Graduate Computational Chemistry/Materials Science - Syllabus

CHEM 529 $\bullet$ PHYS 611

Instructor

  • Michele Pavanello
  • Office: Smith 511
  • Office hours: you are welcome in Smith 511 anytime! Either Michele or a Pavanello Research Group member will be there to help you

Overview

The goal of this 3 credit course for Chemistry, Physics and Materials science graduate and undergraduate students is to provide basic knowledge of the theory of materials science and molecular quantum mechanics when it is applied to determine properties (e.g., photoelectron spectroscopy, IR, UV/VIS, NMR, etc...) as well as reactivity and dynamics.

The lectures are scheduled for Mondays 6:00 to 8:50 PM in ENG 215 and will cover "Theory" and "Applications". Theory lectures will treat the theoretical background (formal proofs, derivations and problem solving). Applications lectures will involve learning Linux, BASH scripting, basic Python and practicing concepts of computational chemistry.

Lectures will be divided in two parts: The first part (1.5 hours) will be devoted to the study of theoretical tools at the foundation of quntum chemistry and quantum materials science. The second part of the lectures will be devoted practical applications of the concepts learned during the first part of the lecture and will involve Python coding or training on the use of off-the-shelf electronic structure software.

Class Slack channel

Join the class Slack channel for asking questions to the instructor and other students in the class

Books & Materials

Learning Goals

  1. The basics of Quantum Mechanics applied to Materials Science and Chemistry
  2. Code in Pyhton (with Psi4 and ASE) or use Gaussian or Quantumm ESPRESSO softwares and building models with Avogadro
  3. Manage data sets and sustainable code development
  4. Support experimental work with "first-principles" quantum simulations

Timeline (subject to corrections)

LectureTheory TopicPractical TopicAssigments Due
9/12Theory (ch 1) Python 1
9/19 Theory (ch 2.1, 2.2) Python 2
9/26
IQC setup and lecture 1
Python 1
10/3 Theory (ch 2.3) Gaussian and AmarelPython 2 and Project abstract
10/10Theory (ch 3.1, 3.2)Python 3 / GaussianRevised project abstract
10/17Theory (ch 3.3, 3.4)IQC lectures 1 and 2Python 3
10/24
Midterm exam
10/31Theory (ch 3.5-8) IQC lectures 3 and 4IQC lecture 2
11/7Theory (ch 4.1) IQC lecture 5IQC lecture 3
11/14 Theory (ch 4.2, 4.3)IQC lecture 6IQC lecture 4
11/21Theory (ch 4.4) Work on projectIQC lecture 5
11/28Theory (ch 4.5, 4.6)Work on projectIQC lecture 6
12/5Theory (ch 2.4, 5.1) Work on projectAssigments Due
12/12 Theory (ch 5.2) Work on projectAssigments Due

Grade distribution


ItemPercentage
Homework20%
Midterm30%
Project50%
Total100%

Grade cut-offs

GradePercentage
A85--100
B65--84
C55--64

Homework rules

Midterm and Final

The midterm exam will be one-hour long and will involve problem solving. It will concern the course material covered until the last lecture before the exam. There will be no final exam for this class.

Computational/Theoretical Project

This project will be either Computational or Theoretical. Title and abstract of the Project need to be agreed upon by Prof. Pavanello no later than lecture 4. The subject of the project should be formulated in collaboration with the student's research advisor.

Computational

It will involve using an established computer software (such as Gaussian) to study a chemical reaction or physical process. A 3--5 page report and a presentation on this project will be graded out of 50 points and will constitute the grade associated with the "Project" grade item. Further instructions will be given later.

Theoretical

It will involve coding from scratch in Python one of the a useful feature for materials science and chemistry in a local orbital basis (PySCF), or plane wave basis (Quantum ESPRESSO or QEpy or other platforms) or finite differences basis:

  • Ground state HF or DFT.
  • Time-dependent HF or DFT in real time or Casida formalism.
  • Time-dependent current DFT in real time or Casida formalism.
  • Phonons / molecular vibrations using the Sternheimer equation.
  • Optical spectra with the Sternheimer equation.
  • ... any other feature agreed upon by Prof Pavanello and the student.

This project also will involve a 3--5 page report preferably on a Jupyter notebook in Markdown language, together with in-line examples of computations run with the computer code as well as a presentation. Alternative computer coding projects can also be considered.

Official Course Website

The official course webpage is

https://rutgers.instructure.com/courses/201103}
On the website you will find additional resources that may be posted. Homeworks, Midterm and Project grades are also posted here.

Disability Services

Rutgers University welcomes students with disabilities into all of the University’s educational programs. In order to receive consideration for reasonable accommodations, you must complete and submit the Registration Form, schedule and complete an intake meeting, and submit appropriate documentation. If your request for reasonable accommodations is approved, you will receive a Letter of Accommodations (LOA), which you should present privately to the instructor as early in the semester as possible. Accommodations are not retroactive and are effective only upon submission of the LOA to the instructor. Please begin the process by completing and submitting the Registration Form, Applying for Services, available at the website https://ods.rutgers.edu/. There you can:

  • Applying for Services
  • Documentation Guidelines
  • Letter of Accommodations (LOA)

Feel free to contact the Office of Disability Services (ODS) Suite 219, Paul Robeson Campus Center (973) 353-5315

Religious Holiday Policy

Students are advised to provide timely notification to instructors about necessary absences for religious observances and are responsible for making up the work or exams according to an agreed-upon schedule.

Counseling Services

Counseling Center Room 101, Blumenthal Hall, (973) 353-5805 or http://counseling.newark.rutgers.edu/.

Students with Temporary Conditions/Injuries

Students experiencing a temporary condition or injury that is adversely affecting their ability to fully participate in their courses should submit a request for assistance at: https://temporaryconditions.rutgers.edu.

Students Who are Pregnant

The Office of Title IX and ADA Compliance is available to assist students with any concerns or potential accommodations related to pregnancy: (973) 353-1906 or TitleIX@newark.rutgers.edu.

Gender or Sex-Based Discrimination or Harassment

Students experiencing any form of gender or sex-based discrimination or harassment, including sexual assault, sexual harassment, relationship violence, or stalking, should know that help and support are available. To report an incident, contact the Office of Title IX and ADA Compliance:

  • (973) 353-1906 or TitleIX@newark.rutgers.edu.
  • To submit an incident report: http://tinyurl.com/RUNReportingForm.
  • To speak with a staff member who is confidential and does NOT have a reporting responsibility, contact the Office for Violence Prevention and Victim Assistance: (973) 353-1918 or run.vpva@rutgers.edu