mcell/mdl/testsuite/reactions/test_reactions.py

#! /usr/bin/env python

from testutils import McellTest
from testutils import get_output_dir
from testutils import cleandir
from reaction_output import RequireCountConstraints
from reaction_output import RequireCountEquilibrium
from reaction_output import RequireCountRxnRate
from reaction_output import RequireCounts
from reaction_output import RequireCountsPositive
from reaction_output import RequireCountsPositiveOrZero
from reaction_output import RequireHitsCrossRelations
from reaction_output import RequireValidTriggerOutput
import unittest
import math

class TestReactionsNumeric(unittest.TestCase):

  def test_volume(self):
    t = McellTest("reactions", "01-volume_highconc.mdl", ["-quiet"])
    t.add_extra_check(RequireCountConstraints("dat/01-volume_highconc/V_out.dat",
                            [(0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0),    # 1000
                             (0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0),    # 1000
                             (0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0),    # 1000
                             (0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0),    # 1000
                             (0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0),    # 1000
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0),    # 1000
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0),    # 1000
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1)],   # 1000
                            [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000],
                            header=True))
    t.add_extra_check(RequireCountEquilibrium("dat/01-volume_highconc/V_out.dat",
                            [500] * 26,
                            [25]  * 26,
                            header=True))
    t.add_extra_check(RequireCountRxnRate("dat/01-volume_highconc/rxn_out.dat",
                            values=[1e5]*7 + [3.33e4]*1 +[1e5]*7 + [3.33e4]*1,
                            tolerances=[1.5e4]*7 + [5e3]*1 +[1.5e4]*7 + [5e3]*1,
                            min_time=5e-3,
                            base_time=0.0,
                            header=True))
    t.invoke(get_output_dir())

  def test_volume_noacc3d(self):
    t = McellTest("reactions", "02-volume_highconc_noacc3d.mdl", ["-quiet"])
    t.add_extra_check(RequireCountConstraints("dat/02-volume_highconc_noacc3d/V_out.dat",
                            [(0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0),    # 0
                             (1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0),    # 1000
                             (0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0),    # 1000
                             (0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0),    # 1000
                             (0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0),    # 1000
                             (0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0),    # 1000
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0),    # 1000
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0),    # 1000
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1)],   # 1000
                            [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000],
                            header=True))
    t.add_extra_check(RequireCountEquilibrium("dat/02-volume_highconc_noacc3d/V_out.dat",
                            [500] * 26,
                            [25]  * 26,
                            header=True))
    t.add_extra_check(RequireCountRxnRate("dat/02-volume_highconc_noacc3d/rxn_out.dat",
                            values=    [1e5] * 5 + [2e4] * 3 + [1e5] * 5 + [2e4] * 3,
                            tolerances=([1.5e4] * 5) + ([6e3] * 3) + ([1.5e4] * 5) + ([6e3] * 3),
                            min_time=5e-3,
                            base_time=0.0,
                            header=True))
    t.invoke(get_output_dir())

  def test_surface(self):
    t = McellTest("reactions", "03-surface.mdl", ["-quiet"])
    t.add_extra_check(RequireCountConstraints("dat/03-surface/V_out.dat",
                            [(0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_b1             == S_b2 */
                             (0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_b3             == S_b4 */
                             (0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_bt1            == S_bt2 */
                             (0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_bt3            == S_bt4 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_t1             == S_t2 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_t1             == S_t3 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_t4             == S_t5 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_t4             == S_t6 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_t7             == S_t8 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_t7             == S_t9 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_b1             == S_vb2 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_bt1            == S_vbt2 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_b3             == S_vb4 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_bt3            == S_vbt4 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_t1             == S_vt2 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_t1             == S_vt3 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_t4             == S_vt5 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_t4             == S_vt6 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_t7             == S_vt8 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_t7             == S_vt9 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_vt1            == S_vvt2 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_vt1            == S_vvt3 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_vt4            == S_vvt5 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_vt4            == S_vvt6 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_vt7            == S_vvt8 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_vt7            == S_vvt9 */
                             (1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 1000    /* S_u   + B_u      == 1000 */
                             (0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 1000    /* S_b1  + B_b      == 1000 */
                             (0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 1000    /* S_b3  + B_b2     == 1000 */
                             (0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 1000    /* S_bt1 + B_bt     == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 1000    /* S_bt3 + B_bt2    == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 1000    /* S_t1  + B_t      == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 1000    /* S_t4  + B_t2     == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 1000    /* S_t7  + B_t3     == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 1000    /* V_b1  + B_vb     == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0),    # 1000    /* V_bt1 + B_vbt    == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0),    # 1000    /* V_b3  + B_vb2    == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0),    # 1000    /* V_bt3 + B_vbt2   == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0),    # 1000    /* V_t1  + B_vt     == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0),    # 1000    /* V_t4  + B_vt2    == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0),    # 1000    /* V_t7  + B_vt3    == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0),    # 1000    /* V_vt1 + B_vvt    == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0),    # 1000    /* V_vt4 + B_vvt2   == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1)],   # 1000    /* V_vt4 + B_vvt2   == 1000 */
                            [0]*26 + [1000]*18,
                            header=True))
    t.add_extra_check(RequireCountEquilibrium("dat/03-surface/V_out.dat",
                            [500] * 62,
                            [25]  * 62,
                            header=True))
    t.add_extra_check(RequireCountRxnRate("dat/03-surface/rxn_out.dat",
                            values=    [1e5] * 15 + [1e4]*3 + [1e5] * 15 + [1e4]*3,
                            tolerances=[1.5e4] * 15 + [7.0e3] * 3 + [1.5e4] * 15 + [7.0e3] * 3,
                            min_time=5e-3,
                            base_time=0.0,
                            header=True))
    t.add_extra_check(RequireCountRxnRate("dat/03-surface/b19_rxn_out.dat",
                            values=    [3.3e4] * 4,
                            tolerances=[0.99e4] * 4,
                            min_time=5e-3,
                            base_time=0.0,
                            header=True))
    t.add_extra_check(RequireCountRxnRate("dat/03-surface/b20_rxn_out.dat",
                            values=    [5.0e4] * 1 + [2.5e4] * 3,
                            tolerances=[1.0e4] * 1 + [0.5e4] * 3,
                            min_time=5e-3,
                            base_time=0.0,
                            header=True))
    t.invoke(get_output_dir())

  def test_surface_with_surface_class(self):
    t = McellTest("reactions", "04-surface.mdl", ["-quiet"])
    t.add_extra_check(RequireCountConstraints("dat/04-surface/V_out.dat",
                            [(0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_b1             == S_b2 */
                             (0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_b3             == S_b4 */
                             (0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_bt1            == S_bt2 */
                             (0,  0,  0,  0,  0,  0,  0,  1, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* S_bt3            == S_bt4 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 0),    # 0       /* V_b1             == S_vb2 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  -1,  0,  0,  0,  0,  0,  0,  0,  0, 0,  0,  0,  0,  0),    # 0       /* V_bt1            == S_vbt2 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),    # 0       /* V_b3             == S_vb4 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  -1,  0,  0,  0,  0,  0,  0,  0,  0, 0),    # 0       /* V_bt3            == S_vbt4 */
                             (1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0),    # 1000    /* S_u   + B_u      == 1000 */
                             (0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0),    # 1000    /* S_b1  + B_b      == 1000 */
                             (0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0),    # 1000    /* S_b3  + B_b2     == 1000 */
                             (0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0),    # 1000    /* S_bt1 + B_bt     == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0),    # 1000    /* S_bt3 + B_bt2    == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0),    # 1000    /* V_b1  + B_vb     == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0),    # 1000    /* V_bt1 + B_vbt    == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0),    # 1000    /* V_b3  + B_vb2    == 1000 */
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1)],    # 1000    /* V_bt3 + B_vbt2   == 1000 */
                            [0]*8 + [1000]*9,
                            header=True))
    t.add_extra_check(RequireCountEquilibrium("dat/04-surface/V_out.dat",
                            [500] * 26,
                            [25]  * 26,
                            header=True))
    t.add_extra_check(RequireCountRxnRate("dat/04-surface/rxn_out.dat",
                            values=    [1e5] * 18,
                            tolerances=[1.5e4] * 18,
                            min_time=5e-3,
                            base_time=0.0,
                            header=True))
    t.add_extra_check(RequireCountEquilibrium("dat/04-surface/b13_u_out.dat",
                            [500] * 2,
                            [50]  * 2,
                            header=True))
    t.add_extra_check(RequireCountRxnRate("dat/04-surface/b13_u_rxn_out.dat",
                            values=    [3.3e4] * 6,
                            tolerances=[0.99e4] * 6,
                            min_time=5e-3,
                            base_time=0.0,
                            header=True))
    t.add_extra_check(RequireCountEquilibrium("dat/04-surface/b14_u_out.dat",
                            [1000] * 2,
                            [50]  * 2,
                            header=True))
    t.add_extra_check(RequireCountRxnRate("dat/04-surface/b14_u_rxn_out.dat",
                            values=    [8.0e4]*2 + [4.0e4]*2 + [2.4e4]*2,
                            tolerances=[2.4e4]*2 + [1.2e4]*2 + [0.72e4]*2,
                            min_time=5e-3,
                            base_time=0.0,
                            header=True))
    t.add_extra_check(RequireCountEquilibrium("dat/04-surface/b15_u_out.dat",
                            [1000] * 2,
                            [50]  * 2,
                            header=True))
    t.add_extra_check(RequireCountRxnRate("dat/04-surface/b15_u_rxn_out.dat",
                            values=    [2.4e4]*2 + [4.0e4]*2 + [8.0e4]*2,
                            tolerances=[0.72e4]*2 + [1.2e4]*2 + [2.4e4]*2,
                            min_time=5e-3,
                            base_time=0.0,
                            header=True))
    t.add_extra_check(RequireCountRxnRate("dat/04-surface/b16_b_rxn_out.dat",
                            values=    [5.1e4] * 3,
                            tolerances=[1.02e4] * 3,
                            min_time=5e-3,
                            base_time=0.0,
                            header=True))
    t.add_extra_check(RequireCountRxnRate("dat/04-surface/b17_b_rxn_out.dat",
                            values=    [7.26e4] + [3.63e4] + [2.18e4],
                            tolerances=[1.04e4]  + [0.73e4] + [0.44e4],
                            min_time=5e-3,
                            base_time=0.0,
                            header=True))

    t.invoke(get_output_dir())

  def test_region_borders_cube(self):
    # The test is done on the cube with simple region border geometry.
    # Region r1 borders are REFLECTIVE for molecule A, ABSORPTIVE for B,
    # and TRANSPARENT for C.  Initially we place 100 molecules of each type
    # inside region r1. We check that all molecules A are contained
    # within r1 and there are none of them in the surrounding region r2.
    # Because B has high diffusion coefficient, they all get absorbed
    # at the border, and after some time we should register none of them
    # inside either r1 or r2. The total count of C as sum across regions
    # r1 and r2 is constant over the simulation.
    # Region r3 borders are REFLECTIVE for molecules D and E. We place
    # 100 molecules D there that also undergo unimolecular reaction
    # D @ surface_class -> E[rate].  We check that total sum of D and E
    # within the region r3 is equal to 100. 
    t = McellTest("reactions", "07-region_borders.mdl", ["-quiet"])
    
    t.add_extra_check(RequireCounts("dat/07-region_borders/box_1_A.dat", [(f*1e-6,100,0) for f in range(0,101)], "# Seconds r1_A r2_A"))
    t.add_extra_check(RequireCounts("dat/07-region_borders/box_1_B.dat", [(f*1e-6,0,0) for f in range(70,101)], "# Seconds r1_B r2_B"))
    t.add_extra_check(RequireCountConstraints("dat/07-region_borders/box_1_C.dat",         constraints=[(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1), 
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1)],
        totals = [100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100],
                  header=True))
    t.add_extra_check(RequireCountConstraints("dat/07-region_borders/box_1_r3.dat",         constraints=[(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1), 
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1)],
        totals = [100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100],
                  header=True))
    t.add_extra_check(RequireCounts("dat/07-region_borders/box_2_r4.dat", [(f*1e-6,0) for f in range(70,101)], "# Seconds r4_A"))
    t.add_extra_check(RequireCountsPositive("dat/07-region_borders/box_2_A.dat","# Seconds r2_A r3_A"))
    t.add_extra_check(RequireCounts("dat/07-region_borders/box_3_r5.dat", [(f*1e-6,200) for f in range(70,101)], "# Seconds r5_A"))
    t.add_extra_check(RequireCounts("dat/07-region_borders/box_3_r6.dat", [(f*1e-6,0) for f in range(70,101)], "# Seconds r6_A"))

    t.invoke(get_output_dir())
  
  def test_region_borders_sphere(self):
    # The test is done on the sphere with complex region border geometry.
    # Region  r1 boundary crosses the apex of the sphere.
    # Region r1 borders are REFLECTIVE for molecule A, ABSORPTIVE for B,
    # and TRANSPARENT for C.  Initially we place 100 molecules of each type
    # inside region r1. We check that all molecules A are contained
    # within r1 and there are none of them in the surrounding region r2.
    # Because B has high diffusion coefficient, they all get absorbed
    # at the border, and after some time we should register none of them
    # inside either r1 or r2. The total count of C as sum across regions
    # r1 and r2 is constant over the simulation.
    # Region r3 borders are REFLECTIVE for molecules D and E. We place
    # 100 molecules D there that also undergo unimolecular reaction
    # D @ surface_class -> E[rate].  We check that total sum of D and E
    # within the region r3 is equal to 100.
    # Also TRIGGER statements are checked. 
    t = McellTest("reactions", "08-region_borders.mdl", ["-quiet"])
    
    t.add_extra_check(RequireCounts("dat/08-region_borders/A.dat", [(f*1e-6,100,0) for f in range(0,101)], "# Seconds r1_A r2_A"))
    t.add_extra_check(RequireCounts("dat/08-region_borders/B.dat", [(f*1e-6,0,0) for f in range(99,101)], "# Seconds r1_B r2_B"))
    t.add_extra_check(RequireCountConstraints("dat/08-region_borders/C.dat",         constraints=[(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1), 
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1)],
        totals = [100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100],
                  header=True))
    t.add_extra_check(RequireCountConstraints("dat/08-region_borders/r2.dat",         constraints=[(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1), 
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),  
       (1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1),(1,1)],
        totals = [100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100, 
                  100,100,100,100,100,100,100,100,100,100],
                  header=True))
    t.add_extra_check(RequireHitsCrossRelations("dat/08-region_borders/A_hits_C_cross.dat", "# Seconds A_fr_hits A_back_hits A_all_hits C_fr_cross C_back_cross C_all_cross"))
    t.add_extra_check(RequireValidTriggerOutput("dat/08-region_borders/C_trigger_fr_hits.dat", 1, False, None, None, xrange=(-10,10),yrange=(-10,10),zrange=(-10,10)))
    t.add_extra_check(RequireValidTriggerOutput("dat/08-region_borders/C_trigger_back_hits.dat", 1, False, None, None, xrange=(-10,10),yrange=(-10,10),zrange=(-10,10)))
    t.add_extra_check(RequireValidTriggerOutput("dat/08-region_borders/C_trigger_all_hits.dat", 1, False, None, None, xrange=(-10,10),yrange=(-10,10),zrange=(-10,10)))
    t.add_extra_check(RequireValidTriggerOutput("dat/08-region_borders/C_trigger_fr_cross.dat", 1, False, None, None, xrange=(-10,10),yrange=(-10,10),zrange=(-10,10)))
    t.add_extra_check(RequireValidTriggerOutput("dat/08-region_borders/C_trigger_back_cross.dat", 1, False, None, None, xrange=(-10,10),yrange=(-10,10),zrange=(-10,10)))
    t.add_extra_check(RequireValidTriggerOutput("dat/08-region_borders/C_trigger_all_cross.dat", 1, False, None, None, xrange=(-10,10),yrange=(-10,10),zrange=(-10,10)))

    t.invoke(get_output_dir())

  def test_region_borders_cube_all_molecules(self):
    # The test is done on the six cubes with simple region 
    # border geometry.
    # Region r1 is TOP, and region r2 consist of all other sides.
    # For each of the above cubes region r1 is assigned surface class
    # that has properties such TRANSPARENT/REFLECTIVE/ABSORPTIVE
    # for ALL_MOLECULES or ALL_SURFACE_MOLECULES.
    # Initially we place surface molecules A and B in the amount of 
    # 100 molecules of each type inside region r1.
    # We count molecules A and B in the regions r1 and r2.
    t = McellTest("reactions", "09-region_borders.mdl", ["-quiet"])
    
    t.add_extra_check(RequireCounts("dat/09-region_borders/refl_all_mols.dat", [(f*1e-6,100,100,0,0) for f in range(0,101)], "# Seconds r1_A r1_B r2_A r2_B"))
    t.add_extra_check(RequireCounts("dat/09-region_borders/refl_all_surface_mols.dat", [(f*1e-6,100,100,0,0) for f in range(0,101)], "# Seconds r1_A r1_B r2_A r2_B"))
    t.add_extra_check(RequireCounts("dat/09-region_borders/absorb_all_mols.dat", [(f*1e-6,0,0,0,0) for f in range(90,101)], "# Seconds r1_A r1_B r2_A r2_B"))
    t.add_extra_check(RequireCounts("dat/09-region_borders/absorb_all_surface_mols.dat", [(f*1e-6,0,0,0,0) for f in range(90,101)], "# Seconds r1_A r1_B r2_A r2_B"))
    t.add_extra_check(RequireCountConstraints("dat/09-region_borders/transp_all_mols.dat", constraints=[(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1), 
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1)],
        totals = [200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200],
                  header=True))
    t.add_extra_check(RequireCountConstraints("dat/09-region_borders/transp_all_surface_mols.dat", constraints=[(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1), 
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),  
       (1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1),(1,1,1,1)],
        totals = [200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200, 
                  200,200,200,200,200,200,200,200,200,200],
                  header=True))


    t.invoke(get_output_dir())

  def test_surf_properties_all_molecules(self):
    #  The test is done on the collection of two cubes, one enclosed inside
    #  the another.  The outer cube has REFLECTIVE mesh for ALL_MOLECULES.
    #  The properties of inner cubes change from REFLECTIVE to TRANSPARENT 
    #  to ABSORPTIVE for ALL_MOLECULES as we move from one collection 
    #  to another.  Volume molecules A,B,C are released inside the inner cube.
    #  We count molecules in the space between the cubes. 

    t = McellTest("reactions", "10-surf_properties_all_molecules.mdl", ["-quiet"])
    t.add_extra_check(RequireCounts("dat/10-surf_properties_all_molecules/refl.dat", [(f*1e-6,0,0,0) for f in range(0,101)], "# Seconds A_diff B_diff C_diff"))
    t.add_extra_check(RequireCounts("dat/10-surf_properties_all_molecules/absorp.dat", [(f*1e-6,0,0,0) for f in range(0,101)], "# Seconds A_diff B_diff C_diff"))
    t.add_extra_check(RequireCountsPositive("dat/10-surf_properties_all_molecules/transp.dat","# Seconds A_diff B_diff C_diff"))

    t.invoke(get_output_dir())

  def test_surf_properties_all_volume_molecules(self):
    #  The test is done on the collection of two cubes, one enclosed inside
    #  the another. The outer cube has REFLECTIVE mesh for ALL_VOLUME_MOLECULES.
    #  The properties of inner cubes change from REFLECTIVE to TRANSPARENT 
    #  to ABSORPTIVE for ALL_VOLUME_MOLECULES as we move from one collection 
    #  to another.  Volume molecules A,B,C are released inside the inner cube.
    #  We count molecules in the space between the cubes. 

    t = McellTest("reactions", "11-surf_properties_all_volume_molecules.mdl", ["-quiet"])
    t.add_extra_check(RequireCounts("dat/11-surf_properties_all_volume_molecules/refl.dat", [(f*1e-6,0,0,0) for f in range(0,101)], "# Seconds A_diff B_diff C_diff"))
    t.add_extra_check(RequireCounts("dat/11-surf_properties_all_volume_molecules/absorp.dat", [(f*1e-6,0,0,0) for f in range(0,101)], "# Seconds A_diff B_diff C_diff"))
    t.add_extra_check(RequireCountsPositive("dat/11-surf_properties_all_volume_molecules/transp.dat","# Seconds A_diff B_diff C_diff"))

    t.invoke(get_output_dir())

  def test_all_enclosed(self):
    #  The test is done on the collection of two cubes, one enclosed inside
    #  the another. The grid molecules A are placed on the surfaces of
    #  both cubes. The statement COUNT[A,outer[whole_mesh], ALL_ENCLOSED]
    #  counts number of molecules A on the "inner" cube.
    #
    #  Failure: The count of molecules A is incorrect.
    #  Success: The count of molecules A is correct.
    t = McellTest("reactions", "12-all_enclosed_test.mdl", ["-quiet"])
    t.add_extra_check(RequireCounts("dat/12-all_enclosed_test/A.dat", [(f*1e-6,100) for f in range(0,101)]))
    t.invoke(get_output_dir())

  def test_restricted_borders_reactions(self):
    # The test is done on five cubes with simple region border geometry.
    # For bimolecular reaction molecules b_A are placed on the RIGHT 
    # side of the cubes, and molecules b_B are placed on the TOP side.  
    # For trimolecular reaction molecules t_A and t_B are placed 
    # on RIGHT side of the cube and molecules t_C are placed on 
    # TOP side of the cube. We declare the region
    # border between TOP and RIGHT restrictive in several different
    # ways.  There should be no reactions and therefore no reaction
    # products D for boxes 1-4. For box_5 the region border is not
    # restrictive and so reactions happened and reaction products
    # are created.
    t = McellTest("reactions", "13-restricted_border_reaction.mdl", ["-quiet"])
    
    t.add_extra_check(RequireCounts("dat/13-restricted_border_reaction/box_1.dat", [(f*1e-6,0) for f in range(0,101)], "# Seconds D"))
    t.add_extra_check(RequireCounts("dat/13-restricted_border_reaction/box_2.dat", [(f*1e-6,0) for f in range(0,101)], "# Seconds D"))
    t.add_extra_check(RequireCounts("dat/13-restricted_border_reaction/box_3.dat", [(f*1e-6,0) for f in range(0,101)], "# Seconds D"))
    t.add_extra_check(RequireCounts("dat/13-restricted_border_reaction/box_4.dat", [(f*1e-6,0) for f in range(0,101)], "# Seconds D"))
    t.add_extra_check(RequireCounts("dat/13-restricted_border_reaction/box_6.dat", [(f*1e-6,0) for f in range(0,101)], "# Seconds D"))
    t.add_extra_check(RequireCounts("dat/13-restricted_border_reaction/box_7.dat", [(f*1e-6,0) for f in range(0,101)], "# Seconds D"))
    t.add_extra_check(RequireCountsPositive("dat/13-restricted_border_reaction/box_5.dat", [(f*1e-6,0) for f in range(90,101)]))
    t.add_extra_check(RequireCountsPositive("dat/13-restricted_border_reaction/box_8.dat", [(f*1e-6,0) for f in range(90,101)]))

  def test_restricted_borders_product_placement(self):
    # The test is done on 19 cubes with simple region border geometry.
    # Unimolecular reaction is tested on the boxes 1 and 2, bimolecular
    # reaction is tested on boxes 3 and 4, and trimolecular reaction
    # on boxes 5 and 6. For these boxes we define region border properties
    # as restrictive for some reaction products and in some cases
    # for the reactant(s). For boxes 1, 3, and 5 there should be
    # no products outside restrictive region r1 boundary.
    # For boxes 2, 4, and 6 products F and G should be placed
    # outside region r1 since its borders are not restrictive
    # for them.
    t = McellTest("reactions", "14-restricted_border_product_placement.mdl", ["-quiet"])
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_1_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_1_r3.dat", [(f,0,0,0,0) for f in range(90,101)], "# Iteration_# r3_D r3_E r3_F r3_G"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_2_r2.dat", [(f,0,0,0,0) for f in range(90,101)], "# Iteration_# r2_D r2_E r2_F r2_G"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_2_r3.dat", "# Iteration_# r3_D r3_E r3_F r3_G"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_3_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_3_r2.dat", "# Iteration_# r2_D r2_E r2_F r2_G"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_4_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_4_r2.dat", [(f,0,0,0,0) for f in range(90,101)], "# Iteration_# r2_D r2_E r2_F r2_G"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_5_r3.dat", "# Iteration_# r3_D r3_E r3_F r3_G"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_5_r4.dat", [(f,0,0,0,0) for f in range(90,101)], "# Iteration_# r4_D r4_E r4_F r4_G"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_6_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_6_r5.dat", [(f,0,0,0,0) for f in range(90,101)], "# Iteration_# r5_D r5_E r5_F r5_G"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_7_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_7_r3.dat", [(f,0,0,0,0) for f in range(90,101)], "# Iteration_# r3_D r3_E r3_F r3_G"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_8_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_8_r4.dat", [(f,0,0,0,0) for f in range(90,101)], "# Iteration_# r4_D r4_E r4_F r4_G"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_9_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_9_r2.dat", [(f,0,0,0,0) for f in range(90,101)], "# Iteration_# r2_D r2_E r2_F r2_G"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_10_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_10_r2.dat", "# Iteration_# r2_D r2_E r2_F r2_G"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_11_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G r1_K r1_L"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_11_r2.dat", [(f,0,0,0,0,0,0) for f in range(90,101)], "# Iteration_# r2_D r2_E r2_F r2_G r2_K r2_L"))
    t.add_extra_check(RequireCountsPositiveOrZero("dat/14-restricted_border_product_placement/box_12_r5.dat", "# Iteration_# r5_D r5_E r5_F r5_G r5_K r5_L"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_12_r6.dat", [(f,0,0,0,0,0,0) for f in range(90,101)], "# Iteration_# r6_D r6_E r6_F r6_G r6_K r6_L"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_13_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G r1_K r1_L"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_13_r3.dat", [(f,0,0,0,0,0,0) for f in range(90,101)], "# Iteration_# r3_D r3_E r3_F r3_G r3_K r3_L"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_14_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G r1_K r1_L"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_14_r3.dat", [(f,0,0,0,0,0,0) for f in range(90,101)], "# Iteration_# r3_D r3_E r3_F r3_G r3_K r3_L"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_15_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G r1_K r1_L"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_15_r2.dat", [(f,0,0,0,0,0,0) for f in range(90,101)], "# Iteration_# r2_D r2_E r2_F r2_G r2_K r2_L"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_16_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G r1_K r1_L"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_16_r2.dat", [(f,0,0,0,0,0,0) for f in range(90,101)], "# Iteration_# r2_D r2_E r2_F r2_G r2_K r2_L"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_17_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G r1_K r1_L"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_17_r2.dat", [(f,0,0,0,0,0,0) for f in range(90,101)], "# Iteration_# r2_D r2_E r2_F r2_G r2_K r2_L"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_18_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G r1_K r1_L"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_18_r2.dat", [(f,0,0,0,0,0,0) for f in range(90,101)], "# Iteration_# r2_D r2_E r2_F r2_G r2_K r2_L"))
    t.add_extra_check(RequireCountsPositive("dat/14-restricted_border_product_placement/box_19_r1.dat", "# Iteration_# r1_D r1_E r1_F r1_G r1_K r1_L"))
    t.add_extra_check(RequireCounts("dat/14-restricted_border_product_placement/box_19_r2.dat", [(f,0,0,0,0,0,0) for f in range(90,101)], "# Iteration_# r2_D r2_E r2_F r2_G r2_K r2_L"))

    t.invoke(get_output_dir())

  def test_restricted_borders_reactions(self):
    # The test is done is done on sphere with three overlapping regions.
    # Here we test the surface products placement that should follow
    # the established policy.
    t = McellTest("reactions", "15-overlappingSRs.mdl", ["-quiet"])
    t.add_extra_check(RequireCountsPositive("dat/15-overlappingSRs/r4.dat", "# Iteration_# r4_B r4_C r4_D"))
    t.add_extra_check(RequireCounts("dat/15-overlappingSRs/r5.dat", [(f,0,0,0) for f in range(90,101)], "# Iteration_# r5_B r5_C r5_D"))

    t.invoke(get_output_dir())

  def test_surface_products_replace_reactants(self):
    # The test is done is done on the number of cubes
    # Here we test how surface products replace surface reactants
    # that should follow the established policy.
    # Mostly here we look into product generation and no segfaults
    # during simulation.
    t = McellTest("reactions", "16-surf_products_replace_reactants.mdl", ["-quiet"])
    t.add_extra_check(RequireCountsPositive("dat/16-surf_products_replace_reactants/box_1.dat"))
    t.add_extra_check(RequireCountsPositive("dat/16-surf_products_replace_reactants/box_2.dat"))
    t.add_extra_check(RequireCountsPositive("dat/16-surf_products_replace_reactants/box_3.dat"))
    t.add_extra_check(RequireCountsPositive("dat/16-surf_products_replace_reactants/box_4_I.dat"))
    t.add_extra_check(RequireCountsPositive("dat/16-surf_products_replace_reactants/box_4_b_A3.dat"))
    t.add_extra_check(RequireCountsPositive("dat/16-surf_products_replace_reactants/box_5.dat"))
    t.add_extra_check(RequireCountsPositive("dat/16-surf_products_replace_reactants/box_6.dat"))
    t.add_extra_check(RequireCountsPositive("dat/16-surf_products_replace_reactants/box_7.dat"))
    t.add_extra_check(RequireCountsPositive("dat/16-surf_products_replace_reactants/box_8.dat"))
    t.add_extra_check(RequireCountsPositive("dat/16-surf_products_replace_reactants/box_9.dat"))
    t.add_extra_check(RequireCountsPositive("dat/16-surf_products_replace_reactants/box_10.dat"))
    t.add_extra_check(RequireCountsPositive("dat/16-surf_products_replace_reactants/box_11.dat"))
    t.add_extra_check(RequireCountsPositive("dat/16-surf_products_replace_reactants/box_12.dat"))

    t.invoke(get_output_dir())





###################################################################
# Generate a test suite for all numeric tests
###################################################################
def numericsuite():
  return unittest.makeSuite(TestReactionsNumeric, "test")

###################################################################
# Default use of this file will invoke all tests
###################################################################
if __name__ == "__main__":
  cleandir(get_output_dir())
  unittest.main()