Screenshot instructions:
Windows
Mac
Red Hat Linux
Ubuntu
Click URL instructions:
Rightclick on ad, choose "Copy Link", then paste here →
(This may not be possible with some types of ads)
From: Tian Lan <tianlan@ca...>  20130322 18:53:41
Attachments:
Message as HTML

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: 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: 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: Tian Lan <tianlan@ca...>  20130324 00:09:34
Attachments:
Message as HTML

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...>  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: 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...>  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@... 
Sign up for the SourceForge newsletter:
No, thanks