[CP2K-user] [CP2K:11982] Re: first principle MD in zeolite
Peiyao Wu
wupeiy... at gmail.com
Wed Jul 17 16:58:20 UTC 2019
That's correct. Thanks!
On Wednesday, July 17, 2019 at 10:04:36 AM UTC-5, Matthias Krack wrote:
>
> 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:* c... at googlegroups.com <javascript:> <c... at googlegroups.com
> <javascript:>> *On Behalf Of *Peiyao Wu
> *Sent:* Mittwoch, 17. Juli 2019 16:31
> *To:* cp2k <c... at googlegroups.com <javascript:>>
> *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
>
>
>
>
>
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