NCSI: Structure Determination and Analysis of Mixed Palladium Silicon Clusters, Si(n)Pd(m) (n

Status	Completed
Mentor Name	Jonathan Lyon
Mentor's XSEDE Affiliation	Research Allocation
Mentor Has Been in XSEDE Community	4-5 years
Project Title	Structure Determination and Analysis of Mixed Palladium Silicon Clusters, Si(n)Pd(m) (n < 13; m = 1-3)
Summary	This position will study strongly bound doped metalloid atomic clusters as models for real world systems in heterogeneous catalysts and electronics. Specifically, we will explore palladium doped silicon clusters here, Si(n)Pd(m) (n < 13; m = 1-3). searching cluster potential energy surfaces for local and global minima and exploring the relationship of cluster size and dopant concentration on different cluster properties. The results from this investigation will then be compared with related cluster systems.
Job Description	The student will perform theoretical chemistry calculations using the Gaussian 16 and NBO 7 programs on the EXPANSE cluster housed at the San Diego Supercomputing Center (SDSC). First, this student will generate candidate structures for each cluster size and composition using global optimization procedures. One program utilizes the artificial bee colony algorithm, whereas the second basin hoping program is written and compiled in-house using Fortran code. Additional structures will be generated by hand from our prior knowledge as well as previous predictions in the literature. All candidate structures will then be further optimized by this student at the B3LYP/6-311++G(d,p)/SDD level of theory first. This method has been shown to reproduce experimental results for similar systems, and will be further tested and validated by this student for select sizes by comparing with other density functional theory and larger ab initio methods (i.e., MP2 and CCSD). Various results from generated outputs will be visualized with the Avogadro, Gabedit, and Gaussview programs on a local machine.
Computational Resources	This project will make use of the EXPANSE high performance computing cluster at the SDSC through XSEDE allocation CHE-130094 (active through 3/31/2022). This computer cluster has the Gaussian 16 program and required compilers already installed. The NBO 7 program, which will also be utilized in this project, was recently purchased and installed on the EXPANSE cluster in January 2021 at PI Lyon's request and efforts. Generated files from all programs will be transferred to a local desktop in PI Lyon's research laboratory for analysis, visualization, and long term storage.
Contribution to Community	This project will contribute to the XSEDE community in several ways. First, it is expected the results from this project will be of significant interest locally and more broadly to the scientific community. The results from this investigation are intertwined with that of other students in the same laboratory who are exploring related systems. It is anticipated this project will result in a presentation by the student at a scientific meeting, a presentation by the mentor at a scientific meeting, and a manuscript submitted for publication to a peer reviewed journal. Second, it is likely the student applying for position will be relatively new to the XSEDE community applying to the EMPOWER program for the first time, and will come from a group typically underrepresented in science and computing fields. This program will allow for the training of this next-generation researcher in computer science and computational chemistry. Lastly, this project will occur at Murray State University, an EPSCoR institution.
Position Type	Apprentice
Training Plan	It is anticipated the student applying for this position will have already began training and completed all safety requirements for work with PI Lyon in the Spring 2021 semester. During the Fall 2021 semester, this student will continue to expand this project and should require minimal training. Regardless, an intensive week long refresher training will occur at the start of the semester to quickly catch the student up to speed after the break. If needed after this refresher training with PI Lyon, the "Expanse 101 Webinar" recorded on 10/8/2020 and the Cornell University's "Introduction to Linux Virtual Workshop," both of which are available on the XSEDE training site, will be utilized as additional training supplements for this student. Any additional new or refresher training needed by the student throughout the remainder of the semester will be performed by the mentor, Dr. Lyon. Although scheduled weekly meetings will occur between the student and mentor where progress and problems encountered will be discussed, in person interactions will likely occur more frequently every couple of days as they have in the past. Monthly progress reports for Shodor will be prepared by the student and discussed with the mentor before all formal deadlines. Dr. Lyon has trained several students in the past in similar techniques, including a previously successful EMPOWER program participant in 2020.
Student Prerequisites/Conditions/Qualifications	Student should be moderately familiar with navigating through Linux operating systems. Student should be a chemistry major, or suitable equivalent. While a prior knowledge of physical chemistry is beneficial, it is not required. A desire to learn physical chemistry concepts as needed is more important.
Duration	Semester
Start Date	08/17/2021
End Date	12/11/2021

NCSI

Structure Determination and Analysis of Mixed Palladium Silicon Clusters, Si(n)Pd(m) (n < 13; m = 1-3)