Hi Dr Dubbeldam:
I am a new user to the RASPA2.0.
I have run the examples from the RASPA2.0 manual and my own tests, warning of atom-pairs with no VDW interactions have been found in the output files.
In manual example "Adsorption of methane in MFI" atom-pairs with no VDW interactions had shown in the last part of output file.
When running my own test "Adsorption of O2 in flexible IRMOF-1" atom-pairs with no VDW interactions such as
Zn1-O_o2 Zn1-O_com O1-O_o2 O1-O_com....... (maximum 50 interactions shown)" were shown in the output file
With respect to the adsorption of methane in the same flexible IRMOF-1, no such warning popped up.
Best
Chao
Warnings are produced for undefined VDW pairs. If you want to get rid of the warnings you can define these VDW potentials explicitly (by listing them as 'none' if they do not need any VDW interaction).
Adsorption of H2, N2 and H2O in IRMOF-1 have been run respectively. The atom-pairs with no VDW interactions appeared in the output file.
With respect to your comment on solving this issue, the VDW interactions of H_h2, N_com, O_com, Hw, and Lw are defined "NONE" as listed in force_field_mixing_rules.def file from force field folder "Dubbeldam2007FlexibleIRMOF-1". The same warning about the atom-pairs still appear.
With the above mentioned modified force field the warning about the atom-pairs with no VDW interactions (such as He-Zn1 He-O1 He-O2 He-C1 He-C2 He-C3 He-H1 Zn1-He ...) pops up during the running of adsorption of helium in IRMOF-1 although no modification happens to He in force_field_mixing_rules.def.
No warning shows for the running of adsorption of helium in IRMOF-1 with "Dubbeldam2007FlexibleIRMOF-1" force field.
Do you have any suggestions about these? Is there anything I am doing wrong?
Best
Chao
The force fields provided with RASPA are examples. If you are doing simulations for your own systems, then construct your own force fields (you can put them in your local directory). Of course you can use the provided examples as a start. If you want to get rid of the warnings you can define these VDW potentials explicitly in the forcefield files (by listing them as 'none' if they do not need any VDW interaction).
Hi David:
For the previous threads, probably I did not explain clearly for the atom-pairs warning during the calculations.
I have run jobs for single component helium and H2 adsorption isotherm simulations in IRMOF-1 with RASPA2.0 code.
With original Dubbeldam2007FlexibleIRMOF-1 force field (from examples in the RASPA2.0 manual) and similar input file shown below, no problem with helium adsorption simulation. But for H2 adsorption simulation, the job is completed with warning of atom-pairs with no VDW interactions.
Input file for H2 adsorption isotherm in flexible IRMOF-1.
SimulationType MonteCarlo
NumberOfCycles 50000
NumberOfInitializationCycles 20000
PrintEvery 5000
RestartFile no
ChargeMethod Ewald
CutOff 12.0
Forcefield Dubbeldam2007FlexibleIRMOF-1
EwaldPrecision 1e-6
Framework 0
FrameworkName IRMOF-1
UnitCells 1 1 1
HeliumVoidFraction 0.801937
FrameworkDefinitions Dubbeldam2007FlexibleIRMOF-1
ExternalTemperature 298.0
ExternalPressure 1.0e4
FlexibleFramework yes
HybridMCMDMoveProbability 1.0
Component 0 MoleculeName H2
StartingBead 0
MoleculeDefinition TraPPE
IdealGasRosenbluthWeight 1.0
TranslationProbability 1.0
RotationProbability 1.0
ReinsertionProbability 1.0
SwapProbability 1.0
CreateNumberOfMolecules 0
The warning in Output file for H2 adsorption isotherm in flexible IRMOF-1.
Simulation finished, 1 warnings
WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION Zn1-H_h2 O1-H_h2 O2-H_h2 C1-H_h2 C2-H_h2 C3-H_h2 H1-H_h2 H_h2-Zn1 H_h2-O1 H_h2-O2 H_h2-C1 H_h2-C2 H_h2-C3 H_h2-H1 H_h2-H_com H_com-H_h2 (maximum 50 interactions shown)
I followed your suggestion to set up 'None' for H_h2 in force_field_mixing_rules.def as shown in the following:
# general rule for shifted vs truncated
shifted
# general rule tailcorrections
no
# number of defined interactions
28
# type interaction
Zn1 LENNARD_JONES 0.42 2.7
O1 LENNARD_JONES 700.0 2.98
O2 LENNARD_JONES 70.5 3.11
C1 LENNARD_JONES 47.0 3.74
C2 LENNARD_JONES 47.86 3.47
C3 LENNARD_JONES 47.86 3.47
H1 LENNARD_JONES 7.65 2.85
He LENNARD_JONES 10.9 2.64
CH4_sp3 LENNARD_JONES 158.5 3.72
CH3_sp3 LENNARD_JONES 108.0 3.76
CH2_sp3 LENNARD_JONES 56.0 3.96
CH_sp3 LENNARD_JONES 17.0 4.67
C_sp3 LENNARD_JONES 0.8 6.38
H_com LENNARD_JONES 36.7 2.958
H_h2 NONE
...
Run the H2 adsorption again, the situation seems worse than before since the job cannot be completed in addition with warning as attached in the following:
(Selected parts from the RASPA output file:)
[Init] Current cycle: 15000 out of 20000
========================================================================================================
Net charge: 7.77156e-15 (F: 7.77156e-15, A: 0, C: 0)
Current Box: 25.83200 0.00000 0.00000 [A]
0.00000 25.83200 0.00000 [A]
0.00000 0.00000 25.83200 [A]
Box-lengths: 25.83200 25.83200 25.83200 Box-angles: 90.00000 90.00000 90.00000 [degrees]
Volume: 17237.49273 [A^3]
Framework center-of-mass drift: -0.0038216342 [A] 0.0058036771 [A] 0.0081836628 [A]
Loadings per component:
----------------------------------------------------------------------------------------------------------------------------------------------------
Component 0 (H2), current number of integer/fractional/reaction molecules: 229/0/0, density: 44.47085 [kg/m^3]
absolute adsorption: 229.00000 [mol/uc], 37.1838 [mol/kg], 74.9581 [mg/g]
833.4370 [cm^3 STP/g], 494.4579 [cm^3 STP/cm^3]
excess adsorption: 228.96640 [mol/uc], 37.1784 [mol/kg], 74.9471 [mg/g]
833.3147 [cm^3 STP/g], 494.3853 [cm^3 STP/cm^3]
----------------------------------------------------------------------------------------------------------------------------------------------------
Degrees of freedom: 2417 1272 1145 0
Number of Framework-atoms: 424
Number of Adsorbates: 229 (229 integer, 0 fractional, 0 reaction)
Number of Cations: 0 (0 integer, 0 fractional, % reaction
Current total potential energy: -71392892107.3171691895 [K]
Current Host-Host energy: -5168103.9700590987 [K]
Current Host-Adsorbate energy: -71391731743.3306274414 [K]
Current Host-Cation energy: 0.0000000000 [K]
Current Adsorbate-Adsorbate energy: 3713442.5821436136 [K]
Current Cation-Cation energy: 0.0000000000 [K]
Current Adsorbate-Cation energy: 0.0000000000 [K]
Current Host-Bond energy: 146101.9216051124 [K]
Current Host-Bend energy: 119276.6359353390 [K]
Current Host-Torsion energy: 21043.0224195453 [K]
Current Host-Improper torsion energy: 7875.8203939654 [K]
WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION Zn1-O1 Zn1-O2 Zn1-C1 Zn1-C2 Zn1-C3 Zn1-H1 Zn1-H_h2 Zn1-H_com O1-Zn1 O1-O2 O1-C1 O1-C2 O1-C3 O1-H1 O1-H_h2 O1-H_com O2-Zn1 O2-O1 O2-C1 O2-C2 O2-C3 O2-H1 O2-H_h2 O2-H_com C1-Zn1 C1-O1 C1-O2 C1-C2 C1-C3 C1-H1 C1-H_h2 C1-H_com C2-Zn1 C2-O1 C2-O2 C2-C1 C2-C3 C2-H1 C2-H_h2 C2-H_com C3-Zn1 C3-O1 C3-O2 C3-C1 C3-C2 C3-H1 C3-H_h2 C3-H_com H1-Zn1 H1-O1 (maximum 50 interactions shown)
Do you have any comment that something wrong with the step for removal of atom-pairs with no VDW interactions?
Best
Chao
See the manual for the format of the file. If you add an interaction you need to increase the number of interactions.
Change
# number of defined interactions
28
to
# number of defined interactions
29
Thanks. That works.
Chao