 Re: Num. of grids overlapping with atom * = 0 ( No.1 ) |
- Date: 2005/04/09 09:33
- Name: T.Ozaki
- Hi,
If you do not mind, please show us the following informations:
(1) Definition.of.Atomic.Species
(2) Atoms.SpeciesAndCoordinates.Unit
(3) Atoms.SpeciesAndCoordinates
(4) Atoms.UnitVectors.Unit
(5) Atoms.UnitVectors
(6) scf.energycutoff
> 2. Under the Key words "Atoms. Species And Coordinates", the coordinates of the atoms
> should be given, are they the coordinates of Cartesian system?
Yes, it is the Cartesian.
Regards,
T.Ozaki
|
| Re: Num. of grids overlapping with atom * = 0 ( No.2 ) |
- Date: 2005/04/18 00:02
- Name: s. j. luo <sjluo@phys.ntu.edu.tw>
- Hi,
The following is the *.dat file, thank you for your help!
sj luo
#
# SCF calculation of a bulk cumn bichain by the GGGA-PBE
# and the band method
#
#
# File Name
#
System.CurrrentDirectory ./ # default=./
System.Name pnpnn
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)
#
# Definition of Atomic Species
#
Species.Number 4
<Definition.of.Atomic.Species
O O8.0-s2p2d2 O_TM_PCC_GGA
N N8.0-s2p2d2 N_TM_PCC_GGA
C C8.0-s2p2d2 C_TM_PCC_GGA
H H8.0-s22p31d11 H_TM_PCC_GGA
Definition.of.Atomic.Species>
#
# Atoms
#
Atoms.Number 72
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 N 1.705376005936 4.462110087967 2.196531321716 4.0 1.0
2 N 9.254624032211 14.887890293503 2.196531321716 4.0 1.0
3 N 1.034624003601 9.299610183334 5.283281352234 4.0 1.0
4 N 4.445376015472 0.375390007401 5.283281352234 4.0 1.0
5 O 0.549096001911 4.123485081291 2.605217025757 4.0 2.0
6 O 10.410904036236 15.226515300179 2.605217025757 4.0 2.0
7 O 2.190904007626 8.960985176659 5.691967056274 4.0 2.0
8 O 3.289096011448 0.714015014076 5.691967056274 4.0 2.0
9 C 2.740000009537 4.837500095367 2.979331129456 3.0 1.0
10 C 0.000000000000 9.675000190735 6.066081159973 3.0 1.0
11 C 2.108704007339 4.371165086174 0.758105807495 3.0 1.0
12 C 8.851296030807 14.978835295296 0.758105807495 3.0 1.0
13 C 0.631296002197 9.208665181541 3.844855838013 3.0 1.0
14 C 4.848704016876 0.466335009193 3.844855838013 3.0 1.0
15 C 2.426544008446 2.910240057373 0.487706504822 3.0 1.0
16 C 8.533456029701 16.439760324097 0.487706504822 3.0 1.0
17 C 0.313456001091 7.747740152740 3.574456535339 3.0 1.0
18 C 5.166544017982 1.927260037994 3.574456535339 3.0 1.0
19 C 0.965576003361 4.936185097313 12.230938320923 3.0 1.0
20 C 9.994424034786 14.413815284157 12.230938320923 3.0 1.0
21 C 1.774424006176 9.773685192680 2.970688229370 3.0 1.0
22 C 3.705576012897 19.251315379524 2.970688229370 3.0 1.0
23 C 2.740000009537 4.837500095367 4.462205844116 3.0 1.0
24 C 0.000000000000 9.675000190735 7.548955874634 3.0 1.0
25 C 2.279680007935 3.719070073318 5.132647950745 3.0 1.0
26 C 8.680320030212 15.630930308151 5.132647950745 3.0 1.0
27 C 0.460320001602 8.556570168686 8.219397981262 3.0 1.0
28 C 5.019680017471 1.118430022049 8.219397981262 3.0 1.0
29 C 2.308176008034 3.693915072823 6.527858964539 3.0 1.0
30 C 8.651824030113 15.656085308647 6.527858964539 3.0 1.0
31 C 0.431824001503 8.531415168190 9.614608995056 3.0 1.0
32 C 5.048176017570 1.143585022545 9.614608995056 3.0 1.0
33 C 2.740000009537 4.837500095367 7.184719371033 3.0 1.0
34 C 0.000000000000 9.675000190735 10.271469401550 3.0 1.0
35 N 2.740000009537 4.837500095367 8.649073585510 4.0 1.0
36 N 0.000000000000 9.675000190735 11.735823616028 4.0 1.0
37 O 2.838640009880 5.899815116310 9.230617291260 4.0 2.0
38 O 8.121360028267 13.450185265160 9.230617291260 4.0 2.0
39 O 10.861360037804 10.737315211678 12.317367321777 4.0 2.0
40 O 5.578640019417 18.287685360527 12.317367321777 4.0 2.0
41 H 1.841280006409 2.844450056076 4.593084045410 0.9 0.1
42 H 9.118720031738 16.505550325394 4.593084045410 0.9 0.1
43 H 0.898720003128 7.681950151443 7.679834075928 0.9 0.1
44 H 4.581280015945 1.993050039291 7.679834075928 0.9 0.1
45 H 1.983760006905 2.941200057983 7.062484069824 0.9 0.1
46 H 8.976240031242 16.408800323486 7.062484069824 0.9 0.1
47 H 0.756240002632 7.778700153351 10.149234100342 0.9 0.1
48 H 4.723760016441 1.896300037384 10.149234100342 0.9 0.1
49 H 3.178400011063 2.612250051498 1.012454010010 0.9 0.1
50 H 7.781600027084 16.737750329971 1.012454010010 0.9 0.1
51 H 10.521600036621 7.449750146866 4.099204040527 0.9 0.1
52 H 5.918400020599 2.225250043869 4.099204040527 0.9 0.1
53 H 2.740000009537 2.805750055313 11.840773117065 0.9 0.1
54 H 8.220000028610 16.544250326157 11.840773117065 0.9 0.1
55 H 0.000000000000 7.643250150681 2.580523025513 0.9 0.1
56 H 5.480000019073 2.031750040054 2.580523025513 0.9 0.1
57 H 1.567280005455 2.360700046539 0.802555007935 0.9 0.1
58 H 9.392720032692 16.989300334930 0.802555007935 0.9 0.1
59 H 1.172720004082 7.198200141907 3.889305038452 0.9 0.1
60 H 4.307280014992 2.476800048828 3.889305038452 0.9 0.1
61 H 0.624720002174 5.805000114441 0.123470001221 0.9 0.1
62 H 10.335280035973 13.545000267029 0.123470001221 0.9 0.1
63 H 2.115280007362 10.642500209808 3.210220031738 0.9 0.1
64 H 3.364720011711 18.382500362396 3.210220031738 0.9 0.1
65 H 0.252080000877 4.315050085068 12.223530120850 0.9 0.1
66 H 10.707920037270 15.034950296402 12.223530120850 0.9 0.1
67 H 2.487920008659 9.152550180435 2.963280029297 0.9 0.1
68 H 2.992080010414 0.522450010300 2.963280029297 0.9 0.1
69 H 1.096000003815 4.914900096893 11.396281112671 0.9 0.1
70 H 9.864000034332 14.435100284576 11.396281112671 0.9 0.1
71 H 1.644000005722 9.752400192261 2.136031021118 0.9 0.1
72 H 3.836000013351 19.272600379944 2.136031021118 0.9 0.1
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
0.0000 9.6750 6.1735
5.4800 0.0000 6.1735
5.4800 9.6750 0.0000
Atoms.UnitVectors>
#
# SCF or Electronic System
#
scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.SpinOrbit.Coupling off # On|Off, default=off
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 150.0 # default=150 (Ry)
scf.maxIter 50 # default=40
scf.EigenvalueSolver band # DC|GDC|Cluster|Band
scf.Kgrid 3 3 3 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.20 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.500 # default=0.40
scf.Mixing.History 7 # default=5
scf.Mixing.StartPulay 7 # default=6
scf.criterion 1.0e-8 # default=1.0e-6 (Hartree)
#
# 1D FFT
#
1DFFT.NumGridK 900 # default=900
1DFFT.NumGridR 900 # default=900
1DFFT.EnergyCutoff 3600.0 # default=3DFFT.EnergyCutoff*3.0 (Ry)
#
# Orbital Optimization
#
orbitalOpt.Method off # Off|Unrestricted|Restricted|species
orbitalOpt.InitCoes Symmetrical # Symmetrical|Free
orbitalOpt.initPrefactor 0.1 # default=0.1
orbitalOpt.scf.maxIter 15 # default=12
orbitalOpt.MD.maxIter 5 # default=5
orbitalOpt.per.MDIter 20 # default=1000000
orbitalOpt.criterion 1.0e-4 # default=1.0e-4 (Hartree/borh)^2
#
# output of contracted orbitals
#
CntOrb.fileout off # on|off, default=off
Num.CntOrb.Atoms 1 # default=1
<Atoms.Cont.Orbitals
1
Atoms.Cont.Orbitals>
#
# SCF Order-N
#
orderN.HoppingRanges 4.0 # default=5.0 (Ang)
orderN.NumHoppings 1 # default=2
#
# MD or Geometry Optimization
#
MD.Type Nomd # Nomd|Constant_Energy_MD|Opt
MD.maxIter 1 # default=1
MD.TimeStep 1 # default=0.5 (fs)
MD.Opt.criterion 1.0e-5 # default=1.0e-4 (Hartree/bohr)
#restart using a restart file, *.rst
scf.restart off #on/off,default=off
#
# Band dispersion
#
Band.dispersion on # on|off, default=off
<Band.KPath.UnitCell
-0.303368495968 0.171830424590 0.269289601993
0.303368495968 -0.171830424590 0.269289601993
0.303368495968 0.171830424590 - 0.269289601993
Band.KPath.UnitCell>
# if <Band.KPath.UnitCell does not exist,
# the reciprical lattice vector is employed.
Band.Nkpath 5
<Band.kpath
25 0.0 0.0 0.0 1.0 0.0 0.0 g X
25 1.0 0.0 0.0 0.5 0.5 0.5 X L
25 0.5 0.5 0.5 1.0 0.5 0.0 L W
25 1.0 0.5 0.0 0.0 0.0 0.0 W g
25 0.0 0.0 0.0 1.0 1.0 0.0 g X
Band.kpath>
#
# MO output
#
MO.fileout off # on|off
num.HOMOs 1 # default=2
num.LUMOs 1 # default=2
MO.Nkpoint 2 # default=1
<MO.kpoint
0.0 0.0 0.0
0.0 0.0 0.2
MO.kpoint>
#
# DOS and PDOS
#
Dos.fileout on # on|off, default=off
Dos.Erange -20.0 20.0 # default = -20 20
Dos.Kgrid 5 5 5 # default = Kgrid1 Kgrid2 Kgrid3
HS.fileout on # on|off, default=off
 |
| Re: Num. of grids overlapping with atom * = 0 ( No.3 ) |
- Date: 2005/04/20 01:47
- Name: T.Ozaki
- Hi,
The coordinates specified by "Atoms.SpeciesAndCoordinates" seems
to protrude from the unit cell specified by "Atoms.UnitVectors".
I have found that the molecular structure is highly fragmented.
OpenMX requires that the structure is defined in the unit cell.
Would you specify the structure in an usual way that the molecule
is not fragmented ?, although I guess that the paper you referred
gives the structure.
Best regards,
T.Ozaki
P.S.
The specification of H8.0-s22p31d11 corresponds to H8.0-s2p3d1
because of no orbital optimization.
The following is just a comment on your calculation.
If you want to know the basis set convergence, starting
from the folloing basis functions,
H4.5-s2,
C5.0-s2p2
N5.0-s2p2d1
O5.0-s2p2d1
it would be better to check how the result can be changed by
the cutoff radii and the number of basis functions.
(I guess that the above basis functions maybe enough for most
purposes)
Also, for this system, I guess that 150 Ryd can be reduced to
around 100-120 Ryd without changing the result.
|
|
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Num. of grids overlapping with atom * = 0