File Structure

The filing should be fairly clear and intuition based. First on the desktop enter the folder Mauro, or enter the hard drive from there, then enter the folder corresponding to composition or enter the density folder for the measurements and workups of the manual density measurements. Next after entering the composition folder there are descriptions of either the constrained work folders or the temperatures and trials of unconstrained work. From here enter the temperature of choice. for Unconstrained files the temperatures labelled are uncorrected but with the constrained files the temperatures are corrected. From here there is all the input and outputs from the RMC process. In this section there are often inserts labelled as such that describe the outputs from the RMC simulation. There are also the visual fits labelled as fits or files 1-4 that correspond to the same numbered figure in matlab. For unconstrained RMC the one fit is of the S(q). For constrained the fits are Ni-Ni, Ni-Zr, Zr-Zr, and S(q) for the fits 1, 2, 3 and 4 respectively. From here you can enter the voronoi folder. The top 20 Voronoi indices are listed in the file labelled as (C_ for constrained and blank if unconstrained)Voronoi_(1 or 2)_(Temp). Here the 1 represents the top 20 voronoi counts with out the outliers being removed and 2 represents the files after the outliers have been removed. For counts of types of indices check the lab notebook. Note:Different runs are labelled differently and usually in a sub folder under the general heading. So for example there where multiple runs, especially in the unconstrained RMC and experiments to test methods. These got there own folder and then were subdivided into temperature or if they were all one temperature then the experiment folder will hold all the proper information under the temperature and type of constraint. Often the Liquid and Glass data were divided by folder.

On the Hard drive is everything up to the first constrained run with the r-spacing of .01 and the full gr files. After this the folder on my desktop labelled Mauro contains the different constrained runs and the manual densities, as well as the results from the first constrained run.The hard drive also has the original experimental files. In a folder called Diff from the desktop path contains a re-configured temperature data for the highest and lowest temperature liquids.


This summer has been an excellent start to the research that I will be doing. I hope to continue this research during the school terms. First let us talk about what has been accomplished. The liquid data for my composition (Zr36Ni64) has been configured in the RMC process and Voronoi analysis has been done. There is continuation to these parts with error analysis, with more iterations, another composition I would also like to investigate. The side project of measuring density manually and the preparation for the Advanced Photon Source went well. At Argonne National Lab the experiment and all the work that we did there was a wonderful experience. I would probably say that that was one of the best weeks for me. Now lastly there was an attempt at serial communication with the microbalance used in density measurements. This went awry and this project’s difficulties hit me the hardest. However I was able to do some troubleshooting and narrow down the possible problems in the communication process. Eventually I hope to be able to communicate successfully. Lastly the work as a whole, being a group member of Professor Mauro’s research team inspired my to try and do great things. Thank you, Professor Mauro. The team we had performed quite well, I would say in the search for what makes a better glass former and I hope to contribute more in the following year(s).

12 min Presentation


Week 4

This week was split into many parts. These parts were finishing Voronoi analysis from the previous week, density workups and the exploration of LabView, varying number density and see how this affects the Reverse Monte Carlo Simulation and its outputs, and lastly beginning Constrained RMC’s. The Voronoi index counts were obtained and the top 20 Voronoi indices were obtained before and after outlier removal.There was a difficulty in finding the outliers at 233C in order to solve this problem the RMC was ran again on a newly generated configuration file. This ran for 24 hours like the rest of the glasses. Afterwards the outliers were able to be found and the top 20 Voronoi indices before and after outlier removal. In addition to this the counts for certain indices were obtained. This week has also been dedicated to measuring the densities of various composition glasses. This was done using Archimedes’ Method. It should be noted that the mass measurements found in the air are easy to obtain and take less than an hour for 10 measurements. However the toluene measurements are much harder to obtain. The process has taken as long as 3 hours obtaining stable measurements. I have found slight ways to decrease this time and increase the stability and precision of these measurements. First the toluene should be removed from the storage, placed in a container, holding the appropriate volume, outside and covered as to approach the room’s temperature before taking measurements. Another method is to look at the minute oscillations that hold fairly stable and find the value that is being fluctuated around. The next method is to use Lab View to automate these measurements, this project has led me to watch many tutorial videos on the National Instruments’ site, doing the programming tutorials found on their site, completing their quizzes, and reading the user manual for the Cahn C-35 micro-balance in order to find how to interface with the balance. To further investigate the Reverse Monte Carlo simulation and the accuracy of the number densities that were given, and used in the earlier runs. This was done by looking at the highest temperature glass and decreasing the number density by 5% and extrapolating the liquid data to get another value that turned out to be 18.5% higher than the original value. These runs were then compared by looking at the fit to the S(q) and the partial g(r)’s. This varying of the number density was also tested on the highest temperature liquid changing the number density by decreasing it by 5%,10%, and 15% of the original value. The comparison was done the same way. The results illustrate for the glass that the given density is likely to be within a 5% of the true value, and probably even more precise than that. The liquid data is harder to interpret however there is a clear difference between the number densities in the fits and that leads me to believe that the value given is more precise than the five percent difference illustrated in my test. Lastly this week I have begun the constrained RMC by including Molecular Dynamic data in the RMC simulation. This was run initially for 12 hours on the highest temperature liquid. The fit was very choppy and could use more time so it was ran for another 12 hour increment. The change in procedure is minimal¬† but more set up is necessary so this process has begun. The main differences when compared to the unconstrained RMC are the additional .gr files and the .dat file that has been altered to accommodate the additional information. Finishing Voronoi from Unconstrained of Zr36Ni64: Voronoi_2_1_233 Voronoi_2_2_233 Voronoi_2_408. Density Spreadsheets were not allowed for “security reasons” in current format. Varying the number density results: Insert_05383 Insert_05666 Insert_06258 Insert_053193 Insert_056322 Insert_059451 Insert_067128 P_VND_1444

ni-ni_partial_grs_vary_number_density ni-zr_partial_grs_vary_number_density partial_grs_w_number_density_005383 partial_grs_w_number_density_005666 partial_grs_w_number_density_0067128

Lastly the Constrained RMC example files were also not allowed to be attached however they w

Week 3

At the beginning of the week the glass RMC’s were finished after 24 hours and the 1175C run was ran with an additional hour to finish moving out the atoms that were below the cutoff. The top 20 Voronoi indices were obtained. The partial g(r)’s were examined to see if there were any obvious physical inconsistencies. The Voronoi index counts were mapped against temperature to see how the structural Voronoi cells evolve across temperatures to hopefully gleam what happens as the liquid transitions into a glass.The partial g(r) at 1175 C had its earlier problem removed, but still retains that discontinuous jump that exist before the actual first peak. This jump id believed to have no physical meaning because it has an atom within the radius excluding other atoms. Why does the simulation do this? The glass partial g(r)’s look very nice. However the first peak happens at the same radius when it should differ between the different partials.The height of the first peak still corresponds as described in last week’s report. There is slight ruggedness to the fits and there still exist a small bump for the Ni-Ni partial g(r). Some of temperatures had their outliers removed and their top 20 Voronoi indices recorded. Note: for all of these glasses the AllStat.txt file was quite odd. The characters were repeated a consistent integer number of times. This integer ranged from 4-6 and the text file was edited so that the correct file was saved using the find and replace function. RMC and Fits: Insert_25 Insert_233 Insert_349 Insert_408 Insert_1175_2. Voronoi Indices: Voronoi_1_25 Voronoi_1_233 Voronoi_1_349 Voronoi_1_408 Voronoi_2_25 Voronoi_2_349 Voronoi_2_1175. Voronoi Index counts across Temperatures:

h_voronoi_index_counts_across_temperatures voronoi_index_counts_across_temperatures.

Partial g(r)’s for different temperatures and different partials: ni-ni_partial_grs_across_the_glass_temperatures ni-zr_partial_grs_across_the_glass_temperatures partial_grs_at_25_c partial_grs_at_233_c partial_grs_at_349_c partial_grs_at_408_c partial_grs_at_1175c_2 zr-zr_partial_grs_across_the_glass_temperatures.

Achievements thus far


Week 2

Throughout the week I was able to run an RMC for every temperature for the Zr36Ni64 system. The top 20 Voronoi indices were obtained before and after outlier removal. Patterns were looked for by analyzing the trends in the Voronoi indices to obtain a basis for either state or even a general trend extending beyond the narrow temperature range of four temperatures per state. However, on Friday morning a hypothesis was tested that proved that the RMC program was being ran incorrectly. This lead to a complete redo. The liquid temperature RMC were redone and the Voronoi indices were obtained before and after outlier removal. The glasses were set up for a 24 hour run to get better results than the previous runs. The RMC details and the visual fits: Insert_1175 Insert_1254 Insert_1360 Insert_1444.The Voronoi indices for the liquid temperatures: Voronoi_1_1175 Voronoi_1_1254 Voronoi_1_1360 Voronoi_1_1444 Voronoi_2_1175 Voronoi_2_1254 Voronoi_2_1360 Voronoi_2_1444. The partial g(r)’s obtained from running the RMC were plotted out and the contents evaluated. The plots:¬†Pg(r)1_LT . The plots look very similar to the overal g(r) plot however here there are some elements that can be more easily examined. The highest peaks are Zr-Zr which makes sense since Zirconium is bigger even though there is less Zr in the sample.The plots do not slowly rise to a peak but rather they have jumps that look rather discontinuous. Another error also arises when examining the 1175 C plots as there are atoms in the area where there should not be any. This does not make much sense as this fit looked quite good and the chi squared value was the lowest out of all of these liquids however another RMC might be in order to eliminate these impossibilities present in the partial g(r). In the near future a revision to the apparatus presentation will be uploaded to have a better flow and to show the most important part in detail not the extraneous details.

Apparatus Presentation


Week 1

I looked at the Zr36Ni64 system. For all of the different temperatures of this system the preliminary files were generated from the experimental results.From this the S(q)’s and g(r)’s for this system were compared with one another at the different temperatures. An unconstrained Reverse Monte Carlo was executed on this system at room temperature. The resulting atom positions were then used in an initial running of the voronoi programs to generate a list of voronoi indices without the removal of outliers.The Procedure: Week 1 Procedure. The plots:1comparing_the_grs_for_the_various_temperatures_for_zr36ni64 comparing_the_sqs_for_the_various_temperatures_for_zr36ni64 glass_and_liquid_height_of_the_first_gr_peak_as_a_function_of_temperature_for_zr36ni64 glass_and_liquid_height_of_the_first_sq_peak_as_a_function_of_temperature_for_zr36ni64. The observations: Observations1. The equations and R^2 for the heights of S(q)1 and g(r) as functions of temperature separated by state: Equations1.