Unconventional absorption energy obtained

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Unconventional absorption energy obtained

Date: 2025/05/29 17:18
Name: dena <daa58768199@gmail.com>: Hello everyone
I am looking to calculate the adsorption energy between the amino acid glycine and nanotube. I have shared the executable files of the total energy in the output files. The important thing is that the structures are properly optimized and apparently there are no problems. But in the end the adsorption energy is much higher than expected.
I need your guidance, researchers, to solve my problem.
Glycine input file and utotal: Utot = -57.304033299868

pecies.Number 4
<Definition.of.Atomic.Species
H H6.0-s2p1 H_PBE19
C C6.0-s2p2d1 C_PBE19
N N6.0-s2p2d1 N_PBE19
O O6.0-s2p2d1 O_PBE19
Definition.of.Atomic.Species>

Atoms.Number 10
Atoms.SpeciesAndCoordinates.Unit Ang
<Atoms.SpeciesAndCoordinates
1 N -14.0680000 -36.8279990 22.5709990 2.5 2.5
2 H -14.4370000 -35.9230000 22.7810000 0.5 0.5
3 H -13.7530000 -36.8559990 21.6220000 0.5 0.5
4 H -13.3100000 -37.0379980 23.1880000 0.5 0.5
5 C -15.1150000 -37.8200000 22.7520010 2.0 2.0
6 H -15.9020000 -37.5719990 22.0529990 0.5 0.5
7 H -15.4140000 -37.7770000 23.7910000 0.5 0.5
8 C -14.6530000 -39.2330020 22.4570010 2.0 2.0
9 O -13.6900000 -39.2109990 22.1870000 3.0 3.0
10 O -15.4170000 -39.8620000 22.6000000 3.0 3.0
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
18.0000000 0.0000000 0.0000000
0.0000000 18.0000000 0.0000000
0.0000000 0.0000000 18.0000000
Atoms.UnitVectors>

#
# SCF or Electronic System
#

scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 250 # default=150 (Ry)
scf.maxIter 100 # default=40
scf.EigenvalueSolver cluster # DC|GDC|Cluster|Band
scf.Kgrid 1 1 1 # means 4x4x4
scf.Mixing.Type rmm-diis # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.10 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.200 # default=0.40
scf.Mixing.History 10 # default=5
scf.Mixing.StartPulay 5 # default=6
scf.criterion 1.0e-9 # default=1.0e-6 (Hartree)

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

nanotube input file and utotal: = -634.576012890136

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
29.999999999999996 0.000000000000000 0.000000000000000
0.000000000000000 29.999999999999996 0.000000000000000
0.000000000000000 0.000000000000000 21.160000000000000
Atoms.UnitVectors>

scf.XcType GGA-PBE
scf.SpinPolarization off
scf.ElectronicTemperature 300.0
scf.energycutoff 200
scf.maxIter 100
scf.EigenvalueSolver band
scf.Kgrid 1 1 2
scf.Mixing.Type rmm-diisk
scf.Init.Mixing.Weight 0.05
scf.Min.Mixing.Weight 0.01
scf.Max.Mixing.Weight 0.30
scf.Mixing.History 25
scf.Mixing.StartPulay 15
scf.criterion 1.0e-7
MD.Type DIIS # Nomd|Opt|NVE|NVT_VS|NVT_NH
# Constraint_Opt|DIIS2|Constraint_DIIS2
MD.Opt.DIIS.History 3 # default=3
MD.Opt.StartDIIS 20 # default=5
MD.Opt.EveryDIIS 50 # default=10
MD.maxIter 100 # default=1
MD.TimeStep 1.0 # default=0.5 (fs)
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr)

#
# MD or Geometry Optimization
#

MD.Type DIIS # Nomd|Opt|NVE|NVT_VS|NVT_NH
# Constraint_Opt|DIIS2|Constraint_DIIS2
MD.Opt.DIIS.History 3 # default=3
MD.Opt.StartDIIS 20 # default=5
MD.Opt.EveryDIIS 10000 # default=10
MD.maxIter 200 # default=1
MD.TimeStep 1.0 # default=0.5 (fs)
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr)
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
nanotube + gly input file and utotal: = -692.526427461150
Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
30.800000000000001 0.000000000000000 0.000000000000000
0.000000000000000 30.800000000000001 0.000000000000000
0.000000000000000 0.000000000000000 21.599799999999995
Atoms.UnitVectors>

scf.XcType GGA-PBE
scf.SpinPolarization off
scf.ElectronicTemperature 300.0
scf.energycutoff 300
scf.maxIter 100
scf.EigenvalueSolver band
scf.Kgrid 1 1 2
scf.Mixing.Type rmm-diisk
scf.Init.Mixing.Weight 0.05
scf.Min.Mixing.Weight 0.01
scf.Max.Mixing.Weight 0.30
scf.Mixing.History 25
scf.Mixing.StartPulay 15
scf.criterion 1.0e-7
scf.dftD on # on|off, default=off
version.dftD 3 # 2|3, default=2
DFTD3.damp bj # zero|bj, default=bj
DFTD.Unit Ang # Ang|AU
DFTD.rcut_dftD 15.0 # default=100 (DFTD.Unit)
DFTD.cncut_dftD 40 # default=40 (DFTD.Unit)
DFTD.IntDirection 1 1 1 # default=1 1 1 (1:on 0:off)

MD.Type DIIS # Nomd|Opt|NVE|NVT_VS|NVT_NH
# Constraint_Opt|DIIS2|Constraint_DIIS2
MD.Opt.DIIS.History 3 # default=3
MD.Opt.StartDIIS 20 # default=5
MD.Opt.EveryDIIS 50 # default=10
MD.maxIter 100 # default=1
MD.TimeStep 1.0 # default=0.5 (fs)
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++===
E abs= -0.66 hartree!!!!!
-0.66 h= -414.15 kcal/mol

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Re: Unconventional absorption energy obtained ( No.1 )

Date: 2025/06/01 07:25
Name: Yung-Ting Lee

To compare the energies of systems correctly, all parameters must be identical.

You may check your input data.

For example,
(1) The unit cells should be the same.
(2) The values for scf.energycutoff should be the same.
(3) Turn on or off DFTD3 in all cases.

If parameters are inconsistent, energy comparison will not be valid.

Best regards,
Yung-Ting Lee

Re: Unconventional absorption energy obtained ( No.2 )

Date: 2025/07/01 19:04
Name: dena <daa58768199@gmail.com>

hello dear Yung-Ting Lee
Thanks,The problem was solved with your help.

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