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#41
General / Re: Inaccurate Adsorption Isot...
Last post by dubbelda - September 30, 2024, 10:58:16 AMI 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.
#42
General / Re: How to make adsorption den...
Last post by dubbelda - September 30, 2024, 10:55:24 AMFirst 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.
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.
#43
General / Re: Single point calculation f...
Last post by dubbelda - September 30, 2024, 10:52:36 AMUse 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).
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).
#44
Different between what and what? What is the expected value and you're getting a wrong value? More info is needed.
#45
General / Re: iRASPA Potential Energy Su...
Last post by dubbelda - September 30, 2024, 10:46:32 AMUnder "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.
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.
#46
Output files / Inconsistency Between Results ...
Last post by Lingxiao Qin - September 08, 2024, 03:17:48 AMDear 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
restart_Cu-BTC_1.1.1_273.000000_2.5e+06
output_Cu-BTC_1.1.1_273.000000_2.5e+06.data
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
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 0restart_Cu-BTC_1.1.1_273.000000_2.5e+06
Code Select
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
Code Select
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
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ #47
Input files and parameters / Re: Run RASPA simulation with ...
Last post by Lingxiao Qin - September 07, 2024, 08:51:18 AMI 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
In a sum, for your purpose of simulating a rigid structure, it is enough to write
Code Select
Framework 0
FrameworkName calf-20
UnitCells 1.0 1.0 1.0 #48
General / Re: helium void fraction
Last post by Lingxiao Qin - September 07, 2024, 05:50:58 AMIt 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.
#49
General / helium void fraction
Last post by alireza_hadi68 - September 06, 2024, 01:17:00 PMI have problem simulating helium void fraction in MOF. I used example code and revised it as follow:
SimulationType MonteCarlo
NumberOfCycles 500000
PrintEvery 10000
PrintPropertiesEvery 10000
Forcefield local
Framework 0
FrameworkName perfect_charge
UnitCells 2 2 2
ExternalTemperature 298.0
Component 0 MoleculeName helium
MoleculeDefinition local
WidomProbability 1.0
CreateNumberOfMolecules 0
but I have the error below:
ReturnPseudoAtomNumber: Error!!!! :He
I would greatly appreciate any assistance in resolving this issue.
Thanks!
SimulationType MonteCarlo
NumberOfCycles 500000
PrintEvery 10000
PrintPropertiesEvery 10000
Forcefield local
Framework 0
FrameworkName perfect_charge
UnitCells 2 2 2
ExternalTemperature 298.0
Component 0 MoleculeName helium
MoleculeDefinition local
WidomProbability 1.0
CreateNumberOfMolecules 0
but I have the error below:
ReturnPseudoAtomNumber: Error!!!! :He
I would greatly appreciate any assistance in resolving this issue.
Thanks!
#50
Input files and parameters / Run RASPA simulation with Rigi...
Last post by AntonioDouglas - August 29, 2024, 04:08:06 AMHi Prof. Dubbeldam and dear RASPA Community.
I am a beginner in using RASPA.
I am trying to simulate adsorption on a MOF with Monte Carlo, and I am following the manual and the RASPA repository on github as guidance. In order to simulate the structure as rigid, I follow the instructions in the manual in the "Framework parameters" section, so I adopt the parameters:
Framework 0
FrameworkName calf-20
UnitCells 1.0 1.0 1.0
FlexibleFramework no
FrameworkDefinitions framework.def
The last parameter was adopted by recommendation of the manual, which states: "The file is read even when 'FlexibleFramework no' is specified (the reason is that framework bond-dipoles are defined using the 'framework.def' file)".
However, the manual does not contain examples or further details about the framework.def file when the intention is to simulate a rigid structure.
In the RASPA github repository, the examples show the specifications of simulation.input and framework.def for adsorption analysis only when the structure is flexible, thus leaving no further information on how to simulate adsorption in rigid structures.
In an attempt to find a solution, my most reasonable guesses were: 1. Consider that the definition of the rigid structure of the framework described in the content of framework.def was exactly the same as the rigid structure of the molecule, in molecule.def. 2. Consider 0 in all #CoreShells bond BondDipoles UreyBradley bend inv tors configurations improper-torsion bond/bond bond/bend bend/bend stretch/torsion bend/torsion, as stated in the framework.def file used as an example for flexible structures.
Nothing worked.
These and countless other attempts proved fruitless, and most of the time they resulted in the same error log: "Error: Unknown group type (should be 'Flexible' or 'Rigid')", except for guess 1, described above, in which I got the error: "ReturnPseudoAtomNumber: Error!!!! :0.22394", referring to the corresponding value of "Acentric factor [-]", as stated in the edited framework.def file, taking as an example the file for the rigid molecule CO2.def, which is in the RASPA github repository.
With no further ideas on how to proceed, I come to ask for your help, a long-time RASPA user, on how to proceed and solve this problem.
How can I correctly define the parameter to establish that the MOF structure used in the adsorption simulation calculated with Monte Carlo is in fact rigid?
Thank you in advance.
Regards,
Antonio Douglas
I am a beginner in using RASPA.
I am trying to simulate adsorption on a MOF with Monte Carlo, and I am following the manual and the RASPA repository on github as guidance. In order to simulate the structure as rigid, I follow the instructions in the manual in the "Framework parameters" section, so I adopt the parameters:
Framework 0
FrameworkName calf-20
UnitCells 1.0 1.0 1.0
FlexibleFramework no
FrameworkDefinitions framework.def
The last parameter was adopted by recommendation of the manual, which states: "The file is read even when 'FlexibleFramework no' is specified (the reason is that framework bond-dipoles are defined using the 'framework.def' file)".
However, the manual does not contain examples or further details about the framework.def file when the intention is to simulate a rigid structure.
In the RASPA github repository, the examples show the specifications of simulation.input and framework.def for adsorption analysis only when the structure is flexible, thus leaving no further information on how to simulate adsorption in rigid structures.
In an attempt to find a solution, my most reasonable guesses were: 1. Consider that the definition of the rigid structure of the framework described in the content of framework.def was exactly the same as the rigid structure of the molecule, in molecule.def. 2. Consider 0 in all #CoreShells bond BondDipoles UreyBradley bend inv tors configurations improper-torsion bond/bond bond/bend bend/bend stretch/torsion bend/torsion, as stated in the framework.def file used as an example for flexible structures.
Nothing worked.
These and countless other attempts proved fruitless, and most of the time they resulted in the same error log: "Error: Unknown group type (should be 'Flexible' or 'Rigid')", except for guess 1, described above, in which I got the error: "ReturnPseudoAtomNumber: Error!!!! :0.22394", referring to the corresponding value of "Acentric factor [-]", as stated in the edited framework.def file, taking as an example the file for the rigid molecule CO2.def, which is in the RASPA github repository.
With no further ideas on how to proceed, I come to ask for your help, a long-time RASPA user, on how to proceed and solve this problem.
How can I correctly define the parameter to establish that the MOF structure used in the adsorption simulation calculated with Monte Carlo is in fact rigid?
Thank you in advance.
Regards,
Antonio Douglas
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