Recent posts

#61

General / Re: Can the cavity of a MOF be...

Last post by dubbelda - September 30, 2024, 01:45:40 PM

There is a 'help' in iRASPA ('help' menu). In principle, this is about understanding the three panes in the top-left: (I) projects, (II) scenes, (III) movie frames. If you select the second tab, you can add structures to the scene.
'File' -> 'New' -> 'Objects' -> 'Ellipsoid' and then edit the properties.

#62

General / Re: Enthalpy of adsorption

Last post by dubbelda - September 30, 2024, 01:07:58 PM

This works in raspa3 now.

#63

General / Re: Inaccurate Adsorption Isot...

Last post by dubbelda - September 30, 2024, 10:58:16 AM

I do not see the charges of the framework. How do you set these? In the input the charges for the framework appear to be zero.

#64

General / Re: How to make adsorption den...

Last post by dubbelda - September 30, 2024, 10:55:24 AM

First in RASPA do a Monte Carlo simulation with some particles and create the 3D density grid.
Page 172 manual:
ComputeDensityProfile3DVTKGrid yes
WriteDensityProfile3DVTKGridEvery 10000
DensityProfile3DVTKGridPoints 150 150 150

Than it creates files which can you import in iRASPA.

In RASPA3, it will write out a cube-file, which you can also import in iRASPA.

#65

General / Re: Single point calculation f...

Last post by dubbelda - September 30, 2024, 10:52:36 AM

Use a restart-file:
Reads the positions, velocities, and force from the directory 'RestartInitial'. Any creation of molecules in the 'simulation.input' file will be in addition and after this first read from file. This is useful to loadinitial positions of cations for example, and after that create adsorbates. The restart file is written at 'PrintEvery' intervals.

Easiest is to first create a system with the desired number of molecules. Then run it to get a restart-file. Move the directory from 'Restart' to 'RestartInitial' and edit the positions. Then rerun with 'RestartFile yes' (and set 'CreateNumberOfMolecules 0' since they now come from the restart-file).

#66

General / Re: MM3

Last post by dubbelda - September 30, 2024, 10:49:15 AM

Different between what and what? What is the expected value and you're getting a wrong value? More info is needed.

#67

General / Re: iRASPA Potential Energy Su...

Last post by dubbelda - September 30, 2024, 10:46:32 AM

Under "Appearances" you have "Volumetric data": click "Show grid data" and set rendering method to "isosurface".

No, you cannot get the energy per molecule, only the total energy of the component. Note however, that all molecules are equivalent, so you could just divide by the amount of molecules.

[a test simulation shows that the number of adsorbates in the restart file (seven, see the snippet attached below) differs from that reported at the last "PrintEvery" interval in the output file (nine, see the snippet attached below)]

#68

Output files / Inconsistency Between Results ...

Last post by Lingxiao Qin - September 08, 2024, 03:17:48 AM

Dear Prof. Dubbeldam and RASPA community,

The "Restart and Crash-Recovery" section of the RASPA manual mentions that "The restart file is written at 'PrintEvery' intervals.". According to this statement, I expect that the positions, velocities and forces of the adsorbate atoms recorded in the restart file to match the results printed at the last "PrintEvery" interval in the output file. However, a test simulation shows that the number of adsorbates in the restart file (seven, see the snippet attached below) differs from that reported at the last "PrintEvery" interval in the output file (nine, see the snippet attached below), which makes me confused. Could you please clarify what is the relationship between the configuration recorded by the restart file and the results documented in the output file?

Here are my simulation.input and snippets of restart and output files.

simulation.input

Code Select Expand

SimulationType                MonteCarlo
NumberOfCycles                1000
NumberOfInitializationCycles  1000
PrintEvery                    200

ContinueAfterCrash no

ChargeMethod                  Ewald
Forcefield                    ExampleMOFsForceField
UseChargesFromCIFFile yes
CutOffVDW                     10
CutOffChargeCharge            10
RemoveAtomNumberCodeFromLabel yes

Framework             0
FrameworkName         Cu-BTC
UnitCells             1 1 1
HeliumVoidFraction    0.745895
ExternalTemperature   273
ExternalPressure    2500000.0


Component 0 MoleculeName              N2
            MoleculeDefinition        ExampleDefinitions
            TranslationProbability    1.0
            RotationProbability       1.0
            ReinsertionProbability    1.0
            SwapProbability           1.0
            CreateNumberOfMolecules   0
restart_Cu-BTC_1.1.1_273.000000_2.5e+06

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Components: 1 (Adsorbates 7, Cations 0)
========================================================================
Component 0 (N2)
Fractional-molecule-id component 0: -1
Lambda-factors component 0:  0.000000 0.000000 0.000000
Number-of-biasing-factors component 0: 21
Biasing-factors component 0:  0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
Maximum-CF-Lambda-change component 0: 0.500000
Maximum-CBCF-Lambda-change component 0: 0.500000

Maximum-translation-change component 0: 1.000000,0.487500,1.000000
Maximum-translation-in-plane-change component 0: 0.000000,0.000000,0.000000
Maximum-rotation-change component 0: 0.490874 1.472622 0.490874

Reactions: 0

Component: 0     Adsorbate    7 molecules of N2
------------------------------------------------------------------------
output_Cu-BTC_1.1.1_273.000000_2.5e+06.data

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Current cycle: 800 out of 1000
========================================================================================================

Net charge: 1.0103e-13 (F: 1.0103e-13, A: 0, C: 0)
Current Box:  26.34300   0.00000   0.00000 [A]   Average Box:  26.34300   0.00000   0.00000 [A]
               0.00000  26.34300   0.00000 [A]                  0.00000  26.34300   0.00000 [A]
               0.00000   0.00000  26.34300 [A]                  0.00000   0.00000  26.34300 [A]
Box-lengths:   26.34300  26.34300  26.34300 [A] Average:  26.34300  26.34300  26.34300 [A]
Box-angles:   90.00000  90.00000  90.00000 [degrees] Average:  90.00000  90.00000  90.00000 [degrees]
Volume: 18280.82098 [A^3] Average Volume: 18280.82098 [A^3]

Loadings per component:
----------------------------------------------------------------------------------------------------------------------------------------------------
Component 0 (N2), current number of integer/fractional/reaction molecules: 9/0/0 (avg.   9.08489), density:  22.90147 (avg.  23.11749) [kg/m^3]
absolute adsorption:   9.00000 (avg.   9.08489) [mol/uc],   0.9302462147 (avg.   0.9390209050) [mol/kg],  26.0594337300 (avg.  26.3052433421) [mg/g]
                      20.8505160951 (avg.  21.0471917914) [cm^3 STP/g],   18.3237652830 (avg.  18.4966070141) [cm^3 STP/cm^3]
excess adsorption:    -0.1951236435 (avg.  -0.1102297608) [mol/uc],  -0.0201681145 (avg.  -0.0113934242) [mol/kg],  -0.5649790729 (avg.  -0.3191694608) [mg/g]
                      -0.4520476299 (avg.  -0.2553719336) [cm^3 STP/g],   -0.3972666493 (avg.  -0.2244249183) [cm^3 STP/cm^3]
----------------------------------------------------------------------------------------------------------------------------------------------------
Degrees of freedom: 45 0 45 0
Number of Framework-atoms:    624
Number of Adsorbates:           9 (9 integer, 0 fractional, 0 reaction)
Number of Cations:              0 (0 integer, 0 fractional, 0 reaction)

Current total potential energy:             -3908.4716378953 [K]  (avg.       -3915.5804048016)
Current Host-Host energy:                     0.0000000000 [K]  (avg.           0.0000000000)
Current Host-Adsorbate energy:            -3762.2229554409 [K]  (avg.       -3738.1974921185)
Current Host-Cation energy:                   0.0000000000 [K]  (avg.           0.0000000000)
Current Adsorbate-Adsorbate energy:        -146.2486824543 [K]  (avg.        -177.3829126831)
Current Cation-Cation energy:                 0.0000000000 [K]  (avg.           0.0000000000)
Current Adsorbate-Cation energy:              0.0000000000 [K]  (avg.           0.0000000000)



+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Finishing simulation
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

["FlexibleFramework"]

#69

Input files and parameters / Re: Run RASPA simulation with ...

Last post by Lingxiao Qin - September 07, 2024, 08:51:18 AM

I do not think "FlexibleFramework" and "FrameworkDefinitions" have to be explicitly specified when simulating a rigid framework. See the RASPA manual examples of Adsorption isotherm of N2 in a metal-organic framework (MOF), Henry coefficients, enthalpy of adsorption and Adsorption isotherm of CO2 in Cu-BTC for a sample simulation.input file. In addition, you may also compare the input files of these two examples (Diffusion of benzene in rigid IRMOF-1 VS in flexible IRMOF-10) to see that "FlexibleFramework" and "FrameworkDefinitions" are not needed for rigid framework simulation.

In a sum, for your purpose of simulating a rigid structure, it is enough to write

Code Select Expand

Framework 0
FrameworkName calf-20
UnitCells 1.0 1.0 1.0

#70

General / Re: helium void fraction

Last post by Lingxiao Qin - September 07, 2024, 05:50:58 AM

It would be best if you could upload your simulation files including force field definition (force_field.def or force_field_mixing_rules.def), pseudo_atoms.def, framework.cif, helium.def and simulation.input so that possible repliers can try to reproduce your error. Currently I would suggest checking the definition of He atom in the force_field.def, force_field_mixing_rules.def, pseudo_atoms.def and helium.def. RASPA documentation has provided an example about how to simulate the helium void-fraction of a structure. Maybe you can use that example as a reference.