repo stringlengths 2 99 | file stringlengths 13 225 | code stringlengths 0 18.3M | file_length int64 0 18.3M | avg_line_length float64 0 1.36M | max_line_length int64 0 4.26M | extension_type stringclasses 1
value |
|---|---|---|---|---|---|---|
espressopp | espressopp-master/testsuite/mean_square_internal_distance/test_mean_square_internal_distance.py | # Copyright (C) 2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the Licens... | 2,677 | 36.71831 | 133 | py |
espressopp | espressopp-master/testsuite/FixedLocalTuple/TestFixedLocalTupleList.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 4,596 | 30.703448 | 112 | py |
espressopp | espressopp-master/testsuite/rattle/test_rattle.py | #!/usr/bin/env python
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ... | 4,969 | 39.737705 | 147 | py |
espressopp | espressopp-master/testsuite/unittest/TestParticle.py | # Copyright (C) 2012,2013, 2017(H)
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the t... | 1,510 | 36.775 | 73 | py |
espressopp | espressopp-master/testsuite/unittest/PTestVerletList.py | # Copyright (C) 2012,2013,2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms... | 2,966 | 24.577586 | 90 | py |
espressopp | espressopp-master/testsuite/unittest/TestEsLogging.py | # Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | 2,198 | 30.869565 | 88 | py |
espressopp | espressopp-master/testsuite/unittest/TestReal3D.py | # Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | 4,531 | 29.829932 | 73 | py |
espressopp | espressopp-master/testsuite/unittest/__init__.py | # Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | 2,714 | 43.508197 | 78 | py |
espressopp | espressopp-master/testsuite/unittest/TestInt3D.py | # Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | 3,565 | 29.220339 | 73 | py |
espressopp | espressopp-master/testsuite/verlet_list_buffer/verlet_list_buffer.py | #!/usr/bin/env python2
# Copyright (C) 2020
# Max Planck Institute for Polymer Research & JGU Mainz
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 3,389 | 32.235294 | 122 | py |
espressopp | espressopp-master/testsuite/cm_velocity/test_CMVelocity.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 2,589 | 32.205128 | 91 | py |
espressopp | espressopp-master/testsuite/python_tools/io/test_python_tools_io.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 4,075 | 35.070796 | 122 | py |
espressopp | espressopp-master/testsuite/python_tools/complex/test_python_tools_complex.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 3,613 | 43.073171 | 157 | py |
espressopp | espressopp-master/testsuite/SubregionTracking/test_SubregionTracking.py | #!/usr/bin/env python
#
# Copyright (C) 2017,2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eithe... | 3,675 | 42.761905 | 158 | py |
espressopp | espressopp-master/testsuite/sub_ens_bond/sub_ens_bond.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 6,834 | 34.414508 | 93 | py |
espressopp | espressopp-master/testsuite/fixed_list_types_test/fixed_list_types_test.py | # Copyright (C) 2016
# Jakub Krajniak (jkrajniak at gmail.com)
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
... | 7,981 | 38.127451 | 139 | py |
espressopp | espressopp-master/testsuite/AdResS/TDforce/test_TDforce.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 16,465 | 49.048632 | 176 | py |
espressopp | espressopp-master/testsuite/AdResS/AdressDensity/test_AdressDensity.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 3,714 | 40.741573 | 111 | py |
espressopp | espressopp-master/testsuite/AdResS/RDFatomistic/test_RDFatomistic.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eith... | 8,264 | 46.774566 | 139 | py |
espressopp | espressopp-master/testsuite/AdResS/FreeEnergyCompensation/test_FreeEnergyCompensation.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 6,885 | 42.859873 | 174 | py |
espressopp | espressopp-master/testsuite/AdResS/MTSAdResS/test_MTSAdResS.py | #!/usr/bin/env python2
#
# Copyright (C) 2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either ve... | 12,977 | 48.534351 | 153 | py |
espressopp | espressopp-master/testsuite/AdResS/HAdResS/test_HAdResS.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eith... | 12,808 | 48.647287 | 297 | py |
espressopp | espressopp-master/testsuite/AdResS/PIAdResS/test_PIAdResS.py | #!/usr/bin/env python
#
# Copyright (C) 2017,2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eithe... | 16,792 | 48.246334 | 459 | py |
espressopp | espressopp-master/testsuite/AdResS/RadGyrXProfilePI/test_RadGyrXProfilePI.py | #!/usr/bin/env python
#
# Copyright (C) 2017,2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eithe... | 3,923 | 46.277108 | 139 | py |
espressopp | espressopp-master/testsuite/AdResS/ForceAdResS/test_AdResS.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eith... | 16,081 | 48.030488 | 153 | py |
espressopp | espressopp-master/testsuite/constrain_rg/test_constrain_rg.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 5,764 | 35.03125 | 110 | py |
espressopp | espressopp-master/testsuite/tabulated_dihedral/tabulated_dihedral.py | #!/usr/bin/env python2
import sys
import unittest
import time
import os
import mpi4py.MPI as MPI
import espressopp
import math
import numpy as np
import logging
from espressopp import Real3D, Int3D
print "Comparison Tabulated dihedral vs Harmonic dihedral"
# Input values for system
N = 10 ... | 4,972 | 33.296552 | 109 | py |
espressopp | espressopp-master/testsuite/minimize_energy/test_minimize_energy.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 2,755 | 33.886076 | 94 | py |
espressopp | espressopp-master/testsuite/lattice_boltzmann/test_LatticeBoltzmann.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 3,672 | 30.663793 | 114 | py |
espressopp | espressopp-master/testsuite/lattice_boltzmann/test_LBMDcoupling.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 7,571 | 33.733945 | 112 | py |
espressopp | espressopp-master/testsuite/lattice_boltzmann/test_extForce.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 4,112 | 31.642857 | 114 | py |
espressopp | espressopp-master/testsuite/LangevinThermostat/test_LangevinThermostat.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 6,355 | 39.484076 | 139 | py |
espressopp | espressopp-master/testsuite/tabulated/polymer_melt_tabulated.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
# Copyright (C) 2019
# Max Planck Computing and Data Facility
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gen... | 8,850 | 36.345992 | 123 | py |
espressopp | espressopp-master/testsuite/ljcos/test_ljcos.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 2,338 | 31.486111 | 111 | py |
espressopp | espressopp-master/testsuite/integrator/PTestVelocityVerlet.py | # Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | 4,251 | 26.79085 | 114 | py |
espressopp | espressopp-master/testsuite/esutil/PTestCollectives.py | # Copyright (C) 2012,2013,2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms... | 1,935 | 35.528302 | 77 | py |
espressopp | espressopp-master/testsuite/NPartSubregion/test_NPartSubregion.py | #!/usr/bin/env python
#
# Copyright (C) 2017,2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eithe... | 3,603 | 42.421687 | 140 | py |
espressopp | espressopp-master/testsuite/pickle_potential/testwarmup.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 2,149 | 26.21519 | 119 | py |
espressopp | espressopp-master/testsuite/pickle_potential/pickle_potential.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 1,526 | 34.511628 | 79 | py |
espressopp | espressopp-master/testsuite/thermo_integration/test_thermo_integration.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 6,548 | 48.240602 | 179 | py |
espressopp | espressopp-master/testsuite/vectorization/test_vectorization.py | #!/usr/bin/env python2
# Copyright (C) 2020
# Max Planck Institute for Polymer Research & JGU Mainz
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 4,384 | 33.527559 | 122 | py |
espressopp | espressopp-master/testsuite/cap_force/test_cap_force.py | # Copyright (C) 2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the Licens... | 9,172 | 41.271889 | 118 | py |
espressopp | espressopp-master/testsuite/pi_water/pathintegral.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 5,640 | 34.929936 | 141 | py |
espressopp | espressopp-master/testsuite/pi_water/water.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 8,192 | 37.646226 | 199 | py |
espressopp | espressopp-master/testsuite/langevin_thermostat_on_group/langevin_thermostat_on_group.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 2,938 | 35.283951 | 98 | py |
espressopp | espressopp-master/testsuite/interaction_potentials/unittest/PTestSoftCosine.py | # Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | 2,039 | 33.576271 | 73 | py |
espressopp | espressopp-master/testsuite/interaction_potentials/unittest/PTestLennardJones.py | # Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | 2,370 | 33.867647 | 84 | py |
espressopp | espressopp-master/testsuite/interaction_potentials/unittest/PTestFENE.py | # Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | 1,424 | 36.5 | 101 | py |
espressopp | espressopp-master/testsuite/interaction_potentials/unittest/PTestMorse.py | # Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | 1,429 | 38.722222 | 109 | py |
espressopp | espressopp-master/testsuite/interaction_potentials/dihedral_harmonic/test_dihedralharmonic.py | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import time
import math
import espressopp
import mpi4py.MPI as MPI
import unittest
def vec_pbc(u,v,cell):
#vector u-v
dx = u[0] - v[0]
dy = u[1] - v[1]
dz = u[2] - v[2]
dx = dx - round(dx/cell[0])*cell[0]
dy = dy - round(dy/cell[1])*cell[1]
... | 5,058 | 36.474074 | 211 | py |
espressopp | espressopp-master/testsuite/potential_array/potential_array_test.py | #!/usr/bin/env python2
import espressopp
from espressopp.tools import replicate, readxyz
from espressopp import Real3D
import time, sys
import numpy as np
def bench_lj(xyz_file):
# read from xyz file
print "reading from: ", xyz_file
pid, type, xpos, ypos, zpos, xvel, yvel, zvel, Lx, Ly, Lz = readxyz(xyz... | 6,079 | 34.555556 | 94 | py |
espressopp | espressopp-master/testsuite/FileIOTests/dump_xyz/test_dump_xyz.py | # Copyright (C) 2016
# Max Planck Institute for Polymer Research & JGU Mainz
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of th... | 7,295 | 50.744681 | 208 | py |
espressopp | espressopp-master/testsuite/FileIOTests/dump_xtc_adress/test_dump_xtc_adress.py | # Copyright (C) 2017
# Jakub Krajniak (jkrajniak at gmail.com)
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
... | 2,612 | 34.794521 | 83 | py |
espressopp | espressopp-master/testsuite/FileIOTests/h5md/dump_topology_test.py | #!/usr/bin/env python
# Copyright (c) 2015-2018
# Jakub Krajniak (jkrajniak at gmail.com)
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either versio... | 7,346 | 33.985714 | 112 | py |
espressopp | espressopp-master/testsuite/FileIOTests/h5md/dump_h5md_test.py | #!/usr/bin/env python
# Copyright (c) 2015-2018
# Jakub Krajniak (jkrajniak at gmail.com)
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either versio... | 4,528 | 30.894366 | 101 | py |
espressopp | espressopp-master/testsuite/FileIOTests/dump_gromacs_adress/test_dump_gromacs_adress.py | # Copyright (C) 2017(H)
# Max Planck Institute for Polymer Research
# Copyright (C) 2016
# Max Planck Institute for Polymer Research & JGU Mainz
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Licen... | 6,837 | 45.202703 | 664 | py |
espressopp | espressopp-master/testsuite/FileIOTests/dump_xtc/test_dump_xtc.py | # Copyright (C) 2016, 2017(H)
# Max Planck Institute for Polymer Research & JGU Mainz
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either versio... | 2,930 | 37.064935 | 152 | py |
espressopp | espressopp-master/testsuite/FileIOTests/dump_gromacs/test_dump_gromacs.py | # Copyright (C) 2017
# Max Planck Institute for Polymer Research
# Copyright (C) 2016
# Max Planck Institute for Polymer Research & JGU Mainz
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License ... | 3,828 | 38.474227 | 164 | py |
espressopp | espressopp-master/testsuite/DPDThermostat/test_DPDThermostat.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 6,256 | 36.692771 | 105 | py |
espressopp | espressopp-master/testsuite/constrain_com/test_constrain_com.py | #!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 5,804 | 34.396341 | 115 | py |
espressopp | espressopp-master/testsuite/system_test/system_test.py | #!/usr/bin/env python
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ... | 2,275 | 34.015385 | 76 | py |
espressopp | espressopp-master/examples/lennard_jones_93_wall/lennard_jones_93_wall.py | #!/usr/bin/env python2
# Copyright (C) 2015-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 6,463 | 36.581395 | 170 | py |
espressopp | espressopp-master/examples/ewald/ewald.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 7,823 | 38.515152 | 138 | py |
espressopp | espressopp-master/examples/lj_cos/lj_cos.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 7,443 | 31.792952 | 118 | py |
espressopp | espressopp-master/examples/adress/piadress_water/AdaptivePIwater.py | #!/usr/bin/env python
# Copyright (C) 2017,2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either ... | 21,537 | 42.86558 | 451 | py |
espressopp | espressopp-master/examples/adress/multiple_time_stepping_fadress/water_mts_fadress.py | #!/usr/bin/env python
# Copyright (C) 2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either versi... | 13,168 | 42.319079 | 220 | py |
espressopp | espressopp-master/examples/adress/fadress_selfadjusting/peptide-adres-selfadjusting.py | #!/usr/bin/env python2
# Copyright (C) 2016, 2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundatio... | 21,548 | 41.419291 | 346 | py |
espressopp | espressopp-master/examples/adress/fadress_protein/ubiquitin.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation,... | 23,695 | 43.04461 | 346 | py |
espressopp | espressopp-master/examples/adress/multiple_time_stepping_hadress/water_mts_hadress.py | #!/usr/bin/env python
# Copyright (C) 2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either versi... | 12,973 | 42.536913 | 220 | py |
espressopp | espressopp-master/examples/adress/fadress_tetraliquid/adress.py | #!/usr/bin/env python2
# Copyright (C) 2016, 2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, e... | 8,788 | 34.297189 | 112 | py |
espressopp | espressopp-master/examples/adress/hadress_tetraliquid/hadress_tetraliquid_FEC/hadressDensityFEC.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ei... | 9,488 | 34.275093 | 124 | py |
espressopp | espressopp-master/examples/adress/hadress_tetraliquid/hadress_tetraliquid_FEC/Tetracryst.py | #!/usr/bin/python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either ... | 2,957 | 30.468085 | 128 | py |
espressopp | espressopp-master/examples/adress/hadress_tetraliquid/hadress_tetraliquid_FEC/hadressPressureFEC.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ei... | 9,519 | 34.522388 | 124 | py |
espressopp | espressopp-master/examples/adress/hadress_tetraliquid/hadress_tetraliquid_KTI/Tetracryst.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ei... | 2,962 | 30.521277 | 128 | py |
espressopp | espressopp-master/examples/adress/hadress_tetraliquid/hadress_tetraliquid_KTI/hadressKTI.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ei... | 11,990 | 33.26 | 133 | py |
espressopp | espressopp-master/examples/adress/hadress_tetraliquid/hadress_tetraliquid_plain/hadress.py | #!/usr/bin/env python2
# Copyright (C) 2016, 2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, e... | 10,266 | 33.921769 | 124 | py |
espressopp | espressopp-master/examples/adress/hadress_tetraliquid/hadress_tetraliquid_plain/Tetracryst.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ei... | 2,957 | 32.235955 | 128 | py |
espressopp | espressopp-master/examples/adress/hadress_water/water.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ei... | 10,312 | 38.51341 | 276 | py |
espressopp | espressopp-master/examples/local_pressure_tensor/local_pressure_tensor.py | #!/usr/bin/env python2
# Copyright (C) 2015-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 6,109 | 35.586826 | 118 | py |
espressopp | espressopp-master/examples/lennard_jones/lennard_jones.py | #!/usr/bin/env python2
# Copyright (C) 2015-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 13,497 | 44.755932 | 145 | py |
espressopp | espressopp-master/examples/simpleGromacs/simpleGromacs.py | #!/usr/bin/env python2
# Copyright (C) 2012-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 8,189 | 34.921053 | 200 | py |
espressopp | espressopp-master/examples/polystyrene_gromacs/polystyrene.py | #!/usr/bin/env python2
# Copyright (C) 2012-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 10,080 | 35.393502 | 247 | py |
espressopp | espressopp-master/examples/force_capping/force_capping.py | #!/usr/bin/env python2
# Copyright (C) 2015-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 2,402 | 34.865672 | 107 | py |
espressopp | espressopp-master/examples/lattice_boltzmann/lb_md_coupling.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 2,698 | 37.557143 | 109 | py |
espressopp | espressopp-master/examples/lattice_boltzmann/extForces/sin_like_with_temp.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 3,936 | 40.882979 | 83 | py |
espressopp | espressopp-master/examples/lattice_boltzmann/extForces/gravity_like.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 3,470 | 40.321429 | 82 | py |
espressopp | espressopp-master/examples/electrostatics/electrostatics_example.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 10,081 | 39.653226 | 112 | py |
espressopp | espressopp-master/examples/analyze_during_integration/analyze_during_integration.py | #!/usr/bin/env python2
# Copyright (C) 2015-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ei... | 2,404 | 40.465517 | 109 | py |
espressopp | espressopp-master/examples/stillinger_weber_Si/stillinger_weber_silicon.py | #!/usr/bin/env python2
# Copyright (C) 2015-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 9,076 | 36.508264 | 142 | py |
espressopp | espressopp-master/examples/vectorization/lennard_jones.py | #!/usr/bin/env python2
# Copyright (C) 2020
# Max Planck Institute for Polymer Research & JGU Mainz
# Copyright (C) 2015-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of ... | 15,515 | 45.178571 | 145 | py |
espressopp | espressopp-master/examples/hierarchical_strategy_for_one-component/polymer_melt_from_restart.py | #!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
import time
import espressopp
import logging
from mpi4py import MPI
# set parameters for simulations
seed = 654321 # seed for random
... | 7,604 | 35.38756 | 134 | py |
espressopp | espressopp-master/examples/hierarchical_strategy_for_one-component/generate_microscopic-c.py | #!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
import time
import espressopp
import logging
from mpi4py import MPI
# set the propertis of microscopic polymer
input_file = open('input.txt')
# def... | 5,926 | 35.361963 | 134 | py |
espressopp | espressopp-master/examples/hierarchical_strategy_for_one-component/softblobs_25.py | #!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
from math import fabs
import time
import espressopp
import logging
from mpi4py import MPI
# set the initial configuration file of microscopic polyme... | 13,709 | 35.56 | 204 | py |
espressopp | espressopp-master/examples/hierarchical_strategy_for_one-component/softblobs_100.py | #!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
from math import fabs
import time
import espressopp
import logging
from mpi4py import MPI
# set the initial configuration file of microscopic polyme... | 11,568 | 33.846386 | 127 | py |
espressopp | espressopp-master/examples/hierarchical_strategy_for_one-component/reinsertion.py | #!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
from math import sqrt, pi, cos, sin
import random
import time
import espressopp
import logging
from mpi4py import MPI
# set the initial configuratio... | 11,634 | 33.020468 | 114 | py |
espressopp | espressopp-master/examples/hierarchical_strategy_for_one-component/fbloop.py | #!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
from math import sqrt, pi, cos, sin, acos, asin, fabs
import time
import espressopp
import logging
from mpi4py import MPI
# set parameters for simul... | 12,797 | 32.241558 | 114 | py |
espressopp | espressopp-master/examples/hierarchical_strategy_for_one-component/softblobs_50.py | #!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
from math import fabs
import time
import espressopp
import logging
from mpi4py import MPI
# set the initial configuration file of microscopic polyme... | 13,700 | 35.342175 | 163 | py |
espressopp | espressopp-master/examples/convert_gromacs_tables/convert_gromacs_table.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 6,888 | 34.147959 | 96 | py |
espressopp | espressopp-master/examples/fix_particles/fix_particles.py | #!/usr/bin/env python2
# Copyright (C) 2015-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 2,406 | 37.206349 | 94 | py |
espressopp | espressopp-master/examples/thd_integration_solvation/methanol-TI.py | #!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | 21,312 | 41.969758 | 425 | py |
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