[Pw_forum] Order of Total Energy in SCF calculations

Giovanni Pizzi giovanni.pizzi at epfl.ch
Fri Dec 20 22:33:47 CET 2013


Dear Manu Hedge,
I don't know what you mean by "perfect", anyway it seems to be that you still have almost overlapping atoms…
Best,
Giovanni


On 20 Dec 2013, at 22:07, Manu Hegde wrote:

Thanks for your kind reply. Yeah I repeated this time by double checking my crystal coordinates with both VESTA and XRYSDYNE. It is perfect. Lorenzo, you are right I think. I will double check my pseudopotentials now. Then I will run the calcuations. Here is my new input data and outfile, still SCF energies are out of order!

 &CONTROL
                 calculation = 'scf' ,
                      outdir = '/home/owner/' ,
                  pseudo_dir = '/host/qexpress/espresso-5.0.2/pseudo/' ,
                      prefix = 'ga2o3' ,
 /
 &SYSTEM
                       ibrav = -12,
                           A = 12.34 ,
                           B = 3.08 ,
                           C = 5.87 ,
                       cosAB = 0 ,
                       cosAC = -0.24 ,
                       cosBC = 0 ,
                         nat = 10,
                        ntyp = 2,
                     ecutwfc = 70 ,
                     ecutrho = 840 ,
                       nosym = .false. ,
                        nbnd = 50,
                  tot_charge = 0.000000,
                 occupations = 'smearing' ,
                     degauss = 0.001 ,
            exxdiv_treatment = 'gygi-baldereschi' ,
 /
 &ELECTRONS
            electron_maxstep = 200,
                    conv_thr = 5.D-14 ,
                 startingpot = 'file' ,
                 startingwfc = 'atomic' ,
                 mixing_mode = 'local-TF' ,
                 mixing_beta = 0.4 ,
                 mixing_ndim = 10,
             diagonalization = 'david' ,
 /
ATOMIC_SPECIES
   Ga   69.72300  Ga.pbe-mt_fhi.UPF
    O   15.99900  O.pbe-kjpaw.UPF
ATOMIC_POSITIONS crystal
   Ga      0.091000000    0.000000000    0.794000000    1  0  1
   Ga      0.090000000    0.000000000    0.795000000    1  0  1
   Ga      0.342000000    0.000000000    0.686000000    1  0  1
   Ga      0.341000000    0.000000000    0.686000000    1  0  1
    O      0.163000000    0.000000000    0.109000000    1  0  1
    O      0.167000000    0.000000000    0.101000000    1  0  1
    O      0.495000000    0.000000000    0.257000000    1  0  1
    O      0.496000000    0.000000000    0.255000000    1  0  1
    O      0.826000000    0.000000000    0.436000000    1  0  1
    O      0.828000000    0.000000000    0.436000000    1  0  1
K_POINTS gamma


Output file is



     Program PWSCF v.5.0.2 (svn rev. 9392) starts on 20Dec2013 at 10:49:16

     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org<http://www.quantum-espresso.org/>",
     in publications or presentations arising from this work. More details at
     http://www.quantum-espresso.org/quote.php

     Serial version

     Current dimensions of program PWSCF are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3
     Waiting for input...
     Reading input from standard input
               file Ga.pbe-mt_fhi.UPF: wavefunction(s)  4d 4f renormalized

     gamma-point specific algorithms are used

     G-vector sticks info
     --------------------
     sticks:   dense  smooth     PW     G-vecs:    dense   smooth      PW
     Sum        9059    3023    749               600859   115693   14483
     Tot        4530    1512    375



     bravais-lattice index     =          -12
     lattice parameter (alat)  =      23.3192  a.u.
     unit-cell volume          =    1461.5653 (a.u.)^3
     number of atoms/cell      =           10
     number of atomic types    =            2
     number of electrons       =        48.00
     number of Kohn-Sham states=           50
     kinetic-energy cutoff     =      70.0000  Ry
     charge density cutoff     =     840.0000  Ry
     convergence threshold     =      5.0E-14
     mixing beta               =       0.4000
     number of iterations used =           10  local-TF  mixing
     Exchange-correlation      =  SLA  PW   PBX  PBC ( 1 4 3 4 0)
     EXX-fraction              =        0.00

     celldm(1)=  23.319220  celldm(2)=   0.249595  celldm(3)=   0.475689
     celldm(4)=   0.000000  celldm(5)=  -0.240000  celldm(6)=   0.000000

     crystal axes: (cart. coord. in units of alat)
               a(1) = (   1.000000   0.000000   0.000000 )
               a(2) = (   0.000000   0.249595   0.000000 )
               a(3) = (  -0.114165   0.000000   0.461786 )

     reciprocal axes: (cart. coord. in units 2 pi/alat)
               b(1) = (  1.000000 -0.000000  0.247226 )
               b(2) = (  0.000000  4.006494 -0.000000 )
               b(3) = (  0.000000  0.000000  2.165506 )


     PseudoPot. # 1 for Ga read from file:
     /host/qexpress/espresso-5.0.2/pseudo/Ga.pbe-mt_fhi.UPF
     MD5 check sum: d2addd91d8bcf9a88adfbbdfd2637de8
     Pseudo is Norm-conserving, Zval =  3.0
     Generated using FHI98PP, converted with fhi2upf.x v.5.0.2
     Using radial grid of  529 points,  3 beta functions with:
                l(1) =   1
                l(2) =   2
                l(3) =   3

     PseudoPot. # 2 for  O read from file:
     /host/qexpress/espresso-5.0.2/pseudo/O.pbe-kjpaw.UPF
     MD5 check sum: 90f4868982d1b5f8aada8373f3a0510a
     Pseudo is Projector augmented-wave + core cor, Zval =  6.0
     Generated using "atomic" code by A. Dal Corso (espresso distribution)
     Shape of augmentation charge: BESSEL
     Using radial grid of 1095 points,  4 beta functions with:
                l(1) =   0
                l(2) =   0
                l(3) =   1
                l(4) =   1
     Q(r) pseudized with 0 coefficients


     atomic species   valence    mass     pseudopotential
        Ga             3.00    69.72300     Ga( 1.00)
        O              6.00    15.99900      O( 1.00)

      2 Sym. Ops. (no inversion) found



   Cartesian axes

     site n.     atom                  positions (alat units)
         1           Ga  tau(   1) = (   0.0003527   0.0000000   0.3666579  )
         2           Ga  tau(   2) = (  -0.0007614   0.0000000   0.3671197  )
         3           Ga  tau(   3) = (   0.2636826   0.0000000   0.3167851  )
         4           Ga  tau(   4) = (   0.2626826   0.0000000   0.3167851  )
         5           O   tau(   5) = (   0.1505560   0.0000000   0.0503347  )
         6           O   tau(   6) = (   0.1554693   0.0000000   0.0466404  )
         7           O   tau(   7) = (   0.4656595   0.0000000   0.1186790  )
         8           O   tau(   8) = (   0.4668878   0.0000000   0.1177554  )
         9           O   tau(   9) = (   0.7762239   0.0000000   0.2013386  )
        10           O   tau(  10) = (   0.7782239   0.0000000   0.2013386  )

     number of k points=     1  gaussian smearing, width (Ry)=  0.0010
                       cart. coord. in units 2pi/alat
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   2.0000000

     Dense  grid:   300430 G-vectors     FFT dimensions: ( 216,  54, 108)

     Smooth grid:    57847 G-vectors     FFT dimensions: ( 125,  32,  60)

     Largest allocated arrays     est. size (Mb)     dimensions
        Kohn-Sham Wavefunctions         5.53 Mb     (   7242,   50)
        NL pseudopotentials            11.93 Mb     (   7242,  108)
        Each V/rho on FFT grid         19.22 Mb     (1259712)
        Each G-vector array             2.29 Mb     ( 300430)
        G-vector shells                 1.18 Mb     ( 154426)
     Largest temporary arrays     est. size (Mb)     dimensions
        Auxiliary wavefunctions        11.05 Mb     (   7242,  200)
        Each subspace H/S matrix        0.31 Mb     ( 200, 200)
        Each <psi_i|beta_j> matrix      0.04 Mb     (    108,   50)
        Arrays for rho mixing         192.22 Mb     (1259712,  10)

     The initial density is read from file :
     /home/owner/ga2o3.save/charge-density.dat


     negative rho (up, down):  0.792E-04 0.000E+00
     Starting wfc are   88 atomic wfcs

     total cpu time spent up to now is       49.4 secs

     per-process dynamical memory:   185.0 Mb

     Self-consistent Calculation

     iteration #  1     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  1.00E-05,  avg # of iterations = 17.0

     negative rho (up, down):  0.598E-05 0.000E+00

     total cpu time spent up to now is       75.3 secs

     total energy              =    4938.29712853 Ry
     Harris-Foulkes estimate   =    4938.22313787 Ry
     estimated scf accuracy    <       0.41754104 Ry

     iteration #  2     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  8.70E-04,  avg # of iterations =  1.0

     total cpu time spent up to now is       87.3 secs

     total energy              =    4938.33592276 Ry
     Harris-Foulkes estimate   =    4938.29279567 Ry
     estimated scf accuracy    <       0.30683623 Ry

     iteration #  3     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  6.39E-04,  avg # of iterations =  1.0

     total cpu time spent up to now is      101.0 secs

     total energy              =    4938.39891566 Ry
     Harris-Foulkes estimate   =    4938.32812563 Ry
     estimated scf accuracy    <       0.16581632 Ry

     iteration #  4     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  3.45E-04,  avg # of iterations =  2.0

     total cpu time spent up to now is      113.9 secs

     total energy              =    4938.39312220 Ry
     Harris-Foulkes estimate   =    4938.38608688 Ry
     estimated scf accuracy    <       0.02721425 Ry

     iteration #  5     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  5.67E-05,  avg # of iterations =  4.0

     total cpu time spent up to now is      127.2 secs

     total energy              =    4938.39390580 Ry
     Harris-Foulkes estimate   =    4938.39118343 Ry
     estimated scf accuracy    <       0.01307994 Ry

     iteration #  6     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  2.72E-05,  avg # of iterations =  5.0

     total cpu time spent up to now is      139.9 secs

     total energy              =    4938.39616138 Ry
     Harris-Foulkes estimate   =    4938.39184943 Ry
     estimated scf accuracy    <       0.12816220 Ry

     iteration #  7     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  2.72E-05,  avg # of iterations =  1.0

     total cpu time spent up to now is      152.2 secs

     total energy              =    4938.39448062 Ry
     Harris-Foulkes estimate   =    4938.39337459 Ry
     estimated scf accuracy    <       0.01271195 Ry

     iteration #  8     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  2.65E-05,  avg # of iterations =  1.0

     total cpu time spent up to now is      164.5 secs

     total energy              =    4938.39419361 Ry
     Harris-Foulkes estimate   =    4938.39378074 Ry
     estimated scf accuracy    <       0.00996928 Ry

     iteration #  9     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  2.08E-05,  avg # of iterations =  1.0

     total cpu time spent up to now is      176.9 secs

     total energy              =    4938.39418124 Ry
     Harris-Foulkes estimate   =    4938.39408487 Ry
     estimated scf accuracy    <       0.00287607 Ry

     iteration # 10     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  5.99E-06,  avg # of iterations =  8.0

     total cpu time spent up to now is      189.8 secs

     total energy              =    4938.39434380 Ry
     Harris-Foulkes estimate   =    4938.39404235 Ry
     estimated scf accuracy    <       0.01438715 Ry

     iteration # 11     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  5.99E-06,  avg # of iterations =  1.0

     total cpu time spent up to now is      202.2 secs

     total energy              =    4938.39410947 Ry
     Harris-Foulkes estimate   =    4938.39408264 Ry
     estimated scf accuracy    <       0.00392466 Ry

     iteration # 12     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  5.99E-06,  avg # of iterations =  1.0

     total cpu time spent up to now is      214.7 secs

     total energy              =    4938.39412353 Ry
     Harris-Foulkes estimate   =    4938.39409606 Ry
     estimated scf accuracy    <       0.00220472 Ry

     iteration # 13     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  4.59E-06,  avg # of iterations =  1.0

     total cpu time spent up to now is      227.1 secs

     total energy              =    4938.39412742 Ry
     Harris-Foulkes estimate   =    4938.39411648 Ry
     estimated scf accuracy    <       0.00077585 Ry

     iteration # 14     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  1.62E-06,  avg # of iterations =  1.0

     total cpu time spent up to now is      239.6 secs

     total energy              =    4938.39412492 Ry
     Harris-Foulkes estimate   =    4938.39412295 Ry
     estimated scf accuracy    <       0.00007273 Ry

     iteration # 15     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  1.52E-07,  avg # of iterations =  1.0

     total cpu time spent up to now is      252.0 secs

     total energy              =    4938.39412350 Ry
     Harris-Foulkes estimate   =    4938.39412342 Ry
     estimated scf accuracy    <       0.00000313 Ry

     iteration # 16     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  6.53E-09,  avg # of iterations =  5.0

     total cpu time spent up to now is      265.4 secs

     total energy              =    4938.39412142 Ry
     Harris-Foulkes estimate   =    4938.39412142 Ry
     estimated scf accuracy    <       0.00000414 Ry

     iteration # 17     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  6.53E-09,  avg # of iterations =  1.0

     total cpu time spent up to now is      277.8 secs

     total energy              =    4938.39412145 Ry
     Harris-Foulkes estimate   =    4938.39412142 Ry
     estimated scf accuracy    <       0.00000408 Ry

     iteration # 18     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  6.53E-09,  avg # of iterations =  1.0

     total cpu time spent up to now is      290.2 secs

     total energy              =    4938.39412145 Ry
     Harris-Foulkes estimate   =    4938.39412143 Ry
     estimated scf accuracy    <       0.00000078 Ry

     iteration # 19     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  1.62E-09,  avg # of iterations =  1.0

     total cpu time spent up to now is      302.7 secs

     total energy              =    4938.39412144 Ry
     Harris-Foulkes estimate   =    4938.39412144 Ry
     estimated scf accuracy    <       0.00000018 Ry

     iteration # 20     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  3.76E-10,  avg # of iterations =  1.0

     total cpu time spent up to now is      315.1 secs

     total energy              =    4938.39412144 Ry
     Harris-Foulkes estimate   =    4938.39412144 Ry
     estimated scf accuracy    <       0.00000002 Ry

     iteration # 21     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  5.12E-11,  avg # of iterations =  1.0

     total cpu time spent up to now is      327.5 secs

     total energy              =    4938.39412144 Ry
     Harris-Foulkes estimate   =    4938.39412144 Ry
     estimated scf accuracy    <          3.1E-09 Ry

     iteration # 22     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  6.50E-12,  avg # of iterations =  3.0

     total cpu time spent up to now is      340.0 secs

     total energy              =    4938.39412144 Ry
     Harris-Foulkes estimate   =    4938.39412144 Ry
     estimated scf accuracy    <          2.0E-09 Ry

     iteration # 23     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  4.16E-12,  avg # of iterations =  1.0

     total cpu time spent up to now is      352.4 secs

     total energy              =    4938.39412144 Ry
     Harris-Foulkes estimate   =    4938.39412144 Ry
     estimated scf accuracy    <          6.7E-11 Ry

     iteration # 24     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  1.40E-13,  avg # of iterations =  4.0

     total cpu time spent up to now is      366.1 secs

     total energy              =    4938.39412144 Ry
     Harris-Foulkes estimate   =    4938.39412144 Ry
     estimated scf accuracy    <          2.8E-11 Ry

     iteration # 25     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  1.00E-13,  avg # of iterations =  1.0

     total cpu time spent up to now is      378.6 secs

     total energy              =    4938.39412144 Ry
     Harris-Foulkes estimate   =    4938.39412144 Ry
     estimated scf accuracy    <          1.1E-12 Ry

     iteration # 26     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  1.00E-13,  avg # of iterations =  1.0

     total cpu time spent up to now is      391.0 secs

     total energy              =    4938.39412144 Ry
     Harris-Foulkes estimate   =    4938.39412144 Ry
     estimated scf accuracy    <          9.0E-13 Ry

     iteration # 27     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  1.00E-13,  avg # of iterations =  1.0

     total cpu time spent up to now is      403.5 secs

     total energy              =    4938.39412144 Ry
     Harris-Foulkes estimate   =    4938.39412144 Ry
     estimated scf accuracy    <          2.0E-13 Ry

     iteration # 28     ecut=    70.00 Ry     beta=0.40
     Davidson diagonalization with overlap
     ethr =  1.00E-13,  avg # of iterations =  1.0

     total cpu time spent up to now is      414.3 secs

     End of self-consistent calculation

          k = 0.0000 0.0000 0.0000 (  7242 PWs)   bands (ev):

   -90.2908 -90.0412 -89.8349 -89.8224 -89.6488 -89.4214 -86.0207 -85.9975
   -85.7751 -40.1704 -39.8801 -39.5302 -10.6308  -9.5392  -2.5414  -1.9632
    -1.1054  -0.2253   0.7544   1.2391   1.9599   2.6234   2.7093   2.7309
     2.7639   3.0767   3.4409   3.4782   4.6520   5.1184   5.8085   6.0575
     6.1719   6.4130   7.0001   7.5031   8.2702   8.3526   8.5260   8.5755
     8.7028   8.8727   9.0694   9.3255   9.3593  10.2785  10.3479  10.9827
    11.0547  11.5075

     the Fermi energy is     2.7474 ev

!    total energy              =    4938.39412144 Ry
     Harris-Foulkes estimate   =    4938.39412144 Ry
     estimated scf accuracy    <          4.8E-14 Ry

     The total energy is the sum of the following terms:

     one-electron contribution =    -416.33496719 Ry
     hartree contribution      =     170.32220332 Ry
     xc contribution           =     -53.05139715 Ry
     ewald contribution        =    5293.56350757 Ry
     one-center paw contrib.   =     -56.10496582 Ry
     smearing contrib. (-TS)   =      -0.00025929 Ry

     convergence has been achieved in  28 iterations

     Writing output data file ga2o3.save

     init_run     :     48.14s CPU     48.76s WALL (       1 calls)
     electrons    :    355.54s CPU    364.84s WALL (       1 calls)

     Called by init_run:
     wfcinit      :      2.04s CPU      2.12s WALL (       1 calls)
     potinit      :      2.63s CPU      2.95s WALL (       1 calls)

     Called by electrons:
     c_bands      :     78.83s CPU     79.80s WALL (      28 calls)
     sum_band     :     90.95s CPU     93.75s WALL (      28 calls)
     v_of_rho     :     53.06s CPU     54.56s WALL (      29 calls)
     newd         :     78.22s CPU     80.58s WALL (      29 calls)
     mix_rho      :     39.71s CPU     39.85s WALL (      28 calls)

     Called by c_bands:
     init_us_2    :      0.96s CPU      0.98s WALL (      57 calls)
     regterg      :     76.77s CPU     77.74s WALL (      28 calls)

     Called by *egterg:
     h_psi        :     47.51s CPU     47.74s WALL (      97 calls)
     s_psi        :      3.90s CPU      3.92s WALL (      97 calls)
     g_psi        :      0.27s CPU      0.27s WALL (      68 calls)
     rdiaghg      :      0.85s CPU      0.88s WALL (      96 calls)

     Called by h_psi:
     add_vuspsi   :      8.73s CPU      8.76s WALL (      97 calls)

     General routines
     calbec       :     13.45s CPU     13.51s WALL (     125 calls)
     fft          :     30.15s CPU     30.24s WALL (     459 calls)
     ffts         :     13.17s CPU     13.21s WALL (    1438 calls)
     fftw         :     23.57s CPU     23.68s WALL (    4118 calls)
     interpolate  :      4.85s CPU      5.08s WALL (      57 calls)
     davcio       :      0.02s CPU      0.66s WALL (      28 calls)


     PAW routines
     PAW_pot      :     15.48s CPU     15.52s WALL (      29 calls)
     PAW_ddot     :      9.30s CPU      9.32s WALL (    1343 calls)
     PAW_symme    :      0.00s CPU      0.00s WALL (      56 calls)

     PWSCF        :  6m44.07s CPU     6m54.45s WALL


   This run was terminated on:  10:56:10  20Dec2013

=------------------------------------------------------------------------------=
   JOB DONE.
=------------------------------------------------------------------------------=

Regards,
Manu


On Fri, Dec 20, 2013 at 7:28 AM, Paolo Giannozzi <paolo.giannozzi at uniud.it<mailto:paolo.giannozzi at uniud.it>> wrote:
Your input data is still wrong. What is the distance
between atoms 1 and 2 in your list? (hint: 0.015 A)

P.
--
 Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216<tel:%2B39-0432-558216>, fax +39-0432-558222<tel:%2B39-0432-558222>

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