Committer: ckloss <ckloss@fluid38.(none)>

On branch master
 Initial commit for lpp, version 2011-10-11

src/chain.py

@@ -0,0 +1,245 @@
+# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
+# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+#
+# 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 
+# the GNU General Public License.
+
+# chain tool
+
+oneline = "Create bead-spring chains for LAMMPS input"
+
+docstr = """
+c = chain(N,rho)            setup box with N monomers at reduced density rho
+c = chain(N,rho,1,1,2)	    x,y,z = aspect ratio of box (def = 1,1,1)
+
+c.seed = 48379              set random # seed (def = 12345)
+c.mtype = 2    		    set type of monomers (def = 1)
+c.btype = 1           	    set type of bonds (def = 1)
+c.blen = 0.97               set length of bonds (def = 0.97)
+c.dmin = 1.02               set min dist from i-1 to i+1 site (def = 1.02)
+
+c.id = "chain"              set molecule ID to chain # (default)
+c.id = "end1"               set molecule ID to count from one end of chain
+c.id = "end2"               set molecule ID to count from either end of chain
+
+c.build(100,10)		    create 100 chains, each of length 10
+
+  can be invoked multiple times interleaved with different settings
+  must fill box with total of N monomers
+  
+c.write("data.file")        write out all built chains to LAMMPS data file
+"""
+
+# History
+#   8/05, Steve Plimpton (SNL): original version
+
+# ToDo list
+
+# Variables
+#   n = number of monomers
+#   rhostar = reduced density
+#   seed = 12345
+#   mtype = type of monomers
+#   btype = type of bonds
+#   blen = length of bonds
+#   dmin = minimum distance from i-1 to i+1
+#   id = "chain","end1",or "end2"
+#   atoms = list of atoms
+#   bonds = list of bonds
+#   xprd,yprd,zprd = x,y,z box size
+#   xlo,ylo,zlo = -xyz prd / 2
+#   xhi,yhi,zhi = x,y,zprd /2
+
+# Imports and external programs
+
+import math
+from data import data
+
+# Class definition
+
+class chain:
+  
+  # --------------------------------------------------------------------
+
+  def __init__(self,n,rhostar,*list):
+    self.n = n
+    self.rhostar = rhostar
+    xaspect = yaspect = zaspect = 1.0
+    if len(list):
+      xaspect = list[0]
+      yaspect = list[1]
+      zaspect = list[2]
+    self.seed = 12345
+    self.mtype = 1
+    self.btype = 1
+    self.blen = 0.97
+    self.dmin = 1.02
+    self.id = "chain"
+    self.atoms = []
+    self.bonds = []
+
+    volume = n/rhostar
+    prd = pow(volume/xaspect/yaspect/zaspect,1.0/3.0)
+    self.xprd = xaspect * prd
+    self.xlo = -self.xprd/2.0
+    self.xhi = self.xprd/2.0
+    self.yprd = yaspect * prd
+    self.ylo = -self.yprd/2.0
+    self.yhi = self.yprd/2.0
+    self.zprd = zaspect * prd
+    self.zlo = -self.zprd/2.0
+    self.zhi = self.zprd/2.0
+
+    print "Simulation box: %g by %g by %g" % (self.xprd,self.yprd,self.zprd)
+
+  # --------------------------------------------------------------------
+
+  def build(self,n,nper):
+    for ichain in xrange(n):
+      atoms = []
+      bonds = []
+      id_atom_prev = id_mol_prev = id_bond_prev = 0
+      if len(self.atoms):
+        id_atom_prev = self.atoms[-1][0]
+        id_mol_prev = self.atoms[-1][1]
+      if len(self.bonds):
+        id_bond_prev = self.bonds[-1][0]
+
+      for imonomer in xrange(nper):
+        if imonomer == 0:
+          x = self.xlo + self.random()*self.xprd
+          y = self.ylo + self.random()*self.yprd
+          z = self.zlo + self.random()*self.zprd
+	  ix = iy = iz = 0
+        else:
+          restriction = True
+          while restriction:
+            rsq = 2.0
+            while rsq > 1.0:
+              dx = 2.0*self.random() - 1.0
+              dy = 2.0*self.random() - 1.0
+              dz = 2.0*self.random() - 1.0
+              rsq = dx*dx + dy*dy + dz*dz
+            r = math.sqrt(rsq)
+            dx,dy,dz = dx/r,dy/r,dz/r
+            x = atoms[-1][3] + dx*self.blen
+            y = atoms[-1][4] + dy*self.blen
+            z = atoms[-1][5] + dz*self.blen
+            restriction = False
+            if imonomer >= 2:
+              dx = x - atoms[-2][3]
+              dy = y - atoms[-2][4]
+              dz = z - atoms[-2][5]
+              if math.sqrt(dx*dx + dy*dy + dz*dz) <= self.dmin:
+                restriction = True
+              
+        x,y,z,ix,iy,iz = self.pbc(x,y,z,ix,iy,iz)
+        idatom = id_atom_prev + imonomer + 1
+        if self.id == "chain":
+          idmol = id_mol_prev + 1
+        elif self.id == "end1":
+          idmol = imonomer + 1
+        elif self.id == "end2":
+          idmol = imonomer + 1
+          if idmol > nper/2:
+            idmol = nper - imonomer
+        else:
+          raise StandardError,"chain ID is not a valid value"
+	        
+        atoms.append([idatom,idmol,self.mtype,x,y,z,ix,iy,iz])
+        if imonomer:
+	  bondid = id_bond_prev + imonomer
+          bonds.append([bondid,self.btype,idatom-1,idatom])
+        
+      self.atoms += atoms
+      self.bonds += bonds
+
+  # --------------------------------------------------------------------
+
+  def write(self,file):
+    if len(self.atoms) != self.n:
+      raise StandardError,"%d monomers instead of requested %d" % \
+                           (len(self.atoms),self.n)
+
+    list = [atom[2] for atom in self.atoms]
+    atypes = max(list)
+
+    btypes = 0
+    if len(self.bonds):
+      list = [bond[1] for bond in self.bonds]
+      btypes = max(list)
+
+    # create the data file
+
+    d = data()
+    d.title = "LAMMPS FENE chain data file"
+    d.headers["atoms"] = len(self.atoms)
+    d.headers["bonds"] = len(self.bonds)
+    d.headers["atom types"] = atypes
+    d.headers["bond types"] = btypes
+    d.headers["xlo xhi"] = (self.xlo,self.xhi)
+    d.headers["ylo yhi"] = (self.ylo,self.yhi)
+    d.headers["zlo zhi"] = (self.zlo,self.zhi)
+
+    lines = []
+    for i in range(atypes): lines.append("%d 1.0\n" % (i+1))
+    d.sections["Masses"] = lines
+    
+    lines = []
+    for atom in self.atoms:
+      line = "%d %d %d %g %g %g %d %d %d\n" % \
+             (atom[0], atom[1], atom[2], atom[3], atom[4], atom[5],
+              atom[6], atom[7], atom[8])
+      lines.append(line)
+    d.sections["Atoms"] = lines
+    
+    lines = []
+    for bond in self.bonds:
+      line = "%d %d %d %d\n" % (bond[0], bond[1], bond[2], bond[3])
+      lines.append(line)
+    d.sections["Bonds"] = lines
+
+    d.write(file)
+
+  # --------------------------------------------------------------------
+
+  def pbc(self,x,y,z,ix,iy,iz):
+    if x < self.xlo:
+      x += self.xprd
+      ix -= 1
+    elif x >= self.xhi:
+      x -= self.xprd
+      ix += 1
+    if y < self.ylo:
+      y += self.yprd
+      iy -= 1
+    elif y >= self.yhi:
+      y -= self.yprd
+      iy += 1
+    if z < self.zlo:
+      z += self.zprd
+      iz -= 1
+    elif z >= self.zhi:
+      z -= self.zprd
+      iz += 1
+    return x,y,z,ix,iy,iz
+
+  # --------------------------------------------------------------------
+
+  def random(self):
+    k = self.seed/IQ
+    self.seed = IA*(self.seed-k*IQ) - IR*k
+    if self.seed < 0:
+      self.seed += IM
+    return AM*self.seed
+
+# --------------------------------------------------------------------
+# random # generator constants
+
+IM = 2147483647
+AM = 1.0/IM
+IA = 16807
+IQ = 127773
+IR = 2836