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Input files and parameters / Re: Density by NPT MC and MD

« Last post by dubbelda on August 20, 2020, 11:18:20 AM »

MD always uses a shifted potential. Did you use the same in the Monte Carlo?
Did you use appropriate MC moves like translation, rotation, reinsertion, partial reinsertion to sample to the phase-space properly?

General / Re: Run RASPA using MPI

« Last post by dubbelda on August 20, 2020, 11:13:30 AM »

RASPA is not a parallel code. There is usually very little reason to in Monte Carlo. Once your system is equilibrated, you can start several independent jobs and just average the results.

General / Re: Running RASPA2 with Python Scripts

« Last post by David Dubbeldam on August 20, 2020, 11:09:36 AM »

The numat-version is a clone of the RASPA software where they added the python workflow.
Please ask the authors of the numat-version.

General / Re: Surface area of MgMOF-74

« Last post by dubbelda on August 20, 2020, 11:04:39 AM »

There is a example in: examples/Tutorial/AdsorptionN2InMIL-47/3-Surface-area

Output:

Average Surface Area:
=====================
Block[ 0] 252.784946 [-]
Block[ 1] 253.629130 [-]
Block[ 2] 253.098236 [-]
Block[ 3] 254.806589 [-]
Block[ 4] 253.473192 [-]
------------------------------------------------------------------------------
Average surface area: 253.558418 +/- 1.379919 [A^2]
1652.157533 +/- 8.991397 [m^2/g]
1652.766655 +/- 8.99471 [m^2/cm^3]

General / Surface area of MgMOF-74

« Last post by imaeda on August 19, 2020, 04:43:51 AM »

Dear all,
I am trying to calculate surface area of MgMOF-74 following the tutorial.
Cif file of MgMOF-74 is in RASPA2-master>structures>mofs>cif.
However, the calculation result is 0.
How can I solve this problem?
The input file is:
SimulationType MonteCarlo
NumberOfCycles 2000
PrintEvery 100
PrintPropertiesEvery 100
Forcefield local
Framework 0
FrameworkName MgMOF-74
UnitCells 2 2 5
ExternalTemperature 298.0
HeliumVoidFraction 0.908459
SurfaceAreaProbeDistance Sigma
Component 0 MoleculeName N2
MoleculeDefinition TraPPE
SurfaceAreaProbability 1.0
CreateNumberOfMolecules 0

General / Running RASPA2 with Python Scripts

« Last post by Busra on August 08, 2020, 11:31:18 PM »

Dear all,

I am trying to run RASPA2 using Python scripts as in https://github.com/numat/RASPA2/wiki/Workflow
However, there was an error about space group that was previously discussed in this forum.
Then I tried to run with ZIF-8.cif since its space group is P1 but the same error occurred once more.

My code is:

import RASPA2
myMOF="ZIF-8.cif"
output=RASPA2.get_geometric_surface_area(myMOF, unit_cells=(1,1,1), cycles=500, input_file_type="cif", units="m^2/g", forcefield="CrystalGenerator")

I have written this according to raspa2.py and run with Python3.8.3

I would be grateful if anyone could help me to realize my mistakes, and run the program.

Output files / Vapor density by NVT-GEMC

« Last post by Jianbo on August 03, 2020, 03:27:20 PM »

Hello Dr. Dubbeldam,

I am doing NVT-Gibbs Ensemble Simulations to obtain SPC/E water vapor density.

I have no idea why negative pressre existed in the liquid box shows negative pressre existed. Is there anything wrong with my input file?

Besides, how can I tell the vapour-liquid equilibrium has been reached? I use averaged Widom chemical potential and averaged pressure to identify the equilibrium state, am I right?

Thanks in advance!

P. S. simulation file is as below:

SimulationType MonteCarlo

NumberOfCycles 200000
NumberOfInitializationCycles 50000

RestartFile no
ContinueAfterCrash no
WriteBinaryRestartFileEvery 1000

PrintEvery 1000
PrintPropertiesEvery 1000

ChargeMethod Ewald
EwaldPrecision 1e-5
Forcefield SPC_E
CutOffVDW 10
CutOffChargeCharge 10

Box 0
BoxLengths 22 22 22
BoxAngles 90 90 90
ExternalTemperature 300.0

Movies yes
WriteMoviesEvery 1000

ComputeEnergyHistogram yes
ComputeNumberOfMoleculesHistogram yes
ComputeMolecularPressure yes

Box 1
BoxLengths 100 100 100
BoxAngles 90 90 90
ExternalTemperature 300.0

Movies yes
WriteMoviesEvery 1000

ComputeEnergyHistogram yes
ComputeNumberOfMoleculesHistogram yes
ComputeMolecularPressure yes

GibbsVolumeChangeProbability 0.1

Component 0 MoleculeName water_SPCE
StartingBead 0
MoleculeDefinition SPC_E
TranslationProbability 40
RotationProbability 40
ReinsertionProbability 3.3
GibbsSwapProbability 10
GibbsWidomProbability 3.3
WidomProbability 3.3
CreateNumberOfMolecules 320 0

Input files and parameters / Density by NPT MC and MD

« Last post by aemelianova on August 02, 2020, 11:35:07 PM »

Dear Prof. Dubbeldam and RASPA users,

I was trying to calculate the density of the bulk liquid using NPT ensemble with MC and validate by NPT MD simulation.
I am using the same force field and the rest of the parameters for the molecule. I got the expected result (close to the experimental value) with MC which also agrees well with MD simulation in LAMMPS. However, MD result by RASPA is much higher (about 60 kg/m3 difference). Both results were well equilibrated.
I was trying to turn on/off tail correction and change the time step, and it did not change the result significantly.
What may be the reason of this discrepancy?

Input files and parameters / Larger amount of molecules in MC calculation of benzene on HZSM-5

« Last post by cbornes on July 20, 2020, 09:23:42 PM »

New user here.

I´m trying to study the adsorption of aromatic compounds on acid zeolites. I´ve built an HZSM-5 supercell cif file and the following input file but for some reason, I´m getting more than 1 benzene molecule (as selected). Since I want to study the adsorption on acid site (H-site) how can I force a single benzene molecule per acid site

----INPUT---
SimulationType MonteCarlo
NumberOfCycles 25000
NumberOfInitializationCycles 10000
PrintEvery 1000
RestartFile no

Forcefield GarciaPerez2006

Framework 0
FrameworkName MFI_1Al
RemoveAtomNumberCodeFromLabel yes
UnitCells 1 1 1
ExternalTemperature 300
ExternalPressure 10000.0
Movies yes
WriteMoviesEvery 100

Component 0 MoleculeName benzene
MoleculeDefinition TraPPE
TranslationProbability 1.0
ReinsertionProbability 1.0
SwapProbability 1.0
ExtraFrameworkMolecule no
CreateNumberOfMolecules 2

-----CIF----

_cell_length_a 20.022
_cell_length_b 19.899
_cell_length_c 26.766
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 10664.1

_symmetry_cell_setting orthorhombic
_symmetry_space_group_name_Hall 'P 1'
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1

_symmetry_equiv_pos_as_xyz 'x,y,z'

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_charge
_atom_site_polarization
_atom_site_anisotropic_displacement
_atom_site_anisotropic_type
_atom_site_print_to_pdb
Si Si 0.42238 0.05650 0.33201 Si4+ 0 0 absolute yes
Si Si 0.30716 0.02772 0.40535 Si4+ 0 0 absolute yes
Si Si 0.27911 0.06127 0.01560 Si4+ 0 0 absolute yes
Si Si 0.12215 0.06298 0.01335 Si4+ 0 0 absolute yes
Si Si 0.07128 0.02722 0.40725 Si4+ 0 0 absolute yes
Si Si 0.18641 0.05896 0.33591 Si4+ 0 0 absolute yes
Si Si 0.42265 0.82750 0.33641 Si4+ 0 0 absolute yes
Si Si 0.30778 0.86984 0.40726 Si4+ 0 0 absolute yes
Si Si 0.27554 0.82721 0.01555 Si4+ 0 0 absolute yes
Si Si 0.12058 0.82690 0.01490 Si4+ 0 0 absolute yes
Si Si 0.07044 0.86963 0.40900 Si4+ 0 0 absolute yes
Si Si 0.18706 0.82673 0.34034 Si4+ 0 0 absolute yes
O O 0.37260 0.05340 0.37790 O2- 0 0 absolute yes
O O 0.30840 0.05870 0.46055 O2- 0 0 absolute yes
O O 0.20070 0.05920 0.01445 O2- 0 0 absolute yes
O O 0.09690 0.06110 0.45720 O2- 0 0 absolute yes
O O 0.11490 0.05410 0.36185 O2- 0 0 absolute yes
O O 0.24350 0.05530 0.37700 O2- 0 0 absolute yes
O O 0.37420 0.84390 0.38140 O2- 0 0 absolute yes
O O 0.30850 0.84480 0.46360 O2- 0 0 absolute yes
O O 0.19800 0.84460 0.01440 O2- 0 0 absolute yes
O O 0.09100 0.83860 0.46115 O2- 0 0 absolute yes
O O 0.11690 0.84220 0.36530 O2- 0 0 absolute yes
O O 0.24480 0.84060 0.37890 O2- 0 0 absolute yes
O O 0.30470 0.94900 0.40670 O2- 0 0 absolute yes
O O 0.07680 0.94810 0.41155 O2- 0 0 absolute yes
.
.
.
Si Si 0.42956 0.36963 0.65900 Si4+ 0 0 absolute yes
Al Al 0.31294 0.32673 0.59034 Al3+ 0 0 absolute yes
.
.
.
O O 0.99600 0.65280 0.89610 O2- 0 0 absolute yes
H H 0.31449 0.25063 0.53431 H1+ 0 0 absolute yes

PS. Iḿ not able to write the full cif file do to a maximum length of the post

Thanks a lot
Carlos

General / Run RASPA using MPI

« Last post by manuelbenavent on July 17, 2020, 09:07:46 AM »

Dear developers,

I was wondering if I could run RASPA using MPI. Or is there any other way to make parallelization?

Thanks
Manuel