Merge remote-tracking branch 'origin/main' into docs

stochasticHydroTools · Apr 29, 2024 · d9607dd · d9607dd
2 parents 2c41006 + 633d3a4
commit d9607dd
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diff --git a/cpp/example.cpp b/cpp/example.cpp
@@ -3,8 +3,8 @@
  For instance, a triply periodic algorithm will need at least a box size.
  */
 #include "MobilityInterface/MobilityInterface.h"
-#include"libMobility/solvers/NBody/mobility.h"
-#include"libMobility/solvers/PSE/mobility.h"
+#include"../solvers/NBody/mobility.h"
+#include"../solvers/PSE/mobility.h"
 #include <type_traits>
 #include<vector>
 #include<random>
@@ -24,9 +24,12 @@ template<class Solver>
 auto initializeSolver(Parameters par){
   std::shared_ptr<MobilityBase> solver;
   if(std::is_same<Solver,NBody>::value){
-    solver = std::make_shared<NBody>(Configuration{.periodicityX = libmobility::periodicity_mode::open,
+    auto nbody = std::make_shared<NBody>(Configuration{.periodicityX = libmobility::periodicity_mode::open,
 						   .periodicityY = libmobility::periodicity_mode::open,
 						   .periodicityZ = libmobility::periodicity_mode::open});
+
+    nbody->setParametersNBody({nbody_rpy::algorithm::advise, 1,par.numberParticles});
+    solver = nbody;
   }
   if(std::is_same<Solver,PSE>::value){
     auto pse = std::make_shared<PSE>(Configuration{.periodicityX = libmobility::periodicity_mode::periodic,
@@ -48,6 +51,7 @@ auto computeMFWithSolver(std::shared_ptr<MobilityBase> solver,
 			 std::vector<scalar> &pos,
 			 std::vector<scalar> &forces){
   std::vector<scalar> result(pos.size(), 0);
+  solver->setPositions(pos.data());
   solver->Mdot(forces.data(), result.data());
   return result;
 }

diff --git a/python/example.py b/python/example.py
@@ -5,11 +5,17 @@
 '''
 import numpy as np
 import libMobility
-#Each solver has its own help available, and libMobility itself offers information about the common interface.
-#help(libMobility)
-#help(libMobility.NBody)
-#help(libMobility.PSE)
-#help(...
+# can also import modules individually by name, e.g.
+# from libMobility import SelfMobility
+# from libMobility import PSE 
+# ... etc
+
+# Each solver has its own help available, and libMobility itself offers information about the common interface.
+# help(libMobility)
+# help(libMobility.NBody)
+# help(libMobility.PSE)
+# help(...
+
 
 numberParticles = 3
 #Each module can be compiled using a different precision, you can know which one with this
@@ -20,21 +26,22 @@
 
 #Any solver can be used interchangeably, some of them need additional initialization via a "setParameters" function
 
-
 nb = libMobility.SelfMobility(periodicityX='open',periodicityY='open',periodicityZ='open')
+# to call with the alternate import, use the below
+# nb = SelfMobility(periodicityX='open',periodicityY='open',periodicityZ='open')
 
-#For NBody periodicityZ can also be single_wall
-#nb = libMobility.NBody(periodicityX='open',periodicityY='open',periodicityZ='open')
-#nb.setParametersNBody(algorithm="advise", Nbatch=-1, NperBatch=-1)
+# For NBody periodicityZ can also be single_wall
+# nb = libMobility.NBody(periodicityX='open',periodicityY='open',periodicityZ='open')
+# nb.setParametersNBody(algorithm="advise", Nbatch=1, NperBatch=numberParticles)
 
-#nb = libMobility.PSE(periodicityX='periodic',periodicityY='periodic',periodicityZ='periodic')
-#nb.setParametersPSE(psi=1, Lx=128, Ly=128, Lz=128,shearStrain=0);
+# nb = libMobility.PSE(periodicityX='periodic',periodicityY='periodic',periodicityZ='periodic')
+# nb.setParametersPSE(psi=1,   Lx=128, Ly=128, Lz=128,shearStrain=1)
 
 nb.initialize(temperature=1.0, viscosity = 1/(6*np.pi),
               hydrodynamicRadius = 1.0,
               numberParticles = numberParticles)
 nb.setPositions(pos)
-#result = M*F
+
 nb.Mdot(forces = force, result = result)
 print(f"{numberParticles} particles located at ( X Y Z ): {pos}")
 print("Forces:", force)

diff --git a/solvers/CMakeLists.txt b/solvers/CMakeLists.txt
@@ -2,3 +2,7 @@ add_subdirectory(DPStokes)
 add_subdirectory(PSE)
 add_subdirectory(NBody)
 add_subdirectory(SelfMobility)
+
+set(INIT_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
+set(INIT_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/path/to/installation/directory")
+file(COPY "${INIT_SOURCE_DIR}/__init__.py" DESTINATION ${Python3_SITEARCH}/libMobility)
diff --git a/solvers/__init__.py b/solvers/__init__.py
@@ -0,0 +1,6 @@
+from .PSE import PSE
+from .SelfMobility import SelfMobility
+from .NBody import NBody
+from .DPStokes import DPStokes
+
+__all__ = ['PSE', 'SelfMobility', 'NBody', 'DPStokes']