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  • job314
    job314 job314
    Basis Sets

    My current activity on this forum is due to the need to calculate Raman spectra. This one is not a problem but more of an observation. For the longest time I thought that CRYSTAL had a basis set problem where basis sets were seemingly randomly optimized and there were many falvors of them and they wer nore standartized in terms of contractions (e.g. 6-31G*). I was very happy to find out that standard basis sets by Peintinger were created, e.g. pob-TZVP which I can simply specify with BASISSET. So in all of my recent work on Raman spectra I used them for simplicity and uniformity.
    Fast forward, my calculated Raman peaks just do not have the right position. I understand there will be an intrinsic error in the calculated peak positions, but the peaks ere 150-200 cm-1 too low for a sulfate ion. So I looked back at CRYSTAL references that did Raman including Roberto's and noticed at that time they still used these old school basis sets. I was curious and for B3LYP-D3 (I have molecular crystals or ionic crystals) with pob-TZVP I recalculated everything with these large 8611 basis sets. Much to my dismay, these old school basis sets yielded calculated Raman peaks in the vicinity of the experimental, e.g. 150-200 cm-1 higher than pob-TZVP with everything else in the input the same.
    This is not a cimplaint, I understand that frequency outcome will depend on the calculation setup, e.g. functional and basis set, but why would pob-TZVP be so spectacularly bad at these Raman vibrations?
    See attached, blue is 86111 old school basis set and orange is pob-TZVP basis set - I have much more data with pob-TZVP (unfortunately).
    Experimental SO4 vibration is around 920 cm-1 in this particular mineral

    573bcbe9-738d-4f7b-abda-2e3c7e43c00b-image.png

    5 0 1 Reply
    job314 job314
    Alessandro, the setback is temporary. What I really appreciate is that you gave CRYSTAL more life via user support than it ever had. I am very grateful for it
  • aimipa
    aimipa aimipa
    Density-of-States

    Hello,

    I performed a dos calculation, projected on two atom groups. each group contains 20 atoms.
    However i am wondering, is there a way to identify from the .dat file or the .out, which projection corresponds to each group?

    Thank you in advance

    1 0 0 Reply
    aerba aerba
    Hi, The first data series corresponds to the first set and the second to the second. If you need more insight on the specifics of your calculation, please share your files. Hope this helps,
  • job314
    job314 job314
    Vibrational Spectroscopies: IR, Raman, INS

    Hi all, it's more of an functional question. I noticed that only limited subset of functionals is available for Raman intensity calculations. I have a molecular crystal and trying all of it, started with range separated, then hybrid... Now I found that PBE can be combined with D3 and trying that one. So my question is - what is the difference between PBE and PBEXC or PBEsol and PBEsolXC?

    Turn out I can simply specify

    DFT
    PBE-D3
    END

    but not

    DFT
    PBEsol
    END

    the latter aborts and I can only make it work if I specify otherwise it returns an error

    DFT
    PBEsolxc
    END

    (EXCHANGE)[CORRELATION] FUNCTIONAL:(PBEsol GGA)[PBEsol]

    The former, however, still returns

    (EXCHANGE)[CORRELATION] FUNCTIONAL:(PERDEW-BURKE-ERNZERHOF)[PERDEW-BURKE-ERNZERHOF]

    I guess my question is why PBE can specified as a single keyword but not PBEsol which needs to be PBEsolXC. What is the significance of xc addition here?

    thank you

    1 0 0 Reply
    aerba aerba
    Hi, In CRYSTAL, the most general syntax to specify exchange-correlation (xc) functionals is, within the DFT input block through the EXCHANGE and CORRELAT keywords as: DFT EXCHANGE label of exchange functional (e.g. VBH, BECKE, PBE, ...) CORRELAT label of correlation functional (e.g. VWN, LYP, PBE, ...) ENDDFT For certain standard combinations of exchange and correlation functionals, we have implemented single keywords. For instance: DFT BLYP ENDDFT is equivalent to DFT EXCHANGE BECKE CORRELAT LYP ENDDFT Another example (here the "XC" letters are appended at the end of the name to reflect that the functional is used for both the exchange and correlation part): DFT PBESOLXC ENDDFT is equivalent to DFT EXCHANGE PBESOL CORRELAT PBESOL ENDDFT For PBE, there are three equivalent ways to define it in CRYSTAL: DFT PBEXC ENDDFT or DFT PBE ENDDFT or DFT EXCHANGE PBE CORRELAT PBE ENDDFT There isn't a general rule, I'm afraid. This syntax aspects are discussed at page 134 of CRYSTAL23 User's Manual. Hope this clarifies things a little,
  • R.Zosiamliana
    R.Zosiamliana R.Zosiamliana
    Elasticity, Piezoelectricity, Photoelasticity

    Hello,

    I’m performing a 2D slab calculation using CRYSTAL17 for a hexagonal monolayer system (a = b = 6.81998 Å, γ = 120°, c = 500 Å to simulate vacuum). Geometry is read from an external file. I enabled piezoelectric property calculation.

    CRYSTAL printed the piezoelectric tensor (in |e|·bohr units) as:

    | 0.000 0.000 -3.931 |
    | -3.931 3.931 0.000 |
    | 0.083 0.083 0.000 |

    My questions:

    1) For slab models, should the full 3D volume be used in the unit conversion to C/m2, or just the in-plane area?

2) Are these piezoelectric constants physically meaningful for 2D systems, or is there a standard post-processing correction needed?

    Thank you in advance for your help.

    Best regards,
    R.Zosiamliana
    PSRC
    3yrs+, CRYSTAL17 user.

    1 0 0 Reply
    aerba aerba
    Hi, Direct piezoelectric constants of a 3D lattice in CRYSTAL are defined and computed as: $$ e_{ci}^{3D} = \left( \frac{\partial P_c}{\partial \eta_i}\right) = \frac{1}{V}\left( \frac{\partial^2 E}{\partial E_c\partial \eta_i}\right) $$ that is as first derivatives of Cartesian components of the polarization (c=x,y,z) with respect to strain components, or, equivalently as second derivatives of the energy density (V is the volume of the 3D lattice cell) with respect to Cartesian components of an electric field \(E_c\) and strain components, where the strain \( \eta \) is dimensionless and thus the direct piezoelectric constants have units of \( \textup{charge/length}^2 \). For 1D and 2D periodic lattices, as the volume (V) is not uniquely defined (or not defined at all in some cases), one may divide by the length \(l \) and area \( A\) of the lattice cell instead: $$ e_{ci}^{1D} = \frac{1}{l}\left( \frac{\partial^2 E}{\partial E_c\partial \eta_i}\right) \quad \textup{and} \quad e_{ci}^{2D} = \frac{1}{A}\left( \frac{\partial^2 E}{\partial E_c\partial \eta_i}\right) $$ that would thus be expressed in units of \( \textup{charge} \) or \( \textup{charge/length} \) for 1D and 2D lattices, respectively. However, in CRYSTAL for 1D and 2D lattices we do not divide by \(l \) or \( A\) , and just define and compute the piezoelectric constants as: $$ e_{ci}^\textup{1D and 2D} = \left( \frac{\partial^2 E}{\partial E_c\partial \eta_i}\right) $$ with units of \( \textup{charge}\cdot\textup{length} \). Yes, these constants are physically meaningful for 1D and 2D systems. For a 2D monolayer system, for instance, depending on what you need to compare with, you can do one of two things: keep them as they are printed in the CRYSTAL output (units of \( \textup{charge}\cdot\textup{length} \)) divide the values you get in the CRYSTAL output by the area of the 2D cell (and thus express them in units of \( \textup{charge/length} \)) I would not divide by a volume because I would not know the physical meaning of the volume of a 2D monolayer system. Hope this helps,
  • esmuigors
    esmuigors esmuigors
    Single-Point Calculations

    We are researching LiF and we are interested in creating a potential energy curve for the crystalline structure of LiF. From what we have already found out, a diatomic case is not described in an asymptotically correct way by any density functional but is described by MP2–MP4 (the internal energy with Coulomb energy subtracted goes to 0 at large distances).

    In the manual, it is mentioned that CRYSTAL can compute MP2 for single points. However, when we launch it, the following error happens:

    4f596dba-7c90-4e62-b0ae-f2bcf8966e52-image.png

    We tried both the parallel and the serial version, the error is the same. Actually, for the parallel version it starts to compute MP2 and then falls out.

    What can be the issue?

    LiF_MP2.pobtzvp_rev2_sp.out

    LiF_MP2.pobtzvp_rev2_sp_parallel.out

    1 0 0 Reply
    aerba aerba
    Hi, The MP2 option is no longer supported in recent versions of the CRYSTAl program. If you are interested in a periodic MP2 calculation, my suggestion is to contact Lorenzo Maschio ([email protected]) and Denis Usvyat ([email protected]) directly, who may provide guidance in the use of the CRYSCOR program.
  • job314
    job314 job314
    Vibrational Spectroscopies: IR, Raman, INS

    I am sorry, I am having a bad stretch with frequency calculations

    SIZE OF GRID= 1268364
    TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MAKE_GRID2 TELAPSE 3087.73 TCPU 3042.39
    BECKE WEIGHT FUNCTION
    RADSAFE = 2.00
    TOLERANCES - DENSITY:10**- 6; POTENTIAL:10**- 9; GRID WGT:10**-14

    RADIAL INTEGRATION - INTERVALS (POINTS,UPPER LIMIT): 1( 75, 4.0*R)

    ANGULAR INTEGRATION - INTERVALS (ACCURACY LEVEL [N. POINTS] UPPER LIMIT):
    1( 4[ 86] 0.2) 2( 8[ 194] 0.5) 3( 12[ 350] 0.9) 4( 16[ 974] 3.5)
    5( 12[ 350]9999.0)
    TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 3150.14 TCPU 3104.48
    forrtl: severe (67): input statement requires too much data, unit 81, file /90daydata/urea_kinetics/struvite/camB3LYP_pobTZVP/restart/fort.81.pe150
    Image PC Routine Line Source
    Pcrystal 0000000007361152 Unknown Unknown Unknown
    Pcrystal 000000000735F4F6 Unknown Unknown Unknown
    Pcrystal 0000000001BA1663 Unknown Unknown Unknown
    Pcrystal 0000000000AED67B Unknown Unknown Unknown
    Pcrystal 0000000000A8D803 Unknown Unknown Unknown
    Pcrystal 0000000000ADD31F Unknown Unknown Unknown
    Pcrystal 0000000000A62692 Unknown Unknown Unknown
    Pcrystal 0000000000D4DAD1 Unknown Unknown Unknown
    Pcrystal 000000000074B942 Unknown Unknown Unknown

    2 0 0 Reply
    job314 job314
    I tried rerunning it with fewer nodes - thought it is some parallel issue. A problem again ANGULAR INTEGRATION - INTERVALS (ACCURACY LEVEL [N. POINTS] UPPER LIMIT): 1( 4[ 86] 0.2) 2( 8[ 194] 0.5) 3( 12[ 350] 0.9) 4( 16[ 974] 3.5) 5( 12[ 350]9999.0) CYCLE 0 ALPHA 227.814788 EPSILON 1.894274 DELTA 2.2781E+02 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 1902.88 TCPU 1885.42 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 1904.27 TCPU 1886.79 DIIS TEST: 0.61205E+01 AT CPHF CYCLE 1 - MIX 60 % CYCLE 1 ALPHA 257.133404 EPSILON 2.009363 DELTA 2.9319E+01 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2002.77 TCPU 1984.78 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2004.16 TCPU 1986.16 DIIS TEST: 0.71887E+01 AT CPHF CYCLE 2 - DIIS ACTIVE - HISTORY: 2 CYCLES CYCLE 2 ALPHA 268.265588 EPSILON 2.053062 DELTA 1.1132E+01 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2102.04 TCPU 2083.54 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2103.42 TCPU 2084.92 DIIS TEST: 0.36370E+00 AT CPHF CYCLE 3 - DIIS ACTIVE - HISTORY: 3 CYCLES CYCLE 3 ALPHA 276.769385 EPSILON 2.086443 DELTA 8.5038E+00 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2202.03 TCPU 2183.04 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2203.42 TCPU 2184.42 DIIS TEST: 0.54051E-01 AT CPHF CYCLE 4 - DIIS ACTIVE - HISTORY: 4 CYCLES CYCLE 4 ALPHA 278.095061 EPSILON 2.091647 DELTA 1.3257E+00 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2302.12 TCPU 2282.64 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2303.51 TCPU 2284.02 DIIS TEST: 0.85023E-02 AT CPHF CYCLE 5 - DIIS ACTIVE - HISTORY: 5 CYCLES CYCLE 5 ALPHA 278.435921 EPSILON 2.092985 DELTA 3.4086E-01 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2402.16 TCPU 2382.20 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2403.54 TCPU 2383.57 DIIS TEST: 0.38480E-03 AT CPHF CYCLE 6 - DIIS ACTIVE - HISTORY: 6 CYCLES CYCLE 6 ALPHA 278.461661 EPSILON 2.093086 DELTA 2.5739E-02 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2502.06 TCPU 2481.62 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2503.45 TCPU 2482.99 DIIS TEST: 0.44991E-03 AT CPHF CYCLE 7 - DIIS ACTIVE - HISTORY: 7 CYCLES CYCLE 7 ALPHA 278.460154 EPSILON 2.093080 DELTA -1.5071E-03 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2601.70 TCPU 2580.74 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2603.08 TCPU 2582.11 DIIS TEST: 0.36243E-03 AT CPHF CYCLE 8 - DIIS ACTIVE - HISTORY: 8 CYCLES CYCLE 8 ALPHA 278.473843 EPSILON 2.093134 DELTA 1.3689E-02 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MOQGAD TELAPSE 2701.77 TCPU 2680.26 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT CP_MONMON TELAPSE 2703.15 TCPU 2681.62 DIIS TEST: 0.85073E-04 AT CPHF CYCLE 9 - DIIS ACTIVE - HISTORY: 9 CYCLES CYCLE 9 ALPHA 278.474328 EPSILON 2.093136 DELTA 4.8487E-04 forrtl: severe (256): unformatted I/O to unit open for formatted transfers, unit 85, file /dev/null Image PC Routine Line Source Pcrystal 0000000007374206 Unknown Unknown Unknown Pcrystal 0000000001BA179E Unknown Unknown Unknown Pcrystal 0000000000A8038B Unknown Unknown Unknown Pcrystal 0000000000A63D97 Unknown Unknown Unknown Pcrystal 0000000000D4DAD1 Unknown Unknown Unknown Pcrystal 000000000074B942 Unknown Unknown Unknown Pcrystal 000000000040591E Unknown Unknown Unknown Pcrystal 00000000004053FD Unknown Unknown Unknown libc.so.6 000014B7C14295D0 Unknown Unknown Unknown libc.so.6 000014B7C1429680 __libc_start_main Unknown Unknown Pcrystal 0000000000405315 Unknown Unknown Unknown
  • matscidanny
    matscidanny matscidanny
    Harmonic and Anharmonic Lattice Dynamics and Thermodynamics

    Hello CRYSTAL team,

    I recently calculated phonon band structures and phonon density of states (PDOS) for a material.

    From the output, it seems that the phonon DOS was calculated three times. It is printed in the output once every time a new band path was calculated. In my case, I followed the Gamma-X-Y-Gamma path so it prints PDOS once after Gamma-X, once after X-Y, once after Y-Gamma.

    I plotted all of these instances independently (including their atomic projections) using a python script, and they all look different. However, when using CRYSPLOT, it only shows the last calculated PDOS instance as the total PDOS.(see attached figure)

    CRYSPLOT_comparison_PDOS.png

    I was wondering if the other two calculated total PDOS are ignored, and how the total PDOS is calculated such that only the last instance is shown. I was hoping to get a better understanding on how the output is organized for future plots.

    Thank you,
    Danny

    7 0 0 Reply
    matscidanny matscidanny
    Hello Dr. Erba, Thank you very much for your thorough explanation! This clarifies all my questions. I will make sure to re-calculate using a larger supercell. Best, Danny
  • alichahine
    alichahine alichahine
    Other Questions

    Hello i am trying to perform COOP calculation for a system of molecular crystals. I have the .f9 file ready with the following .d3 file :
    NEWK
    3 3
    1 0
    COOP
    1 200 239 240 1 12 0
    END

    and the output always gives a DOSS error and says that there is an error in the input deck

    2 0 0 Reply
    mriveraa mriveraa
    Hi! In a COOP calculation you aim to have a description on the interaction between pairs of orbitals or atoms. In order to do that, you need to indicate each pair you are interested to analyze. In your input, in the first line after the COOP keyword, the initial number 1 indicates that you are interested in one pair of orbitals/atoms. You still need to indicate a pair of orbitals or atoms to be considered, writing them in separated lines. Consider this example, taken from the Tutorials webpage: NEWK 6 6 1 0 COOP 1 200 7 14 1 12 0 -1 1 -1 2 END Here, the two lines before the final END keyword indicate which atoms will be considered (atoms, given that the lines start with a negative value, as stated in the manual page 322). COOP will be evaluated considering the first and second atoms of the systems (with indices 1 and 2). From your previous calculations you can recover the indices of the atoms/orbitals you are interested. Let me know if this information has been useful
  • mones19
    mones19 mones19
    Geometry Optimisations

    I have issues with the attached geometry input file. CRYSTAL says some atoms are too close even though the geometry has no issue when the original cif file is visualized. I also noticed the V and O atoms that sits on the C4 axis of the point group are duplicated 8 times. Since the space group is P4/n, having 8 different coordinates does make sense because there are 8 symmetry operation. But since they sit specifically on the rotation axis, some of the operation result in the same equivalent position but the primitive unit cell in the crystal output shows 8 different V atoms. I have never encountered this issue and I am not sure if this is the issue of my input file or something else. I have attached the input file and the output file. TPPVO1_FM_fullopt.d12 TPPVO1_FM_fullopt.txt opt_geom.cif

    2 0 0 Reply
    mones19 mones19
    Thank you very much. Now it works without any issue. I was not aware of the necessity to change this parameter as I did not encounter any issue with other calculations I have done due to it being 0 0 0.
  • job314
    job314 job314
    Running CRYSTAL in Parallel

    Colleagues, this is likely not PCrystal but my HPC problem. When I run PCrystal between several nodes, it always stops at the same point below and just sits there. Job is clearly running if I squeue but no progress is made for many hours, output is not being updated since it reached the point below. I kill it, run it on a single node and it runs no problem. I SSH into the node, I see all the cores occupied with PCrystal nicely.

    Where can it be a problem?

    MAX NUMBER OF SCF CYCLES 200 CONVERGENCE ON DELTAP 10**-16
    WEIGHT OF F(I) IN F(I+1) 30% CONVERGENCE ON ENERGY 10**-10
    SHRINK. FACT.(MONKH.) 4 4 4 NUMBER OF K POINTS IN THE IBZ 30
    SHRINKING FACTOR(GILAT NET) 4 NUMBER OF K POINTS(GILAT NET) 30

    *** K POINTS COORDINATES (OBLIQUE COORDINATES IN UNITS OF IS = 4)
    1-R( 0 0 0) 2-C( 1 0 0) 3-R( 2 0 0) 4-C( 0 1 0)
    5-C( 1 1 0) 6-C( 2 1 0) 7-R( 0 2 0) 8-C( 1 2 0)
    9-R( 2 2 0) 10-C( 0 0 1) 11-C( 1 0 1) 12-C( 2 0 1)
    13-C( 3 0 1) 14-C( 0 1 1) 15-C( 1 1 1) 16-C( 2 1 1)
    17-C( 3 1 1) 18-C( 0 2 1) 19-C( 1 2 1) 20-C( 2 2 1)
    21-C( 3 2 1) 22-R( 0 0 2) 23-C( 1 0 2) 24-R( 2 0 2)
    25-C( 0 1 2) 26-C( 1 1 2) 27-C( 2 1 2) 28-R( 0 2 2)
    29-C( 1 2 2) 30-R( 2 2 2)

    DIRECT LATTICE VECTORS COMPON. (A.U.) RECIP. LATTICE VECTORS COMPON. (A.U.)
    X Y Z X Y Z
    17.8044525 0.0000000 -0.1043147 0.3535604 -0.0000000 0.1127826
    0.0000000 24.2698591 -0.0000000 -0.0000000 0.2588884 -0.0000000
    -3.5260288 0.0000000 11.0536983 0.0033366 0.0000000 0.5694882

    DISK SPACE FOR EIGENVECTORS (FTN 10) 44204368 REALS

    SYMMETRY ADAPTION OF THE BLOCH FUNCTIONS ENABLED

    #!/bin/bash
    #SBATCH --nodes=4
    #SBATCH --tasks-per-node=96
    #SBATCH -t 100:00:00
    #SBATCH -o vasp.out
    #SBATCH -e vasp.err
    #SBATCH -p ceres
    #SBATCH --export=ALL
    #SBATCH --mail-type=ALL
    #SBATCH [email protected]
    #SBATCH -J /90daydata/urea_kinetics/MgNH4SO4/camB3LYP_pob2TZVP/Raman

    module unload intel
    module load crystal
    mpirun -np 384 Pcrystal < INPUT

    6 0 0 Reply
    job314 job314
    OK, here we go. It just is stuck, always the same position in the output (ceres20-compute-46:0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95) (ceres24-compute-18:96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191) export TMPDIR=/local/bgfs/jonas.baltrusaitis/15383115 export TMOUT=5400 export SINGULARITY_TMPDIR=/local/bgfs/jonas.baltrusaitis/15383115 MAX NUMBER OF SCF CYCLES 200 CONVERGENCE ON DELTAP 10**-20 WEIGHT OF F(I) IN F(I+1) 30% CONVERGENCE ON ENERGY 10**-10 SHRINK. FACT.(MONKH.) 6 6 6 NUMBER OF K POINTS IN THE IBZ 64 SHRINKING FACTOR(GILAT NET) 6 NUMBER OF K POINTS(GILAT NET) 64 *** K POINTS COORDINATES (OBLIQUE COORDINATES IN UNITS OF IS = 6) 1-R( 0 0 0) 2-C( 1 0 0) 3-C( 2 0 0) 4-R( 3 0 0) 5-C( 0 1 0) 6-C( 1 1 0) 7-C( 2 1 0) 8-C( 3 1 0) 9-C( 0 2 0) 10-C( 1 2 0) 11-C( 2 2 0) 12-C( 3 2 0) 13-R( 0 3 0) 14-C( 1 3 0) 15-C( 2 3 0) 16-R( 3 3 0) 17-C( 0 0 1) 18-C( 1 0 1) 19-C( 2 0 1) 20-C( 3 0 1) 21-C( 0 1 1) 22-C( 1 1 1) 23-C( 2 1 1) 24-C( 3 1 1) 25-C( 0 2 1) 26-C( 1 2 1) 27-C( 2 2 1) 28-C( 3 2 1) 29-C( 0 3 1) 30-C( 1 3 1) 31-C( 2 3 1) 32-C( 3 3 1) 33-C( 0 0 2) 34-C( 1 0 2) 35-C( 2 0 2) 36-C( 3 0 2) 37-C( 0 1 2) 38-C( 1 1 2) 39-C( 2 1 2) 40-C( 3 1 2) 41-C( 0 2 2) 42-C( 1 2 2) 43-C( 2 2 2) 44-C( 3 2 2) 45-C( 0 3 2) 46-C( 1 3 2) 47-C( 2 3 2) 48-C( 3 3 2) 49-R( 0 0 3) 50-C( 1 0 3) 51-C( 2 0 3) 52-R( 3 0 3) 53-C( 0 1 3) 54-C( 1 1 3) 55-C( 2 1 3) 56-C( 3 1 3) 57-C( 0 2 3) 58-C( 1 2 3) 59-C( 2 2 3) 60-C( 3 2 3) 61-R( 0 3 3) 62-C( 1 3 3) 63-C( 2 3 3) 64-R( 3 3 3) DIRECT LATTICE VECTORS COMPON. (A.U.) RECIP. LATTICE VECTORS COMPON. (A.U.) X Y Z X Y Z 13.1430453 0.0000000 0.0000000 0.4780616 0.0000000 0.0000000 0.0000000 11.6066979 0.0000000 0.0000000 0.5413413 0.0000000 0.0000000 0.0000000 21.1989478 0.0000000 0.0000000 0.2963914 DISK SPACE FOR EIGENVECTORS (FTN 10) 53868000 REALS SYMMETRY ADAPTION OF THE BLOCH FUNCTIONS ENABLED TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT gordsh1 TELAPSE 186.18 TCPU 45.44
  • othmen1983
    othmen1983 othmen1983
    Geometry Optimisations

    Dear all, i want to use GHOST keyword in order to create an oxygen vacancy in the monoclinic structure of HfO2. when trying to lunch this JOB with the input1.d12, i obtain this msg: SCF abnormal end - no wf written in fort.9.
    Also when trying to do that manually by removing one oxygen according to input2.d12 it still fails. How to fix this problem please.
    thank you for your kind help

    1 0 0 Reply
    eascrizzi eascrizzi
    Hi Othmen! I think that you have a problem in the geometry sections of your input files. When dealing with monoclinic structures, only one angle (beta) has to be specified as alfa and gamma are 90 by default, see page 22 of Crystal User's Manual. Furthermore, in input1 the atomic coordinates are missing, while in input2 94 atoms coordinates are written but you specified that 95 atoms are present. Let me know if you have other problems
  • job314
    job314 job314
    Equation-of-State and Pressure

    Alessandro, I am having a blast finding the volume of the crystals using EOS which I can then use for supercell etc. I was wondering about the technically correct sequence here:

    -I run EOS, it prints
    SORTING VOLUMES/ENERGIES

     VOLUME (A^3)    ENERGY (a.u.)

 443.177886   -2.716943460865E+03
 451.049595   -2.716949077158E+03
 458.957263   -2.716952819603E+03
 466.951330   -2.716954739628E+03
 471.547619   -2.716955035989E+03
 475.033963   -2.716954889255E+03
 483.208420   -2.716953349891E+03
 491.475047   -2.716950220038E+03
 499.836229   -2.716945606438E+03

    +++++++ FITTING USING ALL POINTS +++++++

    USERS OF THIS EOS MODULE SHOULD KINDLY CITE THE FOLLOWING REFERENCE:

    A. Erba, A. Mahmoud, D. Belmonte and R. Dovesi, J. Chem. Phys., 140, 124703 (2014)

    EQUATION OF STATE VOL(A^3) E(AU) BM(GPa) BM PRIME

    MURNAGHAN 1944 471.7053 -2716.95501994 53.34 3.41
    BIRCH-MURNAGHAN 1947 471.7038 -2716.95502102 53.40 3.42
    POIRIER-TARANTOLA 1998 471.7006 -2716.95502119 53.41 3.43
    VINET 1987 471.7019 -2716.95502111 53.40 3.43

    POLYNOMIAL FITTING VOL(A^3) E(AU) BM(GPa)

    THIRD ORDER POLYNOMIAL 471.6937 -2716.95502707 53.73
    FOURTH ORDER POLYNOMIAL 471.6893 -2716.95503729 54.28
    FIFTH ORDER POLYNOMIAL 471.6651 -2716.95503712 54.28

    Now, is there a trick to make software plots lattice parameters for that minimum volume? I could not find any

    Since I could not find any, I take the two lattice parameters around that lowest energy volume and extrapolate lattice parameters to it. My second question then is - should I run one more CVOLOPT using that EOS lowest volume extrapolated lattice parameters to arrive to something that is not only lowest volume, but also optimal lattice parameters for that volume OR whatever comes out from EOS is already optimal lattice parameters for that minimal volume?

    thank you

    13 0 0 Reply
    aerba aerba
    For the purpose of finding the minimum energy structure to then do Raman calculations, it is. EOS gives you much more than that of course: the p(V) or, equivalently, V(p) relation (i.e. structure as a function of pressure), the bulk modulus K(p), and allows to compute the enthalpy H(p).
  • aimipa
    aimipa aimipa
    Other Questions

    Hi,

    I need to perform a properties computation, specifically i need to study
    Electron Transport Properties (BOLTZTRA).
    However, i am particularly interested in one direction of the 3D space.
    Is there an option to use an anisotropic grid in the NEWK block?
    If not, is there another way to use an anisotropic grid in properties?

    Thank you in advance

    1 0 0 Reply
    eascrizzi eascrizzi
    Hi aimipa! Yes there is an option to set an anisotropic grid from NEWK, you can find it at page 346 of the CRYSTAL User's Manual, see also the screenshot I attach below. You have to set IS=0 and then you can choose three different shrinking factors along B1, B2 and B3. For example: NEWK 0 12 12 8 4 sets a shrinking factor of 12, 8 and 4 along the three reciprocal lattice vectors. I have never tested this anisotropic option in a BOLTZTRA calculation, would you mind let me know if it works? [image: newk.png]
  • job314
    job314 job314
    Geometry Editing

    I am trying to input the following cif file Mg, Acta Crystallographica 17 (1964) 1478-1479.cif which is P 21/a space group 14. However, in the manual space group 14 is P 21/c and my geometry ends up looking funky. I also tried entering manually, e.g. P 2 1a but that simply does not work. Can you help me enter the correct space group here?

    CRYSTAL
    1 0 0
    P 2 1a
    9.383 12.669 6.220 107.05
    20
    7 0.1321 0.3509 0.3611
    1 0.058 0.337 0.225
    1 0.208 0.305 0.394
    1 0.095 0.344 0.487
    1 0.174 0.421 0.346
    12 0 0 0
    8 0.1603 -0.1094 -0.0307
    8 0.1685 0.1042 0.1656
    8 -0.0017 -0.0687 0.2986
    1 0.2 0.091 0.317
    1 0.227 0.134 0.116
    1 0.252 -0.096 0.059
    1 0.143 -0.176 -0.008
    1 -0.097 -0.066 0.341
    1 0.027 -0.135 0.325
    16 0.0953 -0.3605 0.2575
    8 -0.0469 -0.4174 0.2116
    8 0.2185 -0.4328 0.3718
    8 0.1185 -0.3211 0.0456
    8 0.0951 -0.2702 0.4089

    4 0 0 Reply
    aerba aerba
    Good! The clean way is: CRYSTAL 1 0 0 P 21/A I guess the extra "1"s you put are safe as they correspond to the identity operator.
  • dariag
    dariag dariag
    Vibrational Spectroscopies: IR, Raman, INS

    Is there a way to restart a Raman calculation that crashed, e.g. for wall time limit on a national supercomputer, at the half of the CPHF cycle (like at the point ELECTRIC FIELD APPLIED ALONG CARTESIAN DIRECTIONS XZ)?

    Thank you

    5 0 0 Reply
    dariag dariag
    Yes sure. No problem. I'm copying it here below. Thank you for the help Daria Furfural CRYSTAL 0 0 0 19 7.83542762 10.92181175 14.94182734 90.000000 90.000000 90.000000 33 8 1.907561246186E-01 3.035506248522E-01 4.408415126674E-01 8 -4.953260939445E-01 3.221701934644E-01 3.435788389827E-01 6 2.036695655476E-01 3.000622663369E-01 3.482645168957E-01 6 4.363374159111E-02 2.908170991680E-01 3.122160878064E-01 1 1.581732742072E-02 2.880586476013E-01 2.419150131741E-01 6 -7.402527715589E-02 2.893444053747E-01 3.842913887226E-01 1 -2.109486401803E-01 2.822752418693E-01 3.798189138779E-01 6 2.099722211847E-02 2.968688203007E-01 4.606664256414E-01 1 -9.310483322231E-03 2.937832972654E-01 -4.691825366176E-01 6 3.647591498990E-01 3.132132214593E-01 3.052219591009E-01 1 3.550467304924E-01 3.168499490771E-01 2.320173417360E-01 8 2.803460822693E-01 -3.091160241316E-01 4.442088720927E-01 8 -4.110526913885E-01 -3.641439806750E-01 3.516630126321E-01 6 2.872037985115E-01 -3.695128622796E-01 3.626185432797E-01 6 1.245767077225E-01 -3.991101749711E-01 3.362778399038E-01 1 9.163169834882E-02 -4.467733390550E-01 2.755816936910E-01 6 1.226510841197E-02 -3.550438914407E-01 4.034527830796E-01 1 -1.250093786328E-01 -3.609739865930E-01 4.033488316714E-01 6 1.122081912874E-01 -3.009269785992E-01 4.671425614917E-01 1 8.596288473646E-02 -2.539158941058E-01 -4.709004162095E-01 6 4.474098992917E-01 -3.907868742186E-01 3.203804132925E-01 1 4.349587971852E-01 -4.336723578587E-01 2.540887571847E-01 8 1.068738713332E-01 -3.851604875541E-02 3.194441316968E-01 8 -2.354778627755E-01 -1.170305051641E-02 3.709929081706E-01 6 5.921416878240E-02 -5.109842318475E-03 4.052174692072E-01 6 2.027905991547E-01 1.001107546720E-02 4.563966208009E-01 1 2.038099671676E-01 3.508046669402E-02 -4.738476409789E-01 6 3.453540637796E-01 -1.523126326522E-02 4.003413693017E-01 1 4.790458182320E-01 -1.335338648893E-02 4.173410231626E-01 6 2.808235437569E-01 -4.461452496729E-02 3.184022003331E-01 1 3.367732131084E-01 -7.306049141011E-02 2.558072164743E-01 6 -1.187612609562E-01 6.696688015001E-03 4.250681762815E-01 1 -1.454796120848E-01 3.516201574611E-02 4.940534466886E-01 FREQCALC NUMDERIV 2 INTENS INTRAMAN INTCPHF END END BASISSET POB-TZVP-REV2 DFT B3LYP-D3 XLGRID ENDdft SHRINK 4 4 TOLDEE 10 SCFDIR LEVSHIFT 6 1 FMIXING 30 TOLINTEG 7 7 7 7 14 EXCHSIZE 13220300 BIPOSIZE 13220300 ENDscf
  • Gryffindor
    Gryffindor Gryffindor
    Density-of-States

    Hi
    I’m using HSE06/TZVP LOT to compute band gaps for a series of ZIF frameworks, and I’m noticing a systematic overestimation of ~0.6–1.2 eV when compared with published reference values.

    What level of absolute accuracy should I generally expect from CRYSTAL’s HSE06 band gaps? Are there specific numerical settings you recommend to avoid this discrepancy?
    I am trying to understand what I may be doing wrong.

    Thanks

    3 0 0 Reply
    Aleks Aleks
    Hi, Hmmm...even though the SI file of the paper you have shared does point to using HSE06, it remains not entirely clear whether its parameters were kept default or altered (for all systems together or individually for instance). There are also differences between what different codes consider as "default" settings. For example, within the code used in the paper (VASP, nice code, no doubt), the defaults for HSE06 read (taken from https://www.vasp.at/wiki/index.php/List_of_hybrid_functionals) : $$ \omega= 0.2\ \mathring{A} , \quad c = 0.25, \quad \text{correlation}=\text{PBE}, $$ with the first number reading the range separation parameter (omega) and the second the fraction of exact exchange used (c). Within CRYSTAL (also nice code, no doubt), these read (taken from the manual, page 138): $$ \omega= 0.11\ a_0^{-1}, \quad c = 0.25, \quad \text{correlation}=\text{PBE}, $$ adopting the same labels. Not sure about the exact definition of units (perhaps a developer can comment if this is indeed Bohr radius as assumed?), but you can already see the subtle differences having to be taken into account when comparing between codes. A few other thoughts worth considering: In the paper, the structure was optimized with PBEsol and on top of that geometry HSE06 was applied as a single-point calculation. Not sure about the exact composition of those ZIFs, but the structural differences could play a significant role as well (planewave codes are very costly when optimizing a structure with hybrid functionals). Here is also a good read on this topic: doi.org/10.1088/2516-1075/aafc4b One final small comment. Within the PAW formalism implemented in VASP, scalar relativistic effects are included in the pseudopotentials by default. No problem, cool feature, but should be taken into account when comparing results, especially for heavier elements (longer discussion found here https://blog.vasp.at/forum/viewtopic.php?t=902) Hope this helps! Cheers, Aleks
  • LUXiu
    LUXiu LUXiu
    Spin-Orbit Coupling and SCDFT

    Hi,

    I have recently been running SOC calculations for materials with different types of relativistic basis sets for each element. For instance, NdI2, in which iodine has Stuttgart, but Neodymium only has Columbus based on the manual. Here are my two concerns:

    1. Is running SOC with different relativistic basis sets for each element likely to produce reliable results?

    2. In the CRYSTAL23 manual, page 91:
      "As for the Columbus and Stuttgart-Cologne ECP libraries, molecular basis sets are available online in clickable periodic tables at: http://people.clarkson.edu/~pchristi/reps.html"
      The link is not working. So far, I made the basis set manually from the paper. But it would be useful if users had access to it.

    Btw, thanks for running the forum!

    2 0 1 Reply
    LUXiu LUXiu
    Thanks Jacques! These are very informative. The information for specific basis sets is helpful, I will try them.
  • matscidanny
    matscidanny matscidanny
    Single-Point Calculations

    I wanted to understand better how the Fermi level is determined in CRYSTAL. Looking through the manual, I found that there is mention about this in Section 18.7: "The technique adopted to compute EF and the P matrix in the SCF step is described in reference [100]."

    Ref. [100] is the following: V. R. Saunders et al. Electronic structure theory: from molecules to crystals. private communication, 1999.

    The only thing I could find about ref. [100] was this google scholar entry which does not have a link to the article. I was wondering if there is any information about this somewhere else, or if you know where we could have access to the original paper.

    2 0 0 Reply
    matscidanny matscidanny
    Hello Prof. Erba, Thank you for providing the reference and relevant pages. This is very useful. Best, Danny
  • Ehsangowdini
    Ehsangowdini Ehsangowdini
    Spin-Orbit Coupling and SCDFT

    Dear Crystal Team
    Hi

    I was wondering If I can use the TZVP_rev2 basis set posted in the official website of CRYSTAL for Mg and Si atoms for SOC calculation ?

    e.g.
    Mg_pob_TZVP_rev2

    12 9
    0 0 7 2.0 1.0
    31438.3495550 0.00060912311326
    4715.51533540 0.00470661964650
    1073.16292470 0.02413582065700
    303.572387680 0.09362895983400
    98.6262510420 0.26646742093000
    34.9438084170 0.47890929917000
    12.8597851990 0.33698490286000
    0 0 3 2.0 1.0
    64.8769130040 0.01918088930700
    19.7255207770 0.09091370439200
    2.89518043390 -0.39563756125000
    0 0 2 2.0 1.0
    1.19604547100 1.68276033730000
    0.54329451156 0.52141091954000
    0 0 1 0.0 1.0
    0.83471188300 1.00000000000000
    0 0 1 0.0 1.0
    0.14506887000 1.00000000000000
    0 2 5 6.0 1.0
    179.871896120 0.00537995490180
    42.1200693760 0.03931801409800
    13.1205030320 0.15740129476000
    4.62575036090 0.35919094128000
    1.66952110160 0.45533379310000
    0 2 1 0.0 1.0
    0.56631001000 1.00000000000000
    0 2 1 0.0 1.0
    0.18813966000 1.00000000000000
    0 3 1 0.0 1.0
    0.29355357000 1.00000000000000

    6 0 0 Reply
    Ehsangowdini Ehsangowdini
    Thank you so much this helped a lot
  • Yachao_su
    Yachao_su Yachao_su
    Geometry Optimisations

    Hi all,

    According to the CRYSTAL manual, for optimal parallel performance when using Pcrystal, the number of MPI processes should ideally not exceed the total number of irreducible representations associated with the k-points (assuming symmetry is applied).

    However, after going through the output file from a recent run, I wasn’t able to find this number explicitly printed.Would there be a recommended way to extract or compute this value within CRYSTAL?
    Or is it typically something one estimates manually based on the symmetry and k-point grid? Any guidance would be greatly appreciated!

    2 0 0 Reply
    Yachao_su Yachao_su
    Thank you very much for the detailed explanation—this really helped clarify things for me! The plot and your explanation made it all very clear.