Re: [QE-users] Random seed for MD calculations
ring Dynamics:iteration = 11018 Again, thank you very much for the patch file. I hope this report could provide some useful information for QE development. Best regards, Han Hsu On Thu, Aug 10, 2023 at 9:48 PM Paolo Giannozzi wrote: > Thank you for reporting this. Could you please try the attached patch > and report if it fixes your problem? > > Paolo > > On 8/10/23 12:36, Han Hsu (徐翰) wrote: > > > > You don't often get email from han...@ncu.edu.tw. Learn why this is > > important <https://aka.ms/LearnAboutSenderIdentification> > > > > > > Dear QE developers and users, > > > > I've been performing Born-Oppenheimer molecular dynamics (BOMD) > > calculations for hcp Fe at high-PT conditions using Quantum Espresso > > (pw.x, calculation= 'md'). For the thermostats, I am testing stochastic > > velocity rescaling (svr) and Andersen, as they are the only ones (in QE) > > that generate canonical ensembles. For these two thermostats, random > > numbers are generated in each time step. I find, however, that in > > restart calculations (restart_mode= 'restart'), the random numbers are > > not generated properly. In each restart calculation, the same sequence > > of random numbers are generated, as shown in detail in the next few > > paragraphs. Consequently, the calculation results (e.g pressure, > > temperature) exhibit a periodic behavior, with a period same as the > > length of each restart calculation. My question is: Can we avoid this > > problem by properly setting the random seed in restart calculations? If > > so, how to do that? (For restart_mode= 'from_scratch', such a problem > > does not occur, as also shown in the next few paragraphs). > > > > Note: To print out the random numbers generated in each time step, a few > > more lines (write statements) have to be added to the file > > PW/src/dynamics_module.f90. Also, to obtain lots of data within a short > > time, I use fcc Si (8-atom cells) to run extensive tests. For these > > tests, each run consists of 12000 time steps divided into 12 rounds of > > calculations: A from_scratch round (steps 1–1000) followed by 11 restart > > rounds (steps 1001–2000, 2001–3000, ..., 11001–12000). > > > > For the 'svr' thermostat, random numbers (R1, R2,..., R_Nf) from > > gaussian distribution are generated in teach time step. In the > > from_scratch calculation (steps 1–1000), the random numbers generated in > > steps 1–4 are are as below: > > > > Entering Dynamics:iteration = 1 > > rr**2 = R1**2 = 2.2273 > > sum_of_gaussians2 = R2**2+...+R_Nf**2 = 23.3447 > > Entering Dynamics:iteration = 2 > > rr**2 = R1**2 = 0.0441 > > sum_of_gaussians2 = R2**2+...+R_Nf**2 = 17.0921 > > Entering Dynamics:iteration = 3 > > rr**2 = R1**2 = 0.6032 > > sum_of_gaussians2 = R2**2+...+R_Nf**2 = 16.4800 > > Entering Dynamics:iteration = 4 > > rr**2 = R1**2 = 1.2989 > > sum_of_gaussians2 = R2**2+...+R_Nf**2 = 13.2204 > > > > Next, in the restart calculation for steps 1001–2000, the random numbers > > generated in steps 1001–1004 are are as below: > > > > Entering Dynamics:iteration = 1001 > > rr**2 = R1**2 = 0.0008 > > sum_of_gaussians2 = R2**2+...+R_Nf**2 = 18.0810 > > Entering Dynamics:iteration = 1002 > > rr**2 = R1**2 = 0.8306 > > sum_of_gaussians2 = R2**2+...+R_Nf**2 = 19.9568 > > Entering Dynamics:iteration = 1003 > > rr**2 = R1**2 = 1.0171 > > sum_of_gaussians2 = R2**2+...+R_Nf**2 = 14.5561 > > Entering Dynamics:iteration = 1004 > > rr**2 = R1**2 = 0.0605 > > sum_of_gaussians2 = R2**2+...+R_Nf**2 = 28.3579 > > > > Next, in the restart calculation for steps 2001–3000, the random numbers > > generated in steps 2001–2004 are are as below: > > > > Entering Dynamics:iteration = 2001 > > rr**2 = R1**2 = 0.0008 > > sum_of_gaussians2 = R2**2+...+R_Nf**2 = 18.0810 > > Entering Dynamics:iteration = 2002 > > rr**2 = R1**2 = 0.8306 > > sum_of_gaussians2 = R2**2+...+R_Nf**2 = 19.9568 > > Entering Dynamics:iteration = 2003 > > rr**2 = R1**2 = 1.0171 > > sum_of_gaussians2 = R2**2+...+R_Nf**2 = 14.5561 > > Entering Dynamics:iteration = 2004 > > rr**2 = R1**2 = 0.0605 > > sum_of_gaussians2 = R2**2+...+R_Nf**2 = 28.3579 > > > > Next, in th
[QE-users] Random seed for MD calculations
ubroutine set_random_seed(). To properly set the random seed in restart calculations, perhaps the subroutine set_random_seed() should be called somewhere? (Probably not in dynamics_module.f90, as we do not want to reseed the random number in every time step...) Any suggestions and advice are appreciated. Thank you very much for the help!! Best regards, Han Hsu Department of Physics National Central University (Taiwan) -- === Han Hsu (徐翰) Associate Professor Department of Physics National Central University Taoyuan 32001, Taiwan Email: han...@ncu.edu.tw Web: sites.google.com/site/hanhsuphys Tel: +886-3-422-7151 ext 65303 Fax: +886-3-425-1175 === ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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] Andersen thermostat in QE: random collisions or not?
s not a problem at all? I truly appreciate any comments and suggestions. Best regards, Han pwscf.md.1.in <https://drive.google.com/file/d/1ialx9iPnx8n9Dd6VAIogt_mgy30qmEXq/view?usp=drive_web> pwscf.md.1.out <https://drive.google.com/file/d/1GdPyB4X2_eYrAZl1WEoJZNQmEeDSmqqn/view?usp=drive_web> pwscf.md.2.in <https://drive.google.com/file/d/15ZgVyb00FJeUtZKnDPKAVny9Y8hO4E0b/view?usp=drive_web> pwscf.md.2.out <https://drive.google.com/file/d/1xo_rWYX3FTcgcouHEIAa6_xkpAhDgc7I/view?usp=drive_web> pwscf.md.3.in <https://drive.google.com/file/d/1KwDpT8Exm5ClCmZL6zpMdao5-IpJHv-p/view?usp=drive_web> pwscf.md.3.out <https://drive.google.com/file/d/1R-mdwRht4XdJ-sxym9Q5TkjPf5ZesELT/view?usp=drive_web> pwscf.md.4.in <https://drive.google.com/file/d/1GwNqJ76nHd5ExI5iXdtf3-i98hHCSR3S/view?usp=drive_web> pwscf.md.4.out <https://drive.google.com/file/d/1r3U4EItVQlKU2WEhTgcVZANhonRJEWFl/view?usp=drive_web> -- === Han Hsu (徐翰) Associate Professor Department of Physics National Central University Taoyuan 32001, Taiwan Email: han...@ncu.edu.tw Web: sites.google.com/site/hanhsuphys Tel: +886-3-422-7151 ext 65303 Fax: +886-3-425-1175 === ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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: [Pw_forum] space_group, crystal_sg, and Wyckoff position still implemented in QE?
Dear Prof. Giannozzi, Thank you very much for the clarification. Best regards, Han On Tue, Apr 26, 2016 at 3:38 AM, Paolo Giannozzi wrote: > I agree. It wasn't clearly explained in the documentation (or maybe it > wasn't explained at all) but "nat" for Wyckoff position input is the number > of independent sites, not the total number of atoms > > Paolo > > On Mon, Apr 25, 2016 at 8:23 PM, Youssef Aharbil > wrote: > >> Dear han. >> Because "nat" means simply the number of lines to be input not the number >> of atoms generated via all of wyckoff sites. >> >> Youssef Aharbil. >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > -- === Han Hsu (徐翰) Assistant Professor Department of Physics National Central University Taoyuan 32001, Taiwan Email: han...@ncu.edu.tw Tel: +886-3-422-7151 ext 65303 Fax: +886-3-425-1175 === ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] space_group, crystal_sg, and Wyckoff position still implemented in QE?
Dear PWscf users and developers,
I am currently using Quantum Espresso 5.3.0 to compute a hexagonal system
(R-3c, space group 167). I am wondering if space_group and crystal_sg are
still implemented in QE? I keep getting an error message like below:
Error in routine read_cards (4):
wrong number of columns in ATOMIC_POSITIONS
My input file looks like the following, which I believe (and hope) to be
correct.
&system
space_group= 167, rhombohedral= .false.
ibrav= 4
celldm(1)= 8.0
celldm(3)= 2.0
nat= 30, ntyp= 3
...
ATOMIC_POSITIONS {crystal_sg}
Mg 6b
C 6a
O 18e 0.30
(Notice: 18e only needs a parameter x, while 6b and 6a do not need
anything)
I am thus wondering if the Wyckoff position is still implemented in QE? Or
perhaps the above input file is indeed not written properly?
Thank you very much for any answers.
Best regards,
Han
--
===
Han Hsu (徐翰)
Assistant Professor
Department of Physics
National Central University
Taoyuan 32001, Taiwan
Email: han...@ncu.edu.tw
Tel: +886-3-422-7151 ext 65303
Fax: +886-3-425-1175
===
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