I totally forgot to write something about this paper. But before getting to that, an anecdote: Last month some friends and I were sitting out in a hallway of one of the hotels hosting the ACS national meeting. We were definitely looking tired. A guy, who seemed to be experienced in hiring, started talking to us about not giving up and practice more on elevator conversations: your ability to ultra-summarize your work to others. He did spend some time sharing his experiences with us. We must’ve looked really tired (especially me)…
So here is that elevator report for you (web visitor): We got a paper published on estimating the absorption spectrum of excited-states, here. You select an excited state (based on its symmetry, transition energy and oscillator strength from the ground state), and the program outputs its absorption spectrum (in terms of oscillator strengths).
With some extra details, you run a regular linear-response “TDDFT” calculation (starting from the ground-state orbitals), and choose the state. The algorithm perturbs the orbitals using the transition vectors of the chosen state, and then runs the linear-response calculations once again. At the end it prints out the oscillator strengths for transitions starting from the chosen excited-state. The tests I’ve run indicate the printed results are ok against experimental data. The paper is backed by a theory based on quantum mechanics (exact in principle), and the approximations are improvable.
If somebody paid me for an honest brief review of this paper, I’d say: Incomprehensible, intricate, complicated, but seems useful. I love it, but I understand the formalism is hard, but the implementation is quite simple. Applications to organic semiconductors are coming
Chaotic Microchips
Anarchy(chaos)+Microchip = Happiness
“Chaos” is an interesting word in science, maybe ’cause is synonym of (according to thesaurus.com): anarchy, disorder, lawlessness, pandemonium, among others?. Aren’t those words that draw our attention? (Many movies are about creating disorder and the journey of some folk trying to restore order). Anyway, it’s been a while since the last post… my bad.
El Capitan drinks Quantum Espresso
To compile a slow version of quantum espresso for an iMac: i) Download last version, and extract somewhere. ii), use this script, “qe_conf.sh”:
NWChem in El Capitan
I installed it in a mid 2011 iMac, and used gcc compilers. First, get the right compilers (or make sure gcc5, or alike, is installed).
sudo port install gcc5 +gfortran+universal
(I needed to make symbolic links in /opt/local/bin for gfortran, gcc, g++, and cpp. Port installs them as gsomething-mp-5). Also make sure you have mpich. If not, type
sudo port install mpich-gcc5
then
sudo port select –set mpi mpich-gcc5-fortran
This last step is to use the mpi commands linked to gcc, instead of clang.
Download nwchem-6.6 from here, and extract the .tar.gz file into some folder. The environmental variables are:
Deleting Native Apps in Mac OS X
I like to keep my mac laptop with minimal number of apps. El Capitan comes with an additional protection feature that does not let you delete native apps. The solution is to reboot the computer, while the screen is dark hold command+r to enter recovery mode. Once there open a terminal and type “csrutil disable”. Then restart, find the app, change its permissions, and delete; you could also do this by entering the applications folder and typing “rm -rf /Applications/dying.app”. Then go back to recovery mode, open a terminal and type “csrutil enable” to reactivate the feature.
Finding Cutoffs for Quantum Espresso Calculations
Critical numbers to check before running plane-wave calculations are the kinetic energy and density cut-offs. I found a useful guide to check these cutoffs, http://larrucea.eu/checking-optimum-cutoff-qe/. I uploaded a copy here. The script needs the location of the pseudopotential file and the executable, pw.x, location. One can modify the script, for example changing the numbers in the list of trial cutoffs to search for the best numbers. For ultrasoft potentials I guess one has to make sure the density cutoffs are high enough so the calculations for the last values in the list of kinetic energy cutoffs are reliable enough. [Update: the new QE library based on rrkjus pseudopotentials includes the cut-offs]
2d Silicon Hybrid Material
I noticed an article on a new 2d sheet combining silicon, nitrogen, and boron. It’s another honeycomb-shaped system, challenging the almighty graphene When I first read the news article I thought this had been synthesized, which would’ve been really nice. But at this point the work is only computational, but it’s still quite interesting. There are so many candidates for 2d semiconductors out there… makes me think, which one will be the king? Link
JPCA Paper Out
We finally got our paper on hybrid functionals and the local density approximation (lda) accepted. This work presents some basic conditions hybrid XC functionals should satisfy and a discussion on the balance between correlation, HF, and local exchanges. We suggested an adiabatic functional, cam-lda0, which can be used to speed up calculations a little bit. Copies available at the JPCA website, here
Ravens and the Theory of Mind
These birds are among the smartest flying beings. A recent study claims proving that ravens are capable of anticipating what other birds might do. This would mean ravens have a theory of mind, they could think as if they were other birds. This is simply fascinating. Ravens are quite intelligent mammals, and, I think, very clever. Perhaps, a theory of mind can help them to secure food resources, plan strategies. There are many other studies, even in TV shows, illustrating their relative brilliance. The Washington post announced this study