error in exercise(ETHZ) - Lecture 6
TBLEE
taeb... at gmail.com
Wed Oct 29 13:35:03 UTC 2014
Hello,
I was doing exercise on CP2K.org site but following error message was
generated ....
Does anyone have idea about this error? FYI, I attach input file that I
used.
Thanks,
[tlee8 at crcfe02 EXERCISE_6.1]$ cp2k.popt mybasis.inp
DBCSR| Multiplication driver
SMM
DBCSR| Multiplication stack size
1000
DBCSR| Multiplication size stacks
0
DBCSR| Use subcommunicators
T
DBCSR| Use MPI combined types
F
DBCSR| Use MPI memory allocation
T
DBCSR| Use Communication thread
T
DBCSR| Communication thread load
100
**** **** ****** ** PROGRAM STARTED AT 2014-10-29
09:32:50.518
***** ** *** *** ** PROGRAM STARTED ON
crcfe02.crc.nd.edu
** **** ****** PROGRAM STARTED BY
tlee8
***** ** ** ** ** PROGRAM PROCESS ID
52535
**** ** ******* ** PROGRAM STARTED IN
/pscratch/tlee8/CP2K_TUTORIAL/EXERCIS
E-ETHZ/LECTURE6/EXERCISE_6.1
CP2K| version string: CP2K version
2.4.0
CP2K| source code revision number:
12993
CP2K| is freely available from
http://www.cp2k.org/
CP2K| Program compiled at Mon Oct 28 11:01:26 EDT
2013
CP2K| Program compiled on
opteron.crc.nd.edu
CP2K| Program compiled for
Linux-x86-64-intel
CP2K| Input file name
mybasis.inp
GLOBAL| Force Environment number
1
GLOBAL| Basis set file name
BASIS_SET
GLOBAL| Geminal file name
BASIS_GEMINAL
GLOBAL| Potential file name
POTENTIAL
GLOBAL| MM Potential file name
MM_POTENTIAL
GLOBAL| Coordinate file name
__STD_INPUT__
GLOBAL| Method name
CP2K
GLOBAL| Project name
H-mybasis
GLOBAL| Preferred FFT library
FFTW3
GLOBAL| Run type
ENERGY
GLOBAL| All-to-all communication in single precision
F
GLOBAL| FFTs using library dependent lengths
F
GLOBAL| Global print level
MEDIUM
GLOBAL| Total number of message passing processes
1
GLOBAL| Number of threads for this process
1
GLOBAL| This output is from process
0
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max
average
MEMORY| MemTotal 264498560 264498560 264498560
264498560
MEMORY| MemFree 150235840 150235840 150235840
150235840
MEMORY| Buffers 409384 409384 409384
409384
MEMORY| Cached 105928768 105928768 105928768
105928768
MEMORY| Slab 3076572 3076572 3076572
3076572
MEMORY| SReclaimable 2805852 2805852 2805852
2805852
MEMORY| MemLikelyFree 259379844 259379844 259379844
259379844
*** Fundamental physical constants (SI units) ***
*** Literature: B. J. Mohr and B. N. Taylor,
*** CODATA recommended values of the fundamental physical
*** constants: 2006, Web Version 5.1
*** http://physics.nist.gov/constants
Speed of light in vacuum [m/s]
2.99792458000000E+08
Magnetic constant or permeability of vacuum [N/A**2]
1.25663706143592E-06
Electric constant or permittivity of vacuum [F/m]
8.85418781762039E-12
Planck constant (h) [J*s]
6.62606896000000E-34
Planck constant (h-bar) [J*s]
1.05457162825177E-34
Elementary charge [C]
1.60217648700000E-19
Electron mass [kg]
9.10938215000000E-31
Electron g factor [ ]
-2.00231930436220E+00
Proton mass [kg]
1.67262163700000E-27
Fine-structure constant
7.29735253760000E-03
Rydberg constant [1/m]
1.09737315685270E+07
Avogadro constant [1/mol]
6.02214179000000E+23
Boltzmann constant [J/K]
1.38065040000000E-23
Atomic mass unit [kg]
1.66053878200000E-27
Bohr radius [m]
5.29177208590000E-11
*** Conversion factors ***
[u] -> [a.u.]
1.82288848426455E+03
[Angstrom] -> [Bohr] = [a.u.]
1.88972613288564E+00
[a.u.] = [Bohr] -> [Angstrom]
5.29177208590000E-01
[a.u.] -> [s]
2.41888432650478E-17
[a.u.] -> [fs]
2.41888432650478E-02
[a.u.] -> [J]
4.35974393937059E-18
[a.u.] -> [K]
3.15774647902944E+05
[a.u.] -> [kJ/mol]
2.62549961709828E+03
[a.u.] -> [kcal/mol]
6.27509468713739E+02
[a.u.] -> [Pa]
2.94210107994716E+13
[a.u.] -> [bar]
2.94210107994716E+08
[a.u.] -> [atm]
2.90362800883016E+08
[a.u.] -> [eV]
2.72113838565563E+01
[a.u.] -> [Hz]
6.57968392072181E+15
[a.u.] -> [1/cm] (wave numbers)
2.19474631370540E+05
[a.u./Bohr**2] -> [1/cm]
5.14048714338585E+03
CELL| Volume [angstrom^3]:
1000.000
CELL| Vector a [angstrom]: 10.000 0.000 0.000 |a| =
10.000
CELL| Vector b [angstrom]: 0.000 10.000 0.000 |b| =
10.000
CELL| Vector c [angstrom]: 0.000 0.000 10.000 |c| =
10.000
CELL| Angle (b,c), alpha [degree]:
90.000
CELL| Angle (a,c), beta [degree]:
90.000
CELL| Angle (a,b), gamma [degree]:
90.000
CELL| Orthorhombic:
YES
CELL_REF| Volume [angstrom^3]:
1000.000
CELL_REF| Vector a [angstrom 10.000 0.000 0.000 |a| =
10.000
CELL_REF| Vector b [angstrom 0.000 10.000 0.000 |b| =
10.000
CELL_REF| Vector c [angstrom 0.000 0.000 10.000 |c| =
10.000
CELL_REF| Angle (b,c), alpha [degree]:
90.000
CELL_REF| Angle (a,c), beta [degree]:
90.000
CELL_REF| Angle (a,b), gamma [degree]:
90.000
CELL_REF| Orthorhombic:
YES
CELL_TOP| Volume [angstrom^3]:
1000.000
CELL_TOP| Vector a [angstrom 10.000 0.000 0.000 |a| =
10.000
CELL_TOP| Vector b [angstrom 0.000 10.000 0.000 |b| =
10.000
CELL_TOP| Vector c [angstrom 0.000 0.000 10.000 |c| =
10.000
CELL_TOP| Angle (b,c), alpha [degree]:
90.000
CELL_TOP| Angle (a,c), beta [degree]:
90.000
CELL_TOP| Angle (a,b), gamma [degree]:
90.000
CELL_TOP| Orthorhombic:
YES
GENERATE| WARNING:: No connections detected for Hydrogen - Atom Nr:
1 !
GENERATE| Preliminary Number of Bonds generated:
0
GENERATE| Achieved consistency in connectivity generation.
*******************************************************************************
*******************************************************************************
**
**
** ##### ## ##
**
** ## ## ## ## ##
**
** ## ## ## ######
**
** ## ## ## ## ## ##### ## ## #### ## ##### #####
**
** ## ## ## ## ## ## ## ## ## ## ## ## ## ##
**
** ## ## ## ## ## ## ## #### ### ## ###### ######
**
** ## ### ## ## ## ## ## ## ## ## ## ##
**
** ####### ##### ## ##### ## ## #### ## ##### ##
**
** ## ##
**
**
**
** ... make the atoms dance
**
**
**
** Copyright (C) by CP2K Developers Group (2000 - 2013)
**
**
**
*******************************************************************************
DFT| Spin unrestricted (spin-polarized) Kohn-Sham calculation
UKS
DFT| Multiplicity
2
DFT| Number of spin states
2
DFT| Charge
0
DFT| Self-interaction correction (SIC)
NO
DFT| Cutoffs: density
1.000000E-10
DFT| gradient
1.000000E-10
DFT| tau
1.000000E-10
DFT| cutoff_smoothing_range
0.000000E+00
DFT| XC density smoothing
NONE
DFT| XC derivatives
PW
FUNCTIONAL| NO EXCHANGE-CORRELATION FUNCTIONAL USED.
QS| Method:
GAPW
QS| Density plane wave grid type NON-SPHERICAL
FULLSPACE
QS| Number of grid levels:
4
QS| Density cutoff [a.u.]:
140.0
QS| Multi grid cutoff [a.u.]: 1) grid level
140.0
QS| 2) grid level
46.7
QS| 3) grid level
15.6
QS| 4) grid level
5.2
QS| Grid level progression factor:
3.0
QS| Relative density cutoff [a.u.]:
20.0
QS| Consistent realspace mapping and integration
QS| Interaction thresholds: eps_pgf_orb:
1.0E-05
QS| eps_filter_matrix:
0.0E+00
QS| eps_core_charge:
1.0E-12
QS| eps_rho_gspace:
1.0E-10
QS| eps_rho_rspace:
1.0E-10
QS| eps_gvg_rspace:
1.0E-05
QS| eps_ppl:
1.0E-02
QS| eps_ppnl:
1.0E-07
QS| GAPW| eps_fit:
1.0E-04
QS| GAPW| eps_iso:
1.0E-12
QS| GAPW| eps_svd:
1.0E-08
QS| GAPW| eps_cpc:
1.0E-10
QS| GAPW| atom-r-grid: quadrature: GC_LOG
QS| GAPW| atom-s-grid: max l :
0
QS| GAPW| max_l_rho0 :
2
QS| GAPW| At least one kind is NOT PAW, i.e. it has only soft AO
QS| GAPW| The NOT PAW atoms are treated fully GPW
ATOMIC KIND INFORMATION
1. Atomic kind: H Number of atoms:
1
Orbital Basis Set
Number of orbital shell sets:
2
Number of orbital shells:
2
Number of primitive Cartesian functions:
2
Number of Cartesian basis functions:
2
Number of spherical basis functions:
2
Norm type:
2
Normalised Cartesian orbitals:
Set Shell Orbital Exponent
Coefficient
1 1 1s 0.350000
0.324311
2 1 1s 0.600000
0.485874
Potential information for
ALL
Description: All-electron
potential
Krack, Parrinello, PCCP 2, 2105
(2000)
Gaussian exponent of the core charge distribution:
12.500000
Electronic configuration (s p d ...): 1
0 0
MOLECULE KIND INFORMATION
All atoms are their own molecule, skipping detailed information
TOTAL NUMBERS AND MAXIMUM NUMBERS
Total number of - Atomic kinds:
1
- Atoms:
1
- Shell sets:
2
- Shells:
2
- Primitive Cartesian functions:
2
- Cartesian basis functions:
2
- Spherical basis functions:
2
Maximum angular momentum of the orbital basis functions:
0
MODULE QUICKSTEP: ATOMIC COORDINATES IN angstrom
Atom Kind Element X Y Z Z(eff)
Mass
1 1 H 1 5.000000 5.000000 5.000000 1.00
1.0079
SCF PARAMETERS Density guess:
ATOMIC
--------------------------------------------------------
max_scf:
50
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
--------------------------------------------------------
Mixing method:
DIRECT_P_MIXING
--------------------------------------------------------
No outer SCF
PW_GRID: Information for grid number
1
PW_GRID: Cutoff [a.u.]
140.0
PW_GRID: spherical cutoff:
NO
PW_GRID: Bounds 1 -54 53 Points:
108
PW_GRID: Bounds 2 -54 53 Points:
108
PW_GRID: Bounds 3 -54 53 Points:
108
PW_GRID: Volume element (a.u.^3) 0.5357E-02 Volume (a.u.^3)
6748.3346
PW_GRID: Grid span
FULLSPACE
PW_GRID: Information for grid number
2
PW_GRID: Cutoff [a.u.]
46.7
PW_GRID: spherical cutoff:
NO
PW_GRID: Bounds 1 -30 29 Points:
60
PW_GRID: Bounds 2 -30 29 Points:
60
PW_GRID: Bounds 3 -30 29 Points:
60
PW_GRID: Volume element (a.u.^3) 0.3124E-01 Volume (a.u.^3)
6748.3346
PW_GRID: Grid span
FULLSPACE
PW_GRID: Information for grid number
3
PW_GRID: Cutoff [a.u.]
15.6
PW_GRID: spherical cutoff:
NO
PW_GRID: Bounds 1 -18 17 Points:
36
PW_GRID: Bounds 2 -18 17 Points:
36
PW_GRID: Bounds 3 -18 17 Points:
36
PW_GRID: Volume element (a.u.^3) 0.1446 Volume (a.u.^3)
6748.3346
PW_GRID: Grid span
FULLSPACE
PW_GRID: Information for grid number
4
PW_GRID: Cutoff [a.u.]
5.2
PW_GRID: spherical cutoff:
NO
PW_GRID: Bounds 1 -10 9 Points:
20
PW_GRID: Bounds 2 -10 9 Points:
20
PW_GRID: Bounds 3 -10 9 Points:
20
PW_GRID: Volume element (a.u.^3) 0.8435 Volume (a.u.^3)
6748.3346
PW_GRID: Grid span
FULLSPACE
RS_GRID: Information for grid number
1
RS_GRID: Bounds 1 -54 53 Points:
108
RS_GRID: Bounds 2 -54 53 Points:
108
RS_GRID: Bounds 3 -54 53 Points:
108
RS_GRID: Information for grid number
2
RS_GRID: Bounds 1 -30 29 Points:
60
RS_GRID: Bounds 2 -30 29 Points:
60
RS_GRID: Bounds 3 -30 29 Points:
60
RS_GRID: Information for grid number
3
RS_GRID: Bounds 1 -18 17 Points:
36
RS_GRID: Bounds 2 -18 17 Points:
36
RS_GRID: Bounds 3 -18 17 Points:
36
RS_GRID: Information for grid number
4
RS_GRID: Bounds 1 -10 9 Points:
20
RS_GRID: Bounds 2 -10 9 Points:
20
RS_GRID: Bounds 3 -10 9 Points:
20
DISTRIBUTION OF THE PARTICLES (ROWS)
Process row Number of particles Number of matrix
rows
0 1
-1
Sum 1
-1
DISTRIBUTION OF THE PARTICLES (COLUMNS)
Process col Number of particles Number of matrix
columns
0 1
-1
Sum 1
-1
*****************************************************************************
*** 09:32:51 ERRORL2 in hfx_libint_wrapper:initialize_libint processor 0
***
*** :: err=-300 This CP2K executable has not been linked against the
***
*** library libint, required for HFX.
***
*****************************************************************************
===== Routine Calling Stack =====
3 hfx_create
2 quickstep_create_force_env
1 CP2K
CP2K| This CP2K executable has not been linked against the library
libint, required for HFX.
CP2K| Abnormal program termination, stopped by process number 0
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
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