espressomd · kodiakhq · Feb 14, 2020 · Feb 13, 2020 · Feb 13, 2020 · Feb 13, 2020
diff --git a/doc/doxygen/bibliography.bib b/doc/doxygen/bibliography.bib
@@ -351,6 +351,20 @@ @Article{neumann85b
 doi = {10.1063/1.448553},
 }
 
+@article{panneton06a,
+author = {Panneton, Fran\c{c}ois and L'Ecuyer, Pierre and Matsumoto, Makoto},
+title = {Improved long-period generators based on linear recurrences modulo 2},
+year = {2006},
+publisher = {Association for Computing Machinery},
+address = {New York, NY, USA},
+volume = {32},
+number = {1},
+issn = {0098-3500},
+doi = {10.1145/1132973.1132974},
+journal = {ACM Transactions on Mathematical Software (TOMS)},
+pages = {1-16},
+}
+
 @Book{Pottier2010,
   title={{Nonequilibrium Statistical Physics}},
   subtitle={{Linear Irreversible Processes}},

diff --git a/doc/tutorials/01-lennard_jones/01-lennard_jones.ipynb b/doc/tutorials/01-lennard_jones/01-lennard_jones.ipynb
@@ -168,7 +168,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The next step would be to create an instance of the System class and to seed espresso. This instance is used as a handle to the simulation system. At any time, only one instance of the System class can exist."
+    "The next step would be to create an instance of the System class. This instance is used as a handle to the simulation system. At any time, only one instance of the System class can exist."
    ]
   },
   {
@@ -177,8 +177,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "system = espressomd.System(box_l=BOX_L)\n",
-    "system.seed = 42"
+    "system = espressomd.System(box_l=BOX_L)"
    ]
   },
   {

diff --git a/doc/tutorials/02-charged_system/02-charged_system-1.ipynb b/doc/tutorials/02-charged_system/02-charged_system-1.ipynb
@@ -102,7 +102,6 @@
     "# Setup System\n",
     "box_l = (n_part / density)**(1. / 3.)\n",
     "system = System(box_l=[box_l, box_l, box_l])\n",
-    "system.seed = 42\n",
     "system.periodicity = [True, True, True]\n",
     "system.time_step = time_step\n",
     "system.cell_system.skin = 0.3"

diff --git a/doc/tutorials/02-charged_system/02-charged_system-2.ipynb b/doc/tutorials/02-charged_system/02-charged_system-2.ipynb
@@ -157,7 +157,6 @@
     "box_z = box_l + 2.0 * (lj_sigmas[\"Electrode\"] + wall_margin)\n",
     "elc_gap = box_z * 0.15\n",
     "system = System(box_l=[box_l, box_l, box_z + elc_gap])\n",
-    "system.seed = 42\n",
     "box_volume = numpy.prod([box_l, box_l, box_z])\n",
     "\n",
     "system.periodicity = [True, True, True]\n",

diff --git a/doc/tutorials/02-charged_system/scripts/nacl.py b/doc/tutorials/02-charged_system/scripts/nacl.py
@@ -50,7 +50,6 @@
 # Setup System
 box_l = (n_part / density)**(1. / 3.)
 system = espressomd.System(box_l=[box_l] * 3)
-system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
 system.periodicity = [True, True, True]
 system.time_step = time_step
 system.cell_system.skin = 0.3

diff --git a/doc/tutorials/02-charged_system/scripts/nacl_units.py b/doc/tutorials/02-charged_system/scripts/nacl_units.py
@@ -25,8 +25,7 @@
 assert_features(["ELECTROSTATICS", "MASS", "LENNARD_JONES"])
 
 system = espressomd.System(box_l=[1.0, 1.0, 1.0])
-system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
-numpy.random.seed(system.seed)
+numpy.random.seed(seed=42)
 
 print("\n--->Setup system")
 

diff --git a/doc/tutorials/02-charged_system/scripts/nacl_units_confined.py b/doc/tutorials/02-charged_system/scripts/nacl_units_confined.py
@@ -27,8 +27,7 @@
 assert_features(["ELECTROSTATICS", "MASS", "LENNARD_JONES"])
 
 system = espressomd.System(box_l=[1.0, 1.0, 1.0])
-system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
-numpy.random.seed(system.seed)
+numpy.random.seed(seed=42)
 
 print("\n--->Setup system")
 

diff --git a/doc/tutorials/02-charged_system/scripts/nacl_units_confined_vis.py b/doc/tutorials/02-charged_system/scripts/nacl_units_confined_vis.py
@@ -29,8 +29,7 @@
 assert_features(["ELECTROSTATICS", "MASS", "LENNARD_JONES"])
 
 system = espressomd.System(box_l=[1.0, 1.0, 1.0])
-system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
-numpy.random.seed(system.seed)
+numpy.random.seed(seed=42)
 
 print("\n--->Setup system")
 

diff --git a/doc/tutorials/02-charged_system/scripts/nacl_units_vis.py b/doc/tutorials/02-charged_system/scripts/nacl_units_vis.py
@@ -27,8 +27,7 @@
 assert_features(["ELECTROSTATICS", "MASS", "LENNARD_JONES"])
 
 system = espressomd.System(box_l=[1.0, 1.0, 1.0])
-system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
-numpy.random.seed(system.seed)
+numpy.random.seed(seed=42)
 
 visualizer = visualization_opengl.openGLLive(
     system,

diff --git a/doc/tutorials/05-raspberry_electrophoresis/05-raspberry_electrophoresis.ipynb b/doc/tutorials/05-raspberry_electrophoresis/05-raspberry_electrophoresis.ipynb
@@ -93,7 +93,6 @@
     "# System setup\n",
     "#############################################################\n",
     "system = espressomd.System(box_l=[box_l] * 3)\n",
-    "system.set_random_state_PRNG()\n",
     "system.time_step = time_step"
    ]
   },

diff --git a/doc/tutorials/06-active_matter/EXERCISES/flow_field.py b/doc/tutorials/06-active_matter/EXERCISES/flow_field.py
@@ -60,7 +60,6 @@
 TIME_STEP = 0.01
 
 system = espressomd.System(box_l=[LENGTH, LENGTH, LENGTH])
-system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
 system.cell_system.skin = 0.3
 system.time_step = TIME_STEP
 system.min_global_cut = 1.0

diff --git a/doc/tutorials/08-visualization/08-visualization.ipynb b/doc/tutorials/08-visualization/08-visualization.ipynb
@@ -59,7 +59,6 @@
     "\n",
     "# integration parameters\n",
     "system = espressomd.System(box_l=[box_l, box_l, box_l])\n",
-    "system.seed = system.cell_system.get_state()['n_nodes'] * [1234]\n",
     "system.time_step = 0.0001\n",
     "system.cell_system.skin = 0.4\n",
     "system.thermostat.set_langevin(kT=1.0, gamma=1.0, seed=42)\n",

diff --git a/maintainer/benchmarks/ferrofluid.py b/maintainer/benchmarks/ferrofluid.py
@@ -93,9 +93,8 @@
 
 # PRNG seeds
 #############################################################
-system.random_number_generator_state = list(range(
-    n_proc * (system._get_PRNG_state_size() + 1)))
 # np.random.seed(1)
+
 # Integration parameters
 #############################################################
 system.time_step = 0.01

diff --git a/maintainer/benchmarks/lj.py b/maintainer/benchmarks/lj.py
@@ -91,8 +91,6 @@
 
 # PRNG seeds
 #############################################################
-system.random_number_generator_state = list(range(
-    n_proc * (system._get_PRNG_state_size() + 1)))
 # np.random.seed(1)
 
 # Integration parameters

diff --git a/maintainer/benchmarks/p3m.py b/maintainer/benchmarks/p3m.py
@@ -99,8 +99,8 @@
 
 # PRNG seeds
 #############################################################
-system.random_number_generator_state = list(range(
-    n_proc * (system._get_PRNG_state_size() + 1)))
+# np.random.seed(1)
+
 # Integration parameters
 #############################################################
 system.time_step = 0.01

diff --git a/samples/MDAnalysisIntegration.py b/samples/MDAnalysisIntegration.py
@@ -28,9 +28,7 @@
 # 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)
+np.random.seed(seed=42)
 
 system.time_step = 0.001
 system.cell_system.skin = 0.1

diff --git a/samples/billiard.py b/samples/billiard.py
@@ -38,7 +38,6 @@
 
 # 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]]
 

diff --git a/samples/chamber_game.py b/samples/chamber_game.py
@@ -58,7 +58,6 @@
 
 box = np.array([1500.0, 500.0, 150.0])
 system = espressomd.System(box_l=box)
-system.set_random_state_PRNG()
 
 # PARAMETERS
 

diff --git a/samples/constraints.py b/samples/constraints.py
@@ -34,10 +34,7 @@
 
 box_l = 50.0
 system = espressomd.System(box_l=[box_l] * 3)
-system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
-np.random.seed(seed=system.seed)
-
-# if no seed is provided espresso generates a seed
+np.random.seed(seed=42)
 
 system.time_step = 0.01
 system.cell_system.skin = 10.0

diff --git a/samples/diffusion_coefficient.py b/samples/diffusion_coefficient.py
@@ -31,9 +31,7 @@
 dt = 0.05
 
 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)
+np.random.seed(seed=42)
 
 p = system.part.add(pos=(0, 0, 0), id=0)
 system.time_step = dt

diff --git a/samples/dpd.py b/samples/dpd.py
@@ -41,9 +41,7 @@
 
 # Activate the thermostat
 system.thermostat.set_dpd(kT=kT, seed=123)
-system.set_random_state_PRNG()
-np.random.seed(seed=system.seed)
-#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
+np.random.seed(seed=42)
 
 # Set up the DPD friction interaction
 system.non_bonded_inter[0, 0].dpd.set_params(

diff --git a/samples/drude_bmimpf6.py b/samples/drude_bmimpf6.py
@@ -76,7 +76,6 @@
 
 system = espressomd.System(box_l=[box_l, box_l, box_l])
 system.virtual_sites = VirtualSitesRelative(have_velocity=True)
-system.set_random_state_PRNG()
 
 if args.visu:
     d_scale = 0.988 * 0.5

diff --git a/samples/ekboundaries.py b/samples/ekboundaries.py
@@ -27,8 +27,6 @@
 import os
 
 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

diff --git a/samples/espresso_logo.py b/samples/espresso_logo.py
@@ -27,9 +27,7 @@
 
 box_l = 50
 system = espressomd.System(box_l=[box_l, 15, box_l])
-system.set_random_state_PRNG()
-#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
-np.random.seed(seed=system.seed)
+np.random.seed(seed=42)
 
 yoff = 3
 

diff --git a/samples/grand_canonical.py b/samples/grand_canonical.py
@@ -59,9 +59,7 @@
 # Integration parameters
 #############################################################
 system = espressomd.System(box_l=[box_l, box_l, box_l])
-system.set_random_state_PRNG()
-#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
-np.random.seed(seed=system.seed)
+np.random.seed(seed=42)
 
 system.time_step = 0.01
 system.cell_system.skin = 0.4

diff --git a/samples/h5md.py b/samples/h5md.py
@@ -24,8 +24,6 @@
 from espressomd import interactions
 
 system = espressomd.System(box_l=[100.0, 100.0, 100.0])
-system.set_random_state_PRNG()
-#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
 
 system.time_step = 0.01
 system.thermostat.set_langevin(kT=1.0, gamma=1.0, seed=42)

diff --git a/samples/lbf.py b/samples/lbf.py
@@ -52,7 +52,6 @@
 
 box_l = 50
 system = espressomd.System(box_l=[box_l] * 3)
-system.set_random_state_PRNG()
 
 system.time_step = 0.01
 system.cell_system.skin = 0.1

diff --git a/samples/lj-demo.py b/samples/lj-demo.py
@@ -95,8 +95,6 @@
 # Integration parameters
 #############################################################
 system = espressomd.System(box_l=[box_l, box_l, box_l])
-system.set_random_state_PRNG()
-#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
 
 system.time_step = 0.01
 system.cell_system.skin = 0.4

diff --git a/samples/lj_liquid.py b/samples/lj_liquid.py
@@ -57,9 +57,7 @@
 # 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)
+np.random.seed(seed=42)
 
 system.time_step = 0.01
 system.cell_system.skin = 0.4

diff --git a/samples/lj_liquid_distribution.py b/samples/lj_liquid_distribution.py
@@ -54,9 +54,7 @@
 # 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)
+np.random.seed(seed=42)
 
 system.time_step = 0.01
 system.cell_system.skin = 0.4

diff --git a/samples/lj_liquid_structurefactor.py b/samples/lj_liquid_structurefactor.py
@@ -54,9 +54,7 @@
 # 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)
+np.random.seed(seed=42)
 
 system.time_step = 0.01
 system.cell_system.skin = 0.4

diff --git a/samples/load_checkpoint.py b/samples/load_checkpoint.py
@@ -81,8 +81,6 @@
 print("\n### Integrate until user presses ctrl+c ###")
 print("Integrating...")
 
-system.set_random_state_PRNG()
-#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
-np.random.seed(seed=system.seed)
+np.random.seed(seed=42)
 while True:
     system.integrator.run(1000)
diff --git a/samples/minimal-charged-particles.py b/samples/minimal-charged-particles.py
@@ -44,9 +44,7 @@
 # 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)
+np.random.seed(seed=42)
 
 system.time_step = 0.01
 system.cell_system.skin = 0.4

diff --git a/samples/minimal-diamond.py b/samples/minimal-diamond.py
@@ -30,9 +30,7 @@
 #############################################################
 
 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.seed = system.seed
+np.random.seed(seed=42)
 system.time_step = 0.01
 system.cell_system.skin = 0.4
 system.cell_system.set_n_square(use_verlet_lists=False)

diff --git a/samples/minimal-polymer.py b/samples/minimal-polymer.py
@@ -30,9 +30,7 @@
 #############################################################
 
 system = espressomd.System(box_l=[100, 100, 100])
-system.set_random_state_PRNG()
-#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
-np.random.seed(seed=system.seed)
+np.random.seed(seed=42)
 
 system.time_step = 0.01
 system.cell_system.skin = 0.4

diff --git a/samples/observables_correlators.py b/samples/observables_correlators.py
@@ -26,9 +26,7 @@
 
 # System setup
 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)
+np.random.seed(seed=42)
 
 system.part.add(pos=(0, 0, 0), v=(1, 2, 3))
 system.time_step = 0.01

diff --git a/samples/p3m.py b/samples/p3m.py
@@ -59,9 +59,7 @@
 # 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)
+np.random.seed(seed=42)
 
 system.time_step = 0.01
 system.cell_system.skin = 0.4

diff --git a/samples/reaction_ensemble.py b/samples/reaction_ensemble.py
@@ -48,9 +48,7 @@
 # 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)
+np.random.seed(seed=42)
 
 system.time_step = 0.02
 system.cell_system.skin = 0.4