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Raman Spectroscopy using CRYSTAL

11 min read

How to run

https://tutorials.crystalsolutions.eu/tutorial.html?td=others&tf=howtorun

  • input: inputfilename.d12
  • output: inpsutfilename.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
 
runcryMPP ZrS3.d12

Info

Make sure you modify the runcryMPP script for your own environment.

Run Crystal23 on Aspire2a

!/bin/bash
#PBS -N CyGeI3
#PBS -l select=2:ncpus=128:mpiprocs=128:mem=200G
#PBS -l walltime=24:00:00
#PBS -j oe
#PBS -P 11002122
#PBS -q normal
 
export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
export OMP_NUM_THREADS=1
 
module swap craype-x86-rome craype-x86-milan
module swap PrgEnv-cray PrgEnv-gnu
module load cray-libsci/21.08.1.2
module swap craype-network-ofi craype-network-ucx
 
 
export NCORES=`wc -l $PBS_NODEFILE | awk '{print $(NF-1)}'`
 
cd ${PBS_O_WORKDIR}
 
/home/users/nus/msedz/app/CRYSTAL23/v2/runcryMPP CyGeI3.d12 > stdout.log 2>&1

Files

ExtensionDescription
.d12wave function calculation input (programĀ crystal)
.outwf calculation printed output file (it may be modified by setting environment variable $OUTFILE)
.d3properties calculation input (programĀ properties)
.outpproperties calculation output file (it may be modified by setting environment variable)
.pspostscript file - written by one of the programsof the packageĀ Crgra2006
.mapsmaps06 control file (seeĀ Crgra2006)
.bandband06 control file (seeĀ Crgra2006)
.dossdoss06 control file (seeĀ 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:

  1. convention for the space group identification: sequential number (0) or alphanumeric code (1).
  2. type of cell for rhombohedral groups: hexagonal (0) or rhombohedral (1).
  3. setting of the origin (seeĀ  CRYSTAL Userā€™s ManualĀ 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 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 DFT block
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

Geometry Optimization

CyGeI3
CRYSTAL
0 0 0
33
20.591  8.354  7.886
25
253 0.45183 0.75482 0.85631
253 0.43425 0.26315 0.83032
253 0.61369 0.46481 0.84800
32  0.50153 0.49637 0.65662
7   0.5836  1.0329  0.9641
1   0.548881 0.991594 0.913205
1   0.585958 1.137143 0.941864
1   0.580466 1.018196 1.075590
6   0.6426 0.9527 0.9007
1   0.635755 0.837611 0.916528
6   0.6505 0.979 0.7154
1   0.613390 0.933462 0.656777
1   0.651205 1.092699 0.692759
6   0.7117 0.904 0.646
1   0.717909 0.940699 0.530046
1   0.706531 0.789021 0.643187
6   0.2604 0.578 0.933
1   0.297203 0.530645 0.990360
1   0.260279 0.691818 0.958135
6   0.1996 0.506 0.9991
1   0.204333 0.389987 1.000048
1   0.193247 0.540325 1.115310
6   0.7687 0.944 0.744
1   0.780368 1.054303 0.721935
1   0.804471 0.877157 0.706032
OPTGEOM
TOLDEG
0.00003
TOLDEX
0.00012
FINALRUN
4
MAXTRADIUS
0.25
END
END
253 12
INPUT
25. 0 3 4 4 4 0
  40.033376  49.989649 0
  17.300576 281.006556 0
   8.851720  61.416739 0
  15.720141  67.416239 0
  15.208222 134.807696 0
   8.294186  14.566548 0
   7.753949  28.968422 0
  13.817751  35.538756 0
  13.587805  53.339759 0
   6.947630   9.716466 0
   6.960099  14.977500 0
  18.522950 -20.176618 0
  18.251035 -26.088077 0
   7.557901  -0.220434 0
   7.597404  -0.221646 0
0 0 5 2 1.0
  5899.5791533      0.000241882693
  898.54238765      0.001547404174
  200.37237912      0.004283668446
  31.418053840     -0.039417936275
  15.645987838      0.960866919920
0 0 2 2 1.0
  11.815741857      0.759615240910
  6.4614458287      0.424955018350
0 0 2 0 1.0
  2.2210057600      0.701255197000
  1.0420511800      0.298744803000
0 0 1 0 1.0
  0.2321271300      1.000000000000
0 2 3 6 1.0
  197.30030547      0.000739512269
  20.061411349      0.066168450008
  9.7631460485     -0.285546623480
0 2 4 5 1.0
  12.984316904     -0.049096186164
  3.6199503008      0.389144324820
  2.0232273090      0.656108172620
  1.0367490559      0.318035516470
0 2 1 0 1.0
  0.3995601300      1.000000000000
0 2 1 0 1.0
  0.1221941700      1.000000000000
0 3 6 10 1.0
  119.12671745      0.000825960396
  33.404240134      0.006837767577
  17.805918203     -0.010308158997
  4.8990510353      0.226704576580
  2.4516753106      0.441801139370
  1.1820693432      0.367754722250
0 3 1 0 1.0
  1.0035336200      1.000000000000
0 3 1 0 1.0
  0.5277932300      1.000000000000
0 3 1 0 1.0
  0.2009869100      1.000000000000
32 15
0 0 8 2.0 1.0
  466115.00592      0.0002248726466
  69875.420762      0.0017435426729
  15903.276716      0.0090691482206
  4501.8233453      0.0369061746850
  1466.0570924      0.1205016790700
  527.07841728      0.2874864170300
  205.00395074      0.4162232188500
  81.251596065      0.2239784569500
0 0 4 2.0 1.0
  505.74661282     -0.0251846092910
  156.96593744     -0.1189892972100
  25.761448176      0.5493013587000
  11.106654687      0.5293930912900
0 0 2 2.0 1.0
  17.272059104     -0.2285459572800
  2.9438289048      0.6837793031700
0 0 1 2.0 1.0
  1.4786569600      1.0000000000000
0 0 1 0.0 1.0
  0.4368300500      1.0000000000000
0 0 1 0.0 1.0
  0.1684150250      1.0000000000000
0 2 6 6.0 1.0
  2633.9346241      0.0022143925310
  624.00161628      0.0181408991410
  200.58528404      0.0866321849220
  75.097081525      0.2564902059200
  30.214388474      0.4265861126200
  12.440087567      0.2620052731300
0 2 3 6.0 1.0
  45.981316002     -0.0203217676780
  6.9945654416      0.3201374452700
  2.9686001327      0.5905101455500
0 2 1 2.0 1.0
  1.2044364000      1.0000000000000
0 2 1 0.0 1.0
  0.4237841000      1.0000000000000
0 2 1 0.0 1.0
  0.1518920500      1.0000000000000
0 3 5 10.0 1.0
  119.44887581      0.0105865445210
  35.062915293      0.0696012809450
  12.636924529      0.2280703528700
  4.8888672922      0.4030106722000
  1.8453195392      0.4130484701500
0 3 1 0.0 1.0
  1.5531065900      1.0000000000000
0 3 1 0.0 1.0
  0.6401807200      1.0000000000000
0 3 1 0.0 1.0
  0.2805796200      1.0000000000000
7 8
0 0 6 2.0 1.0
  19730.800647      0.00021887984991
  2957.8958745      0.00169607088030
  673.22133595      0.00879546035380
  190.68249494      0.03535938260500
  62.295441898      0.11095789217000
  22.654161182      0.24982972552000
0 0 2 2.0 1.0
  8.9791477428      0.4062389614800
  3.6863002370      0.2433821717600
0 0 1 0.0 1.0
  0.7865398200      1.0000000000000
0 0 1 0.0 1.0
  0.2677997200      1.0000000000000
0 2 4 3.0 1.0
  49.200380510      0.0055552416751
  11.346790537      0.0380523797230
  3.4273972411      0.1495367102900
  1.1785525134      0.3494930523000
0 2 1 0.0 1.0
  0.3780331700      1.0000000000000
0 2 1 0.0 1.0
  0.1473661500      1.0000000000000
0 3 1 0.0 1.0
  0.3612294900      1.0000000000000
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
  0.5157455100      1.00000000000
0 0 1 0.0 1.0
  0.1795111000      1.00000000000
0 2 1 0.0 1.0
  0.5000000000      1.00000000000
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
  0.1973545000      1.00000000000000
0 3 1 0.0 1.0
  0.5791584200      1.00000000000000
99 0
END
DFT
PBE0
XXLGRID
END
DIIS
CMPLXFAC
1
TOLINTEG
7 7 7 7 16
SHRINK
3 3
TOLDEE
9
EXCHSIZE
12012489
BIPOSIZE
6855600
MAXCYCLE
150
END

Phonon calculations

CyGeI3
EXTERNAL
FREQCALC
END
END
253 12
INPUT
25. 0 3 4 4 4 0
  40.033376  49.989649 0
  17.300576 281.006556 0
   8.851720  61.416739 0
  15.720141  67.416239 0
  15.208222 134.807696 0
   8.294186  14.566548 0
   7.753949  28.968422 0
  13.817751  35.538756 0
  13.587805  53.339759 0
   6.947630   9.716466 0
   6.960099  14.977500 0
  18.522950 -20.176618 0
  18.251035 -26.088077 0
   7.557901  -0.220434 0
   7.597404  -0.221646 0
0 0 5 2 1.0
  5899.5791533      0.000241882693
  898.54238765      0.001547404174
  200.37237912      0.004283668446
  31.418053840     -0.039417936275
  15.645987838      0.960866919920
0 0 2 2 1.0
  11.815741857      0.759615240910
  6.4614458287      0.424955018350
0 0 2 0 1.0
  2.2210057600      0.701255197000
  1.0420511800      0.298744803000
0 0 1 0 1.0
  0.2321271300      1.000000000000
0 2 3 6 1.0
  197.30030547      0.000739512269
  20.061411349      0.066168450008
  9.7631460485     -0.285546623480
0 2 4 5 1.0
  12.984316904     -0.049096186164
  3.6199503008      0.389144324820
  2.0232273090      0.656108172620
  1.0367490559      0.318035516470
0 2 1 0 1.0
  0.3995601300      1.000000000000
0 2 1 0 1.0
  0.1221941700      1.000000000000
0 3 6 10 1.0
  119.12671745      0.000825960396
  33.404240134      0.006837767577
  17.805918203     -0.010308158997
  4.8990510353      0.226704576580
  2.4516753106      0.441801139370
  1.1820693432      0.367754722250
0 3 1 0 1.0
  1.0035336200      1.000000000000
0 3 1 0 1.0
  0.5277932300      1.000000000000
0 3 1 0 1.0
  0.2009869100      1.000000000000
32 15
0 0 8 2.0 1.0
  466115.00592      0.0002248726466
  69875.420762      0.0017435426729
  15903.276716      0.0090691482206
  4501.8233453      0.0369061746850
  1466.0570924      0.1205016790700
  527.07841728      0.2874864170300
  205.00395074      0.4162232188500
  81.251596065      0.2239784569500
0 0 4 2.0 1.0
  505.74661282     -0.0251846092910
  156.96593744     -0.1189892972100
  25.761448176      0.5493013587000
  11.106654687      0.5293930912900
0 0 2 2.0 1.0
  17.272059104     -0.2285459572800
  2.9438289048      0.6837793031700
0 0 1 2.0 1.0
  1.4786569600      1.0000000000000
0 0 1 0.0 1.0
  0.4368300500      1.0000000000000
0 0 1 0.0 1.0
  0.1684150250      1.0000000000000
0 2 6 6.0 1.0
  2633.9346241      0.0022143925310
  624.00161628      0.0181408991410
  200.58528404      0.0866321849220
  75.097081525      0.2564902059200
  30.214388474      0.4265861126200
  12.440087567      0.2620052731300
0 2 3 6.0 1.0
  45.981316002     -0.0203217676780
  6.9945654416      0.3201374452700
  2.9686001327      0.5905101455500
0 2 1 2.0 1.0
  1.2044364000      1.0000000000000
0 2 1 0.0 1.0
  0.4237841000      1.0000000000000
0 2 1 0.0 1.0
  0.1518920500      1.0000000000000
0 3 5 10.0 1.0
  119.44887581      0.0105865445210
  35.062915293      0.0696012809450
  12.636924529      0.2280703528700
  4.8888672922      0.4030106722000
  1.8453195392      0.4130484701500
0 3 1 0.0 1.0
  1.5531065900      1.0000000000000
0 3 1 0.0 1.0
  0.6401807200      1.0000000000000
0 3 1 0.0 1.0
  0.2805796200      1.0000000000000
7 8
0 0 6 2.0 1.0
  19730.800647      0.00021887984991
  2957.8958745      0.00169607088030
  673.22133595      0.00879546035380
  190.68249494      0.03535938260500
  62.295441898      0.11095789217000
  22.654161182      0.24982972552000
0 0 2 2.0 1.0
  8.9791477428      0.4062389614800
  3.6863002370      0.2433821717600
0 0 1 0.0 1.0
  0.7865398200      1.0000000000000
0 0 1 0.0 1.0
  0.2677997200      1.0000000000000
0 2 4 3.0 1.0
  49.200380510      0.0055552416751
  11.346790537      0.0380523797230
  3.4273972411      0.1495367102900
  1.1785525134      0.3494930523000
0 2 1 0.0 1.0
  0.3780331700      1.0000000000000
0 2 1 0.0 1.0
  0.1473661500      1.0000000000000
0 3 1 0.0 1.0
  0.3612294900      1.0000000000000
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
  0.5157455100      1.00000000000
0 0 1 0.0 1.0
  0.1795111000      1.00000000000
0 2 1 0.0 1.0
  0.5000000000      1.00000000000
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
  0.1973545000      1.00000000000000
0 3 1 0.0 1.0
  0.5791584200      1.00000000000000
99 0
END
DFT
PBE0
XXLGRID
END
DIIS
CMPLXFAC
1
TOLINTEG
7 7 7 7 16
SHRINK
2 2
EXCHSIZE
12012489
BIPOSIZE
6855600
MAXCYCLE
150
END

Tips

  • Use MPPcrystal for relaxation and phonon calculations, then use Pcrystal for Raman calculations
  • DIIS should be specified for MPPcrystal to accelerate convergence
  • The dual level parallelism should be activated since I have too much k-points for a very few nodes. I reduced the SHRINK to 2 2, and change CMPLXFAC to 1, so it can fully take advantage of dual parallelism now. Itā€™s running very fast.
  • TOLDEE should be set for some tight values (>= 9)
  • In relaxation (OPTGEOM), tighter parameters should be chosen, default values are
OPTGEOM
TOLDEG
0.00003
TOLDEX
0.00012
FINALRUN
4
MAXTRADIUS
0.25
END

Graph View