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#! /usr/bin/env python |
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|
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"""Dipolar Lattice Builder |
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|
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Creates cubic lattices of dipoles to test the dipole-dipole |
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interaction code. |
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|
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Usage: buildDipolarArray |
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|
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Options: |
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-h, --help show this help |
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-a, --array-type-A use array type "A" (default) |
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-b, --array-type-B use array type "B" |
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-l, --lattice=... use the specified lattice ( SC, FCC, or BCC ) |
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-d, --direction=... use dipole orientation (001, 111, or 011) |
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-c, --constant=... use the specified lattice constant |
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-n use the specified number of unit cells |
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-o, --output-file=... use specified output (.xyz) file |
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|
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Type "A" arrays have nearest neighbor strings of antiparallel dipoles. |
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|
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Type "B" arrays have nearest neighbor strings of antiparallel dipoles |
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if the dipoles are contained in a plane perpendicular to the dipole |
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direction that passes through the dipole. |
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|
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Example: |
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buildDipolarArray -a -l fcc -d 001 -c 5 -n 3 -o A_fcc_001.xyz |
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|
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""" |
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|
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__author__ = "Dan Gezelter (gezelter@nd.edu)" |
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__version__ = "$Revision: 1639 $" |
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__date__ = "$Date: 2011-09-24 16:18:07 -0400 (Sat, 24 Sep 2011) $" |
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|
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__copyright__ = "Copyright (c) 2013 by the University of Notre Dame" |
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__license__ = "OpenMD" |
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|
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import sys |
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import getopt |
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import string |
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import math |
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import numpy |
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|
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def usage(): |
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print __doc__ |
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|
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def createLattice(latticeType, latticeNumber, latticeConstant, dipoleDirection, doTypeA, outputFileName): |
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a1 = numpy.array([1.0,0.0,0.0]) |
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a2 = numpy.array([0.0,1.0,0.0]) |
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a3 = numpy.array([0.0,0.0,1.0]) |
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|
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sc = numpy.array([[0.0,0.0,0.0]]) |
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|
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bcc = numpy.array([[0.0,0.0,0.0], |
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[0.5,0.5,0.5]]) |
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|
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fcc = numpy.array([[0.0,0.0,0.0], |
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[0.5,0.5,0.0], |
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[0.0,0.5,0.5], |
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[0.5,0.0,0.5]]) |
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|
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dipole001 = numpy.array([0.0,0.0,1.0]) |
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dipole011 = numpy.array([0.0,1.0/math.sqrt(2.0),1.0/math.sqrt(2.0)]) |
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dipole111 = numpy.array([1.0/math.sqrt(3.0),1.0/math.sqrt(3.0),1.0/math.sqrt(3.0)]) |
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|
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if (latticeType.lower() == 'sc'): |
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basis_atoms = sc |
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elif(latticeType.lower() == 'fcc'): |
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basis_atoms = fcc |
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elif(latticeType.lower() == 'bcc'): |
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basis_atoms = bcc |
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else: |
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print "unknown lattice type" |
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print __doc__ |
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|
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ijklvector = numpy.array([1,1,1,1]) |
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|
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if (dipoleDirection.lower() == '001'): |
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basis_dipoles = numpy.array([dipole001, -dipole001]) |
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elif(dipoleDirection.lower() == '011'): |
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basis_dipoles = numpy.array([dipole011, -dipole011]) |
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elif(dipoleDirection.lower() == '111'): |
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basis_dipoles = numpy.array([dipole111, -dipole111]) |
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else: |
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print "unknown lattice type" |
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print __doc__ |
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|
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if (not doTypeA): |
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if (latticeType.lower() == 'sc'): |
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if (dipoleDirection.lower() == '001'): |
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ijkl = numpy.array([1,1,0,0]) |
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elif(dipoleDirection.lower() == '011'): |
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ijkl = numpy.array([1,1,-1,0]) |
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elif(dipoleDirection.lower() == '111'): |
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ijkl = numpy.array([1,1,-2,0]) |
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elif(latticeType.lower() == 'fcc'): |
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if (dipoleDirection.lower() == '001'): |
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ijkl = numpy.array([1,1,0,1]) |
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elif(dipoleDirection.lower() == '011'): |
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ijkl = numpy.array([1,1,-1,2]) |
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elif(dipoleDirection.lower() == '111'): |
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ijkl = numpy.array([1,1,-2,1]) |
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elif(latticeType.lower() == 'bcc'): |
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if (dipoleDirection.lower() == '001'): |
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ijkl = numpy.array([1,1,0,1]) |
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elif(dipoleDirection.lower() == '011'): |
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ijkl = numpy.array([1,1,-1,1]) |
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elif(dipoleDirection.lower() == '111'): |
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ijkl = numpy.array([1,1,-2,0]) |
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else: |
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if (latticeType.lower() == 'sc'): |
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ijkl = numpy.array([1,1,1,0]) |
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elif(latticeType.lower() == 'fcc'): |
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ijkl = numpy.array([1,1,1,1]) |
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elif(latticeType.lower() == 'bcc'): |
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ijkl = numpy.array([0,0,0,1]) |
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|
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bravais_lattice = [] |
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bravais_dipoles = [] |
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|
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for i in range(latticeNumber): |
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for j in range(latticeNumber): |
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for k in range(latticeNumber): |
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for l in range(len(basis_atoms)): |
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bravais_lattice.append(i*a1 + j*a2 + k*a3 + basis_atoms[l]) |
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tester = numpy.array([i,j,k,l]) |
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flip = numpy.dot(tester, ijkl) % 2 |
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print flip |
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bravais_dipoles.append(basis_dipoles[flip]) |
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|
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outputFile = open(outputFileName,'w') |
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|
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outputFile.write(repr(len(bravais_lattice)) + '\n') |
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Hxx = latticeConstant * latticeNumber |
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Hyy = latticeConstant * latticeNumber |
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Hzz = latticeConstant * latticeNumber |
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|
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outputFile.write('Hmat: {{%d, 0, 0}, {0, %d, 0}, {0, 0, %d}}\n' % (Hxx, Hyy, Hzz)) |
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|
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for i in range(len(bravais_lattice)): |
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xcart = latticeConstant*(bravais_lattice[i][0]) |
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ycart = latticeConstant*(bravais_lattice[i][1]) |
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zcart = latticeConstant*(bravais_lattice[i][2]) |
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dx = bravais_dipoles[i][0] |
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dy = bravais_dipoles[i][1] |
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dz = bravais_dipoles[i][2] |
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outputFile.write('Ar ' + repr(xcart) + ' ' + repr(ycart) + ' ' + repr(zcart) + ' ' + repr(dx) + ' ' + repr(dy) + ' ' + repr(dz) + '\n') |
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|
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outputFile.close() |
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|
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def main(argv): |
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|
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doTypeA = True |
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haveOutputFileName = False |
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latticeType = "fcc" |
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dipoleDirection = "001" |
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latticeNumber = 3 |
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latticeConstant = 4 |
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try: |
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opts, args = getopt.getopt(argv, "habl:d:c:n:o:", ["help","array-type-A", "array-type-B", "lattice=" "direction=", "constant=", "output-file="]) |
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except getopt.GetoptError: |
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usage() |
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sys.exit(2) |
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for opt, arg in opts: |
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if opt in ("-h", "--help"): |
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usage() |
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sys.exit() |
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elif opt in ("-a", "--array-type-A"): |
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doTypeA = True |
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elif opt in ("-b", "--array-type-B"): |
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doTypeA = False |
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elif opt in ("-l", "--lattice"): |
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latticeType = arg |
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elif opt in ("-d", "--direction"): |
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dipoleDirection = arg |
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elif opt in ("-c", "--constant"): |
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latticeConstant = float(arg) |
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elif opt in ("-n"): |
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latticeNumber = int(arg) |
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elif opt in ("-o", "--output-file"): |
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outputFileName = arg |
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haveOutputFileName = True |
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if (not haveOutputFileName): |
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usage() |
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print "No output file was specified" |
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sys.exit() |
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|
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createLattice(latticeType, latticeNumber, latticeConstant, dipoleDirection, doTypeA, outputFileName); |
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|
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if __name__ == "__main__": |
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if len(sys.argv) == 1: |
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usage() |
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sys.exit() |
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main(sys.argv[1:]) |
