Hi Aleks, I tried but ended up just using LDREMO keyword
Another superstrange thing (that of course was not happening yesterday), that I can't seem to specify initial and final step anymore properly, it divides it by 10... Bizzare. I now have to multiply initial step by 10 (-1.6 start I want I need to specify as 16!) so it startes at -1.6...

My INput is:

EXTERNAL
FREQCALC
RESTART
SCANMODE
1 -16 0 0.1
1
END
END

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SCAN ALONG NORMAL MODES
STARTING POINT: -16 ENDING POINT: 0 STEP: 0.10000
(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( -62.7)
[ 0.028 - 3-]
-1.6000 -0.1610014638959E+04 -0.1610015023766E+04 18 -0.1E-07
-1.5000 -0.1610014685887E+04 -0.1610014979469E+04 29 0.5E-06
-1.4000 -0.1610014719434E+04 -0.1610014938029E+04 13 -0.9E-07
-1.3000 -0.1610014740251E+04 -0.1610014899447E+04 13 -0.2E-06
-1.2000 -0.1610014750671E+04 -0.1610014863723E+04 21 -0.9E-08
-1.1000 -0.1610014754239E+04 -0.1610014830856E+04 15 -0.4E-06
-1.0000 -0.1610014749993E+04 -0.1610014800848E+04 28 0.1E-07
-0.9000 -0.1610014740870E+04 -0.1610014773698E+04 23 0.1E-05

Oh, I see... somewhere among the files I found this. It is unusual since everything converged optimized/converged otherwise. Now wonder I can't restart, it is not restart problem. Why would i become linearly dependent in SCANMODE but not before?

ERROR **** CHOLSK **** BASIS SET LINEARLY DEPENDENT

No idea... I just have no idea... I ran a complete run and all of a sudden the same abort. So frustrating since I do not understand the error

output.out INPUT.d12

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SCAN ALONG NORMAL MODES
STARTING POINT: -1 ENDING POINT: 0 STEP: 20.00000
(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( -62.7)
[ 5.606 - 3-]
Abort(1) on node 31 (rank 31 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 31[output.out](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) [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)

fort.f34 INPUT.d12 job.out Further on this problem - I managed to run this without restart - I am notoriously bad restarting. Tryiong to get rid of this small negative frequenyc. I do not see from the scan any problems, e.g. any local minimum I could restart calculation from. It just decreases monotonically...

MODE(CM-1) DISPLAC TOTAL ENE(DFT)(AU) CLASSICAL HARM ENE(AU) NCYC DE
[MAX DISP -NATOM-]
1( -62.1)
[ 0.113 - 3-]
-4.0000 -0.1610002871486E+04 -0.1610016919330E+04 43 -0.9E-10
-3.6000 -0.1610006913204E+04 -0.1610016489435E+04 32 -0.4E-10
-3.2000 -0.1610009918764E+04 -0.1610016104792E+04 34 0.2E-11
-2.8000 -0.1610012035843E+04 -0.1610015765400E+04 37 -0.8E-11
-2.4000 -0.1610013425826E+04 -0.1610015471261E+04 39 0.2E-08
-2.0000 -0.1610014243529E+04 -0.1610015222375E+04 121 0.4E-09
-1.6000 -0.1610014634134E+04 -0.1610015018740E+04 39 -0.5E-12
-1.2000 -0.1610014749019E+04 -0.1610014860357E+04 78 0.4E-10
-0.8000 -0.1610014729596E+04 -0.1610014747227E+04 54 -0.1E-09
-0.4000 -0.1610014679529E+04 -0.1610014679349E+04 36 0.1E-11
0.0000 -0.1610014656723E+04 -0.1610014656723E+04 CENTRAL POINT

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 Giu, it worked!

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

wonderful, thank you both

thank you, this is very useful for me

Hi, we synthesized a complex material something along the lines of LaFex Niy Coz Cuu Mnv O3 where x+y+z+u+n=1. I know it is not trivial, but I would like to attempt using configuration analysis in TREATMENT OF DISORDERED SYSTEMS / SOLID SOLUTIONS module to generate possible configurations. The parent compound is LaFeO3 perovskite structure. It is Pnma symmetry

Lattice (Primitive)
a 5.60 Å, b 5.66 Å, c 7.94 Å, α 90.00 º, β 90.00 º, ɣ 90.00 º

Wyckoff Element x y z
4b Fe 1/2 0 1/2
4c La 0.009381 0.961741 3/4
4c O 0.08612 0.478265 1/4
8d O 0.712594 0.287975 0.453725

so all the atom substitutions of Ni, Co, Cu and Mn will go into that 4b Fe site. From the analysis, it has 4 symmetry equivalent sites:

 5 T  26 FE    0.000000000000E+00  0.000000000000E+00 -5.000000000000E-01

  6 F  26 FE   -5.000000000000E-01  0.000000000000E+00 -3.095458132887E-17

  7 F  26 FE   -5.000000000000E-01 -5.000000000000E-01  2.220446049250E-16

  8 F  26 FE    0.000000000000E+00 -5.000000000000E-01 -5.000000000000E-01

I know the Fe composition, it is 20 %, the rest are Ni, Co, Cu and Mn, all at the same 20 % compositions - this simplifies the problem. But then I have 4 equivalent Fe sites and 5 elements to fit. Am I correct that I need to construct a supercell here? Ultimately, I would like this module to return me possible combinations of all 20% five elements, but not sure what size of supercell to create

see the attached test structure input.out INPUT.d12

thank you

I admit I am not very good conceptualizing these symetry unique points on Brillouin zone or expressing them in .d3 file as a path. I have two structures below that I fully optimized and calculated vibrational frequencies. Now my task is DOS/BAND. Is there a GUI that would help me read the optimized structures and prepare .d3 file? Or can I use my optimization file somehow to extract those unique points?

SPACE GROUP (CENTROSYMMETRIC) : P 21/N

LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - CONVENTIONAL CELL
A B C ALPHA BETA GAMMA
7.40400 21.53400 5.65700 90.00000 91.05000 90.00000

and

SPACE GROUP (CENTROSYMMETRIC) : P -1

LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - CONVENTIONAL CELL
A B C ALPHA BETA GAMMA
10.70800 10.11400 6.41000 91.30000 88.30000 91.00000

Dear all, I optimized a crystal, got good gradients, but numerical displacements are already suspect as they generate lots of negative energies, it's a big system, I am still running it but decided to preemptively ask why this can be the case?

SYMMETRY ALLOWED FORCES (COORDINATE, FORCE)

1 -7.1019812E-07    2  2.6847537E-07    3  1.7714543E-06    4  1.5380909E-06
5 -8.5713887E-07    6 -7.6313741E-07    7 -1.3777999E-06    8 -4.2292032E-07
9  3.7330006E-07   10 -1.0186152E-07   11  7.8436370E-08   12 -1.0666144E-07

13 7.6024231E-07 14 1.2549944E-07 15 -3.8114243E-07 16 8.3483245E-07
17 1.2719080E-06 18 1.3589256E-07 19 -1.2770755E-06 20 -1.7657611E-06
21 -6.7831105E-07 22 -2.8553633E-06 23 -2.5801301E-06 24 1.6190965E-06
25 2.7986374E-07 26 1.6445538E-06 27 1.5791380E-06 28 3.4913230E-06
29 7.5492284E-07 30 -3.2944974E-06 31 -2.9919538E-06 32 1.2296182E-06
33 4.5466078E-07 34 -1.8564773E-07 35 9.3158783E-07 36 -1.4184621E-07
37 2.8763484E-06 38 -1.7874331E-06 39 -3.3548919E-07 40 -1.0246636E-06
41 7.3025290E-07 42 -7.4914105E-07 43 -1.5527795E-07 44 -5.9189571E-07
45 1.1402401E-07 46 1.1445077E-07 47 5.0641463E-07 48 2.6720325E-07
49 3.9382990E-07 50 1.9265418E-07 51 -5.0025563E-07 52 -1.4722329E-07
53 -3.9032570E-07 54 -1.8660950E-07 55 -3.7294087E-08 56 2.7903845E-07
57 -1.1262719E-07 58 -1.4056720E-06 59 -7.2814440E-07 60 -4.2360016E-07
61 9.6760468E-07 62 -1.1476558E-06 63 5.7400637E-08 64 8.2334616E-07
65 1.7677814E-06 66 1.1935613E-06 67 -5.3996977E-07 68 5.3577787E-07
69 -5.5566146E-07 70 2.5231789E-07 71 -6.3487986E-07 72 7.2284427E-07
73 -8.4328694E-08 74 -5.8224781E-07 75 -1.6946265E-07 76 1.0209263E-06
77 2.9716506E-07 78 2.3838462E-07 79 1.7955521E-06 80 4.0804899E-07
81 1.2100282E-07 82 -1.5099145E-06 83 2.9006726E-07 84 -2.2790446E-07
85 1.4325087E-06 86 -6.8494225E-07 87 -3.3477344E-07 88 -2.2149944E-07
89 1.3328321E-07 90 -1.8330282E-08

ATOM MAX ABS(DGRAD) TOTAL ENERGY (AU) N.CYC DE SYM
CENTRAL POINT -5.463640944184E+03 0 0.0000E+00 8
1 O DX 6.5777E-04 -5.463640944692E+03 11 -5.0781E-07 1
1 O DY 8.9722E-04 -5.463640943824E+03 12 3.6002E-07 1
1 O DZ 2.7715E-03 -5.463640938222E+03 13 5.9626E-06 1
9 O DX 1.4159E-03 -5.463640942796E+03 11 1.3886E-06 1
9 O DY 2.4328E-03 -5.463640939470E+03 13 4.7142E-06 1
9 O DZ 7.5341E-04 -5.463640944273E+03 10 -8.8837E-08 1
17 N DX 3.3298E-03 -5.463640936786E+03 9 7.3979E-06 1
17 N DY 2.6834E-03 -5.463640938932E+03 10 5.2525E-06 1
17 N DZ 2.2061E-03 -5.463640940002E+03 10 4.1826E-06 1
25 H DX 5.8163E-04 -5.463640944625E+03 10 -4.4035E-07 1
25 H DY 9.7068E-04 -5.463640943311E+03 9 8.7315E-07 1
25 H DZ 1.3265E-03 -5.463640942408E+03 11 1.7757E-06 1
33 H DX 1.9126E-03 -5.463640940840E+03 12 3.3445E-06 1
33 H DY 9.0051E-04 -5.463640944155E+03 9 2.8878E-08 1
33 H DZ 6.4300E-04 -5.463640945217E+03 9 -1.0328E-06 1
41 N DX 3.4011E-03 -5.463640936782E+03 10 7.4018E-06 1
41 N DY 2.7133E-03 -5.463640938661E+03 12 5.5236E-06 1
41 N DZ 2.8802E-03 -5.463640937601E+03 11 6.5830E-06 1
49 H DX 1.5489E-03 -5.463640941848E+03 10 2.3365E-06 1
49 H DY 3.3487E-04 -5.463640945255E+03 9 -1.0709E-06 1
49 H DZ 8.9868E-04 -5.463640943999E+03 9 1.8543E-07 1
57 N DX 2.4112E-03 -5.463640939472E+03 9 4.7126E-06 1
57 N DY 3.5207E-03 -5.463640936173E+03 10 8.0110E-06 1
57 N DZ 3.2454E-03 -5.463640936926E+03 12 7.2582E-06 1
65 H DX 4.2444E-04 -5.463640945298E+03 10 -1.1135E-06 1
65 H DY 1.4990E-03 -5.463640942117E+03 10 2.0672E-06 1
65 H DZ 9.8569E-04 -5.463640943558E+03 7 6.2581E-07 1
73 H DX 8.8996E-04 -5.463640943796E+03 11 3.8818E-07 1
73 H DY 4.0635E-04 -5.463640945249E+03 9 -1.0646E-06 1
73 H DZ 1.5526E-03 -5.463640941922E+03 11 2.2623E-06 1
81 N DX 3.0237E-03 -5.463640937800E+03 12 6.3840E-06 1
81 N DY 3.1621E-03 -5.463640937605E+03 12 6.5795E-06 1
81 N DZ 3.3672E-03 -5.463640936782E+03 11 7.4017E-06 1
89 H DX 3.5908E-04 -5.463640945209E+03 8 -1.0249E-06 1
89 H DY 1.0305E-03 -5.463640943313E+03 13 8.7074E-07 1
89 H DZ 1.3452E-03 -5.463640942571E+03 10 1.6132E-06 1
97 H DX 1.1682E-03 -5.463640943082E+03 10 1.1022E-06 1
97 H DY 1.4461E-03 -5.463640941923E+03 12 2.2616E-06 1

output.out attached

I profusely apologize, but how do I visualize vibrations on my browser using JSMol? I know it sounds silly but I have no idea how to install or launch it. Your webpage below did it very well, I can't follow any of the Java related instructions on the developers website, I would like to be able to run JSmol on my home computer on a browser, can somebody give me a brief instruction how to do that?

Your tutorial page does that very well

https://www.crystal.unito.it/prtfreq/jmol.html

Files for scenario 3
INPUT.d12
fort.f34

Hi Alessandro, working hard on this one. Scenario 3 seemed trivial (but did not converge). I assumed some JT distortion, so I used distortion along z axis argument and I shifted dxz down and assumed this is the double populated one. So far no luck in convergence

EIGSHIFT
5
1 8 1 -.5 .5
1 8 2 -.5 -.5
1 8 3 -.5 .5
1 8 4 -.5 .5
1 8 5 -.5 .5

Alessandro,

I am making a large 450 atom supercell of MgNH4PO4*6H2O to study Fe ion incorporation. We experimntally observe about 5% Mg atoms substituted with Fe - we do not know the oxidation state. So my supercell is big and I optimize this ionic solid with PBE-D3. My question is long and related on how to obtain required electronic state and converge in some instances. See below my diagram. I am exploring 3 different substitutional scenarios.

Scenario 1 is substituting Fe3+ and removing one proton to make it neutral. I am getting excellent SCF convergence, my guess is that this octahedral symmetry is broken somehow by removal of proton which helps SCF convergnce but crystal field with nearly 5 inpaired electrons is still preserved after the convergence with PBE-D3/pobDZVP.

Scenario 2 is an SCF problem. To charge balance it I remove NH4+. Immediately I get problems with SCF becoming conducting, I guess it does not want to be perfectly Oh symmetry and needs some distortion. I managed to converged it with PBE-D3/STO-3G in hopes that it will optimize to some solution which I can further optimize with PBE-D3/pobDZVP. But if I wanted to bias it with EIGENSHIFT and start with a large basus set, what would be my logic here? Robert Orlando used to very elegantly explain these things to me in the past.

Scenario 3 I haven't run yet. Seems like perfect Oh symmetry with the corresponding crystal field splitting and 4 unpaired electrons but my guess is it will run into the same problems as Scenario 2 and will need some biasing.

I mean… those are huge HPC nodes… they can’t be possibly out of disk… But certainly I will try this, will it affect my convergence or calculation speed?

Thank you Alessandro

So on my main supercomputer I am getting this error during write problem. Admins do not know why it happens. It only happes with CRYSTAL and sporadically.

CYC 23 ETOT(AU) -2.276909751322E+04 DETOT -2.19E-06 tst 4.04E-07 PX 2.29E-04
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT DIIS TELAPSE 20527.44 TCPU 20346.34
DIIS TEST: 0.38681E-05 AT SCF CYCLE 23 - DIIS ACTIVE - HISTORY: 23 CYCLES
forrtl: No space left on device
forrtl: severe (38): error during write, unit 8, file /90daydata/urea_kinetics/struvite/Fedoped/PBE_D3/2x2x2_FeOH/fort.8.pe280
Image PC Routine Line Source
Pcrystal 0000000007376772 Unknown Unknown Unknown
Pcrystal 00000000073744DB Unknown Unknown Unknown
Pcrystal 0000000001BA179E Unknown Unknown Unknown
Pcrystal 000000000069D509 Unknown Unknown Unknown
Pcrystal 0000000000695494 Unknown Unknown Unknown
Pcrystal 0000000000992FCD Unknown Unknown Unknown
Pcrystal 0000000000609584 Unknown Unknown Unknown
Pcrystal 0000000000605881 Unknown Unknown Unknown
Pcrystal 0000000000405540 Unknown Unknown Unknown
Pcrystal 00000000004053FD Unknown Unknown Unknown
libc.so.6 0000148B7AA295D0 Unknown Unknown Unknown
libc.so.6 0000148B7AA29680 __libc_start_main Unknown Unknown
Pcrystal 0000000000405315 Unknown Unknown Unknown

It makes sense, thank you.

aerba I do not think this is true now that I have spent so much time restarting. I tried restarting frequency job with the old input (e.g. if I do PREOPTGEOM and it is optimized) and restart normally proceeds. I can take the last coordinate file and do EXTARENAL in the restart but in my experience did not matter, frequency restart always proceeds either way