Hello,
Recently I was doing QMMM single point calculations (version of Q-Chem: 6.2). My calculations consist of 3 consecutive jobs (3 inputs in one file): first job was ground state calculation with PCM, second one was ROKS with PCM and the third one was also a ground state but with frozen solvent field (I used rf_ptss_save in ROKS job). Calculations crashed near the beginning of SCF at 3rd job:
There are 1240 shells and 3015 basis functions
Adding 8412 external point charges to one-electron Hamiltonian
Nucleus-charge energy = 16.8387980807 hartrees
Charge-charge energy = 0.0000000000 hartrees
A cutoff of 1.0D-12 yielded 215867 shell pairs
There are 1122352 function pairs
Smallest overlap matrix eigenvalue = 1.87E-06
Guess MOs from SCF MO coefficient file
Reading MOs from coefficient file
Reading MOs from coefficient file
Long-range K will be added via erf
Coulomb attenuation parameter = 0.33 bohr**(-1)
A restricted hybrid HF-DFT SCF calculation will be
performed using Pulay DIIS extrapolation
Polarizable Continuum solvation model will be applied
Exchange: 0.1900 Hartree-Fock + 0.3500 B88 + 0.4600 muB88 + LR-HF
Correlation: 0.1900 VWN5 + 0.8100 LYP
Using SG-3 standard quadrature grid
Dispersion: Grimme D3
SCF converges when DIIS error is below 1.0E-08
Using Q-Chem read-in guess as SCF_GUESS READ specified.
C-PCM solvent model [f = (eps-1)/eps], solve by conjugate gradient
using 48 threads for integral computing
-------------------------------------------------------
OpenMP Integral computing Module
-------------------------------------------------------
---------------------------------------
Cycle Energy DIIS Error
---------------------------------------
1 -5360.6077490752 2.29E-04
### Frozen reaction-field calculation using stored ESP to compute ASC ###
Reading ESP for state 0 (0 is MP-GS) from file...
... done. Computing ASC and self-interaction...
... done. Updating ref-RF self-interaction (-11.1539 eV) ...
... done. Separating ASC into fast and slow part...
Q-Chem fatal error occurred in module include/RefCount.h, line 48:
RefCount::Constructor called with null pointer argument
I want to ask what do you think, what could be causing this crash?
My input: https://sharetext.io/2a81b0c4
Sincerely,
Tiopirfur
I have tried to look into this but it would be helpful if you could find an example that’s not so large.
Hello,
I’m searching for smaller example and I’ll let you know if I find one.
My system consists of acetonitrile molecules and solute molecule. I tried to repeat calculations with only 2 acetonitrile molecules (one QM and one MM) and solute. These calculations completed without crash, but during SCF in 3rd job I got this warning:
---------------------------------------
1 -995.0625872374 5.53E-04
### Frozen reaction-field calculation using stored ESP to compute ASC ###
Reading ESP for state 0 (0 is MP-GS) from file...
... done. Computing ASC and self-interaction...
... done. Updating ref-RF self-interaction (-2.2007 eV) ...
... done. Separating ASC into fast and slow part...
... done. Computing ESP of SCF density and SCF-fRF interaction ...
... done. Initial SCF-fRF interaction is -1.6214 eV.
Now carrying out SCF calculation in frozen ASC:
Adding current polarization work from ref-RF self-interaction (1.1004 eV)
2 -995.7223315939 6.48E-04
3 -995.7760577175 7.97E-05
4 -995.7767451445 4.01E-05
5 -995.7769512443 9.88E-06
6 -995.7769656611 5.85E-06
7 -995.7769707209 2.23E-06
8 -995.7769714761 8.61E-07
9 -995.7769716147 3.85E-07
10 -995.7769716427 1.53E-07
11 -995.7769716488 5.30E-08
12 -995.7769716496 2.61E-08
13 -995.7769716497 1.17E-08
Q-Chem warning in module libscrf/libscrf/pcm/PCM_CLASS/pcm_setman_ss.C, line 706:
SS-PCM is not implemented for CG solver, sorry ~JMM
### RF-ptSS: Non-eq. corr. for transition from EqS-Ref state ####
=> ptSS (<i0|Ri^f - R0^f|i0>) term: 0.000000 eV
14 -995.7769716501 4.74E-09 Convergence criterion met
---------------------------------------
I don’t know if this warning is related with my crash, but I thought it’s worth sharing.
Input for these calculations:
$molecule
0 1
O 2.114000082015991 -1.9329999685287476 -0.7620000243186951 125 3 5 0 0
N -3.7760000228881836 -0.17499999701976776 0.5339999794960022 79 25 31 35 0
C 1.621000051498413 -0.6340000033378601 -1.1119999885559082 37 1 15 16 30
O 3.575000047683716 -2.8980000019073486 0.6850000023841858 124 5 0 0 0
C 3.0829999446868896 -1.843999981880188 0.26100000739097595 123 1 4 6 0
C 3.2780001163482666 -0.492000013589859 0.5659999847412109 13 5 7 15 0
C 4.1519999504089355 0.15000000596046448 1.4900000095367432 11 6 8 9 0
H 4.804999828338623 -0.4309999942779541 2.127000093460083 12 7 0 0 0
C 4.145999908447266 1.5260000228881836 1.5479999780654907 11 7 10 11 0
H 4.807000160217285 2.0230000019073486 2.246999979019165 12 9 0 0 0
C 3.315999984741211 2.306999921798706 0.7319999933242798 11 9 12 13 0
H 3.3389999866485596 3.384999990463257 0.8019999861717224 12 11 0 0 0
C 2.444999933242798 1.6710000038146973 -0.18199999630451202 11 11 14 15 0
H 1.7949999570846558 2.2639999389648438 -0.8130000233650208 12 13 0 0 0
C 2.440999984741211 0.3109999895095825 -0.24899999797344208 13 3 6 13 0
C 1.8329999446868896 -0.4320000112056732 -2.6050000190734863 1 3 17 18 36
H 2.888000011444092 -0.5759999752044678 -2.8259999752044678 6 16 0 0 0
H 1.5549999475479126 0.5740000009536743 -2.9100000858306885 6 16 0 0 0
H -4.265999794006348 -2.1510000228881836 1.0429999828338623 18 35 0 0 0
H -5.421000003814697 -0.9160000085830688 1.562999963760376 18 35 0 0 0
H -3.880000114440918 -1.0959999561309814 2.4159998893737793 18 35 0 0 0
C -0.6460000276565552 0.49799999594688416 -1.1950000524520874 11 23 30 37 0
C -1.9429999589920044 0.628000020980835 -0.7940000295639038 11 22 24 25 0
H -2.5409998893737793 1.4290000200271606 -1.1950000524520874 12 23 0 0 0
C -2.502000093460083 -0.2919999957084656 0.13199999928474426 78 2 23 26 0
C -1.6759999990463257 -1.3370000123977661 0.621999979019165 11 25 27 28 0
H -2.062999963760376 -2.049999952316284 1.3309999704360962 12 26 0 0 0
C -0.3790000081062317 -1.4429999589920044 0.2070000022649765 11 26 29 30 0
H 0.2370000034570694 -2.24399995803833 0.5839999914169312 12 28 0 0 0
C 0.16599999368190765 -0.5350000262260437 -0.7070000171661377 11 3 22 28 0
C -4.611000061035156 0.9269999861717224 0.07400000095367432 80 2 32 33 34
H -4.130000114440918 1.878000020980835 0.29100000858306885 18 31 0 0 0
H -5.561999797821045 0.8830000162124634 0.5889999866485596 18 31 0 0 0
H -4.78000020980835 0.847000002861023 -0.9990000128746033 18 31 0 0 0
C -4.369999885559082 -1.1449999809265137 1.444000005722046 80 2 19 20 21
H 1.246999979019165 -1.149999976158142 -3.177000045776367 6 16 0 0 0
H -0.24899999797344208 1.2120000123977661 -1.899999976158142 12 22 0 0 0
C 4.420928001403809 2.3830971717834473 4.794969081878662 -1 39 40 41 42
H 5.3337273597717285 2.0750107765197754 4.2416157722473145 -4 38 0 0 0
H 4.0875630378723145 3.2775940895080566 4.226583480834961 -4 38 0 0 0
H 3.666041374206543 1.5751404762268066 4.686923980712891 -4 38 0 0 0
C 4.7958550453186035 2.593752384185791 6.205134868621826 -2 38 43 0 0
N 5.115570545196533 2.7171120643615723 7.319411277770996 -3 42 0 0 0
C -5.660177707672119 0.0014052585465833545 -3.7105185985565186 -1 45 46 47 48
H -6.3960862159729 -0.8015046119689941 -3.9298226833343506 -4 44 0 0 0
H -5.950205326080322 0.23080207407474518 -2.662862777709961 -4 44 0 0 0
H -4.610422611236572 -0.3616585433483124 -3.733290672302246 -4 44 0 0 0
C -5.9191460609436035 1.085862636566162 -4.668871879577637 -2 44 49 0 0
N -6.045229434967041 2.0538878440856934 -5.320666790008545 -3 48 0 0 0
$end
$rem
jobtype sp
method cam-b3lyp
dft_d d3_bj
basis mixed
QM_MM_INTERFACE JANUS
FORCE_FIELD OPLSAA
!FORCEMAN_PRINT 4
USER_CONNECT TRUE
PRINT_GENERAL_BASIS true
SCF_CONVERGENCE 8
MAX_SCF_CYCLES 300
scf_final_print true
MEM_STATIC 8500
MEM_TOTAL 85000
XC_GRID 3
SOLVENT_METHOD PCM
$end
$qm_atoms
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
$end
$force_field_params
NumAtomTypes 4
AtomType -1 -0.080 3.300 0.066
AtomType -2 0.460 3.300 0.066
AtomType -3 -0.560 3.200 0.170
AtomType -4 0.060 2.500 0.015
Bond -1 -2 390.0 1.470
Bond -2 -3 650.0 1.157
Bond -1 -4 340.0 1.090
Angle -4 -1 -2 35.00 108.50
Angle -1 -2 -3 150.00 180.00
Angle -4 -1 -4 33.00 107.80
$end
$pcm
Theory CPCM
Solver CG
Method SWIG
!CGthresh 5
!SwitchThresh 6
Radii FF
!SASradius 1.4
!vdwScale 1.0
NoMatrix
Precond
UseMultipole
$end
$solvent
Dielectric 36.6
OpticalDielectric 1.7956
$end
$basis
O 1
def2-TZVPP
***
N 2
def2-TZVPP
***
C 3
def2-TZVPP
***
O 4
def2-TZVPP
***
C 5
def2-TZVPP
***
C 6
def2-TZVPP
***
C 7
def2-TZVPP
***
H 8
def2-TZVPP
***
C 9
def2-TZVPP
***
H 10
def2-TZVPP
***
C 11
def2-TZVPP
***
H 12
def2-TZVPP
***
C 13
def2-TZVPP
***
H 14
def2-TZVPP
***
C 15
def2-TZVPP
***
C 16
def2-TZVPP
***
H 17
def2-TZVPP
***
H 18
def2-TZVPP
***
H 19
def2-TZVPP
***
H 20
def2-TZVPP
***
H 21
def2-TZVPP
***
C 22
def2-TZVPP
***
C 23
def2-TZVPP
***
H 24
def2-TZVPP
***
C 25
def2-TZVPP
***
C 26
def2-TZVPP
***
H 27
def2-TZVPP
***
C 28
def2-TZVPP
***
H 29
def2-TZVPP
***
C 30
def2-TZVPP
***
C 31
def2-TZVPP
***
H 32
def2-TZVPP
***
H 33
def2-TZVPP
***
H 34
def2-TZVPP
***
C 35
def2-TZVPP
***
H 36
def2-TZVPP
***
H 37
def2-TZVPP
***
C 38
def2-SVP
***
H 39
def2-SVP
***
H 40
def2-SVP
***
H 41
def2-SVP
***
C 42
def2-SVP
***
N 43
def2-SVP
***
$end
@@@
$molecule
read
$end
$rem
jobtype sp
method cam-b3lyp
dft_d d3_bj
basis mixed
QM_MM_INTERFACE JANUS
FORCE_FIELD OPLSAA
USER_CONNECT TRUE
PRINT_GENERAL_BASIS true
SCF_GUESS read
SCF_CONVERGENCE 8
MAX_SCF_CYCLES 300
scf_final_print true
MEM_STATIC 8500
MEM_TOTAL 85000
XC_GRID 3
IQMOL_FCHK True
ROKS True
UNRESTRICTED False
SOLVENT_METHOD PCM
$end
$qm_atoms
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
$end
$force_field_params
NumAtomTypes 4
AtomType -1 -0.080 3.300 0.066
AtomType -2 0.460 3.300 0.066
AtomType -3 -0.560 3.200 0.170
AtomType -4 0.060 2.500 0.015
Bond -1 -2 390.0 1.470
Bond -2 -3 650.0 1.157
Bond -1 -4 340.0 1.090
Angle -4 -1 -2 35.00 108.50
Angle -1 -2 -3 150.00 180.00
Angle -4 -1 -4 33.00 107.80
$end
$pcm
Theory CPCM
Solver CG
Method SWIG
!CGthresh 5
!SwitchThresh 6
Radii FF
!SASradius 1.4
!vdwScale 1.0
NoMatrix
Precond
UseMultipole
rf_ptss_save true
$end
$solvent
Dielectric 36.6
OpticalDielectric 1.7956
$end
$basis
O 1
def2-TZVPP
***
N 2
def2-TZVPP
***
C 3
def2-TZVPP
***
O 4
def2-TZVPP
***
C 5
def2-TZVPP
***
C 6
def2-TZVPP
***
C 7
def2-TZVPP
***
H 8
def2-TZVPP
***
C 9
def2-TZVPP
***
H 10
def2-TZVPP
***
C 11
def2-TZVPP
***
H 12
def2-TZVPP
***
C 13
def2-TZVPP
***
H 14
def2-TZVPP
***
C 15
def2-TZVPP
***
C 16
def2-TZVPP
***
H 17
def2-TZVPP
***
H 18
def2-TZVPP
***
H 19
def2-TZVPP
***
H 20
def2-TZVPP
***
H 21
def2-TZVPP
***
C 22
def2-TZVPP
***
C 23
def2-TZVPP
***
H 24
def2-TZVPP
***
C 25
def2-TZVPP
***
C 26
def2-TZVPP
***
H 27
def2-TZVPP
***
C 28
def2-TZVPP
***
H 29
def2-TZVPP
***
C 30
def2-TZVPP
***
C 31
def2-TZVPP
***
H 32
def2-TZVPP
***
H 33
def2-TZVPP
***
H 34
def2-TZVPP
***
C 35
def2-TZVPP
***
H 36
def2-TZVPP
***
H 37
def2-TZVPP
***
C 38
def2-SVP
***
H 39
def2-SVP
***
H 40
def2-SVP
***
H 41
def2-SVP
***
C 42
def2-SVP
***
N 43
def2-SVP
***
$end
@@@
$molecule
read
$end
$rem
jobtype sp
method cam-b3lyp
dft_d d3_bj
basis mixed
QM_MM_INTERFACE JANUS
FORCE_FIELD OPLSAA
USER_CONNECT TRUE
PRINT_GENERAL_BASIS true
SCF_GUESS read
SCF_CONVERGENCE 8
MAX_SCF_CYCLES 300
scf_final_print true
MEM_STATIC 8500
MEM_TOTAL 85000
XC_GRID 3
SOLVENT_METHOD PCM
$end
$qm_atoms
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
$end
$force_field_params
NumAtomTypes 4
AtomType -1 -0.080 3.300 0.066
AtomType -2 0.460 3.300 0.066
AtomType -3 -0.560 3.200 0.170
AtomType -4 0.060 2.500 0.015
Bond -1 -2 390.0 1.470
Bond -2 -3 650.0 1.157
Bond -1 -4 340.0 1.090
Angle -4 -1 -2 35.00 108.50
Angle -1 -2 -3 150.00 180.00
Angle -4 -1 -4 33.00 107.80
$end
$pcm
Theory CPCM
Solver CG
Method SWIG
!CGthresh 5
!SwitchThresh 6
Radii FF
!SASradius 1.4
!vdwScale 1.0
NoMatrix
Precond
UseMultipole
rf_ptss_read true
$end
$solvent
Dielectric 36.6
OpticalDielectric 1.7956
$end
$basis
O 1
def2-TZVPP
***
N 2
def2-TZVPP
***
C 3
def2-TZVPP
***
O 4
def2-TZVPP
***
C 5
def2-TZVPP
***
C 6
def2-TZVPP
***
C 7
def2-TZVPP
***
H 8
def2-TZVPP
***
C 9
def2-TZVPP
***
H 10
def2-TZVPP
***
C 11
def2-TZVPP
***
H 12
def2-TZVPP
***
C 13
def2-TZVPP
***
H 14
def2-TZVPP
***
C 15
def2-TZVPP
***
C 16
def2-TZVPP
***
H 17
def2-TZVPP
***
H 18
def2-TZVPP
***
H 19
def2-TZVPP
***
H 20
def2-TZVPP
***
H 21
def2-TZVPP
***
C 22
def2-TZVPP
***
C 23
def2-TZVPP
***
H 24
def2-TZVPP
***
C 25
def2-TZVPP
***
C 26
def2-TZVPP
***
H 27
def2-TZVPP
***
C 28
def2-TZVPP
***
H 29
def2-TZVPP
***
C 30
def2-TZVPP
***
C 31
def2-TZVPP
***
H 32
def2-TZVPP
***
H 33
def2-TZVPP
***
H 34
def2-TZVPP
***
C 35
def2-TZVPP
***
H 36
def2-TZVPP
***
H 37
def2-TZVPP
***
C 38
def2-SVP
***
H 39
def2-SVP
***
H 40
def2-SVP
***
H 41
def2-SVP
***
C 42
def2-SVP
***
N 43
def2-SVP
***
$end
Sincerely,
Tiopirfur
It means you’re having to diagonalize the solvent response matrix rather than using an iterative solver. That matrix is probably enormous (e.g., 423,445 surface tesserae in my calculation), so that will be incredibly slow and I’m surprised that it even works.
This job has been running on my system for 90+ hours and is in the SCF iterations for the 3rd job, without crashing. (This is Q-Chem v. 6.3.)
I can reproduce your crash, finally after 4 days on 48 threads. The fuller context of the error message that I get is the following:
### Frozen reaction-field calculation using stored ESP to compute ASC ###
Reading ESP for state 0 (0 is MP-GS) from file...
... done. Computing ASC and self-interaction...
... done. Updating ref-RF self-interaction (-11.1539 eV) ...
... done. Separating ASC into fast and slow part...
Q-Chem warning in module libmdc/NewQAlloc.C, line 469:
QAllocGeneral() returns a null pointer when allocating 1434445344200 Bytes memory
Q-Chem fatal error occurred in module include/RefCount.h, line 48:
RefCount::Constructor called with null pointer argument
Note how the calculation is trying to allocate 1 Tb of memory; that is why it crashes. I think this job is just too large. You could try some of the accelerators for PCM (to not store matrices, in addition to CG solver, and maybe multipole approximations), but this may simply be too large of a cavity surface.
Hello,
Big thank you for your investigation. I have to be more carefull with jobs sizes in the future.
Sincerely,
Tiopirfur
You can also reduce HPoints and HeavyPoints in $pcm section (reducing the discretization grid), but this is so enormous I’m not sure that will help. The options that don’t store matrices are your best bet although those can be slower because they are iterative.