[Smeagol-discuss] geometry partial optimization problem
张广平
284107217 at qq.com
Sun Jan 17 02:25:51 GMT 2010
Dear smeaol user:
Now I want use siesta to perform a partial geometry optimization.When I use zmatrix as the manual tell.</:includetail>
The input is :</:includetail>
----------------------------------</:includetail>
SystemName c6H8N2+Au
SystemLabel c6H8N2</:includetail>
NumberOfSpecies 4
NumberOfAtoms 36</:includetail>
%block ChemicalSpeciesLabel
1 6 C
2 1 H
3 7 N
4 79 Au
%endblock ChemicalSpeciesLabel</:includetail>
PAO.EnergyShift 200 meV</:includetail>
PAO.BasisType split
PAO.BasisSize SZP</:includetail>
LatticeConstant 1.0 Ang</:includetail>
%block LatticeVectors
25.00000000 0.00000000 0.00000000
0.00000000 25.00000000 0.00000000
0.00000000 0.00000000 24.05568134
%endblock LatticeVectors</:includetail>
kgrid_cutoff 20. Ang
%block kgrid_Monkhorst_Pack
1 0 0 0.0
0 1 0 0.0
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack</:includetail>
%block PAO.Basis # Define Basis set
C 2 # Species label, number of l-shells
n=2 0 1 # n, l, Nzeta
5.0
1.000
n=2 1 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
8.0
1.000
N 2 # Species label, number of l-shells
n=2 0 1 # n, l, Nzeta
4.0
1.000
n=2 1 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
7.0
1.000
H 1 # Species label, number of l-shells
n=1 0 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
3.5
1.000
Au 2 # Species label, number of l-shells
n=6 0 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
8.0
1.000
n=5 2 1 # n, l, Nzeta
5.8
1.000
%endblock PAO.Basis</:includetail>
%block Ps.lmax
Au 2
%endblock Ps.lmax</:includetail>
# SPIN options</:includetail>
xc.functional GGA # Exchange-correlation functional
xc.authors PBE # Exchange-correlation version
SpinPolarized F # Logical parameters are: yes or no
FixSpin F
TotalSpin 0.0
NonCollinearSpin F # 'T', 'F'
MeshCutoff 150. Ry # Equivalent plane wave cutoff for the grid</:includetail>
#%block DM.InitSpin
# 88 +
# 89 +
# 91 +
# 94 -
# 95 -
#%endblock DM.InitSpin</:includetail>
# SCF options</:includetail>
DM.Tolerance 1.d-3 # Tolerance in maximum difference between input and output DM
MaxSCFIterations 300 # Maximum number of SCF iter
DM.UseSaveDM F # to use continuation files
DM.MixingWeight 0.02 # New DM amount for next SCF cycle
DM.NumberPulay 5
DM.MixSCF1 F
DM.PulayOnFile F # Store in memory ('F') or in files ('T')
# NeglNonOverlapInt T # 'F'=do not neglect
SolutionMethod Diagon # OrderN or Diagon
ElectronicTemperature 300 K # Temp. for Fermi smearing</:includetail>
# MD options</:includetail>
MD.TypeOfRun CG # Type of dynamics:
MD.VariableCell F
MD.NumCGsteps 200 # Number of CG steps for coordinate optimization
ZM.UnitsLength Ang #the units of length used during Z-matrix input
ZM.UnitsAngle deg #the units of angles used during Z-matrix input
ZM.ForceTolLength 0.02 eV/Ang #controls the convergence with respect to forces on Z-matrix lengths
ZM.ForceTolAngle 0.00356549 Ry/rad #controls the convergence with respect to forces on Z-matrix angles
ZM.MaxDisplLength 0.1 Ang # controls the maximum change in a Zmatrix length during an optimisation step
ZM.MaxDisplAngle 0.003 rad # controls the maximum change in a Z-matrix angle during an optimisation step
ZM.CalcAllForces T # Default value</:includetail>
AtomicCoordinatesFormat Ang</:includetail>
%block Zmatrix
cartesian
4 0.832500 1.441900 0.070000 0 0 0
4 0.832500 4.325700 0.070000 0 0 0
4 0.832500 7.209500 0.070000 0 0 0
4 3.329900 0.000000 0.070000 0 0 0
4 3.329900 2.883800 0.070000 0 0 0
4 3.329900 5.767600 0.070000 0 0 0
4 5.827400 -1.441900 0.070000 0 0 0
4 5.827400 1.441900 0.070000 0 0 0
4 5.827400 4.325700 0.070000 0 0 0
1 3.602290 1.731278 6.212320 1 1 1
1 3.319832 2.314888 7.483680 1 1 1
1 2.095981 1.995008 8.160953 1 1 1
1 1.179880 1.055287 7.579063 1 1 1
1 1.463109 0.470284 6.307043 1 1 1
1 2.686364 0.792157 5.629784 1 1 1
2 4.560824 2.006388 5.644557 1 1 1
2 4.060912 3.044923 7.962504 1 1 1
2 0.218799 0.778868 8.141618 1 1 1
2 0.720051 -0.260182 5.831012 1 1 1
2 2.264637 3.524194 9.544223 1 1 1
2 0.774280 2.665518 9.602215 1 1 1
2 4.021096 0.084236 4.221899 1 1 1
2 2.491712 -0.710195 4.216641 1 1 1
3 1.840356 2.531978 9.498710 0 0 1
3 2.958183 0.262423 4.292613 0 0 1
4 2.438337 1.576108 2.385995 0 0 1
4 2.578104 1.329674 11.405459 0 0 1
4 1.665000 0.000000 13.722500 0 0 0
4 1.665000 2.883800 13.722500 0 0 0
4 1.665000 5.767600 13.722500 0 0 0
4 4.162400 -1.441900 13.722500 0 0 0
4 4.162400 1.441900 13.722500 0 0 0
4 4.162400 4.325700 13.722500 0 0 0
4 6.659800 -2.883800 13.722500 0 0 0
4 6.659800 0.000000 13.722500 0 0 0
4 6.659800 2.883800 13.722500 0 0 0
%endblock Zmatrix</:includetail>
# Output options</:includetail>
WriteCoorInitial F
WriteCoorStep T
WriteCoorXmol T
WriteForces T
WriteEigenvalues T
WriteWaveFunctions T # coefficients of the wavefunctions in the basis set orbitals expansion
WriteMullikenPop 1 # Write Mulliken Population Analysis
#WriteKpoints T
#WriteKbands T
#WriteBands T
WriteMDCoorXmol F
WriteMDhistory F</:includetail>
# Options for saving or reading information
MD.UseSaveXV F # Use stored positions and velocities
MD.UseSaveCG F # Use stored positions and velocities
SaveRho T # Write valence pseudocharge at the mesh
SaveDeltaRho T # Write RHOscf-RHOatm at the mesh
SaveElectrostaticPotential T # Write the total elect. pot. at the mesh
SaveTotalPotential T # Write the total pot. at the mesh
WriteSiestaDim F # Write minimum dim to siesta.h and stop
WriteDenchar F # Write information for DENCHAR
---------------------------------------------------------</:includetail>
In "%block Zmatrix",the last three columns either 1 or 0 indicate whether the corresponding cartesian coordinate fixed or variable.</:includetail>
But the results suggest the z component of the last 9 atoms are variable while I fixed them in the input file.</:includetail>
Here is the outputs for the first three CG moves</:includetail>
siesta: ==============================
Begin CG move = 0
==============================</:includetail>
zmatrix: Z-matrix coordinates: (Ang ; deg )
zmatrix: (Fractional coordinates have been converted to cartesian)
cartesian block 1 ( 36 atoms)
0.83250000 1.44190000 0.07000000
0.83250000 4.32570000 0.07000000
0.83250000 7.20950000 0.07000000
3.32990000 0.00000000 0.07000000
3.32990000 2.88380000 0.07000000
3.32990000 5.76760000 0.07000000
5.82740000 -1.44190000 0.07000000
5.82740000 1.44190000 0.07000000
5.82740000 4.32570000 0.07000000
3.60229000 1.73127800 6.21232000
3.31983200 2.31488800 7.48368000
2.09598100 1.99500800 8.16095300
1.17988000 1.05528700 7.57906300
1.46310900 0.47028400 6.30704300
2.68636400 0.79215700 5.62978400
4.56082400 2.00638800 5.64455700
4.06091200 3.04492300 7.96250400
0.21879900 0.77886800 8.14161800
0.72005100 -0.26018200 5.83101200
2.26463700 3.52419400 9.54422300
0.77428000 2.66551800 9.60221500
4.02109600 0.08423600 4.22189900
2.49171200 -0.71019500 4.21664100
1.84035600 2.53197800 9.49871000
2.95818300 0.26242300 4.29261300
2.43833700 1.57610800 2.38599500
2.57810400 1.32967400 11.40545900
1.66500000 0.00000000 13.72250000
1.66500000 2.88380000 13.72250000
1.66500000 5.76760000 13.72250000
4.16240000 -1.44190000 13.72250000
4.16240000 1.44190000 13.72250000
4.16240000 4.32570000 13.72250000
6.65980000 -2.88380000 13.72250000
6.65980000 0.00000000 13.72250000
6.65980000 2.88380000 13.72250000</:includetail>
Z-matrix Symbol Section -------
Variables
Constants
------------ End of Z-matrix Information</:includetail>
</:includetail>
siesta: ==============================
Begin CG move = 1
==============================</:includetail>
zmatrix: Z-matrix coordinates: (Ang ; deg )
zmatrix: (Fractional coordinates have been converted to cartesian)
cartesian block 1 ( 36 atoms)
0.83250000 1.44190000 0.07000000
0.83250000 4.32570000 0.07000000
0.83250000 7.20950000 0.07000000
3.32990000 0.00000000 0.07000000
3.32990000 2.88380000 0.07000000
3.32990000 5.76760000 0.07000000
5.82740000 -1.44190000 0.07000000
5.82740000 1.44190000 0.07000000
5.82740000 4.32570000 0.07000000
3.61525190 1.73684510 6.20693015
3.31888333 2.30920822 7.47096960
2.09209112 1.98551766 8.10096567
1.16613940 1.05031785 7.58451762
1.46180387 0.47787319 6.31687464
2.69059786 0.79758939 5.69011343
4.57210630 2.01534970 5.65736945
4.08089271 3.06268054 7.96758408
0.21932577 0.77906872 8.13442086
0.70765525 -0.27557949 5.82874609
2.26023094 3.53034505 9.54123011
0.78312570 2.67095534 9.58764887
4.02789546 0.07159983 4.23167394
2.50110058 -0.68673582 4.23137434
1.84035600 2.53197800 9.58443012
2.95818300 0.26242300 4.20526795
2.43833700 1.57610800 2.40543244
2.57810400 1.32967400 11.38849143
1.66500000 0.00000000 13.72814796
1.66500000 2.88380000 13.62250000
1.66500000 5.76760000 13.73740495
4.16240000 -1.44190000 13.74582990
4.16240000 1.44190000 13.73576890
4.16240000 4.32570000 13.70164975
6.65980000 -2.88380000 13.70212701
6.65980000 0.00000000 13.71967106
6.65980000 2.88380000 13.71737248</:includetail>
Z-matrix Symbol Section -------
Variables
Constants
------------ End of Z-matrix Information</:includetail>
</:includetail>
siesta: ==============================
Begin CG move = 2
==============================</:includetail>
zmatrix: Z-matrix coordinates: (Ang ; deg )
zmatrix: (Fractional coordinates have been converted to cartesian)
cartesian block 1 ( 36 atoms)
0.83250000 1.44190000 0.07000000
0.83250000 4.32570000 0.07000000
0.83250000 7.20950000 0.07000000
3.32990000 0.00000000 0.07000000
3.32990000 2.88380000 0.07000000
3.32990000 5.76760000 0.07000000
5.82740000 -1.44190000 0.07000000
5.82740000 1.44190000 0.07000000
5.82740000 4.32570000 0.07000000
3.60398977 1.73200805 6.21161320
3.31970760 2.31414318 7.48201321
2.09547090 1.99376347 8.15308649
1.17807811 1.05463537 7.57977830
1.46293785 0.47127922 6.30833228
2.68691921 0.79286938 5.63769537
4.56230352 2.00756320 5.64623718
4.06353219 3.04725166 7.96317018
0.21886808 0.77889432 8.14067419
0.71842547 -0.26220117 5.83071486
2.26405921 3.52500063 9.54383052
0.77543999 2.66623103 9.60030485
4.02198766 0.08257894 4.22318085
2.49294318 -0.70711865 4.21857307
1.84035600 2.53197800 9.50995101
2.95818300 0.26242300 4.28115890
2.43833700 1.57610800 2.38854395
2.57810400 1.32967400 11.40323394
1.66500000 0.00000000 13.72324065
1.66500000 2.88380000 13.70938638
1.66500000 5.76760000 13.72445458
4.16240000 -1.44190000 13.72555939
4.16240000 1.44190000 13.72424003
4.16240000 4.32570000 13.71976578
6.65980000 -2.88380000 13.71982836
6.65980000 0.00000000 13.72212902
6.65980000 2.88380000 13.72182760</:includetail>
Z-matrix Symbol Section -------
Variables
Constants
------------ End of Z-matrix Information</:includetail>
</:includetail>
</:includetail>
What should I do !</:includetail>Can any one help me ?
Any advice is welcome!
BEST REGARDS!
Guangping Zhang
</:includetail>
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