[Pw_forum] equivalent atomic symbols are not found

[Paolo Giannozzi]

Unfortunately QHA is currently unmaintained

P.

On Sat, 2013-12-14 at 18:57 +0100, David Grifith wrote:
> Dear QE users
> 
> at the final steps of calculating Gibbs energy I get an error that you
> can see in the following:
> 
> STOP equivalent atomic symbols are not found
> At line 59 of file Atom_projected_properties.f90 (unit = 9, file =
> 'projected.DOS')
> Fortran runtime error: Bad integer for item 1 in list input
> At line 66 of file Mean_square_displacement.f90 (unit = 5, file = 'stdin')
> Fortran runtime error: End of file
> mv: cannot stat ‘Displacements’: No such file or directory
> STOP equivalent atomic symbols are not found
> At line 59 of file Atom_projected_properties.f90 (unit = 9, file =
> 'projected.DOS')
> Fortran runtime error: Bad integer for item 1 in list input
> At line 66 of file Mean_square_displacement.f90 (unit = 5, file = 'stdin')
> Fortran runtime error: End of file
> mv: cannot stat ‘Displacements’: No such file or directory
> STOP equivalent atomic symbols are not found
> At line 59 of file Atom_projected_properties.f90 (unit = 9, file =
> 'projected.DOS')
> Fortran runtime error: Bad integer for item 1 in list input
> At line 66 of file Mean_square_displacement.f90 (unit = 5, file = 'stdin')
> Fortran runtime error: End of file
> mv: cannot stat ‘Displacements’: No such file or directory
> At line 59 of file Atom_projected_properties.f90 (unit = 9, file =
> 'projected.DOS')
> Fortran runtime error: Bad integer for item 1 in list input
> At line 72 of file Mean_square_displacement.f90 (unit = 1, file =
> 'projected_DOS.H4')
> Fortran runtime error: Bad integer for item 1 in list input
> mv: cannot stat ‘Displacements’: No such file or directory
> At line 59 of file Atom_projected_properties.f90 (unit = 9, file =
> 'projected.DOS')
> Fortran runtime error: Bad integer for item 1 in list input
> At line 72 of file Mean_square_displacement.f90 (unit = 1, file =
> 'projected_DOS.C5')
> Fortran runtime error: Bad integer for item 1 in list input
> mv: cannot stat ‘Displacements’: No such file or directory
>  ndiv from file ===        4505
> 
> my case is a methane molecule:
> 
>  /
>  &system
>     ibrav=  1,
>     celldm(1) =15.0,
>     nat=5,
>     ntyp= 2,
>     ecutwfc =25.0,
>     ecutrho =300.0,
>  /
> ATOMIC_SPECIES
>  H  1.0   H.pz-kjpaw.UPF
>  C  12.0  C.pz-kjpaw.UPF
> ATOMIC_POSITIONS
> H        0.080728893   0.080728893   0.080728893
> H       -0.080728893  -0.080728893   0.080728893
> H        0.080728893  -0.080728893  -0.080728893
> H       -0.080728893   0.080728893  -0.080728893
> C        0.000000000   0.000000000   0.000000000
> K_POINTS {automatic}
> 1 1 1 0 0 0
> 
> the forces have already been computed using ph.x and q2r.x codes:
> 
>  &inputph
>   tr2_ph=4.0d-14,
>   prefix='ch4',
>   outdir='./tmp/',
>   amass(1)=1.d0,
>   amass(2)=12.d0,
>   nq1=2, nq2=2, nq3=2
>   ldisp=.true. ,
>   fildyn='ch4.dyn',
>  /
> 0.0 0.0 0.0
> 
> and
> 
>  &input
>    fildyn='ch4.dyn', zasr='simple', flfrc='ch4.fc'
>  /
> 
> 
> and finally I have used a script very similar to example QHA/AlAs:
> 
> ##############################################################################
> # Optional parameters, any information specific for the system studied
> #
> SysInfo='ch4'
> 
> # Mandatory parameters
> # Specify SystemName and Force Constants matrix
> 
> Sysname='ch4'
> FC_file='ch4.fc'
> 
> #
> # Specify lattice type (used to create ttrinp file). It should be the
> same as in scf.in file
> # Specify atoms in the unit cell as they specified in scf.in file
> # Specify atomic masses for these atoms in the same order as in scf.in
> # Specify the frequency step (delta_e) as well, but 0.75 is a good choice
> 
> ibrav=1
> atoms="H1 H2 H3 H4 C5"
> mass="1.0 1.0 1.0 1.0 12.0 "
> delta_e=0.75
> 
> # Edit ONLY amass parameters
> # Please do not change flfrq='frequency' line
> # leave asr (acoustic sum rule) and flfrc lines
> 
> cat >matdyn.init <<EOF
> &input
>     amass(1)=1.0,
>     amass(2)=12.0,
>     asr='crystal',
>     flfrc='$FC_file',
>     flfrq='frequency'
> /
> EOF
> 
> #
> # In most cases there is no need to edit files listed below, but if you like ...
> #
> 
> # Temperature range for thermodynamic properties
> # T_start, T_end, T_step for QHA calculations
> 
> cat > Temperature <<EOF
> 5 500 5
> EOF
> 
> # Debye Temperature calculations
> # Phonon DOS filename (total phonon DOS, not projected), leave it as PHDOS.out
> # accuracy (limited 1.d-5, more accuracy is not required )
> # Low_temp_start, Low_Temp_end, and Low_Temp_step for LT limit, up to 15-30K
> # Hihg temperature and T_step for HT limit
> 
> cat >T_Debye.in <<EOF
> PHDOS.out
> 0.0001
>  3 15 3
>  500 10
> EOF
> 
> should I use another way to present equivalent atoms to the codes ?
> 
> I appreciate any comment in advance.
> 
> 

-- 
Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222