[CP2K-user] [CP2K:16245] The SCF iteration rate in QM/MM is significantly different from that in vacuo
方业广
bnuyeguangfang at gmail.com
Wed Nov 17 02:14:19 UTC 2021
Dear all,
I have tested the molecular dynamics of the same molecule in the gas
phase and in the QM/MM environment, and found that the SCF iteration of
QM/MM is dozens of times slower than that of vacuum. Is this
reasonable? As far as I know, the coupling between QM and MM should not
affect the speed so much.
The input and output files for the tests are attached.
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DBCSR| CPU Multiplication driver XSMM
DBCSR| Multrec recursion limit 512
DBCSR| Multiplication stack size 1000
DBCSR| Maximum elements for images UNLIMITED
DBCSR| Multiplicative factor virtual images 1
DBCSR| Use multiplication densification T
DBCSR| Multiplication size stacks 3
DBCSR| Use memory pool for CPU allocation F
DBCSR| Number of 3D layers SINGLE
DBCSR| Use MPI memory allocation F
DBCSR| Use RMA algorithm F
DBCSR| Use Communication thread T
DBCSR| Communication thread load 87
DBCSR| MPI: My node id 0
DBCSR| MPI: Number of nodes 64
DBCSR| OMP: Current number of threads 1
DBCSR| OMP: Max number of threads 1
DBCSR| Split modifier for TAS multiplication algorithm 1.0E+00
**** **** ****** ** PROGRAM STARTED AT 2021-11-17 09:47:43.330
***** ** *** *** ** PROGRAM STARTED ON ja0802.para.bscc
** **** ****** PROGRAM STARTED BY scb3056
***** ** ** ** ** PROGRAM PROCESS ID 116292
**** ** ******* ** PROGRAM STARTED IN /public1/home/scb3056/fangyg/test/for
um
CP2K| version string: CP2K version 8.1
CP2K| source code revision number: git:0b61f2f
CP2K| cp2kflags: omp libint fftw3 libxc parallel mpi3 scalapack xsmm max_contr=
CP2K| 4 mkl
CP2K| is freely available from https://www.cp2k.org/
CP2K| Program compiled at Mon Aug 16 10:31:22 CST 2021
CP2K| Program compiled on ln131.para.bscc
CP2K| Program compiled for Linux-x86-64-intel-minimal
CP2K| Data directory path /public1/soft/cp2k/cp2k-8.1.0/data
CP2K| Input file name md.inp
GLOBAL| Force Environment number 1
GLOBAL| Basis set file name BASIS_MOLOPT
GLOBAL| Potential file name POTENTIAL
GLOBAL| MM Potential file name MM_POTENTIAL
GLOBAL| Coordinate file name complex.pdb
GLOBAL| Method name CP2K
GLOBAL| Project name MD
GLOBAL| Preferred FFT library FFTW3
GLOBAL| Preferred diagonalization lib. SL
GLOBAL| Run type MD
GLOBAL| All-to-all communication in single precision F
GLOBAL| FFTs using library dependent lengths F
GLOBAL| Global print level LOW
GLOBAL| MPI I/O enabled T
GLOBAL| Total number of message passing processes 64
GLOBAL| Number of threads for this process 1
GLOBAL| This output is from process 0
GLOBAL| CPU model name AMD EPYC 7452 32-Core Processor
GLOBAL| CPUID 1002
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 264056840 264056840 264056840 264056840
MEMORY| MemFree 240031296 240031296 240054260 240053639
MEMORY| Buffers 0 0 0 0
MEMORY| Cached 9263668 9240356 9263668 9241307
MEMORY| Slab 1656972 1656972 1656972 1656972
MEMORY| SReclaimable 273912 273912 273912 273912
MEMORY| MemLikelyFree 249568876 249568528 249569280 249568859
************* ******** ***********
************* **********************
**** **** **** ***********
******** **** ******* ****
******* **** ******* ****
**** **** **** ****
**** **** ********** ****
**** **** ******** ****
FRONTIERS IN SIMULATION TECHNOLOGY
C.J. Mundy, S. Balasubramanian,
Ken Bagchi, J. Hutter, Ari Seitsonen
IFW Kuo, T. Laino, J. VandeVondele
Version 1.0
EWALD| Summation is done by: SPME
EWALD| Alpha parameter [ ANGSTROM^-1] 0.4000
EWALD| Real Space Cutoff [ ANGSTROM] 8.4348
EWALD| G-space max. Miller index 80 80 80
EWALD| Spline interpolation order 6
----------------------------------------------------------------------
COLVARS| COLVAR INPUT INDEX: 1
COLVARS| BOND >>> ATOMS: 5 8
----------------------------------------------------------------------
FORCEFIELD| WARNING: A non Critical ForceField parameter is missing! CP2K GOES!
FORCEFIELD| Non critical parameters are:Urey-Bradley,Torsions,Impropers, Opbends and 1-4
FORCEFIELD| All missing parameters will not contribute to the potential energy!
FORCEFIELD| Activate the print key FF_INFO to have a list of missing parameters
CHARGE_INFO| Total Charge of the Classical System: -0.000000
SPLINE_INFO| Generating 28 splines for NONBONDED14 interactions
Due to 7 different atomic kinds
...2 ...4 ...6 ...8 ...10 ...12 ...14 ...16 ...18 ...20 ...22
...24 ...26 ...28
SPLINE_INFO| Number of unique splines computed: 12
SPLINE_INFO| Done
SPLINE_INFO| Generating 28 splines for NONBONDED interactions
Due to 7 different atomic kinds
...2 ...4 ...6 ...8 ...10 ...12 ...14 ...16 ...18 ...20 ...22
...24 ...26 ...28
SPLINE_INFO| Number of unique splines computed: 12
SPLINE_INFO| Done
*******************************************************************************
*******************************************************************************
** **
** ##### ## ## **
** ## ## ## ## ## **
** ## ## ## ###### **
** ## ## ## ## ## ##### ## ## #### ## ##### ##### **
** ## ## ## ## ## ## ## ## ## ## ## ## ## ## **
** ## ## ## ## ## ## ## #### ### ## ###### ###### **
** ## ### ## ## ## ## ## ## ## ## ## ## **
** ####### ##### ## ##### ## ## #### ## ##### ## **
** ## ## **
** **
** ... make the atoms dance **
** **
** Copyright (C) by CP2K developers group (2000 - 2020) **
** J. Chem. Phys. 152, 194103 (2020) **
** **
*******************************************************************************
TOTAL NUMBERS AND MAXIMUM NUMBERS
Total number of - Atomic kinds: 3
- Atoms: 10
- Shell sets: 10
- Shells: 46
- Primitive Cartesian functions: 50
- Cartesian basis functions: 122
- Spherical basis functions: 114
Maximum angular momentum of- Orbital basis functions: 2
- Local part of the GTH pseudopotential: 2
- Non-local part of the GTH pseudopotential: 0
SCF PARAMETERS Density guess: RESTART
--------------------------------------------------------
max_scf: 256
max_scf_history: 0
max_diis: 4
--------------------------------------------------------
eps_scf: 1.00E-05
eps_scf_history: 0.00E+00
eps_diis: 1.00E-01
eps_eigval: 1.00E-05
--------------------------------------------------------
level_shift [a.u.]: 0.00
--------------------------------------------------------
No outer SCF
*******************************************************************************
*******************************************************************************
** **
** ####### ## ## ## ## ## ## **
** ## ## ### ### ### ### ### ### **
** ## ## #### #### #### #### #### #### **
** ## ## ## ### ## ## ### ## ## ### ## **
** ## ## ## ## ## ## ## ## ## **
** ## ## ## ## ## ## ## ## T.Laino and F.Mohamed **
** ##### ## ## ## ## ## ## ## 2005 - 2015 **
** **
** Calculation Started.. **
*******************************************************************************
*******************************************************************************
METADYN| Meta Dynamics Protocol
METADYN| Number of interval time steps to spawn hills 50
METADYN| Number of previously spawned hills 0
METADYN| Spawning the Hills
METADYN| Height of the Spawned Gaussian 0.000
METADYN| Number of collective variables 1
----------------------------------------------------------------------
METAVARS| Collective Variable Number 1
METAVARS| Scaling factor 0.056692
METAVARS| Number of Walls present 2
METAVARS| Wall Number: 1 Type of Wall: REFLECTIVE
METAVARS| Wall direction WALL_PLUS
METAVARS| Wall location 4.440856
METAVARS| Wall Number: 2 Type of Wall: REFLECTIVE
METAVARS| Wall direction WALL_MINUS
METAVARS| Wall location 2.267671
----------------------------------------------------------------------
MD_PAR| Molecular dynamics protocol (MD input parameters)
MD_PAR| Ensemble type NVT
MD_PAR| Number of time steps 3
MD_PAR| Time step [fs] 1.000000
MD_PAR| Temperature [K] 300.000000
MD_PAR| Temperature tolerance [K] 0.000000
MD_PAR| Print MD information every 1 step(s)
MD_PAR| File type Print frequency [steps] File names
MD_PAR| Coordinates 1 traj.xyz
MD_PAR| Velocities 1 MD-vel-1.xyz
MD_PAR| Energies 1 MD-1.ener
MD_PAR| Dump 1 MD-1.restart
ROT| Rotational analysis information
ROT| Principal axes and moments of inertia [a.u.]
ROT| 1 2 3
ROT| Eigenvalues 3.88048832733E+10 3.95934872685E+10 4.02510649601E+10
ROT| x 0.998201731624 0.051426277598 -0.030800015501
ROT| y -0.059597866692 0.906562688808 -0.417842297460
ROT| z 0.006434070886 0.418926520089 0.907997342231
ROT| Number of rotovibrational vectors 6
DOF| Calculation of degrees of freedom
DOF| Number of atoms 4594
DOF| Number of intramolecular constraints 0
DOF| Number of intermolecular constraints 0
DOF| Invariants (translations + rotations) 3
DOF| Degrees of freedom 13779
DOF| Restraints information
DOF| Number of intramolecular restraints 0
DOF| Number of intermolecular restraints 0
THERMOSTAT| Thermostat information for PARTICLES
THERMOSTAT| Type of thermostat Nose-Hoover-Chains
THERMOSTAT| Nose-Hoover-Chain length 3
THERMOSTAT| Nose-Hoover-Chain time constant [fs] 100.000000
THERMOSTAT| Order of Yoshida integrator 3
THERMOSTAT| Number of multiple time steps 2
THERMOSTAT| Initial potential energy 0.000000000000E+00
THERMOSTAT| Initial kinetic energy 0.475022301493E-03
THERMOSTAT| End of thermostat information for PARTICLES
MD_VEL| Velocities initialization
MD_VEL| Initial temperature [K] 300.000000
MD_VEL| COM velocity -0.0000000000 -0.0000000000 -0.0000000000
Translating the system in order to center the QM fragment in the QM box.
Number of electrons: 48
Number of occupied orbitals: 24
Number of molecular orbitals: 24
Number of orbital functions: 114
Number of independent orbital functions: 114
Extrapolation method: initial_guess
*** WARNING in qs_initial_guess.F:309 :: User requested to restart the ***
*** wavefunction from the file named: MD-RESTART.wfn. This file does not ***
*** exist. Please check the existence of the file or change properly the ***
*** value of the keyword WFN_RESTART_FILE_NAME. Calculation continues ***
*** using ATOMIC GUESS. ***
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Minimizer : DIIS : direct inversion
in the iterative subspace
using 7 DIIS vectors
safer DIIS on
Preconditioner : FULL_SINGLE_INVERSE : inversion of
H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T
Precond_solver : DEFAULT
stepsize : 0.08000000 energy_gap : 0.08000000
eps_taylor : 0.10000E-15 max_taylor : 4
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.80E-01 6.0 0.16007137 -112.1488486533 -1.12E+02
2 OT DIIS 0.80E-01 3.2 0.10289018 -114.9512177831 -2.80E+00
3 OT DIIS 0.80E-01 3.2 0.06910800 -116.1316481868 -1.18E+00
4 OT DIIS 0.80E-01 3.2 0.05160064 -117.0607653975 -9.29E-01
5 OT DIIS 0.80E-01 3.2 0.03318113 -117.6851558299 -6.24E-01
6 OT DIIS 0.80E-01 3.2 0.02662863 -117.8354762340 -1.50E-01
7 OT DIIS 0.80E-01 3.2 0.01737838 -118.0378220901 -2.02E-01
8 OT DIIS 0.80E-01 3.2 0.01148663 -118.1358287526 -9.80E-02
9 OT DIIS 0.80E-01 3.2 0.00871590 -118.1879631232 -5.21E-02
10 OT DIIS 0.80E-01 3.2 0.00586993 -118.2117692138 -2.38E-02
11 OT DIIS 0.80E-01 3.2 0.00442134 -118.2274686274 -1.57E-02
12 OT DIIS 0.80E-01 3.2 0.00323829 -118.2363652142 -8.90E-03
13 OT DIIS 0.80E-01 3.2 0.00238978 -118.2425174726 -6.15E-03
14 OT DIIS 0.80E-01 3.2 0.00184652 -118.2455302170 -3.01E-03
15 OT DIIS 0.80E-01 3.2 0.00140522 -118.2475262554 -2.00E-03
16 OT DIIS 0.80E-01 3.2 0.00112472 -118.2487631427 -1.24E-03
17 OT DIIS 0.80E-01 3.2 0.00090748 -118.2495449265 -7.82E-04
18 OT DIIS 0.80E-01 3.2 0.00073238 -118.2500676834 -5.23E-04
19 OT DIIS 0.80E-01 3.2 0.00060771 -118.2504537585 -3.86E-04
20 OT DIIS 0.80E-01 3.2 0.00051078 -118.2507357619 -2.82E-04
21 OT DIIS 0.80E-01 3.2 0.00044551 -118.2509072153 -1.71E-04
22 OT DIIS 0.80E-01 3.2 0.00038139 -118.2510687779 -1.62E-04
23 OT DIIS 0.80E-01 3.2 0.00032880 -118.2511922294 -1.23E-04
24 OT DIIS 0.80E-01 3.2 0.00029120 -118.2512676739 -7.54E-05
25 OT DIIS 0.80E-01 3.2 0.00025435 -118.2513462350 -7.86E-05
26 OT DIIS 0.80E-01 3.2 0.00022785 -118.2513969240 -5.07E-05
27 OT DIIS 0.80E-01 3.2 0.00020223 -118.2514417142 -4.48E-05
28 OT DIIS 0.80E-01 3.2 0.00017913 -118.2514811192 -3.94E-05
29 OT DIIS 0.80E-01 3.2 0.00015217 -118.2515190006 -3.79E-05
30 OT DIIS 0.80E-01 3.2 0.00012977 -118.2515455258 -2.65E-05
31 OT DIIS 0.80E-01 3.2 0.00010997 -118.2515649547 -1.94E-05
32 OT DIIS 0.80E-01 3.2 0.00009006 -118.2515790498 -1.41E-05
33 OT DIIS 0.80E-01 3.2 0.00007304 -118.2515879752 -8.93E-06
34 OT DIIS 0.80E-01 3.2 0.00005973 -118.2515933985 -5.42E-06
35 OT DIIS 0.80E-01 3.2 0.00004989 -118.2515961838 -2.79E-06
36 OT DIIS 0.80E-01 3.2 0.00004143 -118.2515980114 -1.83E-06
37 OT DIIS 0.80E-01 3.2 0.00003501 -118.2515991627 -1.15E-06
38 OT DIIS 0.80E-01 3.2 0.00003053 -118.2515998622 -6.99E-07
39 OT DIIS 0.80E-01 3.2 0.00002698 -118.2516003501 -4.88E-07
40 OT DIIS 0.80E-01 3.2 0.00002412 -118.2516007278 -3.78E-07
41 OT DIIS 0.80E-01 3.2 0.00002204 -118.2516009772 -2.49E-07
42 OT DIIS 0.80E-01 3.2 0.00002017 -118.2516012406 -2.63E-07
43 OT DIIS 0.80E-01 3.2 0.00001871 -118.2516014677 -2.27E-07
44 OT DIIS 0.80E-01 3.2 0.00001728 -118.2516016701 -2.02E-07
45 OT DIIS 0.80E-01 3.2 0.00001586 -118.2516018837 -2.14E-07
46 OT DIIS 0.80E-01 3.2 0.00001449 -118.2516020913 -2.08E-07
47 OT DIIS 0.80E-01 3.2 0.00001322 -118.2516022675 -1.76E-07
48 OT DIIS 0.80E-01 3.2 0.00001193 -118.2516024360 -1.69E-07
49 OT DIIS 0.80E-01 3.2 0.00001068 -118.2516025716 -1.36E-07
50 OT DIIS 0.80E-01 3.2 0.00000933 -118.2516026955 -1.24E-07
*** SCF run converged in 50 steps ***
Electronic density on regular grids: -47.9999998061 0.0000001939
Core density on regular grids: 47.9999999987 -0.0000000013
Total charge density on r-space grids: 0.0000001927
Total charge density g-space grids: 0.0000001927
Overlap energy of the core charge distribution: 0.00000013217887
Self energy of the core charge distribution: -301.67942807122279
Core Hamiltonian energy: 85.89072308802810
Hartree energy: 125.35411776354471
Exchange-correlation energy: -20.36523697676691
Hartree-Fock Exchange energy: -6.04683879625239
QM/MM Electrostatic energy: -1.40493983497391
Total energy: -118.25160269546434
ENERGY| Total FORCE_EVAL ( QMMM ) energy [a.u.]: -136.905472697818425
MD_INI| MD initialization
MD_INI| Potential energy [hartree] -0.136905472698E+03
MD_INI| Total kinetic energy [hartree] 0.654533229227E+01
MD_INI| QM kinetic energy [hartree] 0.173943669988E-01
MD_INI| Total temperature [K] 300.000000
MD_INI| QM temperature [K] 366.180008
MD_INI| Pressure [bar] 1.373018828856E+04
MD_INI| Cell volume [bohr^3] 4.336220625571E+05
MD_INI| Cell volume [ang^3] 6.425615938541E+04
MD_INI| Cell lengths [bohr] 7.66102391E+01 7.55113899E+01 7.49569814E+01
MD_INI| Cell lengths [ang] 4.05403925E+01 3.99589065E+01 3.96655262E+01
MD_INI| Cell angles [deg] 9.00000000E+01 9.00000000E+01 9.00000000E+01
Translating the system in order to center the QM fragment in the QM box.
Number of electrons: 48
Number of occupied orbitals: 24
Number of molecular orbitals: 24
Number of orbital functions: 114
Number of independent orbital functions: 114
Extrapolation method: ASPC
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Minimizer : DIIS : direct inversion
in the iterative subspace
using 7 DIIS vectors
safer DIIS on
Preconditioner : FULL_SINGLE_INVERSE : inversion of
H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T
Precond_solver : DEFAULT
stepsize : 0.08000000 energy_gap : 0.08000000
eps_taylor : 0.10000E-15 max_taylor : 4
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.80E-01 3.7 0.00126811 -118.2671862014 -1.18E+02
2 OT DIIS 0.80E-01 3.2 0.00076142 -118.2674604204 -2.74E-04
3 OT DIIS 0.80E-01 3.2 0.00032059 -118.2676185359 -1.58E-04
4 OT DIIS 0.80E-01 3.2 0.00012169 -118.2676506413 -3.21E-05
5 OT DIIS 0.80E-01 3.2 0.00006034 -118.2676544707 -3.83E-06
6 OT DIIS 0.80E-01 3.2 0.00002348 -118.2676555559 -1.09E-06
7 OT DIIS 0.80E-01 3.2 0.00001167 -118.2676557060 -1.50E-07
8 OT DIIS 0.80E-01 3.2 0.00000515 -118.2676557509 -4.49E-08
*** SCF run converged in 8 steps ***
Electronic density on regular grids: -47.9999998049 0.0000001951
Core density on regular grids: 47.9999999987 -0.0000000013
Total charge density on r-space grids: 0.0000001939
Total charge density g-space grids: 0.0000001939
Overlap energy of the core charge distribution: 0.00000010455794
Self energy of the core charge distribution: -301.67942807122279
Core Hamiltonian energy: 85.79786358195773
Hartree energy: 125.42239461270066
Exchange-correlation energy: -20.34636039364445
Hartree-Fock Exchange energy: -6.03960641819669
QM/MM Electrostatic energy: -1.42251916705332
Total energy: -118.26765575090091
ENERGY| Total FORCE_EVAL ( QMMM ) energy [a.u.]: -135.810374045537571
MD| ***************************************************************************
MD| Step number 1
MD| Time [fs] 1.000000
MD| Conserved quantity [hartree] -0.130069776626E+03
MD| ---------------------------------------------------------------------------
MD| Instantaneous Averages
MD| CPU time per MD step [s] 340.511154 340.511154
MD| Energy drift per atom [K] 0.199258859648E+02 0.000000000000E+00
MD| Potential energy [hartree] -0.135810374046E+03 -0.135810374046E+03
MD| Total kinetic energy [hartree] 0.573909355676E+01 0.573909355676E+01
MD| QM kinetic energy [hartree] 0.159489175516E-01 0.159489175516E-01
MD| Total temperature [K] 263.046701 263.046701
MD| QM temperature [K] 335.750922 335.750922
MD| Pressure [bar] 6.002965231874E+03 6.002965231874E+03
MD| ***************************************************************************
Translating the system in order to center the QM fragment in the QM box.
Number of electrons: 48
Number of occupied orbitals: 24
Number of molecular orbitals: 24
Number of orbital functions: 114
Number of independent orbital functions: 114
Extrapolation method: ASPC
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Minimizer : DIIS : direct inversion
in the iterative subspace
using 7 DIIS vectors
safer DIIS on
Preconditioner : FULL_SINGLE_INVERSE : inversion of
H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T
Precond_solver : DEFAULT
stepsize : 0.08000000 energy_gap : 0.08000000
eps_taylor : 0.10000E-15 max_taylor : 4
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.80E-01 3.6 0.00055483 -118.2910525250 -1.18E+02
2 OT DIIS 0.80E-01 3.1 0.00031662 -118.2911039542 -5.14E-05
3 OT DIIS 0.80E-01 3.2 0.00013094 -118.2911302711 -2.63E-05
4 OT DIIS 0.80E-01 3.2 0.00004280 -118.2911357593 -5.49E-06
5 OT DIIS 0.80E-01 3.2 0.00002358 -118.2911361994 -4.40E-07
6 OT DIIS 0.80E-01 3.1 0.00000674 -118.2911363772 -1.78E-07
*** SCF run converged in 6 steps ***
Electronic density on regular grids: -47.9999997819 0.0000002181
Core density on regular grids: 47.9999999988 -0.0000000012
Total charge density on r-space grids: 0.0000002169
Total charge density g-space grids: 0.0000002169
Overlap energy of the core charge distribution: 0.00000009549439
Self energy of the core charge distribution: -301.67942807122279
Core Hamiltonian energy: 85.74935823296528
Hartree energy: 125.45879098389440
Exchange-correlation energy: -20.33660714955371
Hartree-Fock Exchange energy: -6.03577414037640
QM/MM Electrostatic energy: -1.44747632841449
Total energy: -118.29113637721333
ENERGY| Total FORCE_EVAL ( QMMM ) energy [a.u.]: -135.816542786673722
MD| ***************************************************************************
MD| Step number 2
MD| Time [fs] 2.000000
MD| Conserved quantity [hartree] -0.130133162721E+03
MD| ---------------------------------------------------------------------------
MD| Instantaneous Averages
MD| CPU time per MD step [s] 93.621338 217.066246
MD| Energy drift per atom [K] 0.155689591859E+02 0.778447959295E+01
MD| Potential energy [hartree] -0.135816542787E+03 -0.135813458416E+03
MD| Total kinetic energy [hartree] 0.568104502113E+01 0.571006928895E+01
MD| QM kinetic energy [hartree] 0.145935682172E-01 0.152712428844E-01
MD| Total temperature [K] 260.386094 261.716397
MD| QM temperature [K] 307.218591 321.484756
MD| Pressure [bar] -6.381292500983E+03 -1.891636345546E+02
MD| ***************************************************************************
Translating the system in order to center the QM fragment in the QM box.
Number of electrons: 48
Number of occupied orbitals: 24
Number of molecular orbitals: 24
Number of orbital functions: 114
Number of independent orbital functions: 114
Extrapolation method: ASPC
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Minimizer : DIIS : direct inversion
in the iterative subspace
using 7 DIIS vectors
safer DIIS on
Preconditioner : FULL_SINGLE_INVERSE : inversion of
H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T
Precond_solver : DEFAULT
stepsize : 0.08000000 energy_gap : 0.08000000
eps_taylor : 0.10000E-15 max_taylor : 4
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.80E-01 3.7 0.00038766 -118.3225296351 -1.18E+02
2 OT DIIS 0.80E-01 3.2 0.00022039 -118.3225547008 -2.51E-05
3 OT DIIS 0.80E-01 3.2 0.00009133 -118.3225674044 -1.27E-05
4 OT DIIS 0.80E-01 3.2 0.00003042 -118.3225700673 -2.66E-06
5 OT DIIS 0.80E-01 3.2 0.00001736 -118.3225702806 -2.13E-07
6 OT DIIS 0.80E-01 3.2 0.00000474 -118.3225703785 -9.79E-08
*** SCF run converged in 6 steps ***
Electronic density on regular grids: -47.9999997457 0.0000002543
Core density on regular grids: 47.9999999987 -0.0000000013
Total charge density on r-space grids: 0.0000002530
Total charge density g-space grids: 0.0000002530
Overlap energy of the core charge distribution: 0.00000009886945
Self energy of the core charge distribution: -301.67942807122279
Core Hamiltonian energy: 85.75162869605586
Hartree energy: 125.45792107133452
Exchange-correlation energy: -20.33752073875611
Hartree-Fock Exchange energy: -6.03596625566824
QM/MM Electrostatic energy: -1.47920517910945
Total energy: -118.32257037849675
ENERGY| Total FORCE_EVAL ( QMMM ) energy [a.u.]: -136.396260252041372
MD| ***************************************************************************
MD| Step number 3
MD| Time [fs] 3.000000
MD| Conserved quantity [hartree] -0.130254811854E+03
MD| ---------------------------------------------------------------------------
MD| Instantaneous Averages
MD| CPU time per MD step [s] 93.626603 175.919698
MD| Energy drift per atom [K] 0.720724560173E+01 0.759206826254E+01
MD| Potential energy [hartree] -0.136396260252E+03 -0.136007725695E+03
MD| Total kinetic energy [hartree] 0.613839878414E+01 0.585284578735E+01
MD| QM kinetic energy [hartree] 0.143958407657E-01 0.149794421782E-01
MD| Total temperature [K] 281.348533 268.260442
MD| QM temperature [K] 303.056103 315.341872
MD| Pressure [bar] -9.925144784124E+03 -3.434490684411E+03
MD| ***************************************************************************
-------------------------------------------------------------------------------
- -
- DBCSR STATISTICS -
- -
-------------------------------------------------------------------------------
COUNTER TOTAL BLAS SMM ACC
flops 5 x 24 x 24 46080 0.0% 100.0% 0.0%
flops 5 x 5 x 24 295200 0.0% 100.0% 0.0%
flops 5 x 24 x 5 792000 0.0% 100.0% 0.0%
flops 5 x 13 x 24 2046720 0.0% 100.0% 0.0%
flops 13 x 5 x 24 2046720 0.0% 100.0% 0.0%
flops 18 x 24 x 18 4603392 0.0% 100.0% 0.0%
flops 13 x 24 x 5 8236800 0.0% 100.0% 0.0%
flops 5 x 24 x 13 8236800 0.0% 100.0% 0.0%
flops 13 x 24 x 18 9974016 0.0% 100.0% 0.0%
flops 18 x 24 x 13 9974016 0.0% 100.0% 0.0%
flops 24 x 24 x 18 11612160 0.0% 100.0% 0.0%
flops 18 x 24 x 24 14349312 0.0% 100.0% 0.0%
flops 24 x 24 x 24 15261696 0.0% 100.0% 0.0%
flops 13 x 13 x 24 23946624 0.0% 100.0% 0.0%
flops 24 x 24 x 13 25159680 0.0% 100.0% 0.0%
flops 13 x 24 x 24 31569408 0.0% 100.0% 0.0%
flops 13 x 24 x 13 107273088 0.0% 100.0% 0.0%
flops inhomo. stacks 0 0.0% 0.0% 0.0%
flops total 275.423712E+06 0.0% 100.0% 0.0%
flops max/rank 74.941824E+06 0.0% 100.0% 0.0%
matmuls inhomo. stacks 0 0.0% 0.0% 0.0%
matmuls total 31346 0.0% 100.0% 0.0%
number of processed stacks 31346 0.0% 100.0% 0.0%
average stack size 0.0 1.0 0.0
marketing flops 298.766016E+06
-------------------------------------------------------------------------------
# multiplications 1507
max memory usage/rank 2.293146E+09
# max total images/rank 1
# max 3D layers 1
# MPI messages exchanged 1350272
MPI messages size (bytes):
total size 422.011296E+06
min size 0.000000E+00
max size 4.608000E+03
average size 312.537994E+00
MPI breakdown and total messages size (bytes):
size <= 128 1159494 0
128 < size <= 8192 190778 422011296
8192 < size <= 32768 0 0
32768 < size <= 131072 0 0
131072 < size <= 4194304 0 0
4194304 < size <= 16777216 0 0
16777216 < size 0 0
-------------------------------------------------------------------------------
- -
- DBCSR MESSAGE PASSING PERFORMANCE -
- -
-------------------------------------------------------------------------------
ROUTINE CALLS AVE VOLUME [Bytes]
MP_Bcast 18 12.
MP_Allreduce 8159 8.
MP_Alltoall 5335 5696.
MP_ISend 48208 580.
MP_IRecv 48208 432.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
- -
- GRID STATISTICS -
- -
-------------------------------------------------------------------------------
LP KERNEL BACKEND COUNT PERCENT
4 collocate ortho REF 54714 32.66%
4 integrate ortho REF 52895 31.58%
3 collocate ortho REF 21009 12.54%
3 integrate ortho REF 20170 12.04%
2 collocate ortho REF 5476 3.27%
2 integrate ortho REF 5180 3.09%
5 integrate ortho REF 2954 1.76%
0 collocate general REF 2560 1.53%
1 integrate general REF 2560 1.53%
-------------------------------------------------------------------------------
MEMORY| Estimated peak process memory [MiB] 2188
-------------------------------------------------------------------------------
- -
- MESSAGE PASSING PERFORMANCE -
- -
-------------------------------------------------------------------------------
ROUTINE CALLS AVE VOLUME [Bytes]
MP_Group 5
MP_Bcast 5036 459769.
MP_Allreduce 9305 599186.
MP_Sync 467
MP_Alltoall 1490 46406982.
MP_ISendRecv 29232 67698.
MP_Wait 37556
MP_comm_split 50
MP_ISend 7044 902823.
MP_IRecv 7040 902503.
MP_Recv 42 2736.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
- -
- R E F E R E N C E S -
- -
-------------------------------------------------------------------------------
CP2K version 8.1, the CP2K developers group (2020).
CP2K is freely available from https://www.cp2k.org/ .
Kuehne,Thomas D.; Iannuzzi,Marcella; Del Ben,Mauro;
Rybkin,Vladimir V.; Seewald,Patrick; Stein,Frederick; Laino,Teodoro;
Khaliullin,Rustam Z.; Schuett,Ole; Schiffmann,Florian; Golze,Dorothea;
Wilhelm,Jan; Chulkov,Sergey; Bani-Hashemian,Mohammad Hossein;
Weber,Valery; Borstnik,Urban; Taillefumier,Mathieu;
Jakobovits,Alice Shoshana; Lazzaro,Alfio; Pabst,Hans; Mueller,Tiziano;
Schade,Robert; Guidon,Manuel; Andermatt,Samuel; Holmberg,Nico;
Schenter,Gregory K.; Hehn,Anna; Bussy,Augustin; Belleflamme,Fabian;
Tabacchi,Gloria; Gloess,Andreas; Lass,Michael; Bethune,Iain;
Mundy,Christopher J.; Plessl,Christian; Watkins,Matt;
VandeVondele,Joost; Krack,Matthias; Hutter,Juerg.
The Journal of Chemical Physics, 152 (19), (2020).
CP2K: An electronic structure and molecular dynamics software package -
Quickstep: Efficient and accurate electronic structure calculations.
https://doi.org/10.1063/5.0007045
Schuett, Ole; Messmer, Peter; Hutter, Juerg; VandeVondele, Joost.
Electronic Structure Calculations on Graphics Processing Units, John
Wiley & Sons, Ltd, 173-190 (2016).
GPU-Accelerated Sparse Matrix-Matrix Multiplication for
Linear Scaling Density Functional Theory.
https://doi.org/10.1002/9781118670712.ch8
Borstnik, U; VandeVondele, J; Weber, V; Hutter, J.
PARALLEL COMPUTING, 40 (5-6), 47-58 (2014).
Sparse matrix multiplication: The distributed block-compressed sparse
row library.
https://doi.org/10.1016/j.parco.2014.03.012
Hutter, J; Iannuzzi, M; Schiffmann, F; VandeVondele, J.
WIREs Comput Mol Sci., 4 (1), 15-25 (2014).
CP2K: atomistic simulations of condensed matter systems.
https://doi.org/10.1002/wcms.1159
Guidon, M; Hutter, J; VandeVondele, J.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5 (11), 3010-3021 (2009).
Robust Periodic Hartree-Fock Exchange for Large-Scale Simulations Using
Gaussian Basis Sets.
https://doi.org/10.1021/ct900494g
Guidon, M; Schiffmann, F; Hutter, J; VandeVondele, J.
JOURNAL OF CHEMICAL PHYSICS, 128 (21), 214104 (2008).
Ab initio molecular dynamics using hybrid density functionals.
https://doi.org/10.1063/1.2931945
VandeVondele, J; Hutter, J.
JOURNAL OF CHEMICAL PHYSICS, 127 (11), 114105 (2007).
Gaussian basis sets for accurate calculations on molecular systems in
gas and condensed phases.
https://doi.org/10.1063/1.2770708
Kuhne, TD; Krack, M; Mohamed, FR; Parrinello, M.
PHYSICAL REVIEW LETTERS, 98 (6), 066401 (2007).
Efficient and accurate Car-Parrinello-like approach to
Born-Oppenheimer molecular dynamics.
https://doi.org/10.1103/PhysRevLett.98.066401
Laino, T; Mohamed, F; Laio, A; Parrinello, M.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 1 (6), 1176-1184 (2005).
An efficient real space multigrid QM/MM electrostatic coupling.
https://doi.org/10.1021/ct050123f
Krack, M.
THEORETICAL CHEMISTRY ACCOUNTS, 114 (1-3), 145-152 (2005).
Pseudopotentials for H to Kr optimized for gradient-corrected
exchange-correlation functionals.
https://doi.org/10.1007/s00214-005-0655-y
VandeVondele, J; Krack, M; Mohamed, F; Parrinello, M; Chassaing, T;
Hutter, J. COMPUTER PHYSICS COMMUNICATIONS, 167 (2), 103-128 (2005).
QUICKSTEP: Fast and accurate density functional calculations using a
mixed Gaussian and plane waves approach.
https://doi.org/10.1016/j.cpc.2004.12.014
Frigo, M; Johnson, SG.
PROCEEDINGS OF THE IEEE, 93 (2), 216-231 (2005).
The design and implementation of FFTW3.
https://doi.org/10.1109/JPROC.2004.840301
Kolafa, J.
JOURNAL OF COMPUTATIONAL CHEMISTRY, 25 (3), 335-342 (2004).
Time-reversible always stable predictor-corrector method for molecular dynamics of polarizable molecules.
https://doi.org/10.1002/jcc.10385
VandeVondele, J; Hutter, J.
JOURNAL OF CHEMICAL PHYSICS, 118 (10), 4365-4369 (2003).
An efficient orbital transformation method for electronic structure
calculations.
https://doi.org/10.1063/1.1543154
Hartwigsen, C; Goedecker, S; Hutter, J.
PHYSICAL REVIEW B, 58 (7), 3641-3662 (1998).
Relativistic separable dual-space Gaussian pseudopotentials from H to Rn.
https://doi.org/10.1103/PhysRevB.58.3641
Lippert, G; Hutter, J; Parrinello, M.
MOLECULAR PHYSICS, 92 (3), 477-487 (1997).
A hybrid Gaussian and plane wave density functional scheme.
https://doi.org/10.1080/002689797170220
Perdew, JP; Burke, K; Ernzerhof, M.
PHYSICAL REVIEW LETTERS, 77 (18), 3865-3868 (1996).
Generalized gradient approximation made simple.
https://doi.org/10.1103/PhysRevLett.77.3865
Goedecker, S; Teter, M; Hutter, J.
PHYSICAL REVIEW B, 54 (3), 1703-1710 (1996).
Separable dual-space Gaussian pseudopotentials.
https://doi.org/10.1103/PhysRevB.54.1703
ESSMANN, U; PERERA, L; BERKOWITZ, ML; DARDEN, T; LEE, H; PEDERSEN, LG.
JOURNAL OF CHEMICAL PHYSICS, 103 (19), 8577-8593 (1995).
A SMOOTH PARTICLE MESH EWALD METHOD.
https://doi.org/10.1063/1.470117
NOSE, S. JOURNAL OF CHEMICAL PHYSICS, 81 (1), 511-519 (1984).
A UNIFIED FORMULATION OF THE CONSTANT TEMPERATURE MOLECULAR-DYNAMICS
METHODS.
https://doi.org/10.1063/1.447334
NOSE, S. MOLECULAR PHYSICS, 52 (2), 255-268 (1984).
A MOLECULAR-DYNAMICS METHOD FOR SIMULATIONS IN THE CANONICAL ENSEMBLE.
https://doi.org/10.1080/00268978400101201
-------------------------------------------------------------------------------
- -
- T I M I N G -
- -
-------------------------------------------------------------------------------
SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
CP2K 1 1.0 0.107 0.122 529.153 529.155
qs_mol_dyn_low 1 2.0 0.015 0.016 527.819 527.854
qs_forces 4 3.8 0.001 0.004 310.811 310.814
velocity_verlet 3 3.0 0.005 0.007 287.436 287.438
rebuild_ks_matrix 74 8.1 0.000 0.000 253.413 253.422
qs_ks_build_kohn_sham_matrix 74 9.1 0.018 0.026 253.413 253.422
qs_energies 4 4.8 0.025 0.026 234.862 234.862
scf_env_do_scf 4 5.8 0.000 0.002 229.573 229.573
scf_env_do_scf_inner_loop 70 6.3 0.020 0.036 212.808 212.810
qs_ks_update_qs_env 74 7.3 0.001 0.001 177.483 177.492
pw_transfer 1450 11.7 0.271 0.334 157.786 161.976
fft_wrap_pw1pw2 1282 12.8 0.028 0.036 155.109 159.276
fft_wrap_pw1pw2_150 822 14.0 17.073 19.058 151.008 154.414
qs_vxc_create 74 10.1 0.003 0.005 120.034 120.080
xc_vxc_pw_create 74 11.1 2.462 3.117 120.031 120.076
qmmm_forces 4 3.8 0.001 0.003 117.781 117.782
qmmm_forces_with_gaussian 4 4.8 0.088 0.098 115.457 116.497
fft3d_ps 1282 14.8 63.372 66.540 107.554 110.807
pw_restrict_s3 12 5.8 31.639 32.981 101.177 102.309
qmmm_el_coupling 4 3.8 0.000 0.000 97.206 98.164
qmmm_elec_with_gaussian 4 4.8 0.062 0.104 97.185 98.142
pw_integral_ab 2336 7.5 82.084 83.640 83.270 86.197
qmmm_elec_with_gaussian:spline 4 5.8 0.000 0.000 81.168 82.139
pw_prolongate_s3 12 6.8 25.699 27.005 81.168 82.139
qs_ks_update_qs_env_forces 4 4.8 0.000 0.000 75.935 75.935
hfx_ks_matrix 74 10.1 0.004 0.009 72.446 72.477
derivatives_four_center 4 8.8 0.027 0.207 65.565 65.569
derivatives_four_center_main 4 9.8 0.001 0.001 65.338 65.343
derivatives_four_center_bin 416 10.8 60.894 63.407 60.894 63.407
xc_rho_set_and_dset_create 74 12.1 1.005 1.153 53.163 56.295
qs_rho_update_rho 74 7.4 0.001 0.001 52.625 52.632
calculate_rho_elec 74 8.4 0.361 0.395 52.624 52.631
density_rs2pw 74 9.4 0.007 0.008 44.493 45.720
sum_up_and_integrate 74 10.1 1.412 1.511 33.604 33.631
integrate_v_rspace 74 11.1 0.004 0.005 32.192 32.368
potential_pw2rs 74 12.1 0.019 0.021 31.510 31.689
rs_pw_transfer 616 11.6 0.012 0.018 29.324 29.917
mp_alltoall_z22v 1282 16.8 21.797 28.477 21.797 28.477
x_to_yz 682 16.2 13.350 14.330 24.354 25.901
mp_sum_dm3 20 5.8 25.243 25.347 25.243 25.347
pw_axpy 1708 8.5 23.368 24.574 23.368 24.574
yz_to_x 600 15.3 8.850 10.001 19.643 23.647
pw_zero 1922 7.3 20.498 21.752 20.498 21.752
pw_scatter_p 682 15.2 16.207 17.849 16.207 17.849
init_scf_loop 4 6.8 0.000 0.001 16.758 16.759
pw_gather_p 600 14.3 13.940 15.214 13.940 15.214
pw_derive 456 12.5 12.329 13.159 12.329 13.159
rs_pw_transfer_PW2RS_150 78 13.9 6.744 7.016 10.587 10.863
-------------------------------------------------------------------------------
The number of warnings for this run is : 1
-------------------------------------------------------------------------------
**** **** ****** ** PROGRAM ENDED AT 2021-11-17 09:56:33.329
***** ** *** *** ** PROGRAM RAN ON ja0802.para.bscc
** **** ****** PROGRAM RAN BY scb3056
***** ** ** ** ** PROGRAM PROCESS ID 116292
**** ** ******* ** PROGRAM STOPPED IN /public1/home/scb3056/fangyg/test/for
um
-------------- next part --------------
DBCSR| CPU Multiplication driver XSMM
DBCSR| Multrec recursion limit 512
DBCSR| Multiplication stack size 1000
DBCSR| Maximum elements for images UNLIMITED
DBCSR| Multiplicative factor virtual images 1
DBCSR| Use multiplication densification T
DBCSR| Multiplication size stacks 3
DBCSR| Use memory pool for CPU allocation F
DBCSR| Number of 3D layers SINGLE
DBCSR| Use MPI memory allocation F
DBCSR| Use RMA algorithm F
DBCSR| Use Communication thread T
DBCSR| Communication thread load 87
DBCSR| MPI: My node id 0
DBCSR| MPI: Number of nodes 64
DBCSR| OMP: Current number of threads 1
DBCSR| OMP: Max number of threads 1
DBCSR| Split modifier for TAS multiplication algorithm 1.0E+00
**** **** ****** ** PROGRAM STARTED AT 2021-11-17 09:50:09.749
***** ** *** *** ** PROGRAM STARTED ON ga2008.para.bscc
** **** ****** PROGRAM STARTED BY scb3056
***** ** ** ** ** PROGRAM PROCESS ID 129715
**** ** ******* ** PROGRAM STARTED IN /public1/home/scb3056/fangyg/test/for
um/vacuo
CP2K| version string: CP2K version 8.1
CP2K| source code revision number: git:0b61f2f
CP2K| cp2kflags: omp libint fftw3 libxc parallel mpi3 scalapack xsmm max_contr=
CP2K| 4 mkl
CP2K| is freely available from https://www.cp2k.org/
CP2K| Program compiled at Mon Aug 16 10:31:22 CST 2021
CP2K| Program compiled on ln131.para.bscc
CP2K| Program compiled for Linux-x86-64-intel-minimal
CP2K| Data directory path /public1/soft/cp2k/cp2k-8.1.0/data
CP2K| Input file name vacuo.inp
GLOBAL| Force Environment number 1
GLOBAL| Basis set file name BASIS_MOLOPT
GLOBAL| Potential file name POTENTIAL
GLOBAL| MM Potential file name MM_POTENTIAL
GLOBAL| Coordinate file name vacuo.pdb
GLOBAL| Method name CP2K
GLOBAL| Project name md
GLOBAL| Preferred FFT library FFTW3
GLOBAL| Preferred diagonalization lib. SL
GLOBAL| Run type MD
GLOBAL| All-to-all communication in single precision F
GLOBAL| FFTs using library dependent lengths F
GLOBAL| Global print level LOW
GLOBAL| MPI I/O enabled T
GLOBAL| Total number of message passing processes 64
GLOBAL| Number of threads for this process 1
GLOBAL| This output is from process 0
GLOBAL| CPU model name AMD EPYC 7452 32-Core Processor
GLOBAL| CPUID 1002
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 263793368 263793368 263793368 263793368
MEMORY| MemFree 239345284 239345284 239345284 239345284
MEMORY| Buffers 0 0 0 0
MEMORY| Cached 9224172 9224172 9224172 9224172
MEMORY| Slab 1737256 1737256 1737256 1737256
MEMORY| SReclaimable 326520 326520 326520 326520
MEMORY| MemLikelyFree 248895976 248895976 248895976 248895976
----------------------------------------------------------------------
COLVARS| COLVAR INPUT INDEX: 1
COLVARS| BOND >>> ATOMS: 5 8
----------------------------------------------------------------------
GENERATE| Preliminary Number of Bonds generated: 8
GENERATE| WARNING in connectivity generation!
GENERATE| Two molecules/residues named (MOL1) have different number of atoms.
GENERATE| Molecule starting at position (8) has Nr. <2> of atoms.
GENERATE| while the other same molecules have Nr. <6> of atoms!
GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the generated
GENERATE| connectivity. Retry...
GENERATE| Present value of BONDPARM_FACTOR ( 1.155000 ).
GENERATE| Preliminary Number of Bonds generated: 8
GENERATE| WARNING in connectivity generation!
GENERATE| Two molecules/residues named (MOL1) have different number of atoms.
GENERATE| Molecule starting at position (8) has Nr. <2> of atoms.
GENERATE| while the other same molecules have Nr. <6> of atoms!
GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the generated
GENERATE| connectivity. Retry...
GENERATE| Present value of BONDPARM_FACTOR ( 1.212750 ).
GENERATE| Preliminary Number of Bonds generated: 8
GENERATE| WARNING in connectivity generation!
GENERATE| Two molecules/residues named (MOL1) have different number of atoms.
GENERATE| Molecule starting at position (8) has Nr. <2> of atoms.
GENERATE| while the other same molecules have Nr. <6> of atoms!
GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the generated
GENERATE| connectivity. Retry...
GENERATE| Present value of BONDPARM_FACTOR ( 1.273388 ).
GENERATE| Preliminary Number of Bonds generated: 8
GENERATE| WARNING in connectivity generation!
GENERATE| Two molecules/residues named (MOL1) have different number of atoms.
GENERATE| Molecule starting at position (8) has Nr. <2> of atoms.
GENERATE| while the other same molecules have Nr. <6> of atoms!
GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the generated
GENERATE| connectivity. Retry...
GENERATE| Present value of BONDPARM_FACTOR ( 1.337057 ).
GENERATE| Preliminary Number of Bonds generated: 8
GENERATE| WARNING in connectivity generation!
GENERATE| Two molecules/residues named (MOL1) have different number of atoms.
GENERATE| Molecule starting at position (8) has Nr. <2> of atoms.
GENERATE| while the other same molecules have Nr. <6> of atoms!
GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the generated
GENERATE| connectivity. Retry...
GENERATE| Present value of BONDPARM_FACTOR ( 1.403910 ).
GENERATE| Preliminary Number of Bonds generated: 8
GENERATE| WARNING in connectivity generation!
GENERATE| Two molecules/residues named (MOL1) have different number of atoms.
GENERATE| Molecule starting at position (8) has Nr. <2> of atoms.
GENERATE| while the other same molecules have Nr. <6> of atoms!
GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the generated
GENERATE| connectivity. Retry...
GENERATE| Present value of BONDPARM_FACTOR ( 1.474105 ).
GENERATE| Preliminary Number of Bonds generated: 8
GENERATE| WARNING in connectivity generation!
GENERATE| Two molecules/residues named (MOL1) have different number of atoms.
GENERATE| Molecule starting at position (8) has Nr. <2> of atoms.
GENERATE| while the other same molecules have Nr. <6> of atoms!
GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the generated
GENERATE| connectivity. Retry...
GENERATE| Present value of BONDPARM_FACTOR ( 1.547810 ).
GENERATE| Preliminary Number of Bonds generated: 12
GENERATE| WARNING in connectivity generation!
GENERATE| Two molecules/residues named (MOL1) have different number of atoms.
GENERATE| Molecule starting at position (8) has Nr. <2> of atoms.
GENERATE| while the other same molecules have Nr. <6> of atoms!
GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the generated
GENERATE| connectivity. Retry...
GENERATE| Present value of BONDPARM_FACTOR ( 1.625201 ).
GENERATE| Preliminary Number of Bonds generated: 14
GENERATE| WARNING in connectivity generation!
GENERATE| Two molecules/residues named (MOL1) have different number of atoms.
GENERATE| Molecule starting at position (8) has Nr. <2> of atoms.
GENERATE| while the other same molecules have Nr. <6> of atoms!
GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the generated
GENERATE| connectivity. Retry...
GENERATE| Present value of BONDPARM_FACTOR ( 1.706461 ).
GENERATE| Preliminary Number of Bonds generated: 14
GENERATE| WARNING in connectivity generation!
GENERATE| Two molecules/residues named (MOL1) have different number of atoms.
GENERATE| Molecule starting at position (8) has Nr. <2> of atoms.
GENERATE| while the other same molecules have Nr. <6> of atoms!
GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the generated
GENERATE| connectivity. Retry...
GENERATE| Present value of BONDPARM_FACTOR ( 1.791784 ).
GENERATE| Preliminary Number of Bonds generated: 15
GENERATE| WARNING in connectivity generation!
GENERATE| Two molecules/residues named (MOL1) have different number of atoms.
GENERATE| Molecule starting at position (8) has Nr. <2> of atoms.
GENERATE| while the other same molecules have Nr. <6> of atoms!
GENERATE| Increasing bondparm_factor by 1.05.. An error was found in the generated
GENERATE| connectivity. Retry...
GENERATE| Present value of BONDPARM_FACTOR ( 1.881373 ).
GENERATE| Preliminary Number of Bonds generated: 18
GENERATE| Achieved consistency in connectivity generation.
GENERATE| Number of Bonds generated: 18
GENERATE| Preliminary Number of Bends generated: 60
GENERATE| Number of Bends generated: 60
GENERATE| Number of UB generated: 60
GENERATE| Preliminary Number of Torsions generated: 166
GENERATE| Number of Torsions generated: 166
GENERATE| Number of Impropers generated: 3
GENERATE| Number of 1-4 interactions generated: 10
*******************************************************************************
*******************************************************************************
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** ##### ## ## **
** ## ## ## ## ## **
** ## ## ## ###### **
** ## ## ## ## ## ##### ## ## #### ## ##### ##### **
** ## ## ## ## ## ## ## ## ## ## ## ## ## ## **
** ## ## ## ## ## ## ## #### ### ## ###### ###### **
** ## ### ## ## ## ## ## ## ## ## ## ## **
** ####### ##### ## ##### ## ## #### ## ##### ## **
** ## ## **
** **
** ... make the atoms dance **
** **
** Copyright (C) by CP2K developers group (2000 - 2020) **
** J. Chem. Phys. 152, 194103 (2020) **
** **
*******************************************************************************
TOTAL NUMBERS AND MAXIMUM NUMBERS
Total number of - Atomic kinds: 10
- Atoms: 10
- Shell sets: 10
- Shells: 46
- Primitive Cartesian functions: 50
- Cartesian basis functions: 122
- Spherical basis functions: 114
Maximum angular momentum of- Orbital basis functions: 2
- Local part of the GTH pseudopotential: 2
- Non-local part of the GTH pseudopotential: 0
SCF PARAMETERS Density guess: RESTART
--------------------------------------------------------
max_scf: 256
max_scf_history: 0
max_diis: 4
--------------------------------------------------------
eps_scf: 1.00E-05
eps_scf_history: 0.00E+00
eps_diis: 1.00E-01
eps_eigval: 1.00E-05
--------------------------------------------------------
level_shift [a.u.]: 0.00
--------------------------------------------------------
No outer SCF
METADYN| Meta Dynamics Protocol
METADYN| Number of interval time steps to spawn hills 50
METADYN| Number of previously spawned hills 0
METADYN| Spawning the Hills
METADYN| Height of the Spawned Gaussian 0.000
METADYN| Number of collective variables 1
----------------------------------------------------------------------
METAVARS| Collective Variable Number 1
METAVARS| Scaling factor 0.226767
METAVARS| Number of Walls present 2
METAVARS| Wall Number: 1 Type of Wall: REFLECTIVE
METAVARS| Wall direction WALL_PLUS
METAVARS| Wall location 6.614041
METAVARS| Wall Number: 2 Type of Wall: REFLECTIVE
METAVARS| Wall direction WALL_MINUS
METAVARS| Wall location 5.669178
----------------------------------------------------------------------
MD_PAR| Molecular dynamics protocol (MD input parameters)
MD_PAR| Ensemble type NVT
MD_PAR| Number of time steps 3
MD_PAR| Time step [fs] 1.000000
MD_PAR| Temperature [K] 300.000000
MD_PAR| Temperature tolerance [K] 0.000000
MD_PAR| Print MD information every 1 step(s)
MD_PAR| File type Print frequency [steps] File names
MD_PAR| Coordinates 10 traj.xyz
MD_PAR| Velocities 1 md-vel-1.xyz
MD_PAR| Energies 1 md-1.ener
MD_PAR| Dump 20 md-1.restart
ROT| Rotational analysis information
ROT| Principal axes and moments of inertia [a.u.]
ROT| 1 2 3
ROT| Eigenvalues 1.12824771224E+06 2.11271414485E+06 2.60002565658E+06
ROT| x 0.933516582996 -0.162493784059 0.319597495945
ROT| y 0.332751610941 0.724581723408 -0.603537647143
ROT| z -0.133503388302 0.669758983699 0.730479122950
ROT| Number of rotovibrational vectors 6
DOF| Calculation of degrees of freedom
DOF| Number of atoms 10
DOF| Number of intramolecular constraints 0
DOF| Number of intermolecular constraints 0
DOF| Invariants (translations + rotations) 3
DOF| Degrees of freedom 27
DOF| Restraints information
DOF| Number of intramolecular restraints 0
DOF| Number of intermolecular restraints 0
THERMOSTAT| Thermostat information for PARTICLES
THERMOSTAT| Type of thermostat Nose-Hoover-Chains
THERMOSTAT| Nose-Hoover-Chain length 5
THERMOSTAT| Nose-Hoover-Chain time constant [fs] 5.000000
THERMOSTAT| Order of Yoshida integrator 3
THERMOSTAT| Number of multiple time steps 2
THERMOSTAT| Initial potential energy 0.000000000000E+00
THERMOSTAT| Initial kinetic energy 0.475022301493E-03
THERMOSTAT| End of thermostat information for PARTICLES
MD_VEL| Velocities initialization
MD_VEL| Initial temperature [K] 300.000000
MD_VEL| COM velocity -0.0000000000 0.0000000000 -0.0000000000
Number of electrons: 48
Number of occupied orbitals: 24
Number of molecular orbitals: 24
Number of orbital functions: 114
Number of independent orbital functions: 114
Extrapolation method: initial_guess
*** WARNING in qs_initial_guess.F:309 :: User requested to restart the ***
*** wavefunction from the file named: geom-RESTART.wfn. This file does ***
*** not exist. Please check the existence of the file or change properly ***
*** the value of the keyword WFN_RESTART_FILE_NAME. Calculation continues ***
*** using ATOMIC GUESS. ***
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Minimizer : DIIS : direct inversion
in the iterative subspace
using 7 DIIS vectors
safer DIIS on
Preconditioner : FULL_SINGLE_INVERSE : inversion of
H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T
Precond_solver : DEFAULT
stepsize : 0.08000000 energy_gap : 0.08000000
eps_taylor : 0.10000E-15 max_taylor : 4
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.80E-01 18.9 0.12487494 -112.2582270690 -1.12E+02
2 OT DIIS 0.80E-01 0.1 0.10855209 -114.0048973417 -1.75E+00
3 OT DIIS 0.80E-01 0.1 0.06831030 -114.9314352147 -9.27E-01
4 OT DIIS 0.80E-01 0.1 0.05272501 -115.6960003460 -7.65E-01
5 OT DIIS 0.80E-01 0.1 0.04083096 -116.1312640101 -4.35E-01
6 OT DIIS 0.80E-01 0.1 0.03046176 -116.3934102316 -2.62E-01
7 OT DIIS 0.80E-01 0.1 0.02138618 -116.5842086039 -1.91E-01
8 OT DIIS 0.80E-01 0.1 0.01770227 -116.6652306114 -8.10E-02
9 OT DIIS 0.80E-01 0.1 0.01169782 -116.7362610745 -7.10E-02
10 OT DIIS 0.80E-01 0.1 0.00899540 -116.7761586265 -3.99E-02
11 OT DIIS 0.80E-01 0.1 0.00843082 -116.7966829193 -2.05E-02
12 OT DIIS 0.80E-01 0.1 0.00528658 -116.8179964126 -2.13E-02
13 OT DIIS 0.80E-01 0.1 0.00442094 -116.8278291872 -9.83E-03
14 OT DIIS 0.80E-01 0.1 0.00291102 -116.8376270293 -9.80E-03
15 OT DIIS 0.80E-01 0.1 0.00226607 -116.8419035554 -4.28E-03
16 OT DIIS 0.80E-01 0.1 0.00172590 -116.8448536826 -2.95E-03
17 OT DIIS 0.80E-01 0.1 0.00137824 -116.8464264011 -1.57E-03
18 OT DIIS 0.80E-01 0.1 0.00107383 -116.8472850202 -8.59E-04
19 OT DIIS 0.80E-01 0.1 0.00086632 -116.8478026936 -5.18E-04
20 OT DIIS 0.80E-01 0.1 0.00060392 -116.8482859791 -4.83E-04
21 OT DIIS 0.80E-01 0.1 0.00046215 -116.8485124506 -2.26E-04
22 OT DIIS 0.80E-01 0.1 0.00035630 -116.8485927384 -8.03E-05
23 OT DIIS 0.80E-01 0.1 0.00027620 -116.8486447544 -5.20E-05
24 OT DIIS 0.80E-01 0.1 0.00021539 -116.8486784310 -3.37E-05
25 OT DIIS 0.80E-01 0.1 0.00017945 -116.8486959855 -1.76E-05
26 OT DIIS 0.80E-01 0.1 0.00015116 -116.8487087741 -1.28E-05
27 OT DIIS 0.80E-01 0.1 0.00013114 -116.8487171605 -8.39E-06
28 OT DIIS 0.80E-01 0.1 0.00010832 -116.8487256577 -8.50E-06
29 OT DIIS 0.80E-01 0.1 0.00009587 -116.8487315565 -5.90E-06
30 OT DIIS 0.80E-01 0.1 0.00008842 -116.8487357493 -4.19E-06
31 OT DIIS 0.80E-01 0.1 0.00007416 -116.8487405861 -4.84E-06
32 OT DIIS 0.80E-01 0.1 0.00006315 -116.8487441214 -3.54E-06
33 OT DIIS 0.80E-01 0.1 0.00005567 -116.8487463814 -2.26E-06
34 OT DIIS 0.80E-01 0.1 0.00004821 -116.8487484545 -2.07E-06
35 OT DIIS 0.80E-01 0.1 0.00004274 -116.8487498102 -1.36E-06
36 OT DIIS 0.80E-01 0.1 0.00003631 -116.8487510848 -1.27E-06
37 OT DIIS 0.80E-01 0.1 0.00003219 -116.8487520449 -9.60E-07
38 OT DIIS 0.80E-01 0.1 0.00002998 -116.8487525736 -5.29E-07
39 OT DIIS 0.80E-01 0.1 0.00002667 -116.8487531310 -5.57E-07
40 OT DIIS 0.80E-01 0.1 0.00002451 -116.8487535298 -3.99E-07
41 OT DIIS 0.80E-01 0.1 0.00002270 -116.8487539070 -3.77E-07
42 OT DIIS 0.80E-01 0.1 0.00002090 -116.8487542706 -3.64E-07
43 OT DIIS 0.80E-01 0.1 0.00001952 -116.8487545391 -2.69E-07
44 OT DIIS 0.80E-01 0.1 0.00001798 -116.8487548169 -2.78E-07
45 OT DIIS 0.80E-01 0.1 0.00001653 -116.8487551386 -3.22E-07
46 OT DIIS 0.80E-01 0.1 0.00001547 -116.8487553628 -2.24E-07
47 OT DIIS 0.80E-01 0.1 0.00001395 -116.8487556148 -2.52E-07
48 OT DIIS 0.80E-01 0.1 0.00001263 -116.8487558063 -1.91E-07
49 OT DIIS 0.80E-01 0.1 0.00001117 -116.8487559883 -1.82E-07
50 OT DIIS 0.80E-01 0.1 0.00000983 -116.8487561267 -1.38E-07
*** SCF run converged in 50 steps ***
Electronic density on regular grids: -47.9999999774 0.0000000226
Core density on regular grids: 47.9999999987 -0.0000000013
Total charge density on r-space grids: 0.0000000213
Total charge density g-space grids: 0.0000000213
Overlap energy of the core charge distribution: 0.00000013217887
Self energy of the core charge distribution: -301.67942807122284
Core Hamiltonian energy: 85.89391241443138
Hartree energy: 125.34944820741946
Exchange-correlation energy: -20.36577040356821
Hartree-Fock Exchange energy: -6.04691840597645
Total energy: -116.84875612673781
ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -116.848756217926649
MD_INI| MD initialization
MD_INI| Potential energy [hartree] -0.116848756218E+03
MD_INI| Kinetic energy [hartree] 0.128256021403E-01
MD_INI| Temperature [K] 300.000000
MD_INI| Cell volume [bohr^3] 6.748334583090E+03
MD_INI| Cell volume [ang^3] 1.000000000000E+03
MD_INI| Cell lengths [bohr] 1.88972613E+01 1.88972613E+01 1.88972613E+01
MD_INI| Cell lengths [ang] 1.00000000E+01 1.00000000E+01 1.00000000E+01
MD_INI| Cell angles [deg] 9.00000000E+01 9.00000000E+01 9.00000000E+01
Number of electrons: 48
Number of occupied orbitals: 24
Number of molecular orbitals: 24
Number of orbital functions: 114
Number of independent orbital functions: 114
Extrapolation method: ASPC
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Minimizer : DIIS : direct inversion
in the iterative subspace
using 7 DIIS vectors
safer DIIS on
Preconditioner : FULL_SINGLE_INVERSE : inversion of
H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T
Precond_solver : DEFAULT
stepsize : 0.08000000 energy_gap : 0.08000000
eps_taylor : 0.10000E-15 max_taylor : 4
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.80E-01 3.2 0.00112695 -116.8477295812 -1.17E+02
2 OT DIIS 0.80E-01 0.1 0.00069136 -116.8479473161 -2.18E-04
3 OT DIIS 0.80E-01 0.1 0.00030810 -116.8480769687 -1.30E-04
4 OT DIIS 0.80E-01 0.1 0.00012197 -116.8481061733 -2.92E-05
5 OT DIIS 0.80E-01 0.1 0.00004754 -116.8481107865 -4.61E-06
6 OT DIIS 0.80E-01 0.1 0.00002152 -116.8481114731 -6.87E-07
7 OT DIIS 0.80E-01 0.1 0.00001156 -116.8481116044 -1.31E-07
8 OT DIIS 0.80E-01 0.1 0.00000479 -116.8481116509 -4.65E-08
*** SCF run converged in 8 steps ***
Electronic density on regular grids: -47.9999999571 0.0000000429
Core density on regular grids: 47.9999999987 -0.0000000013
Total charge density on r-space grids: 0.0000000416
Total charge density g-space grids: 0.0000000416
Overlap energy of the core charge distribution: 0.00000012911475
Self energy of the core charge distribution: -301.67942807122284
Core Hamiltonian energy: 85.85598627021145
Hartree energy: 125.37823521764788
Exchange-correlation energy: -20.35863635957127
Hartree-Fock Exchange energy: -6.04426883707062
Total energy: -116.84811165089063
ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -116.848111658696013
MD| ***************************************************************************
MD| Step number 1
MD| Time [fs] 1.000000
MD| Conserved quantity [hartree] -0.116835418936E+03
MD| ---------------------------------------------------------------------------
MD| Instantaneous Averages
MD| CPU time per MD step [s] 100.716271 100.716271
MD| Energy drift per atom [K] 0.115754274049E+01 0.000000000000E+00
MD| Potential energy [hartree] -0.116848111659E+03 -0.116848111659E+03
MD| Kinetic energy [hartree] 0.113061479493E-01 0.113061479493E-01
MD| Temperature [K] 264.458881 264.458881
MD| ***************************************************************************
Number of electrons: 48
Number of occupied orbitals: 24
Number of molecular orbitals: 24
Number of orbital functions: 114
Number of independent orbital functions: 114
Extrapolation method: ASPC
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Minimizer : DIIS : direct inversion
in the iterative subspace
using 7 DIIS vectors
safer DIIS on
Preconditioner : FULL_SINGLE_INVERSE : inversion of
H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T
Precond_solver : DEFAULT
stepsize : 0.08000000 energy_gap : 0.08000000
eps_taylor : 0.10000E-15 max_taylor : 4
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.80E-01 3.2 0.00032882 -116.8472640767 -1.17E+02
2 OT DIIS 0.80E-01 0.1 0.00019855 -116.8472827557 -1.87E-05
3 OT DIIS 0.80E-01 0.1 0.00006723 -116.8472938766 -1.11E-05
4 OT DIIS 0.80E-01 0.1 0.00003036 -116.8472951264 -1.25E-06
5 OT DIIS 0.80E-01 0.1 0.00001150 -116.8472953913 -2.65E-07
6 OT DIIS 0.80E-01 0.1 0.00000477 -116.8472954301 -3.88E-08
*** SCF run converged in 6 steps ***
Electronic density on regular grids: -47.9999999493 0.0000000507
Core density on regular grids: 47.9999999987 -0.0000000013
Total charge density on r-space grids: 0.0000000494
Total charge density g-space grids: 0.0000000494
Overlap energy of the core charge distribution: 0.00000013627888
Self energy of the core charge distribution: -301.67942807122284
Core Hamiltonian energy: 85.84021573065401
Hartree energy: 125.39096972285142
Exchange-correlation energy: -20.35580294981887
Hartree-Fock Exchange energy: -6.04324999884880
Total energy: -116.84729543010624
ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -116.847295435643915
MD| ***************************************************************************
MD| Step number 2
MD| Time [fs] 2.000000
MD| Conserved quantity [hartree] -0.116835379616E+03
MD| ---------------------------------------------------------------------------
MD| Instantaneous Averages
MD| CPU time per MD step [s] 35.476671 68.096471
MD| Energy drift per atom [K] 0.239917588885E+01 0.119958794443E+01
MD| Potential energy [hartree] -0.116847295436E+03 -0.116847703547E+03
MD| Kinetic energy [hartree] 0.981199679810E-02 0.105590723737E-01
MD| Temperature [K] 229.509617 246.984249
MD| ***************************************************************************
Number of electrons: 48
Number of occupied orbitals: 24
Number of molecular orbitals: 24
Number of orbital functions: 114
Number of independent orbital functions: 114
Extrapolation method: ASPC
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Minimizer : DIIS : direct inversion
in the iterative subspace
using 7 DIIS vectors
safer DIIS on
Preconditioner : FULL_SINGLE_INVERSE : inversion of
H + eS - 2*(Sc)(c^T*H*c+const)(Sc)^T
Precond_solver : DEFAULT
stepsize : 0.08000000 energy_gap : 0.08000000
eps_taylor : 0.10000E-15 max_taylor : 4
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.80E-01 3.1 0.00026414 -116.8468718871 -1.17E+02
2 OT DIIS 0.80E-01 0.1 0.00016213 -116.8468840351 -1.21E-05
3 OT DIIS 0.80E-01 0.1 0.00005273 -116.8468915665 -7.53E-06
4 OT DIIS 0.80E-01 0.1 0.00002494 -116.8468922949 -7.28E-07
5 OT DIIS 0.80E-01 0.1 0.00000738 -116.8468924857 -1.91E-07
*** SCF run converged in 5 steps ***
Electronic density on regular grids: -47.9999999602 0.0000000398
Core density on regular grids: 47.9999999987 -0.0000000013
Total charge density on r-space grids: 0.0000000385
Total charge density g-space grids: 0.0000000385
Overlap energy of the core charge distribution: 0.00000014043946
Self energy of the core charge distribution: -301.67942807122284
Core Hamiltonian energy: 85.83882444381089
Hartree energy: 125.39274746399474
Exchange-correlation energy: -20.35573733221211
Hartree-Fock Exchange energy: -6.04329913050111
Total energy: -116.84689248569097
ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -116.846892499927975
MD| ***************************************************************************
MD| Step number 3
MD| Time [fs] 3.000000
MD| Conserved quantity [hartree] -0.116835392655E+03
MD| ---------------------------------------------------------------------------
MD| Instantaneous Averages
MD| CPU time per MD step [s] 35.096049 57.096331
MD| Energy drift per atom [K] 0.198743204794E+01 0.146220264560E+01
MD| Potential energy [hartree] -0.116846892500E+03 -0.116847433198E+03
MD| Kinetic energy [hartree] 0.891199327799E-02 0.100100460085E-01
MD| Temperature [K] 208.457892 234.142130
MD| ***************************************************************************
-------------------------------------------------------------------------------
- -
- DBCSR STATISTICS -
- -
-------------------------------------------------------------------------------
COUNTER TOTAL BLAS SMM ACC
flops 5 x 24 x 24 46080 0.0% 100.0% 0.0%
flops 5 x 5 x 24 291600 0.0% 100.0% 0.0%
flops 5 x 24 x 5 782400 0.0% 100.0% 0.0%
flops 13 x 5 x 24 2021760 0.0% 100.0% 0.0%
flops 5 x 13 x 24 2021760 0.0% 100.0% 0.0%
flops 18 x 24 x 18 4541184 0.0% 100.0% 0.0%
flops 13 x 24 x 5 8136960 0.0% 100.0% 0.0%
flops 5 x 24 x 13 8136960 0.0% 100.0% 0.0%
flops 13 x 24 x 18 9839232 0.0% 100.0% 0.0%
flops 18 x 24 x 13 9839232 0.0% 100.0% 0.0%
flops 24 x 24 x 18 11446272 0.0% 100.0% 0.0%
flops 18 x 24 x 24 14141952 0.0% 100.0% 0.0%
flops 24 x 24 x 24 14819328 0.0% 100.0% 0.0%
flops 13 x 13 x 24 23654592 0.0% 100.0% 0.0%
flops 24 x 24 x 13 24800256 0.0% 100.0% 0.0%
flops 13 x 24 x 24 31120128 0.0% 100.0% 0.0%
flops 13 x 24 x 13 105942720 0.0% 100.0% 0.0%
flops inhomo. stacks 0 0.0% 0.0% 0.0%
flops total 271.582416E+06 0.0% 100.0% 0.0%
flops max/rank 73.677744E+06 0.0% 100.0% 0.0%
matmuls inhomo. stacks 0 0.0% 0.0% 0.0%
matmuls total 30939 0.0% 100.0% 0.0%
number of processed stacks 30939 0.0% 100.0% 0.0%
average stack size 0.0 1.0 0.0
marketing flops 294.646464E+06
-------------------------------------------------------------------------------
# multiplications 1478
max memory usage/rank 167.968768E+06
# max total images/rank 1
# max 3D layers 1
# MPI messages exchanged 1324288
MPI messages size (bytes):
total size 415.876608E+06
min size 0.000000E+00
max size 4.608000E+03
average size 314.037903E+00
MPI breakdown and total messages size (bytes):
size <= 128 1136121 0
128 < size <= 8192 188167 415876608
8192 < size <= 32768 0 0
32768 < size <= 131072 0 0
131072 < size <= 4194304 0 0
4194304 < size <= 16777216 0 0
16777216 < size 0 0
-------------------------------------------------------------------------------
- -
- DBCSR MESSAGE PASSING PERFORMANCE -
- -
-------------------------------------------------------------------------------
ROUTINE CALLS AVE VOLUME [Bytes]
MP_Bcast 18 12.
MP_Allreduce 8005 8.
MP_Alltoall 5263 5728.
MP_ISend 47280 581.
MP_IRecv 47280 434.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
- -
- GRID STATISTICS -
- -
-------------------------------------------------------------------------------
LP KERNEL BACKEND COUNT PERCENT
4 collocate ortho REF 60710 30.36%
4 integrate ortho REF 59022 29.51%
3 collocate ortho REF 29857 14.93%
3 integrate ortho REF 28597 14.30%
2 collocate ortho REF 6862 3.43%
2 integrate ortho REF 6486 3.24%
5 integrate ortho REF 3324 1.66%
0 collocate general REF 2560 1.28%
1 integrate general REF 2560 1.28%
-------------------------------------------------------------------------------
MEMORY| Estimated peak process memory [MiB] 161
-------------------------------------------------------------------------------
- -
- MESSAGE PASSING PERFORMANCE -
- -
-------------------------------------------------------------------------------
ROUTINE CALLS AVE VOLUME [Bytes]
MP_Group 4
MP_Bcast 3841 277066.
MP_Allreduce 9568 118.
MP_Sync 457
MP_Alltoall 1737 1040931.
MP_ISendRecv 38052 10763.
MP_Wait 49910
MP_comm_split 50
MP_ISend 11088 38592.
MP_IRecv 11088 38592.
MP_Recv 42 2736.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
- -
- R E F E R E N C E S -
- -
-------------------------------------------------------------------------------
CP2K version 8.1, the CP2K developers group (2020).
CP2K is freely available from https://www.cp2k.org/ .
Kuehne,Thomas D.; Iannuzzi,Marcella; Del Ben,Mauro;
Rybkin,Vladimir V.; Seewald,Patrick; Stein,Frederick; Laino,Teodoro;
Khaliullin,Rustam Z.; Schuett,Ole; Schiffmann,Florian; Golze,Dorothea;
Wilhelm,Jan; Chulkov,Sergey; Bani-Hashemian,Mohammad Hossein;
Weber,Valery; Borstnik,Urban; Taillefumier,Mathieu;
Jakobovits,Alice Shoshana; Lazzaro,Alfio; Pabst,Hans; Mueller,Tiziano;
Schade,Robert; Guidon,Manuel; Andermatt,Samuel; Holmberg,Nico;
Schenter,Gregory K.; Hehn,Anna; Bussy,Augustin; Belleflamme,Fabian;
Tabacchi,Gloria; Gloess,Andreas; Lass,Michael; Bethune,Iain;
Mundy,Christopher J.; Plessl,Christian; Watkins,Matt;
VandeVondele,Joost; Krack,Matthias; Hutter,Juerg.
The Journal of Chemical Physics, 152 (19), (2020).
CP2K: An electronic structure and molecular dynamics software package -
Quickstep: Efficient and accurate electronic structure calculations.
https://doi.org/10.1063/5.0007045
Schuett, Ole; Messmer, Peter; Hutter, Juerg; VandeVondele, Joost.
Electronic Structure Calculations on Graphics Processing Units, John
Wiley & Sons, Ltd, 173-190 (2016).
GPU-Accelerated Sparse Matrix-Matrix Multiplication for
Linear Scaling Density Functional Theory.
https://doi.org/10.1002/9781118670712.ch8
Borstnik, U; VandeVondele, J; Weber, V; Hutter, J.
PARALLEL COMPUTING, 40 (5-6), 47-58 (2014).
Sparse matrix multiplication: The distributed block-compressed sparse
row library.
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- -
- T I M I N G -
- -
-------------------------------------------------------------------------------
SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
CP2K 1 1.0 0.022 0.025 171.571 171.571
qs_mol_dyn_low 1 2.0 0.111 0.112 171.345 171.348
qs_forces 4 3.8 0.001 0.002 171.003 171.004
rebuild_ks_matrix 73 8.1 0.000 0.000 167.000 167.004
qs_ks_build_kohn_sham_matrix 73 9.1 0.009 0.012 167.000 167.004
hfx_ks_matrix 73 10.1 0.003 0.004 163.687 163.697
qs_ks_update_qs_env_forces 4 4.8 0.000 0.000 135.809 135.810
derivatives_four_center 4 8.8 0.032 0.192 135.550 135.553
derivatives_four_center_main 4 9.8 0.001 0.001 135.338 135.345
derivatives_four_center_bin 417 10.8 123.457 134.139 123.457 134.139
velocity_verlet 3 3.0 0.063 0.063 106.376 106.377
qs_energies 4 4.8 0.001 0.002 35.174 35.174
scf_env_do_scf 4 5.8 0.000 0.000 34.791 34.792
qs_ks_update_qs_env 73 7.3 0.001 0.001 31.195 31.198
init_scf_loop 4 6.8 0.000 0.000 28.288 28.289
integrate_four_center 73 11.1 0.069 0.488 28.130 28.132
mp_sum_lv 31 5.3 11.882 19.738 11.882 19.738
integrate_four_center_main 73 12.1 0.008 0.009 12.157 12.570
integrate_four_center_bin 7738 13.1 12.149 12.561 12.149 12.561
calc_screening_functions 1 12.0 8.268 8.368 9.346 9.455
scf_env_do_scf_inner_loop 69 6.3 0.002 0.012 6.497 6.499
calc_pair_dist_radii 1 12.0 4.713 4.757 5.312 5.365
-------------------------------------------------------------------------------
The number of warnings for this run is : 1
-------------------------------------------------------------------------------
**** **** ****** ** PROGRAM ENDED AT 2021-11-17 09:53:02.163
***** ** *** *** ** PROGRAM RAN ON ga2008.para.bscc
** **** ****** PROGRAM RAN BY scb3056
***** ** ** ** ** PROGRAM PROCESS ID 129715
**** ** ******* ** PROGRAM STOPPED IN /public1/home/scb3056/fangyg/test/for
um/vacuo
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