Hello everyone! Happy holidays!
I have been using RASPA for the past few months, and recently I started incorporating the charge equilibration feature in my simulation pipeline. Initially, everything went fine, but then I started having problems.
When the
ChargeFromChargeEquilibration option is set to
yes, the simulation crashes with a
Segmentation Fault for some (but not all) CIF files.
One example of a CIF file that leads to a crash is TER.cif from the Database of Zeolite Structures:
https://asia.iza-structure.org/IZA-SC/cif/TER.cif.
The simulation.input file is as simple as
SimulationType MonteCarlo
NumberOfCycles 0
Framework 0
FrameworkName TER
UnitCells 3 2 2
ChargeFromChargeEquilibration yes
ChargeEquilibrationPeriodic yes
ChargeEquilibrationEwald yes
SymmetrizeFrameworkCharges noThe purpose of this
MonteCarlo simulation is simply to create a new CIF file containing a 3x2x2 supercell with P1 symmetry.
To help with debugging, I recompiled
RASPA v2.0.39 with
CFLAGS="-w -ggdb -O0" and executed
gdb ~/RASPA2-2.0.39/bin/simulate
(gdb) run
Starting program: ~/RASPA2-2.0.39/bin/simulate
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff6492e18 in __strcpy_sse2_unaligned () from /lib64/libc.so.6
(gdb) bt
#0 0x00007ffff6492e18 in __strcpy_sse2_unaligned () from /lib64/libc.so.6
#1 0x00007ffff718e543 in WriteFrameworkDefinitionShell (string=0x7ffff7bff6f8 "initial") at framework.c:2103
#2 0x00007ffff793de5e in run (inputData=0x408910 "simulation.input", inputCrystal=0x408930 "",
raspaDir=0x7fffffffd8cb "~/RASPA2-2.0.39/", stream=false) at run.c:101
#3 0x00000000004013e1 in main (argc=1, argv=0x7fffffffd398) at main.c:106
(gdb) frame 1
#1 0x00007ffff718e543 in WriteFrameworkDefinitionShell (string=0x7ffff7bff6f8 "initial") at framework.c:2103
2103 strcpy(symbol,PseudoAtoms[Type].ChemicalElement);
(gdb) p Type
$2 = -415391835
(gdb) p PseudoAtoms[Type].ChemicalElement
Cannot access memory at address 0xffffffce7b817de4The source of the Segmentation Fault seems to be that we are trying to access the
PseudoAtoms array at a
negative index (
Type = -415391835), which does not exist. This occurs at
https://github.com/iRASPA/RASPA2/blob/master/src/framework.c#L2103.
So I investigated further why/where the
Type index variable was set to a negative value and found it at
https://github.com/iRASPA/RASPA2/blob/master/src/framework.c#L2101.
(gdb) p CurrentSystem
$3 = 0
(gdb) p CurrentFramework
$4 = 0
(gdb) p i
$5 = 0
(gdb) p Framework[CurrentSystem].Atoms[CurrentFramework][i].Type
$6 = -415391835
gdb) p Framework[CurrentSystem].Atoms[CurrentFramework][i]
$14 = {
"Type": -415391835,
"Charge": 0.10504292071040217,
"CFVDWScalingParameter": 0.60642472553108762,
"CFChargeScalingParameter": -0.79514090088772649,
"CFStoredScalingParameter": 0.99604382482586074,
"Modified": 159528,
"OriginalType": -1078542400,
"CreationState": -845529396,
"AssymetricType": 1068764949,
"temp": 0.99692550651848566,
"Position": {
"x": 0.42480330804058136,
"y": 0.9052856728556895,
"z": -0.13602553641904541
},
"AnisotropicPosition": {
"x": 0.99070533128772031,
"y": 0.93363353366682034,
"z": -0.35822956998662936
},
"ReferencePosition": {
"x": -0.73270495495271304,
"y": -0.68054643411580806,
"z": 0.9831752294314593
},
"ReferenceAnisotropicPosition": {
"x": 0.18266490695368287,
"y": 0.74724584781165182,
"z": 0.6645476980083872
},
"RattleReferencePosition": {
"x": 0.99913704083225319,
"y": -0.041535209605439771,
"z": 0.93363353366682034
},
"Velocity": {
"x": -0.35822956998662936,
"y": 0.74724584781165182,
"z": 0.6645476980083872
},
"ReferenceVelocity": {
"x": 0.99913704083225319,
"y": -0.041535209605439771,
"z": 0.93363353366682034
},
"Force": {
"x": -0.35822956998662936,
"y": 0.74724584781165182,
"z": 0.6645476980083872
},
"ReferenceForce": {
"x": 0.99913704083225319,
"y": -0.041535209605439771,
"z": 0.93363353366682034
},
"RattleGradient": {
"x": -0.35822956998662936,
"y": 0.74724584781165182,
"z": 0.6645476980083872
},
"ElectricField": {
"x": 0.99913704083225319,
"y": -0.041535209605439771,
"z": 0.93363353366682034
},
"ReferenceElectricField": {
"x": -0.35822956998662936,
"y": 0.75562487546411949,
"z": 0.65500461645688624
},
"InducedElectricField": {
"x": -0.50000000000000122,
"y": -0.86602540378443804,
"z": -0.50000000000000122
},
"InducedDipole": {
"x": -0.86602540378443804,
"y": -0.50000000000000122,
"z": -0.86602540378443804
},
"HessianIndex": {
"x": 11,
"y": -1075838976,
"z": -396866395
},
"HessianAtomIndex": -1075071366,
"Fixed": {
"x": -1725695833,
"y": -1075481023,
"z": 1040166342
}
}I notice that both
Type and
OriginalType are negative, but
AssymetricType is positive.
I have read here several times that is typically something in the CIF files that generates these Segmentation Faults. I also agree that is probably easier to fix the non-standard CIF rather than implementing safeguards in the code to deal with rare situations. I hope that I was able to pinpoint the issue well enough to make it easier for the experts identify its origin. I also posted this as an issue in the RASPA Github repository for proper documentation.
Is there anything we can do (preferably) to the CIF file (otherwise, to the code itself) to prevent this Segmentation Fault from happening?
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