[DFTB-Plus-User] Printing of Dipole Moment
Bálint Aradi
aradi at uni-bremen.de
Mon Jun 12 14:48:29 CEST 2023
Dear Saleh,
in periodic system, the absolute value of the dipole is generally ill
defined, since you can shift the cell boundaries arbitrarily around. If
you think about a 1D example of periodic alternating charges, depending
how you lay your periodic boundaries, the dipole vector points points
either to the right or to the left (as you calculate if from the charges
within your unit cell):
... | - + | - + | - + | ...
... - | + - | + - | + ...
The warning should just ensure, that you do not use the printed dipole
vector for something, you are not supposed to.
Best regards,
Bálint
On 08.06.23 02:40, Saleh Md Abu wrote:
> 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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> DFTB-Plus-User at mailman.zfn.uni-bremen.de
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--
Dr. Bálint Aradi
Bremen Center for Computational Materials Science, University of Bremen
http://www.bccms.uni-bremen.de/cms/people/b-aradi/
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