first principle MD in zeolite
Assigned to mit...@gmail.com by me
Peiyao Wu
I'm trying to run a first principle MD for a box with nitrogen and zeolite (structure with xyz coordinate). The job started running with no error message and terminate in about five minutes with "OT -----killed-----". What are some things that might be wrong in my input file?
&GLOBAL
PROJECT MOF
RUN_TYPE MD
! limit the runs to 5min
WALLTIME
! reduce the amount of IO
IOLEVEL LOW
&END GLOBAL
&FORCE_EVAL
METHOD QS
!STRESS_TENSOR DIAGONAL_NUMERICAL
&DFT
BASIS_SET_FILE_NAME ~/cp2k/data/BASIS_MOLOPT
POTENTIAL_FILE_NAME ~/cp2k/data/GTH_POTENTIALS
&MGRID
CUTOFF 300
NGRIDS 5
&END
&QS
METHOD GPW
EPS_DEFAULT 1.0E-10
EXTRAPOLATION ASPC
&END QS
&POISSON
PERIODIC XYZ
&END
&SCF
EPS_SCF 1.0E-6
SCF_GUESS ATOMIC
MAX_SCF 20
&OT
MINIMIZER DIIS
PRECONDITIONER FULL_KINETIC
&END OT
&OUTER_SCF
EPS_SCF 1.0E-6
MAX_SCF 10
&END OUTER_SCF
&END SCF
&XC
&XC_FUNCTIONAL PBE
&END
&VDW_POTENTIAL
POTENTIAL_TYPE PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD3
REFERENCE_C9_TERM .TRUE.
LONG_RANGE_CORRECTION .TRUE.
PARAMETER_FILE_NAME dftd3.dat
REFERENCE_FUNCTIONAL PBE
R_CUTOFF [angstrom] 10.0
EPS_CN 1.0E-6
&END PAIR_POTENTIAL
&END VDW_POTENTIAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC 24.188 24.188 24.188
ALPHA_BETA_GAMMA 90.0 90.0 90.0
&END CELL
&COORD
@INCLUDE box1config.xyz
&END COORD
&KIND Si
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND Al
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q3
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q6
ELEMENT O
&END KIND
&KIND Ca
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q10
&END KIND
&KIND N
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q5
&END KIND
&END SUBSYS
&END FORCE_EVAL
&MOTION
&GEO_OPT
OPTIMIZER LBFGS ! Good choice for 'small' systems (use LBFGS for large systems)
MAX_ITER 100
MAX_DR [bohr] 0.003 ! adjust target as needed
&LBFGS
&END
&END
&MD
ENSEMBLE NVT ! sampling the canonical ensemble, accurate properties might need NVE
TEMPERATURE [K] 77.0
TIMESTEP [fs] 0.5
STEPS 100
# GLE thermostat as generated at http://epfl-cosmo.github.io/gle4md
# GLE provides an effective NVT sampling.
&THERMOSTAT
TYPE NOSE
REGION MASSIVE
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON [wavenumber_t] 1000.0
MTS 2
&END NOSE
&END THERMOSTAT
&END
&TRAJECTORY
&EACH
MD 1
&END EACH
&END TRAJECTORY
&VELOCITIES OFF
&END VELOCITIES
&FORCES OFF
&END FORCES
&RESTART_HISTORY
&EACH
MD 500
&END EACH
&END RESTART_HISTORY
&RESTART
BACKUP_COPIES 3
&EACH
MD 1
&END EACH
&END RESTART
&END PRINT
&END MOTION
Vladimir Rybkin
среда, 17 июля 2019 г., 15:34:08 UTC+2 пользователь Peiyao Wu написал:
Peiyao Wu
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.
*******************************************************************************
*******************************************************************************
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** ## ## ## ## ## ##### ## ## #### ## ##### ##### **
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** ## ## ## ## ## ## ## #### ### ## ###### ###### **
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** ####### ##### ## ##### ## ## #### ## ##### ## **
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** **
** ... 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
Krack Matthias (PSI)
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.
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Peiyao Wu
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