Changeset 1718 for Tutorials/MCsimanneal

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Timestamp:
Mar 16, 2015 4:18:34 PM (7 years ago)
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updating images in tutorials

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Tutorials/MCsimanneal
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8 edited

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• Tutorials/MCsimanneal/MCSA in GSAS.htm

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1Å or better.

Step 2. Peak picking & fitting

Step 2. Peak picking & fitting

Next you need to select limits so that ~20 peaks are selected for indexing; go to Limits and choose 9-25° 2Θ. Next go to Peak List and pick all the peaks you can see between the limits. This is most easily done by hand as the Auto search routine gives a lot of spurious peaks for this rather noisy and weak data; I picked 21 peaks, skipping a few very weak ones. Then use Peak fitting/LSQ PeakFit to fit them. You will need to vary at least X & Y in Peak fitting/LSQ PeakFit to fit them. You will need to vary at least X & Y in Instrument Parameters along with pos & int in the Peak List to get a reasonable fit suitable for indexing.

Step 3. Indexing

Parameters along with pos & int in the Peak List to get a reasonable fit suitable for indexing.

Step 3. Indexing

Next go to Index Peak List and do Operations/Load/Reload to set up the peaks for indexing. Then go to Unit Cells List for indexing. The most likely Bravais lattice for these small organic molecules is either Orthorhombic-P or Monoclinic-P; you can try both and see what comes out (Hint: its Orthorhombic-P). The correct unit cell should almost immediately appear with an M20 ~330 with a=7.748, b=7.651, c=12.736, Vol=755.01. Do Cell Index/Refine/Copy Cell; you can then try various space groups. Press the Show HKL positions to see the lines with extinctions (Hint: its Orthorhombic-P). The correct unit cell should almost immediately appear with an M20 ~330 with a=7.748, b=7.651, c=12.736, Vol=755.01. Do Cell Index/Refine/Copy Cell; you can then try various space groups. Press the Show HKL positions to see the lines with extinctions (Hint: its P 21 21 21). You can then do Cell Index/Refine/Refine Cell to improve the lattice parameters with M20 ~380. Finally do Cell Index/Refine/Make new phase to create the phase; I named it 3-aminoquinoline.

Step 4. Setup for Pawley refinement

Step 4. Setup for Pawley refinement

There are a number of steps that must be done in preparation style='mso-fareast-font-family:"Times New Roman"'>1.      Select Limits in the GSAS-II data tree for the PWDR data set and expand the plot so that the style='mso-fareast-font-family:"Times New Roman"'>2.      Select Instrument Parameters and uncheck all Refine flags and do Operations/Reset profile to recover the default values. The peak fitting done earlier style='mso-fareast-font-family:"Times New Roman"'>3.      Select Sample Parameters and uncheck refinement of Histogram scale factor.

Sample Parameters and uncheck refinement of Histogram scale factor.

4.      Go to Phases/3-aminoquinoline to find the Pawley controls. Check the Do Pawley refinement box and enter the d-spacing (1.8133) into the Pawley dmin box.

normal'>Pawley dmin box.

When done the General tab should look like

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Next find the Data tab; it will be empty except for a single line of text. Do Edit/Add powder histograms; a dialog box will appear

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Select either choice; the desired data set will be added to this phase for analysis. The data tab now shows the new data set; check the Show button to see the full information

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This is the location for all the phase dependent parameters for this histogram. Notice that it includes phase fraction, size & mustrain as well as preferred orientation, elastic strain and extinction corrections. The Babinet correction is intended for protein work where a significant region of the structure is disordered solvent. There are buttons for plotting size and mustrain surfaces and preferred orientation correction curves.

for this histogram. Notice that it includes phase fraction, size & mustrain as well as preferred orientation, elastic strain and extinction corrections. The Babinet correction is intended for protein work where a significant region of the structure is disordered solvent. There are buttons for plotting size and mustrain surfaces and preferred orientation correction curves.

Next find the Pawley reflections tab; it will be empty except for column headings. Do Operations/Pawley create; this makes the reflection set over the range covered by setting Pawley dmin. The table should list reflections 0-91. Select and check the refine column using the same technique you used for the peak list.

empty except for column headings. Do Operations/Pawley create; this makes the reflection set over the range covered by setting Pawley dmin. The table should list reflections 0-91. Select and check the refine column using the same technique you used for the peak list.

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you didnt skip a step as it might not work correctly if you did.

Step 5. Pawley refinement

Step 5. Pawley refinement

To start the refinement, do Calculate/Refine on the main GSAS-II data tree window. Before it begins a backup of the project file is made; the name will be aminoquinoline.bck0.gpx. It can be used to recover from a bad refinement. A progress dialog box will appear showing the residual as the refinement proceeds. My refinement completed with Rwp ~12.9%; a dialog box appears asking if you wish to load the result. Press OK. To see the plot select the PWDR line in the GSAS-II data tree (Ive adjusted the width and height).

showing the residual as the refinement proceeds. My refinement completed with Rwp ~12.9%; a dialog box appears asking if you wish to load the result. Press OK. To see the plot select the PWDR line in the GSAS-II data tree (Ive adjusted the width and height).

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background model. One easy way to fit that broad hump is to add a peak to the background. Go to Background and set No. peaks to 1, then change pos to 19, int to 100000 and sig to pos to 19, int to 100000 and sig to 100000; for the peak only refine int. I also set No. coeff. to No. coeff. to 5; the window shows

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Do a Calculate/Refine; my Rwp fell to ~8.5%. In Background select pos & sig for refinement and in Instrument Parameters select X & Y for refinement; then do Calculate /Refine again. I got Rwp~7.5% at convergence and the fit looked like

style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; mso-hansi-theme-font:minor-latin'>Calculate/Refine; my Rwp fell to ~8.5%. In Background select pos & sig for refinement and in Instrument Parameters select X & Y for refinement; then do Calculate /Refine again. I got Rwp~7.5% at convergence and the fit looked like

c

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Annealing.

Step 6. Setup for Monte Carlo/Simulated Annealing

The molecular structure of 3-aminoquinoline is two aromatic rings with one N-substituted position and an amino side group

Step 6. Setup for Monte Carlo/Simulated Annealing

The molecular structure of 3-aminoquinoline is two aromatic rings with one N-substituted position and an amino side group

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MC/SA structure solution consists of optimizing the position freedom. Thus we need to determine essentially six parameters. To do this in GSAS-II we need to put a model of this molecule in as a rigid body. One must create the model outside of GSAS-II, it has no facilities for model building. I used the Avogadro (http://avogadro.cc/wiki/Main_Page) create the model outside of GSAS-II, it has no facilities for model building. I used the Avogadro (http://avogadro.cc/wiki/Main_Page) package for this and created a simple xyz Cartesian coordinate file for it (if you have Avogadro or something equivalent you can try this for yourself). To start go to Rigid bodies in the main GSAS-II data tree. You will see a window with two tabs; select Residue rigid bodies and then do Edit/Import XYZ. Change the file type to XYZ file (*.xyz) and select aminoquinoline.xyz. The Rigid bodies style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz) and select aminoquinoline.xyz. The Rigid bodies window will show

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If you select the Plot? box a drawing will appear

If you select the Plot? box a drawing will appear

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needed for MC/SA and will just make computation times a bit longer than necessary. You should change the Residue name to something meaningful, I used amino.

style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; mso-hansi-theme-font:minor-latin'>Residue name to something meaningful, I used amino.

Next go to Phases/3-aminoquinoline and select the MC/SA tab and do MC/SA/Add rigid body; select the only choice (amino) from the popup selection box. The MC/SA window shows

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You see the four equivalent molecules for space group P212121 whose centers fall within the unit cell; the reference one is that in the lower left corner with C1 at the origin. You can enter values in the x,y,z boxes and see how the structure changes. Similarly, you can enter an angle in Oa or a vector in the Oi,Oj,Okx,y,z boxes and see how the structure changes. Similarly, you can enter an angle in Oa or a vector in the Oi,Oj,Ok  box to see the effects of rotating the molecule. Each of these parameters has a defined range for the MC/SA with the default. We want to optimize the position and orientation of this molecule; check the x, y & z boxes and select AV from the Oa, Oi,Oj,Ok Vary? pulldown. The MC/SA window should look like

"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: minor-latin'>AV from the Oa, Oi,Oj,Ok Vary? pulldown. The MC/SA window should look like

This completes the set up for MC/SA processing.

Step 7. Monte Carlo/Simulated Annealing

Step 7. Monte Carlo/Simulated Annealing

Now go to the General tab; the MC/SA controls are at the bottom of the window. To begin the setup of these controls, select a source of the Reflection set to be used in the MC/SA runs. The choice is to use either the Pawley reflections or the Reflection List for the PWDR data set. If you choose Pawley reflections then the structure factors will be Pawley model values, Fsq(hkl) in Pawley table, and the covariance matrix developed from the refinement will be used for peak overlap effects in the MC/SA calculations. Alternatively, if you choose PWDR Quinoli.gda Bank 1 then the structure factors will be those, Fosq in structure factors will be Pawley model values, Fsq(hkl) in Pawley table, and the covariance matrix developed from the refinement will be used for peak overlap effects in the MC/SA calculations. Alternatively, if you choose PWDR Quinoli.gda Bank 1 then the structure factors will be those, Fosq in Reflection table, extracted during the Pawley refinement and the peak FWHMs will be used for peak overlap effects in the MC/SA calculations. Notice that the Pawley Fsq(hkl) values are the same as the Fcsq Reflection List values. Here I chose Pawley reflections for the Reflection set as it give slightly better performance in MC/SA.

the Pawley Fsq(hkl) values are the same as the Fcsq Reflection List values. Here I chose Pawley reflections for the Reflection set as it give slightly better performance in MC/SA.

Next, you need to set the minimum d-spacing (d-min). Smaller values gives minima in the MC/SA minimization surface that are more should have 5-8 reflections for each MC/SA parameter; in this case 35-50 reflections are needed. If you examine the reflection list (either Pawley or Reflection List) youll see that a d-min of 2.5 will give sufficient reflections.

Lastly, you need to set the run controls. I used 500 for the No. trials; this is the number of random tries at each temperature in the annealing schedule. When done the General window should look like

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When ready, you can start the MC/SA calculation by doing Compute/MC/SA from the General window menu. A progress bar will appear that shows the MC/SA residual (an as indicating which MC/SA run is being done. When it finishes, control is shifted to the MC/SA window which gives a list of the solutions it found at the bottom of the window (scroll down to see them).

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molecules clashing), then you should just rerun MC/SA perhaps using more runs or more trials. Be sure to set the Keep box for any solutions you want to retain; the others will be cleared before the next MC/SA run starts. When you think you have a good one, Select it; the parameters will be copied to the appropriate boxes in the upper part of the MC/SA window and the structure is drawn again. Next we want to refine this solution so go back to the General tab.

When you think you have a good one, Select it; the parameters will be copied to the appropriate boxes in the upper part of the MC/SA window and the structure is drawn again. Next we want to refine this solution so go back to the General tab.

MC/SA refinement is achieved by narrowing the search ranges and rerunning the MC/SA calculations. This is done by checking the MC/SA Refine box. Using 10% of the ranges reduces the search volume in this case by ~6 orders of magnitude so that the true minimum is much easier to find. Now rerun Compute/MC/SA; be sure to select the best one before starting. The residual should drop to a id="Picture_x0020_22" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:569.25pt; height:285pt;visibility:visible;mso-wrap-style:square'>

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This is clearly a good result (R ~ 0.4%!) and the structure

This is clearly a good result (R ~ 0.4%!) and the structure

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is identical to the published one

is identical to the published one

as drawn by the Mercury program

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as drawn by the Mercury program

(https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx). To save this solution to the Atoms list do MC/SA/Move MC/SA solution; the drawing will show the new atom positions

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And they will be listed in the Atoms table.

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It is now ready for Rietveld refinement; this needs to use the rigid body as the data will not support independent atom position refinement.

Step 8. Initial Rietveld refinement

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It is now ready for Rietveld refinement; this needs to use the rigid body as the data will not support independent atom position refinement.

Step 8. Initial Rietveld refinement

After a few simple steps the 3-aminoquinoline structure will be ready for the first Rietveld refinement: 1) On the General tab uncheck the Do Pawley refinement? box, 2) check the Histogram scale factor box in Sample Parameters and 3) zero both X & Y and uncheck their refine boxes in Instrument Parameters. Then do Calculate/Refine from the main GSAS-II data tree window; my Rwp was ~9%. Next check the Refine unit cell in the General window and in the Data window, using the uniaxial model for mustrain, check both Cryst. size & mustrain be ready for the first Rietveld refinement: 1) On the General tab uncheck the Do Pawley refinement? box, 2) check the Histogram scale factor box in Sample Parameters and 3) zero both X & Y and uncheck their refine boxes in Instrument Parameters. Then do Calculate/Refine from the main GSAS-II data tree window; my Rwp was ~9%. Next check the Refine unit cell in the General window and in the Data window, using the uniaxial model for mustrain, check both Cryst. size & mustrain boxes and do another Calculate/Refine; I got an Rwp ~8.5% for this. Weve not refined atom positions or thermal parameters; to do this we need to describe the structure as a rigid body.

Step 9. Rigid body model

style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; mso-hansi-theme-font:minor-latin'>Calculate/Refine; I got an Rwp ~8.5% for this. Weve not refined atom positions or thermal parameters; to do this we need to describe the structure as a rigid body.

Step 9. Rigid body model

The rigid body itself has already been defined; it was used for the MC/SA structure solution. Now we have to place it in the unit cell matching the atom positions obtained from the MC/SA runs. First go to the Draw Atoms tab and change the Style to balls & sticks and the Label to name. Double click on the column headings and select the item from the popup control. Next go to the RB Models tab; it will be empty. Do Edit/Assign atoms to rigid body; then select amino in the Select rigid body model pull down (the only choice). The RB Models window will show

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You will orient the rigid body against the atoms by matching up the 3 reference atoms in the rigid body (C1, C2 & C5) to the corresponding atoms in the structure (C(2), C(3) & C(6)). Do these in order; the drawing will show the shift of molecular origin and then its reorientation as the three atoms are selected. Press Ready when done; the structure will be drawn with yellow bonds indicating that it is now a rigid body and not independent atoms. The RB Models window shows the new rigid body

corresponding atoms in the structure (C(2), C(3) & C(6)). Do these in order; the drawing will show the shift of molecular origin and then its reorientation as the three atoms are selected. Press Ready when done; the structure will be drawn with yellow bonds indicating that it is now a rigid body and not independent atoms. The RB Models window shows the new rigid body

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To refine the rigid body parameters check the Refine? box, select AV from the pull down, choose Uiso from the thermal parameter model and check its Refine? box. Then do Calculate/Refine; after a couple of refinement runs I got an Rwp ~7.9% and the RBModels window shows the new parameters

box, select AV from the pull down, choose Uiso from the thermal parameter model and check its Refine? box. Then do Calculate/Refine; after a couple of refinement runs I got an Rwp ~7.9% and the RBModels window shows the new parameters

and the profile shows the fit

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and the profile shows the fit

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This completes the structure analysis for 3-aminoquinoline. Next is a more complex case involving some internal degrees of freedom in the molecule of a-d-lactose.

molecule of a-d-lactose.

• Tutorials/MCsimanneal/MCSA in GSAS_files/filelist.xml

 r1705
• Tutorials/MCsimanneal/MCSA in GSAS_files/props061.xml

 r1705
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