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From: Xiaoliang Zhang <zhangxiaoliang@ie...>  20100724 02:36:43

OK, thanks > Hi, > > Lattice vectors in reciprocal space are calculated from lattice > vectors in real space in usual manner. Qvector in phonopy input and > output is represented in fractional value, where the periodic unit > corresponds to 1. The following is a small code that I used for this > test. > > import numpy as np > > a = np.array( [[ 0.5, 0.5, 0.0 ], > [ 0.0, 0.5, 0.5 ], > [ 0.5, 0.0, 0.5 ]] ) > > b = np.linalg.inv( a ).T > > print a > print b > > print 0.5 * ( b[1] + b[2] ) > > > b is calculated same as you, where the definition is without 2pi. Then > Si[001] is, if I understand correctly, the direction has to be along a > Cartesian axis in reciprocal space, because Si[001] is defined for > conventional unit cell, but not for primitive cell (am I correct?). > Therefore, the vector in reciprocal space has to be also along a > Cartesian axis. I think that this is not a specific definition of > phonopy. > > Cheers, > > Togo > > > 2010/7/23 Xiaoliang Zhang <zhangxiaoliang@...>: > > Hi, Togo, > > Could you please help me with the definition of qvector? thanks, I just > > don't understand. > > > > For Si diamond crystal structure, I want to get the phonon dispersion of > > Si[001] direction. > > Before, I tried to use > > QI = 0.0 0.0 0.0 > > QF = 0.0 0.0 1.0 > > You said that it's wrong, and the qpoints should be like this: > > QI = 0.0 0.0 0.0 > > QF = 0.0 0.5 0.5 > > > > I just don't exactly understand what you said above. > > > > I know that for diamond crystal, the primitive lattice vector is(as in > > POSCAR): > > a1 = 0.5 0.5 0.0 > > a2 = 0.0 0.5 0.5 > > a3 = 0.5 0.0 0.5 > > so the reciprocal lattice vector should be > > b1 = 1.0 1.0 1.0 > > b2 = 1.0 1.0 1.0 > > b3 = 1.0 1.0 1.0 > > Am I right? > > > > Then why QF should be [0.0 0.5 0.5] for Si[001] direction? Thanks. > > > > > > > > > > > >  > > This SF.net email is sponsored by Sprint > > What will you do first with EVO, the first 4G phone? > > Visit sprint.com/first  http://p.sf.net/sfu/sprintcomfirst > > _______________________________________________ > > Phonopyusers mailing list > > Phonopyusers@... > > https://lists.sourceforge.net/lists/listinfo/phonopyusers > > > > > > > >  > Atsushi Togo > http://atztogo.users.sourceforge.net/ > atz.togo@... > 
From: Atz Togo <atz.togo@gm...>  20100724 01:55:29

Hi, Lattice vectors in reciprocal space are calculated from lattice vectors in real space in usual manner. Qvector in phonopy input and output is represented in fractional value, where the periodic unit corresponds to 1. The following is a small code that I used for this test. import numpy as np a = np.array( [[ 0.5, 0.5, 0.0 ], [ 0.0, 0.5, 0.5 ], [ 0.5, 0.0, 0.5 ]] ) b = np.linalg.inv( a ).T print a print b print 0.5 * ( b[1] + b[2] ) b is calculated same as you, where the definition is without 2pi. Then Si[001] is, if I understand correctly, the direction has to be along a Cartesian axis in reciprocal space, because Si[001] is defined for conventional unit cell, but not for primitive cell (am I correct?). Therefore, the vector in reciprocal space has to be also along a Cartesian axis. I think that this is not a specific definition of phonopy. Cheers, Togo 2010/7/23 Xiaoliang Zhang <zhangxiaoliang@...>: > Hi, Togo, > Could you please help me with the definition of qvector? thanks, I just > don't understand. > > For Si diamond crystal structure, I want to get the phonon dispersion of > Si[001] direction. > Before, I tried to use > QI = 0.0 0.0 0.0 > QF = 0.0 0.0 1.0 > You said that it's wrong, and the qpoints should be like this: > QI = 0.0 0.0 0.0 > QF = 0.0 0.5 0.5 > > I just don't exactly understand what you said above. > > I know that for diamond crystal, the primitive lattice vector is(as in > POSCAR): > a1 = 0.5 0.5 0.0 > a2 = 0.0 0.5 0.5 > a3 = 0.5 0.0 0.5 > so the reciprocal lattice vector should be > b1 = 1.0 1.0 1.0 > b2 = 1.0 1.0 1.0 > b3 = 1.0 1.0 1.0 > Am I right? > > Then why QF should be [0.0 0.5 0.5] for Si[001] direction? Thanks. > > > > > >  > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first  http://p.sf.net/sfu/sprintcomfirst > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers > >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Atz Togo <atz.togo@gm...>  20100724 01:52:01

Hi, Lattice vectors in reciprocal space are calculated from lattice vectors in real space in usual manner. Qvector in phonopy input and output is represented in fractional value, where the periodic unit corresponds to 1. The following is a small code that I used for this test. import numpy as np a = np.array( [[ 0.5, 0.5, 0.0 ], [ 0.0, 0.5, 0.5 ], [ 0.5, 0.0, 0.5 ]] ) b = np.linalg.inv( a ).T print a print b print 0.5 * ( b[1] + b[2] ) b is calculated same as you, where the definition is without 2pi. Then Si[001] is, if I understand correctly, the direction has to be along a Cartesian axis in reciprocal space, because Si[001] is defined for conventional unit cell, but not for primitive cell (am I correct?). Therefore, the vector in reciprocal space has to be also along a Cartesian axis. I think that this is not a specific definition of phonopy. Cheers, Togo 2010/7/23 Xiaoliang Zhang <zhangxiaoliang@...>: > Hi, Togo, > Could you please help me with the definition of qvector? thanks, I just > don't understand. > > For Si diamond crystal structure, I want to get the phonon dispersion of > Si[001] direction. > Before, I tried to use > QI = 0.0 0.0 0.0 > QF = 0.0 0.0 1.0 > You said that it's wrong, and the qpoints should be like this: > QI = 0.0 0.0 0.0 > QF = 0.0 0.5 0.5 > > I just don't exactly understand what you said above. > > I know that for diamond crystal, the primitive lattice vector is(as in > POSCAR): > a1 = 0.5 0.5 0.0 > a2 = 0.0 0.5 0.5 > a3 = 0.5 0.0 0.5 > so the reciprocal lattice vector should be > b1 = 1.0 1.0 1.0 > b2 = 1.0 1.0 1.0 > b3 = 1.0 1.0 1.0 > Am I right? > > Then why QF should be [0.0 0.5 0.5] for Si[001] direction? Thanks. > > > > > >  > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first  http://p.sf.net/sfu/sprintcomfirst > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers > >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Xiaoliang Zhang <zhangxiaoliang@ie...>  20100723 14:36:06

Hi, Togo, Could you please help me with the definition of qvector? thanks, I just don't understand. For Si diamond crystal structure, I want to get the phonon dispersion of Si[001] direction. Before, I tried to use QI = 0.0 0.0 0.0 QF = 0.0 0.0 1.0 You said that it's wrong, and the qpoints should be like this: QI = 0.0 0.0 0.0 QF = 0.0 0.5 0.5 I just don't exactly understand what you said above. I know that for diamond crystal, the primitive lattice vector is(as in POSCAR): a1 = 0.5 0.5 0.0 a2 = 0.0 0.5 0.5 a3 = 0.5 0.0 0.5 so the reciprocal lattice vector should be b1 = 1.0 1.0 1.0 b2 = 1.0 1.0 1.0 b3 = 1.0 1.0 1.0 Am I right? Then why QF should be [0.0 0.5 0.5] for Si[001] direction? Thanks. 
From: Atz Togo <atz.togo@gm...>  20100722 14:54:02

Hi, Frequencies are written in mesh.yaml. Even if some information is written, if the user can not find it, it means nothing. Currently, the document is written only by me. It is extremely difficult to improve it without other's advice. This project of a harmonic phonon code, which is scientifically nothing new, is a kind of my hobby (nobody pays money for it), and I have not strong motivation (or say no strong pressure from outside) to continue it. So user's or developer's contribution really encourages me :) Togo On Thu, Jul 22, 2010 at 9:52 PM, Ujjal Das <ujjal@...> wrote: > > Thank you for the reply. > > Yes, it is related to phonopy operation. > > I have all the required files (INPHON, FORCES, POSCAR, DISP). I can > compute the > thermal properties using "phonopy t" command. But I don't know how to extract > phonon frequencies. What command should I use or how the INPHON file should > look like. > > If you mean that it is already in the manual, I should look at it more > carefully. > > Ujjal > > > > Quoting Atz Togo <atz.togo@...>: > >> Hi, >> >> I don't understand your question. Physics question, computational >> question, or just a question of operation of phonopy? If it is the >> last one, it means that the manual is written so badly, and I need >> your advise to improve it! >> >> Cheers! >> >> Togo >> >> On Thu, Jul 22, 2010 at 1:05 PM, Ujjal Das <ujjal@...> wrote: >>> >>> Dear phonopyusers, >>> >>> How to extract frequencies once the forces (of the supercells) are >>> calculated >>> using VASP? What should be the command options? >>> >>> Thank you, >>> >>> Ujjal >>> >>> >>>  >>> Ujjal Das, Ph.D. >>> Chemical Engineering, MIT >>> 66264, Phone: 8123227402 >>> >>> >>> >>>  >>> This SF.net email is sponsored by Sprint >>> What will you do first with EVO, the first 4G phone? >>> Visit sprint.com/first  http://p.sf.net/sfu/sprintcomfirst >>> _______________________________________________ >>> Phonopyusers mailing list >>> Phonopyusers@... >>> https://lists.sourceforge.net/lists/listinfo/phonopyusers >>> >> >> >> >>  >> Atsushi Togo >> http://atztogo.users.sourceforge.net/ >> atz.togo@... >> >>  >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first  http://p.sf.net/sfu/sprintcomfirst >> _______________________________________________ >> Phonopyusers mailing list >> Phonopyusers@... >> https://lists.sourceforge.net/lists/listinfo/phonopyusers >> > > > >  > Ujjal Das, Ph.D. > Chemical Engineering, MIT > 66264, Phone: 8123227402 > > > > > > >  > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first  http://p.sf.net/sfu/sprintcomfirst > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Ujjal Das <ujjal@MIT.EDU>  20100722 12:53:05

Thank you for the reply. Yes, it is related to phonopy operation. I have all the required files (INPHON, FORCES, POSCAR, DISP). I can compute the thermal properties using "phonopy t" command. But I don't know how to extract phonon frequencies. What command should I use or how the INPHON file should look like. If you mean that it is already in the manual, I should look at it more carefully. Ujjal Quoting Atz Togo <atz.togo@...>: > Hi, > > I don't understand your question. Physics question, computational > question, or just a question of operation of phonopy? If it is the > last one, it means that the manual is written so badly, and I need > your advise to improve it! > > Cheers! > > Togo > > On Thu, Jul 22, 2010 at 1:05 PM, Ujjal Das <ujjal@...> wrote: >> >> Dear phonopyusers, >> >> How to extract frequencies once the forces (of the supercells) are >> calculated >> using VASP? What should be the command options? >> >> Thank you, >> >> Ujjal >> >> >>  >> Ujjal Das, Ph.D. >> Chemical Engineering, MIT >> 66264, Phone: 8123227402 >> >> >> >>  >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first  http://p.sf.net/sfu/sprintcomfirst >> _______________________________________________ >> Phonopyusers mailing list >> Phonopyusers@... >> https://lists.sourceforge.net/lists/listinfo/phonopyusers >> > > > >  > Atsushi Togo > http://atztogo.users.sourceforge.net/ > atz.togo@... > >  > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first  http://p.sf.net/sfu/sprintcomfirst > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers >  Ujjal Das, Ph.D. Chemical Engineering, MIT 66264, Phone: 8123227402 
From: Atz Togo <atz.togo@gm...>  20100722 06:30:05

Hi, I don't understand your question. Physics question, computational question, or just a question of operation of phonopy? If it is the last one, it means that the manual is written so badly, and I need your advise to improve it! Cheers! Togo On Thu, Jul 22, 2010 at 1:05 PM, Ujjal Das <ujjal@...> wrote: > > Dear phonopyusers, > > How to extract frequencies once the forces (of the supercells) are calculated > using VASP? What should be the command options? > > Thank you, > > Ujjal > > >  > Ujjal Das, Ph.D. > Chemical Engineering, MIT > 66264, Phone: 8123227402 > > > >  > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first  http://p.sf.net/sfu/sprintcomfirst > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Ujjal Das <ujjal@MIT.EDU>  20100722 04:05:32

Dear phonopyusers, How to extract frequencies once the forces (of the supercells) are calculated using VASP? What should be the command options? Thank you, Ujjal  Ujjal Das, Ph.D. Chemical Engineering, MIT 66264, Phone: 8123227402 
From: Masato YOSHIYA <yoshiya@am...>  20100715 16:15:03

Dear Evgeny, I guess I understand what kind of answer you wish to hear: I used to do so. But I'm afraid there is no general answer to your question. Somebody else might answer to your question based on his/her experiences, but it is different from material to material. First of all, abinitio calculation has finite numerical and physical accuracy whichever code or method you use as long as you conduct the calculation within practical time. In addition, physical constraints you impose to your model, such as, assumptions, cell size, or criteria of convergencies, for example, add up physical errors. These factors put your obtained value away from ideal value achievable by computation. It should be noted that the ideal value is not necessarily equial to experimental value which might contain error. As a rule of thumb, computational value will tell you how accurate experimental value would be. At the same time, experimental value will tell you how accurate computational value would be. Thus, my best advise to you is, to put both computational and experimental values on your sides, and to try to improve each. As for computational side, there are a number of ways to improve numerical and physical accuracy, about which you may be asked in this mailing list, I suppose. Good luck! Masato (2010/07/16 0:48), Evgeny Blokhin wrote: > Good day! Please could You comment on the precision of the heat > capacities and Helmholtz free energies calculated with Phonopy? How > many digits after dot do you usually consider? > Thanks, > Evgeny > >  > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first  http://p.sf.net/sfu/sprintcomfirst > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers 
From: Evgeny Blokhin <jam31@ja...>  20100715 15:48:18

Good day! Please could You comment on the precision of the heat capacities and Helmholtz free energies calculated with Phonopy? How many digits after dot do you usually consider? Thanks, Evgeny 
From: Atz Togo <atz.togo@gm...>  20100715 03:38:32

Hi, You have to specify the tag EIGENVECTORS. EIGENVECTORS = .TRUE. The document of phonopy is not clear enough.... Togo On Thu, Jul 15, 2010 at 11:29 AM, Atz Togo <atz.togo@...> wrote: > Hi, > > I hope that it's not a bug of the code. Could you show your INPHON and POSCAR? > > Togo > > On Thu, Jul 15, 2010 at 7:42 AM, jiajun liu <onephyman@...> wrote: >> Dear Prof. Togo >> >> I have tried several attempts in order to get the >> partial density of states of the phonons (use PDOS tags) without any >> successes. The phonopy (phonopy0.9.1) which I used can only give me the >> total density of states, but not the partial density of states. >> >> >> I look into the scripts and bin directory and I found that actually the >> partial DOS and total DOS functions are actually the same! Is it a >> bug/error in the code? Can you please look into it? >> >> Thank you very much for your times & helps. >> >> regards >> KC >> >> >> > > > >  > Atsushi Togo > http://atztogo.users.sourceforge.net/ > atz.togo@... >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Atz Togo <atz.togo@gm...>  20100715 02:29:52

Hi, I hope that it's not a bug of the code. Could you show your INPHON and POSCAR? Togo On Thu, Jul 15, 2010 at 7:42 AM, jiajun liu <onephyman@...> wrote: > Dear Prof. Togo > > I have tried several attempts in order to get the > partial density of states of the phonons (use PDOS tags) without any > successes. The phonopy (phonopy0.9.1) which I used can only give me the > total density of states, but not the partial density of states. > > > I look into the scripts and bin directory and I found that actually the > partial DOS and total DOS functions are actually the same! Is it a > bug/error in the code? Can you please look into it? > > Thank you very much for your times & helps. > > regards > KC > > >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: jiajun liu <onephyman@gm...>  20100714 22:43:00

Dear Prof. Togo I have tried several attempts in order to get the partial density of states of the phonons (use PDOS tags) without any successes. The phonopy (phonopy0.9.1) which I used can only give me the total density of states, but not the partial density of states. I look into the scripts and bin directory and I found that actually the partial DOS and total DOS functions are actually the same! Is it a bug/error in the code? Can you please look into it? Thank you very much for your times & helps. regards KC 