undefined species name in Atoms.SpeciesAndCoordinates

Top Page > Browsing

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!

Page: [1]

Re: undefined species name in Atoms.SpeciesAndCoordinates ( No.1 )

Date: 2026/03/01 16:29
Name: Kazume NISHIDATE <kazume.nishidate@gmail.com>

> �M �*c�A

These errors may be due to your language's coding system.
Try converting the character encoding to ASCII.

The 'iconv' command can do it.

西館数芽
Kazume NISHIDATE Ph.D

Department of Systems Innovation Engineering,
Graduate School of Science and Engineering, Iwate University
4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
Phone:+81-19-621-6391
kazume.nishidate@gmail.com, nisidate@iwate-u.ac.jp
https://sites.google.com/site/nisidatelab/

Page: [1]