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convert tabs to spaces, remove extra spaces, fix comments

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danielque
2023-08-09 16:49:09 +02:00
parent 633058e1ab
commit d560b34214
47 changed files with 1263 additions and 1266 deletions
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68
src/pair.py
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@ -3,7 +3,7 @@
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# pair tool
@ -15,15 +15,15 @@ p = pair("lj/charmm/coul/charmm") create pair object for specific pair style
available styles: lj/cut, lj/cut/coul/cut, lj/charmm/coul/charmm
p.coeff(d) extract pairwise coeffs from data object
p.init(cut1,cut2,...) setup based on coeffs and cutoffs
p.coeff(d) extract pairwise coeffs from data object
p.init(cut1,cut2,...) setup based on coeffs and cutoffs
init args are specific to pair style:
lj/cut = cutlj
lj/cut/coul/cut = cutlj,cut_coul (cut_coul optional)
lj/charmm/coul/charmm = cutlj_inner,cutlj,cutcoul_inner,cut_coul
(last 2 optional)
e_vdwl,e_coul = p.single(rsq,itype,jtype,q1,q2,...) compute LJ/Coul energy
pairwise energy between 2 atoms at distance rsq with their attributes
@ -96,9 +96,9 @@ class pair:
epsilon = data.get("Pair Coeffs",2)
sigma = data.get("Pair Coeffs",3)
ntypes = len(epsilon)
self.lj3 = []
self.lj4 = []
self.lj4 = []
for i in xrange(ntypes):
self.lj3.append(ntypes * [0])
self.lj4.append(ntypes * [0])
@ -107,7 +107,7 @@ class pair:
sigma_ij = sqrt(sigma[i]*sigma[j])
self.lj3[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,12.0);
self.lj4[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,6.0);
# --------------------------------------------------------------------
# args = cutlj
@ -117,20 +117,20 @@ class pair:
# --------------------------------------------------------------------
# args = rsq,itype,jtype
def single_lj_cut(self,list):
rsq = list[0]
itype = list[1]
jtype = list[2]
r2inv = 1.0/rsq
if rsq < self.cut_ljsq:
r6inv = r2inv*r2inv*r2inv
eng_vdwl = r6inv*(self.lj3[itype][jtype]*r6inv-self.lj4[itype][jtype])
else: eng_vdwl = 0.0
return eng_vdwl
return eng_vdwl
# --------------------------------------------------------------------
# --------------------------------------------------------------------
@ -140,9 +140,9 @@ class pair:
epsilon = data.get("Pair Coeffs",2)
sigma = data.get("Pair Coeffs",3)
ntypes = len(epsilon)
self.lj3 = []
self.lj4 = []
self.lj4 = []
for i in xrange(ntypes):
self.lj3.append(ntypes * [0])
self.lj4.append(ntypes * [0])
@ -151,41 +151,41 @@ class pair:
sigma_ij = sqrt(sigma[i]*sigma[j])
self.lj3[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,12.0);
self.lj4[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,6.0);
# --------------------------------------------------------------------
# args = cutlj, cut_coul (cut_coul optional)
def init_lj_cut_coul_cut(self,list):
self.qqr2e = 332.0636 # convert energy to kcal/mol
self.qqr2e = 332.0636 # convert energy to kcal/mol
cut_lj = list[0]
self.cut_ljsq = cut_lj*cut_lj
if len(list) == 1: cut_coul = cut_lj
else: cut_coul = list[1]
self.cut_coulsq = cut_coul*cut_coul
# --------------------------------------------------------------------
# args = rsq,itype,jtype,q1,q2
def single_lj_cut_coul_cut(self,list):
rsq = list[0]
itype = list[1]
jtype = list[2]
q1 = list[3]
q2 = list[4]
r2inv = 1.0/rsq
if rsq < self.cut_coulsq: eng_coul = self.qqr2e * q1*q2*sqrt(r2inv)
else: eng_coul = 0.0
if rsq < self.cut_ljsq:
r6inv = r2inv*r2inv*r2inv
eng_vdwl = r6inv*(self.lj3[itype][jtype]*r6inv-self.lj4[itype][jtype])
else: eng_vdwl = 0.0
return eng_coul,eng_vdwl
return eng_coul,eng_vdwl
# --------------------------------------------------------------------
# --------------------------------------------------------------------
# lj/charmm/coul/charmm methods
@ -194,9 +194,9 @@ class pair:
epsilon = data.get("Pair Coeffs",2)
sigma = data.get("Pair Coeffs",3)
ntypes = len(epsilon)
self.lj3 = []
self.lj4 = []
self.lj4 = []
for i in xrange(ntypes):
self.lj3.append(ntypes * [0])
self.lj4.append(ntypes * [0])
@ -205,18 +205,18 @@ class pair:
sigma_ij = 0.5 * (sigma[i] + sigma[j])
self.lj3[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,12.0);
self.lj4[i][j] = 4.0 * epsilon_ij * pow(sigma_ij,6.0);
# --------------------------------------------------------------------
# args = cutlj_inner,cutlj,cutcoul_inner,cut_coul (last 2 optional)
def init_lj_charmm_coul_charmm(self,list):
self.qqr2e = 332.0636 # convert energy to kcal/mol
self.qqr2e = 332.0636 # convert energy to kcal/mol
cut_lj_inner = list[0]
cut_lj = list[1]
self.cut_lj_innersq = cut_lj_inner*cut_lj_inner
self.cut_ljsq = cut_lj*cut_lj
if len(list) == 2:
cut_coul_inner = cut_lj_inner
cut_coul = cut_lj
@ -235,16 +235,16 @@ class pair:
# --------------------------------------------------------------------
# args = rsq,itype,jtype,q1,q2
def single_lj_charmm_coul_charmm(self,list):
rsq = list[0]
itype = list[1]
jtype = list[2]
q1 = list[3]
q2 = list[4]
r2inv = 1.0/rsq
if rsq < self.cut_coulsq:
eng_coul = self.qqr2e * q1*q2*sqrt(r2inv)
if rsq > self.cut_coul_innersq:
@ -253,7 +253,7 @@ class pair:
self.denom_coul
eng_coul *= switch1
else: eng_coul = 0.0
if rsq < self.cut_ljsq:
r6inv = r2inv*r2inv*r2inv
eng_vdwl = r6inv*(self.lj3[itype][jtype]*r6inv-self.lj4[itype][jtype])
@ -263,5 +263,5 @@ class pair:
self.denom_lj
eng_vdwl *= switch1
else: eng_vdwl = 0.0
return eng_coul,eng_vdwl