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Committer: ckloss <ckloss@fluid38.(none)>
On branch master Initial commit for lpp, version 2011-10-11
This commit is contained in:
ckloss
267
src/pair.py
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267
src/pair.py
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# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
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# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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#
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# Copyright (2005) Sandia Corporation. Under the terms of Contract
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# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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# certain rights in this software. This software is distributed under
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# the GNU General Public License.
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# pair tool
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oneline = "Compute LAMMPS pairwise energies"
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docstr = """
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p = pair("lj/charmm/coul/charmm") create pair object for specific pair style
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available styles: lj/cut, lj/cut/coul/cut, lj/charmm/coul/charmm
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p.coeff(d) extract pairwise coeffs from data object
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p.init(cut1,cut2,...) setup based on coeffs and cutoffs
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init args are specific to pair style:
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lj/cut = cutlj
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lj/cut/coul/cut = cutlj,cut_coul (cut_coul optional)
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lj/charmm/coul/charmm = cutlj_inner,cutlj,cutcoul_inner,cut_coul
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(last 2 optional)
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e_vdwl,e_coul = p.single(rsq,itype,jtype,q1,q2,...) compute LJ/Coul energy
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pairwise energy between 2 atoms at distance rsq with their attributes
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args are specific to pair style:
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lj/cut = rsq,itype,jtype
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lj/cut/coul/cut = rsq,itype,jtype,q1,q2
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lj/charmm/coul/charmm = rsq,itype,jtype,q1,q2
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"""
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# History
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# 8/05, Steve Plimpton and Paul Crozier (SNL): original version
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# 9/05, Paul Crozier (SNL): added lj/cut and lj/cut/coul/cut
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# ToDo list
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# Variables
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# Imports and external programs
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from math import sqrt
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# Class definition
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class pair:
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# --------------------------------------------------------------------
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def __init__(self,style):
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# map generic methods to style-specific methods
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if style == "lj/cut":
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self.coeff_func = self.coeff_lj_cut
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self.init_func = self.init_lj_cut
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self.single_func = self.single_lj_cut
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elif style == "lj/cut/coul/cut":
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self.coeff_func = self.coeff_lj_cut_coul_cut
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self.init_func = self.init_lj_cut_coul_cut
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self.single_func = self.single_lj_cut_coul_cut
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elif style == "lj/charmm/coul/charmm":
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self.coeff_func = self.coeff_lj_charmm_coul_charmm
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self.init_func = self.init_lj_charmm_coul_charmm
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self.single_func = self.single_lj_charmm_coul_charmm
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else:
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raise StandardError, "this pair style not yet supported"
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# --------------------------------------------------------------------
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# generic coeff method
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def coeff(self,data):
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self.coeff_func(data)
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# --------------------------------------------------------------------
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# generic init method, as many args as needed
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def init(self,*list):
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self.init_func(list)
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# --------------------------------------------------------------------
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# generic single method, as many args as needed
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def single(self,*list):
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return self.single_func(list)
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# --------------------------------------------------------------------
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# --------------------------------------------------------------------
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# lj/cut methods
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def coeff_lj_cut(self,data):
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epsilon = data.get("Pair Coeffs",2)
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sigma = data.get("Pair Coeffs",3)
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ntypes = len(epsilon)
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self.lj3 = []
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self.lj4 = []
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for i in xrange(ntypes):
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self.lj3.append(ntypes * [0])
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self.lj4.append(ntypes * [0])
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for j in xrange(ntypes):
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epsilon_ij = sqrt(epsilon[i]*epsilon[j])
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sigma_ij = sqrt(sigma[i]*sigma[j])
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self.lj3[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,12.0);
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self.lj4[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,6.0);
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# --------------------------------------------------------------------
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# args = cutlj
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def init_lj_cut(self,list):
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cut_lj = list[0]
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self.cut_ljsq = cut_lj*cut_lj
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# --------------------------------------------------------------------
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# args = rsq,itype,jtype
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def single_lj_cut(self,list):
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rsq = list[0]
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itype = list[1]
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jtype = list[2]
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r2inv = 1.0/rsq
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if rsq < self.cut_ljsq:
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r6inv = r2inv*r2inv*r2inv
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eng_vdwl = r6inv*(self.lj3[itype][jtype]*r6inv-self.lj4[itype][jtype])
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else: eng_vdwl = 0.0
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return eng_vdwl
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# --------------------------------------------------------------------
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# --------------------------------------------------------------------
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# lj/cut/coul/cut methods
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def coeff_lj_cut_coul_cut(self,data):
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epsilon = data.get("Pair Coeffs",2)
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sigma = data.get("Pair Coeffs",3)
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ntypes = len(epsilon)
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self.lj3 = []
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self.lj4 = []
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for i in xrange(ntypes):
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self.lj3.append(ntypes * [0])
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self.lj4.append(ntypes * [0])
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for j in xrange(ntypes):
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epsilon_ij = sqrt(epsilon[i]*epsilon[j])
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sigma_ij = sqrt(sigma[i]*sigma[j])
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self.lj3[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,12.0);
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self.lj4[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,6.0);
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# --------------------------------------------------------------------
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# args = cutlj, cut_coul (cut_coul optional)
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def init_lj_cut_coul_cut(self,list):
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self.qqr2e = 332.0636 # convert energy to kcal/mol
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cut_lj = list[0]
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self.cut_ljsq = cut_lj*cut_lj
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if len(list) == 1: cut_coul = cut_lj
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else: cut_coul = list[1]
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self.cut_coulsq = cut_coul*cut_coul
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# --------------------------------------------------------------------
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# args = rsq,itype,jtype,q1,q2
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def single_lj_cut_coul_cut(self,list):
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rsq = list[0]
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itype = list[1]
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jtype = list[2]
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q1 = list[3]
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q2 = list[4]
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r2inv = 1.0/rsq
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if rsq < self.cut_coulsq: eng_coul = self.qqr2e * q1*q2*sqrt(r2inv)
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else: eng_coul = 0.0
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if rsq < self.cut_ljsq:
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r6inv = r2inv*r2inv*r2inv
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eng_vdwl = r6inv*(self.lj3[itype][jtype]*r6inv-self.lj4[itype][jtype])
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else: eng_vdwl = 0.0
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return eng_coul,eng_vdwl
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# --------------------------------------------------------------------
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# --------------------------------------------------------------------
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# lj/charmm/coul/charmm methods
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def coeff_lj_charmm_coul_charmm(self,data):
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epsilon = data.get("Pair Coeffs",2)
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sigma = data.get("Pair Coeffs",3)
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ntypes = len(epsilon)
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self.lj3 = []
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self.lj4 = []
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for i in xrange(ntypes):
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self.lj3.append(ntypes * [0])
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self.lj4.append(ntypes * [0])
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for j in xrange(ntypes):
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epsilon_ij = sqrt(epsilon[i]*epsilon[j])
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sigma_ij = 0.5 * (sigma[i] + sigma[j])
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self.lj3[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,12.0);
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self.lj4[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,6.0);
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# --------------------------------------------------------------------
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# args = cutlj_inner,cutlj,cutcoul_inner,cut_coul (last 2 optional)
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def init_lj_charmm_coul_charmm(self,list):
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self.qqr2e = 332.0636 # convert energy to kcal/mol
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cut_lj_inner = list[0]
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cut_lj = list[1]
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self.cut_lj_innersq = cut_lj_inner*cut_lj_inner
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self.cut_ljsq = cut_lj*cut_lj
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if len(list) == 2:
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cut_coul_inner = cut_lj_inner
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cut_coul = cut_lj
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else:
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cut_coul_inner = list[2]
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cut_coul = list[3]
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self.cut_coul_innersq = cut_coul_inner*cut_coul_inner
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self.cut_coulsq = cut_coul*cut_coul
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self.denom_lj = (self.cut_ljsq-self.cut_lj_innersq) * \
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(self.cut_ljsq-self.cut_lj_innersq) * \
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(self.cut_ljsq-self.cut_lj_innersq);
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self.denom_coul = (self.cut_coulsq-self.cut_coul_innersq) * \
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(self.cut_coulsq-self.cut_coul_innersq) * \
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(self.cut_coulsq-self.cut_coul_innersq);
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# --------------------------------------------------------------------
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# args = rsq,itype,jtype,q1,q2
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def single_lj_charmm_coul_charmm(self,list):
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rsq = list[0]
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itype = list[1]
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jtype = list[2]
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q1 = list[3]
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q2 = list[4]
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r2inv = 1.0/rsq
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if rsq < self.cut_coulsq:
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eng_coul = self.qqr2e * q1*q2*sqrt(r2inv)
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if rsq > self.cut_coul_innersq:
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switch1 = (self.cut_coulsq-rsq) * (self.cut_coulsq-rsq) * \
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(self.cut_coulsq + 2.0*rsq - 3.0*self.cut_coul_innersq) / \
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self.denom_coul
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eng_coul *= switch1
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else: eng_coul = 0.0
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if rsq < self.cut_ljsq:
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r6inv = r2inv*r2inv*r2inv
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eng_vdwl = r6inv*(self.lj3[itype][jtype]*r6inv-self.lj4[itype][jtype])
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if rsq > self.cut_lj_innersq:
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switch1 = (self.cut_ljsq-rsq) * (self.cut_ljsq-rsq) * \
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(self.cut_ljsq + 2.0*rsq - 3.0*self.cut_lj_innersq) / \
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self.denom_lj
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eng_vdwl *= switch1
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else: eng_vdwl = 0.0
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return eng_coul,eng_vdwl
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