def get(self):
if lpsolve('get_Nrows', self.__lp) == 0:
self.__lp_setting()
lpsolve('solve', self.__lp)
obj = lpsolve('get_objective', self.__lp)
var = lpsolve('get_variables', self.__lp)[0][self.__nc:]
return (obj, var)
def __node_constraints(self, lp):
coeff = [0] * ((self.__nv + self.__ne) * self.__k)
for v in self.__g.nodes_iter():
for i in range(self.__k):
coeff[v * self.__k + i] = 1
lpsolve('add_constraint', lp, coeff, 'EQ', 1)
for i in range(self.__k):
coeff[v * self.__k + i] = 0
def __lin_prog(self):
lp = lpsolve('make_lp', 0, (self.__nv + self.__ne) * self.__k)
self.__set_objective(lp)
self.__constraints(lp)
self.__bounds(lp)
self.__config(lp)
lpsolve('solve', lp)
return lpsolve('get_variables', lp)[0][:self.__nv * self.__k]
def __total_order(self): # 3
T, x, y = self.zeros, self.__x, self.__y
for i, j in product(self.g.nodes(), repeat=2):
if i == j:
continue
T[x(i, j)] = 1
T[x(j, i)] = 1
lpsolve('add_constraint', self.lp, T, 'EQ', 1)
T[x(i, j)], T[x(j, i)] = 0, 0
def __gearing_xy(self): # 5
T, x, y = self.zeros, self.__x, self.__y
for i, j in product(self.g.nodes(), repeat=2):
if i == j:
continue
T[x(i, j)] = -1
T[y(i, j)] = 1
lpsolve('add_constraint', self.lp, T, 'LE', 0)
T[x(i, j)], T[y(i, j)] = 0, 0
def __transitivity(self): # 4
T, x, y = self.zeros, self.__x, self.__y
for i, j, k in product(self.g.nodes(), repeat=3):
if i == j or j == k or i == k:
continue
T[x(i, j)] = 1
T[x(j, k)] = 1
T[x(i, k)] = -1
lpsolve('add_constraint', self.lp, T, 'LE', 1)
T[x(i, j)], T[x(j, k)], T[x(i, k)] = 0, 0, 0
def __counting_chord(self): # 7
T, x, y = self.zeros, self.__x, self.__y
for i, j, k in product(self.g.nodes(), repeat=3):
if i == j or j == k or i == k:
continue
T[x(j, k)] = 1
T[y(i, j)] = 1
T[y(i, k)] = 1
T[y(j, k)] = -1
lpsolve('add_constraint', self.lp, T, 'LE', 2)
T[x(j, k)], T[y(i, j)], T[y(i, k)], T[y(j, k)] = 0, 0, 0, 0
def start_new_objective(self, kind=2, last_r=-1):
if kind=='random':
lpsolve('set_obj_fn', self.lp, random(lpsolve('get_Ncolumns', self.lp)) - 0.5)
elif kind=='facet':
r = self.ineqs[random_integers(len(self.ineqs))-1]
lpsolve('set_obj_fn', self.lp, r[0])
return r
def __counting_edges(self): # 6
T, x, y = self.zeros, self.__x, self.__y
for i, j in self.g.edges():
T[x(i, j)] = -1
T[y(i, j)] = 1
lpsolve('add_constraint', self.lp, T, 'EQ', 0)
T[x(i, j)], T[y(i, j)] = 0, 0
T[x(j, i)] = -1
T[y(j, i)] = 1
lpsolve('add_constraint', self.lp, T, 'EQ', 0)
T[x(j, i)], T[y(j, i)] = 0, 0
def __set_constraints(self):
for j, c in enumerate(self.__clauses):
v = [0] * self.__N
v[j] = 1
d = 0
for i in c:
if i < 0:
v[self.__nc - 1 + abs(i)] = 1
d += 1
else:
v[self.__nc - 1 + i] = -1
lpsolve('add_constraint', self.__lp, v, 'LE', d)
def leq(self, a):
#-----------------------------------------------------------------------
# We convert <= constraints to >= so that in package_solution we can
# simply subtract the current contraint value in the tableau from the
# original right hand side values given here to derive the amount of
# slack on each constraint. This is important to have in
# interior_point().
#-----------------------------------------------------------------------
if not self.set_bound(a, 'up'):
if self.add_noise: a = self.noise(a)
lpsolve('add_constraint', self.lp, -a[1:], GE, a[0])
self.leq_count += 1
self.ineqs.append([-a[1:], GE, a[0]])
def __init__(self, **kw):
self.ncols = kw.get('ncols', None)
self.nthreads = kw.get('nthreads', 1)
self.random_seed = kw.get('rngseed', None)
self.objf_choice = kw.get('objf choice', 'random')
self.sol_type = kw.get('solution type', 'interior')
self.add_noise = kw.get('add noise', False)
ran_set_seed(self.random_seed)
self.lp = lpsolve('make_lp', 0, self.ncols)
#lpsolve('set_bounds_tighter', self.lp, True) # important so that we don't loosen tight bounds
self.ineqs = []
self.eq_count = 0
self.leq_count = 0
self.geq_count = 0
self.bnd_count = 0
self.iteration = 0
self.prev_sol = None
self.sum_ln_k = 0
self.curr_sol = None
self.n_solutions = 0
def __init__(self, nv, clauses, costs=None):
self.__nc = len(clauses)
self.__nv = nv
self.__clauses = clauses
self.__N = self.__nc + self.__nv
self.__costs = costs if costs else [1] * self.__nc
self.__lp = lpsolve('make_lp', 0, self.__N)
def __edge_constraints(self, lp):
node_offset = self.__nv * self.__k
coeff = [0] * ((self.__nv + self.__ne) * self.__k)
for e, (u, v) in enumerate(self.__g.edges_iter()):
uk, vk = u * self.__k, v * self.__k
for i in range(self.__k):
coeff[node_offset + e * self.__k + i] = 1
coeff[uk + i] = 1
coeff[vk + i] = -1
lpsolve('add_constraint', lp, coeff, 'GE', 0)
coeff[uk + i] = -1
coeff[vk + i] = 1
lpsolve('add_constraint', lp, coeff, 'GE', 0)
coeff[node_offset + e * self.__k + i] = 0
coeff[uk + i] = 0
coeff[vk + i] = 0
def __determine_max_clique_size(self): # 2
T, x, y = self.zeros, self.__x, self.__y
T[0] = 1
for i in self.g.nodes():
for j in self.g.nodes():
if i == j:
continue
T[y(i, j)] = -1
lpsolve('add_constraint', self.lp, T, 'GE', 0)
for j in self.g.nodes():
if i == j:
continue
T[y(i, j)] = 0
assert (T.count(1) == 1)
T[0] = 0
assert (self.zeros.count(1) == 0)
def set_bound(self, a, type):
return False
func = {'low': 'set_lowbo',
'up': 'set_upbo'}.get(type, None)
if func is None:
assert 0, 'Bad type to set_bound'
w = a.nonzero()[0]
if w.size == 2 and w[0] == 0:
bnd = -a[0] / a[w[1]]
lpsolve(func, self.lp, w[1], bnd)
self.bnd_count += 1
return True
return False
def assign_placements():
num_tas = len(all_tas)
num_times = len(ID_TO_TIMES)
upper = [1 for _ in range(num_tas * num_times)] # max value must be 1
obj_func = make_obj_func()
constr_mat = make_constr_mat(num_tas, num_times)
b_vector = make_b_vector()
e_vector = make_e_vector(num_tas, num_times)
lp = lpm.lp_maker(obj_func, constr_mat, b_vector, e_vector)
lps.lpsolve('set_bb_depthlimit', lp, 0) # set branch and bound depth limit
lps.lpsolve('set_binary', lp, upper) # all values must be either 0 or 1
lps.lpsolve('solve', lp)
vars = lps.lpsolve('get_variables', lp)[0]
lps.lpsolve('delete_lp', lp)
output_results(vars)
def start(self):
Log( '=' * 80 )
Log( 'SAMPLEX' )
Log( '=' * 80 )
Log( 'Using lpsolve %s' % lpsolve('lp_solve_version') )
Log( "ncols = %i" % self.ncols )
Log( "random seed = %s" % self.random_seed )
Log( "threads = %s" % self.nthreads )
Log( "objf choice = %s" % self.objf_choice )
Log( "solution type = %s" % self.sol_type )
Log( "add noise = %s" % self.add_noise )
Log( "%6s %6s %6s %6s\n%6i %6i %6i %6i"
% (">=", "<=", "=", "bnd", self.geq_count, self.leq_count, self.eq_count, self.bnd_count) )
#lpsolve('set_verbose', self.lp, DETAILED)
#lpsolve('set_verbose', self.lp, DETAILED)
lpsolve('set_verbose', self.lp, IMPORTANT)
def __bounds(self, lp):
nv, ne = self.__nv * self.__k, self.__ne * self.__k
# lpsolve('set_binary', lp, [1] * nv + [0] * ne)
lpsolve('set_upbo', lp, [1] * nv + [Infinite] * ne)
lpsolve('set_lowbo', lp, [0] * nv + [0] * ne)
for i, v in enumerate(self.__s):
lpsolve('set_lowbo', lp, v * self.__k + i + 1, 1)
def set_constraints(lp, n):
for v in incomming_constraints(n):
lpsolve('add_constraint', lp, v, 'EQ', 1)
for v in outgoing_constraints(n):
lpsolve('add_constraint', lp, v, 'EQ', 1)
for v in subtour_constraints(n):
lpsolve('add_constraint', lp, v, 'LE', n - 1)
def assign_placements():
"""
Takes in an option for which to assign placements for.
Outputs nothing, but calls output_results which prints all placements.
"""
num_tutors = len(all_tutors)
num_times = len(ID_TO_TIMES)
upper = [1 for _ in range(num_tutors * num_times)] # max value must be 1
obj_func = make_obj_func()
constr_mat = make_constr_mat(num_tutors, num_times)
b_vector = make_b_vector()
e_vector = make_e_vector(num_tutors, num_times)
lp = lpm.lp_maker(obj_func, constr_mat, b_vector, e_vector)
lps.lpsolve('set_bb_depthlimit', lp, 0) # set branch and bound depth limit
lps.lpsolve('set_binary', lp, upper) # all values must be either 0 or 1
lps.lpsolve('solve', lp)
vars = lps.lpsolve('get_variables', lp)[0]
lps.lpsolve('delete_lp', lp)
output_results(vars)
def package_solution(self):
objv = array(lpsolve('get_objective', self.lp))
vars = array(lpsolve('get_variables', self.lp)[0])
slack = array(lpsolve('get_constraints', self.lp)[0]) - array(lpsolve('get_rh', self.lp)[1:])
slack[abs(slack) < 1e-5] = 0
nvars = len(vars)
nslack = len(slack)
s = SamplexSolution()
s.sol = empty(nvars + 1)
s.sol[1:] = vars
s.sol[0] = objv
s.vertex = empty(nvars + nslack + 1)
s.vertex[1:nvars+1] = vars
s.vertex[1+nvars:1+nvars+nslack] = slack
s.vertex[0] = objv
assert all(s.vertex[1:] >= 0), s.vertex[s.vertex < 0]
return s
def next_solution(self):
while True:
r = self.start_new_objective(kind=self.objf_choice)
result = lpsolve('solve', self.lp)
if result in [OPTIMAL, TIMEOUT]: break
elif result == SUBOPTIMAL: continue
elif result == INFEASIBLE: raise SamplexNoSolutionError()
elif result == UNBOUNDED: raise SamplexUnboundedError()
else:
Log( result )
raise SamplexUnexpectedError("unknown pivot result = %i" % result)
objv = lpsolve('get_objective', self.lp)
if self.objf_choice == 'facet' and abs(objv) > 1e-6:
print 'BAD VARIABLE', objv
del self.ineqs[r]
else:
break
print 'Solution after %i steps.' % lpsolve('get_total_iter', self.lp)
def get_mtz_ilp_tour(P):
dmat = distance_matrix(P)
n, N = len(P), len(dmat)
lp = lpsolve('make_lp', 0, N + n)
lpsolve('set_obj_fn', lp, dmat + [0] * len(P))
set_constraints(lp, n)
set_bounds(lp, N, n)
config_lp(lp)
lpsolve('solve', lp)
tour = [0] * (n + 1)
for i, v in enumerate(lpsolve('get_variables', lp)[0][N:]):
tour[int(v)] = i
return tour
def get_mtz_ilp_tour(P):
n, N = len(P), len(P)**2
d = [np.linalg.norm(P[i] - P[j]) for i, j in product(range(n), range(n))]
lp = lpsolve('make_lp', 0, N + n)
lpsolve('set_obj_fn', lp, d + [0] * len(P))
set_constraints(lp, n)
set_bounds(lp, N, n)
config_lp(lp)
lpsolve('solve', lp)
tour = [0] * (n + 1)
for i, v in enumerate(lpsolve('get_variables', lp)[0][N:]):
tour[int(v)] = i
return tour
def eq(self, a):
#if self.add_noise: a = noise(a)
lpsolve('add_constraint', self.lp, a[1:], EQ, -a[0])
self.eq_count += 1
def solve_lp_knapsack_lpsolve(scores, costs, budget):
import lpsolve55 as lps
relax = True
n = len(scores)
lp = lps.lpsolve('make_lp', 0, n)
# Set verbosity level. 3 = only warnings and errors.
lps.lpsolve('set_verbose', lp, 3)
lps.lpsolve('set_obj_fn', lp, -scores)
lps.lpsolve('add_constraint', lp, costs, lps.LE, budget)
lps.lpsolve('set_lowbo', lp, np.zeros(n))
lps.lpsolve('set_upbo', lp, np.ones(n))
if not relax:
lps.lpsolve('set_int', lp, [True] * n)
else:
lps.lpsolve('set_int', lp, [False] * n)
# Solve the ILP, and call the debugger if something went wrong.
ret = lps.lpsolve('solve', lp)
assert ret == 0
# Retrieve solution and return
x, _ = lps.lpsolve('get_variables', lp)
x = np.array(x)
return x
def solve_lp(scp_gen):
print "--- SOLVE LINEAR PROGRAMMING ---"
n = scp_gen.universal_set_size
lp = lpsolve('make_lp', 0, n)
lpsolve('set_maxim', lp)
lpsolve('set_obj_fn', lp, [1] * n)
for i, v in enumerate(scp_gen.get_cols()):
lpsolve('add_constraint', lp, v, 'LE', scp_gen.cost[i])
lpsolve('set_lowbo', lp, [0] * n)
lpsolve('write_lp', lp, 'd.lp')
lpsolve('set_verbose', lp, IMPORTANT)
lpsolve('solve', lp)
res = lpsolve('get_objective', lp)
print "solution of lp:", res
V = lpsolve('get_variables', lp)[0]
print "solution vector:", V
ans = 0
AV = []
for i, v in enumerate(scp_gen.get_cols()):
s = sum(V[j] for j, e in enumerate(v) if e != 0)
if s == scp_gen.cost[i]:
AV.append(1)
ans += s
else:
AV.append(0)
_, f = scp_gen.get_f()
print "f:", f, "1/f", 1.0 / float(f)
print "deterministic rounding:", AV
print "result of linear relaxation:", ans
print "alpha: ", ans / res, "\n"
if scp_gen.is_covered([i for i, v in enumerate(AV) if v == 1]):
print 'covered'
else:
print 'uncovered'
lpsolve('delete_lp', lp)
def _find_error_canceling_reaction(self,
reference_subset,
milp_software=None):
"""
Automatically find a valid error canceling reaction given a subset of the available benchmark species. This
is done by solving a mixed integer linear programming (MILP) problem similiar to
Buerger et al. (https://doi.org/10.1016/j.combustflame.2017.08.013)
Args:
reference_subset (list): A list of indices from self.reference_species that can participate in the reaction
milp_software (list, optional): Solvers to try in order. Defaults to ['lpsolve'] or if pyomo is available
defaults to ['lpsolve', 'pyomo']. lpsolve is usually faster.
Returns:
tuple(ErrorCancelingReaction, np.ndarray)
- Reaction with the target species (if a valid reaction is found, else ``None``)
- Indices (of the subset) for the species that participated in the return reaction
"""
if milp_software is None:
milp_software = ['lpsolve']
if pyo is not None:
milp_software.append('pyomo')
# Define the constraints based on the provided subset
c_matrix = np.take(self.constraint_matrix, reference_subset, axis=0)
c_matrix = np.tile(c_matrix, (2, 1))
sum_constraints = np.sum(c_matrix, 1, dtype=int)
targets = -1 * self.target_constraint
m = c_matrix.shape[0]
n = c_matrix.shape[1]
split = int(m / 2)
for solver in milp_software:
if solver == 'pyomo':
# Check that pyomo is available
if pyo is None:
raise ImportError(
'Cannot import optional package pyomo. Either install this dependency with '
'`conda install -c conda-forge pyomo glpk` or set milp_software to `lpsolve`'
)
# Setup the MILP problem using pyomo
lp_model = pyo.ConcreteModel()
lp_model.i = pyo.RangeSet(0, m - 1)
lp_model.j = pyo.RangeSet(0, n - 1)
lp_model.r = pyo.RangeSet(
0, split -
1) # indices before the split correspond to reactants
lp_model.p = pyo.RangeSet(
split,
m - 1) # indices after the split correspond to products
lp_model.v = pyo.Var(lp_model.i,
domain=pyo.NonNegativeIntegers
) # The stoich. coef. we are solving for
lp_model.c = pyo.Param(
lp_model.i,
lp_model.j,
initialize=lambda _, i_ind, j_ind: c_matrix[i_ind, j_ind])
lp_model.s = pyo.Param(
lp_model.i,
initialize=lambda _, i_ind: sum_constraints[i_ind])
lp_model.t = pyo.Param(
lp_model.j, initialize=lambda _, j_ind: targets[j_ind])
lp_model.obj = pyo.Objective(rule=_pyo_obj_expression)
lp_model.constraints = pyo.Constraint(
lp_model.j, rule=_pyo_constraint_rule)
# Solve the MILP problem using the GLPK MILP solver (https://www.gnu.org/software/glpk/)
opt = pyo.SolverFactory('glpk')
results = opt.solve(lp_model, timelimit=1)
# Return the solution if a valid reaction is found. Otherwise continue to next solver
if results.solver.termination_condition == pyo.TerminationCondition.optimal:
# Extract the solution and find the species with non-zero stoichiometric coefficients
solution = lp_model.v.extract_values().values()
break
elif solver == 'lpsolve':
# Save the current signal handler
sig = signal.getsignal(signal.SIGINT)
# Setup the MILP problem using lpsolve
lp = lpsolve('make_lp', 0, m)
lpsolve('set_verbose', lp,
2) # Reduce the logging from lpsolve
lpsolve('set_obj_fn', lp, sum_constraints)
lpsolve('set_minim', lp)
for j in range(n):
lpsolve(
'add_constraint', lp,
np.concatenate(
(c_matrix[:split, j], -1 * c_matrix[split:, j])),
EQ, targets[j])
lpsolve('add_constraint', lp, np.ones(m), LE,
20) # Use at most 20 species (including replicates)
lpsolve('set_timeout', lp,
1) # Move on if lpsolve can't find a solution quickly
# Constrain v_i to be 4 or less
for i in range(m):
lpsolve('set_upbo', lp, i, 4)
# All v_i must be integers
lpsolve('set_int', lp, [True] * m)
status = lpsolve('solve', lp)
# Reset signal handling since lpsolve changed it
try:
signal.signal(signal.SIGINT, sig)
except ValueError:
# This is not being run in the main thread, so we cannot reset signal
pass
# Return the solution if a valid reaction is found. Otherwise continue to next solver
if status == 0:
_, solution = lpsolve('get_solution', lp)[:2]
break
else:
raise ValueError(
f'Unrecognized MILP solver {solver} for isodesmic reaction generation'
)
else:
return None, None
reaction = ErrorCancelingReaction(self.target, dict())
subset_indices = []
for index, v in enumerate(solution):
if v > 0:
subset_indices.append(index % split)
if index < split:
reaction.species.update(
{self.reference_species[reference_subset[index]]: -v})
else:
reaction.species.update({
self.reference_species[reference_subset[index % split]]:
v
})
return reaction, np.array(subset_indices)
def inner_point(self, newp):
lp = lpsolve('make_lp', 0, self.nVars+1) # +1 for variable used to find the first inner point
lpsolve('set_epsb', lp, 1e-14)
lpsolve('set_epsd', lp, 1e-14)
lpsolve('set_epsint', lp, 1e-14)
lpsolve('set_epsel', lp, 1e-8)
lpsolve('set_verbose', lp, FULL)
lpsolve('set_sense', lp, False)
for eq,a in self.eq_list:
l = (a[1:]).tolist()
if eq == 'eq': l.append(0); lpsolve('add_constraint', lp, l, EQ, -a[0])
if eq == 'leq': l.append(1); lpsolve('add_constraint', lp, l, LE, -a[0])
if eq == 'geq': l.append(1); lpsolve('add_constraint', lp, l, GE, -a[0])
for i in range(self.nVars):
q = np.zeros(self.nVars+1)
q[[i,-1]] = -1, 1
lpsolve('add_constraint', lp, q.tolist(), LE, 0)
o = np.zeros(self.nVars+1)
o[-1] = 1
lpsolve('set_obj_fn', lp, o.tolist())
while True:
result = lpsolve('solve', lp)
if result in [OPTIMAL, TIMEOUT]: break
elif result == SUBOPTIMAL: continue
elif result == INFEASIBLE: raise SamplexNoSolutionError()
elif result == UNBOUNDED: raise SamplexUnboundedError()
else:
Log( result )
raise SamplexUnexpectedError("unknown pivot result %i from linear solver." % result)
objv = np.array(lpsolve('get_objective', lp))
v1 = np.array(lpsolve('get_variables', lp)[0])
assert len(v1) == lpsolve('get_Norig_columns', lp)
assert len(v1) == self.nVars+1
del lp
v1 = v1[:-1] # Remove the temporary variable that tracks the distance from the simplex boundary
v1[np.abs(v1) < 1e-14] = 0
assert np.all(v1 >= 0), v1[v1 < 0]
ok,fail_count = self.in_simplex(v1, eq_tol=1e-12, tol=0, verbose=1)
ok,fail_count = self.in_simplex(v1, eq_tol=1e-12, tol=-1e-13, verbose=1)
assert ok, len(fail_count)
newp[:] = v1
self.project(newp)
ok,fail_count = self.in_simplex(newp, eq_tol=1e-12, tol=0, verbose=1)
ok,fail_count = self.in_simplex(newp, eq_tol=1e-12, tol=-1e-5, verbose=1)
tmp += [1]
if examinee in examinees:
examinees[examinee] += [variable]
else:
examinees[examinee] = [variable]
# one examination at most per timeslot
constraints += [tmp + [0] * (len(function) - len(possibilities))]
for examinee in examinees:
tmp = [0] * len(function)
for variable in examinees[examinee]:
tmp[variable] = 1
# one examination at most per examinee
constraints += [tmp]
lp = lpsolve('make_lp', len(constraints), len(function))
lpsolve('set_verbose', lp, 'IMPORTANT')
lpsolve('set_mat', lp, constraints)
lpsolve('set_rh_vec', lp, [1] * len(constraints))
lpsolve('set_constr_type', lp, ['LE'] * len(constraints))
lpsolve('set_obj_fn', lp, function)
lpsolve('set_maxim', lp)
lpsolve('set_binary', lp, [True] * len(function))
#lpsolve('write_lp', lp, 'a.lp')
lpsolve('solve', lp)
variables = lpsolve('get_variables', lp)[0]
'''
for date, times in examinations:
for time, possibilities in times:
for variable, examinee, examiners in possibilities:
def _clarOptimization(mol, constraints=None, maxNum=None):
"""
Implements linear programming algorithm for finding Clar structures. This algorithm maximizes the number
of Clar sextets within the constraints of molecular geometry and atom valency.
Returns a list of valid Clar solutions in the form of a tuple, with the following entries:
[0] Molecule object
[1] List of aromatic rings
[2] List of bonds
[3] Optimization solution
The optimization solution is a list of boolean values with sextet assignments followed by double bond assignments,
with indices corresponding to the list of aromatic rings and list of bonds, respectively.
Method adapted from:
Hansen, P.; Zheng, M. The Clar Number of a Benzenoid Hydrocarbon and Linear Programming.
J. Math. Chem. 1994, 15 (1), 93–107.
"""
cython.declare(molecule=Molecule, asssr=list, exo=list, l=cython.int, m=cython.int, n=cython.int,
a=list, objective=list, status=cython.int, solution=list, innerSolutions=list)
from lpsolve55 import lpsolve
# Make a copy of the molecule so we don't destroy the original
molecule = mol.copy(deep=True)
asssr = molecule.getAromaticSSSR()[0]
if not asssr:
return []
# Get list of atoms that are in rings
atoms = set()
for ring in asssr:
atoms.update(ring)
atoms = list(atoms)
# Get list of bonds involving the ring atoms, ignoring bonds to hydrogen
bonds = set()
for atom in atoms:
bonds.update([atom.bonds[key] for key in atom.bonds.keys() if key.isNonHydrogen()])
bonds = list(bonds)
# Identify exocyclic bonds, and save their bond orders
exo = []
for bond in bonds:
if bond.atom1 not in atoms or bond.atom2 not in atoms:
if bond.isDouble():
exo.append(1)
else:
exo.append(0)
else:
exo.append(None)
# Dimensions
l = len(asssr)
m = len(atoms)
n = l + len(bonds)
# Connectivity matrix which indicates which rings and bonds each atom is in
# Part of equality constraint Ax=b
a = []
for atom in atoms:
inRing = [1 if atom in ring else 0 for ring in asssr]
inBond = [1 if atom in [bond.atom1, bond.atom2] else 0 for bond in bonds]
a.append(inRing + inBond)
# Objective vector for optimization: sextets have a weight of 1, double bonds have a weight of 0
objective = [1] * l + [0] * len(bonds)
# Solve LP problem using lpsolve
lp = lpsolve('make_lp', m, n) # initialize lp with constraint matrix with m rows and n columns
lpsolve('set_verbose', lp, 2) # reduce messages from lpsolve
lpsolve('set_obj_fn', lp, objective) # set objective function
lpsolve('set_maxim', lp) # set solver to maximize objective
lpsolve('set_mat', lp, a) # set left hand side to constraint matrix
lpsolve('set_rh_vec', lp, [1] * m) # set right hand side to 1 for all constraints
lpsolve('set_constr_type', lp, ['='] * m) # set all constraints as equality constraints
lpsolve('set_binary', lp, [True] * n) # set all variables to be binary
# Constrain values of exocyclic bonds, since we don't want to modify them
for i in range(l, n):
if exo[i - l] is not None:
# NOTE: lpsolve indexes from 1, so the variable we're changing should be i + 1
lpsolve('set_bounds', lp, i + 1, exo[i - l], exo[i - l])
# Add constraints to problem if provided
if constraints is not None:
for constraint in constraints:
lpsolve('add_constraint', lp, constraint[0], '<=', constraint[1])
status = lpsolve('solve', lp)
objVal, solution = lpsolve('get_solution', lp)[0:2]
lpsolve('delete_lp', lp) # Delete the LP problem to clear up memory
# Check that optimization was successful
if status != 0:
raise ILPSolutionError('Optimization could not find a valid solution.')
# Check that we the result contains at least one aromatic sextet
if objVal == 0:
return []
# Check that the solution contains the maximum number of sextets possible
if maxNum is None:
maxNum = objVal # This is the first solution, so the result should be an upper limit
elif objVal < maxNum:
raise ILPSolutionError('Optimization obtained a sub-optimal solution.')
if any([x != 1 and x != 0 for x in solution]):
raise ILPSolutionError('Optimization obtained a non-integer solution.')
# Generate constraints based on the solution obtained
y = solution[0:l]
new_a = y + [0] * len(bonds)
new_b = sum(y) - 1
if constraints is not None:
constraints.append((new_a, new_b))
else:
constraints = [(new_a, new_b)]
# Run optimization with additional constraints
try:
innerSolutions = _clarOptimization(mol, constraints=constraints, maxNum=maxNum)
except ILPSolutionError:
innerSolutions = []
return innerSolutions + [(molecule, asssr, bonds, solution)]
def assign_sections(tas, prioritize=False, analyze=False):
"""
tas: a list of ta objects
i = index of sections
j = index of tas
The columns, x_i_j, go as follows:
x_0_0, x_1_0, x_2_0, ..., x_0_1, ..., x_M_N
"""
M = len(tas[0].rankings) # number of section
N = len(tas) # number of tas
f = make_obj_f(tas, prioritize)
A = make_coeff_m(M, N)
b = make_b_v(tas, M, N)
e = make_e_v(M, N)
v = [1 for _ in range(M*N)]
lp = lpm.lp_maker(f, A, b, e, None, v)
# set branch and bound depth
lps.lpsolve('set_bb_depthlimit', lp, 0)
# set all variables to binary
lps.lpsolve('set_binary', lp, v)
# set lp to minimize the objective function
lps.lpsolve('set_minim', lp)
lps.lpsolve('write_lp', lp, LP_OUT)
lps.lpsolve('solve', lp)
res = lps.lpsolve('get_variables', lp)[0]
lps.lpsolve('delete_lp', lp)
parse_results(res, tas, M, analyze)
def next(self, nsolutions=None):
Log( "Getting solutions" )
self.start_new_objective('random')
#lpsolve('set_simplextype', self.lp, lp.SIMPLEX_DUAL_DUAL)
#lpsolve('set_simplextype', self.lp, lp.SIMPLEX_PRIMAL_PRIMAL)
#lpsolve('set_pivoting', self.lp, PRICER_DANTZIG)
#lpsolve('set_pivoting', self.lp, lp.PRICER_DANTZIG | lp.PRICE_ADAPTIVE)
#lpsolve('set_pivoting', self.lp, lp.PRICER_STEEPESTEDGE | lp.PRICE_ADAPTIVE)
#lpsolve('set_presolve', self.lp, PRESOLVE_LINDEP)
#lpsolve('set_timeout', self.lp, 0)
res = lpsolve('solve', self.lp)
#lpsolve('set_presolve', self.lp, PRESOLVE_NONE)
restxt = {NOMEMORY: 'NOMEMORY',
OPTIMAL: 'OPTIMAL',
SUBOPTIMAL: 'SUBOPTIMAL',
INFEASIBLE: 'INFEASIBLE',
UNBOUNDED: 'UNBOUNDED',
DEGENERATE: 'DEGENERATE',
NUMFAILURE: 'NUMFAILURE',
USERABORT: 'USERABORT',
TIMEOUT: 'TIMEOUT',
PRESOLVED: 'PRESOLVED'}[res]
print 'solve result %s (%i)' % (restxt, res)
if res != OPTIMAL: return
#lpsolve('set_timeout', self.lp, 1)
Log( "------------------------------------" )
Log( "Found feasible" )
Log( "------------------------------------" )
self.curr_sol = self.package_solution()
self.prev_sol = self.curr_sol.vertex.copy()
if self.sol_type in ['vertex', 'interior']:
self.sum_ln_k = 0
self.n_solutions = 0
while self.n_solutions != nsolutions:
self.iteration=0
self.n_solutions += 1
while True:
self.next_solution()
self.curr_sol = self.package_solution()
p = self.prepare_return_sol()
if p is not None:
break
print 'SAME VERTEX!'
yield p
else:
self.sum_ln_k = 0
self.n_solutions = 0
all = []
while self.n_solutions != nsolutions*100:
self.iteration=0
self.n_solutions += 1
while True:
self.next_solution()
self.curr_sol = self.package_solution()
all.append(self.curr_sol)
break
while nsolutions > 0:
yield self.CLT(all)
nsolutions -= 1
def test_lpsolve(self):
""" test lpsolve
(http://lpsolve.sourceforge.net)
"""
try:
from lpsolve55 import lpsolve
except ImportError:
raise SkipTest('lpsolve is not available')
print '\n------------------------------ lpsolve ------------------------------'
obj = self.f.tolist()
lp = lpsolve('make_lp', 0, len(obj))
lpsolve('set_verbose', lp, 'IMPORTANT')
lpsolve('set_obj_fn', lp, obj)
i = 0
for con in self.A:
lpsolve('add_constraint', lp, con.tolist(), 'LE', self.b[i])
i = i + 1
for i in range(len(self.lb)):
lpsolve('set_lowbo', lp, i + 1, self.lb[i])
lpsolve('set_upbo', lp, i + 1, self.ub[i])
results = lpsolve('solve', lp)
result_text = [
'OPTIMAL An optimal solution was obtained',
'SUBOPTIMAL The model is sub-optimal. Only happens if there are integer variables and there is already an integer solution found. The solution is not guaranteed the most optimal one.',
'INFEASIBLE The model is infeasible',
'UNBOUNDED The model is unbounded',
'DEGENERATE The model is degenerative',
'NUMFAILURE Numerical failure encountered',
'USERABORT The abort routine returned TRUE. See put_abortfunc',
'TIMEOUT A timeout occurred. A timeout was set via set_timeout',
'N/A'
'PRESOLVED The model could be solved by presolve. This can only happen if presolve is active via set_presolve',
'PROCFAIL The B&B routine failed',
'PROCBREAK The B&B was stopped because of a break-at-first (see set_break_at_first) or a break-at-value (see set_break_at_value)',
'FEASFOUND A feasible B&B solution was found',
'NOFEASFOUND No feasible B&B solution found'
]
print 'results: (%d)' % results, result_text[results]
print 'f:', lpsolve('get_objective', lp)
print 'x:', lpsolve('get_variables', lp)[0]
lpsolve('delete_lp', lp)
def next(self, nsolutions=None):
# this does the first part of the cpu intensive tasks
Log( '=' * 80 )
Log( 'Simplex Random Walk' )
Log( '=' * 80 )
Log( " %i equations" % len(self.eq_list) )
Log( "%6s %6s %6s\n%6i %6i %6i"
% (">=", "<=", "=", self.geq_count, self.leq_count, self.eq_count) )
if nsolutions == 0: return
assert nsolutions is not None
dim = self.nVars
dof = dim - self.eq_count
burnin_len = max(10, int(self.burnin_factor * dof))
redo = max(100, int((dof ** self.redo_exp) * self.redo_factor))
nmodels = nsolutions
nthreads = self.nthreads
self.stride = int(dim+1)
n_stored = 0
self.dim = dim
self.dof = dof
self.redo = redo
self.burnin_len = burnin_len
accept_rate = self.accept_rate
accept_rate_tol = self.accept_rate_tol
store = np.zeros((dim, 1+burnin_len), order='Fortran', dtype=np.float64)
newp = np.zeros(dim, order='C', dtype=np.float64)
eval = np.zeros(dim, order='C', dtype=np.float64)
evec = np.zeros((dim,dim), order='F', dtype=np.float64)
self.eqs = np.zeros((self.eqn_count+dim,dim+1), order='C', dtype=np.float64)
for i,[c,e] in enumerate(self.eq_list):
self.eqs[i,:] = e
for i in xrange(dim):
self.eqs[self.eqn_count+i,1+i] = 1
self.dist_eqs = np.zeros((self.eqn_count-self.eq_count,dim+1), order='C', dtype=np.float64)
i=0
for c,e in self.eq_list:
if c == 'eq':
continue
elif c == 'leq':
p = e
elif c == 'geq':
p = -e
self.dist_eqs[i,:] = p
i += 1
Log( 'Using lpsolve %s' % lpsolve('lp_solve_version') )
Log( "random seed = %s" % self.random_seed )
Log( "threads = %s" % self.nthreads )
Log( "acceptence rate = %s" % self.accept_rate )
Log( "acceptence rate tolerance = %s" % self.accept_rate_tol )
Log( "dof = %s" % self.dof)
Log( "sample distance = max(100,%s * %s^%s) = %s" % (self.redo_factor, self.dof, self.redo_exp, redo) )
Log( "starting twiddle = %s" % self.twiddle )
Log( "burn-in length = %s" % burnin_len )
time_begin_next = time.clock()
#-----------------------------------------------------------------------
# Create pseudo inverse matrix to reproject samples back into the
# solution space.
#-----------------------------------------------------------------------
P = np.eye(dim)
if self.eq_count > 0:
self.A = np.zeros((self.eq_count, dim), order='C', dtype=np.float64)
self.b = np.zeros(self.eq_count, order='C', dtype=np.float64)
for i,[c,e] in enumerate(self.eq_list[:self.eq_count]):
self.A[i] = e[1:]
self.b[i] = e[0]
self.Apinv = pinv(self.A)
P -= np.dot(self.Apinv, self.A)
else:
self.A = None
self.B = None
self.Apinv = None
ev, evec = eigh(P)
#-----------------------------------------------------------------------
#-----------------------------------------------------------------------
# Find a point that is completely inside the simplex
#-----------------------------------------------------------------------
Log('Finding first inner point')
time_begin_inner_point = time.clock()
self.inner_point(newp)
time_end_inner_point = time.clock()
ok,fail_count = self.in_simplex(newp, eq_tol=1e-12, tol=0, verbose=1)
assert ok
self.avg0 = newp
# eqs = self.eqs.copy('A')
# eqs[:,1:] = np.dot(self.eqs[:,1:], evec)
# print newp
# S = zeros(self.eqs.shape[0])
# newp[:] = np.dot(evec.T, newp)
# newp0 = newp.copy()
# steps = newp.copy()
# for q in range(100):
# csamplex.refine_center(self, eqs, newp, ev, S, steps)
# d = newp - newp0
# #print d
# print norm(d)
# #print
# newp0 = newp.copy()
# #assert 0
# newp[:] = np.dot(evec, newp)
store[:,0] = newp
n_stored = 1
#-----------------------------------------------------------------------
# Estimate the eigenvectors of the simplex
#-----------------------------------------------------------------------
Log('Estimating eigenvectors')
time_begin_est_eigenvectors = time.clock()
self.measured_ev(newp, ev, eval, evec)
time_end_est_eigenvectors = time.clock()
#-----------------------------------------------------------------------
# Now we can start the random walk
#-----------------------------------------------------------------------
Log( "Getting solutions" )
q = MP.Queue()
#-----------------------------------------------------------------------
# Launch the threads
#-----------------------------------------------------------------------
threads = []
models_per_thread = nmodels // nthreads
models_under = nmodels - nthreads*models_per_thread
id,N = 0,0
while id < nthreads and N < nmodels:
n = models_per_thread
if id < models_under:
n += 1
assert n > 0
Log( 'Thread %i gets %i' % (id,n) )
cmdq = MP.Queue()
ackq = MP.Queue()
thr = MP.Process(target=rwalk_burnin, args=(id, n, int(np.ceil(burnin_len/nthreads)), self, q, cmdq, ackq, newp, self.twiddle, eval.copy('A'), evec.copy('A')))
thr.daemon = False # RK: make non daemonic threads. Make sure to
# shut them down afterwards! But this way, one
# can use glass inside a celery worker (which
# is a daemon. since daemonic processes are not
# allowed to start daemonic processes, this has
# to be non daemonic)
threads.append([thr,cmdq,ackq])
N += n
id += 1
assert N == nmodels
for thr,cmdq,_ in threads:
thr.start()
cmdq.put(['CONT'])
def drainq(q):
try:
while True:
q.get(block=False)
except QueueEmpty:
pass
def pause_threads(threads):
for _,cmdq,ackq in threads:
cmdq.put(['WAIT'])
assert ackq.get() == 'OK'
def adjust_threads(i, cont_cmd):
pause_threads(threads)
drainq(q)
Log( 'Computing eigenvalues... [%i/%i]' % (i, burnin_len) )
self.compute_eval_evec(store, eval, evec, n_stored)
# new twiddle <-- average twiddle
t = 0
for _,cmdq,ackq in threads:
cmdq.put(['REQ TWIDDLE'])
t += ackq.get()
t /= len(threads)
Log( 'New twiddle %f' % t )
for _,cmdq,_ in threads:
cmdq.put(['NEW DATA', [eval.copy('A'), evec.copy('A'), t]])
cmdq.put([cont_cmd])
#-----------------------------------------------------------------------
# Burn-in
#-----------------------------------------------------------------------
Status("computing eigenvalues", i=0, of=burnin_len)
time_begin_burnin = time.clock()
compute_eval_window = 2 * self.dof
j = 0
for i in xrange(burnin_len):
Status("computing eigenvalues", i=i, of=burnin_len)
j += 1
k,vec = q.get()
store[:, n_stored] = vec
n_stored += 1
if j == compute_eval_window:
j = 0
adjust_threads(i+1,'CONT')
compute_eval_window = int(0.1*burnin_len + 1)
elif len(threads) < compute_eval_window:
threads[k][1].put(['CONT'])
time_end_burnin = time.clock()
Status("computing eigenvalues", i=burnin_len, of=burnin_len)
#-----------------------------------------------------------------------
# Actual random walk
#-----------------------------------------------------------------------
Status("generating models", i=0, of=nmodels)
time_begin_get_models = time.clock()
adjust_threads(burnin_len, 'RWALK')
i=0
while i < nmodels:
k,vec = q.get()
t = np.zeros(dim+1, order='Fortran', dtype=np.float64)
t[1:] = vec
i += 1
Log( '%i models left to generate' % (nmodels-i), overwritable=True)
Status("generating models", i=i, of=nmodels)
yield t
time_end_get_models = time.clock()
Status("generating models", i=nmodels, of=nmodels)
#-----------------------------------------------------------------------
# Stop the threads and get their running times.
#-----------------------------------------------------------------------
time_threads = []
for thr,cmdq,ackq in threads:
cmdq.put(['STOP'])
m,t = ackq.get()
assert m == 'TIME'
time_threads.append(t)
#thr.terminate()
time_end_next = time.clock()
max_time_threads = np.amax(time_threads) if time_threads else 0
avg_time_threads = np.mean(time_threads) if time_threads else 0
Log( '-'*80 )
Log( 'SAMPLEX TIMINGS' )
Log( '-'*80 )
Log( 'Initial inner point %.2fs' % (time_end_inner_point - time_begin_inner_point) )
Log( 'Estimate eigenvectors %.2fs' % (time_end_est_eigenvectors - time_begin_est_eigenvectors) )
Log( 'Burn-in %.2fs' % (time_end_burnin - time_begin_burnin) )
Log( 'Modeling %.2fs' % (time_end_get_models - time_begin_get_models) )
Log( 'Max/Avg thread time %.2fs %.2fs' % (max_time_threads, avg_time_threads) )
Log( 'Total wall-clock time %.2fs' % (time_end_next - time_begin_next) )
Log( '-'*80 )
from lpsolve55 import lpsolve, IMPORTANT
lp = lpsolve('make_lp', 0, 4)
lpsolve('set_obj_fn', lp, [1, 3, 6.24, 0.1])
lpsolve('add_constraint', lp, [0, 78.26, 0, 2.9], 'GE', 92.3)
lpsolve('add_constraint', lp, [0.24, 0, 11.31, 0], 'LE', 14.8)
lpsolve('add_constraint', lp, [12.68, 0, 0.08, 0.9], 'GE', 4)
lpsolve('set_lowbo', lp, 1, 28.6)
lpsolve('set_lowbo', lp, 4, 18)
lpsolve('set_upbo', lp, 4, 48.98)
lpsolve('set_col_name', lp, 1, 'x1')
lpsolve('set_col_name', lp, 2, 'x2')
lpsolve('set_col_name', lp, 3, 'x3')
lpsolve('set_col_name', lp, 4, 'x4')
lpsolve('set_row_name', lp, 1, 'CONST1')
lpsolve('set_row_name', lp, 2, 'CONST2')
lpsolve('set_row_name', lp, 3, 'CONST3')
lpsolve('write_lp', lp, 'a.lp')
lpsolve('set_verbose', lp, IMPORTANT)
lpsolve('solve', lp)
print lpsolve('get_objective', lp)
print lpsolve('get_variables', lp)
print lpsolve('get_constraints', lp)[0]
def calculate_lpsolve(f, A, b, resolution):
n=len(f)
lp = lpsolve('make_lp', 0, len(f))
if not debug:
lpsolve('set_verbose', lp, IMPORTANT)
lpsolve('set_obj_fn', lp, [ -x for x in f ])
for i in range(len(A)):
lpsolve('add_constraint', lp, A[i], LE, b[i])
lpsolve('set_lowbo', lp, [0]*n)
lpsolve('set_upbo', lp, [slot_size(resolution)]*n)
lpsolve('solve', lp)
result = lpsolve('get_variables', lp)[0]
if not type(result) == list:
result = [ result ]
lpsolve('delete_lp', lp)
return result
def geq(self, a):
if not self.set_bound(a, 'low'):
if self.add_noise: a = self.noise(a)
lpsolve('add_constraint', self.lp, a[1:], GE, -a[0])
self.geq_count += 1
self.ineqs.append([a[1:], GE, -a[0]])
def det_rounding(scp_gen):
# linear reluxation
n = scp_gen.universal_set_size
lp = lpsolve('make_lp', 0, n)
lpsolve('set_maxim', lp)
lpsolve('set_obj_fn', lp, [1] * n)
for i, v in enumerate(scp_gen.get_cols()):
lpsolve('add_constraint', lp, v, 'LE', scp_gen.cost[i])
lpsolve('set_lowbo', lp, [0] * n)
lpsolve('set_verbose', lp, IMPORTANT)
lpsolve('solve', lp)
# deterministic rounding
float_ans = lpsolve('get_variables', lp)[0]
lpsolve('delete_lp', lp)
I = []
for i, v in enumerate(scp_gen.get_cols()):
s = sum(float_ans[j] for j, e in enumerate(v) if e != 0)
if s == scp_gen.cost[i]:
I.append(1)
else:
I.append(0)
return I
from lpsolve55 import lpsolve, LE #@UnresolvedImport
lp = lpsolve('make_lp', 0, 8)
#lpsolve('set_verbose', lp, IMPORTANT)
lpsolve('set_obj_fn', lp, [-1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0])
lpsolve('add_constraint', lp, [1.0, 1.0, 1.0, 0, 0, 0, 0, 0], LE, 8.0)
lpsolve('add_constraint', lp, [0, 0, 0, 1.0, 1.0, 0, 0, 0], LE, 4.0)
lpsolve('add_constraint', lp, [0, 0, 0, 0, 0, 1.0, 0, 0], LE, 8.0)
lpsolve('add_constraint', lp, [0, 0, 0, 0, 0, 0, 1.0, 1.0], LE, 12.0)
lpsolve('add_constraint', lp, [1.0, 0, 0, 1.0, 0, 0, 0, 0], LE, 10.0)
lpsolve('add_constraint', lp, [0, 1.0, 0, 0, 1.0, 1.0, 1.0, 0], LE, 10.0)
lpsolve('add_constraint', lp, [0, 0, 1.0, 0, 0, 0, 0, 1.0], LE, 10.0)
lpsolve('set_lowbo', lp, [0, 0.0, 0, 0, 0, 0, 0, 0])
lpsolve('set_upbo', lp, [10.0, 10.0, 10.0, 10.0, 10.0, 10.0, 10.0, 10.0])
lpsolve('solve', lp)
print lpsolve('get_variables', lp)[0]
lpsolve('delete_lp', lp)
def solve_bp(scp_gen):
print "--- SOLVE BINARY PROGRAMMING ---"
lp = lpsolve('make_lp', 0, scp_gen.covering_set_num)
lpsolve('set_obj_fn', lp, scp_gen.cost)
lpsolve('set_binary', lp, range(scp_gen.covering_set_num))
for v in scp_gen.get_rows():
lpsolve('add_constraint', lp, v, 'GE', 1)
lpsolve('set_verbose', lp, IMPORTANT)
lpsolve('write_lp', lp, 'b.lp')
lpsolve('solve', lp)
print "solution of bp:", lpsolve('get_objective', lp)
V = lpsolve('get_variables', lp)[0]
print "solution vector:", V
print scp_gen.is_covered([i for i, v in enumerate(V) if v != 0.0]), "\n"
lpsolve('delete_lp', lp)
def next(self, nsolutions=None):
Log("=" * 80)
Log("Simplex Random Walk")
Log("=" * 80)
Log(" %i equations" % len(self.eq_list))
Log("%6s %6s %6s\n%6i %6i %6i" % (">=", "<=", "=", self.geq_count, self.leq_count, self.eq_count))
if nsolutions == 0:
return
assert nsolutions is not None
dim = self.nVars
dof = dim - self.eq_count
burnin_len = max(10, int(self.burnin_factor * dof))
redo = max(100, int((dof ** self.redo_exp) * self.redo_factor))
nmodels = nsolutions
nthreads = self.nthreads
self.stride = int(dim + 1)
n_stored = 0
self.dim = dim
self.dof = dof
self.redo = redo
self.burnin_len = burnin_len
accept_rate = self.accept_rate
accept_rate_tol = self.accept_rate_tol
store = np.zeros((dim, 1 + burnin_len), order="Fortran", dtype=np.float64)
newp = np.zeros(dim, order="C", dtype=np.float64)
eval = np.zeros(dim, order="C", dtype=np.float64)
evec = np.zeros((dim, dim), order="F", dtype=np.float64)
self.eqs = np.zeros((self.eqn_count + dim, dim + 1), order="C", dtype=np.float64)
for i, [c, e] in enumerate(self.eq_list):
self.eqs[i, :] = e
for i in xrange(dim):
self.eqs[self.eqn_count + i, 1 + i] = 1
self.dist_eqs = np.zeros((self.eqn_count - self.eq_count, dim + 1), order="C", dtype=np.float64)
i = 0
for c, e in self.eq_list:
if c == "eq":
continue
elif c == "leq":
p = e
elif c == "geq":
p = -e
self.dist_eqs[i, :] = p
i += 1
Log("Using lpsolve %s" % lpsolve("lp_solve_version"))
Log("random seed = %s" % self.random_seed)
Log("threads = %s" % self.nthreads)
Log("acceptence rate = %s" % self.accept_rate)
Log("acceptence rate tolerance = %s" % self.accept_rate_tol)
Log("dof = %s" % self.dof)
Log("sample distance = max(100,%s * %s^%s) = %s" % (self.redo_factor, self.dof, self.redo_exp, redo))
Log("starting twiddle = %s" % self.twiddle)
Log("burn-in length = %s" % burnin_len)
time_begin_next = time.clock()
# -----------------------------------------------------------------------
# Create pseudo inverse matrix to reproject samples back into the
# solution space.
# -----------------------------------------------------------------------
P = np.eye(dim)
if self.eq_count > 0:
self.A = np.zeros((self.eq_count, dim), order="C", dtype=np.float64)
self.b = np.zeros(self.eq_count, order="C", dtype=np.float64)
for i, [c, e] in enumerate(self.eq_list[: self.eq_count]):
self.A[i] = e[1:]
self.b[i] = e[0]
self.Apinv = pinv(self.A)
P -= np.dot(self.Apinv, self.A)
else:
self.A = None
self.B = None
self.Apinv = None
ev, evec = eigh(P)
# -----------------------------------------------------------------------
# -----------------------------------------------------------------------
# Find a point that is completely inside the simplex
# -----------------------------------------------------------------------
Log("Finding first inner point")
time_begin_inner_point = time.clock()
self.inner_point(newp)
time_end_inner_point = time.clock()
ok, fail_count = self.in_simplex(newp, eq_tol=1e-12, tol=0, verbose=1)
assert ok
self.avg0 = newp
# eqs = self.eqs.copy('A')
# eqs[:,1:] = np.dot(self.eqs[:,1:], evec)
# print newp
# S = zeros(self.eqs.shape[0])
# newp[:] = np.dot(evec.T, newp)
# newp0 = newp.copy()
# steps = newp.copy()
# for q in range(100):
# csamplex.refine_center(self, eqs, newp, ev, S, steps)
# d = newp - newp0
# #print d
# print norm(d)
# #print
# newp0 = newp.copy()
# #assert 0
# newp[:] = np.dot(evec, newp)
store[:, 0] = newp
n_stored = 1
# -----------------------------------------------------------------------
# Estimate the eigenvectors of the simplex
# -----------------------------------------------------------------------
Log("Estimating eigenvectors")
time_begin_est_eigenvectors = time.clock()
self.measured_ev(newp, ev, eval, evec)
time_end_est_eigenvectors = time.clock()
# -----------------------------------------------------------------------
# Now we can start the random walk
# -----------------------------------------------------------------------
Log("Getting solutions")
q = MP.Queue()
# -----------------------------------------------------------------------
# Launch the threads
# -----------------------------------------------------------------------
threads = []
models_per_thread = nmodels // nthreads
models_under = nmodels - nthreads * models_per_thread
id, N = 0, 0
while id < nthreads and N < nmodels:
n = models_per_thread
if id < models_under:
n += 1
assert n > 0
Log("Thread %i gets %i" % (id, n))
cmdq = MP.Queue()
ackq = MP.Queue()
thr = MP.Process(
target=rwalk_burnin,
args=(
id,
n,
int(np.ceil(burnin_len / nthreads)),
self,
q,
cmdq,
ackq,
newp,
self.twiddle,
eval.copy("A"),
evec.copy("A"),
),
)
threads.append([thr, cmdq, ackq])
N += n
id += 1
assert N == nmodels
for thr, cmdq, _ in threads:
thr.start()
cmdq.put(["CONT"])
def drainq(q):
try:
while True:
q.get(block=False)
except QueueEmpty:
pass
def pause_threads(threads):
for _, cmdq, ackq in threads:
cmdq.put(["WAIT"])
assert ackq.get() == "OK"
def adjust_threads(i, cont_cmd):
pause_threads(threads)
drainq(q)
Log("Computing eigenvalues... [%i/%i]" % (i, burnin_len))
self.compute_eval_evec(store, eval, evec, n_stored)
# new twiddle <-- average twiddle
t = 0
for _, cmdq, ackq in threads:
cmdq.put(["REQ TWIDDLE"])
t += ackq.get()
t /= len(threads)
Log("New twiddle %f" % t)
for _, cmdq, _ in threads:
cmdq.put(["NEW DATA", [eval.copy("A"), evec.copy("A"), t]])
cmdq.put([cont_cmd])
# -----------------------------------------------------------------------
# Burn-in
# -----------------------------------------------------------------------
time_begin_burnin = time.clock()
compute_eval_window = 2 * self.dof
j = 0
for i in xrange(burnin_len):
j += 1
k, vec = q.get()
store[:, n_stored] = vec
n_stored += 1
if j == compute_eval_window:
j = 0
adjust_threads(i + 1, "CONT")
compute_eval_window = int(0.1 * burnin_len + 1)
elif len(threads) < compute_eval_window:
threads[k][1].put(["CONT"])
time_end_burnin = time.clock()
# -----------------------------------------------------------------------
# Actual random walk
# -----------------------------------------------------------------------
time_begin_get_models = time.clock()
adjust_threads(burnin_len, "RWALK")
i = 0
while i < nmodels:
k, vec = q.get()
t = np.zeros(dim + 1, order="Fortran", dtype=np.float64)
t[1:] = vec
i += 1
Log("%i models left to generate" % (nmodels - i), overwritable=True)
yield t
time_end_get_models = time.clock()
# -----------------------------------------------------------------------
# Stop the threads and get their running times.
# -----------------------------------------------------------------------
time_threads = []
for thr, cmdq, ackq in threads:
cmdq.put(["STOP"])
m, t = ackq.get()
assert m == "TIME"
time_threads.append(t)
# thr.terminate()
time_end_next = time.clock()
max_time_threads = np.amax(time_threads) if time_threads else 0
avg_time_threads = np.mean(time_threads) if time_threads else 0
Log("-" * 80)
Log("SAMPLEX TIMINGS")
Log("-" * 80)
Log("Initial inner point %.2fs" % (time_end_inner_point - time_begin_inner_point))
Log("Estimate eigenvectors %.2fs" % (time_end_est_eigenvectors - time_begin_est_eigenvectors))
Log("Burn-in %.2fs" % (time_end_burnin - time_begin_burnin))
Log("Modeling %.2fs" % (time_end_get_models - time_begin_get_models))
Log("Max/Avg thread time %.2fs %.2fs" % (max_time_threads, avg_time_threads))
Log("Total wall-clock time %.2fs" % (time_end_next - time_begin_next))
Log("-" * 80)
def assign_sections(students, prioritize=False, debug=False):
"""
students: a list of student objects
i = index of sections
j = index of students
The columns, x_i_j, go as follows:
x_0_0, x_1_0, x_2_0, ..., x_0_1, ..., x_M_N
"""
M = len(students[0].rankings) # number of section
N = len(students) # number of students
f = make_obj_f(students, prioritize)
A = make_coeff_m(M, N)
b = make_b_v(students, M, N)
e = make_e_v(M, N)
v = [1 for _ in range(M * N)]
lp = lpm.lp_maker(f, A, b, e, None, v)
# set branch and bound depth to be unlimited
lps.lpsolve("set_bb_depthlimit", lp, 0)
# set all variables to binary
lps.lpsolve("set_binary", lp, v)
# set lp to minimize the objective function
lps.lpsolve("set_minim", lp)
lps.lpsolve("write_lp", lp, LP_OUT)
lps.lpsolve("solve", lp)
res = lps.lpsolve("get_variables", lp)[0]
lps.lpsolve("delete_lp", lp)
parse_results(res, students, M, debug)
def __del__(self):
if self.lp:
lpsolve('delete_lp', self.lp)
def det_rounding(scp_gen):
# linear reluxation
lp = lpsolve('make_lp', 0, scp_gen.covering_set_num)
lpsolve('set_obj_fn', lp, scp_gen.cost)
for v in scp_gen.get_rows():
lpsolve('add_constraint', lp, v, 'GE', 1)
for i in range(1, scp_gen.covering_set_num + 1):
lpsolve('set_lowbo', lp, i, 0)
lpsolve('set_verbose', lp, IMPORTANT)
lpsolve('solve', lp)
# deterministic rounding
float_ans = lpsolve('get_variables', lp)[0]
_, f = scp_gen.get_f()
return [1 if x >= 1.0 / float(f) else 0 for x in float_ans]
def test_lpsolve(self):
""" test lpsolve
(http://lpsolve.sourceforge.net)
"""
try:
from lpsolve55 import lpsolve
except ImportError:
raise SkipTest('lpsolve is not available')
print '\n------------------------------ lpsolve ------------------------------'
obj = self.f.tolist()
lp = lpsolve('make_lp', 0, len(obj))
lpsolve('set_verbose', lp, 'IMPORTANT')
lpsolve('set_obj_fn', lp, obj)
i = 0
for con in self.A:
lpsolve('add_constraint', lp, con.tolist(), 'LE', self.b[i])
i = i+1
for i in range (len(self.lb)):
lpsolve('set_lowbo', lp, i+1, self.lb[i])
lpsolve('set_upbo', lp, i+1, self.ub[i])
results = lpsolve('solve', lp)
result_text = [
'OPTIMAL An optimal solution was obtained',
'SUBOPTIMAL The model is sub-optimal. Only happens if there are integer variables and there is already an integer solution found. The solution is not guaranteed the most optimal one.',
'INFEASIBLE The model is infeasible',
'UNBOUNDED The model is unbounded',
'DEGENERATE The model is degenerative',
'NUMFAILURE Numerical failure encountered',
'USERABORT The abort routine returned TRUE. See put_abortfunc',
'TIMEOUT A timeout occurred. A timeout was set via set_timeout',
'N/A'
'PRESOLVED The model could be solved by presolve. This can only happen if presolve is active via set_presolve',
'PROCFAIL The B&B routine failed',
'PROCBREAK The B&B was stopped because of a break-at-first (see set_break_at_first) or a break-at-value (see set_break_at_value)',
'FEASFOUND A feasible B&B solution was found',
'NOFEASFOUND No feasible B&B solution found'
]
print 'results: (%d)' % results, result_text[results]
print 'f:', lpsolve('get_objective', lp)
print 'x:', lpsolve('get_variables', lp)[0]
lpsolve('delete_lp', lp)