- Welcome to iRASPA Community.
Recent posts
#11
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
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ #12
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 #13
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.
#14
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!
#15
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
#16
Input files and parameters / Bulk Density Validation by MC
Last post by Bourne - August 07, 2024, 04:04:41 AMDear Dr. Dubbeldam and RASPA users,
I am a beginner with the RASPA software and am conducting a study on gas occurrence behaviors within porous rock. As part of my study, I am performing validation work on the fluid model by calculating the bulk density within an empty box at 333K using MC simulations. I have tested the TraPPE and EPM2 models. However, the results are unsatisfactory, as both bulk density values deviate from the data provided by NIST and the P-R equation, despite the systems being well equilibrated. This discrepancy is confusing, and I've tried various approaches without success. I have checked all the input files, and they appear to be correct. Could you please advise on how I might resolve this issue?
Thank you for your time.
Best regards,
Input files for TraPPE Model Validation:
SimulationType MonteCarlo
NumberOfCycles 20000
NumberOfInitializationCycles 6000
PrintEvery 1000
RestartFile no
ChargeMethod Ewald
EwaldPrecision 1e-5
Forcefield TraPPE
RemoveAtomNumberCodeFromLabel no
Box 0
BoxLengths 25 25 25
ExternalTemperature 333.0
ExternalPressure 5e6 10e6 15e6 20e6 25e6 30e6
Movies yes
WriteMoviesEvery 2000
Component 0 MoleculeName CO2
MoleculeDefinition TraPPE
TranslationProbability 0.5
RotationProbability 0.5
ReinsertionProbability 0.5
SwapProbability 1.0
CreateNumberOfMolecules 0
I am a beginner with the RASPA software and am conducting a study on gas occurrence behaviors within porous rock. As part of my study, I am performing validation work on the fluid model by calculating the bulk density within an empty box at 333K using MC simulations. I have tested the TraPPE and EPM2 models. However, the results are unsatisfactory, as both bulk density values deviate from the data provided by NIST and the P-R equation, despite the systems being well equilibrated. This discrepancy is confusing, and I've tried various approaches without success. I have checked all the input files, and they appear to be correct. Could you please advise on how I might resolve this issue?
Thank you for your time.
Best regards,
Input files for TraPPE Model Validation:
SimulationType MonteCarlo
NumberOfCycles 20000
NumberOfInitializationCycles 6000
PrintEvery 1000
RestartFile no
ChargeMethod Ewald
EwaldPrecision 1e-5
Forcefield TraPPE
RemoveAtomNumberCodeFromLabel no
Box 0
BoxLengths 25 25 25
ExternalTemperature 333.0
ExternalPressure 5e6 10e6 15e6 20e6 25e6 30e6
Movies yes
WriteMoviesEvery 2000
Component 0 MoleculeName CO2
MoleculeDefinition TraPPE
TranslationProbability 0.5
RotationProbability 0.5
ReinsertionProbability 0.5
SwapProbability 1.0
CreateNumberOfMolecules 0
#17
Output files / Calculation of MSD from GCMC a...
Last post by thor - August 03, 2024, 05:39:00 AMDear Professor David:
I want to use the final configuration of GCMC adsorption as the initial configuration for MD simulation to calculate MSD. So I renamed the Restart file obtained by adsorption to RestartInitial and used the following file as input. After the simulation is completed, I did not get the corresponding MSDOrderN. Why is this? Is my input file setting correct?
SimulationType MolecularDynamics
NumberOfCycles 1000000
NumberOfInitializationCycles 0
NumberOfEquilibrationCycles 1000000
PrintEvery 5000
PrintPropertiesEvery 1000
RestartFile yes
Ensemble NVT
TimeStep 0.0005
ComputeMSD yes
PrintMSDEvery 5000
Forcefield UFF-Direding
UseChargesFromCIFFile yes
ChargeMethod Ewald
Framework 0
FrameworkName COF2207-8
CutOffVDW 12.8
UnitCells 1 1 1
ExternalTemperature 298
ExternalPressure 1e5
Component 0 MoleculeName CO2
MoleculeDefinition TraPPE
TranslationProbability 0.5
RotationProbability 0.5
ReinsertionProbability 0.5
SwapProbability 1.0
CreateNumberOfMolecules 0
I want to use the final configuration of GCMC adsorption as the initial configuration for MD simulation to calculate MSD. So I renamed the Restart file obtained by adsorption to RestartInitial and used the following file as input. After the simulation is completed, I did not get the corresponding MSDOrderN. Why is this? Is my input file setting correct?
SimulationType MolecularDynamics
NumberOfCycles 1000000
NumberOfInitializationCycles 0
NumberOfEquilibrationCycles 1000000
PrintEvery 5000
PrintPropertiesEvery 1000
RestartFile yes
Ensemble NVT
TimeStep 0.0005
ComputeMSD yes
PrintMSDEvery 5000
Forcefield UFF-Direding
UseChargesFromCIFFile yes
ChargeMethod Ewald
Framework 0
FrameworkName COF2207-8
CutOffVDW 12.8
UnitCells 1 1 1
ExternalTemperature 298
ExternalPressure 1e5
Component 0 MoleculeName CO2
MoleculeDefinition TraPPE
TranslationProbability 0.5
RotationProbability 0.5
ReinsertionProbability 0.5
SwapProbability 1.0
CreateNumberOfMolecules 0
#18
General / iRASPA Potential Energy Surfac...
Last post by Cecilia - July 23, 2024, 11:46:59 AMHello,
I was wondering how I can use iRASPA to generate a potential energy surface a MOF. I had tried downloaded iRASPA from the Microsoft store and the Apple store but neither seems to have the "Adsorption Surface" section under the "Appearance" tab that I saw in the photos.
Furthermore, I was wondering if it is possible to get the energies of each molecule per MC step from RASPA simulations with the grand canonical ensemble?
Many thanks in advance!
I was wondering how I can use iRASPA to generate a potential energy surface a MOF. I had tried downloaded iRASPA from the Microsoft store and the Apple store but neither seems to have the "Adsorption Surface" section under the "Appearance" tab that I saw in the photos.
Furthermore, I was wondering if it is possible to get the energies of each molecule per MC step from RASPA simulations with the grand canonical ensemble?
Many thanks in advance!
#19
General / RUPTURA - fitting file
Last post by inangoi - July 10, 2024, 01:57:45 PMHi,
I'm trying to produce an isotherm using RUPTURA. I tried to do the example (MAF-X8-xylenes - fitting) but I don't know how to get the 'Result.dat-MAF-x8...' file
It is said in the documentation the this file (Results.dat) consists of the
equilibrium loading data computed using grand-canonical Monte Carlo simulations. But when I run a MC simulation using RASPA the output file is different from the example
Results.dat-MAF-x8 ... from the example:
# 1: pressure [Pa]
# 2: fugacity coefficient [-]
# 3: fugacity [Pa]
# 4: (absolute) loading [molecules per total cell]
# 5: (absolute) error [molecules per total cell]
# 6: (absolute) loading [molecules per unit cell]
# 7: (absolute) error [molecules per unit cell]
# 8: (absolute) loading [mol/kg]
# 9: (absolute) error [mol/kg]
# 10: (absolute) loading [mg/g]
# 11: (absolute) error [mg/g]
# 12: (excess) loading [molecules per total cell]
# 13: (excess) error [molecules per total cell]
# 14: (excess) loading [molecules per unit cell]
# 15: (excess) error [molecules per unit cell]
# 16: (excess) loading [mol/kg]
# 17: (excess) error [mol/kg]
# 18: (excess) loading [mg/g]
# 19: (excess) error [mg/g]
# 20: heat of desorption [K]
# 21: heat of desorption error [K]
# MAF-x8-P1-Repeat, 433K, o-xylene
0.00000000010000 1.0000000000 0.00000000010000 0.0074480000 0.0029671913 0.0009310000 0.0003708989 0.0002080881 0.0000828997 0.0220916711 0.0088010491 0.0074480000 0.0029671913 0.0009310000 0.0003708989 0.0002080881 0.0000828997 0.0220916711 0.0088010491 18782.43092 380.146898
0.00000000030703 1.0000000000 0.00000000030703 0.0216080000 0.0085091424 0.0027010000 0.0010636428 0.0006037013 0.0002377351 0.0640919481 0.0252391481 0.0216080000 0.0085091424 0.0027010000 0.0010636428 0.0006037013 0.0002377351 0.0640919481 0.0252391481 18795.78499 282.730668
0.00000000094267 1.0000000000 0.00000000094267 0.0563380000 0.0363284911 0.0070422500 0.0045410614 0.0015740153 0.0010149740 0.1671053393 0.1077547096 0.0563380000 0.0363284911 0.0070422500 0.0045410614 0.0015740153 0.0010149740 0.1671053393 0.1077547096 18686.98457 432.402570
0.00000000289427 1.0000000000 0.00000000289427 0.1611820000 0.0512807588 0.0201477500 0.0064100949 0.0045032295 0.0014327222 0.4780853563 0.1521049487 0.1611820000 0.0512807588 0.0201477500 0.0064100949 0.0045032295 0.0014327222 0.4780853563 0.1521049487 18690.29605 178.637466
0.00000000888624 1.0000000000 0.00000000888624 0.5160240000 0.1673997422 0.0645030000 0.0209249678 0.0144170843 0.0046769456 1.5305897550 0.4965279337 0.5160240000 0.1673997422 0.0645030000 0.0209249678 0.0144170843 0.0046769456 1.5305897550 0.4965279337 18640.31467 243.501202
0.00000002728330 1.0000000000 0.00000002728330 1.7657580000 0.5404926327 0.2207197500 0.0675615791 0.0493331356 0.0151007082 5.2374523367 1.6031666865 1.7657580000 0.5404926327 0.2207197500 0.0675615791 0.0493331356 0.0151007082 5.2374523367 1.6031666865 18758.00885 286.259478
0.00000008376780 1.0000000000 0.00000008376780 5.4241680000 0.9562926569 0.6780210000 0.1195365821 0.151544
.
.
.
.
-------------------------------
input
SimulationType MonteCarlo
NumberOfCycles 25000
NumberOfInitializationCycles 5000
PrintEvery 1000
Forcefield ExampleZeolitesForceField
RemoveAtomNumberCodeFromLabel yes
Framework 0
FrameworkName MFI_SI
UnitCells 2 2 2
HeliumVoidFraction 0.29
ExternalTemperature 300.0
ExternalPressure 1e4 1e5
ComputeNumberOfMoleculesHistogram yes
WriteNumberOfMoleculesHistogramEvery 5000
NumberOfMoleculesHistogramSize 1100
NumberOfMoleculesRange 80
ComputeEnergyHistogram yes
WriteEnergyHistogramEvery 5000
EnergyHistogramSize 400
EnergyHistogramLowerLimit -110000
EnergyHistogramUpperLimit -20000
Component 0 MoleculeName methane
MoleculeDefinition ExampleDefinitions
TranslationProbability 0.5
ReinsertionProbability 0.5
SwapProbability 1.0
CreateNumberOfMolecules 0
----------------
output_...
Compiler and run-time data
===========================================================================
RASPA 2.0.45
Compiled as a 64-bits application
Compiler: gcc Apple LLVM 12.0.5 (clang-1205.0.22.9)
Compile Date = May 18 2021, Compile Time = 12:54:12
Tue May 18 12:55:50 2021
Simulation started on Tuesday, May 18.
The start time was 12:55 PM.
Cpu data: x86_64
Cpu Model: MacPro7,1
Host name: MacPro.local
OS release: 20.4.0
OS type: Darwin
OS version: 20E232
Simulation
===========================================================================
Dimensions: 3
Random number seed: 1621335350
RASPA directory set to: /Users/dubbelda/RASPA/simulations/
String appended to output-files:
Number of cycles: 25000
Number of initializing cycles: 5000
Number of equilibration cycles: 0
Print every: 1000
Rectangular boundary condition applied
Timestep: 0.000500
Degrees of freedom: 0
Translational Degrees of freedom: 0
Rotational Degrees of freedom: 0
Degrees of freedom Framework: 0
.
.
.
.
What should I change in the input file? or what am I doing wrong?
Thank you in advance for any help
I'm trying to produce an isotherm using RUPTURA. I tried to do the example (MAF-X8-xylenes - fitting) but I don't know how to get the 'Result.dat-MAF-x8...' file
It is said in the documentation the this file (Results.dat) consists of the
equilibrium loading data computed using grand-canonical Monte Carlo simulations. But when I run a MC simulation using RASPA the output file is different from the example
Results.dat-MAF-x8 ... from the example:
# 1: pressure [Pa]
# 2: fugacity coefficient [-]
# 3: fugacity [Pa]
# 4: (absolute) loading [molecules per total cell]
# 5: (absolute) error [molecules per total cell]
# 6: (absolute) loading [molecules per unit cell]
# 7: (absolute) error [molecules per unit cell]
# 8: (absolute) loading [mol/kg]
# 9: (absolute) error [mol/kg]
# 10: (absolute) loading [mg/g]
# 11: (absolute) error [mg/g]
# 12: (excess) loading [molecules per total cell]
# 13: (excess) error [molecules per total cell]
# 14: (excess) loading [molecules per unit cell]
# 15: (excess) error [molecules per unit cell]
# 16: (excess) loading [mol/kg]
# 17: (excess) error [mol/kg]
# 18: (excess) loading [mg/g]
# 19: (excess) error [mg/g]
# 20: heat of desorption [K]
# 21: heat of desorption error [K]
# MAF-x8-P1-Repeat, 433K, o-xylene
0.00000000010000 1.0000000000 0.00000000010000 0.0074480000 0.0029671913 0.0009310000 0.0003708989 0.0002080881 0.0000828997 0.0220916711 0.0088010491 0.0074480000 0.0029671913 0.0009310000 0.0003708989 0.0002080881 0.0000828997 0.0220916711 0.0088010491 18782.43092 380.146898
0.00000000030703 1.0000000000 0.00000000030703 0.0216080000 0.0085091424 0.0027010000 0.0010636428 0.0006037013 0.0002377351 0.0640919481 0.0252391481 0.0216080000 0.0085091424 0.0027010000 0.0010636428 0.0006037013 0.0002377351 0.0640919481 0.0252391481 18795.78499 282.730668
0.00000000094267 1.0000000000 0.00000000094267 0.0563380000 0.0363284911 0.0070422500 0.0045410614 0.0015740153 0.0010149740 0.1671053393 0.1077547096 0.0563380000 0.0363284911 0.0070422500 0.0045410614 0.0015740153 0.0010149740 0.1671053393 0.1077547096 18686.98457 432.402570
0.00000000289427 1.0000000000 0.00000000289427 0.1611820000 0.0512807588 0.0201477500 0.0064100949 0.0045032295 0.0014327222 0.4780853563 0.1521049487 0.1611820000 0.0512807588 0.0201477500 0.0064100949 0.0045032295 0.0014327222 0.4780853563 0.1521049487 18690.29605 178.637466
0.00000000888624 1.0000000000 0.00000000888624 0.5160240000 0.1673997422 0.0645030000 0.0209249678 0.0144170843 0.0046769456 1.5305897550 0.4965279337 0.5160240000 0.1673997422 0.0645030000 0.0209249678 0.0144170843 0.0046769456 1.5305897550 0.4965279337 18640.31467 243.501202
0.00000002728330 1.0000000000 0.00000002728330 1.7657580000 0.5404926327 0.2207197500 0.0675615791 0.0493331356 0.0151007082 5.2374523367 1.6031666865 1.7657580000 0.5404926327 0.2207197500 0.0675615791 0.0493331356 0.0151007082 5.2374523367 1.6031666865 18758.00885 286.259478
0.00000008376780 1.0000000000 0.00000008376780 5.4241680000 0.9562926569 0.6780210000 0.1195365821 0.151544
.
.
.
.
-------------------------------
input
SimulationType MonteCarlo
NumberOfCycles 25000
NumberOfInitializationCycles 5000
PrintEvery 1000
Forcefield ExampleZeolitesForceField
RemoveAtomNumberCodeFromLabel yes
Framework 0
FrameworkName MFI_SI
UnitCells 2 2 2
HeliumVoidFraction 0.29
ExternalTemperature 300.0
ExternalPressure 1e4 1e5
ComputeNumberOfMoleculesHistogram yes
WriteNumberOfMoleculesHistogramEvery 5000
NumberOfMoleculesHistogramSize 1100
NumberOfMoleculesRange 80
ComputeEnergyHistogram yes
WriteEnergyHistogramEvery 5000
EnergyHistogramSize 400
EnergyHistogramLowerLimit -110000
EnergyHistogramUpperLimit -20000
Component 0 MoleculeName methane
MoleculeDefinition ExampleDefinitions
TranslationProbability 0.5
ReinsertionProbability 0.5
SwapProbability 1.0
CreateNumberOfMolecules 0
----------------
output_...
Compiler and run-time data
===========================================================================
RASPA 2.0.45
Compiled as a 64-bits application
Compiler: gcc Apple LLVM 12.0.5 (clang-1205.0.22.9)
Compile Date = May 18 2021, Compile Time = 12:54:12
Tue May 18 12:55:50 2021
Simulation started on Tuesday, May 18.
The start time was 12:55 PM.
Cpu data: x86_64
Cpu Model: MacPro7,1
Host name: MacPro.local
OS release: 20.4.0
OS type: Darwin
OS version: 20E232
Simulation
===========================================================================
Dimensions: 3
Random number seed: 1621335350
RASPA directory set to: /Users/dubbelda/RASPA/simulations/
String appended to output-files:
Number of cycles: 25000
Number of initializing cycles: 5000
Number of equilibration cycles: 0
Print every: 1000
Rectangular boundary condition applied
Timestep: 0.000500
Degrees of freedom: 0
Translational Degrees of freedom: 0
Rotational Degrees of freedom: 0
Degrees of freedom Framework: 0
.
.
.
.
What should I change in the input file? or what am I doing wrong?
Thank you in advance for any help
#20
Visualization / Adsorption density distributio...
Last post by Z.GAO - July 03, 2024, 05:25:02 AMHi everyone,
In the post-processing of gas adsorption MOF, I want to make an adsorption density distribution map. MOF is a triclinic system, and the adsorption density map drawn by VisIt software is still a cubic structure. So I use iRASPA software to draw it. Although iRASPA can show the triclinic structure, there is no color scale, only one color, which makes it difficult to intuitively judge the priority adsorption site. How can I solve this problem?
In addition, when I use iRASPA to present the molecular structure, I find that some atoms are not bonded. How should I deal with this?
Best wishes!
Zheng
In the post-processing of gas adsorption MOF, I want to make an adsorption density distribution map. MOF is a triclinic system, and the adsorption density map drawn by VisIt software is still a cubic structure. So I use iRASPA software to draw it. Although iRASPA can show the triclinic structure, there is no color scale, only one color, which makes it difficult to intuitively judge the priority adsorption site. How can I solve this problem?
In addition, when I use iRASPA to present the molecular structure, I find that some atoms are not bonded. How should I deal with this?
Best wishes!
Zheng