[CP2K:2494] Test files -H2O

Teodoro Laino teodor... at gmail.com
Wed Jan 6 09:26:28 CET 2010


Hello,

If I would be you I would first try to check if a popt works! If it is 
working (with same compiler/libraries setup) then I would go for trying 
the psmp.

Teo

Sandeep Kumar Reddy wrote:
> 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 <mailto: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
>
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>
>
> -- 
>
> 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,
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>
>
>
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