Cu FCC vc-relax method error

Question

Reference: Density Functional Theory: A Practical Introduction, David Sholl, Janice A. Steckel, Chapter 2, Page No. 48

Section 2.2 The fcc Cu calculations in Fig. 2.3 used a cubic supercell with 4 Cu atoms, a cutoff energy of 292 eV, and 12 x 12 x 12 k points.

I approached this problem like this,
[cu_fcc.vcr.in]

 &CONTROL
                 calculation = 'vc-relax' ,
                restart_mode = 'from_scratch' ,
                      outdir = '../outdir' ,
                  pseudo_dir = '../pseudo' ,
                      prefix = 'cu' ,
 /
 &SYSTEM
                       ibrav = 2,
                   celldm(1) = 4.91,
                         nat = 4,
                        ntyp = 1,
                     ecutwfc = 21 ,
                 occupations = 'smearing' ,
                     degauss = 0.02 ,
                    smearing = 'gaussian' ,
 /
 &ELECTRONS
 /
 &IONS
 /
 &CELL
               cell_dynamics = 'bfgs' ,
 /
ATOMIC_SPECIES
   Cu   63.55000  Cu.pbe-kjpaw.UPF 
ATOMIC_POSITIONS {alat} 
   Cu      0.000000000    0.000000000    0.000000000    
   Cu      0.500000000    0.000000000    0.500000000    
   Cu      0.000000000    0.500000000    0.500000000    
   Cu      0.500000000    0.500000000    0.000000000    
K_POINTS automatic 
  12 12 12   0 0 0

[cu_fcc.vcr.out]

     Program PWSCF v.6.8 starts on 27Sep2021 at 20:15:59 

     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);
         "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
         "P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
          URL http://www.quantum-espresso.org", 
     in publications or presentations arising from this work. More details at
     http://www.quantum-espresso.org/quote

     Parallel version (MPI), running on     1 processors

     MPI processes distributed on     1 nodes
     2319 MiB available memory on the printing compute node when the environment starts

     Reading input from cu_fcc.vcr.in

     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) =  4

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     Error in routine check_atoms (1):
     atoms #   1 and #   2 differ by lattice vector ( 0,-1, 1) in crystal axis
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

Unfortunately, Am getting an error, which is posted above. Where is the problem in my input file?

Edit 1:
As suggested by @tyberius, I changed the values from 0.5 to 0.25 and re-run the calculations. Now am getting a different error.

[cu_fcc.vcr.out]

     Program PWSCF v.6.8 starts on 27Sep2021 at 22:43:53 

     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);
         "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
         "P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
          URL http://www.quantum-espresso.org", 
     in publications or presentations arising from this work. More details at
     http://www.quantum-espresso.org/quote

     Parallel version (MPI), running on     1 processors

     MPI processes distributed on     1 nodes
     934 MiB available memory on the printing compute node when the environment starts

     Reading input from cu_fcc.vcr.in

     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) =  4

     Subspace diagonalization in iterative solution of the eigenvalue problem:
     a serial algorithm will be used


     G-vector sticks info
     --------------------
     sticks:   dense  smooth     PW     G-vecs:    dense   smooth      PW
     Sum          73      73     31                  387      387     113

     Using Slab Decomposition



     bravais-lattice index     =            2
     lattice parameter (alat)  =       4.9100  a.u.
     unit-cell volume          =      29.5927 (a.u.)^3
     number of atoms/cell      =            4
     number of atomic types    =            1
     number of electrons       =        44.00
     number of Kohn-Sham states=           26
     kinetic-energy cutoff     =      21.0000  Ry
     charge density cutoff     =      84.0000  Ry
     scf convergence threshold =      1.0E-06
     mixing beta               =       0.7000
     number of iterations used =            8  plain     mixing
     energy convergence thresh.=      1.0E-04
     force convergence thresh. =      1.0E-03
     press convergence thresh. =      5.0E-01
     Exchange-correlation= SLA  PW   PBX  PBC
                           (   1   4   3   4   0   0   0)
     nstep                     =           50


     celldm(1)=   4.910000  celldm(2)=   0.000000  celldm(3)=   0.000000
     celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000

     crystal axes: (cart. coord. in units of alat)
               a(1) = (  -0.500000   0.000000   0.500000 )  
               a(2) = (   0.000000   0.500000   0.500000 )  
               a(3) = (  -0.500000   0.500000   0.000000 )  

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


     PseudoPot. # 1 for Cu read from file:
     ../pseudo/Cu.pbe-kjpaw.UPF
     MD5 check sum: fe769b0ab65dca5f3352e2411ad4c6f8
     Pseudo is Projector augmented-wave + core cor, Zval = 11.0
     Generated using "atomic" code by A. Dal Corso (espresso distribution)
     Shape of augmentation charge: BESSEL
     Using radial grid of 1199 points,  6 beta functions with: 
                l(1) =   2
                l(2) =   2
                l(3) =   0
                l(4) =   0
                l(5) =   1
                l(6) =   1
     Q(r) pseudized with 0 coefficients 


     atomic species   valence    mass     pseudopotential
        Cu            11.00    63.55000     Cu( 1.00)

     48 Sym. Ops., with inversion, found (36 have fractional translation)



   Cartesian axes

     site n.     atom                  positions (alat units)
         1           Cu  tau(   1) = (   0.0000000   0.0000000   0.0000000  )
         2           Cu  tau(   2) = (   0.2500000   0.0000000   0.2500000  )
         3           Cu  tau(   3) = (   0.0000000   0.2500000   0.2500000  )
         4           Cu  tau(   4) = (   0.2500000   0.2500000   0.0000000  )

     number of k points=    72  Gaussian smearing, width (Ry)=  0.0200
                       cart. coord. in units 2pi/alat
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0011574
        k(    2) = (  -0.0833333   0.0833333  -0.0833333), wk =   0.0092593
        k(    3) = (  -0.1666667   0.1666667  -0.1666667), wk =   0.0092593
        k(    4) = (  -0.2500000   0.2500000  -0.2500000), wk =   0.0092593
        k(    5) = (  -0.3333333   0.3333333  -0.3333333), wk =   0.0092593
        k(    6) = (  -0.4166667   0.4166667  -0.4166667), wk =   0.0092593
        k(    7) = (   0.5000000  -0.5000000   0.5000000), wk =   0.0046296
        k(    8) = (   0.0000000   0.1666667   0.0000000), wk =   0.0069444
        k(    9) = (  -0.0833333   0.2500000  -0.0833333), wk =   0.0277778
        k(   10) = (  -0.1666667   0.3333333  -0.1666667), wk =   0.0277778
        k(   11) = (  -0.2500000   0.4166667  -0.2500000), wk =   0.0277778
        k(   12) = (  -0.3333333   0.5000000  -0.3333333), wk =   0.0277778
        k(   13) = (   0.5833333  -0.4166667   0.5833333), wk =   0.0277778
        k(   14) = (   0.5000000  -0.3333333   0.5000000), wk =   0.0277778
        k(   15) = (   0.4166667  -0.2500000   0.4166667), wk =   0.0277778
        k(   16) = (   0.3333333  -0.1666667   0.3333333), wk =   0.0277778
        k(   17) = (   0.2500000  -0.0833333   0.2500000), wk =   0.0277778
        k(   18) = (   0.1666667  -0.0000000   0.1666667), wk =   0.0138889
        k(   19) = (   0.0000000   0.3333333   0.0000000), wk =   0.0069444
        k(   20) = (  -0.0833333   0.4166667  -0.0833333), wk =   0.0277778
        k(   21) = (  -0.1666667   0.5000000  -0.1666667), wk =   0.0277778
        k(   22) = (  -0.2500000   0.5833333  -0.2500000), wk =   0.0277778
        k(   23) = (   0.6666667  -0.3333333   0.6666667), wk =   0.0277778
        k(   24) = (   0.5833333  -0.2500000   0.5833333), wk =   0.0277778
        k(   25) = (   0.5000000  -0.1666667   0.5000000), wk =   0.0277778
        k(   26) = (   0.4166667  -0.0833333   0.4166667), wk =   0.0277778
        k(   27) = (   0.3333333   0.0000000   0.3333333), wk =   0.0138889
        k(   28) = (   0.0000000   0.5000000   0.0000000), wk =   0.0069444
        k(   29) = (  -0.0833333   0.5833333  -0.0833333), wk =   0.0277778
        k(   30) = (  -0.1666667   0.6666667  -0.1666667), wk =   0.0277778
        k(   31) = (   0.7500000  -0.2500000   0.7500000), wk =   0.0277778
        k(   32) = (   0.6666667  -0.1666667   0.6666667), wk =   0.0277778
        k(   33) = (   0.5833333  -0.0833333   0.5833333), wk =   0.0277778
        k(   34) = (   0.5000000   0.0000000   0.5000000), wk =   0.0138889
        k(   35) = (   0.0000000   0.6666667   0.0000000), wk =   0.0069444
        k(   36) = (  -0.0833333   0.7500000  -0.0833333), wk =   0.0277778
        k(   37) = (   0.8333333  -0.1666667   0.8333333), wk =   0.0277778
        k(   38) = (   0.7500000  -0.0833333   0.7500000), wk =   0.0277778
        k(   39) = (   0.6666667  -0.0000000   0.6666667), wk =   0.0138889
        k(   40) = (   0.0000000   0.8333333   0.0000000), wk =   0.0069444
        k(   41) = (   0.9166667  -0.0833333   0.9166667), wk =   0.0277778
        k(   42) = (   0.8333333   0.0000000   0.8333333), wk =   0.0138889
        k(   43) = (   0.0000000  -1.0000000   0.0000000), wk =   0.0034722
        k(   44) = (  -0.1666667   0.3333333   0.0000000), wk =   0.0277778
        k(   45) = (  -0.2500000   0.4166667  -0.0833333), wk =   0.0555556
        k(   46) = (  -0.3333333   0.5000000  -0.1666667), wk =   0.0555556
        k(   47) = (   0.5833333  -0.4166667   0.7500000), wk =   0.0555556
        k(   48) = (   0.5000000  -0.3333333   0.6666667), wk =   0.0277778
        k(   49) = (  -0.1666667   0.5000000   0.0000000), wk =   0.0277778
        k(   50) = (  -0.2500000   0.5833333  -0.0833333), wk =   0.0555556
        k(   51) = (   0.6666667  -0.3333333   0.8333333), wk =   0.0555556
        k(   52) = (   0.5833333  -0.2500000   0.7500000), wk =   0.0555556
        k(   53) = (   0.5000000  -0.1666667   0.6666667), wk =   0.0555556
        k(   54) = (   0.4166667  -0.0833333   0.5833333), wk =   0.0555556
        k(   55) = (   0.3333333   0.0000000   0.5000000), wk =   0.0277778
        k(   56) = (  -0.1666667   0.6666667  -0.0000000), wk =   0.0277778
        k(   57) = (   0.7500000  -0.2500000   0.9166667), wk =   0.0555556
        k(   58) = (   0.6666667  -0.1666667   0.8333333), wk =   0.0555556
        k(   59) = (   0.5833333  -0.0833333   0.7500000), wk =   0.0555556
        k(   60) = (   0.5000000   0.0000000   0.6666667), wk =   0.0277778
        k(   61) = (   0.8333333  -0.1666667   1.0000000), wk =   0.0277778
        k(   62) = (   0.7500000  -0.0833333   0.9166667), wk =   0.0555556
        k(   63) = (   0.6666667   0.0000000   0.8333333), wk =   0.0277778
        k(   64) = (  -0.1666667  -1.0000000  -0.0000000), wk =   0.0138889
        k(   65) = (   0.6666667  -0.3333333   1.0000000), wk =   0.0277778
        k(   66) = (   0.5833333  -0.2500000   0.9166667), wk =   0.0555556
        k(   67) = (   0.5000000  -0.1666667   0.8333333), wk =   0.0277778
        k(   68) = (   0.6666667  -0.1666667   1.0000000), wk =   0.0277778
        k(   69) = (   0.5833333  -0.0833333   0.9166667), wk =   0.0555556
        k(   70) = (   0.5000000   0.0000000   0.8333333), wk =   0.0277778
        k(   71) = (  -0.3333333  -1.0000000   0.0000000), wk =   0.0138889
        k(   72) = (  -0.5000000  -1.0000000   0.0000000), wk =   0.0069444

     Dense  grid:      387 G-vectors     FFT dimensions: (  12,  12,  12)

     Estimated max dynamical RAM per process >       4.38 MB

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     Error in routine memory_report (1):
     more bands than PWs!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. — Community, Sep 27, 2021 at 15:50
I attached the output file, which clearly mentions the error. My question is all about why am I getting this error and how to proceed further with the calculation. — 147875, Sep 27, 2021 at 15:57

Tyberius · Accepted Answer · 2021-09-27 16:42:15Z

5

As the error message states, your atoms 1 and 2 are related by translation vectors, so you can't specify both of them.

Note the lattice vectors used for an FCC system in QE:

2 cubic F (fcc)

v1 = (a/2)(-1,0,1), v2 = (a/2)(0,1,1), v3 = (a/2)(-1,1,0)

As you can see, -v2+v3= (-.5,0,-.5), which is the distance between atoms 1 and 2.

I haven't done much with Quantum Espresso, but I believe you just need to set the coordinates in your input to 0.25 rather than 0.50.

answered Sep 27, 2021 at 16:42

Tyberius♦

14.2k3 gold badges24 silver badges111 bronze badges

$\begingroup$ I changed the values as suggested by you. Now am getting a different error, which I posted in question. Please go through it. $\endgroup$
– 147875
Sep 27, 2021 at 17:24
$\begingroup$ @147875 Best I can tell, this is a memory issue. The source code for memory_report suggests that it calculates the maximum number of plane waves that can be used given the amount of memory and if this is is less than the number of bands, the calculation throws an error. $\endgroup$
– Tyberius ♦
Sep 27, 2021 at 17:34
$\begingroup$ Thank you! It does makes sense. Is there any quantity I can reduce, so that I can work within my limitations? $\endgroup$
– 147875
Sep 27, 2021 at 17:51
$\begingroup$ For fcc Cu in the primitive cell there should be just one atom, not four. $\endgroup$
– Brandon Bocklund
Sep 28, 2021 at 1:33
$\begingroup$ @BrandonBocklund The author clearly mentions in the question to use 4 Cu atoms. How do one know how many atoms should one consider in calculations? $\endgroup$
– 147875
Sep 28, 2021 at 7:25

| Show 2 more comments

Brandon Bocklund · Accepted Answer · 2021-09-28 15:30:55Z

ibrav = 2 in Quantum Espresso gives an fcc Bravis lattice, as mentioned in the answer by Tyberius, with the lattice vectors:

a(1) = (  -0.500000   0.000000   0.500000 )
a(2) = (   0.000000   0.500000   0.500000 )
a(3) = (  -0.500000   0.500000   0.000000 )

Using an fcc Bravis lattice, which the primitive cell for fcc structures contains one atom. The cubic, conventional fcc cell contains four atoms, which is the source of confusion.

I set up a relaxation file based on the one you had for fcc Cu like this:

 &CONTROL
                 calculation = 'vc-relax' ,
                restart_mode = 'from_scratch' ,
                      outdir = '../outdir' ,
                  pseudo_dir = '../pseudo' ,
                      prefix = 'cu' ,
 /
 &SYSTEM
                       ibrav = 2,
                   celldm(1) = 7.2,
                         nat = 1,
                        ntyp = 1,
                     ecutwfc = 21 ,
                 occupations = 'smearing' ,
                     degauss = 0.02 ,
                    smearing = 'gaussian' ,
 /
 &ELECTRONS
 /
 &IONS
 /
 &CELL
               cell_dynamics = 'bfgs' ,
 /
ATOMIC_SPECIES
   Cu   63.55000  Cu.pbe-kjpaw.UPF 
ATOMIC_POSITIONS {alat} 
   Cu      0.000000000    0.000000000    0.000000000    
K_POINTS automatic 
  12 12 12   0 0 0

The differences are in the choice of celldm(1) = 7.2 for the initial guess, nat = 1 and the single Cu atom in the ATOMIC_POSITIONS card.

I'm not sure what celldm(1) you were using once you tried only one atom. The way I determined 7.2 as a guess was to perform several SCF calculations at different values of celldm(1) and add those cell dimensions and energies to a file called alat-e.dat:

6.0 -212.99886753
6.5 -213.12777832
6.8 -213.15585359
7.0 -213.16375461
7.2 -213.16506950
7.5 -213.16053932
8.0 -213.13825503

Then I ran Quantum Espresso's ev.x with the input:

$ ev.x
     Lattice parameter or Volume are in (au, Ang) > au
     Enter type of bravais lattice (fcc, bcc, sc, noncubic) > fcc
     Enter type of equation of state :
     1=birch1, 2=birch2, 3=keane, 4=murnaghan > 4
     Input file > alat-e.dat
     Output file >

which gives the output

# equation of state: murnaghan.        chisq =   0.2682D-07
# a0 =  7.1754 a.u., k0 = 1018 kbar, dk0 =  4.51 d2k0 =  0.000 emin = -213.16545
# a0 =  3.79708 Ang, k0 = 101.9 GPa,  V0 =    92.36 (a.u.)^3,  V0 =   13.69 A^3

#########################################################################
# Lat.Par       E_calc        E_fit       E_diff    Pressure      Enthalpy
# a.u.            Ry           Ry            Ry        GPa           Ry
#########################################################################
  6.00000    -212.99887    -212.99887    -0.00000     231.74     -212.14819
  6.50000    -213.12778    -213.12781     0.00004      63.49     -212.83147
  6.80000    -213.15585    -213.15581    -0.00004      24.15     -213.02679
  7.00000    -213.16375    -213.16357    -0.00019       8.99     -213.11137
  7.20000    -213.16507    -213.16541     0.00034      -1.02     -213.17154
  7.50000    -213.16054    -213.16037    -0.00017     -10.17     -213.23347
  8.00000    -213.13826    -213.13828     0.00003     -17.40     -213.28964

The celldm(1) = 7.2 I rounded from the a0 = 7.1754 a.u. value in the output. The value of a0 in Å, a0 = 3.79708 Ang, seems reasonable, but I haven't checked it.

I know what you have done, fitting Birch-Murnaghan's equation to E_vs_alat curve to get physical properties of the crystal. What I wanted is to find the 'alat' using "variable cell relaxation method", where you guess the celldm(1) and it does geometric and structural optimization to find out 'alat'. — 147875, Sep 28, 2021 at 16:17
Sure, the input file at the top is for vc-relax and works well for me. I suggested the EV curve just to get a reasonable starting point for the lattice parameter. — Brandon Bocklund, Sep 28, 2021 at 18:04

147875 · Accepted Answer · 2021-10-02 10:19:18Z

With the help of @Tyberius and @BrandonBocklund, I did the calculation of Cu in FCC lattice. Calculated lattice constant $a = 3.62613952 \, A^\circ$, where as experimental value is $a = 3.6149 \, A^\circ$. The major source of confusion is, I interpreted the question as FCC primitive cell has 4 Atoms.

 &CONTROL
                 calculation = 'vc-relax' ,
                restart_mode = 'from_scratch' ,
                      outdir = '../../tmp' ,
                  pseudo_dir = '../../pseudo' ,
                      prefix = 'cu_fcc' ,
 /
 &SYSTEM
                       ibrav = 2,
                   celldm(1) = 7.1754,
                         nat = 1,
                        ntyp = 1,
                     ecutwfc = 40 ,
                 occupations = 'smearing' ,
                     degauss = 0.02 ,
                    smearing = 'methfessel-paxton' ,
 /
 &ELECTRONS
                    conv_thr = 1d-8 ,
                 mixing_mode = 'plain' ,
                 mixing_beta = 0.7 ,
 /
 &IONS
                ion_dynamics = 'bfgs' ,
 /
 &CELL
               cell_dynamics = 'bfgs' ,
                       press = 0 ,
              press_conv_thr = 0.5 ,
 /
ATOMIC_SPECIES
   Cu   63.55000  Cu.pbe-dn-rrkjus_psl.1.0.0.UPF 
ATOMIC_POSITIONS alat 
   Cu      0.000000000    0.000000000    0.000000000    
K_POINTS automatic 
  8 8 8   0 0 0

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