Embedded Files
Example of input for IR, TS,...
Example of input for IR, TS,...
If you prefer to use the standard/default settings, you can use:
Example input MIL53_Cr with NO2
CRYSTAL
0 0 0
26
17.8802 11.4337 6.9031 90 90 90
24
13 0.00000 1.00000 1.16408
13 0.50000 0.50000 0.66408
8 0.57997 0.60872 1.25083
6 0.71576 0.72242 1.23941
1 0.68793 0.69960 1.10562
8 0.07997 1.10872 0.75083
6 0.21576 1.22242 0.73941
1 0.18793 1.19960 0.60562
8 0.42003 0.60872 0.57733
6 0.28424 0.72242 0.58875
1 0.31207 0.69960 0.72254
8 0.92003 1.10872 1.07733
6 0.78424 1.22242 1.08875
7 0.81207 1.19960 1.22254
6 0.68130 0.69488 0.41408
6 0.60835 0.63299 0.41408
6 0.18130 1.19488 0.91408
6 0.10835 1.13299 0.91408
8 -0.87258 1.78175 -0.25907
8 -0.78014 1.84248 -0.15848
8 0.00000 1.07983 0.41408
1 0.00000 1.16381 0.41408
8 0.50000 0.57983 0.91408
1 0.50000 0.66381 0.91408
FREQCALC
PREOPTGEOM
FULLOPTG
ENDOPT
INTENS
INTRAMAN
INTCPHF
ENDCPHF
RAMEXP
295 532 #K nm_laser
ENDFREQ
ENDG
#BASISSETSECTION
#99 0
#END
DFT
SPIN
B3LYP-D3
XLGRID
END
TOLINTEG
7 7 7 7 14
TOLDEE
7
SHRINK
0 8
8 8 8
SCFDIR
BIPOSIZE
110000000
EXCHSIZE
110000000
SPINLOCK
0 5 #alpha-beta ncycles
MAXCYCLE
800
FMIXING
30
ANDERSON
PPAN
END
The PREOPTGEOM part, automatically assigns a tighter convergence for the optimization (the vibration modes are dependent on a good optimized geometry).
If you want to set this manually, you will do something like this:
[...]
FREQCALC
PREOPTGEOM
FULLOPTG
MAXCYCLE
900 # We have modified the default cycle from 500 to 900
TOLDEG # More info about tight energy conversion, see page 182 of manual: http://www.crystal.unito.it/Manuals/crystal17.pdf
0.00003
TOLDEX # More info about tight energy conversion, see page 182 of manual: http://www.crystal.unito.it/Manuals/crystal17.pdf
0.00012
FINALRUN
4
MAXTRADIUS # To limit the maximum displacement in the geometry cycle.
0.25
#TRUSTRADIUS
#0.001
ENDOPT
INTENS
INTRAMAN
INTCPHF
ENDCPHF
RAMEXP # Here you make it more comparable to the experimental laser used for the measuring the Raman
295 532 # K nm_laser
ENDFREQ
ENDG
[...]
Sometimes, you need a very tight convergence for the SCF or your electronic density. For such cases, you need to run a calculations that takes longer than usual. Some cases includes the optimization of organic molecular crystals, or the calculation of the IR or when the TS is hard to converge.
"The conditions adopted by default in geometry optimization before frequency calculation are
different than those considered for normal optimizations in order to obtain much more accurate
minima numerical second derivatives. This ensures a good accuracy in the computation of the
frequencies and modes. The defaults are:
TOLDEG 0.00003
TOLDEX 0.00012
FINALRUN 4
MAXTRADIUS 0.25
TRUSTRADIUS .TRUE."
Page 182 of the manual.
Remember that TOLDEE default changes for single point, geometry optimization and frequencies:
TOLDEE - SCF convergence threshold on total energy
rec variable meaning
• ∗ ITOL 10−IT OL threshold for convergence on total energy
Different default values are set for different type of calculation:
SCF single point 6
Geometry optimization OPTGEOM 7
Frequency calculation FREQCALC 10
Elastic constants ELASTCON 8
Equation of state EOS 8
Example
Optimization with very tight constrains when the opt. part gives you trouble (ex. for PE orthorhombic lattice)
CRYSTAL
0 0 1
62
7.43200 2.54700 4.94300 90 90 90
3
6 0.043000 0.250000 -0.930000 Biso 1.000000 C
1 0.167000 0.250000 -0.016000 Biso 1.000000 H
1 0.044000 0.250000 -0.678000 Biso 1.000000 H
OPTGEOM
FULLOPTG
MAXCYCLE
900 #It always works!!!! However use this only when necessary because the cycles needed are much more, see example to the left.
TOLDEG #More info about tight energy conversion, see page 182 of manual: http://www.crystal.unito.it/Manuals/crystal14.pdf
0.00003
TOLDEX
0.00004
FINALRUN
4
#MAXTRADIUS # To limit the maximum displacement in geometry cycle.
#0.01
#TRUSTRADIUS
#0.001
ENDOPT
END
6 8
.... # Everything else is the same as above
If you need to run IR, you need to calculate the dielectric tensor first, with the CPHF method, and add the output format SETPRINT, such that the dielectric tensor is printed in different formats. Example below.
CPHF calculation for getting the dielectric tensor (ex. for polyethylene, PE, orthorhombic lattice)
CRYSTAL
0 0 1
62
8.64992873 2.55236562 4.77040804 90.000000 90.000000 90.000000
3
6 4.219457125923E-02 2.500000000000E-01 4.260242859622E-02
1 1.581384601366E-01 2.500000000000E-01 -4.959642885797E-02
1 5.933897545132E-02 2.500000000000E-01 2.701567899197E-01
CPHF # Notice these are the lines we add to calculate the dielectric tensor
FMIXING
50
MAXCYCLE
150
ENDCPHF
END
6 8
0 0 6 2.0 1.0
13575.349682 0.00022245814352
2035.2333680 0.00172327382520
463.22562359 0.00892557153140
131.20019598 0.03572798450200
42.853015891 0.11076259931000
15.584185766 0.24295627626000
0 0 2 2.0 1.0
6.2067138508 0.41440263448000
2.5764896527 0.23744968655000
0 0 1 0.0 1.0
0.4941102000 1.00000000000000
0 0 1 0.0 1.0
0.1644071000 1.00000000000000
0 2 4 2.0 1.0
34.697232244 0.00533336578050
7.9582622826 0.03586410909200
2.3780826883 0.14215873329000
0.8143320818 0.34270471845000
0 2 1 0.0 1.0
0.5662417100 1.00000000000000
0 2 1 0.0 1.0
0.2673545000 1.00000000000000
0 3 1 0.0 1.0
0.8791584200 1.00000000000000
1 4
0 0 3 1.0 1.0
34.061341000 0.00602519780
5.1235746000 0.04502109400
1.1646626000 0.20189726000
0 0 1 0.0 1.0
0.4157455100 1.00000000000
0 0 1 0.0 1.0
0.1795111000 1.00000000000
0 2 1 0.0 1.0
0.8000000000 1.00000000000
99 0
END
DFT
B3LYP
XLGRID
END
TOLINTEG
7 7 7 7 14
TOLDEE
7
SHRINK
0 25
25 25 25
BIPOSIZE
8000000
EXCHSIZE
8000000
MAXCYCLE
600
FMIXING
80
ANDERSON
PPAN
SETPRINT #These lines print out the Dielectric Tensor in different formats (This is a very advance feature)
1
18 1
END
GRIMME # Grimme D2, only H and C will be used, taken from Table 1: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20495/full
1.05 20. 25.
4 # only H and C is used but is shown how to put other elements
1 0.14 1.001
6 1.75 1.452
235 12.47 1.749
238 24.67 1.606
END
This input.d12 will generate .out with the following lines at the end. These lines will be used for the input to calculate IR.
DIELECTRIC TENSOR
TENSOR IN ORIGINAL CARTESIAN AXES
XX 1.930068E+00 YY 2.084255E+00 ZZ 1.931386E+00 XY 0.000000E+00 XZ 0.000000E+00 YZ 0.000000E+00
TENSOR IN PRINCIPAL AXES SYSTEM
AA 1.930068E+00 BB 2.084255E+00 CC 1.931386E+00
If you want to see the full output files, check the attachment below or go this link.
This dielectric tensor, then can be used for the input of the IR calculations. Remember that this optimized structure, if possible the tight convergence criteria mentioned above for the optimization for the structure needs to be used, specially for compounds that have a flat energy surface, for example molecular crystals and surfaces. (see more in: )
Example of IR calculation for PE orthorhombic lattice
CRYSTAL
0 0 1
62
8.64992873 2.55236562 4.77040804 90.000000 90.000000 90.000000
3
6 4.219457125923E-02 2.500000000000E-01 4.260242859622E-02
1 1.581384601366E-01 2.500000000000E-01 -4.959642885797E-02
1 5.933897545132E-02 2.500000000000E-01 2.701567899197E-01
FREQCALC # This is the block that will calculate the IR.
INTENS
DIELTENS # This is where the dielectric tensor is used. It is comparable to exp. literature values.
1.930068 0 0
0 2.084255 0
0 0 1.931386
IRSPEC
REFRIND
DIELFUN
DAMPFAC
5.0
GAUSS
ENDIR
ENDFREQ
END
6 8
0 0 6 2.0 1.0
13575.349682 0.00022245814352
2035.2333680 0.00172327382520
463.22562359 0.00892557153140
131.20019598 0.03572798450200
42.853015891 0.11076259931000
15.584185766 0.24295627626000
0 0 2 2.0 1.0
6.2067138508 0.41440263448000
2.5764896527 0.23744968655000
0 0 1 0.0 1.0
0.4941102000 1.00000000000000
0 0 1 0.0 1.0
0.1644071000 1.00000000000000
0 2 4 2.0 1.0
34.697232244 0.00533336578050
7.9582622826 0.03586410909200
2.3780826883 0.14215873329000
0.8143320818 0.34270471845000
0 2 1 0.0 1.0
0.5662417100 1.00000000000000
0 2 1 0.0 1.0
0.2673545000 1.00000000000000
0 3 1 0.0 1.0
0.8791584200 1.00000000000000
1 4
0 0 3 1.0 1.0
34.061341000 0.00602519780
5.1235746000 0.04502109400
1.1646626000 0.20189726000
0 0 1 0.0 1.0
0.4157455100 1.00000000000
0 0 1 0.0 1.0
0.1795111000 1.00000000000
0 2 1 0.0 1.0
0.8000000000 1.00000000000
99 0
END
DFT
B3LYP
XLGRID
END
TOLINTEG
8 8 8 8 16
TOLDEE
11
SHRINK
0 20
20 20 20
BIPOSIZE
8000000
EXCHSIZE
8000000
MAXCYCLE
600
FMIXING
80
ANDERSON
PPAN
END
GRIMME # Grimme D2, only H and C will be used, taken from Table 1: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20495/full
1.05 20. 25.
4 # only H and C is used but is shown how to put other elements
1 0.14 1.001
6 1.75 1.452
235 12.47 1.749
238 24.67 1.606
END
If you want to see the full output file, check the attachment below or go this link.
RESTART a vibration calculation
RESTART a vibration calculation
http://tutorials.crystalsolutions.eu/tutorial.html?td=vibfreq&tf=vibfreq_tut
Page updated
Google Sites
Report abuse