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1
Input files and parameters / Choosing space group
« Last post by Eliyhau on March 12, 2020, 01:43:23 PM »
Hello,
I am importing a CIF file to the iRaspa program, but for some reason the space group is not imported with it. According to Mercury software, the spacegroup should be C2/c, monoclinic; however, I cannot find it in the list of spacegroups under 'symmetry properties'.
Is there a way to get iRaspa to read the spacegroup directly from the CIF file? or perhaps a simple method to manually select the correct spacegroup?
Thanks!
2
Yes, the first component is then not changing it's number of molecules, while the second component is swapped in and out.
3
General / Re: error run simulate
« Last post by David Dubbeldam on March 01, 2020, 09:40:13 AM »
Since I see some python stuff, so it is probably that you are using the numat-code (https://github.com/numat/RASPA2).
You could ask them about their additional python routines.
Our version is strictly C, and is at: https://github.com/iraspa/raspa2
4
General / error run simulate
« Last post by moondog on February 28, 2020, 04:45:44 PM »
Hi,
I'm running a simulation with raspa2
my simulation input is

SimulationType                 MonteCarlo
NumberOfCycles                 10000
NumberOfInitializationCycles   5000
PrintEvery                     1000
RestartFile                    no

Forcefield                     UFF
CutOff                         12.00

Framework                      0
FrameworkName                  ZIF-8
UnitCells                      2 2 2
ExternalTemperature            298.0
ExternalPressure               10000000.0

Movies                         yes
WriteMoviesEvery               1000

Component 0 MoleculeName               RFP
            MoleculeDefinition         Drugs
            TranslationProbability     1.0
            RotationProbability        1.0
            ReinsertionProbability     1.0
            SwapProbability            1.0
            CreateNumberOfMolecules    0

and UFF force field il correctly in raspa-dir

I obtain this error

Process Process-1:
Traceback (most recent call last):
  File "/usr/lib/python3.5/multiprocessing/process.py", line 249, in _bootstrap
    self.run()
  File "/usr/lib/python3.5/multiprocessing/process.py", line 93, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/lib/python3.5/dist-packages/RASPA2-2.0.3-py3.5-linux-x86_64.egg/RASPA2/raspa2.py", line 119, in _script_subprocess
    libraspa = cdll.LoadLibrary(os.path.join(libraspa_dir, libraspa_file))
  File "/usr/lib/python3.5/ctypes/__init__.py", line 425, in LoadLibrary
    return self._dlltype(name)
  File "/usr/lib/python3.5/ctypes/__init__.py", line 347, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: /usr/local/lib/python3.5/dist-packages/RASPA2-2.0.3-py3.5-linux-x86_64.egg/RASPA2/simulations/lib/libraspa2.py: invalid ELF header

How could I fix it?
regards

Alberto
5
General / Cation Doping to a Structure and then Calculate Adsorption of Hydrogen
« Last post by cud on February 25, 2020, 01:32:56 PM »
Hello,

First of all, sorry for this noob question.

I have an user generated structure(CIF file). I want to dope some cation and then calculate the hydrogen storage capacity of the cation doped structure. I have prepared the following input file considering the "RASPA 2.0: Molecular Software Package for Adsorption and Diffusion in (Flexible) Nanoporous Materials" PDF file. I have a questions at this point.

Does this input file I prepared work for the purpose I intended? Or is there a fatal error?

Thank you very much for your time.

SimulationType                          MonteCarlo
NumberOfCycles                        25000
NumberOfInitializationCycles      10000
RestartFile                                no
PrintEvery                                1000
Forcefield                                 (Select based on structure)

Framework                    0
FrameworkName           (USER DEFINED STRUCTURE - CIF File)
UnitCells                       (Adjust considering cut-off and unitcell dimensions)
ExternalTemperature      (Temperature Kelvin)
ExternalPressure           (Pressure Pascal)

Component 0                MoleculeName                         (the cation to be doped)
                                   MoleculeDefinition                    TraPPE
                                   TranslationProbability                1.0
                                   RandomTranslationProbability    1.0
                                   ExtraFrameworkMolecule           yes
                                   CreateNumberOfMolecules        (according to the calculated percentage of doping)

Component 1                MoleculeName                          H2
                                   MoleculeDefinition                     TraPPE
                                   TranslationProbability                1.0
                                   ReinsertionProbability                1.0
                                   SwapProbability                        1.0
                                   ExtraFrameworkMolecule           no
                                   CreateNumberOfMolecules         0


6
Input files and parameters / Re: Question on how to describe ions' chemical potential
« Last post by Haolong on February 12, 2020, 05:49:39 AM »
Dear David:

Thanks for your reply! I am looking forward to simulating the distribution of ions in aqueous solution, the electrolyte in another word, where the chemical potential of ions might be influenced by the concentration or mole fraction of ions in the reservoir instead of pressure. In this situation, can I find a way to link the activity coefficient of ions to the fugacity coefficient, which is used in RASPA to manipulate the chemical potential?

Kind regards,
Haolong
7
Simulation algorithms and theory / Re: about CFCMC potential
« Last post by zhaoli2023 on February 08, 2020, 08:50:57 AM »
Thanks for your reply!
I get it.

Best,
Zhao
8
Visualization / Re: Visualisation using Para View
« Last post by David Dubbeldam on February 03, 2020, 09:32:40 PM »
I guess you need to figure out how Paraview scales these. For the density file, it is by default 150x150x150 points, and this needs to be converted to the real unit cell.
9
Visualization / Re: Imported PDB file
« Last post by David Dubbeldam on February 03, 2020, 09:25:16 PM »
There are many pdb-files out there that are not according to the PDB specification. You could try to use "openbabel" to create a good pdb-file and see if that works.
10
Visualization / Imported PDB file
« Last post by catenate19 on February 01, 2020, 05:05:09 AM »
Hello, please I am having trouble viewing an imported PDB file (a protein structure) on iRASPA. The program just seems to hang unlike the PDBs that exist in the gallery.
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