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11
Input files and parameters / SLURM Script help...???
« Last post by monuplamoodu@yahoo.com on September 08, 2020, 05:30:25 PM »
Hi Everyone

I am new to RASPA and recently we have installed the same at our internal cluster and I am trying to run a test calculation with the following SLURM script but I keep getting an error that is "Permission Denied". The below script is basically from the RASPA manual but I was wondering what's wrong with this script. It would be highly appreciated if someone can help me out here!
Thanks in advance...

#!/bin/bash
#SBATCH -J Name
#SBATCH -p highmem
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --export=ALL

module load RASPA2/May-2020

valhost=$SLURM_JOB_NODELIST
export RASPA_DIR=${HOME}/RASPA/
$RASPA_DIR/monu.input


-Monu

Monu Joy
Graduate Student & Teaching Assistant
Functional Materials Design & X-ray Diffraction Lab (Office: CAMP 328)
Department of Chemistry & Biomolecular Science, Box 5814
Clarkson University, Potsdam, NY 13699, USA

E-mail: joym@clarkson.edu | Mob: +1 (315) 323-4313
12
General / Defination of absorbates in RASPA
« Last post by Haolong on August 29, 2020, 09:33:48 AM »
Dear Dr. Dubbeldam,

According to your paper, RASPA seems designed to simulate gases and liquids as absorbates.

Can I use RASPA to simulate ions as absorbates in dense systems with Ewald Summation?

Kind regards
Haolong
13
Input files and parameters / Change input file when restart
« Last post by Haolong on August 29, 2020, 03:13:50 AM »
Hello Dr. Dubbeldam,

Can I change my input file before restarting from crash?

Kind regards
Haolong

14
Output files / The absorption of ions stuck at a certain number
« Last post by Haolong on August 29, 2020, 03:07:21 AM »
Hello Dr. Dubbeldam,

I am trying to simulate the absorption of ions. One of the outputs are shown as below.

It shows that the number of ions stuck at 201 (or some other number in other outputs). Meanwhile the number of water atoms keep increasing at each step.

Is the RASPA stuck in simulating the ions here? Or it's working but I can't see from the number of ions?

Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0, density:   0.00000 [kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 0/1/0 (average   0.00000/  1.00000), density:   0.00000 (average   0.00000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average   1.72934/  1.00000), density: 438.22578 (average   3.77035) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average   8.15732/  1.00000), density: 438.22578 (average  17.78482) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  14.18356/  1.00000), density: 438.22578 (average  30.92339) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  19.84458/  1.00000), density: 438.22578 (average  43.26570) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  25.17260/  1.00000), density: 438.22578 (average  54.88200) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  30.19617/  1.00000), density: 438.22578 (average  65.83453) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  34.94065/  1.00000), density: 438.22578 (average  76.17858) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  39.42868/  1.00000), density: 438.22578 (average  85.96351) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  43.68050/  1.00000), density: 438.22578 (average  95.23345) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  47.71429/  1.00000), density: 438.22578 (average 104.02801) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  51.54638/  1.00000), density: 438.22578 (average 112.38285) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  55.19155/  1.00000), density: 438.22578 (average 120.33014) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  58.66313/  1.00000), density: 438.22578 (average 127.89900) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  61.97326/  1.00000), density: 438.22578 (average 135.11581) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  65.13292/  1.00000), density: 438.22578 (average 142.00460) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  68.15215/  1.00000), density: 438.22578 (average 148.58722) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  71.04012/  1.00000), density: 438.22578 (average 154.88364) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  73.80519/  1.00000), density: 438.22578 (average 160.91213) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  76.45506/  1.00000), density: 438.22578 (average 166.68944) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  78.99677/  1.00000), density: 438.22578 (average 172.23094) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  81.43681/  1.00000), density: 438.22578 (average 177.55079) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  83.78116/  1.00000), density: 438.22578 (average 182.66201) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  86.03535/  1.00000), density: 438.22578 (average 187.57665) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  88.20447/  1.00000), density: 438.22578 (average 192.30584) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  90.29326/  1.00000), density: 438.22578 (average 196.85987) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  92.30609/  1.00000), density: 438.22578 (average 201.24830) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  94.24703/  1.00000), density: 438.22578 (average 205.48000) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  96.11988/  1.00000), density: 438.22578 (average 209.56322) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  97.92814/  1.00000), density: 438.22578 (average 213.50565) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average  99.67510/  1.00000), density: 438.22578 (average 217.31443) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average 101.36384/  1.00000), density: 438.22578 (average 220.99626) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average 102.99720/  1.00000), density: 438.22578 (average 224.55737) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average 104.57788/  1.00000), density: 438.22578 (average 228.00360) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average 106.10838/  1.00000), density: 438.22578 (average 231.34044) kg/m^3]
Component 1 (Cl), current number of integer/fractional/reaction molecules: 201/1/0 (average 107.59105/  1.00000), density: 438.22578 (average 234.57300) kg/m^3]

Kind regards
Haolong
15
Output files / Exactly the same output from different simulations
« Last post by Haolong on August 29, 2020, 02:58:45 AM »
Hello Dr. Dubbeldam,

I got exactly the same output from different simulations, which have the same input files.

This happens around 2 out of 10 works with same input files.

Does it mean these 2 works are using the same array of random numbers?

Kind regards
Haolong
16
Output files / Re: Vapor density by NVT-GEMC
« Last post by Jianbo on August 22, 2020, 01:32:30 PM »
Thanks for your kindly response!

I have checked the result:
The vapor pressure seems to fluactuate around the average pressure value which indicates the system are well equilibrated.
However, the average widom chemical potential of vapor phase differs a lot from the liquid phase which indicates the system are not equilibrated.

So, I am confused how can I tell the system is well equilbrated?
17
Simulation algorithms and theory / Re: Heat Capacity (MC-NPT)
« Last post by dcyanoura on August 20, 2020, 12:49:48 PM »
Dear Dr Dubbeldam,

according to the RASPA output in NPT-MC simulations, the formula
related to the enthalpy fluctuations is used to calculate the isobaric heat capacity Cp:

[1/(kB T^2)]*[<H^2>-<H>^2]

The results are expressed in the output as [J/mol/K.]
However, my question is if these values need to be divided by the number of molecules in
the NPT simulation to get the correct values, since this seems to be the case.

Is this correct?

Your answer will be highly appreciated.


PS: Note also that in the case of Monte Carlo, only the configurational enthalpy is taken into account. Therefore,
the value of the isobaric heat capacity calculated with RASPA corresponds to the configurational Cp.
In order to calculate the overall isobaric heat capacity Cp, the kinetic energy contributions need to be taken into account
as well. There are several ways to do so, which are already presented in the literature, e.g.

M. Lagache, P. Ungerer, A. Boutin, A. H. Fuchs, Prediction of thermodynamic derivative properties of fluids by Monte Carlo simulation, Phys.Chem.Chem.Phys., 2001,3, 4333-4339

18
Output files / Re: Vapor density by NVT-GEMC
« Last post by dubbelda on August 20, 2020, 11:36:25 AM »
The pressure of the liquid-phase contains a large error (because of the strong molecular interactions). Usually people take the gas-phase value after the simulation is equilibrated.
19
Input files and parameters / Re: 1_2_ethanediol TraPPE modell
« Last post by dubbelda on August 20, 2020, 11:31:22 AM »
I copied your input, and see no problems.
Have you tried to run it with zero cycles? Does it finish? is the output precisely (pseudo-atoms, force field etc) exactly what you put in?
If that works, run it with 10 cycles and see if it works.

One thing that could go wrong is that your input files are not ascci-files, but utf8 or windows-files that contain different newlines.
With utilities like 'dos2unix' and 'unix2dos' you convert between windows and linux/Mac.
20
You're swapping molecules in and out, and hence use the grand-canonical ensemble. In this ensemble, you fix the chemical potential (via the pressure/fugacity) and the amount of molecules fluctuates. So you're not able to control how many of where the molecules are. But that is the nature of adsorption.


Btw. you're missing a rotation move (although you could say this is also achieved via insertion of molecules, this is much less efficient).
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