|Posted on October 19, 2012 at 8:05 PM|
Last wednesday I submmited the project DFTCorr, A New Strategy in DFT: Density Functionals Adapted to Electron Correlation, to the Starting Grant (StG). The European Reserach Councill finances a few excellent research projects of young scientists (maximum 7 years from PhD defense) through the StG call. It took quite a lot of time to prepare the proposal and I am literally exhausted after this last three-week effort. I want to thank the twenty people who patiently read and reviewed various versions of my proposal. Thank you all for your help!!
Now it's time for a short break. I go trekking to the Basque Country for a week time or so.
|Posted on September 30, 2012 at 3:35 PM|
This september I went back to Donosti. I'm involved in an on-going project with many people from Jesus Ugalde's group, which aims at paralellizing the PNOF program of Mario Piris. So far, we had parallelized the main bottleneck of the program (the utilization of two-electron integrals to construct the pseudo-Fockian matrix), producing very high parallelization performance yields. However, as the number of cores increases, other processes in the code gain importance and these yields drop. The aim on this three-week incursion in Donosti has been the parallelization of the second most important process in the code. The Donosti InternationalPhysics Center (DIPC), which had employed me in the past, paid for my expenses.
In addition, I have also been busy writing the second Barcelona Supercomputer Centre (BSC) application on PNOF5 calculations. This time, we turn our sight to transition metal (TM) complexes, in a project which would be the very first one to address TMs from a density-matrix functional theory (DMFT) perpective (actually PNOF5 it is not a pure DMFT approach, it is rather an effective-pairing theory but the different is subtle). Little by little PNOF5 it is making its own way among other computational chemistry tools.
Finally, together with Pedro Salvador and Eloy Ramos we have also been working on the local spin decomposition of a few PNOF functionals. Interestingly, the local-spin decomposition has reaveled itself as an stringent test for the cumulant part of the second-order density matrices, and this decomposition has been used to unveil some limitations of natural orbital functionals.
Now I'm back in Girona, and full-time focused on writing the Starting Grant. Results are ready. The idea is clear. Some people have give his opinion on the topic. Some writing has been done. I just need to polish the whole thing in the next few weeks.
|Posted on September 30, 2012 at 3:25 PM|
This year's (most likely) last conference have been in Prague. I attended EUCheMS together with many other people from the Institute of Computational Chemistry and Catalysis (IQCC). I gave a talk on the electronic characterization of electrides and presented a poster on the work of reduced density matrices which will be submitted anytime soon.
These conference days have been a sort of short fake vacations, since I am employing my vacations days in the elaboration of Starting Grant proposal. I shall give a more detailed description of the project in a forthcoming post.
Besides, since last July Mauricio Rodriguez joined the IQCC, and he will be working on the development of density and density-matrix functionals, the subject of the Career Integration Grant. Together with Marc Garcia and Eloy Ramos, they have produced a wealth of data that will be used as a proof of concept for the Starting Grant proposal.
|Posted on August 8, 2012 at 9:00 AM|
The call for the Catalan Governtment PhD grants (FI2012) is opened. In our group we are looking for good candidates to work mainly on a DFT development project (see this link) who can apply for such grants. However, candidates with more chemistry-oriented preferences are also welcome to join other research lines in our group. The requisites include:
- BSc. on Chemistry, Physics or Mathematics.
- Having a Master of Sci. with completion date between 1st of January 2010 and 31st of December 2012.
- Not having a PhD.
- The grades on your BSc. should be above 2.00 according to our 'national rates'. You can find the conversion rates for your country in the following link (see pages 15-24).
Interested candidates should send their CVs (including a grade count as explained above) to ematito(at)gmail.com before 10th of September.
|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.