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RUNNING , /scratch/pdelugas/qe_gitlab/test-suite/..//bin/cp.x -input sio2-us-pbe-1.in
Program CP v.7.1 starts on 7Dec2022 at 9:51:59
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
"P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Parallel version (MPI), running on 1 processors
MPI processes distributed on 1 nodes
2336 MiB available memory on the printing compute node when the environment starts
Reading input from sio2-us-pbe-1.in
Job Title: MD Simulation
Atomic Pseudopotentials Parameters
----------------------------------
Reading pseudopotential for specie # 1 from file :
/scratch/pdelugas/qe_gitlab/test-suite/..//pseudo/O.pbe-rrkjus.UPF
file type is xml
Reading pseudopotential for specie # 2 from file :
/scratch/pdelugas/qe_gitlab/test-suite/..//pseudo/Si.pbe-nl-rrkjus_psl.1.0.0.UPF
file type is xml
file O.pbe-rrkjus.UPF: wavefunction(s) 2S renormalized
Main Simulation Parameters (from input)
---------------------------------------
Restart Mode = -1 from_scratch
Number of MD Steps = 20
Print out every 20 MD Steps
Reads from unit = 90
Writes to unit = 91
MD Simulation time step = 5.00
Electronic fictitious mass (emass) = 700.00
emass cut-off = 3.00
Simulation Cell Parameters (from input)
external pressure = 0.00 [KBar]
wmass (calculated) = 49868.25 [AU]
ibrav = 8
alat = 9.28990000
a1 = 9.28990000 0.00000000 0.00000000
a2 = 0.00000000 16.09066419 0.00000000
a3 = 0.00000000 0.00000000 10.21470954
b1 = 0.10764379 0.00000000 0.00000000
b2 = 0.00000000 0.06214784 0.00000000
b3 = 0.00000000 0.00000000 0.09789804
omega = 1526.90153773
Energy Cut-offs
---------------
Ecutwfc = 20.0 Ry, Ecutrho = 150.0 Ry, Ecuts = 80.0 Ry
Gcutwfc = 6.6 , Gcutrho = 18.1 Gcuts = 13.2
modified kinetic energy functional, with parameters:
ecutz = 150.0000 ecsig = 2.0000 ecfix = 16.00
NOTA BENE: refg, mmx = 0.050000 3600
Eigenvalues calculated without the kinetic term contribution
Orthog. with lagrange multipliers : eps = 0.10E-08, max = 300
verlet algorithm for electron dynamics
with friction frice = 0.2000 , grease = 1.0000
Electron dynamics : the temperature is not controlled
initial random displacement of el. coordinates with amplitude= 0.010000
Electronic states
-----------------
Number of Electrons= 96, of States = 48
Occupation numbers :
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
Exchange and correlations functionals
-------------------------------------
Exchange-correlation= PBE
( 1 4 3 4 0 0 0)
Ions Simulation Parameters
--------------------------
Ions are not allowed to move
Ionic position (from input)
sorted by specie, and converted to real a.u. coordinates
Species 1 atoms = 12 mass = 29166.22 (a.u.), 16.00 (amu) rcmax = 1.00 (a.u.)
3.188294 14.832370 1.228830
7.832315 6.787040 1.228830
2.074435 5.995380 4.737583
6.720314 14.042319 4.737583
3.963071 11.269898 7.878606
8.608021 3.222959 7.878606
3.963071 4.819153 9.146251
8.608021 12.864483 9.146251
3.187365 1.256681 5.580296
7.833244 9.302011 5.580296
2.075364 10.092062 2.073586
6.719385 2.046732 2.073586
Species 2 atoms = 6 mass = 51040.88 (a.u.), 28.00 (amu) rcmax = 1.00 (a.u.)
0.288916 8.045330 3.404563
4.933866 0.000000 3.404563
2.133890 12.277174 -0.041880
6.778840 4.231844 -0.041880
2.133890 3.813486 6.852027
6.778840 11.858816 6.852027
Ionic position read from input file
Cell Dynamics Parameters (from STDIN)
-------------------------------------
Starting cell generated from CELLDM
Constant VOLUME Molecular dynamics
cell parameters are not allowed to move
Verbosity: iverbosity = 1
Simulation dimensions initialization
------------------------------------
unit vectors of full simulation cell
in real space: in reciprocal space (units 2pi/alat):
1 9.2899 0.0000 0.0000 1.0000 0.0000 0.0000
2 0.0000 16.0907 0.0000 0.0000 0.5773 0.0000
3 0.0000 0.0000 10.2147 0.0000 0.0000 0.9095
G-vector sticks info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Sum 1783 951 239 47285 18431 2305
Using Slab Decomposition
Real Mesh
---------
Global Dimensions Local Dimensions Processor Grid
.X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z.
40 64 40 40 64 40 1 1 1
Array leading dimensions ( nr1x, nr2x, nr3x ) = 40 64 40
Local number of cell to store the grid ( nrxx ) = 102400
Number of x-y planes for each processors:
| 64, 40 |
Using Slab Decomposition
Smooth Real Mesh
----------------
Global Dimensions Local Dimensions Processor Grid
.X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z.
27 45 30 27 45 30 1 1 1
Array leading dimensions ( nr1x, nr2x, nr3x ) = 27 45 30
Local number of cell to store the grid ( nrxx ) = 36450
Number of x-y planes for each processors:
| 45, 30 |
Using Slab Decomposition
Small Box Real Mesh
-------------------
Global Dimensions Local Dimensions Processor Grid
.X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z.
24 24 24 24 24 24 1 1 1
Array leading dimensions ( nr1x, nr2x, nr3x ) = 24 24 24
Local number of cell to store the grid ( nrxx ) = 13824
unit vectors of box grid cell
in real space: in reciprocal space:
5.5739 0.0000 0.0000 1.0000 0.0000 0.0000
0.0000 6.0340 0.0000 0.0000 0.9238 0.0000
0.0000 0.0000 6.1288 0.0000 0.0000 0.9095
Reciprocal Space Mesh
---------------------
Large Mesh
Global(ngm_g) MinLocal MaxLocal Average
23643 23643 23643 23643.00
Smooth Mesh
Global(ngms_g) MinLocal MaxLocal Average
9216 9216 9216 9216.00
Wave function Mesh
Global(ngw_g) MinLocal MaxLocal Average
1153 1153 1153 1153.00
Small box Mesh
ngb = 3183 not distributed to processors
System geometry initialization
------------------------------
ibrav = 8 cell parameters read from input file
unit vectors of box grid cell
in real space: in reciprocal space:
5.5739 0.0000 0.0000 1.0000 0.0000 0.0000
0.0000 6.0340 0.0000 0.0000 0.9238 0.0000
0.0000 0.0000 6.1288 0.0000 0.0000 0.9095
Subspace diagonalization in iterative solution of the eigenvalue problem:
a serial algorithm will be used
Matrix Multiplication Performances
ortho mmul, time for parallel driver = 0.00001 with 1 procs
Constraints matrixes will be distributed block like on
ortho sub-group = 1* 1 procs
Pseudopotentials initialization
-------------------------------
is, nh(is), ngb, kkbeta, lmaxq = 1 8 3183 865 3
qqq
-0.1022 0.5410 0.0000 0.0000
0.5410 -2.5883 0.0000 0.0000
0.0000 0.0000 0.2297 0.2861
0.0000 0.0000 0.2861 0.3565
is, nh(is), ngb, kkbeta, lmaxq = 2 8 3183 829 3
qqq
-0.0772 -0.0666 0.0000 0.0000
-0.0666 -0.0419 0.0000 0.0000
0.0000 0.0000 -0.0095 -0.0249
0.0000 0.0000 -0.0249 -0.0561
Common initialization
Specie: 1
1 indv= 1 ang. mom= 0
2 indv= 2 ang. mom= 0
3 indv= 3 ang. mom= 1
4 indv= 3 ang. mom= 1
5 indv= 3 ang. mom= 1
6 indv= 4 ang. mom= 1
7 indv= 4 ang. mom= 1
8 indv= 4 ang. mom= 1
dion
0.4798 -1.3236 0.0000 0.0000
-1.3236 2.2757 0.0000 0.0000
0.0000 0.0000 0.6278 0.8512
0.0000 0.0000 0.8512 1.1500
Specie: 2
1 indv= 1 ang. mom= 0
2 indv= 2 ang. mom= 0
3 indv= 3 ang. mom= 1
4 indv= 3 ang. mom= 1
5 indv= 3 ang. mom= 1
6 indv= 4 ang. mom= 1
7 indv= 4 ang. mom= 1
8 indv= 4 ang. mom= 1
dion
0.3872 0.3449 0.0000 0.0000
0.3449 0.7963 0.0000 0.0000
0.0000 0.0000 0.1675 0.1356
0.0000 0.0000 0.1356 0.3372
Cell parameters from input file are used in electron mass preconditioning
init_tpiba2= 0.45744371
Short Legend and Physical Units in the Output
---------------------------------------------
NFI [int] - step index
EKINC [HARTREE A.U.] - kinetic energy of the fictitious electronic dynamics
TEMPH [K] - Temperature of the fictitious cell dynamics
TEMP [K] - Ionic temperature
ETOT [HARTREE A.U.] - Scf total energy (Kohn-Sham hamiltonian)
ENTHAL [HARTREE A.U.] - Enthalpy ( ETOT + P * V )
ECONS [HARTREE A.U.] - Enthalpy + kinetic energy of ions and cell
ECONT [HARTREE A.U.] - Constant of motion for the CP lagrangian
Wave Initialization: random initial wave-functions
Occupation number from init
nbnd = 48
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
formf: eself= 210.64152
formf: vps(g=0)= -0.0099197 rhops(g=0)= -0.0039295
formf: vps(g=0)= -0.0096913 rhops(g=0)= -0.0037826
formf: vps(g=0)= -0.0093631 rhops(g=0)= -0.0035749
formf: vps(g=0)= -0.0092512 rhops(g=0)= -0.0035049
formf: vps(g=0)= -0.0091485 rhops(g=0)= -0.0034412
formf: sum_g vps(g)= -2.3739121 sum_g rhops(g)= -0.5407261
formf: vps(g=0)= -0.0084471 rhops(g=0)= -0.0026197
formf: vps(g=0)= -0.0082679 rhops(g=0)= -0.0025217
formf: vps(g=0)= -0.0080097 rhops(g=0)= -0.0023832
formf: vps(g=0)= -0.0079213 rhops(g=0)= -0.0023366
formf: vps(g=0)= -0.0078401 rhops(g=0)= -0.0022941
formf: sum_g vps(g)= -1.6238694 sum_g rhops(g)= -0.3604841
Delta V(G=0): 0.197520Ry, 5.374780eV
from rhoofr: total integrated electronic density
in g-space = 96.000000 in r-space = 96.000000
nfi ekinc temph tempp etot enthal econs econt vnhh xnhh0 vnhp xnhp0
1 8.050478466836569 0.0 0.00 -25.433376939645 -25.433376939645 -25.433376939645 -17.382898472808 0.0000 0.0000 0.0000 0.0000
2 19.241701957635019 0.0 0.00 -48.241151411268 -48.241151411268 -48.241151411268 -28.999449453633 0.0000 0.0000 0.0000 0.0000
3 28.410034157438069 0.0 0.00 -77.301247074586 -77.301247074586 -77.301247074586 -48.891212917148 0.0000 0.0000 0.0000 0.0000
4 32.639556933845768 0.0 0.00 -106.634078626968 -106.634078626968 -106.634078626968 -73.994521693122 0.0000 0.0000 0.0000 0.0000
5 31.840696417104041 0.0 0.00 -131.976588913902 -131.976588913902 -131.976588913902 -100.135892496798 0.0000 0.0000 0.0000 0.0000
6 27.640647499729731 0.0 0.00 -151.597226211910 -151.597226211910 -151.597226211910 -123.956578712180 0.0000 0.0000 0.0000 0.0000
7 22.104811301710370 0.0 0.00 -165.800284248778 -165.800284248778 -165.800284248778 -143.695472947068 0.0000 0.0000 0.0000 0.0000
8 16.788074029249188 0.0 0.00 -175.826942809725 -175.826942809725 -175.826942809725 -159.038868780476 0.0000 0.0000 0.0000 0.0000
9 12.453488107738387 0.0 0.00 -182.999286445096 -182.999286445096 -182.999286445096 -170.545798337357 0.0000 0.0000 0.0000 0.0000
10 9.247256426343338 0.0 0.00 -188.333577957829 -188.333577957829 -188.333577957829 -179.086321531485 0.0000 0.0000 0.0000 0.0000
11 6.998743573253689 0.0 0.00 -192.490533058934 -192.490533058934 -192.490533058934 -185.491789485680 0.0000 0.0000 0.0000 0.0000
12 5.449260822463960 0.0 0.00 -195.861602889943 -195.861602889943 -195.861602889943 -190.412342067479 0.0000 0.0000 0.0000 0.0000
13 4.367870146132796 0.0 0.00 -198.670394660438 -198.670394660438 -198.670394660438 -194.302524514306 0.0000 0.0000 0.0000 0.0000
14 3.586775809940515 0.0 0.00 -201.047444211945 -201.047444211945 -201.047444211945 -197.460668402004 0.0000 0.0000 0.0000 0.0000
15 2.997665786089332 0.0 0.00 -203.075643032323 -203.075643032323 -203.075643032323 -200.077977246233 0.0000 0.0000 0.0000 0.0000
16 2.535754235872847 0.0 0.00 -204.814657966538 -204.814657966538 -204.814657966538 -202.278903730665 0.0000 0.0000 0.0000 0.0000
17 2.163799143330720 0.0 0.00 -206.312502731279 -206.312502731279 -206.312502731279 -204.148703587948 0.0000 0.0000 0.0000 0.0000
18 1.860064186707398 0.0 0.00 -207.610015502824 -207.610015502824 -207.610015502824 -205.749951316116 0.0000 0.0000 0.0000 0.0000
19 1.610629720906617 0.0 0.00 -208.742003776360 -208.742003776360 -208.742003776360 -207.131374055454 0.0000 0.0000 0.0000 0.0000
* Physical Quantities at step: 20
total energy = -209.73735544761 Hartree a.u.
kinetic energy = 103.13573 Hartree a.u.
electrostatic energy = -198.21990 Hartree a.u.
esr = 0.42693 Hartree a.u.
eself = 210.64152 Hartree a.u.
pseudopotential energy = -97.05342 Hartree a.u.
n-l pseudopotential energy = 38.61088 Hartree a.u.
exchange-correlation energy = -56.21064 Hartree a.u.
average potential = 0.00000 Hartree a.u.
Eigenvalues (eV), kp = 1 , spin = 1
-26.83 -25.21 -24.49 -24.22 -23.61 -23.38 -22.80 -22.51 -22.02 -21.66
-20.83 -19.25 -12.36 -11.81 -10.67 -9.97 -9.67 -9.39 -9.13 -8.87
-8.52 -8.20 -8.01 -7.14 -6.97 -6.62 -6.34 -6.14 -5.72 -5.61
-5.55 -5.20 -4.93 -4.71 -4.48 -4.10 -3.85 -3.69 -3.24 -2.70
-1.03 1.05 1.22 4.03 4.73 7.64 9.01 10.41
CELL_PARAMETERS
9.28990000 0.00000000 0.00000000
0.00000000 16.09066419 0.00000000
0.00000000 0.00000000 10.21470954
System Density [g/cm^3] : 2.6420799903
System Volume [A.U.^3] : 1526.9015377315
Center of mass square displacement (a.u.): 0.000000
ATOMIC_POSITIONS
O 0.31882936800000E+01 0.14832370390000E+02 0.12288296100000E+01
O 0.78323146900000E+01 0.67870403900000E+01 0.12288296100000E+01
O 0.20744346700000E+01 0.59953799200000E+01 0.47375825000000E+01
O 0.67203136600000E+01 0.14042318980000E+02 0.47375825000000E+01
O 0.39630713400000E+01 0.11269898260000E+02 0.78786058200000E+01
O 0.86080213400000E+01 0.32229592000000E+01 0.78786058200000E+01
O 0.39630713400000E+01 0.48191526700000E+01 0.91462513300000E+01
O 0.86080213400000E+01 0.12864482670000E+02 0.91462513300000E+01
O 0.31873646900000E+01 0.12566805500000E+01 0.55802960700000E+01
O 0.78332436800000E+01 0.93020105500000E+01 0.55802960700000E+01
O 0.20753636600000E+01 0.10092061950000E+02 0.20735861300000E+01
O 0.67193846700000E+01 0.20467319500000E+01 0.20735861300000E+01
Si 0.28891589000000E+00 0.80453300000000E+01 0.34045628400000E+01
Si 0.49338658900000E+01 0.00000000000000E+00 0.34045628400000E+01
Si 0.21338900300000E+01 0.12277173580000E+02 -0.41880310000000E-01
Si 0.67788400300000E+01 0.42318435800000E+01 -0.41880310000000E-01
Si 0.21338900300000E+01 0.38134864200000E+01 0.68520274700000E+01
Si 0.67788400300000E+01 0.11858816420000E+02 0.68520274700000E+01
ATOMIC_VELOCITIES
O 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
O 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
O 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
O 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
O 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
O 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
O 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
O 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
O 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
O 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
O 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
O 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
Si 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
Si 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
Si 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
Si 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
Si 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
Si 0.00000000000000E+00 0.00000000000000E+00 0.00000000000000E+00
Partial temperatures (for each ionic specie)
Species Temp (K) Mean Square Displacement (a.u.)
1 0.00E+00 0.0000E+00
2 0.00E+00 0.0000E+00
20 1.405215218126730 0.0 0.00 -209.737355447613 -209.737355447613 -209.737355447613 -208.332140229486 0.0000 0.0000 0.0000 0.0000
writing restart file (with schema): ./sio2_91.save/
restart : 0.00s CPU 0.08s WALL ( 1 calls)
Averaged Physical Quantities
accumulated this run
ekinc : 12.06963 12.06963 (AU)
ekin : 117.29658 117.29658 (AU)
epot : -312.84562 -312.84562 (AU)
total energy : -164.12530 -164.12530 (AU)
temperature : 0.00000 0.00000 (K )
enthalpy : -164.12530 -164.12530 (AU)
econs : -164.12530 -164.12530 (AU)
pressure : 0.00000 0.00000 (Gpa)
volume : 1526.90154 1526.90154 (AU)
Called by MAIN_LOOP:
initialize : 1.41s CPU 1.42s WALL ( 1 calls)
main_loop : 4.49s CPU 4.62s WALL ( 20 calls)
cpr_total : 4.49s CPU 4.70s WALL ( 1 calls)
Called by INIT_RUN:
Called by CPR:
cpr_md : 4.49s CPU 4.70s WALL ( 20 calls)
move_electro : 4.41s CPU 4.53s WALL ( 20 calls)
Called by move_electrons:
rhoofr : 0.37s CPU 0.37s WALL ( 21 calls)
vofrho : 0.63s CPU 0.70s WALL ( 21 calls)
dforce : 0.39s CPU 0.39s WALL ( 504 calls)
calphi : 0.02s CPU 0.02s WALL ( 21 calls)
newd : 3.19s CPU 3.23s WALL ( 21 calls)
Called by ortho:
ortho_iter : 0.01s CPU 0.01s WALL ( 21 calls)
rsg : 0.01s CPU 0.01s WALL ( 21 calls)
rhoset : 0.01s CPU 0.01s WALL ( 21 calls)
sigset : 0.00s CPU 0.01s WALL ( 21 calls)
tauset : 0.00s CPU 0.01s WALL ( 21 calls)
ortho : 0.07s CPU 0.08s WALL ( 21 calls)
updatc : 0.01s CPU 0.01s WALL ( 21 calls)
Small boxes:
rhov : 0.16s CPU 0.16s WALL ( 21 calls)
fftb : 2.50s CPU 2.53s WALL ( 14114 calls)
set_cc : 0.04s CPU 0.04s WALL ( 21 calls)
Low-level routines:
prefor : 0.01s CPU 0.01s WALL ( 21 calls)
nlsm1 : 0.00s CPU 0.00s WALL ( 22 calls)
nlsm1us : 0.03s CPU 0.03s WALL ( 42 calls)
fft : 0.14s CPU 0.14s WALL ( 211 calls)
ffts : 0.01s CPU 0.01s WALL ( 42 calls)
fftw : 0.42s CPU 0.42s WALL ( 1512 calls)
betagx : 0.66s CPU 0.67s WALL ( 1 calls)
qradx : 0.32s CPU 0.32s WALL ( 1 calls)
gram : 0.01s CPU 0.01s WALL ( 1 calls)
nlinit : 1.15s CPU 1.16s WALL ( 1 calls)
init_dim : 0.00s CPU 0.01s WALL ( 1 calls)
newnlinit : 0.04s CPU 0.04s WALL ( 1 calls)
from_scratch : 0.25s CPU 0.25s WALL ( 1 calls)
strucf : 0.00s CPU 0.00s WALL ( 1 calls)
calbec : 0.00s CPU 0.00s WALL ( 22 calls)
exch_corr : 0.56s CPU 0.62s WALL ( 21 calls)
CP : 5.95s CPU 6.17s WALL
This run was terminated on: 9:52: 5 7Dec2022
=------------------------------------------------------------------------------=
JOB DONE.
=------------------------------------------------------------------------------=
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