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add more unit tests for neighbor list access

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This commit is contained in:
Axel Kohlmeyer
2021-04-02 21:00:26 -04:00
parent 51212e62d9
commit c74bb9b56b
2 changed files with 209 additions and 22 deletions
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1
unittest/python/CMakeLists.txt
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@ -28,6 +28,7 @@ endif()
if(Python_EXECUTABLE)
# prepare to augment the environment so that the LAMMPS python module and the shared library is found.
set(PYTHON_TEST_ENVIRONMENT PYTHONPATH=${LAMMPS_PYTHON_DIR}:$ENV{PYTHONPATH})
list(APPEND PYTHON_TEST_ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
if(APPLE)
list(APPEND PYTHON_TEST_ENVIRONMENT "DYLD_LIBRARY_PATH=${CMAKE_BINARY_DIR}:$ENV{DYLD_LIBRARY_PATH};LAMMPS_CMAKE_CACHE=${CMAKE_BINARY_DIR}/CMakeCache.txt")
else()

230
unittest/python/python-commands.py
View File

@ -1,6 +1,17 @@
import sys,os,unittest
from lammps import lammps, LMP_VAR_ATOM
from lammps import lammps, LMP_VAR_ATOM, LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR
has_manybody=False
try:
machine=None
if 'LAMMPS_MACHINE_NAME' in os.environ:
machine=os.environ['LAMMPS_MACHINE_NAME']
lmp=lammps(name=machine)
has_manybody = lmp.has_style("pair","sw")
lmp.close()
except:
pass
class PythonCommand(unittest.TestCase):
@ -85,35 +96,34 @@ create_atoms 1 single &
natoms = self.lmp.get_natoms()
self.assertEqual(natoms,2)
def testNeighborList(self):
self.lmp.command("units lj")
self.lmp.command("atom_style atomic")
self.lmp.command("atom_modify map array")
self.lmp.command("boundary f f f")
self.lmp.command("region box block 0 2 0 2 0 2")
self.lmp.command("create_box 1 box")
x = [
1.0, 1.0, 1.0,
1.0, 1.0, 1.5
]
def testNeighborListSimple(self):
self.lmp.commands_string("""
units lj
atom_style atomic
atom_modify map array
boundary f f f
region box block 0 2 0 2 0 2
create_box 1 box""")
x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5 ]
types = [1, 1]
self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2)
nlocal = self.lmp.extract_global("nlocal")
self.assertEqual(nlocal, 2)
self.lmp.command("mass 1 1.0")
self.lmp.command("velocity all create 3.0 87287")
self.lmp.command("pair_style lj/cut 2.5")
self.lmp.command("pair_coeff 1 1 1.0 1.0 2.5")
self.lmp.command("neighbor 0.1 bin")
self.lmp.command("neigh_modify every 20 delay 0 check no")
self.lmp.commands_string("""
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.1 bin
neigh_modify every 20 delay 0 check no
run 0 post no""")
self.lmp.command("run 0")
self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"), 0)
idx = self.lmp.find_pair_neighlist("lj/cut")
self.assertEqual(0, 0)
self.assertEqual(self.lmp.find_pair_neighlist("morse"), -1)
nlist = self.lmp.get_neighlist(0)
self.assertEqual(len(nlist), 2)
atom_i, numneigh_i, neighbors_i = nlist[0]
@ -127,6 +137,182 @@ create_atoms 1 single &
self.assertEqual(1, neighbors_i[0])
def testNeighborListHalf(self):
self.lmp.commands_string("""
boundary f f f
units real
region box block -5 5 -5 5 -5 5
create_box 1 box
mass 1 1.0
pair_style lj/cut 4.0
pair_coeff 1 1 0.2 2.0
""")
x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0,
0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1,
0.0, 0.0, 1.0 ]
tags = [1, 2, 3, 4, 5, 6, 7]
types = [1, 1, 1, 1, 1, 1, 1]
self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
nlocal = self.lmp.extract_global("nlocal")
self.assertEqual(nlocal, 7)
self.lmp.command("run 0 post no")
self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"),0)
nlist = self.lmp.get_neighlist(0)
self.assertEqual(nlist.size, 7)
for i in range(0,nlist.size):
idx, num, neighs = nlist.get(i)
self.assertEqual(idx,i)
self.assertEqual(num,nlocal-1-i)
@unittest.skipIf(not has_manybody,"Full neighbor list test for manybody potential")
def testNeighborListFull(self):
self.lmp.commands_string("""
boundary f f f
units metal
region box block -5 5 -5 5 -5 5
create_box 1 box
mass 1 1.0
pair_style sw
pair_coeff * * Si.sw Si
""")
x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0,
0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1,
0.0, 0.0, 1.0 ]
tags = [1, 2, 3, 4, 5, 6, 7]
types = [1, 1, 1, 1, 1, 1, 1]
self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
nlocal = self.lmp.extract_global("nlocal")
self.assertEqual(nlocal, 7)
self.lmp.command("run 0 post no")
self.assertEqual(self.lmp.find_pair_neighlist("sw"),0)
nlist = self.lmp.get_neighlist(0)
self.assertEqual(nlist.size, 7)
for i in range(0,nlist.size):
idx, num, neighs = nlist.get(i)
self.assertEqual(idx,i)
self.assertEqual(num,nlocal-1)
@unittest.skipIf(not has_manybody,"Hybrid neighbor list test for manybody potential")
def testNeighborListHybrid(self):
self.lmp.commands_string("""
boundary f f f
units metal
region box block -5 5 -5 5 -5 5
create_box 2 box
mass * 1.0
pair_style hybrid/overlay morse 4.0 lj/cut 4.0 lj/cut 4.0 sw
pair_coeff * * sw Si.sw Si NULL
pair_coeff 1 2 morse 0.2 2.0 2.0
pair_coeff 2 2 lj/cut 1 0.1 2.0
pair_coeff * * lj/cut 2 0.01 2.0
""")
x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0,
0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1,
0.0, 0.0, 1.0 ]
tags = [1, 2, 3, 4, 5, 6, 7]
types = [1, 1, 1, 1, 2, 2, 2]
self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
nlocal = self.lmp.extract_global("nlocal")
self.assertEqual(nlocal, 7)
self.lmp.command("run 0 post no")
# valid and invalid lookups
self.assertNotEqual(self.lmp.find_pair_neighlist("sw"),-1)
self.assertNotEqual(self.lmp.find_pair_neighlist("morse"),-1)
self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut",nsub=1),-1)
self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut",nsub=2),-1)
self.assertEqual(self.lmp.find_pair_neighlist("lj/cut"),-1)
self.assertEqual(self.lmp.find_pair_neighlist("hybrid/overlay"),-1)
self.assertNotEqual(self.lmp.get_neighlist(4).size,0)
self.assertEqual(self.lmp.get_neighlist(5).size,-1)
# full neighbor list for 4 type 1 atoms
# all have 3 type 1 atom neighbors
nlist = self.lmp.get_neighlist(self.lmp.find_pair_neighlist("sw"))
self.assertEqual(nlist.size, 4)
for i in range(0,nlist.size):
idx, num, neighs = nlist.get(i)
self.assertEqual(idx,i)
self.assertEqual(num,3)
# half neighbor list for all pairs between type 1 and type 2
# 4 type 1 atoms with 3 type 2 neighbors and 3 type 2 atoms without neighbors
nlist = self.lmp.get_neighlist(self.lmp.find_pair_neighlist("morse"))
self.assertEqual(nlist.size, 7)
for i in range(0,nlist.size):
idx, num, neighs = nlist.get(i)
if (i < 4): self.assertEqual(num,3)
else: self.assertEqual(num,0)
# half neighbor list between type 2 atoms only
# 3 pairs with 2, 1, 0 neighbors
nlist = self.lmp.get_neighlist(self.lmp.find_pair_neighlist("lj/cut",nsub=1))
self.assertEqual(nlist.size, 3)
for i in range(0,nlist.size):
idx, num, neighs = nlist.get(i)
self.assertEqual(num,2-i)
# half neighbor list between all pairs. same as simple lj/cut case
nlist = self.lmp.get_neighlist(self.lmp.find_pair_neighlist("lj/cut",nsub=2))
self.assertEqual(nlist.size, 7)
for i in range(0,nlist.size):
idx, num, neighs = nlist.get(i)
self.assertEqual(num,nlocal-1-i)
def testNeighborListCompute(self):
self.lmp.commands_string("""
boundary f f f
units real
region box block -5 5 -5 5 -5 5
create_box 1 box
mass 1 1.0
pair_style lj/cut 4.0
pair_coeff 1 1 0.2 2.0
compute dist all pair/local dist
fix dist all ave/histo 1 1 1 0.0 3.0 4 c_dist mode vector
thermo_style custom f_dist[*]
""")
x = [ 0.0, 0.0, 0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0,
0.0, -1.1, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.1,
0.0, 0.0, 1.0 ]
tags = [1, 2, 3, 4, 5, 6, 7]
types = [1, 1, 1, 1, 1, 1, 1]
self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
nlocal = self.lmp.extract_global("nlocal")
self.assertEqual(nlocal, 7)
self.lmp.command("run 0 post no")
# check compute data from histogram summary
nhisto = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=0)
nskip = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=1)
minval = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=2)
maxval = self.lmp.extract_fix("dist",LMP_STYLE_GLOBAL,LMP_TYPE_VECTOR,nrow=3)
# 21 pair distances counted, none skipped, smallest 1.0, largest 2.1
self.assertEqual(nhisto,21)
self.assertEqual(nskip,0)
self.assertEqual(minval,1.0)
self.assertEqual(maxval,2.1)
self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut"),-1)
self.assertNotEqual(self.lmp.find_compute_neighlist("dist"),-1)
# the compute has a half neighbor list
nlist = self.lmp.get_neighlist(self.lmp.find_compute_neighlist("dist"))
self.assertEqual(nlist.size, 7)
for i in range(0,nlist.size):
idx, num, neighs = nlist.get(i)
self.assertEqual(idx,i)
self.assertEqual(num,nlocal-1-i)
def test_extract_box_non_periodic(self):
self.lmp.command("boundary f f f")
self.lmp.command("region box block 0 2 0 2 0 2")