consistent style in samples

samples/MDAnalysisIntegration.py

@@ -12,6 +12,10 @@
 # set up a minimal sample system
 
 system = espressomd.System(box_l=[10.0, 10.0, 10.0])
+system.set_random_state_PRNG()
+#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
+np.random.seed(seed=system.seed)
+
 system.time_step = 0.001
 system.cell_system.skin = 0.1
 

samples/billard.py

@@ -8,7 +8,7 @@
 from espressomd import electrostatics
 from espressomd import minimize_energy
 from espressomd.interactions import *
-import numpy
+import numpy as np
 from threading import Thread
 from math import *
 from espressomd.visualization_opengl import *
@@ -18,6 +18,7 @@
 
 #ESPRESSO
 system = espressomd.System(box_l=[1.0, 1.0, 1.0])
+system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
 table_dim = [2.24,1.12]
 system.box_l = [table_dim[0], 3, table_dim[1]]
 
@@ -34,7 +35,7 @@
         light_brightness = 5.0)
 
 stopped = True
-angle = numpy.pi*0.5
+angle = np.pi*0.5
 impulse = 10.0
 
 def decreaseAngle():
@@ -168,7 +169,7 @@ def mix_sig(sig1,sig2,rule='LB'):
 
         vsum = 0
         for p in system.part:
-            vsum += numpy.linalg.norm(p.v)
+            vsum += np.linalg.norm(p.v)
 
             for h in hole_pos:
 

samples/bonds-tst.py

@@ -2,7 +2,8 @@
 import espressomd
 from espressomd.interactions import *
 
-S = espressomd.System(box_l=[1.0, 1.0, 1.0])
+system = espressomd.System(box_l=[1.0, 1.0, 1.0])
+system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
 
 h = HarmonicBond(r_0=0, k=1)
 f = FeneBond(k=1, d_r_max=1)
@@ -14,61 +15,61 @@
 print(f2)
 
 # note the order of the printed bond types
-S.bonded_inter[0] = h
-S.bonded_inter[2] = f
-S.bonded_inter.add(f2)
+system.bonded_inter[0] = h
+system.bonded_inter[2] = f
+system.bonded_inter.add(f2)
 
 print("\n**Added bond types to the system:")
-for b in S.bonded_inter:
+for b in system.bonded_inter:
     print(b)
 
-S.part.add(id=0, pos=(0., 0., 0.))
-S.part.add(id=1, pos=(0, 0, 0))
-S.part.add(id=2, pos=(0, 0, 0))
+system.part.add(id=0, pos=(0., 0., 0.))
+system.part.add(id=1, pos=(0, 0, 0))
+system.part.add(id=2, pos=(0, 0, 0))
 print("\n**Defined three particles")
 print("Bonds for particle '0':")
-print(S.part[0].bonds)
+print(system.part[0].bonds)
 
 print("\n**Bonding particle 0 to particle 1 with bond referred by \"f2\'")
-S.part[0].add_bond((f2, 1))
+system.part[0].add_bond((f2, 1))
 print("Bonds for particle '0':")
-print(S.part[0].bonds)
+print(system.part[0].bonds)
 
 
 print("\n**Bonding particle 0 to particle 2 with bond referred by index 0")
-S.part[0].add_bond((0, 2))
+system.part[0].add_bond((0, 2))
 print("Bonds for particle 0:")
-print(S.part[0].bonds)
+print(system.part[0].bonds)
 
 print("Bonds for particle 1:")
-print(S.part[1].bonds)
+print(system.part[1].bonds)
 print("Bonds for particle 2:")
-print(S.part[2].bonds)
+print(system.part[2].bonds)
 
 
 print("\n**creating holder for bonds on particle 0")
-tmp = S.part[0].bonds
+tmp = system.part[0].bonds
 print("\n**deleted all bonds of 0")
-S.part[0].delete_all_bonds()
+system.part[0].delete_all_bonds()
 print("Bonds for particle 0:")
-print(S.part[0].bonds)
+print(system.part[0].bonds)
 
 print("\n**setting particle 0 bonds from holder")
-S.part[0].bonds = tmp
+system.part[0].bonds = tmp
 print("Bonds for particle 0:")
-print(S.part[0].bonds)
+print(system.part[0].bonds)
 
 print("\n**deleting bond referred by \"h\" to particle 2 :")
-S.part[0].delete_bond((h, 2))
+system.part[0].delete_bond((h, 2))
 print("Bonds for particle '0':")
-print(S.part[0].bonds)
+print(system.part[0].bonds)
 
 print("\n**Bonding particle 0 to particle 1 with bond referred by index 0 :")
 print("**Bonding particle 0 to particle 2 with bond referred by index 2 :")
-S.part[0].bonds = ((0, 1), (2, 2))
+system.part[0].bonds = ((0, 1), (2, 2))
 print("Bonds for particle '0':")
-print(S.part[0].bonds)
+print(system.part[0].bonds)
 
 print("**Listing bonds held by all particles")
-for p in S.part:
+for p in system.part:
     print(p.bonds)

samples/cellsystem_test.py

@@ -19,7 +19,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 from __future__ import print_function
-import espressomd as es
+import espressomd
 from espressomd import polymer
 from espressomd import interactions
 import time
@@ -29,31 +29,33 @@
 def profile():
     cs.skin = skin
     ti = time.time()
-    S.integrator.run(n_steps)
+    system.integrator.run(n_steps)
     tf = time.time()
     print("\t with skin={} ran {:d} steps in {:f} seconds. steps/sec:{:f} ".format(skin,
                                                                                    n_steps, tf - ti, n_steps * 1. / (tf - ti)))
 
 
-S = es.System(box_l = [100, 100, 100])
-cs = S.cell_system
+system = espressomd.System(box_l = [100, 100, 100])
+system.set_random_state_PRNG()
+#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
+cs = system.cell_system
 
 
 # domain decomposition with verlet list: three equivalent commands
 cs.set_domain_decomposition()
 cs.set_domain_decomposition(True)
 cs.set_domain_decomposition(use_verlet_lists=True)
 
-S.thermostat.set_langevin(kT=1.0, gamma=1.0)
-S.time_step = 0.01
+system.thermostat.set_langevin(kT=1.0, gamma=1.0)
+system.time_step = 0.01
 
 
 # Create a minimal polymer
-S.non_bonded_inter[0, 0].lennard_jones.set_params(
+system.non_bonded_inter[0, 0].lennard_jones.set_params(
     epsilon=1, sigma=1,
     cutoff=2**(1. / 6), shift="auto")
 fene = interactions.FeneBond(k=10, d_r_max=1.5)
-S.bonded_inter.add(fene)
+system.bonded_inter.add(fene)
 polymer.create_polymer(N_P=1, bond_length=0.97, MPC=100, bond=fene)
 
 n_steps = 1000

samples/coulomb_debye_hueckel.py

@@ -17,7 +17,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 from __future__ import print_function
-import numpy
+import numpy as np
 import espressomd
 from espressomd import thermostat
 from espressomd import electrostatics
@@ -63,6 +63,10 @@
 # Integration parameters
 #############################################################
 system = espressomd.System(box_l=[box_l]*3)
+system.set_random_state_PRNG()
+#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
+np.random.seed(seed=system.seed)
+
 system.time_step = 0.01
 system.cell_system.skin = 0.4
 
@@ -99,7 +103,7 @@
 #############################################################
 
 for i in range(n_part):
-    system.part.add(id=i, pos=numpy.random.random(3) * system.box_l)
+    system.part.add(id=i, pos=np.random.random(3) * system.box_l)
 
 for i in range(n_part / 2):
     system.part[2 * i].q = -1.0
@@ -115,7 +119,7 @@
 # means that lj_sig is 0.714 nm in SI units.
 coulomb_prefactor = 1
 # inverse Debye length for 1:1 electrolyte in water at room temperature (nm)
-dh_kappa = numpy.sqrt(mol_dens) / 0.304
+dh_kappa = np.sqrt(mol_dens) / 0.304
 # convert to MD units
 dh_kappa = dh_kappa / 0.714
 dh = electrostatics.CDH(prefactor=coulomb_prefactor, kappa=dh_kappa,

samples/debye_hueckel.py

@@ -17,7 +17,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 from __future__ import print_function
-import numpy
+import numpy as np
 import espressomd
 from espressomd import thermostat
 from espressomd import electrostatics
@@ -63,6 +63,9 @@
 # Integration parameters
 #############################################################
 system = espressomd.System(box_l=[box_l]*3)
+system.set_random_state_PRNG()
+np.random.seed(seed=system.seed)
+
 system.time_step = 0.01
 system.cell_system.skin = 0.4
 
@@ -99,7 +102,7 @@
 #############################################################
 
 for i in range(n_part):
-    system.part.add(id=i, pos=numpy.random.random(3) * system.box_l)
+    system.part.add(id=i, pos=np.random.random(3) * system.box_l)
 
 for i in range(n_part / 2):
     system.part[2 * i].q = -1.0
@@ -112,7 +115,7 @@
 # means that lj_sig is 0.714 nm in SI units.
 coulomb_prefactor =1
 # inverse Debye length for 1:1 electrolyte in water at room temperature (nm)
-dh_kappa = numpy.sqrt(mol_dens) / 0.304
+dh_kappa = np.sqrt(mol_dens) / 0.304
 # convert to MD units
 dh_kappa = dh_kappa / 0.714
 dh = electrostatics.DH(

samples/diffusion_coefficient.py

@@ -7,22 +7,26 @@
 """
 
 from __future__ import division, print_function
+import espressomd
+from espressomd.correlators import Correlator 
+from espressomd.observables import ParticlePositions, ParticleVelocities
+import numpy as np
 
 gamma=2.4
 kT=1.37
 dt=0.05
 
-import espressomd
-from espressomd.correlators import Correlator 
-from espressomd.observables import ParticlePositions, ParticleVelocities
-import numpy as np
+system=espressomd.System(box_l=[1.0, 1.0, 1.0])
+system.set_random_state_PRNG()
+#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
+np.random.seed(seed=system.seed)
+
 
-s=espressomd.System(box_l=[1.0, 1.0, 1.0])
-p=s.part.add(pos=(0,0,0),id=0)
-s.time_step=dt
-s.thermostat.set_langevin(kT=kT,gamma=gamma)
-s.cell_system.skin =0.4
-s.integrator.run(1000)
+p=system.part.add(pos=(0,0,0),id=0)
+system.time_step=dt
+system.thermostat.set_langevin(kT=kT,gamma=gamma)
+system.cell_system.skin =0.4
+system.integrator.run(1000)
 
 pos_obs=ParticlePositions(ids=(0,))
 vel_obs=ParticleVelocities(ids=(0,))
@@ -31,10 +35,10 @@
     corr_operation="square_distance_componentwise", compress1="discard1")
 c_vel = Correlator(obs1=vel_obs, tau_lin=16, tau_max=20., dt=dt,
     corr_operation="scalar_product", compress1="discard1")
-s.auto_update_correlators.add(c_pos)
-s.auto_update_correlators.add(c_vel)
+system.auto_update_correlators.add(c_pos)
+system.auto_update_correlators.add(c_vel)
 
-s.integrator.run(1000000)
+system.integrator.run(1000000)
 
 c_pos.finalize()
 c_vel.finalize()

samples/dpd.py

@@ -3,9 +3,9 @@
 import numpy as np
 
 # Set up the box and time step
-s = espressomd.System(box_l = 3 * [10])
-s.time_step = 0.01
-s.cell_system.skin=0.4
+system = espressomd.System(box_l = 3 * [10])
+system.time_step = 0.01
+system.cell_system.skin = 0.4
 
 # DPD parameters
 n_part = 200
@@ -16,31 +16,34 @@
 F_max=1.
 
 # Activate the thermostat
-s.thermostat.set_dpd(kT=kT)
+system.thermostat.set_dpd(kT=kT)
+system.set_random_state_PRNG()
+np.random.seed(seed=system.seed)
+#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
 
 # Set up the DPD friction interaction
-s.non_bonded_inter[0,0].dpd.set_params(
+system.non_bonded_inter[0,0].dpd.set_params(
     weight_function=0, gamma=gamma, r_cut=r_cut,
     trans_weight_function=0, trans_gamma=gamma, trans_r_cut=r_cut)
 
 # Set up the repulsive interaction
-s.non_bonded_inter[0,0].hat.set_params(F_max=F_max,
+system.non_bonded_inter[0,0].hat.set_params(F_max=F_max,
                                        cutoff=r_cut)
 
 # Add the particles randomly distributed over the box
-s.part.add(pos=s.box_l * np.random.random((n_part,3)))
+system.part.add(pos=system.box_l * np.random.random((n_part,3)))
 
 # As a usage example, we calculate the pressure at serveral
 # particle densities.
 for V in range(100, 1000, 100):
     # Rescale the system to the new volume
-    s.change_volume_and_rescale_particles(V**0.3333)
+    system.change_volume_and_rescale_particles(V**0.3333)
 
     # List of samples
     p_samples = []
     for i in range(100):
-        s.integrator.run(1000)
-        p_samples.append(s.analysis.pressure()['total'])
+        system.integrator.run(1000)
+        p_samples.append(system.analysis.pressure()['total'])
 
     # Average pressure
     p_avg = np.mean(p_samples)

samples/ekboundaries.py

@@ -1,6 +1,11 @@
+
 from espressomd import System, shapes, electrokinetics
 import sys
+
 system = System(box_l = [10, 10, 10])
+system.set_random_state_PRNG()
+#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
+
 system.cell_system.skin = 0.4
 system.time_step = 0.1