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#71
Visualization / Adsorption density distributio...
Last post by Z.GAO - July 03, 2024, 05:25:02 AMHi 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
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
#72
General / Difficult to install RASPA3 on...
Last post by Yu_Zhuochen - June 20, 2024, 12:10:33 PMI'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?
$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?
#73
General / Re: iRASPA cannot display the ...
Last post by Lingxiao Qin - June 10, 2024, 10:23:58 AMI 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
Code Select
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. #74
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
#75
General / Single point calculation for a...
Last post by Sara - June 04, 2024, 04:50:09 PMHi 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.
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.
#76
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？
#77
General / iRASPA cannot display the dens...
Last post by John Walker - May 29, 2024, 09:16:10 AMDear:
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
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
#78
Input files and parameters / Ideal Gas Rosenbluth Weight Gr...
Last post by ngantzler - May 28, 2024, 08:15:16 PMHi Dr. Dubbeldam,
I am putting together a molecular model and have gotten an IGRW > 1.0. Similar models such as the PFOA model used in The role of surface thermodynamics and kinetics in the removal of PFOA from aqueous solutions give an IGRW~3.69 (T=298 K).
My understanding is that the IGRW = 1.0 for small molecules (e.g. butane) where we can neglect intra-molecular interactions; however, for larger molecules (e.g. octane) we expect an IGRW < 1.0, so I don't understand what it means to have a value greater then 1.0.
Is an IGRW > 1.0 physically meaningful? What is the physical intuition to apply here? Could this be due to degenerate energy states?
Thanks,
Nick
I am putting together a molecular model and have gotten an IGRW > 1.0. Similar models such as the PFOA model used in The role of surface thermodynamics and kinetics in the removal of PFOA from aqueous solutions give an IGRW~3.69 (T=298 K).
My understanding is that the IGRW = 1.0 for small molecules (e.g. butane) where we can neglect intra-molecular interactions; however, for larger molecules (e.g. octane) we expect an IGRW < 1.0, so I don't understand what it means to have a value greater then 1.0.
Is an IGRW > 1.0 physically meaningful? What is the physical intuition to apply here? Could this be due to degenerate energy states?
Thanks,
Nick
#79
General / Re: Defining a parametric flex...
Last post by iwanchemist - May 25, 2024, 12:03:29 PMI have same problem, how to define flexible structure in .def file
what we have to manual definition flexible structure?
what we have to manual definition flexible structure?
#80
Simulation algorithms and theory / GCMD-Example 13: MD MuPT
Last post by iwanchemist - May 25, 2024, 08:44:50 AMHello Prof. Dubbeldam,
I wanna ask you about GCMD (MC/MD) skrip in module RASPA like this:
SimulationType MolecularDynamics
NumberOfCycles 1000000
NumberOfEquilibrationCycles 100000
PrintEvery 1000
ContinueAfterCrash yes
WriteBinaryRestartFileEvery 1000
Ensemble MuPT
Forcefield Local
CutOff 10.0
Movies yes
WriteMoviesEvery 1000
Framework 0
FrameworkName Framework_0_final_1_1_1_VASP
HeliumVoidFraction 0.801937
UnitCells 1 1 1
ExternalTemperature 298.0
ExternalPressure 1000000
ComputeRDF yes
WriteRDFEvery 1000
FlexibleFramework yes
FrameworkDefinitions Local
Component 0 MoleculeName CO2
MoleculeDefinition Local
IdealGasRosenbluthWeight 1.0
SwapProbability 1.0
CreateNumberOfMolecules 1
Based on this script, I am confused. If the MD script is simulated for 1,000,000 cycles, what is the default duration of the Monte Carlo simulation?
I wanna ask you about GCMD (MC/MD) skrip in module RASPA like this:
SimulationType MolecularDynamics
NumberOfCycles 1000000
NumberOfEquilibrationCycles 100000
PrintEvery 1000
ContinueAfterCrash yes
WriteBinaryRestartFileEvery 1000
Ensemble MuPT
Forcefield Local
CutOff 10.0
Movies yes
WriteMoviesEvery 1000
Framework 0
FrameworkName Framework_0_final_1_1_1_VASP
HeliumVoidFraction 0.801937
UnitCells 1 1 1
ExternalTemperature 298.0
ExternalPressure 1000000
ComputeRDF yes
WriteRDFEvery 1000
FlexibleFramework yes
FrameworkDefinitions Local
Component 0 MoleculeName CO2
MoleculeDefinition Local
IdealGasRosenbluthWeight 1.0
SwapProbability 1.0
CreateNumberOfMolecules 1
Based on this script, I am confused. If the MD script is simulated for 1,000,000 cycles, what is the default duration of the Monte Carlo simulation?
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