[DFTB-Plus-User] Printing of Dipole Moment
Saleh Md Abu
saleh.md.abu.314 at s.kyushu-u.ac.jp
Thu Jun 8 02:40:22 CEST 2023
Dear concern,
I have recently updated DFTB+ 20.1 to DFTB+ 22.2. After that, I ran an NPT simulation of 50 water molecules and got a warning message; Dipole moment is not defined absolutely!. I ran the same simulation in the previous version but didn't see any warning message of dipole moment. I do not understand the meaning of this warning. I am afraid I have prepared poor systems, or is there something wrong with my systems?
Can anyone help me in this regard?
Thanks and best regards,
Saleh
Input file as below
Geometry = genFormat {
<<< "geometry.gen"
}
Driver = VelocityVerlet{
TimeStep [fs] = 1.0
Thermostat = NoseHoover {
Temperature [Kelvin] = 300
CouplingStrength [cm^-1] = 3200
}
Barostat = {
Pressure = 3.44396E-09
# Coupling
Timescale = 10.0
}
Steps = 1000000
MovedAtoms = 1:-1
MDRestartFrequency = 100
}
Hamiltonian = DFTB {
Scc = Yes
MaxSCCIterations = 2000
MaxAngularMomentum {
O = "p"
H = "s"
# C = "p"
# N = "p"
# Cl = "d"
# S = "d"
# P = "d"
}
# Charge = 1.0
SlaterKosterFiles = Type2FileNames { # File names with two atom type names
Prefix = "~/3ob-3-1/" # Prefix before first type name
Separator = "-" # Dash between type names
Suffix = ".skf" # Suffix after second type name
}
ThirdOrderFull = Yes
HubbardDerivs {
# C = -0.1492
H = -0.1857
O = -0.1575
# N = -0.1535
# Cl = -0.0697
# S = -0.11
# P = -0.14
}
HCorrection = H5 {
RScaling = 0.68
WScaling = 0.23
H5Scaling {
O = 0.045
# N = 0.0675
}
}
Dispersion = DftD3 {
Damping = ZeroDamping {
sr6 = 1.25 #3OB
alpha6 = 29.61 #3OB
}
s6 = 1.0
s8 = 0.49 # 3OB
HHRepulsion = Yes
}
SCCTolerance = 1e-4
Mixer = Anderson {
MixingParameter = 0.05
Generations = 8
}
Solver = DivideAndConquer {}
Filling = Fermi {
Temperature [Kelvin] = 1000.0
}
KPointsAndWeights = {
0.000000000000E+000 0.000000000000E+000 0.000000000000E+000 1.00000000000
}
}
Options {
WriteChargesAsText = Yes
}
Analysis {
CalculateForces = Yes
}
ParserOptions {
ParserVersion = 8
}
#Parallel {
# Groups = 4
# UseOmpThreads = Yes
#}
Part of the output as below
MD step: 10100
Nose-Hoover chain variables
x:
0.9709126675E+00 0.5095393583E+01 -0.1201993198E+02
v:
0.1172380185E-03 -0.6143591866E-04 -0.9400160624E-03
g:
-0.5122282026E-06 0.7590791869E-06 -0.5381051028E-05
Lattice vectors (A)
0.11511686E+02 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.11511686E+02 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.11511686E+02
Volume: 0.102947E+05 au^3 0.152552E+04 A^3
Pressure: -0.435908E-05 au -0.128249E+09 Pa
Gibbs free energy: -203.6228907991 H -5540.8608 eV
Gibbs free energy including KE: -203.4334648600 H -5535.7062 eV
Potential Energy: -203.6229262537 H -5540.8617 eV
MD Kinetic Energy: 0.1894259385 H 5.1545 eV
Total MD Energy: -203.4335003152 H -5535.7072 eV
MD Temperature: 0.0008475433 au 267.6327 K
Warning: dipole moment is not defined absolutely!
Dipole moment: -16.09138492 -13.84621712 3.59721433 au
Dipole moment: -40.90022412 -35.19357631 9.14320756 Debye
MD step: 10200
Nose-Hoover chain variables
x:
0.9443649828E+00 0.6825341898E+01 -0.1345300994E+02
v:
0.1130087503E-03 0.5289183249E-03 -0.1920912684E-02
g:
-0.2748048030E-06 0.3238016101E-06 -0.5105070806E-05
Lattice vectors (A)
0.11516625E+02 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.11516625E+02 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.11516625E+02
Volume: 0.103079E+05 au^3 0.152748E+04 A^3
Pressure: 0.149716E-06 au 0.440480E+07 Pa
Gibbs free energy: -203.6199934071 H -5540.7819 eV
Gibbs free energy including KE: -203.4232467089 H -5535.4282 eV
Potential Energy: -203.6200289073 H -5540.7829 eV
MD Kinetic Energy: 0.1967466983 H 5.3538 eV
Total MD Energy: -203.4232822090 H -5535.4291 eV
MD Temperature: 0.0008802984 au 277.9759 K
Warning: dipole moment is not defined absolutely!
Dipole moment: -9.66148980 -15.98281037 -0.30577511 au
Dipole moment: -24.55705956 -40.62425512 -0.77720286 Debye
MD step: 10300
Nose-Hoover chain variables
x:
0.8823886131E+00 0.8379095854E+01 -0.1387168258E+02
v:
0.1058884319E-03 -0.9580387030E-03 0.9837814733E-03
g:
0.7523473872E-07 -0.3729004755E-06 -0.4466987244E-05
Lattice vectors (A)
0.11528007E+02 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.11528007E+02 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.11528007E+02
Volume: 0.103385E+05 au^3 0.153201E+04 A^3
Pressure: -0.152318E-04 au -0.448135E+09 Pa
Gibbs free energy: -203.6052263574 H -5540.3801 eV
Gibbs free energy including KE: -203.3982624316 H -5534.7483 eV
Potential Energy: -203.6052619629 H -5540.3811 eV
MD Kinetic Energy: 0.2069639236 H 5.6318 eV
Total MD Energy: -203.3982980394 H -5534.7493 eV
MD Temperature: 0.0009260131 au 292.4115 K
Warning: dipole moment is not defined absolutely!
Dipole moment: -12.68722536 -22.05729297 17.53312324 au
Dipole moment: -32.24771287 -56.06405106 44.56475768 Debye
MD step: 10400
Nose-Hoover chain variables
x:
0.8346498308E+00 0.6569701582E+01 -0.1188304703E+02
v:
-0.1442483628E-04 0.7331923441E-03 0.6808164405E-03
g:
0.1603784843E-06 -0.5291815472E-05 -0.4847254387E-05
Lattice vectors (A)
0.11532605E+02 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.11532605E+02 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.11532605E+02
Volume: 0.103509E+05 au^3 0.153385E+04 A^3
Pressure: 0.977452E-05 au 0.287576E+09 Pa
Gibbs free energy: -203.5923194080 H -5540.0289 eV
Gibbs free energy including KE: -203.3778966071 H -5534.1941 eV
Potential Energy: -203.5923550562 H -5540.0299 eV
MD Kinetic Energy: 0.2144228023 H 5.8347 eV
Total MD Energy: -203.3779322538 H -5534.1951 eV
MD Temperature: 0.0009593861 au 302.9498 K
Warning: dipole moment is not defined absolutely!
Dipole moment: -0.26787305 0.89270894 16.61393390 au
Dipole moment: -0.68086544 2.26903997 42.22841124 Debye
MD step: 10500
Nose-Hoover chain variables
x:
0.9051690473E+00 0.7504479737E+01 -0.1183789952E+02
v:
0.3205883830E-04 -0.2075510106E-02 -0.9431590510E-03
g:
-0.8509819391E-07 -0.4925412607E-05 -0.1077083201E-05
Lattice vectors (A)
0.11540175E+02 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.11540175E+02 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.11540175E+02
Volume: 0.103713E+05 au^3 0.153687E+04 A^3
Pressure: -0.468445E-06 au -0.137821E+08 Pa
Gibbs free energy: -203.6140395857 H -5540.6199 eV
Gibbs free energy including KE: -203.4081380876 H -5535.0171 eV
Potential Energy: -203.6140753041 H -5540.6209 eV
MD Kinetic Energy: 0.2059014980 H 5.6029 eV
Total MD Energy: -203.4081738061 H -5535.0180 eV
MD Temperature: 0.0009212595 au 290.9104 K
Warning: dipole moment is not defined absolutely!
Dipole moment: -4.06856578 -13.63431827 14.24332489 au
Dipole moment: -10.34126354 -34.65498313 36.20292366 Debye
MD step: 10600
Nose-Hoover chain variables
x:
0.9056278317E+00 0.6487463254E+01 -0.1048597708E+02
v:
0.8879065586E-04 0.4594279028E-02 0.2246002129E-03
g:
-0.4339333373E-06 -0.1860775486E-05 0.1572257438E-04
Lattice vectors (A)
0.11540304E+02 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.11540304E+02 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.11540304E+02
Volume: 0.103717E+05 au^3 0.153692E+04 A^3
Pressure: -0.262813E-05 au -0.773222E+08 Pa
Gibbs free energy: -203.6008275147 H -5540.2604 eV
Gibbs free energy including KE: -203.4105803559 H -5535.0835 eV
Potential Energy: -203.6008632343 H -5540.2614 eV
MD Kinetic Energy: 0.1902471584 H 5.1769 eV
Total MD Energy: -203.4106160759 H -5535.0845 eV
MD Temperature: 0.0008512177 au 268.7930 K
Warning: dipole moment is not defined absolutely!
Dipole moment: 7.22136767 -16.73774786 -7.02930762 au
Dipole moment: 18.35488726 -42.54311496 -17.86671928 Debye
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