Nuclephile Substitution CH3Cl - mMD3 - Revision history

Karsai: /* 2D free-energy profile */

2022-04-15T15:33:11Z

2D free-energy profile

← Older revision		Revision as of 15:33, 15 April 2022
Line 151:		Line 151:

	<div class="toccolours mw-customtoggle-script">'''Click to show/calcprofile2D.py'''</div>		<div class="toccolours mw-customtoggle-script">'''Click to show/calcprofile2D.py'''</div>
	<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:~~calcprofile2D}}~~</div>		<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script"><pre>
			#!/usr/bin/python

			from math import *

			def gauss_pot(x,y,x0,y0,h,w):
			en=he(-((x-x0)2+(y-y0)2)/2.0/w*2)
			return en

			ff=raw_input('File name?\n')

			f=open(ff,'r')
			data=[]
			h=[]
			w=[]
			for line in f.readlines():
			line=line.split()
			x=[]
			if (len(line)>2):
			for i in range(len(line)-2):
			x.append(float(line[i]))
			data.append(x)
			h.append(float(line[-2]))
			w.append(float(line[-1]))
			f.close()

			name=raw_input('x1_min x1_max M:\n')
			name=name.split()
			a0=float(name[0])
			a1=float(name[1])
			num1=int(name[2])

			name=raw_input('x2_min x2_max N:\n')
			name=name.split()
			b0=float(name[0])
			b1=float(name[1])
			num2=int(name[2])

			ff=ff+'.xyz'

			f=open(ff,'w')

			stepA=(a1-a0)/num1
			stepB=(b1-b0)/num2
			x=a0
			for i in range(1,num1):
			x=x+stepA
			y=b0
			for k in range(1,num2):
			en=0.0
			y=y+stepB
			x_=(x+y)/2.
			y_=(x-y)/2.
			for j in range(len(data)):
			x0=data[j][0]
			y0=data[j][1]
			en_=gauss_pot(x,y,x0,y0,h[j],w[j])
			en+=en_
			f.write(`x`+'\t'+`y`+'\t'+`-en`+'\n')
			f.write('\n')

			f.close()
			</pre>
			</div>

Karsai: /* Download */

2019-11-14T09:45:44Z

Download

← Older revision		Revision as of 09:45, 14 November 2019
Line 195:		Line 195:
	== Download ==		== Download ==

	[~~http~~:~~//www.vasp.at/vasp-workshop/examples/~~CH3Cl_mMD3.tgz CH3Cl_mMD3.tgz]		[[Media:CH3Cl_mMD3.tgz\| CH3Cl_mMD3.tgz]]

	{{Template:Molecular dynamics - Tutorial}}		{{Template:Molecular dynamics - Tutorial}}

	[[Category:Examples]]		[[Category:Examples]]

Karsai at 08:50, 3 October 2019

2019-10-03T08:50:13Z

← Older revision		Revision as of 08:50, 3 October 2019
Line 75:		Line 75:

	=== Running the calculation ===		=== Running the calculation ===
	The mass for hydrogen in this example is set 3.016 a.u. corresponding to the tritium isotope. This way larger timesteps can be chosen for the MD.		The mass for hydrogen in this example is set 3.016 a.u. corresponding to the tritium isotope. This way larger timesteps can be chosen for the MD (note that the free energy is independent of the masses of atoms).

	The bias potential is specified in the {{TAG\|PENALTYPOT}} file.		The bias potential is specified in the {{TAG\|PENALTYPOT}} file.

Karsai: /* 2D free-energy profile */

2019-10-01T11:46:48Z

2D free-energy profile

← Older revision		Revision as of 11:46, 1 October 2019
Line 149:		Line 149:
	=== 2D free-energy profile ===		=== 2D free-energy profile ===
	To calculate the free-energy profile in 2D we use the script ''calcprofile2D.py'' attached with this example:		To calculate the free-energy profile in 2D we use the script ''calcprofile2D.py'' attached with this example:

	<div class="toccolours mw-customtoggle-script">'''Click to show/calcprofile2D.py'''</div>		<div class="toccolours mw-customtoggle-script">'''Click to show/calcprofile2D.py'''</div>
	<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:calcprofile2D}}</div>		<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:calcprofile2D}}</div>


	This script projects a set of two-dimmensional Gaussians defined in the input file (such as {{TAG\|PENALTYPOT}} or {{TAG\|HILLSPOT}}) onto a regular 2D grid of <math> M \times N </math> points defined by the user. The user is asked to provide the following data: (a) the name of the input file, (b) the initial (''x1_min'') and final (''x1_max'') grid points, and the number of grid points (''M'') for the axis corresponding to the first collective variable, and (c) the initial (''x2_min'') and final (''x2_max'') grid points and the number of grid points (''N'') for the axis corresponding to the second collective variable. The result is written to a file with extension ''.xyz'' and it can be visualized by regular plotting tools like Gnuplot.		This script projects a set of two-dimmensional Gaussians defined in the input file (such as {{TAG\|PENALTYPOT}} or {{TAG\|HILLSPOT}}) onto a regular 2D grid of <math> M \times N </math> points defined by the user. The user is asked to provide the following data: (a) the name of the input file, (b) the initial (''x1_min'') and final (''x1_max'') grid points, and the number of grid points (''M'') for the axis corresponding to the first collective variable, and (c) the initial (''x2_min'') and final (''x2_max'') grid points and the number of grid points (''N'') for the axis corresponding to the second collective variable. The result is written to a file with extension ''.xyz'' and it can be visualized by regular plotting tools like Gnuplot.

Karsai: /* 2D free-energy profile */

2019-10-01T11:46:38Z

2D free-energy profile

@@ Line 148: / Line 148: @@
 === 2D free-energy profile ===
+To calculate the free-energy profile in 2D we use the script ''calcprofile2D.py'' attached with this example:
 <div class="toccolours mw-customtoggle-script">'''Click to show/calcprofile2D.py'''</div>
 <div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:calcprofile2D}}</div>
 This script projects a set of two-dimmensional Gaussians defined in the input file (such as {{TAG|PENALTYPOT}} or {{TAG|HILLSPOT}}) onto a regular 2D grid of <math> M \times N </math> points defined by the user. The user is asked to provide the following data: (a) the name of the input file, (b) the initial (''x1_min'') and final (''x1_max'') grid points, and the number of grid points (''M'') for the axis corresponding to the first collective variable, and (c) the initial (''x2_min'') and final (''x2_max'') grid points and the number of grid points (''N'') for the axis corresponding to the second collective variable. The result is written to a file with extension ''.xyz'' and it can be visualized by regular plotting tools like Gnuplot.

Karsai: /* 2D free-energy profile */

2019-10-01T11:43:22Z

2D free-energy profile

← Older revision		Revision as of 11:43, 1 October 2019
Line 150:		Line 150:

	<div class="toccolours mw-customtoggle-script">'''Click to show/calcprofile2D.py'''</div>		<div class="toccolours mw-customtoggle-script">'''Click to show/calcprofile2D.py'''</div>
	<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{[[calcprofile2D]]}}</div>		<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{:calcprofile2D}}</div>

Karsai: /* 2D free-energy profile */

2019-10-01T11:42:35Z

2D free-energy profile

← Older revision		Revision as of 11:42, 1 October 2019
Line 148:		Line 148:

	=== 2D free-energy profile ===		=== 2D free-energy profile ===

			<div class="toccolours mw-customtoggle-script">'''Click to show/calcprofile2D.py'''</div>
			<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-script">{{[[calcprofile2D]]}}</div>



	To calculate the free-energy profile in 2D we use the script ''calcprofile2D.py'' attached with this example:		To calculate the free-energy profile in 2D we use the script ''calcprofile2D.py'' attached with this example:

Karsai at 10:26, 1 October 2019

2019-10-01T10:26:07Z

← Older revision		Revision as of 10:26, 1 October 2019
Line 252:		Line 252:

	== Download ==		== Download ==

			[http://www.vasp.at/vasp-workshop/examples/CH3Cl_mMD3.tgz CH3Cl_mMD3.tgz]

	{{Template:Molecular dynamics - Tutorial}}		{{Template:Molecular dynamics - Tutorial}}

	[[Category:Examples]]		[[Category:Examples]]

Karsai: /* 2D free-energy profile */

2019-10-01T10:15:54Z

2D free-energy profile

← Older revision		Revision as of 10:15, 1 October 2019
Line 246:		Line 246:
	Please execute this script with the following command:		Please execute this script with the following command:
	gnuplot plot_2D_profile.gp		gnuplot plot_2D_profile.gp

			The resulting free energy profile should look like the following:

			[[File:PENALTYPOT mMD3 2D profile.jpg\|500px]]

	== Download ==		== Download ==

Karsai: /* 2D free-energy profile */

2019-10-01T09:48:53Z

2D free-energy profile

← Older revision		Revision as of 09:48, 1 October 2019
Line 240:		Line 240:

	set cntrparam levels incremental 0., 0.02, 0.5		set cntrparam levels incremental 0., 0.02, 0.5

	set out "PENALTYPOT.jpg"		set out "PENALTYPOT.jpg"
	splot "PENALTYPOT.xyz" with lines title 'bias potential (eV)'		splot "PENALTYPOT.xyz" with lines title 'bias potential (eV)'