I11 User Manual - Diamond Light Source
Contents
1. 5 Constant Velocity Scanning Commands MAC data collection 5 1 Constant velocity scan cvscan The user specifies only the total time for the scan seconds A motion trajectory is calculated so that the diffractometer 20 circle moves at a constant angular speed The detectors are gated at sufficient frequency to give a nominal 20 interval of 1 mdeg cvscan time Perform constant velocity scan cvscan 1800 Either command performs 20 cvscan with a cvscan 1800 total counting time of 30 minutes scan ds 1 3 1 cvscan 1800 Perform 3 20 cvscans with a counting time of 30 minutes each cvscan stop Stops the current cvscan Constant velocity scans with sample stage translation motor stagescan scan spos start stop Perform a constant velocity scan of specified step cvscan time time at each position of spos scan spos 20 0 4 ovscan 120 Performs a 2 minute constant velocity scan of specified time at each position of spos 20 16 12 8 4 and 0 Constant velocity scan with theta rocking In use the PheniX cryostat 11 300 K gas cell or other user sample environment that is mounted on the theta circle of the diffractometer can be oscillated during a 20 scan This can be done by appending rocktheta at the end of a scan command or switching on off the rocking when required Science Division diamond Doc No BLS I11 MAN 001 Issue 1 7 9 Date 23 April 2015 Page 35 of 542. Science Division diamond Doc No BLS I1 1 MAN 001 Issue 1 7 9 Date 23 April 2015 Page 1 of 54 Beamline I11 User Manual Prepared by Paul Adamson Alistair Lennie Claire Murray Julia Parker Jonathan Potter Chiu Tang Steve Thompson and Fajin Yuan Doc No BLS I11 MAN 001 Science KA Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 2 of 54 Contents 1 Introduction to U1 I nU Em 4 1 1 SCOPE of this COCUMICIU METER T 8 1 2 R lated documents accer eean aaa qaa Rete oh pOUU REN OP EE UR eR NN a opu A DUE RA CU pM PROP RENS 8 EE RB li e 9 3 Sample environment Options aadctoest instinto tide en o E ou nta E EE orn pa M diete E cS EE 10 3 1 Sample ATTN oases TE 11 2 2 Sample Spinners and Doltletsu os OI Odo aes aod a ee eee 12 20 Cryostream 30 300 K I uie sede enas eee ni eraat aeeai See Ea aS EEEN nudes M aM dM 13 3 4 Cyberstar hot air blower RT 1000 9C sees eee eene eee en nennen enne eee netten nonna 14 3 5 PheniX Era e SCENES SN X oem 15 3 0 Cryostat 5 UN qu 19 3 7 Humidity CHAINS Jseseancarersascervizenchseacanserscedecousmeuatwnnsamnseee u Error Bookmark not defined 3 9 Capillary furnace RT 15D0 OC ierse ocideso iced gosuelu ie utu Rete ipud pM RR E id
3. scan ds 13 1 cvscan 1800 rocktheta rocktheta start rocktheta stop rocktheta setLowerLimit 20 rocktheta setUpperLimit 20 6 Step Scanning Commands Single motor or step scan scan scan motor start finish stepsize detector count time scan toh L0 20 0 005 Io 2 Concurrent multi motor scans scan motori startl finishl stepl motor2 start2 step2 detector count time scan tth 10 30 0 002 theta 5 O QUI macis I Perform 3 20 cvscans with a counting time of 30 minutes each whilst rocking the theta circle Starts the theta rocking Stops the theta rocking Sets the lower limit of the rocking motion to be 0 20 Do not change the limits of rocking without checking the range of Sets the lower limit of the rocking motion to be 0 20 Move the motor from start to finish in steps allowing the detector to count for count time seconds at each motor position Scan 20 from 10 to 20 in steps of 0 005 allowing Io to count for 2 seconds at each motor position Scan motor 1 from start1 to finish1 in steps of stepl simultaneously with motor 2 etc collecting data at each point for count time seconds Scan 0 20 concurrently starting at 10 finishing at 30 with 0 steps of 0 001 1 second per step using the MACIS detector Doc No BLS I11 MAN 001 Science CD Issue 1 7 9 wi diamond Date
4. 3 8 Flat plate furnace RT 1700 K Additional instructions will be provided by beamline staff Doc No BLS I11 MAN 001 Science KA M Issue 1 7 9 v Y diamond Date 23 April 2015 Division Page 20 of 54 4 Controlling the instrument All control takes place using two Linux control PCs ws 001 and ws 002 in the control cabin Each PC duplicates the other 4 1 First steps All users need to log in to the data acquisition software GDA as follows e Log on to a linux control PC using your FedID and password supplied by the User Office e using menu bar Applications Data Acquisition 1 start GDA log display This starts a log file which will run continuously e using menu bar Applications Data Acquisition 2 start GDA servers This restarts the GDA servers to load your user visit information e using menu bar Applications Data Acquisition start GDA Client e select OK This starts the GDA client window Figure 12Figure 12 GDA client display Division dip diamond Doc No BLS I11 MAN 001 Issue 1 7 9 Date 23 April 2015 Page 21 of 54 Main Terminal window l Scripting Terminal x r Terminal Tum the acutal trajectory from XPS the acutal trajectory from XPS the acutal trajectory from XPS the acutal trajectory from XPS Scan complete to to to to SSeS yp eS ree ex EPICS please wait EPICS please wait EPICS p
5. Issue 1 7 9 Division i diamond Date 23 April 2015 Page 25 of 54 Nudge motor position UP 1 step Current motor position To change motor position enter new value Step size Nudge motor position DOWN 1 step Figure 15 Diffractometer motor control window DO NOT move the vertical jacks or the X translation you will mis align the diffractometer Care must be taken when moving 0 20 and 6 to avoid collision anti collision switches are in place 4 23 Large sample table Select to open a window for direct control of the position of the large sample table Science Doc No BLS I1 1 MAN 001 Issue 1 7 9 Division diamond Date 23 April 2015 Page 26 of 54 To change motor position enter new value mm Nudge motor position DOWN st PME Kills power to motor Horizontal X direction TL BLIII MO TAELE 02 Nudge motor position UP 1 step Current Position Step Size Figure 16 Motor control for large sample table Users should only make adjustments to the Horizontal Motor 300 Table OUT 0 Table IN Science Division diamond Doc No BLS I11 MAN 001 Issue 1 7 9 Date 23 April 2015 Page 27 of 54 4 2 4 Sample environment options e Select EL to open a window for control of the sample environment options Figure 17 Select the appropriate option for your experiment to open another w
6. startpos to endpos in steps of posstep posstep cvscan time with 2theta start counting for time at each position Robot error codes If the robotic arm fails an error code will be reported in the terminal panel Use this to help beamline staff identify the problem The most common error codes are 2010 Diffractometer move not completed 2450 Interlock problem 3540 Robot interlock key missing 2070 Server not active Doc No BLS I11 MAN 001 Science KA Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 41 of 54 9 Sample environment control commands Command syntax is identical for all variable temperature options with some minor exceptions A 3 letter code is used to distinguish between hardware as follows e ocs Oxford Cryostream e csb Cyberstar Hot air blower e pcs PheniX cryostat e capf STOE capillary furnace e mri flat plate furnace humidity chamber e cs4 4 K cryostat e linkam linkam DSC 9 Fast Temperature Scanning The use of the pos command to set the temperature see below will wait for the temperature to be achieved before returning and allowing the next command e g data collection to be run For fast temperature scanning e g using the PSD with cryostream or hot air blower you may simply wish to set the temperature ramping and be able to collect data as it is changing Please note that an extra command is required for the Cryostream caput BLllI C
7. 23 April 2015 IVISIOD as Page 37 of 54 psdrt 10 A 10 sec PSD data collection with the theta scan delta anglel angle2 anglestep mythen t scan delta 5 5 25 D 25 smythen 1 Scan delta 5 5 25 0 25 mythen 1 Scan tempdevice start T end T T step ds 1 0 n 1 0 mythen t scan oos 200 300 5 ds tL 10 0 1 0 mythen t 0 circle rocking Collects data for one frame at anglel and one frame at angle 2 Two dat files will be written to your data directory eg 12345 mythen 0001 dat and 12345 mythen 0002 dat Using the object smythen in place of mythen means the 2 files will subsequently be summed and the merged file saved 12345 mythen data also summed dat Collects one frame of 1 second at 5 degrees and a second frame at 5 25 degrees Then sums the frames Collects one frame of 1 second at 5 degrees and a second frame at 5 25 degrees A temperature scan can be called to collect multiple frames with the PSD over a range of temperatures Cryostream scan ocs changing temperature from 200 to 300 K in 5 K steps collecting 10 frames of 1 sec at each temperature Note that the number of frames you wish to collect at each temperature needs to be written with a decimal place ie 10 0 not 10 Doc No BLS I11 MAN 001 Science KA Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 38 of 54 The file number 12345 dat for this scan will contain 3 columns
8. 23 April 2015 Division Page 36 of 54 Multi motor nested or grid scans scan motorl start1 endi Perform a grid of scans using motorl from St pl motorz tarr start to endl in steps of stepl and ends stepz detector likewise motor2 Collect data for time at name time each point using detector scan tth 10 30 0 002 theta 5 Perform a grid of scans 20 moves from 10 10 0 001 macis 1 to 30 in 0 001 steps At each 20 0 moves from 5 to 10 in steps of 0 001 Detector MACIS records intensity for 1 second at each point 7 PSD Data Collection Before using the PSD Mythen detector from GDA the NewMythenlI GUI must be started in order to load the trimbits to the detector modules and set the correct thresholds A beamline scientist will do this for you The fast shutter is opened at the beginning of any scan and closed at the end to protect sample from beam damage 7 1 Data Collection A file 12345 dat is created listing the frame number and corresponding mythen data file for each frame Data for multiple frames has the same file number but with an extension indexing mythen and the frame number e g 12345 mythen 0001 dat psd t collects one frame exposed for t seconds psd 1 frame of 1 sec exposure pad t n collects n frames exposed for t seconds each psd 1 10 10 frames of 1 sec each s Doc No BLS I11 MAN 001 Science CD di d Issue 1 7 9 Di e e A lamon Date
9. and raise to close gas ballast valve Twist knurled ring and lower to open gas ballast valve Gas ballast valve on Cryoseal pump Figure 11 Pumping set for PheniX cryostat rear view To change your sample the cryostat must be fully warmed to room temperature and the vacuum released see instructions below e Once the data collection is completed in the cryostat controller window select The PhaseID changes to Warm This will heat the cryostat to 300K and hold this temperature for half an hour to remove any water from the system After 30min the Run mode indicates Shutdown OK For a view of the complete window see Figure 19 To run this from a scripts use the command pcs purge Doc No BLS I11 MAN 001 Science CA Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 19 of 54 Figure 10 e Figure 10 Do not vent the system until the system is fully warm and the turbo pump has completely stopped Failure to do this risks damaging the cryocooler and the pump e Release the 4 clips and remove the outer cover e Loosen but do not remove the 4 screws holding the inner cover in place Slide the inner cover off e Loosen 2 grub screws and remove sample holder with sample 3 6 Cryostat 5 295 K Additional instructions will be provided by beamline staff 3 7 Capillary furnace RT 1500 K Additional instructions will be provided by beamline staff
10. return twice If failed in rebin messages are still being returned check your typing 11 4 Data Processing PSD data 11 4 1 Automatic data merging Using the detector object smythen in place of mythen will automatically merge data files after collection see 7 1 11 4 2 Data Merging If you forget to use the smythen object or chose not to and wish to sum the data collected from two delta positions using the scan delta command the two frames from a scan can be merged together afterwards using a routine called mythenbin py From a linux terminal window cd to your data directory e g dls 11 1 data 2009 ee0 Then call the mythenbin script to merge the two files Note that the merged file will need to be written to your data processing directory as you do not have write permissions to your data directory mythenbin py FILE1 FILE2 gt processing NEWFILE E g To merge 12345 mythen 0001 dat and 12345 mythen 0002 dat mythenbin py 12345 mythen 0001 dat 12345 mythen 0002 dat gt processing 12345 merged dat Doc No BLS I11 MAN 001 Science D M Issue 1 7 9 v Y diamond Date 23 April 2015 Division Page 52 of 54 11 4 3 Mythen Data Summing A program for summing Mythen data mythensum py is also available Remember that if a sample is changing structure or even expanding or contracting during a series of data collections summing these data together won t help you very much Summed smythen files can also
11. used to open and close the fast shutter at other times eg to take a burn of the beam position during experimental alignment and set up pos fastshutter OPEN pos fastshutter CLOSE 4 3 4 Sample spinner spin on spin ortri spin setspeed speed spin setspeed 35 spin getSpeed 4 3 5 Beam monitor Turn on the sample spinner Turn off the sample spinner Set or change the spin speed Set spin speed to 3596 of maximum Returns the current spin speed The beam monitor command monitors the value of the ion chamber Ic4 If Ic4 falls below a threshold value this means there is no X ray beam because e the shutter is closed or e the synchrotron has lost beam Science Division Doc No BLS I11 MAN 001 diamond is en 2015 4 Page 32 of 54 The scan will pause and the warning message SCAN PAUSED WAITING FOR BEAM ON will appear in the GDA window When beam is restored step scan will resume constant velocity trajectory scan will stop and restart from the beginning bm on Turn on the beam monitor facility bm off Turn off the beam monitor facility bm isMonitorOn Is the beam monitor on yes 0 no 4 3 6 Controlling Position Motors The command syntax is identical for all motors A code is used to distinguish between motors as follows e Diffractometer 0 circle sample theta e Diffractometer 20 circle MACs tth e Diffractometer circ
12. where a parameter or other option is enclosed in square brackets as parameter the brackets should be omitted in the final command commands should be typed into a single line even when examples extend over more than 1 line 4 3 1 Generic commands sleep time Pause all GDA activities for the specified time in seconds to be used in a script if a wait time is required sleep 300 Pause all GDA activity for 300 seconds perhaps to allow temperature stabilisation pwd Lists the present working directory as for linux lwf Gives the full file path of the last working file nwf Gives the full file path of the next working file nfn Gives the next file number no directory path Division Science CD M Issue 1 7 9 wi diamond Date 23 April 2015 Doc No BLS I11 MAN 001 Page 31 of 54 4 3 0 Experimental hutch shutter ehshutter EE cios Experiment Shutter 4 3 3 Fast shutter Open the experimental hutch shutter by clicking the ehshutter Open button in the GDA window Close the shutter by clicking the Close button Indicates shutter status on beamline synoptic There is a fast shutter embedded in the beamline after the last ion chamber This is to protect radiation sensitive samples from unnecessary exposure when not collecting data This is linked in to data collection so should open and close automatically at the beginning and end of data collection The commands below can be
13. 1 Doc No BLS I11 MAN 001 Science CD M Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 23 of 54 4 2 1 Webcam controls E Vacuum M Controls xj tnt a te AR WES we wg E e E P Webcams are labelled WB1 WB11 Five webcams are located in the experimental hutch 1 2 are fixed and permanently displayed in the control cabin Figure 2 e Double click the required WB icon in the synoptic view to open the corresponding webcam window ac ukiviewAndex shtml Ge fr Most Visited v jetwork Support JShop DPoductsv JTaningv 6 Webmail AXISA AXIS 214 PTZ Network Camera Live View Setup Help http A11 webcam diamond ac uk axis cgi com ptz cgi camera 1 amp rzoom 2500 Figure 14 Typical webcam image webcam 1 e WBI WB10 and WB11 can be further controlled by the user e Use the controls at the bottom of the display to pan and zoom Doc No BLS I11 MAN 001 Science D M Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 24 of 54 Ctrl panel e Click to open a further menu This includes the option of removing the red cross marking the centre of the image and to switch on the auto focussing 4 2 2 Diffractometer motors Select to open a window for direct control of some of the diffractometer La es motors ROBOT DIFF Ic4 E Figure 15 Science Doc No BLS I11 MAN 001 D
14. AC data This takes place after every constant velocity scan cvscan as follows e Data rebinned to step size 0 001 degree e Data file gt your data directory For example raw data file number 3051 mac 001 raw gt 3051 mac 001 dat If data collection has been paused part way through a cvscan eg due to a beam loss then only the processed dat file is saved not the raw data 11 3 Rebinning MAC data Rebinning MAC data through windows This software is currently only installed on the local drives for ws003 and ws005 Steps 1 3 only need to be done once per IDL session 1 Double click the IDL 6 3 icon on the desk top this opens the interactive IDL environment 2 Atthe top of the IDL window go to open and navigate to the C rebin directory and select the file rebin idl delta tau pro this will load the rebin program into the top right pane of the IDL environment Science f 7 Doe No BLS III MAN 001 ww y diamond Date 23 April 2015 4 b Division Page 49 of 54 T E sah Pun Poi Manse mde rm BaduS c amp mezjor eEm I zeei u 1028595 amp E Qesnuvax COLETA Nare 0 de Vale 4 e wD Ready oO a ae Baw i Oise owes psisanmpenimee cen _ Snarmorac nateos T nnuvtnt netoad B mt seeasze curwn iB wedgus 3 Click on run at the top of the IDL window and select the first entry in the drop down menu compile rebin idl delta tau pro Thi
15. G CSTBHM Sets the Cryostream target temperature to O l RTEMP 100 100K and the temperature will begin to change until it reached the set temperature Note that the cryostream cannot be set to another temperature The ocs stop command a few times must be used to stop the asynchronous command see 9 2 caput BLIII CG CSTRM This extra command is required to make the 01 RAMP PROC 1 Cryostream to ramp to the required Science Division diamond Doc No BLS I11 MAN 001 Issue 1 7 9 Date 23 April 2015 Page 42 of 54 scan ds 1 0 10 0 1 0 mythen 1 OCS caput BL111 EA BLOW 01 SP 700 scan os 1 0 10 0 1 0 mythen 1 cab csb stop esb stop osb stopt 9 2 Oxford Cryostream cs start pos ocs ocs pos ocs 270 ocs getRampRate ocs setRampRate 180 GCS stop ocs end temperature It is only necessary for the Cryostream Command to take 10 frames of 1 sec each with the PSD The appending of ocs to the command line means the temperature will be read from the Cryostream after each frame and written as an extra column in the dat file see 7 1 These are the equivalent commands to heat a sample to 700 degrees Celsius for example Initialise the Cryostream Get current temperature K Get current temperature K Set temperature to 270 K Get current ramp rate K hour Set the temperature ramp rate to 180 K hour Maximum is 360 K hour
16. Stop ramp immediately and hold temperature Run Cryostream shutdown procedure Science Division diamond Doc No BLS I11 MAN 001 Issue 1 7 9 Date 23 April 2015 Page 43 of 54 9 3 Cyberstar Hot Air blower pos pos esky pos cab 9 4 PheniX cryostat operation pos pos pcs pos pcs pcs pes pcs pcs csb csb 500 stop csb 23 setRampRate 0 1 Start pcs pes 50 getRampRate setRampRate 180 stop end end Get current temperature C Set temperature to 500 C Stop ramp immediately and hold temperature Set temperature to 23 C Use this command to ramp down the temperature before switching off Set the temperature ramp rate to 0 08 C sec 2 5 C min Maximum is 0 16 C sec 10 C min Initialise the PheniX cryostat Get current temperature K Get current temperature K Set temperature to 50 K Get current ramp rate K hour Set the temperature ramp rate to 180K hour Maximum is 360 K hour Stop ramp immediately and hold temperature Run PheniX shutdown procedure see 3 5 Runs the warm phase see 3 5 Science gD Doc No BLS I11 MAN 001 z Issue 1 7 9 Ivici diamond Date 23 April 2015 Division vay Page 44 of 54 10 Writing and running scripts Use the JythonEditor window in the GDA to write sequences of commands 7 ythonEditor x 1 Flat plate thet
17. a 19 3 9 Plat plate t rmace RT 1700 56 tees diet pet rbe ien cat enay spica pia alu oi o taa cedit pits ad 19 4 Controlling the TuS CORO TIE oisi en eee FEY EYE PASO RIF Rd den PAR Mn epu me Rt R QUIA n UV Di PU 20 A 1 PARSE SUG PS Tr 20 QNA yO DUC iie SM r a 22 4 3 GDA Cri an ERREUR 30 5 Constant Velocity Scanning Commands MAC data collection sese 34 5 1 Constant velocity scan CVSCAM icuiecis repere pa YR e epo REEF I NIMES eda Fo EON Mb Resa LU Fa ro ERU Fu ERE Va RUE 34 D Step Scanning CONImatlsus oce ERR MERO buta es uim DM eM Seas vA M EDU M TUE M DUM 35 7 JIESDDSSCoOlBOUOaeneddvsciba nus bits tnnt aa rti but td Mus me fa s D pM m pl DB M ta 36 dal stu ole CHO eos ii ensi ene raids dac deed etia Renditen cat are Cer re emer rarer 36 ROBO Arm and eurOuSel ouo ds e ota D EI dv tias te DeC OmU eR itu RE Taa 38 8 1 Manual Sample Change Commands eee eee esee eene eene enne nnne trennen 38 5 2 M ltipl Simple SCANS ucsesrascerki tea uva tr exa uv oes VERI ET E E RO eda CROP MO E NU REENE QU AR HUP DUE E ETE 39 9 Sample environment control commands sesssesssseeeseseeeeee enne enne enne 41 9 T Fast Temperature Scanning oiosoch Gaston tuu eene ban nena oat OD oai t eE Gen cuu Kop dup Md 41 92 Oxford CryostreaM EET 42 9 3 Cyberstar HotAir Oye r
18. a 2theta scan 2 MAC 1 3 pos theta 3 4 cvscan tth 5 900 Redo last action 5 pos theta 5 6 cvscan tth 5 900 7 pos theta 10 Undo last action 8 cvscan tth 5 900 9 cvscan tth 5 900 theta 30 11 Filename of displayed script _optimise_pitch py a wm Si py Save Save As Close Opens a new script Run saved script Opens a Close JythonEditor window saved script B Saves the displayed script with new filename Saves the displayed script Notes on the JythonEditor e The JythonEditor does not check for syntax except capitalization e Comments require the character at the beginning of the line e Some commands are given pre programmed colour codes to make the script easier to read e There are no end or stop commands e Tabs allow many files to be edited at once e Use ctrl c and ctrl v to copy paste between scripts e you must SAVE your script before it can be RUN Doc No BLS I11 MAN 001 Science CD M Issue 1 7 9 v Y diamond Date 23 April 2015 Division Page 45 of 54 e Ifthe RUN button is not highlighted either the script is not saved or GDA is busy The current scan or an entire script can be paused or halted from the GDA display Pause scan Pause script Halt current scans scripts storan Figure 20 Control of scripts 10 1 Script commands e Scripts use the jython programming language e Commands can be entered line by line in a script exactly as they woul
19. be added together using this method mythensum py 12345 mythen 0001 dat 12345 mythen 0002 dat gt processing 12345 summed dat OR mythensum py 12345 mythen dat gt processing 12345 summed dat 12 Data Plotting Data from the MAC and PSD will be plotted in the DataPlot windows of GDA To plot data from an older visit use the full file path in place of the scan number e g dl1s ill data 2010 ee0 12345 mythen 001 dat plot MAC 12345 mac 001 dat Plots the MAC file 12345 mac 001 dat as a new plot overwrites any existing plot plotover MAC 12345 mac Adds 12345 mac 002 dat to the existing plot 002 dat in the Data Plot window plot PSD 12345 mythen Plots the chosen PSD data frame overwrites 0003 gat any existing plot plotover PSD 12234 mythen Plots the chosen frame onto the existing plot 0004 dat in the Data Plot window plot PSD 12345 mythen To plot a merged PSD data file summed dat Division Doc No BLS I11 MAN 001 Science CD Issue 1 7 9 wi diamond Date 23 April 2015 Page 53 of 54 13 Troubleshooting All motors return to their original positions after a scan including the Cryostream hot air blower temperatures The GDA window has completely frozen and I cannot input any commands The GDA window shows at the line prompt instead of gt gt gt and won t carry out any commands To turn OFF the return to original positions flag on the gda command lin
20. d on the command line e For example a script to change the temperature of the cryostream ocs wait 5 minutes at each temperature to allow the sample to equilibrate and then collect a cvscan could be written as follows pos ocs 100 sleep 300 cyscan 1800 pos ocs 120 sleep 300 cvscan 1800 pos ocs 140 sleep 300 cvscan 1800 pos ocs 160 sleep 300 cyscan 1800 pos ocs l90 sleep 300 cvscan 1800 e Alternatively this could be written in a loop every command that is indented is included in the loop for i in range 100 200 20 Science Doc No BLS I11 MAN 001 Issue 1 7 9 Division M diamond Date 23 April 2015 Page 46 of 54 pos ocs i sleep 300 cvscan 1800 interruptable e When using a range in this way e g start stop step the stop point is not included in the loop so for this example the final cvscan will be run at 180 K e Theinterruptable command is important and MUST be placed at the beginning or end of every loop this enables the loop to be paused halted for example if the beam is lost Doc No BLS I11 MAN 001 Science D Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 47 of 54 11 Data Handling 11 1 Data Directories and Subdirectories 11 1 1 Where is my data Your main experimental directory has the same name as your visit number e g EE1234 1 This directory is in the I11 directory for the current year so From a windows machine open an e
21. e type scansReturnToOriginalPositions 0 To switch back ON type scansReturnToOriginalPositions 1 Check if GDA really has frozen and isn t just waiting for a scan to finish Try and close the client window using the cross in the top right corner If nothing happens then you will need to force a close from a linux terminal window at a command line prompt type killall java This will close the GDA client You will then need to restart the GDA server and client by following the instructions in 4 1 If you are at all unsure then contact beamline staff before proceeding You have missed out a close bracket at the end of a command Type then hit return Doc No BLS I11 MAN 001 Science Issue 1 7 9 Division diamond Date 23 April 2015 Page 54 of 54 14 Corrections Changes New Commands for the Next Version
22. estare er a vedo 43 Doc No BLS I11 MAN 001 Science KA Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 3 of 54 9 4 Phenix cryostat 0perauiOn TH ie ee eee ee 43 10 Writing and fonning SOT sessios i aiiud tubi ba oboe Dun aaea a tin Leu IE ua M ees dtu D e Md 44 T0 1 SGCIDUCOTDETIHHUS icit robbed dien o beo r deca E E ba odii and tona eui iip Rd tne 45 11 Data Handilin Seeya a e E M E De Lum Ea uie 47 11 1 Data Directories and Subdirectories esseseesseseseseeseesrtsstserrsttsstsersstesstseresrenseterertesstestesresseesee 47 11 2 Automatic processing of MAC data eeeseseseseeeseeeerstsrrseresressteeresressrserestensessrsstesseestesresseesee 48 11 3 Rebinning MAC dat aa 48 114 Data Proc ssing PSD Cali siirre i mens Ei ub EEE E EA Racca 51 12 Data PIONIN enee E A RON E E O A 52 T3 Troubleshooting i ead E E E rece a 53 14 Corrections Changes New Commands for the Next Version eesssesseeesesrsssesressresrrsresseseresresss 54 Science KA M Issue 1 7 9 wi diamond Date 23 April 2015 Division Doc No BLS I11 MAN 001 Page 4 of 54 1 Introduction to I11 Beamline Figure 1 shows an overview of the beamline facilities These consist of A support laboratory for sample preparation Control room 1 also known as CC1 which also incorporates a user training area CC1 has duplicate beamline control PCs four Windows PCs and one Linux PC ava
23. g is a troubleshooting guide 1 2 Related documents e Diamond User Office Welcome e SCI SAD 0008 Computing Services for Diamond Users e Beamline I11 technical papers 1 Design of powder diffraction beamline BL I11 at Diamond C C Tang S P Thompson T P Hill G R Wilkin U H Wagner Z Kristallogr Suppl 26 153 158 2007 2 A new instrument for high resolution powder diffraction S P Thompson J E Parker J Potter T P Hill A Birt T M Cobb F Yuan and C C Tang Rev Sci Instrum 80 075107 2009 Doc No BLS I11 MAN 001 Science CA M Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 9 of 54 2 Safety issues All users are required to attend a Safety induction provided via the User Office before using the beamline This will cover safety issues and procedures applicable throughout Diamond Light Source The I11 beamline staff or Experimental Hall Coordinators will provide e Beamline induction e Personnel Safety System PSS training The beamline induction will describe e the location of the nearest fire exit e the location of the emergency motor stop e the location of oxygen depletion monitor e beamline specific safety information A set of staff telephone numbers is located close to every telephone in case of any problems For out of hours support please control the Experimental Hall Coordinators ext 8787 or the Control Room ext 8899 No user is
24. gure 7 Hot air blower with protective cover in position Even with the protective cover users should take care when changing Doc No BLS I11 MAN 001 Science CA Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 15 of 54 3 5 PheniX cryostat 11 295 K The cryostat will be set up by DLS staff on the diffractometer and all necessary ancillary equipment connected e Mount your sample capillary on to the PheniX brass sample holder as shown in Figure 8 Use a small amount of vacuum grease to secure the capillary if necessary Aluminium capillaries are available for improve thermal contact e Fit sample holder to the cold stage of the PheniX cryostat There are 2 grub screws that lock it into place e Check sample alignment Figure 8 e Fit the first cover and tighten the 4 screws holding it in place e Fit the outer cover as shown in Figure 9 and close the 4 clips to hold it in place s Camera cross hairs r Sample capillary Maximum length 40mm different Sample capillary diameters possible side view top view Figure 8 Sample holder for PheniX cryostat Doc No BLS I11 MAN 001 Science Issue 1 7 9 e o e Date 23 April 2015 Division Page 16 of 54 Outer cover fitted into position Sample holder in position on cold stage Clips 4 for securing outer cover Figure 9 Views of PheniX cryostat in position on diffractometer left both cove
25. ilable for users There are also storage ring status displays camera displays and synoptic displays see Figure 2 Control room 2 also known as CC2 CC2 has benches for setting up cells for long duration experiments and EH2 beamline control pcs Experimental hutch 1 This is the experimental space containing the diffractometer and other ancillary equipment Experimental hutch 2 This is the experimental space for long duration experiments and is accessible only to DLS staff and approved users EH2 is still under construction so the door linking EH1 and EH2 should remain closed at all times and must only be used in an emergency Control racks These contain beamline electronics and are accessible only to DLS staff Optics hutch This houses beamline optics and is accessible only to DLS staff This will be searched and locked by DLS staff before your experiment Figure 1 I11 beamline layout DONE diamond A e ee ate 11 Division Page 5 of 54 Beamline synoptic ES N NNN i display see 4 2 W Display showing Fixed webcams status of DLS gt ES 2 in experimental hutch storage ring 2 in optics hutch Control PC d Control PC ws 002 ws 001 2 monitors 2 monitors Figure 2 View of beamline control cabin Doc No BLS I1 1 MAN 001 Science Dp H Issue 1 7 9 d diamond 55554 Division Page 6 of 54 Diffractometer MACs Beam pipe Robo
26. indow These are provided for reference as Figure 18 and Figure 19 but will not be discussed further as users normally control temperature from scripts using GDA Hot air blower 11 300K cryostat Enable disable sample spinner Set spin speed BLIII EZ ENV OI Oxford Cryostream Figure 17 Sample environment options Science Division diamond Doc No BLS I1 1 MAN 001 Issue 1 7 9 Date 23 April 2015 Page 28 of 54 The hot air blower capillary furnace and flat plate furnace all use Eurotherm controllers similar to Figure 18 Figure 18 Eurotherm controller window for hot air blower capillary and flat plate furnaces Doc No BLS I11 MAN 001 Science Issue 1 7 9 Division diamond Date 23 April 2015 Page 29 of 54 The Cryostream and PheniX cryostats both use Oxford Cryosystems controllers similar to Figure 19 i gt r EIE re A eries 700 setup BL11I CG CSTAT 01 180 00 K Figure 19 Oxford Cryosystems controller window for PheniX and Cryostream Doc No BLS I11 MAN 001 Science CA Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 30 of 54 4 3 GDA Commands Note that some commands are case sensitive there is no syntax check where a parameter is enclosed in round brackets as parameter the brackets are an essential part of the command syntax There is no space before the first bracket
27. le PSD delta e sample X position across the beam Spos e large table X position across the beam tlx A number of general commands are available to control the motors pos motor pos ttn pos motor pos tth 10 Spos value Read and return the position of a motor Read and return the position of the 20 circle requested value Move the motor to the requested value Move the 20 circle motor to 10 degrees Move the sample position allowed range 20 to 5 mm Doc No BLS I11 MAN 001 Science aD Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 33 of 54 If you move the sample with the spos command use the appropriate camera to ensure that the sample is still in the beam spos 0 Move sample to default position beam hits sample 10mm from end of brass holder spos 20 Move the sample so that the beam is 10 20 30mm from end of brass holder spos 5 Move the sample so that the beam is 10 5 5mm from end of brass holder pos tix 0 Move the table to location close to diffractometer pos tlx 300 Move table 300mm away from diffractometer Moving the large table towards and away from the diffractometer provides a convenient way to move variable temperature equipment out of the way to change samples See examples in sections 3 3 and 3 4 Doc No BLS I1 1 MAN 001 Science CA Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 34 of 54
28. lease wait EPICS please wait Script Editor window E jythonEditor x 1 Flat plate theta 2theta scan end 2 MAC 1 Reading the acutal trajectory from XPS to EPICS please wait one 3 pos theta 3 Reading the acutal trajectory from XPS to EPICS please wait 4 cvscan tth 5 900 5 pos theta 5 6 cvscan tth 5 900 jjacutal pulses is 45000 7 pos theta 10 Writing data to file d1s ill data 2009 0 0 11918 dat Please wait 8 cvscan tth 5 900 riting data to file dls ill data 2009 0 0 11918 dat completed 9 cvscan tth 5 900 theta 30 Post Scan data reduction rebinning Please Wait Data Rebin Completed Successfully Trying to opens d1s ill data 2009 0 0 processing 11918_red dat Data plotting please wait Post processing completed GDA AcquisitionGUI Version 7 14 0 logged in as ILluser SOK E ivihontanor x a Ye Ts lie ya Yaz as 34 35 16 Wrrting data to fil eduction rebinni Data Rebin Completed Successfully lrying to opens dls 111 duta 2009 0 0 pracessing 11918 red dat Data plotting please wait Current File Name 11908 dat Legend Post processing completed i C a pL mouse position 33 68 12 791 77 gt gt gt levscan tth 5 900 clear i Create new graph S Clear old graph tine Iv Disconnect esc aph onty ehshutter Beam lambda tse san Pause script Maitowrent scan
29. listing the temperature frame number at that T and PSD data file For faster temperature scanning with the PSD see section 9 1 8 Robotic Arm and carousel The robotic arm and carousel are identified in blue in Figure 3 Each of 4 carousel trays can hold 50 samples 200 total Every 5 location is numbered The robotic arm is interlocked with the experimental hutch door so will not operate unless the hutch has been searched and locked The user has complete freedom when loading the carousel but is responsible for recording where samples are The marked area of the large table must remain totally clear otherwise the robot arm could be obstructed or cause damage Pleae note that the robot commands do not switch on the sample spinner Check that the spinner is running before activating the robot 8 1 Manual Sample Change Commands Use these commands to insert and remove individual samples from the diffractometer sample stage The following commands must be run before any use of the robot sample start Switch on the robot server sample recover Check for the presence of a sample on the diffractometer Remove any sample present and place in the recovery tray on the carousel stand Doc No BLS I11 MAN 001 Science CD M Issue 1 7 9 v Y diamond Date 23 April 2015 Division Page 39 of 54 sample stop Stop robot and switch off server pos sample samplenumber Pick up sample from locati
30. n Page 13 of 54 3 3 Cryostream 80 500 K Dry air supply shield gas Liquid nitrogen Gas nozzle supply line Figure 6 Cryostream The Cryostream will be set up by DLS staff on the large sample table and all ancillary equipment connected For manual sample changes Mount sample capillary on standard sample holder Execute pos tlx 300 command or use control window Figure 16 to move large table out of position allowing access to diffractometer Place sample on diffractometer Execute pos tlx 0 command or use control window Figure 16 to move large table with Cryostream back into position Execute spin on command in GDA to switch on sample spinner section 4 3 4 Or use the Enable Disable button on the EPICS screen Set temperature as described in section 9 1 Beware of hot or cold gas jet from Cryostream nozzle when changing samples Science Division diamond Doc No BLS I11 MAN 001 Issue 1 7 9 Date 23 April 2015 Page 14 of 54 3 4 Cyberstar hot air blower RT 1000 C The hot air blower will be set up by DLS staff on the large sample table and all ancillary equipment connected e Manual sample changing is as for the Cryostream described above section 3 3 Temperature control is described in section 9 3 Use quartz capillaries for temperatures above 650C Hot air blower samples if the hot air blower is ON Protective cover Fi
31. n cross hairs are positioned inside the experimental hutch to allow users to check their sample alignment Figure 5 Beamline staff will position the cross hairs in the beam path and will provide sample alignment training if required The monitors are located on the wall of the experimental hutch Cross hairs Cross hairs Figure 5 Images from sample alignment cameras Doc No BLS I11 MAN 001 Science amp e Issue 1 7 9 Division e diamond Date 23 April 2015 Page 12 of 54 3 2 Sample spinners and holders Both capillary and flat plate room temperature sample holders fit directly to magnetic spinners mounted at the centre of the 0 circle face plate The sample holders are magnetic Please note Capillaries must be under 4 cm long to ensure compatibility with the robot When operating in transmission geometry absorption by the sample can be a significant problem Therefore it is important to choose the correct diameter capillary for your sample the most commonly used capillary diameters are 0 3 0 5 and 0 7 mm A sample absorption calculator is available at http 11bm xray aps anl gov absorb absorb php 3 2 1 Capillary spinner Capillary sample Upper brass body This screws on to the lower brass body Lower brass body with internal magnetic body This fits to the diffractometer Doc No BLS I11 MAN 001 Science CA M Issue 1 7 9 wi diamond Date 23 April 2015 Divisio
32. ng Edit the lt file_list gt variable to contain a comma separated list of all the files you want to rebin note the space after the first quotation mark for each file If you have so many files that you need to go to a new line after the last comma of the line put a dollar sign and press return eg 79123 mac 001 file_list 81369 mac 001 81370 mac 001 Edit the choice of a rebin variable called argument to select sum or batch rebin Edit the lt step_size gt variable to your desired rebin step size Edit the lt user_comment gt variable to contain a string that is added to the end of the rebinned file Note the space after the 1 quotation mark this is only necessary if the comment string starts with a number As a default I recommend setting the string to the step size Doc No BLS I11 MAN 001 Science CA Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 51 of 54 g Save this file and leave notepad open if you want to do more rebinning 5 Back at the IDL window in the bottom command line entry line type the following run c rebin run_rebin txt And watch the printed output To rebin more files simply repeat step 4a g and use the up arrow key to recall the run command NOTE sometimes the Diamond network fails to make a connection to the data directory and rebin returns a failed in type message In this instance type close all into the command line and press
33. on samplenumber on carousel and place on diffractometer sample clearSample Pick up sample from spinner and replace in original position on carousel sample finish Switch off the robot You must also use the sample start and sample recover commands to initialise the robot following an emergency stop or opening of the hutch door 8 2 Multiple sample scans In this mode the robotic arm e picks up a sample from the carousel and places it on the diffractometer e performs a cvscan e removes the sample and returns it to the carousel e The sample start and recover commands are run automatically at the beginning of the scan and the sample stop commands is run at the end You will therefore need to run a start and recover command before using the robot again unless it s in a scan sample command scan sample firstsample last Perform 20 cvscan for the sample step cvscan time specified time for every step sample between firstsample and lastsample scan sample 1 21 1 cvscan 1800 Perform 30 minute 20 cvscan on Science Doc No BLS I11 MAN 001 Issue 1 7 9 Division M diamond Date 23 April 2015 Page 40 of 54 every sample between 1 and 21 Multiple sample scans with sample position translation for each sample scan sample firstsample Perform a cvscan for samples firstsample lastsample samplestep to lastsample at each position from spos startpos endpos
34. permitted to work inside the experimental hutch unless trained by Beamline staff or the Experimental Hall Coordinators Doc No BLS I11 MAN 001 Science D Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 10 of 54 3 Sample environment options There are a number of sample environment options available depending on the temperature range required for measurements Temperature control commands are described in chapter 9 Temperature range NET Te Notes Capillary Spinner Sample changer with robotic arm available Flat plate spinner 80 500 K Oxford Cryostream For use with capillary spinner Can be used with the robot for automated sample changes RT 1000 C Cyberstar hot air For use with capillary spinner Can be used 295 1273 K blower with the robot for automated sample changes Temperature control less precise below 250 C RT 1500 C STOE capillary 295 1773 K furnace RT 1700 C Flat plate furnace 295 1973 K 11 295 K PheniX cryostat Closed cycle cooler Allow at least 3 hours to change samples 5 295 K 4K Cryostat Closed cycle cooler beamtime shift to set up and cooldown Allow 1 day per sample Table 1 Sample environment options Doc No BLS I11 MAN 001 Science CA H Issue 1 7 9 d diamond 5 554 Division Page 11 of 54 3 Sample alignment Two cameras with built i
35. rs removed right both covers fitted e Switch on vacuum diaphragm pump connected to the cryo seal On first use it is necessary to briefly pump with the gas ballast valve open Pull and twist the sleeve DOWN to open see Figure 10 leave for 10 minutes then pull and twist the sleeve UP to close This cryo seal pump remains ON throughout the experiment e Check that the vent valve on the side of turbo station is closed e Switch on the turbo pumping station to pump out the sample space Open the gas ballast valve as required usually approx 10 minutes only The turbo will accelerate to 1500Hz over the next few minutes e Figure 10 shows the turbo controller display Doc No BLS I11 MAN 001 Science CD H Issue 1 7 9 d diamond 555 Division Page 17 of 54 Display ON OFF Mains ON OFF Figure 10 Pumping set used with PheniX cryostat front view The PheniX cryostat is ready for use when the pressure has fallen below about 10 mbar This will take up to 90 minutes for first use and typically 45 minutes thereafter e Switch on the controller Initialise by pressing the Start button or by using the pcs start command see 9 4 e Set start temperature for experiment see 9 4 Doc No BLS I11 MAN 001 Science aD M Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 18 of 54 Vent valve Gas ballast valve on turbo backing pump Twist knurled ring
36. s scripts NN uuu es theta 2theta sfn 3 pos theta 3 4 cyscan tth 5 900 5 pos theta 5 6 cyscan tth 5 900 7 pos theta 10 B cyscan tth 5 900 9 cvscan tth 5 900 theta 30 FI ao ai 3 Command 5 4 as 6 1 s ine s 5 ER 52 ss El ss E E E e le 63 E es 66 s 68 E x opumise pitchpy Flat plate Stpy C new open Save Save As Close Run undo redo 55000 z 50000 gt 45000 Data display window rehshutter Pause scan Pause script Halt current scans scripts OSTOPALL Open Commands for controlling scripts and operating the shutter Figure 12 GDA client display Science Division diamond Doc No BLS I11 MAN 001 Issue 1 7 9 Date 23 April 2015 Page 22 of 54 4 2 The synoptic window From a Linux terminal window type launcher then select IBeamlineslI1 1 powder diffraction to display the synoptic window Figure 13 As the name suggests this window provides a synopsis or summary of the beamline topology and hardware from the storage ring to the diffractometer The user need be concerned only with parts of the information presented These are indicated by CD and described in more detail in the remainder of this section Vacuum system Beamline hardware I11 diagnostics Storage ring information Figure 13 The synoptic window for I1
37. s will produce some compiler messages in the middle pane of the IDL environment Fle Edt Search Ruy Project Macos Window Hep algjxj zee s s 08 9SEkER ILLECTED AFTER CVSCAN VAS UPDATED TO 7 DEG 2THETA OTHERWISE USE OLD acd file suaned_file_stemtstrconprers ds renove_all 4strconpress string j rexove_oll jee dat y lw 4 24 eX lera i C NNI Banj BDO rimmat cuba L stsoeceltesnimesie cibeben E Abra mac ds throu Brn rebebit Notepsd fb WL 604528 Demo CE LET Science ai oe Division gt Date 23 April 2015 Page 50 of 54 alaiz ei xi QeevMuwrpr XT we n Ege j a vo Dany u E hn Distan B CJ C rbon rrot ook C sisdenceinesninesian C cive E Rate Pac dta throu I nnrebn tt motecad 88 WOK 404570 Drama BH 9eacdus 4 On the desktop open a my computer and navigate to C rebin and open run rebin txt preferably using notepad This is a small IDL file that contains all the necessary information about your data needed to run the rebin and is split into fairly obvious sections a Edit the last section of the path variable to give the right directory for your data path data i1 1 data 201 1 ee1234 1 Do same for the lt out_path gt directory note the output directory must be the processing folder inside your data directory out_path i1 1 storage il 1 data 201 1 ee6547 1 processi
38. tic arm XYZ table Carousel Figure 3 The I11 experimental hutch PSD is not on this photo The experimental hutch is dominated by the diffractometer which has 3 coaxial high precision rotary stages 0 20 and 6 and is shown in Figure 3 Figure 3 also shows the robotic arm and 200 sample carousel for automated sample change giving high throughput for room temperature measurements The robotic arm can also be used with the Cryostream and hot air blower For room temperature measurements capillary or flat plate a spinner is mounted on the circle The MAC detectors high resolution are mounted on the 20 circle and the PSD high speed is mounted on the 6 circle Doc No BLS I1 1 MAN 001 Science ap H Issue 1 7 9 diamond sepia Division Page 7 of 54 For non contact variable temperature techniques the ancillary equipment can be mounted on the large XYZ table MAC arm 1 of 5 beampipe 1111 crystals x9 Sample stage Figure 4 Close up of MAC detector array Each of the 5 MAC arms consists of 9 Si crystals giving a total of 45 crystals Full 20 scan 3 150 degrees achieved by 40 degrees of motion with overlap between detectors Data from a total of 45 detectors is integrated to produce the final pattern I11 is designed to operate in Constant Velocity trajectory mode The user specifies the total count time and the diffractometer motion trajectory is calculated to gi
39. ve a constant 20 angular speed Unless specified in advance the I11 optics will be set up to use the maximum X ray flux at 15keV about 0 827A A beamline scientist will determine the precise wavelength at the beginning of the experiment using a standard silicon sample Science KA Issue 1 7 9 wi diamond Date 23 April 2015 Division Doc No BLS I11 MAN 001 Page 8 of 54 1 1 Scope of this document This is a guide for users of DLS beamline I11 Its contents are restricted to aspects of the hardware and software that users need to know in order to collect high quality data from the I11 beamline It will be updated in line with beamline developments New users are strongly recommended to read this document before the start of their experimental time Chapter 2 Chapter 3 Chapters 0 7 Chapter 8 Chapter 9 Chapter 10 Chapter 11 Chapter 12 Chapter 13 describes essential safety issues describes basic operations for the various sample environment options including loading and unloading of samples describe the software and commands graphical and text used to control and collect data from the diffractometer describes how to use the robot arm and carousel to change samples automatically describes the commands used to control the sample environment options is a guide to writing scripts gives a summary of the data handling protocol used with the I11 beamline gives a guide to data plottin
40. xplorer window and type in the address bar il 1 storage il 1 data 2010 ee1234 1 And from a linux terminal window d dls ili data 2010 ee1234 1 Run numbers will automatically increment by 1 for each scan it is your responsibility to keep a record of which scan is of which sample Each scan will consist of an SRS file 12345 dat which list the data files for that scan and any other information you have appended such as the cryostream temperature see section 9 1 The data files for MAC data will be in the form 12345 mac 001 raw raw data and 12345 mac 002 dat rebinned data 11 1 2 Creating sub directories For experiments creating a LARGE number of data files you may wish to divide you data directory into sub directories e g a new sub directory for each sample setSubdirectoy myfirstsample Creates a new subdirectory within ee1234 1 called myfirstsample All subsequent data will be written into this subdirectory until you set a new subdirectory or return to the main directory setSubdirectory Returns to the main directory ie no subdirectory set Doc No BLS I11 MAN 001 Science gD Issue 1 7 9 wi diamond Date 23 April 2015 Division Page 48 of 54 11 1 3 Adding a title to the file SRSWriteAtFileCreation MyTitle Sets the title in the header file to be MyTitle Warning This will be applied to all subsequent data files until you change it 11 2 Automatic processing of M
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