|Posted on April 24, 2014 at 8:10 AM|
On March we meet with the working team for a group photo. The group is slowly growing and now it includes one PhD student, one full-time postdoctoral fellow and partial-time one as well as three undergraduate students. They have all been employed by the Europa Excelencia project from MINECO.
From left to right: Mr. Mauricio Rodríguez, Ms. Natàlia Abulí, Ms. Irene Casademont, Dr. Eloy Ramos-Córdoba, Mr. Jesus Antonio Luque, Dr. Eduard Matito and Dr. Ferran Feixas.
Mauricio is currently on the second year of his PhD thesis and works on the development of DFT functionals with the use of model systems. Natàlia is a last-year undergradute student working in the development of DFT functionals for the calculation of non-linear optical properties. Irene is a third-year undergraduate student working on Dye Sensitized Solar Cells using time-dependent DFT and several tools developed in the group to study the charge-transfer process. Eloy is a postdoctoral fellow working on method development, including DFT, DMFT, electron-correlation measures and local spin analysis. Jesus A. is a third-year undergraduate working on chemical bonding analysis with focus on multicenter interactions. Ferran is a postdoctoral fellow focused on protein dynamics (his own research line) and working with us on the construction of approximate high-order density matrices and chemical bonding analysis.
|Posted on February 3, 2014 at 9:40 AM|
2013 has been a great year. I started the year knowing that my project DFTCorr was selected for the final stage of the Starting Grant (StG). I had the interview in Brussels on April. Unfortunately, it did not went as good as I would like to; one of the members of the committee was clearly against my proposal. On June I got the outcome. It was very good (A) but it was not enough to be granted the StG. I was on the 53%-55% ranking range (the 1-50% range was awarded). Since then, I started working on the Consolidator Grant 2014 proposal, which I will submit at the end of May 2014.
On May 2013, I got the outcome of the Ramon y Cajal grant (Spanish five-year tenure track). It did not matter that I have passed to the final stage of the StG... this time they did not even rank me among the first fifty. I gave up on this proposal, is too much biased towards high-IF research. My research does not get published in JACS or Angewandte. In my humble opinion it is completely unfair to those of us who work on more theoretically-oriented research, but I cannot help it. I better focus on non-Spanish calls, which are less driven by this IF craziness.
At the end of the year I got two good news. On one side, I was one of the eight researchers awarded a Europa Excelencia project (€75,000). Only those researchers that submitted a StG in the last call (2013), passed to the last stage in Brussels and get the maximum score (A), could apply. IMHO it is a bit unfair that other researchers who also made it to the final stage in Brussels but got a B could not apply for these projects. I'm using this money to purchase a small workstation and hire several people to work on the DFTCorr project.
On December I learnt I was awarded a five-year position at the Basque Country with possibility of permanent position after evaluation on the fourth year. The position comes also with some startup money and a travel allowance from the Ikerbasque foundation [total funding: €215,408].
Research-wise it was also a very good year. Several important results have been obtained, including a very precise approximation for the third-order reduced density matrix (3-RDM) [work submitted], a new stringent condition for the density matrix functional theory (DMFT) [work to be submitted soon] -that in principle can be extended to DFT- and several partial results on the DFT project that can be used to reinforce the CoG application of 2014. I just need the time to write down all this stuff... :-) Hopefully I can start before the end of May!
Addendum 1 (March 2014): Several newspapers and websites published the news about the Europa Excelencia and the Ikerbasque position. Local News: UdG, Science & Technology Park. Catalan Newspapers: Punt Avui, Diari de Girona and La Vanguardia. Spanish Newspaper: ABC.
Addendum 2 (April 2014): My PhD student, Mauricio Rodriguez, who is working on the DFTcorr project, was awarded the Master Thesis award and obtained a national PhD grant. On the other hand, Eloy Ramos obtained his PhD diploma, and he will be soon hired as postdoc to continue his work on DFTcorr.
Addendum 3 (May 2014): Verònica Postils was awarded the Sant Jordi award for his work 'Electrides. Tomorrow's compounds', based on her Master Thesis (September 2013) that I co-supervised.
|Posted on January 4, 2014 at 6:40 PM|
Anyone working on research knows that very seldom one has the chance to start and finish a paper within a short period of time. Usually a research project extends over a long period, with some lapses of time when the project gets stuck or halt for this or that reason. Namely, projects in collaboration with people from different institutions tend to be slow running projects. The story I explain in this post completely feels in this category. The research started on November 2004 and it got published on September 2013.
It all started back in 2004, when I was a PhD student visiting for the first time the University of Szczecin (Poland). I went to Szczecin to work with Jerzy Cioslowski, who agreed on hosting me for three months. I had read some paper of Jerzy and I was enthusiastic to have the chance to work with him. So, I got quite disappointed when I realized that he would be on a short stay in Dresden for most of my time in Szczecin. At least, he arranged someone to look after me. He was Jacek Styszynski, a physicist working on relativistic effects on molecules. Jacek took good care of me and had the patience to teach me about (relativistic) four-components calculations. Under his guidance in no more than three months we completed a research project that we published in Chemical Physics. This is the counterexample of how much time a collaborative project takes. Afterwards, Jacek suggested to work on a more ambitious project, which pretended to produce benchmark results for several carbonyl complexes and explain some controversial results obtained in the literature. The work was very appealing from both the chemical and the computational viewpoints. By then, there were very few relativistic codes and none of them could perform geometry optimization. So we would have to implement the optimization and the frequency calculations of these species. In 2004 I started working on this project for a few weeks before Jerzy came back. Then, I switched to some research project about the homogeneous electron gas. Short after Jerzy returned I went back to Girona and basically left Jacek's work aside for a while.
In 2005 I visited again Szczecin. This time I worked on both projects full time, and we got some results on the project with Jacek. However, at the end of my stay, after careful check of our results we noticed a large deviation of some vibrational frequencies as compared to the experimental ones. This result made no sense and it was Jerzy who noticed that our scheme to calculate vibrational frequencies (taken from an old German manuscript) missed some important coupling effects. On Christmas 2005 I left Szczecin with the feeling we still had plenty of work to do.
On July 2006 I defended my thesis, and right after that I went to Szczecin for another four-month stay. This time the focus of my stay in Szczecin was completing with Jerzy some paper on aromaticity and preparing the postdoc project I would carry out in Szczecin. I also spent quite some time working on Jacek's project but I left Szczecin with the feeling that the metal carbonyl project needed some re-thinking and we were far from the end...
On 2006 I was not awarded two (Spanish and Catalan) postdoctorals to go to Szczecin, so I look for another postdoc possibility. That is how I ended up in Aarhus, working with Ove Christiansen. I had a great time in Denmark and learnt a lot about vibrational calculations, potential energy surfaces, coupled-cluster methods and even some QM/MM theory. If you want to learn these techniques, visiting Aarhus (and Ove) is a must. At the beginning of 2007 I was awarded the Marie Curie fellowship to work in Szczecin but I enjoyed so much my time in Aarhus that I postponed my start in Szczecin more than one year. (I wish it could have been more!) Nonetheless, I started in Szczecin full of enthusiasm, because I was giving the chance to start doing some research on model systems, and I needed this background to later work on theory development as I really wanted to do.
Altogether, I had abandoned my project with Jacek two years and I took it back ion Spring 2009. After my experience in Aarhus I knew how to deal with the vibrational problem of metal carbonyls. Since I was mostly focused on the research about harmonium it took one year to obtain the first optimization results from Dirac (which was now capable of geometry optimization) and realize that the optimizations were neither efficient nor reliable. This finding coincided with Pedro Salvador visit to Szczecin, and he got enrolled in the project. Using a modified code of his, we interfaced a modified version of Dirac to obtain more reliable geometry optimizations and harmonic frequencies. Some months later we obtained our first final results. So, at the end of my postdoctoral stay in Szczecin we had most of our geometries and frequencies for the lightest transition metals.
On 2011 I moved to the Basque Country, where I had basically no time to work on Jacek's project. On 2012 I moved back to Girona but, once again, it took me a few months to find the time to work on the metal carbonyl work. By then, Jacek had completed most calculations. I started writing the manuscript at the beginning of 2013 and generated the chemical bonding analysis of these complexes. On Spring we submitted our manuscript, which got finally accepted on Autumn. It got published before the end of 2013.
This project took longer than expected because it was never part of my main research subject but also because of the research itself. If you are familiar with computational chemistry you may wonder how a project of three-atom molecules can take so long. The reason is four-component calculations. Unlike (regular) two-component methods, there are very few basis sets (sometime none!) available for these complexes. We had to change the basis sets when better ones were available (Prof. Dyall kindly sent us these basis set in advance). On top of this, one should take into account that there was no gradients available in Dirac for four-components CCSD(T) and, therefore, the optimization and frequency calculations are done numerically with the aid of an external software. The nature of the potential energy surface of MCO molecules also complicated both the geometry optimization and the frequency calculations. Our results included forth-row transition metals without the use of pseupotentials (they are not available); these were by far the most expensive calculations. Hopefully, we proved that Sadley's X2C methods, which are much more less demanding than pure four-component methods, give good results for geometries, dissociation energies and CO stretching frequencies (although a few bending frequencies are wrongly estimated with this method).
I am happy that despite the difficulties we could complete the paper with Jacek and Pedro. The metal carbonyl project was a good excuse to keep in touch with Jacek, who was my neighbor in Szczecin for two years and he is now also a very good friend. Jadwiga and him made my time in Szczecin a great and fruitful experience. If we ever get enrolled in a research project together with him let us hope it will take far less time. My feeling is that I will have the opportunity to see it by myself :-)
|Posted on October 28, 2013 at 10:20 PM|
This year I have attended four different conferences and I have presented a few works, including some results for aromaticity, multicenter indices, third-order densities, electrides and DFT development.
On June I participated in the NCI Workshop Topological Approaches to Intermolecular Interactions organized, among others, by Julia Contreras from the CNRS in Paris. The conference included a training session, in which the authors and developers of NCI software gave us a good introduction to the theory and the software. It was a very well organized conference which included four talks from people from the IQCC (Verònica Postils, Marc Garcia-Borràs, Sílvia Simon and myself) and one excellent presentation by Ferran Feixas, a former IQCC member. I presented a summary of the results we have obtained in the past years using the multicenter indices. In addition, I got the chance to perform as a session chairman.
On July I was invited to give the course Molecular vibrations: From Vibrational Wavefunctions to Potential Energy Surfaces in the 9th SEADIM Intensive Course organized in Havana (Cuba). As a curiosity I got a fever the day of the lecture and I did my best to give a good talk... but I can only certainly say that this is the lecture in which I have sweated the most :-) A few days later I took part in the 9th Seminars of Advanced Studies on Molecular Design and Bioinformatics: Energy (SEADIM) organized in Varadero, giving a talk entitled A New Means to Characterize and Identify of Electrides.
On September I attended the 15th DFT conference held in Durham (UK) which, so far, has been the most fruitful conference of the year. I brought a poster presenting new hybrids functionals for two and three-electron harmonium. In Durham I enjoyed very good lectures, including those of Axel Becke, Erin Johnson and Marcel Swart. The last one was particularly enlightening and, IMHO, the best conference of Marcel I have attended (Marcel is also part of the IQCC).
Finally, on October I was invited to give a lecture in Advances in Quantum Chemical Topology, a very well-organized symposium that took place in Mexico City. My talk summarized the last results obtained with multicenter indices but with particular focus on the new approximation for the third-order density we have designed (work to be submitted soon).
And basically that's it for 2013. In a forthcoming post I shall give more details of my stay in Mexico.
|Posted on March 28, 2013 at 11:40 AM|
The call for the Marie Curie Actions (MCA) for postdoctoral grants opened recently. There are two postdoctoral fellows that we can host in our group:
- European candidates: International European Fellowship (IEF).
- Non-European candidates: International Incoming Fellowship (IIF).
The candidates should have an excellent CV (these grants are very competitive) and they should write a 25-page project proposal. Despite we are looking for candidates to work on a DFT/DMFT development project we are also interested on candidates with his own idea for a research project. We would provide guidance to write the application (the group is experienced on writing MCA proposals) and the group would host the fellow and provide him with all the resources needed to carry out the research project.
Interested candidates: please contact ematito(at)gmail.com before 30th of June
|Posted on February 9, 2013 at 6:35 PM|
Last October I submmitted the project DFTCorr, A New Strategy in DFT: Density Functionals Adapted to Electron Correlation, to the Starting Grant (StG) program from the European Research Council (ERC). I just learnt that my proposal made it to the second stage and, therefore, I will be interviewed in Brussels by the ERC. About 50% of the candidates interviewed are granted. I am glad I could get this far and I will try my best in Brussels.
|Posted on January 30, 2013 at 6:30 PM|
The Carolina Foundation (link and call in Spanish) has opened calls for PhD grants and short postdoc stays (up to three months) for Latinamerican people willing to visit Spain. The University of Girona is among the host institutions and it helps cofinancing the doctorate studies.
Candidates interested on working with me (see a possible topic) at the Institute of Computational Chemistry and Catalysis in the University of Girona should contact me (please include a CV) at least three weeks before the deadline (19th of April 2013).
|Posted on January 21, 2013 at 7:00 PM|
Update: You can download the talks from this link.
In 2011 I did my third postdoc stay in Prof. Ugalde's group at the Euskal Herriko Unibertsitatea (EHU). Last week three researchers from this group visited our institute. Prof. Mario Piris, Dr. Jon M. Matxain and Dr. Fernando Ruipérez spent the whole week in Girona working with Dr. Pedro Salvador, Eloy Ramos and myself.
Since I left Donosti I pay a visit to the group once in a while (I visited the group on Spring and Autumn 2012), so now I was happy to host some basque visitors in Girona. The topic of the Career Integration Grant (CIG) I was granted in 2011 focused on the study of density matrix functional theory (DMFT) and its applications, and thus the collaboration with Basque country is particularly relevant. Since Prof. Piris joint the EHU, the group of Prof. Ugalde is actively working on a particular form of DMFT known as the natural orbital functional theory (NOFT) through the development and application of Piris-NOFs (PNOF). Recently, I programmed a parallel (MPI) version of PNOFid code which yields very promising efficiencies. Hence, together with the people at the EHU we obtained computer time at the Mare Nostrum (MN) supercomputer center (more than one million hours were granted on different PNOF projects thus far). These hours have been used to prove PNOF5 capabilities in small biological systems and transition metal complexes. This year three publications will be submitted concerning these topics.
Now, together with Dr. Pedro Salvador and Eloy Ramos, we are analyzing the performance of PNOF5-PT2 (the ontop second-order perturbation correction to PNOF5, recently implemented by Prof. Piris) as a benchmarking tool. To this aim, we have requested more computer time in MN in order to test PNOF5-PT2 in a series of difficult molecular systems.
In addition, also with Pedro, Eloy and Mario, we are also improving the convergence speed with PNOF5, which is the main weakness of the method. And, last but not least, we have also applied our recently developed spin decomposition scheme to PNOF5. Interestingly, this scheme does not only unveils the limitations of PNOF5 to attain the local atomic spin value upon dissociation, but it also points out which part of PNOF5 functional needs to be improved to fulfill this property. Therefore, local spin values can be used as an stringent test for DMFT and DFT functionals. The reduced number of such tests makes this finding particularly relevant for the development of new functional expressions.
|Posted on December 14, 2012 at 1:35 PM|
This week I was invited to visit the group of Ricardo Mata in Göttingen. They are working in many fields, from Molecular Dynamics to local correlated methods. They even programmed a molecular application for android that can open xyz and pdb files, design new molecules and optimize them with a force field. The program has been downloaded over 8000 times!
Recently, together with his postdoc Diego Andrada, they started to work in the fields of molecular bonding and aromaticity. Therefore, they became interested in the research of our group, which I tried to summarize in a seminar. I talked about the works I carried out in collaboration with many people (see talk) and the ESI-3D program, which I developed during the last years. Recently, I have been working on the update of this software which include many new possibilities. This new version will be released any time soon.
Over the weekend I also shortly visited Frankfurt and its Weihnachtsmarkts, which I missed from the time I spent near Berlin.
|Posted on December 14, 2012 at 12:55 PM|
The use of parallel architectures opens the possibility to address challenges that would be impossible otherwise. The biggest supercomputer in Catalonia is Mare Nostrum, which has been recently extended with Mare Nostrum 3 and belongs to the Barcelona Supercomputer Center (BSC). I have benefited from BSC resources in the past and currently I'm involved into two projects granted by BSC:
- Benchmark Calculations on Few-Electron Harmonium Atoms.
- Transition metal chemistry with PNOF5.
The first deals with the continuation of the benchmark calculation for harmonium we started with Jerzy Cioslowski during my postdoc in Szczecin. Now thanks to Krzysztof Strasburger we have a method which not only provides highly accurate energetics but also wavefunctions. The time granted in this period we partially cover our computational needs to deal with four-electron harmonium. These results will be used to calibrate and develop new DFT functionals. Indeed, the three electron results have already been used to elaborate the Starting grant project proposal DFTCorr.
The second project is the continuation of the applicability of PNOF5 code of Mario Piris (recently parallelized by me) to molecular relevant systems. First we focus on small biological systems now we turn our sight to transition metal chemistry. This work is tightly related to the Marie-Curie Career-Integration-Grant Project that I was awarded in 2011. Other people in the IQCC has been granted computational time in BSC.
In addition, lately I had the opportunity to attend a free course on parallel computing. In the course they gave the basics of OpenMP, MPI and many debugging tools to enhance the performance of a parallel code. Some of these tools will be soon installed in our own cluster and they will be certainly used to tune the programs behind the aforementioned projects.