cleanup and compilation for python off

python/lammps.py

@@ -505,7 +505,7 @@ class lammps(object):
     self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, py_object, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
     self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, py_object]
     self.lib.lammps_set_fix_external_callback.restype = None
-    
+
     self.mliappy = MLIAPPY(self)
 
   # -------------------------------------------------------------------------
@@ -2931,12 +2931,12 @@ class MLIAPPY():
     def __init__(self,lammps):
         self._module = None
         self.lammps = lammps
-        
+
     @property
     def module(self):
         if self._module:
             return self._module
-            
+
         try:
             # Begin Importlib magic to find the embedded python module
             # This is needed because the filename for liblammps does not
@@ -2959,10 +2959,10 @@ class MLIAPPY():
             # End Importlib magic to find the embedded python module
         except:
             raise ImportError("Could not load MLIAPPY coupling module")
-    
+
     def activate(self):
         self.module
-        
+
     def load_model(self,model):
         self.module.load_from_python(model)
-            
+

src/MLIAP/mliap_data.cpp

@@ -29,7 +29,7 @@ MLIAPData::MLIAPData(LAMMPS *lmp, int gradgradflag_in, int *map_in,
                      class MLIAPModel* model_in,
                      class MLIAPDescriptor* descriptor_in,
                      class PairMLIAP* pairmliap_in) :
-  Pointers(lmp), gradforce(nullptr), betas(nullptr), 
+  Pointers(lmp), gradforce(nullptr), betas(nullptr),
   descriptors(nullptr), eatoms(nullptr), gamma(nullptr),
   gamma_row_index(nullptr), gamma_col_index(nullptr), egradient(nullptr),
   numneighs(nullptr), iatoms(nullptr), ielems(nullptr), jatoms(nullptr), jelems(nullptr),

src/MLIAP/mliap_model_python.cpp

@@ -15,6 +15,8 @@
    Contributing author: Nicholas Lubbers (LANL)
 ------------------------------------------------------------------------- */
 
+#ifdef MLIAP_PYTHON
+
 #include <Python.h>
 #include "mliap_model_python.h"
 #include "mliap_model_python_couple.h"
@@ -43,9 +45,9 @@ MLIAPModelPython::MLIAPModelPython(LAMMPS* lmp, char* coefffilename) :
     PyGILState_Release(gstate);
     error->all(FLERR,"Could not initialize embedded Python");
   }
-  
+
   PyObject* coupling_module = PyImport_ImportModule("mliap_model_python_couple");
-  
+
   if (!coupling_module) {
     PyErr_Print();
     PyErr_Clear();
@@ -97,7 +99,7 @@ void MLIAPModelPython::read_coeffs(char * fname)
     error->all(FLERR,"Loading python model failure.");
   }
   PyGILState_Release(gstate);
-  
+
   if (loaded) {
     this->connect_param_counts();
   }
@@ -113,7 +115,7 @@ void MLIAPModelPython::connect_param_counts()
   nelements = MLIAPPY_nelements(this);
   nparams = MLIAPPY_nparams(this);
   ndescriptors = MLIAPPY_ndescriptors(this);
-  
+
   if (PyErr_Occurred()) {
     PyErr_Print();
     PyErr_Clear();
@@ -137,7 +139,7 @@ void MLIAPModelPython::compute_gradients(MLIAPData* data)
   if (not model_loaded) {
     error->all(FLERR,"Model not loaded.");
   }
-  
+
   PyGILState_STATE gstate = PyGILState_Ensure();
   MLIAPPY_compute_gradients(this, data);
   if (PyErr_Occurred()) {
@@ -196,3 +198,5 @@ double MLIAPModelPython::memory_usage()
   // todo: get approximate memory usage in coupling code.
   return 0;
 }
+
+#endif

src/MLIAP/mliap_model_python.h

@@ -38,7 +38,7 @@ protected:
   virtual void read_coeffs(char *);
 
 private:
-  
+
 };
 
 }

src/MLIAP/mliap_model_python_couple.pyx

@@ -1,12 +1,5 @@
 # cython: language_level=3
 # distutils: language = c++
-# distutils: define_macros="LMP_MLIAPPY"
-# distutils: extra_compile_args= -stdlib=libc++ -std=c++11
-# distutils: include_dirs = ../STUBS .. ../MLIAP 
-# distutils: extra_link_args= -stdlib=libc++
-# Note: only the language_level and language commands are needed, the rest pertain
-# to building mliap_model_python_couple as a standalone python extension, which
-# is experimental.
 
 cimport cython
 
@@ -88,11 +81,11 @@ def load_from_python(model):
         LOADED_MODELS[c_id]=model
         lmp_model = <MLIAPModelPython *> <uintptr_t> c_id
         lmp_model.connect_param_counts()
-        
+
 
 cdef public void MLIAPPY_unload_model(MLIAPModelPython * c_model) with gil:
     del LOADED_MODELS[c_id(c_model)]
-    
+
 cdef public int MLIAPPY_nparams(MLIAPModelPython * c_model) with gil:
     return int(retrieve(c_model).n_params)
 
@@ -107,7 +100,7 @@ cdef public void MLIAPPY_compute_gradients(MLIAPModelPython * c_model, MLIAPData
 
     n_d = data.ndescriptors
     n_a = data.natoms
-    
+
     # Make numpy arrays from pointers
     beta_np = np.asarray(<double[:n_a,:n_d] > &data.betas[0][0])
     desc_np = np.asarray(<double[:n_a,:n_d]> &data.descriptors[0][0])
@@ -116,7 +109,7 @@ cdef public void MLIAPPY_compute_gradients(MLIAPModelPython * c_model, MLIAPData
 
     # Invoke python model on numpy arrays.
     model(elem_np,desc_np,beta_np,en_np)
-    
+
     # Get the total energy from the atom energy.
     energy = np.sum(en_np)
     data.energy = <double> energy

src/MLIAP/pair_mliap.cpp

@@ -73,17 +73,17 @@ PairMLIAP::~PairMLIAP()
 
 void PairMLIAP::compute(int eflag, int vflag)
 {
-  
+
   // consistency checks
 
   if (data->ndescriptors != model->ndescriptors) {
     error->all(FLERR,"Incompatible model and descriptor descriptor count");
   };
-  
+
   if (data->nelements != model->nelements) {
     error->all(FLERR,"Incompatible model and descriptor element count");
   };
-  
+
   ev_init(eflag,vflag);
 
   data->generate_neighdata(list, eflag, vflag);
@@ -249,7 +249,7 @@ void PairMLIAP::coeff(int narg, char **arg)
 void PairMLIAP::e_tally(MLIAPData* data)
 {
   if (eflag_global) eng_vdwl += data->energy;
-  if (eflag_atom) 
+  if (eflag_atom)
     for (int ii = 0; ii < data->natoms; ii++) {
       const int i = data->iatoms[ii];
       eatom[i] += data->eatoms[ii];