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Messages - lifesmiel

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Output files / Re: atom-pairs with no VDW interaction(s)
« on: April 03, 2018, 06:54:47 PM »
Thanks. That works.


Output files / Re: atom-pairs with no VDW interaction(s)
« on: April 03, 2018, 12:44:23 AM »
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
# general rule tailcorrections
# number of defined interactions
# 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?



Output files / Re: atom-pairs with no VDW interaction(s)
« on: March 29, 2018, 12:42:53 AM »
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?



Output files / atom-pairs with no VDW interaction(s)
« on: March 28, 2018, 07:06:11 PM »
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.



Input files and parameters / turning on polarizability
« on: March 28, 2018, 06:55:10 PM »
Hi Dr Dubbeldam:

I am a new user to the RASPA2.0.
I am wondering how to turn on the polarization for absorbate and MOF? Is there any specification I need to make in input file or force-field files?



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