Professional Documents
Culture Documents
Contents
1 Conventions Used in this Document
1.1 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.2 Additional Input Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2 Using the ICSD: Starting Structures
2.1 Performing A Search . . . . . . . . . . .
2.2 Saving the cif Files . . . . . . . . . . . .
2.3 A Sample cif File . . . . . . . . . . . . .
2.4 Opening the cif File in GaussView . . .
2.5 Saving a Job File Derived from a cif File
6
6
7
.
.
.
.
.
8
9
12
14
16
17
.
.
.
.
.
.
.
.
.
18
18
19
19
19
20
22
22
23
25
.
.
.
.
.
26
26
27
27
28
29
.
.
.
.
30
30
30
31
32
6 Spin-Orbit Calculations
6.1 Example 1: Ge with ECP . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.2 Example 2: Hg with ECP . . . . . . . . . . . . . . . . . . . . . . . . . . . .
33
33
35
7 Dispersion Calculations
36
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
37
37
39
39
39
40
40
40
41
42
9 Symmetry
9.1 A Sample band.inp File . . . . . . .
9.2 Determining the SG for 3-D Systems
9.3 2-D Slabs/Films . . . . . . . . . . . .
9.4 1-D Monolayers . . . . . . . . . . . .
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
43
44
45
47
47
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
48
48
49
50
50
50
51
52
53
53
53
.
.
.
.
.
.
54
54
56
57
57
57
57
.
.
.
.
.
58
59
59
60
60
61
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
3
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
Jobs
. . . .
. . . .
. . . .
. . . .
. . . .
. . . .
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
61
61
61
62
63
64
13 Scripts
13.1 PBS Submission Scripts (Rice-Specific) . . . . . . . . . . . .
13.1.1 STIC Serial Job PBS Submission Script . . . . . . .
13.1.2 STIC Parallel (Linda) Job PBS Submission Script . .
13.1.3 DaVinci Parallel (Linda) Job PBS Submission Script
13.1.4 BioU Serial Job PBS Submission Script . . . . . . . .
13.2 PDOS Vertical Template . . . . . . . . . . . . . . . . . . . .
13.3 PDOS Horizontal Template . . . . . . . . . . . . . . . . . .
13.4 Band Structure: gpband Default . . . . . . . . . . . . . . .
13.5 Band Structure: Modified AlSb (HISS) gpt File . . . . . . .
13.6 BS and PDOS Multiplot Example . . . . . . . . . . . . . . .
13.6.1 Header and Multiplot Set-Up . . . . . . . . . . . . .
13.6.2 Band Structure Plot . . . . . . . . . . . . . . . . . .
13.6.3 Band Structure PlotII . . . . . . . . . . . . . . . . .
13.6.4 The Rotated PDOS Plot-I . . . . . . . . . . . . . . .
13.6.5 The Rotated PDOS Plot-II . . . . . . . . . . . . . .
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
65
66
66
67
68
69
70
71
72
73
74
74
75
76
77
78
14 PBC Functionals
14.1 Scuseria Functionals . . .
14.2 Just-For-Solids Functionals
14.3 (Semi)Local Functionals .
14.4 Global Hybrids . . . . . .
14.5 Functional Bibliography .
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
80
80
80
81
81
81
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
82
82
83
84
84
85
86
88
88
89
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
90
90
1.1
Examples
1.2
Please note that there are numerous additional examples of PBC jobs that are small enough
to run relatively quickly. Many of these may be taken from the Heyd 2005 paper on HSE,
(#265).
The unmodified (HSE03) input files and basis sets from this paper are located at online.
Simply replace the route line below in those *.com files, with the recommended route in
Sections 3.2.2-3.2.3).
%chk= file.chk
#p HSEh1PBE/GenECP Int(Grid=UltraFine) Pop=Regular FMM=(print)
IOp1=timestamp IOp(5/13=1,5/33=1)
SCF=(NoVarAcc,NoIncFock,Tight)
The ICSD Web database is located at icsd.fiz-karlsruhe.de. For Rice users free access is
available via IP address at icsd.fiz-karlsruhe.de.ezproxy.rice.edu.
The red rectangle in the center shows you how you are logged in. If it does not show that
you are logged in through Rice then you have access to the full database. You cannot access
the full database at home, or remotely, since the license is via IP address.)
The orange arrow to the right indicates how you can log in, and personalize your account.
This feature allows you to save your searches, which is very handy.
The yellow rectangle to the right shows you all of the options available for the different
searches. Chemistry is the most frequently used option.
NOTE: The contents of the center section change, depending upon the chosen option, while
the choices to the far left and right remain the same.
2.1
Performing A Search
Once you have logged in, you should see a page similar to that depicted in Figure 1. Go to
the left column and click Chemistry,as is delineated by the red arrow.
Figure 1: The ICSD page once you have logged in and are ready to begin a search.
Once you have clicked on Chemistry you will be provided with an empty form, as in
Figure 2.
1. Type in the element/compound/alloy/system you are interested in the line marked by
thered arrow This example is for bcc Cr.
2. Enter the number of elements in the system.orange arrow. (In this case 1.)
3. Hit Run Query on the left. green arrow.
Figure 2: The ICSD page once you have logged in and are ready to begin a search.
Notice that the lower right of Figure 2 has saved searches, indicated by the blue arrow in
the lower left corner. You can save your searches and recall them as necessary.
9
The various crystal structures for your system available in the database then appear, as in
the Cr example discussed and in Figure 3, below.
1. It is better to use the most recent and/or highest quality structures, but in this example,
the High Quality Data only option does not reduce the number of structures. (See
the red arrow to the far left.)
2. The ICSD generally reports only the Hermann-Mauguin notation (HMN) to report the
symmetry elements in the space groups. See the orange arrow to the left. (The space
group in HMN and as number(s) are in the *.cif files.)
The 4th column has the Structure Type, which is also listed in the band.inp file
names. So, since, we know we want bcc-Cr and it is a metal like W (Tungsten)
select the Im3m structure.
- BUT - what if you do not know that much? Refer to Section ?? for more
information on determining symmetry in various dimensions.
3. Simply select the structure(s) with the space group(s) you need. See the Green arrow.
4. Click Export Selected Data at the top, right, as indicated by the blue arrow.
10
Figure 3: Some of the many crystal structures available for Cr on the ICSD.
Note that if the Show Detailed View button is clicked once the structure has been
selected (purple arrow of Figure 3), that significantly more information about the structure
appears, as shown in Figure 4.
1. The structure is a Jmol animation with free rotation in and out of the ICSD window/tab.
2. The Experimental section summarizes what can be found in the articles of the Bibliography section.
3. The Warnings and Comments may be helpful in determining the quality of the structure
4. Once satisfied, click the Export CIF File button. (Circled in red.)
11
2.2
3. Notice that there are two other formats: *.csv and *.xls, if tabulated data is desired.
Figure 5: The Export Selected Data page for Cr cif file ID #44731.
NOTE:
GaussView can read *.cif files as is,
so once they are downloaded, you are ready to go!
13
2.3
14
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 z, y, -x
2 y, x, -z
3 x, z, -y
4 z, x, -y
5 y, z, -x
6 x, y, -z
7 z, -y, x
8 y, -x, z
9 x, -z, y
10 z, -x, y
11 y, -z, x
12 x, -y, z
13 -z, y, x
14 -y, x, z
15 -x, z, y
16 -z, x, y
17 -y, z, x
18 -x, y, z
19 -z, -y, -x
20 -y, -x, -z
(TRUNCATED)
. . .
96 x+1/2, y+1/2, z+1/2
loop_
_atom_type_symbol
_atom_type_oxidation_number
Cr0+ 0
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_B_iso_or_equiv
_atom_site_occupancy
_atom_site_attached_hydrogens
Cr1 Cr0+ 2 a 0 0 0 . 1. 0
#End of data_44731-ICSD
15
2.4
Figure 7: GaussView for cif files. Left: The window to select and open a cif file in your
directory. Right: The periodic system with cell axes and atoms constructed from the cif
file by GaussView.
16
2.5
17
3.1
0.00000000
0.00000000
2.06825000
2.06825000
4.13650000
-2.06825000
0.00000000
2.38820939
2.38820939
1.19410469
1.19410469
0.00000000
3.58231408
0.00000000
0.00000000
2.53193200
3.35800000
5.88993200
0.00000000
0.00000000
6.71600000
@/projects/guscus/basis/cd-heyd.gbs/N
@/projects/guscus/basis/s-mHeyd2005.gbs/N
18
3.2
3.2.1
Link 0 Commands
1. A checkpoint, *.chk file is vital: PBC jobs run long, are prone to crash, and are necessary
for BS/PDOS calculations.
2. %mem, %NProcShared, scratch file names/locations and other commands will be added
via the various PBS scripts and are not necessarily PBC-related other than that memory
requirements will be much larger than those of molecules, and running in parallel becomes
especially useful.
3.2.2
19
Using the Pop=FULL option will result in an... overly large file.
6. FMM=Print and IOp1=timestamp are useful for debugging and timings
Odds are, you will use these at some point: put them in your template and be glad
later.
7. Other important PBC IOps: (Check the G09 IOps Page for more details. These are all
Overlay 5 Direct link to Overlay 5)
5/13=1 continue running even in spite of non-convergence, ILSW flag ON
5/33=1 eigenvalues and MOs printed at end
5/181=10 run a PDOS calculation (See Section 8.2.)
5/184=### look for a band.inp file of space group ### and compute the band
structure.
e.g., 186 = Wurtzite/hexagonal; 216 = Zincblende; 227 = Diamond, ...
See Sections 8.3 and 9.1.
8. The SCF settings are key for both energy calculations and optimizations. Again,this is the
minimal route for a PBC job. See the specific keyword pages for more details.
NoVarAcc Do not use the default of modest integral accuracy early in direct SCF,
switching to full accuracy later on.
NoIncFock Prevents the use of incremental Fock matrix formation, and it is the
default for conventional SCF
Tight SCF=Tight, should be default: SCF details.
Note that "tight" varies by Gaussian version for PBC, so explicitly stating this is
a safety measure.
If in doubt, check your output file.
There is a definite difference between HSE03 and HSE06.
3.2.3
20
For a neutral singlet, will usually see 0 1, but be aware of an older notation using
commas: 0,1
3. The unit cell coordinates.
xyz Cartesian coordinates
Usually from a *.cif file downloaded from a database, like the ICSD, see Section 2.
Can be aprimitive, the full unit cell or a supercell. NOTE:
Databases generally provide the unit cell, not the primitive cell.
4. The translation vectors always follow the cell coordinates
Labeled by Tv, or numerically as -2.
Correspond to the x, y and z directions, respectively.
Note that these directions/planes do not necessarily correlate with those for various
Miller Indices of interest: when going from 3-D to a 2-D slab or 1-D monolayer, simply
deleting one (or two) of the rows from the bulk structure may not result in the desired
lower dimensional structure.
Always followed by a blank line.
5. The basis set specification using a path
The/N prevents the basis set from being printed at the beginning if the output file
Alternatively, the basis set and/or ECP can be added to the end of the file, as in
molecular calculations
6. There are cases where additional specifications may be added to a file. For examples, review
the sample input files in Sections 4, 5, and 6.
This example, with the complete input file (including both basis sets)
and the corresponding output file is provided locally at:
guscus:/projects/guscus/Manuals/examples/CdS-wu/.
21
3.3
Geometry Optimizations
Note that both the lattice parameters *and* the atomic positions
are relaxed within a gaussian PBC optimization.
%chk=CdS-wu_x.chk
#p HSEh1pbe/GenEcp Int(Grid=UltraFine) Pop=Regular FMM=(Print)
IOp1=timestamp IOpp(5/13=1,5/33=1,5/181=10,5/184=186)
SCF=(NoVarAcc,NoIncFock,Tight) Opt Guess=(Read,Fock)
3.3.1
Line-By-Line Description
22
3.4
The best way to apply constraints in these geometry optimizations would be to use the keyword
Opt=ModRedundant, symbolic Z-matrices would not work well for PBC optimizations.
The trick in applying constraints to PBC geometry optimizations is to get the correct
numbering right. Note that the translation vectors count for the purpose of atom numbering even
though they are obviously not atoms and thus their numbers cannot be used directly to apply a
constraint. So, for example, if one wants to freeze the length of a translation vector, the constraint
would be to freeze the interatomic distance between an atom in the origin cell and the same atom
in the contiguous cell along the direction of the translation vector of interest.
In a 3-D periodic calculation, there are 8 cells to consider, the origin cell (O) and seven contiguous
cells (one along each one of the three translation vector, T1, T2 and T3, plus the four contiguous
cells along the diagonals, T1+T2, T1+T3, T2+T3, and T1+T2+T3). The following shows how
these cells are ordered for atom numbering purposes:
Cell Start End
O
1
T3
N+1
T2
2N+1
T2+T3
3N+1
T1
4N+1
T1+T3
5N+1
T1+T2
6N+1
T1+T2+T3
7N+1
N
2N
3N
4N
5N
6N
7N
8N
where N is the number of entries in the input file, that is the number of "real" atoms plus the three
translation vectors.
For instance, in the input file you sent here, you have 12 atoms plus the three translation vectors,
that makes N=15. If you were to freeze the length of the first translation vector (T1), you could
freeze, for instance, the interatomic distance between atom 1 (in cell O) and atom 61 (same atom
but in cell T1).
In your case, I see that you would like to constrain the lengths of T1 and T2 to be the same, not just
freeze the length. Unfortunately, the redundant internal set does not allow to impose the identity
condition between two coordinates. However, for this particular case, it would still be possible to
do what you are trying here.
In order to keep the lengths of T1 and T2 equal during the optimization, you could freeze the angle
between an atom in cell T1, the same atom in cell O, and the same atom in cell T1+T2. This angle
23
should bisect the angle between T1-O-T2. So, given that your translation vectors form an angle
of 90 degrees, the T1-O-T1+T2 angle should be frozen to be 45.0 degrees, exactly at the bisection
(which implies that the two translation vectors will be equal in length). Below is an example of how
to do this for your input file.
#p uTPSStpss/Gen PBC=(nkpoint=2000) pop=regular
SCF=(convergence=7,maxcycles=64,NoVarAcc)
Guess=(Read,Fock) OPT=modredun
V4O8 tetragonal rutile
0 5
V
O
O
V
V
V
O
O
O
O
O
O
Tv
Tv
Tv
A 61 1 31 90.0 F
A 61 1 91 45.0 F
(high temperature);
1.27880629
0.27860530
1.81959437
3.48744003
2.73205066
0.52341693
4.48764102
3.73225165
-0.47678407
2.94665196
2.19126259
1.06420500
4.55460000
0.00000000
0.00000000
4.44482660
0.95052300
3.32683050
2.18167660
0.08147340
2.34462340
3.21367300
3.57577700
1.31262700
1.06368050
1.19946950
3.46261950
0.00000000
4.55460000
0.00000000
-0.22374016
0.87756065
0.96076224
1.19205909
3.77512190
2.35932265
0.09075828
2.67382109
3.46062345
0.00755669
2.59061950
3.54382505
0.00000000
0.00000000
5.70280000
@v_towler.bas
@o_towler.bas
24
3.5
Restarts
For both energy calculations and optimizations, adding Restart is sufficient, i.e.,
Energy Calculation: SCF=(NoVarAcc,NoIncFock,Tight,Restart)
Optimization: SCF=(NoVarAcc,NoIncFock,Tight) OPT=Restart
See also Section 3.4 for instructions on how to run constrained geometry optimizations
25
4.1
Input
If the AFM guess is turned on, a list of atoms whose spin densities are to be flipped should be
specified after a blank line from the input file. This is best accomplished by running a two-part
calculation using Link 1. (See Section 4.2 for more details.)
1. The first part of the input file should be the "unflipped" system
2. Add a blank space
3. Add Link1
4. The new route will include Guess=(Read,Fock), IOp(5/150=1) and NoSymm. The
NoSymm keyword prevents the reorientation and causes all computations to be performed
in the input orientation.
5. Add the new spin multiplicity, e.g., 0 3 0 1
6. Input the coordinates again (could Geom=Allchk be used)
7. Input ONE (1) blank line after the last Tv
8. Add the list of atoms that will be spin flipped
Specify according to the atom numbers
Apparently vertically specified (See 4.5.)
26
4.2
In the following example, the comments are actually *in* the G09 input file.
%chk=H.chk
#p PBEPBE/cc-pvtz
PBE H note this starts out as a triplet and will be flipped
0,3
H
H
TV
--Link1-%chk=H.chk
#p PBEPBE/cc-pvtz Guess={Read,Fock} IOp(5/150=1) NoSymm
PBE H note that the total spin multiplicity is now 1
0,1
H
H
TV
4.3
At the beginning of the SCF, the output file should contain the following message:
"AfmFkG: AFM guess by flipping spin density"
followed by the list of atoms and basis sets involved in the spin flipping.
The input and output files with comments are located locally at:
guscus:/projects/guscus/Manuals/AFMGuess/Example1-H.
27
4.4
--Link1-%chk=Cr.chk
#p PBEPBE/LANL2DZ guess=read IOp(5/150=1)
PBE Cr
!
! **** note that total spin multiplicity here is 1.
!
0,1
Cr
0.0000 0.000 0.0000
Cr
0.0000 0.000 2.4000
TV
0.0000 0.000 4.8000
!LIST OF ATOMS WHERE THE SPIN SHOULD BE FLIPPED
1
A.U. after
A.U. after
55 cycles
30 cycles
A sample version of the input and output with comments is located locally at:
guscus:/projects/guscus/Manuals/AFMGuess/Example2-Cr.
28
4.5
In the following example, the comments are actually *in* the G09 input file.
Notice the free-format of the G09 input files...
%chk=LTO.chk
#p UPBEpbe/GEN pseudo=read Int=Grid=Ultrafine
iop(5/13=1,5/33=1,3/18=1,3/65=-25) GFInput pop=regular SCF=tight
Ferro magnetic LaTiO3 Spin UP for all
Ti atoms 2,8,9,10
0,5
La,0,3.0649514287,-2.2692554128,-1.580103775
Ti,0,0.27940315,-2.4932384439,-3.5559414972
O,0,-2.2052614311,0.2766559378,-1.5802918116
O,0,1.4815133703,-0.890960693,-3.3214858263
La,0,-2.5045921227,2.8229404289,2.3702238711
La,0,0.2660765836,0.0554120936,2.3713792713
La,0,0.2942660209,0.4982535617,-1.5812458804
Ti,0,0.2793469199,-2.490041081,0.3961952352
Ti,0,-2.5196374746,0.2743011984,-3.5568557237
Ti,0,-2.5197041276,0.2775004992,0.3952969214
O,0,2.7656449004,0.277038938,2.3704292974
O,0,0.5937990896,-2.4894430993,2.3716929806
O,0,-0.0334301204,3.0431335943,-1.5815593191
O,0,-0.922206137,1.443200864,0.6296615465
O,0,-1.3188302628,-1.3219594526,4.112984379
O,0,1.8777073771,1.8772833843,0.1591920659
O,0,-0.9211487908,1.4446548897,4.1116294151
O,0,1.4825626149,-0.8895175017,0.1604564175
O,0,1.8791897066,1.8756333904,-3.322861073
O,0,-1.3173586107,-1.3236264087,0.6309382415
TV,0,5.5997593459,-0.0013274988,-0.0004424492
TV,0,0.0016897946,5.5337445538,-0.0022507369
TV,0,-0.0001024768,0.0064109731,7.9042794351
! used basis sets @2_mod_SVP_Ti.gbs, SVP_O.gbs, 2_SVP_La.gbs get from Fadwa El-Mellouhi
! fadwa.el_mellouhi@qatar.tamu.edu
%-------------------------------------------------%chk=LTO.chk
#p UPBEpbe/GEN pseudo=read Int=Grid=Ultrafine
Guess(Read,Fock) IOp(5/13=1,5/33=1,3/18=1,3/65=-25,5/150=1) GFInput pop=regular SCF=tight
AntiFerromagnetic state will be obtained from the previous run by activating the IOP 5/150=1 indicating
to flip spin for the Ti atoms. Atoms 8 and 9 will have spin DOWN while 2 and 10 will keep spin UP.
0,1
La,0,3.0649514287,-2.2692554128,-1.580103775
Ti,0,0.27940315,-2.4932384439,-3.5559414972
O,0,-2.2052614311,0.2766559378,-1.5802918116
O,0,1.4815133703,-0.890960693,-3.3214858263
La,0,-2.5045921227,2.8229404289,2.3702238711
La,0,0.2660765836,0.0554120936,2.3713792713
La,0,0.2942660209,0.4982535617,-1.5812458804
Ti,0,0.2793469199,-2.490041081,0.3961952352
Ti,0,-2.5196374746,0.2743011984,-3.5568557237
Ti,0,-2.5197041276,0.2775004992,0.3952969214
O,0,2.7656449004,0.277038938,2.3704292974
O,0,0.5937990896,-2.4894430993,2.3716929806
O,0,-0.0334301204,3.0431335943,-1.5815593191
O,0,-0.922206137,1.443200864,0.6296615465
O,0,-1.3188302628,-1.3219594526,4.112984379
O,0,1.8777073771,1.8772833843,0.1591920659
O,0,-0.9211487908,1.4446548897,4.1116294151
O,0,1.4825626149,-0.8895175017,0.1604564175
O,0,1.8791897066,1.8756333904,-3.322861073
O,0,-1.3173586107,-1.3236264087,0.6309382415
TV,0,5.5997593459,-0.0013274988,-0.0004424492
TV,0,0.0016897946,5.5337445538,-0.0022507369
TV,0,-0.0001024768,0.0064109731,7.9042794351
! basis sets @2_mod_SVP_Ti.gbs @Basis/SVP_O.gbs @2_SVP_La.gbs
9
8
Local versions of the input and output files (with comments) are located at:
guscus:/projects/guscus/Manuals/AFMGuess/Example3-LTO.
29
The Variable Magnetic Moment (VMM) code is similar to that of the AFM Guess.
For version G09-b1-pbc-2.3 the IOps are:
1. 5/150=-1 turn on the VMM code
2. 5/150=0 turn off the VMM guess (default)
3. NOTE: These IOps change by version please check before running.
5.1
Input
1. The first part of the input file should be the "unflipped" system
2. Specify orbitals of interest, e.g., 5D 7F in Example ??
3. Add a blank space
4. Add Link1
5. The new route will include Guess=(Read,Fock), IOp(5/150=-1)
6. Input the coordinates again (could Geom=Allchk be used?)
5.2
Output
A.U. after
A.U. after
37 cycles
16 cycles
30
5.3
%chk=Pd.ccpvtzpp.SVWN5.5.V06.chk
#p USVWN5/Gen Pseudo=read 5D 7F IOp1=timestamp
SCF=(Conver=8,MaxCycle=300,CDIIS,NoIncFock,NoVarAcc)
iop(5/33=1,5/13=1) PBC(NCellMin=120)
Pd linear monostrand SVWN5 /
0,5
Pd
Pd
Tv
.000000
0.000
0.0
.00000
.000000
0.000
3.000
0.0
6.0000
multipl = 5
.000000
0.000
0.0
.00000
.000000
0.000
3.000
0.0
6.000
31
5.4
In the following example, the comments are actually *in* the G09 input file.
32
Spin-Orbit Calculations
The key is to use a gdv version that has Spin-Orbit Coupling implemented and to use IOp(3/117=1).
As of April 1, 2012, G09-B1 and gdv-H11 may be used with confidence, although gdv-H13 has
been tested.
6.1
%subst l302 ..
%KJob l302
#p USVWN5/Gen Pseudo=Read 5d 7F IOp1=tstamp gfprint
iop(3/117=1) NosSmm
Bulk Ge with ECP spin-orbit. This is the "molecular" calculation
only to generate the intracell SO matrix elements in the cell 0.
@Ge.cell.geom ! Coordinates, basis sets and ECP are all online
@Ge.bas
@Ge-SO.ecp
--Link1-%subst l502 ..
#p USVWN5/Gen Pseudo=Read 5d 7F IOp1=tstamp
SCF(maxcycle=60,conver=5)
PBC(cellrange=60,NKPoint=1000)
IOp(5/193=1)
IOp(5/155=3)
!
!
!
!
33
The output file provides the magnitude of the coupling via the cmd line: grep A300 SCF D00
[sgu1@gw test-Ge-con]$
SCF Done: E(US-VWN5)
NFock= 8
Spin-orb: E(2nd v) =
TOTAL
E(US-VWN5)
8 cycles
34
6.2
0.0000
0.0000
*.log
A.U. after
23 cycles
-V/T= 3.9834
A.U.
A.U.
35
Dispersion Calculations
36
8.1
For the example route below, both PDOS and band data will be computed for the HSE single point
energy calculation of a monolayer of MoS2 .[1]
%chk=monohse.chk
#p HSEh1PBE/GenECP Int(Grid=UltraFine) pop=regular FMM=print
IOp1=timestamp iop(5/13=1,5/33=1)
SCF=(NoVarAcc,NoIncFock,Tight)
IOp(5/181=10,5/184=194)
NOTE:
1. Both band structure and projected densities of states data will be produced at the end of this
SPE calculation.
If this had been an optimization, band structure data would appear at the end of each
opt cycle.
Some PDOS data files appear during an energy calculation (see Section 8.2 but all files
do not appear until the job completes.
2. The IOp 5/181=10 indicates that G09 should calculate the PDOS.
3. The IOp 5/184=194 indicates that the k-path and labels for space group 194 (hexagonal)
have been provided in the band.inp file.
The band.inp files are described in Section 9.1 and located locally at
guscus:/projects/guscus/Manuals/binps/.
A band.inp file with the correct symmetry (see Section 9 must be copied, renamed and
placed in the same directory as your job.
4. The monolayer is a 2-D system, so a modified band.inp file was used for this calculation.
5. Ensure that your pbs or other submission file has the following line at the very end:
mkpdos
37
All relevant files to reproduce the plot in Figure 10 may be copied from:
guscus:/projects/guscus/Manuals/examples/MoS2mono
See Section 10 for explicit details on using Gnuplot for BS/PDOS plots.
12
10
8
Energy (eV)
12
Ss
Sp
Sd
Mos
Mop
Mod
Total
10
8
2
MoS2 Monolayer SPE
EF
KPath
Figure 10: An example of BS and PDOS as plotted using multiplot. The data is from the
HSE SP calc of an MoS2 monolayer, with a calculated direct band gap Eg of 2.33 eV. (See
#386, Appl. Phys. Lett. 99, 261908 (2011).)
38
8.2
PDOS Only
PDOS only jobs are fairly straightforward:
1. Add IOp 5/181=10 to the route.
2. Place the following command at the end of your *.gjf or *pbs file:
mkpdos bias from 0 $InpBase.out0 f v > & mkpdos.log
8.2.1
Input Example
%chk=Si-dia_o.chk
#p HSE1PBE/Gen Pop=Regular Int(Grid=UltraFine) FMM=Print
IOp1=timestamp IOp(5/13=1,5/33=1)
SCF(NoVarAcc,NoIncFock,Tight) IOp(5/181=10,5/184=227)
OPT Guess=(Read,Fock)
8.2.2
PDOS Output
Several PDOS-related files will appear once a job has finished. NOTE: A job will appear to be
running until all PDOS-related files finish writing. These files include:
pdos.dat contains the data to plot Useful.
pdos.legend.txt Legend for orbital populations on specific nuclei. Useful.
fort.121 appears as the job runs and indicates that PDOS will be calculated.
zpratl-pdos.inp a file necessary for the calculation, appears as jobs runs.
mkpdos.log describes what happened during the PDOS calculation.
pdos.d additional data that may be deleted at the end.
2.5
Sis
Sip
Sid
Total
Fermi level
Si (dia)
HSE OPT
Eg = 1.22 eV (I)
Expt. = 1.17 eV (I)
1.5
0.5
0
-10
-8
-6
-4
-2
0
2
Energy (eV)
39
10
8.3
Band structure jobs are also easy to run and set up, but require some knowledge of the symmetry of
the system because of the necessary band.inp files. The band.inp files will be discussed in detail
in Subsection 9.1.
8.3.1
8.3.2
Output Files
In addition to the *.out and *.chk files that are necessary for processing the BS data, two (2) new
files are produced:
1. band.dat This contains everything you need to plot band structure. The last 6 lines of the
file (tail -6 band.dat) provide the number of electrons, the HOCO and LUCO values, the
indirect gap (after scaling) and mGap1/MGap1.
2. bandk.dat This is in the work-up, but it is not as large as band.dat and is not necessary
once a gnuplot file has been set up.
Last updated: March 26, 2012
40
8.4
If a *chk file is available for either an opt or energy calculation, band structure and PDOS can be
calculated after the fact. This requires a truly minimal input file assuming pop=regular was used
in the job that generate the *chk file:
%chk=AlN_x.chk
#p HSEh1PBE/ChkBas Geom=AllCheck Guess=(Read,Fock)
IOp1=timestamp iop(5/13=1,5/33=1)
IOp(5/181=10,5/184=227,5/14=20)
ChkBas reads the basis set information from the *chk file
Geom=AllCheck takes the title, charge, multiplicity and coordinates from the *chk file.
IOp 5/14=20 uses the BS data from the already computed real-space Fock matrix.
These 4 lines are sufficient to produce, in this case, both PDOS and BS for a FCC system in space
group 227.
To turn off PDOS, which should usually run automatically as it is in most *pbs scripts, (See
Section 13) change the PDOS IOp to IOp(5/181=200).
This restart is much faster than re-doing a full energy calculation, but is generally not
instant unless it is PDOS only.
This usually works, but if the *chk file was corrupted or there was not band.inp file in place
for the restart from an good *chk file, all sorts of weirdness will ensue.
Last updated: March 26, 2012
41
8.5
IOp
IOp 5/181
Arguments
0
1
2
10
20
00
200
IOp 5/184
EE
00 00
99 00 00
FF
00
01
02
03
10
20
30
KK
KK 00
0
SpG
1-228
IOp 5/183
0
-1
42
Symmetry
To run band structure jobs, the argument of IOp (5/184=SG)
is the space group number (SG) of the system.
Formally, the space group number refers to the unique numbers (1-230) assigned to all space group
types, as defined by the International Union of Crystallography.
Groups within the same crystal system or point group have consecutive numbers, otherwise,
the numbering is arbitrary.
Not all space groups are represented by known compounds.
To locate the appropriate *.inp file:
1. Note that the files are named first by the SG that would complete the argument of IOp
(5/184=SG), then the prototype, followed finally by packing type e.g., 186_MoS2-hex.inp.
(For more information, refer Section 9.1.)
2. Copy and rename the *.inp file with the appropriate SG to band.inp in the running directory
3. This enables gaussian to read the k-path and label the high symmetry points.
4. Recall that band.inp files are stored locally in guscus:/projects/guscus/Manuals/binps/
Other instances where knowing the SG is helpful:
1. When the conventional/crystallographic unit cells are large, creating a smaller primitive is
useful and requires knowledge of the SG before and after the cell size is reduced.
2. If a supercell is created (e.g., for doping), then the symmetry changes must be noted.
NOTE:
There are numerous systems to designate symmetry, so familiarity with the more
common systems will prove helpful when information other than SG is provided.
Currently Available Information:
A sample band.inp file Section 9.1
3-D (Bulk) systems Section 9.2
2-D Slabs/films/monolayers Section 9.3
1-D Chains Section 9.4
Creating supercells and primitives Section under construction
Other symmetry designations Section under construction
List of additional resources Section under construction
43
Sec. 9: Symmetry
9.1
Below is an example of the band.inp copied from 227-Diamond-fcc.inp in the /binps directory
[needs a path] and renamed band.inp. Notice that other symmetry designations in addition to
space group are listed; nevertheless, G09 uses the SPACE GROUP as the argument to IOp(5/184).
!
!
!
!
!
!
!
!
KLABELS:
GM
0
K
3/8
L
1/2
U
5/8
W
1/2
X
1/2
0
3/8
1/2
1/4
1/4
0
0
3/4
1/2
5/8
3/4
1/2
KPATH: GM X W K GM L U W L K|U X
IMPORTANT:
This external band.inp file is necessary because the internal library cannot always correctly
identify the symmetry, especially for space groups lower than 200. (The band structure code
looks for the band.inp file by default.)
More importantly, band.inp files allow the path to be changed as necessary to match the
literature or, in the case of optimizations where the symmetry has changed, re-run the job
with the correct space group and path
Again, the band.inp template files are in the /binps directory on guscusgw and
are named (1) according to space group and lattice and/or (2) labeled to indicate
any modifications or use in publications.
Notice that fractions or decimal representations can be used, e.g., 1/2 or 0.5 for the coordinates.
Last updated: March 26, 2012
44
Sec. 9: Symmetry
9.2
The space group of crystal structure is usually included in the *.cif (or, less frequently *.pdf ) file
downloaded from a database, e.g., the ICSD or the AMS.
The space groups are numbers ranging from 1-230, as is seen to the far left column of Figure 13, which
contains also the short symbols to the far right, another commonly used symmetry designation.
45
Sec. 9: Symmetry
Figure 13: Table of Space Groups in 3-D. The SGs used as the argument for IOp 5/184
are located in the far left column, as numbers 1-230. The other common system, the International Short System designations, are an abbreviated version of Hermman-Mauguin
notation and form the column to the far right. Other systems such as the Pearson for Struckturbericht designations are as not universally applicable, and are thus not as widely used.
(From: en.wikipedia.org/wiki/Space_group)
46
Sec. 9: Symmetry
9.3
2-D Slabs/Films
Generally, the initial space group of your system in terms of how g09 identifies the point group is
in the *.cif file downloaded from a database, e.g., the ICSD or the AMS. Other means of acquiring
this information include:
1. The literature the papers you start with
2. The ACONVASP Online site (Curtarolos group at Duke)
3. The 2-D Space Groups Table (See Figure 14)
4. Materials software like Materials Studio, Vesta, etc.
Figure 14: 2D-Brillouin Zones. (a) Square, with lattice constant a, (b) Rectangular, with
lattice contants 1 , 2 , and, (c) Hexagonal with lattice constant a. (Taken from: Economou,
2010, Ref. [2])
9.4
1-D Monolayers
Generally, the initial space group of your system is in the *.cif file downloaded from a database.
Other means of acquiring this information:
1. The literature
2. Non-Gaussview software
47
10
10.1
Density of states plots are generally *MUCH* easier to work-up than BS data: simply use the
pdos.dat, pdos.legend.txt files generated by your job output and a *.gpt template file.
The pdos.dat file for am MgInS2 LSDA OPT looks like this:
#
E/eV
-42.0000
-41.9800
-41.9600
-41.9400
-41.9200
-41.9000
-41.8800
-41.8600
-41.8400
-41.8200
-41.8000
-41.7800
-41.7600
-41.7400
-41.7200
-41.7000
-41.6800
-41.6600
-41.6400
-41.6200
. . .
0 Mg S a
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
-0.0000
-0.0000
-0.0000
-0.0000
-0.0000
-0.0000
-0.0000
0 Mg P a
0.0000
0.0000
0.0000
0.0000
0.0006
0.0026
0.0097
0.0335
0.1067
0.3143
0.8543
2.1437
4.9656
10.6178
20.9583
38.1885
64.2341
99.7368
142.9556
189.1489
0 In S a
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
-0.0000
-0.0000
-0.0000
-0.0000
-0.0000
-0.0001
-0.0001
-0.0003
-0.0004
-0.0007
-0.0009
-0.0012
0 In P a
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
-0.0000
-0.0000
-0.0000
-0.0000
-0.0000
-0.0001
-0.0002
-0.0003
-0.0005
-0.0008
-0.0011
-0.0014
0 In D a
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
-0.0000
-0.0000
-0.0000
-0.0000
-0.0000
-0.0000
-0.0000
-0.0000
0 S S a
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0001
0.0001
0.0004
0.0009
0.0018
0.0036
0.0066
0.0111
0.0172
0.0246
0.0326
0 S P a
0.0000
0.0000
0.0000
0.0000
-0.0000
-0.0000
-0.0000
-0.0000
-0.0001
-0.0004
-0.0011
-0.0027
-0.0063
-0.0136
-0.0268
-0.0488
-0.0821
-0.1274
-0.1827
-0.2417
0 S D a
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0001
0.0002
0.0003
0.0005
0.0007
0.0011
0.0014
Total a
0.0000
0.0000
0.0000
0.0000
0.0006
0.0026
0.0097
0.0334
0.1066
0.3139
0.8534
2.1413
4.9601
10.6060
20.9350
38.1460
64.1627
99.6258
142.7966
188.9385
E(eV)
0 Mg S a
0 Mg P a
0 InS a
0 In P a
0 In D a
0 S S a
0 S P a
0 S D a
Total a
where the different orbitals for each atom are listed followed by the Total electron density. This
helps you determine the color scheme of your gnuplot output.
48
10.2
= DIRECT Mg_8In_{16}S_{32}:
. xc . / . bas .
Fully-Relaxed XTAL
Gap_I=Gap_D=2.5 eV
HOCO = 0
LUCO = 4.1252
set xrange [-5.0:8.0] # range of x-axis will vary by system
set yrange [-2:80] # range of y-axis will vary by system
# Line styles and color
set style line 1 lt 0
set style line 2 lt 1
set style line 3 lt 2
set style line 4 lt 1
set style line 5 lt 1
set style line 6 lt 1
set style line 7 lt 1
set style line 8 lt 1
set style line 9 lt 1
set style line 10 lt 3
scheme
lc rgbcolor "black"
lc rgbcolor "magenta"
lc rgbcolor "magenta"
lc rgbcolor "red"
lc rgbcolor "blue"
lc rgbcolor "cyan
lc rgbcolor "green"
lc rgbcolor "gray"
lc rgbcolor "orange"
lc rgbcolor "orange"
pt
pt
pt
pt
pt
pt
pt
pt
pt
pt
0
2
1
1
1
5
2
3
4
5
ps
ps
ps
ps
ps
ps
ps
ps
ps
ps
1.5
1.5
1.5
1.5
1.5
1.5
1.5
1.5
1.5
1.5
49
10.3
Currently, the easiest way to plot band structure data is to use the gpband Perl script written by
Dr. Cristian Diaconu. As it is to large to include in Section 13, the gpband script is stored at
guscus:/projects/guscus/Manuals/scripts/gpband.
10.3.1
1. Place a copy of gpbandon each machine where gaussian PBC code will be run.
2. Run gpband in the jobs working directory: gpband band.dat
The files that are processed include band.dat bandk.dat and the *.out, hence the
admonition to run gpband in the jobs working directory.
Note the numerous annotations within the script, describing the program and how the
band*.dat files are arranged.
Of the many options, gpband nameoffile.dat seems to work the best, but feel
free to explore.
3. Copy the gnuplot and *.dat files to your desktop to plot the data. (There is no Gnuplot on
most Rice clusters.)
4. gpband prepares a basic gp file that runs to produce eps output see Figure 15.
The default color scheme is most likely not what will be used in the final plot.
The lowest gap is generally plotted, but may be adjusted for aesthetic reasons.
Labels, I-bars, additional lines and comments must be added by hand.
10.3.2
20
10
Energy (eV)
10
20
30
40
W K|U X
k path
50
Figure 15:
The band structure for AlSb optimized using
HISS. The command gpband
band.dat produced a Gnuplot
file, band-p.gp, ran it and created band.eps (to the left) automatically. Notice the default energy scale (taken from the gaussian PBC code defaults) is intentionally large and that the color
scheme has each band coded in
different linestyles and/or colors.
10.3.3
Annotated sections of the gp file that produced Figure 15. (The full script is in Section 13.4.)
x1_GM = 0.000000
x2_X = 0.862114
x3_W = 1.293143
x4_K = 1.597934
x5_GM = 2.512322
x6_L = 3.258914
x7_U = 3.786839
x8_W = 4.091633
x9_K = 4.396424
x10_X = 4.701213
=
=
=
=
=
=
=
=
=
10.371738
10
10.371738
11
12.420518
10.371738
3.058369
8.405779
2.048780
E(y) = y - E0
set
set
set
. .
set
arrow
arrow
arrow
.
arrow
set arrow 11 \
from graph 0, first E(HOCO) \
to
graph 1, first E(HOCO) nohead lt 19
set arrow 12 \
from graph 0, first E(LUCO) \
to
graph 1, first E(LUCO) nohead lt 20
\
data
data
data
data
data
data
data
data
data
data
data
data
data
data
data
data
data
data
using
using
using
using
using
using
using
using
using
using
using
using
using
using
using
using
using
using
51
10.3.4
Modified BS Output
The gp file in Section 10.3.3 has been modified in the following ways to produce Figure 16:
The scale of the y-axis is now from -7 to 10, so it is easier to see the camel-back structure
of AlSb.
The valence band are all colored red.
The conduction bands are all labeled in blue
The Fermi Level E = 0 is now labeled and the energy denoted as a horizontal black line
The conduction band maximum is depicted as a dashed orange line.
The favored, indirect transition from to somewhere near X is marked by both an arrow
and a green I-bar.
The slightly higher in energy direct gap is marked only with an I-bar.
Structure analysis, e.g., locating points on the bands that are not along the high-symmetry
k-lines for energy comparisons. Mining the data in the band*.dat files will be discussed in
Section 10.4.
10
8
6
Energy (eV)
4
2
2.33 eV (I)
2.05 eV (I)
0
2
4
6
K
W K|U X
All files necessary to produce this plot and that of Figure 15 are locally
available at guscus:/projects/guscus/Manuals/examples/AlSb-HISS.
The full gp files are also listed in Sections 10.3.4 and 13.5.
52
10.4
Locating k-Points
This section is for locating points so that arrows can be drawn in Gnuplot to
mark direct and indirect transitions. Not all points of import are located on the
lines corresponding to the symmetry points specified in the path of the band.inp
file, so this becomes something of an art.
10.4.1
This should be the easy case for an indirect gap from one k-point to another.
1. Search band.dat file for energy via grep
2. Also need to do the reverse case.
10.4.2
Special Gaps
53
11
11.1
For Starters: Read the Gaussian 09 manual entries for Molecule Specifications and the keywords:
PBC and FMM. (The input file information in Section 3 has more information for PBC.
Perhaps an FMM section would be useful...)
What not to do: If you want to put your computer system on its knees, try B3LYP with a diffuse
basis set on your favorite 3D system, e.g., diamond.
1. The near-field portion of the FMM without symmetry included will be very costly.
2. Symmetry is not implemented, yet, but we are working on it and even when it is, doping
and disorder lower the symmetry, anyway.
3. The HFx (Hartree Fock exchange) portion with diffuse basis functions (bfs), a full-range
1/r potential, and default cutoffs will take forever, and it is almost guaranteed that a
single iteration will exceed your patience.
Hybrids: Any with full (global) or long-range 1/r potential are significantly more expensive (1020x or even more) than short-range hybrids like HSE that were designed with solids in mind.
Be extremely careful if you want to do a PBC full or long-range hybrid.
Dimensionality: 3D calculations are more expensive than 2D, which are, in turn, much more
expensive than 1D. If you are not familiar with the PBC code and how to tune up its options,
we recommend that you start playing in 1D and move your way up to 2D/3D slowly.
Diffuse bfs: They may be needed in some specific cases and for some specific properties but in
general, it is a good idea to carefully analyze whether your chosen MOLECULAR basis set
(i.e., a basis set that was developed for atoms/molecules and usually contain fairly diffuse bfs
to describe atomic tails) is really needed for your PERIODIC system, which does not have
any density tail (well... it does if you are doing 1D or 2D, but not in 3D).
Linear dependencies: Our PBC code does not suffer from linear dependencies, i.e., if you use
a dense basis on a dense system and you end up with product bfs that are almost linearly
dependent (overlap matrix eigenvalue at some k-point below a certain threshold), the code
will remove the offending linear combination. However, there may be cases where the overall
accuracy is affected because of
1. Aggressive thresholds
2. A sloppy (or not accurate enough) xc quadrature grid, or,
3. A sloppy (or not accurate enough) Brillouin zone (k-point) integration grid.
In these cases, the SCF will die with some error message (with the cause not
trivially identifiable form the error message) being a combination of the above.
54
bf Exponents: As a practical matter, bfs with exponents smaller than 0.10-0.15 are problematic
and usually not needed. Removing them (i.e., adapting a molecular basis for an efficient
periodic calculation) is not required in our code (our numerics are usually robust enough to
deal with them) but it will surely make your calculations much faster and your life
much easier on thresholds.
Metals: Tread very carefully if your system is metallic. Metal calculations are tricky and costly.
1. Integration in k-point space is arduous. There are several options that can be tried
here if one has convergence problems in the SCF. A radical solution is to start from a
finite temperature calculation at ca. 1000 K and then try to cool off the system some
or converge ILT (or similar) from there.
2. Most PW calculations on metals are done at finite temperature, otherwise convergence
is rather difficult to achieve even with PW codes.
3. Diffuse and polarization functions are generally important for metals. Your cpu time will
go up because to achieve convergence you will need a larger basis than for semiconductors
or insulators and lots of k-points.
Semiconductors and Insulators: If you feel that your calculations are slow, there is plenty of
room of improvement by playing with many of the accuracy thresholds (explained in detail in
Izmaylovs piece). The record for this type improvement may be the InAs case finely-tuned
by Ed Brothers: he was able to achieve a 20x speed-up by tuning thresholds (from default
values) with a minimal loss of accuracy for the band gap (less than 0.01 eV)
Density Fitting Gaussian provides the density fitting approximation for pure DFT calculations.
The desired fitting basis set is specified as a third component of the model chemistry, as in
this example:
#p BLYP/6-31G(d)/Auto
Note that the slashes are required when a density fitting basis set is specified. See the Basis
Sets entry in the Gaussian manual for more information.
CPU Time Monitor your cpu time with flags like #p and IOp1=timestamp, which will increase
cpu time printing and allow you to spot portions that are particularly expensive and amenable
to improvement by fine-tuning thresholds. See Section 3.
55
11.2
Diffuse Functions
Contributed by Dr. Cristian V. Diaconu with comments from Drs. Artur F.
Izmaylov, and Ionut D. Prodan for the October 2009 version of this guide.
NMtPBC is determined for k = 0. Unfortunately, the convergence of the Bloch sums with the
numberof cells depends on k for the Bloch sum form currently used in Gaussian. This is
usually not a problem; however, for diffuse functions, this may become a huge problem. The
number of cells may increase toward k = . While the number of cells is enough at k = 0,
it may not be enough as k = , and Gaussian will die with the error:
Possibly not enough cells included in PBC.
Numerical problems in PBC.
If this happens the only way around it is to increase the number of cells by forcing a larger
range: PBC=(CellRange=N). See the PBC keyword page. -OR- use less-diffuse basis
functions, since the calculations become prohibitively expensive with diffuse functions anyway.
Due to the same problem of the form of the Bloch functions, the norms of the Bloch functions
become exponentially small when the exponents become small (norm ca. exp(k 2 /a). The
norms are also k-dependent, so even if the near linear dependencies are eliminated at k = 0,
the norms of the Bloch functions may still be too small at other values of k. This condition
leads to warnings from subroutine ZFrmV2 of the form:
ZFrmV2: there are 14 very small orbitals for k= 617 kxyz= 7 15 3.
The only solution to this problem is to prune the diffuse basis functions (especially the p-type).
Gaussian removes the culprits, (see Section ?? but when this happens the basis functions are
too diffuse and is usually associated with the previous problem (not enough cells included in
PBC) or Gaussian dies with an error of the following type:
-------------------- ATTENTION-------------------Total charge is not ZERO --- -0.002902253251
-------------------- ATTENTION-------------------There is a problem with the total charge.
There is also a problem with 5d/6d basis sets. See the Basis Sets entry in the Gaussian 09
manual. This problem can be exacerbated for periodic calculations, especially when using
a 5d basis set as a 6done, thus having an extra s-type function that can be nearly linear
dependent with the existing s-type functions. This is true the other way, too: a 6d basis set
may assume to have an extra s-type functions from the d-type shells.
The rule of thumb for diffuse functions: the smallest exponent for s-type functions should be
larger than about min = 2/d2 , where d is the smallest distance between two atoms. The
exponent input in Gaussian is in Bohr 2 , so use d in Bohr.
56
11.3
11.3.1
Description
The PBC keyword allows you to specify options for Periodic Boundary Conditions jobs.
Note: PBC is turned on simply by including translation vectors in the input structure, and this
keyword is used only to control how PBC calculations are performed.
If you do not need any of these options, you do not have to include the keyword PBC to perform
a PBC calculation.
11.3.2
Options
11.3.3
Availability
HF and DFT energy and optimizations. Not valid with SCRF or Charge. For periodic systems of
any reasonable size, acceptable performance may only be feasible by using a pure DFT functional
in combination with density fitting.
57
12
The module system is employed on Scuseria Group workstations as well as on the shared computational resources at Rice: BlueBioU, DaVinci and STIC. (An older machine, SUG@R is also
available, but is is non-ideal for PBC jobs.) A condo of Scuseria-Group-Only nodes exists on each
of the Rice clusters. Normally, it is more efficient to use the guscus condo (see Section 13), but
change the queue name to common, for access to the public nodes.
58
12.1
The following is the procedure for STIC, but the procedure works the same on all Rice computers.
1. Login via ssh
2. Source the .bashrc file containing the Gaussian paths in it: source /projects/guscus/.bashrc
3. cd to shared.scratch, e.g., cd /shared.scratch/sgu1
4. Type module avail to see what modules are available (See Section 12.3.1) for the output.)
-OR5. Type module list to confirm which modules are already loaded. (See Section 12.3.3)
6. Type module load gdv-h11-hiss-and-pbc.2.3 to load the module for PBC calculations
(See Section 12.3.2.)
7. Check to see that the module loaded successfully by typing module list (See Section 12.3.3)
8. Run the script to create the *.pbs file (See Section 13 for the necessary scripts.)
9. Type qsub *.pbs to submit your job
10. Type qstat to see that your job was submitted and is in the queue you want it to be in...
12.2
# THIS STEP 1b
sgu1@stic.rcsg.rice.edus password:
********************************************
-bash-3.2$ source . /projects/guscus/.bashrc
-bash-3.2$ cd /shared.scratch/sgu1
# THIS IS STEP 2
# THIS IS STEP 3
59
12.3
12.3.1
Module Commands
Module Avail
Typing module avail will allow you to see which modules are currently available on the machine
you have logged into, as in the example, below:
[sgu1@login1 sgu1]$ module avail
The gaussian-related codes are listed in the top section, which includes G09, all usable gdv versions
and the Portland Group compilers. The bottom section lists various applications that may be of
use, like matlab.
The g09- series are actual g09 versions, not development versions of the gaussian code.
The gdv- series are developement versions of gaussian.
The most stable for PBC, with the most features and options is gdv-h11-hiss-and-pbc.2.3.
USE THIS unless otherwise instructed.
gdv-h11-sol has PBEsol incorporated in it, but no PBC features like BS, PDOS, AFM,
VMM, SO or Dispersion.
60
12.3.2
Module Load
12.3.3
Module List
To CONFIRM the module was loaded, or LIST modules already loaded, type: module list
[sgu1@login1 sgu1]$ module list
Currently Loaded Modulefiles:
1) pgi-10
2) gdv-h11
3) gdv-h11-hiss-and-pbc.2.3
Notice that at least 3 files are loaded. The module you want
usually has the highest number.
12.3.4
Module Unload
To UNLOAD a module, type module unload ModuleName, confirm with module list
[sgu1@login1 sgu1]$ module unload gdv-h11-hiss-and-pbc.2.3
[sgu1@login1 sgu1]$ module list
No Module Files Currently Loaded
12.3.5
Put it all together: Load/confirm modules, submit job and check the queue as in Section 12.1.
[mjl3@login1 mjl3]$ module load gdv-h11-hiss-and-pbc.2.3
[mjl3@login1 mjl3]$ module list
Currently Loaded Modulefiles:
1) pgi-10
2) gdv-h11
3) gdv-h11-hiss-and-pbc.2.3
LiMoS2-hse11_o
LiMoS2-pbe_o
20
n2-ksghf
PCBInputFile
mjl3
mjl3
ks19
rmi1
sgu1
190:28:0
187:12:3
235:00:3
04:32:08
00:02:08
R
R
R
R
R
guscus
guscus
guscus
guscus
guscus
61
12.4
The availability on the other machines will vary, but will tend to have the same versions of the
more recent codes. Source /projects/guscus/.bashrc and then type module avail to see the
list below...
Table 2: Gaussian Modules Currently Available (as of March 27, 2012) on STIC
Module
G09 Versions
g09-b1
g09-b1-linda
g09-b1-pbc-2.3
g09-b1-pbc-2.3.t
g09-c1
g09-c1-linda
G09 Development
gdv-g1
gdv-h1
gdv-h1-D
gdv-h1-extra-HISS
gdv-h10
gdv-h11
gdv-h11-hiss-and-pbc.2.3
gdv-h11-ib3
gdv-h11-sol
gdv-h12p
gdv-h12p-D
gdv-h13
PGI Compilers
pgi-10
pgi-10.9
pgi-11
Description
Notes
Oldest
Old
Latest
[1] This version will eventually also include PBEsol, Ireks dispersion code, any new Bulik
functionals and any other code that is to be used by many, PBC or not. This will be the version
that will be kept current.
62
12.4.1
Source /projects/guscus/.bashrc and then type module avail to see the list below...
Table 3: Applications Modules Currently Available on STIC (As of March 27, 2012), sorted
according to potential interest to the Scuseria Group.
Module
gaussian/g09-c1-linda
intel/2011.0.13(default)
intel/3.2.1.015
jdk/1.6.0_12
matlab/2008b(default)
matlab/2009b
matlab/2011a
pgi/9.0.4
pgi/10.9
python3/3.2.1
R/2.11.1-gcc
siesta/3.0-rc2
Description
Parallel G09
compiler
compiler
Jasons PQT code
Check w/Irek
Check w/Irek
Check w/Irek
Check w/Irek
Can we use this?
openmpi/1.3.3-gcc
openmpi/1.3.3-intel
openmpi/1.3.3-pgi
openmpi/1.4.4-gcc
openmpi/1.4.4-intel(default)
openmpi/1.4.4-pgi
63
Module
Notes
amber/11
Bio FF code
cilk++/8503
cmake/2.8.5
comsol/3.5a
comsol/4.0a
comsol/4.1
fftw/3.2.2-intel
globus/5.0.4-xsede
gmt/4.5.3
gromacs/4.5.5
Bio visualizer
hdf5/1.8.4p1
hdf5/1.8.8(default)
hpctoolkit/2011-05-16
hypre/2.0.0-intel
lammps/20Aug11
lumerical/6.5.5(default)
lumerical/7.5.1
lumerical/7.5.3
mvapich/1.2rc1-intel
namd/2.7
namd/2.8
netcdf/4.1.1
papi/3.7.0
opencl/2.5rc2
slog2sdk/1.2.6
totalview/8.7.0
totalview/8.9.2
turnin/2.0
turnin/2.1
turnin/3.0(default)
12.5
You need to source /projects/guscus/.bashrc and then type module avail to see the list below.
To run gnuplot and others APPS, type module load Apps
64
13
Scripts
The scripts provided herein are optimized for quick cut-N-paste.
Alternatively, local users may copy them from:
guscus:/projects/guscus/Manuals/scripts
Questions, comments or better implementations are welcome.
Please feel free to contact Melissa Lucero.
65
13.1
13.1.1
#!/bin/bash
set -o errexit
set -o pipefail
# exit on errors
# or failure in a pipe
if [ $# -eq 0 ]; then
cat <<EOF
USAGE:
${0##*/} Input NNodes WallTime_in_days
EOF
exit 1
fi
Inp=$1
# test if we got needed data
if [ -z "$Inp" ]; then
echo "No Input File Specified"
exit 1
fi
if [ -z "$2" ]; then
echo "Wall Time Not Specified"
exit 1
fi
WALLTIME=$(( 24 * $2 )):00:00
InpBase=${Inp%.*}
SubFile=$InpBase.pbs #Prepare submission script
cat <<EOFPBS >$SubFile
#!/bin/bash
#PBS -N $InpBase
#PBS -V
#PBS -m n
#PBS -r n
#PBS -o $InpBase.pbserr
#PBS -j oe
#PBS -l nodes=1:ppn=12,walltime=$WALLTIME
#PBS -l mem=24000mb
#PBS -q guscus
InpBase=$InpBase
TIMEFORMAT="TIMING: %3R %3U %3S"
GAUSS_SCRDIR=/shared.scratch/\$USER/tmp/\$PBS_JOBID
export GAUSS_SCRDIR
\${GAUSS_MEMDEF:=2415919104}
cd \$PBS_O_WORKDIR
exec &>$InpBase.err
set -x
trap "rm -rf \$GAUSS_SCRDIR" EXIT
mkdir -p \$GAUSS_SCRDIR
df -h
uname -a
printenv
time \$GAU <<EOGJF >"\$InpBase.out"
%mem=23500mb
EOFPBS
cat $Inp
>> $SubFile
echo "EOGJF"
>> $SubFile
cat << EOF >> $SubFile
echo \$?
mkpdos -bias-from "\$InpBase.out" -f -v >& mkpdos.log # Required to run PDOS, comment out if no PBC code
EOF
66
13.1.2
#!/bin/bash
set -o errexit
set -o pipefail
# exit on errors
# or failure in a pipe
if [ $# -eq 0 ]; then
cat <<EOF
USAGE:
${0##*/} Input NNodes WallTime_in_days
EOF
exit 1
fi
Inp=$1
NNodes=$3
if [ -z "$Inp" ]; then # test if we got needed data
echo "No Input File Specified"
exit 1
fi
if [ -z "$2" ]; then
echo "Wall Time Not Specified"
exit 1
fi
if [ -z "$NNodes" ]; then
echo "Number Of Nodes Not Specified"
exit 1
fi
WALLTIME=$(( 24 * $2 )):00:00
InpBase=${Inp%.*}
SubFile=$InpBase.pbs #Prepare submission script
cat <<EOFPBS >$SubFile
#!/bin/bash
#PBS -N $InpBase
#PBS -V
#PBS -m n
#PBS -r n
#PBS -o $InpBase.pbserr
#PBS -j oe
#PBS -l nodes=$NNodes:ppn=12,walltime=$WALLTIME
#PBS -l mem=24000mb
#PBS -q guscus
InpBase=$InpBase
TIMEFORMAT="TIMING: %3R %3U %3S"
# Format for bash time builtin
GAUSS_SCRDIR=/shared.scratch/\$USER/tmp/\$PBS_JOBID
export GAUSS_SCRDIR
\${GAUSS_MEMDEF:=2415919104}
cd \$PBS_O_WORKDIR
exec &>$InpBase.err
set -x
trap "rm -rf \$GAUSS_SCRDIR" EXIT
mkdir -p \$GAUSS_SCRDIR
df -h
uname -a
printenv
LINDA_WORKERS=\$(cat \$PBS_NODEFILE |sort -u |tr \n , |sed s/,$//)
time \$GAU <<EOGJF >"\$InpBase.out"
%nprocsh=6
%mem=23500mb
%LindaWorkers=\$LINDA_WORKERS
EOFPBS
cat $Inp
>> $SubFile
echo "EOGJF"
>> $SubFile
cat << EOF >> $SubFile
echo \$?
EOF
67
13.1.3
#!/bin/bash
set -o errexit
set -o pipefail
# exit on errors
# or failure in a pipe
if [ $# -eq 0 ]; then
cat <<EOF
USAGE:
${0##*/} INPut NNODES
EOF
exit 1
fi
INP=$1
NNODES=$2
# test if we got needed data
if [ -z "$INP" ]; then
echo "No Input File Specified"
exit 1
fi
if [ -z "$NNODES" ]; then
echo "Number Of Nodes Not Specified"
exit 1
fi
INPBASE=${INP%.*}
#Prapare submission script
SUBFILE=$INPBASE.pbs
cat <<EOFPBS >$SUBFILE
#!/bin/bash
#PBS -N $INPBASE
#PBS -V
#PBS -m n
#PBS -r n
#PBS -o $INPBASE.pbserr
#PBS -j oe
#PBS -l nodes=$NNODES:ppn=12,pmem=4000mb
#PBS -q parallel
INPBASE=$INPBASE
TIMEFORMAT="TIMING: %3R %3U %3S"
GAUSS_SCRDIR=/scratch/\$USER/tmp/\$PBS_JOBID
export GAUSS_SCRDIR
: \${GAUSS_MEMDEF:=2415919104}
cd \$PBS_O_WORKDIR
exec &>$INPBASE.err
set -x
trap "rm -rf \$GAUSS_SCRDIR" EXIT
mkdir -p \$GAUSS_SCRDIR
df -h
uname -a
printenv
LINDA_WORKERS=\$(cat \$PBS_NODEFILE |sort -u |tr \n , |sed s/,$//)
time \$GAU <<EOGJF >"\$INPBASE.out"
%nprocsh=12
%mem=42GB
%LindaWorkers=\$LINDA_WORKERS
EOFPBS
cat $INP
>> $SUBFILE
echo "EOGJF"
>> $SUBFILE
cat << EOF >> $SUBFILE
echo \$?
EOF
68
13.1.4
#!/bin/bash
set -o errexit
set -o pipefail
# exit on errors
# or failure in a pipe
df -h
uname -a
printenv
time \$GAU <<EOGJF >"\$InpBase.out"
%mem=23500mb
EOFPBS
cat $Inp
>> $SubFile
echo "EOGJF"
>> $SubFile
cat << EOF >> $SubFile
echo \$?
mkpdos -bias-from "\$InpBase.out" -F -v >& mkpdos.log
EOF
69
13.2
reset
set term postscript portrait enhanced dashed lw 2.0 color Times-Roman 20
# DEFINE INPUT AND OUTPUT
set output output.ps # name of output file
data = pdos.dat
# dat file
# DEFINE PLOT RANGES
set lmargin 5.5
set rmargin 0.5
set yrange [-10.0:10.0] # THESE WILL CHANGE BASED ON YOUR SYSTEM
set xrange [-0.03:2.5] # LEAVES A LITTLE SPACE TO SEE IF BASIS SET IS OKAY
set ylabel Energy (eV) offset 1.3,0
set xlabel PDOS (states/eV/unit cell)
set ytics 2.0 # THIS IS BASED ON A SMALL UNIT CELL, ADJUST AS NECESSARY
set xtics 0.5
# ARROWS
# The gray baseline along the y-axis
set arrow 1 from 0, graph 0 to 0, graph 1 nohead lc rgb dark-gray
lw 1.0
# PLOT THE DATA -- FIRST LINE IS DASHED BLACK LINE FOR FERMI LEVEL
plot 0 w l lt 2 lw 2.0 lc rgb black not,\
data using 2:1 w l ls 2 t Q_{/Helvetica-oblique s},\
data using 3:1 w l ls 3 t Q_{/Helvetica-oblique p},\
data using 4:1 w l ls 4 t Q_{/Helvetica-oblique d},\
data using 5:1 w l ls 1 t Total
70
13.3
reset
set term postscript eps enhanced dashed dl 2.0 color Times-Roman 20
# INPUT AND OUTPUT
set output pdos.eps # name of output file
data = pdos.dat # dat file
# PLOT RANGES
set lmargin 5.5
set xrange [-10.0:10.0]
set yrange [-0.1:2.5] # Allows view of baseline
set xlabel Energy (eV)
set ylabel PDOS (states/eV/unit cell) offset 1.3,0
set xtics 2.0
set ytics 0.5
# ARROWS and LABELS
set arrow 1 from 0, graph 0 to 0, graph 1 nohead lc rgb dark-gray lw 1.0
set label 1 Fermi level at 0, graph 1 right rotate offset character 1, character -1 tc rgb navy
set label 2 at -9,2.3 {/Helvetica=20 Si (dia) } tc rgb dark-red
set label 3 at -9,2.1 {/Helvetica=16 HSE OPT} tc rgb navy
set label 4 at -9,1.9 {/Helvetica-Italic=16 E_{g} = }{/Helvetica=16 1.22 eV (I)} tc rgb navy
set label 5 at -9,1.7 {/Helvetica=16 Expt. = 1.17 eV (I)} tc rgb red
set key at 9.7,2.45 right
71
2.5
Si (dia)
2
Sis
Sip
Sid
Total
Fermi level
HSE OPT
Eg = 1.22 eV (I)
Expt. = 1.17 eV (I)
1.5
0.5
0
-10
-8
-6
-4
-2
0
2
Energy (eV)
10
13.4
=
=
=
=
=
=
=
=
=
10.371738
10
10.371738
11
12.420518
10.371738
3.058369
8.405779
2.048780
E(y) = y - E0
set
set
set
set
set
set
set
set
set
set
arrow
arrow
arrow
arrow
arrow
arrow
arrow
arrow
arrow
arrow
set arrow 11 \
from graph 0, first E(HOCO) to
set arrow 12 \
from graph 0, first E(LUCO) to
\
data
data
data
data
data
data
data
data
data
data
data
data
data
data
data
data
data
data
using
using
using
using
using
using
using
using
using
using
using
using
using
using
using
using
using
using
72
13.5
reset
set terminal postscript eps enhanced color dl 2 "Helvetica,18"
set output AlSb-hiss2.eps
data = AlSb-hiss.dat
set rmargin 4
unset key
set ylabel "Energy (eV)" offset 1.5,0
x1_GM = 0.000000
x2_X = 0.862114
x3_W = 1.293143
x4_K = 1.597934
x5_GM = 2.512322
x6_L = 3.258914
x7_U = 3.786839
x8_W = 4.091633
x9_K = 4.396424
x10_X = 4.701213
set xtics ( "{/Symbol G}" x1_GM, "X" x2_X, "W" x3_W, "K" x4_K, "{/Symbol G}" x5_GM, "L" x6_L, "U" x7_U, "W" x8_W, "K | U" x9_K, "X" x10_X )
E0
cHOCO
HOCO
cLUCO
LUCO
EF
mGap
MGap
iGap
UCO2
=
=
=
=
=
=
=
=
=
=
10.371738
10
10.371738
11
12.420518
10.371738
3.058369
8.405779
2.048780
12.700369
E(y) = y - E0
# LINE STYLES
set style
set style
set style
set style
set style
set
set
set
set
set
set
set
set
set
set
arrow
arrow
arrow
arrow
arrow
arrow
arrow
arrow
arrow
arrow
line
line
line
line
line
1
2
3
4
5
lt
lt
lt
lt
lt
4
1
1
1
1
lw
lw
lw
lw
lw
0.7
1.0
2.5
2.5
2.5
lc
lc
lc
lc
lc
rgbcolor
rgbcolor
rgbcolor
rgbcolor
rgbcolor
dark-turquoise
black
black
red
blue
# I-Bars and
set arrow
set arrow
set arrow
# Labels
set label
set label
set label
Transition Arrows
11 from 0.735264,0 to 0.735264,E(LUCO) size 0.2,90 heads lw 2.5 lc rgb green front
13 from x5_GM,0 to 0.735264,E(LUCO) heads lw 1.5 front
15 from x6_L,0 to 3.258914,E(UCO2) size 0.2,90 heads lw 2.5 lc rgb magenta front
1 {/Helvetica-Oblique=28 E_{F}} at 4.7,0.00 tc rgbcolor dark-red
2 {2.05 eV (I)} at 0.9,0.6
3 {2.33 eV (I)} at 3.3, 0.8
-1 not,\
2 lc rgbcolor "orange" not, \
1:(E($19)) t "27" with l ls 5, \
1:(E($18)) t "26" with l ls 5, \
1:(E($17)) t "25" with l ls 5, \
1:(E($16)) t "24" with l ls 5, \
1:(E($15)) t "23" with l ls 5, \
1:(E($14)) t "22" with l ls 5, \
1:(E($13)) t "21" with l ls 5, \
1:(E($12)) t "20" with l ls 5, \
1:(E($11)) t "19" with l ls 5, \
1:(E($10)) t "18-occ" with l ls 4, \
1:(E($9)) t "17-occ" with l ls 4, \
1:(E($8)) t "16-occ" with l ls 4, \
1:(E($7)) t "15-occ" with l ls 4, \
1:(E($6)) t "14-occ" with l ls 4, \
1:(E($5)) t "13-occ" with l ls 4, \
1:(E($4)) t "12-occ" with l ls 4, \
1:(E($3)) t "11-occ" with l ls 4, \
1:(E($2)) t "10-occ" with l ls 4
73
13.6
13.6.1
# TERMINAL SET-UP
reset
set encoding iso_8859_1
set terminal postscript eps enhanced lw 2 color
# SET INPUT AND OUTPUT FILE NAMES
set output both.eps
data = band.dat
# SET MARGINS, AXES and DECORATIONS
set lmargin 5.5
set rmargin 0
set xlabel "K-Path"
set ylabel "Energy (eV)" offset 1.3,0
unset key
unset colorbox
# SET MULTIPLOT
# --> 1 ROW, 2 COLUMNS, NO TITLE
set multiplot layout 1,2
74
"Times-Roman,16"
13.6.2
# LINE STYLES & EXTRA COLORS FOR LABELING VARIOUS BANDS WHEN NECESSARY
# ----->
Note, there are more in the actual gpt file on guscus...
set
set
set
set
set
set
set
set
set
set
set
set
set
set
set
style
style
style
style
style
style
style
style
style
style
style
style
style
style
style
line
line
line
line
line
line
line
line
line
line
line
line
line
line
line
75
13.6.3
# SET VERTICAL
set arrow 1
set arrow 2
set arrow 3
set arrow 4
# LOWEST
VBMx
VBMy
CBMx
CBMy
1 nohead ls 1
nohead ls 1
nohead ls 1
1 nohead ls 1
76
13.6.4
77
13.6.5
78
79
14
14.1
PBC Functionals
Scuseria Functionals
Table 5: Functionals developed in the Scuseria Group sorted according to type. Note that
availability is variable. SR=Short -range, MR=Middle-range, and LR=Long-range.
Keyword and/or IOp
Acronym(s)
Global Hybrids
TPSSh
TPSSh
SR Screened Hybrids
HSEh1HSE
HSE1PBE
HSE2PBE
MR Screened Hybrids
3/74=-61
3/74=-56
3/74=-62
3/74=-57
LR Screened Hybrids
LC-wPBE
Citation(s)
[5, 6]
HSE, HSE06H
HSE, HSE06
HSE03
[7, 8, 9]
[8, 9]
[10]
HISS, HISSb
[11]
HISS, HISSb
HISS-a
HISS-a
[11]
[12]
[12]
Use this!
G09-B, gdv-h11 (PBC)
Use this gdv-h1 (PBC)
Dont use; gdv-h11 (PBC)
Dont use; gdv-h1 (PBC)
LC-PBE
[13]
Semilocal
PBEPBE + 3/74=5050 PBEsol
TPSSTPSS
TPSS
14.2
Availability/Notes
[14, 15]
[16]
Just-For-Solids Functionals
Table 6: Functionals developed explicitly for solids, discussed and compared in the literature,
but not necessarily implemented widely. (Not an exhaustive list.)
Keyword and/or IOp
Acronym(s)
Citation(s)
Availability/Notes
PBEPBE + 3/74=5050
AMO5
HSEsol
HTBS
MBJLDA
PBEsol
[17]
[18]
[19]
[20]
[14, 15]
Not available
Not available
Not available
Not available
gdv-h11-sol; no PBC, yet...
80
14.3
(Semi)Local Functionals
Table 7: Functionals commonly encountered by the solid state theoretician that are known
not to work well, but continue to be used, anyway. Arranged roughly according to the rungs
of the functional Jacobs Ladder.[21]
Keyword and/or IOp
Acronym(s)
Citation(s)
SVWN5
LSDA
[22]
LSDA
M06L
PBEPBE
PW91
PW92
TPSSTPSS
revTPSS
WC
LSDA, LDA
M06L
PBE
PW91
PW92
TPSS
revTPSS
WC
[23]
[24]
[25, 26]
[27]
[28]
[16]
[29, 30, 31]
[32]
14.4
Availability/Notes
Global Hybrids
Table 8: Global hybrid functionals that have been applied to the extended systems. Note:
expect to expend extensive amounts of CPU time.
Keyword and/or IOp
Acronym(s)
Citation(s)
Availability/Notes
B3LYP
PBEh1PBE
M06
M06HF
M062X
TPSSh
B3LYP
PBEh,PBE0
M06
M06HF
M062X
TPSSh
[33]
[34, 35]
[36]
[37]
[38]
[5, 6]
14.5
Functional Bibliography
For LaTex users, a BibTex file, functionals.bib file with all of the citations used here and more is
provided at guscus:/projects/guscus/Manuals/functionals.bib.
81
15
The format for PBC basis sets is the same as that for molecular basis sets. See the G09 Basis Set
and Gen/GenECP pages for more details. Generally, the basis sets will be called externally via
Gen/GenECP(or Pseudo=Read) or by specifying the path to the basis set preceded by an @
and terminated with a /N to prevent writing to the output file. (As in Section 3) The anatomy of
a G09 basis set file is as follows:
Type/Constraint
1
2
3
...
n
nGauss
d1
d2
d3
dn
ScaleFactor
#
#
#
#
#
1. The shell descriptor line contains: the shell type, the number of primitive gaussians, and the scale factor.
The type/constraint specification is for shells: S, P, D, DP, SPD, F, G... for
s-, p-, d, dp... shells, respectively.
NGauss specifies the number of primitive gaussian shells (the degree of contraction) for the shell being defined.
Scale Factor (#) refers to the shell scale factor, e.g. if #=2, all primitive
exponents are scaled by 2.
2. The remaining lines are primitive gaussian specifications
There are nGauss of them
Each line defines the exponents k and dk contraction coefficients.
Comments are made using an exclamation point
15.1
0.00180093
0.0137419
0.0681334
0.2333250
0.5890860
0.2995050
0.1145360
0.9205120
-0.00337804
0.0354609
0.2374510
0.8204580
1.0000000
1.0000000
1.0000000
1.0000000
82
15.2
Before running a PBC job, it is important to ensure that the chosen MOLECULAR basis set i.e., a
basis set developed for atoms/molecules is reasonable for extended systems. (Basis sets are generally
downloaded from the EMSL or a similar ES database see Section 15.2.1.)
WHY?
Molecular basis sets typically contain one or more few diffuse basis functions (bfs) in order
to properly describe atomic tails.
A periodic system in 3-D does not need these tails, which will slow down your jobs.
(They slow the Coulomb near field of the fast multipole method.)[39]
There are are some tails in lower dimensions, but these calculations are not as sensitive.
See also Sections 11.1 and 11.2 and References [40, 41, 42] for additional, more detailed
discussion.
The Gaussian Basis Set FAQ prepared by Mike Towler provides a nice
introduction to the use of gaussian basis sets in PBC calculations.
A copy is also kept at: gusucs:/projects/guscus/Manuals/Towler.pdf
CAUTION:
A basis set properly optimized for previous PBC calculations may not
work as well when applied to a different system.
83
15.2.1
Sites from which gaussian-type basis sets may be downloaded prior to modification include:
EMSL https://bse.pnl.gov/bse/portal
Mike Towlers Page http://www.tcm.phy.cam.ac.uk/ mdt26/crystal.html
Crystal Periodic Table http://www.crystal.unito.it/Basis_Sets/Ptable.html
15.2.2
This example contains the basis sets for -SiC (zincblende polytype) used in References [12, 11,
43] and many other papers. As is clear from the arrows, Si p shell exponents are edited as in
Reference [44], but nothing is modified in the C basis set.
MODIFIED Si and C m-6-311G* basis sets
****
S 0
S
6
1.00
69379.2300
10354.9400
2333.87960
657.142950
214.301130
77.6291680
S
3 1.00
77.6291680
30.6308070
12.8012950
S
1 1.00
3.92686600
S
1 1.00
1.45234300
S
1 1.00
0.256234000
S
1 1.00
0.120000000
P
4 1.00
335.483190
78.9003660
24.9881500
9.21971100
P
2 1.00
3.62114000
1.45131000
P
1 1.00
0.504977000
P
1 1.00
0.250000000
P
1 1.00
0.120000000
D
1 1.00
0.450000000
****
C
0
S
6 1.00
4563.24000
682.024000
154.973000
44.4553000
13.0290000
1.82773000
SP 3 1.00
20.9642000
4.80331000
1.45933000
SP 1 1.00
0.483456000
SP 1 1.00
0.145585000
D
1 1.00
0.626000000
****
0.0007570
0.0059320
0.0310880
0.1249670
0.3868970
0.5548880
0.1778810
0.6277650
0.2476230
1.0000000
1.0000000
1.0000000
1.0000000
0.0088660
0.0682990
0.2909580
0.7321170
0.6198790
0.4391480
1.0000000
1.0000000
1.0000000
1.0000000
0.00196665
0.0152306
0.0761269
0.2608010
0.6164620
0.2210060
0.1146600
0.9199990
-0.00303068
0.0402487
0.2375940
0.8158540
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
84
0.757000000E-03
0.593200000E-02
0.310880000E-01
0.124967000
0.386897000
0.554888000
0.177881000
0.627765000
0.247623000
1.00000000
1.00000000
1.00000000
1.00000000
0.886600000E-02
0.682990000E-01
0.290958000
0.732117000
0.619879000
0.439148000
1.00000000
1.00000000
1.00000000
1.00000000
0.196665000E-02
0.152306000E-01
0.761269000E-01
0.260801000
0.616462000
0.221006000
0.114660000
0.919999000
-0.303068000E-02
0.402487000E-01
0.237594000
0.815854000
1.00000000
1.00000000
1.00000000
1.00000000
1.00000000
15.2.3
Note the modifications marked in the original As basis set (right) downloaded from the EMSL. The
basis set modification for gaussian PBC calculations (left) is discussed in Reference [44] and is
acompanied by the appropriate ECP at the bottom.
MODIFIED As m-pVDZ-PP basis set
As
S
As
S
0.0011370
0.0060550
0.0841250
-0.4052850
0.7129260
0.4733760
0.0180130
<-------- deleted
-0.0037200
<-------- deleted
Goes from 8 to 6 bc of deletions
-0.0003900
-0.0021900
-0.0268530
0.1368780
-0.3204570
-0.3373910
0.6763840
<-------- deleted
0.5349800
<-------- deleted
1.0000000
1.0000000
<--------
set to 0.12
1.0000000
<-------- deleted
Goes from 7 to 6 bc of deletion
0.0038570
-0.0851010
0.4047620
0.5314780
0.1840120
0.0057640
-0.0003520
<-------- deleted
Goes from 7 to 6 bc of deletion
-0.0007720
0.0199410
-0.1072100
-0.1722590
0.0087610
0.5697440
0.5356530
<-------- deleted
1.0000000
<--------
set to 0.12
1.0000000
Goes from 7 to 6 bc of deletion
0.0119800
0.0795440
0.2367550
0.4015340
0.4066860
0.1731620
0.0087300
<-------- deleted
1.00
2542.81000
381.169000
40.2342000
16.1217000
3.20189000
1.42096000
S
6 1.00
2542.81000
381.169000
40.2342000
16.1217000
3.20189000
1.42096000
S
1 1.00
0.321443000
S
1 1.00
0.120000000
P
6 1.00
99.5349000
24.1195000
5.84196000
2.56010000
1.09308000
0.318424000
P
6 1.00
99.5349000
24.1195000
5.84196000
2.56010000
1.09308000
0.318424000
P
1 1.00
0.120000000
D
6 1.00
113.509000
36.8872000
13.6893000
5.38964000
2.08046000
0.737568000
D
1 1.00
0.307800000
****
AS 0
AS-ECP
4
10
G POTENTIAL
1
2
1.00000000
S-G POTENTIAL
2
2
28.72512200
2
6.76768100
P-G POTENTIAL
4
2
45.33106400
2
44.76741500
2
19.53909000
2
18.97347100
D-G POTENTIAL
6
2
51.05715200
2
50.15134000
2
16.10893600
2
14.67222300
2
3.85192700
2
3.81350200
F-G POTENTIAL
2
2
11.94058400
2
17.76116000
1.0000000
1.0000000
0
6
<-------- deleted
85
0.113700000E-02
0.605500000E-02
0.841250000E-01
-0.405285000
0.712926000
0.473376000
-0.390000000E-03
-0.219000000E-02
-0.268530000E-01
0.136878000
-0.320457000
-0.337391000
1.00000000
1.00000000
0.385700000E-02
-0.851010000E-01
0.404762000
0.531478000
0.184012000
0.576400000E-02
-0.772000000E-03
0.199410000E-01
-0.107210000
-0.172259000
0.876100000E-02
0.569744000
1.00000000
0.119800000E-01
0.795440000E-01
0.236755000
0.401534000
0.406686000
0.173162000
1.00000000
0.00000000
370.11402500
9.34929600
99.14210300
198.30788000
28.38307300
56.87146400
-18.48514500
-28.11353000
-1.22389500
-1.34576500
0.10175700
0.17033800
-0.77523000
-2.15725900
15.2.4
On the left is the original 6-311++G(3df) basis set for chlorine: all exponents with values of
0.15 have been marked with arrows. (Note that in Section 15.2.3, 0.12 is the minimum.) In the
column to the right, the values of the 2 marked exponents have been changed to 0.15.
1st MODIFICATION Cl 6-311++G(3df ) basis set
Cl
0
S
6
1.00
0.0007380
105819.0000000
0.0057180
15872.0000000
0.0294950
3619.6500000
0.1172860
1030.8000000
0.3629490
339.9080000
0.5841490
124.5380000
S
3
1.00
0.1341770
124.5380000
0.6242500
49.5135000
0.2917560
20.8056000
S
1
1.00
1.0000000
6.5834600
S
1
1.00
1.0000000
2.5646800
S
1
1.00
1.0000000
0.5597630
S
1
1.00
1.0000000
0.1832730
P
5
1.00
0.0023910
589.7760000
0.0185040
139.8490000
0.0813770
45.1413000
0.2215520
16.8733000
0.7725690
6.7411000
P
2
1.00
-1.5722440
6.7411000
0.9923890
2.7715200
P
1
1.00
1.0000000
1.0238700
P
1
1.00
1.0000000
0.3813680
P
1
1.00
1.0000000 <--------------------------------------->
0.1500000
SP
1
1.00
1.0000000
1.0000000
<---------------------->
0.1500000
D
1
1.00
1.0000000
3.0000000
D
1
1.00
1.0000000
0.7500000
D
1
1.00
1.0000000
0.1875000
F
1
1.00
1.0000000
0.7000000
****
86
0.0007380
0.0057180
0.0294950
0.1172860
0.3629490
0.5841490
0.1341770
0.6242500
0.2917560
1.0000000
1.0000000
1.0000000
1.0000000
0.0023910
0.0185040
0.0813770
0.2215520
0.7725690
-1.5722440
0.9923890
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
0.0007380
0.0057180
0.0294950
0.1172860
0.3629490
0.5841490
0.1341770
0.6242500
0.2917560
1.0000000
1.0000000
1.0000000
1.0000000
0.0023910
0.0185040
0.0813770
0.2215520
0.7725690
-1.5722440
0.9923890
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
Cl
0
S
6
1.00
105819.0000000
15872.0000000
3619.6500000
1030.8000000
339.9080000
124.5380000
S
3
1.00
124.5380000
49.5135000
20.8056000
S
1
1.00
6.5834600
S
1
1.00
2.5646800
S
1
1.00
0.5597630
S
1
1.00
<------------------ Sim3 --------------------->
0.1832730
P
5
1.00
589.7760000
139.8490000
45.1413000
16.8733000
6.7411000
P
2
1.00
6.7411000
2.7715200
P
1
1.00
1.0238700
P
1
1.00
0.3813680
P
1
1.00
<----------------- Sim1 ---------------------->
0.1500000
<----------------- Sim2 ---------------->
# SP
1
1.00
1.0000000
<------ Sim2 ------>
#
0.1500000
D
1
1.00
3.0000000
D
1
1.00
0.7500000
D
1
1.00
0.1875000
F
1
1.00
0.7000000
****
0.0007380
0.0057180
0.0294950
0.1172860
0.3629490
0.5841490
0.1341770
0.6242500
0.2917560
1.0000000
1.0000000
1.0000000
1.0000000
0.0023910
0.0185040
0.0813770
0.2215520
0.7725690
-1.5722440
0.9923890
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
1.0000000
87
15.3
The EMSL site is very easy to use. The key features of the homepage are shown below.
1. Use the periodic table (red arrow) to select
one (or more) elements.
2. The program window (green arrow) allows
selction of the appropriate format for common ES codes.
3. The basis set window (blue arrow)for choosing the basis set.
4. Information about the basis set (purple arrow).
15.3.1
Example: Ge
The process for acquiring the Ge 6-311G* basis set for use in gaussian is illustrated in Figure 18.
Specifically:
1. Ensure Gaussian94 is the ES code format selected (red oval).
2. Click Ge (green oval).
3. Select 6-311G* in the basis set window (blue oval).
Notice that information about the basis set chosen appears in the bottom section (purple rectangle).
Figure 18: The process for acquiring the Ge 6-311G* basis set in gaussian format.
88
15.4
After downloading gaussian basis sets from Mike Towlers or the Crystal web sites, they must be
converted into the gaussian format. Notice the differences in format, below, for Scandium.
ORIGINAL Crystal09 (cry) Basis Set
Sc_864-11G*_harrison_2006
! Sc_864-11G*_harrison_2006
! N. M. Harrison, B. Montanari, Ling Ge, 2006, unpublished.
! It is being used for Sc@C82 and Sc@C82@SWNT
! (single-wall carbon nanotube).
Sc
0
S
8
1.0
208000.0000000000
2.2500000000E-04
29700.0000000000
1.9270000000E-03
6280.0000000000
1.1094000000E-02
1642.0000000000
4.9970000000E-02
494.6400000000
1.7014000000E-01
170.6200000000
3.6880000000E-01
66.6200000000
4.0290000000E-01
27.7200000000
1.4490000000E-01
SP
6
1.0
499.4000000000
-5.5800000000E-03 8.5100000000E-03
118.5300000000
-7.3800000000E-02 6.0210000000E-02
39.0100000000
-1.1600000000E-01 2.1290000000E-01
15.2000000000
2.4930000000E-01 3.8470000000E-01
6.5110000000
6.9850000000E-01 4.0280000000E-01
1.9980000000
3.2300000000E-01 1.8300000000E-01
SP
4
1.0
25.0900000000
1.6000000000E-03 -3.3100000000E-02
9.6200000000
-1.3600000000E-01 -7.1300000000E-02
3.9790000000
-7.0590000000E-01 1.4650000000E-01
1.6120000000
1.0180000000
1.4520000000
SP
1
1.0
0.7800000000
1.0
1.0
SP
1
1.0
0.3900000000
1.0
1.0
D
3
1.0
3.9400000000
1.6000000000E-01
1.0720000000
3.1300000000E-01
0.3940000000
4.0600000000E-01
****
21 6
0 0 8 2. 1.
208000.
29700.
6280.0
1642.0
494.64
170.62
66.62
27.72
0 1 6 8. 1.
499.4
118.53
39.01
15.20
6.511
1.998
0 1 4 8. 1.
25.09
9.62
3.979
1.612
0 1 1 2. 1.
0.780
0 1 1 0. 1.
0.390
0 3 3 1. 1.
3.940
1.072
0.394
0.000225
0.001927
0.011094
0.04997
0.17014
0.3688
0.4029
0.1449
-0.00558
-0.0738
-0.1160
0.2493
0.6985
0.323
0.0016
-0.1360
-0.7059
1.018
0.00851
0.06021
0.2129
0.3847
0.4028
0.183
-0.0331
-0.0713
0.1465
1.452
1.
1.
1.
1.
0.160
0.313
0.406
The Sc_864-11G*_harrison_2006 Crystal basis set *.cry on the left was converted to a gaussianformatted *.gbs file using the gbsutil script written by Cris Diaconu.
To use this script:
1. Move all of the information at the bottom of the *.cry file to the TOP
2. Comment out all non-basis set data using exclamation points:
The basis set description line (already at the top).
All references and notes information moved from the bottom in Step 1.
3. Remove ALL extra spaces at the top or bottom, either by deletion or !
4. Run the script:
[sgu1@login2]$ ./gbsutil Sc-864-11G*.cry Sc-864-11G*.gbs
Download the original Sc.cry file at the link above, or copy it locally, along
with the Sc.gbs file from: guscus:/projects/guscus/Manuals/examples/.
The gbsutil script is too long to include in Section 13, so a copy is available
at guscus:/projects/guscus/Manuals/scripts/gbsutil.
89
16
Given that the state-of-the-art filesystems can crash and there are monthly purges of /shared.scratch/
on all Rice clusters (See Section 12) it is a good idea to back up all data you might want. Especially
since PBC jobs tend to run long, the gjf , out, chk and all BS and PDOS dat files may be of import
later. The easiest and fasted way to accomplish routine backups is via the rsync command: rsync
-aHVhu, where
a - archive, archive mode; same as rlptgoD (no -H)
H - hard links, preserve hard links
V - verbose, increase verbosity
h - human readable, output numbers in a human readable format
16.1
(1) Assume user sgu1 has directories for each of the clusters on guscus, e.g.:
[sgu1@guscus ~]$ ls
Bluebiou
Davinci
STIC
Sugar
(2) Alternatively, an exclude file may be used. This is useful to prevent backing up all *err files,
pdos.d directories, large chk files for unfinished jobs and anything else not needing to be saved.
[sgu1@guscus ~]$ vi xclude
tmp/
*.chk
*err
fort*
mkpdos.log
pdos.d/
zpratl*
90
Notice that none of the files or directories specified in the xclud file on the previous page are downloaded, while non-gaussian-generated files including text (README, deleteme, etc.), image
(eps, png), Gnuplot (gpt), and BS/PDOS dat files are all copied recursively.
rsync cmds as aliases are very convenient, e.g., in the .bashrc file:
alias stics=rsync -aHvhu
-
-exclude-from /users/sgu1/xclud sgu1@stic:/shared.scratch/sgu1/ ./
91
References
[1] J. K. Ellis, M. J. Lucero, and G. E. Scuseria, 99, 26190 (2011).
[2] E. N. Economou, The Physics of Semiconductors Essentials and Beyond, Springer, Berlin,
2010.
[3] H. Matthieu, D. Auvergne, P. Merle, and K. C. Rustagi, Phys. Rev. B 12, 5846 (1975).
[4] A. Joullie, B. Girault, A. M. Joullie, and A. Zien-Eddine, Phys. Rev. B 25, 7830
(1982).
[5] J. M. Tao, J. P. Perdew, V. N. Staroverov, and G. E. Scuseria, Phys. Rev. Lett. 91,
146401 (2003).
[6] V. N. Staroverov, G. E. Scuseria, J. Tao, and J. P. Perdew, J. Chem. Phys. 119,
12129 (2003).
[7] T. M. Henderson, A. F. Izmaylov, G. Scalmani, and G. E. Scuseria, J. Chem. Phys.
131, 044108 (2009), Specifically, the HSEh parameterization of HSE06[8, 9], called by the
gaussian keyword HSEh1PBE.
[8] J. Heyd, G. E. Scuseria, and M. Ernzerhof, J. Chem. Phys. 124, 219906 (2006).
[9] J. Heyd, G. E. Scuseria, and M. Ernzerhof, J. Chem. Phys. 124, 219906 (2006).
[10] J. Heyd, G. E. Scuseria, and M. Ernzerhof, J. Chem. Phys. 118, 8207 (2003).
[11] T. M. Henderson, A. F. Izmaylov, G. E. Scuseria, and A. Savin, J. Theor. Comput.
Chem. 4, 1254 (2008).
[12] T. M. Henderson, A. F. Izmaylov, G. E. Scuseria, and A. Savin, J. Chem. Phys. 127,
221103 (2007).
[13] O. A. Vydrov and G. E. Scuseria, J. Chem. Phys. 125, 234109 (2006).
[14] J. P. Perdew, A. Ruzsinszky, G. I. Csonka, O. A. Vydrov, G. E. Scuseria, L. A.
Constantin, X. Zhou, and K. Burke, Phys. Rev. Lett. 100, 136406 (2008), See also the
2009 Erratum in Reference[15].
[15] J. P. Perdew, A. Ruzsinszky, M. Ernzerhof, G. I. Csonka, O. A. Vydrov, G. E.
Scuseria, L. A. Constantin, X. Zhou, and K. Burke, Phys. Rev. Lett. 102, 039902
(2009).
[16] J. Tao, J. P. Perdew, V. N. Staroverov, and G. E. Scuseria, Phys. Rev. Lett. 91,
146401 (2003).
[17] R. Armiento and A. E. Mattsson, Phys. Rev. B 72, 085108 (2005).
[18] L. Schimk, J. Harl, and G. Kresse, Phys. Rev. B 72, 085108 (2005).
[19] P. Haas, F. Tran, P. Blaha, and K. Schwarz, Phys. Rev. B 83, 205117 (2011).
92
REFERENCES
[20] F. Tran and P. Blaha, Phys. Rev. Lett. 102, 226401 (2009).
[21] J. P. Perdew and K. Schmidt, in Density Functional Theory and Its Applications to Materials, edited by V. V. et al., American Institute of Physics, New York, 2001.
[22] S. H. Vosko, L. Wilk, and M. Nusair, Can. J. Phys 58, 1200 (1980).
[23] J. P. Perdew and Y. Wang, Phys. Rev. B 45, 13244 (1992).
[24] Y. Zhao and D. G. Truhlar, J. Chem. Phys. 125, 194101 (2006).
[25] J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996), E78, 1396
(1997), Ref. [?].
[26] J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 78, 1396 (1997).
[27] J. P. Perdew, in Electronic Structure of Solids 91, edited by P. Ziesche and H. Eschrig,
p. 11, Akademie Verlag, Berlin, 1991.
[28] J. P. Perdew and Y. Wang, Phys. Rev. B 45, 13244 (1992).
[29] J. P. Perdew, A. Ruzsinszky, G. I. Csonka, L. A. Constantin, and J. Sun, Phys. Rev.
Lett. 103, 026403 (2009), See also the Erratum[30], Phys. Rev. Lett., 106, 179902 (2011).
[30] J. P. Perdew, A. Ruzsinszky, G. I. Csonka, L. A. Constantin, and J. Sun, Phys. Rev.
Lett. 106, 179902 (2011).
[31] J. Sun, M. Marsman, G. I. Csonka, A. Ruzsinszky, P. Hao, Y.-S. Kim, G. Kresse,
and J. P. Perdew, Phys. Rev. B 84, 035117 (2011).
[32] Z. Wu and R. E. Cohen, Phys. Rev. B 73, 235116 (2006).
[33] P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch, J. Phys. Chem. ,
11623 (1994).
[34] M. Ernzerhof and G. E. Scuseria, J. Chem. Phys. 110, 5029 (1999).
[35] C. Adamo and V. Barone, J. Chem. Phys. 110, 6158 (1999).
[36] Y. Zhao, N. E. Schultz, and D. G. Truhlar, J. Chem. Phys. 123, 19410 (2005).
[37] Y. Zhao and D. G. Truhlar, J. Phys. Chem. A 110, 13126 (2006).
[38] Y. Zhao and D. G. Truhlar, Theor. Chem. Acc. 120, 215 (2008).
[39] M. C. Strain, G. E. Scuseria, and M. J. Frisch, Science 271, 51 (1996).
[40] T. M. Henderson, J. Paier, and G. E. Scuseria, Physica Status Solidi B 248, 767 (2011).
[41] B. G. Janesko, T. M. Henderson, and G. E. Scuseria, Phys. Chem. Chem. Phys. 11,
443 (2009).
[42] J. Paier, C. V. Diaconu, G. E. Scuseria, M. Guidon, J. VandeVondele, and J. Hutter, Phys. Rev. B 80, 174114 (2009).
93
REFERENCES
94