Recent Posts

Pages: 1 2 [3] 4 5 ... 10
21
Visualization / Re: iRASPA unable to visualize 13X zeolite file
« Last post by rshukre on September 26, 2021, 01:00:51 AM »
Please see the attachment for the Movie file generated.
22
Input files and parameters / RandomAlSubstitution_13X
« Last post by rshukre on September 26, 2021, 12:58:13 AM »
Hello,

I have a question regarding RandomAlSubstitution to modify the Si/Al ratio in zeolite 13X. In the manual, it is written that the 'Substitute' command is useful to have the same structure, whereas the 'RandomlySubstitute' command may not keep the same space group. I want to substitute 10 Al atoms by 10 Si atoms in the framework. How many 'Substitute' commands do I need to consider in the input file, so as to keep the space group in the fd-3, with 96 elements ? How do I check if the same space group is followed at the end of simulation.

Regards,
Rajasi

23
Visualization / iRASPA unable to visualize 13X zeolite file
« Last post by rshukre on September 26, 2021, 12:42:38 AM »
Hello,

I have modified the base file of NaX, available in RASPA to suit the Si/Al ratio, which I want. The base file in RASPA has Si/Al = 1 (96 Si, 96 Al). For my simulations, I need Si/Al = 1.23 (106 Si, 86 Al), differentiating the oxygen atoms based on connectivity to Si or Al. I have changed the base file using RASPA simulations, whose input file is given below.  RASPA generates an output file in the Movie folder, titled 'Framework_0_final_1_1_1.cif',  which I have attached in this post. This file has 86 Al and 106 Si, meaning that random substitution has worked. My question is as follows :

Why is iRASPA unable to visualize this file? There are total 576 atoms/ unit cell. When I upload the modified file, it only reads 232 atoms and the structure generated is not right. However, VESTA is able to generate the correct structure. I would really appreciate it if you could help me with this.

Thanks,
Rajasi

INPUT :

SimulationType                MC
NumberOfCycles                0
NumberOfInitializationCycles  0
PrintEvery                    10
     
Forcefield                      local
UseChargesFromCIFFile           yes

RandomlySubstitute 10 Al1 Si1

ModifyFrameworkAtomConnectedTo O1 Oa1 Al1
ModifyFrameworkAtomConnectedTo O2 Oa2 Al1
ModifyFrameworkAtomConnectedTo O3 Oa3 Al1
ModifyFrameworkAtomConnectedTo O4 Oa4 Al1
     
Framework 0
FrameworkName NaX
UnitCells 1 1 1
ExternalTemperature 293


24
Input files and parameters / Re: The usage of block_file
« Last post by rshukre on September 25, 2021, 06:27:31 PM »
Hello Dr. Dubbeldam,

Please see attached the simulation input file and the block file. I obtained the block file for the 13X structure ( Si = 86, Al = 106) using Zeo++ and the format is the same as that required in RASPA. The block file has 8 pockets, which should be for the sodalite units in the 13X structure.
I have also defined the input for switching on the block using the format followed in the RASPA examples. 

INPUT FILE :

SimulationType        MonteCarlo
NumberOfCycles        100000
PrintEvery            1000
PrintPropertiesEvery  1000

Forcefield             local
UseChargesFromCIFFile  yes

Framework 0
FrameworkName NaX
UnitCells 1 1 1
ExternalTemperature 298.0

Component 0 MoleculeName             helium
            MoleculeDefinition       local
            BlockPockets             yes
            BlockPocketsFileName     zeoNaX
            WidomProbability         1.0
            CreateNumberOfMolecules  0

BLOCK FILE :

8
0.920026 0.868617 0.846936 3.49194
0.126382 0.106569 0.0971705 3.71214
0.350113 0.356273 0.881404 3.84527
0.61603 0.611122 0.13383 3.75885
0.418688 0.884354 0.342678 3.14328
0.882809 0.374691 0.426361 3.61778
0.65533 0.130399 0.617683 3.96516
0.155449 0.630486 0.585976 3.53465


25
General / Re: RASPA Simulations Directory not Found
« Last post by amogh on September 24, 2021, 08:48:44 PM »
For setting the RASPA_DIR variable, what is the ideal path to do so? After cloning from Github and running the install commands in the RASPA2 main directory, I just want to make sure I set RASPA_DIR correctly as it often looks for files that don't exist when I have done it before.
26
Input files and parameters / Re: The usage of block_file
« Last post by David Dubbeldam on September 22, 2021, 03:06:43 PM »
Just checked the code: the Widom move _does_ check for blocking.
How did you define the blocking-pockets and what is your input-file to switch on blocking for that component?
27
Announcements / RASPA workshop announced (online) 20 January 2022
« Last post by David Dubbeldam on September 22, 2021, 03:01:20 PM »
This workshop/school focuses on a practical understanding of visualization and molecular simulation of nanoporous materials and fluids, using iRASPA and RASPA. RASPA is well known for force field-based molecular simulation of adsorption and diffusion in nanoporous materials (such as MOFs and zeolites), as well as studying thermodynamic and transport properties of complex fluids. The combination with the visualization software iRASPA enables obtaining direct molecular insight. In this 1-day workshop, besides lectures on the basics of MD/MC, we will also consider the practical side of simulations using iRASPA/RASPA: setting up the system, constructing input files for molecules and frameworks, setting up a force field, understanding input settings, and analyzing the output. The workshop will be online.

https://iraspa.org/workshops/iraspa-raspa-online-workshop-2022/
28
General / Re: Grid potentials for mobile cations in MC/GCMC simulations
« Last post by David Dubbeldam on September 22, 2021, 02:58:55 PM »
The grids are tested by random insertion. So there is no mechanism that avoids overlap of the ions.
You can get: large negative Coulombic energy + large repulsive energy, that nearly cancels out.
So, this is more a problem of the test then of the grid itself.
You can run a simulation with and without the grid and see if you get the same answers.
29
General / Re: RASPA Simulations Directory not Found
« Last post by David Dubbeldam on September 22, 2021, 02:52:10 PM »
You should not install it on /lib, which is indeed a read-only systems directory.
Better just install it in your home account.

In the raspa-directory do:
rm -rf autom4te.cache 
mkdir m4 
aclocal 
autoreconf -i 
automake --add-missing 
autoconf 
./scripts/CompileScript/make-gcc-local
make
make install
30
Input files and parameters / Rigid/Flexible Siloxane
« Last post by JY on September 17, 2021, 10:40:26 PM »
Hello,

I would like to have some hints and help - I have been getting the same error:

Shift all potentials
Error:  Unknown group type (should be 'Flexible' or 'Rigid')

despite various edits made in the molecule.def file.

The only difference between mine and the rigid/flexible example in the raspa handbook is the sequence and direction of numbering the atoms. I came across someone asking about the same question on GitHub and a person suggested to have the flexible or rigid keyword first and then the number of atoms. That did not work too.

RASPA:
Code: [Select]
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
0.0
0.0
0.0
#Number Of Atoms
16
# Number of groups
3
# carboxyl-group
3
flexible
0 Mof_Ob
1 Mof_Ca
2 Mof_Ob
# phenyl-ring
10
rigid
3 Mof_Cb 6.458 6.458 11.526
4 Mof_Cc 7.308 7.308 12.221
5 Mof_Cc 5.608 5.608 12.221
6 Mof_H 7.876 7.876 11.759
7 Mof_H 5.04 5.04 11.759
8 Mof_Cc 7.308 7.308 13.611
9 Mof_Cc 5.608 5.608 13.611
10 Mof_H 7.876 7.876 14.073
11 Mof_H 5.04 5.04 14.073
12 Mof_Cb 6.458 6.458 14.306
# carboxyl-group
3
flexible
13 Mof_Ca
14 Mof_Ob
15 Mof_Ob

Mine:
Code: [Select]
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
586.5
1332000
0.5890
# Number Of Atoms
40
# Number Of Groups
9
# Siloxane ring
8
rigid
0 Si 0.000000 0.000000 0.000000
1 Si -0.022992 3.123492 0.020456
2 Si 3.123592 0.022792 0.020256
3 Si 3.100800 3.146484 0.000299
4 O -0.226719 1.556842 0.505651
5 O 1.566549 -0.204327 -0.484996
6 O 1.534151 3.351011 -0.484096
7 O 3.327919 1.589341 0.505451
# methyl group 1
4
flexible
8 C
16 H
17 H
18 H
# methyl group 2
4
flexible
9 C
19 H
20 H
21 H
# methyl group 3
4
flexible
10 C
22 H
23 H
24 H
# methyl group 4
4
flexible
11 C
25 H
26 H
27 H
# methyl group 5
4
flexible
12 C
28 H
29 H
30 H
# methyl group 6
4
flexible
13 C
31 H
32 H
33 H
# methyl group 7
4
flexible
14 C
34 H
35 H
36 H
# methyl group 8
4
flexible
15 C
37 H
38 H
39 H

Pages: 1 2 [3] 4 5 ... 10