News:

SMF - Just Installed!

Main Menu
Menu

Show posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.

Show posts Menu

Messages - David Dubbeldam

#211
General / Re: 'CrashRestart' taking long time
October 24, 2018, 11:59:04 AM
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).
#212
General / Re: 'CrashRestart' taking long time
October 18, 2018, 01:48:00 PM
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).
#213
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.
#214
Input files and parameters / Re: Error in connectivity
September 29, 2018, 06:50:46 AM
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
#215
Input files and parameters / Re: Error in connectivity
September 23, 2018, 08:40:12 AM
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.
#216
Input files and parameters / Re: Error in connectivity
September 22, 2018, 09:41:07 AM
Remove the empty line after "11 H_xyl    0.48371800   -2.55620700   -0.00016000"
#217
Input files and parameters / Re: Error in connectivity
September 21, 2018, 07:54:11 PM
The most common reason is that your molecule contains a ring. RASPA can not handle flexible rings.
#218
General / Re: Issue with the forcefield
September 21, 2018, 05:44:04 PM
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.
#219
General / Re: Issue with the forcefield
September 20, 2018, 10:23:48 AM
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.
#220
Output files / Re: Excess adsorption
July 29, 2018, 12:52:41 PM
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).
#221
Output files / Re: Excess adsorption
July 27, 2018, 09:12:40 PM
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).
#222
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).
#223
What do you mean with a "totally destroyed structure"? Are you using a flexible model? In that case you need a good force field to describe the flexibility of the framework.
For a rigid structure, the end and begin structure should of course be identical. In case you meant a rigid structure, then check whether the space-group is given correctly. You can always change your structure to a P1 structure, so that there are no space group issues.
#224
Output files / Re: MSD calculation
May 23, 2018, 10:39:03 AM
See the manual for these options.

'ComputeMSDConventional'  for conventional MSD, and 'ComputeMSD' for order-n MSD (works in log-scale).

Correlation times are usually much smaller than total simulation time, because you need to average a lot to get good statistics. You could only have one measurement of a correlation time equal to your simulation length and that point would be useless.
#225
If you use a flexible framework, then all atoms should move. In MD that is done automatically; in MC you need MC-moves to do that.