[Phonopy-users] vibrational free energy From: Dr. Ravi Chinnappan - 2013-05-27 13:07:55 Attachments: Message as HTML Dear Dr. Togo, You may remember that you helped me obtaining irreducible representations for KMnAg3C6N6. Science Vol. 319, p794 (2008) is an article on related substance Ag3CoC6N6. Fig4 of this paper provides partial vibrational free energy for Ag, Co and CN. (The discussion is on the 3rd column, 2nd para.) Assuming that they really mean the partial vibrational free energy, I would like to do similar analysis for our study. Ponopy provides partial DOS. I used following option to plot using pdosplot: pdosplot -i '1 2 3, 4 5 6, 7 8 9 10 11 12 13 14 15, 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 38 39 40 41 42 43 44 45 46 47 48 49 50 51' -o 'pdos.pdf' partial_dos.dat. However, it is not clear how to obtain partial vibrational free energy. Please help me with this. Great regards, Ravi 
 Re: [Phonopy-users] vibrational free energy From: Atsushi Togo - 2013-05-28 01:02:15 Hi, I spent some time to understand it. But unfortunately, I could not see the mathematical definition and physical concept of the mean partial phonon frequencies. I will consider the implementation in phonopy if you let me understand it. Togo On Mon, May 27, 2013 at 10:07 PM, Dr. Ravi Chinnappan wrote: > Dear Dr. Togo, > You may remember that you helped me obtaining irreducible representations > for KMnAg3C6N6. > Science Vol. 319, p794 (2008) is an article on related substance Ag3CoC6N6. > Fig4 of this paper provides partial vibrational free energy for Ag, Co and > CN. (The discussion is on the 3rd column, 2nd para.) Assuming that they > really mean the partial vibrational free energy, I would like to do similar > analysis for our study. > > Ponopy provides partial DOS. I used following option to plot using > pdosplot: > pdosplot -i '1 2 3, 4 5 6, 7 8 9 10 11 12 13 14 15, 16 17 18 19 20 21 22 23 > 24 25 26 27 28 29 30 31 32 33 34 35 36 38 39 40 41 42 43 44 45 46 47 48 49 > 50 51' -o 'pdos.pdf' partial_dos.dat. > > However, it is not clear how to obtain partial vibrational free energy. > > Please help me with this. > > Great regards, > Ravi > ------------------------------------------------------------------------------ > Try New Relic Now & We'll Send You this Cool Shirt > New Relic is the only SaaS-based application performance monitoring service > that delivers powerful full stack analytics. Optimize and monitor your > browser, app, & servers with just a few lines of code. Try New Relic > and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may > _______________________________________________ > Phonopy-users mailing list > Phonopy-users@... > https://lists.sourceforge.net/lists/listinfo/phonopy-users > -- Atsushi Togo http://atztogo.github.com/ atz.togo@... 
 Re: [Phonopy-users] vibrational free energy From: Atsushi Togo - 2013-05-28 09:57:45 Hi, Could you describe the formulation? In addition, as far as I read the paper, they don't provide partial vibrational free energy, but the mean partial phonon frequencies. As I wrote, I can't figure out the physical meaning of both of partial vibrational free energy and mean partial phonon frequencies. Phonon is quantized as a collective motion and the quantized energies are used to calculate thermal properties. How can we divide thermal properites into atomic fractions? Togo On Tue, May 28, 2013 at 5:18 PM, Dr. Ravi Chinnappan wrote: > Dear Dr. Togo, > > phonopy -t prints phonon free energy, entropy and specific heat. We know > the formulation. Phonopy computes atom resolved PDOS. I would like to be > able to use phonopy to compute free energy, entropy and specific heat for > each atom resolved PDOS. > > Please help me with this. > > Kind regards, > Ravi > > > > On Tue, May 28, 2013 at 10:34 AM, Atsushi Togo wrote: >> >> Dear Dr. Chinnappan, >> >> WIthout formulation, it's difficult to implement what really you need. >> I guess the formula would be like, >> >> \sum_\lambda \omega_\lambda |e_i|^2 >> >> \lambda is the index of phonon mode. \omega is the frequency. e_i is >> the i-th component of the eigenvector. If for a specific atom, i >> should be summed up for x, y, z of the atom. >> >> But I can't understand it physically because the thermal properties >> are calculated from the statistical mechanics and the statistics are >> made for phonon modes or frequencies. It intuitively sounds strange >> for me to divide frequencies. >> >> Best regards, >> >> Togo >> >> On Tue, May 28, 2013 at 1:44 PM, Dr. Ravi Chinnappan >> wrote: >> >> Hi, >> >> >> >> I spent some time to understand it. But unfortunately, I could not see >> >> the mathematical definition and physical concept of the mean partial >> >> phonon frequencies. I will consider the implementation in phonopy if >> >> you let me understand it. >> >> >> >> Togo >> >> >> >> On Mon, May 27, 2013 at 10:07 PM, Dr. Ravi Chinnappan >> >> wrote: >> >> > Dear Dr. Togo, >> >> > You may remember that you helped me obtaining irreducible >> >> > representations >> >> > for KMnAg3C6N6. >> >> > Science Vol. 319, p794 (2008) is an article on related substance >> >> > Ag3CoC6N6. >> >> > Fig4 of this paper provides partial vibrational free energy for Ag, >> >> > Co >> >> > and >> >> > CN. (The discussion is on the 3rd column, 2nd para.) Assuming that >> >> > they >> >> > really mean the partial vibrational free energy, I would like to do >> >> > similar >> >> > analysis for our study. >> >> > >> >> > Ponopy provides partial DOS. I used following option to plot using >> >> > pdosplot: >> >> > pdosplot -i '1 2 3, 4 5 6, 7 8 9 10 11 12 13 14 15, 16 17 18 19 20 21 >> >> > 22 >> >> > 23 >> >> > 24 25 26 27 28 29 30 31 32 33 34 35 36 38 39 40 41 42 43 44 45 46 47 >> >> > 48 >> >> > 49 >> >> > 50 51' -o 'pdos.pdf' partial_dos.dat. >> >> > >> >> > However, it is not clear how to obtain partial vibrational free >> >> > energy. >> >> > >> >> > Please help me with this. >> >> > >> >> > Great regards, >> >> > Ravi >> >> > >> >> > >> >> > ------------------------------------------------------------------------------ >> >> > Try New Relic Now & We'll Send You this Cool Shirt >> >> > New Relic is the only SaaS-based application performance monitoring >> >> > service >> >> > that delivers powerful full stack analytics. Optimize and monitor >> >> > your >> >> > browser, app, & servers with just a few lines of code. Try New Relic >> >> > and get this awesome Nerd Life shirt! >> >> > http://p.sf.net/sfu/newrelic_d2d_may >> >> > _______________________________________________ >> >> > Phonopy-users mailing list >> >> > Phonopy-users@... >> >> > https://lists.sourceforge.net/lists/listinfo/phonopy-users >> >> > >> >> >> >> >> >> >> >> -- >> >> Atsushi Togo >> >> http://atztogo.github.com/ >> >> atz.togo@... >> > >> > >> >> >> >> -- >> Atsushi Togo >> http://atztogo.github.com/ >> atz.togo@... > > -- Atsushi Togo http://atztogo.github.com/ atz.togo@... 
 Re: [Phonopy-users] vibrational free energy From: Atsushi Togo - 2013-05-28 13:28:03 I need mathematical expression to discuss. How do you divide Helmholtz free energy into atoms? The formula is shown here. http://phonopy.sourceforge.net/theory.html#helmholtz-free-energy In the case of phonon (internal) energy, http://phonopy.sourceforge.net/theory.html#harmonic-phonon-energy it would be possible to divide using eigenvectors systematically, because of the linear function form to omega. Togo On Tue, May 28, 2013 at 9:06 PM, Dr. Ravi Chinnappan wrote: > Dear Dr. Togo, > > Yes, phonon is quantized as a collective motion and the quantized energies > are used to calculate thermal properties. But there are 3N phonon modes > for a crystal with N atoms. These collective motions are distinguished by > characteristic patterns of atomic displacements. Consider the substance is > made of three species, 1, 2, and 3. We can think of collective motion of 1 > or 2, or 1 & 2 or 2 & 3, or 3 or 1 & 2 & 3,etc. > > Phonopy documentation provides two presentations, phonopy-workshop.pdf and > introduction-phonon-calc.pdf, besides the manual. In these presentations > (p29 and p14), expressions for vibrational free energy, entropy and specific > heat are given. > (http://exciting-code.org/ref:phonons also provides such expressions as well > as the constraint on the phonon DOS. These are easy on-line references). > > Consider the mode label 's' in the expression for vibrational free energy. > Consider that the given value of 's' involves displacement of only species > 1. This mode has a given value of frequency, omega. DOS would tell us > how may such modes are there in the substance. With these, the free > energy, entropy and specific heat can be computed. > > These quantities can be considered contributed by species 1 (partial > vibrational free energy of species 1, etc.), which is a constituent of the > lattice. We don't mean contribution from free species or atom 1. > > This is my understanding. I don't have complete clarity. I too felt > strange when I first read that part of the paper. But phonopy provides > partial phonon dos. Therefore, I convince myself that respective partial > free energy is meaningful. > > I can use the expression for free energy with partial phonon dos to compute > the respective energies. It is doable, but would require more tuning. > > Please help with this. > > Great regards, > Ravi > > > > On Tue, May 28, 2013 at 3:27 PM, Atsushi Togo wrote: >> >> Hi, >> >> Could you describe the formulation? In addition, as far as I read the >> paper, they don't provide partial vibrational free energy, but the >> mean partial phonon frequencies. >> >> As I wrote, I can't figure out the physical meaning of both of partial >> vibrational free energy and mean partial phonon frequencies. Phonon is >> quantized as a collective motion and the quantized energies are used >> to calculate thermal properties. How can we divide thermal properites >> into atomic fractions? >> >> Togo >> >> On Tue, May 28, 2013 at 5:18 PM, Dr. Ravi Chinnappan >> wrote: >> > Dear Dr. Togo, >> > >> > phonopy -t prints phonon free energy, entropy and specific heat. We >> > know >> > the formulation. Phonopy computes atom resolved PDOS. I would like to >> > be >> > able to use phonopy to compute free energy, entropy and specific heat >> > for >> > each atom resolved PDOS. >> > >> > Please help me with this. >> > >> > Kind regards, >> > Ravi >> > >> > >> > >> > On Tue, May 28, 2013 at 10:34 AM, Atsushi Togo >> > wrote: >> >> >> >> Dear Dr. Chinnappan, >> >> >> >> WIthout formulation, it's difficult to implement what really you need. >> >> I guess the formula would be like, >> >> >> >> \sum_\lambda \omega_\lambda |e_i|^2 >> >> >> >> \lambda is the index of phonon mode. \omega is the frequency. e_i is >> >> the i-th component of the eigenvector. If for a specific atom, i >> >> should be summed up for x, y, z of the atom. >> >> >> >> But I can't understand it physically because the thermal properties >> >> are calculated from the statistical mechanics and the statistics are >> >> made for phonon modes or frequencies. It intuitively sounds strange >> >> for me to divide frequencies. >> >> >> >> Best regards, >> >> >> >> Togo >> >> >> >> On Tue, May 28, 2013 at 1:44 PM, Dr. Ravi Chinnappan >> >> wrote: >> >> >> Hi, >> >> >> >> >> >> I spent some time to understand it. But unfortunately, I could not >> >> >> see >> >> >> the mathematical definition and physical concept of the mean partial >> >> >> phonon frequencies. I will consider the implementation in phonopy if >> >> >> you let me understand it. >> >> >> >> >> >> Togo >> >> >> >> >> >> On Mon, May 27, 2013 at 10:07 PM, Dr. Ravi Chinnappan >> >> >> wrote: >> >> >> > Dear Dr. Togo, >> >> >> > You may remember that you helped me obtaining irreducible >> >> >> > representations >> >> >> > for KMnAg3C6N6. >> >> >> > Science Vol. 319, p794 (2008) is an article on related substance >> >> >> > Ag3CoC6N6. >> >> >> > Fig4 of this paper provides partial vibrational free energy for >> >> >> > Ag, >> >> >> > Co >> >> >> > and >> >> >> > CN. (The discussion is on the 3rd column, 2nd para.) Assuming >> >> >> > that >> >> >> > they >> >> >> > really mean the partial vibrational free energy, I would like to >> >> >> > do >> >> >> > similar >> >> >> > analysis for our study. >> >> >> > >> >> >> > Ponopy provides partial DOS. I used following option to plot >> >> >> > using >> >> >> > pdosplot: >> >> >> > pdosplot -i '1 2 3, 4 5 6, 7 8 9 10 11 12 13 14 15, 16 17 18 19 20 >> >> >> > 21 >> >> >> > 22 >> >> >> > 23 >> >> >> > 24 25 26 27 28 29 30 31 32 33 34 35 36 38 39 40 41 42 43 44 45 46 >> >> >> > 47 >> >> >> > 48 >> >> >> > 49 >> >> >> > 50 51' -o 'pdos.pdf' partial_dos.dat. >> >> >> > >> >> >> > However, it is not clear how to obtain partial vibrational free >> >> >> > energy. >> >> >> > >> >> >> > Please help me with this. >> >> >> > >> >> >> > Great regards, >> >> >> > Ravi >> >> >> > >> >> >> > >> >> >> > >> >> >> > ------------------------------------------------------------------------------ >> >> >> > Try New Relic Now & We'll Send You this Cool Shirt >> >> >> > New Relic is the only SaaS-based application performance >> >> >> > monitoring >> >> >> > service >> >> >> > that delivers powerful full stack analytics. Optimize and monitor >> >> >> > your >> >> >> > browser, app, & servers with just a few lines of code. Try New >> >> >> > Relic >> >> >> > and get this awesome Nerd Life shirt! >> >> >> > http://p.sf.net/sfu/newrelic_d2d_may >> >> >> > _______________________________________________ >> >> >> > Phonopy-users mailing list >> >> >> > Phonopy-users@... >> >> >> > https://lists.sourceforge.net/lists/listinfo/phonopy-users >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> Atsushi Togo >> >> >> http://atztogo.github.com/ >> >> >> atz.togo@... >> >> > >> >> > >> >> >> >> >> >> >> >> -- >> >> Atsushi Togo >> >> http://atztogo.github.com/ >> >> atz.togo@... >> > >> > >> >> >> >> -- >> Atsushi Togo >> http://atztogo.github.com/ >> atz.togo@... > > -- Atsushi Togo http://atztogo.github.com/ atz.togo@...