undefined species name in Atoms.SpeciesAndCoordinates |
- Date: 2026/02/12 01:31
- Name: Gibu
- Hello users,
I am new to this software. I am trying to run a noncollinear DFT single-point calculation with spin–orbit coupling (SOC) for my system. But I constantly get error related to the input. Following is the content from the log file;
The number of threads in each node for OpenMP parallelization is 1.
*******************************************************
*******************************************************
Welcome to OpenMX Ver. 3.9
Copyright (C), 2002-2019, T. Ozaki
OpenMX comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to
redistribute it under the constitution of the GNU-GPL.
*******************************************************
*******************************************************
Found an undefined species name �M �*c�A
in Atoms.SpeciesAndCoordinates or Hubbard.U.values
Please check your input file
Found an undefined species name �M �*c�A
in Atoms.SpeciesAndCoordinates or Hubbard.U.values
Please check your input file
Found an undefined species name �^P^K�*c�A
in Atoms.SpeciesAndCoordinates or Hubbard.U.values
Please check your input file
Found an undefined species name �~S^K�*c�A
in Atoms.SpeciesAndCoordinates or Hubbard.U.values
Please check your input file
Found an undefined species name ^N^P^M�*c�A
in Atoms.SpeciesAndCoordinates or Hubbard.U.values
Please check your input file
Found an undefined species name �~I^N�*c�A
in Atoms.SpeciesAndCoordinates or Hubbard.U.values
Please check your input file
Found an undefined species name N&^P�*c�A
in Atoms.SpeciesAndCoordinates or Hubbard.U.values
Please check your input file
Found an undefined species name g&^P�*c�A
in Atoms.SpeciesAndCoordinates or Hubbard.U.values
Please check your input file
Following is my .dat input file;
############################################
# System
############################################
System.Name CsPbI3_C60_IC001
System.CurrentDirectory ./
System.Unit Ang
############################################
# Atomic species and basis sets
############################################
Species.Number 5
<Definition.of.Atomic.Species
Cs Cs12.0-s3p2d2 Cs_PBE19
Pb Pb8.0-s3p2d2f1 Pb_PBE19
I I7.0-s3p2d2f1 I_PBE19
C C6.0-s2p2d1 C_PBE19
Li Li8.0-s3p2 Li_PBE19
Definition.of.Atomic.Species>
############################################
# Atoms
############################################
Atoms.Number 196
Atoms.SpeciesAndCoordinates.Unit Ang
<Atoms.SpeciesAndCoordinates
# === paste ALL atoms from IC_pos xyz ===
1 Cs 9.1561500652 3.3254766144 9.0816267717
2 Cs 9.5492055257 2.7800741732 15.5065982650
.
.
26 Cs 3.5277274182 15.8422667365 15.6386799700
27 Cs 3.0229236990 15.4071266297 21.4601788077
.
48 Pb 0.1948776971 12.5765549587 12.4564436376
49 Pb -0.0692476871 12.3357434846 18.6555858258
50 Pb 12.4946716762 -0.1278964188 6.6456620569
51 Pb 12.4408766088 -0.1220663446 12.5552740477
52 Pb -0.1367289150 -0.1127758644 6.1496222888
53 Pb -0.1573043576 0.2891888825 12.5479669582
54 Pb 0.0214155037 -0.3961867717 19.0522584236
55 I 13.0970178358 12.8121708163 22.0031901969
56 I 12.9131855154 2.7532044782 19.2372776280
.
.
.
.
134 I 2.8989975731 0.1628993826 12.9469616218
135 I 2.8924753354 0.1084355388 18.6186544776
136 C 9.8943453376 11.9859457937 24.4427277452
137 C 10.1466860591 13.3641645490 24.6409362828
138 C 11.4770976504 13.5104391342 25.1956346836
139 C 11.9849774277 12.1297303604 25.3859816053
.
.
.
.
195 C 9.1881489305 12.4703975478 31.5191418883
196 Li 8.4541446214 12.8553670913 28.6123580839
Atoms.SpeciesAndCoordinates>
############################################
# Unit cell
############################################
Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
18.8594990000 0.0000000000 0.0000000000
0.0000000000 18.8594990000 0.0000000000
0.0000000000 0.0000000000 40.0000000000
Atoms.UnitVectors>
############################################
# DFT settings
############################################
scf.XcType GGA-PBE
scf.energycutoff 450.0
scf.maxIter 200
scf.Min.Mixing.Weight 0.001
scf.Mixing.Weight 0.02
scf.Mixing.Type rmm-diis
scf.ElectronicTemperature 300.0
scf.EigenvalueSolver Band
############################################
# k-points (Gamma only)
############################################
scf.Kgrid 3 3 1
############################################
# Spin–orbit coupling (CRITICAL)
############################################
scf.SpinPolarization NC
scf.SpinOrbit.Coupling on
############################################
# States (for electron transfer)
############################################
scf.Num.Occupied auto
scf.Num.Unoccupied 20
############################################
# Output for NAMD
############################################
scf.output.eigenvalues on
scf.output.wavefunctions on
scf.output.overlap on
scf.output.Hamiltonian on
############################################
# SCF convergence
############################################
scf.criterion.energy 1.0e-7
############################################
# End
############################################
Could you please help me to figure out the mistake in this input file. Thanks in advance!
 | |