243 lines
10 KiB
Python
243 lines
10 KiB
Python
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import sys,os,unittest
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from lammps import lammps
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has_full=False
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try:
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machine=None
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if 'LAMMPS_MACHINE_NAME' in os.environ:
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machine=os.environ['LAMMPS_MACHINE_NAME']
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lmp=lammps(name=machine)
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has_full = lmp.has_style("atom","full")
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lmp.close()
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except:
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pass
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class PythonGather(unittest.TestCase):
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def setUp(self):
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machine=None
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if 'LAMMPS_MACHINE_NAME' in os.environ:
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machine=os.environ['LAMMPS_MACHINE_NAME']
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self.lmp=lammps(name=machine,
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cmdargs=['-nocite',
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'-log','none',
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'-echo','screen'])
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self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR'])
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# clean up temporary files
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def tearDown(self):
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self.lmp.close()
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# bond data comparison
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def checkBond(self, vals, btype, batom1, batom2):
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if ((vals[1] == batom1 and vals[2] == batom2)
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or (vals[1] == batom2 and vals[2] == batom1)):
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self.assertEqual(vals[0], btype)
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return 1
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else:
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return 0
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# angle data comparison
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def checkAngle(self, vals, atype, aatom1, aatom2, aatom3):
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set1 = {aatom1, aatom2, aatom3}
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set2 = {vals[1], vals[2], vals[3]}
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if len(set1.intersection(set2)) == 3:
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self.assertEqual(vals[0], atype)
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return 1
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else:
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return 0
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# dihedral data comparison
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def checkDihedral(self, vals, dtype, datom1, datom2, datom3, datom4):
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set1 = {datom1, datom2, datom3, datom4}
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set2 = {vals[1], vals[2], vals[3], vals[4]}
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if len(set1.intersection(set2)) == 4:
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self.assertEqual(vals[0], dtype)
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return 1
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else:
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return 0
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# improper data comparison
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def checkImproper(self, vals, itype, iatom1, iatom2, iatom3, iatom4):
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set1 = {iatom1, iatom2, iatom3, iatom4}
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set2 = {vals[1], vals[2], vals[3], vals[4]}
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if len(set1.intersection(set2)) == 4:
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self.assertEqual(vals[0], itype)
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return 1
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else:
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return 0
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##############################
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@unittest.skipIf(not has_full, "Gather_bonds test")
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def testGatherBond_newton_on(self):
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"""Test gather_bonds() with newton on"""
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self.lmp.command("newton on on")
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self.lmp.file("in.fourmol")
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self.lmp.command("run 0 post no")
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nbonds, bonds = self.lmp.gather_bonds()
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self.assertEqual(nbonds, 24)
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self.assertEqual(len(bonds), 3*24)
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count = 0;
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for i in range(0,nbonds):
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count += self.checkBond(bonds[3*i:3*i+3], 5, 1, 2)
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count += self.checkBond(bonds[3*i:3*i+3], 3, 1, 3)
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count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 4)
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count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 5)
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count += self.checkBond(bonds[3*i:3*i+3], 1, 6, 3)
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count += self.checkBond(bonds[3*i:3*i+3], 3, 6, 8)
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count += self.checkBond(bonds[3*i:3*i+3], 4, 6, 7)
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count += self.checkBond(bonds[3*i:3*i+3], 5, 8, 9)
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count += self.checkBond(bonds[3*i:3*i+3], 5, 27, 28)
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count += self.checkBond(bonds[3*i:3*i+3], 5, 29, 27)
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self.assertEqual(count,10)
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@unittest.skipIf(not has_full, "Gather_bonds test")
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def testGatherBond_newton_off(self):
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"""Test gather_bonds() with newton off"""
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self.lmp.command("newton off off")
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self.lmp.file("in.fourmol")
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self.lmp.command("run 0 post no")
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nbonds, bonds = self.lmp.gather_bonds()
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self.assertEqual(nbonds, 24)
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self.assertEqual(len(bonds), 3*24)
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count = 0;
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for i in range(0,nbonds):
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count += self.checkBond(bonds[3*i:3*i+3], 5, 1, 2)
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count += self.checkBond(bonds[3*i:3*i+3], 3, 1, 3)
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count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 4)
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count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 5)
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count += self.checkBond(bonds[3*i:3*i+3], 1, 3, 6)
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count += self.checkBond(bonds[3*i:3*i+3], 3, 6, 8)
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count += self.checkBond(bonds[3*i:3*i+3], 4, 6, 7)
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count += self.checkBond(bonds[3*i:3*i+3], 5, 8, 9)
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count += self.checkBond(bonds[3*i:3*i+3], 5, 27, 28)
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count += self.checkBond(bonds[3*i:3*i+3], 5, 27, 29)
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self.assertEqual(count,10)
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@unittest.skipIf(not has_full, "Gather_angles test")
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def testGatherAngle_newton_on(self):
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"""Test gather_angles() with newton on"""
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self.lmp.command("newton on on")
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self.lmp.file("in.fourmol")
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self.lmp.command("run 0 post no")
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nangles, angles = self.lmp.gather_angles()
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self.assertEqual(nangles, 30)
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self.assertEqual(len(angles), 120)
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count = 0;
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for i in range(0,nangles):
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count += self.checkAngle(angles[4*i:4*i+4], 4, 2, 1, 3)
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count += self.checkAngle(angles[4*i:4*i+4], 4, 1, 3, 6)
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count += self.checkAngle(angles[4*i:4*i+4], 2, 4, 3, 6)
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count += self.checkAngle(angles[4*i:4*i+4], 3, 7, 6, 8)
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count += self.checkAngle(angles[4*i:4*i+4], 3, 8, 10, 16)
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count += self.checkAngle(angles[4*i:4*i+4], 2, 8, 10, 11)
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count += self.checkAngle(angles[4*i:4*i+4], 1, 12, 10, 16)
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count += self.checkAngle(angles[4*i:4*i+4], 2, 10, 12, 14)
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count += self.checkAngle(angles[4*i:4*i+4], 1, 19, 18, 20)
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count += self.checkAngle(angles[4*i:4*i+4], 1, 28, 27, 29)
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self.assertEqual(count,10)
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@unittest.skipIf(not has_full, "Gather_angles test")
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def testGatherAngle_newton_off(self):
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"""Test gather_angles() with newton off"""
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self.lmp.command("newton off off")
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self.lmp.file("in.fourmol")
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self.lmp.command("run 0 post no")
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nangles, angles = self.lmp.gather_angles()
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self.assertEqual(nangles, 30)
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self.assertEqual(len(angles), 120)
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count = 0;
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for i in range(0,nangles):
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count += self.checkAngle(angles[4*i:4*i+4], 4, 2, 1, 3)
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count += self.checkAngle(angles[4*i:4*i+4], 4, 1, 3, 6)
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count += self.checkAngle(angles[4*i:4*i+4], 2, 4, 3, 6)
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count += self.checkAngle(angles[4*i:4*i+4], 3, 7, 6, 8)
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count += self.checkAngle(angles[4*i:4*i+4], 3, 8, 10, 16)
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count += self.checkAngle(angles[4*i:4*i+4], 2, 8, 10, 11)
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count += self.checkAngle(angles[4*i:4*i+4], 1, 12, 10, 16)
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count += self.checkAngle(angles[4*i:4*i+4], 2, 10, 12, 14)
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count += self.checkAngle(angles[4*i:4*i+4], 1, 19, 18, 20)
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count += self.checkAngle(angles[4*i:4*i+4], 1, 28, 27, 29)
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self.assertEqual(count,10)
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@unittest.skipIf(not has_full, "Gather_dihedrals test")
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def testGatherDihedral_newton_on(self):
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"""Test gather_dihedrals() with newton on"""
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self.lmp.command("newton on on")
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self.lmp.file("in.fourmol")
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self.lmp.command("run 0 post no")
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ndihedrals, dihedrals = self.lmp.gather_dihedrals()
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self.assertEqual(ndihedrals, 31)
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self.assertEqual(len(dihedrals), 155)
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count = 0;
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for i in range(0,ndihedrals):
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 2, 2, 1, 3, 6)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 3, 2, 1, 3, 5)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 1, 1, 3, 6, 7)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 5, 4, 3, 6, 7)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 4, 3, 6, 8, 9)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 2, 6, 8, 10, 16)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 5, 8, 10, 12, 13)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 1, 8, 10, 12, 14)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 2, 11, 10, 16, 17)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 5, 16, 10, 12, 14)
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self.assertEqual(count,10)
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@unittest.skipIf(not has_full, "Gather_dihedrals test")
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def testGatherDihedral_newton_off(self):
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"""Test gather_dihedrals() with newton off"""
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self.lmp.command("newton off off")
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self.lmp.file("in.fourmol")
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self.lmp.command("run 0 post no")
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ndihedrals, dihedrals = self.lmp.gather_dihedrals()
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self.assertEqual(ndihedrals, 31)
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self.assertEqual(len(dihedrals), 155)
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count = 0;
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for i in range(0,ndihedrals):
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 2, 2, 1, 3, 6)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 3, 2, 1, 3, 5)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 1, 1, 3, 6, 7)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 5, 4, 3, 6, 7)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 4, 3, 6, 8, 9)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 2, 6, 8, 10, 16)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 5, 8, 10, 12, 13)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 1, 8, 10, 12, 14)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 2, 11, 10, 16, 17)
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count += self.checkDihedral(dihedrals[5*i:5*i+5], 5, 16, 10, 12, 14)
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self.assertEqual(count,10)
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@unittest.skipIf(not has_full, "Gather_impropers test")
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def testGatherImproper_newton_on(self):
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"""Test gather_impropers() with newton on"""
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self.lmp.command("newton on on")
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self.lmp.file("in.fourmol")
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self.lmp.command("run 0 post no")
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nimpropers, impropers = self.lmp.gather_impropers()
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self.assertEqual(nimpropers, 2)
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self.assertEqual(len(impropers), 10)
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count = 0;
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for i in range(0,nimpropers):
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count += self.checkImproper(impropers[5*i:5*i+5], 1, 6, 3, 8, 7)
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count += self.checkImproper(impropers[5*i:5*i+5], 2, 8, 6, 10, 9)
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self.assertEqual(count,10)
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@unittest.skipIf(not has_full, "Gather_impropers test")
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def testGatherImproper_newton_off(self):
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"""Test gather_impropers() with newton off"""
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self.lmp.command("newton off off")
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self.lmp.file("in.fourmol")
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self.lmp.command("run 0 post no")
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nimpropers, impropers = self.lmp.gather_impropers()
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self.assertEqual(nimpropers, 2)
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self.assertEqual(len(impropers), 10)
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count = 0;
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for i in range(0,nimpropers):
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count += self.checkImproper(impropers[5*i:5*i+5], 1, 6, 3, 8, 7)
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count += self.checkImproper(impropers[5*i:5*i+5], 2, 8, 6, 10, 9)
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self.assertEqual(count,10)
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##############################
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if __name__ == "__main__":
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unittest.main()
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