Solved the problem with erfc

Removed unused preprocessor generated files

Src/ewald.c

@@ -17,7 +17,7 @@
  * Include erfc code, unless user wants to use an erfc from libm.
  */
 #ifndef LIBM_HAS_ERFC
-#include "ndtr.h"
+#include "MMTK/ndtr.h"
 #endif
 #ifndef M_PI
 #define M_PI   3.14159265358979323846264338327950288

Src/ewald1.i

-for (k = 0; k < nblist->npairs; k++, pair++) {
-  if (cutoff_sq == 0. || pair->r_sq <= cutoff_sq) {
-    int i = pair->i1;
-    int j = pair->i2;
-    double r_sq = pair->r_sq;
-    double r = sqrt(r_sq);
-    double f1 = erfc(beta*r);
-    double f2 = erfc_cutoff;
-    vector3 rij;
-    if (pair->one_four)
-      f1 += one_four_factor-1.;
-#ifdef NBLIST_WITH_VECTORS
-    vector_copy(rij, pair->d);
-#else
-    distance_vector_function(rij, x[j], x[i], universe_data);
-#endif
-#   include "ewald2.i"
-  }
-}
-
-for (k = 0; k < n_ex; k += 2) {
-  int i = excluded[k];
-  int j = excluded[k+1];
-  double r_sq, r, f1, f2;
-  vector3 rij;
-  distance_vector_function(rij, x[j], x[i], universe_data);
-  r_sq = vector_length_sq(rij);
-  r = sqrt(r_sq);
-  f1 = erfc(beta*r)-1.;
-  f2 = erfc_cutoff;
-# include "ewald2.i"
-}

Src/ewald2.i

-{
-  double qiqj = charge[i]*charge[j]*electrostatic_energy_factor;
-  double ef = 2./sqrt(M_PI);
-  self->energy += qiqj*(f1/r-f2*inv_cutoff);
-  if (gradients != NULL || force_constants != NULL) {
-    double deriv = -qiqj*(f1/r_sq-f2*inv_cutoff
-	                  +ef*beta*(exp(-beta*beta*r_sq)/r
-                                    -inv_cutoff*exp(-beta*beta*cutoff_sq)))/r;
-    if (gradients != NULL) {
-      vector3 grad;
-      grad[0] = deriv*rij[0];
-      grad[1] = deriv*rij[1];
-      grad[2] = deriv*rij[2];
-      if (gradient_fn != NULL) {
-	(*gradient_fn)(self, gradients, i, grad);
-	vector_changesign(grad);
-	(*gradient_fn)(self, gradients, j, grad);
-      }
-      else {
-	vector3 *f = (vector3 *)((PyArrayObject *)gradients)->data;
-	f[i][0] += grad[0];
-	f[i][1] += grad[1];
-	f[i][2] += grad[2];
-	f[j][0] -= grad[0];
-	f[j][1] -= grad[1];
-	f[j][2] -= grad[2];
-      }
-    }
-    if (force_constants != NULL) {
-      double deriv2 = 2.*qiqj*(f1/(r*r_sq) - f2*cube(inv_cutoff)
-	                       + ef*beta*exp(-beta*beta*r_sq)
-                                               * (beta*beta+1./r_sq));
-      if (inv_cutoff > 0.)
-	deriv2 -= 2.*qiqj*ef*beta*exp(-beta*beta*cutoff_sq)
-                         * (beta*beta+sqr(inv_cutoff));
-      add_pair_fc(self, force_constants, fc_fn, i, j,
-		  rij, r_sq, deriv, deriv2);
-    }
-  }
-}

Src/ndtr.c

@@ -145,8 +145,9 @@ Direct inquiries to 30 Frost Street, Cambridge, MA 02140
 */
 
 
-#include "polevl.h"
-#include "ndtr.h"
+#include "MMTK/mconf.h"
+#include "MMTK/ndtr.h"
+#include "MMTK/polevl.h"
 
 #ifdef UNK
 static double P[] = {

Src/nonbonded.c

@@ -8,7 +8,7 @@
 #define PY_ARRAY_UNIQUE_SYMBOL PyArray_MMTKFF_API
 
 #ifndef LIBM_HAS_ERFC
-#include "ndtr.h"
+#include "MMTK/ndtr.h"
 #endif
 
 #include "MMTK/forcefield.h"

Src/nonbonded1.i

-for (k = 0; k < n_ex; k += 2) {
-  int i = excluded[k];
-  int j = excluded[k+1];
-  double qiqj = charge[i]*charge[j]*electrostatic_energy_factor;
-  pair_es_energy(-qiqj, distance_vector_function);
-}
-for (k = 0; k < n_14; k += 2) {
-  int i = one_four[k];
-  int j = one_four[k+1];
-  double qiqj = charge[i]*charge[j]*electrostatic_energy_factor;
-  pair_es_energy(qiqj*(es_one_four_factor-1.), distance_vector_function);
-}

Src/polevl.c

@@ -50,7 +50,7 @@ Direct inquiries to 30 Frost Street, Cambridge, MA 02140
 */
 
 
-#include "polevl.h"
+#include "MMTK/polevl.h"
 
 double polevl( double x, double coef[], int N )
 {

setup.py

@@ -337,7 +337,7 @@ simulations.
                       Extension('MMTK_forcefield',
                                 ['Src/MMTK_forcefield.c',
                                  'Src/bonded.c', 'Src/nonbonded.c',
-                                 'Src/ewald.c', 'Src/sparsefc.c'],
+                                 'Src/ewald.c', 'Src/sparsefc.c','Src/ndtr.c','Src/polevl.c'],
                                 extra_compile_args = compile_args + high_opt,
                                 include_dirs=include_dirs + ['Src'],
                                 define_macros = [('SERIAL', None),