[CP2K:2493] Test files -H2O

Sandeep Kumar Reddy kuma... at gmail.com
Wed Jan 6 09:21:31 CET 2010


Hello,
       Thank you for your quick reply. Following are the details about
compilers, arch etc.

Intel Compiler(ifort) Version : 10.1

My Arch File : "Linux-x86-64-intel.psmp"

# by default some intel compilers put temporaries on the stack
# this might lead to segmentation faults is the stack limit is set to low
# stack limits can be increased by sysadmins or e.g with ulimit -s 256000
# furthermore new ifort (10.0?) compilers support the option
# -heap-arrays 64
# add this to the compilation flags is the other options do not work
# The following settings worked for:
# - AMD64 Opteron
# - SUSE Linux Enterprise Server 10.0 (x86_64)
# - Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version
10.0
# - AMD acml library version 3.6.0
# - MPICH2-1.0.5p4
# - FFTW 3.1.2
#
CC       = cc
CPP      =
FC       = ifort -openmp -FR -O0
LD       = ifort -openmp -FR -O0
AR       = ar -r
DFLAGS   = -D__INTEL -D__FFTSG -D__FFTW3
CPPFLAGS = -C -traditional $(DFLAGS) -I$(INTEL_INC)
INTEL_INC= -I/sfs1/intel_012008/mkl/10.0.011/include
-I/sfs1/intel_012008/mkl/10.0.011/include/fftw
INTEL_LIB= /sfs1/intel_012008/mkl/10.0.011/lib/em64t
FCFLAGS  = $(DFLAGS) $(INTEL_INC) -heap-arrays 64
FCFLAGS2 = $(DFLAGS) $(INTEL_INC) -heap-arrays 64
LDFLAGS  = $(FCFLAGS) -i-static
MKLPATH  = /sfs1/intel_012008/mkl/10.0.011/lib/em64t/
LIBS     = -L$(MKLPATH) -lfftw3xf_intel $(MKLPATH)/libmkl_solver_lp64.a
-Wl,--start-group $(MKLPATH)/libmkl_intel_lp64.a
$(MKLPATH)/libmkl_intel_thread.a $(M
KLPATH)/libmkl_core.a -Wl,--end-group -openmp -lpthread

# $(INTEL_LIB)/libmkl_scalapack_lp64.a \

#           $(INTEL_LIB)/libmkl_core.a \

#           $(INTEL_LIB)/libfftw3.a

OBJECTS_ARCHITECTURE = machine_intel.o

graphcon.o: graphcon.F
      $(FC) -c $(FCFLAGS2) $<
Linux-jnc.psmp (END)


Regards,
Sandeep kumar reddy

On Wed, Jan 6, 2010 at 12:27 PM, Laino Teodoro <teodor... at gmail.com>wrote:

> Hello Sandeep,
>
> your executable is giving almost random numbers:
>
>
>     1 P_Mix/Diag. 0.40E+00    0.3     1.96524988       -17.0390500821
> -1.70E+01
>     2 P_Mix/Diag. 0.40E+00    0.4     1.17914993       -13.5426292836
>  3.50E+00
>     3 P_Mix/Diag. 0.40E+00    0.4     0.70748996        -9.9067192962
>  3.64E+00
>     4 P_Mix/Diag. 0.40E+00    0.4     0.42449397        -7.1955092465
>  2.71E+00
>     5 P_Mix/Diag. 0.40E+00    0.4     0.25469638        -5.3903907002
>  1.81E+00
>
> while a correct executable should give more reasonable numbers:
>
>     1 P_Mix/Diag. 0.40E+00    0.7     0.94986401       -17.0390500821
> -1.70E+01
>     2 P_Mix/Diag. 0.40E+00    0.7     0.55704339       -17.1017974052
> -6.27E-02
>     3 P_Mix/Diag. 0.40E+00    0.8     0.33374888       -17.1395184934
> -3.77E-02
>     4 P_Mix/Diag. 0.40E+00    0.8     0.19743634       -17.1616212665
> -2.21E-02
>     5 P_Mix/Diag. 0.40E+00    0.9     0.11691752       -17.1746976329
> -1.31E-02
>
> (Please check the 6th column)
>
>  You need to provide your arch file, compiler, version, libraries and first
> of all look through all the past messages to see if somebody experienced the
> same problem you have (very probably you have a bugged compiler version or
> wrong libraries).
>
> Teo
>
>
> On 6 Jan 2010, at 07:47, Sandeep Kumar Reddy wrote:
>
>  Hello,
>>          Please help a new user of CP2K.  I am trying to learn CP2K. When
>> i try to execute H2O.inp  given in tests directory of cp2k, the output file
>> terminated after reading the contents of the input file. I am using a serial
>> executable. Following is the input file.
>>
>> &FORCE_EVAL
>>  METHOD Quickstep
>>  &DFT
>>    &MGRID
>>      CUTOFF 280
>>    &END MGRID
>>    &QS
>>      EPS_DEFAULT 1.0E-12
>>    &END QS
>>    &SCF
>>      SCF_GUESS ATOMIC
>>      EPS_SCF 3.0E-7
>>      MAX_SCF 50
>>      &DIAGONALIZATION
>>         ALGORITHM STANDARD
>>      &END DIAGONALIZATION
>>    &END SCF
>>    &XC
>>      &XC_FUNCTIONAL BLYP
>>      &END XC_FUNCTIONAL
>>    &END XC
>>  &END DFT
>>  &SUBSYS
>>    &CELL
>>      ABC 5.0 5.0 5.0
>>    &END CELL
>>    &COORD
>>    O   0.000000    0.000000   -0.065587
>>    H   0.000000   -0.757136    0.520545
>>    H   0.000000    0.757136    0.520545
>>    &END COORD
>>    &KIND H
>>      BASIS_SET DZVP-GTH-BLYP
>>      POTENTIAL GTH-BLYP-q1
>>    &END KIND
>>    &KIND O
>>      BASIS_SET DZVP-GTH-BLYP
>>      POTENTIAL GTH-BLYP-q6
>>    &END KIND
>>  &END SUBSYS
>> &END FORCE_EVAL
>> &GLOBAL
>>  PROJECT H2O
>>  RUN_TYPE ENERGY_FORCE
>>  PRINT_LEVEL MEDIUM
>> &END GLOBAL
>>
>> The  output file is
>> ----------------------------
>>
>>  SCF PARAMETERS         Density guess:
>>  ATOMIC
>>
>>  --------------------------------------------------------
>>                        max_scf:
>>    50
>>                        max_scf_history:
>>     0
>>                        max_diis:
>>    4
>>
>>  --------------------------------------------------------
>>                        eps_scf:
>>  3.00E-07
>>                        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            -27      26                Points:
>>    54
>>  PW_GRID:   Bounds   2            -27      26                Points:
>>    54
>>  PW_GRID:   Bounds   3            -27      26                Points:
>>    54
>>  PW_GRID: Volume element (a.u.^3)  0.5357E-02     Volume (a.u.^3)
>> 843.5418
>>  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            -15      14                Points:
>>    30
>>  PW_GRID:   Bounds   2            -15      14                Points:
>>    30
>>  PW_GRID:   Bounds   3            -15      14                Points:
>>    30
>>  PW_GRID: Volume element (a.u.^3)  0.3124E-01     Volume (a.u.^3)
>> 843.5418
>>  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             -9       8                Points:
>>    18
>>  PW_GRID:   Bounds   2             -9       8                Points:
>>    18
>>  PW_GRID:   Bounds   3             -9       8                Points:
>>    18
>>  PW_GRID: Volume element (a.u.^3)  0.1446         Volume (a.u.^3)
>> 843.5418
>>  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             -4       4                Points:
>>     9
>>  PW_GRID:   Bounds   2             -4       4                Points:
>>     9
>>  PW_GRID:   Bounds   3             -4       4                Points:
>>     9
>>  PW_GRID: Volume element (a.u.^3)   1.157         Volume (a.u.^3)
>> 843.5418
>>  PW_GRID: Grid span
>>  FULLSPACE
>>
>>  RS_GRID: Information for grid number
>>      1
>>  RS_GRID:   Bounds   1            -27      26                Points:
>>    54
>>  RS_GRID:   Bounds   2            -27      26                Points:
>>    54
>>  RS_GRID:   Bounds   3            -27      26                Points:
>>    54
>>
>>  RS_GRID: Information for grid number
>>      2
>>  RS_GRID:   Bounds   1            -15      14                Points:
>>    30
>>  RS_GRID:   Bounds   2            -15      14                Points:
>>    30
>>  RS_GRID:   Bounds   3            -15      14                Points:
>>    30
>>
>>  RS_GRID: Information for grid number
>>      3
>>  RS_GRID:   Bounds   1             -9       8                Points:
>>    18
>>  RS_GRID:   Bounds   2             -9       8                Points:
>>    18
>>  RS_GRID:   Bounds   3             -9       8                Points:
>>    18
>>
>>  RS_GRID: Information for grid number
>>      4
>>  RS_GRID:   Bounds   1             -4       4                Points:
>>     9
>>  RS_GRID:   Bounds   2             -4       4                Points:
>>     9
>>  RS_GRID:   Bounds   3             -4       4                Points:
>>     9
>>
>>  2D_CM| distribution_2d cost model info
>>  2D_CM| molecular_distribution
>>    NO
>>  2D_CM| account for symmetry
>>   YES
>>  2D_CM| cost model                                                 BLOCK
>> SURFACE
>>
>>  2D_MC| Monte Carlo annealing to optimize the distribution_2d
>>  2D_MC| Number of moves
>> 400000
>>  2D_MC| Number of annealing cycles
>>    10
>>  2D_MC| Number of reduction steps per cycle
>>      5
>>  2D_MC| Reduction factor per step
>> 0.8000000000
>>  2D_MC| Termination tolerance
>> 0.0200000000
>>  2D_MC| Maximum temperature
>> 0.5000000000
>>  2D_MC| Swap probability
>>  0.9000000000
>>  2D_MC| Number of processor rows
>>     1
>>  2D_MC| Number of processor cols
>>     1
>>  2D_MC| Number of elements
>>     3
>>  2D_MC| What do we minimize                                     SMALLEST
>> MAXIMUM
>>  2D_MC| Cost of optimal distribution
>>   374
>>  2D_MC| Cost of found distribution
>>   374
>>  2D_MC| Difference in percent
>>      0
>>
>>
>>  DISTRIBUTION OF THE PARTICLES (ROWS)
>>
>>  Process row   Number of particles      Number of matrix rows
>>
>>            0                     3                         -1
>>
>>          Sum                     3                         -1
>>
>>
>>  DISTRIBUTION OF THE PARTICLES (COLUMNS)
>>
>>  Process col   Number of particles   Number of matrix columns
>>
>>            0                     3                         -1
>>
>>          Sum                     3                         -1
>>
>>  DISTRIBUTION OF THE NEIGHBOR LISTS
>>
>>  Total number of particle pairs:                          155
>>  Total number of matrix elements:                        9763
>>  Average number of particle pairs:                        155
>>  Maximum number of particle pairs:                        155
>>  Average number of matrix element:                       9763
>>  Maximum number of matrix elements:                      9763
>>
>>
>>  DISTRIBUTION OF THE OVERLAP MATRIX
>>
>>  Number  of non-zero blocks:                                6
>>  Percentage non-zero blocks:                           100.00
>>  Average number of blocks per CPU:                          6
>>  Maximum number of blocks per CPU:                          6
>>  Average number of matrix elements per CPU:               374
>>  Maximum number of matrix elements per CPU:               374
>>
>>  Number of electrons:
>>      8
>>  Number of occupied orbitals:
>>      4
>>  Number of molecular orbitals:
>>     4
>>
>>  Number of orbital functions:
>>     23
>>  Number of independent orbital functions:
>>     23
>>
>>  Extrapolation method: initial_guess
>>
>>  Atomic guess: The first density matrix is obtained in terms of atomic
>> orbitals
>>               and electronic configurations assigned to each atomic kind
>>
>>  Guess for atomic kind: O
>>
>>  Electronic structure
>>    Total number of core electrons
>>  2.00
>>    Total number of valence electrons
>> 6.00
>>    Total number of electrons
>> 8.00
>>    Multiplicity                                                   not
>> specified
>>    S   [  2.00] 2.00
>>    P      4.00
>>
>>
>>
>>  *******************************************************************************
>>                  Iteration          Convergence                     Energy
>> [au]
>>
>>  *******************************************************************************
>>                          1         1.66618
>> -14.807077685535
>>                          2         2.18144
>> -14.856922221361
>>                          3        0.941861E-01
>> -15.651433198989
>>                          4        0.311542E-02
>> -15.652878316096
>>                          5        0.129713E-02
>> -15.652879617314
>>                          6        0.810331E-03
>> -15.652879783588
>>                          7        0.223809E-04
>> -15.652879889876
>>                          8        0.143180E-06
>> -15.652879889960
>>
>>  Energy components [Hartree]           Total Energy ::
>>  -15.652879889960
>>                                        Band Energy ::
>> -2.992123709411
>>                                     Kinetic Energy ::
>> 11.832933160969
>>                                        Core Energy ::
>>  -26.139880136201
>>                                          XC Energy ::
>> -3.155492704318
>>                                     Coulomb Energy ::
>> 13.642492950559
>>                       Total Pseudopotential Energy ::
>>  -38.007855496846
>>                       Local Pseudopotential Energy ::
>>  -39.320898599300
>>                    Nonlocal Pseudopotential Energy ::
>>  1.313043102454
>>                                        Confinement ::
>>  0.350421996757
>>
>>  Orbital energies  State     L     Occupation   Energy[a.u.]
>>  Energy[eV]
>>
>>                       1     0          2.000      -0.861204
>>  -23.434552
>>                       2     0          0.000       0.744977
>> 20.271849
>>
>>                       1     1          4.000      -0.317429
>> -8.637681
>>                       2     1          0.000       0.561513
>> 15.279549
>>
>>
>>  Guess for atomic kind: H
>>
>>  Electronic structure
>>    Total number of core electrons
>>  0.00
>>    Total number of valence electrons
>> 1.00
>>    Total number of electrons
>> 1.00
>>    Multiplicity                                                   not
>> specified
>>    S      1.00
>>
>>
>>
>>  *******************************************************************************
>>                  Iteration          Convergence                     Energy
>> [au]
>>
>>  *******************************************************************************
>>                          1        0.316896E-02
>>  -0.422453501026
>>                          2        0.328845E-03
>>  -0.422462494147
>>                          3        0.113312E-06
>>  -0.422462591984
>>
>>  Energy components [Hartree]           Total Energy ::
>> -0.422462591984
>>                                        Band Energy ::
>> -0.193030813655
>>                                     Kinetic Energy ::
>>  0.475635387250
>>                                        Core Energy ::
>> -0.478998252516
>>                                          XC Energy ::
>> -0.248263936733
>>                                     Coulomb Energy ::
>>  0.304799597265
>>                       Total Pseudopotential Energy ::
>> -0.972153085242
>>                       Local Pseudopotential Energy ::
>> -0.972153085242
>>                    Nonlocal Pseudopotential Energy ::
>>  0.000000000000
>>                                        Confinement ::
>>  0.175194454757
>>
>>  Orbital energies  State     L     Occupation   Energy[a.u.]
>>  Energy[eV]
>>
>>                       1     0          1.000      -0.193031
>> -5.252636
>>                       2     0          0.000       0.807984
>> 21.986353
>>
>>  Re-scaling the density matrix to get the right number of electrons
>>                  # Electrons              Trace(P)               Scaling
>> factor
>>                            8                 8.002
>>  1.000
>>
>>
>>  SCF WAVEFUNCTION OPTIMIZATION
>>
>>  Step     Update method      Time    Convergence         Total energy
>>  Change
>>
>>  ------------------------------------------------------------------------------
>>
>>  Total electronic density (r-space):          -7.9999999948
>>  0.0000000052
>>  Total core charge density (r-space):          8.0000000000
>>  0.0000000000
>>  Total charge density (r-space):
>> 0.0000000052
>>  Total charge density (g-space):
>> 0.0000000052
>>     1 P_Mix/Diag. 0.40E+00    0.3     1.96524988       -17.0390500821
>> -1.70E+01
>>
>>  Total electronic density (r-space):          -4.7999999969
>>  3.2000000031
>>  Total core charge density (r-space):          8.0000000000
>>  0.0000000000
>>  Total charge density (r-space):
>> 3.2000000032
>>  Total charge density (g-space):
>> 3.2000000032
>>     2 P_Mix/Diag. 0.40E+00    0.4     1.17914993       -13.5426292836
>>  3.50E+00
>>
>>  Total electronic density (r-space):          -2.8799999981
>>  5.1200000019
>>  Total core charge density (r-space):          8.0000000000
>>  0.0000000000
>>  Total charge density (r-space):
>> 5.1200000019
>>  Total charge density (g-space):
>> 5.1200000019
>>     3 P_Mix/Diag. 0.40E+00    0.4     0.70748996        -9.9067192962
>>  3.64E+00
>>
>>  Total electronic density (r-space):          -1.7279999989
>>  6.2720000011
>>  Total core charge density (r-space):          8.0000000000
>>  0.0000000000
>>  Total charge density (r-space):
>> 6.2720000011
>>  Total charge density (g-space):
>> 6.2720000011
>>     4 P_Mix/Diag. 0.40E+00    0.4     0.42449397        -7.1955092465
>>  2.71E+00
>>
>>  Total electronic density (r-space):          -1.0367999993
>>  6.9632000007
>>  Total core charge density (r-space):          8.0000000000
>>  0.0000000000
>>  Total charge density (r-space):
>> 6.9632000007
>>  Total charge density (g-space):
>> 6.9632000007
>>     5 P_Mix/Diag. 0.40E+00    0.4     0.25469638        -5.3903907002
>>  1.81E+00
>>
>>  Total electronic density (r-space):          -0.6220799996
>>  7.3779200004
>>  Total core charge density (r-space):          8.0000000000
>>  0.0000000000
>>  Total charge density (r-space):
>> 7.3779200004
>>  Total charge density (g-space):
>> 7.3779200004
>> Aborted
>>
>>
>> Could anyone help me please ?
>>
>> Thank you,
>> Regards,
>> Sandeep kumar reddy
>> Molecular simulations lab,
>> JNCASR
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "cp2k" group.
>> To post to this group, send email to cp... at googlegroups.com.
>> To unsubscribe from this group, send email to cp2k+
>> unsub... at googlegroups.com.
>> For more options, visit this group at http://groups.google.com/
>> group/cp2k?hl=en.
>>
>
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To post to this group, send email to cp... at googlegroups.com.
> To unsubscribe from this group, send email to
> cp2k+uns... at googlegroups.com <cp2k%2Bun... at googlegroups.com>.
> For more options, visit this group at
> http://groups.google.com/group/cp2k?hl=en.
>
>
>
>


-- 

Sandeep Kumar Reddy
Molecular Simulations Lab
Chemistry and Physics of Materials Unit JNCASR
Bangalore-560064
Ph: 080 22082809
---------------------------------------------------------
Sometimes our ambitions get flop,
Sometimes our assumtions go wrong,
But our goal is still wating for us,
Let us be positive and be active,
Our life is simply what our thoughts makes it,
Why not we think  good, positive
and big and make our life
a Grand celebration.
Have a wonderful day.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20100106/08b3a117/attachment.html>


More information about the CP2K-user mailing list