[CP2K-user] [CP2K:18785] Bad condition number R_COND
Nilesh Dhumal
nil.dhumal0 at gmail.com
Tue May 9 14:17:30 UTC 2023
Hello User,
I installed the latest version of cp2k (2323.1) on our cluster.
I am getting the Bad condition number R_COND error for my every input file.
We have 8.2 version installed on the cluster. The simulation finished
successfully using the older version (8.2) of cp2k.
Attached is input and output file.
Is the issue in input file or compilation ?
Thanks,
Nilesh
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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| OMP: Current number of threads 40
DBCSR| OMP: Max number of threads 40
DBCSR| Split modifier for TAS multiplication algorithm 1.0E+00
**** **** ****** ** PROGRAM STARTED AT 2023-05-09 00:54:17.851
***** ** *** *** ** PROGRAM STARTED ON stcg02
** **** ****** PROGRAM STARTED BY casgaussian
***** ** ** ** ** PROGRAM PROCESS ID 2507397
**** ** ******* ** PROGRAM STARTED IN /home/casgaussian/water
CP2K| version string: CP2K version 2022.2
CP2K| source code revision number: git:a95ec40
CP2K| cp2kflags: omp libint fftw3 libxc xsmm spglib libvori libbqb
CP2K| is freely available from https://www.cp2k.org/
CP2K| Program compiled at Tue May 9 12:37:54 AM UTC 2023
CP2K| Program compiled on stcg02
CP2K| Program compiled for local
CP2K| Data directory path /home/software/cp2k-2022.2/data
CP2K| Input file name npt_equ.inp
GLOBAL| Force Environment number 1
GLOBAL| Basis set file name /home/software/cp2k-2022.2/data/BASIS_SE
GLOBAL| Potential file name /home/software/cp2k-2022.2/data/POTENTIA
GLOBAL| MM Potential file name MM_POTENTIAL
GLOBAL| Coordinate file name ./water_64.xyz
GLOBAL| Method name CP2K
GLOBAL| Project name H2O
GLOBAL| Run type MD
GLOBAL| FFT library FFTW3
GLOBAL| Diagonalization library ScaLAPACK
GLOBAL| Orthonormality check for eigenvectors DISABLED
GLOBAL| Matrix multiplication library ScaLAPACK
GLOBAL| All-to-all communication in single precision F
GLOBAL| FFTs using library dependent lengths F
GLOBAL| Grid backend AUTO
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 40
GLOBAL| This output is from process 0
GLOBAL| Stack size for threads created by OpenMP (OMP_STACKSIZE) default
GLOBAL| CPU model name Intel(R) Xeon(R) CPU E5-2640 v4 @ 2.40GHz
GLOBAL| CPUID 1002
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 65848796 65848796 65848796 65848796
MEMORY| MemFree 47247164 47247164 47247164 47247164
MEMORY| Buffers 384352 384352 384352 384352
MEMORY| Cached 16348732 16348732 16348732 16348732
MEMORY| Slab 1221748 1221748 1221748 1221748
MEMORY| SReclaimable 982740 982740 982740 982740
MEMORY| MemLikelyFree 64962988 64962988 64962988 64962988
GENERATE| Preliminary Number of Bonds generated: 0
GENERATE| Achieved consistency in connectivity generation.
*******************************************************************************
*******************************************************************************
** **
** ##### ## ## **
** ## ## ## ## ## **
** ## ## ## ###### **
** ## ## ## ## ## ##### ## ## #### ## ##### ##### **
** ## ## ## ## ## ## ## ## ## ## ## ## ## ## **
** ## ## ## ## ## ## ## #### ### ## ###### ###### **
** ## ### ## ## ## ## ## ## ## ## ## ## **
** ####### ##### ## ##### ## ## #### ## ##### ## **
** ## ## **
** **
** ... make the atoms dance **
** **
** Copyright (C) by CP2K developers group (2000-2022) **
** J. Chem. Phys. 152, 194103 (2020) **
** **
*******************************************************************************
TOTAL NUMBERS AND MAXIMUM NUMBERS
Total number of - Atomic kinds: 2
- Atoms: 192
- Shell sets: 384
- Shells: 704
- Primitive Cartesian functions: 960
- Cartesian basis functions: 1536
- Spherical basis functions: 1472
Maximum angular momentum of- Orbital basis functions: 2
- Local part of the GTH pseudopotential: 2
- Non-local part of the GTH pseudopotential: 0
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.]: 0.000000
--------------------------------------------------------
Mixing method: PULAY_MIXING
charge density mixing in g-space
--------------------------------------------------------
No outer SCF
MD_PAR| Molecular dynamics protocol (MD input parameters)
MD_PAR| Ensemble type NPT_F
MD_PAR| Number of time steps 10000
MD_PAR| Time step [fs] 1.000000
MD_PAR| Temperature [K] 300.000000
MD_PAR| Temperature tolerance [K] 0.000000
MD_PAR| Pressure [bar] 1.000000
MD_PAR| Barostat time constant [fs] 1000.000000
MD_PAR| Print MD information every 1 step(s)
MD_PAR| File type Print frequency [steps] File names
MD_PAR| Coordinates 1 H2O-pos-1.xyz
MD_PAR| Cell 1 H2O-1.cell
MD_PAR| Velocities 1 H2O-vel-1.xyz
MD_PAR| Energies 1 H2O-1.ener
MD_PAR| Dump 20 H2O-1.restart
ROT| Rotational analysis information
ROT| Principal axes and moments of inertia [a.u.]
ROT| 1 2 3
ROT| Eigenvalues 1.76295814137E+08 1.96733343491E+08 1.97242116479E+08
ROT| x 0.697117735727 0.547668170908 -0.462694755869
ROT| y -0.623358600825 0.781814530245 -0.013787497056
ROT| z 0.354190509913 0.298036264356 0.886410439817
ROT| Number of rotovibrational vectors 6
DOF| Calculation of degrees of freedom
DOF| Number of atoms 192
DOF| Number of intramolecular constraints 0
DOF| Number of intermolecular constraints 0
DOF| Invariants (translations + rotations) 0
DOF| Degrees of freedom 576
DOF| Restraints information
DOF| Number of intramolecular restraints 0
DOF| Number of intermolecular restraints 0
THERMOSTAT| Thermostat information for PARTICLES
THERMOSTAT| Type of thermostat Nose-Hoover-Chains
THERMOSTAT| Nose-Hoover-Chain length 3
THERMOSTAT| Nose-Hoover-Chain time constant [fs] 1000.000000
THERMOSTAT| Order of Yoshida integrator 3
THERMOSTAT| Number of multiple time steps 2
THERMOSTAT| Initial potential energy 0.000000000000E+00
THERMOSTAT| Initial kinetic energy 0.912042818867E-01
THERMOSTAT| End of thermostat information for PARTICLES
THERMOSTAT| Thermostat information for BAROSTAT
THERMOSTAT| Type of thermostat Nose-Hoover-Chains
THERMOSTAT| Nose-Hoover-Chain length 3
THERMOSTAT| Nose-Hoover-Chain time constant [fs] 1000.000000
THERMOSTAT| Order of Yoshida integrator 3
THERMOSTAT| Number of multiple time steps 2
THERMOSTAT| Initial potential energy 0.000000000000E+00
THERMOSTAT| Initial kinetic energy 0.475022301493E-03
THERMOSTAT| End of thermostat information for BAROSTAT
MD_VEL| Velocities initialization
MD_VEL| Initial temperature [K] 300.000000
MD_VEL| COM velocity 0.0000000000 -0.0000000000 -0.0000000000
Number of electrons: 512
Number of occupied orbitals: 256
Number of molecular orbitals: 256
Number of orbital functions: 1472
Number of independent orbital functions: 1472
Extrapolation method: initial_guess
SCF WAVEFUNCTION OPTIMIZATION
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 NoMix/Diag. 0.50E+00 17.9 1.15190345 -1089.6673475560 -1.09E+03
2 Pulay/Diag. 0.50E+00 19.5 0.37199647 -1031.4837793156 5.82E+01
3 Pulay/Diag. 0.50E+00 19.6 0.10356247 -1111.3348618475 -7.99E+01
4 Pulay/Diag. 0.50E+00 19.8 0.05656877 -1093.1044442674 1.82E+01
5 Pulay/Diag. 0.50E+00 19.8 0.03375459 -1097.4859200042 -4.38E+00
6 Pulay/Diag. 0.50E+00 19.8 0.00542590 -1097.3184238791 1.67E-01
7 Pulay/Diag. 0.50E+00 19.6 0.00323418 -1097.1041226568 2.14E-01
8 Pulay/Diag. 0.50E+00 19.8 0.00126838 -1097.0593817469 4.47E-02
9 Pulay/Diag. 0.50E+00 19.0 0.00058817 -1097.0767239353 -1.73E-02
10 Pulay/Diag. 0.50E+00 19.3 0.00046154 -1097.0834965631 -6.77E-03
11 Pulay/Diag. 0.50E+00 19.6 0.00021587 -1097.0643330192 1.92E-02
12 Pulay/Diag. 0.50E+00 19.5 0.00010385 -1097.0698941487 -5.56E-03
13 Pulay/Diag. 0.50E+00 19.3 0.00006890 -1097.0730404766 -3.15E-03
14 Pulay/Diag. 0.50E+00 19.7 0.00002731 -1097.0695573677 3.48E-03
15 Pulay/Diag. 0.50E+00 19.8 0.00001326 -1097.0700252459 -4.68E-04
16 Pulay/Diag. 0.50E+00 19.5 0.00000583 -1097.0705334822 -5.08E-04
*** SCF run converged in 16 steps ***
Electronic density on regular grids: -511.9999966424 0.0000033576
Core density on regular grids: 511.9999878047 -0.0000121953
Total charge density on r-space grids: -0.0000088378
Total charge density g-space grids: -0.0000088378
Overlap energy of the core charge distribution: 0.00000081423004
Self energy of the core charge distribution: -2850.59943771439157
Core Hamiltonian energy: 822.32635780304167
Hartree energy: 1195.13580971414171
Exchange-correlation energy: -263.93326409917893
Total energy: -1097.07053348215686
ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -1097.070324309342141
MD_INI| MD initialization
MD_INI| Potential energy [hartree] -0.109707032431E+04
MD_INI| Kinetic energy [hartree] 0.273612845660E+00
MD_INI| Temperature [K] 300.000000
MD_INI| Barostat temperature [K] 300.000000
MD_INI| Pressure [bar] -2.158312695477E+04
MD_INI| Cell volume [bohr^3] 1.261911012238E+04
MD_INI| Cell volume [ang^3] 1.869959168000E+03
MD_INI| Cell lengths [bohr] 2.32814260E+01 2.32814260E+01 2.32814260E+01
MD_INI| Cell lengths [ang] 1.23200000E+01 1.23200000E+01 1.23200000E+01
MD_INI| Cell angles [deg] 9.00000000E+01 9.00000000E+01 9.00000000E+01
Number of electrons: 512
Number of occupied orbitals: 256
Number of molecular orbitals: 256
Number of orbital functions: 1472
Number of independent orbital functions: 1472
Extrapolation method: ASPC
SCF WAVEFUNCTION OPTIMIZATION
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 Pulay/Diag. 0.50E+00 18.8 0.08213927 -1097.0242234432 -1.10E+03
2 Pulay/Diag. 0.50E+00 19.6 15.30158723 586.6013705871 1.68E+03
3 Pulay/Diag. 0.50E+00 19.4 0.00081141 1177.5620451315 5.91E+02
4 Pulay/Diag. 0.50E+00 19.1 0.00036298 1177.5620530778 7.95E-06
5 Pulay/Diag. 0.50E+00 19.2 0.00173929 1177.5738052157 1.18E-02
6 Pulay/Diag. 0.50E+00 19.7 15.37113911 -515.4651028752 -1.69E+03
7 Pulay/Diag. 0.50E+00 19.6 43.64152639 -939.8464651106 -4.24E+02
8 Pulay/Diag. 0.50E+00 19.8 43.57449261 -876.5051094119 6.33E+01
9 Pulay/Diag. 0.50E+00 19.5 0.29868422 -1090.7742456269 -2.14E+02
10 Pulay/Diag. 0.50E+00 19.7 0.07500820 -1092.9996366358 -2.23E+00
11 Pulay/Diag. 0.50E+00 19.9 0.03388564 -1094.6025451797 -1.60E+00
12 Pulay/Diag. 0.50E+00 19.3 0.08676773 -1095.7994858545 -1.20E+00
13 Pulay/Diag. 0.50E+00 19.4 0.01119117 -1097.0541364761 -1.25E+00
14 Pulay/Diag. 0.50E+00 19.7 0.00542308 -1097.0868962466 -3.28E-02
15 Pulay/Diag. 0.50E+00 19.7 0.00263718 -1097.0067806907 8.01E-02
16 Pulay/Diag. 0.50E+00 19.5 0.00212467 -1097.0409215031 -3.41E-02
17 Pulay/Diag. 0.50E+00 19.4 0.00193455 -1097.0643615495 -2.34E-02
18 Pulay/Diag. 0.50E+00 19.4 0.00106932 -1097.0427468071 2.16E-02
19 Pulay/Diag. 0.50E+00 19.7 0.00070191 -1097.0341242385 8.62E-03
20 Pulay/Diag. 0.50E+00 20.1 0.00035164 -1097.0400920524 -5.97E-03
21 Pulay/Diag. 0.50E+00 19.5 0.00022496 -1097.0437705757 -3.68E-03
22 Pulay/Diag. 0.50E+00 19.7 0.00012807 -1097.0403699037 3.40E-03
23 Pulay/Diag. 0.50E+00 19.5 0.00009717 -1097.0397940195 5.76E-04
24 Pulay/Diag. 0.50E+00 19.7 0.00008381 -1097.0414002175 -1.61E-03
25 Pulay/Diag. 0.50E+00 19.5 0.00007936 -1097.0417463547 -3.46E-04
26 Pulay/Diag. 0.50E+00 19.7 0.00002953 -1097.0411358972 6.10E-04
27 Pulay/Diag. 0.50E+00 19.3 0.00001709 -1097.0410258644 1.10E-04
28 Pulay/Diag. 0.50E+00 19.5 0.00001409 -1097.0412563693 -2.31E-04
29 Pulay/Diag. 0.50E+00 19.4 0.00000455 -1097.0412367775 1.96E-05
*** SCF run converged in 29 steps ***
Electronic density on regular grids: -511.9997109557 0.0002890443
Core density on regular grids: 511.9999874356 -0.0000125644
Total charge density on r-space grids: 0.0002764799
Total charge density g-space grids: 0.0002764799
Overlap energy of the core charge distribution: 0.00000098280740
Self energy of the core charge distribution: -2850.59943771439157
Core Hamiltonian energy: 822.30682861617026
Hartree energy: 1195.17352706922225
Exchange-correlation energy: -263.92215573132717
Total energy: -1097.04123677751909
ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -1097.041170585418286
MD| ***************************************************************************
MD| Step number 1
MD| Time [fs] 1.000000
MD| Conserved quantity [hartree] -0.109669802417E+04
MD| ---------------------------------------------------------------------------
MD| Instantaneous Averages
MD| CPU time per MD step [s] 881.650064 881.650064
MD| Energy drift per atom [K] 0.442396903982E+01 0.000000000000E+00
MD| Potential energy [hartree] -0.109704117059E+04 -0.109704117059E+04
MD| Kinetic energy [hartree] 0.247143908357E+00 0.247143908357E+00
MD| Temperature [K] 270.978405 270.978405
MD| Pressure [bar] -2.151377982471E+04 -2.151377982471E+04
MD| Barostat temperature [K] 3.009894020436E+02 3.009894020436E+02
MD| Cell volume [bohr^3] 1.261888637929E+04 1.261888637929E+04
MD| Cell volume [ang^3] 1.869926012695E+03 1.869926012695E+03
MD| ---------------------------------------------------------------------------
MD| Cell lengths [bohr] 2.32816944E+01 2.32789102E+01 2.32832614E+01
MD| Cell lengths [ang] 1.23201420E+01 1.23186687E+01 1.23209713E+01
MD| Average cell lengths [bohr] 2.32816944E+01 2.32789102E+01 2.32832614E+01
MD| Average cell lengths [ang] 1.23201420E+01 1.23186687E+01 1.23209713E+01
MD| Cell angles [deg] 8.99981912E+01 9.00128515E+01 8.99954413E+01
MD| Average cell angles [deg] 8.99981912E+01 9.00128515E+01 8.99954413E+01
MD| ***************************************************************************
MD| Estimated peak process memory after this step [MiB] 1692
Number of electrons: 512
Number of occupied orbitals: 256
Number of molecular orbitals: 256
Number of orbital functions: 1472
Number of independent orbital functions: 1472
Extrapolation method: ASPC
SCF WAVEFUNCTION OPTIMIZATION
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 Pulay/Diag. 0.50E+00 19.0 0.04107655 -1097.0063819327 -1.10E+03
2 Pulay/Diag. 0.50E+00 19.6 0.44953409 -1092.5490126983 4.46E+00
3 Pulay/Diag. 0.50E+00 19.8 0.00004493 -1057.2376331395 3.53E+01
4 Pulay/Diag. 0.50E+00 19.7 0.09157255 -1056.1530579893 1.08E+00
5 Pulay/Diag. 0.50E+00 19.6 0.00000566 -1050.6572544146 5.50E+00
*** SCF run converged in 5 steps ***
Electronic density on regular grids: -511.9829060674 0.0170939326
Core density on regular grids: 511.9999875816 -0.0000124184
Total charge density on r-space grids: 0.0170815142
Total charge density g-space grids: 0.0170815142
Overlap energy of the core charge distribution: 0.00000127176537
Self energy of the core charge distribution: -2850.59943771439157
Core Hamiltonian energy: 863.09780962560296
Hartree energy: 1222.19504237656975
Exchange-correlation energy: -285.35066997418238
Total energy: -1050.65725441463564
ENERGY| Total FORCE_EVAL ( QS ) energy [a.u.]: -1093.371589795000091
MD| ***************************************************************************
MD| Step number 2
MD| Time [fs] 2.000000
MD| Conserved quantity [hartree] -0.109303451696E+04
MD| ---------------------------------------------------------------------------
MD| Instantaneous Averages
MD| CPU time per MD step [s] 99.885196 490.767630
MD| Energy drift per atom [K] 0.602964635920E+04 0.301482317960E+04
MD| Potential energy [hartree] -0.109337158980E+04 -0.109520638019E+04
MD| Kinetic energy [hartree] 0.241055310088E+00 0.244099609223E+00
MD| Temperature [K] 264.302624 267.640514
MD| Pressure [bar] -3.622312452287E+04 -2.886845217379E+04
MD| Barostat temperature [K] 3.027672623568E+02 3.018783322002E+02
MD| Cell volume [bohr^3] 1.261847219765E+04 1.261867928847E+04
MD| Cell volume [ang^3] 1.869864637309E+03 1.869895325002E+03
MD| ---------------------------------------------------------------------------
MD| Cell lengths [bohr] 2.32818508E+01 2.32762807E+01 2.32849729E+01
MD| Cell lengths [ang] 1.23202248E+01 1.23172772E+01 1.23218770E+01
MD| Average cell lengths [bohr] 2.32817726E+01 2.32775954E+01 2.32841172E+01
MD| Average cell lengths [ang] 1.23201834E+01 1.23179730E+01 1.23214241E+01
MD| Cell angles [deg] 8.99963422E+01 9.00256459E+01 8.99909248E+01
MD| Average cell angles [deg] 8.99972667E+01 9.00192487E+01 8.99931831E+01
MD| ***************************************************************************
MD| Estimated peak process memory after this step [MiB] 1776
Number of electrons: 512
Number of occupied orbitals: 256
Number of molecular orbitals: 256
Number of orbital functions: 1472
Number of independent orbital functions: 1472
Extrapolation method: ASPC
SCF WAVEFUNCTION OPTIMIZATION
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 Pulay/Diag. 0.50E+00 18.7 2.68298776 -1075.7875451247 -1.08E+03
2 Pulay/Diag. 0.50E+00 19.5 67.81188168 ******************** 3.56E+09
*******************************************************************************
* ___ *
* / \ *
* [ABORT] *
* \___/ Bad condition number R_COND = 1.943E-20 (smaller than the machine *
* | working precision) *
* O/| *
* /| | *
* / \ common/mathlib.F:741 *
*******************************************************************************
===== Routine Calling Stack =====
9 pulay_mixing
8 gspace_mixing
7 scf_env_do_scf_inner_loop
6 scf_env_do_scf
5 qs_energies
4 qs_forces
3 velocity_verlet
2 qs_mol_dyn_low
1 CP2K
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