Messages

In the literature and articles on "Reactive ensemble" the authors usually cite articles that describe how to compute these (either using QM calculations or using experimental date tables).

You can select which atoms to use for interpolation. The other ones will be computed in the usual way without interpolation.
The test at the beginning is limited and just meant to catch obvious wrong interpolations. But it is up to the user to judge whether the interpolation is sufficiently accurate or not. A few test of e.g. isotherms with and without grids can shows whether the grid is accurate enough.

These are warnings, it is up to you to judge how good the interpolation is.
For atom-types that have no VDW interaction, the atoms can be placed on top of other atoms during the test. This lead to large errors in the energy/force interpolation, but this would not occur during a real simulation.
Also, you can select which atom types to use with grid-interpolation (and which not).

The binary-restart should immediately pick up where it left. So at most 10000 cycles before catching up again with the output. Make sure it really reads the binary restart and does not restart from scratch (for example, by testing it using WriteBinaryRestartFileEvery with a smaller number and run it interactively in a console). Also, you have the source code, and you can use a debugger to see what is happening).

What is "CrashRestart yes"? Please check the manual "Restart and crash-recovery".
There is an option to restart from a restart-file containing positions, velocities, forces, and one option to continue from a binary file.
The binary-file format is not transferable between different versions of the code, so make sure you are using the latest version of the code (2.0.35).

No, but you can convert your 'chemical potential' to 'fugacity'.
Then, to use your own equation of state, simply input your computed 'fugacity coefficient'.
For example:
ExternalPressure 1e5
FugacityCoefficient 1.0
means the pressure is fugacity (because the fugacity coefficient is 1.0 and then pressure is equal to fugacity) and at 1 bar.
With your equation of state you can compute the fugacity coefficient.

We do not have anything to do with python (that is an addition by 'numat' and their github version).
For our version (see the manual) you install with:
1 ) rm -rf autom4te.cache
2 ) mkdir m4
3 ) aclocal
4 ) autoreconf -i
5 ) automake --add-missing
6 ) autoconf
7 ) ./configure --prefix=${RASPA_DIR}
   or
   ./scripts/CompileScript/make-gcc-local
8 ) make
9 ) make install

For our version of the code, this should not happen (on a standard unix system) and indicates something very strange on your system. Use a debugger to found out why it fails.
If you're using a version by other people (for example the numat github version) then it could be that their python additions might cause this problem.

Remove the empty line after "11 H_xyl    0.48371800   -2.55620700   -0.00016000"

The most common reason is that your molecule contains a ring. RASPA can not handle flexible rings.

The forcefield and molecules present in RASPA are examples. For your system you need to define your own force field (for the adsorbate, the ZIF-8, and the cross-interactions). All relevant interactions needs to be defined.

Higher adsorption capacity compared to what? experiments? other simulations?
For the first, you need to make sure you use a reliable force field and a structure that corresponds to the experiments (taking inaccessibility for example into account). For the latter, you need to make sure you do the simulations exactly as published in the literature.

No, there is nothing wrong. With the fugacity coefficient specified as 1.0, the code will not compute the excess adsorption. For that it needs to use an equation of state using the critical constants.
Note that you can also trivially compute excess adsorption from absolute adsorption by hand (see literature).

The computation of excess adorption is done using an equation of state (Peng-Robinson), which requires that you specify the critical constants for your molecule (at the top of the molecule definition).

So in iRASPA you import both files at the same time (on a mac you use cmd-click to add to the selection in the file-import).