add pitorsions to tinker2lmp.py
This commit is contained in:
Steve Plimpton
@ -351,20 +351,25 @@ class data:
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# data file keywords, both header and main sections
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hkeywords = ["atoms","ellipsoids","lines","triangles","bodies",
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"bonds","angles","dihedrals","impropers",
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"bonds","angles","dihedrals","impropers","pitorsions",
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"atom types","bond types","angle types","dihedral types",
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"improper types","xlo xhi","ylo yhi","zlo zhi","xy xz yz"]
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"improper types","pitorsion types",
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"xlo xhi","ylo yhi","zlo zhi","xy xz yz"]
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skeywords = [["Masses","atom types"],
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["Atoms","atoms"],["Ellipsoids","ellipsoids"],
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["Lines","lines"],["Triangles","triangles"],["Bodies","bodies"],
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["Bonds","bonds"],
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["Angles","angles"],["Dihedrals","dihedrals"],
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["Impropers","impropers"],["Velocities","atoms"],
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["Angles","angles"],
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["Dihedrals","dihedrals"],
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["Impropers","impropers"],
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["PiTorsions","pitorsions"],
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["Velocities","atoms"],
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["Pair Coeffs","atom types"],
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["Bond Coeffs","bond types"],["Angle Coeffs","angle types"],
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["Dihedral Coeffs","dihedral types"],
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["Improper Coeffs","improper 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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["MiddleBondTorsion Coeffs","dihedral types"],
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@ -13,8 +13,6 @@
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# Author: Steve Plimpton
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import sys,os,math
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path = os.environ["LAMMPS_PYTHON_TOOLS"]
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sys.path.append(path)
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from data import data
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BIG = 1.0e20
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@ -107,10 +105,21 @@ class PRMfile:
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self.angleparams = self.angles()
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self.bondangleparams = self.bondangles()
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self.torsionparams = self.torsions()
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self.ureyparams = self.ureybonds()
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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.ntypes = len(self.masses)
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# find a section in the PRM file
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def find_section(self,txt):
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txt = "## %s ##" % txt
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for iline,line in enumerate(self.lines):
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if txt in line: return iline
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return -1
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# scalar params
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def force_field_definition(self):
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iline = self.find_section("Force Field Definition")
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iline += 3
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@ -125,7 +134,9 @@ class PRMfile:
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elif words[0] == "angle-pentic": self.angle_pentic = float(words[1])
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elif words[0] == "angle-sextic": self.angle_sextic = float(words[1])
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iline += 1
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# atom classes and masses
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def peratom(self):
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classes = []
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masses = []
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@ -143,6 +154,8 @@ class PRMfile:
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iline += 1
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return classes,masses
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# polarization groups
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def polarize(self):
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polgroup = []
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iline = self.find_section("Dipole Polarizability Parameters")
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@ -297,33 +310,7 @@ 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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# coeffs for K2,K3 = 0.0 since Urey-Bradley is simple harmonic
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def ureybonds(self):
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params = []
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iline = self.find_section("Urey-Bradley 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] == "ureybrad":
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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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value1 = float(words[4])
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value2 = float(words[5])
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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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iline += 1
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return params
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# Dihedral interactions
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# dihedral interactions
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def torsions(self):
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params = []
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@ -363,7 +350,7 @@ class PRMfile:
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iline += 1
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return params
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# Improper or out-of-plane bend interactions
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# improper or out-of-plane bend interactions
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def opbend(self):
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params = []
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@ -385,11 +372,53 @@ class PRMfile:
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iline += 1
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return params
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def find_section(self,txt):
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txt = "## %s ##" % txt
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for iline,line in enumerate(self.lines):
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if txt in line: return iline
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return -1
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# convert PRMfile params to LAMMPS bond_style class2 bond 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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params = []
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iline = self.find_section("Urey-Bradley 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] == "ureybrad":
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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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value1 = float(words[4])
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value2 = float(words[5])
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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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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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def pitorsions(self):
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params = []
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iline = self.find_section("Pi-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] == "pitors":
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class1 = int(words[1])
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class2 = int(words[2])
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value1 = float(words[3])
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lmp1 = value1
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params.append((class1,class2,lmp1))
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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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@ -639,6 +668,49 @@ 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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# 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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type = xyz.type
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classes = prm.classes
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bonds = xyz.bonds
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pitorsionlist = []
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for atom1 in id:
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for atom2 in bonds[atom1-1]:
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if atom1 < atom2:
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if len(bonds[atom1-1]) != 3: continue
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if len(bonds[atom2-1]) != 3: continue
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if bonds[atom1-1][0] == atom2:
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atom3 = bonds[atom1-1][1]
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atom4 = bonds[atom1-1][2]
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elif bonds[atom1-1][1] == atom2:
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atom3 = bonds[atom1-1][0]
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atom4 = bonds[atom1-1][2]
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elif bonds[atom1-1][2] == atom2:
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atom3 = bonds[atom1-1][0]
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atom4 = bonds[atom1-1][1]
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if bonds[atom2-1][0] == atom1:
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atom5 = bonds[atom2-1][1]
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atom6 = bonds[atom2-1][2]
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elif bonds[atom2-1][1] == atom1:
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atom5 = bonds[atom2-1][0]
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atom6 = bonds[atom2-1][2]
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elif bonds[atom2-1][2] == atom1:
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atom5 = bonds[atom2-1][0]
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atom6 = bonds[atom2-1][1]
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pitorsionlist.append((atom3,atom4,atom1,atom2,atom5,atom6))
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# ----------------------------------------
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# create lists of bond/angle/dihedral/improper types
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# ----------------------------------------
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@ -954,7 +1026,53 @@ for atom1,atom2,atom3,atom4 in olist:
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# replace original olist with reduced version
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olist = olist_reduced
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# generate pitorsiontype = LAMMPS type of each pitorsion
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# generate pitorsionparams = LAMMPS params for each pitorsion type
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# flags[i] = which LAMMPS pitorsion type (1-N) the Ith Tinker PRM file ptors is
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# 0 = none
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# convert prm.pitorsionparams to a dictionary for efficient searching
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# key = (class1,class2)
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# value = (M,params) where M is index into prm.pitorsionparams
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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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pitdict = {}
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for m,params in enumerate(prm.pitorsionparams):
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pitdict[(params[0],params[1])] = (m,params)
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flags = len(prm.pitorsionparams)*[0]
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pitorsiontype = []
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pitorsionparams = []
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for tmp1,tmp2,atom1,atom2,tmp3,tmp4 in pitorsionlist:
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type1 = type[atom1-1]
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type2 = type[atom2-1]
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c1 = classes[type1-1]
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c2 = classes[type2-1]
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if (c1,c2) in pitdict: m,params = pitdict[(c1,c2)]
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elif (c2,c1) in pitdict: m,params = pitdict[(c2,c1)]
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else:
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# NOTE: probably this PiT should be deleted from enumeration list
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# similar to olist for impropers above
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# IMPORTANT: look at other errors and messages t2lmp.py is producing
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error("PiTorsion not found: %d %d: %d %d" % (atom1,atom2,c1,c2))
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pitorsiontype.append(0)
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continue
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if not flags[m]:
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v1 = params[2:]
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pitorsionparams.append(v1)
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flags[m] = len(pitorsionparams)
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pitorsiontype.append(flags[m])
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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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# ----------------------------------------
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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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@ -1009,6 +1127,7 @@ nbonds = len(blist)
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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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# data file header values
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@ -1119,6 +1238,24 @@ if nimpropers:
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lines.append(line+'\n')
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d.sections["Impropers"] = lines
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if npitorsions:
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d.headers["pitorsions"] = len(pitorsionlist)
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d.headers["pitorsion types"] = len(pitorsionparams)
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lines = []
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for i,one in enumerate(pitorsionparams):
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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["PiTorsion Coeffs"] = lines
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lines = []
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for i,one in enumerate(pitorsionlist):
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line = "%d %d %d %d %d %d %d %d" % \
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(i+1,pitorsiontype[i],one[0],one[1],one[2],one[3],one[4],one[5])
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lines.append(line+'\n')
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d.sections["PiTorsions"] = lines
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d.write(datafile)
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# print stats to screen
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@ -1129,11 +1266,13 @@ print "Tinker XYZ types =",len(tink2lmp)
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print "Tinker PRM types =",prm.ntypes
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#print "Tinker groups =",ngroups
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print "Nmol =",nmol
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print "Nbonds =",len(blist)
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print "Nangles =",len(alist)
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print "Ndihedrals =",len(dlist)
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print "Nimpropers =",len(olist)
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print "Nbonds =",nbonds
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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 "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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