World

Hi!

I am trying to compile Crystal 23 on Xeon E-2695v2 processors, but they are not supported by the Intel Toolkit. I am missing the instruction vfmadd231sd, giving GDB output:

Program received signal SIGILL, Illegal instruction.
0x0000000000e915a2 in timer_module_mp_init_timer_ ()
(gdb) bt full
#0 0x0000000000e915a2 in timer_module_mp_init_timer_ ()
No symbol table info available.
#1 0x0000000006828517 in initpp_ ()
No symbol table info available.
#2 0x00000000004073bd in MAIN__ ()
No symbol table info available.
(gdb) info registers
Missing register name
(gdb) x/i $rip
=> 0xe915a2 <timer_module_mp_init_timer_+82>:
vfmadd231sd 0x73c02ed(%rip),%xmm0,%xmm3 # 0x8251898

Could you please suggest a compilation method, such as using GCC or any other compiler? Is there a way to compile it using CMake?

Thank you!

Hello,

I am trying to run a single-point calculation in a 2D heterostructure that I had optimized in the past using a different code.

I am taking the following error in the output file, which implies a problem with geometry.

**NEIGHBORS OF THE NON-EQUIVALENT ATOMS

 N = NUMBER OF NEIGHBORS AT DISTANCE R
    ATOM  N     R/ANG      R/AU   NEIGHBORS (ATOM LABELS AND CELL INDICES)
 DISTANCE BETWEEN ATOMS   1 290 TOO SMALL: 0.3226 ANGSTROM
 PLEASE CHECK GEOMETRY
 ERROR **** NEIGHB **** USE KEYWORD SMALLDIST TO RUN ANYWAY**

However, I haven't yet managed to find in the tutorials or in the manual the keyword SMALLDIST.
Any suggestions?

Thanks in advance,
Ilias

Hello,

Is there a way to print the eigenvectors and eigenvalues of a system after a simulation has finished running?

Chris

Dear developers and others.

I am a bit confused about the output of the second hyperpolarizability calculation:

*******************************************************************************
 SECOND HYPERPOLARIZABILITY (GAMMA) TENSOR
  COMPONENT      GAMMA
 *******************************************************************************

     XXXX    1.0077E+04 (   1.0077E+04)
     XXXY    4.1650E-13 (   1.9458E-08)
     XXXZ    5.9072E-13 (   2.5339E-08)
     XXYY    3.9702E+03 (   3.9702E+03)
     XXYZ   -1.0917E+03 (  -1.0917E+03)
     XXZZ    3.2158E+03 (   3.2158E+03)
     XYYY    7.0166E-13 (   1.4903E-07)
     XYYZ    5.2035E-14 (   2.4139E-08)
     XYZZ    1.9596E-13 (   1.3356E-08)
     XZZZ    6.7898E-13 (  -7.7814E-09)
     YYYY    7.2247E+03 (   7.2247E+03)
     YYYZ   -4.5162E+02 (  -4.5162E+02)
     YYZZ    3.0331E+03 (   3.0331E+03)
     YZZZ   -1.5476E+01 (  -1.5476E+01)
     ZZZZ    1.1089E+04 (   1.1089E+04)

What are the quantities in parentheses? Are these a result of some rotation? If so, then why only the minor components change? Which ones are the real ones I should use?

Thank You in advance.

Hello,

I would like to run CRYSTAL23 on a machine where the host CPU is an Intel Xeon Phi KNL 7250 (Knights Landing) — the KNL is used as the main host processor, not as a coprocessor. I’d like advice on how to build and run CRYSTAL23 to get the best possible performance on this platform.

Specifically, could you please advise on what hybrid MPI+OpenMP layout tends to perform best on KNL for CRYSTAL23?
Do you recommend running KNL in Cache mode (MCDRAM as L3 cache) or Flat mode (explicit allocation), for a CRYSTAL23?

Thank you in advance for any guidance and best practices you can share.

Best regards

Hello!
In many articles where CRYSTAL is used, I have come across the following phrase

The energy optimization of the basis sets was undertaken using the Billy software.

which is accompanied by a link to the manual. But there is no information about it in the manual or anywhere else. Can anyone explain what it is? Thank you in advance!

Dear CRYSTAL community,

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Hello,

I'm running an elastic and piezolectric calculation that stops due to an error when reading the fort.62 file. Please find below the error message provided by Slurm (scheduler manager):

forrtl: Invalid argument
forrtl: severe (24): end-of-file during read, unit 62, file fort.62

The error happens at the end of the first strain step or at the beginning of the second, though the output file was not updated.

Is there a solution to this error? It happened twice in a row. Is it possible to restart a piezoelectric/elastic calculation?

Kind regards,
Pierre

Hi all, trying to eliminate a negative frequency via SCANMODE. Job aborts with no particular message before scanning. I have FREQINFO file for the restart
FREQINFO.DAT INPUT.d12 input.f34 input.out

EXTERNAL
FREQCALC
RESTART
SCANMODE
1 -10 10 0.4
1
END
END

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SCAN ALONG NORMAL MODES
STARTING POINT: -10 ENDING POINT: 10 STEP:   0.40000
(THE STEP IS GIVEN AS TIMES OF THE CLASSICAL AMPLITUDE AT THE QUANTUM GROUND
STATE ENERGY. THE MAX ATOMIC DISPLACEMENT IN THE STEP IS GIVEN IN BOHR
WITHIN SQUARE BRACKETS)

 MODE(CM-1) DISPLAC   TOTAL ENE(DFT)(AU)  CLASSICAL HARM ENE(AU)  NCYC    DE
[MAX DISP -NATOM-]
  1( -62.1)
[   0.113 -    3-]

Hi

I have two questions regarding Band Plot,

1- Is there a way to plot Orbital-Resolved bands from CRYSTAL output?
2- Is there a way to create .d3 file for 2D bands?

Thank you so much

Hi,

I am curious if Crystal accepts something like the cc-pVDZ-DK Gaussian basis set for the calculation of SOC effects in transition metals? From what I gather, it is an all electron basis set (https://www.basissetexchange.org/basis/cc-pvdz-dk/format/crystal/?version=0&elements=28). Would this require the keyword INPSOC in the basis set block of the input file?

Chris

Hi,

I am trying to simulate a slab model of thin film on substrate. When I ran the job, there was a convergence problem in the SCF cycle. My initial suspect was the interface, since I don't have extract geometrical configuration it was only a pure guess.

So I ran a calculation with only the substrate, but still it did not convergence in SCF cycle with MPPcrystal. I reran the same calculation of only substrate with Pcrystal it converged in 20 cycles. So why is there discrepancy between both versions. I am attaching the input and output for both calculation here.
Substrate_MPP.out
Substrate_MPP.d12
Substrate_Pcrystal.out
Substrate_Pcrystal.d12

To check if there is any issue with the MPP compilation, I added the REPLDATA tag in MPP input, so that it runs as Pcrystal, this time it again converged in 20 cycles.

I would like to use MPPcrystal for my final structure of thin film to speedup the calculation and avoid memory issues, so could you let me what is the issue I am encountering with both the versions.

Thanks & Regards,
Rams

Hello all. I have a question about CRYSTAL23 and how it works when it comes to calculating eigenvalues for certain k-points. Let's look at the example of SiO2 cell with 12 ions:

*** 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( 1 1 0) 6-C( 2 1 0) 7-C( 2 2 0) 8-C( 0 0 1)
9-C( 1 0 1) 10-C( 2 0 1) 11-C( 3 0 1) 12-C( 1 1 1)
13-C( 2 1 1) 14-C( 2 2 1) 15-C( 0 0 2) 16-C( 1 0 2)
17-C( 2 0 2) 18-C( 3 0 2) 19-C( 1 1 2) 20-C( 2 1 2)
21-C( 2 2 2) 22-R( 0 0 3) 23-C( 1 0 3) 24-C( 2 0 3)
25-R( 3 0 3) 26-C( 1 1 3) 27-C( 2 1 3) 28-C( 2 2 3)

So here it shows 28 k-points for the 6x6x6 Monkhorst-Pack grid, and if I understand correctly, the reason why it's not showing all 216 points is because the program recognizes the crystal symmetry so it knows that the energy at (1 0 0) is the same as at (0 1 0), (0 0 1), (-1 0 0), etc?

If that is the case, then to build a high-symmetry path along Gamma-X-K-Gamma, for example... we could just take the points 4-R( 3 0 0) and 7-C( 2 2 0) and divide them by IS, which in this case is 6 to get the points (0.5, 0, 0) and (1/3, 1/3, 0). Would that be correct? Because that would make the extraction of eigenvalues quite simple for this path.

Thanks in advance,

Chris

Dear CRYSTAL support and others,

I am new to CRYSTAL, hence the error is probably on my side.

I am trying to perform a geometry optimization of a molecular crystal and then use it to compute the dielectric susceptibilities. If I understand it correctly, I need to use the keyword EXTPRT within the OPTGEOM section to export the optimized geometry and get a fort.34 file, which I then have to use in my next calculation with EXTERNAL keyword for the geometry.

However, the run fails with an error message:

ERROR **** CONOPT_ **** KEYWORD EXTPRT      NOT ALLOWED
forrtl: error (78): process killed (SIGTERM)

If I remove the EXTPRT keyword, the optimization runs just fine (at least with some of the functionals)! But I cannot get the geometry out of the .OUT file. I tried using the cell parameters I got after "CRYSTALLOGRAPHIC CELL" and run an elastic constant calculation; however, it failed with "WARNING!! FORCE 9 AT CENTRAL POINT IS GREATER THAN 10^-4. OPTIMIZE THE STRUCTURE AND RE-RUN" (there were multiple such messages for multiple force vectors) and the error

 ERROR **** BFGS_ **** PXK TOO SMALL

So I am now at loss trying to get the geometry out of my optimization. Can anyone help please?

Please find inputs for the jobs attached.
CS2_normalP_r2SCANh.pob_tzvp_rev2_opt_withEXTPRT.out CS2_normalP_r2SCANh.pob_tzvp_rev2_opt_withoutEXTPRT.out CS2_r2SCANh.pob_tzvp_rev2_elconst_manualCOORDS.out

Dear Admin,
I hope this message finds you well.
I did an HSE06 calculation to find the band gap in a 2D material.
I got the value of 1.4 eV for the band gap, but VBM and CBM positions are not correct in the output of CRYSTAL:
TOP OF VALENCE BANDS - BAND 15; K 1; EIG -8.7684392E-01 AU
BOTTOM OF VIRTUAL BANDS - BAND 16; K 48; EIG -2.2555491E-01 AU
Can you help me solving this problem in this case?
I have attached the input and output files.INPUT.d12 output.out

Thank you in advance,
Masoud

Dear CRYSTAL developers and users,

I would like to perform a band edge alignment calculation by referencing the valence/conduction band edges to the vacuum level in the context of photocatalysis. For this purpose, I need the planar-averaged electrostatic potential along the slab normal direction.

I have already generated the electrostatic potential in Gaussian cube format using the POTCUBE keyword (file: POT_CUBE.DAT).

My questions are:

Does CRYSTAL provide any direct tool or utility to compute the planar average of the electrostatic potential from POT_CUBE.DAT (or other related output files)?

If not, is it recommended to post-process the cube file externally (e.g., with scripts, VESTA, or custom Python routines)?

Any guidance, example workflows, or scripts would be greatly appreciated.

Best regards,
Chhatra Subba

Hi,

I am trying to calculate defect formation energies following Bailey's method (10.1103/PhysRevB.81.205214). In the paper they deal with anion vacancies by removing the anion and retaining its basis sets. When I follow this method I end up with a negative value in the SCF on the anion. For example, for Ca2ZnN2 I replaced one of the nitrogens with a 0 basis set (shown below), and using ATOMONLY to optimise (neutral defect). The calculation converged but the value on the anion vacancy was -1.3085951 (shown below) and when checking the geometry I found that the vacancy has merged with a neighbouring Zn atom. I can get the calculation to converge without producing a negative value in the SCF using FRAGMENT to keep the vacancy and the cation it merges with in place, but if I restart the calculation without FRAGMENT it will not converge. For Ca2ZnN2 this happens across all charge states of the anion vacancy I have tried (-2,-1,0,1,2). I have so far looked at five nitride compounds and this behaviour happens in three of them.

What does the negative value here mean?
Is there a way around this besides using FRAGMENT?

I would appreciate any help.
Thanks!

0 4
0 0 6 0 1.0
 4150.0 0.001845
 620.1 0.01416
 141.7 0.06863
 40.34 0.2286
 13.03 0.4662
 4.47 0.3657
0 1 2 0 1.0
 5.425 -0.4133 0.238
 1.149 1.224 0.859
0 1 1 0.0 1.0
 0.2832 1.0 1.0
0 3 1 0.0 1.0
 0.8 1.0 1.0

 TOTAL ATOMIC CHARGES:
   8.1376632   8.1212165   8.1248702   8.1206438   8.1229391   8.1124523
   8.1236540   8.1193919   8.1205622   8.1248273   8.1212382   8.1375264
   8.1125477  -1.3072013   8.1125440   8.1257835   8.1206284   8.1377578
   8.1194311   8.1236914   8.1124840   8.1226134   8.1377863   8.1205830
   8.1173933   8.1258681   8.1207059   8.1240065   8.1199368   8.1207339
   8.1194493   8.1236090   8.1239754   8.1207282   8.1258496   8.1174264
   8.1206901   8.1197740   8.1207285   8.1206837   8.1239699   8.1174550
   8.1236610   8.1194374   8.1206695   8.1199530   8.1174242   8.1240181
  29.6808307  29.6816377  29.6812243  29.6819752  29.6710460  29.6849333
  29.6759320  29.6852850  29.6820377  29.6812695  29.6815737  29.6808892
  29.6849531  31.6491331  29.6849573  29.6819626  29.6819686  29.6807771
  29.6852479  29.6759483  29.6849717  29.6711835  29.6807525  29.6819924
  19.0454220  19.0459330  19.0431780  19.0431020  19.0432569  19.0451214
  19.0452198  19.0462440  19.0451348  19.0432244  19.0430908  19.0432040
  19.0459080  19.0452863  19.0925535  19.0432123  19.0444657  19.0432576
  19.0459533  19.0430879  19.0462163  19.0453976  19.0430765  19.0459700
  19.0634872  19.0436933  19.0366981  19.0429866  19.0441015  19.0430915
  19.0628392  19.0436877  19.0430659  19.0443015  19.0429753  19.0368146
  19.0436806  19.0628125  19.0649399  19.0442844  19.0435415  19.0442819
  19.0437081  19.0456880  19.0436812  19.0634794  19.0457099  19.0436711

Hi all, I am not getting the right geometry inputs for 1/3 and 2/3 positions. For example, for the structure below, I am trying to enter for the group 164:

CRYSTAL
0 0 0
164
3.186 4.653
3
27	0.0 0.0 0.0
1 0.333 0.6666 0.4134
8	 0.3333 0.666 0.2128

and it ends up being incorrect stoichiometry, which tells me these fractional positions were not parsed correctly.

 CRYSTAL CALCULATION
 (INPUT ACCORDING TO THE INTERNATIONAL TABLES FOR X-RAY CRYSTALLOGRAPHY)
 CRYSTAL FAMILY                       :  HEXAGONAL   
 CRYSTAL CLASS  (GROTH - 1921)        :  DITRIGONAL SCALENOHEDRAL             

 SPACE GROUP (CENTROSYMMETRIC)        :  P -3 M 1        

 LATTICE PARAMETERS  (ANGSTROMS AND DEGREES) - CONVENTIONAL CELL
        A           B           C        ALPHA        BETA       GAMMA
     3.18600     3.18600     4.65300    90.00000    90.00000   120.00000


 NUMBER OF IRREDUCIBLE ATOMS IN THE CONVENTIONAL CELL:    3

 INPUT COORDINATES

 ATOM AT. N.              COORDINATES
   1  27     0.000000000000E+00  0.000000000000E+00  0.000000000000E+00
   2   1     3.330000000000E-01  6.666000000000E-01  4.134000000000E-01
   3   8     3.333000000000E-01  6.660000000000E-01  2.128000000000E-01

 *******************************************************************************

 << INFORMATION >>: FROM NOW ON, ALL COORDINATES REFER TO THE PRIMITIVE CELL

 *******************************************************************************

 LATTICE PARAMETERS  (ANGSTROMS AND DEGREES) - PRIMITIVE CELL
       A          B          C        ALPHA      BETA     GAMMA        VOLUME
    3.18600    3.18600    4.65300    90.00000  90.00000 120.00000     40.903006

 COORDINATES OF THE EQUIVALENT ATOMS (FRACTIONAL UNITS)

 N. ATOM EQUIV AT. N.          X                  Y                  Z

   1   1   1   27 CO    0.00000000000E+00  0.00000000000E+00  0.00000000000E+00

   2   2   1    1 H     3.33000000000E-01 -3.33400000000E-01  4.13400000000E-01
   3   2   2    1 H     3.33400000000E-01 -3.33600000000E-01  4.13400000000E-01
   4   2   3    1 H     3.33600000000E-01 -3.33000000000E-01  4.13400000000E-01
   5   2   4    1 H    -3.33600000000E-01  3.33400000000E-01 -4.13400000000E-01
   6   2   5    1 H    -3.33000000000E-01  3.33600000000E-01 -4.13400000000E-01
   7   2   6    1 H    -3.33400000000E-01  3.33000000000E-01 -4.13400000000E-01
   8   2   7    1 H    -3.33000000000E-01  3.33400000000E-01 -4.13400000000E-01
   9   2   8    1 H    -3.33400000000E-01  3.33600000000E-01 -4.13400000000E-01
  10   2   9    1 H    -3.33600000000E-01  3.33000000000E-01 -4.13400000000E-01
  11   2  10    1 H     3.33600000000E-01 -3.33400000000E-01  4.13400000000E-01
  12   2  11    1 H     3.33000000000E-01 -3.33600000000E-01  4.13400000000E-01
  13   2  12    1 H     3.33400000000E-01 -3.33000000000E-01  4.13400000000E-01

  14   3   1    8 O     3.33300000000E-01 -3.34000000000E-01  2.12800000000E-01
  15   3   2    8 O     3.34000000000E-01 -3.32700000000E-01  2.12800000000E-01
  16   3   3    8 O     3.32700000000E-01 -3.33300000000E-01  2.12800000000E-01
  17   3   4    8 O    -3.32700000000E-01  3.34000000000E-01 -2.12800000000E-01
  18   3   5    8 O    -3.33300000000E-01  3.32700000000E-01 -2.12800000000E-01
  19   3   6    8 O    -3.34000000000E-01  3.33300000000E-01 -2.12800000000E-01
  20   3   7    8 O    -3.33300000000E-01  3.34000000000E-01 -2.12800000000E-01
  21   3   8    8 O    -3.34000000000E-01  3.32700000000E-01 -2.12800000000E-01
  22   3   9    8 O    -3.32700000000E-01  3.33300000000E-01 -2.12800000000E-01
  23   3  10    8 O     3.32700000000E-01 -3.34000000000E-01  2.12800000000E-01
  24   3  11    8 O     3.33300000000E-01 -3.32700000000E-01  2.12800000000E-01
  25   3  12    8 O     3.34000000000E-01 -3.33300000000E-01  2.12800000000E-01

Dear everyone,
we are trying to calculate nanotube and we expected that the system owe the band gap about 2.0 eV, in the optimization process, words "POSSIBLY CONDUCTING STATE" appeared in the SCF file. Finally, the band gap converge to about 0.5 eV with incompact structure . we tried some methods as the follows: 1) reoptimization, sometime the structure changes a lot, the result seems to be correct, but it does not work for most cases. 2) try different keyword in optgeom section , such as, TOLDEG TOLDEX TOLDEE change to default value *0.1 , respectively; Hessian updating method change default to OLDCG; NoGUESS was added; ALLOWTRUSTR was added, while try different MAXTRADIUS TRUSTRADIUS for different number; the ICODE for FINALRUN was also 4; 3) try different parameter in SCF section: change the DFT functional (HSE06, B3LPY, PBE0); change convergence method( DIIS; LEVSHIFT; ANDERSON; BROYSDEN); the number of K point in K point sample was also changed with different value (8, 10 ,16); 4) the basis set also change, in most cases the pob_TZVP_rev2 were adopted.
Unfortunately, the optimized structures seem to be unreasonable with different trying mentioned above.
The system and basis parameter can be seen from the INPUT file as attachment. All the jobs were finished in Pcrystal, in the crystal user's Manual, it is noted that the keyword "FINALRUN" does not work in Pcrystal, we want to know whether it is true(crystal17, page 338).
I would appreciate any help.
Thanks!
[INPUT](Invalid file type. Allowed types are: .png, .jpg, .bmp, .txt, .gif, .d12, .out, .dat, .d3, .outp, .input, .output, .dat, .f34, .cif, .pdf, .f9, .f20, .f13, .freqinfo, .out2, .log, .jpeg)

Hello,
I am a user of CRYSTAL17 and would like to consult about some fundamental issues related to structural optimization and vibrational (frequency) calculations.
It is possible to calculate IR and Raman intensities and phonon DOS under various pressures using the "FREQCALC" block and specifying the "PRESSURE" (in MPa) after performing structural optimization. However, I am confused about the following:
Q1:
If structural optimization is performed using the default settings without specifying "EXTPRESS" (external pressure, in Hartree/Bohr³), the resulting structure corresponds to a (local or global) minimum on the potential energy surface at zero pressure. If a frequency calculation is then carried out with a non-zero "PRESSURE" applied, the potential energy surface effectively changes. This could result in imaginary vibrational modes, which is the source of my confusion.
Q2:
Similarly, if I perform a full structural optimization (including both cell parameters and atomic positions) under an applied external pressure (e.g., setting "EXTPRESS" to 0.001 Hartree/Bohr³ ≈ 29.457 GPa), I obtain a "contracted" structure with reduced cell parameters and shorter chemical bonds. If I then perform a frequency calculation on this optimized structure but set a "PRESSURE" value lower than the pressure used during optimization (e.g., less than 29.457 GPa), it seems reasonable to expect that imaginary modes might appear due to the mismatch between the pressure used in optimization and that used in the vibrational analysis. It is quite confusing.

Thanks~!