
import sys,os,unittest,ctypes
from lammps import lammps, LMP_VAR_ATOM, LMP_STYLE_GLOBAL, LMP_STYLE_LOCAL
from lammps import LMP_TYPE_VECTOR, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS
from lammps import LAMMPS_DOUBLE_2D, LAMMPS_AUTODETECT
import math

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

has_streitz=False
try:
    machine=None
    if 'LAMMPS_MACHINE_NAME' in os.environ:
        machine=os.environ['LAMMPS_MACHINE_NAME']
    lmp=lammps(name=machine)
    has_streitz = lmp.has_style("pair","coul/streitz")
    lmp.close()
except:
    pass

class PythonCommand(unittest.TestCase):

    def setUp(self):
        machine=None
        if 'LAMMPS_MACHINE_NAME' in os.environ:
            machine=os.environ['LAMMPS_MACHINE_NAME']
        self.lmp=lammps(name=machine,
                        cmdargs=['-nocite',
                                 '-log','none',
                                 '-echo','screen',
                                 '-var','zpos','1.5',
                                 '-var','x','2'])
        # create demo input strings and files
        # a few commands to set up a box with a single atom
        self.demo_input="""
region       box block 0 $x 0 2 0 2
create_box 1 box
create_atoms 1 single 1.0 1.0 ${zpos}
"""
        # another command to add an atom and use a continuation line
        self.cont_input="""
create_atoms 1 single &
            0.2 0.1 0.1
"""
        self.demo_file='in.test'
        with open(self.demo_file,'w') as f:
            f.write(self.demo_input)
        self.cont_file='in.cont'
        with open(self.cont_file,'w') as f:
            f.write(self.cont_input)

    # clean up temporary files
    def tearDown(self):
        if os.path.exists(self.demo_file):
            os.remove(self.demo_file)
        if os.path.exists(self.cont_file):
            os.remove(self.cont_file)

    ##############################
    def testFile(self):
        """Test reading commands from a file"""
        natoms = self.lmp.get_natoms()
        self.assertEqual(natoms,0)
        self.lmp.file(self.demo_file)
        natoms = self.lmp.get_natoms()
        self.assertEqual(natoms,1)
        self.lmp.file(self.cont_file)
        natoms = self.lmp.get_natoms()
        self.assertEqual(natoms,2)

    def testNoFile(self):
        """Test (not) reading commands from no file"""
        self.lmp.file(None)
        natoms = self.lmp.get_natoms()
        self.assertEqual(natoms,0)

    def testCommand(self):
        """Test executing individual commands"""
        natoms = self.lmp.get_natoms()
        self.assertEqual(natoms,0)
        cmds = self.demo_input.splitlines()
        for cmd in cmds:
            self.lmp.command(cmd)
        natoms = self.lmp.get_natoms()
        self.assertEqual(natoms,1)

    def testCommandsList(self):
        """Test executing commands from list of strings"""
        natoms = self.lmp.get_natoms()
        self.assertEqual(natoms,0)
        cmds = self.demo_input.splitlines()+self.cont_input.splitlines()
        self.lmp.commands_list(cmds)
        natoms = self.lmp.get_natoms()
        self.assertEqual(natoms,2)

    def testCommandsString(self):
        """Test executing block of commands from string"""
        natoms = self.lmp.get_natoms()
        self.assertEqual(natoms,0)
        self.lmp.commands_string(self.demo_input+self.cont_input)
        natoms = self.lmp.get_natoms()
        self.assertEqual(natoms,2)

    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.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""")

        idx = self.lmp.find_pair_neighlist("lj/cut")
        self.assertNotEqual(idx, -1)
        self.assertEqual(self.lmp.find_pair_neighlist("morse"), -1)
        nlist = self.lmp.get_neighlist(idx)
        self.assertEqual(len(nlist), 2)
        atom_i, numneigh_i, neighbors_i = nlist[0]
        atom_j, numneigh_j, _ = nlist[1]

        self.assertEqual(atom_i, 0)
        self.assertEqual(atom_j, 1)

        self.assertEqual(numneigh_i, 1)
        self.assertEqual(numneigh_j, 0)

        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)

        # look up neighbor list by atom index
        num, neighs = nlist.find(2)
        self.assertEqual(num,4)
        self.assertIsNotNone(neighs,None)
        # this one will fail
        num, neighs = nlist.find(10)
        self.assertEqual(num,-1)
        self.assertIsNone(neighs,None)

    @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)

    def testNeighborListZeroHalf(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 zero 4.0
        pair_coeff 1 1
        """)
        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("zero"),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)

        # look up neighbor list by atom index
        num, neighs = nlist.find(2)
        self.assertEqual(num,4)
        self.assertIsNotNone(neighs,None)
        # this one will fail
        num, neighs = nlist.find(10)
        self.assertEqual(num,-1)
        self.assertIsNone(neighs,None)

    def testNeighborListZeroFull(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 zero 4.0 full
        pair_coeff * *
        """)
        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("zero"),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)

        ndist1 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_VECTOR)
        ndist2 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_ROWS)
        ndist3 = self.lmp.extract_compute("dist",LMP_STYLE_LOCAL,LMP_SIZE_COLS)

        self.assertEqual(ndist1,21)
        self.assertEqual(ndist2,21)
        self.assertEqual(ndist3,0)

        self.assertNotEqual(self.lmp.find_pair_neighlist("lj/cut"),-1)
        self.assertNotEqual(self.lmp.find_compute_neighlist("dist"),-1)
        self.assertEqual(self.lmp.find_compute_neighlist("xxx"),-1)
        self.assertEqual(self.lmp.find_fix_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")
        self.lmp.command("create_box 1 box")

        boxlo, boxhi, xy, yz, xz, periodicity, box_change = self.lmp.extract_box()

        self.assertEqual(boxlo, [0.0, 0.0, 0.0])
        self.assertEqual(boxhi, [2.0, 2.0, 2.0])
        self.assertEqual(xy, 0.0)
        self.assertEqual(yz, 0.0)
        self.assertEqual(xz, 0.0)
        self.assertEqual(periodicity, [0, 0, 0])
        self.assertEqual(box_change, 0)

    def test_extract_box_periodic(self):
        self.lmp.command("boundary p p p")
        self.lmp.command("region box block 0 2 0 2 0 2")
        self.lmp.command("create_box 1 box")

        boxlo, boxhi, xy, yz, xz, periodicity, box_change = self.lmp.extract_box()

        self.assertEqual(boxlo, [0.0, 0.0, 0.0])
        self.assertEqual(boxhi, [2.0, 2.0, 2.0])
        self.assertEqual(xy, 0.0)
        self.assertEqual(yz, 0.0)
        self.assertEqual(xz, 0.0)
        self.assertEqual(periodicity, [1, 1, 1])
        self.assertEqual(box_change, 0)

    def test_extract_box_triclinic(self):
        self.lmp.command("boundary p p p")
        self.lmp.command("region box prism 0 2 0 2 0 2 0.1 0.2 0.3")
        self.lmp.command("create_box 1 box")

        boxlo, boxhi, xy, yz, xz, periodicity, box_change = self.lmp.extract_box()

        self.assertEqual(boxlo, [0.0, 0.0, 0.0])
        self.assertEqual(boxhi, [2.0, 2.0, 2.0])
        self.assertEqual(xy, 0.1)
        self.assertEqual(xz, 0.2)
        self.assertEqual(yz, 0.3)
        self.assertEqual(periodicity, [1, 1, 1])
        self.assertEqual(box_change, 0)

    def test_reset_box(self):
        self.lmp.command("boundary p p p")
        self.lmp.command("region box block 0 2 0 2 0 2")
        self.lmp.command("create_box 1 box")
        self.lmp.command("change_box all triclinic")
        self.lmp.command("change_box all xy final 0.1 yz final 0.2 xz final 0.3")
        self.lmp.reset_box([0,0,0], [1,1,1], 0, 0, 0)

        boxlo, boxhi, xy, yz, xz, periodicity, box_change = self.lmp.extract_box()

        self.assertEqual(boxlo, [0.0, 0.0, 0.0])
        self.assertEqual(boxhi, [1.0, 1.0, 1.0])
        self.assertEqual(xy, 0)
        self.assertEqual(yz, 0)
        self.assertEqual(xz, 0)
        self.assertEqual(periodicity, [1, 1, 1])
        self.assertEqual(box_change, 0)

    def test_extract_variable_equalstyle(self):
        self.lmp.command("variable a equal 100")
        a = self.lmp.extract_variable("a")
        self.assertEqual(a, 100)

        self.lmp.command("variable a equal 3.14")
        a = self.lmp.extract_variable("a")
        self.assertEqual(a, 3.14)

    def test_extract_variable_stringstyle(self):
        self.lmp.command("variable a string xxx")
        a = self.lmp.extract_variable("a")
        self.assertEqual(a, 'xxx')

        rv = self.lmp.set_string_variable("a","20")
        a = self.lmp.extract_variable("a")
        self.assertEqual(a, '20')
        self.assertEqual(rv, 0)

    def test_extract_variable_internalstyle(self):
        self.lmp.command("variable a internal 2.0")
        a = self.lmp.extract_variable("a")
        self.assertEqual(a, 2.0)

        rv = self.lmp.set_internal_variable("a",-4.5)
        a = self.lmp.extract_variable("a")
        self.assertEqual(a, -4.5)
        self.assertEqual(rv, 0)

    def test_extract_variable_atomstyle(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
        ]

        types = [1, 1]

        self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2)
        self.lmp.command("variable a atom x*x+y*y+z*z")
        a = self.lmp.extract_variable("a", "all", LMP_VAR_ATOM)
        self.assertEqual(a[0], x[0]*x[0]+x[1]*x[1]+x[2]*x[2])
        self.assertEqual(a[1], x[3]*x[3]+x[4]*x[4]+x[5]*x[5])

    def test_get_thermo(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
        ]

        types = [1, 1]
        self.lmp.create_atoms(2, id=None, type=types, x=x)

        state = {
            "step": 0,
            "dt" : 0.005,
            "time" : 0.0,
            "atoms" : 2.0,
            "vol" : 8.0,
            "lx" : 2.0,
            "ly" : 2.0,
            "lz" : 2.0,
            "xlo" : 0,
            "xhi" : 2.0,
            "ylo" : 0,
            "yhi" : 2.0,
            "zlo" : 0,
            "zhi" : 2.0
        }

        for key, value in state.items():
            result = self.lmp.get_thermo(key)
            self.assertEqual(value, result, key)


    def test_last_thermo(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")
        self.lmp.command("mass * 1")

        x = [
          0.5, 0.5, 0.5,
          1.5, 1.5, 1.5
        ]
        types = [1, 1]
        self.lmp.create_atoms(2, id=None, type=types, x=x)

        self.assertEqual(self.lmp.last_thermo(), None)
        self.lmp.command("run 2 post no")
        ref = { "Step" : 2,
                "Temp" : 0.0,
                "E_pair" : 0.0,
                "E_mol" : 0.0,
                "TotEng" : 0.0,
                "Press" : 0.0}
        self.assertDictEqual(self.lmp.last_thermo(), ref)

    def test_extract_setting(self):
        self.assertEqual(self.lmp.extract_setting("dimension"), 3)
        self.assertEqual(self.lmp.extract_setting("box_exist"), 0)
        self.assertEqual(self.lmp.extract_setting("kokkos_active"), 0)
        self.assertEqual(self.lmp.extract_setting("kokkos_nthreads"), 0)
        self.assertEqual(self.lmp.extract_setting("kokkos_ngpus"), 0)
        self.lmp.command("region box block -1 1 -2 2 -3 3")
        self.lmp.command("create_box 1 box")
        self.lmp.command("special_bonds lj 0.0 0.5 0.8 coul 0.1 0.5 1.0")
        self.assertEqual(self.lmp.extract_setting("newton_bond"), 1)
        self.assertEqual(self.lmp.extract_setting("newton_pair"), 1)
        self.assertEqual(self.lmp.extract_setting("triclinic"), 0)
        self.assertEqual(self.lmp.extract_setting("universe_rank"), 0)
        self.assertEqual(self.lmp.extract_setting("universe_size"), 1)
        self.assertEqual(self.lmp.extract_setting("world_rank"), 0)
        self.assertEqual(self.lmp.extract_setting("world_size"), 1)
        self.assertEqual(self.lmp.extract_setting("triclinic"), 0)
        self.assertEqual(self.lmp.extract_setting("comm_style"), 0)
        self.assertEqual(self.lmp.extract_setting("comm_layout"), 0)
        self.assertEqual(self.lmp.extract_setting("comm_mode"), 0)
        self.assertEqual(self.lmp.extract_setting("ghost_velocity"), 0)
        self.lmp.command("comm_style tiled")
        self.lmp.command("comm_modify vel yes")
        self.lmp.command("mass 1 1.0")
        self.lmp.command("run 0 post no")
        self.lmp.command("balance 0.1 rcb")
        self.assertEqual(self.lmp.extract_setting("comm_style"), 1)
        self.assertEqual(self.lmp.extract_setting("comm_layout"), 2)
        self.assertEqual(self.lmp.extract_setting("comm_mode"), 0)
        self.assertEqual(self.lmp.extract_setting("ghost_velocity"), 1)

    def test_extract_global(self):
        self.lmp.command("region box block -1 1 -2 2 -3 3")
        self.lmp.command("create_box 1 box")
        self.lmp.command("special_bonds lj 0.0 0.5 0.8 coul 0.1 0.5 1.0")
        self.assertEqual(self.lmp.extract_global("units"), "lj")
        self.assertEqual(self.lmp.extract_global("ntimestep"), 0)
        self.assertEqual(self.lmp.extract_global("dt"), 0.005)

        self.assertEqual(self.lmp.extract_global("boxxlo"), -1.0)
        self.assertEqual(self.lmp.extract_global("boxxhi"), 1.0)
        self.assertEqual(self.lmp.extract_global("boxylo"), -2.0)
        self.assertEqual(self.lmp.extract_global("boxyhi"), 2.0)
        self.assertEqual(self.lmp.extract_global("boxzlo"), -3.0)
        self.assertEqual(self.lmp.extract_global("boxzhi"), 3.0)
        self.assertEqual(self.lmp.extract_global("boxlo"), [-1.0, -2.0, -3.0])
        self.assertEqual(self.lmp.extract_global("boxhi"), [1.0, 2.0, 3.0])
        self.assertEqual(self.lmp.extract_global("sublo"), [-1.0, -2.0, -3.0])
        self.assertEqual(self.lmp.extract_global("subhi"), [1.0, 2.0, 3.0])
        self.assertEqual(self.lmp.extract_global("periodicity"), [1,1,1])
        self.assertEqual(self.lmp.extract_global("triclinic"), 0)
        self.assertEqual(self.lmp.extract_global("special_lj"), [1.0, 0.0, 0.5, 0.8])
        self.assertEqual(self.lmp.extract_global("special_coul"), [1.0, 0.1, 0.5, 1.0])
        self.assertEqual(self.lmp.extract_global("sublo_lambda"), None)
        self.assertEqual(self.lmp.extract_global("subhi_lambda"), None)
        self.assertEqual(self.lmp.extract_global("respa_levels"), None)
        self.assertEqual(self.lmp.extract_global("respa_dt"), None)
        self.lmp.command("special_bonds lj/coul 0.0 1.0 1.0")
        self.assertEqual(self.lmp.extract_global("special_lj"), [1.0, 0.0, 1.0, 1.0])
        self.assertEqual(self.lmp.extract_global("special_coul"), [1.0, 0.0, 1.0, 1.0])
        self.assertEqual(self.lmp.extract_global("map_style"), 0)
        self.assertEqual(self.lmp.extract_global("map_tag_max"), -1)
        self.assertEqual(self.lmp.extract_global("sortfreq"), 1000)
        self.assertEqual(self.lmp.extract_global("nextsort"), 0)
        self.assertEqual(self.lmp.extract_global("xlattice"), 1.0)
        self.assertEqual(self.lmp.extract_global("ylattice"), 1.0)
        self.assertEqual(self.lmp.extract_global("zlattice"), 1.0)

        # set and initialize r-RESPA
        self.lmp.command("run_style respa 3 5 2 pair 2 kspace 3")
        self.lmp.command("mass * 1.0")
        self.lmp.command("run 1 post no")
        self.assertEqual(self.lmp.extract_global("ntimestep"), 1)
        self.assertEqual(self.lmp.extract_global("respa_levels"), 3)
        self.assertEqual(self.lmp.extract_global("respa_dt"), [0.0005, 0.0025, 0.005])

        # checks only for triclinic boxes
        self.lmp.command("change_box all triclinic")
        self.assertEqual(self.lmp.extract_global("triclinic"), 1)
        self.assertEqual(self.lmp.extract_global("sublo_lambda"), [0.0, 0.0, 0.0])
        self.assertEqual(self.lmp.extract_global("subhi_lambda"), [1.0, 1.0, 1.0])

        # processor grid
        self.assertEqual(self.lmp.extract_global("procgrid"), [1,1,1])
        self.lmp.command("comm_style tiled")
        self.lmp.command("run 0 post no")
        self.lmp.command("balance 0.1 rcb")
        self.assertEqual(self.lmp.extract_global("procgrid"), None)

    def test_extract_pair1(self):
        self.lmp.command("region box block 0 1 0 1 0 1")
        self.lmp.command("create_box 3 box")
        self.lmp.command("mass * 1.0")
        self.lmp.command("pair_style lj/cut 3.0")
        self.lmp.command("pair_coeff 1 1 1.0 1.0")
        self.lmp.command("pair_coeff 2 2 1.5 2.0")
        self.lmp.command("pair_coeff 3 3 1.0 3.0")
        self.lmp.command("run 0 post no")
        self.assertEqual(self.lmp.extract_pair_dimension("epsilon"), 2)
        self.assertEqual(self.lmp.extract_pair_dimension("sigma"), 2)
        self.assertEqual(self.lmp.extract_pair_dimension("cut_coul"), None)
        sigma = self.lmp.extract_pair("sigma")
        self.assertEqual(sigma[1][1], 1.0)
        self.assertEqual(sigma[2][2], 2.0)
        self.assertEqual(sigma[3][3], 3.0)
        self.assertEqual(sigma[1][2], math.sqrt(2.0))

    @unittest.skipIf(not has_streitz, "Pair extract for coul/streitz test")
    def test_extract_pair2(self):
        self.lmp.command("units metal")
        self.lmp.command("atom_style charge")
        self.lmp.command("region box block 0 1 0 1 0 1")
        self.lmp.command("create_box 2 box")
        self.lmp.command("mass * 1.0")
        self.lmp.command("pair_style coul/streitz 12.0 wolf 0.31")
        self.lmp.command("pair_coeff * * AlO.streitz Al O")
        self.lmp.command("run 0 post no")

        self.assertEqual(self.lmp.extract_pair_dimension("chi"), 1)
        self.assertEqual(self.lmp.extract_pair_dimension("scale"), 2)
        self.assertEqual(self.lmp.extract_pair_dimension("cut_coul"), 0)
        self.assertEqual(self.lmp.extract_pair_dimension("epsilon"), None)

        self.assertEqual(self.lmp.extract_pair("cut_coul"), 12.0)
        self.assertEqual(self.lmp.extract_pair("chi"), [0.0, 0.0, 5.484763])
        scale = self.lmp.extract_pair("scale")
        self.assertEqual(scale[0][0], 0.0);
        self.assertEqual(scale[0][1], 0.0);
        self.assertEqual(scale[1][1], 1.0);
        self.assertEqual(scale[1][2], 1.0);
        self.assertEqual(scale[2][2], 1.0);

    def test_create_atoms(self):
        self.lmp.command("boundary f p m")
        self.lmp.command("region box block 0 10 0 10 0 10")
        self.lmp.command("create_box 2 box")
        # second atom is outside the box -> dropped
        self.lmp.create_atoms(2, [1,2], [1,1], [1.0, 1.0, 3.0, 5.0, 8.0, 12.0])
        self.assertEqual(self.lmp.get_natoms(),1)
        # non-zero velocities
        self.lmp.create_atoms(2, None, [2,2], [2.0, 2.0, 1.0, 3.0, 4.0, 6.0], v=[0.1, 0.2, 0.3, -0.1, -0.2, -0.3])
        self.assertEqual(self.lmp.get_natoms(),3)
        # first atom is dropped, extend shrinkwrapped box for second atom, third atoms is wrapped around PBC.
        self.lmp.create_atoms(3, [5,8,10], [1,2,1], [-1.0, 1.0, 3.0, 5.0, 8.0, 12.0, 1.0, -1.0, 1.0], shrinkexceed=True)
        self.assertEqual(self.lmp.get_natoms(),5)
        # set image flags
        self.lmp.create_atoms(1, None, [2], [5.0, 8.0, 1.0], image=[self.lmp.encode_image_flags(1,0,-1)])
        self.assertEqual(self.lmp.get_natoms(),6)
        tag = self.lmp.extract_atom("id")
        typ = self.lmp.extract_atom("type")
        pos = self.lmp.extract_atom("x",LAMMPS_DOUBLE_2D)
        vel = self.lmp.extract_atom("v",LAMMPS_DOUBLE_2D)
        img = self.lmp.extract_atom("image",LAMMPS_AUTODETECT)
        # expected results: tag, type, x, v, image
        result = [ [ 1, 1, [1.0, 1.0,  3.0], [ 0.0,  0.0,  0.0], [0, 0,  0]],\
                   [ 2, 2, [2.0, 2.0,  1.0], [ 0.1,  0.2,  0.3], [0, 0,  0]],\
                   [ 3, 2, [3.0, 4.0,  6.0], [-0.1, -0.2, -0.3], [0, 0,  0]],\
                   [ 8, 2, [5.0, 8.0, 12.0], [ 0.0,  0.0,  0.0], [0, 0,  0]],\
                   [10, 1, [1.0, 9.0,  1.0], [ 0.0,  0.0,  0.0], [0, 0,  0]],\
                   [11, 2, [5.0, 8.0,  1.0], [ 0.0,  0.0,  0.0], [1, 0, -1]] ]
        for i in range(len(result)):
            self.assertEqual(tag[i],result[i][0])
            self.assertEqual(typ[i],result[i][1])
            for j in range(3):
                self.assertEqual(pos[i][0:3],result[i][2])
                self.assertEqual(vel[i][0:3],result[i][3])
                self.assertEqual(self.lmp.decode_image_flags(img[i]), result[i][4])

    def test_map_atom(self):
        self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR'])
        self.lmp.command("newton on on")
        self.lmp.file("in.fourmol")
        self.lmp.command("run 4 post no")
        sometags = [1, 10, 25, 29]
        tags = self.lmp.extract_atom("id")
        sametag = self.lmp.extract_global("sametag")
        for mytag in sometags:
            myidx = self.lmp.map_atom(mytag)
            self.assertEqual(mytag, tags[myidx])
            if sametag[myidx] < 0: continue
            self.assertEqual(mytag, tags[sametag[myidx]])

##############################
if __name__ == "__main__":
    unittest.main()
