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Viewing changes to tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py

  • Committer: Package Import Robot
  • Author(s): Anton Gladky
  • Date: 2015-04-29 23:44:49 UTC
  • mfrom: (5.1.3 experimental)
  • Revision ID: package-import@ubuntu.com-20150429234449-mbhy9utku6hp6oq8
Tags: 0~20150313.gitfa668e1-1
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tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
 
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#!/usr/bin/env python
 
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# Calculate a table of pairwise energies and forces between "INT" atoms
 
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# in the lipid membrane model described in 
 
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#   Brannigan et al, Phys Rev E, 72, 011915 (2005)
 
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# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
 
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# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity)
 
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def U(r, eps, sigma):
 
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    return eps*   (0.4*pow((sigma/r),12)  -  3.0*sigma*sigma/(r*r))
 
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def F(r, eps, sigma):
 
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    return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
 
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epsilon = 2.75/4.184 # kCal/mole
 
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sigma   = 7.5
 
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Rmin    = 0.02
 
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Rmax    = 22.6
 
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rcut    = 22.5
 
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N       = 1130
 
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for i in range(0,N):
 
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    r = Rmin + i*(Rmax-Rmin)/(N-1)
 
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    U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
 
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    F_r = F(r, epsilon, sigma)
 
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    if r > rcut:
 
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        U_r = 0.0
 
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        F_r = 0.0
 
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    print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
 
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