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From: Atsushi Togo <atz.togo@gm...>  20130327 02:13:30

Hi, Which phonopy version do you use? By the way, please join the mailing list. Otherwise, your post is not automatically distributed. I have to login the administration web page, check the post and approve, etc., which bother me. Togo On Thu, Mar 21, 2013 at 12:57 PM, <polivia@...> wrote: > Hi! > I´m new with this. I tried to install phonopy in my new Mac and after > running setup.py script I get this message: > > fatal error: 'omp.h' file not found > #include <omp.h> > > Could you give me an idea for solving this? > > Thanks a lot. > > > Patricia > >  > Own the FutureIntel® Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. > Compete for recognition, cash, and the chance to get your game > on Steam. $5K grand prize plus 10 genre and skill prizes. > Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers  Atsushi Togo http://atztogo.github.com/ atz.togo@... 
From: Atsushi Togo <atz.togo@gm...>  20130326 22:57:47

Hi, I don't understand what kind of technique you expect. The handling of tensor using matrix representations of space group can be found in the books for group theory for solids. I think the best is to read one of those books. By the way, phonopy does not directly apply symmetry constrains numerically. http://phonopy.sourceforge.net/theory.html#thepalinskilikawazoemethod Togo On Wed, Mar 27, 2013 at 4:02 AM, Iyad ALQASIR <iyad.ne@...> wrote: > Dear Phonopy users, > > Phonopy calcualted the nonequivalent set of force constants and distribute > them to those are equivalent. It applies also symmetry operations on the > force constants to conserve the clousre relations ( constraints). But all of > this is done numerically. > > My question, how for a system of given number of atoms, I can extract > analytically using phonopy the list of the nonequivalent force constants > and the equations connect these force constants based on the symmetry > operations. As an example for a system of Nb using 54 atoms which means > there are 54 x 54 matrix element where each element is 3x3 matrix, that is, > there are 26244 force constants, only 16 force constants are nonequivalent. > I did that by hand which is time consuming. If I want to know the > relations between these force constants, please advice how. > > Thank you > ___________________________ > IYAD I. ALQASIR, PhD > Postdoc Research Associate > > XRay and Neutron Scattering and Spectroscopy Group > Materials Science and Technology Division > Oak Ridge National Lab > Oak Ridge, TN > >  > Own the FutureIntel® Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. > Compete for recognition, cash, and the chance to get your game > on Steam. $5K grand prize plus 10 genre and skill prizes. > Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers >  Atsushi Togo http://atztogo.github.com/ atz.togo@... 
From: Iyad ALQASIR <iyad.ne@gm...>  20130326 19:02:17

Dear Phonopy users, Phonopy calcualted the nonequivalent set of force constants and distribute them to those are equivalent. It applies also symmetry operations on the force constants to conserve the clousre relations ( constraints). But all of this is done numerically. My question, how for a system of given number of atoms, I can extract analytically using phonopy the list of the nonequivalent force constants and the equations connect these force constants based on the symmetry operations. As an example for a system of Nb using 54 atoms which means there are 54 x 54 matrix element where each element is 3x3 matrix, that is, there are 26244 force constants, only 16 force constants are nonequivalent. I did that by hand which is time consuming. If I want to know the relations between these force constants, please advice how. Thank you ___________________________ IYAD I. ALQASIR, PhD Postdoc Research Associate XRay and Neutron Scattering and Spectroscopy Group Materials Science and Technology Division Oak Ridge National Lab Oak Ridge, TN 
From: Atsushi Togo <atz.togo@gm...>  20130326 08:21:10

Hi, I personally don't know your system. If nobody can answer this, you may try to install Ubuntu on your computer. http://phonopy.sourceforge.net/virtualmachine.html Togo On Tue, Mar 26, 2013 at 2:30 PM, Tian Lan <tianlan@...> wrote: > Hi all, > > When I am running qha calculation. I met the error : You need to install > pythonscipy. In phonopy website, this was mentioned. > I checked our cluster, there is a package 'pythonpkg/scipy'. Are they the > same thing or not? > I am not familiar with those things. I could not find an accurate source to > get this particular pythonscipy, could someone help me? > Thanks! > > Best, > Tian > >  > Lan, Tian > Ph.D. Candidate, Department of Applied Physics and Materials Science > California Institute of Technology, > Caltech M/C 13878, Pasadena, CA, 91125 > >  > Own the FutureIntel® Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. > Compete for recognition, cash, and the chance to get your game > on Steam. $5K grand prize plus 10 genre and skill prizes. > Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers >  Atsushi Togo http://atztogo.github.com/ atz.togo@... 
From: Tian Lan <tianlan@ca...>  20130326 05:30:10

Hi all, When I am running qha calculation. I met the error : You need to install pythonscipy. In phonopy website, this was mentioned. I checked our cluster, there is a package 'pythonpkg/scipy'. Are they the same thing or not? I am not familiar with those things. I could not find an accurate source to get this particular pythonscipy, could someone help me? Thanks! Best, Tian  Lan, Tian Ph.D. Candidate, Department of Applied Physics and Materials Science California Institute of Technology, Caltech M/C 13878, Pasadena, CA, 91125 
From: Atsushi Togo <atz.togo@gm...>  20130325 05:13:13

Hi, Phonopy employs the supercell approach, which is the real space approach. In phonopy, usually properties are normalized for the size of input cell, and it is irrespective of supercell size. Supercell size is a kind of a convergence parameter which is used to approximate phonon modulation at qpoints. Togo On Mon, Mar 25, 2013 at 1:41 PM, Tian Lan <tianlan@...> wrote: > Hi, > > I think my concern is whether the phonon free energy in phonop has already > been normalized to that from the building block of the supercell, instead of > the supercell itself. > > In the README of Al example, it says the phonon was calculated with a 2 by 2 > by 2 supercell. Is the building block a conventional one? I guess this > supercell is established upon a conventional unit cell instead of the > primitive one (sorry about the word, my primitive cell in the former message > should mean the conventional one). Maybe I am wrong. > > I also did calculation for my own structure. The structure has 6 atoms for > conventional cell, then I used a 3 by 3 by 3 supercell to do the phonon > calculation. However, in the thermal_properties, I saw "natom=6", so the > free energy looks like being normalized to the building block of the > supercell, i.e, the 6 atoms one, Otherwise, natom should be equal to 162. > > Sorry about this, but I am confused here. > > Best, > Tian > > On Sun, Mar 24, 2013 at 7:50 PM, Atsushi Togo <atz.togo@...> wrote: >> >> >> > > > >> >> >> > Thank you! I will work more on it. >> > >> > I found some inconsistency in the QHA example. Maybe I misunderstood >> > your >> > instruction 'The quantities have to be normalized to a cell having the >> > same >> > number of atoms'. I am using a 1.1 version. >> > >> > When I looked at the QHA example for Al. The README said it was >> > calcuated >> > with a 2 by 2 by 2 supercell. But in the ev.dat, the energies are for a >> > primitive cell. Also in each thermal_properties.yaml, 'natom' is said >> > equal >> > to 4, which is the number of atoms for a primitive cell. So the >> > thermal_properties has normalize the atoms number to one primitive cell >> > already, I think. I run my own structure. I am using a supercell, the >> > thermalproperites still give a primitive cell instead, at least the >> > natom >> > said so. >> > >> > So, my observation is thermal_properties always normalize the cell to a >> > primitive cell, even though you calculate phonons using a 2*2*2 or >> > others. >> > If this is true, then ev.dat should correspond to a primitive one as >> > well. >> >> The primitive cell of Al contains one atom. 4 is for the conventional >> unit cell (cubic one). Phonopy calculates properties for the input >> cell. However you can reduce it if the input cell contains further >> smaller translational period. In Al example case, POSCAR's are the >> conventional unit cells. If you want to calculate for the primitive >> cell, you can set 'PRIMITIVE_AXIS = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0'. >> >> Togo >> >> >> > >> > Best, >> > Tian >> > >> > On Sun, Mar 24, 2013 at 7:23 AM, Atsushi Togo <atz.togo@...> >> > wrote: >> >> >> >> Hi, >> >> >> >> > I have a further question about the phonon frequency. I used the VASP >> >> > relaxed structure, and got some negative frequencies. The magnitude >> >> > is >> >> > small >> >> > though~ 0.3THz. I would not worry if only 3 lowest bands at Gamma >> >> > point >> >> > behave so, which might be from the numerical accuracy I guess. >> >> >> >> I feel 0.3 THz is not very small. But it depends on your over all >> >> calculation. >> >> >> >> > Surprisingly, I found negative frequencies for some acoustic modes in >> >> > some >> >> > other q points, and somewhere even a little more negative than at >> >> > Gamma. >> >> > I >> >> > guess it might imply the structure is not so stable at 0 K, at least >> >> > in >> >> > the >> >> > harmonic approximation? >> >> >> >> It depends on the qpoint. If it is the commensurate point, it >> >> indicates definitely instability or numerical error (at harmonic >> >> approximation). >> >> >> >> > Nevertheless, since all optical modes are good, I >> >> > think it may not be a big problem. >> >> >> >> It's not related to optical modes, usually. >> >> >> >> > I only care about the quasiharmonic >> >> > thermal expansion, I am not sure whether such a small negative >> >> > frequencies >> >> > in acoustic bands would hurt the thermal expansion calculation much? >> >> >> >> Yes. Thermal properties at constant volume can not be calculated >> >> correctly. >> >> >> >> > If so, >> >> > can I slightly adjust the lattice parameters to make those modes >> >> > positive? >> >> >> >> I don't think so. >> >> >> >> > In all, my question is how much would this situation affect the >> >> > thermal >> >> > expansion calculation? Can I slightly fix it. >> >> >> >> I have no idea. >> >> >> >> Togo >> >> >> >> >> >> > >> >> > Thank you, >> >> > Tian >> >> > >> >> > On Sat, Mar 23, 2013 at 7:30 AM, Atsushi Togo <atz.togo@...> >> >> > wrote: >> >> >> >> >> >> I added the sentence in the manual. Thank you for your comment. >> >> >> http://phonopy.sourceforge.net/qha.html#phonopyqha >> >> >> >> >> >> Togo >> >> >> >> >> >> On Sat, Mar 23, 2013 at 11:28 PM, Atsushi Togo <atz.togo@...> >> >> >> wrote: >> >> >> > Hi, >> >> >> > >> >> >> > The quantities have to be normalized to the cell having the same >> >> >> > number of atoms. >> >> >> > >> >> >> > Togo >> >> >> > >> >> >> > On Sat, Mar 23, 2013 at 3:53 AM, Tian Lan <tianlan@...> >> >> >> > wrote: >> >> >> >> Dear all, >> >> >> >> >> >> >> >> I just started to use phonopy with VASP to calculate the thermal >> >> >> >> expansion. >> >> >> >> >> >> >> >> I think I will use the following commands and files to extract >> >> >> >> the >> >> >> >> thermal >> >> >> >> expansion. >> >> >> >> phonopyqha ev.dat thermal_properties{1..10}.yaml >> >> >> >> >> >> >> >> thermal_properties.yaml contains the phonon free energy, while >> >> >> >> ev.dat >> >> >> >> contains the electronic part. It is quite clear though, but my >> >> >> >> question >> >> >> >> is, >> >> >> >> I will use, say a 2 by 2 by 2 supercell to calculate phonons, >> >> >> >> then >> >> >> >> should >> >> >> >> ev.dat come from the calculation with the same supercell or it >> >> >> >> could >> >> >> >> be a >> >> >> >> primitive cell instead? I mean is the phonon free energy in >> >> >> >> thermal_properties normalized to some form? I have not tried it >> >> >> >> yet >> >> >> >> and >> >> >> >> unclear at this step, I want to make sure that E and F from the >> >> >> >> above >> >> >> >> two >> >> >> >> calculations associated with the same. >> >> >> >> >> >> >> >> Thank you for your help ! >> >> >> >> >> >> >> >> Best, >> >> >> >> Tian >> >> >> >> >> >> >> >>  >> >> >> >> Lan, Tian >> >> >> >> Ph.D. Candidate, Department of Applied Physics and Materials >> >> >> >> Science >> >> >> >> California Institute of Technology, >> >> >> >> Caltech M/C 13878, Pasadena, CA, 91125 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>  >> >> >> >> Everyone hates slow websites. So do we. >> >> >> >> Make your web apps faster with AppDynamics >> >> >> >> Download AppDynamics Lite for free today: >> >> >> >> http://p.sf.net/sfu/appdyn_d2d_mar >> >> >> >> _______________________________________________ >> >> >> >> Phonopyusers mailing list >> >> >> >> Phonopyusers@... >> >> >> >> https://lists.sourceforge.net/lists/listinfo/phonopyusers >> >> >> >> >> >> >> > >> >> >> > >> >> >> > >> >> >> >  >> >> >> > Atsushi Togo >> >> >> > http://atztogo.github.com/ >> >> >> > atz.togo@... >> >> >> >> >> >> >> >> >> >> >> >>  >> >> >> Atsushi Togo >> >> >> http://atztogo.github.com/ >> >> >> atz.togo@... >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>  >> >> >> Everyone hates slow websites. So do we. >> >> >> Make your web apps faster with AppDynamics >> >> >> Download AppDynamics Lite for free today: >> >> >> http://p.sf.net/sfu/appdyn_d2d_mar >> >> >> _______________________________________________ >> >> >> Phonopyusers mailing list >> >> >> Phonopyusers@... >> >> >> https://lists.sourceforge.net/lists/listinfo/phonopyusers >> >> > >> >> > >> >> > >> >> > >> >> >  >> >> > Lan, Tian >> >> > Ph.D. Candidate, Department of Applied Physics and Materials Science >> >> > California Institute of Technology, >> >> > Caltech M/C 13878, Pasadena, CA, 91125 >> >> >> >> >> >> >> >>  >> >> Atsushi Togo >> >> http://atztogo.github.com/ >> >> atz.togo@... >> > >> > >> > >> > >> >  >> > Lan, Tian >> > Ph.D. Candidate, Department of Applied Physics and Materials Science >> > California Institute of Technology, >> > Caltech M/C 13878, Pasadena, CA, 91125 >> >> >> >>  >> Atsushi Togo >> http://atztogo.github.com/ >> atz.togo@... > > > > >  > Lan, Tian > Ph.D. Candidate, Department of Applied Physics and Materials Science > California Institute of Technology, > Caltech M/C 13878, Pasadena, CA, 91125  Atsushi Togo http://atztogo.github.com/ atz.togo@... 
From: Atsushi Togo <atz.togo@gm...>  20130325 02:50:25

Hi, > Thank you! I will work more on it. > > I found some inconsistency in the QHA example. Maybe I misunderstood your > instruction 'The quantities have to be normalized to a cell having the same > number of atoms'. I am using a 1.1 version. > > When I looked at the QHA example for Al. The README said it was calcuated > with a 2 by 2 by 2 supercell. But in the ev.dat, the energies are for a > primitive cell. Also in each thermal_properties.yaml, 'natom' is said equal > to 4, which is the number of atoms for a primitive cell. So the > thermal_properties has normalize the atoms number to one primitive cell > already, I think. I run my own structure. I am using a supercell, the > thermalproperites still give a primitive cell instead, at least the natom > said so. > > So, my observation is thermal_properties always normalize the cell to a > primitive cell, even though you calculate phonons using a 2*2*2 or others. > If this is true, then ev.dat should correspond to a primitive one as well. The primitive cell of Al contains one atom. 4 is for the conventional unit cell (cubic one). Phonopy calculates properties for the input cell. However you can reduce it if the input cell contains further smaller translational period. In Al example case, POSCAR's are the conventional unit cells. If you want to calculate for the primitive cell, you can set 'PRIMITIVE_AXIS = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0'. Togo > > Best, > Tian > > On Sun, Mar 24, 2013 at 7:23 AM, Atsushi Togo <atz.togo@...> wrote: >> >> Hi, >> >> > I have a further question about the phonon frequency. I used the VASP >> > relaxed structure, and got some negative frequencies. The magnitude is >> > small >> > though~ 0.3THz. I would not worry if only 3 lowest bands at Gamma point >> > behave so, which might be from the numerical accuracy I guess. >> >> I feel 0.3 THz is not very small. But it depends on your over all >> calculation. >> >> > Surprisingly, I found negative frequencies for some acoustic modes in >> > some >> > other q points, and somewhere even a little more negative than at Gamma. >> > I >> > guess it might imply the structure is not so stable at 0 K, at least in >> > the >> > harmonic approximation? >> >> It depends on the qpoint. If it is the commensurate point, it >> indicates definitely instability or numerical error (at harmonic >> approximation). >> >> > Nevertheless, since all optical modes are good, I >> > think it may not be a big problem. >> >> It's not related to optical modes, usually. >> >> > I only care about the quasiharmonic >> > thermal expansion, I am not sure whether such a small negative >> > frequencies >> > in acoustic bands would hurt the thermal expansion calculation much? >> >> Yes. Thermal properties at constant volume can not be calculated >> correctly. >> >> > If so, >> > can I slightly adjust the lattice parameters to make those modes >> > positive? >> >> I don't think so. >> >> > In all, my question is how much would this situation affect the thermal >> > expansion calculation? Can I slightly fix it. >> >> I have no idea. >> >> Togo >> >> >> > >> > Thank you, >> > Tian >> > >> > On Sat, Mar 23, 2013 at 7:30 AM, Atsushi Togo <atz.togo@...> >> > wrote: >> >> >> >> I added the sentence in the manual. Thank you for your comment. >> >> http://phonopy.sourceforge.net/qha.html#phonopyqha >> >> >> >> Togo >> >> >> >> On Sat, Mar 23, 2013 at 11:28 PM, Atsushi Togo <atz.togo@...> >> >> wrote: >> >> > Hi, >> >> > >> >> > The quantities have to be normalized to the cell having the same >> >> > number of atoms. >> >> > >> >> > Togo >> >> > >> >> > On Sat, Mar 23, 2013 at 3:53 AM, Tian Lan <tianlan@...> >> >> > wrote: >> >> >> Dear all, >> >> >> >> >> >> I just started to use phonopy with VASP to calculate the thermal >> >> >> expansion. >> >> >> >> >> >> I think I will use the following commands and files to extract the >> >> >> thermal >> >> >> expansion. >> >> >> phonopyqha ev.dat thermal_properties{1..10}.yaml >> >> >> >> >> >> thermal_properties.yaml contains the phonon free energy, while >> >> >> ev.dat >> >> >> contains the electronic part. It is quite clear though, but my >> >> >> question >> >> >> is, >> >> >> I will use, say a 2 by 2 by 2 supercell to calculate phonons, then >> >> >> should >> >> >> ev.dat come from the calculation with the same supercell or it >> >> >> could >> >> >> be a >> >> >> primitive cell instead? I mean is the phonon free energy in >> >> >> thermal_properties normalized to some form? I have not tried it yet >> >> >> and >> >> >> unclear at this step, I want to make sure that E and F from the >> >> >> above >> >> >> two >> >> >> calculations associated with the same. >> >> >> >> >> >> Thank you for your help ! >> >> >> >> >> >> Best, >> >> >> Tian >> >> >> >> >> >>  >> >> >> Lan, Tian >> >> >> Ph.D. Candidate, Department of Applied Physics and Materials Science >> >> >> California Institute of Technology, >> >> >> Caltech M/C 13878, Pasadena, CA, 91125 >> >> >> >> >> >> >> >> >> >> >> >>  >> >> >> Everyone hates slow websites. So do we. >> >> >> Make your web apps faster with AppDynamics >> >> >> Download AppDynamics Lite for free today: >> >> >> http://p.sf.net/sfu/appdyn_d2d_mar >> >> >> _______________________________________________ >> >> >> Phonopyusers mailing list >> >> >> Phonopyusers@... >> >> >> https://lists.sourceforge.net/lists/listinfo/phonopyusers >> >> >> >> >> > >> >> > >> >> > >> >> >  >> >> > Atsushi Togo >> >> > http://atztogo.github.com/ >> >> > atz.togo@... >> >> >> >> >> >> >> >>  >> >> Atsushi Togo >> >> http://atztogo.github.com/ >> >> atz.togo@... >> >> >> >> >> >> >> >>  >> >> Everyone hates slow websites. So do we. >> >> Make your web apps faster with AppDynamics >> >> Download AppDynamics Lite for free today: >> >> http://p.sf.net/sfu/appdyn_d2d_mar >> >> _______________________________________________ >> >> Phonopyusers mailing list >> >> Phonopyusers@... >> >> https://lists.sourceforge.net/lists/listinfo/phonopyusers >> > >> > >> > >> > >> >  >> > Lan, Tian >> > Ph.D. Candidate, Department of Applied Physics and Materials Science >> > California Institute of Technology, >> > Caltech M/C 13878, Pasadena, CA, 91125 >> >> >> >>  >> Atsushi Togo >> http://atztogo.github.com/ >> atz.togo@... > > > > >  > Lan, Tian > Ph.D. Candidate, Department of Applied Physics and Materials Science > California Institute of Technology, > Caltech M/C 13878, Pasadena, CA, 91125  Atsushi Togo http://atztogo.github.com/ atz.togo@... 
From: Atsushi Togo <atz.togo@gm...>  20130324 14:23:26

Hi, > I have a further question about the phonon frequency. I used the VASP > relaxed structure, and got some negative frequencies. The magnitude is small > though~ 0.3THz. I would not worry if only 3 lowest bands at Gamma point > behave so, which might be from the numerical accuracy I guess. I feel 0.3 THz is not very small. But it depends on your over all calculation. > Surprisingly, I found negative frequencies for some acoustic modes in some > other q points, and somewhere even a little more negative than at Gamma. I > guess it might imply the structure is not so stable at 0 K, at least in the > harmonic approximation? It depends on the qpoint. If it is the commensurate point, it indicates definitely instability or numerical error (at harmonic approximation). > Nevertheless, since all optical modes are good, I > think it may not be a big problem. It's not related to optical modes, usually. > I only care about the quasiharmonic > thermal expansion, I am not sure whether such a small negative frequencies > in acoustic bands would hurt the thermal expansion calculation much? Yes. Thermal properties at constant volume can not be calculated correctly. > If so, > can I slightly adjust the lattice parameters to make those modes positive? I don't think so. > In all, my question is how much would this situation affect the thermal > expansion calculation? Can I slightly fix it. I have no idea. Togo > > Thank you, > Tian > > On Sat, Mar 23, 2013 at 7:30 AM, Atsushi Togo <atz.togo@...> wrote: >> >> I added the sentence in the manual. Thank you for your comment. >> http://phonopy.sourceforge.net/qha.html#phonopyqha >> >> Togo >> >> On Sat, Mar 23, 2013 at 11:28 PM, Atsushi Togo <atz.togo@...> wrote: >> > Hi, >> > >> > The quantities have to be normalized to the cell having the same >> > number of atoms. >> > >> > Togo >> > >> > On Sat, Mar 23, 2013 at 3:53 AM, Tian Lan <tianlan@...> wrote: >> >> Dear all, >> >> >> >> I just started to use phonopy with VASP to calculate the thermal >> >> expansion. >> >> >> >> I think I will use the following commands and files to extract the >> >> thermal >> >> expansion. >> >> phonopyqha ev.dat thermal_properties{1..10}.yaml >> >> >> >> thermal_properties.yaml contains the phonon free energy, while ev.dat >> >> contains the electronic part. It is quite clear though, but my question >> >> is, >> >> I will use, say a 2 by 2 by 2 supercell to calculate phonons, then >> >> should >> >> ev.dat come from the calculation with the same supercell or it could >> >> be a >> >> primitive cell instead? I mean is the phonon free energy in >> >> thermal_properties normalized to some form? I have not tried it yet and >> >> unclear at this step, I want to make sure that E and F from the above >> >> two >> >> calculations associated with the same. >> >> >> >> Thank you for your help ! >> >> >> >> Best, >> >> Tian >> >> >> >>  >> >> Lan, Tian >> >> Ph.D. Candidate, Department of Applied Physics and Materials Science >> >> California Institute of Technology, >> >> Caltech M/C 13878, Pasadena, CA, 91125 >> >> >> >> >> >>  >> >> Everyone hates slow websites. So do we. >> >> Make your web apps faster with AppDynamics >> >> Download AppDynamics Lite for free today: >> >> http://p.sf.net/sfu/appdyn_d2d_mar >> >> _______________________________________________ >> >> Phonopyusers mailing list >> >> Phonopyusers@... >> >> https://lists.sourceforge.net/lists/listinfo/phonopyusers >> >> >> > >> > >> > >> >  >> > Atsushi Togo >> > http://atztogo.github.com/ >> > atz.togo@... >> >> >> >>  >> Atsushi Togo >> http://atztogo.github.com/ >> atz.togo@... >> >> >>  >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_mar >> _______________________________________________ >> Phonopyusers mailing list >> Phonopyusers@... >> https://lists.sourceforge.net/lists/listinfo/phonopyusers > > > > >  > Lan, Tian > Ph.D. Candidate, Department of Applied Physics and Materials Science > California Institute of Technology, > Caltech M/C 13878, Pasadena, CA, 91125  Atsushi Togo http://atztogo.github.com/ atz.togo@... 
From: Tian Lan <tianlan@ca...>  20130324 00:09:34

Thank you, I think it becomes clear. I have a further question about the phonon frequency. I used the VASP relaxed structure, and got some negative frequencies. The magnitude is small though~ 0.3THz. I would not worry if only 3 lowest bands at Gamma point behave so, which might be from the numerical accuracy I guess. Surprisingly, I found negative frequencies for some acoustic modes in some other q points, and somewhere even a little more negative than at Gamma. I guess it might imply the structure is not so stable at 0 K, at least in the harmonic approximation? Nevertheless, since all optical modes are good, I think it may not be a big problem. I only care about the quasiharmonic thermal expansion, I am not sure whether such a small negative frequencies in acoustic bands would hurt the thermal expansion calculation much? If so, can I slightly adjust the lattice parameters to make those modes positive? In all, my question is how much would this situation affect the thermal expansion calculation? Can I slightly fix it. Thank you, Tian On Sat, Mar 23, 2013 at 7:30 AM, Atsushi Togo <atz.togo@...> wrote: > I added the sentence in the manual. Thank you for your comment. > http://phonopy.sourceforge.net/qha.html#phonopyqha > > Togo > > On Sat, Mar 23, 2013 at 11:28 PM, Atsushi Togo <atz.togo@...> wrote: > > Hi, > > > > The quantities have to be normalized to the cell having the same > > number of atoms. > > > > Togo > > > > On Sat, Mar 23, 2013 at 3:53 AM, Tian Lan <tianlan@...> wrote: > >> Dear all, > >> > >> I just started to use phonopy with VASP to calculate the thermal > expansion. > >> > >> I think I will use the following commands and files to extract the > thermal > >> expansion. > >> phonopyqha ev.dat thermal_properties{1..10}.yaml > >> > >> thermal_properties.yaml contains the phonon free energy, while ev.dat > >> contains the electronic part. It is quite clear though, but my question > is, > >> I will use, say a 2 by 2 by 2 supercell to calculate phonons, then > should > >> ev.dat come from the calculation with the same supercell or it could > be a > >> primitive cell instead? I mean is the phonon free energy in > >> thermal_properties normalized to some form? I have not tried it yet and > >> unclear at this step, I want to make sure that E and F from the above > two > >> calculations associated with the same. > >> > >> Thank you for your help ! > >> > >> Best, > >> Tian > >> > >>  > >> Lan, Tian > >> Ph.D. Candidate, Department of Applied Physics and Materials Science > >> California Institute of Technology, > >> Caltech M/C 13878, Pasadena, CA, 91125 > >> > >> >  > >> Everyone hates slow websites. So do we. > >> Make your web apps faster with AppDynamics > >> Download AppDynamics Lite for free today: > >> http://p.sf.net/sfu/appdyn_d2d_mar > >> _______________________________________________ > >> Phonopyusers mailing list > >> Phonopyusers@... > >> https://lists.sourceforge.net/lists/listinfo/phonopyusers > >> > > > > > > > >  > > Atsushi Togo > > http://atztogo.github.com/ > > atz.togo@... > > > >  > Atsushi Togo > http://atztogo.github.com/ > atz.togo@... > > >  > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_mar > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers >  Lan, Tian Ph.D. Candidate, Department of Applied Physics and Materials Science California Institute of Technology, Caltech M/C 13878, Pasadena, CA, 91125 
From: Atsushi Togo <atz.togo@gm...>  20130323 14:32:40

Now I updated the manual on entropy. Thank you. Togo On Wed, Mar 13, 2013 at 6:30 PM, Atsushi Togo <atz.togo@...> wrote: > Hi, > > Thank you. I will fix it! > > Togo > > On Tue, Mar 12, 2013 at 6:28 PM, Søren Smidstrup > <soren.smidstrup@...> wrote: >> Hey Phononpy users. >> >> On the page with the theory, I have spotted two errors in the last >> equation for the entropy. >> http://phonopy.sourceforge.net/theory.html >> >> The bold k should of course be a bold q instead, but more important >> there is a sign error on >> the second term. >> >> Best regards, >> Søren Smidstrup >> QuantumWise A/S >> >>  >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_mar >> _______________________________________________ >> Phonopyusers mailing list >> Phonopyusers@... >> https://lists.sourceforge.net/lists/listinfo/phonopyusers > > > >  > Atsushi Togo > http://atztogo.users.sourceforge.net/ > atz.togo@...  Atsushi Togo http://atztogo.github.com/ atz.togo@... 
From: Atsushi Togo <atz.togo@gm...>  20130323 14:30:39

I added the sentence in the manual. Thank you for your comment. http://phonopy.sourceforge.net/qha.html#phonopyqha Togo On Sat, Mar 23, 2013 at 11:28 PM, Atsushi Togo <atz.togo@...> wrote: > Hi, > > The quantities have to be normalized to the cell having the same > number of atoms. > > Togo > > On Sat, Mar 23, 2013 at 3:53 AM, Tian Lan <tianlan@...> wrote: >> Dear all, >> >> I just started to use phonopy with VASP to calculate the thermal expansion. >> >> I think I will use the following commands and files to extract the thermal >> expansion. >> phonopyqha ev.dat thermal_properties{1..10}.yaml >> >> thermal_properties.yaml contains the phonon free energy, while ev.dat >> contains the electronic part. It is quite clear though, but my question is, >> I will use, say a 2 by 2 by 2 supercell to calculate phonons, then should >> ev.dat come from the calculation with the same supercell or it could be a >> primitive cell instead? I mean is the phonon free energy in >> thermal_properties normalized to some form? I have not tried it yet and >> unclear at this step, I want to make sure that E and F from the above two >> calculations associated with the same. >> >> Thank you for your help ! >> >> Best, >> Tian >> >>  >> Lan, Tian >> Ph.D. Candidate, Department of Applied Physics and Materials Science >> California Institute of Technology, >> Caltech M/C 13878, Pasadena, CA, 91125 >> >>  >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_mar >> _______________________________________________ >> Phonopyusers mailing list >> Phonopyusers@... >> https://lists.sourceforge.net/lists/listinfo/phonopyusers >> > > > >  > Atsushi Togo > http://atztogo.github.com/ > atz.togo@...  Atsushi Togo http://atztogo.github.com/ atz.togo@... 
From: Atsushi Togo <atz.togo@gm...>  20130323 14:28:57

Hi, The quantities have to be normalized to the cell having the same number of atoms. Togo On Sat, Mar 23, 2013 at 3:53 AM, Tian Lan <tianlan@...> wrote: > Dear all, > > I just started to use phonopy with VASP to calculate the thermal expansion. > > I think I will use the following commands and files to extract the thermal > expansion. > phonopyqha ev.dat thermal_properties{1..10}.yaml > > thermal_properties.yaml contains the phonon free energy, while ev.dat > contains the electronic part. It is quite clear though, but my question is, > I will use, say a 2 by 2 by 2 supercell to calculate phonons, then should > ev.dat come from the calculation with the same supercell or it could be a > primitive cell instead? I mean is the phonon free energy in > thermal_properties normalized to some form? I have not tried it yet and > unclear at this step, I want to make sure that E and F from the above two > calculations associated with the same. > > Thank you for your help ! > > Best, > Tian > >  > Lan, Tian > Ph.D. Candidate, Department of Applied Physics and Materials Science > California Institute of Technology, > Caltech M/C 13878, Pasadena, CA, 91125 > >  > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_mar > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers >  Atsushi Togo http://atztogo.github.com/ atz.togo@... 
From: Tian Lan <tianlan@ca...>  20130322 18:53:41

Dear all, I just started to use phonopy with VASP to calculate the thermal expansion. I think I will use the following commands and files to extract the thermal expansion. phonopyqha ev.dat thermal_properties{1..10}.yaml thermal_properties.yaml contains the phonon free energy, while ev.dat contains the electronic part. It is quite clear though, but my question is, I will use, say a 2 by 2 by 2 supercell to calculate phonons, then should ev.dat come from the calculation with the same supercell or it could be a primitive cell instead? I mean is the phonon free energy in thermal_properties normalized to some form? I have not tried it yet and unclear at this step, I want to make sure that E and F from the above two calculations associated with the same. Thank you for your help ! Best, Tian  Lan, Tian Ph.D. Candidate, Department of Applied Physics and Materials Science California Institute of Technology, Caltech M/C 13878, Pasadena, CA, 91125 
From: Aldo Humberto Romero <aromero@qr...>  20130321 10:26:55

I do not think, this is a problem of phonopy, are you sure your electronic structure calculation is correct? the geometry is reproduced with reported results? atomic distances? which exchange correlation are you using?.. before jumping into phonon you have to test your pseudos and your exchange correlations... are the pseudos for W with d electrons? Regards aldo. > Hi all, > > Could anyone calculate the correct phonon dispersion for MoS2 or other > transition metal dichalcogenides using DFPT method in phonopy? I am > getting > three optical modes overlapping on the acoustic modes and a very huge gap > between optical and acoustic modes. LOTO splitting is also not solving > the > problem. I followed exactly the same procedure as in the tutorial. Tried > with more kpoints, bigger supercells, but no success. Can someone suggest > if I am missing something. > > > Thanks in advance. >  > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_mar_______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers >  Prof. Aldo Humberto Romero CINVESTAVUnidad Queretaro Libramiento Norponiente 2000 CP 76230, Queretaro, QRO, Mexico tel: 442 211 9909 fax: 442 211 9938 email: aromero@... aldorome@... www: qro.cinvestav.mx/~aromero 
From: S Bhatta <sb.quantum@gm...>  20130321 07:47:59

Hi all, Could anyone calculate the correct phonon dispersion for MoS2 or other transition metal dichalcogenides using DFPT method in phonopy? I am getting three optical modes overlapping on the acoustic modes and a very huge gap between optical and acoustic modes. LOTO splitting is also not solving the problem. I followed exactly the same procedure as in the tutorial. Tried with more kpoints, bigger supercells, but no success. Can someone suggest if I am missing something. Thanks in advance. 
From: <polivia@qr...>  20130321 03:57:07

Hi! I´m new with this. I tried to install phonopy in my new Mac and after running setup.py script I get this message: fatal error: 'omp.h' file not found #include <omp.h> Could you give me an idea for solving this? Thanks a lot. Patricia 
From: Atsushi Togo <atz.togo@gm...>  20130313 09:30:37

Hi, Thank you. I will fix it! Togo On Tue, Mar 12, 2013 at 6:28 PM, Søren Smidstrup <soren.smidstrup@...> wrote: > Hey Phononpy users. > > On the page with the theory, I have spotted two errors in the last > equation for the entropy. > http://phonopy.sourceforge.net/theory.html > > The bold k should of course be a bold q instead, but more important > there is a sign error on > the second term. > > Best regards, > Søren Smidstrup > QuantumWise A/S > >  > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_mar > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Søren Smidstrup <soren.smidstrup@qu...>  20130312 17:46:41

Hey Phononpy users. On the page with the theory, I have spotted two errors in the last equation for the entropy. http://phonopy.sourceforge.net/theory.html The bold k should of course be a bold q instead, but more important there is a sign error on the second term. Best regards, Søren Smidstrup QuantumWise A/S 
From: Atsushi Togo <atz.togo@gm...>  20130311 18:20:33

Hi, You can download the latest one here, http://sourceforge.net/projects/phonopy/files/phonopy/phonopy1.6/ Togo On Mon, Mar 11, 2013 at 3:21 PM, Xiaoqiu Ye <xy83@...> wrote: > I am not. I don't know the latest one. Do you go to class tonight? > > Xiaoqiu > ________________________________________ > From: Atsushi Togo [atz.togo@...] > Sent: Monday, March 11, 2013 4:36 AM > To: Xiaoqiu Ye > Cc: phonopyusersowner@... > Subject: Re: Forgotten the command to produce DOS with phonopy 0.9.1.4, who can help me? > > Hi, > > I have completely forgotten about older versions. Can't you use the latest one? > > Togo > > On Sun, Mar 10, 2013 at 12:19 AM, Xiaoqiu Ye <xy83@...> wrote: >> Hello , every one . >> I have forgotten the command to produce DOS with phonopy 0.9.1.4, who >> can help me? >> Or a manual of Phonopy 0.9.1.4 is needed. >> Thanks. >> Xiaoqiu > > > >  > Atsushi Togo > http://atztogo.users.sourceforge.net/ > atz.togo@... > >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Atsushi Togo <atz.togo@gm...>  20130305 11:19:37

Hi, Frequency unit has to be in THz, but not in angular frequency. http://phonopy.sourceforge.net/phonopymodule.html#thermalproperties Togo On Tue, Mar 5, 2013 at 6:47 PM, "Alejandro Rébola" <arebol2@...> wrote: > Dear users, > > I'm using the phonopy modules to obtain the frequencies and then I > calculate some thermal properties. The omega I use is omega=2pi*f, where f > is the frequency I get from phonopy (using default units and VASP). > However, I'm checking the source code for similar calculations, and I > don't see this frequency being multiplied by the factor 2pi. Does anybody > know where in the source code this factor is taken into account? > Thank you in advance, > > Alejandro > > >  > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Alejandro Rébola <arebol2@ui...>  20130305 09:47:39

Dear users, I'm using the phonopy modules to obtain the frequencies and then I calculate some thermal properties. The omega I use is omega=2pi*f, where f is the frequency I get from phonopy (using default units and VASP). However, I'm checking the source code for similar calculations, and I don't see this frequency being multiplied by the factor 2pi. Does anybody know where in the source code this factor is taken into account? Thank you in advance, Alejandro 
From: Atsushi Togo <atz.togo@gm...>  20130305 01:28:25

Hi, It is difficult to help without enough information. At least, you need to show the lattice vectors of your unit cell in Cartesian coordinates and also those of the primitive cell. Togo On Tue, Mar 5, 2013 at 12:59 AM, Sebastian Christensen <sebastian@...> wrote: > The space group you mention has no centering. So I would assume your primitive cell is the same as the one defined in your POSCAR file. So you should set PRIMITIVE_AXIS = [1 0 0 0 1 0 0 0 1] > > Sebastian > > Original Message > From: bdsahoo@... [mailto:bdsahoo@...] > Sent: 4. marts 2013 14:47 > To: Phonopyusers@... > Subject: [Phonopyusers] (no subject) > > yes i am getting p63/mmm space group also there is no problem in the convergence .the problem is that how can i get 9 branches inthis p63/mmm(hexagonal omega phase) . what should be my primitive axis for my structure > > >  > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers > >  > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Sebastian Christensen <sebastian@ch...>  20130304 16:18:42

The space group you mention has no centering. So I would assume your primitive cell is the same as the one defined in your POSCAR file. So you should set PRIMITIVE_AXIS = [1 0 0 0 1 0 0 0 1] Sebastian Original Message From: bdsahoo@... [mailto:bdsahoo@...] Sent: 4. marts 2013 14:47 To: Phonopyusers@... Subject: [Phonopyusers] (no subject) yes i am getting p63/mmm space group also there is no problem in the convergence .the problem is that how can i get 9 branches inthis p63/mmm(hexagonal omega phase) . what should be my primitive axis for my structure  Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb _______________________________________________ Phonopyusers mailing list Phonopyusers@... https://lists.sourceforge.net/lists/listinfo/phonopyusers 
From: Cinves <aromero@qr...>  20130304 13:51:50

How many atoms per unit cell? Are the 27 branches very different of what you expect? Sent from my iPhone On Mar 4, 2013, at 8:46 AM, bdsahoo@... wrote: > yes i am getting p63/mmm space group also there is no problem in the > convergence .the problem is that how can i get 9 branches inthis > p63/mmm(hexagonal omega phase) . what should be my primitive axis for my > structure > > >  > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers 
From: <bdsahoo@ba...>  20130304 13:47:10

yes i am getting p63/mmm space group also there is no problem in the convergence .the problem is that how can i get 9 branches inthis p63/mmm(hexagonal omega phase) . what should be my primitive axis for my structure 