World

Hello!
I am struggling to understand the way in which CRYSTAL rotates the atoms. Here is my structure:
reference.f34
I want to rotate all atoms so that Mn remains in place, and oxygens NN 21&23 move to the ac (xz) plane. This, in essence, is a rotation around the axis 10Mn-12P, the result of which should be that
Y coordinate of Mn = Y(O21) = Y(O23). The angle that should work is +-24.7159 degrees, depending on the direction that CRYSTAL uses.
So, I tried

ATOMROT
0 # include all atoms
999 1 # no translation & rotation around a specified axis
10 12 # atom labels that define rotation axis
+/-24.7159 # angle (degrees)

To the effect of

ALL THE  36 ATOMS IN THE REFERENCE CELL ARE MANIPULATED

SELECTED ATOMS ARE ROTATED AROUND THE AXIS DEFINED BY TWO ATOMS:  10  12
(DIRECTION COSINES  0.000  0.000 -1.000) BY AN ANGLE:  24.72

ATOM  10 AT.N.  25 COORDINATES   4.46889   0.00000   2.24246
ATOM  21 AT.N.   8 COORDINATES  -2.74300   2.67751   3.17915
ATOM  23 AT.N.   8 COORDINATES   3.56177   1.05955   3.17915

and

ALL THE  36 ATOMS IN THE REFERENCE CELL ARE MANIPULATED

SELECTED ATOMS ARE ROTATED AROUND THE AXIS DEFINED BY TWO ATOMS:  10  12
(DIRECTION COSINES  0.000  0.000 -1.000) BY AN ANGLE:  -24.72

ATOM  10 AT.N.  25 COORDINATES   4.46889   0.00000   2.24246
ATOM  21 AT.N.   8 COORDINATES  -2.25530  -3.73706   3.17915
ATOM  23 AT.N.   8 COORDINATES   3.07407   0.00001   3.17915

So the second method maybe worked? Except that I have been unable to visualize/confirm it using VESTA, because the output of edited geometry section looks the same as the input*.

So, my questions are:

1. how to validate the result of rotation?
2. when using ROTCRY+MATROT, where is the origin of rotation?
3. which method of rotation I should use in this situation?

*VESTA, of course, does not open .f34 files, so my usual workflow is to convert CRYSTAL output to a VASP-POSCAR format:

Structure description line
1.0 #scaling factor
[DIRECT LATTICE VECTORS CARTESIAN COMPONENTS (ANGSTROM)]
List-of-elements
Amounts-of-each-element
Direct or Cartesian # coordinate format
[list of coordinates in the selected format]

Hi,

I am doing a frequency with intensities calculation on an Iron complex with four Fe atoms in the unit cell. I am trying to do the ferromagnetic state with HSE06-D3 functional and the POB-tzvp-rev2 basis. I have optimised the cell, copied the optimised cell to fort.34 and copied the fort.9 file of the optimised calculation to fort.20, ready for a frequency calculation with intensities.

The calculation is being run on 24 cores on a single node, with up to 4GBs of memory /core. The run uses intel mpi for interprocess communication.

After reporting the hyperpolarisability and electric susceptibility tensors (Beta and Chi), the program crashes with:

COMPUTING IR TENSOR ALONG DIRECTION X
forrtl: severe (67): input statement requires too much data, unit 2, file /mnt/scratch/chmjke/SpinCrossover/CRYSTAL/HSE06/AFM2/fort.2.pe15

I attach the input file: frequencies.d12
A tar file of the output and fort.34: info.tgz

Any help would be grateful received.
Thanks John

Dear All,

I'm looking at upgrading to crystal23 but in the meantime has anyone had success in compiling from objects on an apple silicon system? I was thinking of using brew installed openmpi.

Does anyone have a suitable include file?

Jack

Dear All,
I have successfully run the serial version of test11. When I swap to the parallel version, however, I get the following errors:
SCF abnormal end - no wf written in fort.9
ls: No match.
ls: No match.
ls: No match.

The full output is:

~ [jack] Squirrel? ~>runPcry23 8 test11
output data in /Users/jack/test11.out
mpirun executable in /opt/homebrew/Cellar/open-mpi/5.0.9/bin
Pcrystal executable in /Users/jack/Code/CRYSTAL23/bin/v1.0.1
input data in /Users/jack/Code/CRYSTAL23/test_cases/inputs/test11.d12
file machines.LINUX in /Users/jack/Code/CRYSTAL23/utils23
list of nodes in /Users/jack/Code/CRYSTAL23/utils23/nodes.par
creating temporary directories /Users/jack/tmp/tmp_p84659_jack on each node
([email protected]) Password:
temporary dir created on d-i184-6-123.staff.eduroam.uq.edu.au
copying Pcrystal executable on each node
([email protected]) Password:
copying input file on each node
([email protected]) Password:
Pcrystal job running in /Users/jack/tmp/tmp_p84659_jack on each node ...
SCF abnormal end - no wf written in fort.9
ls: No match.
ls: No match.
ls: No match.
removing temporary directories /Users/jack/tmp/tmp_p84659_jack from each node
([email protected]) Password:

I am running an apple silicon machine with open-mpi 5.0.9 installed via homebrew.

Thanks,
Jack

Dear all,

Thank you for reading this topic.

I got this error:

INPUT COORDINATES

ATOM AT. N.              COORDINATES
  1   8     0.000000000000E+00  2.500000000000E-01  3.140000000000E-01
  2   8     1.500000000000E-01  1.660000000000E-01  1.570000000000E-01
  3   6     1.960000000000E-01  4.000000000000E-02  1.800000000000E-02
  4   6     0.000000000000E+00  5.400000000000E-02  3.900000000000E-02
  5   6     0.000000000000E+00  1.250000000000E-01  1.120000000000E-01
ERROR **** geometry ****  FORMAT ERROR IN INPUT DECK

It looks like the program can not read the coordination of Cr.
the input and cif are attached:
mil53crtest.d12
181154opt.cif

Thank you again,
Wang

Dear CRYSTAL Development Team,

I am currently experiencing consistent MPI_ABORT terminations when attempting to run hybrid functional (HSE06) calculations including spin–orbit coupling (SOC) using CRYSTAL23.

The calculations start correctly, but the code terminates early during execution with an MPI_ABORT message on a specific rank. This behavior persists across a wide range of tested MPI/OpenMP parallelization layouts, including very conservative memory-safe configurations, as well as in reduced MPI mode. The issue appears independent of the batch system or cluster configuration.

Before proceeding further, I would like to kindly ask:

Is the combination of HSE06 and SOC fully supported and considered stable in CRYSTAL23 for periodic systems?

To help with diagnosis, I have attached:

the input file used for the calculation,

the corresponding output file showing the error,

and the batch submission script.

These files are provided only for technical reference and reproducibility. I would greatly appreciate any confirmation regarding the current support status of HSE06 + SOC in CRYSTAL23, as well as any known limitations, restrictions, or recommended settings for such calculations.
Thank you very much for your time and support.

Kind regards,
Masoud

Hi,

I am performing doping in a material that initially has space group 225, but the application of the substitution block from the manual the symmetry to be reduced to space group P1.
How can I calculate the band structure in P1?

Thanks!

Hello!
I was running several jobs with different combinations of FDOCCUP, SPINLOCK, and EIGSHIFT. I abandoned most of them, but two crashed with an error message that I have never seen before. All jobs were using the same external geometry file.

alpo4_186_mn_conf_01_ddd.out

alpo4_186_mn_conf_22_ddd.out

For the isolated molecule such as CO2 which is D infinity h, what is the symmetry group? I could not find this one in the manual

How can I plot the PDOS for each individual orbital component separately?
Actually could not able to decode the last four line from the crystal23 manual :

NEWK
12 12
1 0
DOSS
3 100 3 6 1 12 0
4 1 2 3 7 s
4 4 5 8 9 px py
2 6 10 pz
END

In my system, if I need to plot px, py, and pz orbitals of Zn and Cl separately, then how to modify these last 3 lines?

CRYSTAL
0 0 0
230
19.52502047
6
30 9.713891360990E-17 -2.500000000000E-01 -3.750000000000E-01
17 9.427017681292E-02 -3.049312792878E-01 -2.362267967025E-01
7 -1.501875525291E-02 -3.310379606087E-01 -3.160580056873E-01
6 2.209194576296E-02 -3.478572492153E-01 -2.592622821244E-01
6 4.327400041674E-01 1.250000000000E-01 1.827400041674E-01
1 3.934409884276E-01 1.250000000000E-01 1.434409884276E-01

I have this 600 atom Ih symmetry molecular cage. I am seeking help extracting the asymmetric unit from it to enter into CRYSTAL so I can use Ih symmetry. If anybody could help me with it, I would appreciate it.

B60C300H120O120[Ih].txt

JB

Dear CRYSTAL team,

I am trying to execute a spin polarized single point calculation on a metal-organic framework. The calculation I am trying to run is very similar to earlier work from your group (10.1021/acs.jpcc.9b06533).

I have tried many different settings and keywords, but I cannot obtain SCF convergence and I am hoping you can provide me some tips. Similar to the publication, I am using a 6-311G** basis set for the elements H, C, N, O and F. For the Fe atoms, I am using the POB-TZVP basis set.

I am trying to find the high spin state (all Fe atoms should have +5 spin).

Previous unsuccesful attempts include:

• SPINLOCK 120 (all Fe atoms, instead of only those closes to F atoms)
• ATOMSPIN +1 for all Fe atoms
• UHF
• Other functionals (PBE/PBE0/BLYP)
• EIGSHIFT/LEVSHIFT
• Various FMIXING values

I have attached the INPUT, fort.34 and BASISSETS.DAT files as a single .zip for the most promising set of input parameters, in which I directly modify the shell occupancy of 8 Fe atoms and 8 F atoms. Unfortunately, SCF convergence remains very slow (150+ SCF loops so far and still no convergence).

Are there other things I could try to obtain SCF convergence?

crystal23_mil127.zip

Best regards,
Wim Temmerman - Ghent University

Hello!
Help with the problem! When you try to run geometry optimization for configurations, only the geometry optimization of the original connection is started. I am attaching a view of a part of the input file, as it is all set.

CRYSTAL
0 0 0
194
3.065 17.656
4
22    0        0        0.5
14    0        0        0.75
22    0.666666 0.333333 0.364919
6     0.333333 0.666666 0.427507
SCELCONF
1 0 0
0 1 0
0 0 1
RUNCONFS
ATOMSUBS
22 273
END
OPTGEOM
MAXCYCLE
500
END
END

Dear all, I am getting the IO error when scanning modes and no idea why. I copied HESSFREQ.DAT and FREQINFO.DAT files into the scan directory. I would appreciate your help

Unfortunately, it is a large system and I can't upload the files here, I will move them via Dropbox, see the link below

https://www.dropbox.com/t/uVxYAZdbhCFpM79K

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(  -8.5)
[   0.030 -  390-]
io error
Read_int_1d
        300          -1
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

Good evening,

please how to write the input to design a double walled from a slab between 2 different layer sheet ?

Dear CRYSTAL Support Team,

I hope this message finds you well.

I have been using the CRYSTAL software for some time and have generally found it to perform very well, particularly for organic molecular systems. However, I have recently encountered persistent SCF convergence issues when working with inorganic materials.

Specifically, I observe that during the self-consistent field (SCF) cycles, the calculations often converge to a metallic solution instead of the expected insulating state. This behavior occurs for several inorganic systems I have tested. For instance, in my current study of a CdS slab (input file attached), calculations using various functionals converge to a metallic state, whereas bulk CdS correctly yields an insulating band gap of approximately 3 eV at the HSE06 level.

For comparison, my VASP calculations for the same systems converge reliably to the correct insulating solution. This suggests that the issue may be related to the SCF procedure in CRYSTAL, particularly for slab or defect systems.

Could you please advise on strategies or recommended settings to avoid this incorrect metallic convergence? Any suggestions or example input configurations would be greatly appreciated.slab-m06.d12.txt

Hello,

I have been attempting to incorporate composite methods such as HFSOL3C into my computations, however, it appears that CRYSTAL does not recognize the keyword. This appears the same for any composite method, but not if I put in something like STO-3G.

After going back to the basic MgO test case, I still receive an error that states: "SELECTED BASIS SET IS UNAVAILABLE OR WRONG KEYWORD"

I have attached the output file.

Any help would be greatly appreciated,

George
mgo (1).out

Hello,

I am studying a particular Perovskite structure. I performed COHP calculation to understand the bond strength. As per the paper mentioned in the manual (PCCP,17,31023-31029 (2015) -"Integration of the COHP diagram is a measure of bond strength (in units of energy)).

But when I perform the COHP analysis and integrated till Fermi level, I am getting a positive value for the integrated COHP, that means the bond is unstable right ?, which is not possible since it is a very well experimentally observed structure. Attached below are the COHP and integrated COHP plot between oxygen and Ni atom within the considered unit cell.

Any suggestions ? I am attaching the input and COHP files from properties calculation.

Thanks in advance for your help !

COHP.dat
INPUT.d3

Regards,
Rams

Hi,

I'm currently running some molecular calculation as tests before going to periodic one of porphyrin with Co2+.
I'm using spin DFT with a spinloc2 1 -5 setting (with HSEsol).
With POB-DZVP, the calculation finishes successfully while with rev2 it fails after the 4th SCF cycle (sometimes the 3rd) with the good old "NaN at SCF".
I'm not sure what to try beside giving it more memory (which gives the same results) as those are my first calculation with metals.

I'm not sure if it's even a bug but since POB-DZVP works and not POB-DZVP-REV2, I figure that there's something that I cannot control at play.

Best,
Jean

PS: I also tried with FMIXING 60, spinlock instead of spinloc2, tighter tolinteg but got the same problem.

por_co-opt-pob_dzvp_rev2.d12 por_co-opt-pob_dzvp_rev2.out

I'm working on electron density maps using CRYSPLOT and I’m trying to generate contour plots in different planes—specifically XY, XZ, and a custom diagonal like XY-Z. I’ve successfully used RECTANGU for XZ plots, but I’m not sure how to define the input for other orientations.
Here’s a simplified version of my current input:

ECHG
0
50
ATOMS
1 0 0 0
2 0 0 0
2 0 0 1
RECTANGU
MARGINS
3 3 3 3
END
END

How can I modify this to get a plot in the XY and XY-Z plane and if 2 atoms are in the same cell as 0 0 0, they overlap or no? *