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
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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 the restart calculation for steps 3001–4000, the random numbers
generated in steps 3001–3004 are are as below:
Entering Dynamics: iteration = 3001
rr**2 = R1**2 = 0.0008
sum_of_gaussians2 = R2**2+...+R_Nf**2 = 18.0810
Entering Dynamics: iteration = 3002
rr**2 = R1**2 = 0.8306
sum_of_gaussians2 = R2**2+...+R_Nf**2 = 19.9568
Entering Dynamics: iteration = 3003
rr**2 = R1**2 = 1.0171
sum_of_gaussians2 = R2**2+...+R_Nf**2 = 14.5561
Entering Dynamics: iteration = 3004
rr**2 = R1**2 = 0.0605
sum_of_gaussians2 = R2**2+...+R_Nf**2 = 28.3579
Clearly, the same sequence of random numbers are generated in all
restart rounds (steps 1001–2000, 2001–3000, 3001–4000, ..., etc.), while
the from_scratch round (steps 1–1000) is an exception. I am thus
wondering how to properly generate/seed the random numbers in restart
calculations?
A few more remarks:
(1) I have done this test on different facilities at different
institutes. The same pattern persists.
(2) For Andersen thermostat, the same pattern persists: In the restart
calculations, at the same respective time steps (e.g. steps 1001, 2001,
3001, ...), the same atoms are "randomly" chosen to interact with the
heat bath.
Finally, my understanding is that in Quantum Espresso, generation and
seed of random numbers are controlled by Modules/random_numbers.f90 and
a subroutine 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 <mailto:han...@ncu.edu.tw>
Web: sites.google.com/site/hanhsuphys
<https://sites.google.com/site/hanhsuphys/>
Tel: +886-3-422-7151 ext 65303
Fax: +886-3-425-1175
===============================
_______________________________________________
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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
_______________________________________________
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users mailing list users@lists.quantum-espresso.org
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--
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Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
diff --git a/PW/src/dynamics_module.f90 b/PW/src/dynamics_module.f90
index 37416c268..5ea6f9564 100644
--- a/PW/src/dynamics_module.f90
+++ b/PW/src/dynamics_module.f90
@@ -237,7 +237,7 @@ CONTAINS
is_restart = .FALSE.
ENDIF
ENDIF
-
+ !
IF (.NOT.is_restart) THEN
!
CLOSE( UNIT = 4, STATUS = 'DELETE' )
@@ -711,17 +711,13 @@ CONTAINS
USE symm_base, ONLY : invsym, nsym, irt
USE cell_base, ONLY : alat
USE ions_base, ONLY : nat, if_pos
- USE random_numbers, ONLY : gauss_dist, set_random_seed
+ USE random_numbers, ONLY : gauss_dist
!
IMPLICIT NONE
!
INTEGER :: na, nb
REAL(DP) :: total_mass, kt, sigma, ek, ml(3), system_temp
!
- ! ... next command prevents different MD runs to start
- ! ... with exactly the same "random" velocities
- !
- CALL set_random_seed( )
kt = temperature / ry_to_kelvin
!
! ... starting velocities have a Maxwell-Boltzmann distribution
diff --git a/PW/src/setup.f90 b/PW/src/setup.f90
index fcbc9a0f7..22f4efb57 100644
--- a/PW/src/setup.f90
+++ b/PW/src/setup.f90
@@ -97,6 +97,8 @@ SUBROUTINE setup()
USE additional_kpoints, ONLY : add_additional_kpoints
USE control_flags, ONLY : sic
USE sic_mod, ONLY : init_sic, occ_f2fn, sic_energy
+ USE random_numbers, ONLY : set_random_seed
+ USE dynamics_module, ONLY : control_temp
!
IMPLICIT NONE
!
@@ -703,7 +705,10 @@ SUBROUTINE setup()
IF (sic_energy) CALL occ_f2fn()
END IF
!
- RETURN
+ ! ... next command prevents different MD runs to start
+ ! ... with exactly the same "random" velocities
+ !
+ IF (lmd.AND.control_temp) CALL set_random_seed( )
!
END SUBROUTINE setup
!
_______________________________________________
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
