interpreting Raman calculation output
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I found this forum very useful and very informative. I would like to ask help with Raman spectra calculation interpretation. We normally run 532 nm Raman on our powders and I would like to calculate said spectrum. However, I find it difficult as I view through the calculation output to find out which one is which. In particular, first I run
EXTERNAL FREQCALC FRAGMENT 10 9 106 131 175 191 192 193 194 195 196 197 PREOPTGEOM ATOMONLY END INTENS INTRAMAN INTCPHF END END ENDand obtain Raman.out this output. This provides these modes
27- 27 0.1614E-04 881.8618 26.4376 (A ) A ( 1850.51) A 28- 28 0.1776E-04 925.0155 27.7313 (A ) A ( 528.78) A 29- 29 0.1840E-04 941.4794 28.2248 (A ) A ( 120.15) A 30- 30 0.2223E-04 1034.8768 31.0248 (A ) A ( 89.10) Athen polycrystalline
27- 27 881.8618 (A ) 48.11 27.86 20.26 28- 28 925.0155 (A ) 198.27 175.12 23.16 29- 29 941.4794 (A ) 571.74 518.42 53.32 30- 30 1034.8768 (A ) 1000.00 947.97 52.03and crystalline printouts
27- 27 881.8618 (A ) 8.45 24.41 40.44 9.34 6.13 11.78 28- 28 925.0155 (A ) 120.61 24.34 1.57 214.59 57.50 53.57 29- 29 941.4794 (A ) 51.70 47.91 33.81 449.39 12.69 878.42 30- 30 1034.8768 (A ) 949.93 32.47 88.71 1000.00 45.46 356.43At this point I am lost as I am not sure which ones CRYSPLOT extracts.
Then I try to obtain those for 532 nm laser so I restart withEXTERNAL FREQCALC RESTART FRAGMENT 10 9 106 131 175 191 192 193 194 195 196 197 INTENS INTRAMAN RAMANREA RAMEXP 295. 532. ENDFREQ ENDbut in the file I obtain it is pretty much the same information Ramexp.out
[...] 27- 27 0.1614E-04 881.8618 26.4376 (A ) A ( 1850.51) A 28- 28 0.1776E-04 925.0155 27.7313 (A ) A ( 528.78) A 29- 29 0.1840E-04 941.4794 28.2248 (A ) A ( 120.15) A 30- 30 0.2223E-04 1034.8768 31.0248 (A ) A ( 89.10) A [...] <RAMAN><RAMAN><RAMAN><RAMAN><RAMAN><RAMAN><RAMAN><RAMAN><RAMAN><RAMAN><RAMAN> [...] 27- 27 881.8618 (A ) 42.48 24.60 17.89 28- 28 925.0155 (A ) 164.88 145.62 19.26 29- 29 941.4794 (A ) 465.01 421.64 43.37 30- 30 1034.8768 (A ) 721.86 684.30 37.56 [...] 27- 27 881.8618 (A ) 4.11 11.87 19.67 4.54 2.98 5.73 28- 28 925.0155 (A ) 55.23 11.14 0.72 98.27 26.33 24.53 29- 29 941.4794 (A ) 23.15 21.46 15.14 201.27 5.68 393.41 30- 30 1034.8768 (A ) 377.60 12.91 35.26 397.50 18.07 141.68 [...] <RAMAN><RAMAN><RAMAN><RAMAN><RAMAN><RAMAN><RAMAN><RAMAN><RAMAN><RAMAN><RAMAN>I think I am after one of these below but I am simply not sure what CRYSPLOT is plotting or which ones are written into RAMSPEC.DAT (and what is the difference between first and second run, honestly).
I was wondering if somebody could read this long email, look at the two files and elaborate a little on these results since all the Raman vibrations are plotted at least thrice in each file.
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Dear Jonas,
Thanks for reaching out and being one of the most active users of these early days of the forum. Your question gives us the chance to clarify some aspects of the output file that might not be obvious to non expert users. Below, I will refer to your output file.
Harmonic Frequencies and IR intensities
To compute harmonic frequencies and IR intensities (with the default approach of the Berry phase) the input looks like:
FREQCALC INTENS ENDFREQIn the output file, the following table is printed:
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH EIGENVALUES (EIGV) OF THE MASS WEIGHTED HESSIAN MATRIX AND HARMONIC TRANSVERSE OPTICAL (TO) FREQUENCIES. IRREP LABELS REFER TO SYMMETRY REPRESENTATION ANALYSIS; A AND I INDICATE WHETHER THE MODE IS ACTIVE OR INACTIVE, RESPECTIVELY, FOR IR AND RAMAN; INTEGRATED IR INTENSITIES IN BRACKETS. CONVERSION FACTORS FOR FREQUENCIES: 1 CM**(-1) = 0.4556335E-05 HARTREE 1 THZ = 0.3335641E+02 CM**(-1) HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH MODES EIGV FREQUENCIES IRREP IR INTENS RAMAN (HARTREE**2) (CM**-1) (THZ) (KM/MOL) 1- 1 0.3488E-07 40.9894 1.2288 (A ) A ( 0.40) A 2- 2 0.6077E-07 54.1037 1.6220 (A ) A ( 0.96) A 3- 3 0.6801E-07 57.2344 1.7158 (A ) A ( 2.45) A 4- 4 0.2238E-06 103.8371 3.1130 (A ) A ( 11.47) A [...]For each mode (or set of degenerate modes) its eigenvalue (in Ha\(^2\)), harmonic frequency (in cm\(^{-1}\) and THz) and irreducible representation get printed. In addition, labels specifying whether the mode is IR/Raman active are also displayed (A and I indicate whether the mode is active or inactive, respectively).
Raman intensities
Raman intensities can be computed via a coupled-perturbed approach by inserting the INTRAMAN keyword followed by the INTCPHF block in the input deck:
FREQCALC INTRAMAN INTCPHF END ENDFREQRaman intensities are computed for each independent component of the polarizability tensor (xx, xy, xz, yy, yz, zz, labeled as "Single Crystal" in the output file) and are also averaged to mimic polycrystalline powder samples (total, parallel polarisation, perpendicular polarisation averages are printed in the output).
POLYCRYSTALLINE ISOTROPIC INTENSITIES (ARBITRARY UNITS) MODES FREQUENCIES I_tot I_par I_perp ---------------------------------------------------------------- 1- 1 40.9894 (A ) 0.46 0.27 0.19 2- 2 54.1037 (A ) 7.35 4.23 3.12 3- 3 57.2344 (A ) 12.79 8.82 3.96 4- 4 103.8371 (A ) 13.66 7.89 5.77SINGLE CRYSTAL DIRECTIONAL INTENSITIES (ARBITRARY UNITS) MODES FREQUENCIES I_xx I_xy I_xz I_yy I_yz I_zz ---------------------------------------------------------------------------- 1- 1 40.9894 (A ) 0.00 0.37 0.02 0.63 0.00 0.21 2- 2 54.1037 (A ) 3.17 0.69 0.00 4.35 3.66 10.05 3- 3 57.2344 (A ) 3.82 3.54 0.02 3.50 0.03 27.53 4- 4 103.8371 (A ) 2.57 1.81 0.01 16.25 3.34 19.62For more details on such polycrystalline averages, please refer to sections 8.4 and 8.7 of the CRYSTAL23 manual.
Raman spectrum
A continuous Raman spectrum can be simulated by use of the RAMSPEC block, as in:
FREQCALC INTRAMAN INTCPHF END RAMSPEC END ENDFREQThe simulated spectrum is printed in an external file named RAMSPEC.DAT that contains several columns: column 1 with frequencies in cm\(^{-1}\), columns 2-4 with polycrystalline intensities (total, parallel, perpendicular), columns 5-10 with single crystal intensities (xx, xy, xz, yy, yz, zz).
Effect of Temperature and Laser wavelength
The effect of temperature and laser wavelength on computed Raman intensities can be accounted for by use of the RAMANEXP keyword, as in:
FREQCALC INTRAMAN INTCPHF END RAMANEXP 298 532 RAMSPEC END ENDFREQHere we set 298 K for the temperature and 532 nm for the laser wavelength. This option modifies the values of all computed Raman intensities (in the output and in the RAMSPEC.DAT file accordingly).
Please, note that other properties (harmonic frequencies and IR intensities) are not affected by this option and thus remain unchanged in the output.
Plots
When CRYSPLOT reads the CRYSTAL output file it only plots the total intensity of the polycrystalline powder model.
When CRYSPLOT reads the RAMSPEC.DAT file it plots all components:
Other plotting tools can be used to plot specific columns of the RAMSPEC.DAT file (e.g., CRYSTALClear, gnuplot).
