219 lines
9.5 KiB
Python
219 lines
9.5 KiB
Python
import sys,os,unittest
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from ctypes import *
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from lammps import lammps, LMP_STYLE_GLOBAL, LMP_STYLE_ATOM, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY
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try:
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import numpy
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NUMPY_INSTALLED = True
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except ImportError:
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NUMPY_INSTALLED = False
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# add timestep dependent force
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def callback_one(lmp, ntimestep, nlocal, tag, x, f):
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lmp.fix_external_set_virial_global("ext",[1.0, 1.0, 1.0, 0.0, 0.0, 0.0])
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for i in range(nlocal):
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f[i][0] = float(ntimestep)
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f[i][1] = float(ntimestep)
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f[i][2] = float(ntimestep)
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if ntimestep < 10:
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lmp.fix_external_set_energy_global("ext", 0.5)
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lmp.fix_external_set_vector("ext", 1, ntimestep)
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lmp.fix_external_set_vector("ext", 3, 1.0)
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lmp.fix_external_set_vector("ext", 4, -0.25)
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else:
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lmp.fix_external_set_energy_global("ext", 1.0)
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lmp.fix_external_set_vector("ext", 2, ntimestep)
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lmp.fix_external_set_vector("ext", 5, -1.0)
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lmp.fix_external_set_vector("ext", 6, 0.25)
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eatom = [0.0,0.1,0.2,0.3,0.4,0.5,0.6,0.7]
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vatom = [ [0.1,0.0,0.0,0.0,0.0,0.0],
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[0.0,0.2,0.0,0.0,0.0,0.0],
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[0.0,0.0,0.3,0.0,0.0,0.0],
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[0.0,0.0,0.0,0.4,0.0,0.0],
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[0.0,0.0,0.0,0.0,0.5,0.0],
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[0.0,0.0,0.0,0.0,0.0,0.6],
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[0.0,0.0,0.0,0.0,-7.0,0.0],
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[0.0,-8.0,0.0,0.0,0.0,0.0] ]
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if ntimestep < 5:
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lmp.fix_external_set_energy_peratom("ext",eatom)
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lmp.fix_external_set_virial_peratom("ext",vatom)
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else:
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import numpy as np
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eng = np.array(eatom)
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vir = np.array(vatom)
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lmp.numpy.fix_external_set_energy_peratom("ext",eng)
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lmp.numpy.fix_external_set_virial_peratom("ext",vir)
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# ------------------------------------------------------------------------
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class PythonExternal(unittest.TestCase):
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@unittest.skipIf(not NUMPY_INSTALLED, "NumPy is not available")
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def testExternalCallback(self):
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"""Test fix external from Python with pf/callback"""
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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, cmdargs=['-nocite', '-log','none', '-echo', 'screen'])
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# a few commands to set up simple system
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basic_system="""lattice sc 1.0
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region box block -1 1 -1 1 -1 1
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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pair_style zero 0.1
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pair_coeff 1 1
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velocity all set 0.1 0.0 -0.1
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thermo_style custom step temp pe ke etotal press
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thermo 5
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fix 1 all nve
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fix ext all external pf/callback 5 1
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compute eatm all pe/atom fix
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compute vatm all stress/atom NULL fix
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compute sum all reduce sum c_eatm c_vatm[*]
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thermo_style custom step temp pe ke etotal press c_sum[*]
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fix_modify ext energy yes virial yes
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"""
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lmp.commands_string(basic_system)
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lmp.fix_external_set_vector_length("ext",6);
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lmp.set_fix_external_callback("ext",callback_one,lmp)
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# check setting per-atom data with python lists
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lmp.command("run 0 post no")
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reduce = lmp.extract_compute("sum", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR)
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self.assertAlmostEqual(reduce[0],2.8,14)
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self.assertAlmostEqual(reduce[1],-0.1,14)
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self.assertAlmostEqual(reduce[2],7.8,14)
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self.assertAlmostEqual(reduce[3],-0.3,14)
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self.assertAlmostEqual(reduce[4],-0.4,14)
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self.assertAlmostEqual(reduce[5],6.5,14)
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self.assertAlmostEqual(reduce[6],-0.6,14)
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fext = lmp.extract_fix("ext", LMP_STYLE_ATOM, LMP_TYPE_ARRAY)
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self.assertAlmostEqual(float(fext[0][0]), 0.0)
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self.assertAlmostEqual(float(fext[0][1]), 0.0)
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self.assertAlmostEqual(float(fext[0][2]), 0.0)
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self.assertAlmostEqual(float(fext[1][0]), 0.0)
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self.assertAlmostEqual(float(fext[1][1]), 0.0)
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self.assertAlmostEqual(float(fext[1][2]), 0.0)
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self.assertAlmostEqual(float(fext[2][0]), 0.0)
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self.assertAlmostEqual(float(fext[2][1]), 0.0)
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self.assertAlmostEqual(float(fext[2][2]), 0.0)
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lmp.command("run 10 post no")
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self.assertAlmostEqual(lmp.get_thermo("temp"),1.0/30.0,14)
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self.assertAlmostEqual(lmp.get_thermo("pe"),1.0/8.0,14)
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self.assertAlmostEqual(lmp.get_thermo("press"),0.15416666666666667,14)
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# check setting per-atom data numpy arrays
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reduce = lmp.extract_compute("sum", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR)
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self.assertAlmostEqual(reduce[0],2.8,14)
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self.assertAlmostEqual(reduce[1],-0.1,14)
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self.assertAlmostEqual(reduce[2],7.8,14)
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self.assertAlmostEqual(reduce[3],-0.3,14)
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self.assertAlmostEqual(reduce[4],-0.4,14)
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self.assertAlmostEqual(reduce[5],6.5,14)
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self.assertAlmostEqual(reduce[6],-0.6,14)
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val = 0.0
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for i in range(0,6):
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val += lmp.extract_fix("ext",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=i)
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self.assertAlmostEqual(val,15.0,14)
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fext = lmp.extract_fix("ext", LMP_STYLE_ATOM, LMP_TYPE_ARRAY)
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self.assertAlmostEqual(float(fext[0][0]), 10.0)
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self.assertAlmostEqual(float(fext[0][1]), 10.0)
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self.assertAlmostEqual(float(fext[0][2]), 10.0)
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self.assertAlmostEqual(float(fext[1][0]), 10.0)
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self.assertAlmostEqual(float(fext[1][1]), 10.0)
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self.assertAlmostEqual(float(fext[1][2]), 10.0)
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self.assertAlmostEqual(float(fext[2][0]), 10.0)
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self.assertAlmostEqual(float(fext[2][1]), 10.0)
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self.assertAlmostEqual(float(fext[2][2]), 10.0)
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def testExternalArray(self):
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"""Test fix external from Python with pf/array"""
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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, cmdargs=['-nocite', '-log','none', '-echo', 'screen'])
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# a few commands to set up simple system
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basic_system="""lattice sc 1.0
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region box block -1 1 -1 1 -1 1
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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pair_style zero 0.1
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pair_coeff 1 1
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velocity all set 0.1 0.0 -0.1
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fix 1 all nve
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fix ext all external pf/array 1
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fix_modify ext energy yes virial yes
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thermo_style custom step temp pe ke press
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thermo 5
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"""
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lmp.commands_string(basic_system)
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force = lmp.fix_external_get_force("ext");
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nlocal = lmp.extract_setting("nlocal");
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for i in range(nlocal):
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force[i][0] = 0.0
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force[i][1] = 0.0
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force[i][2] = 0.0
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lmp.fix_external_set_energy_global("ext", 0.5)
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lmp.fix_external_set_virial_global("ext",[0.5, 0.5, 0.5, 0.0, 0.0, 0.0])
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fext = lmp.extract_fix("ext", LMP_STYLE_ATOM, LMP_TYPE_ARRAY)
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self.assertAlmostEqual(float(fext[0][0]), 0.0)
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self.assertAlmostEqual(float(fext[0][1]), 0.0)
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self.assertAlmostEqual(float(fext[0][2]), 0.0)
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self.assertAlmostEqual(float(fext[1][0]), 0.0)
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self.assertAlmostEqual(float(fext[1][1]), 0.0)
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self.assertAlmostEqual(float(fext[1][2]), 0.0)
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self.assertAlmostEqual(float(fext[2][0]), 0.0)
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self.assertAlmostEqual(float(fext[2][1]), 0.0)
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self.assertAlmostEqual(float(fext[2][2]), 0.0)
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lmp.command("run 5 post no")
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self.assertAlmostEqual(lmp.get_thermo("temp"),4.0/525.0,14)
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self.assertAlmostEqual(lmp.get_thermo("pe"),1.0/16.0,14)
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self.assertAlmostEqual(lmp.get_thermo("press"),0.06916666666666667,14)
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if NUMPY_INSTALLED:
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npforce = lmp.numpy.fix_external_get_force("ext")
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self.assertEqual(len(npforce),8)
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self.assertEqual(len(npforce[0]),3)
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self.assertEqual(npforce[1][1],0.0)
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force = lmp.fix_external_get_force("ext");
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nlocal = lmp.extract_setting("nlocal");
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for i in range(nlocal):
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force[i][0] = 6.0
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force[i][1] = 6.0
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force[i][2] = 6.0
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lmp.fix_external_set_energy_global("ext", 1.0)
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lmp.fix_external_set_virial_global("ext",[1.0, 1.0, 1.0, 0.0, 0.0, 0.0])
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lmp.command("run 5 post no")
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self.assertAlmostEqual(lmp.get_thermo("temp"),1.0/30.0,14)
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self.assertAlmostEqual(lmp.get_thermo("pe"),1.0/8.0,14)
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self.assertAlmostEqual(lmp.get_thermo("press"),0.15416666666666667,14)
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if NUMPY_INSTALLED:
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npforce = lmp.numpy.fix_external_get_force("ext")
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self.assertEqual(npforce[0][0],6.0)
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self.assertEqual(npforce[3][1],6.0)
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self.assertEqual(npforce[7][2],6.0)
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fext = lmp.extract_fix("ext", LMP_STYLE_ATOM, LMP_TYPE_ARRAY)
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self.assertAlmostEqual(float(fext[0][0]), 6.0)
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self.assertAlmostEqual(float(fext[0][1]), 6.0)
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self.assertAlmostEqual(float(fext[0][2]), 6.0)
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self.assertAlmostEqual(float(fext[1][0]), 6.0)
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self.assertAlmostEqual(float(fext[1][1]), 6.0)
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self.assertAlmostEqual(float(fext[1][2]), 6.0)
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self.assertAlmostEqual(float(fext[2][0]), 6.0)
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self.assertAlmostEqual(float(fext[2][1]), 6.0)
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self.assertAlmostEqual(float(fext[2][2]), 6.0)
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##############################
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if __name__ == "__main__":
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unittest.main()
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