Greetings!
I got the forrtl: severe (174): SIGSEGV, segmentation fault occurred
error during a transition state search in a system of interaction between an acetate anion and a single Zn2+ cation.
The following is the input:
set_num_threads(16)
molecule {
+1 1
--
-1 1
O 1.1701300000 0.1654470000 -0.0947420000
O 3.1276960000 -0.8622710000 0.4937720000
C 3.2066180000 1.1786520000 -0.6749440000
C 2.4258700000 0.0481420000 -0.0275680000
H 2.9541340000 1.2423440000 -1.7375930000
H 2.9541350000 2.1273840000 -0.1920510000
H 4.2856690000 1.0209270000 -0.5846250000
--
2 1
Zn 0.8640000000 -2.2140000000 1.2660000000
}
set optking {
opt_coordinates = cartesian
}
set {
maxiter 500
geom_maxiter 500
basis def2-QZVPPD
scf_type df
guess sad
reference rks
opt_type ts
frag_mode MULTI
}
optimize('b3lyp-d')
The process went until the following part:
Back-transformation to cartesian coordinates...
Successfully converged to displaced geometry.
--- Internal Coordinate Step in ANG or DEG, aJ/ANG or AJ/DEG ---
---------------------------------------------------------------------------
Coordinate Previous Force Change New
---------- -------- ------ ------ ------
1 R(1,X) = -0.471628 0.153137 0.000441 -0.471186
2 R(1,Y) = 1.251632 -0.165398 -0.063903 1.187729
3 R(1,Z) = -0.715786 0.094543 0.037681 -0.678105
4 R(2,X) = 1.485938 -0.129646 0.012853 1.498791
5 R(2,Y) = 0.223914 0.114420 -0.014956 0.208957
6 R(2,Z) = -0.127272 -0.065609 0.009723 -0.117549
7 R(3,X) = 1.564860 0.226283 -0.007627 1.557233
8 R(3,Y) = 2.264837 0.208281 -0.009731 2.255105
9 R(3,Z) = -1.295988 -0.119175 0.004979 -1.291009
10 R(4,X) = 0.784112 -0.162924 -0.001743 0.782369
11 R(4,Y) = 1.134327 -0.220971 -0.031031 1.103296
12 R(4,Z) = -0.648612 0.126513 0.018732 -0.629880
13 R(5,X) = 1.312376 -0.039272 -0.022157 1.290219
14 R(5,Y) = 2.328529 -0.025754 -0.017270 2.311259
15 R(5,Z) = -2.358637 0.034111 0.009435 -2.349202
16 R(6,X) = 1.312377 -0.039251 -0.021381 1.290997
17 R(6,Y) = 3.213569 -0.042436 -0.016566 3.197003
18 R(6,Z) = -0.813095 0.004928 0.008017 -0.805078
19 R(7,X) = 2.643911 -0.054663 -0.010395 2.633516
20 R(7,Y) = 2.107112 -0.030229 -0.009523 2.097589
21 R(7,Z) = -1.205669 0.017317 0.004492 -1.201176
---------------------------------------------------------------------------
Back-transformation to cartesian coordinates...
Successfully converged to displaced geometry.
--- Internal Coordinate Step in ANG or DEG, aJ/ANG or AJ/DEG ---
---------------------------------------------------------------------------
Coordinate Previous Force Change New
---------- -------- ------ ------ ------
1 R(8,X) = -0.777758 0.046208 0.049893 -0.727864
2 R(8,Y) = -1.127815 0.161888 0.162799 -0.965016
3 R(8,Z) = 0.644956 -0.092512 -0.092952 0.552004
---------------------------------------------------------------------------
The output file just suddenly stopped, while the following error popped up in the terminal:
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libgdma.so 00007F61BFEE40DC for__signal_handl Unknown Unknown
libpthread-2.17.s 00007F61CD6995E0 Unknown Unknown Unknown
core.cpython-39-x 00007F61C254AA76 Unknown Unknown Unknown
core.cpython-39-x 00007F61C249F9F7 Unknown Unknown Unknown
core.cpython-39-x 00007F61C23FE666 Unknown Unknown Unknown
core.cpython-39-x 00007F61C4C136AD Unknown Unknown Unknown
core.cpython-39-x 00007F61C4D1C7C2 Unknown Unknown Unknown
core.cpython-39-x 00007F61C48EBB8F Unknown Unknown Unknown
python3.9 0000000000507357 Unknown Unknown Unknown
python3.9 00000000004F06EC _PyObject_MakeTpC Unknown Unknown
python3.9 00000000004ECC13 _PyEval_EvalFrame Unknown Unknown
python3.9 00000000004E6ABA Unknown Unknown Unknown
python3.9 00000000004F7DE4 _PyFunction_Vecto Unknown Unknown
python3.9 00000000004E7D89 _PyEval_EvalFrame Unknown Unknown
python3.9 00000000004E6ABA Unknown Unknown Unknown
python3.9 00000000004E6747 _PyEval_EvalCodeW Unknown Unknown
python3.9 00000000004E66F9 PyEval_EvalCodeEx Unknown Unknown
python3.9 00000000005932FB PyEval_EvalCode Unknown Unknown
python3.9 00000000005C0B77 Unknown Unknown Unknown
python3.9 00000000005BCB90 Unknown Unknown Unknown
python3.9 00000000005B47AB PyRun_StringFlags Unknown Unknown
python3.9 0000000000597FC8 Unknown Unknown Unknown
python3.9 00000000004F8854 Unknown Unknown Unknown
python3.9 00000000004E7D89 _PyEval_EvalFrame Unknown Unknown
python3.9 00000000004E6ABA Unknown Unknown Unknown
python3.9 00000000004E6747 _PyEval_EvalCodeW Unknown Unknown
python3.9 00000000004E66F9 PyEval_EvalCodeEx Unknown Unknown
python3.9 00000000005932FB PyEval_EvalCode Unknown Unknown
python3.9 00000000005C0B77 Unknown Unknown Unknown
python3.9 00000000005BCB90 Unknown Unknown Unknown
python3.9 0000000000456493 Unknown Unknown Unknown
python3.9 00000000005B6872 PyRun_SimpleFileE Unknown Unknown
python3.9 00000000005B3DEE Py_RunMain Unknown Unknown
python3.9 00000000005873A9 Py_BytesMain Unknown Unknown
libc-2.17.so 00007F61CCBDFC05 __libc_start_main Unknown Unknown
python3.9 000000000058725E Unknown Unknown Unknown
The matter seems to only pop up once frag_mode MULTI
is included as a setting in the input. As additional information, that option was added due to failure of optimization convergence during a previous transition state search due to splitting of acetate molecule into CH3 and CO2 during the search. Hence, I considered using fragments to preserve the molecule during optimization. I would appreciate a feedback on this matter, or any suggestions that can help this calculation reach convergence!