[QE-users] Negative pressure convention
Hello everyone, I am trying to run some MD with pw.x, and I am modifying the lattice parameter of my cell until I reach 60 kBar. However, I was noticing that it printed some negative pressures. I was wondering if the convention is that negative pressure indicates expansion, or what would be the case? Thank you in advance, Valeria ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Atomic velocities units
Hello, Thanks Kazume and Lorenzo for your time. I think having them printed would be great for users, in the meantime I will calculate them with what you gave me. And Kazume, I took a look to the module you mentioned (thanks for that, it was really useful) and I could see that the starting velocities therefore follow a Maxwell-Boltzmann distribution. That means that the system is already thermalized? I know this is not a technical question, but I was wondering so since when I run a MD simulation in pw.x in the past without inputting velocities, the variation in temperature was high at the beginning of the simulation. Thanks, Valeria From: Kazume NISHIDATE<mailto:nisid...@iwate-u.ac.jp> Sent: Monday, August 9, 2021 7:02 PM To: Quantum ESPRESSO users Forum<mailto:users@lists.quantum-espresso.org> Subject: Re: [QE-users] Atomic velocities units Hello Valeria: As the manual says that the 'dt’ is "time step for molecular dynamics, in Rydberg atomic units (1 a.u.=4.8378 * 10^-17 s : beware, the CP code uses Hartree atomic units, half that much!!!)” https://www.quantum-espresso.org/Doc/INPUT_PW.html If you did not supply the initial velocities, the initial velocities at the specified temperature are given by (dynamics_module.f90): ! ... N.B. velocities must in a.u. units of alat and are zero ! ... for fixed ions ! vel(:,na) = DBLE( if_pos(:,na) ) * & gauss_dist( 0.D0, sigma, 3 ) / alat So the unit is a.u. divided by 'alat'. And the kinetic energy 'ekin' is calculated by (dynamics_module.f90): ekin = ekin + 0.5D0 * mass(na) * & ( vel(1,na)**2 + vel(2,na)**2 + vel(3,na)**2 ) then it is rescaled as ekin = ekin*alat**2 to recover the atomic unit in the above vel**2 operation. > Another question; is there a way to grep or look for the velocities > in some kind of output file from a pw.x run? Possible. We can extract the atomic positions at each MD time steps from the output file. The velocities can be directly calculated by (r(t2)-r(t1))/dt. But I think QE may save the velocities at the final MD step in the working dir to make it possible the restart run. To check this you can calculate some short time MD run and investigate the directory if there is the final velocity data. > 2021/08/10 8:43、valeria arteaga muñiz のメール: > > Hello Lorenzo, > > Thank you again. I don’t know how could I fix that bug since the version of > QE I am currently using is installed on a supercomputer, and I don’t think I > have access to the main directories. > Another question; is there a way to grep or look for the velocities in some > kind of output file from a pw.x run? > best regards kazume NISHIDATE 敬具 西館数芽 nisid...@iwate-u.ac.jp kazume.nishid...@gmail.com ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu<http://www.max-centre.eu>) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Atomic velocities units
Hello Lorenzo, Thank you again. I don’t know how could I fix that bug since the version of QE I am currently using is installed on a supercomputer, and I don’t think I have access to the main directories. Another question; is there a way to grep or look for the velocities in some kind of output file from a pw.x run? Thanks, Valeria From: Lorenzo Paulatto<mailto:paul...@gmail.com> Sent: Tuesday, August 3, 2021 3:17 PM To: Quantum ESPRESSO users Forum<mailto:users@lists.quantum-espresso.org> Subject: Re: [QE-users] Atomic velocities units It is a trivial fix, but I'm away from my pc for a couple of weeks. It is fixed in my gitlab fork https://gitlab.com/paulatz/q-e/-/commit/2c1e1d3d8b5c47639ba1af3842d187d5903115c5 -- Lorenzo Paulatto On Mon, Aug 2, 2021, 17:18 valeria arteaga muñiz mailto:valitze...@hotmail.com>> wrote: Thank you both for your replies. Okay, I will take that into consideration. Actually I wanted to use the atomic velocities together with the svr thermostat, do you suggest any other method since that one doesn't work well with the atomic velocities? Best, Valeria Valeria From: users mailto:users-boun...@lists.quantum-espresso.org>> on behalf of Paolo Giannozzi mailto:p.gianno...@gmail.com>> Sent: Monday, August 2, 2021 8:47:07 AM To: Quantum ESPRESSO users Forum mailto:users@lists.quantum-espresso.org>> Subject: Re: [QE-users] Atomic velocities units From a quick look at the code, it seems to me that the documentation is correct for both pw.x and cp.x. For cp.x, the velocities are given with the same logic as for the atomic positions (in A, Bohr, units of lattice parameter, crystal units) divided by time in hartree a.u. (2.4189*10^-17 s) ; for pw.x, the velocities are always given in Bohr divided by Rydberg a.u. for time (4.8378*10^-17 s). I am rather puzzled by the cp.x logic, but this is how it works right now Paolo On Fri, Jul 30, 2021 at 3:07 PM Lorenzo Paulatto mailto:paul...@gmail.com>> wrote: I'm not sure, actually the time conversion I gave you is for pw.x, as cp.x use Hartree units instead of Rydberg for the energy there is a possible factor 2 difference (the base to find out this conversion is keep in mind that [ħ]=J·s=1 in atomic units. The input manual says that pw.x velocities are just "atomic units", no conversion is done in the code as far as I could see. Also keep in mind that ATOMIC_VELOCITIES is a seldom used feature, and may have bugs (i.e. I recently found out that it does not work with svr thermostat because of a little bug) hth -- Lorenzo Paulatto - Paris On Jul 29 2021, at 8:17 pm, valeria arteaga muñiz mailto:valitze...@hotmail.com>> wrote: Hello Lorenzo, Thanks for your reply. This is also for the pw.x code, right? Best, Valeria From: Lorenzo Paulatto<https://link.getmailspring.com/link/17a87165-f0ab-4c7c-9c86-aee213369...@getmailspring.com/0?redirect=mailto%3Apaulatz%40gmail.com&recipient=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D> Sent: Thursday, July 29, 2021 11:18 AM To: Quantum ESPRESSO users Forum<https://link.getmailspring.com/link/17a87165-f0ab-4c7c-9c86-aee213369...@getmailspring.com/1?redirect=mailto%3Ausers%40lists.quantum-espresso.org&recipient=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D> Cc: users@lists.quantum-espresso.org<https://link.getmailspring.com/link/17a87165-f0ab-4c7c-9c86-aee213369...@getmailspring.com/2?redirect=mailto%3Ausers%40lists.quantum-espresso.org&recipient=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D> Subject: Re: [QE-users] Atomic velocities units It depends on which units you have specified for atomic positions. Regarding time, 1 a.u.=4.8378 * 10^-17 s kind regards -- Lorenzo Paulatto - Paris On Jul 29 2021, at 5:20 am, valeria arteaga muñiz mailto:valitze...@hotmail.com>> wrote: Hello everyone. I am trying to perform a MD run using the pw.x code. I'd like to use the atomic positions and also velocities from another run in Angstroms and Å/picoseconds to the QE input, but I am not sure about the units I need to use. In the documentation, there says it should be atomic units, and when I read the co.c documentation it was the same, but in the description they mentioned we needed to use the units as they're in the atomic positions card and time in a.u. does anyone have an idea of what convertion should I use? Thanks for your time ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu<http://www.max-centre.eu>) users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu<http://www.max-centre.eu>) users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum
Re: [QE-users] Atomic velocities units
Thank you both for your replies. Okay, I will take that into consideration. Actually I wanted to use the atomic velocities together with the svr thermostat, do you suggest any other method since that one doesn't work well with the atomic velocities? Best, Valeria Valeria From: users on behalf of Paolo Giannozzi Sent: Monday, August 2, 2021 8:47:07 AM To: Quantum ESPRESSO users Forum Subject: Re: [QE-users] Atomic velocities units From a quick look at the code, it seems to me that the documentation is correct for both pw.x and cp.x. For cp.x, the velocities are given with the same logic as for the atomic positions (in A, Bohr, units of lattice parameter, crystal units) divided by time in hartree a.u. (2.4189*10^-17 s) ; for pw.x, the velocities are always given in Bohr divided by Rydberg a.u. for time (4.8378*10^-17 s). I am rather puzzled by the cp.x logic, but this is how it works right now Paolo On Fri, Jul 30, 2021 at 3:07 PM Lorenzo Paulatto mailto:paul...@gmail.com>> wrote: I'm not sure, actually the time conversion I gave you is for pw.x, as cp.x use Hartree units instead of Rydberg for the energy there is a possible factor 2 difference (the base to find out this conversion is keep in mind that [ħ]=J·s=1 in atomic units. The input manual says that pw.x velocities are just "atomic units", no conversion is done in the code as far as I could see. Also keep in mind that ATOMIC_VELOCITIES is a seldom used feature, and may have bugs (i.e. I recently found out that it does not work with svr thermostat because of a little bug) hth -- Lorenzo Paulatto - Paris On Jul 29 2021, at 8:17 pm, valeria arteaga muñiz mailto:valitze...@hotmail.com>> wrote: Hello Lorenzo, Thanks for your reply. This is also for the pw.x code, right? Best, Valeria From: Lorenzo Paulatto<https://link.getmailspring.com/link/17a87165-f0ab-4c7c-9c86-aee213369...@getmailspring.com/0?redirect=mailto%3Apaulatz%40gmail.com&recipient=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D> Sent: Thursday, July 29, 2021 11:18 AM To: Quantum ESPRESSO users Forum<https://link.getmailspring.com/link/17a87165-f0ab-4c7c-9c86-aee213369...@getmailspring.com/1?redirect=mailto%3Ausers%40lists.quantum-espresso.org&recipient=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D> Cc: users@lists.quantum-espresso.org<https://link.getmailspring.com/link/17a87165-f0ab-4c7c-9c86-aee213369...@getmailspring.com/2?redirect=mailto%3Ausers%40lists.quantum-espresso.org&recipient=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D> Subject: Re: [QE-users] Atomic velocities units It depends on which units you have specified for atomic positions. Regarding time, 1 a.u.=4.8378 * 10^-17 s kind regards -- Lorenzo Paulatto - Paris On Jul 29 2021, at 5:20 am, valeria arteaga muñiz mailto:valitze...@hotmail.com>> wrote: Hello everyone. I am trying to perform a MD run using the pw.x code. I'd like to use the atomic positions and also velocities from another run in Angstroms and Å/picoseconds to the QE input, but I am not sure about the units I need to use. In the documentation, there says it should be atomic units, and when I read the co.c documentation it was the same, but in the description they mentioned we needed to use the units as they're in the atomic positions card and time in a.u. does anyone have an idea of what convertion should I use? Thanks for your time ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu<http://www.max-centre.eu>) users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu<http://www.max-centre.eu>) users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu<http://www.max-centre.eu>) users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 206, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Atomic velocities units
Hello Lorenzo, Thanks for your reply. This is also for the pw.x code, right? Best, Valeria From: Lorenzo Paulatto<mailto:paul...@gmail.com> Sent: Thursday, July 29, 2021 11:18 AM To: Quantum ESPRESSO users Forum<mailto:users@lists.quantum-espresso.org> Cc: users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> Subject: Re: [QE-users] Atomic velocities units It depends on which units you have specified for atomic positions. Regarding time, 1 a.u.=4.8378 * 10^-17 s kind regards -- Lorenzo Paulatto - Paris On Jul 29 2021, at 5:20 am, valeria arteaga muñiz wrote: Hello everyone. I am trying to perform a MD run using the pw.x code. I'd like to use the atomic positions and also velocities from another run in Angstroms and Å/picoseconds to the QE input, but I am not sure about the units I need to use. In the documentation, there says it should be atomic units, and when I read the co.c documentation it was the same, but in the description they mentioned we needed to use the units as they're in the atomic positions card and time in a.u. does anyone have an idea of what convertion should I use? Thanks for your time ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Atomic velocities units
Hello everyone. I am trying to perform a MD run using the pw.x code. I'd like to use the atomic positions and also velocities from another run in Angstroms and Å/picoseconds to the QE input, but I am not sure about the units I need to use. In the documentation, there says it should be atomic units, and when I read the co.c documentation it was the same, but in the description they mentioned we needed to use the units as they're in the atomic positions card and time in a.u. does anyone have an idea of what convertion should I use? Thanks for your time ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] crystal definition
Could you please be more specific on this? From: Husak Michal<mailto:michal.hu...@vscht.cz> Sent: Saturday, January 30, 2021 11:39 PM To: Quantum ESPRESSO users Forum<mailto:users@lists.quantum-espresso.org> Subject: Re: [QE-users] crystal definition Forget this method. Get a CIF file for the structure you want to stady and use the space group based crystal definition ... From: users on behalf of valeria arteaga muñiz Sent: Sunday, January 31, 2021 5:26:37 AM To: users@lists.quantum-espresso.org Subject: [QE-users] crystal definition Hello everyone. I have been working for a couple of months with quantum espresso and still there are some things that get me confused. I hope you can help me. If we wanted to define a BCC crystal (lets say) we could make use of the ibrav=3 parameter. With this, we would have a bcc structure with one atom per cell (?). I don’t know how can that be possible if the bcc cell is supposed to have two atoms per cell (1/8 contribution of 8 corner atoms + 1 contribution of a middle atom). When I use xcrysden for visualization just setting ibrav =3, I get the complete bcc structure. I also have tried to create my bcc crystal from scratch using ibrav=0 and placing the atomic positions at the corner and other atom at 0.5 0.5 0.5 (center), which leads to 2 atoms per unit cell. When I make scf calculations for this case I get around twice the total energy I get in previous case (using ibrav=3). I wonder what is the correct way to use this. Thanks for your clarifications, Valeria ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu<http://www.max-centre.eu>) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] crystal definition
Hello everyone. I have been working for a couple of months with quantum espresso and still there are some things that get me confused. I hope you can help me. If we wanted to define a BCC crystal (lets say) we could make use of the ibrav=3 parameter. With this, we would have a bcc structure with one atom per cell (?). I don’t know how can that be possible if the bcc cell is supposed to have two atoms per cell (1/8 contribution of 8 corner atoms + 1 contribution of a middle atom). When I use xcrysden for visualization just setting ibrav =3, I get the complete bcc structure. I also have tried to create my bcc crystal from scratch using ibrav=0 and placing the atomic positions at the corner and other atom at 0.5 0.5 0.5 (center), which leads to 2 atoms per unit cell. When I make scf calculations for this case I get around twice the total energy I get in previous case (using ibrav=3). I wonder what is the correct way to use this. Thanks for your clarifications, Valeria ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
