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#1
General / Re: How to make adsorption den...
Last post by John Walker - Today at 10:14:56 AM大佬，你会了吗？
#2
General / iRASPA cannot display the dens...
Last post by John Walker - Today at 09:16:10 AMDear:
I have recently been using MOF materials for methane adsorption, and have attempted to import VTK files generated by RASPA2.0.4 into the IRASPA software. I am only able to generate MOF structure diagrams, but not the methane diagrams. I imported using 'DensityProfile_methane' and 'COMDensityProfile_methane' from the VTK folder, and received the error 'Import failed, Cannot read VTK header (line: 910 file: iraspagui/mainwindow.cpp)'. Importing 'Framework_final.pdb' from the Movies folder does display the molecular structure, which confuses me. How can I produce a methane adsorption density map? I can do it with VisIt.
SimulationType MonteCarlo
NumberOfCycles 30000
NumberOfInitializationCycles 5000
PrintEvery 1000
ContinueAfterCrash no
#WriteBinaryRestartFileEvery 1000
ChargeMethod Ewald
EwaldPrecision 1e-6
Ensemble NVT
TimeStep 0.0005
Forcefield GenericMOFs
CutOffVDW 12
RemoveAtomNumberCodeFromLabel yes
Movies yes
WriteMoviesEvery 1000
RemoveAtomNumberCodeFromLabel yes
UseChargesFromCIFFile yes
Framework 0
FrameworkName HKUST-1
UnitCells 2 2 2
HeliumVoidFraction 0.39778
ExternalTemperature 298.15
ExternalPressure 1.0e+06
ComputeDensityProfile3DVTKGrid yes
WriteDensityProfile3DVTKGridEvery 1000
DensityProfile3DVTKGridPoints 150 150 150
AverageDensityOverUnitCellsVTK yes
DensityAveragingTypeVTK FullBox
Component 0 MoleculeName methane
MoleculeDefinition TraPPE
IdealGasRosenbluthWeight 1.0
TranslationProbability 1.0
RotationProbability 1.0
ReinsertionProbability 1.0
##CBMCProbability 1.0
SwapProbability 1.0
CreateNumberOfMolecules 0
I have recently been using MOF materials for methane adsorption, and have attempted to import VTK files generated by RASPA2.0.4 into the IRASPA software. I am only able to generate MOF structure diagrams, but not the methane diagrams. I imported using 'DensityProfile_methane' and 'COMDensityProfile_methane' from the VTK folder, and received the error 'Import failed, Cannot read VTK header (line: 910 file: iraspagui/mainwindow.cpp)'. Importing 'Framework_final.pdb' from the Movies folder does display the molecular structure, which confuses me. How can I produce a methane adsorption density map? I can do it with VisIt.
SimulationType MonteCarlo
NumberOfCycles 30000
NumberOfInitializationCycles 5000
PrintEvery 1000
ContinueAfterCrash no
#WriteBinaryRestartFileEvery 1000
ChargeMethod Ewald
EwaldPrecision 1e-6
Ensemble NVT
TimeStep 0.0005
Forcefield GenericMOFs
CutOffVDW 12
RemoveAtomNumberCodeFromLabel yes
Movies yes
WriteMoviesEvery 1000
RemoveAtomNumberCodeFromLabel yes
UseChargesFromCIFFile yes
Framework 0
FrameworkName HKUST-1
UnitCells 2 2 2
HeliumVoidFraction 0.39778
ExternalTemperature 298.15
ExternalPressure 1.0e+06
ComputeDensityProfile3DVTKGrid yes
WriteDensityProfile3DVTKGridEvery 1000
DensityProfile3DVTKGridPoints 150 150 150
AverageDensityOverUnitCellsVTK yes
DensityAveragingTypeVTK FullBox
Component 0 MoleculeName methane
MoleculeDefinition TraPPE
IdealGasRosenbluthWeight 1.0
TranslationProbability 1.0
RotationProbability 1.0
ReinsertionProbability 1.0
##CBMCProbability 1.0
SwapProbability 1.0
CreateNumberOfMolecules 0
#3
Input files and parameters / Ideal Gas Rosenbluth Weight Gr...
Last post by ngantzler - May 28, 2024, 08:15:16 PMHi Dr. Dubbeldam,
I am putting together a molecular model and have gotten an IGRW > 1.0. Similar models such as the PFOA model used in The role of surface thermodynamics and kinetics in the removal of PFOA from aqueous solutions give an IGRW~3.69 (T=298 K).
My understanding is that the IGRW = 1.0 for small molecules (e.g. butane) where we can neglect intra-molecular interactions; however, for larger molecules (e.g. octane) we expect an IGRW < 1.0, so I don't understand what it means to have a value greater then 1.0.
Is an IGRW > 1.0 physically meaningful? What is the physical intuition to apply here? Could this be due to degenerate energy states?
Thanks,
Nick
I am putting together a molecular model and have gotten an IGRW > 1.0. Similar models such as the PFOA model used in The role of surface thermodynamics and kinetics in the removal of PFOA from aqueous solutions give an IGRW~3.69 (T=298 K).
My understanding is that the IGRW = 1.0 for small molecules (e.g. butane) where we can neglect intra-molecular interactions; however, for larger molecules (e.g. octane) we expect an IGRW < 1.0, so I don't understand what it means to have a value greater then 1.0.
Is an IGRW > 1.0 physically meaningful? What is the physical intuition to apply here? Could this be due to degenerate energy states?
Thanks,
Nick
#4
General / Re: Defining a parametric flex...
Last post by iwanchemist - May 25, 2024, 12:03:29 PMI have same problem, how to define flexible structure in .def file
what we have to manual definition flexible structure?
what we have to manual definition flexible structure?
#5
Simulation algorithms and theory / GCMD-Example 13: MD MuPT
Last post by iwanchemist - May 25, 2024, 08:44:50 AMHello Prof. Dubbeldam,
I wanna ask you about GCMD (MC/MD) skrip in module RASPA like this:
SimulationType MolecularDynamics
NumberOfCycles 1000000
NumberOfEquilibrationCycles 100000
PrintEvery 1000
ContinueAfterCrash yes
WriteBinaryRestartFileEvery 1000
Ensemble MuPT
Forcefield Local
CutOff 10.0
Movies yes
WriteMoviesEvery 1000
Framework 0
FrameworkName Framework_0_final_1_1_1_VASP
HeliumVoidFraction 0.801937
UnitCells 1 1 1
ExternalTemperature 298.0
ExternalPressure 1000000
ComputeRDF yes
WriteRDFEvery 1000
FlexibleFramework yes
FrameworkDefinitions Local
Component 0 MoleculeName CO2
MoleculeDefinition Local
IdealGasRosenbluthWeight 1.0
SwapProbability 1.0
CreateNumberOfMolecules 1
Based on this script, I am confused. If the MD script is simulated for 1,000,000 cycles, what is the default duration of the Monte Carlo simulation?
I wanna ask you about GCMD (MC/MD) skrip in module RASPA like this:
SimulationType MolecularDynamics
NumberOfCycles 1000000
NumberOfEquilibrationCycles 100000
PrintEvery 1000
ContinueAfterCrash yes
WriteBinaryRestartFileEvery 1000
Ensemble MuPT
Forcefield Local
CutOff 10.0
Movies yes
WriteMoviesEvery 1000
Framework 0
FrameworkName Framework_0_final_1_1_1_VASP
HeliumVoidFraction 0.801937
UnitCells 1 1 1
ExternalTemperature 298.0
ExternalPressure 1000000
ComputeRDF yes
WriteRDFEvery 1000
FlexibleFramework yes
FrameworkDefinitions Local
Component 0 MoleculeName CO2
MoleculeDefinition Local
IdealGasRosenbluthWeight 1.0
SwapProbability 1.0
CreateNumberOfMolecules 1
Based on this script, I am confused. If the MD script is simulated for 1,000,000 cycles, what is the default duration of the Monte Carlo simulation?
#6
General / No strings attached dating
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#7
Output files / absoulte and excess adsorption
Last post by Junran Lu - May 24, 2024, 04:09:26 AMDear Professor David:
In the simulation of toluene adsorption on MFI-type zeolite, the output-file shows, adsorption load is postive, and excess load is negative; in the simluation.input, we set the external temperature and pressure are 298K and 1e5Pa, respeactively; which adsorption result is correct under 298K/1e5Pa tolulene adsorption simulation?
the detail amount of adsorption is following:
Component 0 [toluene]
-------------------------------------------------------------
Block[ 0] 57.54390 [-]
Block[ 1] 61.49325 [-]
Block[ 2] 62.96655 [-]
Block[ 3] 63.05500 [-]
Block[ 4] 64.06460 [-]
------------------------------------------------------------------------------
Average 61.8246600000 +/- 4.5842966097 [-]
Average loading absolute [molecules/unit cell] 7.7280825000 +/- 0.5730370762 [-]
Average loading absolute [mol/kg framework] 1.3397983817 +/- 0.0993460082 [-]
Average loading absolute [milligram/gram framework] 123.4325701655 +/- 9.1525212259 [-]
Average loading absolute [cm^3 (STP)/gr framework] 30.0302084340 +/- 2.2267390183 [-]
Average loading absolute [cm^3 (STP)/cm^3 framework] 54.7548092722 +/- 4.0600673988 [-]
Block[ 0] 57.54390 [-]
Block[ 1] 61.49325 [-]
Block[ 2] 62.96655 [-]
Block[ 3] 63.05500 [-]
Block[ 4] 64.06460 [-]
------------------------------------------------------------------------------
Average -24.1753400000 +/- 4.5842966097 [-]
Average loading excess [molecules/unit cell] -3.0219175000 +/- 0.5730370762 [-]
Average loading excess [mol/kg framework] -0.5239022974 +/- 0.0993460082 [-]
Average loading excess [milligram/gram framework] -48.2659241607 +/- 9.1525212259 [-]
Average loading excess [cm^3 (STP)/gr framework] -11.7427333877 +/- 2.2267390183 [-]
Average loading excess [cm^3 (STP)/cm^3 framework] -21.4108113298 +/- 4.0600673988 [-]
while during the simluation, the toluene molecule is defined as a rigid molecule(as following):
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
591.75
4126257.975
0.264
# Number Of Atoms
7
# Number Of Groups
1
# Alkane-group
7
rigid
0 CH3 0.0 1.54 0.0
1 C_arc 0.0 0.0 0.0
2 CH_arc 1.2124 -0.7 0.0
3 CH_arc 1.2124 -2.1 0.0
4 CH_arc 0.0 -2.8 0.0
5 CH_arc -1.2124 -2.1 0.0
6 CH_arc -1.2124 -0.7 0.0
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 7 0 0 0 0 0 0 0 0 0 0 0 0 0
# Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
1 2 RIGID_BOND
3 4 RIGID_BOND
2 3 RIGID_BOND
4 5 RIGID_BOND
5 6 RIGID_BOND
6 1 RIGID_BOND
# Number of config moves
0
In the simulation of toluene adsorption on MFI-type zeolite, the output-file shows, adsorption load is postive, and excess load is negative; in the simluation.input, we set the external temperature and pressure are 298K and 1e5Pa, respeactively; which adsorption result is correct under 298K/1e5Pa tolulene adsorption simulation?
the detail amount of adsorption is following:
Component 0 [toluene]
-------------------------------------------------------------
Block[ 0] 57.54390 [-]
Block[ 1] 61.49325 [-]
Block[ 2] 62.96655 [-]
Block[ 3] 63.05500 [-]
Block[ 4] 64.06460 [-]
------------------------------------------------------------------------------
Average 61.8246600000 +/- 4.5842966097 [-]
Average loading absolute [molecules/unit cell] 7.7280825000 +/- 0.5730370762 [-]
Average loading absolute [mol/kg framework] 1.3397983817 +/- 0.0993460082 [-]
Average loading absolute [milligram/gram framework] 123.4325701655 +/- 9.1525212259 [-]
Average loading absolute [cm^3 (STP)/gr framework] 30.0302084340 +/- 2.2267390183 [-]
Average loading absolute [cm^3 (STP)/cm^3 framework] 54.7548092722 +/- 4.0600673988 [-]
Block[ 0] 57.54390 [-]
Block[ 1] 61.49325 [-]
Block[ 2] 62.96655 [-]
Block[ 3] 63.05500 [-]
Block[ 4] 64.06460 [-]
------------------------------------------------------------------------------
Average -24.1753400000 +/- 4.5842966097 [-]
Average loading excess [molecules/unit cell] -3.0219175000 +/- 0.5730370762 [-]
Average loading excess [mol/kg framework] -0.5239022974 +/- 0.0993460082 [-]
Average loading excess [milligram/gram framework] -48.2659241607 +/- 9.1525212259 [-]
Average loading excess [cm^3 (STP)/gr framework] -11.7427333877 +/- 2.2267390183 [-]
Average loading excess [cm^3 (STP)/cm^3 framework] -21.4108113298 +/- 4.0600673988 [-]
while during the simluation, the toluene molecule is defined as a rigid molecule(as following):
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
591.75
4126257.975
0.264
# Number Of Atoms
7
# Number Of Groups
1
# Alkane-group
7
rigid
0 CH3 0.0 1.54 0.0
1 C_arc 0.0 0.0 0.0
2 CH_arc 1.2124 -0.7 0.0
3 CH_arc 1.2124 -2.1 0.0
4 CH_arc 0.0 -2.8 0.0
5 CH_arc -1.2124 -2.1 0.0
6 CH_arc -1.2124 -0.7 0.0
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 7 0 0 0 0 0 0 0 0 0 0 0 0 0
# Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
1 2 RIGID_BOND
3 4 RIGID_BOND
2 3 RIGID_BOND
4 5 RIGID_BOND
5 6 RIGID_BOND
6 1 RIGID_BOND
# Number of config moves
0
#8
Output files / Re: ENERGY DRIFT
Last post by neumannrf - April 10, 2024, 12:28:49 AMDear Dr. Dubbeldam,
We are having a similar problem with C2H2 and would like to try your suggestion, but we could not find in the manual how to set up a hard-sphere potential on the Hydrogen. What are the keyword and parameters?
We are having a similar problem with C2H2 and would like to try your suggestion, but we could not find in the manual how to set up a hard-sphere potential on the Hydrogen. What are the keyword and parameters?
#9
General / The name of RASPA
Last post by sara abbasi - March 18, 2024, 08:07:55 PMHello everyone
In RASPA name, what does each capital letter mean?
I appreciate all your kind responses.
Thank you
Sara
In RASPA name, what does each capital letter mean?
I appreciate all your kind responses.
Thank you
Sara
#10
General / Installation on ubuntu
Last post by Aleksandr Volkov - March 09, 2024, 11:48:36 AMGood afternoon!
Faced with the problem of installing on ububntu, I understand you need to install as written in the manual or differently? Is there an instruction for installing on ububntu?
Faced with the problem of installing on ububntu, I understand you need to install as written in the manual or differently? Is there an instruction for installing on ububntu?