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1
Input files and parameters / How to use Feymann-Hibbs correction to Lennard-Jones?
« Last post by Cheng on January 20, 2022, 10:35:48 AM »
Hello,
       I am trying to calculate the adsorption of hydrogen molecular. In a lot of papers Feymann-Hibbs correction is used and I'm wondering how I can specify the input file in RASPA to use such correction? Is it some parameters in force_field.def or force_field_mixing_rule.def?
Thanks very much!
2
General / Energy Drift - Cations
« Last post by isaaraujo on January 08, 2022, 09:52:04 AM »
Dear Dr. Dubbeldam,

I am simulating adsorption of water and salt on a clay slit pore using MD simulations. First I minimized the clay structure + cations in the NPT ensemble using the Baker minimization method. Subsequently I equilibrated the structure in the NPT ensemble. However I notice that during the equilibration, the energy drifts increase gradually at each step. For structures that do not have cations as extra framework, I don't observe this issue. Is there a way to address this problem in RASPA?
I have another question regarding energy drifts in the simulation. For another system that I am simulating and that does not contain any cations I can reach an energy drift around 1x10^-5 during equilibration. However, when production steps start, the energy drift started gradually increasing. What could be a reason for that? 

SimulationType                   MolecularDynamics
NumberOfCycles                         20000
NumberOfInitializationCycles     20000
NumberOfEquilibrationCycles      500000
RestartFile                      yes
PrintEvery      10000
ContinueAfterCrash            no
WriteBinaryRestartFileEvery   2000
Ensemble          NPT

CutOff                           9.0
Movies yes
WriteMoviesEvery 20000
PrintEvery       25000
PrintPropertiesEvery 25000

TimeStep          0.0005
Forcefield                       CLAYFF
RemoveAtomNumberCodeFromLabel yes

Framework 0
FrameworkName superillite_complete20
UnitCells       1 1 1
ExternalTemperature 330.0
ComputeMolecularPressure yes

FlexibleFramework yes
FrameworkDefinitions CLAYFFLEXIBLE
ExternalPressure 5000000.0

Component 0 MoleculeName                 kalium
       MoleculeDefinition           Cations
       TranslationProbability       1.0
       RandomTranslationProbability 1.0
       ExtraFrameworkMolecule       yes
       CreateNumberOfMolecules      0

Thank you
Isa
 
3
Simulation algorithms and theory / Question with RASPA minimization
« Last post by zhaoli2023 on January 06, 2022, 07:23:04 AM »
Hi,

I have a question regarding the minimization method in RASPA.

During a minimization, I sometimes encounter a message that says "Too many iterations in tqli", and then RASPA seems stopped.

Is this a warning that indicates that some of my setup is wrong? Can I ignore this message?

Thanks for your help! :)
4
Input files and parameters / The input file for the system with large numbers of atoms
« Last post by xiaoboy on December 30, 2021, 10:15:30 AM »
Dear friends

I am trying to calculate a system with about 3000 atoms. However the simulation crashed with Segmentation fault.
The simulation will be normally terminated for the system with less atoms.
The attachment is the cif file for my simulation, and my simulation.input file is as following:
Could anyone help me solve this issue, Do I need to modify this input file?
Thanks very much!

SimulationType                MonteCarlo
NumberOfCycles                20000
NumberOfInitializationCycles  20000
PrintEvery                    1000
RestartFile                   no

ChargeMethod                  Ewald
EwaldPrecision                1e-6
Forcefield                    local
CutOffVDW                     13.0
RemoveAtomNumberCodeFromLabel no
ChargeFromChargeEquilibration           yes
Movies                 no

Framework             0
FrameworkName 1201
UnitCells             2  2  1
HeliumVoidFraction 0.294706
ExternalTemperature   298
ExternalPressure      100000
PrintForcefieldToOutput No
PrintPseudoAtomsToOutput No
PrintMoleculeDefinitionToOutput No


Component 0 MoleculeName              M1
            StartingBead              0
            MoleculeDefinition        local
            IdealGasRosenbluthWeight  1
            TranslationProbability    1.0
            RotationProbability       1.0
            ReinsertionProbability    1.0
            CBMCProbability           1.0
            IdentityChangeProbability 1.0
              NumberOfIdentityChanges 2
              IdentityChangesList     0 1
            SwapProbability           1.0
            CreateNumberOfMolecules   0
            MolFraction 0.9

Component 1 MoleculeName              M2
            StartingBead              0
            MoleculeDefinition        local
            IdealGasRosenbluthWeight  1
            TranslationProbability    1.0
            RotationProbability       1.0
            ReinsertionProbability    1.0
            CBMCProbability           1.0
            IdentityChangeProbability 1.0
              NumberOfIdentityChanges 2
              IdentityChangesList     0 1
            SwapProbability           1.0
            CreateNumberOfMolecules   0
            MolFraction 0.1
5
Input files and parameters / Using RestartInitial
« Last post by vgd_127 on December 28, 2021, 01:00:06 PM »
Hi,

I am simulating zeolites with extra framework cations.
I first performed the equilibration of the cations without guest molecules and a restart file was generated with the position of cations.

I now tried using that restart file from the previous simulation to fix the initial position of cations in a new simulation which will now include the adsorbate component as well. The code is throwing the following error:

Could NOT open file: RestartInitial/System_0/restart_
Could somebody help out in troubleshooting this issue?
Thanks a lot.
6
Bug reports / Segmentation fault related to flexible MOFs
« Last post by Monica_Gao on December 12, 2021, 06:42:11 PM »
Dear Dr. David Dubbeldam

   I met something wrong when I studied the effect of flexibility of MOFs on gas separation. There was a segmentation fault occuring in my result when the pressure ranges from 0.1 bar to 10 bar.

_cell_length_a: 16.733000
_cell_length_b: 13.038000
_cell_length_c: 6.812000
_cell_length_alpha: 90.000000
_cell_length_beta: 90.000000
_cell_length_gamma: 90.000000
_symmetry_space_group_name_Hall: -I 2 2a found space group: 347
_symmetry_space_group_name_H-M: I m c m found space group: 347
_symmetry_Int_Tables_number: 343
space group found from symmetry elements: 347 (nr elements: 16)
End reading cif-file
Number of bonds: 0 0 1
Shift all potentials
Writing Crash-file!: 0
/var/spool/torque/mom_priv/jobs/794.localhost.SC: line 16: 19513 Segmentation fault      (core dumped) $RASPA_DIR/bin/simulate simulation.input



   The MOFs proposed in the study are MIL-53 series, including MIL-53(Al), MIL-53(Cr) and so on.  Refering to the example (IRMOF-1) you gave to us, I defined the information of framework. Taking MIL-53 (Cr) as example,


the cif file we defined is:

data_MIL-53ht

_audit_creation_method RASPA-1.0
_audit_creation_date 2011-3-9
_audit_author_name '?'

_citation_author_name        'C. Serre, F. Millange, C. Thouvenot, M. Nogues, G. Marsolier, D. Louer, and G. Ferey'
_citation_title              'Very large breathing effect in the first nanoporous chromium(III)-based solids: MIL-53 or Cr-III(OH).{O2C-C6H4-CO2}.{HO2C-C6H4-CO2H}(x).H2Oy'
_citation_journal_abbrev     'J. Am. Chem. Soc.'
_citation_journal_volume     124
_citation_journal_number     45
_citation_page_first         13519
_citation_page_last          13526
_citation_year               2002

_cell_length_a    16.733
_cell_length_b    13.038
_cell_length_c    6.812
_cell_angle_alpha 90
_cell_angle_beta  90
_cell_angle_gamma 90
_cell_volume      1486.14

_symmetry_cell_setting          orthorhombic
_symmetry_space_group_name_Hall '-I 2 2a'
_symmetry_space_group_name_H-M  'I m c m'
_symmetry_Int_Tables_number     74

loop_
_symmetry_equiv_pos_as_xyz
 'x,y,z'
 '-x+1/2,y,-z'
 'x+1/2,-y,-z'
 '-x,-y,z'
 '-x,-y,-z'
 'x+1/2,-y,z'
 '-x+1/2,y,z'
 'x,y,-z'
 'x+1/2,y+1/2,z+1/2'
 '-x,y+1/2,-z+1/2'
 'x,-y+1/2,-z+1/2'
 '-x+1/2,-y+1/2,z+1/2'
 '-x+1/2,-y+1/2,-z+1/2'
 'x,-y+1/2,z+1/2'
 '-x,y+1/2,z+1/2'
 'x+1/2,y+1/2,-z+1/2'

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z   
_atom_site_charge

Cr1      Cr     0.25000    0.75000   0.25    0.574 
O1       O      0.25000    0.686     0       -0.486
O2       O     -0.168      0.161     0.167   -0.211
C3       C     -0.033      0.032     0.179   -0.073
C2       C     -0.066      0.063     0       -0.043
C1       C     -0.137      0.132     0       0.083 
Ho1      H      0.25000    0.611     0       0.121 
H1       H     -0.060      0.058     0.329   0.035



The structure as well as the corresponding atom names are shown in the attach file, named MIL-53(Cr)ht.bmp

The flexiblity of framework was defined as follow:

#CoreShells bond  BondDipoles UreyBradley bend  inv  tors improper-torsion bond/bond bond/bend bend/bend stretch/torsion bend/torsion
          0    5            0           0    7    0     8                3         0         0         0               0            0
#bond stretch atom n1-n2, equilibrium distance, bondforce-constant
C3 H1  HARMONIC_BOND  366001.13136396  0.95
C3 C3  HARMONIC_BOND  483413.91047488  1.36
C2 C3  HARMONIC_BOND  483413.91047488  1.36
C1 C2  HARMONIC_BOND  353750.919316375 1.42
O2 C1  HARMONIC_BOND  543840.64928424  1.25
#bond bending atom n1-n2-n3, equilibrium angle, bondforce-constant
C1 C2 C3 HARMONIC_BEND 34926.5543205787 120.0
C2 C3 H1 HARMONIC_BEND 37263.15559911 120.0
C3 C3 H1 HARMONIC_BEND 37263.15559911 120.0
C3 C2 C3 HARMONIC_BEND 90640.10821404 120.0
C3 C3 C2 HARMONIC_BEND 90640.10821404 120.0
O2 C1 O2 HARMONIC_BEND 135960.162321060 130.0
O2 C1 C2 HARMONIC_BEND 54882.4848123699 115.0
#torsion atom n1-n2-n3-n4,
O2 C1 C2  C3  TRAPPE_DIHEDRAL      0.0   0.0   1258.890391861  0.0
C1 C2 C3  H1  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
C1 C2 C3  C3  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
H1 C3 C3  H1  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
C2 C3 C3  H1  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
C2 C3 C3  C2  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
H1 C3 C2  C3  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
C3 C2 C3  C3  TRAPPE_DIHEDRAL      0.0   0.0   1510.668470234  0.0
#improper torsion atom n1-n2-n3-n4,
C2 C1 O2  O2  TRAPPE_IMPROPER_DIHEDRAL 0.0 0.0   5035.561567446  0.0
C3 C2 C3  C1  TRAPPE_IMPROPER_DIHEDRAL 0.0 0.0   5035.561567446  0.0
C2 C3 C3  H1  TRAPPE_IMPROPER_DIHEDRAL 0.0 0.0   186.3157779955  0.0



There is a question here: Is it necessary to define the bond, bend, torsion information between Cr(III) and surrounding O or C? And how to obtain these information and change them into the form that RASPA can identify

The force_field_mixing_rules.def file was defined as follow:

# general rule for shifted vs truncated
shifted
# general rule tailcorrections
no
# number of defined interactions
28
# type interaction
Al_      Lennard-jones      254.09      4.01
Br_      Lennard-jones      126.29      3.73
C_      Lennard-jones      52.83      3.43
Ca_      Lennard-jones      119.75      3.03
Cl_      Lennard-jones      114.21      3.52
Cr_      Lennard-jones      7.55      2.69
F_      Lennard-jones      25.16      3
Fe_      Lennard-jones      6.54      2.59
Ga_      Lennard-jones      208.81      3.9
H_      Lennard-jones      22.14      2.57
In_      Lennard-jones      301.39      3.98
N_      Lennard-jones      34.72      3.26
O_      Lennard-jones      30.19      3.12
Os_      Lennard-jones      18.62      2.78
V_      Lennard-jones      8.05      2.8
CH4_sp3        lennard-jones    148.0     3.72
CH3_sp3        lennard-jones    98     3.76
CH2_sp3        lennard-jones    46      3.96
CH_sp3         lennard-jones    17.0      4.67
C_sp3          lennard-jones     0.8      6.38
O_co2          lennard-jones    79    3.05
C_co2          lennard-jones    27.0    2.8
Ow             lennard-jones    81.9    3.16
Hw             lennard-jones    0             0
Lw            lennard-jones    0             0
S_S          lennard-jones    122     3.6
H_S         lennard-jones      50    2.5
M_S        lennard-jones       0    0
# general mixing rule for Lennard-Jones
Lorentz-Berthelot


The pseudo_atoms.def file was defined as follow:

#number of pseudo atoms
23
#type      print   as    chem  oxidation   mass        charge   polarization B-factor radii  connectivity anisotropic anisotropic-type   tinker-type
Cr1         yes     Zn     Zn     0       65.37       0.574         0           1.0     1.6      0            0          relative             0
O1          yes     O      O      0       15.9994     -0.486        0           1.0     0.68     2            0          relative             0
O2          yes     O      O      0       15.9994     -0.211        0           1.0     0.68     2            0          relative             0
C3          yes     C      C      0       12.0107     -0.073        0           1.0     0.720    0            0          relative             0
C2          yes     C      C      0       12.0107     -0.043        0           1.0     0.720    0            0          relative             0
C1          yes     C      C      0       12.0107     0.083         0           1.0     0.720    0            0          relative             0
Ho1         yes     H      H      0       1.00794     0.121         0           1.0     0.320    0            0          relative             0
H1          yes     H      H      0       1.00794     0.035         0           1.0     0.320    0            0          relative             0
He          yes     He     He     0       4.002602     0            0           1.0     1        0            0          relative             0
CH4_sp3     yes     C      C      0       16.04246     0            0           1.0     1        0            0          relative             0
CH3_sp3     yes     C      C      0       15.03452     0            0           1.0     1        0            0          relative             0
CH2_sp3     yes     C      C      0       14.02658     0            0           1.0     1        0            0          relative             0
CH_sp3      yes     C      C      0       13.01864     0            0           1.0     1        0            0          relative             0
CH2_sp2     yes     C      C      0       14.02658     0            0           1.0     1        0            0          relative             0
C_sp3       yes     C      C      0       12           0            0           1.0     1        0            0          relative             0
C_co2       yes     C      C      0       12.0107     0.7         1.508         1.0     0.720    0            0          relative             0
O_co2       yes     O      O      0       15.9994    -0.35        0.9475        1.0     0.68     0            0          relative             0
Ow          yes     O      O      0       15.9994     0             0           1.0     0.5      2            0          relative             0
Hw          yes     H      H      0       1.00794     0.524         0           1.0     1        1            0          relative             0
Lw          no      L      -      0       0           -1.048        0           1.0     1        1            0          relative             0
S_S         yes     S      S      0       32.06        0            0           1.0     1        0            0          relative             0
H_S         yes     H      H      0       1            0.21         0           1.0     1        0            0          relative             0
M_S         no      M      -      0       0            -0.42        0           1.0     1        0            0          relative             0


No extra force field defined in the force_field.def

As for the input file, we used the hybrid MCMD method to calculate the adsorption capacity of CH4 in MIL-53(Cr)

SimulationType                MonteCarlo
NumberOfCycles                100000
NumberOfInitializationCycles  100000
PrintEvery                    5000
RestartFile                   no

ContinueAfterCrash no
WriteBinaryRestartFileEvery 5000

ChargeMethod                  Ewald
Forcefield                    MIL-53-Cr-ht-pri
CutOffVDW                     12.5
RemoveAtomNumberCodeFromLabel yes

Framework             0
FrameworkName         MIL-53-Cr-ht-pri
ChargeFromChargeEquilibration yes
UnitCells             2 2 4
HeliumVoidFraction    0.5093
FrameworkDefinitions  MIL-53-Cr-ht-pri
ExternalTemperature   298.15
ExternalPressure    61000

FlexibleFramework yes

HybridMCMDMoveProbability 1.0

Movies        yes
WriteMoviesEvery 5000


Component 0 MoleculeName              CH4
            StartingBead              0           
            MoleculeDefinition        gwq_trappe   
            TranslationProbability    1.0         
            RotationProbability       1.0         
            SwapProbability           1.0         
            RegrowProbability         1.0         
            IdealGasRosenbluthWeight  1.0       
            CreateNumberOfMolecules   0           


I would be very very grateful if you can give me some suggestions.   ;D ;D ;D ;D ;D ;D

In addition, I'd like to ask you some questions:


In the first example listed in the Advanced Example, you said the adsorption of CO2 in a totally flexible IRMOF-1 using a hybrid MC and MD simulation in μVT ensemble . However, you listed another example to illustrate the CO2 adsorption in flexible IRMOF-1 in osmotic ensemble.

1. If I want to obtain the gas separation capability of a flexible MOF, which method is better for us to use? In which condition should I used the instruction of the  first example, and in which condition I should use the instruction in the second example.

2. According to Sven M. J. Rogge (Adv. Theory Simul. 2019, 2, 1800177, doi: 10.1002/adts.201800177), the hybrid MCMD is the best way to predict the adsorption behaviors in a flexible MOF in a restricted osmotic ensemble, which seems to be the combination of the first and second example (Scheme 4). In that work, he did a MD at the very beginning, but in the case of hybridMCMD method in RASPA, it seems no MD relative defination involved.  So, how does it manange to do MD simulation.
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I am really looking forward to your respond ;D ;D ;D


Sincere
Monica
7
General / Re: Why the excess adsorption is negative, when doing MC
« Last post by sara abbasi on December 09, 2021, 08:06:45 AM »
Dear Dr. Dubbeldum
I am using RASPA to calculate propane/propene selectivity of pure silica zeolite LTA using the following code. In output absolute loading for both propane and propene is positive, But excess loading is negative.  Then I tried this simulation in 1 bar pressure, But excess loading is negative. Thanks a lot for guiding me.
SimulationType                MonteCarlo
NumberOfCycles                100000
NumberOfInitializationCycles  10000
PrintEvery                    1000
RestartFile                   no

ContinueAfterCrash            no
WriteBinaryRestartFileEvery   500

Forcefield                    local
UseChargesFromCIFFile         yes

Framework 0
FrameworkName Framework_0_final_1_1_1
UnitCells 3 3 3
HeliumVoidFraction 0.460673
ExternalTemperature 308.37
ExternalPressure 1970000
Movies yes
WriteMoviesEvery 1000

Component 0 MoleculeName               propene
            MoleculeDefinition         local
            IdealGasRosenbluthWeight   1.0
            MoleFraction               0.91
            TranslationProbability     0.5
            RotationProbability        0.5
            ReinsertionProbability     0.5
            IdentityChangeProbability  1.0
            NumberOfIdentityChanges    2
            IdentityChangesList        0 1
            SwapProbability            1.0
            CreateNumberOfMolecules    0
           
Component 1 MoleculeName               propane
            MoleculeDefinition         local
            IdealGasRosenbluthWeight   1.0
            MoleFraction               0.09
            TranslationProbability     0.5
            RotationProbability        0.5
            ReinsertionProbability     0.5
            IdentityChangeProbability  1.0
            NumberOfIdentityChanges    2
              IdentityChangesList      0 1
            SwapProbability            1.0
            CreateNumberOfMolecules    0
           
8
Dear RASPA community,

I am simulating water adsorption in a rigid hydrophobic Zeolite. I am puzzling to grasp the relationship that links the external pressure "ExternalPressure" and the fugacity coefficent "FugacityCoefficient" in RASPA input script with the chemical potential calculated by RASPA to perform a GCMC simulation.

Instead of using the peng-Robinson state equation to calculate the fugacity, I input indeed myself the fugacity properly calculated before running a simulation for my water model. However, by using the widom insertion method to calculate the chemical potential of a box with only water (for tests), there is a mismatch with the expect chemical potential corresponding to the input fugacity coefficient.

For information, I used the relationship from statistical physics to compute the fugacity coefficient phi for input in RASPA:

phi = fugacity/P_ext = exp((mu_real(P_ext,T)-mu_perfect_gas(P_ext,T))/RT)

Is this relation used in RASPA or am I wrong?

Any help would be greatly appreciated!  :)
9
Input files and parameters / Making OPLS benzene molecules
« Last post by don on December 02, 2021, 05:20:06 PM »
I am trying to make benzene molecules using the OPLS 1990 JACS paper, which is simply LJ+Coulomb and has no bonds, angles, or torsion.
If I do the following, I get "Error in CBMC growing scheme.. No atoms can be grown, check the connectivity of your molecule." How do I solve this error?
I also changed the end of the force_field_mixing_rules file from "Lorentz-Berthelot" to "Jorgensen"
I would like to avoid implementing bonds and angles in the topology if possible because I believe the calculations will be faster.

-------------------------------------------------------------------------------------
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
562.05
4894000.0
0.2092
# Number Of Atoms
12
# Number of groups
1
# benzene-group
rigid
# number of atoms
12
# atomic positions
 0 C_benz  0.00000000    0.00000000    0.00000000
 1 C_benz  1.39200000    0.00000000    0.00000000
 2 C_benz  2.08800000    1.20550736    0.00000000
 3 C_benz  1.39200051    2.41101443   -0.00119599
 4 C_benz  0.00000000    2.41101459   -0.00167420
 5 C_benz -0.69600000    1.20550717   -0.00068061
 6 H_benz -0.54000000   -0.93530733    0.00044182
 7 H_benz  1.93200000   -0.93530654    0.00129125
 8 H_benz  3.16799982    1.20550747    0.00062273
 9 H_benz  1.93200056    3.34632183   -0.00125416
10 H_benz -0.53999901    3.34632180   -0.00260212
11 H_benz -1.77600000    1.20550708   -0.00085731
# Chiral centers Bond  BondDipoles Bend  UrayBradley InvBend  Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Bend/Torsion IntraVDW IntraCoulomb
               0   0            0    0            0       0        0            0         0            0         0            0        0            0
10
Pictures and movies / Re: creating movies in iRASPA
« Last post by David Dubbeldam on December 02, 2021, 10:58:18 AM »
Select both files when loading them into iRASPA. The first tab in the project-pane shows the project. The second tab shows the two "movies" that you have loaded: the cif file with 1 frame, and the pdb with many frames. The third tab shows the frames of the movie.

Note: there is help in iRASPA (see menu item 'Help').
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