Cleanup cython

src/core/particle_data.cpp

@@ -1366,7 +1366,7 @@ void remove_id_from_map(int part_id, int type) {
 int get_random_p_id(int type, int random_index_in_type_map) {
   if (random_index_in_type_map + 1 > particle_type_map.at(type).size())
     throw std::runtime_error("The provided index exceeds the number of "
-                             "particles listed in the type_map");
+                             "particle types listed in the particle_type_map");
   return *std::next(particle_type_map[type].begin(), random_index_in_type_map);
 }
 
@@ -1376,6 +1376,9 @@ void add_id_to_type_map(int part_id, int type) {
 }
 
 int number_of_particles_with_type(int type) {
+  if (particle_type_map.count(type) == 0)
+    throw std::runtime_error("The provided particle type does not exist in "
+                             "the particle_type_map");
   return static_cast<int>(particle_type_map.at(type).size());
 }
 

src/python/espressomd/__init__.py

@@ -20,11 +20,11 @@
 # Define the espressomd package
 
 # Initialize MPI, start the main loop on the slaves
-import espressomd._init
+from . import _init
 
-from espressomd.system import System
-from espressomd.code_info import features, all_features
-from espressomd.cuda_init import gpu_available
+from .system import System
+from .code_info import features, all_features
+from .cuda_init import gpu_available
 
 
 class FeaturesError(Exception):

src/python/espressomd/actors.pyx

@@ -16,7 +16,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 include "myconfig.pxi"
 from .highlander import ThereCanOnlyBeOne
-from .utils import handle_errors
+from .utils cimport handle_errors
 
 cdef class Actor:
 

src/python/espressomd/analyze.pxd

@@ -20,11 +20,8 @@
 # For C-extern Analysis
 
 cimport numpy as np
-from espressomd.utils cimport *
-from .utils cimport Vector9d
-from libcpp.string cimport string  # import std::string as string
+from .utils cimport Vector3i, Vector3d, Vector9d, List
 from libcpp.vector cimport vector  # import std::vector as vector
-from libcpp.map cimport map  # import std::map as map
 
 cdef extern from "<array>" namespace "std" nogil:
     cdef cppclass array4 "std::array<double, 4>":

src/python/espressomd/analyze.pyx

@@ -19,25 +19,21 @@
 # For C-extern Analysis
 include "myconfig.pxi"
 from . cimport analyze
-from . cimport utils
-from . cimport particle_data
-from . import utils
-from . import code_info
-from . import particle_data
-from libcpp.string cimport string  # import std::string as string
 from libcpp.vector cimport vector  # import std::vector as vector
-from libcpp.map cimport map  # import std::map as map
-from .interactions import *
-from espressomd.interactions cimport *
+from .interactions cimport BONDED_IA_NONE
+from .interactions cimport bonded_ia_params
 import numpy as np
 cimport numpy as np
-from globals cimport n_configs
-
-from .utils import array_locked
+from .globals import Globals
 
 from collections import OrderedDict
 from .system import System
-from espressomd.utils import is_valid_type
+from .utils import array_locked, is_valid_type
+from .utils cimport Vector3i, Vector3d, Vector9d, List
+from .utils cimport handle_errors, check_type_or_throw_except
+from .utils cimport create_nparray_from_double_array, \
+    create_nparray_from_int_list, \
+    create_int_list_from_python_object
 
 
 class Analysis:
@@ -54,7 +50,7 @@ class Analysis:
     def append(self):
         """Append configuration for averaged analysis."""
         assert analyze.n_part, "No particles to append!"
-        if analyze.n_configs > 0:
+        if n_configs > 0:
             assert analyze.n_part_conf == analyze.n_part, \
                 "All configurations stored must have the same length"
 
@@ -846,7 +842,7 @@ class Analysis:
                 n_conf = n_configs
 
         if r_max is None:
-            r_max = min_box_l / 2.0
+            r_max = min(Globals().box_l) / 2
 
         cdef vector[double] rdf
         rdf.resize(r_bins)
@@ -921,7 +917,7 @@ class Analysis:
             raise ValueError("type_list_b has to be a list!")
 
         if r_max is None:
-            r_max = min_box_l / 2.0
+            r_max = min(Globals().box_l) / 2
 
         assert r_min >= 0.0, "r_min was chosen too small!"
         assert not log_flag or r_min != 0.0, "r_min cannot include zero"

src/python/espressomd/cellsystem.pxd

@@ -23,8 +23,6 @@ from libcpp cimport bool
 from libcpp.vector cimport vector
 from libcpp.pair cimport pair
 
-from .utils cimport Vector3i
-
 cdef extern from "communication.hpp":
     void mpi_bcast_cell_structure(int cs)
     int n_nodes

src/python/espressomd/cellsystem.pyx

@@ -16,19 +16,19 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-from grid cimport node_grid
-from . cimport cellsystem
+from .grid cimport node_grid
 from . cimport integrate
-from globals cimport *
+from .globals cimport FIELD_SKIN, FIELD_NODEGRID, FIELD_MAXNUMCELLS, FIELD_MINNUMCELLS
+from .globals cimport max_cut, verlet_reuse, n_layers, dd, cell_structure, \
+    min_num_cells, max_num_cells, skin
+from .globals cimport mpi_bcast_parameter, calc_processor_min_num_cells
 import numpy as np
-from espressomd.utils cimport handle_errors
-from espressomd.utils import is_valid_type
+from .utils cimport handle_errors
+from .utils import is_valid_type
 
 cdef class CellSystem:
     def set_domain_decomposition(self, use_verlet_lists=True,
-                                 fully_connected=[False,
-                                                  False,
-                                                  False]):
+                                 fully_connected=[False, False, False]):
         """
         Activates domain decomposition cell system.
 

src/python/espressomd/checkpointing.py

@@ -21,7 +21,7 @@
 import os
 import re
 import signal
-from espressomd.utils import is_valid_type
+from .utils import is_valid_type
 
 try:
     import cPickle as pickle

src/python/espressomd/collision_detection.pyx

@@ -15,7 +15,8 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 from .script_interface import ScriptInterfaceHelper, script_interface_register
-from .utils import handle_errors, to_str
+from .utils import to_str
+from .utils cimport handle_errors
 from .interactions import BondedInteraction, BondedInteractions
 
 

src/python/espressomd/drude_helpers.py

@@ -14,8 +14,8 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
-import espressomd.interactions
-from espressomd import has_features
+from . import interactions
+from .__init__ import has_features
 
 # Dict with Drude type infos
 drude_dict = {}
@@ -35,29 +35,35 @@ def add_drude_particle_to_core(system, harmonic_bond, thermalized_bond,
     """
     Adds a Drude particle with specified id, type, and mass to the system.
     Checks if different Drude particles have different types.
-    Collects types/charges/polarizations/Thole factors for intramol. core-Drude short-range exclusion and Thole interaction.
+    Collects types/charges/polarizations/Thole factors for intramolecular
+    core-Drude short-range exclusion and Thole interaction.
 
     Attributes
     ----------
 
-    system : Instance of :attr:`espressomd.system.System`
-    harmonic_bond: This method adds this harmonic bond to between Drude particle and core
-    thermalized_bond: This method adds this thermalized_bond to between Drude particle and core
-    p_core: The existing core particle
+    system : :class:`espressomd.system.System`
+    harmonic_bond: :class:`espressomd.interactions.HarmonicBond`
+        Add this harmonic bond to between Drude particle and core
+    thermalized_bond: :class:`espressomd.interactions.ThermalizedBond`
+        Add this thermalized_bond to between Drude particle and core
+    p_core: :class:`espressomd.particle_data.ParticleHandle`
+        The existing core particle
     id_drude: :obj:`int`
-              This method creates the Drude particle and assigns this id.
+        This method creates the Drude particle and assigns this id.
     type_drude: :obj:`int`
-                The type of the newly created Drude particle
+        The type of the newly created Drude particle
     alpha : :obj:`float`
-            The polarizability in units of inverse volume. Related to the charge of the Drude particle.
+        The polarizability in units of inverse volume. Related to the charge
+        of the Drude particle.
     mass_drude : :obj:`float`
-                 The mass of the newly created Drude particle
+        The mass of the newly created Drude particle
     coulomb_prefactor : :obj:`float`
-                        Required to calculate the charge of the Drude particle.
+        Required to calculate the charge of the Drude particle.
     thole_damping : :obj:`float`
-                    Thole damping factor of the Drude pair. Comes to effect if add_all_thole() method is used.
+        Thole damping factor of the Drude pair. Comes to effect if
+        :meth:`add_all_thole()` method is used.
     verbose : :obj:`bool`
-             Turns on verbosity.
+        Turns on verbosity.
 
     """
 
@@ -132,13 +138,13 @@ def add_thole_pair_damping(system, t1, t2, verbose=False):
     Attributes
     ----------
 
-    system : Instance of :attr:`espressomd.system.System`
+    system : :class:`espressomd.system.System`
     t1 : :obj:`int`
         Type 1
     t2 : :obj:`int`
         Type 2
     verbose : :obj:`bool`
-             Turns on verbosity.
+        Turns on verbosity.
 
     """
 
@@ -155,14 +161,15 @@ def add_thole_pair_damping(system, t1, t2, verbose=False):
 
 def add_all_thole(system, verbose=False):
     """
-    Calls add_thole_pair_damping() for all necessary combinations to create the interactions.
+    Calls :meth:`add_thole_pair_damping()` for all necessary combinations to
+    create the interactions.
 
     Attributes
     ----------
 
-    system : Instance of :attr:`espressomd.system.System`
+    system : :class:`espressomd.system.System`
     verbose : :obj:`bool`
-             Turns on verbosity.
+        Turns on verbosity.
 
     """
 
@@ -191,9 +198,9 @@ def setup_and_add_drude_exclusion_bonds(system, verbose=False):
     Attributes
     ----------
 
-    system : Instance of :attr:`espressomd.system.System`
+    system : :class:`espressomd.system.System`
     verbose: :obj:`bool`
-             Turns on verbosity.
+        Turns on verbosity.
 
     """
 
@@ -203,7 +210,7 @@ def setup_and_add_drude_exclusion_bonds(system, verbose=False):
         #...exclusions with core
         qd = drude_dict[td]["q"]  # Drude charge
         qc = drude_dict[td]["qc"]  # Core charge
-        subtr_sr_bond = espressomd.interactions.BondedCoulombSRBond(
+        subtr_sr_bond = interactions.BondedCoulombSRBond(
             q1q2=-qd * qc)
         system.bonded_inter.add(subtr_sr_bond)
         drude_dict[td]["subtr_sr_bonds_drude-core"] = subtr_sr_bond
@@ -232,12 +239,15 @@ def setup_intramol_exclusion_bonds(system, mol_drude_types, mol_core_types,
     Attributes
     ----------
 
-    system : Instance of :attr:`espressomd.system.System`
-    mol_drude_types : List of types of Drude particles within the molecule
-    mol_core_types : List of types of core particles within the molecule
-    mol_core_partial_charges : List of partial charges of core particles within the molecule
+    system : :class:`espressomd.system.System`
+    mol_drude_types :
+        List of types of Drude particles within the molecule
+    mol_core_types :
+        List of types of core particles within the molecule
+    mol_core_partial_charges :
+        List of partial charges of core particles within the molecule
     verbose : :obj:`bool`
-             Turns on verbosity.
+        Turns on verbosity.
 
     """
 
@@ -250,7 +260,7 @@ def setup_intramol_exclusion_bonds(system, mol_drude_types, mol_core_types,
             #...excluding the Drude core partner
             if drude_dict[td]["core_type"] != tc:
                 qd = drude_dict[td]["q"]  # Drude charge
-                subtr_sr_bond = espressomd.interactions.BondedCoulombSRBond(
+                subtr_sr_bond = interactions.BondedCoulombSRBond(
                     q1q2=-qd * qp)
                 system.bonded_inter.add(subtr_sr_bond)
                 drude_dict[td]["subtr_sr_bonds_intramol"][
@@ -268,11 +278,13 @@ def add_intramol_exclusion_bonds(system, drude_ids, core_ids, verbose=False):
     Attributes
     ----------
 
-    system : Instance of :attr:`espressomd.system.System`
-    drude_ids : IDs of Drude particles within a molecule.
-    core_ids : IDs of core particles within a molecule.
+    system : :class:`espressomd.system.System`
+    drude_ids :
+        IDs of Drude particles within a molecule.
+    core_ids :
+        IDs of core particles within a molecule.
     verbose : :obj:`bool`
-             Turns on verbosity.
+        Turns on verbosity.
 
     """
 

src/python/espressomd/electrokinetics.pxd

@@ -17,8 +17,6 @@
 include "myconfig.pxi"
 from libcpp cimport bool
 
-from .utils cimport Vector3i
-
 IF ELECTROKINETICS and CUDA:
     cdef extern from "grid_based_algorithms/electrokinetics.hpp":
 

src/python/espressomd/electrokinetics.pyx

@@ -26,9 +26,9 @@ from . import utils
 import os
 import tempfile
 import shutil
-from .utils cimport Vector6d
+from .utils import is_valid_type
+from .utils cimport Vector3i, Vector6d, handle_errors
 import numpy as np
-from espressomd.utils import is_valid_type
 
 IF ELECTROKINETICS:
     cdef class Electrokinetics(HydrodynamicInteraction):

src/python/espressomd/electrostatic_extensions.pxd

@@ -16,14 +16,12 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Handling of electrostatics
 
 include "myconfig.pxi"
-from espressomd.system cimport *
-from espressomd.utils cimport *
-from espressomd.electrostatics cimport *
-from libcpp cimport vector
-from utils cimport Vector3d
+from .electrostatics cimport *
+from libcpp.vector cimport vector
+from libcpp cimport bool
+from .utils cimport Vector3d
 
 IF ELECTROSTATICS and P3M:
 

src/python/espressomd/electrostatic_extensions.pyx

@@ -19,10 +19,10 @@
 
 from . cimport utils
 include "myconfig.pxi"
-from espressomd cimport actors
+from . cimport actors
 from . import actors
 import numpy as np
-from espressomd.utils cimport handle_errors
+from .utils cimport handle_errors, check_type_or_throw_except, check_range_or_except
 
 IF ELECTROSTATICS and P3M:
     from espressomd.electrostatics import check_neutrality