TODO

src/core/interactions.cpp

@@ -78,6 +78,7 @@ bool long_range_interactions_sanity_checks() {
   return false;
 }
 
+// TODO: remove this function
 void mpi_bcast_ia_params_local(int i, int j) {
   boost::mpi::broadcast(comm_cart, get_ia_param(i, j), 0);
   on_short_range_ia_change();

src/core/nonbonded_interactions/lj.cpp

@@ -25,10 +25,10 @@
 #include "lj.hpp"
 
 #ifdef LENNARD_JONES
-#include "interactions.hpp"
+#include "interactions.hpp" // TODO: remove include
 #include "nonbonded_interaction_data.hpp"
 
-#include <utils/constants.hpp>
+#include <utils/constants.hpp> // TODO: remove include
 #include <utils/math/int_pow.hpp>
 
 #include <algorithm>

src/core/nonbonded_interactions/lj.hpp

@@ -37,6 +37,7 @@
 #include <utils/math/int_pow.hpp>
 #include <utils/math/sqr.hpp>
 
+// TODO: remove function
 int lennard_jones_set_params(int part_type_a, int part_type_b, double eps,
                              double sig, double cut, double shift,
                              double offset, double min);

src/core/nonbonded_interactions/nonbonded_interaction_data.cpp

@@ -48,7 +48,7 @@
  * variables
  *****************************************/
 int max_seen_particle_type = 0;
-std::vector<IA_parameters> old_nonbonded_ia_params;
+std::vector<IA_parameters> old_nonbonded_ia_params; // TODO: delete
 std::vector<std::shared_ptr<IA_parameters>> nonbonded_ia_params;
 
 /** Minimal global interaction cutoff. Particles with a distance
@@ -230,7 +230,7 @@ double maximal_cutoff_nonbonded() {
   return max_cut_nonbonded;
 }
 
-void reset_ia_params() {
+void reset_ia_params() { // TODO: delete
   boost::fill(old_nonbonded_ia_params, IA_parameters{});
   mpi_bcast_all_ia_params();
 }

src/core/nonbonded_interactions/nonbonded_interaction_data.hpp

@@ -282,7 +282,7 @@ struct IA_parameters {
 #endif
 };
 
-extern std::vector<IA_parameters> old_nonbonded_ia_params;
+extern std::vector<IA_parameters> old_nonbonded_ia_params; // TODO: delete
 extern std::vector<std::shared_ptr<IA_parameters>> nonbonded_ia_params;
 
 /** Maximal particle type seen so far. */
@@ -323,11 +323,11 @@ IA_parameters *get_ia_param_safe(int i, int j);
 
 /** @brief Get the state of all non-bonded interactions.
  */
-std::string ia_params_get_state();
+std::string ia_params_get_state(); // TODO: delete
 
 /** @brief Set the state of all non-bonded interactions.
  */
-void ia_params_set_state(std::string const &);
+void ia_params_set_state(std::string const &); // TODO: delete
 
 void mpi_realloc_ia_params_local(int new_size);
 
@@ -343,7 +343,7 @@ void make_particle_type_exist_local(int type);
 /**
  * @brief Reset all interaction parameters to their defaults.
  */
-void reset_ia_params();
+void reset_ia_params(); // TODO: delete
 
 /** Check if a non-bonded interaction is defined */
 inline bool checkIfInteraction(IA_parameters const &data) {

src/core/nonbonded_interactions/wca.cpp

@@ -23,10 +23,10 @@
 #include "wca.hpp"
 
 #ifdef WCA
-#include "interactions.hpp"
+#include "interactions.hpp" // TODO: remove include
 #include "nonbonded_interaction_data.hpp"
 
-#include <utils/constants.hpp>
+#include <utils/constants.hpp> // TODO: remove include
 
 #include <cmath>
 #include <stdexcept>

src/core/nonbonded_interactions/wca.hpp

@@ -35,6 +35,7 @@
 #include <utils/math/int_pow.hpp>
 #include <utils/math/sqr.hpp>
 
+// TODO: remove function
 int wca_set_params(int part_type_a, int part_type_b, double eps, double sig);
 
 /** Calculate WCA force factor */

src/python/espressomd/interactions.pyx

@@ -16,15 +16,16 @@
 # 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 libcpp.string cimport string
+from libcpp.string cimport string  # TODO: delete include
 cimport cpython.object
-import collections
+import collections  # TODO: delete include
 
 include "myconfig.pxi"
 from . import utils
 from .script_interface import ScriptObjectMap, ScriptInterfaceHelper, script_interface_register
 
 
+# TODO: delete class
 cdef class NonBondedInteraction:
     """
     Represents an instance of a non-bonded interaction, such as Lennard-Jones.
@@ -206,6 +207,7 @@ cdef class NonBondedInteraction:
             "Subclasses of NonBondedInteraction must define the required_keys() method.")
 
 
+# TODO: rename class to NonBondedInteraction
 class NewNonBondedInteraction(ScriptInterfaceHelper):
     """
     Represents an instance of a non-bonded interaction, such as Lennard-Jones.
@@ -1647,7 +1649,7 @@ class NonBondedInteractions(ScriptInterfaceHelper):
         self.call_method("insert", key=key, object=value)
 
     def __getstate__(self):
-        cdef string core_state = ia_params_get_state()
+        cdef string core_state = ia_params_get_state()  # TODO: delete line
         n_types = self.call_method("get_n_types")
         state = []
         for i in range(n_types):
@@ -1664,14 +1666,14 @@ class NonBondedInteractions(ScriptInterfaceHelper):
             obj = NonBondedInteractionHandle(_types=types, **objects)
             self.call_method("insert", key=types, object=obj)
 
-    def reset(self):
+    def reset(self):  # TODO: delete this method and uncomment _so_bind_methods
         reset_ia_params()
         self.call_method("reset")
 
     @classmethod
     def _restore_object(cls, so_callback, so_callback_args, state):
-        cdef string core_state = state["core_state"]
-        ia_params_set_state(core_state)
+        cdef string core_state = state["core_state"]  # TODO: delete line
+        ia_params_set_state(core_state)  # TODO: delete line
         so = so_callback(*so_callback_args)
         so.__setstate__(state)
         return so