[CP2K-user] [CP2K:11982] Re: first principle MD in zeolite

Krack Matthias (PSI) matthi... at psi.ch
Wed Jul 17 15:03:32 CET 2019


Running a 686 atoms system on a single CPU core might exceed the available memory and cause an out-of-memory from the system.

M.

From: cp... at googlegroups.com <cp... at googlegroups.com> On Behalf Of Peiyao Wu
Sent: Mittwoch, 17. Juli 2019 16:31
To: cp2k <cp... at googlegroups.com>
Subject: [CP2K:11982] Re: first principle MD in zeolite


I'm running on a supercomputer in a research institute. I also added a line "LSD .TRUE." because it had an error of odd number of electrons.

The out put is this:



 DBCSR| CPU Multiplication driver                                           BLAS

 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| Number of 3D layers                                               SINGLE

 DBCSR| Use MPI memory allocation                                              T

 DBCSR| Use RMA algorithm                                                      F

 DBCSR| Use Communication thread                                               T

 DBCSR| Communication thread load                                             87





  **** **** ******  **  PROGRAM STARTED AT               2019-07-17 09:18:47.903

 ***** ** ***  *** **   PROGRAM STARTED ON                                ln0006

 **    ****   ******    PROGRAM STARTED BY                                   pwu

 ***** **    ** ** **   PROGRAM PROCESS ID                                  3398

  **** **  *******  **  PROGRAM STARTED IN /panfs/roc/groups/12/siepmann/pwu/tes

                                           t-cp2k/BCR-10-4-NPT



 CP2K| version string:                    CP2K version 7.0 (Development Version)

 CP2K| source code revision number:                                  git:a55c4e4

 CP2K| cp2kflags: fftw3 parallel mpi3 scalapack

 CP2K| is freely available from                            https://www.cp2k.org/

 CP2K| Program compiled at                          Fri Jul 12 17:38:01 CDT 2019

 CP2K| Program compiled on                                                ln0004

 CP2K| Program compiled for                                   Linux-x86-64-intel

 CP2K| Data directory path           /panfs/roc/groups/12/siepmann/pwu/cp2k/data

 CP2K| Input file name                                                    md.inp



 GLOBAL| Force Environment number                                              1

 GLOBAL| Basis set file name            /home/siepmann/pwu/cp2k/data/BASIS_MOLOP

 GLOBAL| Potential file name            /home/siepmann/pwu/cp2k/data/GTH_POTENTI

 GLOBAL| MM Potential file name                                     MM_POTENTIAL

 GLOBAL| Coordinate file name                                      __STD_INPUT__

 GLOBAL| Method name                                                        CP2K

 GLOBAL| Project name                                                        MOF

 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                             1

 GLOBAL| Number of threads for this process                                    1

 GLOBAL| This output is from process                                           0

 GLOBAL| CPU model name                Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz



 MEMORY| system memory details [Kb]

 MEMORY|                        rank 0           min           max       average

 MEMORY| MemTotal             65670968      65670968      65670968      65670968

 MEMORY| MemFree               4173760       4173760       4173760       4173760

 MEMORY| Buffers                  4220          4220          4220          4220

 MEMORY| Cached               56787252      56787252      56787252      56787252

 MEMORY| Slab                  1140136       1140136       1140136       1140136

 MEMORY| SReclaimable           893684        893684        893684        893684

 MEMORY| MemLikelyFree        61858916      61858916      61858916      61858916





 GENERATE|  Preliminary Number of Bonds generated:                             0

 GENERATE|  Achieved consistency in connectivity generation.



 *******************************************************************************

 *******************************************************************************

 **                                                                           **

 **     #####                         ##              ##                      **

 **    ##   ##            ##          ##              ##                      **

 **   ##     ##                       ##            ######                    **

 **   ##     ##  ##   ##  ##   #####  ##  ##   ####   ##    #####    #####    **

 **   ##     ##  ##   ##  ##  ##      ## ##   ##      ##   ##   ##  ##   ##   **

 **   ##  ## ##  ##   ##  ##  ##      ####     ###    ##   ######   ######    **

 **    ##  ###   ##   ##  ##  ##      ## ##      ##   ##   ##       ##        **

 **     #######   #####   ##   #####  ##  ##  ####    ##    #####   ##        **

 **           ##                                                    ##        **

 **                                                                           **

 **                                                ... make the atoms dance   **

 **                                                                           **

 **            Copyright (C) by CP2K developers group (2000 - 2019)           **

 **                                                                           **

 *******************************************************************************





 TOTAL NUMBERS AND MAXIMUM NUMBERS



  Total number of            - Atomic kinds:                                   5

                             - Atoms:                                        686

                             - Shell sets:                                   686

                             - Shells:                                      3467

                             - Primitive Cartesian functions:               3276

                             - Cartesian basis functions:                   9641

                             - Spherical basis functions:                   8955



  Maximum angular momentum of- Orbital basis functions:                        2

                             - Local part of the GTH pseudopotential:          2

                             - Non-local part of the GTH pseudopotential:      3





 SCF PARAMETERS         Density guess:                                    ATOMIC

                        --------------------------------------------------------

                        max_scf:                                              20

                        max_scf_history:                                       0

                        max_diis:                                              4

                        --------------------------------------------------------

                        eps_scf:                                        1.00E-06

                        eps_scf_history:                                0.00E+00

                        eps_diis:                                       1.00E-01

                        eps_eigval:                                     1.00E-05

                        --------------------------------------------------------

                        level_shift [a.u.]:                                 0.00

                        --------------------------------------------------------

                        Outer loop SCF in use

                        No variables optimised in outer loop

                        eps_scf                                         1.00E-06

                        max_scf                                               10

                        No outer loop optimization

                        step_size                                       5.00E-01



 MD| Molecular Dynamics Protocol

 MD| Ensemble Type                                                           NVT

 MD| Number of Time Steps                                                    100

 MD| Time Step [fs]                                                         0.50

 MD| Temperature [K]                                                       77.00

 MD| Temperature tolerance [K]                                              0.00

 MD| Print MD information every                                        1 step(s)

 MD| File type     Print frequency[steps]                             File names

 MD| Coordinates            1                                      MOF-pos-1.xyz

 MD| Velocities             1                                      MOF-vel-1.xyz

 MD| Energies               1                                         MOF-1.ener

 MD| Dump                   1                                      MOF-1.restart



 ROT| Rotational Analysis Info

 ROT| Principal axes and moments of inertia in atomic units:

 ROT|                                1                 2                 3

 ROT| EIGENVALUES            0.865428622E+10   0.875228727E+10   0.934185610E+10

 ROT|      X                     0.811895120       0.355981637       0.462713073

 ROT|      Y                    -0.583698550       0.479959905       0.654930907

 ROT|      Z                     0.011059654      -0.801820157       0.597463070

 ROT| Number of Rotovibrational vectors:     6



 Calculation of degrees of freedom

                                                      Number of atoms:       686

                                 Number of Intramolecular constraints:         0

                                 Number of Intermolecular constraints:         0

                                  Invariants(translation + rotations):         0

                                                   Degrees of freedom:      2058





 Restraints Information

                                  Number of Intramolecular restraints:         0

                                  Number of Intermolecular restraints:         0



 THERMOSTAT| Thermostat Info for PARTICLES

 THERMOSTAT| Type of thermostat                               Nose-Hoover-Chains

 THERMOSTAT| Nose-Hoover-Chain length                                          3

 THERMOSTAT| Nose-Hoover-Chain time constant [  fs]                        33.36

 THERMOSTAT| Order of Yoshida integrator                                       3

 THERMOSTAT| Number of multiple time steps                                     2

 THERMOSTAT| Initial Potential Energy                                   0.000000

 THERMOSTAT| Initial Kinetic Energy                                     0.250916

 THERMOSTAT| End of Thermostat Info for PARTICLES



 ************************** Velocities initialization **************************

 Initial Temperature                                                     77.00 K

 COM velocity:           -0.000000000000     -0.000000000000     -0.000000000000

 *******************************************************************************





 Spin 1



 Number of electrons:                                                       1868

 Number of occupied orbitals:                                               1868

 Number of molecular orbitals:                                              1868



 Spin 2



 Number of electrons:                                                       1867

 Number of occupied orbitals:                                               1867

 Number of molecular orbitals:                                              1867



 Number of orbital functions:                                               8955

 Number of independent orbital functions:                                   8955



 Extrapolation method: initial_guess





 SCF WAVEFUNCTION OPTIMIZATION



  ----------------------------------- OT ---------------------------------------

  Minimizer      : DIIS                : direct inversion

                                         in the iterative subspace

                                         using   7 DIIS vectors

                                         safer DIIS on

  Preconditioner : FULL_KINETIC        : inversion of T + eS

  Precond_solver : DEFAULT

  stepsize       :    0.15000000                  energy_gap     :    0.20000000

  eps_taylor     :   0.10000E-15                  max_taylor     :             4

  ----------------------------------- OT ---------------------------------------



  Step     Update method      Time    Convergence         Total energy    Change

  ------------------------------------------------------------------------------

Killed




--
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp... at googlegroups.com<mailto:cp... at googlegroups.com>.
To post to this group, send email to cp... at googlegroups.com<mailto:cp... at googlegroups.com>.
Visit this group at https://groups.google.com/group/cp2k.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/887ae44b-998f-4935-8ad4-f98c5d5a5c44%40googlegroups.com<https://groups.google.com/d/msgid/cp2k/887ae44b-998f-4935-8ad4-f98c5d5a5c44%40googlegroups.com?utm_medium=email&utm_source=footer>.
For more options, visit https://groups.google.com/d/optout.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20190717/b96edc90/attachment-0001.html>


More information about the CP2K-user mailing list