Roll out ScriptInterface

doc/sphinx/integration.rst

@@ -352,7 +352,7 @@ The following minimal example illustrates how to use the SDM in |es|::
     system.periodicity = [False, False, False]
     system.time_step = 0.01
     system.cell_system.skin = 0.4
-    system.part.add(pos=[0, 0, 0], rotation=[1, 0, 0])
+    system.part.add(pos=[0, 0, 0], rotation=[True, False, False])
     system.integrator.set_stokesian_dynamics(viscosity=1.0, radii={0: 1.0})
     system.integrator.run(100)
 
@@ -690,7 +690,7 @@ needs to be activated via::
     system.periodicity = [False, False, False]
     system.time_step = 0.01
     system.cell_system.skin = 0.4
-    system.part.add(pos=[0, 0, 0], rotation=[1, 0, 0], ext_force=[0, 0, -1])
+    system.part.add(pos=[0, 0, 0], rotation=[True, False, False], ext_force=[0, 0, -1])
     system.thermostat.set_stokesian(kT=1.0, seed=43)
     system.integrator.set_stokesian_dynamics(viscosity=1.0, radii={0: 1.0})
     system.integrator.run(100)

doc/sphinx/magnetostatics.rst

@@ -32,8 +32,8 @@ Magnetostatic interactions are activated via the actor framework::
 
     system = espressomd.System(box_l=[10, 10, 10])
     system.time_step = 0.01
-    system.part.add(pos=[[0, 0, 0], [1, 1, 1]],
-                    rotation=2 * [(1, 1, 1)], dip=2 * [(1, 0, 0)])
+    system.part.add(pos=[[0, 0, 0], [1, 1, 1]], dip=2 * [(1, 0, 0)],
+                    rotation=2 * [(True, True, True)])
 
     actor = espressomd.magnetostatics.DipolarDirectSumCpu(prefactor=1.)
     system.actors.add(actor)

doc/sphinx/particles.rst

@@ -654,7 +654,7 @@ Lattice-Boltzmann swimmers
 
     import espressomd
     system = espressomd.System(box_l=[1, 1, 1])
-    system.part.add(pos=[2, 0, 0], rotation=[1, 1, 1], swimming={
+    system.part.add(pos=[2, 0, 0], rotation=[True, True, True], swimming={
         'f_swim': 0.01, 'mode': 'pusher', 'dipole_length': 2.0})
 
 For an explanation of the parameters ``v_swim`` and ``f_swim`` see the previous

doc/sphinx/visualization.rst

@@ -209,12 +209,12 @@ feature)::
 
     for i in range(10):
         system.part.add(pos=np.random.random(3) * box_l,
-                        rotation=[1, 1, 1],
+                        rotation=[True, True, True],
                         ext_torque=[5, 0, 0],
                         v=[10, 0, 0],
                         type=0)
         system.part.add(pos=np.random.random(3) * box_l,
-                        rotation=[1, 1, 1],
+                        rotation=[True, True, True],
                         ext_torque=[0, 5, 0],
                         v=[-10, 0, 0],
                         type=1)

doc/tutorials/ferrofluid/ferrofluid_part1.ipynb

@@ -432,7 +432,8 @@
    "outputs": [],
    "source": [
     "# Add particles\n",
-    "system.part.add(pos=pos, rotation=N_PART * [(1, 1, 1)], dip=dip, fix=N_PART * [(0, 0, 1)])"
+    "system.part.add(pos=pos, rotation=N_PART * [(True, True, True)],\n",
+    "                dip=dip, fix=N_PART * [(False, False, True)])"
    ]
   },
   {

maintainer/benchmarks/ferrofluid.py

@@ -97,7 +97,7 @@
 #############################################################
 system.part.add(
     pos=np.random.random((n_part, 3)) * system.box_l,
-    rotation=n_part * [(1, 1, 1)],
+    rotation=n_part * [(True, True, True)],
     dipm=n_part * [args.dipole_moment])
 
 #  Warmup Integration

maintainer/benchmarks/lj.py

@@ -105,9 +105,11 @@
     system.bonded_inter.add(hb)
     for _ in range(0, n_part, 2):
         pos = np.random.random(3) * system.box_l
+        vec = np.random.random(3)
+        vec /= np.linalg.norm(vec)
         p1 = system.part.add(pos=pos)
-        p2 = system.part.add(pos=pos + np.random.random(3) / np.sqrt(3))
-        system.part[p1].add_bond((hb, p2))
+        p2 = system.part.add(pos=pos + vec * hb.r_0)
+        p1.add_bond((hb, p2))
 
 #  Warmup Integration
 #############################################################

samples/dancing.py

@@ -52,9 +52,9 @@
 system.integrator.set_stokesian_dynamics(
     viscosity=1.0, radii={0: 1.0}, approximation_method=sd_method)
 
-system.part.add(pos=[-5, 0, 0], rotation=[1, 1, 1])
-system.part.add(pos=[0, 0, 0], rotation=[1, 1, 1])
-system.part.add(pos=[7, 0, 0], rotation=[1, 1, 1])
+system.part.add(pos=[-5, 0, 0], rotation=[True, True, True])
+system.part.add(pos=[0, 0, 0], rotation=[True, True, True])
+system.part.add(pos=[7, 0, 0], rotation=[True, True, True])
 
 gravity = espressomd.constraints.Gravity(g=[0, -1, 0])
 system.constraints.add(gravity)

samples/drude_bmimpf6.py

@@ -211,7 +211,7 @@ def combination_rule_sigma(rule, sig1, sig2):
     cation_com = system.part.add(
         type=types["BMIM_COM"], pos=pos_com,
         mass=masses["BMIM_COM"], rinertia=[646.284, 585.158, 61.126],
-        gamma=0, rotation=[1, 1, 1])
+        gamma=0, rotation=[True, True, True])
 
     cation_c1 = system.part.add(type=types["BMIM_C1"],
                                 pos=pos_com + [0, -0.527, 1.365], q=charges["BMIM_C1"])

samples/grand_canonical.py

@@ -95,7 +95,7 @@
     reactant_types=[], reactant_coefficients=[], product_types=[1, 2],
     product_coefficients=[1, 1], default_charges={1: -1, 2: +1})
 print(RE.get_status())
-system.setup_type_map([0, 1, 2])
+system.setup_type_map(type_list=[0, 1, 2])
 
 # Set the hidden particle type to the lowest possible number to speed
 # up the simulation

samples/lj_liquid_structurefactor.py

@@ -78,7 +78,7 @@
 structurefactor_type_list = [0, 1]
 structurefactor_order = 20
 structurefactor_bins = len(system.analysis.structure_factor(
-    [0], structurefactor_order)[0])
+    sf_types=[0], sf_order=structurefactor_order)[0])
 structurefactor_k = np.zeros(structurefactor_bins)
 structurefactor_Sk = np.zeros(structurefactor_bins)
 
@@ -153,7 +153,7 @@
     system.integrator.run(int_steps)
 
     structurefactor_k, structurefactor_Sk = system.analysis.structure_factor(
-        structurefactor_type_list, structurefactor_order)
+        sf_types=structurefactor_type_list, sf_order=structurefactor_order)
 
     energies = system.analysis.energy()
     print(energies['total'])

samples/reaction_methods.py

@@ -98,7 +98,7 @@
 assert RE is not None, "Please choose a reaction ensemble from the command line"
 
 print(RE.get_status())
-system.setup_type_map(list(types.values()))
+system.setup_type_map(type_list=list(types.values()))
 
 
 # Set the hidden particle type to the lowest possible number to speed

samples/rigid_body.py

@@ -106,7 +106,8 @@ def rotate_vector(vector, axis, angle):
 # place center bead
 p_center = system.part.add(
     pos=center_of_mass, mass=branch_len * 6 + 1, rinertia=principal_moments,
-    rotation=[1, 1, 1], type=ParticleTypes.CENTER.value, quat=espressomd.rotation.matrix_to_quat(principal_axes))
+    rotation=[True, True, True], type=ParticleTypes.CENTER.value,
+    quat=espressomd.rotation.matrix_to_quat(principal_axes))
 
 # Relate the particles that make up the rigid body to the central particle.
 # This will also mark them as `virtual = True`

samples/widom_insertion.py

@@ -111,7 +111,7 @@
                    reactant_coefficients=[], product_types=[1, 2],
                    product_coefficients=[1, 1], default_charges={1: -1, 2: +1})
 print(widom.get_status())
-system.setup_type_map([0, 1, 2])
+system.setup_type_map(type_list=[0, 1, 2])
 
 
 # Set the hidden particle type to the lowest possible number to speed

src/config/gen_featureconfig.py

@@ -1,3 +1,4 @@
+#
 # Copyright (C) 2013-2022 The ESPResSo project
 # Copyright (C) 2012 Olaf Lenz
 #
@@ -16,9 +17,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-# This script generates the files featureconfig.h and featureconfig.c.
-#
-import time
+
 import string
 import inspect
 import sys
@@ -32,67 +31,78 @@
     print(f"Usage: {sys.argv[0]} DEFFILE HPPFILE CPPFILE", file=sys.stderr)
     exit(2)
 
-deffilename, hfilename, cfilename = sys.argv[1:5]
-
-print("Reading definitions from " + deffilename + "...")
-defs = featuredefs.defs(deffilename)
-print("Done.")
-
-print("Writing " + hfilename + "...")
-hfile = open(hfilename, 'w')
-
-hfile.write("""/*
-WARNING: This file was autogenerated by
+path_def, path_hpp, path_cpp = sys.argv[1:5]
 
-   %s on %s
+print(f"Reading definitions from {path_def}")
+defs = featuredefs.defs(path_def)
 
-   Do not modify it or your changes will be overwritten!
-   Modify features.def instead.
+disclaimer = f"""/*
+    WARNING: This file was generated automatically.
+    Do not modify it or your changes will be overwritten!
+    Modify features.def instead.
 */
-#ifndef ESPRESSO_FEATURECONFIG_HPP
-#define ESPRESSO_FEATURECONFIG_HPP
-
-#include "cmake_config.hpp"
-#include "myconfig-final.hpp"
+"""
 
-""" % (sys.argv[0], time.asctime()))
+print(f"Writing {path_hpp}")
+hfile = open(path_hpp, 'w')
+hfile.write(disclaimer)
+hfile.write("""
+#ifndef ESPRESSO_SRC_CONFIG_CONFIG_FEATURES_HPP
+#define ESPRESSO_SRC_CONFIG_CONFIG_FEATURES_HPP
+""")
 
 # external features can only be set by the build
 # system, so in case the user has defined some of
 # them, we undef all external features and include
 # the config from the build system again, to make
 # sure only the detected ones are set.
-hfile.write('/* Guards for externals */')
+hfile.write("""
+/*********************************/
+/* Handle definitions from CMake */
+/*********************************/
+
+#include "cmake_config.hpp"
+#include "myconfig-final.hpp"
+""")
 external_template = string.Template("""
 // $feature is external
 #if defined($feature)
 #undef $feature
 #endif
 """)
-for feature in defs.externals:
+for feature in sorted(defs.externals):
     hfile.write(external_template.substitute(feature=feature))
 
 # Include definitions from CMake
 hfile.write("""
-/* Definitions from CMake */
 #include "cmake_config.hpp"
 
 """)
 
 # handle implications
-hfile.write('/* Handle implications */')
+hfile.write("""\
+/***********************/
+/* Handle implications */
+/***********************/
+""")
 implication_template = string.Template("""
 // $feature implies $implied
 #if defined($feature) && !defined($implied)
 #define $implied
 #endif
 """)
-for feature, implied in defs.implications:
+for feature, implied in sorted(defs.implications):
     hfile.write(implication_template.substitute(
         feature=feature, implied=implied))
 
+hfile.write("\n")
+
 # output warnings if internal features are set manually
-hfile.write('/* Warn when derived switches are specified manually */')
+hfile.write("""\
+/*****************************************************/
+/* Warn when derived switches are specified manually */
+/*****************************************************/
+""")
 derivation_template = string.Template("""
 // $feature equals $expr
 #ifdef $feature
@@ -101,58 +111,52 @@
 #define $feature
 #endif
 """)
-for feature, expr, cppexpr in defs.derivations:
+for feature, expr, cppexpr in sorted(defs.derivations):
     hfile.write(derivation_template.substitute(
         feature=feature, cppexpr=cppexpr, expr=expr))
 
-# write footer
-# define external FEATURES and NUM_FEATURES
 hfile.write("""
-extern const char* FEATURES[];
-extern const int NUM_FEATURES;
 
-#endif /* of _FEATURECONFIG_HPP */""")
-hfile.close()
-print("Done.")
+extern char const *const FEATURES[];
+extern char const *const FEATURES_ALL[];
+extern unsigned int const NUM_FEATURES;
+extern unsigned int const NUM_FEATURES_ALL;
 
-print("Writing " + cfilename + "...")
-cfile = open(cfilename, 'w')
-
-# handle requirements
-
-cfile.write(f"""/*
-WARNING: This file was autogenerated by
+#endif
+""")
 
-   {sys.argv[0]}
-   on
-   {time.asctime()}
+hfile.close()
 
-   Do not modify it or your changes will be overwritten!
-   Modify features.def instead.
-*/
+print(f"Writing {path_cpp}")
+cfile = open(path_cpp, "w")
 
-/* config.hpp includes config-features.hpp and myconfig.hpp */
+cfile.write(disclaimer)
+cfile.write(f"""
+#include "config-features.hpp"
 #include "config.hpp"
 
+/***********************/
+/* Handle requirements */
+/***********************/
 """)
 
-cfile.write('/* Handle requirements */')
-
 requirement_string = """
 // {feature} requires {expr}
 #if defined({feature}) && !({cppexpr})
 #error Feature {feature} requires {expr}
 #endif
 """
-for feature, expr, cppexpr in defs.requirements:
+for feature, expr, cppexpr in sorted(defs.requirements):
     cfile.write(
         requirement_string.format(
             feature=feature, cppexpr=cppexpr, expr=expr))
 
 cfile.write("""
-
+/****************/
 /* Feature list */
-const char* FEATURES[] = {
+/****************/
+
+char const *const FEATURES[] = {
 """)
 
 feature_string = """
@@ -161,14 +165,31 @@
 #endif
 """
 
-for feature in defs.externals.union(defs.features, defs.derived):
+for feature in sorted(defs.externals.union(defs.features, defs.derived)):
     cfile.write(feature_string.format(feature=feature))
 
 cfile.write("""
 };
+unsigned int const NUM_FEATURES = sizeof(FEATURES) / sizeof(char*);
+""")
 
-const int NUM_FEATURES = sizeof(FEATURES)/sizeof(char*);
+cfile.write("""
+/*********************/
+/* Feature full list */
+/*********************/
+
+char const *const FEATURES_ALL[] = {\
+""")
+
+feature_string = """
+  "{feature}","""
+
+for feature in sorted(defs.allfeatures):
+    cfile.write(feature_string.format(feature=feature))
+
+cfile.write("""
+};
+unsigned int const NUM_FEATURES_ALL = sizeof(FEATURES_ALL) / sizeof(char*);
 """)
 
 cfile.close()
-print("Done.")