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))