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#41
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?
#42
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?
#43
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
#44
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?
#45
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
#46
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?
#47
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?
#48
Output files / Re: heat of adsorption method ...
Last post by dddD - December 23, 2023, 04:34:20 AMI want to know, too!
#49
General / Can anyone recommend some lite...
Last post by WuJH - December 21, 2023, 04:03:29 PMDear professors:
Can anyone recommend some literatures that can use raspa to reproduce the GCMC simulation process？
Thanks very much!
Can anyone recommend some literatures that can use raspa to reproduce the GCMC simulation process？
Thanks very much!
#50
Output files / heat of adsorption method in G...
Last post by Nourissa - December 19, 2023, 01:02:34 PMI am trying to find the equation or method that is used to compute heat of adsorption in GCMC. if anyone knows please share a reference paper.
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