Hi there,

I’m running into issues using Q-CHEM v5.4 to optimize the locations of the protons on hydronium ion above a carbon flake adsorbed metalloporphyrin (203 atoms) while using constrained DFT to enforce charge localization on the graphitic flake. I’m freezing all of the atoms except for the protons on the hydronium ion in the optimization. The first SCF cycle seems to finish fine and the coordinates get updated, but then the this error is printed:

" Q-Chem fatal error occurred in module libmdc/newfileman.C, line 384:

FileMan error: End of file reached prematurely reading (6930168) bytes in file FILE_SPARSE_DENSITY_MATRIX"

This only seems to happen on a handful of jobs, but the inputs only differ in the coordinates of the atoms and not the REM variables. I have put a sample input below without the atomic coordinates to save space (I can provide those if needed). Any advice will be very helpful. Thank you.

$rem

JOBTYPE = OPT

ECP = General

BASIS = General

METHOD = BP86

DFT_D = D3

SCF_Guess = AUTOSAD

SCF_ALGORITHM = RCA_DIIS

MAX_SCF_CYCLES = 1000

THRESH = 14

SCF_CONVERGENCE = 8

CDFT = TRUE

CDFT_THRESH = 8

BECKE_SHIFT = UNSHIFTED

SYM_IGNORE = TRUE

SYMMETRY = FALSE

$end

$cdft

1.0

1.0 79 200

$end

$basis

N 0

6-31g(d,p)

C 0

6-31g(d,p)

O 0

6-31g(d,p)

Co 0

lanl2dz

H 0

6-31g(d,p)

$end

$ecp

Co 0

fit-lanl2dz

$end

Do you get any warnings about linear dependencies or about the number of linearly-independent orbitals? I can imagine a scenario in that case…

(Unrelated: please use the preformatted text button </> to paste inputs/outputs. Otherwise some characters get dropped, which makes it hard to copy/paste your input, or you get a bunch of markup due to special characters.)

Hi there,

Thanks for the quick response. I don’t see any warnings about linear dependencies, only an expected warning about the constrained geometry optimization not being able to use internal coordinates. I can share my output file or specific portions of it if that will help diagnose the problem.

Hmm, okay, that was a guess. In a small example that I cooked up for this purpose, you would see something like the following:

```
Linear dependence detected in AO basis
Tighter screening thresholds may be required for diffuse basis sets
Use S2THRESH > 12 and THRESH = 14 in case of SCF convergence issues
Number of orthogonalized atomic orbitals = 48
```

whereas a few lines above, Q-Chem had told you there were 49 basis functions:

```
There are 25 shells and 49 basis functions
```

This is because this example has one numerical (below threshold) linear dependence. This example is small but with an extremely diffuse basis set, but another scenario for linear dependencies is large molecules (even if the basis set isn’t diffuse). If the number of basis functions changes along the optimization, it might give you a problem like this and the solution would be to (a) increase THRESH, which often leads to faster convergence anyway (I think the default is too loose, prefer THRESH=12) ,or (b) increase BASIS_LIN_DEP_THRESH (default is 6) to keep those linear dependencies from being removed.

This may not be the problem, though, it is a guess.

Okay, I’ll try working with BASIS_LIN_DEP_THRESH and see what happens. Thank you for the advice.

Interestingly, I’m still not getting linear dependencies in the outputs and I’m getting a few geometry optimization steps in before QCHEM stops with the same error message. I’ve been setting BASIS_LIN_DEP_THRESH = 9. I’m getting the same behavior when I run a standard DFT calculation on the metalloporrphyrin without the graphitic surface or charge constraints, which leads me to believe that the cDFT protocol is not the issue. I have provided that sample input below.

```
$comment
CoTPP w H3O
$end
$molecule
1 2
N 0.4519020175 1.5178454465 2.2645739761
N -2.6345629840 -0.8498759077 1.7918282036
N -2.2655044154 1.8949260440 1.8340475692
N 0.1152431359 -1.2100956814 1.8877243088
C 0.4281092678 2.9009635872 2.4908732146
C 1.7766226178 1.1354332272 2.5215605046
C -3.9876873022 -0.4864203128 1.8489325846
C -2.6361429222 -2.2427498028 1.8902448546
C -0.6532933922 3.7447948772 2.2228976446
C 2.3227760578 -0.1284777528 2.2668463346
C -4.4921243822 0.8055571572 1.6637635346
C -1.5197431222 -3.0709509328 1.7381746946
C -1.8923480322 3.2420219172 1.8197597246
C 1.5213213078 -1.2059787928 1.8736191646
C -3.6399115922 1.9108893972 1.5719936146
C -0.2277442522 -2.5448162228 1.6428455246
C 1.6892282278 3.3429046672 3.0190753746
C 2.5205762378 2.2513354472 3.0418024046
C -4.8053385622 -1.6446270628 2.1074897646
C -3.9697976422 -2.7304831628 2.1362110046
C -0.5209356522 5.1994716072 2.4749980646
C 3.7718434278 -0.3550549728 2.4958015846
C -5.9579105322 1.0260134472 1.6404293346
C -1.6901591522 -4.5436573828 1.7882450146
C -3.0077962622 4.0790017972 1.4563084446
C 2.0301339178 -2.5162721028 1.5458359546
C -4.0905329422 3.2561086072 1.3047185646
C 0.9494617978 -3.3458009228 1.4077461546
C -1.4472664622 5.8425328872 3.3246524846
C 4.7481848978 0.5207300872 1.9769158346
C 0.5279935478 5.9540130472 1.9153497446
C 4.2009671878 -1.4463776728 3.2826233846
C -6.8119090822 0.2425207072 0.8363398146
C -0.9325080822 -5.2961036428 2.7118952646
C -6.5285941422 2.0254543672 2.4587973946
C -2.6164996722 -5.2167744528 0.9682296046
C -1.3238873322 7.2058087972 3.6148771546
C 6.1116833978 0.2886930072 2.1993089346
C 0.6469480978 7.3204198172 2.1995996346
C 5.5620338578 -1.6720723528 3.5175707246
C -8.1928845922 0.4749786472 0.8274557446
C -1.0847226122 -6.6838619128 2.8057871446
C -7.9083133322 2.2544260872 2.4542868446
C -2.7623027622 -6.6075922428 1.0561547946
C -0.2744976622 7.9497802072 3.0519384246
C 6.5247738778 -0.8129116028 2.9633798946
C -8.7449026322 1.4848505672 1.6295903746
C -1.9969905722 -7.3472172828 1.9715366546
H 1.8989481278 4.3605507672 3.3358039546
H 3.5482958178 2.1981373372 3.3876438846
H -5.8789957822 -1.6120980828 2.2647024846
H -4.2195962822 -3.7715637828 2.3207552346
H -2.9426245022 5.1532637572 1.3086175946
H 3.0836899378 -2.7576946628 1.4329375346
H -5.1066130622 3.5218049172 1.0238782146
H 0.9357738678 -4.4040170828 1.1591640746
H -2.2624196822 5.2534323572 3.7565451246
H 4.4322851678 1.3800830972 1.3816798346
H 1.2374004078 5.4683693972 1.2424059346
H 3.4478100278 -2.1069095428 3.7231275846
H -6.3825199322 -0.5364924728 0.2037762346
H -0.2294727922 -4.7724855528 3.3686491646
H -5.8699570822 2.6098813572 3.1072292846
H -3.2190747122 -4.6480732228 0.2566534846
H -2.0386207122 7.6824493072 4.2941982346
H 6.8514761578 0.9711077172 1.7676248546
H 1.4606228278 7.8934692072 1.7423014146
H 5.8670885578 -2.5112156728 4.1527431946
H -8.8383059222 -0.1309011728 0.1843432846
H -0.5021762322 -7.2418787428 3.5464822246
H -8.3304715722 3.0219607672 3.1118336646
H -3.4774992122 -7.1131545128 0.3977518646
H -0.1763007722 9.0162593872 3.2779840546
H 7.5891256778 -0.9950811528 3.1383894246
H -9.8245473222 1.6638316072 1.6237976546
H -2.1173961722 -8.4322273828 2.0421259446
Co -1.0818084014 0.3403084153 1.8658673704
O -1.1786571184 0.3377660690 4.6725617767
H -0.6211339144 -0.4615118462 4.4594790140
H -2.0732477855 0.1135720822 4.2803413359
H -0.8202912172 1.0124517828 3.9494318931
$end
$rem
JOBTYPE = OPT
ECP = General
BASIS = General
METHOD = BP86
DFT_D = D3
SCF_Guess = AUTOSAD
SCF_ALGORITHM = RCA_DIIS
MAX_SCF_CYCLES = 4000
SYMMETRY = FALSE
SYMMETRY_IGNORE = 1
THRESH = 14
S2THRESH = 14
SCF_CONVERGENCE = 8
GEOM_OPT_MAX_CYCLES = 150
BASIS_LIN_DEP_THRESH = 9
$end
$opt
FIXED
5 XYZ
6 XYZ
7 XYZ
8 XYZ
9 XYZ
10 XYZ
11 XYZ
12 XYZ
13 XYZ
14 XYZ
15 XYZ
16 XYZ
17 XYZ
18 XYZ
19 XYZ
20 XYZ
21 XYZ
22 XYZ
23 XYZ
24 XYZ
25 XYZ
26 XYZ
27 XYZ
28 XYZ
29 XYZ
30 XYZ
31 XYZ
32 XYZ
33 XYZ
34 XYZ
35 XYZ
36 XYZ
37 XYZ
38 XYZ
39 XYZ
40 XYZ
41 XYZ
42 XYZ
43 XYZ
44 XYZ
45 XYZ
46 XYZ
47 XYZ
48 XYZ
49 XYZ
50 XYZ
51 XYZ
52 XYZ
53 XYZ
54 XYZ
55 XYZ
56 XYZ
57 XYZ
58 XYZ
59 XYZ
60 XYZ
61 XYZ
62 XYZ
63 XYZ
64 XYZ
65 XYZ
66 XYZ
67 XYZ
68 XYZ
69 XYZ
70 XYZ
71 XYZ
72 XYZ
73 XYZ
74 XYZ
75 XYZ
76 XYZ
ENDFIXED
$end
$ecp
Co 0
fit-lanl2dz
****
$end
$basis
N 0
6-31g(d,p)
****
C 0
6-31g(d,p)
****
H 0
6-31g(d,p)
****
O 0
6-31g(d,p)
****
Co 0
lanl2dz
****
$end
```

Using that input file, I can reproduce the crash and the error message after 3 optimization steps, using the latest trunk version of Q-Chem. I will investigate a little further and submit a bug ticket if I can’t figure out the reason.

Update: forget about BASIS_LIN_DEP_THRESH, this is not a linear dependency issue.

The proximate reason that Q-Chem is failing is because the number of function pairs is changing (you can see this by searching for “function pairs”). Q-Chem crashes when the number of function pairs is larger than it was at the previous geometry, so it’s trying to read more density matrix data than were written at the previous geometry.

I’m not sure why Q-Chem doesn’t catch this (I will submit a bug report), though it appears to be related to the use of constraints because when I remove the constraints, the optimization makes it through more steps (still running).

The workaround is to set SCF_GUESS_ALWAYS = TRUE in $rem. That will force Q-Chem to generate a new SCF guess at each geometry, rather than read it in from the previous step.

Ok great! I figured it was a problem with the geometry constraints given all of the different modifications I had tried, but it’s good to know that there is a workaround. Thank you for all of the help!