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#81
General / About Atoms named xx+number in...
Last post by Yu_Zhuochen - February 14, 2023, 03:10:01 AMDear 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?
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?
#82
Input files and parameters / Re: pseudo_atom radii
Last post by Yu_Zhuochen - February 09, 2023, 03:54:22 AMDear Prof. :
I wonder how to calculate the radii when we simulate a flexible molecue or framework indeed.
Sincerely.
I wonder how to calculate the radii when we simulate a flexible molecue or framework indeed.
Sincerely.
#83
General / Atomization energies in partit...
Last post by w_wonder - February 07, 2023, 08:57:30 PMHi,
This is related to https://forums.iraspa.org/index.php?topic=1227.0
In RASPA2, if I understand correctly, https://pure.tudelft.nl/ws/portalfiles/portal/71296377/Thesis_Ahmadreza_Rahbari.pdf, A73, including an exponential factor exp(D_e/(kT)).
If the system includes a charged species, e.g., OH^-, will the atomization energy be calculated from negatively charged atom, e.g., OH^- -> O^- and H?
From what I understand, the atomization energy is for setting up zero point, as long as the references (e.g., neutral atoms for neutral molecules) are consistent, the calculations should be fine. But, I know very little about the implementation of RASPA2 (go through the source code is quite complicated), does OH^- -> O^- and H OK for simulating charged molecules? Or should I use a different approach?
Thank you very much
This is related to https://forums.iraspa.org/index.php?topic=1227.0
In RASPA2, if I understand correctly, https://pure.tudelft.nl/ws/portalfiles/portal/71296377/Thesis_Ahmadreza_Rahbari.pdf, A73, including an exponential factor exp(D_e/(kT)).
If the system includes a charged species, e.g., OH^-, will the atomization energy be calculated from negatively charged atom, e.g., OH^- -> O^- and H?
From what I understand, the atomization energy is for setting up zero point, as long as the references (e.g., neutral atoms for neutral molecules) are consistent, the calculations should be fine. But, I know very little about the implementation of RASPA2 (go through the source code is quite complicated), does OH^- -> O^- and H OK for simulating charged molecules? Or should I use a different approach?
Thank you very much
#84
General / How to make adsorption density...
Last post by Zihan Zhou - February 07, 2023, 03:59:43 AMHow to make adsorption density maps using RASPA and iRASPA?
#85
General / Re: About the relation between...
Last post by w_wonder - February 02, 2023, 04:35:26 PMHi, one more question, in https://github.com/iRASPA/RASPA2/blob/master/examples/Tutorial/ReactionEnsembleAmmonia/simulation.input
ExternalPressure 4e7
but, for the data in Table A5 https://pure.tudelft.nl/ws/portalfiles/portal/71296377/Thesis_Ahmadreza_Rahbari.pdf
I can reproduce (~20% accuracy) with 1e5 pressure (standard) based on Gaussian output (multiplying /V and exp(beta T) terms; V = RT/p), if I use 4e7, that will lead to orders of magnitude difference.
Question 1: for the data in Table A5, what pressure was used?
Question 2: if the answer to question 1 is the standard pressure, does the partition function needs to be consistent with ExternalPressure? If the answer to question 1 is the ExternalPressure, how it was evaluated?
Thanks
ExternalPressure 4e7
but, for the data in Table A5 https://pure.tudelft.nl/ws/portalfiles/portal/71296377/Thesis_Ahmadreza_Rahbari.pdf
I can reproduce (~20% accuracy) with 1e5 pressure (standard) based on Gaussian output (multiplying /V and exp(beta T) terms; V = RT/p), if I use 4e7, that will lead to orders of magnitude difference.
Question 1: for the data in Table A5, what pressure was used?
Question 2: if the answer to question 1 is the standard pressure, does the partition function needs to be consistent with ExternalPressure? If the answer to question 1 is the ExternalPressure, how it was evaluated?
Thanks
#86
General / Inquiry regarding reconvening ...
Last post by saif - January 26, 2023, 09:30:50 PMHello everyone,
I hope you are all doing well,
I am currently working on a project related to gas separation by adsorption on MOFs using GCMC on RASPA on an HPC. I made a run of 120,000 cycles thinking that they will be enough to equilibrate, yet I found that couple of 10,000 cycles are additionally needed. After my first run was completed, I wanted to continue running the job for the additional cycles instead of repeating the entire run from the beginning. I tried the option of ContinueAfterCrash, and RestartFile but neither worked and showed the same previous output file. Are there any other possible ways to reconvene the run from where it stopped without the need to repeat it?
Your guidance is appreciated and many thanks in advance.
I hope you are all doing well,
I am currently working on a project related to gas separation by adsorption on MOFs using GCMC on RASPA on an HPC. I made a run of 120,000 cycles thinking that they will be enough to equilibrate, yet I found that couple of 10,000 cycles are additionally needed. After my first run was completed, I wanted to continue running the job for the additional cycles instead of repeating the entire run from the beginning. I tried the option of ContinueAfterCrash, and RestartFile but neither worked and showed the same previous output file. Are there any other possible ways to reconvene the run from where it stopped without the need to repeat it?
Your guidance is appreciated and many thanks in advance.
#87
General / Re: About the relation between...
Last post by w_wonder - January 25, 2023, 04:16:11 AMThanks.
Looks like exp(D0/kT) and total atomic energy are the keys. I managed to verified ~ 20%.
Looks like exp(D0/kT) and total atomic energy are the keys. I managed to verified ~ 20%.
#88
Bug reports / Two frameworks in the same sim...
Last post by TFabiani - January 20, 2023, 12:53:16 PMDear,
I faced up the following issue. When using more than one framework in the simulation, the charges are applied only to the second framework. The simulation of one framework of the two (separately) show a regular behavior of the software, while using two is always the first to have -nan in the Output file in the field "charges", even swapping the two or using other files.
I am using charges from CIF file.
Is there any way to avoid it and to run the simulation with two frameworks at the same time?
Thank you in advance for your help,
Best regards,
Thomas
Input File
SimulationType MonteCarlo
NumberOfCycles 500000
NumberOfInitializationCycles 1000
NumberOfEquilibrationCycles 5000
PrintEvery 10000
UseChargesFromCIFFile yes
Forcefield Local
Framework 0
FrameworkName Tf-DHzDPr-COF
UnitCells 2 2 9
Framework 1
FrameworkName MFI_SI_Olson
ShiftUnitCells 0.0 0.0 0.0
UnitCells 5 2 3
[...]
Output file
Pseudo Atom[ 97] Name C60 Oxidation: Element: C pdb-name: C Scat. Types: 7 6 Mass=12.0107
35897 B-factor:0.000
Charge=-nan (av) Polarization=1.760000000 [A^3] (considered a charged atom and no pol
arization) Interactions: yes
I faced up the following issue. When using more than one framework in the simulation, the charges are applied only to the second framework. The simulation of one framework of the two (separately) show a regular behavior of the software, while using two is always the first to have -nan in the Output file in the field "charges", even swapping the two or using other files.
I am using charges from CIF file.
Is there any way to avoid it and to run the simulation with two frameworks at the same time?
Thank you in advance for your help,
Best regards,
Thomas
Input File
SimulationType MonteCarlo
NumberOfCycles 500000
NumberOfInitializationCycles 1000
NumberOfEquilibrationCycles 5000
PrintEvery 10000
UseChargesFromCIFFile yes
Forcefield Local
Framework 0
FrameworkName Tf-DHzDPr-COF
UnitCells 2 2 9
Framework 1
FrameworkName MFI_SI_Olson
ShiftUnitCells 0.0 0.0 0.0
UnitCells 5 2 3
[...]
Output file
Pseudo Atom[ 97] Name C60 Oxidation: Element: C pdb-name: C Scat. Types: 7 6 Mass=12.0107
35897 B-factor:0.000
Charge=-nan (av) Polarization=1.760000000 [A^3] (considered a charged atom and no pol
arization) Interactions: yes
#89
Simulation algorithms and theory / Re: How to do Monte Carlo simu...
Last post by alireza_hadi68 - January 15, 2023, 12:03:02 PMDear Dr. Dubbeldam,
Thanks a lot for your helpful reply!
Thanks a lot for your helpful reply!
#90
General / Re: error message on restart a...
Last post by David Dubbeldam - January 11, 2023, 08:08:05 PMNote sure, but could be that the crash damage the restart-file. This could happen when the crash happens at the exact time the binary-restart-file is written to disk.