Recent Posts

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21
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?
22
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.
23
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.
24
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]
25
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
26
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.




27
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
28
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?
29
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
30
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
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