Jesse Guzman's Lab Book

ClosR Widget

2009-04-13T23:59:00.003-07:00

ClosR Widget

2009-04-13T23:59:00.001-07:00

ClosR Widget

2009-04-13T23:22:00.001-07:00

ClosR Widget

2009-04-13T23:21:00.001-07:00

Schedule

2006-11-02T14:24:00.000-08:00

Morning (8am-5pm) Evening(5pm-12am) Night(12am-8am) [Approx]

Wed - 11/8 Setup (Bud/Justin/Jacob) Geza (post-class ~7) Jesse

Th- 11/9 Bud/Jacob Justin Jesse

Fri-11/10 Bud Geza/Jacob Justin

Sat - 11/11 Bud Geza/Jacob Jesse

Sun - 11/12 Geza/Jacob Justin Jesse

Mon - 11/13 Geza in @6am then Bud/Justin tear down

Tu - 11/14 NO BEAMTIME NO BEAMTIME NO BEAMTIME

Wed - 11/15 Bud/Justin/Jacob set up in afternoon/evening Jesse

Th - 11/16 Bud Justin/Jacob Jesse

Fri - 11/17 Bud Geza Justin

Sat - 11/18 Bud Geza Jesse

Sun - 11/19 Geza Justin Jesse

Mon 11/20 Geza @ 6am/Bud Justin Jesse

Tu 11/21 Bud/Geza/Justin/Jacob Tear down/Pack up

Sig plot of lsmo c-axis x=0.34

2006-06-30T14:15:00.000-07:00

Old Data on LSMO x=0.34, 0.36

2006-06-30T12:34:00.000-07:00

Sig plot of lsmo_36_c

2006-06-29T15:01:00.000-07:00

Sample Scan Count

2006-06-29T14:10:00.000-07:00

Ok folks, we'll be doing 6 different samples with the following number of scans:
LCMO 18% ------------17
LCMO 20% -----------17
TbMnO3 ----------------10 --Tb
TbMnO3 ---------------- 6 --Mn
Bi2Ru2O7 -------------- 8
Pr2Ru2O7 -------------- 8
Pr1.2Bi0.8Ru2O7 ---- 8 --Pr
Pr1.2Bi0.8Ru2O7 ---- 8 --Bi
CuIr2S4 ----------------- 6 --Ir
------------------------------------
Total: 86 hrs

Sig plot of lsmo_36_ab

2006-06-28T16:01:00.000-07:00

PProc

2006-06-28T15:14:00.000-07:00

PProc is a program which takes the output from rsfit- and plots the sigma's of the files using gnuplot.

Here's how to use it:
you need to make a inparam.dat file which has some info in it like directory and base filename

you need to make a filelist.equiv two columns ###filename ####temp

Then type 'pproc -n #' where # is the filename.# you want to plot the sigma.

LSMO 0.34/0.36 ab/c-axis

2006-06-15T12:56:00.000-07:00

So here's the r-space plots of all of the new data collected on the lsmo 0.34/0.36 ab/c samples.

Tc Comparison

2006-04-21T13:49:00.000-07:00

First Sigma Plot (Yay!)

2006-04-19T17:47:00.000-07:00

This is my first sigma vs. temperature- not great; not terrible. You can kinda see the transition temperature ~125K so that's good. There's a few data points with huge error bars, this need to be fixed.

Figuring out E0

2006-04-19T14:29:00.000-07:00

So to figure out what E0 is, we simply take the standard file and do a Fourier transform from k-space to r-space (using the same range of course) and plot it on top of a low temperature data file. You look at the zero crossings and then change the field "E0 shift in (eV)". Try 5.0eV and -5.0eV to get an idea of how to shift it. You can either shift the standard file, or the actual data file. Here's what I got:

Ok so the black trace (hard to see) is the actual real data file. The red trace is the UNshifted standard file. The blue trace is -5.0eV shifted, the green trace is +5.0eV, the cyan trace is shifted +6.0eV, and the magenta trace is at +8.0eV.

Start Fit #2

2006-04-18T12:52:00.000-07:00

So the black trace is a sample trace of our lsmo sample in the ab-plane, and the red trace is the mn-o ab-plane standard file. I think they look reasonable, but I'll have to wait to see what Bud has to say.

ZOOM:

Ok so I looked up Travis' rsfit files and changed some stuff and ran it here's what I got:

ZOOM:

Travis is GOD

2006-04-14T12:25:00.000-07:00

good standard from travis:

lsmo_mn_o_ab_1.9372.scf.4.f8

feff.inp file for c-axis: go up one lvl for ab plane:
/home/staff/tobrien/fit/structures/bilayer_lsmo/old/feff8/c

SSRL end of run form

2006-04-14T12:01:00.000-07:00

Collecting good polarized EXAFS data on single crystal samples for both transmission and fluoresence is difficult because of Bragg diffraction from the sample, which changes the x-ray absorption in the sample. Usually one collects the data at a series of angles, and then combines the data to overcome this issue. For the bilayer CMR manganites we are studying, we have very thin oriented single crystals (mounted over a hole in a larger piece of the same single crystal material); however our first attempts to obtain transmission data (2+ years ago at the APS) failed because the Bragg spikes were too large.
Since then we have been using fluorescence data collection which is time consuming and has poorer data quality than for transmission. Last summer together with A. Mehta we showed on a diffraction beamline, that the problems in the transmission EXAFS were indeed caused by a number of Bragg diffractions; further we showed that oscillating the sample about vertical and horizontal axes, effectively averaged out the Bragg spikes if the oscillation angle was large enough (+- 2 deg) - we have now designed a wobbler to rotate the samples by a few degrees about horizontal and vertical axes (while the sample is in a He cryostat) and obtained the first good transmission data on one of the bilayer samples La(1.28)Sr(1.72)Mn2O7. Our preliminary data
reduction indicates consistent data. We also collected some fluorescence data using the same
method.

Post-trial Wrap-up

2006-04-13T16:35:00.000-07:00

So this is what I think is the reduction so far:

The input parameters are as follows:
Power of E-E0 = 0.7
# of knots = 6
End of E-K trans = 10.5
End of K-R trans = 10.25
Begin of K-R tr = 3
y2 = 1.3

Split them up

2006-04-13T13:43:00.000-07:00

So now I need to break up the larger set into three smaller sets:

3K-50K: 049b1-2; 050b1;051b1-3;053b1-3
100K-124K: 056b1-3; 057b1-2; 058b1; 059b1; 060b1-2; 061b1-3; 062b1; 063b1-2
128K-160K: 065b1-3; 066b1-3; 067b1-3; 068b1-3; 069b1-3
180K-325K: 070b1-3; 071b1-4; 072b1-3; 0731-4; 074b1-3

Ok so after looking at all of these files we didn't really notice anything strange besides the fact that the peaks were shifting around atonically. Decided there's a background issue and went back to re-re-re-reduce the data.

I'm slowly varying the fourier transform range, the power of (E-E0), and the # of knots. Here's the two best settings so far:

Above used a power of 1, and 6 knots with a window from 3 to 10:

Above used a power of 0.5, and 5 knots with a window from 3 to 10:

Re-re-Reduce

2006-04-13T12:58:00.000-07:00

So came in today and tweeked up the pre-edge and background removal. I moved the "start XXXeV above edge" parameter to 170eV. It was at ~150eV and looked like it was falling on the top of a peak. I also pushed the low end of the fit range up a little bit, also looked like it was coming in on a peak. Then I just Fourier transformed it and got this:

In K-space:

In R-space:

It looks to me like I got rid of the shoulder problem. I still need to check Lisa's suggestion for the outlyer (06xb-whatever), which is that E-E0 is varying.

Reducing AB-plane data

2006-04-12T15:40:00.001-07:00

So all of the earlier stuff was from the c-axis data:

Here's the normalized plot in energy space of the ab-plane data:

Things get kinda funky in k-space. Here's the plot:

Notice the black highlighted outlying trace. That's 060b1:

Here's is the real space data:

And here's the real space data post- y2 correction:

Guess what that red- low r outlier is...060b1- who would've thought?

Reducing AB-plane data

2006-04-12T15:40:00.000-07:00

Start Fit

2006-04-11T14:11:00.000-07:00

Ok so now I need to begin fitting the data. We use a program called RSFIT. It works pretty good: here's what I've got so far. Here's my input file:

And here's what it looks like plotted with the actual data (data is in red):

Not the best...the phase is off...why is that? And the peak of the fit is a little bit low.

Weird Traces: the Search cont'd

2006-04-11T13:41:00.000-07:00

Ok so now I'm still trying to find out what traces are strange. We now have our data overlapping very nicely in energy space, and mostly overlapping in k-space. However, there is a bad section from ~10.6 A^-1 to the end of the trace. Here's a graph:

List of weirdness:
022b1
025b2 (maybe)
038b2
042b1

Not sure of the glitch...

2006-04-10T16:18:00.000-07:00

We re-did the pre edge using 185eV above the edge for our background removal.

Here's the new normalized post pre-edge removal spectra:

And the zoom:

Now I need to re-do the k-space data and the r-space data and see how it turns out.

I'm going to leave the last bit of data out with the crazy up turn at the end:
use k_max = 12.6 and fft k_max of 12.1;
K-space plot:

Here's what I got:

Now you can see that I've gotten rid of that horrible shoulder problem, and most (~80%) of the traces don't have the "wiggle" problem either, this one which happens to be the first data set, is the worst by far:

Found a Glitch

2006-04-10T15:52:00.000-07:00

Ok so we need to remove a glitch at:
6980

Here's some examples:

And here's all of the files on top of each other:

Weird Shoulders

2006-04-10T14:35:00.000-07:00

028b1
029b1-2
030b1-3 (b2 is ok...)
031b1-3
032b1-3

Above has weird shoulders around 1.2-1.3A. Here's a plot (the highlighted trace is in black):

-------------
022b1
023b1
023b2
024b1
042b1
Above doesn't have shoulders- but had weird dips in the less than 1.2A area. Here's a plot:

---------
039b3
043b1
043b2
044b1

Above has a flatened top, and in some cases looks like two peaks. Here's a plot:

Reduce Numero Tres

2006-04-10T12:09:00.000-07:00

This is the E-space file that has been normalized and pre-edged.

So, in this next plot is just a blown up view of the middle section of the energy space file. You can see how the different traces seperate? That's bad!

This is the real space plot of the lsmo c-axis data. See the shoulder below ~1.2A. That can't be there since an atom is only ~1A or maybe even a little bit more. We think that the pre-edge was not done corretly and I want to check to see if it is correct or not.

And finally this is my input parameters into the Fourier transform from K-space to real space.

Reduced Woes Part 2

2006-04-06T03:53:00.000-07:00

Ok so I made a little more progress tonight:
I decided to just try to do the pre edge without worring about the normalization, using [ret] mode, and got it to work so I was encouraged. Next, I tried victoreen mode and got that to work out as well. Then when I tried normalizing to edge height, I got the blank file again. so I'm definately doing that wrong. Here is my best pre-edge graph and my comdata file.

The red plot is the original data, and the black plot is the "pre-edge reduced" data (of course its not really since its wrong!)

My Reduced Woes

2006-04-06T01:37:00.000-07:00

This is the un-reduced data.

This is my comdata file. I thought I was setting this up correctly...but I didn't get any data out when I tried using these values. Obviously something I'm doing is just plain WRONG! What is it?

Wobbler Data (beginnings...)

2006-04-05T19:45:00.000-07:00

This is what the Io looks like. So this is where I should find mono glitches.

Here is the difference between a scan with the oscillator on, and a scan with the oscillator off.

Here's all of the scans in one plot. Where is the mono glitches? I can't tell anymore.

Wobbler Pictures

2006-04-05T17:58:00.000-07:00

This is a picture of the center oscillator, which rotates the sample horizontally about the vertical axis. The pivots are connected to the sample holder vertically.

This is the back side of the center oscillator. You can see the two magnets which are epoxied in place. The stack of magnets which moves in and out of the driving coil are held in place by these small magnets.

This is a view of the fully assembled oscillator connected to the cryostat probe. The sample is also mounted and held in place by a springy metal, I belive copper-berilium- need to check this: if you could comment on this Bud. This is the front end. One major improvement needs to be in how the wires are held in place. This grey terminal block is too large, and the connectors we were using are too large.

This is the back side of the oscillator connected to the probe. This is where the most improvement needs to be. Having the two coils (one driving- one pickup) horizontally in line created some issue with the cryostat. They would get pushed in by the sides of the cryostat and would then become misaligned. They need to be smaller and more robust.

Changing to Flouresence

2006-04-01T11:49:00.000-08:00

1. Go to "Detectors" and then "current" to get a list of the currently used
2. Go to "Detectors" and then "File" gives a list of possible file detectors can be used
3. Trans.DET for transmission and GE30SCA1.DET is germanium with one scalar; GE30 SCA2.DET is a germanium detector with two scalars (we're using sca1)
4. Then you turn the beam OFF and do offsets by going to "Detectors"/"Current"/"Offsets"
5. Then run GE30 form command prompt, or restore from background
6. So this application is used to select what energy range you want to make counts (you are setting a window)
7.

Computer Notes

2006-03-31T05:46:00.000-08:00

XAS Data Collector:
System crash: Type "xas" to restart in the same window it in which is crashes, look for register dump;
R0= hex, R1 = hex, etc.
Highlighting graphs: Setup, Linestyles

Shift Notes

2006-03-31T00:33:00.000-08:00

Shut off beam
Move the mono to the detune energy
Change the temperature
Open the hutch
Check the oscillator pickup and input voltage
Do a vert/horiz scan
Detune the mono
Change the info in the scan log and write file number in lab book
Start Scan

NOTE: When you first get on shift, its a good idea to think about what time the beam gets refilled, so that you can plan your scans around that.

1. Kinda self-explanatory

2. Typically its ~50% of the max voltage on I0, but it really depends on the setup: for example if you have mirrors, such as mirrors that cut out the higher harmonics you detune less- using Matt Valdimir's harmonic rejection mirrors we were detuning at 25%. Typical energies are 100-200eV above the edge. For LSMO 6.6keV- which is a little low, but typically we're a little above or below the rule of thumb.

3. Changing the temperature on the temperature controller is just a matter of holding down the "set" button and then clicking the "raise/lower" buttons until you set it to the right energy. The controller does the rest. When making larger temperature jumps, first switch off the toggle that is in-line on the controler cable to the probe. This allows the cryo to heat up, since it takes alot longer than the probe. Wait until it is 15 deg or so away from set temp and then switch the toggle again. Keep an eye on the cryo temp we don't want it getting much less than 5 deg below the set, or more than 10 deg below set temp. If it is rising or falling quickly, increase the flow or decrease the flow accordingly. Make sure that the flow meter is still moving, and that the needle is pointing higher than 1 o'clock.

4. Der

5. 0.2 V/div scale on the oscilliscope means that you want ~300mV on the pickups and ~400mV on one signal and ~800mV on the other signal. To do this, first check the DC level on the scope by switching to DC mode. Second, shut of the horiz. signal generator by unselecting the waveform (DO NOT TURN THE POWER OFF- this ruins the DC offset) and look at channel two (the pickups). Then, turn the horiz. back on and shut off the vert by turning the attenuation all the way up (DO NOT TURN IT OFF). Be sure to check the DC offset of the pickups, making sure its centered, if not adjust the pots on the box.

6. Go to "Motors" and then "Scan Motor" then click on "select devices" then click on "select motor" choose VERT2 or HORIZ2, then click on "select detector" and choose I1. Then change the "start" and "end" to approx. -0.9mm and 0.9mm, finally click on start scan. After scanning, choose the position according to the setup charactistics, and click on "accept position".

7. Go to "Motors" and then "Move Motor" then see #2 for info on this.

8. Change the temperature information. Change the beam current information. Change the sample information. *all of this depends on what's been changed (der). Afterwards, be sure to remember to plot the current scan because you need to see if something catastrophic happens. Go to the plot window, click on "Files" then click on the box labeled "Plot All Sweeps" finally click on button "Plot Std." Finally, click on "Start Scan." Sit back relax and wait for the next one (or work on papers like Bud wants).

A. Extra "der" notes:
1. When you unplug the probe to switch samples (for example) be sure to put the resistor plug in the end of the cable, and SHUT OFF the heater. Select "manual" and turn the heater output to zero.

Setup Notes

2006-03-29T11:15:00.000-08:00

1. Unloaded all stuff

2. Get out lab notebook
a. Tape in the checkout list

3. Get stuff ready for Cryostat:
a. There's three temperature controlers- #1 is for probe A: #2 is for the cryostat: #3 is for probe B (be sure to use the right sensor port bc they are calibrated for that specific probe)
b. You need to use the shorted connector on the unused controller port
c. feed the cables through into the hutch
d. inside the hutch plug everything into the cryo- the black mark on the probe is for the
temperature controller- no mark is for the osciallator (if its being used)- the last cable is
plugged into the cryo
e. get power in the hutch
f. get out the aluminum mounting plate to connect the cryostat to the stepper motors
g. put it together with the cryo hanging off the motor UPSTREAM: move the vertical plate connection point where it needs to be so that the cryo's windows are centered in the beam. Make sure that the motor is not at its limit, preferably centered.
h. next, connect the turbo pump to the cryostat- keeping the valve closed, turn on the pump to make sure its working correctly, then open the cryo valve and wait for it to pump down
i. check the detectors- gas is flowing, have enough gas for the run, get them aligned, use the correct gain for each of them (you don't want the detector to read more than 6V and less than 0.1V-usually)

4. Oscillator setup notes:
a. the sample is mounted in the same vertical position as slot 8 (1.86" from mounting holes)
b. the sample is mounted on the probe that was designed for 15 deg alignment, so you need to set it 3 marks off from a 45 deg mark (45-30=15deg)
c. be sure to note the orientation of the oscillator before putting it in the cryo
d. every time you take the probe out, check to make sure the coils haven't moved
e. follow Geza' Kurczveil's Manual on the electronic setup of the oscillator:
-i) in short- pwr, signal generators, oscilascope, connect output signal from box to scope, using DC mode on the scope- adjust the position of zero,
use the DC off-set on the sig. generators to make sure the output isn't clipping, then use the pots on the box to center the sine wave

5. Alignment
a. First do an "eye-ball" check of the vertical and horizontal alignment- do this wrt the windows
b. Secondly, get an idea of what the sample looks like (for powder this isn't an issue)
c. Make sure you start with the slits realatively wide open (~0.7mm vert x ~10mm horiz unfocused powder- THIS IS A RULE OF THUMB) (if you are doing single crystal- start much bigger, maybe 2mm vert x 20 mm horiz)
d. Do vertical and horizontal scans to get an idea of where the sample is located
e. Close the slits down (~0.7mm x ~10mm) if they are bigger
f. Do another scan

Osciallator Calibration

2006-03-28T14:35:00.000-08:00

In calculating the sample's angular displacement, we found that we need to measure a trace on the wall of 30" which corresponds to a plus-minus angular displacement of the sample of 2 deg. This means that we have 15" per deg plus-minus on sample.

Heater Pictures

2006-02-14T01:04:00.000-08:00

I think this picture isn't shown connected correctly...check this one. Otherwise it's pretty self explainatory.

2006-01-31T15:00:00.000-08:00

Things to do:
1. Prepare samples
2. Order Helium
3. Geza safty talk
4. Re-do oscillator
5. Transport of transfer tube
6. Pump cryostat/transfer tube 1 week in advance
7. Request lab combination @ SSRL
8. LiqN2 Feb. 7th
9. Schedule shifts Feb. 7-14
10. Make sure we have the right windows

Setup:
Low T (3 days- done second)
1. N2 ionization chamber x3
2. slits 0.7x10mm

Samples:
Ba Clathrate (n-type) --> Ba L3 edge; 5.2keV; 5-7 T's; 1-2 dbl layers
Ba Clathrate (p-type) --> Ba L3 edge; 5.2keV; 5-7 T's; 1-2 dbl layers
NiGa2S4 ----------------> Ni K edge; 8.3keV; 4-6 T's < 40K; 4 T's > 40K; 3 dbl layer ??
LCMO (16%) -------------> Mn K edge; 6.5keV; 10-13 T's; 2 dbl layers
LCMO (22%) -------------> Mn K edge; 6.5keV; 10-13 T's; 2 dbl layers

Setup
High T (2 days - done first)
1. Oven (setup, align, He gas)
2. Water on hand

Samples:
LCMO (22%)w/Bn-----------> Mn K edge; 6.5keV; 8-10T's up 8-10T's dn-hyster;
LCMO (35%)w/Bn-----------> Mn K edge; 6.5keV; 8-10T's up 8-10T's dn-hyster;

2005-12-08T09:16:00.000-08:00

STDFILE ni1ab_O_1.943.ff8 1.9430 # 2 2.0
STDFILE ni2ab_O_1.94.ff8 1.94 # 1,2 4.0
STDFILE ni2ab_Y_3.203.ff8 3.203 #
STDFILE ni2ab_Ba_3.386.ff8 3.386 #
STDFILE ni1ab_Ba_3.471.ff8 3.471 #
STDFILE ni1ab_Cu_3.85.ff8 3.85 #
STDFILE ni2ab_Cu_3.85.ff8 3.85 #
STDFILE ni1ab_CuO_3.886.ff8 3.886 #
STDFILE ni2ab_CuO_3.8387.ff8 3.8387 #
STDFILE ni2ab_CuO_3.905.ff8 3.905 #
STDFILE ni2ab_O-O_3.307.ff8 3.307
STDFILE ni2ab_O-O_3.8387.ff8 3.8387
STDFILE ni2ab_O-O_3.8544.ff8 3.8544
STDFILE ni1ab_BaO_4.1452.ff8 4.1452
STDFILE ni1ab_CuO-O_3.886.ff8 3.886
STDFILE ni1ab_O_4.2882.ff8 4.2882

2005-12-07T15:15:00.000-08:00

So this is the first note in the lab notebook:

Working on fitting the ab-plane
First some nomenclature:
A1 = Ni1-O peak
A2 = Ni2-O peak
A3 = Ni2-Y peak
A4 = Ni2-Ba peak
A5 = Ni1-Ba peak
A6 = Ni1-Cu peak
A7 = Ni2-Cu peak

and

x=consentration of Ni on Cu1 per layer
(x-1)/2 = consentration of Ni on Cu2 per layer

now, using this nomenclature, and an S02 = 3/4

A2 = 3-2A1
A3 = 0.5 (A2)
A4 = A3
A5 = 2A1
A6 = A5
A7 = A2

Now the multi-leg needs to be done:
Add together multi's within +- 0.05 angs.
Only include multi's within ~5% of the max amplitude peak.
Remember to add similar paths
Only add multi's which start in the ab-plane
Also, constrain by (1) (# of same multi-leg) (concentration per layer)

N1 (c-axis: 113,114) (ab-plane: 130,131) Grown in Ar
N2 (c-axis: 120,121) (ab-plane: 133,134) Grown in air; annealed in O2
N3 (c-axis: 123,124) (ab-plane: 137) Grown in air; annealed in Ar; annealed in O2
N4 (c-axis: 127,128,129) (ab-plane: 138) Grown in air; annealed in Ar; cooled in Ar)