31
General / Re: How to make snapshots
« on: October 20, 2020, 06:54:17 PM »
You can use the 'Movie'-option to write snapshots at regular intervals to a pdb-file. That pdb-file can then be viewed with a molecular viewer.
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32
Simulation algorithms and theory / Re: Heat Capacity (MC-NPT)
« on: September 25, 2020, 12:34:30 PM »
There are many different formulas given in the literature, so there is not one unique number.
So compute it in the way to that you choose (but write down what formula you used for it).
So compute it in the way to that you choose (but write down what formula you used for it).
33
Output files / Re: Vapor density by NVT-GEMC
« on: September 25, 2020, 12:26:22 PM »
Using the Widom-insertion in dense system is known to fail. That is why people take the value from the vapor phase assuming you have run long enough to be equilibrated.
34
Output files / Re: The absorption of ions stuck at a certain number
« on: September 25, 2020, 12:24:08 PM »
Adsorption of ions is very difficult because the the molecule is charged. Net-charge is not allowed in a real periodic system.
35
Output files / Re: Exactly the same output from different simulations
« on: September 25, 2020, 12:05:18 PM »
The randomseed is taken from the system time. if you submit lots of jobs to a cluster which start at the same time, they might use the same random seed.
The random-seed can also be set by hand in the input file.
The random-seed can also be set by hand in the input file.
36
Input files and parameters / Re: Change input file when restart
« on: September 25, 2020, 11:57:07 AM »
No, it will read all values from the binary-restart-file.
When restarting from "RestartInitial" it is fine to change the input parameters.
When restarting from "RestartInitial" it is fine to change the input parameters.
37
General / Re: Defination of absorbates in RASPA
« on: September 25, 2020, 11:49:55 AM »
In the source, the design is that you have a framework, and at most two types of molecules: adsorbates and cations. Adsorbates are usually fluctuation in an adsorption simulations, and you would use the cation-type for molecules that are fixed in number.
So you could leave out the framework, and you're simulating a fluid. They are still called adsorbates, although they are strictly not. it is just a naming for different types of molecules.
The main reason is that the energy-decompositions is based on these types. So, you would also get the evaregs adsorbate-adsorbate, cation-cation, and adsorbate-cation energies.
So you could leave out the framework, and you're simulating a fluid. They are still called adsorbates, although they are strictly not. it is just a naming for different types of molecules.
The main reason is that the energy-decompositions is based on these types. So, you would also get the evaregs adsorbate-adsorbate, cation-cation, and adsorbate-cation energies.
38
General / Re: error run simulate
« on: September 25, 2020, 11:46:35 AM »
It is the same version, but I have no idea about the python part or how it works. So for any questions, you will need to ask Numat.
39
General / Re: Running RASPA2 with Python Scripts
« on: August 20, 2020, 12:09:36 PM »
The numat-version is a clone of the RASPA software where they added the python workflow.
Please ask the authors of the numat-version.
Please ask the authors of the numat-version.
40
Input files and parameters / Re: 1_2_ethanediol TraPPE modell
« on: July 14, 2020, 12:43:18 PM »
Are you using the latest version? (2.0.37).
I see no immediate issues with it.
number of intra VDW interactions: 6
--------------------------------------------
interaction 0: A=0 B=3 scaling factor: 0
interaction 1: A=0 B=3 scaling factor: 0
interaction 2: A=0 B=3 scaling factor: 0
interaction 3: A=0 B=3 scaling factor: 0
interaction 4: A=0 B=3 scaling factor: 0
interaction 5: A=0 B=3 scaling factor: 0
number of intra charge-charge Coulomb interactions: 6
-----------------------------------------------------------
interaction 0: A=0 B=3 scaling factor: 0.5
interaction 1: A=0 B=4 scaling factor: 1
interaction 2: A=0 B=5 scaling factor: 1
interaction 3: A=1 B=4 scaling factor: 0.5
interaction 4: A=1 B=5 scaling factor: 1
interaction 5: A=2 B=5 scaling factor: 0.5
Are you getting this?
I see no immediate issues with it.
number of intra VDW interactions: 6
--------------------------------------------
interaction 0: A=0 B=3 scaling factor: 0
interaction 1: A=0 B=3 scaling factor: 0
interaction 2: A=0 B=3 scaling factor: 0
interaction 3: A=0 B=3 scaling factor: 0
interaction 4: A=0 B=3 scaling factor: 0
interaction 5: A=0 B=3 scaling factor: 0
number of intra charge-charge Coulomb interactions: 6
-----------------------------------------------------------
interaction 0: A=0 B=3 scaling factor: 0.5
interaction 1: A=0 B=4 scaling factor: 1
interaction 2: A=0 B=5 scaling factor: 1
interaction 3: A=1 B=4 scaling factor: 0.5
interaction 4: A=1 B=5 scaling factor: 1
interaction 5: A=2 B=5 scaling factor: 0.5
Are you getting this?
41
General / Re: Mg and K cations .def file
« on: May 26, 2020, 05:57:06 PM »
All structure, molecule and force field files are examples. For you own use case, you need to construct these files with the exact parameters that you want.
42
General / Re: Why the excess adsorption is negative, absolute adsorption is zero when doing MC
« on: May 14, 2020, 08:10:12 PM »
Negative excess adsorption indicates that you are in the liquid phase. That happens when you go above the vapor pressure.
43
Input files and parameters / Re: MC and MD inconsistency
« on: May 14, 2020, 08:07:21 PM »
A common inconstancy between MC and MD is the VDW potential. Make sure you use a shifted VDW potential for MC.
44
Input files and parameters / Re: Torsional potential with phase angle term
« on: May 14, 2020, 08:05:08 PM »
Depending on the value of 'f' you could probably rewrite that functional form into into another form that is supported (using cosine and sine rules). If that is not possible, another option is add the functional form in the code.
45
Input files and parameters / Re: setup for energy-bias GCMC?
« on: April 24, 2020, 07:41:49 PM »
The energy-bias method is not implemented in RASPA (it is implemented in the code 'MUSIC').