10

6.4 Sample and Blank Positions..................................................................................................... 11

6.5 Instrument Control .................................................................................................................. 12

6.6 Data Format .......................................................................................................................... 12

6.7 Cosmic Background Rejection ................................................................................................. 13

7 Sample Mounting .......................................................................................................................... 14

7.1 General Considerations ........................................................................................................... 14

7.2 Solid Samples ......................................................................................................................... 15

7.3 Inviscid Liquids ........................................................................................................................ 16

3



7.4 Viscous Liquids and Pastes ...................................................................................................... 16

7.5 Heating, Cooling, and Humidity Control .................................................................................. 17

7.6 Sample Holders ....................................................................................................................... 18

7.6.1 Ambient Plate ................................................................................................................. 18

7.6.2 Sandwich Cell Holder ...................................................................................................... 21

7.6.3 JSP Re-Usable Capillary Holder ........................................................................................ 22

7.6.4 Linkam Sample Holder ..................................................................................................... 24

7.6.5 Environmental Chamber .................................................................................................. 27

8 Capillary Filling & Cleaning Procedure ............................................................................................ 28

8.1 Before Measurements ............................................................................................................. 28

8.2 After Measurements ................................................................................................................ 29

9 Measurement Procedure ................................................................................................................ 30

9.1 Setup ...................................................................................................................................... 30

9.2 Sample Loading ...................................................................................................................... 30

9.3 Heating and Cooling ............................................................................................................... 33

9.3.1 Julabo Heater/Chiller ....................................................................................................... 33

9.3.2 Linkam Sample Holder ..................................................................................................... 34

9.4 Transmission Mode X-Ray Scattering ....................................................................................... 36

4



9.4.1 Measurements Using GICC Interactive Mode.................................................................... 36

9.4.2 Measurements Using Macros ........................................................................................... 41

9.5 Exporting Data ........................................................................................................................ 43

9.6 Sample Unloading ................................................................................................................... 44

10 spec Command Quick Reference .................................................................................................... 46

10.1 Most Frequently Used Commands ........................................................................................... 46

10.2 Standard spec Commands ....................................................................................................... 47

10.3 Configuration Related Commands ........................................................................................... 47

10.4 X-Ray Source and Detector Commands .................................................................................... 48

10.5 Configuration Commands ....................................................................................................... 48

10.6 Commands for Time-sequences ............................................................................................... 48

10.7 Julabo Heater/Chiller Commands ............................................................................................. 49

10.8 Linkam Thermal Stage Commands ........................................................................................... 49

11 Configurations ............................................................................................................................... 50

11.1 2 Slit Configurations ............................................................................................................... 50

11.2 3 Slit Configurations ............................................................................................................... 51

5



1 Purpose

This document describes how to measure scattering produced by an x-ray beam, which is transmitted

through a sample, using the SAXSLAB Ganesha 300XL small angle x-ray scattering (SAXS) system in 4D

Labs. This document is intended to be a reference for trained users of the system; it is not a substitute for

training by staff of the 4D Labs Nanofabrication Facility. Readers of this document are expected to have a

basic familiarity with x-ray scattering and vacuum systems.

Measurement of grazing incidence x-ray scattering will added to a future version of this document.

Data reduction is not described in this document. Instead, refer to the SAXSGUI user's manual.1

2 Definitions

ESAXS: Extreme Small Angle X-ray Scattering. q-range (0.003 Å-1 to 0.2 Å-1).

GICC: Ganesha Interactive Control Center. Graphical user interface for acquisition of XRD data.

GI-XS: Grazing Incidence X-ray Scattering. X-ray scattering produced when the angle between the x-ray

beam and sample surface is close to the critical angle for total external reflection. The main applications

are for surface nanostructure and thin films.

LN2: Liquid nitrogen.

MAXS: Medium Angle X-ray Scattering. q-range (0.013 Å-1 to 0.7 Å-1).

SAXS: Small Angle X-ray Scattering. q-range (0.005 Å-1 to 0.3 Å-1).2

1 SAXSGUI User’s Guide, Rev. 2.05.02, Rigaku Innovative Technologies 7 JJ X-Ray Systems (2010/03/17).

2 Note that the term "SAXS" is somewhat ambiguous in the manufacturer's documentation and may refer to either of two dif-

ferent angular ranges. When acquiring data one may choose any one of four q-ranges denoted WAXS (0.6 Å-1 to 2.6 Å-1), MAXS

(0.013 Å-1 to 0.7 Å-1), SAXS (0.005 Å-1 to 0.3 Å-1), or ESAXS (0.003 Å-1 to 0.2 Å-1). Sometimes, the term SAXS refers to x-ray

scattering in the limited range (0.005 Å-1 to 0.3 Å-1). On the other hand, the Ganesha 300XL is called a SAXS system by the

manufacturer so sometimes SAXS refers to x-ray scattering over the entire q-range of the Ganesha 300XL, i.e., (0.003 Å-1 to 2.6

Å-1). In this document, SAXS will refer to the smaller q-range only. For the larger range, i.e., 0.003 Å-1 to 2.6 Å-1, the term x-ray

scattering will be used.

6



WAXS: Wide Angle X-ray Scattering. q-range (0.6 Å-1 to 2.6 Å-1).

T-XS: Transmission X-ray Scattering. X-ray scattering produced when the x-ray beam is transmitted the

angle between the x-ray beam and sample surface is large, typically 90°.

3 Conventions

In this document, the following items are italicized.

Hardware units

Software menu items

Software windows and panels

Software box names

The following items are underlined.

Hardware buttons and switches

Software buttons and check boxes

Special keyboard keys, e.g., Enter.

Text to be typed is shown inside double quotation marks.

spec commands are in boldface type and are preceded by the spec prompt >. After typing each spec com-

mand, press the Enter key. In this document, this is assumed implicitly.

Hazard conventions:

CAUTION indicates a hazard which may cause damage to equipment.

WARNING indicates a hazard which may cause injury to personnel. It may cause damage to equip-

ment as well.

4 References

Beamstop Alignment, Rev. 1.0, SAXSLAB document ID-001-R1.0 (2013/03/18).

Expert Users FAQ, Rev. 1.0, SAXSLAB document EUF-001-R1.0 (2012/10/08).

7



Ganesha 300 XL Operation Manual, Rev. 1.2, SAXSLAB document OM-300-R1.2 (2014/12/10).

Ganesha Interactive Control Center, Rev. 1.0, SAXSLAB (2015/05/27).

GISAXS/GIWAXS, Rev. 1.1, SAXSLAB document ID-002-R1.1 (2013/03/20).

SAXS2 Operating Procedure: GI-SAXS, GI-WAXS & GI-MAXS Measurements, SAXS Labs Ganesha, Rev.

3, J. Thostenson, SAXSLAB (2013/08/14).

SAXS2 Operating Procedure: SAXS, WAXS & MAXS Measurements, SAXS Labs Ganesha, Rev. 3, J.

Thostenson, SAXSLAB (2013/08/14).

SAXSGUI User’s Guide, Rev. 2.05.02, Rigaku Innovative Technologies 7 JJ X-Ray Systems

(2010/03/17).

spec™ X-Ray Diffraction Software User Manual, Rev. 2.8, Certified Scientific Software (June 3, 2008).

Training folder on the SAXS computer.

5 Contact

Questions or comments concerning this document or operation of the system should be directed to the cur-

rent tool owner at 4D Labs Nanofabrication Facility, Simon Fraser University, Burnaby, BC, Canada. The

current tool owner is listed on the web page for the tool on the 4D Labs Nanofabrication Facility web site.

6 Overview

6.1 Transmission and Grazing Incidence Modes

Two modes of x-ray scattering are defined by the angle of the x-ray beam with respect to the sample sur-

face:

Transmission mode.

Grazing incidence.

In transmission mode, the angle of the x-ray beam with respect to the sample is large, typically 90°. The

sample must be thin enough that a significant fraction of the beam is transmitted through the sample or

8



the scattered x-rays will be mostly absorbed. On the other hand, samples must be thick enough to produce

significant scattering (see Section 6.3).

In grazing incidence mode, the angle of the x-ray beam with respect to the sample is small. Specifically, it

is close to the critical angle for total external reflection. Under these conditions, measurements are surface

sensitive so this technique is suitable for measuring the nanostructure of surfaces and thin films.3

Sample holders for transmission and grazing incidence measurements are different or, at least, oriented

differently. Furthermore, grazing incidence measurements require optimization of the angle of incidence.

Otherwise, the measurement procedures are similar.

6.2 X-Ray Scattering Measurements 4

Before measuring the x-ray scattering from your samples, you should think about what you want to get

from your measurement. Answering the following questions will help you to determine how you should set

up your x-ray scattering measurements and how long they should take.

1) How strongly does your sample scatter?

2) What information do you wish to obtain from x-ray scattering?

a) Peak Positions and peak-width?

b) Particle sizes?

c) Data that can be accurately modeled over a large q-range.

3) What is the q-range of interest to you?

In general, it is best to start with WAXS or MAXS because these measurements are much quicker than

SAXS and ESAXS. If there is a problem with your sample, it is to your advantage to find it quickly.

3 Films ranging in thickness from a few nm to several hundred nm.

4 This section is based on:


9



The first step in the measurement procedure is to select the configuration. The standard configurations and

their properties (aperture sizes, detector distances, q-range, intensities, and resolution) are listed in Section

11.

Your first decision should be whether to use 2 slits or 3 slits. In most cases, 2 slits is the best choice be-

cause the incident intensity in a 2 slit configuration is 2 – 4 times higher than the intensity in the corre-

sponding 3 slit configuration but the resolution is only a little worse with 2 slits.

Next, you need to decide in which region(s) of the total q-range (0.0035 Å-1 ≤ q ≤ 2.8 Å-1) you wish to

make measurements. The incident intensity in the WAXS region (0.07 Å-1 ≤ q ≤ 2.8 Å-1) is a factor of 4-5

higher than in the MAXS region (0.15 Å-1 ≤ q ≤ 0.65 Å-1), which is a factor of 4-5 higher than in the SAXS

region (0.007 Å-1 ≤ q ≤ 0.25 Å-1), which is again a factor 4- 5 more than in the ESAXS region (0.0035 Å-1

≤ q ≤ 0.18 Å-1).

The final question is whether to use a 2 mm or a 4 mm beam stop. The beam stop is a circular disk imme-

diately in front of the detector. Its purpose is to prevent the direct beam from striking the detector. In most

cases, the 2 mm beam stop will block the direct beam sufficiently. Now, you have all of the information

necessary to select the configuration.

Whenever the configuration is changed, it is necessary to fine tune the beam stop position so that it blocks

the direct beam as well as possible at the detector. In order to do so, it is necessary that the stage be in a

position in which there is no absorption or scattering, i.e., a blank position. Fine tuning the beam stop po-

sition is an automatic procedure.

In each measurement, the user has the option to:

1) Measure the sample transmission and incident x-ray beam intensity.

2) Block the direct beam at the detector with the beam stop.

3) Place a mask over the beam stop position when the 2D x-ray scattering image is displayed.

4) Include the sample thickness.

10



In general, it is advisable to check all of these options. Measuring the sample transmission and the incident

x-ray beam intensity and including the sample thickness allow the absolute scattering intensity to be calcu-

lated.

Finally, you need to choose the data acquisition time. Once you have done measured the x-ray scattering of

your sample in one configuration, you can estimate the time needed in other configurations by comparing

the incident intensities in the different configurations from the configurations list (see Section 11).

If you are only looking for peak positions or particle sizes don't spend a lot of time getting the low-intensity

portions of the curve to look nice. Think about what you are looking for, measure it to the accuracy that

you need, and move on.

For some samples, especially those in capillaries or, to a lesser extent, those in sandwich cells, there may

be significant scattering from the sample container and/or matrix. In such cases, it is desirable to measure

the x-ray scattering from the empty sample container or the sample container filled with the matrix and

subtract that measurement from the measurement of the sample in the container. In the case of capillaries,

the identical capillary should be used and, if possible, it should be filled with the sample matrix.

6.3 Sample Preparation

In the SAXSLAB Ganesha, x-ray scattering is measured in a vacuum chamber in order to reduce the back-

ground intensity. Consequently, samples may need to be enclosed appropriately, e.g., by wrapping them or

placing them in a capillary or sandwich cell. Details may be found in Section 7. Obviously, samples which

are enclosed are not appropriate for grazing incidence measurements.

Scattering intensity depends on the thickness of your sample. In transmission mode, the optimum sample

thickness is the inverse of mass attenuation coefficient μ/ρ of your sample at the energy of the Cu Kα x-

rays emitted by the x-ray source. In other words, the optimum thickness toptimum is given by:

toptimum ≅ ρ/μ at E = 8.0 keV (λ = 1.54 Å)

11



For polymers, typically toptimum ≅ 1 mm.

Samples or sample enclosures should be mounted on a sample holder which can be inserted onto the sam-

ple stage in the Ganesha vacuum chamber. There are a variety of sample holders to accommodate different

types of samples, e.g., films, sheets, plates, powders, inviscid liquids, viscous liquids, and pastes. Some

sample holders allow measurements at ambient temperature only but others allow heating, cooling, and

humidity control. Details may be found in Section 7.

6.4 Sample and Blank Positions

After the sample holder with the samples has been loaded into the vacuum chamber and the chamber has

been evacuated, the positions of the samples and a blank position must be identified. The blank position

may be any position in which it is possible to measure the x-ray intensity without any absorption or scatter-

ing; the beam should simply pass through vacuum. Typically, in a blank position, the x-ray beam will pass

through an empty hole in the sample holder.

Large motions of the sample stage may require a significant amount of time, so it is desirable for multiple

samples to be close together and for the blank position to be close to the sample positions.

First the approximate sample and blank positions should be identified by moving the stage until the desired

position aligned with the cursor on the RayCam camera viewer. That cursor is set to the position of the

incident x-ray beam. For many samples, this coarse alignment procedure will be sufficient.

In some cases, sample alignment should be fine-tuned. For capillaries, more accurate alignment is required

due to the strong curvature of the capillary. The Align Capillary function of the GICC5 performs this func-

tion. For small or indistinct samples, the Scan Sample function of the GICC will align the centre of the sam-

ple with the x-ray beam. For holes, the Align Hole function of the GICC will align the centre of the hole

with the x-ray beam.

5 Ganesha Interactive Control Center

12



6.5 Instrument Control

Full control of the operation of the SAXSLAB Ganesha is possible via the spec command line interface. spec

is commonly used to control synchrotrons. On the other hand, many measurements can be created and run

more simply using a graphical user interface called the Ganesha Interactive Control Center (GICC). GICC

has two modes of operation.

1) Interactive mode, in which buttons in the GICC window control the Ganesha directly.

2) Macro mode, in which buttons in the GICC window creates commands in a macro. Macros can be ed-

ited by a text editor so often it is simpler to modify and existing macro with a text editor than to create

a macro from scratch using GICC. A macro can run by a single spec command.

Currently, temperature and humidity can only be controlled from spec; however, normally one would set

the temperature and/or humidity using spec and then initiate a measurement in spec by running a macro.

When using spec, the GICC should be in pause mode or spec commands may not run.

6.6 Data Format 6

Image data is saved in tiff format and should be readable by most data-handling packages. However, since

the header is full of information about the measurement,7 full utilization of this information requires that

SAXSGUI or other programs have custom read-in modules. The measurements are numbered consecutively

with prefixes and suffixes indicating the actually type of tile.

A measurement is actually a string of measurements By default, rather than making one long exposure for

each measurement, many short exposures are made and added together. In order to preserve the experi-

ment history, each short exposure is saved for later use.

6 This section is more or less copied from:


7 For details about the header, see Ganesha 300 XL Operation Manual, Rev. 1.2, SAXSLAB document OM-300-R1.2, Appendix 1

(2014/12/10).

13



There are several advantages to this approach:

1) The dynamic range of the measurement is higher.

2) The experiment progression may be observed each time a short measurement finishes.

3) If at some point the measurement fails, useful data is still saved.

4) The time evolution of the scattering is tracked.

5) Advanced noise reduction could be performed by comparing the short measurements with each other in

various ways (not implemented yet).

A 15 s time interval for the short measurements has been chosen. A 3,600 second measurement therefore

actually consists of 240 images.

The following files are generated:

Table 6-1: Data file descriptions.

Filename Description

/disk2/data/latest/latest_nnnnn_craw.tiff A .tiff file that is updated to include the latest data acquired. This file is the real-time sum of all the short measurements. The full header information is included.

/disk2/data/images/im_nnnnn_craw.tiff A tiff file that is created at the end of the measurement, which is the sum of all the short measurements. It should therefore be identical to the latest_nnnnn_craw.tiff. This file has the full header information inserted.

/disk2/data/frames/frames_nnnnn_craw.zip A .zip file containing the short measurements as well as a file with the Metadata. This file is not readable by SAXSGUI.

6.7 Cosmic Background Rejection

Cosmic radiation may contribute significantly to the scattering measurements; however, SAXSLAB has de-

veloped a method to remove up to 65% of cosmic radiation events, based on a signature of such events.

As a result, corrected data files, from which suspected cosmic radiation events have been removed, are

automatically generated. Usually, the corrected files are created within 2 min of completion of data acquisi-

14



tion and are located in sub-directories labelled "Corrected" in the directories listed above. These data files

have the same names as the original files but with -caz substituted for -craw.

7 Sample Mounting

7.1 General Considerations

In the SAXSLAB Ganesha, x-ray scattering is measured in a vacuum chamber in order to reduce the back-

ground intensity. Consequently,

Volatile samples must be contained in an enclosure, which is sealed to pressures <1 x 10-2 mbar.

Powders must be contained in order to prevent the powder from blowing away when the vacuum

chamber is either pumped down or vented.

In this document, a sample enclosure contains a sample such as a liquid, paste, or powder which can flow.

Methods of containing samples are described in Sections 7.2, 7.3, and 7.4. Examples are capillaries,

sandwich cells, and wrappers. Films, sheets and plates do not require a sample enclosure. In the environ-

mental chamber, samples are not exposed to vacuum but an enclosure may be required to prevent the

sample from flowing; however, the enclosure should not be sealed if humidity control is desired.

Samples and/or sample enclosures are mounted on a sample holder which is inserted into the sample

stage. Some sample holders allow ambient temperature x-ray scattering measurements in vacuum but oth-

ers allow the sample environment to be controlled. Available sample holders are the ambient plate holder,

sandwich cell holder, JSP re-usable capillary holder, Linkam holder, and environmental chamber (see Sec-

tion 7.4).

Tape may be used in the vacuum chamber to attach samples or sample enclosures to a sample holder;

however, it is important to choose a tape which has weak x-ray scattering in order to reduce interference

with the scattering from your sample. Suitable tapes include:

3M Scotch tape.

15



Kapton tape

The range of motion of the sample stage is 80 mm in the y and z directions. This may be insufficient to al-

low all available sample positions to be placed in the x-ray beam, e.g., for the ambient plate and the re-

usable capillary holders. Be sure that you are aware of the motion limitations of your sample holder before

mounting samples.

WARNING

When heating and cooling, it is the operator's responsibility to be aware of the thermal characteristics of

their samples and sample enclosures, including, but not limited to, melting point, boiling point, and de-

composition temperature. Furthermore, it is the operator's responsibility to ensure that sample heating or

cooling does not result in danger to personnel or damage to equipment.

WARNING

When installing a sample holder onto the sample stage or removing a sample holder, avoid touching the

mirror on the right. If I it touched, it may be misaligned and interfere with the x-ray beam. Consequently, it

is preferable to use your left hand to install or remove sample holders.

7.2 Solid Samples

For room temperature measurements, solid samples may be placed over a convenient hole in the ambient

plate sample holder (see Section 7.6.1) and held in place with tape, vacuum grease, or wax. Powders must

be enclosed in order to prevent the powder from:

1) Blowing away when the vacuum chamber is either pumped down or vented.

2) Falling under gravity.

Powders may be contained by one of the following methods.

16



Wrapping in aluminum foil. The aluminum foil will produce strong x-ray diffraction peaks at the

upper end of the Ganesha's q-range but this may be acceptable at low q values.

Sandwiching between two layers of tape. It may be beneficial to place the powder within an o-ring

or washer between the two layers of tape.

Placing in a sandwich cell, as described for pastes and viscous liquids (cf. Section 7.4).

Placing in a capillary, as described for inviscid liquids (cf. Section 7.3).

7.3 Inviscid Liquids

Inviscid liquids and some powders may be placed in sealed, thin-walled (e.g., 0.01 mm), quartz capillaries.

Both disposable and re-usable capillaries are available but must be purchased. Treat both types of capillar-

ies with care; they are expensive. Instructions for filling and cleaning capillaries may be found in Section 8.

Capillaries containing volatile samples must be sealed. Disposable capillaries may be sealed by flame seal-

ing or with glue or wax. Re-usable capillaries are sealed with o-rings. Before sealing, remove as much air

as possible and avoid creating bubbles. Capillaries may shatter under the pressure from residual air when

the vacuum chamber is evacuated.

Liquid samples which are too viscous to be easily placed in a capillary, may be put into a sandwich cell (cf.

Section 7.4).

7.4 Viscous Liquids and Pastes

Viscous liquids, pastes, and powders may be placed in a sandwich cell, which consists of a stainless steel

disk with a 10 mm diameter hole sandwiched between two 10 mm dia. sheets of mica or Kapton (see Fig-

ure 7-1). Mica scatters weakly but uniformly over the q-range; however, absorption is high so mica sheets

must be thin. Kapton has scatters more strongly and less uniformly but is much cheaper. Users must supply

their own mica or Kapton discs. Mica discs (10 mm dia. x 0.005 mm thick) may be purchased from 4D

Labs.

17



a b

Figure 7-1: Sandwich cell: a) assembled and b) disassembled.

Sandwich cells may be mounted on the sandwich cell holder (see Section 7.6.2) for room temperature

measurements or on the Linkam holder (see Section 7.6.4) for measurements in the temperature range -

150°C to 300°C.

7.5 Heating, Cooling, and Humidity Control

Two sample holders, the Linkam holder and the JSP re-usable capillary holder allow heating and cooling. In

addition, there is an environmental chamber, which allows heating of solid samples in controlled humidity

at atmospheric pressure. Characteristics of these samples holders and the environmental chamber are

listed in Table 7-1. Bear in mind that the temperatures listed are those of the sample holder, not the sam-

ple. The temperature of the sample is not measured. Equilibrium sample temperatures may be different due

to poor thermal conduction between the sample and the sample holder and heat losses to the environ-

ment. Furthermore, it may take up to 30 min for the sample temperature to reach equilibrium.

18



Table 7-1: Options for sample temperature and humidity control.

Sample

Holder

Sample Types &

Containers

Temperature

Range (°C)

Relative

Humidity

Range

(%)

Ambient

Pressure

Controller

Linkam Film, sheet, plate,

wrapped powder

-150 to 300 N/A Vacuum Linkam

Linkam sandwich cell, dis-

posable capillary

-150 to 300 N/A Atm. 1 Linkam

JSP Re-usable capillary 5 to 70 2 N/A Atm. 1 Julabo Heater / Chiller

Environmental

Chamber

Film, sheet, plate,

wrapped powder

room to 90 0 to 95 Atm. Humidity Generator &

Julabo Heater/Chiller

1 The sample holder is sealed so although the sample holder is in vacuum, the sample is at atmospheric pressure.

2 The recommended temperature range for aqueous solutions is 5°C to 70°C. Outside this range, the risk of the ca-

pillary breakage increases. With care, temperatures up to 80°C are permissible. For non-aqueous solutions, tempera-

tures down to -20°C may be permissible, depending on the solution.

7.6 Sample Holders

7.6.1 Ambient Plate

The ambient plate sample holder (see Figure 7-2) is suitable for room temperature measurements of the

following types of samples.

Films, sheets, or thin plates. Typically, these are taped to the ambient plate.

Powders enclosed appropriately, e.g., wrapped in aluminum foil, placed in an o-ring or washer

sandwiched between two layers of tape, or placed in a sealed, disposable capillary. The wrapper

should be taped to the ambient plate.

Inviscid liquids in sealed, disposable capillaries.

19



Figure 7-2: Ambient plate sample holder with samples taped to the plate.

The ambient plate sample holder has a set of 4 mm dia. holes, which are 8 mm centre to centre, arrayed in

ten columns of four holes in the centre and one column of six holes at each end; however, the column at

each end is not accessible for measurements because the sample stage has insufficient range. In addition,

there are three larger rectangular holes across the top, which are accessible.

Disposable, 1.5 mm diameter, thin-walled (e.g., 0.01 mm) quartz capillaries may be clamped to the ambi-

ent plate with the accessory capillary plate (see Figure 7-3). Users must provide their own capillaries, which

may be purchased from 4D Labs. If the capillary fits loosely, it may be necessary to hold it in place with

tape.

20



Figure 7-3: Ambient plate sample holder with capillary plate and a disposable 1.5 mm diam-eter, 80 mm long capillary.

When viewed from one end, the ambient plate is L-shaped and should be mounted on the sample stage

with the bottom of the L pointing left and the label to the front (see Figure 7-4). In this orientation, sam-

ples should be on the left side and the label on the end should face the vacuum chamber door.

Figure 7-4: Ambient plate sample holder mounted on the sample stage. Viewed from the left side of the vacuum chamber door.

21



7.6.2 Sandwich Cell Holder

The sandwich cell holder can accommodate six sandwich cells and is suitable for ambient temperature

measurements of viscous liquids, pastes, and powders (see Figure 7-5).

Figure 7-5: Sandwich cell holder with five sandwich cells mounted.

Like the ambient plate, the sandwich cell holder is L-shaped when viewed from the end but, unlike the

ambient plate, the bottom of the L should point to the right when the holder is installed on the sample

stage (see Figure 7-6).

22



Figure 7-6: Sandwich cell holder on the sample stage. Viewed from the vacuum chamber door.

7.6.3 JSP Re-Usable Capillary Holder

The JSP re-usable capillary holder (see Figure 7-7) can accommodate five re-usable, thin-walled (e.g., 0.01

mm) quartz capillaries, which are sealed with o-rings. Users must provide their own capillaries, which may

be purchased from 4D Labs.

23



Figure 7-7: JSP re-usable capillary holder. There is a temperature probe in position 1 (far right) and a capillary in position 2 (second from right).

The JSP re-usable capillary holder may be heated or cooled by the Julabo chiller. The temperature of the

sample holder is measured by in temperature probe in position 1, leaving positions 2 – 6 available for re-

usable capillaries. For aqueous samples, the recommended temperature range is 5°C – 70°C. It is possible

to go up to 80°C but the risk of breaking the capillaries increases.8 Non-aqueous and some aqueous sam-

ples may be cooled below 5°C but thermal expansion of aqueous samples may break the capillaries. The

lower limit is about -20°C.

When the JSP re-usable capillary holder is inserted into the sample stage, the electrical cable and two

chiller fluid connectors should be at the front (see Figure 7-8). The fluid connectors are interchangeable.

When joining the fluid connectors push them on firmly. Afterwards, try to pull each connector apart to en-

sure the connections are secure.

After disconnecting the chiller fluid connectors, they should be wiped with a lint-free tissue to remove any

residual chiller fluid.

8 The plastic tubing will soften at 90°C so do not exceed 90°C under any circumstances.

24



Figure 7-8: JSP re-usable capillary holder mounted on the sample stage, as viewed from the detector. The vacuum chamber door is to the right. On the capillary holder, there is a tem-perature probe in position 1 (far right) and a capillary in position 2 (second from right).

7.6.4 Linkam Sample Holder

The Linkam holder may be heated or cooled over the temperature range -150°C to 300°C. Cooling is ac-

complished by flowing liquid nitrogen through the stage and heating with an electrical heater. Note that,

for temperatures below room temperature, the heater is used in conjunction with liquid nitrogen cooling in

order to get a faster and more accurate response. For temperatures above room temperature, it is advisa-

ble to allow air to flow through the Linkam holder (instead of LN2). Otherwise, when cooling of the sample

is desired, the cooling rate will be very low.

25



The following samples and sample enclosures may be mounted on the Linkam holder.

Film, sheet, or plate held in place with the circular clip (see Figure 7-9a).

One sandwich cell held in place with the circular clip (see Figure 7-9b).

One disposable capillary,1.0 – 1.5 mm dia. and at least 90 mm long, held in place by a pair of PTFE blocks with 1.6 mm diameter holes (see Figure 7-9c).

a b c

Figure 7-9: Linkam sample holder configured for transmission with a) sheet sample, b) sandwich cell, and c) capillary.

The L-shaped Linkam holder is inserted onto the sample stage in a similar manner to the ambient plate

holder, i.e., the bottom of the L points to the left and the sample is mounted on the left side. One electrical

connector and two silicone tubes should be connected to the top of the Linkam stage. The tubing and elec-

trical cable pass through a vacuum feedthrough to the outside of the chamber.

For temperatures below room temperature, on the outside of the feedthrough, the tube from the LN2 dew-

ar should be connected to the stainless tube stub in the vacuum feedthrough labelled "IN". A silicone tube

from the Linkam controller should be connected to the other stainless tube stub in the vacuum feed-

through, labelled "OUT". The Linkam controller controls the flow of LN2 by pumping on this tube.

26



For heating above room temperature the LN2 dewar is not necessary but a cooling gas is still useful or the

cooling rate will be very low. In this case, room air may be used as the cooling gas so the IN tube on the

outside of the vacuum feedthrough is simply left open. The OUT tube should still be connected to the

Linkam controller so that the air flow can be controlled.

Figure 7-10: Linkam sample holder on the sample stage, viewed from the vacuum chamber door.

Whenever the silicone tubes inside the vacuum chamber are not connected to the Linkam holder, the two

stainless tube stubs on the outside should be connected to each other with a short length of silicone tub-

ing. Otherwise, air will leak into the vacuum chamber through the tube stubs.

27



7.6.5 Environmental Chamber

Figure 7-11: Environmental chamber.

28



Figure 7-12: Sample holder removed from environmental chamber. The sample holder is ro-tated 90° clockwise when it is inserted in the environmental chamber.

8 Capillary Filling & Cleaning Procedure

Both disposable and re-usable capillaries must be purchased.

CAUTION

Wear safety glasses and gloves when handling capillaries.

8.1 Before Measurements

1) Remove the caps from the capillary, noting which end of the capillary the caps are from.

2) Wash the caps with DI water, isopropanol, and then DI water.

3) Flush the capillary with DI water. This can be done with the squirt bottles or with a syringe.

4) If required, flush the capillary with 10 mL of 10% Contrad™ detergent (or equivalent) using a syringe.

5) Flush the capillary with isopropanol. This can be done with the squirt bottles or with a syringe.

6) Flush the capillary with DI water.

7) Dry the capillary with air using a syringe. DO NOT use any other method to dry the capillary.

29



8) Wash the capillary with about 100 μL of buffer solution.

9) Load the capillary with sample or buffer for SAXS analysis. If using the SAXS1 capillary, load with 35

μL of sample. If using the SAXS2 capillary, use 100 μL, but only add enough sample to fill the capillary.

a) It is best to hold the capillary horizontal to the table when loading sample.

b) Avoid air bubbles in the measurement region of the capillary.

10) Place the caps on the capillary by alternately tightening each end. The liquid in the capillary will move

as the caps are tightened. Makes sure the liquid ends up in the center of the analysis window.

11) If using a disposable capillary,

a) seal the ends of the capillary and

b) test the capillary in a vacuum chamber to ensure there are no leaks.

8.2 After Measurements

1) Remove the caps from the capillary, noting which end of the capillary the caps are from.

2) Wash the caps with DI water, isopropanol, and then DI water.

3) Flush the capillary with DI water. This can be done with the squirt bottles or with a syringe.

4) If needed, flush with 10 mL of 10% Contrad™ detergent (or equivalent) using a syringe.

5) Flush the capillary with isopropanol. This can be done with the squirt bottles or with a syringe.

6) Flush the capillary with DI water.

7) Dry the capillary with air using the syringe. DO NOT use any other method to dry the capillary.

30



9 Measurement Procedure

9.1 Setup

1) Create a ticket on the 4D Labs Nanofabrication web site.

2) Create a record in the SAXS user log book.

3) Check the vacuum chamber pressure. It should be < 1 x 10-1 mbar.9

4) Observe whether the yellow lamp on the light tower is on, indicating that the x-ray source is on. If not,

contact the tool owner.

5) Check that the x-ray voltage and current on the Xenocs GeniX x-ray source controller are at the normal

operating values, i.e., 50 kV and 0.60 mA, respectively. If not,

a) Check whether the x-ray source controller warns the tube warm-up is required. If so, contact the

tool owner. Otherwise, proceed.

b) Ensure the GICC is off or paused.

c) Ramp up the x-ray source voltage and current by typing in the spec window:

>x_start

The x-ray source should ramp up to normal operating conditions within 3 min.

6) If the vacuum chamber lamp is off, it may be switched on as follows.

a) Ensure the GICC is off or paused.

b) In the spec window, type: >light_on The vacuum chamber lamp should illuminate. If not, ensure that the switch hanging from the cam-era is on and that the brightness is adjusted appropriately.

9.2 Sample Loading

1) Ensure that vacuum chamber door latch is off.

2) Ensure that GICC is running and not paused.

9 Base pressure is 1 x 10-2 mbar.

31



3) In the GICC window, press Vent.

4) Wait for venting to complete (a little over 1 minute).

5) Open the vacuum chamber door.

6) With your left hand, loosen the two screws which hold the sample holder onto the sample stage.10

7) With your left hand, slide the sample stage out and place it in the sample stage drawer.

8) Close the vacuum chamber door.

9) Mount your samples on an appropriate sample holder (see Section 0).11 Ensure that no sample will leak

when placed in the vacuum chamber. If using tape to mount samples on the sample holder, ensure

that there is a beam path which avoids the tape.

10) Make a note of the sample positions and a blank position nearby.

11) Open the vacuum chamber door and, with your left hand, slide the sample holder onto the sample

stage, pushing it all the way back.

CAUTION

Do not touch the mirror to the right of the sample stage. It is easily misaligned.

12) Ensure that the sample holder is installed in the correct orientation (see Section 7.6).

13) With your fingers, tighten the two screws required to keep the sample holder in place.12

14) If heating, cooling, or humidity control is required, connect the electrical connector and tubing as fol-

lows (cf. Section 7.6).

a) JSP re-usable capillary holder (see Figure 7-8):

i) Ensure the coolant tubing and electrical connector are on top and at the front of the sample

holder.

ii) Push the Julabo electrical cable onto the electrical connector of the holder.

10 The screws should be only finger tight.

11 In general, your samples should be fairly close together and close to the desired blank position in order to minimize the time

taken for the stage to move between samples and the blank position.

12 A wrench is neither necessary nor desired.

32



iii) Push the two female Julabo coolant connectors firmly onto the male connectors of the sample

holder.

iv) Attempt to pull apart each pair of connectors. They must not come apart.

b) Linkam sample holder (see Figure 7-10):

i) Push the Linkam electrical cable onto the electrical connector of the sample holder.

ii) Push the two silicone tubes onto the tube stubs on top of the sample holder.

c) Environmental chamber:

15) Close and latch the vacuum chamber door.

16) Let the software know which sample stage is installed as follows.

a) Select GICC pause mode, by pressing the black pause button ( || ). The button should turn red ( || ).

b) In spec, type

> change_sample_stage

A numbered list of sample holders should appear.

c) Type the correct sample holder number.

d) Select GICC run mode, by pressing the red pause button ( || ). The button should turn black ( || ).

17) Warn everyone else in the room that there will be a loud noise.

18) In the GICC window, press Evacuate.

19) After a few seconds, the latch should release. If it does not, release the latch and inform the tool own-

er.

20) The system is ready when the spec window no longer displays > sleeping t, where t is a time in sec-

onds, and spec is ready to accept a new command.

21) Measurements should commence after the vacuum chamber pressure has dropped below 2 x 10-1

mbar. This should take < 5 min.13, 14

13 If the pressure has not dropped below 2 x 10-1 mbar in 5 min, check for vacuum leaks. If the pressure remains above 2 x 10-1

mbar, inform the tool owner.

14 Measurements may be made at pressures > 2 x 10-1 mbar, but the background signal will be high.

33



9.3 Heating and Cooling

9.3.1 Julabo Heater/Chiller

The Julabo chiller is used to heat or cool the JSP re-usable capillary holder and the environmental chamber.

JSP Re-usable Capillary Holder: For aqueous samples, the recommended temperature range is 5°C –

70°C. It is possible to go up to 80°C but the risk of breaking the capillaries increases. Do not exceed 90°C

under any circumstances because the plastic tubing will soften. Non-aqueous and some aqueous samples

may be cooled below 5°C but thermal expansion of aqueous samples may break the capillaries. The lower

limit is about -20°C.

Set the sample temperature with the Julabo heater/chiller as follows. Times are always in seconds and

temperatures in °C.

1) Ensure that the electrical cable and tubing from the Julabo heater/chiller is securely connect to the

sample holder.

2) Ensure that the power to the Julabo heater/chiller is switched on (top unit).

3) Ensure that the power to the Julabo controller is switched on (bottom unit).

4) Ensure that the Julabo heater/chiller is set to external control.

5) Ensure that the GICC is closed or paused.

6) Go to the spec window.

7) Start temperature control.

>julabo_start

The Julabo heater/chiller pump should switch on and the fluid should begin to cool. Go to the next

step promptly.

8) Use the PT100 temperature probe on the JSP re-usable capillary holder for temperature control.

>julabo_pt100_control

9) Set the desired temperature T1 and hold for time ts.

>julabo_stabilise T1 ts tmax

34



where

T1 = temperature set point

ts = time for which temperature is kept constant after reaching T1

tmax = the upper time limit for the temperature to reach T1.

If the temperature has not stabilized at T1 in time tmax, the command is aborted.

10) (Optional) Display the current temperature.

>julabo_get_temperature

11) (Optional) Log the temperature for time tw.

>julabo_watch tw

12) When finished, end temperature control.

>julabo_end

Ensure that the sample holder is close to room temperature before venting and removing the sample hold-

er.

9.3.2 Linkam Sample Holder

Set the temperature of the Linkam sample holder as follows. Times are always in seconds and tempera-

tures in °C.

1) Ensure that the electrical cable and tubing from the vacuum feedthrough is securely connect to the

sample holder.

2) Ensure that the silicone tubing from the Linkam controller is connected to the vacuum feedthrough

OUT tube stub.

3) If LN2 cooling is required:

a) Fill the LN2 dewar with LN2.

b) Connect the LN2 dewar tubing to the vacuum feedthrough IN tube stub.

4) If LN2 cooling is not required, leave the IN tube stub open.

5) Ensure that the power to the Linkam pump is switched on (top unit).

6) Ensure that the power to the Linkam controller is switched on (bottom unit).

35



7) Ensure that the GICC is closed or paused.

8) Go to the spec window.

9) Start temperature control.

>linkam_start

10) Set the pump mode depending upon whether LN2 or air is used for cooling.

a) LN2 cooling

>linkam_pump_auto

b) Air cooling

>linkam_pump_manual

11) Set the temperature ramp rate dT/dt in °C/s.

>linkam_set_rate dT/dt

12) Set the desired temperature T1.

>linkam_set_setpoint T1

13) Set the desired temperature T1 and hold. Temperature is logged until T1 is reached. Abort if it the time

required to reach T1 exceeds tmax.

>linkam_stabilise T1 tmax

14) (Optional) Display the current temperature in °C.

>linkam_get_temperature

15) (Optional) Log the temperature for time tw in seconds.

>linkam_watch tw

16) When finished, end temperature control.

>linkam_end

Ensure that the sample holder is close to room temperature before venting and removing the sample hold-

er.

36



9.4 Transmission Mode X-Ray Scattering

9.4.1 Measurements Using GICC Interactive Mode

This section describes the procedure for measuring the scattering from an x-ray beam, which is transmitted

through a sample, using interactive commands from the Ganesha Interactive Control Center (GICC).

Figure 9-1: GICC window with Sample Positions panel expanded.

1) Set the temperature of the sample holder using spec and make a note of the time.

2) Ensure that GICC is running and not paused. The pause button ( || ) at the upper right of the GICC

window (see Figure 9-1) should be black. If it is red, click it and it should turn black.

3) Ensure that the macro panel (which would be on the far right) is collapsed (as shown in Figure 9-1).

4) Ensure that the RayCam video window is open and visible. If it is open, the CAM1 button in the Gane-

sha Control Panel will be blue. If it is closed, the button will be yellow. In that case, press the button

and the RayCam video window should open.

37



5) Move the sample into the path of the x-ray beam, which is marked by the cursor in the RayCam video

window, by any of the following methods. If the sample is taped in to the sample holder, avoid moving

the tape into the x-ray beam.

a) Relative movements using the Horizontal and Vertical + and - buttons in the Placement panel.

b) Absolute movements by typing the desired positions in the Horizontal and Vertical absolute posi-

tion boxes and pressing the respective Go buttons in the Placement panel.

c) Selecting the desired position on the appropriate sample holder schematic and pressing the Go To

button in the Sample Positions panel.15 If the Sample Positions panel is collapsed, expand it by

clicking on the arrowhead ( < ) in the vertical bar on the left side of the GICC window.

The current values of the horizontal and vertical coordinates are displayed in the blue boxes in the

Placement panel.

6) (Optional but strongly recommended if the sample is in a capillary). Fine tune the sample position, ac-

cording to whether the sample is in a capillary or not.

a) If the Configuration is set to 2 Apertures MAX, proceed to the next step. Otherwise,

i) Scroll to 2 Apertures MAX in the Configuration panel.

ii) Press the Go button, immediately to the right of the configurations list.

iii) Wait for the configuration to change.

b) If the sample is not in a capillary, perform the following alignment procedure. If the sample is

in a capillary, skip this step.

i) Press the Scan Sample button in the Scans section of the Placement panel. The Scan Sample

window should open.

ii) Select the Scan Direction (Horizontal or Vertical).

iii) Enter the scan range (Start and Finish), number of measurements (Intervals), and measurement

duration (Time).

iv) Press OK. The x-ray intensity will be measured by the pin diode and the results displayed in the

scan plot window.

15 Here, it is assumed that the sample holder is correctly referenced.

38



v) Determine the optimal position and move to that position, using the controls in the Placement

panel.

vi) Repeat steps ii) to v) for the other Scan Direction.

c) If the sample is in a capillary, perform the following alignment procedure. If the sample is not

in a capillary, skip this step.

d) Press the Align Capillary button in the Scans section of the Placement panel. The Align Capillary

window should open.

e) Select the Scan Direction (Horizontal or Vertical), which is normal to the axis of the capillary.

f) Enter the scan Half-range and number of measurements (Intervals).

g) Press OK. The x-ray intensity will be measured by the pin diode and the results displayed in the

scan plot window. The optimal position will be determined automatically and the sample holder

will move to that position.

7) Record the sample position.

8) Define the blank position as follows.

a) Move the sample holder to a position in which nothing lies in the path of the x-ray beam, which is

marked by the cursor in the RayCam video window, by any of the following methods. An empty

hole in the sample holder is usually most convenient.16

i) Relative movements using the Horizontal and Vertical + and - buttons in the Placement panel.

ii) Absolute movements by typing the desired positions in the Horizontal and Vertical absolute

position boxes and pressing the respective Go buttons in the Placement panel.

iii) Selecting the desired position on the appropriate sample holder schematic and pressing the Go

To button in the Sample Positions panel.17 If the Sample Positions panel is collapsed, expand it

by clicking on the arrowhead ( < ) in the vertical bar on the left side of the GICC window.

b) (Optional). Fine tune the blank position.

i) If the Configuration is set to 2 Apertures MAX, proceed to the next step. Otherwise,

16 For efficient measurements, the blank position should be close to the sample position.

17 Here, it is assumed that the sample holder is correctly referenced.

39



(1) Scroll to 2 Apertures MAX in the Configuration panel.

(2) Press the Go button, immediately to the right of the configurations list.

(3) Wait for the configuration to change.

ii) Press the Align Hole button in the Scans section of the Placement panel. The Align Hole win-

dow should open.

iii) Select the Scan Direction (Horizontal or Vertical).

iv) Enter the scan range (Start and Finish), number of measurements (Intervals), and measurement

duration (Time).

v) Press OK. The x-ray intensity will be measured by the pin diode and the results displayed in the

scan plot window.

vi) Determine the optimal position and move to that position.

vii) Repeat steps iii) to vi) for the other Scan Direction.

c) Press the Set button in the Blank Position section of the Direct Control panel. The Blank Position

coordinates boxes should be updated to the current position.18

9) Scroll to the number of apertures and q-range in the Configuration panel, using the configurations list

(Section 11) as a guide. If using multiple q-ranges, start with the highest range first because it will be

fastest.

10) Press the Go button immediately to the right of the scroll box.

11) Scroll to the desired beam stop configuration in the Configuration panel.

12) Press the Go button immediately to the right of the scroll box.

13) Ensure that the sample holder is in the blank position, e.g., by clicking the Go to button in the Blank

Position section of the Direct Control panel.

14) Press the Fine Tune BS button in the Configuration panel.

15) Wait for beam stop tuning to be completed. Its progress may be followed in the spec window.

16) Press the Fine Tune BS button in the Configuration panel a second time.19

18 Now, it is possible to return to the Blank Position quickly by pressing the Go to button in the Blank Position section.

19 Actually, this should only be necessary if the beam stop reference position has changed substantially, e.g., if changing be-

tween centred and off-centre beam stop configurations. Nevertheless, it is safer to fine tune the beam stop twice regardless.

40



17) Wait for beam stop tuning to be completed.

18) Move to the sample position.

19) Specify the optional measurement parameters in the Measurement Details panel.

a) Transmission + IO: If checked, sample transmission and x-ray beam intensity are measured. Re-

quired for calculation of absolute scattering intensities.

b) BS Mask: If checked, a mask is placed over the beam stop in the 2D scattering images. Recom-

mended.

c) BS In: If checked, the direct beam is blocked in front of the detector. Strongly recommended.

d) Overwrite Thickness: If checked, allows the sample thickness (in cm) to be entered in the box at

the right. Required for accurate calculation of absolute scattering intensities.

e) Description: Labels 2D scattering images with the description typed in the box, e.g., sample name,

q-range, measurement time. Recommended.

20) Enter the measurement time in the Time box. Use the configurations list (Section 11) as a guide.

21) If necessary, wait for the sample temperature to equilibrate.

22) Check that the vacuum pressure < 2 x 10-1 mbar.20

23) To start the measurement, press the red Measure button. When the measurement commences, the

Abort button should appear.

24) (Recommended). Record the Description and the measurement number, immediately to the left of the

Measure button, and. The data filename will include this number.

25) Monitor the measurement as follows.

a) Open SAXSGUI.

b) In the file menu, select File: Open Latest. SAXSGUI image viewer should open and display the 2D

data.

A measurement may be aborted at any time by pressing the Abort button. After aborting, check whether

the shutter is open or closed. 21 If the shutter remains open, close it by pressing the Close button in the

Shutter section of the Direct Control panel.

20 Measurements may be made at pressures > 2 x 10-1 mbar, but the background signal will be high.

41



9.4.2 Measurements Using Macros

9.4.2.1 Introduction

This section describes the procedure for measuring the scattering from an x-ray beam, by creating and run-

ning a macro. Macros are especially convenient when making multiple measurements of a single sample

(e.g., different q-ranges) or measurements of multiple samples.

A macro may be created and modified by using GICC macro mode or a text editor. In GICC macro mode,

commands are created by the graphical user interface without any knowledge of the spec command lan-

guage; however, GICC does not allow temperature control. Using a text editor requires some knowledge of

spec but if one is only making simple modifications to an existing macro, only rudimentary knowledge of

spec may be required.

In this document, only the GICC macro mode will be described.

9.4.2.2 Creating and Modifying a Macro with GICC

The procedure for creating a macro follows.

1) Find, set, and record the sample position, as described for GICC's interactive mode (see Section 9.4.1).

2) Find, set, and record a convenient blank position, as described for GICC's interactive mode (see Section

9.4.1).

3) Expand the macro panel by clicking on the arrowhead ( > ) in the vertical bar on the right side of the

GICC window.

21 An open shutter is indicated by illumination of the red lamp on the light tower and Open is displayed in the blue shutter status

box in the Direct Control panel of the GICC.

42



Figure 9-2: GICC window with Macro panel expanded.

4) Start the macro recorder by clicking the New button in the macro toolbar, at the top of the macro pan-

el. Subsequently, each time that a GICC button is pressed, instead of performing that action, a macro

command for that action will be created and displayed in the macro panel.

5) Move to the blank position.

6) Perform steps 9) - 23) in Section 9.4.1.

7) When recording the macro has been completed, save the macro in your own Macros folder in either or

both of two formats.

a) To save in .gicc format, click either the Save or Save as button. Files in the .gicc format, can be

opened by GICC.

b) To save in .macro format, click the Export button.

Macros saved in the .gicc format may be modified by:

1) Click the Open button in the GICC macro toolbar.

2) Navigate to your Macros folder and open the desired macro. It should appear in the macro pane.

3) Right click on any command in the macro to open a menu.

43



4) Left click to select Remove, Replace, or Insert Before.

Macros in .mac format may be opened and modified by a text editor.

Lines beginning with # are ignored when the macro is run so # is useful as a prefix for comments.

9.4.2.3 Running a Macro

Macros in the .gicc format may be run from GICC by opening them and then clicking Run in the GICC mac-

ro toolbar. Macros in the .macro format may be run from spec, by executing the command:

>qdo /home/saxslab/Users/UserFolderName/Macros/filename.macro

Here, it is assumed that the macro is in the Macros folder in your personal folder in the Users folder.

9.5 Exporting Data

Data are saved in the saxsgui\Data, which can be reached via the desktop shortcut Link to Data. In the Da-

ta directory, data are stored in three directories.

1) Latest – real-time live sum of all short measurements, equals Images equivalent when measurement

finishes

2) Images – end product after measurement finishes

3) Frames – zipped folder of all 15 second frames collected during measurement associated with specific

image number

Images and Latest have raw and corrected sub-directories. The latter contain corrected data, in which sus-

pected cosmic ray events have been removed.

You should export your data to your personal folder. Export multiple data files to your personal Data direc-

tory as follows.

1) In the menu bar of the SAXSGUI image viewer, select Processing: AutoProcess: AP From MetaData.

44



2) Select all of the images you want to export.

3) Click Open.

4) Select the destination folder, which should be in your personal folder.

5) Click OK

9.6 Sample Unloading

It is your responsibility to retrieve your samples promptly after your measurements are completed and to

dispose of them. Unless you have made other arrangements with the tool owner, you will be responsible

for tool charges as long as your samples remain in the vacuum chamber. Completely remove tape or other

adhesives from the sample holder. Do not remove any calibration samples such as AgBeh.

The procedure for unloading samples is as follows.

1) Ensure that vacuum chamber door latch is off.

2) Ensure that GICC is running and not paused.

3) In the GICC window, press Vent.

4) Wait for venting to complete (a little over 1 minute).

5) Open the vacuum chamber door.

CAUTION

Do not touch the mirror to the right of the sample stage. It is easily misaligned.

6) Disconnect any cables or tubing from the sample holder as follows (cf. Section 7.6).

a) JSP re-usable capillary holder (see Figure 7-8):

i) Disconnect the two Julabo coolant connectors from the sample holder.

ii) Wipe each of the four connectors with a tissue to remove residual coolant.

iii) Disconnect the Julabo electrical cable from the sample holder.

b) Linkam sample holder (see Figure 7-10):

45



i) Disconnect the Linkam electrical cable from the sample holder.

ii) Gently pull off the two silicone tubes on the tube stubs on top of the sample holder.

iii) Go to the outside of the Linkam vacuum feedthrough.

iv) If applicable, disconnect the LN2 dewar tube from the IN tube stub in feedthrough.

v) Disconnect the silicone Linkam controller tube from the OUT tube stub in feedthrough.

vi) Connect the IN and OUT tube stubs with a short length of silicone tubing.

c) Environmental chamber:

7) Place the cables and tubing which will be left in vacuum in positions which will interfere with the stage

motion or x-ray beam.

8) With your left hand, loosen the two screws which hold the sample holder onto the sample stage by

about ½ turn each.

9) With your left hand, slide the sample stage out and place it in the sample stage drawer.

10) Close and latch the vacuum chamber door.

11) Warn everyone else in the room that there will be a loud noise.

12) In the GICC window, press Evacuate.

13) After a few seconds, the latch should release. If it does not, release the latch and inform the tool own-

er.

14) The system is ready when the spec window no longer displays > sleeping t, where t is a time in sec-

onds, and spec is ready to accept a new command.

15) Select GICC pause mode, by pressing the black pause button ( || ). The button should turn red ( || ).

16) In the spec window, type:

>light_off

46



10 spec Command Quick Reference

spec is software developed by Certified Scientific Software for x-ray diffraction instrument control and data

acquisition. Documentation for spec, including manuals and user guides, may be found at:

http://www.certif.com/content/spec/

spec commands commonly used to control the Ganesha SAXS system are listed and described in this sec-

tion.

10.1 Most Frequently Used Commands

Command Description

vent_system Vent the vacuum chamber

evacuate_system Evacuate the vacuum chamber

c_shut Close the Shutter

o_shut Open the Shutter

conf_go conf_ugo what_conf

Go to a predefined configuration, update

mv umv mvr umrv

Moves motors in different ways

wu Shows motor positions

ascan dscan lup

Different types of motor scans

pd_in Move pin-diode into beam

pd_out Move pin-diode out of beam

SAMPLE_DESCRIPTION=”hello” Sets a parameter that is written to master.dat and image header

saxsmeasure Starts the measurement and saves it

killsaxsmeasure Abort the measurement

transmission_measure Measures the transmission of a sample

blankpos_def Define blank position

qdo macro-file Execute the commands in the macro file (quiet do)

mv_beam2bstop Centers the beam on the beam stop

light_on, light_off Turns the light in the chamber on and off

http://www.certif.com/content/spec/

47



10.2 Standard spec Commands

Command Description

wa list of all defined motors with its user and dial values

wu list of all defined motors with its user values

wm motor-name1 motor-name2 ... where motors: user and dial values, soft limits of motors

mv motor-name number absolute move of a motor by number [mm] or [º]

mvr motor-name number relative move of a motor by number [mm] or [º]

umv motor-name number updated absolute move of a motor by number [mm] or [º]

umvr motor-name number updated relative move of a motor by number [mm] or [º]

ascan motor-name init_value final_value nº_of_steps time_per_step

absolute scan – remember to open shutter before running this

dscan motor-name init_value final_value nº_of_steps time_per_step

relative scan – remember to open shutter before running this

lup motor-name init_value final_value nº_of_steps time_per_step

relative scan, which goes to the peak afterwards

counters define your counters

setplot define parameters of the plot on the screen

plotselect define counters to be plotted

Ctrl-C stop execution of a command

newsample Allows to define parameters for new sample (filename, plot window, etc.)

prdef macro-name listing of commands in a known macro

lsdef *name* list of known macros containing string name

change_bstop_conf Change the desired beam stop position/configuration

bstop_in Move the beam stop into nominal position

bstop_out Move the beam stop out of the detector area

pd_in Move pin-diode into beam

pd_out Move pin-diode out of beam

do_sleep wait_time Wait for wait_time in seconds

10.3 Configuration Related Commands

Command Description

what_conf Ask what configuration is most likely the present

conf_go conf# Go to the configuration specified (using configuration variables)

conf_ugo conf# Go to the configuration specified (using configuration variables) – updating positions

conf_lineup conf# Create lineup procedure for configuration specified

full_conf_lineup conf# Create lineup procedure for configuration specified including detector alignment

detpos_go conf# detpos_ugo conf#

Go to the detector position in the specified configuration

conf_save conf# Save the present pinhole location to the pinhole configuration variables

conf_save2disk Saves the present pinhole configuration variables to a file that can later be reloaded

conf_load_latest Loads latest saved pinhole positions

conf_load_default_positions Loads old default positions

48



10.4 X-Ray Source and Detector Commands

spec can only control the x-ray source if the Xenocs GeniX x-ray source controller is set to re-

mote control.

Command Description

o_shut Open X-ray Shutter

c_shut Close X-ray Shutter

x_start Starts X-ray generator and goes to standby mode

x_ramp Ramps the X-ray generator and goes to full power

x_standby Moves the X-ray generator to standby values

x_off Turns the generator off

change_bstop_conf Change the desired beam stop position/configuration

bstop_in Move the beam stop into nominal position

bstop_out Move the beam stop out of the detector area

pd_in Move Pin-diode into beam

pd_out Move Pin-diode out of beam

10.5 Configuration Commands

Command Description

what_conf Ask what configuration is most likely the present

conf_go conf# Go to the configuration specified (using configuration variables)

conf_ugo conf# Go to the configuration specified (using configuration variables) – updating positions

conf_lineup conf# Create lineup procedure for configuration specified

full_conf_lineup conf# Create lineup procedure for configuration specified including detector alignment

detpos_go conf# detpos_ugo conf#

Go to the detector position in the specified configuration

conf_save conf# Save the present pinhole location to the pinhole configuration variables

conf_save2disk Saves the present pinhole configuration variables to a file that can later be reloaded

conf_load_latest Loads latest saved pinhole positions

conf_load_default_positions Loads old default positions

10.6 Commands for Time-sequences

Command Description

timescan counting-time sleep-time Counts until it is stopped. In-between each counting time there is a sleep time.

loopscan npoints counting-time sleep-time As time scan but stops after npoints

49



10.7 Julabo Heater/Chiller Commands

Command Description

julabo_start Switches ON communication with Julabo Controller (overhead cost = 4 seconds)

julabo_end Switches OFF communication with Julabo Controller

julabo_counter_on Start using Julabo as a counter (to Julabos and Julaboe)

julabo_counter_off Stop using Julabo as a counter

julabo_get_temperature Get current temperature of Julabo stage

julabo_get_setpoint Get current setpoint for Julabo stage

julabo_set_setpoint(temp) Sets the temperature setpoint to temp

julabo_stabilise s_p stabiliza-tion_time maxtime

Sets setpoint to s_p and logs temperature until the temperature is reached. After the temperature is reached it stabilizes for the given time. If reaching the tem-perature takes more than maxtime then the command is stopped

julabo_watch maxtime Logs the temperature for maxtime

julabo_cool Cools the Julabo stage as fast as possible

10.8 Linkam Thermal Stage Commands

Command Description

linkam_start Switches ON communication with Linkam Controller (overhead cost = 4 seconds)

linkam_end Switches OFF communication with Linkam Controller

linkam_pump_auto Start the Linkam pump in auto mode. Manual mode can also be set Linkam_pump_manual, and then Linkam_set_pump speed. But this is not recom-mended

linkam_stabilise s_p max-time

Sets setpoint to s_p and logs temperature until the temperature is reached. Unless maxtime is exceeded.

_linkam_get_temperature() Returns current temperature of Linkam holder

linkam_get_temperature Get current temperature of Linkam holder

linkam_get_rate Get current ramp rate for Linkam holder

linkam_get_setpoint Get current setpoint for Linkam holder

linkam_set_rate rate Sets the temperature ramp rate to rate degrees per minute

linkam_set_setpoint temp Sets the temperature to temp degrees

linkam_set_pumpseed nn Sets the pump speed to nn%

linkam_watch maxtime Logs the temperature for maxtime

linkam_cool Cools the Linkam holder as fast as possible

50



11 Configurations

11.1 2 Slit Configurations

Conf. Name Description DETX value

Nom. Beam Stop

qmin qmax Io Aperture Dimensions

Resolution

S1 S3 Incident Scattered Total q

mm mm Å-1

Å-1

Mph/s mm mm Radians Radians Radians Å-1

0 Open Open Apertures

21 WAXS Wide Angle, 2 mm beam stop

10 2 0.07 2.8 55 0.9 0.9 0.00160 0.01061 0.0107 0.0438

22 MAXS Medium Angle, 2 mm beam stop

350 2 0.015 0.65 31 0.9 0.4 0.00116 0.00130 0.0017 0.0071

23 SAXS Small Angle, 2 mm beam stop

950 2 0.007 0.25 4.5 0.4 0.3 0.00062 0.00045 0.0008 0.0031

24 ESAXS Extreme Small Angle, 2 mm beam stop

1400 2 0.0035 0.18 2.2 0.4 0.2 0.00053 0.00025 0.0006 0.0024

25 MAXS-4

Medium Angle, 4 mm beam stop

600 4 0.015 0.4 62 1 0.77 0.00157 0.00136 0.0021 0.0085

26 SAXS-4 Small Angle, 4 mm beam stop

1400 4 0.007 0.18 17 0.6 0.46 0.00094 0.00042 0.0010 0.0042

Sample – Detector Distance ≅ DETX value + 91 mm

Distance = 1125 mm

51



11.2 3 Slit Configurations

Conf. Name Description DETX value

Nom. Beam Stop

qmin qmax Io Aperture Dimensions

Resolution

S1 S2 S3 Incident Scattered Total q

mm mm Å-1

Å-1

Mph/s mm mm mm Radians Radians Radians Å-1

0 Open Open Apertures

1 WAXS Wide Angle, 2 mm beam stop

10 2 0.07 2.8 25 0.7 0.4 0.76 0.00152 0.0092 0.0094 0.0382

2 MAXS Medium Angle, 2 mm beam stop

350 2 0.015 0.65 6.5 0.4 0.3 0.54 0.00097 0.0016 0.0019 0.0077

3 SAXS Small Angle, 2 mm beam stop

950 2 0.007 0.25 1.3 0.3 0.15 0.34 0.00062 0.0005 0.0008 0.0032

4 ESAXS Extreme Small Angle, 2 mm beam stop

1400 2 0.0035 0.18 0.28 0.2 0.1 0.24 0.00041 0.0003 0.0005 0.0020

5 MAXS-4

Medium Angle, 4 mm beam stop

600 4 0.015 0.4 24 0.7 0.4 0.66 0.00152 0.0012 0.0019 0.0079

6 SAXS-4

Small Angle, 4 mm beam stop

1400 4 0.007 0.18 3.5 0.4 0.2 0.42 0.00083 0.0004 0.0009 0.0037

Sample – Detector Distance ≅ DETX value + 91 mm

Distance = 725 mm

Documents

Small Angle X-Ray Scattering System (SAXS) · Simon Fraser University 8888 University Drive, Burnaby, B.C. V5A 1S6 E [email protected] T 778.782.8158 F 778.782.3765 1 Purpose This document