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#71
Simulation algorithms and theory / Initialization phase of CFCMC
Last post by wei123 - March 10, 2023, 10:12:16 AM
Hello RASPA community,

I tried using the CFCMC method in RASPA according to the example which specified an initialization, equilibration and production phase. As far as I know, the equilibration phase is used to calculate the biasing factor for a flat distribution of lambda. Based on the simulation resutls that I have obtained (attachment), it seems like there is not much going on during the initialization phase (input file also attached).

Can someone tell me what happens in the initialization phase of CFCMC and if the initialization phase is even necessary, when the equilibration phase is defined?

Thank you!

Regards,
Wei
#72
General / Can the cavity of a MOF be ind...
Last post by Lingxiao Qin - February 25, 2023, 04:12:12 AM
Dear Prof. Dubbeldam,

In some literatures the cavity of a MOF is indicated by a sphere, can such an image be created by iRASPA? If not, could you please suggest me a suitable way to create such an image?

Thanks for your help.
#73
General / Is measuring distance function...
Last post by Lingxiao Qin - February 25, 2023, 04:06:22 AM
Dear Prof. Dubbeldam,

In the manual via the help menu of iRASPA, I found that the distance between two atoms coule be measured by "alt + left mouse clicking on atoms 1 and 2". However, I could not use this function on my Windows desktop. Since the manual seems to be written for Macs, I wonder whether the measuring distance function is available on Windows.

Thans for your help.
#74
Simulation algorithms and theory / Re: MSD of MD
Last post by Yu_Zhuochen - February 24, 2023, 01:47:10 PM
I met the same problem. How to solve it?
#75
General / Re: About the relation between...
Last post by w_wonder - February 22, 2023, 05:43:11 PM
Quote from: David Dubbeldam on November 22, 2022, 10:32:28 AM
These value come from: https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.7b00092/suppl_file/ct7b00092_si_001.pdf
and to reduce under/overflow you input them as the log of these numbers in Table S3.

One more question. Does RASPA have two conventions in the partition function, that previously, the exp(D0/kT) term was not included
as in https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.5b00160/suppl_file/ct5b00160_si_001.pdf
later the exp(D0/kT) was included, as in
https://pure.tudelft.nl/ws/portalfiles/portal/71296377/Thesis_Ahmadreza_Rahbari.pdf

Thanks.
#76
General / radial distribution function
Last post by kokojiang - February 20, 2023, 09:57:47 AM
Dear Prof. Dubbeldam and RASPA community,

I am now comparing the RDF of the same molecule towards different atoms in MOF. In the output RDF files, like "RDF_H2_Ow.dat", I want to switch the positions of H2 and Ow,so I can get "RDF_Ow_H2.dat"  to avoid the influence of the radius of the center atom. I don't know whether RASPA can do this or not, but if it's possible, could you please tell me how?

Thank you!
#77
Bug reports / Re: Draw isotherms using a per...
Last post by Zihan Zhou - February 16, 2023, 08:58:30 AM
This problem has been solved.
#78
Bug reports / Draw isotherms using a perl sc...
Last post by Zihan Zhou - February 15, 2023, 12:17:33 PM
usage: simulate [ -h] [-v] [-s] [-C CRYSTAL] input simulate: error: the following arguments are required: input. After a lot of attemptance, I still can not figure it out.
#79
Output files / Re: ENERGY DRIFT
Last post by kokojiang - February 15, 2023, 08:10:07 AM
Dear Dr. Dubbeldam,

    I am getting the same error too. Like what you explained, the error happened as the number of adsorbates increased. When the number of adsorbates is low, it works well. But when the number of adsorbates is large, like 2500, the error appeared. In the forcefield I use, hydrogens did have no lennard-jones potential. How can I solve this warning? Should I change the forcefield or just run a larger simulation cycle?

Thank you!.
Jiang
#80
General / About Atoms named xx+number in...
Last post by Yu_Zhuochen - February 14, 2023, 03:10:01 AM
Dear Prof. Dubbeldam:
I am trying to use GenericMOFs forcefield to make simulations of CO2/H2 adsorption among a database containing 600 COFs. Previouse researchers have already reported some results about 10 COFs with the best performance from the CORE-COF-2020 database(CO2/H2 separation, 0.15:0.85, 1bar-298K&0.1bar-298K).
When I try to reproduce simulation from a previous paper(J. Phys. Chem. C 2020, 124, 22577−22590), even if I set all parameters totally the same as the paper did(forcefiled:DREIDING(I choose GenericMOFs in RASPA), CutOFFVDW 14.0, CO2&H2 are found from share/molecues/TraPPE).
I choosed 5 COFs structures: NPN-2, COF-42-gra, FLT-COF-1, COF-JLU3, PyTTA-BFBIm-iCOF as a test case.

However, my simulation results don't match the paper at all!
I found that some cifs have such a form:
data_TpMA
_audit_creation_date              2022-07-26
_audit_creation_method            'Materials Studio'
_symmetry_space_group_name_H-M    'P1'
_symmetry_Int_Tables_number       1
_symmetry_cell_setting            triclinic
loop_
_symmetry_equiv_pos_as_xyz
  x,y,z
_cell_length_a                    11.2024
_cell_length_b                    11.2061
_cell_length_c                    3.4772
_cell_angle_alpha                 97.1070
_cell_angle_beta                  91.6120
_cell_angle_gamma                 119.7344
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_occupancy
xx1    C     0.47506   0.43704   0.52016   0.00000  Uiso   1.00
xx2    N     0.50682   0.55667   0.42256   0.00000  Uiso   1.00
xx3    O     0.77447   0.62245   0.71005   0.00000  Uiso   1.00
xx4    C     0.41472   0.61064   0.42851   0.00000  Uiso   1.00
xx5    N     0.27729   0.52657   0.44818   0.00000  Uiso   1.00
xx6    C     0.57467   0.38607   0.51378   0.00000  Uiso   1.00
xx7    C     0.71912   0.47896   0.59883   0.00000  Uiso   1.00
xx8    C     0.56333   0.03745   0.42485   0.00000  Uiso   1.00
xx9    N     0.43518   0.94910   0.46020   0.00000  Uiso   1.00
xx10   O     0.38447   0.14605   0.30057   0.00000  Uiso   1.00
xx11   C     0.38143   0.80299   0.44908   0.00000  Uiso   1.00
xx12   N     0.46618   0.74843   0.42631   0.00000  Uiso   1.00
xx13   C     0.61505   0.18930   0.46498   0.00000  Uiso   1.00
xx14   C     0.52400   0.24103   0.42915   0.00000  Uiso   1.00
xx15   C     0.96190   0.52887   0.59917   0.00000  Uiso   1.00
xx16   N     0.04773   0.48874   0.48793   0.00000  Uiso   1.00
xx17   O     0.84383   0.22694   0.60631   0.00000  Uiso   1.00
xx18   C     0.19208   0.58005   0.47129   0.00000  Uiso   1.00
xx19   N     0.24457   0.71864   0.47369   0.00000  Uiso   1.00
xx20   C     0.81129   0.42768   0.58297   0.00000  Uiso   1.00
xx21   C     0.75811   0.28227   0.54563   0.00000  Uiso   1.00
xx22   H     0.37400   0.37256   0.61288   0.00000  Uiso   1.00
xx23   H     0.71304   0.64860   0.86224   0.00000  Uiso   1.00
xx24   H     0.63606   0.00100   0.38331   0.00000  Uiso   1.00
xx25   H     0.33038   0.18685   0.19256   0.00000  Uiso   1.00
xx26   H     0.99955   0.63885   0.68662   0.00000  Uiso   1.00
xx27   H     0.92695   0.28844   0.80338   0.00000  Uiso   1.00

When RASPA load an atom named xx, it cannot be read.
How can I do to solve this problem?