[CP2K-user] first principle MD in zeolite
Peiyao Wu
wupeiy... at gmail.com
Wed Jul 17 14:31:03 UTC 2019
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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** ####### ##### ## ##### ## ## #### ## ##### ##
**
** ## ##
**
**
**
** ... 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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