Recent posts

#91

General / Re: About the relation between...

Last post by w_wonder - January 25, 2023, 04:16:11 AM

Thanks.

Looks like exp(D0/kT) and total atomic energy are the keys. I managed to verified ~ 20%.

[When using more than one framework in the simulation, the charges are applied only to the second framework]

#92

Bug reports / Two frameworks in the same sim...

Last post by TFabiani - January 20, 2023, 12:53:16 PM

Dear,

I faced up the following issue. When using more than one framework in the simulation, the charges are applied only to the second framework. The simulation of one framework of the two (separately) show a regular behavior of the software, while using two is always the first to have -nan in the Output file in the field "charges", even swapping the two or using other files.

I am using charges from CIF file.

Is there any way to avoid it and to run the simulation with two frameworks at the same time?

Thank you in advance for your help,
Best regards,
Thomas

Input File

SimulationType                  MonteCarlo
NumberOfCycles                  500000
NumberOfInitializationCycles    1000
NumberOfEquilibrationCycles    5000
PrintEvery                                 10000
UseChargesFromCIFFile            yes
Forcefield                                   Local

Framework                        0
FrameworkName       Tf-DHzDPr-COF
UnitCells                           2 2 9


Framework         1
FrameworkName               MFI_SI_Olson
ShiftUnitCells                   0.0 0.0 0.0
UnitCells                        5 2 3

[...]

Output file


Pseudo Atom[  97] Name C60      Oxidation:          Element: C    pdb-name: C    Scat. Types:   7   6 Mass=12.0107
35897 B-factor:0.000
Charge=-nan           (av)  Polarization=1.760000000  [A^3] (considered a charged atom and no pol
arization)  Interactions: yes

#93

Simulation algorithms and theory / Re: How to do Monte Carlo simu...

Last post by alireza_hadi68 - January 15, 2023, 12:03:02 PM

Dear Dr. Dubbeldam,

Thanks a lot for your helpful reply!

#94

General / Re: error message on restart a...

Last post by David Dubbeldam - January 11, 2023, 08:08:05 PM

Note sure,  but could be that the crash damage the restart-file. This could happen when the crash happens at the exact time the binary-restart-file is written to disk.

#95

Simulation algorithms and theory / Re: How to do Monte Carlo simu...

Last post by David Dubbeldam - January 11, 2023, 08:05:51 PM

For running multiple simulations, you would use/create scripts that generate the needed input.
MOF simulations time depend on the size of the system, and how accurate you need the results.
Small systems, about a day. Larger system, a week or longer.

#96

Simulation algorithms and theory / How to do Monte Carlo simulati...

Last post by alireza_hadi68 - December 31, 2022, 07:00:36 AM

Hello everyone,

I want to work on a database containing a large number of MOFs, and I need their gas adsorption data (in a defined temperature and pressure). I am not familiar with RASPA and I want to learn it. There are lots of papers using RASPA for this purpose. I have some questions about this:
How could I use RASPA for a large number of MOFs?
Are there any algorithms to do simulations automatically?
How long does it take to do a simulation for each MOF?
What are the system requirements for such simulations?

Your answer could really help me.  :-[

Thanks!

#97

General / error message on restart after...

Last post by virginia314 - December 16, 2022, 02:27:38 AM

I am running a GCMC simulation for adsorption in a MOF that will run for several million steps. I wrote the binary restart file and when my job crashed, I tried to restart it. It read in the binary file and immediately crashed with this error:

read binary file
DONE!!!
Failed to Reposition output-file at 398119 ( beyond file-length 396809)

I tried running a small test case and the restart worked fine. What does this error mean?

#98

General / Re: About the relation between...

Last post by David Dubbeldam - December 02, 2022, 04:00:28 PM

For a detailed explanation see:
https://homepage.tudelft.nl/v9k6y/thesis-Rahbari.pdf
Page 262 and following, and see Table  A5.

#99

Simulation algorithms and theory / Re: can I simulate the adsorpt...

Last post by lzhzzz - November 30, 2022, 04:09:19 PM

That can not really be done without implementing that. The system must stay charge-neutral, so you cannot individually swap na and cl in and out. You will need to do that in pairs.

Hello dear David
If it is a neutral heavy metal molecule in solution, can it be calculated with raspa.
Thank you very much.

#100

Visualization / Re: Vector image export

Last post by David Dubbeldam - November 24, 2022, 10:55:40 AM

No, the data is inherently pixel-based. Exporting to pdf would just put a picture in a pdf.