enable tinker2lmp.py to generate bitorsions
This commit is contained in:
Steve Plimpton
@ -7,6 +7,7 @@
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# -amoeba file = AMOEBA PRM force field file name (required, or hippo)
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# -hippo file = HIPPO PRM force field file name (required, or amoeba)
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# -data file = LAMMPS data file to output (required)
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# -bitorsion file = LAMMPS fix bitorsion file to output (required if BiTorsions)
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# -nopbc = non-periodic system (default)
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# -pbc xhi yhi zhi = periodic system from 0 to hi in each dimension (optional)
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@ -31,6 +32,7 @@ def error(txt=""):
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print " -amoeba file"
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print " -hippo file"
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print " -data file"
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print " -bitorsion file"
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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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@ -108,6 +110,7 @@ class PRMfile:
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self.opbendparams = self.opbend()
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self.ureyparams = self.ureybonds()
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self.pitorsionparams = self.pitorsions()
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self.bitorsionparams = self.bitorsions()
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self.ntypes = len(self.masses)
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# find a section in the PRM file
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@ -329,10 +332,10 @@ class PRMfile:
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class4 = int(words[4])
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if len(words) <= 5:
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error("Torsion has no params: %d %d %d %d" % \
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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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error("Torsion does not have triplets of params: %d %d %d %d" % \
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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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@ -399,7 +402,7 @@ class PRMfile:
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iline += 1
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return params
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# Pi Torsion params, will be read from data file by fix pitorsion
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# PiTorsion params, will be read from data file by fix pitorsion
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def pitorsions(self):
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params = []
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@ -421,6 +424,43 @@ class PRMfile:
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iline += 1
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return params
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# BiTorsion params, will be read from data file by fix bitorsion
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def bitorsions(self):
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params = []
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iline = self.find_section("Torsion-Torsion Parameters")
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if iline < 0: return params
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iline += 3
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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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if words[0].startswith("###########"): break
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if words[0] == "tortors":
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class1 = int(words[1])
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class2 = int(words[2])
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class3 = int(words[3])
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class4 = int(words[4])
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class5 = int(words[5])
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nx = int(words[6])
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ny = int(words[7])
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iline += 1
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array = []
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for iy in range(ny):
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xrow = []
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for ix in range(nx):
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words = self.lines[iline].split()
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xgrid = float(words[0])
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ygrid = float(words[1])
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value = float(words[2])
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tuple3 = (xgrid,ygrid,value)
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xrow.append(tuple3)
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iline += 1
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array.append(xrow)
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params.append((class1,class2,class3,class4,class5,nx,ny,array))
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iline += 1
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return params
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# ----------------------------------------
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# main program
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# ----------------------------------------
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@ -434,6 +474,7 @@ amoeba = hippo = 0
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xyzfile = ""
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prmfile = ""
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datafile = ""
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bitorsionfile = ""
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pbcflag = 0
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iarg = 0
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@ -456,6 +497,10 @@ while iarg < narg:
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if iarg + 2 > narg: error()
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datafile = args[iarg+1]
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iarg += 2
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elif args[iarg] == "-bitorsion":
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if iarg + 2 > narg: error()
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bitorsionfile = args[iarg+1]
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iarg += 2
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elif args[iarg] == "-nopbc":
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pbcflag = 0
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iarg += 1
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@ -673,11 +718,7 @@ for atom1,atom2,atom3 in alist:
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elif (c3,c2,c1) in ubdict:
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ublist.append((atom3,atom2,atom1))
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# ----------------------------------------
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# create list of 6-body Pi-Torsion interactions
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# ----------------------------------------
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# create ptorslist = list of 6-body interactions
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# create pitorslist = list of 6-body interactions
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# based on central bond, each bond atom is bonded to exactly 2 other atoms
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# avoid double counting by requiring atom1 < atom2
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# NOTE: need more info on how to order the 6 atoms for Tinker to compute on
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@ -716,9 +757,28 @@ 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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# create bitorslist = list of 5-body interactions
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# generate topology via double loop over neighbors of central atom3
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# additional double loop over bonds of atom2 and bonds of atom4
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# avoid double counting the reverse bitorsion by use of btdict dictionary
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#pitorsionlist = []
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type = xyz.type
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classes = prm.classes
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bonds = xyz.bonds
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bitorsionlist = []
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btdict = {}
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for atom3 in id:
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for atom2 in bonds[atom3-1]:
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for atom4 in bonds[atom3-1]:
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if atom2 == atom4: continue
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for atom1 in bonds[atom2-1]:
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for atom5 in bonds[atom4-1]:
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if atom1 == atom3 or atom5 == atom3 or atom1 == atom5: continue
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if (atom5,atom4,atom3,atom2,atom1) in btdict: continue
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bitorsionlist.append((atom1,atom2,atom3,atom4,atom5))
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btdict[(atom1,atom2,atom3,atom4,atom5)] = 1
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# ----------------------------------------
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# create lists of bond/angle/dihedral/improper types
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@ -752,7 +812,7 @@ 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: error("Bond not found: %d %d: %d %d" % (atom1,atom2,c1,c2))
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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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@ -869,7 +929,7 @@ for i,one in enumerate(alist):
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m += 2
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else:
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error("Angle not found: %d %d %d: %d %d %d" % (atom1,atom2,atom3,c1,c2,c3))
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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,ubflag,v1,v2,v3,v4,v5,v6 = params[3][which-1]
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@ -979,7 +1039,7 @@ 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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error("Dihedral not found: %d %d %d %d: %d %d %d %d" % \
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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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@ -1063,7 +1123,7 @@ for tmp1,tmp2,atom1,atom2,tmp3,tmp4 in pitorsionlist:
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c1 = classes[type1-1]
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c2 = classes[type2-1]
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# 6-tuple is only a PiTorsion if central 2 atoms math an entry in PRM file
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# 6-tuple is only a PiTorsion if central 2 atoms match an entry in PRM file
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# pitorsionlist_reduced = list of just these 6-tuples
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if (c1,c2) in pitdict or (c2,c1) in pitdict:
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@ -1081,6 +1141,57 @@ for tmp1,tmp2,atom1,atom2,tmp3,tmp4 in pitorsionlist:
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pitorsionlist = pitorsionlist_reduced
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# generate bitorsiontype = LAMMPS type of each bitorsion
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# generate bitorsionparams = LAMMPS params for each bitorsion type
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# flags[i] = which LAMMPS bitorsion type (1-N) the Ith Tinker PRM file btors is
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# 0 = none
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# convert prm.bitorsionparams to a dictionary for efficient searching
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# key = (class1,class2,class3,class4,class5)
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# value = (M,params) where M is index into prm.bitorsionparams
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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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bitdict = {}
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for m,params in enumerate(prm.bitorsionparams):
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bitdict[(params[0],params[1],params[2],params[3],params[4])] = (m,params)
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flags = len(prm.bitorsionparams)*[0]
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bitorsiontype = []
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bitorsionparams = []
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bitorsionlist_reduced = []
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for atom1,atom2,atom3,atom4,atom5 in bitorsionlist:
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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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type4 = type[atom4-1]
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type5 = type[atom5-1]
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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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c4 = classes[type4-1]
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c5 = classes[type5-1]
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# 5-tuple is only a BiTorsion if 5 atoms match an entry in PRM file
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# bitorsionlist_reduced = list of just these 5-tuples
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if (c1,c2,c3,c4,c5) in bitdict or (c5,c4,c3,c2,c1) in bitdict:
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if (c1,c2,c3,c4,c5) in bitdict: m,params = bitdict[(c1,c2,c3,c4,c5)]
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else: m,params = bitdict[(c5,c4,c3,c2,c1)]
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bitorsionlist_reduced.append((atom1,atom2,atom3,atom4,atom5))
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if not flags[m]:
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v1 = params[5:]
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bitorsionparams.append(v1)
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flags[m] = len(bitorsionparams)
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bitorsiontype.append(flags[m])
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# replace original bitorsionlist with reduced version
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bitorsionlist = bitorsionlist_reduced
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# ----------------------------------------
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# assign each atom to a Tinker group
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# NOTE: doing this inside LAMMPS now
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@ -1136,6 +1247,7 @@ nangles = len(alist)
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ndihedrals = len(dlist)
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nimpropers = len(olist)
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npitorsions = len(pitorsionlist)
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nbitorsions = len(bitorsionlist)
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# data file header values
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@ -1271,6 +1383,36 @@ if npitorsions:
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lines.append(line+'\n')
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d.sections["PiTorsions"] = lines
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if nbitorsions:
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d.headers["bitorsions"] = len(pitorsionlist)
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# if there are bitorsions, then -bitorsion file must have been specified
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if not bitorsionfile:
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error("no -bitorsion file was specified, but %d bitorsions exist" % \
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nbitorsions)
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fp = open(bitorsionfile,'w')
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print >>fp,"Tinker BiTorsion parameter file for fix bitorsion\n"
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print >>fp,"%d bitorsion types" % len(bitorsionparams)
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itype = 0
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for nx,ny,array in bitorsionparams:
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itype += 1
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print >>fp
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print >>fp,itype,nx,ny
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for ix in range(nx):
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for iy in range(ny):
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xgrid,ygrid,value = array[ix][iy]
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print >>fp," ",xgrid,ygrid,value
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fp.close()
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lines = []
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for i,one in enumerate(bitorsionlist):
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line = "%d %d %d %d %d %d %d" % \
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(i+1,bitorsiontype[i],one[0],one[1],one[2],one[3],one[4])
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lines.append(line+'\n')
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d.sections["BiTorsions"] = lines
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d.write(datafile)
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# print stats to screen
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@ -1286,8 +1428,10 @@ print "Nangles =",nangles
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print "Ndihedrals =",ndihedrals
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print "Nimpropers =",nimpropers
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print "Npitorsions =",npitorsions
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print "Nbitorsions =",nbitorsions
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print "Nbondtypes =",len(bparams)
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print "Nangletypes =",len(aparams)
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print "Ndihedraltypes =",len(dparams)
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print "Nimpropertypes =",len(oparams)
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print "Npitorsiontypes =",len(pitorsionparams)
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print "Nbitorsiontypes =",len(bitorsionparams)
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