- Welcome to iRASPA Community.
Recent posts
#91
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?
#92
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
#93
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?
#94
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
#95
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?
#96
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?
#97
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!
#98
General / Inaccurate Adsorption Isotherm...
Last post by sridhar - November 24, 2023, 07:51:38 AMDear Prof. Dubbeldam and RASPA community,
I would like to calculate the adsorption isotherm for hydrogen at 77K on IRMOF-1. The absolute adsorption uptake of the RASPA results showed higher values, almost two times more at high pressures (i.e., 100 bar) compared to the experimental results and GCMC calculations in the literature. I am sure that the force-field interactions taken are accurate. The forcefield, pseduoatoms, molecule files, simulation.input used in my RASPA calculations are given below. The IRMOF-1 cif file was used from RASPA software (i.e., raspa/structures/mofs/cif/IRMOF-1.cif). Can you please go through the input files and let me know incase any issues?
1. Simulation.input
SimulationType MonteCarlo
NumberOfCycles 100000
NumberOfInitializationCycles 50000
PrintEvery 5000
RestartFile no
Forcefield ExampleMOFsForceField
Framework 0
FrameworkName IRMOF-1
UnitCells 1 1 1
HeliumVoidFraction 0.81
ExternalTemperature 77
ExternalPressure 100e5
Component 0 MoleculeName H2
MoleculeDefinition ExampleDefinitions
TranslationProbability 0.5
RotationProbability 0.5
ReinsertionProbability 0.5
SwapProbability 1.0
CreateNumberOfMolecules 0
2. pseudoatoms file
#number of pseudo atoms
6
#type print as chem oxidation mass charge polarization B-factor radii connectivity anisotropic anisotropic-type tinker-type
C yes C C 0 12.0 0.0 0.0 1.0 0.67 0 0 relative 0
H_h2 yes H H 0 1.01588 0.468 0.0 1.0 0.53 0 0 relative 0
H_com no H - 0 0.0 -0.936 0.0 1.0 0.53 0 0 relative 0
H yes H H 0 1.01588 0 0.0 1.0 0.53 0 0 relative 0
Zn yes Zn Zn 0 65.39 1.8529 0.0 1.0 1.42 0 0 relative 0
O yes O O 0 15.9994 -1.6 0.0 1.0 0.48 0 0 relative 0
3. force_field_mixing_rules.def
# general rule for shifted vs truncated
shifted
# general rule tailcorrections
no
# number of defined interactions
6
# type interaction
Zn_ lennard-jones 62.4 2.46 // D. Dubbeldam, K.S. Walton, D.E. Ellis, R.Q. Snurr, Angew. Chem. Int. Ed. 2007, 46, 4496-4499.
O_ lennard-jones 30.19 3.12 // idem
C_ lennard-jones 52.84 3.43 // idem
H_ lennard-jones 22.14 2.57 // idem
H_h2 lennard-jones 15 2
H_com none
# general mixing rule for Lennard-Jones
Lorentz-Berthelot
4. H2.def file
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
33
1300000.0
-0.216
#Number Of Atoms
3
# Number of groups
1
# H2-group
rigid
# number of atoms
3
# atomic positions
0 H_h2 0.0 0.0 0.37
1 H_com 0.0 0.0 0.0
2 H_h2 0.0 0.0 -0.37
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 2 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
# Number of config moves
0
I would like to calculate the adsorption isotherm for hydrogen at 77K on IRMOF-1. The absolute adsorption uptake of the RASPA results showed higher values, almost two times more at high pressures (i.e., 100 bar) compared to the experimental results and GCMC calculations in the literature. I am sure that the force-field interactions taken are accurate. The forcefield, pseduoatoms, molecule files, simulation.input used in my RASPA calculations are given below. The IRMOF-1 cif file was used from RASPA software (i.e., raspa/structures/mofs/cif/IRMOF-1.cif). Can you please go through the input files and let me know incase any issues?
1. Simulation.input
SimulationType MonteCarlo
NumberOfCycles 100000
NumberOfInitializationCycles 50000
PrintEvery 5000
RestartFile no
Forcefield ExampleMOFsForceField
Framework 0
FrameworkName IRMOF-1
UnitCells 1 1 1
HeliumVoidFraction 0.81
ExternalTemperature 77
ExternalPressure 100e5
Component 0 MoleculeName H2
MoleculeDefinition ExampleDefinitions
TranslationProbability 0.5
RotationProbability 0.5
ReinsertionProbability 0.5
SwapProbability 1.0
CreateNumberOfMolecules 0
2. pseudoatoms file
#number of pseudo atoms
6
#type print as chem oxidation mass charge polarization B-factor radii connectivity anisotropic anisotropic-type tinker-type
C yes C C 0 12.0 0.0 0.0 1.0 0.67 0 0 relative 0
H_h2 yes H H 0 1.01588 0.468 0.0 1.0 0.53 0 0 relative 0
H_com no H - 0 0.0 -0.936 0.0 1.0 0.53 0 0 relative 0
H yes H H 0 1.01588 0 0.0 1.0 0.53 0 0 relative 0
Zn yes Zn Zn 0 65.39 1.8529 0.0 1.0 1.42 0 0 relative 0
O yes O O 0 15.9994 -1.6 0.0 1.0 0.48 0 0 relative 0
3. force_field_mixing_rules.def
# general rule for shifted vs truncated
shifted
# general rule tailcorrections
no
# number of defined interactions
6
# type interaction
Zn_ lennard-jones 62.4 2.46 // D. Dubbeldam, K.S. Walton, D.E. Ellis, R.Q. Snurr, Angew. Chem. Int. Ed. 2007, 46, 4496-4499.
O_ lennard-jones 30.19 3.12 // idem
C_ lennard-jones 52.84 3.43 // idem
H_ lennard-jones 22.14 2.57 // idem
H_h2 lennard-jones 15 2
H_com none
# general mixing rule for Lennard-Jones
Lorentz-Berthelot
4. H2.def file
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
33
1300000.0
-0.216
#Number Of Atoms
3
# Number of groups
1
# H2-group
rigid
# number of atoms
3
# atomic positions
0 H_h2 0.0 0.0 0.37
1 H_com 0.0 0.0 0.0
2 H_h2 0.0 0.0 -0.37
# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
0 2 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
# Number of config moves
0
#99
General / Enthalpy of adsorption
Last post by Mohammad Ahmadi - November 21, 2023, 12:01:00 AMHi.
How can I calculate the enthalpy of adsorption in the state of adsorption on the adsorbent with extra cation?
The software is not able to calculate the enthalpy for adsorption in this case.
How can I calculate the enthalpy of adsorption in the state of adsorption on the adsorbent with extra cation?
The software is not able to calculate the enthalpy for adsorption in this case.
#100
General / How to change the atom index i...
Last post by kokojiang - October 24, 2023, 06:56:23 AMDear all,
I have the cif file of the MOF structure, the atoms and their indexes goes like this:
C1 1.0 0.3521 0.68248 0.49724
Cr2 1.0 0.6727 0.73299 0.90674
C3 1.0 0.9812 0.86236 0.85294
C4 1.0 0.29174 0.5265 0.71863
...
C1185 1.0 0.17108 0.59341 0.61745
C1186 1.0 0.14289 0.58226 0.66194
C1187 1.0 0.1861 0.67126 0.70408
Cr1188 1.0 0.25915 0.66547 0.69122
...
But in the simulation, we divided the atoms to different types,e.g. only 3 types of carbon atom and 2 types of Cr and so on. The force field is made for the type of atoms such as:
C1 lennard-jones 47.8562 3.47299
C2 lennard-jones 47.8562 3.47299
Cr1 lennard-jones 7.54829 2.69319
Cr2 lennard-jones 7.54829 2.69319
So the data need to be like:
C1 1.0 0.3521 0.68248 0.49724
Cr2 1.0 0.6727 0.73299 0.90674
C1 1.0 0.9812 0.86236 0.85294
C2 1.0 0.29174 0.5265 0.71863
...
C1 1.0 0.17108 0.59341 0.61745
C1 1.0 0.14289 0.58226 0.66194
C2 1.0 0.1861 0.67126 0.70408
Cr2 1.0 0.25915 0.66547 0.69122
...
How do I change the atom index? There are too many atoms for me to do it manually. Is there any software that can do this ?
I have the cif file of the MOF structure, the atoms and their indexes goes like this:
C1 1.0 0.3521 0.68248 0.49724
Cr2 1.0 0.6727 0.73299 0.90674
C3 1.0 0.9812 0.86236 0.85294
C4 1.0 0.29174 0.5265 0.71863
...
C1185 1.0 0.17108 0.59341 0.61745
C1186 1.0 0.14289 0.58226 0.66194
C1187 1.0 0.1861 0.67126 0.70408
Cr1188 1.0 0.25915 0.66547 0.69122
...
But in the simulation, we divided the atoms to different types,e.g. only 3 types of carbon atom and 2 types of Cr and so on. The force field is made for the type of atoms such as:
C1 lennard-jones 47.8562 3.47299
C2 lennard-jones 47.8562 3.47299
Cr1 lennard-jones 7.54829 2.69319
Cr2 lennard-jones 7.54829 2.69319
So the data need to be like:
C1 1.0 0.3521 0.68248 0.49724
Cr2 1.0 0.6727 0.73299 0.90674
C1 1.0 0.9812 0.86236 0.85294
C2 1.0 0.29174 0.5265 0.71863
...
C1 1.0 0.17108 0.59341 0.61745
C1 1.0 0.14289 0.58226 0.66194
C2 1.0 0.1861 0.67126 0.70408
Cr2 1.0 0.25915 0.66547 0.69122
...
How do I change the atom index? There are too many atoms for me to do it manually. Is there any software that can do this ?
SMF spam blocked by CleanTalk