Raman Spectroscopy using CRYSTAL
How to run
https://tutorials.crystalsolutions.eu/tutorial.html?td=others&tf=howtorun
runcry17 inputfilename [wf_file]- input:
inputfilename.d12 - output:
inputfilename.out
Run CRYSTAL17 on Fornax
Submission script:
#!/bin/sh --login
#PBS -N raman
#PBS -l walltime=48:00:00
#PBS -q smallmem
#PBS -j oe
#PBS -l select=8:ncpus=8:mpiprocs=8
#PBS -l place=excl
module load crystal/crystal-17
cd ${PBS_O_WORKDIR}
# number of cores per node used
export NCORES=`wc -l $PBS_NODEFILE | awk '{print $(NF-1)}'`
# number of processes
export NPROCESSES=`wc -l $PBS_NODEFILE | awk '{print $(NF-1)}'`
# Make sure any symbolic links are resolved to absolute path
export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
export SHAREDTMP="YES"
# Set the number of threads to 1
# This prevents any system libraries from automatically
# using threading.
export OMP_NUM_THREADS=1
runcryP ZrS3.d12
Files
| Extension | Description |
|---|---|
| .d12 | wave function calculation input (program crystal) |
| .out | wf calculation printed output file (it may be modified by setting environment variable $OUTFILE) |
| .d3 | properties calculation input (program properties) |
| .outp | properties calculation output file (it may be modified by setting environment variable) |
| .ps | postscript file - written by one of the programsof the package Crgra2006 |
| .maps | maps06 control file (see Crgra2006) |
| .band | band06 control file (see Crgra2006) |
| .doss | doss06 control file (see Crgra2006 |
Input Example
Below is an example of CRYSTAL input for Raman calculation (ZrS3.d12)
ICSD_CollCode42073.cif # title
Geometry block
CRYSTAL # Dimensionality of the system
1 0 0
Three integer numbers:
- convention for the space group identification: sequential number (0) or alphanumeric code (1).
- type of cell for rhombohedral groups: hexagonal (0) or rhombohedral (1).
- setting of the origin (see CRYSTAL User's Manual for further details).
P 1 21/m 1 # space group
5.124300000000 3.624400000000 8.980000000000 97.280000000000 # Lattice parameters
4 # number of atoms in the asymmetric unit
# atomic number and fractional coordinates
240 0.283700000000 0.250000000000 0.655300000000
16 0.472500000000 0.250000000000 0.171600000000
16 0.879900000000 0.250000000000 0.169900000000
16 0.763100000000 0.250000000000 0.554300000000
FREQCALC # FREQCALC opens the vibrational frequencies calculation input
PREOPTGEOM # perform optimization before starting the vibrational modes calculation
FULLOPTG # full geometry optimization
END # end FULLOPTG
INTENS # intensities calculation active
INTRAMAN # Raman intensities calculation on
INTCPHF # IR and Raman intensities via Coupled-Perturbed Hartree-Fock/Kohn-Sham approach (CPHF)
END # end CPHF
RAMANEXP # Raman intensities including xperimental conditions
298, 514 # Temperature, Frequency of the incoming laser (in nm)
END # end RAMANEXP
END # end of the geometry input section
Basis set block
You can get basis set from https://www.crystal.unito.it/basis_sets.html
240 11 # basis set for Zr Zr_POB_TZVP_rev2
INPUT
12. 0 2 4 4 2 0
8.636528 150.242994 0
3.717639 18.780036 0
7.626728 33.192791 0
7.453207 66.389039 0
3.358389 4.620726 0
3.229738 9.260270 0
5.938086 13.993383 0
5.825544 20.995882 0
2.205019 2.285166 0
2.206292 3.441260 0
4.800215 -5.239320 0
4.798992 -6.987424 0
0 0 2 2 1.0
11.0000000000 -0.190755952570
9.50000000000 0.338955887540
0 0 1 2 1.0
5.15504020000 1.000000000000
0 0 1 0 1.0
1.55493930000 1.000000000000
0 0 1 0 1.0
0.62126150000 1.000000000000
0 2 4 6 1.0
8.60663055430 0.040404260236
4.44009799580 -0.211877452010
1.12810269460 0.491642668910
0.54346076310 0.573033706580
0 2 1 0 1.0
0.49792620000 1.000000000000
0 2 1 0 1.0
0.16451000000 1.000000000000
0 3 3 2 1.0
4.55679577950 -0.009619056902
1.29049397970 0.205699901550
0.51646987222 0.418313818510
0 3 1 0 1.0
0.32949280000 1.000000000000
0 3 1 0 1.0
0.18034710000 1.000000000000
0 4 1 0 1.0
0.39261000000 1.000000000000
16 10 # basis set for S S_pob_TZVP_rev2
0 0 7 2.0 1.0
60700.928104 0.00054695944225
9102.6106854 0.00422972245570
2071.4166009 0.02174782415900
586.02476821 0.08510005358900
190.55395021 0.24799128459000
67.630384260 0.46703640406000
25.127306905 0.36434587550000
0 0 3 2.0 1.0
112.57463010 0.02167004024000
34.795554217 0.09360230176000
6.5115556215 -0.26068001422000
0 0 2 2.0 1.0
3.2399032261 1.28420894350000
1.5477160881 0.66036416584000
0 0 1 0.0 1.0
0.4487335200 1.00000000000000
0 0 1 0.0 1.0
0.1553457200 1.00000000000000
0 2 5 6.0 1.0
564.36716027 0.00247967963170
133.42624379 0.01967793025000
42.468271189 0.08998000825800
15.616527580 0.25705880575000
6.1093988469 0.43515167292000
0 2 1 4.0 1.0
2.0359436000 1.00000000000000
0 2 1 0.0 1.0
0.4337928300 1.00000000000000
0 2 1 0.0 1.0
0.1305009100 1.00000000000000
0 3 1 0.0 1.0
0.4107010100 1.0000000000000
99 0 3 # end of pre-defined atomic orbital basis set
END # end of basis set definition
SCF block
DFT # DFT calculations will be performed
PBE0 # PBE0 functional is used
XXLGRID # numerical accuracy: extra extra large predefined grid is used
CHUNKS # max N points in a batch for numerical integration, load balancing
200 # for CHUNKS
END # end for CHUNKS
TOLINTEG # tolerances of Coulomb and exchange infinite sums control;
7 7 7 9 30 # default: 6 6 6 6 12; more accurate calculations may require an increase on the default values, e.g., magnetic properties, etc.
SHRINK # Monkhorst-Pack shrinking factor
8 8 # first is for reciprocal space, the second number is a denser k-point mesh for Fermi energy and density matrix
TOLDEE # tolerance in changing energy for SCF
11 # tolerance in changing energy for SCF 10^-11 Hartree (1 Ha = 27.21 eV) here
EXCHSIZE # size of exchange bipolar expansion buffer (memory per core)
12012489
MAXCYCLE # max number of SCF cycles
150
END # end of DFT