Messages

1

Output files / Abnormal atoms position output when Stiffness is smaller than 1

« on: March 13, 2021, 01:30:58 PM »

 Dear Dubbeldam,

There is abnormal position output for atoms in the molecule with extremely low stiffness(1e-20), which is shown as below:

ATOM      1  O   MOL            24.547   0.074   0.871  1.00  0.00           O 
ATOM      2  H   MOL            24.330  -0.629   1.483  1.00  0.00           H 
ATOM      3  H   MOL            24.677  -0.370   0.033  1.00  0.00           H 
ATOM      4  O   MOL            28.454  26.114   3.621  1.00  0.00           O 
ATOM      5  H   MOL            28.578  25.307   4.121  1.00  0.00           H 
ATOM      6  H   MOL            29.160  26.107   2.976  1.00  0.00           H 
ATOM      7  K   MOL          -54312228503.48764424509490.218-8260815321.219  1.00  0.00           K 
ATOM      8 Cl   MOL          59751111813.535-73398710417.3009088062024.881  1.00  0.00          Cl 
ATOM      9  K   MOL          -7045318285.63313304773408.7447403388878.031  1.00  0.00           K 
ATOM     10 Cl   MOL          7750843838.857-14637127284.649-8144771966.366  1.00  0.00          Cl 

The reason why I set the stiffness as 1e-20 is that I want to insert the K and CL ions in pairs and make sure these ions can be distributed freely in the system to simulate the condense system with water molecules and ions, at the meantime, maintain the electric neutrality.

However, it turns out that when the stiffness is lower than 1,e.g: 1e-5,1e-10 and 1e-15, the output of the ions' position becomes higher than the box length of the system.

At first, I think that's because of the wrap-up issue, so I wrap those coordinates up by the length of the box, but the ions aggregate on one side and even overlap with each other, which is shown in the attachment.

Could you please tell me: 1. Can I set the stiffness lower than 1 in RASPA?
                                     2. How can I wrap up properly in this situation?

Thanks a lot!

Kind regards
Haolong

2

Input files and parameters / Density histograms

« on: January 25, 2021, 12:59:16 PM »

Dear Dubbeldam,

I am trying to use the function: "ComputeDensityHistograms".

However, I couldn't find any output file from it. Could you tell me how could I use this function properly?

Besides, this function doesn't need to set commands such as "WriteDensityHistogramEvery" or "DensityHistogramSize", which is like the other histograms commands,  since I didn't find any in this section of manual, am I correct?

Thanks a lot!
Kind regards
Haolong

3

Output files / Re: The absorption of ions stuck at a certain number

« on: October 23, 2020, 03:28:43 PM »

Dear Dubbeldam,

If this isn't reasonable, do you think it's possible for us to modify the source code to achieve our goal to simulate ions in condense system?

Thanks a lot!

Kind regards,
Haolong

4

Output files / Re: The absorption of ions stuck at a certain number

« on: October 23, 2020, 03:22:06 PM »

Dear Dubbeldam,

Thanks a lot for your reply, I am trying to do the Adsorption of ions by introducing pseudo molecules which have extremely low bond connection between each other to insert the ions as pair into the system. In this way, the charge issue could be solved hopefully. Do you think this is reasonable?

Kind regards,
Haolong

5

General / Defination of absorbates in RASPA

« on: August 29, 2020, 10:33:48 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

6

Input files and parameters / Change input file when restart

« on: August 29, 2020, 04:13:50 AM »

Hello Dr. Dubbeldam,

Can I change my input file before restarting from crash?

Kind regards
Haolong

7

Output files / The absorption of ions stuck at a certain number

« on: August 29, 2020, 04:07:21 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

8

Output files / Exactly the same output from different simulations

« on: August 29, 2020, 03:58:45 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

9

Input files and parameters / Re: Question on how to describe ions' chemical potential

« on: February 12, 2020, 05:49:39 AM »

Dear David:

Thanks for your reply! I am looking forward to simulating the distribution of ions in aqueous solution, the electrolyte in another word, where the chemical potential of ions might be influenced by the concentration or mole fraction of ions in the reservoir instead of pressure. In this situation, can I find a way to link the activity coefficient of ions to the fugacity coefficient, which is used in RASPA to manipulate the chemical potential?

Kind regards,
Haolong

10

Input files and parameters / Question on how to describe ions' chemical potential

« on: January 09, 2020, 05:34:13 AM »

Hi, Professor David:

How can I describe ions' chemical potential instead of fugacity, which is mainly used to describe the property of gas, in the input file?

Kind regards,
Haolong