Messages

[1. Simulation.input]

Dear 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

Hi,

I am getting the following warning while calculating the enthalpy of the adsorption in ZIF-8.

WARNING: THE SYSTEM HAS A NET CHARGE
WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION Zn1-H2 Zn1-N1 Zn1-H3A Zn1-H3B Zn1-H3C C1-H2 C1-N1 C1-H3A C1-H3B C1-H3C C2-H2 C2-N1 C2-H3A C2-H3B C2-H3C C3-H2 C3-N1 C3-H3A C3-H3B C3-H3C C_co2-H2 C_co2-N1 C_co2-H3A C_co2-H3B C_co2-H3C O_co2-H2 O_co2-N1 O_co2-H3A O_co2-H3B O_co2-H3C H2-Zn1 H2-C1 H2-C2 H2-C3 H2-C_co2 H2-O_co2 H2-N1 H2-H3A H2-H3B H2-H3C N1-Zn1 N1-C1 N1-C2 N1-C3 N1-C_co2 N1-O_co2 N1-H2 N1-H3A N1-H3B N1-H3C  (maximum 50 interactions shown)

The simulation.input file is attached. What could be the reason behind the warning, and would it affect the final solution ?

Thank you.

Regards
Sridhar

Thanks for the reply,

I compared with the experiments and i want to make sure my force fields and input file are correct because in the warnings of each simulation it shows max 50 interactions are missing which are Eg: Zn_H_O, C1_C2_Zn etc.

Near 77K in the literature mentioned that quantum effects are considered to get accurate experimental results. Is it possible to include that in raspa?

[b]My input file]

Hi Prof. Dubbeldam,

I'm using raspa for hydrogen adsorption simulation in ZIF-8, I had edited the input file and  force field file of MOF-5 given in the examples for the using ZIF-8 (lennard jones parameters are also changed according to ZIF-8) as adsorbate . After running the simulation i got high adsorption capacities of hydrogen than reported in literature, it happened for 77K and 300K. I would like to know what might be the problem in this simulation.

[b]My input file [/b]
SimulationType                MonteCarlo
NumberOfCycles                50000
NumberOfInitializationCycles  1000
PrintEvery                    2000

Forcefield                    GenericMOFs1

Framework 0
FrameworkName ZIF-8
UnitCells 1 1 1 
HeliumVoidFraction 0.484279
ExternalTemperature 300 
ExternalPressure   5e5 10e5 15e5 20e5 30e5 40e5 50e5 60e5 10e6 20e6

Component 0 MoleculeName             H2
            MoleculeDefinition       TraPPE
            TranslationProbability   1
            ReinsertionProbability   1
            SwapProbability          1
            CreateNumberOfMolecules  0


I edited only forcefield mixing.def file and left forcefield and psuedo atoms.def file as it is

Edited force field is
# general rule for shifted vs truncated
shifted
# general rule tailcorrections
no
# number of defined interactions
55
# type interaction, parameters.    IMPORTANT: define shortest matches first, so that more specific ones overwrites these
O_             lennard-jones    30.19     3.12
N_             lennard-jones    34.72    3.26256
C_             lennard-jones    52.84    3.4299
F_             lennard-jones    36.4834   3.0932
B_             lennard-jones    47.8058   3.58141
P_             lennard-jones   161.03     3.69723
S_             lennard-jones   173.107    3.59032
Cl_            lennard-jones   142.562    3.51932
Br_            lennard-jones   186.191    3.51905
H_             lennard-jones    22.14     2.57
Zn_            lennard-jones    62.3992   2.46155
Be_            lennard-jones    42.7736   2.44552
Cr_            lennard-jones     7.54829  2.69319
Fe_            lennard-jones     6.54185  2.5943
Mn_            lennard-jones     6.54185  2.63795
Cu_            lennard-jones     2.5161   3.11369
Co_            lennard-jones     7.04507  2.55866
Ga_            lennard-jones   208.836    3.90481
Ti_            lennard-jones     8.55473  2.8286
Sc_            lennard-jones     9.56117  2.93551
V_             lennard-jones     8.05151  2.80099
Ni_            lennard-jones     7.54829  2.52481
Zr_            lennard-jones    34.7221   2.78317
Mg_            lennard-jones    55.8574   2.69141
Ne_            lennard-jones    21.1352   2.88918
Ag_            lennard-jones    18.1159   2.80455
In_            lennard-jones   301.428    3.97608
Cd_            lennard-jones   114.734    2.53728
Sb_            lennard-jones   225.946    3.93777
Te_            lennard-jones   200.281    3.98232
Al_            lennard-Jones   155.998    3.91105
Si_            lennard-Jones   155.998    3.80414
He             lennard-jones    10.9      2.64
CH4_sp3        lennard-jones    148     3.73
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    30        2.58
H_h2           lennard-jones    36.7      2.59   
O_co2          lennard-jones    79.0      3.05
C_co2          lennard-jones    27.0      2.80
C_benz         lennard-jones    30.70     3.60
H_benz         lennard-jones    25.45     2.36
N_n2           lennard-jones    36.0      3.31
N_com          none
Ow             lennard-jones    89.633    3.097
N_dmf          lennard-jones    80.0      3.2
Co_dmf         lennard-jones    50.0      3.7
Cm_dmf         lennard-jones    80.0      3.8
O_dmf          lennard-jones    100.0     2.96
H_dmf          lennard-jones    8.0       2.2
Ar             lennard-jones    119.8     3.34
Kr             lennard-jones    166.4     3.636
Xe             lennard-jones    221.0     4.1
# general mixing rule for Lennard-Jones
Lorentz-Berthelot


Thanks.