Segmentation fault QM/MM polarizable water
ghislain.m... at gmail.com
ghislain.m... at gmail.com
Tue Jun 9 10:09:07 UTC 2015
Hello,
I set up a QM/MM input file for a hydrated iron ion (QM region) within
polarizable TIP4P water (MM region) but have issues with the temperature
(and the constant quantity not being constant). It rises to 1000K within
tens of time step and crashes eventually. If I set up a temperature
tolerance control, it seg fault within 60 time step:
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x2538BBD in _gfortrani_backtrace
#1 0x2514D60 in _gfortrani_backtrace_handler
#2 0x7EFF1D718D3F
#3 0x138A7E5 in __qmmm_gpw_energy_MOD_qmmm_elec_with_gaussian_lr
#4 0x138C6BD in __qmmm_gpw_energy_MOD_qmmm_elec_with_gaussian_low at
qmmm_gpw_energy.F:?
#5 0x138CBF2 in __qmmm_gpw_energy_MOD_qmmm_elec_with_gaussian
#6 0x138E6CA in __qmmm_gpw_energy_MOD_qmmm_el_coupling
#7 0xF977E4 in __force_env_methods_MOD_qmmm_energy_and_forces_low at
force_env_methods.F:?
#8 0xF90C4F in __force_env_methods_MOD_force_env_calc_energy_force
#9 0x65675C in __integrator_MOD_nvt
#10 0x59AFCD in __velocity_verlet_control_MOD_velocity_verlet
#11 0x4A47D3 in __md_run_MOD_qs_mol_dyn_low at md_run.F:?
#12 0x4A52A9 in __md_run_MOD_qs_mol_dyn
#13 0x42A72D in __cp2k_runs_MOD_cp2k_run at cp2k_runs.F:?
#14 0x42D7B9 in __cp2k_runs_MOD_run_input
#15 0x425A12 in MAIN__ at cp2k.F:?
srun: error: n05: task 0: Segmentation fault
If I deactivate the dipole section for the polarizable water together with
a temptol, the MD runs but I can see from the .ener file that there is
still something wrong because the constant quantity is not stable :
# Step Nr. Time[fs] Kin.[a.u.]
Temp[K] Pot.[a.u.] Cons Qty[a.u.] UsedTime[s]
0 0.000000 6.123512489 300.000000000
-1688.376614953 -1681.233704606 0.000000000
1 0.500000 6.200944615 303.793515217
-1688.454674919 -1681.234455916 1584.053616034
2 1.000000 6.123512489 300.000000000
-1688.651403569 -1681.508734516 781.486486735
3 1.500000 6.123512489 300.000000000
-1688.936712726 -1681.794143037 613.747086097
4 2.000000 6.123512489 300.000000000
-1689.280054766 -1682.137559996 698.548601538
5 2.500000 6.123512489 300.000000000
-1689.653313928 -1682.510865139 656.035917521
6 3.000000 6.123512489 300.000000000
-1690.036203449 -1682.893769915 715.674252495
7 3.500000 6.123512489 300.000000000
-1690.415686766 -1683.273238079 717.593677139
8 4.000000 6.123512489 300.000000000
-1690.784930772 -1683.642438308 821.530676678
9 4.500000 6.123512489 300.000000000
-1691.144932014 -1684.002369830 955.069705691
10 5.000000 6.123512489 300.000000000
-1691.493357786 -1684.350703028 733.752208665
11 5.500000 6.123512489 300.000000000
-1691.828854461 -1684.686087450 770.332362851
12 6.000000 6.123512489 300.000000000
-1692.154407988 -1685.011512055 803.700799942
13 6.500000 6.123512489 300.000000000
-1692.468266250 -1685.325227389 752.917658262
14 7.000000 6.123512489 300.000000000
-1692.769471149 -1685.626277542 657.358616944
15 7.500000 6.123512489 300.000000000
-1693.058578687 -1685.915220190 604.465238662
16 8.000000 6.123512489 300.000000000
-1693.335615281 -1686.192082966 763.148569925
17 8.500000 6.123512489 300.000000000
-1693.601932422 -1686.458218289 611.582926672
18 9.000000 6.123512489 300.000000000
-1693.856951366 -1686.713048246 763.643155105
19 9.500000 6.123512489 300.000000000
-1694.104831169 -1686.960732789 673.061728137
20 10.000000 6.123512489 300.000000000
-1694.344842063 -1687.200543177 767.700982925
21 10.500000 6.123512489 300.000000000
-1694.577323506 -1687.432819974 805.056688491
22 11.000000 6.123512489 300.000000000
-1694.801711264 -1687.657000019 704.207761740
23 11.500000 6.123512489 300.000000000
-1695.018478826 -1687.873557735 751.591828816
24 12.000000 6.123512489 300.000000000
-1695.227205612 -1688.082073258 866.602900986
25 12.500000 6.321527006 309.701026220
-1695.426180697 -1688.082821574 838.221928451
26 13.000000 6.123512489 300.000000000
-1695.618814809 -1688.473250078 661.379231634
27 13.500000 6.304023666 308.843511526
-1695.799682166 -1688.473392012 673.915761631
28 14.000000 6.123512489 300.000000000
-1695.975824481 -1688.829824167 650.976668453
29 14.500000 6.290711285 308.191318127
-1696.143197005 -1688.829782371 706.452777896
30 15.000000 6.123512489 300.000000000
-1696.306870006 -1689.160432810 676.588798001
31 15.500000 6.279965001 307.664841665
-1696.463669856 -1689.160565221 704.510466747
32 16.000000 6.123512489 300.000000000
-1696.617065127 -1689.470193771 781.046899080
33 16.500000 6.267655708 307.061791078
-1696.761434897 -1689.470208000 737.074181454
34 17.000000 6.123512489 300.000000000
-1696.900836949 -1689.753537638 716.894849787
35 17.500000 6.252395941 306.314192333
-1697.031012847 -1689.754620901 599.609765597
36 18.000000 6.123512489 300.000000000
-1697.154234813 -1690.006514070 605.681155665
37 18.500000 6.238047527 305.611242186
-1697.269663768 -1690.007201125 722.627675435
38 19.000000 6.123512489 300.000000000
-1697.381301608 -1690.233164213 611.757272663
39 19.500000 6.228293347 305.133370367
-1697.487152306 -1690.234029002 710.501011999
40 20.000000 6.123512489 300.000000000
-1697.588981438 -1690.440431491 732.978617050
41 20.500000 6.220439451 304.748596307
-1697.687213279 -1690.441533531 814.034562116
I most likely have some inconsistency in my input file but could not
identify it. The QS and FIST energies in the input file are within the
expected range, I have healthy looking coordinates, even at the seg fault
step ...
Any suggestions would be appreciated,
Many thanks
G
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