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1
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.




2
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
3
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?
4
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
5
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
6
Input files and parameters / Re: 1_2_ethanediol TraPPE modell
« Last post by Christopher on July 16, 2020, 04:51:46 PM »
Maybe simulation.input would be interessting:

SimulationType                    MonteCarlo
NumberOfCycles                    50000
NumberOfInitializationCycles      50000
PrintEvery                        10
RestartFile                       no

CutOff                            14.0
CutOffVDW                         14.0
CutOffCoulomb                     14.0
EwaldPrecision                    1e-12
Forcefield                        local
WriteBinaryRestartFileEvery       1000
ContinueAfterCrash                no

Box 0
BoxLengths 40 40 40
BoxAngles 90 90 90
ExternalTemperature 600
ComputeMolecularPressure yes

Box 1
BoxLengths 40 40 40
BoxAngles 90 90 90
ExternalTemperature 600
ComputeMolecularPressure yes

GibbsVolumeChangeProbability 0.1

Component 0 MoleculeName                      1_2_ethanediol
            StartingBead                      0
            MoleculeDefinition                local
            Intra14ChargeChargeScalingValue   0.5
            Intra14VDWScalingValue            0
            TranslationProbability            1.0
            RandomTranslationProbability      1.0
            RotationProbability               1.0
            GibbsSwapProbability              1.0
            ReinsertionProbability            1.0
            CBMCProbability                   1.0
            CreateNumberOfMolecules           100 100


I varied EwaldPrecision from 1e-6 to 1e-12 and also other starting conditions like box lenghts or the number of molecules in a box. But everytime the simulation get's stuck.

Best Christopher
7
Input files and parameters / Re: 1_2_ethanediol TraPPE modell
« Last post by Christopher on July 16, 2020, 04:49:28 PM »
Dear Dr. Dubbeldam:
thanks for taking the time to help me!
I'm getting the same output. And also the forcefield in the output file looks fine. The version in the outputfile is
RASPA 2.0.38
Compiled as a 64-bits application
Compiler: gcc 7.4.1 20190905 [gcc-7-branch revision 275407]
Compile Date = Jul  1 2020, Compile Time = 13:22:41

I use this version of force_field_mixing_rules.def:
# general rule for shifted vs truncated
truncated
# general rule tailcorrections
yes
# number of defined interactions
13
# type interaction
He             LENNARD_JONES    10.9     2.64
CH4_sp3        LENNARD_JONES   148.0     3.73
CH3_sp3        LENNARD_JONES    98.0     3.75
CH2_sp3        LENNARD_JONES    46.0     3.95
CH_sp3         LENNARD_JONES    10.0     4.68
C_sp3          LENNARD_JONES     0.5     6.4
O_co2          LENNARD_JONES    79.0     3.05
C_co2          LENNARD_JONES    27.0     2.80
N_n2           LENNARD_JONES    36.0     3.31
O_alc          LENNARD_JONES    93.0     3.02
H_alc          LENNARD_JONES     0.0     0.0
CH2_alc        LENNARD_JONES    46.0     3.95
dummy          LENNARD_JONES     0.0     0.0
# general mixing rule for Lennard-Jones
Lorentz-Berthelot


And pseudo_atoms.def
#number of pseudo atoms
13
#type      print   as    chem  oxidation   mass        charge   polarization B-factor radii  connectivity anisotropic anisotropic-type   tinker-type
CH4_sp3    yes     C     C     0           16.04246    0.0      0.0          1.0      1.00   0            0           absolute           0
CH3_sp3    yes     C     C     0           15.03452    0.0      0.0          1.0      1.00   0            0           absolute           0
CH2_sp3    yes     C     C     0           14.02658    0.0      0.0          1.0      1.00   0            0           absolute           0
CH_sp3     yes     C     C     0           13.01864    0.0      0.0          1.0      1.00   0            0           absolute           0
C_sp3      yes     C     C     0           12.0        0.0      0.0          1.0      1.00   0            0           absolute           0
O_alc      yes     O     O     0           15.9994    -0.7      0.0          1.0      1.00   0            0           relative           0
H_alc      yes     H     H     0            1.00794    0.435    0.0          1.0      1.00   0            0           relative           0
CH2_alc    yes     C     C     0           14.02658    0.265    0.0          1.0      1.00   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
N_n2       yes     N     N     0           14.00674   -0.482    0.0          1.0      0.7    0            0           relative           0
N_com      no      N     N     0           0.0         0.964    0.0          1.0      0.7    0            0           relative           0
dummy      no      N     N     0           0.0         0.0      0.0          1.0      1.00   0            0           relative           0

Have you ever tried TraPPE models of diols? I still can't figure out any reason, why it is not working.
If you have any hint, I would really appreciate!

Best
Christopher
8
The positions are relative to each other. In the output file you can see that it reorients the molecule anyway (according to the matrix of inertia).

Dear Dubbelda

But is this ok for me to define the pyridine´s atoms in such a way?

Allow me another question. I want to prepare an MFI zeolite structure in a 1x1x2 with a single Al atom and a corresponding H as counterion. What is the best way for me to prepare such input? I´ve tried to open an MFI.cif file, build a 1x1x2 supercell, and adding both the Al and the H in Avogadro. But it seems that the way is written by Avogadro is not compatible with RASPA. Can you also provide some insight into this?

Thanks
Manuel
9
Input files and parameters / Re: pseudo_atom radii
« Last post by dubbelda on July 14, 2020, 11:57:09 AM »
The radii are used to compute bonding in flexible frameworks.
For small rigid molecules you define the relative positions of all atoms (including for example dummy atoms).
10
Yes, when FugacityCoefficient is set to 1.0, then ExternalPressure is the fugacity which you input.
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