[CP2K:386] Re: Block after " Adding QM/MM electrostatic....."
Teodoro Laino
teodor... at gmail.com
Sun Nov 4 10:06:44 UTC 2007
yep, though this does not help me..
have some time today.. send me the files and I will look into that..
On 4 Nov 2007, at 11:02, Luca wrote:
>
> Ciao Teo,
> thanks for fast response..
> Ok. I work for you request..
>
> at this moment I tried to run with HIGH printing and
> program block at first step after SCF
> .....
> .........
>
> 19 DIIS/Diag. 0.95E-06 4.39 0.0000008858
> -148.2044296893
>
> *** SCF run converged in 19 steps ***
>
>
> Total electronic density (r-space): -116.0000002903
> -0.0000002903
> Total core charge density (r-space): 116.0000000000
> 0.0000000000
> Total charge density (r-space):
> -0.0000002903
> Total charge density (g-space):
> -0.0000002903
>
> Overlap energy of the core charge distribution:
> 0.00000839724822
> Self energy of the core charge distribution:
> -422.48901359943301
> Core Hamiltonian energy:
> 129.97430504509265
> Hartree energy:
> 171.41209987875129
> Exchange-correlation energy:
> -51.57087955822965
> Coulomb Electron-Electron Interaction Energy
> - Already included in the total Hartree term
> 409.92475143294126
> QM/MM Electrostatic energy:
> 24.4690501472
>
> Total energy:
> -148.20442968933276
> Mulliken charges : iteration level:
> 1_0
>
>
> ...........................................
> 127 5888.55511261962 0.1009E-02 0.2658E-04
> 128 5888.55511257744 0.9661E-03 0.2544E-04
> Wannier localization finished in 128 iterations
> D Eq. 11 1 14.3042429464
> D Eq. 11 2 13.5761904129
> D Eq. 11 3 9.5879832646
>
> CP2K| Stopped by processor
> number 0
> CP2K| mpi_allreduce @ mp_min_rv
> CP2K| Error number was
> 134808585
>
>
>
> Tahnks
>
>
> On Nov 4, 10:49 am, Teodoro Laino <teodor... at gmail.com> wrote:
>> Ciao Luca,
>>
>> it could be everything and " Adding QM/MM electrostatic....." is only
>> the latest thing buffered out from cp2k.
>> It could be a bug. So please you should send me:
>> 1) PSF file
>> 2) POT file
>> 3) PDB file
>> 4) Input file
>> 5) BASIS_SET and POTENTIAL files
>>
>> Please put all the files in a .tgz archive.
>> I will wait these files to look further into the problem.
>>
>> Teo
>>
>> On 4 Nov 2007, at 10:44, Luca wrote:
>>
>>
>>
>>> Hi all,
>>> when i run my MD i have strange behavior after 94 steps of MD.
>>> It seems infinite loop in
>>> " Adding QM/MM electrostatic potential to the Kohn-Sham potential.."
>>> in SCF procedure (see output).
>>> I tried some check but nothing to do.
>>> I noted the similar behavior on GEOP_OPT with CG procedure(not
>>> reported).
>>> The minimization with LBFGS is ok.
>>> Follows input section and latest step
>>> Thanks in advance.
>>> Luca
>>
>>> &FORCE_EVAL
>>> METHOD QMMM
>>> &DFT
>>> BASIS_SET_FILE_NAME GTH_BASIS_SETS
>>> POTENTIAL_FILE_NAME GTH_POTENTIALS
>>
>>> &MGRID
>>> COMMENSURATE
>>> CUTOFF 300
>>
>>> &QS
>>> MAP_CONSISTENT
>>> EXTRAPOLATION PS
>>> EPS_DEFAULT 1.0E-10
>>> EXTRAPOLATION_ORDER 3
>>> &END QS
>>
>>> &SCF
>>> MAX_SCF 150
>>> EPS_SCF 1.0E-6
>>> SCF_GUESS ATOMIC
>>> &END SCF
>>
>>> &XC
>>> &XC_FUNCTIONAL BLYP
>>> &END XC_FUNCTIONAL
>>> &END XC
>>
>>> &END DFT
>>
>>> &MM
>>> &FORCEFIELD
>>> PARM_FILE_NAME ./par_amber2charmm.inp
>>> PARMTYPE CHM
>>> EI_SCALE14 0.8333
>>> VDW_SCALE14 1.0
>>> &SPLINE
>>> UNIQUE_SPLINE T
>>> RCUT_NB 10.0
>>> &END SPLINE
>>> &END FORCEFIELD
>>
>>> &POISSON
>>> &EWALD
>>> EWALD_TYPE NONE
>>> ALPHA 0.44
>>> GMAX 64
>>> O_SPLINE 6
>>> &END EWALD
>>> PERIODIC NONE
>>> &END POISSON
>>
>>> &END MM
>>
>>> &QMMM
>>> MM_POTENTIAL_FILE_NAME MM_POTENTIAL
>>> &CELL
>>> UNITS ANGSTROM
>>> ABC 12.0 12.0 18.0
>>> PERIODIC NONE
>>> &END CELL
>>> NOCOMPATIBILITY T
>>> E_COUPL GAUSS
>>> USE_GEEP_LIB 10
>>
>>> &MM_KIND H
>>> RADIUS 0.44
>>> &END MM_KIND
>>> &MM_KIND HO
>>> RADIUS 0.44
>>> &END MM_KIND
>>> &MM_KIND HS
>>> RADIUS 0.44
>>> &END MM_KIND
>>> &MM_KIND HC
>>> RADIUS 0.44
>>> &END MM_KIND
>>> &MM_KIND H1
>>> RADIUS 0.44
>>> &END MM_KIND
>>> &MM_KIND H2
>>> RADIUS 0.44
>>> &END MM_KIND
>>> &MM_KIND H3
>>> RADIUS 0.44
>>> &END MM_KIND
>>> &MM_KIND HP
>>> RADIUS 0.44
>>> &END MM_KIND
>>> &MM_KIND HA
>>> RADIUS 0.44
>>> &END MM_KIND
>>> &MM_KIND H4
>>> RADIUS 0.44
>>> &END MM_KIND
>>> &MM_KIND H5
>>> RADIUS 0.44
>>> &END MM_KIND
>>> &MM_KIND HW
>>> RADIUS 0.44
>>> &END MM_KIND
>>
>>> &MM_KIND O
>>> RADIUS 0.73
>>> &END MM_KIND
>>> &MM_KIND O2
>>> RADIUS 0.73
>>> &END MM_KIND
>>> &MM_KIND OW
>>> RADIUS 0.73
>>> &END MM_KIND
>>> &MM_KIND OH
>>> RADIUS 0.73
>>> &END MM_KIND
>>> &MM_KIND OS
>>> RADIUS 0.73
>>> &END MM_KIND
>>
>>> &MM_KIND CT
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CA
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND C
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CM
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CS
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CB
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CC
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CN
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CK
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CQ
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CW
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CV
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CR
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CX
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CY
>>> RADIUS 0.77
>>> &END MM_KIND
>>> &MM_KIND CD
>>> RADIUS 0.77
>>> &END MM_KIND
>>
>>> &MM_KIND N
>>> RADIUS 0.75
>>> &END MM_KIND
>>> &MM_KIND NA
>>> RADIUS 0.75
>>> &END MM_KIND
>>> &MM_KIND NB
>>> RADIUS 0.75
>>> &END MM_KIND
>>> &MM_KIND NC
>>> RADIUS 0.75
>>> &END MM_KIND
>>> &MM_KIND N2
>>> RADIUS 0.75
>>> &END MM_KIND
>>> &MM_KIND N3
>>> RADIUS 0.75
>>> &END MM_KIND
>>> &MM_KIND NS
>>> RADIUS 0.75
>>> &END MM_KIND
>>
>>> &MM_KIND S
>>> RADIUS 1.02
>>> &END MM_KIND
>>> &MM_KIND SH
>>> RADIUS 1.02
>>> &END MM_KIND
>>
>>> &QM_KIND C
>>> MM_INDEX 4631 4632 4635
>>> MM_INDEX 4636 4637 4638
>>> MM_INDEX 4639 4640 4641 4642 4643 4644
>>> MM_INDEX 1297
>>> MM_INDEX 4099 4104 4106
>>> &END QM_KIND
>>
>>> &QM_KIND H
>>> MM_INDEX 4645 4646 4647 4648 4649 4650
>>> MM_INDEX 4651 4652 4653 4654 4655
>>> MM_INDEX 4656 4657 4658 4659 4660
>>> MM_INDEX 1301 1298 1299
>>> MM_INDEX 4105 4098 4107
>>> &END QM_KIND
>>
>>> &QM_KIND O
>>> MM_INDEX 4633 4634
>>> MM_INDEX 1300
>>> &END QM_KIND
>>
>>> &QM_KIND N
>>> MM_INDEX 4097 4103
>>> &END QM_KIND
>>
>>> &LINK
>>> ALPHA 1.20
>>> LINK_TYPE IMOMM
>>> MM_INDEX 1295
>>> QM_INDEX 1297
>>> &END LINK
>>
>>> &LINK
>>> ALPHA 1.20
>>> LINK_TYPE IMOMM
>>> MM_INDEX 4100
>>> QM_INDEX 4099
>>> &END LINK
>>> &END QMMM
>>
>>> &SUBSYS
>>
>>> &CELL
>>> ABC 64.000 64.0 57.000
>>> UNIT ANGSTROM
>>> PERIODIC NONE
>>> &END CELL
>>
>>> &TOPOLOGY
>>> COORD_FILE_NAME As_THI_T2.pdb
>>> COORDINATE PDB
>>> CONN_FILE_NAME As.psf
>>> CONNECTIVITY PSF
>>> &END TOPOLOGY
>>
>>> &KIND H
>>> BASIS_SET TZV2P-GTH # DZVP-GTH #
>>> POTENTIAL GTH-BLYP-q1
>>> &END KIND
>>
>>> &KIND
>>> O
>>> BASIS_SET TZV2P-GTH # DZVP-GTH #
>>> POTENTIAL GTH-BLYP-q6
>>> &END
>>> KIND
>>
>>> &KIND
>>> C
>>> BASIS_SET TZV2P-GTH # DZVP-GTH #
>>> POTENTIAL GTH-BLYP-q4
>>> &END
>>> KIND
>>
>>> &KIND
>>> N
>>> BASIS_SET TZV2P-GTH # DZVP-GTH #
>>> POTENTIAL GTH-BLYP-q5
>>> &END
>>> KIND
>>
>>> &KIND
>>> S
>>> BASIS_SET TZV2P-GTH # DZVP-GTH #
>>> POTENTIAL GTH-BLYP-q6
>>> &END KIND
>>
>>> &COLVAR
>>> &DISTANCE
>>> ATOMS 4632 1300
>>> &END DISTANCE
>>> &END COLVAR
>>
>>> &COLVAR
>>> &DISTANCE
>>> ATOMS 4634 4103
>>> &END DISTANCE
>>> &END COLVAR
>>
>>> &COLVAR
>>> &DISTANCE
>>> ATOMS 1300 1301
>>> &END DISTANCE
>>> &END COLVAR
>>
>>> &COLVAR
>>> &DISTANCE
>>> ATOMS 1300 4103
>>> &END DISTANCE
>>> &END COLVAR
>>
>>> &END SUBSYS
>>> &END FORCE_EVAL
>>
>>> &GLOBAL
>>> PRINT_LEVEL MEDIUM
>>> PROJECT AS_THI_T2
>>> RUN_TYPE MD
>>> SAVE_MEM F
>>> &END GLOBAL
>>
>>> &MOTION
>>
>>> &GEO_OPT
>>> OPTIMIZER CG
>>> MAX_ITER 125
>>> RMS_DR 1.0E-02
>>> MAX_DR 1.0E-02
>>> RMS_FORCE 1.0E-02
>>> MAX_FORCE 1.0E-02
>>> &END GEO_OPT
>>
>>> &MD
>>> ENSEMBLE NVE
>>> STEPS 1000
>>> TIMESTEP 0.20
>>> TEMPERATURE 20.0
>>> TEMP_TOL 1.0
>>> ANNEALING 1.0
>>> &END MD
>>
>>> &PRINT
>>> &RESTART OFF
>>> &END
>>> &RESTART_HISTORY OFF
>>> &END
>>
>>> &TRAJECTORY
>>> EACH 1
>>> FORMAT XMOL
>>> &END
>>
>>> &VELOCITIES OFF
>>> &END
>>> &END PRINT
>>
>>> &CONSTRAINT
>>
>>> # &COLLECTIVE
>>> # COLVAR 1
>>> # INTERMOLECULAR T
>>> # TARGET [angstrom] 1.46
>>> # &END COLLECTIVE
>>
>>> # &COLLECTIVE
>>> # COLVAR 2
>>> # INTERMOLECULAR T
>>> # TARGET [angstrom] 3.22
>>> # &END COLLECTIVE
>>
>>> # &COLLECTIVE
>>> # COLVAR 3
>>> # INTERMOLECULAR T
>>> # TARGET [angstrom] 2.34
>>> # &END COLLECTIVE
>>
>>> # &COLLECTIVE
>>> # COLVAR 4
>>> # INTERMOLECULAR T
>>> # TARGET [angstrom] 3.16
>>> # &END COLLECTIVE
>>
>>> &FIXED_ATOMS
>>> # Residues within 5 ang. to QM region are free to move,
>>> # other residues are
>>> # fixed
>>> LIST 1
>>> LIST 2
>>> LIST 3
>>> LIST 4
>>> ......
>>> ......
>>
>>> ********************************************************************
>>> **
>>> *********
>>> ENSEMBLE TYPE
>>> = nve
>>> STEP NUMBER
>>> = 94
>>> TIME [FS] =
>>> 18.800000
>>> CONSERVED QNTY =
>>> -0.184128334053E+03
>>
>>> INSTANTANEOUS
>>> AVERAGES
>>> CPU [S] =
>>> 138.16 87.80
>>> {E-E0}/{k_b*N_at} = 0.176474183833E+01
>>> 0.139196951545E+01
>>> POTENTIAL ENERGY[hartree] = -0.184159882198E+03
>>> -0.184167340405E+03
>>> MM KINETIC ENERGY[hartree] = 0.315481442922E-01
>>> 0.328358730418E-01
>>> QM KINETIC ENERGY[hartree] = 0.397864210092E-02
>>> 0.434631302514E-02
>>> MM TEMPERATURE[K] =
>>> 19.139 19.921
>>> QM TEMPERATURE[K] =
>>> 18.613 20.333
>>
>>> ********************************************************************
>>> **
>>> *********
>>
>>> Translating the system in order to center the QM fragment in
>>> the QM
>>> box.
>>> QMMM| Information on the QM/MM Electrostatic Potential:
>>> QMMM| QM/MM Coupling computed collocating the Gaussian Potential
>>> Functions.
>>> MM DIPOLE BERRY PHASE ( A.U.)| 6.055006
>>> 4.833916 8.639664
>>> MM DIPOLE BERRY PHASE (Debye)| 15.390288
>>> 12.286586
>>> 21.959832
>>> MM DIPOLE (NON BERRY PHASE) DERIVATIVE (A.U.)| -0.000156
>>> 0.000728 0.000320
>>
>>> DISTRIBUTION OF THE NEIGHBOR LISTS
>>
>>> Process Number of particle pairs Number of matrix elements
>>
>>> 0 112 28351
>>> 1 107 28856
>>> 2 149
>>
>> ...
>>
>> read more »
>
>
> >
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