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gurobi.py
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Fri, Apr 19, 03:19

gurobi.py
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import numpy as np
import timeit
import gurobipy as gp
from gurobipy import GRB
# This function places the molecule M optimally within the target T such that
# the charges of the molecule CM and the charges of the target CT are
# compatible
def OptimalPlacement(M,CM,T,CT):
try:
#Dimemsion of the Molecule and Target
m = len(M)
n = len(T)
print("-----------------------------------")
print("Sizes of Matrices to match: ", m, n)
print("-----------------------------------")
# Create a new model
Z = gp.Model("QP")
Z.setParam('OutputFlag', 0)
start=timeit.default_timer()
#Create Variables
x = Z.addVars(m, n, name='X', vtype=GRB.BINARY)
Z.addConstrs(x.sum(i, '*') == 1 for i in range(m))
Z.addConstrs(x.sum('*',j) <= 1 for j in range(n))
# if the charges of atom i in molecule and atom j in target do not
# match, then we forbid the assignment i-> j
for i in range(m):
for j in range(n):
if(CM[i] != CT[j]):
Z.addConstr(x[i,j] == 0)
# Set objective by building a long expression
# this takes the most time by far, to optimize?
expr = 2*x[1,1] * x[1,2]
expr.clear()
for i in range(m):
for j in range(m):
for k in range(n):
for l in range(n):
expr.add(x[i,k] * x[j,l], (T[k,l]-M[i,j])**2)
expr.addConstant(-m)
Z.setObjective(expr, GRB.MINIMIZE)
stop=timeit.default_timer()
print("Time to define objective function:", stop-start, "s")
# Optimize model
print("\n----------------\n Optimisation... \n----------------\n")
Z.optimize()
assert Z.status == 2
print("\n------------------\n Best match... \n------------------\n")
matched_target = []
for v in Z.getVars():
if v.x == 1:
i,j = v.varName.split("[")[-1].split("]")[0].split(",")
j = int(j)
matched_target.append(j)
print("Indices of the target:")
print(matched_target)
print("Objective value:")
print(Z.ObjVal)
print("Runtime:")
print(Z.Runtime, "s")
return [matched_target, Z.ObjVal]
except gp.GurobiError as e:
print('Error code ' + str(e.errno) + ': ' + str(e))
return [[], -1]
except AttributeError:
print('Encountered an attribute error')
return [[],-1]
except AssertionError:
print("No optimal solution has been found")
return [[],-1]
#A shortcut to call the OptimalPlacement function
def Assignment(database_index, target_index):
target_CM = data['target_CMs'][target_index]
target_ncharges = data['target_ncharges'][target_index]
target_label = data['target_labels'][target_index]
assert len(target_CM) == len(target_ncharges)
database_CM = data['database_CMs'][database_index]
database_ncharges = data['database_ncharges'][database_index]
database_label = data['database_labels'][database_index]
assert len(database_CM) == len(database_ncharges)
print("----------------------------------------")
print("Trying to place", database_label, "inside", target_label, "...")
print("----------------------------------------")
[target_indices, objval] = OptimalPlacement(database_CM, database_ncharges, target_CM, target_ncharges)
return [target_indices, objval]
if __name__ == "__main__":
data = np.load("data.npz", allow_pickle=True)
#fixed target index (value in {0, 1, 2})
target_index = 2
# loops over all candidates M, looking for minimal objective value
size_database=len(data['database_ncharges'])
m_index=0
[target_indices, objval]=[[], -1]
#for database_index in range(size_database):
for database_index in [0,1]:
print(database_index, " / ", size_database)
[tempindices, tempobjval]=Assignment(database_index, target_index)
if objval==-1 or (tempobjval!=-1 and tempobjval < objval):
objval = tempobjval
target_indices=tempindices
molecule_index=database_index
print("Best molecule M found:")
print("Name:", data['database_labels'][m_index])
print("Target indices:", target_indices)
print("Objective value:", objval)

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