move UB bonds to angle amoeba
This commit is contained in:
Steve Plimpton
@ -372,6 +372,7 @@ skeywords = [["Masses","atom types"],
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["PiTorsion Coeffs","pitorsion types"],
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["BondBond Coeffs","angle types"],
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["BondAngle Coeffs","angle types"],
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["UreyBradley Coeffs","angle types"],
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["MiddleBondTorsion Coeffs","dihedral types"],
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["EndBondTorsion Coeffs","dihedral types"],
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["AngleTorsion Coeffs","dihedral types"],
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@ -206,6 +206,7 @@ class PRMfile:
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def angles(self):
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r2d = 180.0 / math.pi
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ubflag = 0
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params = []
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iline = self.find_section("Angle Bending Parameters")
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if iline < 0: return params
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@ -236,17 +237,17 @@ class PRMfile:
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lmp5 = self.angle_pentic * value1 * r2d*r2d*r2d
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lmp6 = self.angle_sextic * value1 * r2d*r2d*r2d*r2d
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option1 = (pflag,lmp1,lmp2,lmp3,lmp4,lmp5,lmp6)
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option1 = (pflag,ubflag,lmp1,lmp2,lmp3,lmp4,lmp5,lmp6)
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if len(words) >= 7:
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value3 = float(words[6])
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lmp1 = value3
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option2 = (pflag,lmp1,lmp2,lmp3,lmp4,lmp5,lmp6)
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option2 = (pflag,ubflag,lmp1,lmp2,lmp3,lmp4,lmp5,lmp6)
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if len(words) == 8:
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value4 = float(words[7])
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lmp1 = value4
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option3 = (pflag,lmp1,lmp2,lmp3,lmp4,lmp5,lmp6)
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option3 = (pflag,ubflag,lmp1,lmp2,lmp3,lmp4,lmp5,lmp6)
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if not option2 and not option3:
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params.append((class1,class2,class3,[option1]))
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@ -272,7 +273,7 @@ class PRMfile:
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bdict = {}
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for m,bparams in enumerate(self.bondparams):
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bdict[(bparams[0],bparams[1])] = bparams[2]
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while iline < self.nlines:
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words = self.lines[iline].split()
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if len(words):
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@ -372,7 +373,7 @@ class PRMfile:
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iline += 1
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return params
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# convert PRMfile params to LAMMPS bond_style class2 bond params
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# convert PRMfile params to LAMMPS angle_style amoeba UB params
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# coeffs for K2,K3 = 0.0 since Urey-Bradley is simple harmonic
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def ureybonds(self):
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@ -394,7 +395,7 @@ class PRMfile:
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lmp1 = value1
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lmp2 = value2
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params.append((class1,class2,class3,lmp1,lmp2,0.0,0.0))
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params.append((class1,class2,class3,lmp1,lmp2))
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iline += 1
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return params
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@ -715,6 +716,10 @@ for atom1 in id:
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pitorsionlist.append((atom3,atom4,atom1,atom2,atom5,atom6))
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# DEBUG - if uncommented, no PiTorsions appear in data file
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pitorsionlist = []
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# ----------------------------------------
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# create lists of bond/angle/dihedral/improper types
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# ----------------------------------------
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@ -754,44 +759,6 @@ for atom1,atom2 in blist:
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bparams.append((v1,v2,v3,v4))
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flags[m] = len(bparams)
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btype.append(flags[m])
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# extend btype and bparams with Urey-Bradley H-H bond info
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# loop over ublist of UB bonds
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# convert prm.ureyparams to a dictionary for efficient searching
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# key = (class1,class2,class3)
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# value = (M,params) where M is index into prm.ureyparams
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# also add the c1,c3 H-H bond to blist
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id = xyz.id
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type = xyz.type
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classes = prm.classes
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ubdict = {}
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for m,params in enumerate(prm.ureyparams):
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ubdict[(params[0],params[1],params[2])] = (m,params)
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flags = len(prm.ureyparams)*[0]
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for atom1,atom2,atom3 in ublist:
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type1 = type[atom1-1]
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type2 = type[atom2-1]
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type3 = type[atom3-1]
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c1 = classes[type1-1]
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c2 = classes[type2-1]
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c3 = classes[type3-1]
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if (c1,c2,c3) in ubdict:
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m,params = ubdict[(c1,c2,c3)]
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blist.append((atom1,atom3))
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elif (c3,c2,c1) in ubdict:
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m,params = ubdict[(c3,c2,c1)]
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blist.append((atom3,atom1))
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if not flags[m]:
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v1,v2,v3,v4 = params[3:]
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bparams.append((v1,v2,v3,v4))
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flags[m] = len(bparams)
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btype.append(flags[m])
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# generate atype = LAMMPS type of each angle
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# generate aparams = LAMMPS params for each angle type
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@ -905,19 +872,19 @@ for i,one in enumerate(alist):
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error("Angle not found: %d %d %d: %d %d %d" % (atom1,atom2,atom3,c1,c2,c3))
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if not flags[m]:
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pflag,v1,v2,v3,v4,v5,v6 = params[3][which-1]
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aparams.append((pflag,v1,v2,v3,v4,v5,v6))
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pflag,ubflag,v1,v2,v3,v4,v5,v6 = params[3][which-1]
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aparams.append((pflag,ubflag,v1,v2,v3,v4,v5,v6))
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flags[m] = len(aparams)
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atype.append(flags[m])
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# augment the aparams with bond-angle cross terms from bondangleparams
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# generate baparams = LAMMPS bond-angle params for each angle type
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# sbdict = dictionary for angle tuples in bongangleparams
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# badict = dictionary for angle tuples in bongangleparams
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sbdict = {}
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badict = {}
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for v1,v2,v3,v4,v5,v6,v7 in prm.bondangleparams:
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if (v1,v2,v3) in sbdict: continue
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sbdict[(v1,v2,v3)] = (v4,v5,v6,v7)
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if (v1,v2,v3) in badict: continue
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badict[(v1,v2,v3)] = (v4,v5,v6,v7)
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baparams = []
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@ -931,16 +898,54 @@ for itype in range(len(aparams)):
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c2 = classes[type2-1]
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c3 = classes[type3-1]
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if (c1,c2,c3) in sbdict:
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n1,n2,r1,r2 = sbdict[(c1,c2,c3)]
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elif (c3,c2,c1) in sbdict:
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n1,n2,r1,r2 = sbdict[(c3,c2,c1)]
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if (c1,c2,c3) in badict:
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n1,n2,r1,r2 = badict[(c1,c2,c3)]
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elif (c3,c2,c1) in badict:
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n1,n2,r1,r2 = badict[(c3,c2,c1)]
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else:
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print "Bond-stretch angle triplet not found: %d %d %d" % (c1,c2,c3)
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n1,n2,r1,r2 = 4*[0.0]
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baparams.append((n1,n2,r1,r2))
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# augment the aparams with Urey_Bradley terms from ureyparams
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# generate ubparams = LAMMPS UB params for 1-3 bond in each angle type
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# ubdict = dictionary for angle tuples in ureyparams
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ubdict = {}
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for v1,v2,v3,v4,v5 in prm.ureyparams:
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if (v1,v2,v3) in ubdict: continue
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ubdict[(v1,v2,v3)] = (v4,v5)
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ubparams = []
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for itype in range(len(aparams)):
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iangle = atype.index(itype+1)
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atom1,atom2,atom3 = alist[iangle]
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type1 = type[atom1-1]
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type2 = type[atom2-1]
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type3 = type[atom3-1]
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c1 = classes[type1-1]
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c2 = classes[type2-1]
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c3 = classes[type3-1]
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# if UB settings exist for this angle type, set ubflag in aparams to 1
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if (c1,c2,c3) in ubdict:
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r1,r2 = ubdict[(c1,c2,c3)]
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pflag,ubflag,v1,v2,v3,v4,v5,v6 = aparams[itype]
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ubflag = 1
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aparams[itype] = (pflag,ubflag,v1,v2,v3,v4,v5,v6)
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elif (c3,c2,c1) in ubdict:
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r1,r2 = ubdict[(c3,c2,c1)]
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pflag,ubflag,v1,v2,v3,v4,v5,v6 = aparams[itype]
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ubflag = 1
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aparams[itype] = (pflag,ubflag,v1,v2,v3,v4,v5,v6)
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else:
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r1,r2 = 2*[0.0]
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ubparams.append((r1,r2))
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# generate dtype = LAMMPS type of each dihedral
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# generate dparams = LAMMPS params for each dihedral type
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# flags[i] = which LAMMPS dihedral type (1-N) the Tinker FF file dihedral I is
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@ -1075,7 +1080,7 @@ for tmp1,tmp2,atom1,atom2,tmp3,tmp4 in pitorsionlist:
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print "PRM pitor param",len(prm.pitorsionparams)
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print "PiTor list",len(pitorsionlist)
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print "Flags",flags
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#print "Flags",flags
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# ----------------------------------------
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# assign each atom to a Tinker group
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@ -1202,6 +1207,13 @@ if nangles:
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lines.append(line+'\n')
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d.sections["BondAngle Coeffs"] = lines
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lines = []
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for i,one in enumerate(ubparams):
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strone = [str(single) for single in one]
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line = "%d %s" % (i+1,' '.join(strone))
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lines.append(line+'\n')
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d.sections["UreyBradley Coeffs"] = lines
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lines = []
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for i,one in enumerate(alist):
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line = "%d %d %d %d %d" % (i+1,atype[i],one[0],one[1],one[2])
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