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Messages - Lingxiao Qin

#1
Visualization / Re: Density Plot
September 29, 2023, 03:06:14 PM
Are you sure your DensityProfile.vtk file is correct? It seems the file should contain totally 3375000 data points, but you just list 10 points. (Maybe you omit other data points for clarity?) Check /RASPA/RASPA2/examples/Visualization/FullCell/Density/MFI/hexane/RASPA/simulation.input for a sample input file. By the way, iRASPA can import the DensityProfile.vtk file generated by RASPA (with a newest version) to visualize the density plot, but I find it lacks some functions such as displaying the colorbar. Perhaps you can try iRASPA to see if it can generate the correct results.
#2
Quote from: David Dubbeldam on June 13, 2023, 01:45:24 PM
In the gallery, then primitives, then IRMOF-1, you can see such an example.

Thank you for your reply. I do find the example. However, I am struggling to reproduce such a picture. The illustrations in the gallery are very compelling, but I think it may be difficult for a beginner like me to figure out how to draw those pictures without a tutorial. I was wondering if it would be possible for you to write a tutorial about how to draw the pictures in the gallery in the future. I understand that creating tutorials requires time and effort, but I believe this tutorial would be invaluable to the community.
#3
Dear Prof. Dubbeldam,

In some literatures the cavity of a MOF is indicated by a sphere, can such an image be created by iRASPA? If not, could you please suggest me a suitable way to create such an image?

Thanks for your help.
#4
Dear Prof. Dubbeldam,

In the manual via the help menu of iRASPA, I found that the distance between two atoms coule be measured by "alt + left mouse clicking on atoms 1 and 2". However, I could not use this function on my Windows desktop. Since the manual seems to be written for Macs, I wonder whether the measuring distance function is available on Windows.

Thans for your help.
#5
Dear Prof. Dubbeldam and RASPA community,

I would like to report a problem that I encountered. When I used the 'charge-equilibration' method to compute the charges of some relatively large MOFs, the simulation crashed with a Segmentation Fault.

Take ZIF-20.cif as an example. This cif file is in the original 'structures' directory of RASPA (~/RASPA/simulations/share/raspa/structures/cif), whose cell length a, b and c are all equal to 45.4725 Å.

My simulation.input file is as

SimulationType                MonteCarlo
NumberOfCycles                0
NumberOfInitializationCycles  0
PrintEvery                    100
RestartFile                   no

Forcefield                    ExampleMOFsForceField
CutOff                        12.8

ChargeFromChargeEquilibration    yes
ChargeEquilibrationPeriodic      yes
ChargeEquilibrationEwald         yes
SymmetrizeFrameworkCharges       no

Framework             0
FrameworkName         ZIF-20
UnitCells             1 1 1
ExternalTemperature   298.0
ExternalPressure      0.0


The simulation terminated with a Segmentation Fault.
Quote
29555 Segmentation fault      (core dumped) ${RASPA_DIR}/bin/simulate $1

However, if I change the simulated MOF from ZIF-20 to Cu-BTC (simply modify the 'FrameworkName' in the above simulation.input file), whose cell length a, b and c are all equal to 26.343 Å, the simulation can run correctly.

In addition, if I run the simulation of Cu-BTC with 2*2*2 unit cells rather than 1*1*1 unit cell, the simulation will also crash with a Segmentation Fault.

A similar problem had been reported previously in this forum by neumannrf:

https://forums.iraspa.org/index.php?topic=1018.msg1252#msg1252


neumannrf simulated TER.cif (cell length a, b and c are 9.8070 Å,  23.6460 Å and 20.2420 Å, respectivly) with 3*2*2 unit cells and got a Segmentation Fault, but when he used 1*1*1 unit cell, the calculation ran correctly. This is similar to the case of Cu-BTC, but for ZIF-20, even running the simulation with 1*1*1 unit cell leads to a Segmentation Fault.

Following neumannrf's debug steps, I also recompiled RASPA (v2.0.47) with CFLAGS="-w -ggdb -O0" and executed (in the case of ZIF-20 with 1*1*1 unit cell)

gdb ~/RASPA/simulations/bin/simulate

(gdb) run
Starting program: ~/RASPA/simulations/bin/simulate
_cell_length_a: 45.472500
_cell_length_b: 45.472500
_cell_length_c: 45.472500
_cell_length_alpha: 90.000000
_cell_length_beta: 90.000000
_cell_length_gamma: 90.000000
_symmetry_space_group_name_Hall: P 1 found space group: 1
_symmetry_space_group_name_H-M: P 1 found space group: 1
_symmetry_Int_Tables_number: 1
space group found from symmetry elements: 1 (nr elements: 1)
End reading cif-file
'force_field.def' file not found and therefore not used

Program received signal SIGSEGV, Segmentation fault.
0x00007ffffe82d2f4 in PrecomputeFixedEwaldContributions () at ewald.c:1078
1078          Eikx[j*MaxNumberOfCoulombicSites+i].re=Eikx[(j-1)*MaxNumberOfCoulombicSites+i].re*Eikx[MaxNumberOfCoulombicSites+i].re-

(gdb) bt
#0  0x00007ffffe82d2f4 in PrecomputeFixedEwaldContributions () at ewald.c:1078
#1  0x00007ffffeb2b015 in ReadInput (
    input=0x8009b90 "SimulationType", ' ' <repeats 16 times>, "MonteCarlo\nNumberOfCycles", ' ' <repeats 16 times>, "0\nNumberOfInitializationCycles  0\nPrintEvery", ' ' <repeats 20 times>, "100\nRestartFile", ' ' <repeats 19 times>, "no\n\nForcefield", ' ' <repeats 17 times>...) at input.c:9030
#2  0x00007ffffeae35b0 in ReadInputFile (filename=0x8008910 "simulation.input") at input.c:208
#3  0x00007fffff117c7f in run (inputData=0x8008910 "simulation.input", inputCrystal=0x8008930 "",
    raspaDir=0x7ffffffee268 "~/RASPA/simulations/", stream=false) at run.c:97
#4  0x00000000080014ba in main (argc=1, argv=0x7ffffffedf28) at main.c:106

(gdb) frame 0
#0  0x00007ffffe82d2f4 in PrecomputeFixedEwaldContributions () at ewald.c:1078
1078          Eikx[j*MaxNumberOfCoulombicSites+i].re=Eikx[(j-1)*MaxNumberOfCoulombicSites+i].re*Eikx[MaxNumberOfCoulombicSites+i].re-

(gdb) p MaxNumberOfCoulombicSites
$1 = 1024
(gdb) p i
$2 = 4351
(gdb) p j
$3 = 9
(gdb) p  Eikx[j*MaxNumberOfCoulombicSites+i].re
Cannot access memory at address 0x7fff8c505000
(gdb) p Eikx[(j-1)*MaxNumberOfCoulombicSites+i].re
$4 = 0.99841316505325695


It seems the fault is due to the inaccessible memory, so I guess the charge equilibration method for relatively large MOFs might require a lot of memory. However, I observed that during the simulation, only abount 2 G memory was used whereas my computer has a total memory of 32 G. By the way, I ran the simulation in WSL (Windows Subsystem for Linux).

In a sum, my questions are: is the segmentation fault described above due to the implementation of the charge equilibration method in RASPA? Or is it because I do something wrong? How can I compute the charges of relatively large frameworks (such as ZIF-20) in RASPA?

Any suggestions would be greatly appreciated.

Best regards,
Lingxiao Qin