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