I compiled this the following in order to obtain the DFT bandgap of my material, however this error of "Cannot find atomic number for a" came up and I am not sure of the reason for it. If anyone can offer some advice I would greatly appreciate it.
Siesta Version : school--MaX-1.3.0-1
Architecture : Master-template
Compiler version: GNU Fortran (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
Compiler flags : mpif90 -O2
PP flags : -DF2003 -DCDF -DNCDF -DNCDF_4 -DSIESTA__FLOOK -DMPI -DMPI_TIMING
Libraries : libncdf.a libfdict.a libfdict.a -lnetcdff -lnetcdf -L/usr/local/lib -lflookall -ldl -lscalapack-openmpi -llapack -lblas
Directory : /home/max/Desktop/HAP
PARALLEL version
NetCDF support
NetCDF-4 support
Lua support
- Running in serial mode with MPI
Start of run: 6-FEB-2025 12:12:11
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.15514
************************** Dump of input data file ****************************
SystemName Siesta Relaxation
SystemLabel Ca10(PO4)6(OH)2
NumberOfAtoms 44
NumberOfSpecies 4
%block Chemical_Species_label
1 20 Ca
2 15 P
3 1 H
4 8 O
%endblock Chemical_Species_label
LatticeConstant 1.0 Ang
%block LatticeVectors
4.6984272792 -8.1379147632 0.0000000000
4.6984272792 8.1379147632 0.0000000000
0.0000000000 0.0000000000 6.8640256100
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
4.6984 -2.7126 6.8586 1
8.1731 -2.0147 5.1534 1
2.3567 -0.0524 5.1534 1
3.5655 -6.0708 5.1534 1
4.6984 -2.7126 3.4426 1
4.6984 2.7126 3.4266 1
5.8314 6.0708 1.7214 1
1.2237 2.0147 1.7214 1
7.0402 0.0524 1.7214 1
4.6984 2.7126 0.0106 1
2.0234 2.9932 5.1605 2
6.2789 4.8890 5.1605 2
5.7930 0.2557 5.1605 2
3.6039 -0.2557 1.7285 2
3.1180 -4.8890 1.7285 2
7.3734 -2.9932 1.7285 2
0.0000 0.0000 6.3894 3
0.0000 0.0000 2.9574 3
6.5402 0.7322 6.4114 4
5.4926 5.2979 6.4114 4
2.0624 2.1078 6.4114 4
0.0000 0.0000 5.4197 4
3.0037 -2.6796 5.1707 4
5.5744 -1.2615 5.1707 4
5.5172 -4.1968 5.1707 4
3.3464 3.7839 5.1236 4
4.4467 1.0062 5.1236 4
6.3021 3.3479 5.1236 4
5.4978 5.3831 3.9350 4
6.6115 0.6851 3.9350 4
1.9860 2.0696 3.9350 4
7.3344 -2.1078 2.9794 4
2.8566 -0.7322 2.9794 4
3.9042 -5.2979 2.9794 4
0.0000 0.0000 1.9877 4
6.3932 2.6796 1.7387 4
3.8224 1.2615 1.7387 4
3.8797 4.1968 1.7387 4
3.0947 -3.3479 1.6916 4
4.9501 -1.0062 1.6916 4
6.0504 -3.7839 1.6916 4
7.4108 -2.0696 0.5030 4
2.7854 -0.6851 0.5030 4
3.8991 -5.3831 0.5030 4
%endblock AtomicCoordinatesAndAtomicSpecies
%block kgrid_Monkhorst_Pack
2 0 0 0.0
0 2 0 0.0
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
MeshCutoff 400 Ry
PAO.BasisType split
PAO.BasisSize DZP
PAO.EnergyShift 0.03 eV
XC.functional GGA
XC.authors PBE
MaxSCFIterations 1000
SolutionMethod diagon
MD.TypeOfRun CG
MD.NumCGsteps 50
MD.MaxForceTol 0.04
MD.VariableCell T
MD.ConstantVolume F
MD.UseSaveXV T
MD.UseSaveCG T
MD.MaxStressTol 0.0010
WriteMDHistory T
WriteMDXMol T
MD.MaxCGDispl 0.02 Bohr
WriteKbands F
WriteBands T
WriteCoorXmol T
WriteCoorStep T
WriteKpoints T
WriteCoorCerius T
WriteHS T
WriteForces T
WriteMullikenPop 1
SaveHS T
XML.Write T
BandLinesScale ReciprocalLatticeVectors
%block BandLines
1 0.0000 0.0000 0.5000 A
20 0.5000 0.0000 0.5000 L
25 0.5000 0.0000 0.0000 M
30 0.0000 0.0000 0.0000 \Gamma
35 0.0000 0.0000 0.5000 A
40 0.6666 0.3333 0.5000 H
45 0.6666 0.3333 0.0000 K
50 0.0000 0.0000 0.0000 \Gamma
%endblock BandLines
************************** End of input data file *****************************
reinit: -----------------------------------------------------------------------
reinit: System Name: Siesta Relaxation
reinit: -----------------------------------------------------------------------
reinit: System Label: Ca10(PO4)6(OH)2
reinit: -----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 20 Label: Ca
Species number: 2 Atomic number: 15 Label: P
Species number: 3 Atomic number: 1 Label: H
Species number: 4 Atomic number: 8 Label: O
---- Processing specs for species: Ca
Ground state valence configuration: 4s02
Reading pseudopotential information in formatted form from Ca.psf
---- Processing specs for species: P
Ground state valence configuration: 3s02 3p03
Reading pseudopotential information in formatted form from P.psf
---- Processing specs for species: H
Ground state valence configuration: 1s01
Reading pseudopotential information in formatted form from H.psf
---- Processing specs for species: O
Ground state valence configuration: 2s02 2p04
Reading pseudopotential information in formatted form from O.psf
Cannot find atomic number for a
Stopping Program from Node: 0
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
I compiled this the following in order to obtain the DFT bandgap of my material, however this error of "Cannot find atomic number for a" came up and I am not sure of the reason for it. If anyone can offer some advice I would greatly appreciate it.
Siesta Version : school--MaX-1.3.0-1
Architecture : Master-template
Compiler version: GNU Fortran (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
Compiler flags : mpif90 -O2
PP flags : -DF2003 -DCDF -DNCDF -DNCDF_4 -DSIESTA__FLOOK -DMPI -DMPI_TIMING
Libraries : libncdf.a libfdict.a libfdict.a -lnetcdff -lnetcdf -L/usr/local/lib -lflookall -ldl -lscalapack-openmpi -llapack -lblas
Directory : /home/max/Desktop/HAP
PARALLEL version
NetCDF support
NetCDF-4 support
Lua support
reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.15514
************************** Dump of input data file ****************************
SystemName Siesta Relaxation
SystemLabel Ca10(PO4)6(OH)2
NumberOfAtoms 44
NumberOfSpecies 4
%block Chemical_Species_label
1 20 Ca
2 15 P
3 1 H
4 8 O
%endblock Chemical_Species_label
LatticeConstant 1.0 Ang
%block LatticeVectors
4.6984272792 -8.1379147632 0.0000000000
4.6984272792 8.1379147632 0.0000000000
0.0000000000 0.0000000000 6.8640256100
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
4.6984 -2.7126 6.8586 1
8.1731 -2.0147 5.1534 1
2.3567 -0.0524 5.1534 1
3.5655 -6.0708 5.1534 1
4.6984 -2.7126 3.4426 1
4.6984 2.7126 3.4266 1
5.8314 6.0708 1.7214 1
1.2237 2.0147 1.7214 1
7.0402 0.0524 1.7214 1
4.6984 2.7126 0.0106 1
2.0234 2.9932 5.1605 2
6.2789 4.8890 5.1605 2
5.7930 0.2557 5.1605 2
3.6039 -0.2557 1.7285 2
3.1180 -4.8890 1.7285 2
7.3734 -2.9932 1.7285 2
0.0000 0.0000 6.3894 3
0.0000 0.0000 2.9574 3
6.5402 0.7322 6.4114 4
5.4926 5.2979 6.4114 4
2.0624 2.1078 6.4114 4
0.0000 0.0000 5.4197 4
3.0037 -2.6796 5.1707 4
5.5744 -1.2615 5.1707 4
5.5172 -4.1968 5.1707 4
3.3464 3.7839 5.1236 4
4.4467 1.0062 5.1236 4
6.3021 3.3479 5.1236 4
5.4978 5.3831 3.9350 4
6.6115 0.6851 3.9350 4
1.9860 2.0696 3.9350 4
7.3344 -2.1078 2.9794 4
2.8566 -0.7322 2.9794 4
3.9042 -5.2979 2.9794 4
0.0000 0.0000 1.9877 4
6.3932 2.6796 1.7387 4
3.8224 1.2615 1.7387 4
3.8797 4.1968 1.7387 4
3.0947 -3.3479 1.6916 4
4.9501 -1.0062 1.6916 4
6.0504 -3.7839 1.6916 4
7.4108 -2.0696 0.5030 4
2.7854 -0.6851 0.5030 4
3.8991 -5.3831 0.5030 4
%endblock AtomicCoordinatesAndAtomicSpecies
%block kgrid_Monkhorst_Pack
2 0 0 0.0
0 2 0 0.0
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
MeshCutoff 400 Ry
PAO.BasisType split
PAO.BasisSize DZP
PAO.EnergyShift 0.03 eV
XC.functional GGA
XC.authors PBE
MaxSCFIterations 1000
SolutionMethod diagon
MD.TypeOfRun CG
MD.NumCGsteps 50
MD.MaxForceTol 0.04
MD.VariableCell T
MD.ConstantVolume F
MD.UseSaveXV T
MD.UseSaveCG T
MD.MaxStressTol 0.0010
WriteMDHistory T
WriteMDXMol T
MD.MaxCGDispl 0.02 Bohr
WriteKbands F
WriteBands T
WriteCoorXmol T
WriteCoorStep T
WriteKpoints T
WriteCoorCerius T
WriteHS T
WriteForces T
WriteMullikenPop 1
SaveHS T
XML.Write T
BandLinesScale ReciprocalLatticeVectors
%block BandLines
1 0.0000 0.0000 0.5000 A
20 0.5000 0.0000 0.5000 L
25 0.5000 0.0000 0.0000 M
30 0.0000 0.0000 0.0000 \Gamma
35 0.0000 0.0000 0.5000 A
40 0.6666 0.3333 0.5000 H
45 0.6666 0.3333 0.0000 K
50 0.0000 0.0000 0.0000 \Gamma
%endblock BandLines
************************** End of input data file *****************************
reinit: -----------------------------------------------------------------------
reinit: System Name: Siesta Relaxation
reinit: -----------------------------------------------------------------------
reinit: System Label: Ca10(PO4)6(OH)2
reinit: -----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 20 Label: Ca
Species number: 2 Atomic number: 15 Label: P
Species number: 3 Atomic number: 1 Label: H
Species number: 4 Atomic number: 8 Label: O
---- Processing specs for species: Ca
Ground state valence configuration: 4s02
Reading pseudopotential information in formatted form from Ca.psf
---- Processing specs for species: P
Ground state valence configuration: 3s02 3p03
Reading pseudopotential information in formatted form from P.psf
---- Processing specs for species: H
Ground state valence configuration: 1s01
Reading pseudopotential information in formatted form from H.psf
---- Processing specs for species: O
Ground state valence configuration: 2s02 2p04
Reading pseudopotential information in formatted form from O.psf
Cannot find atomic number for a
Stopping Program from Node: 0
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.