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#1
General / RUPTURA - fitting file
Last post by inangoi - July 10, 2024, 01:57:45 PM
Hi,

I'm trying to produce an isotherm using RUPTURA. I tried to do the example (MAF-X8-xylenes - fitting) but I don't know how to get the 'Result.dat-MAF-x8...' file

It is said in the documentation the this file (Results.dat) consists of the
equilibrium loading data computed using grand-canonical Monte Carlo simulations. But when I run a MC simulation using RASPA the output file is different from the example

Results.dat-MAF-x8 ... from the example:

#  1: pressure [Pa]
#  2: fugacity coefficient [-]
#  3: fugacity [Pa]
#  4: (absolute) loading [molecules per total cell]
#  5: (absolute) error [molecules per total cell]
#  6: (absolute) loading [molecules per unit cell]
#  7: (absolute) error [molecules per unit cell]
#  8: (absolute) loading [mol/kg]
#  9: (absolute) error [mol/kg]
# 10: (absolute) loading [mg/g]
# 11: (absolute) error [mg/g]
# 12: (excess) loading [molecules per total cell]
# 13: (excess) error [molecules per total cell]
# 14: (excess) loading [molecules per unit cell]
# 15: (excess) error [molecules per unit cell]
# 16: (excess) loading [mol/kg]
# 17: (excess) error [mol/kg]
# 18: (excess) loading [mg/g]
# 19: (excess) error [mg/g]
# 20: heat of desorption [K]
# 21: heat of desorption error [K]
# MAF-x8-P1-Repeat, 433K, o-xylene
0.00000000010000  1.0000000000  0.00000000010000  0.0074480000 0.0029671913  0.0009310000 0.0003708989  0.0002080881 0.0000828997  0.0220916711 0.0088010491  0.0074480000 0.0029671913 0.0009310000 0.0003708989  0.0002080881 0.0000828997  0.0220916711 0.0088010491  18782.43092 380.146898
0.00000000030703  1.0000000000  0.00000000030703  0.0216080000 0.0085091424  0.0027010000 0.0010636428  0.0006037013 0.0002377351  0.0640919481 0.0252391481  0.0216080000 0.0085091424 0.0027010000 0.0010636428  0.0006037013 0.0002377351  0.0640919481 0.0252391481  18795.78499 282.730668
0.00000000094267  1.0000000000  0.00000000094267  0.0563380000 0.0363284911  0.0070422500 0.0045410614  0.0015740153 0.0010149740  0.1671053393 0.1077547096  0.0563380000 0.0363284911 0.0070422500 0.0045410614  0.0015740153 0.0010149740  0.1671053393 0.1077547096  18686.98457 432.402570
0.00000000289427  1.0000000000  0.00000000289427  0.1611820000 0.0512807588  0.0201477500 0.0064100949  0.0045032295 0.0014327222  0.4780853563 0.1521049487  0.1611820000 0.0512807588 0.0201477500 0.0064100949  0.0045032295 0.0014327222  0.4780853563 0.1521049487  18690.29605 178.637466
0.00000000888624  1.0000000000  0.00000000888624  0.5160240000 0.1673997422  0.0645030000 0.0209249678  0.0144170843 0.0046769456  1.5305897550 0.4965279337  0.5160240000 0.1673997422 0.0645030000 0.0209249678  0.0144170843 0.0046769456  1.5305897550 0.4965279337  18640.31467 243.501202
0.00000002728330  1.0000000000  0.00000002728330  1.7657580000 0.5404926327  0.2207197500 0.0675615791  0.0493331356 0.0151007082  5.2374523367 1.6031666865  1.7657580000 0.5404926327 0.2207197500 0.0675615791  0.0493331356 0.0151007082  5.2374523367 1.6031666865  18758.00885 286.259478
0.00000008376780  1.0000000000  0.00000008376780  5.4241680000 0.9562926569  0.6780210000 0.1195365821  0.151544
.
.
.
.

-------------------------------
input


SimulationType                MonteCarlo
NumberOfCycles                25000
NumberOfInitializationCycles  5000
PrintEvery                    1000

Forcefield                    ExampleZeolitesForceField
RemoveAtomNumberCodeFromLabel yes

Framework 0
FrameworkName MFI_SI
UnitCells 2 2 2
HeliumVoidFraction 0.29
ExternalTemperature 300.0
ExternalPressure 1e4 1e5

ComputeNumberOfMoleculesHistogram yes
WriteNumberOfMoleculesHistogramEvery 5000
NumberOfMoleculesHistogramSize 1100
NumberOfMoleculesRange 80

ComputeEnergyHistogram yes
WriteEnergyHistogramEvery 5000
EnergyHistogramSize 400
EnergyHistogramLowerLimit -110000
EnergyHistogramUpperLimit -20000

Component 0 MoleculeName             methane
            MoleculeDefinition       ExampleDefinitions
            TranslationProbability   0.5
            ReinsertionProbability   0.5
            SwapProbability          1.0
            CreateNumberOfMolecules  0

----------------
output_...

Compiler and run-time data
===========================================================================
RASPA 2.0.45
Compiled as a 64-bits application
Compiler: gcc Apple LLVM 12.0.5 (clang-1205.0.22.9)
Compile Date = May 18 2021, Compile Time = 12:54:12

Tue May 18 12:55:50 2021
Simulation started on Tuesday, May 18.
The start time was 12:55 PM.

Cpu data:    x86_64
Cpu Model:   MacPro7,1
Host name:   MacPro.local
OS release:  20.4.0
OS type:     Darwin
OS version:  20E232


Simulation
===========================================================================
Dimensions: 3
Random number seed: 1621335350
RASPA directory set to: /Users/dubbelda/RASPA/simulations/
String appended to output-files:
Number of cycles: 25000
Number of initializing cycles: 5000
Number of equilibration cycles: 0
Print every: 1000
Rectangular boundary condition applied
Timestep: 0.000500
        Degrees of freedom:                        0
        Translational Degrees of freedom:          0
        Rotational Degrees of freedom:             0
        Degrees of freedom Framework:              0
.
.
.
.



What should I change in the input file? or what am I doing wrong?

Thank you in advance for any help


#2
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#3
Visualization / Adsorption density distributio...
Last post by Z.GAO - July 03, 2024, 05:25:02 AM
Hi everyone,

In the post-processing of gas adsorption MOF, I want to make an adsorption density distribution map. MOF is a triclinic system, and the adsorption density map drawn by VisIt software is still a cubic structure. So I use iRASPA software to draw it. Although iRASPA can show the triclinic structure, there is no color scale, only one color, which makes it difficult to intuitively judge the priority adsorption site. How can I solve this problem?

In addition, when I use iRASPA to present the molecular structure, I find that some atoms are not bonded. How should I deal with this?

Best wishes!

Zheng
#4
General / Prettys Womans in your city fo...
Last post by harveyking - June 24, 2024, 04:55:43 PM
#5
General / Difficult to install RASPA3 on...
Last post by Yu_Zhuochen - June 20, 2024, 12:10:33 PM
I've run these following commands,and try to install raspa3 on ubuntu:
$sudo apt install build-essential git cmake
$sudo add-apt-repository 'deb http://apt.llvm.org/jammy/ llvm-toolchain-jammy-18 main'
$sudo add-apt-repository 'deb-src http://apt.llvm.org/jammy/ llvm-toolchain-jammy-18 main'
$sudo apt install libllvm-18-ocaml-dev libllvm18 llvm-18 llvm-18-dev llvm-18-runtime
$sudo apt install libc++-18-dev libc++abi-18-dev libomp-18-dev pybind11-dev python3-pybind11 liblapack-dev clang-tools-18
$cd src
$vi makefile-manual  and set CXX=clang++-18
$make -f makefile-manual
However, there are several errors during installation:

In module 'std_atomic' imported from foundationkit/threadpool.ixx:31:
In module 'std_private_atomic_aliases' imported from /usr/lib/llvm-18/bin/../include/c++/v1/atomic:591:
In module 'std_cstdlib' imported from /usr/lib/llvm-18/bin/../include/c++/v1/__atomic/aliases.h:21:
/usr/lib/llvm-18/bin/../include/c++/v1/stdlib.h:123:59: error: 'abs' has different definitions in different modules; definition in module 'std_cstdlib' first difference is function body
  123 | _LIBCPP_NODISCARD_EXT inline _LIBCPP_HIDE_FROM_ABI double abs(double __lcpp_x) _NOEXCEPT {
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  124 |   return __builtin_fabs(__lcpp_x);
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  125 | }
      | ~
/usr/lib/llvm-18/bin/../include/c++/v1/stdlib.h:123:59: note: but in '' found a different body
  123 | _LIBCPP_NODISCARD_EXT inline _LIBCPP_HIDE_FROM_ABI double abs(double __lcpp_x) _NOEXCEPT {
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  124 |   return __builtin_fabs(__lcpp_x);
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  125 | }
      | ~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [makefile-manual:47: foundationkit/threadpool.pcm] Error 1

How can I solve this problem?
#6
General / Re: iRASPA cannot display the ...
Last post by Lingxiao Qin - June 10, 2024, 10:23:58 AM
I have tried your input file, and both the 'DensityProfile_methane.vtk' and 'COMDensityProfile_methane.vtk' output files can be successfully imported into iRASPA. I suggest checking the versions of RASPA and iRASPA that you have installed. The latest version of RASPA is v2.0.47, so I doubt whether you really installed RASPA v2.0.4 (released in 2016) or it is just a typo. The VTK files generated by such an old version of RASPA might not be readable by iRASPA. I am not sure of the exact version of RASPA I am using, but it was at least released after 2022. I downloaded iRASPA from the Windows store, which was released in 2018. By the way, the lines Ensemble NVT
TimeStep 0.0005
in your input file seem unusual. From my understanding, these options are used for molecular dynamics simulations and should not be used in a Grand Canonical Monte Carlo simulation, so I commented these two lines when testing your input file.
#7
General / MM3
Last post by Sara - June 04, 2024, 04:52:28 PM
I am trying to use the MM3_VDW but when I calculate the vDW energy for 2 atoms only using the same equation in the manual I am getting different value from the printed one in the output file
#8
General / Single point calculation for a...
Last post by Sara - June 04, 2024, 04:50:09 PM
Hi Dr David Dubbeldam,

Is there a way to compute the adsorbate-adsorbate energy for a defined XYZ coordinates for the both adsorbates? I mean I tried to put them in a box but raspa keeps changing the positions, I want it to read the exact positions in the .def file. Is that possible? it is like a single point calculation.
#9
General / Re: How to make adsorption den...
Last post by John Walker - May 29, 2024, 10:14:56 AM
大佬,你会了吗?
#10
General / iRASPA cannot display the dens...
Last post by John Walker - May 29, 2024, 09:16:10 AM
Dear:
    I have recently been using MOF materials for methane adsorption, and have attempted to import VTK files generated by RASPA2.0.4 into the IRASPA software. I am only able to generate MOF structure diagrams, but not the methane diagrams. I imported using 'DensityProfile_methane' and 'COMDensityProfile_methane' from the VTK folder, and received the error 'Import failed, Cannot read VTK header (line: 910 file: iraspagui/mainwindow.cpp)'. Importing 'Framework_final.pdb' from the Movies folder does display the molecular structure, which confuses me. How can I produce a methane adsorption density map? I can do it with VisIt.

SimulationType                   MonteCarlo
NumberOfCycles                   30000
NumberOfInitializationCycles     5000
PrintEvery                       1000
ContinueAfterCrash               no
#WriteBinaryRestartFileEvery     1000

ChargeMethod                     Ewald
EwaldPrecision                   1e-6

Ensemble                         NVT
TimeStep                         0.0005

Forcefield                       GenericMOFs

CutOffVDW                        12

RemoveAtomNumberCodeFromLabel    yes

Movies                           yes
WriteMoviesEvery                 1000
RemoveAtomNumberCodeFromLabel    yes         

UseChargesFromCIFFile            yes
Framework                        0
FrameworkName                    HKUST-1
UnitCells                        2 2 2
HeliumVoidFraction               0.39778
ExternalTemperature              298.15
ExternalPressure                 1.0e+06

ComputeDensityProfile3DVTKGrid   yes
WriteDensityProfile3DVTKGridEvery 1000
DensityProfile3DVTKGridPoints    150 150 150
AverageDensityOverUnitCellsVTK   yes
DensityAveragingTypeVTK          FullBox

Component 0        MoleculeName                 methane
                   MoleculeDefinition           TraPPE
                   IdealGasRosenbluthWeight     1.0
                   TranslationProbability   1.0         
                   RotationProbability      1.0       
                   ReinsertionProbability   1.0         
                   ##CBMCProbability          1.0
                   SwapProbability          1.0         
                   CreateNumberOfMolecules  0