Hi, I’m trying to run a CC2 calculation with mixed basis set to obtain electron transfer coupling between to molecules. The calculation proceeds through the SCF cycle and runs into an error I have not seen before. Please let me know how to resolve it or what is the error related to. Thanks!
I’m running this calculation on a 64 core (threads) node. This error does not seem to be related to memory usage. Any insights would be helpful, not sure if STS_GMH is incompatible with CC2 or something of that sort.
…
User input:
$molecule
-1 2
C 1.2248647 0.7243188 -1.7494543
C 2.4792601 1.4077446 -1.7501207
C 3.6638166 0.7120805 -1.7507998
C 3.6638166 -0.7120805 -1.7507998
C 2.4792601 -1.4077446 -1.7501207
C 1.2248647 -0.7243188 -1.7494543
H 2.4781698 2.4997912 -1.7501791
H 4.6135615 1.2488859 -1.7514656
H 4.6135615 -1.2488859 -1.7514656
H 2.4781698 -2.4997912 -1.7501791
C 0.0000000 -1.4059204 -1.7487002
C -1.2248647 -0.7243188 -1.7494543
C -1.2248647 0.7243188 -1.7494543
C 0.0000000 1.4059204 -1.7487002
H 0.0000000 -2.4992250 -1.7485718
H 0.0000000 2.4992250 -1.7485718
C -2.4792601 -1.4077446 -1.7501207
C -3.6638166 -0.7120805 -1.7507998
C -3.6638166 0.7120805 -1.7507998
C -2.4792601 1.4077446 -1.7501207
H -2.4781698 -2.4997912 -1.7501791
H -4.6135615 -1.2488859 -1.7514656
H -4.6135615 1.2488859 -1.7514656
H -2.4781698 2.4997912 -1.7501791
C 1.2248647 0.7243188 1.7494543
C 2.4792601 1.4077446 1.7501207
C 3.6638166 0.7120805 1.7507998
C 3.6638166 -0.7120805 1.7507998
C 2.4792601 -1.4077446 1.7501207
C 1.2248647 -0.7243188 1.7494543
H 2.4781698 2.4997912 1.7501791
H 4.6135615 1.2488859 1.7514656
H 4.6135615 -1.2488859 1.7514656
H 2.4781698 -2.4997912 1.7501791
C 0.0000000 -1.4059204 1.7487002
C -1.2248647 -0.7243188 1.7494543
C -1.2248647 0.7243188 1.7494543
C 0.0000000 1.4059204 1.7487002
H 0.0000000 -2.4992250 1.7485718
H 0.0000000 2.4992250 1.7485718
C -2.4792601 -1.4077446 1.7501207
C -3.6638166 -0.7120805 1.7507998
C -3.6638166 0.7120805 1.7507998
C -2.4792601 1.4077446 1.7501207
H -2.4781698 -2.4997912 1.7501791
H -4.6135615 -1.2488859 1.7514656
H -4.6135615 1.2488859 1.7514656
H -2.4781698 2.4997912 1.7501791
$end
$rem
JOBTYPE = SP
METHOD = CC2 ! Use resolution of identity CC2
BASIS = GEN ! Use a general/mixed orbital basis set
AUX_BASIS = GEN ! Use a general/mixed auxiliary basis set
SYMMETRY = FALSE
SYMMETRY_IGNORE = 1
SCS = 1
UNRESTRICTED = FALSE ! Enforce an ROHF reference
STS_GMH = true
STS_DONOR 1-24 !define the donor fragment
STS_ACCEPTOR 25-48 !define the acceptor fragment
MEM_STATIC = 4000
MEM_TOTAL = 238000
SCF_MAX_CYCLES = 250
$end
$basis
! Assign aug-cc-pVTZ to the heavy atoms (Carbon)
C
aug-cc-pVTZ
! Assign cc-pVDZ to the Hydrogen atoms
H
cc-pVDZ
$end
$aux_basis
! Assign the corresponding RI auxiliary basis for Carbon
C
rimp2-aug-cc-pVTZ
! Assign the corresponding RI auxiliary basis for Hydrogen
H
rimp2-cc-pVDZ
$end
Standard Nuclear Orientation (Angstroms)
I Atom X Y Z
1 C 1.2248647000 0.7243188000 -1.7494543000
2 C 2.4792601000 1.4077446000 -1.7501207000
3 C 3.6638166000 0.7120805000 -1.7507998000
4 C 3.6638166000 -0.7120805000 -1.7507998000
5 C 2.4792601000 -1.4077446000 -1.7501207000
6 C 1.2248647000 -0.7243188000 -1.7494543000
7 H 2.4781698000 2.4997912000 -1.7501791000
8 H 4.6135615000 1.2488859000 -1.7514656000
9 H 4.6135615000 -1.2488859000 -1.7514656000
10 H 2.4781698000 -2.4997912000 -1.7501791000
11 C 0.0000000000 -1.4059204000 -1.7487002000
12 C -1.2248647000 -0.7243188000 -1.7494543000
13 C -1.2248647000 0.7243188000 -1.7494543000
14 C 0.0000000000 1.4059204000 -1.7487002000
15 H 0.0000000000 -2.4992250000 -1.7485718000
16 H 0.0000000000 2.4992250000 -1.7485718000
17 C -2.4792601000 -1.4077446000 -1.7501207000
18 C -3.6638166000 -0.7120805000 -1.7507998000
19 C -3.6638166000 0.7120805000 -1.7507998000
20 C -2.4792601000 1.4077446000 -1.7501207000
21 H -2.4781698000 -2.4997912000 -1.7501791000
22 H -4.6135615000 -1.2488859000 -1.7514656000
23 H -4.6135615000 1.2488859000 -1.7514656000
24 H -2.4781698000 2.4997912000 -1.7501791000
25 C 1.2248647000 0.7243188000 1.7494543000
26 C 2.4792601000 1.4077446000 1.7501207000
27 C 3.6638166000 0.7120805000 1.7507998000
28 C 3.6638166000 -0.7120805000 1.7507998000
29 C 2.4792601000 -1.4077446000 1.7501207000
30 C 1.2248647000 -0.7243188000 1.7494543000
31 H 2.4781698000 2.4997912000 1.7501791000
32 H 4.6135615000 1.2488859000 1.7514656000
33 H 4.6135615000 -1.2488859000 1.7514656000
34 H 2.4781698000 -2.4997912000 1.7501791000
35 C 0.0000000000 -1.4059204000 1.7487002000
36 C -1.2248647000 -0.7243188000 1.7494543000
37 C -1.2248647000 0.7243188000 1.7494543000
38 C 0.0000000000 1.4059204000 1.7487002000
39 H 0.0000000000 -2.4992250000 1.7485718000
40 H 0.0000000000 2.4992250000 1.7485718000
41 C -2.4792601000 -1.4077446000 1.7501207000
42 C -3.6638166000 -0.7120805000 1.7507998000
43 C -3.6638166000 0.7120805000 1.7507998000
44 C -2.4792601000 1.4077446000 1.7501207000
45 H -2.4781698000 -2.4997912000 1.7501791000
46 H -4.6135615000 -1.2488859000 1.7514656000
47 H -4.6135615000 1.2488859000 1.7514656000
48 H -2.4781698000 2.4997912000 1.7501791000
Nuclear Repulsion Energy = 2493.71376614 hartrees
There are 95 alpha and 94 beta electrons
Requested basis set is non-standard
There are 452 shells and 1388 basis functions
WARNING: MEM_STATIC is adjusted to be 2000 MB!
Total memory of 238000 MB is distributed as follows:
MEM_STATIC is set to 2000 MB
QALLOC/CCMAN JOB total memory use is 236000 MB
Warning: actual memory use might exceed 238000 MB
Total QAlloc Memory Limit 238000 MB
Mega-Array Size 1956 MB
MEM_STATIC part 2000 MB
Requested basis set is non-standard
There are 904 shells and 3248 basis functions
A cutoff of 1.0D-14 yielded 91860 shell pairs
There are 855716 function pairs ( 1192848 Cartesian)
Smallest overlap matrix eigenvalue = 3.57E-08
Linear dependence detected in AO basis
Tighter screening thresholds may be required for diffuse basis sets
Use S2THRESH > 14 and THRESH = 14 in case of SCF convergence issues
Number of orthogonalized atomic orbitals = 1376
Maximum deviation from orthogonality = 1.920E-10
Scale SEOQF with 1.000000e-01/1.000000e-01/1.000000e-01
Standard Electronic Orientation quadrupole field applied
Nucleus-field energy = 0.0000000022 hartrees
================ Generating on-the-fly SAD Guess ================
Attempting to make child job directory: /tmp/SLURM_2390535/qchem3199068//Frg1/
Attempting to make child job directory: /tmp/SLURM_2390535/qchem3199068//Frg2/
Creating input file /tmp/SLURM_2390535/qchem3199068/Frg1.input
using default PutDataFrgm: nothing
calling putenv with: QCSCRATCH=/tmp/SLURM_2390535/qchem3199068/
calling putenv with: QCLOCALSCR=/tmp/SLURM_2390535/qchem3199068/
Spawning Job For Fragment 0
Done Job For Fragment 0
calling putenv with: QCSCRATCH=/scratch1/ranek
calling putenv with: QCLOCALSCR=/tmp/SLURM_2390535
calling putenv with: QCTHREADS=64
Creating input file /tmp/SLURM_2390535/qchem3199068/Frg2.input
using default PutDataFrgm: nothing
calling putenv with: QCSCRATCH=/tmp/SLURM_2390535/qchem3199068/
calling putenv with: QCLOCALSCR=/tmp/SLURM_2390535/qchem3199068/
Spawning Job For Fragment 1
Done Job For Fragment 1
calling putenv with: QCSCRATCH=/scratch1/ranek
calling putenv with: QCLOCALSCR=/tmp/SLURM_2390535
calling putenv with: QCTHREADS=64
Time for running child jobs: CPU 0.00 s wall 1.26 s
============= Method Specific SAD Guess Constructed =============
Guess from on-the-fly superposition of atomic densities
Warning: Energy on first SCF cycle will be non-variational
General SCF calculation program by
Eric Jon Sundstrom, Paul Horn, Yuezhi Mao, Dmitri Zuev, Alec White,
David Stuck, Shaama M.S., Shane Yost, Joonho Lee, David Small,
Daniel Levine, Susi Lehtola, Hugh Burton, Evgeny Epifanovsky,
Bang C. Huynh
Hartree-Fock
ROSCF diagonal coefficients according to McWeeny and Diercksen:
DD AA BB VV
Fa 0.333 0.333 0.000 0.667
Fb 0.667 0.333 0.000 0.333
See [McWeeny and Diercksen, JCP 49, 4852 (1968)]
(DOI:10.1063/1.1669970) for details.
Orthonormalizing orbitals
using 64 threads for integral computing
OpenMP Integral computing Module
Release: version 1.0, May 2013, Q-Chem Inc. Pittsburgh
A restricted open-shell SCF calculation will be
performed using GDM
SCF converges when RMS gradient is below 1.0e-08
User-specified cutoff of 10e-14
used for neglect of 2-electron integrals.
A cutoff of 10e-14
used for neglect of overlap integrals.
Incremental Fock algorithm is on at the start.
Cycle Energy RMS Gradient
1 -1067.1093293033 8.16e-01 Descent step
2 -1068.0309888253 7.23e-01 Descent step
3 -1068.8427411857 6.25e-01 Descent step
4 -1069.5582932523 5.23e-01 Descent step
5 -1070.1972263654 4.12e-01 Descent step
6 -1070.7117689075 3.38e-01 Descent step
7 -1071.1248055303 2.90e-01 Descent step
8 -1071.4435718672 2.29e-01 Descent step
9 -1071.6730590019 2.61e-01 Descent step
Fro norm of D 1.048969597314e+00
transformation scaled by 2
10 -1071.8684791326 5.27e-01 Descent step
11 -1072.0496627391 9.80e-02 Dog-leg BFGS step
12 -1072.0765698327 5.69e-02 Dog-leg BFGS step
13 -1072.0686726866 8.85e-02 Line search: overstep
14 -1072.0858600616 2.40e-02 Normal BFGS step
15 -1072.0607547404 6.81e-02 Line search: overstep
16 -1072.0869665287 1.08e-02 Normal BFGS step
17 -1072.0876014157 8.53e-03 Normal BFGS step
18 -1072.0878263987 1.01e-03 Normal BFGS step
19 -1072.0878379201 7.51e-04 Normal BFGS step
20 -1072.0878407647 4.28e-04 Normal BFGS step
21 -1072.0878411950 2.62e-04 Normal BFGS step
22 -1072.0878414318 6.24e-04 Normal BFGS step
23 -1072.0878472557 6.92e-03 Line search: understep
Fro norm of D 1.275148951494e+00
transformation scaled by 2
24 -1072.0882366182 6.40e-02 Line search: understep
Fro norm of D 1.131500728885e+00
transformation scaled by 2
25 -1072.0935524547 4.65e-01 Descent step
26 -1072.2309376821 7.69e-02 Dog-leg BFGS step
27 -1072.2252497893 1.49e-01 Line search: overstep
28 -1072.2394797354 6.12e-02 Dog-leg BFGS step
29 -1072.2392195123 8.89e-02 Line search: overstep
30 -1072.2504239022 5.05e-02 Normal BFGS step
31 -1072.2538284704 1.14e-02 Normal BFGS step
32 -1072.2549374501 8.75e-03 Normal BFGS step
33 -1072.2553921812 4.21e-03 Normal BFGS step
34 -1072.2554647218 2.38e-03 Normal BFGS step
35 -1072.2554791371 5.53e-04 Normal BFGS step
36 -1072.2554809672 1.85e-04 Normal BFGS step
37 -1072.2554812785 6.14e-05 Normal BFGS step
38 -1072.2554813349 3.50e-05 Normal BFGS step
39 -1072.2554813457 1.45e-05 Normal BFGS step
40 -1072.2554813480 5.54e-06 Normal BFGS step
41 -1072.2554813485 1.99e-06 Normal BFGS step
42 -1072.2554813485 7.16e-07 Normal BFGS step
43 -1072.2554813485 2.24e-07 Normal BFGS step
44 -1072.2554813485 1.32e-07 Normal BFGS step
45 -1072.2554813486 5.79e-08 Normal BFGS step
GDM::WARNING energy changes are now smaller than effective accuracy.
GDM:: calculation will continue, but THRESH should be increased
GDM:: or SCF_CONVERGENCE decreased.
GDM:: effective_thresh = 1.64e-07
46 -1072.2554813485 1.68e-08 Normal BFGS step
GDM::WARNING energy changes are now smaller than effective accuracy.
GDM:: calculation will continue, but THRESH should be increased
GDM:: or SCF_CONVERGENCE decreased.
GDM:: effective_thresh = 1.64e-07
47 -1072.2554813485 7.63e-09 Convergence criterion met
The disked orbital energies are calculated using alpha and beta Focks
SCF time: CPU 454072.65s wall 14851.00s
<S^2> = 0.750000000
SCF energy = -1072.25548135
Total energy = -1072.25548135
CCMAN2: suite of methods based on coupled cluster
and equation of motion theories.
Components:
- libvmm-1.3-trunk
by Evgeny Epifanovsky, Ilya Kaliman. - libtensor-2.5-trunk
by Evgeny Epifanovsky, Michael Wormit, Dmitry Zuev, Sam Manzer,
Ilya Kaliman. - libcc-2.5-trunk
by Evgeny Epifanovsky, Arik Landau, Tomasz Kus, Kirill Khistyaev,
Dmitry Zuev, Prashant Manohar, Xintian Feng, Anna Krylov,
Matthew Goldey, Alec White, Thomas Jagau, Kaushik Nanda,
Anastasia Gunina, Alexander Kunitsa, Joonho Lee.
CCMAN original authors:
Anna I. Krylov, C. David Sherrill, Steven R. Gwaltney,
Edward F. C. Byrd (2000)
Sergey V. Levchenko, Lyudmila V. Slipchenko, Tao Wang,
Ana-Maria C. Cristian (2003)
Piotr A. Pieniazek, C. Melania Oana, Evgeny Epifanovsky (2007)
Prashant Manohar (2009)
Allocating and initializing 236000MB of RAM (this may take a while)…
Calculation will run on 64 cores.
Alpha MOs, Restricted
– Doubly Occupied –
-11.117 -11.117 -11.117 -11.117 -11.116 -11.116 -11.116 -11.116
1 A 2 A 3 A 4 A 5 A 6 A 7 A 8 A
-11.111 -11.111 -11.111 -11.111 -11.110 -11.110 -11.110 -11.110
9 A 10 A 11 A 12 A 13 A 14 A 15 A 16 A
-11.108 -11.108 -11.108 -11.108 -11.108 -11.108 -11.108 -11.108
17 A 18 A 19 A 20 A 21 A 22 A 23 A 24 A
-11.097 -11.097 -11.097 -11.097 -1.054 -1.049 -1.017 -1.013
25 A 26 A 27 A 28 A 29 A 30 A 31 A 32 A
-0.955 -0.951 -0.933 -0.929 -0.895 -0.890 -0.877 -0.873
33 A 34 A 35 A 36 A 37 A 38 A 39 A 40 A
-0.832 -0.827 -0.754 -0.749 -0.713 -0.710 -0.684 -0.683
41 A 42 A 43 A 44 A 45 A 46 A 47 A 48 A
-0.680 -0.679 -0.619 -0.615 -0.579 -0.576 -0.557 -0.554
49 A 50 A 51 A 52 A 53 A 54 A 55 A 56 A
-0.523 -0.519 -0.513 -0.511 -0.497 -0.493 -0.487 -0.485
57 A 58 A 59 A 60 A 61 A 62 A 63 A 64 A
-0.464 -0.461 -0.448 -0.445 -0.442 -0.440 -0.438 -0.419
65 A 66 A 67 A 68 A 69 A 70 A 71 A 72 A
-0.417 -0.411 -0.409 -0.397 -0.391 -0.370 -0.368 -0.357
73 A 74 A 75 A 76 A 77 A 78 A 79 A 80 A
-0.355 -0.350 -0.342 -0.339 -0.314 -0.301 -0.271 -0.262
81 A 82 A 83 A 84 A 85 A 86 A 87 A 88 A
-0.244 -0.212 -0.205 -0.168 -0.161 -0.119
89 A 90 A 91 A 92 A 93 A 94 A
– Singly Occupied (Occupied) –
0.007
95 A
– Virtual –
0.124 0.124 0.124 0.134 0.134 0.135 0.138 0.140
96 A 97 A 98 A 99 A 100 A 101 A 102 A 103 A
0.146 0.148 0.149 0.150 0.164 0.165 0.165 0.162
(other virtual orbitals …)
*** A
Beta MOs, Restricted
– Doubly Occupied –
-11.117 -11.117 -11.117 -11.117 -11.116 -11.116 -11.116 -11.116
1 A 2 A 3 A 4 A 5 A 6 A 7 A 8 A
-11.111 -11.111 -11.111 -11.111 -11.110 -11.110 -11.110 -11.110
9 A 10 A 11 A 12 A 13 A 14 A 15 A 16 A
-11.107 -11.107 -11.107 -11.107 -11.107 -11.107 -11.107 -11.107
17 A 18 A 19 A 20 A 21 A 22 A 23 A 24 A
-11.096 -11.096 -11.096 -11.096 -1.051 -1.046 -1.014 -1.010
25 A 26 A 27 A 28 A 29 A 30 A 31 A 32 A
-0.952 -0.947 -0.929 -0.925 -0.892 -0.888 -0.874 -0.870
33 A 34 A 35 A 36 A 37 A 38 A 39 A 40 A
-0.828 -0.824 -0.747 -0.744 -0.712 -0.709 -0.681 -0.680
41 A 42 A 43 A 44 A 45 A 46 A 47 A 48 A
-0.677 -0.677 -0.616 -0.613 -0.578 -0.575 -0.555 -0.552
49 A 50 A 51 A 52 A 53 A 54 A 55 A 56 A
-0.521 -0.518 -0.512 -0.509 -0.496 -0.492 -0.486 -0.484
57 A 58 A 59 A 60 A 61 A 62 A 63 A 64 A
-0.463 -0.460 -0.446 -0.444 -0.440 -0.439 -0.428 -0.418
65 A 66 A 67 A 68 A 69 A 70 A 71 A 72 A
-0.416 -0.410 -0.408 -0.388 -0.380 -0.369 -0.367 -0.355
73 A 74 A 75 A 76 A 77 A 78 A 79 A 80 A
-0.354 -0.340 -0.341 -0.338 -0.299 -0.289 -0.260 -0.251
81 A 82 A 83 A 84 A 85 A 86 A 87 A 88 A
-0.233 -0.193 -0.196 -0.158 -0.140 -0.103
89 A 90 A 91 A 92 A 93 A 94 A
– Singly Occupied (Vacant) –
0.160
95 A
– Virtual –
0.124 0.124 0.125 0.135 0.134 0.135 0.138 0.140
96 A 97 A 98 A 99 A 100 A 101 A 102 A 103 A
0.146 0.150 0.149 0.150 0.164 0.166 0.166 0.197
(other virtual orbitals …)
*** A
Occupation and symmetry of molecular orbitals
Point group: C1 (1 irreducible representation).
A All
All molecular orbitals:
- Alpha 1376 1376
- Beta 1376 1376
Alpha orbitals:
- Frozen occupied 28 28
- Active occupied 67 67
- Active virtual 1281 1281
- Frozen virtual 0 0
Beta orbitals:
- Frozen occupied 28 28
- Active occupied 66 66
- Active virtual 1282 1282
- Frozen virtual 0 0
Import integrals: CPU 0.00 s wall 0.00 s
Molecular orbitals will be canonicalized.
/apps/generic/qchem/6.3.0/openmp/bin/qchem: line 129: 3199081 Killed ${QCPROG_S} ${inp} ${scr}
Error in Q-Chem run part 1
remove work dirs /tmp/SLURM_2390535/qchem3199068.0 – /tmp/SLURM_2390535/qchem3199068.0
rm -rf /tmp/SLURM_2390535/qchem3199068.0
rm -rf /tmp/SLURM_2390535/qchem3199068
Error in the Q-Chem run
slurmstepd: error: Detected 1 oom_kill event in StepId=2390535.batch. Some of the step tasks have been OOM Killed.