start_time = time.clock()
for i in range(check):
T = temperature.compute()
P = pressure.compute()
Eb = 0
EAng = 0
for bd in bondedinteractions.values():
Eb += bd.computeEnergy()
for ang in angleinteractions.values():
EAng += ang.computeEnergy()
ELj = ljinteraction.computeEnergy()
EQQ = qq_interactions.computeEnergy()
T = temperature.compute()
Ek = 0.5 * T * (3 * num_particles)
Etotal = Ek + Eb + EAng + EQQ + ELj
outfile.write(
fmt % (i * steps / check * timestep, Eb, EAng, ELj, EQQ, Ek, Etotal))
print(fmt % (i * steps / check * timestep, Eb, EAng, ELj, EQQ, Ek, Etotal))
#espressopp.tools.pdb.pdbwrite("traj.pdb", system, append=True)
integrator.run(steps / check) # print out every steps/check steps
#system.storage.decompose()
# print timings and neighbor list information
end_time = time.clock()
timers.show(integrator.getTimers(), precision=2)
sys.stdout.write('Integration steps = %d\n' % integrator.step)
sys.stdout.write('CPU time = %.1f\n' % (end_time - start_time))
Pij = pressureTensor.compute()
Ek = 0.5 * T * (3 * num_particles)
Ep = interLJ.computeEnergy()
Eb = interFENE.computeEnergy()
Ea = interCosine.computeEnergy()
Etotal = Ek + Ep + Eb + Ea
sys.stdout.write(
' step T P Pxy etotal ekinetic epair ebond eangle\n'
)
sys.stdout.write(fmt % (0, T, P, Pij[3], Etotal, Ek, Ep, Eb, Ea))
start_time = time.clock()
integrator.run(steps)
T = temperature.compute()
P = pressure.compute()
Pij = pressureTensor.compute()
Ek = 0.5 * T * (3 * num_particles)
Ep = interLJ.computeEnergy()
Eb = interFENE.computeEnergy()
Ea = interCosine.computeEnergy()
Etotal = Ek + Ep + Eb + Ea
sys.stdout.write(fmt % (steps, T, P, Pij[3], Etotal, Ek, Ep, Eb, Ea))
sys.stdout.write('\n')
end_time = time.clock()
timers.show(integrator.getTimers(), system)
#os.system('rm '+tabfileLJ+' '+tabfileFENE+' '+tabfileCosine)
print '\nDone.'
P = pressure.compute()
Eb = 0
EAng = 0
ETab=0
#for bd in bondedinteractions.values(): Eb+=bd.computeEnergy()
#for ang in angleinteractions.values(): EAng+=ang.computeEnergy()
#ELj= ljinteraction.computeEnergy()
#EQQ= qq_interactions.computeEnergy()
ETab= tabulatedinteraction.computeEnergy()
T = temperature.compute()
Ek = 0.5 * T * (3 * num_particles)
Etotal = Ek+Eb+EAng+ETab
print (fmt%(i*timestep,Eb, EAng, ETab, Ek, Etotal, T))
outfile.write(fmt%(i*timestep,Eb, EAng, ETab, Ek, Etotal, T))
#espressopp.tools.pdb.pdbfastwrite("traj.pdb", system, append=True)
espressopp.tools.fastwritexyz("traj.xyz", system, append=True, scale=10)
integrator.run(steps/check) # print out every steps/check steps
#espressopp.tools.vmd.imd_positions(system, sock)
# print timings and neighbor list information
end_time = time.clock()
timers.show(integrator.getTimers(), precision=2)
espressopp.tools.analyse.final_info(system, integrator, verletlist, start_time, end_time)
sys.stdout.write('Integration steps = %d\n' % integrator.step)
sys.stdout.write('CPU time = %.1f\n' % (end_time - start_time))
#sock = espressopp.tools.vmd.connect(system)
filename = "prod.pdb"
start_time = time.process_time()
for step in range(prod_nloops):
integrator2.run(prod_isteps)
espressopp.tools.analyse.info(system, integrator2)
# espressopp.tools.xyzfilewrite(filename, system, velocities = False, charge = False, append=True, atomtypes={0:'X'})
# espressopp.tools.pdbwrite("prod.pdb", system, molsize=Npart,append=True)
end_time = time.process_time()
print("production finished")
if (ifbond):
T = temperature.compute()
P = pressure.compute()
Pij = pressureTensor.compute()
Ek = 0.5 * T * (3 * num_particles)
Ep = interLJ.computeEnergy()
Eb = interFENE.computeEnergy()
Ea = interCosine.computeEnergy()
Etotal = Ek + Ep + Eb + Ea
sys.stdout.write(fmt % (prod_nloops*prod_isteps, T, P, Pij[3], Etotal, Ek, Ep, Eb, Ea))
sys.stdout.write('\n')
# print timings and neighbor list information
timers.show(integrator2.getTimers(), precision=3)
sys.stdout.write('Total # of neighbors = %d\n' % vl.totalSize())
sys.stdout.write('Ave neighs/atom = %.1f\n' % (vl.totalSize() / float(num_particles)))
sys.stdout.write('Neighbor list builds = %d\n' % vl.builds)
sys.stdout.write('Integration steps = %d\n' % integrator2.step)
sys.stdout.write('CPUs = %i CPU time per CPU = %.1f\n' % (comm.size,end_time - start_time))
