|Posted on January 20, 2012 at 12:55 PM|
PhD position available in the framework of the Career Integration Grant 2011 titled:
Development of New Non-Empirical DFT Functionals
This is a four year project in computational and theoretical chemistry, which started in December 2011 and is devoted to the development of new DFT and DMFT functionals.
The PhD position (3 years) will start no later than 2013. A background in computational and theoretical chemistry is welcome. However, the candidate will be offered a 1 year grant to perform the master on 'Computational and Theoretical Chemistry'.
THIS POSITION IS CLOSED. INTERESTED CANDIDATES WITH GOOD GRADES MAY APPLY FOR NATIONAL GRANTS SEE THIS LINK.
|Posted on November 19, 2011 at 8:10 PM|
I moved out of the Donosti and went back to Girona on the 1st of December. In a sense, my postdoctoral adventure finished there. However, I do not have a permanent position or whatsoever, and I'm still living out of postdoctoral grants, like the one I just got for the next two years. Yet, taking into account the current economical situation I cannot complain.
My stay in Donosti has been short (8 months) but intense. Apart from some personal issues I have been through, my time in the Basque Country has been great. I confirmed that Prof. Ugalde's group is doing very high-quality research, but I also found myself surrounded by many amiable people. That certainly made my stay very pleasant and the interaction with the members of the group extremely easy. Small wonder I left Donosti with bittersweet feeling ... I was 'coming back home' but I would have stayed there longer.
In Donosti I have had the opportunity to work on different subjects, including the most interesting Natural Orbital Functional Theory (NOFT). Altogether I learnt quite a lot about this theory, which -I believe- it has still a long way to go. I came back to Girona with a few ideas for new projects, some of them to be implemented in NewDFTfunct, which also started on December 2011.
I have to admit that so far I have not had much time to do research... let's see if I can settle down soon and start working!
|Posted on November 4, 2011 at 11:05 AM|
I first learnt about parallelization when I was still in Aarhus. Where else? I still have the impression I spent most of my time in Aarhus learning... this or that thing. We had a brief introduction to MPI and OpenMP protocols and like many other things I learnt, I left it aside for 'some time'. That time turned out to be a couple of years... After a year in Poland, it was pretty obvious that I had to retake those notions if I wanted to perform highly accurate calculations on harmonium.
After browsing the net for tutorials (there is tones of information about parallel computing) I started teaching myself some basics of MPI. A few weeks later I had parallelized a simple matrix multiplication program, and after a few months I got an MPI version of a the FCI code we were working with. Right after that, I parallelized a joint version of this FCI code with an external interface, so that we could use this software in the Barcelona Supercomputer Center (BSC, aka Mare Nostrum) with up to 64 cores. Thereafter, I converted many different versions of this code to MPI protocol.
A few months passed and I left Poland, with many ongoing projects behind. One of those needed the calculation of very expensive four-components CCSD(T) frequency calculations. We already had the software for that (thanks to Pedro Salvador) but it seems it would take ages to obtain the results we needed. So, once again, I undertook to parallelize the software. Last summer I finally fulfilled my promise and we got a twelve-fold parallel version of Pedro's code. I still have to parallelize the geometry optimization with the same code, but as many other things that are not in a rush... it's on the todo list.
Recently, we started working with Jerzy and Krzysztof Strasburger on three-electron harmonium for small values of the confinement parameter. These calculations are even tougher than those I did in BSC, so that we had to use Krzystof's code with explicit correlated gaussians to obtain some meaningful results. His code produced very accurate energies and wavefunctions that had to be treated by a software that Jerzy developed in order to obtain natural orbitals and their occupancies. Soon enough, it became clear that we would need to parallelize Jerzy's code in order to get those results asap. This time we achieved a succesful parallelization on up to 256-cores [personal best ;-)] with BSC resources. I have the feeling the code is good enough to do 1024-fold parallelizations, but we did not need that much.
Two weeks ago I put myself a new challenge, to parallelize a quite large code that performs calculations using a natural-orbital based energy functional (NOF theory, NOFT). The code is known as PNOFID and was developed by Mario Piris. This is the first of such codes (to the best of my knowledge) and the success of this parallelization could open the way for NOFT calculations on 'big' molecules. If we get something parallel-worthy I will post something here...
Obviously, parallelization can become very tricky, especially when want to parallelize different tasks inside the same code, or when the problems we are dealing with are not embarassingly parallel or almost-embarassing parallel. Then, parallelizing a code can become a real pain. However, after these short experiences on parallelization I draw some conclusions:
Almost anything is paralellizable. In many cases, there is a unique task that is consuming most of time, and often enough, this task is simple. We just need to detect the bottleneck and apply the divide-and-conquer strategy that fits. Most of tasks we routinely perform in computing are trivial and thus can be parallelized.
Parallelization can be achieved easily. Sometimes it can be done really easily. Once you learn the MPI commands and gain some experience, you realize that the things to change to obtain a paralell code are relatively few and identical from code to code.
So, sometimes it is just a matter of getting some basic training on MPI (which I guess may take up to a month time) and try to parallelize our favorite code. Things may get easier than you thought.
|Posted on October 13, 2011 at 1:25 PM|
Last year Miquel Solà and myself accepted an invitation from Current Organic Chemistry (Bentham) to edit an especial issue in this journal. We decided for the topic of electron delocalization applied to the field of organic chemistry. We invited some reputed experts in this field -Bernard Silvi, Juan Andrés, Ángel R. de Lera, Fernando P. Cossío, Janos G. Ángyán, Patricio Fuentealba and Tomás Rocha-Rinza-, to write a paper on this topic. They wrote seven reviews with special emphasis in the tools of Atoms-in-Molecules (due to Bader), the electron localization function (ELF) and even some new tools currently being developed (Ángyán's). They use these tools to analyze the electron delocalization and the aromaticity in several organic compounds and reactions, such as several electrocyclic reactions (including pericyclic reactions) and the electrophilic aromatic substitution.
The issue is available here.
|Posted on July 26, 2011 at 6:10 PM|
The Starting Grant (StG) is a prestigious research award from the seventh framework program (FP7), the EU's chief instrument for funding research. This award gives a considerable amount of money [ca. 1.5M€] to young talented researchers. This call is very competitive and it can be taken as a rough measure of the young talent in a given country. 2010's call reported 23 researchers awarded in Spain (9 Catalonia, 6 Madrid, 3 Basque Country, 1 Navarra).
The Advanced Grant (AdG) is the equivalent of the StG for senior researchers. It awards more money [ca. 2.5M€] to brilliant consolidated researchers and thus one can also take the number of AdG per country as a measure of research excellence. 2010's call reported 13 researchers awarded in Spain (7 Catalonia, 2 Madrid, 1 Basque Country).
Let us make some plain statistics. 78% StGs and 76% AdG are accumulated in three autonomous communities (CA) of Spain: Catalonia, Madrid and the Basque Country. Catalonia gets 39% StGs and 53% AdGs. But Catalonia is big enough; 7.54M people live in Catalonia, 2.15M people live in the Basque Country and 6.44M people in Madrid. We may calculate the number of awards per inhabitant to make reliable comparisons among CAs. The number of StG per million people are: 1.19 (Catalonia), 0.93 (Madrid) and 1.40 (Basque Country); the AdGs numbers are 0.92, 0.31 and 0.46 respectively. It is indisputable that Catalonia is particularly good at attracting senior talented researchers, but the Basque Country attracts more young brilliant researchers per inhabitant. Particularly worrying is the situation in the rest of Spain which shares less than 25% of the StGs and AdGs among 29.9M people, i.e. it gets 0.16 StG and 0.10 AdG per million inhabitant.
Smaller wonder... if we look at how much each CA invests in research as compared to its GDP (País Vasco = Basque Country):
Among the four CAs that invest more GDP we find Catalonia, Madrid and the Basque Country which accumulate more than 75% of the StG and AdG awards given to Spain. I'm particularly surprised at the good performance of Catalonia taking into account that it gets much less %GDP [1.68%] than the Basque Country and Madrid [2.06%]. Excepting for Catalonia, Madrid, the Basque Country and Navarra, the other CAs invest below 1.15% of GDP in research.
Look at the %GDP investment over the years. Catalonia's investment has increased about 58% over the last ten years, Madrid's 30% and the Basque Country's 78% (!). So again, it comes as no surprise that the Basque Country is leading the attraction of young researchers. I guess it is just a matter of time for them to lead also the attraction of consolidated researchers in Spain.
All in all, Spain [1.38%] is well below the average investment of %GDP in research for the EU-27 [2.01%]; only Madrid, the Basque Country and Navarra reach the EU-27 standards. Catalonia is so-so [1.68%]. Obtaining funds for research is getting more and more complicated in Spain and many talented researchers are leaving the country to never come back. Only a few CAs can resist the unavoidable brain drain.
|Posted on July 6, 2011 at 6:48 PM|
Lately there have been a few events that well deserve a new post.
I was recently awarded a Career Integration Grant (CIG) that will support my research for the next four years (100,000€;). I will try to use this money to buy some consumables, attend to some conferences and to employ some Ph.D. student.
Yet another year passes and I have not been awarded the Ramon y Cajal (RyC) contract. The RyC is a sort of five-year tenure-track from the Spanish government. Basically my chances of getting a permanent position are extremely low if I am not awarded a RyC. The good news is that this time I got the 23rd position and I am on the reserve list (18 were awarded) but there is no chance for this year.
Together with Jerzy we were granted 20,000 hours of computation in Mare Nostrum. Finally, they grant us time in MN but we requested 150,000 hours and we cannot do much with these 20,000 hours.
I am waiting for a Catalan two-year postdoctoral grant with deadline on November 2010. The decision should have been given by the end of April (6 months... for comparision let me say that the CIG takes much more time to be prepared and the decision was given within 3 months). To make it worse a few months ago the Catalan govenment postponed the decision until July and today I learnt that the decision will be hopefully [sic] postponed until September! It is completely unacceptable that they need 10-11 months to make a decision. If they actually ever make it... Obviously there is an economic reason behind: the Catalan government ran out of money. Yet, they should realize that many people depend on these grants, and awarded or not, they need to know it asap in order to find another source for funds if not granted.
Finally, let me say that I will be attending to WATOC meeting the third week of this month and starting vacation right after it.
|Posted on May 16, 2011 at 5:38 PM|
On April I moved to Donostia to start a postdoctoral stay in the group of Prof. Jesús Ugalde. I'm employed in the Donostia International Physics Center (DIPC) and work in the Faculty of Chemistry in the Euskal Herriko Unibersitatea (EHU). The group is about 15 people and they work on a wide variety of research subjects which, to my convenience, includes harmonium. My experience this first month could not be better. People in the group is very nice and the city, Donostia, is charming. I will stay in Donostia until the of November, then I will move back to Girona.
I'm hosted in the Talent House a residence for postdoctoral researchers that has been recently inaugurated. This residence is just an example of the investment that the city (and the Basque Country) is doing on research. Some time ago Catalunya invested on research and started the program ICREA, whose results are showing in the most competitive european research projects. Spain was awarded 23 grants in the last call of the Starting Grant, 9 of which were to Catalan institutions and 3 to Basque research centers. More recently the Basque Country started the ikerbasque program, quite similar to ICREA. Nowadays, ICREA program has reduced its budget (initially ICREA hired both senior and junior researchers, lately only seniors) while the Basque Country is investing more on research. I believe it's matter of time for the Basque Country to catch up to Catalunya.
|Posted on May 14, 2011 at 8:03 AM|
About a year ago I posted an entry in this blog discussing peer-review process. Today, via twitter I received an article from the editors of the Journal of the American Chemical Society (JACS) to draw our attention on "the moral responsibilities of our referees". Basically the article is critical with those researchers that refuse to write reviews or write a late report that it is of no use. After this article I get the impression JACS editors are mainly concerned about getting reports and getting them on time.
I was startled to see no reference to the quality of the report. They mention all sorts of malpractices (not answering, refusing to report, consulting othe rscientists without editor's consent, removing oneself for long periods from the list of active referees) but they do not mention about writing bad scientific reports. Maybe they do not want to put the researcher's competence into question. Fair enough; but then, they shouldn't mention about these other malpractices either; they all concern the 'moral responsibility' of the reviewers.
The editors should put as much effort on getting good-quality reports as they do on getting quick reports. Lousy reports are potentially more harmful than no report at all. Lousy reports often refuse or accept the paper directly, without much explanation of why the paper merits such qualification. Lousy reports make lousy papers published. If the author feels mistreated, he may appeal. However, experience indicates that his success will mostly depend on his relationship with the editor, rather than on the quality of his paper.
Let me mention a recent episode I experienced while reviewing for JPCA (ACS) and PCCP (RSC). I received a paper to review from these journals and they gave a deadline to respond (between two-three weeks). I read both papers and, in both cases, when I was about to write the report I received e-mail from the editor saying that my report was not longer necessary. In both cases it happened before the deadline. I was pissed. I get the impression editors contact more referees than necessary and then they discard those that come latest. Obviously, such practice increases the demand of referees.
Scientific publishing is business. Let's not forget it. Apparently any strategy is good to increase the publication speed. And if such strategy uses reviewer's time, it does not bear any cost to the journal.
If editors want ((good-quality)) quick reports, they should acknowledge referee's task. It does not make any difference how many papers I review every year. At most I get a Xmas card, lately not even that. I am not sure which should be the mechanism to reward the reviewers, but something has to be done.
I advocated here for responsible reviewer performance. My idea is that anyone should cover the demand of reports his papers generate; I guess this is (morally) responsible. But I also claim for editors' moral responsibility to acknowledge the referee's task and appreciate their time.
|Posted on May 9, 2011 at 6:21 PM|
My time in Szczecin came to an end. After two short years filled with all sort of adventures I'm moving on. My next destination is Donostia, in the Basque Country... but that will be the issue of a coming post. In the following lines I will sum up my experience in Poland.
The group was very small but people were nice to me (Jerzy, Jacek, Marcin, Ewa,Stan and lately Joanna). Scientifically, I have no complaints. I already knew Jerzy, both the guy and the scientist and we understood each other quite well. He is the most knowledgeable scientist I have ever met, and probably I will ever meet. I have learnt a great deal of things from him, and together we have put the basis (algorithm and software) for the study of few-electron harmonium systems. I had also time to learn on my own some basic guidelines to program in parallel (mostly with MPI protocol), which I used to parallelize a few codes of mine. I familiarized myself with literature in the field and got a couple of ideas, which little by little turned into a four-year research project to(hopefully) develop at some point in the coming years. The number of papers published on the main research subject of this postdoc is not large (three so far), but this is mostly because the development of the code/algorithm toke most of my time, the calculations were time consuming and they needed large computational resources that were not easy to obtain. We are actually still looking for resources to finish four-electron harmonium calculations (ideas welcome!). Therefore, some more publications should appear in the coming years. Besides, I also dedicated a not-so-small fraction of my (free) time to work on other research projects because, no matter how much I learn, no papers is no future. The competition is really high. I started collaborations with Prof. Kallol Ray (computational calculations), Prof. István Mayer (decomposition of total spin angular momentum), Prof. Mihai Putz (conceptual DFT), Prof. Gabriel Merino (aromaticity) and my former group in Girona (Prof. Solà's). These collaborations and the last papers from my postdoctoral stay in Denmark with Prof. Ove Christiansen provided the gross publication record during these two years of postdoc.
My only problem on my stay in Szczecin was the university administration. Unfortunately the university did not have (and it doesn't) the adequate infrastructure to hold a Marie Curie fellow (IEF). People who were supposed to take care of my fellowship did not know anything about it and sometimes simply noone took responsibility for it. Everytime there was an issue with my grant it was a nightmare for them... and for me. Someway, somehow (Polska!) it went through, but not without much time and effort from my side. Here I should mention Jacek who did not benefit from this fellowship (and it was not his duty) and carried on his shoulders the paperwork and problems related with the IEF. What is more, he bore my complaints with cheerful equanimity. Without him I would have surely packed and left after the second month. Don't get me wrong, I had an ample office, broadcast connection and nice atmosphere to work (all that a theoretical chemist needs), but every little paper work was a big deal and lots of mess.
On the personal side I had a great time in Szczecin, mostly because of Jacek (yep, the same guy!) and Jadwiga. They were my neighbors and my friends; we shared dinners, Sunday lunches, bottles of wine and Easter parties. Basically any excuse was good to meet. They also helped me with many issues of my apartment that I could not take care by myself because of the language barrier. There are not enough words to acknowledge what they did for me.
All in all, I do not regret a single day I spent in Szczecin. It was a worthwhile experience that I will never forget.
Last dinner in Zbójnicka. From left to right: Jerzy, Jacek, my long-hair-no-shaved me and Marcin.
|Posted on April 13, 2011 at 12:11 PM|
My last month in Poland I organized a mixture of vacation and lab-visiting. I had the opportunity to give talks on the 'Vibrational Auto-adjunting theory' and 'The Electron Localization Function' (see papers 26 and 36) in the Wroclaw University of Technology and the Technical University of Lodz respectively. I was invited to Wroclaw by Robert Zalesny who was a formidable host. In Lodz I was visiting Kasia Pernal and staying at her place. I was impressed by the size of the group in Wroclaw. Kasia's group just started but it is already producing very interesting papers.
On my vacation with Anna we visited Wieliczka, Krákow and Zakopane. Hard to decide which one was best. Krákow is probably my favourite city in Poland (with permission of Torun). In Zakopane we enjoyed the folklore in Chata Zbójnicka. The salt mine in Wielczka is simply impressive, worth a visit. I had almost no time to visit Wroclaw but I was already familar with this charming city. My visit in Lodz was brief, but apparently there is no much to see there, excepting for the Manufaktura (see photo).