[CP2K-user] An error I met when I run MD tasks
汤羽
tangshua... at gmail.com
Fri Mar 19 14:12:24 UTC 2021
Dear cp2k users and developers,
When I use cp2k.popt to run MD tasks, It always give me this
error"Cholesky decomposition failed. Matrix ill conditioned ? ". Can you
give me a suggestion on how to solve this error. The input and output files
are listed as follow. I use centos 8.3 and cp2k-8.1.
Thank you in advance.
The follow is output file:
DBCSR| CPU Multiplication driver
XSMM
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| Use memory pool for CPU allocation
F
DBCSR| Number of 3D layers
SINGLE
DBCSR| Use MPI memory allocation
F
DBCSR| Use RMA algorithm
F
DBCSR| Use Communication thread
T
DBCSR| Communication thread load
87
DBCSR| MPI: My node id
0
DBCSR| MPI: Number of nodes
12
DBCSR| OMP: Current number of threads
1
DBCSR| OMP: Max number of threads
1
DBCSR| Split modifier for TAS multiplication algorithm
1.0E+00
**** **** ****** ** PROGRAM STARTED AT 2021-03-19
22:03:08.501
***** ** *** *** ** PROGRAM STARTED ON
localhost.localdomain
** **** ****** PROGRAM STARTED BY
root
***** ** ** ** ** PROGRAM PROCESS ID
64904
**** ** ******* ** PROGRAM STARTED IN
/tangshuai/inputfile/water_AIMD
CP2K| version string: CP2K
version 8.1
CP2K| source code revision number:
git:0b61f2f
CP2K| cp2kflags: omp libint fftw3 libxc elpa parallel mpi3 scalapack xsmm
plume
CP2K| d2 spglib mkl libvori libbqb
CP2K| is freely available from
https://www.cp2k.org/
CP2K| Program compiled at 2021年 03月 18日 星期四 20:58:14 CST
CP2K| Program compiled on
localhost.localdomain
CP2K| Program compiled for
local
CP2K| Data directory path
/tangshuai/cp2k-8.1/date
CP2K| Input file name
spc216.inp
GLOBAL| Force Environment number
1
GLOBAL| Basis set file name
BASIS_SET
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
spc216
GLOBAL| Preferred FFT library
FFTW3
GLOBAL| Preferred diagonalization lib.
ELPA
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
12
GLOBAL| Number of threads for this process
1
GLOBAL| This output is from process
0
GLOBAL| CPU model name Intel(R) Xeon(R) CPU X5650 @
2.67GHz
GLOBAL| CPUID
0
GLOBAL| Compiled for CPUID
1000
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max
average
MEMORY| MemTotal 16381804 16381804 16381804
16381804
MEMORY| MemFree 9823960 9823960 9823960
9823960
MEMORY| Buffers 2540 2540 2540
2540
MEMORY| Cached 2972888 2972888 2972888
2972888
MEMORY| Slab 561124 561124 561124
561124
MEMORY| SReclaimable 186368 186368 186368
186368
MEMORY| MemLikelyFree 12985756 12985756 12985756
12985756
GENERATE| Preliminary Number of Bonds generated:
0
GENERATE| Achieved consistency in connectivity generation.
*** WARNING in qs_kind_types.F:2026 :: Information provided in the input
***
*** file regarding BASIS for KIND <O> will be ignored!
***
*** WARNING in qs_kind_types.F:2026 :: Information provided in the input
***
*** file regarding BASIS for KIND <H> will be ignored!
***
##### ##### # ####### ######
# # # # # # # #
# # # # ## ## # # #
# # ##### # ## ## # ######
# # # # # ### # # #
# # # # # ## ## # # #
#### # ##### # ## ## # ######
Version 1.0
J. Hutter and A. Hehn
EWALD| Summation is done by:
SPME
EWALD| Alpha parameter [ ANGSTROM^-1]
1.8897
EWALD| Real Space Cutoff [ ANGSTROM]
1.7854
EWALD| G-space max. Miller index 125 125
125
EWALD| Spline interpolation order
6
TOTAL NUMBERS AND MAXIMUM NUMBERS
Total number of - Atomic kinds:
2
- Atoms:
648
- Shell sets:
1296
- Shells:
1296
- Primitive Cartesian functions:
9504
- Cartesian basis functions:
1728
- Spherical basis functions:
1728
Maximum angular momentum of the orbital basis functions:
1
SCF PARAMETERS Density guess:
ATOMIC
--------------------------------------------------------
max_scf:
200
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
--------------------------------------------------------
No outer SCF
MD_PAR| Molecular dynamics protocol (MD input parameters)
MD_PAR| Ensemble type
NVT
MD_PAR| Number of time steps
200
MD_PAR| Time step [fs]
1.000000
MD_PAR| Temperature [K]
298.150000
MD_PAR| Temperature tolerance [K]
0.000000
MD_PAR| Print MD information every 1
step(s)
MD_PAR| File type Print frequency [steps] File
names
MD_PAR| Coordinates 1
spc216-pos-1.xyz
MD_PAR| Velocities 1
spc216-vel-1.xyz
MD_PAR| Energies 1
spc216-1.ener
MD_PAR| Dump 10
spc216-1.restart
ROT| Rotational analysis information
ROT| Principal axes and moments of inertia [a.u.]
ROT| 1 2 3
ROT| Eigenvalues 1.39507247992E+09 1.48002146529E+09
1.51111924487E+09
ROT| x -0.504874912862 -0.790021985783
-0.347802507671
ROT| y 0.564873449390 -0.607055622662
0.558928848037
ROT| z -0.652701546295 0.085724751234
0.752749598797
ROT| Number of rotovibrational vectors
6
DOF| Calculation of degrees of freedom
DOF| Number of atoms
648
DOF| Number of intramolecular constraints
0
DOF| Number of intermolecular constraints
0
DOF| Invariants (translations + rotations)
3
DOF| Degrees of freedom
1941
DOF| Restraints information
DOF| Number of intramolecular restraints
0
DOF| Number of intermolecular restraints
0
THERMOSTAT| Thermostat information for PARTICLES
THERMOSTAT| Type of thermostat Canonical Sampling/Velocity
Rescaling
THERMOSTAT| CSVR time constant [fs]
200.000000
THERMOSTAT| Initial kinetic energy
0.000000000000E+00
THERMOSTAT| End of thermostat information for PARTICLES
MD_VEL| Velocities initialization
MD_VEL| Initial temperature [K]
298.150000
MD_VEL| COM velocity -0.0000000000 0.0000000000
-0.0000000000
Number of electrons:
1728
Number of occupied orbitals:
864
Number of molecular orbitals:
864
Number of orbital functions:
1728
Number of independent orbital functions:
1728
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_SINGLE_INVERSE : inversion of
H + eS -
2*(Sc)(c^T*H*c+const)(Sc)^T
Precond_solver : DEFAULT
stepsize : 0.08000000 energy_gap :
0.08000000
eps_taylor : 0.10000E-15 max_taylor :
4
----------------------------------- OT
---------------------------------------
Step Update method Time Convergence Total energy
Change
------------------------------------------------------------------------------
*******************************************************************************
* ___
*
* / \
*
* [ABORT]
*
* \___/ Cholesky decomposition failed. Matrix ill conditioned ?
*
* |
*
* O/|
*
* /| |
*
* / \
cp_dbcsr_cholesky.F:120 *
*******************************************************************************
===== Routine Calling Stack =====
12 cp_dbcsr_cholesky_decompose
11 qs_ot_get_derivative
10 ot_mini
9 ot_scf_mini
8 qs_scf_loop_do_ot
7 qs_scf_new_mos
6 scf_env_do_scf_inner_loop
5 scf_env_do_scf
4 qs_energies
3 qs_forces
2 qs_mol_dyn_low
1 CP2K
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