Workshop on Computational Ab initio Quantum Thermodynamics (Nov. 28 - Dec. 1)

Columbia Global Center, Nairobi, and Technical University of Kenya

Organizers: Renata Wentzcovitch, George Amolo, Michael Atambo

Click to preview the [schedule in pdf]

Click to preview the [related resources]

Day 1 (Nov. 29)
Kenya Time Sessions
08:45 – 09:00 Welcome
09:00 – 10:00 Renata Wentzcovitch – Thermodynamics with QHA overview (slides)
10:00 – 11:00 John Perdew – DFT Introduction (video)
11:00 – 11:15 Coffee break
11:15 – 12:15 Pietro Delugas – Introduction to DFPT (video, slides)
12:15 – 13:30 Lunch
13:30 – 15:30 Pietro Delugas – Hands-on with QE SCF calculations
15:30 – 15:45 Coffee break
15:45 – 18:00 Qi Zhang – Hands-on with QE SCF calculations and EOS Express workflow (slides)
18:00 – 19:30 Dinner

Day 2 (Nov. 30)
Kenya Time Sessions
09:00 – 10:00 John Perdew – DFT State-of-the-art (video)
10:00 – 11:00 Pietro Delugas – DFPT and phonon calculations with the Quantum ESPRESSO
11:00 – 11:15 Coffee break
11:15 – 12:15 Qi Zhang – The qha Python package (slides)
12:15 – 13:30 Lunch
13:30 – 15:30 Pietro Delugas – Hands-on with QE and Phonon calculations
15:30 – 15:45 Coffee break
15:45 – 18:00 Chenxing Luo – The cij Python package (slides, video)
18:00 – 20:30 Reception at Columbia Global Center in Nairobi

Day 3 (Dec. 1)
Kenya Time Sessions
09:00 – 10:00 Zhen Zhang – Phonon Quasiparticle Calculations (slides)
10:00 – 11:00 Renata Wentzcovitch – Thermodynamics of and thermoelasticity of spin crossovers (slides, video)
11:00 – 11:15 Coffee break
11:15 – 12:15 Zhen Zhang – The phq package (resources)
12:15 – 13:30 Lunch
13:30 – 15:30 Chenxing Luo – Hands-on with QE and thermoelasticity calculations (resources, video)
15:30 – 15:45 Coffee break
15:45 – 18:00 Chenxing Luo – Hands-on with QE and thermoelasticity calculations
18:00 – 19:30 Dinner

Visit of Omololu Akin-Ojo: Bringing Research Excellence To Africa

Guest: Omololu Akin-Ojo (Visit Date: Nov. 12-19, 2022)

Director, ICTP East African Institute for Fundamental Research, University of Rwanda, Kigali Rwanda

Host: Renata Wentzcovitch

APAM and Earth/Environmental Sciences Departments, Columbia University

Materials Simulations in Earth and Planetary Sciences Seminar Series

This virtual seminar series consists of talks on current applications of Materials Simulations to Earth and Planetary Sciences. It meets on select Mondays at 3:00 PM ET.

Host: Renata Wentzcovitch, APAM and DEES, Columbia Engineering

Click to see the introduction. This area of research has expanded dramatically in recent years and has become an integral part of this research field. It is not an overstatement that the future of planetary sciences depends heavily on the ability to simulate processes taking place on planetary interiors, e.g., the unveiling of the internal structure of super-Earths. This seminar series aims to present state-of-the-art activities in this area not just by computational scientists but also by experimental scientists willing to motivate computational research in their respective areas of interest.
The attendance and speakers will be beyond Columbia University’s borders, and researchers from prominent centers will be invited to participate and/or give invited talks. Computational studies of planetary materials have focused to a great extent on very high pressures since this is the most challenging condition for experiments. We hope to bring to the forefront and motivate more research on lower pressures, e.g., < 10 GPa. This is a very challenging pressure range for materials simulations for multiple reasons, e.g., the approximations used in simulations are less accurate at low pressures, and the abundance of complex experimental information at these pressures forces simulations to deal with controversial data.

International Conference in Computational Physics (CCP'22)

Hosted by the University of Texas at Austin, August 1-4, 2022

Organized by Renata Wentzcovitch, James R. Chelikowsky, Ellen Zweibel, Feliciano, Giustino

Gordon Research Conference: Research at High Pressure 2022

Hosted at Holderness School, NH, July 17 - 22, 2022

Session “Earth: From Crust to Inner Core”, Discussion Leader: Renata Wentzcovitch

During the poster session

2022 US-Africa Initiative in Electronic Structure Workshop

Held online Wednesday-Friday, May 25 - 27, 2022, and hosted by Columbia University

Co-organizers: Renata Wentzcovitch, Richard Martin, Omololu Akin-Ojo, Sinead Griffin.

*Photo taken at ES22 (Jun-2-2022).

Mini Seminar by Catherine and Olugbenga, June 14, 2022, at Columbia University

Photo with Catherine, Olugbenga, and Urban’s Group


APS March Meeting 2021

March 15th - 19th, 2021 - Online

Abstracts presented by the Wentzcovitch Group:

  1. M19.00002 - Prediction of a temperature-induced phase transition in Mg2GeO4 by first principles
  2. M19.00004 - Prediction of crystal structures and motifs in the Fe-Mg-O system under Earth’s core pressures
  3. M19.00006 - Phase relations in iron monoxides from LDA + Usc calculations
  4. M19.00008 - Spin state and structural stability of ferropericlase up to 3 Mbar
  5. M19.00009 - Iron oxide motifs and structures from 0.1 to 3 TPa
  6. M19.00010 - Anharmonic thermodynamic properties of cubic CaSiO3 perovskite from phonon quasiparticles
  7. M19.00011 - Prediction of Fe-Mg and Fe-Mg-O compounds at exoplanetary interior pressures
  8. P19.00001 - Cij: A Python code for thermoelasticity
  9. P19.00003 - pgm: A Python package for free energy calculation
  10. P19.00008 - Express: nonstop calculations with Quantum ESPRESSO
  11. V20.00009 - Thermal Conductivity of CaSiO3 Perovskite at Lower Mantle Conditions (Invited)

Workshop for the US-Africa Initiative in Electronic Structure

A virtual mini-workshop at the 2021 APS March Meeting, Sunday March 14, 2021, 8am - 12pm Central Daylight Time.

USAfrI Speakers

  • Omololu Akin-Ojo, East African Institute for Fundamental Research
  • Sinead Griffin, Lawrence Berkeley National Laboratory
  • Richard Martin, University of Illinois and Stanford University
  • Renata Wentzcovitch, Columbia University

Posters presented by the Wentzcovitch Group:

  1. Research and APS March Meeting presentations − Wentzcovitch et al.
  2. cij: A Python code for quasiharmonic thermoelasticity
  3. pgm: A Python package for free energy calculation
  4. Software Advances for Mineral Physics Applications (SAMPA)


AGU Fall Meeting 2020

December 1th - 17th, 2020 -Online Everywhere

Abstracts presented by the Wentzcovitch Group:

  1. Phase relations in iron monoxides from LDA + Usc calculations
  2. pgm: A Python package for free energy calculation
  3. Cij: A Python package for quasiharmonic thermoelasticity
  4. Express: nonstop calculations with ab initio software
  5. Anharmonic thermodynamic properties of cubic CaSiO3 perovskite from phonon quasiparticles
  6. Spin State and Structural Stability of Ferropericlase up to 30 Mbar
  7. Ab initio prediction of a temperature-induced phase transition in Mg2GeO4
  8. Detection of the spin crossover in ferropericlase in the Earth’s lower mantle; an interdisciplinary approach. (Invited)

Sessions co-organized by Renata Wentzcovitch

MR016 - Mineral Physics: Connecting Mineral Properties to Planetary Models II Posters

Primary Convener

  • Elizabeth Colette Thompson, Sewanee: The University of the South


  • Sally June Tracy, Carnegie Institution for Science Washington
  • Han Hsu, NCU National Central University of Taiwan
  • Renata Wentzcovitch, Columbia University
MR027 - Mineral Physics: Connecting Mineral Properties to Planetary Models I

Primary Convener

  • Elizabeth Colette Thompson, Sewanee: The University of the South


  • Sally June Tracy, Carnegie Institution for Science Washington
  • Han Hsu, NCU National Central University of Taiwan
  • Renata Wentzcovitch, Columbia University


AGU Fall Meeting 2019

December 9th - 13th, 2019 - San Francisco, CA

Abstracts presented by the Wentzcovitch Group:

  1. Express: nonstop calculations with the Quantum ESPRESSO
  2. The post-perovskite transition in Fe- and Al-bearing bridgmanite: effects on seismic observables
  3. Thermal Conductivity of CaSiO3 Perovskite at Lower Mantle Conditions (Invited)
  4. Structures of high-pressure iron oxides from adaptive genetic algorithm
  5. Ab initio investigation of order-disorder transition in δ-AlOOH

Sessions co-organized by Renata Wentzcovitch

U42B - Emergent Views of the Earth’s Deep Interior

Primary Convener

  • Renata Wentzcovitch Columbia University


  • Jeroen Tromp, Princeton University
  • Kei Hirose, Tokyo Inst Tech
  • Paul Tackley, ETH Zurique
MR23A - Advances and Applications in Computational Mineral Physics and Geochemistry I

Primary Convener

  • Renata Wentzcovitch Columbia University


  • Bijaya B. Karki, Louisiana State University
  • Koichiro Umemoto, Tokyo Institute of Technoloty
  • Han Hsu, NCU National Central University of Taiwan

Materials Science and Engineering Colloquium: Gilbert 'Rip' Collins

Matter in extreme conditions

April 19, 2019

Speaker: Gilbert ‘Rip’ Collins

Dean’s Professor, Department of Mechanical Engineering, Dean’s Professor, Department of Physics and Astronomy, University of Rochester


Earth Science Colloquium: Kanani K. M. Lee

Facilitating oxidation of the atmosphere through mantle convection

November 30, 2018

Speaker: Kanani K. M. Lee

Associate Professor of Geology and Geophysics, Yale University

Here we show a redox-induced density contrast affects mantle convection and may potentially cause the oxidation of the upper mantle.

(View full abstract here)

Data Science Institute Colloquium: Dan Stanzione

Computing for the Endless Frontier

Tuesday, November 27, 2018 - 2:30pm to 4:00pm

Host: Prof. Renata Wentzcovitch

APAM and Earth/Environmental Sciences Departments

Speaker: Dan Stanzione

Executive Director, Texas Advanced Computing Center, Associate Vice President for Research, The University of Texas at Austin


Data Science Institute Colloquium: Dr. William T.C. Kramer

Blue Waters: A Super System for Highly Productive Frontier Science – Experiences and Lessons Learned

October 3, 2017 - 11:00 AM - 12:15 PM

Speaker: Dr. William T.C. Kramer

The Blue Waters system is the first general purpose, open science, sustained-petaflop supercomputer. It is a powerful resource for the nation’s open-science researchers.


Infrastructure For Computational Mineral Physics

A Community Consultation Workshop, August 29-31, 2010

University of Minnesota 3-111 Keller Hall, 200 Union Street SE Minneapolis, MN 55455-0170


  • Renata Wentzcovitch (UMN)

Steering Committee:

  • Renata Wentzcovitch (UMN)
  • Artem Oganov (Stony Brook)
7:20 am
8:00 am
Renata and Artem
8:10 am
COMPRES: Organization overview
Quentin Williams (UCSC)
part 1 part 2
8:25 am
COMPRES: planning for the next five years
Don Weidner
(Stony Brook)
part 1 part 2
8:40 am
First principles thermoelasticity of minerals
Renata Wentzcovitch (UMN)
part 1 part 2 part 3
9:10 am
Structure prediction: minerals, materials, and some new science ahead of us
Artem Oganov (Stony Brook)
part 1 part 2 part 3
9:40 am
10:00 am
An overview of the Minnesota Supercomputing Institute
Jorge Vinals (MSI)
10:30 am
Time dependent density functional theory in PARSEC and in the Quantum ESPRESSO
Yousef Saad (UMN)
part 1 part 2
10:55 am
CIG: Overview of goals, implementation, and evolution
Peter Van Keken (Ann Arbor)
part 1 part 2
11:20 am
Cluster, surface, and bulk calculations in geochemical applications: Challenges
in finding the right approach
Udo Becker (Ann Arbor)
part 1 part 2
11:45 am
1:00 pm
Density functional theory for mineral physics
Don Truhlar (UMN)
part 1 part 2 part 3
1:25 pm
Interface between experiments and computations
Kanani Lee (Yale)
part 1 part 2
1:45 pm
Insights into the nature of hydrous ringwoodite from experiment and theory
Wendy Panero (Ohio State)
part 1 part 2
2:05 pm
Isotope signatures of high pressure / high temperature processes
Edwin Schauble (UCLA)
part 1 part 2
2:25 pm
Phase transitions in ice: a multi-level challenge calculation
Koichiro Umemoto (UMN)
2:45 pm
Mineral properties at high pressure using ab
initio methods
Li Li (Stony Brook)
part 1 part 2
3:05 pm
3:30 pm
Computer simulation and visualization
studies of disordered and defective systems
Bijaya Karki (LSU)
part 1 part 2
3:55 pm
Alloy theory tools for mineral physics
Dane Morgan (UW)
part 1 part 2
4:20 pm
Long break for dinner
6:45 pm
Evening discussion

Sample Themes
  1. The dream: uninterrupted funding for code development/maintenance/support.
  2. The other dream: hardware for code development and interactivity jobs
  3. Technical personnel
  4. Database development
  5. Specialized toolkits
  6. Tutorials, interships, travel grants, and other outreach activities.
7:00 am
8:00 am
Transition metals in nature
Boris Kiefer
(U of NM)
part 1 part 2
8:25 am
DFT+U calculations in strongly correlated minerals
Matteo Cococcioni (UMN)
part 1 part 2 part 3
8:50 am
First-principles calculations of thermal conductivity of minerals
JJ Dong (Auburn U)
part 1 part 2 part 3
9:15 am
Computational Research: Reflections from PhD to Postdoc
Amy Bengtson (Ann Arbor)
9:30 am
Calculations of spin crossovers with DFT+U
Han Hsu (UMN)
9:45 am
USPEX - evolutionary crystal structure prediction
Andriy Lyakhov
(Stony Brook)
10:00 am
10:30 am
A cyberinfrastructure for first principles calculations and searchable databases.
Vlab (MSI)
part 1 part 2
10:50 am
Resources at the Minnesota Supercomputing Institute
Birali Runesha
(MSI) </a>
part 1 part 2
11:10 am
Discussion of wiki content
12:10 pm
1:00 pm
Discussion, meeting summary, report outline, etc.


Seminars Fall 2009


Quantum simulations of materials and nano-scale processes are a fundamental research approach that have infiltrated virtually all fields of chemical and materials sciences. This seminar series will give an overview of the state-of-the-art in materials and nano-particle simulations and quantum chemistry methods as well as their applications to materials and chemistry in a broad range of thermodynamic conditions. This series will introduce students to this fast evolving field of research. It will also cross fertilize theoretical and computational inter-departmental research on campus by bringing together the faculty involved in related research areas. If appropriate, experimentalists will be invited to present their work to stimulate computational research. The vast majority of seminar speakers are UMN based researchers. It consists of one hour seminars once a week.

List of Talks of Seminars Fall 2009

Date Location Speaker Title
9/11/2009 Walter Library 402 Don Truhlar
University of Minnesota, Chesmistry
Density functional theory: New developments
9/18/2009 Walter Library 402 Renata Wentzcovitch
University of Minnesota, Chemical Engineering and Materials Science
Applications of density functional theory I: thermodynamic phase boundaries of silicate minerals
9/25/2009 Walter Library 404 Traian Dumitrica
University of Minnesota, Mechanical Engineering
Understanding Nano-mechanical Response via Modeling and Simulations
10/02/2009 Walter Library 404 Ilja Siepmann
University of Minnesota, Chemistry
Structure, Solvation, and Phase Equilibria in Hydrogen-bonding Systems
10/09/2009 Walter Library 402 Jiali Gao
University of Minnesota, Chemistry
Quantum mechanical simulations of biological systems: From one electron to tens of thousands of atoms
10/16/2009 Walter Library 402 Matteo Cococcioni
University of Minnesota, Chemical Engineering and Materials Science
Extended LDA+U functional for covalent systems
10/23/2009 Walter Library 402 Chris Cramer
University of Minnesota, Chemistry
Activation of O2 and N2O by Mono- and Polynuclear Supported Metal Complexes
10/30/2009 Walter Library 402 Ellad Tadmor
University of Minnesota, Aerospace Engineering and Mechanics
A unified interpretation of stress in molecular systems
11/06/2009 Walter Library 405 Richard James
University of Minnesota, Aerospace Engineering and Mechanics
Objective molecular dynamics
11/13/2009 Walter Library 402 Ryan Elliott
University of Minnesota, Aerospace Engineering and Mechanics
A Quasicontinuum for Multilattice Crystals Exhibiting Martensitic Phase Transformations: Cascading Cauchy-Born Kinematics
11/20/2009 Walter Library 402 Koichiro Umemoto
University of Minnesota, Geophysics
Applications of density functional theory II: H2O-ice
12/04/2009 Walter Library 402 Darrin York
University of Minnesota, Chemistry
Multiscale simulations of chemical catalysis in strained electrostatic environments of RNA molecules
12/11/2009 Walter Library 402 TBA


Second Vlab Tutorial

2nd Vlab Tutorial on Computational Mineral Physics

Jointly with CIDER and the DEMOCRITOS Simulation Center of Italy

Kavli Institute, UC-Santa Barbara, 07/28 to 08/01, 2008

Organizers: Renata M. Wentzcovitch and Stefano de Gironcoli

The Virtual Laboratory for Earth and Planetary Materials, VLab, the Minnesota Supercomputing Institute for Digital Technology and Advanced Computation (MSI), and the Italian National Simulation Center DEMOCRITOS announce a 1-week tutorial on first principles calculations. The tutorial will take place between July28 and August 01, 2008, at the Kavli Institute for Theoretical Physics, UC-Santa Barbara as part of the Cooperative Institute for Deep Earth Research, CIDER, 2008 program

The tutorial will consist of lectures on the theoretical foundations of first principles calculations of structural, elastic, and thermodynamics properties of minerals at extreme conditions of pressures and temperatures, and hands-on experience using the VLab cyberinfrastructure. The latter uses the Quantum ESPRESSO as back-end computational package and has been developed to enable distributed and automatic execution of the extensive workflows spanned by realistic and demanding computations of minerals’ properties through a consolidated user-friendly interface. Participants will need to bring their own laptop computers with an installed web browser (Firefox is strongly recommended).

Confirmed instructors are:

  • Matteo Cococcioni (University of Minnesota),
  • Cesar da Silva (University of Minnesota),
  • Stefano de Gironcoli (DEMOCRITOS/SISSA),
  • Bijaya Karki (LSU),
  • Boris Kiefer (University of New Mexico),
  • Lars Stixrude (UCL/CIDER),
  • Koichiro Umemoto (University of Minnesota),
  • Renata Wentzcovitch (University of Minnesota).
Click here to preview the registration details.

The VLab will cover lodging and meal costs for all participants. The number of participants will be limited and the selection is on a first-come first-served basis. Please write asap to Debbie Schutta ( to request a place.


Click here to preview the program details.


Second VLab Workshop

2nd VLab Workshop and Meeting of the Elasticity Grand Challenge of the COMPRES Initiative


The second VLab workshop will take place at the University of Minnesota Walter Library Room 402, August 5-10, 2007. It will offer an opportunity for researchers interested in planetary materials and/or planetary processes to exchange information and ideas. This will be a joint meeting of the VLab and of the Elasticity Grand Challenge (EGC) of the COMPRES initiative. The themes to be addressed and confirmed speakers are:

  • D’’ layer Don Helmberger, Thorn Lay, Maarten de Hoop, Ed Garnero, John Hernlund, Xiaodong Song, Wendy Mao, Shige Maruyam,Richard Peltier, Paul Tackley, Taras Gerya, Artem Oganov, Marc Monnereau, Arie Van de Berg, Bruce Buffett, Ulli Hansen

  • Spin transition in iron in the lower mantle Jennifer Jackson, Wolfgang Sturham, Afu Lin, Michael Brown, Renata M Wentzcovitch, Koichiro Umemoto, Catherine McCammon, Dane Morgan, Dipta Bhany Ghosh

  • Transport properties of mantle minerals Anne Hoffmeister, Alex Goncharov, Victor Struzhkin, Philip B. Allen, Tao Sun, Frank Spera

  • Water in the mantle Shun-ichiro Karato, Marc Hirschmann, David Kohlstedt, Suzan Van der Lee, Michael Wysession, Bjorn Winkler, Tom Duffy, Ilja Siepmann

  • Transition zone Lars Stixrude, Don Weidner, Baosheng Li, Yang Shen, Justin Ravenaugh, Jay Bass, Gabriel Gwanmesia, Adam Dziewonski

There will be a session on information technology and demonstration of software for materials computations at some point during the meeting.

  • IT Tone Kokalje, Gordon Erlebacher, Bijaya B. Karki, Marlon Pierce, Cesar da Silva, Dave Yuen, Pedro da Silveira, Jamie Rintelman

View Abstracts


First Vlab Tutorial

VLab tutorial on computational materials / mineral physics

The Virtual Laboratory for Earth and Planetary Materials, VLab, the Minnesota Supercomputing Institute for Digital Technology and Advanced Computation (MSI), and the Italian National Simulation Center DEMOCRITOS announce a 2-week tutorial on first principles calculations. The tutorial will take place between May 21 and June 03, 2006, at MSI, University Of Minnesota, Minneapolis.

The first week will consist of presentations on theoretical foundations. Whole-day lectures will be intercalated by recitations. The second week will consist of hands-on experience with the open source (and free!!) package Quantum ESPRESSO and will invlove whole- day instruction with exercises on predetermined problems.

The syllabus will include some of these topics: 1st-2nd weeks: electron gas, Bloch functions and band structure, phonons, Hartree-Fock method, Density Functional Theory, exchange correlation functionals, pseudopotentials, density functional perturbation theory, molecular dynamics. 2nd week: Quantum ESPRESSO package, i.e., PWSCF, PHONON, CPWe, plus auxiliary programs.

Confirmed instructors at present: Dario Alfe’ (UCL), Philip B. Allen (Stony Brook), Stefano Baroni (DEMOCRITOS & SISSA), Matteo Cococcioni (MIT/U of Minnesota), Stefano de Gironcoli (DEMOCRITOS & SISSA), Nicola Marzari (MIT), Ilja Siepmann (U of Minnesota), Don Truhlar (U of Minnesota), Renata Wentzcovitch (U of Minnesota).

Click here to preview the registration details.

The VLab, with the aid of MSI, will cover registration fees and will try to cover 100% of lodging and meals for all participants. The final level of financial support will be established after the pre-registration deadline. Please write asap to Debbie Schutta ( to pre-register and guarantee a spot. The number of participants will be limited. The pre-registration deadline is January 15, 2006.


Lectures in the first week are in Walter 402, except 5/22. Lectures on 5/22 and 5/26 afternoons, and in the second week are in Lind 24.

Lectures are from 9-noon and 2-5 pm everyday. There will be 15 minute breaks in the morning and afternoon.

Click here to preview the program details.

1st week

(5/21) Sunday

  • Arrival and reception at the Walter Library Bldg. room 401 at 6 pm.

(5/22) Monday (Siepmann, Wentzcovitch, and Kiefer)

  • MD (various ensembles) + VCSMD (Walter 402)
  • Practice with VCSMD code (Lind 24) (5/23) Tuesday (Allen, Wentzcovitch, Kiefer) (Walter 402)
  • Phonons
  • Bloch's theorem
  • k-space
  • QHA (Lind 24)

(5/24) Wednesday (Allen, Wentzcovitch, Kiefer) (Walter 402 all day) (Lind 24 available after hours also)

  • Tight binding
  • Band structures
  • Introduction to plane wave calculations (including forces and stresses)

(5/25) Thursday (Dahlke, Zhou, Wentzcovitch, Kiefer) (Walter 402 all day) (Lind 24 available after hours also)

  • DFT (Kohn-Sham + Mermin) functionals
  • Self-consistency cycle
  • Hartree-Foch
  • Exchage/correlation functionals

(5/26) Friday (Baroni, Kohlmeyer, Kokalj) (Walter 402 in the morning) (Lind 24 in the afternoon)

  • Plane-wave pseudopotential calculations (SB)
  • DFPT (SB)
  • Introduction to the package (SB)
  • Code installation (Kohlmeyer)
  • GUI + XCRYSDEN (Kokalj)

(5/27) Saturday (de Gironcoli, A. Kokalj, da Silva ) (Lind 24 all day)

  • Input build up (SdG)
  • How to translate Wyckoff Xtal structures into QE inputs (SdG)
  • Simple examples of band-structure calculations + simple cell optimization
  • How to submit jobs
  • Introduction to auxiliary programs ((p)DOS, charge density, Xtal structure drawing) (AK)

(5/28) Sunday (no instructors assigned) (Lind 24 all day)

  • Computer Lab available for use 2nd week (5/29) Monday (Sbraccia, Kokalj, da Silva, Wentzcovitch) (Lind 24 all day)
  • Spin polarized super-cell calculations w/ constrained occupation combined with cell optimization
  • Draw outputs from calculation

(5/30) Tuesday (Sbraccia, Cococcioni) (Lind 24 all day)

  • Morning: exploring the energy landscape - NEB, metadynamics and the like (CB)
  • Afternoon: Computer lab (a detailed worked out example + discussion with the instructors)

(5/31) Wednesday (de Gironcoli, Bonini, da Silva, Umemoto ) (Lind 24 all day)

  • Phonons
  • Draw phonon dispersions
  • Prepare input for thermodynamics program
  • Calculation of thermodynamic properties

(6/1) Thursday (Cococcioni, da Silva, Umemoto) (Lind 24 all day)

  • LDA+U
  • Repeat calculations in Mg3Fe1Si4O12 using now LDA+U

(6/2) Friday (Marzari, Bonini) (Lind 24 all day)

  • Car-Parrinello MD
  • Car Parrinello code + hands-on experience

(6/3) Saturday (da Silva, Umemoto) (Lind 24)

  • Work in the lab
  • Departure after lunch

Seminars Spring 2006

List of Talks of Seminars Spring 2006

Date Speaker Title
Jan. 27 Dr. Bruce Buffett
University of Chicago, Department of Geophysical Sciences
Sediments at the Top of Earth's Core
Feb 1
Dr. Koichiro Umemoto
Chemical Engineering and Materials Science, University of Minnesota
Structural Transformations and Structural Anomalies in H2O-ice Under Pressure
Feb. 10 Dr. Wolfgang Bach
Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry Division
Seafloor Serpentinization - where, how and why care?
Feb. 21 Dr. David J. Stevenson
California Institute of Technology, Division of Geological Sciences
What's Going on at the Core-Mantle Boundary?
May 5 Dr. Raymond Jeanloz
University of California-Berkeley, Department of Earth and Planetary Science
Effects of Pressure on Chemical Bonding and Mineralogy Inside the Earth
Feb. 21, 2006 Dr. Joshua Feinberg
University of Cambridge, UK, Department of Earth Sciences
Single Crystal Paleomagnetism: A New Approach to Measuring the Ancient Magnetic Field of the Earth and Solar System
Mar. 2, 2006 Dr. Steven Jacobsen, Carnegie Institute of Washington, Geophysical Laboratory Seismic Structure of a Hydrous Transition Zone: the Emerging Picture from Mineral Physics
Mar. 9, 2006 Dr. Wendy Li-Wen Mao, Los Alamos National Laboratory Mineral Physics through a Diamond Window


First VLab Workshop

First VLab Workshop


The first VLab workshop took place at the Minnesota Supercomputing Institute, July 20-23, 2005. It offered an opportunity for scientists involved in research related to planetary materials and/or planetary processes to exchange information and ideas. The main underlying themes were:

  1. planetary science grand challenges (thermochemical state of the lower mantle, water in the deep mantle)
  2. materials science grand challenges (strongly correlated systems, solid solutions and phase equilibrium, electronic correlation and quantum dynamics in ices)
  3. advances in first principles methodologies (methods, approximations, codes)
  4. Information technology applicable to materials computations


The workshop was primarily a meeting of the VLab group and the community of scientists with overlapping interests. Despite the targeted nature of the science, the spectrum of areas of expertise covered was very broad. Theoretical chemists and materials physicists, along with information technology scientists, came together with Earth and planetary scientists to define novel key problems, identify technologies, and outline strategies to advance planetary materials science.

Program & Talks

CINECA 2005 Meeting

CINECA 2005 Minutes

  1. Presentation from the ESPRESSO development team.

    • History
    • Current state of development and main issues
    • Future plans
  2. An overall discussion that focused mostly on questions about ESPRESSO and how information technology (IT) can improve it.

  3. VLab available to a wider audience brings a problem:

    • Crude-to-wrong calculations made by people without good background on quantum physics and electronic structure. Most are related to choice of pseudo-potentials (PPs) and associated energy cut-off.
    • Solution proposed: A database of good pseudo-potentials and means to upload PPs for a given project. No availability of online tools for PPs generation.
  4. Discussion on the distributed computing problem. Typical problem is to run parameter space studies. Each point in the parameter space is decoupled of each other –> Parallel workflow suitable for implementing in distributed systems. VLab must have means to monitor and steer the execution of a workflow.

  5. We agree that four Web services are very basic to get the VLab up:

    • Build the PWSCF environment (create directories, install input in the compute nodes) and run PWSCF
    • PseudoPotentials data base access
    • Build the PHONON environment
    • Workflow management

Day 1

Click here to see Notes from the ESPRESSO group presentation
  • CINECA ("Chinaca"): consortium of universities. High performance computing research and development. Developing Web applications, portals, common file systems, etc. Portal development is high on the list of their projects. Common schedular.

Currently: all codes have same input structure, output structure is not quite consistent among each other. (for human readable output). Working on common file structure to store huge datasets.

Ideally, should try to merge the internal datastructure (probably to reduce human development costs). Lower priority work.

Main objective: independent codes that can communicate easily one with another.

CP (Lausanne, Princeton) and FPMD (Bologna, Trieste) will be merged into a unique code.

PWscf will remain a separate code

PHONON will remain a separate code

Also there is a number of post processing applications

  • Heavily based on 3d FFT and level 3 linear algebra. BLAS packages and other common routines.

    Plans to integrate other codes that do completely different things (e.g. electronic codes, devel. in Trieste by Ralph) and time-dependent responses developed by Ralph and Baroni. Will become available in the Espresso package.

    Most groups have chosen to implement one application with many functionalities. It is not necessarily the best idea. Problem: must be maintained by the upgrades.

  • Current attempts are to merge the splinter applications: make them interoperable rather than one giant application. First step is to unify the exterior shell of the codes (the user interaction step). To also make the codes use a unified input structure. Currently the output structure is not the same. Also working on a common file structure to store huge data sets produced by the code.

  • Main target is to have independent codes that can communicate with one another easily. All use common data sets, common file formats, interoperable data. Important to maintain as much flexibility as you can in terms of adding functionalities. Must agree on the smallest number possible of rules, to allow interoperability. Should allow a contributor, shoudl be possible to write the application, interfacing to other codes, but should be free not to follow the future upgrades, etc. In the same distribution, could have redundancy: same codes might do the same thing.

At the highest level, one communicates through files.

Common data structures are useful for faster updates. e.g., choice of smaller


protocols: XML-like structures.

Four main codes (in ESPRESSO): PWSCF, CP, FPMD, PHONON:

I/O and data files only refer to these three codes.

PHONON code: uses a perturbation method code that requires some sort of base state.

Currently: inputs identical. Variables are a superset of variables used in each.

Output: initial idea: library of I/O blocks to be called in a pre-defined sequence (to write restart file, etc.)

However: not as flexible as desired.

Switched to XML-like structure for output.

Want the freedom to add information without worrying about order.

Idea: HDF5: not sufficiently flexible. Therefore, used XML approach.

Notes from the overall discussion

Some files can be Gbytes in size. For main usage, single matrices remain binary file.

GE: issues of Fortran Unformatted format

Other issue: input file: is XML required, because namelists not standardized.

Graphical user interface: heavily based on namelist structure. Should perhaps be low priority if not proven to necessary.

  • XML interfaces: first priority is that all the codes should share the same input format. Can restart code with its own output in most cases, and there is some limited ability to make the codes share i/o as files.

  • Gordon: is there a library of i/o classes for handling the files? No, it is a mess.

  • Codes are Fortran. Fortran binary can be incompatible between different versions of Fortran. Gordon suggests writing simple C/C++ libraries to make this more portable.

Pseudopotential files:

  • 1 file per element Input files: described by 6-7 namelists

Discussion on PPs (not very interesting -- jump to basic conclusion)

For each atomic species: name of element + name of pseudo-potential files.

200k per file, 1000 files.

Should not expect the users to understand reliability and accuracy of pseudopotential (PP). Must include description of suggested planewaves, etc.

Should introduce some kind of accuracy indicator (Baroni):

1 PP per element is necessary for a PWSCF run, 10 elements, and 10 different PP based on various code/method/approximations.

  • Why is it hard to make the pseudo potential files available from a database or a few databases? These don't have to be local. Also, how often do these pseudopotential files change?

  • Sounds like it pseudo potential sharing is an important community/gridproblem.

  • Must be able to guarantee different versions of the pseudo potential for backward compatibility. It is a problem of backward compatibility.

  • I would say that the managment of PsP is important, should be separated from code distribution, should be searchable online. I will use PsP for PseudoPotential.

  • Problems with PsP is that non-specialists can't judge the quality of a pseudo potential. It should be a) blessed by particular groups, and b) it should describe how and which problems it should be used for, and c) the accuracy. This should be automated. But is this a Vlab problem?

  • Cesar: only a small subset of elements really interesting in geophysics. So PsP management is not really a huge problem. O, Si, Mg, Ca, maybe C.

Basic conclusion (from the discussion on pseudo-potentials)

  • A databased wrapped service for online PseudoPotential files interesting to Vlab problems, curated and described by various criteria. Must determine the criteria for the entries. Can use this eventually to build an expert system.

Back to overall Discussion

What is the purpose of VLab? What do we want to use all of this grid stuff for?

What is the distributed computing problem? Too much discussion on user interface issues and job management. Typical problem is to run parameter space studies. Very decoupled. (The boldface is my idea)

They (espresso group) plan to use common file system and common schedular for all collaborators in Europe. File system: SFS (an nfs variant from IBM). The schedular they will use is LSF. Currently using many different schedulars (LSF, LoadLeveler, PBS, etc). They are building a portal interface to LSF. They use Unicore for workflow/job managemnet. You can specify dependecies, graphs of jobs, etc.

Gordon: Purpose of VLab is this. Renata needs to run a series of codes. Must run many many many of these since she wants to calculate the free energy and its derivatives. Must minimize the management of these complicated goals and maximize the number of collaborators.

How do novice users determine if their results are acceptable? How to you prevent code from being misused?

Back from lunch.

Recap, what do we want? System that will connect Espresso codes with clients, doing so using a inherently collaborative framework.

Basic portal: upload input (prepare input, instead), run, and get output. The GUI is used separately to generate an input file on the user's desktop (I disagree with this part).

Basic problem: provide a Web service for the solver. Some discussion on using Unicore.

Their portal approach is based on product of company called Nice, "EnginFrame". They say that it should be compatible with portlets ( They are tightly coupled with Platform Computing.

Web services:

  • run PwSCF
  • access PseudoPotentials
  • workflow
  • We want to better understand the workflow specific to this application.

One issue is that "convergence" is tricky. The user must provide the guidance on how long to run, when convergence is obtained.

Some discussion of collaborative, vendor independent visualization over NB.

Back to workflow. Cesar will answer all questions.

  • First, create input file
  • Run PwSCF
  • Get two files: standard output and very big data file
  • For 10 atoms of MgSiO3 (small) takes about 2 hours
  • Need to do individual calculations at many different
  • parameter points. Convergence at different points can
  • vary widely
  • How do you know when a code has converged?
  • When structure has converged, run phonon
  • wave form files can be very large (GB's or larger)
  • 34 MB is typical output file size according to Cesar
  • 100 atoms is 1-2 GB output file for each parameter point
  • At a minimum, you can store charge density file and throw away the wave functions that you calculate The wF can be regenerated from the charge density. This regeneration time is not trivial but an order of magnitude less (or less) than the original full calculations.
  • Typically 12 deformations and 15 pressures define your phase space.
  • Some discussion on how to do steering to avoid restart.

Day 2

  • Installing ESPRESSO. Have to download a fortran compiler.

  • Marlon will build web services for running the codes, uploading and downloading the files.

  • Baroni: PHONON code that we depend upon is probably the least well maintained.

Things to do:

  • Install software (Espresso)
  • Web-service for input files (Italians)
  • Web service to run code on at 2 machines
  • Web service to access pseudopotential database
  • Create a simple workflow: run PWSCF followed by PHONON without any output checking
  • investigate use of binary file on multiple computers. Try to find C library
  • interface to Fortran I/O