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#11
General / iRASPA cannot display the dens...
Last post by John Walker - May 29, 2024, 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
#12
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
#13
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?
#14
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?
#15
General / No strings attached dating
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#16
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
#17
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?
#18
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
#19
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?
#20
General / Defining a parametric flexible...
Last post by gunjanauti - January 23, 2024, 11:08:35 AMHow can I define a flexible molecules in a def file such that bond length between 0-3 is a function of bond lengths of 0-1 and 0-2 and the angle between 0-1-2? (d3 = d1cos(theta) + d2cos(theta)).
How can we use functions in .def file? And being a flexible model, this length should change every timestep, but since the .def file is only read at the start of this simulation, is there any other way to define this molecule?
How can we use functions in .def file? And being a flexible model, this length should change every timestep, but since the .def file is only read at the start of this simulation, is there any other way to define this molecule?