add stretch-bend cross term
This commit is contained in:
Steve Plimpton
@ -36,7 +36,7 @@ def error(txt=""):
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print " -nopbc"
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print " -pbc xhi yhi zhi"
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else: print "ERROR:",txt
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sys.exit()
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#sys.exit()
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# read and store values from a Tinker xyz file
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@ -251,13 +251,13 @@ class PRMfile:
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def bondangles(self):
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params = []
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iline = self.find_section("Stretch Bend Parameters")
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iline = self.find_section("Stretch-Bend Parameters")
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if iline < 0: return params
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iline += 3
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bdict = {}
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for m,params in enumerate(self.bondparams):
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bdict[(params[0],params[1])] = params[2]
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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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@ -271,14 +271,27 @@ class PRMfile:
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value2 = float(words[5])
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lmp1 = value1
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lmp2 = value2
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lmp3 = lmp4 = 0.0
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if (class2,class1) in bdict: lmp3 = bdict[(class2,class1)]
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if (class1,class2) in bdict: lmp3 = bdict[(class1,class2)]
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if (class2,class3) in bdict: lmp4 = bdict[(class2,class3)]
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if (class3,class2) in bdict: lmp4 = bdict[(class3,class2)]
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if lmp3 == 0.0 or lmp4 == 0.0:
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print "Bond in BondAngle term not found",class1,class2,class3
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sys.exit()
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if (class1,class2) in bdict:
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lmp3 = bdict[(class1,class2)]
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elif (class2,class1) in bdict:
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lmp3 = bdict[(class2,class1)]
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else:
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error("1st bond in BondAngle term not found: %d %d %d" % \
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(class1,class2,class3))
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# NOTE: just for debugging
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lmp3 = 0.0
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if (class2,class3) in bdict:
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lmp4 = bdict[(class2,class3)]
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elif (class3,class2) in bdict:
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lmp4 = bdict[(class3,class2)]
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else:
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error("2nd bond in BondAngle term not found: %d %d %d" % \
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(class1,class2,class3))
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# NOTE: just for debugging
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lmp4 = 0.0
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params.append((class1,class2,class3,lmp1,lmp2,lmp3,lmp4))
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iline += 1
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return params
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@ -301,12 +314,11 @@ class PRMfile:
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class4 = int(words[4])
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if len(words) <= 5:
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print "Torsion has no params",class1,class2,class3,class4
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sys.exit()
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error("Torsion has no params: %d %d %d %d" % \
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(class1,class2,class3,class4))
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if (len(words)-5) % 3:
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print "Torsion does not have triplets of params", \
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class1,class2,class3,class4
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sys.exit()
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error("Torsion does not have triplets of params: %d %d %d %d" % \
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(class1,class2,class3,class4))
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mfourier = (len(words)-5) / 3
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oneparams = [class1,class2,class3,class4,mfourier]
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@ -603,9 +615,7 @@ for atom1,atom2 in blist:
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if (c1,c2) in bdict: m,params = bdict[(c1,c2)]
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elif (c2,c1) in bdict: m,params = bdict[(c2,c1)]
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else:
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print "Bond not found",atom1,atom2,c1,c2
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sys.exit()
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else: error("Bond not found: %d %d: %d %d" % (atom1,atom2,c1,c2))
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if not flags[m]:
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v1,v2,v3,v4 = params[2:]
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@ -615,7 +625,6 @@ for atom1,atom2 in blist:
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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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# generate baparams = LAMMPS bond-angle params for each angle type
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# flags[i] = which LAMMPS angle type (1-N) the Tinker FF file angle I is
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# 0 = none
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# Tinker FF file angle entries can have 1, 2, or 3 options
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@ -636,12 +645,11 @@ for m,params in enumerate(prm.angleparams):
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noptions += n
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flags = noptions*[0]
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#baflags = len(baprm)*[0]
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atype = []
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aparams = []
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baparams = []
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for atom1,atom2,atom3 in alist:
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for i,one in enumerate(alist):
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atom1,atom2,atom3 = one
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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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@ -651,8 +659,19 @@ for atom1,atom2,atom3 in alist:
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if (c1,c2,c3) in adict or (c3,c2,c1) in adict:
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if (c1,c2,c3) in adict: m,params = adict[(c1,c2,c3)]
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if (c3,c2,c1) in adict: m,params = adict[(c3,c2,c1)]
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# IMPORTANT subtlety
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# flip order of 3 atoms in alist if the angle
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# matches Angle Bending section of PRM file in reverse order
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# necessary b/c BondAngle coeffs will be generated with r1,r2 params
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# from Bond Stretching section of PRM file
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# since in general r1 != r2, the LAMMPS AngleAmoeba class requires
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# the 3 atoms in the angle be in the order that matches r1 and r2
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if (c3,c2,c1) in adict:
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m,params = adict[(c3,c2,c1)]
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alist[i] = (atom3,atom2,atom1)
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# params is a sequence of 1 or 2 or 3 options
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# which = which of 1,2,3 options this atom triplet matches
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# for which = 2 or 3, increment m to index correct position in flags
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@ -679,7 +698,7 @@ for atom1,atom2,atom3 in alist:
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print " angle atom classes:",c1,c2,c3
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print " Tinker FF file param options:",len(params[3])
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print " Nbonds and hydrogen count:",nbonds,hcount
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#sys.exit() // NOTE: allow this for now
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#sys.exit() NOTE: allow this for now
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if hcount == 0: which = 1
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elif hcount == 1:
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@ -702,7 +721,7 @@ for atom1,atom2,atom3 in alist:
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print " angle atom classes:",c1,c2,c3
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print " Tinker FF file param options:",len(params[3])
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print " Nbonds and hydrogen count:",nbonds,hcount
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#sys.exit() // NOTE: allow this for now
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#sys.exit() NOTE: allow this for now
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if hcount == 0: which = 1
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elif hcount == 1:
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@ -713,8 +732,7 @@ for atom1,atom2,atom3 in alist:
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m += 2
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else:
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print "Angle not found",atom1,atom2,atom3,c1,c2,c3
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sys.exit()
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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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@ -722,24 +740,36 @@ for atom1,atom2,atom3 in alist:
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flags[m] = len(aparams)
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atype.append(flags[m])
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# NOTE: baparams may need to be flipped if match is 3,2,1 instead of 1,2,3
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# NOTE: mismatch between angle and bondangle params may not be handled right
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# should be a new LAMMPS type if either angle or bondangle params do not match?
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#for m,params in enumerate(baprm):
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# c1,c2,c3,v1,v2,v3,v4 = params
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# if (c1 == class1 and c2 == class2 and c3 == class3) or \
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# (c1 == class3 and c2 == class2 and c3 == class1):
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# found += 1
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# if baflags[m]:
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# continue
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# #atype.append(baflags[m])
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# else:
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# baparams.append((v1,v2,v3,v4))
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# baflags[m] = len(baparams)
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# #atype.append(baflags[m])
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# break
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# if found != 1: print "Not found",atom1,atom2,atom3,class1,class2,class3
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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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sbdict = {}
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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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baparams = []
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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 (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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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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# generate dtype = LAMMPS type of each dihedral
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# generate dparams = LAMMPS params for each dihedral type
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@ -774,8 +804,8 @@ for atom1,atom2,atom3,atom4 in dlist:
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if (c1,c2,c3,c4) in ddict: m,params = ddict[(c1,c2,c3,c4)]
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elif (c4,c3,c2,c1) in ddict: m,params = ddict[(c4,c3,c2,c1)]
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else:
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print "Dihedral not found",atom1,atom2,atom3,atom4,c1,c2,c3,c4
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sys.exit()
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error("Dihedral not found: %d %d %d %d: %d %d %d %d" % \
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(atom1,atom2,atom3,atom4,c1,c2,c3,c4))
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if not flags[m]:
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oneparams = params[4:]
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@ -948,17 +978,12 @@ if nangles:
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lines.append(line+'\n')
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d.sections["Angle Coeffs"] = lines
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#lines = []
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#for i,one in enumerate(aparams):
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# line = "%d %g %g %g" % (i+1,0.0,0.0,0.0)
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# lines.append(line+'\n')
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#d.sections["BondBond Coeffs"] = lines
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#lines = []
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#for i,one in enumerate(aparams):
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# line = "%d %g %g %g %g" % (i+1,0.0,0.0,0.0,0.0)
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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(baparams):
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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["BondAngle Coeffs"] = lines
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lines = []
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for i,one in enumerate(alist):
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