 Re: variable cell optimization ( No.1 ) |
- Date: 2017/05/30 21:12
- Name: Kylin
- Dear mosahar
The OptC1 was designed for a box relaxation, where the local minimal of energy/volume configuration was obtained. Thus the inner coordinate of the atoms are still constant same without the release of force.
If you want to relax the box size and the inner coordinates, the option of OptC5 or RFC5 is necessary, while I prefer the later.
If just to relax the atom position, you should refer to the geometry optimization with " MD.Type EF # Opt|DIIS|BFGS|RF|EF" http://www.openmx-square.org/openmx_man3.8/node51.html
Cheers
Kylin
|
| Re: variable cell optimization ( No.2 ) |
- Date: 2017/05/30 23:26
- Name: mosahar <mosahar_bagheri@yahoo.com>
- Dear Kylin
thank you for your answer. however, I have tested OptC5 and RFC5 methods but the doped nano tube has been deformed after optimization at both ends!
as a side point, after cell optimization with OptC1, the bond lengths and stretched and axial length of tube stretched from 11 A to 13 A. can't I regard it as optimized structure?
|
| Re: variable cell optimization ( No.3 ) |
- Date: 2017/05/31 20:10
- Name: Kylin
- Dear mosahar
the geomoetry optimization or the Molecular Mechanics (MM) is not a trivial work in simulation field. The mentioned OptC5 and RFC5 methods just try to find the local minima configuration for your molecules. Thus if you want to avoid the strange results for both atom position and the cell vectors. You should try to fix the position and the direction of cell vectors.
For the side point, have you reach the optimization criterion? The openmx may finished the calculation after 100 loops.
Cheers
Kylin
|
| Re: variable cell optimization ( No.4 ) |
- Date: 2017/06/01 03:17
- Name: mosahar <mosahar_bagheri@yahoo.com>
- Dear Kylin
yes, the calculation have reached the optimization criterion normally (less than 0.0001 H/B).
the input file is as follows:
#
# File Name
#
System.CurrrentDirectory ./ # default=./
System.Name BN-B-Au1
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)
#
# Definition of Atomic Species
#
Species.Number 3
<Definition.of.Atomic.Species
N N7.0-s2p2d1 N_PBE13
B B7.0-s2p2d1 B_PBE13
Au Au9.0-s4p3d2f2 Au_PBE13
Definition.of.Atomic.Species>
#
# Atoms
#
Atoms.Number 120
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 N -5.318 3.573 -3.331 2.5 2.5
2 B -4.762 2.295 -3.752 1.5 1.5
3 N -3.308 2.153 -3.800 2.5 2.5
4 B -2.472 3.203 -3.223 1.5 1.5
5 N -3.089 4.257 -2.422 2.5 2.5
6 B -4.545 4.377 -2.395 1.5 1.5
7 N -5.152 5.166 -1.332 2.5 2.5
8 B -4.461 5.211 -0.050 1.5 1.5
9 N -3.004 5.105 -0.048 2.5 2.5
10 B -2.312 4.739 -1.281 1.5 1.5
11 N -5.156 5.189 1.230 2.5 2.5
12 B -4.551 4.418 2.308 1.5 1.5
13 N -3.096 4.299 2.341 2.5 2.5
14 B -2.316 4.760 1.195 1.5 1.5
15 N -5.327 3.630 3.255 2.5 2.5
16 B -4.772 2.359 3.699 1.5 1.5
17 N -3.319 2.218 3.754 2.5 2.5
18 B -2.481 3.259 3.162 1.5 1.5
19 N -5.590 1.179 3.942 2.5 2.5
20 B -5.028 -0.132 3.654 1.5 1.5
21 N -3.576 -0.293 3.743 2.5 2.5
22 B -2.728 0.887 3.876 1.5 1.5
23 N -5.830 -1.243 3.153 2.5 2.5
24 B -5.201 -2.233 2.299 1.5 1.5
25 N -3.763 -2.382 2.376 2.5 2.5
26 B -2.950 -1.495 3.199 1.5 1.5
27 N -5.869 -3.024 1.276 2.5 2.5
28 B -5.150 -3.234 0.020 1.5 1.5
29 N -3.667 -3.448 0.024 2.5 2.5
30 B -3.060 -3.238 1.438 1.5 1.5
31 N -5.866 -3.045 -1.240 2.5 2.5
32 B -5.196 -2.273 -2.276 1.5 1.5
33 N -3.758 -2.424 -2.347 2.5 2.5
34 B -3.058 -3.264 -1.393 1.5 1.5
35 N -5.822 -1.297 -3.148 2.5 2.5
36 B -5.019 -0.195 -3.666 1.5 1.5
37 N -3.567 -0.358 -3.747 2.5 2.5
38 B -2.942 -1.550 -3.182 1.5 1.5
39 N -1.019 3.086 -3.274 2.5 2.5
40 B -0.205 3.902 -2.376 1.5 1.5
41 N -0.856 4.647 -1.301 2.5 2.5
42 B -0.121 4.727 -0.040 1.5 1.5
43 N -0.860 4.669 1.220 2.5 2.5
44 B -0.212 3.943 2.310 1.5 1.5
45 N -1.028 3.142 3.220 2.5 2.5
46 B -0.430 1.902 3.708 1.5 1.5
47 N -1.277 0.735 3.933 2.5 2.5
48 B -0.675 -0.579 3.716 1.5 1.5
49 N -1.505 -1.696 3.294 2.5 2.5
50 B -0.895 -2.825 2.569 1.5 1.5
51 N -1.773 -3.746 1.892 2.5 2.5
52 Au -1.252 -4.386 0.035 8.5 8.5
53 N -1.770 -3.781 -1.835 2.5 2.5
54 B -0.890 -2.871 -2.524 1.5 1.5
55 N -1.497 -1.754 -3.268 2.5 2.5
56 B -0.665 -0.644 -3.707 1.5 1.5
57 N -1.266 0.667 -3.948 2.5 2.5
58 B -2.718 0.820 -3.898 1.5 1.5
59 N -5.579 1.111 -3.978 2.5 2.5
60 B -0.420 1.837 -3.740 1.5 1.5
61 N 1.030 1.705 -3.806 2.5 2.5
62 B 1.867 2.754 -3.229 1.5 1.5
63 N 1.248 3.799 -2.415 2.5 2.5
64 B 2.027 4.271 -1.272 1.5 1.5
65 N 1.335 4.635 -0.037 2.5 2.5
66 B 2.024 4.294 1.206 1.5 1.5
67 N 1.242 3.841 2.355 2.5 2.5
68 B 1.858 2.811 3.188 1.5 1.5
69 N 1.019 1.772 3.781 2.5 2.5
70 B 1.615 0.444 3.915 1.5 1.5
71 N 0.774 -0.743 3.768 2.5 2.5
72 B 1.390 -1.942 3.200 1.5 1.5
73 N 0.578 -2.904 2.434 2.5 2.5
74 B 1.275 -3.537 1.305 1.5 1.5
75 N 0.677 -3.962 0.035 2.5 2.5
76 B 1.279 -3.560 -1.241 1.5 1.5
77 N 0.583 -2.948 -2.383 2.5 2.5
78 B 1.398 -1.999 -3.163 1.5 1.5
79 N 0.784 -0.809 -3.752 2.5 2.5
80 N 3.319 2.641 -3.284 2.5 2.5
81 B 4.134 3.430 -2.367 1.5 1.5
82 N 3.482 4.166 -1.289 2.5 2.5
83 B 4.217 4.230 -0.030 1.5 1.5
84 N 3.478 4.189 1.228 2.5 2.5
85 B 4.128 3.472 2.321 1.5 1.5
86 N 3.310 2.699 3.250 2.5 2.5
87 B 3.911 1.472 3.761 1.5 1.5
88 N 3.063 0.310 4.004 2.5 2.5
89 B 3.669 -0.994 3.772 1.5 1.5
90 N 2.843 -2.086 3.269 2.5 2.5
91 B 3.510 -3.015 2.370 1.5 1.5
92 N 2.738 -3.622 1.295 2.5 2.5
93 B 3.451 -3.821 0.037 1.5 1.5
94 N 2.742 -3.645 -1.227 2.5 2.5
95 B 3.516 -3.057 -2.309 1.5 1.5
96 N 2.851 -2.144 -3.226 2.5 2.5
97 B 1.625 0.376 -3.917 1.5 1.5
98 N 3.074 0.240 -4.000 2.5 2.5
99 B 3.679 -1.060 -3.745 1.5 1.5
100 B 3.921 1.406 -3.773 1.5 1.5
101 N 5.377 1.282 -3.852 2.5 2.5
102 B 6.212 2.333 -3.278 1.5 1.5
103 N 5.593 3.326 -2.405 2.5 2.5
104 B 6.371 3.821 -1.273 1.5 1.5
105 N 5.677 4.132 -0.027 2.5 2.5
106 B 6.367 3.843 1.227 1.5 1.5
107 N 5.586 3.369 2.365 2.5 2.5
108 B 6.203 2.391 3.257 1.5 1.5
109 N 5.367 1.350 3.846 2.5 2.5
110 B 5.958 0.031 4.048 1.5 1.5
111 N 5.122 -1.151 3.867 2.5 2.5
112 B 5.750 -2.341 3.301 1.5 1.5
113 N 4.961 -3.195 2.420 2.5 2.5
114 B 5.637 -3.825 1.291 1.5 1.5
115 N 4.903 -3.994 0.040 2.5 2.5
116 B 5.640 -3.847 -1.211 1.5 1.5
117 N 4.967 -3.238 -2.353 2.5 2.5
118 B 5.758 -2.399 -3.246 1.5 1.5
119 N 5.132 -1.219 -3.833 2.5 2.5
120 B 5.969 -0.040 -4.031 1.5 1.5
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
11.65 0.0 0.0
0.0 25.0 0.0
0.0 0.0 25.0
Atoms.UnitVectors>
#
# SCF or Electronic System
#
scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW
scf.SpinPolarization off # On|Off
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 170.0 # default=150 (Ry)
scf.maxIter 1000 # default=40
scf.EigenvalueSolver Band # Recursion|Cluster|Band
scf.lapack.dste dstevx # dstevx|dstedc|dstegr,default=dstegr
scf.Kgrid 3 1 1 # means 4x4x4
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay
scf.Init.Mixing.Weight 0.05 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.100 # default=0.40
scf.Mixing.History 50 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.criterion 1.0e-8 # default=1.0e-6 (Hartree)
#
# MD or Geometry Optimization
#
MD.Type OptC2 # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH
MD.Opt.DIIS.History 3 # default=4
MD.Opt.StartDIIS 10 # default=5
MD.Opt.EveryDIIS 10000 # default=10
MD.maxIter 300 # default=200
MD.TimeStep 1.0 # default=0.5 (fs)
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr)
scf.restart off # on|off,default=off
as a side note, I have not included Hubbard term at this point which is off-topic. If possible, please check your results with various optimization schemes (for variable cell).
Thank you very much.
sincerely
Mosahar
 |
| Re: variable cell optimization ( No.5 ) |
- Date: 2017/06/01 11:29
- Name: T. Ozaki
- Hi,
Your structure is not physically acceptable.
Because of the short a-axis, atoms in periodic cells along the a-axis
nearly overlap with atoms in the original cell.
Before going to serious calculations, you should check if the structure
is properly constructed.
Regards,
TO
|
| Re: variable cell optimization ( No.6 ) |
- Date: 2017/06/01 17:18
- Name: mosahar <mosahar_bagheri@yahoo.com>
- Dear professor Ozaki,
thank you for your answer.
|
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variable cell optimization