Merge pull request #3162 from phankl/mesocnt_memory

Optimized memory usage for pair style mesocnt

doc/src/pair_mesocnt.rst

@@ -94,10 +94,6 @@ boron nitride nanotubes.
    Atoms belonging to different CNTs need to be assigned
    different molecule IDs.
 
-A full summary of the method and LAMMPS implementation details
-is expected to soon become available in Computer Physics
-Communications.
-
 ----------
 
 Mixing, shift, table, tail correction, restart, rRESPA info

src/MESONT/pair_mesocnt.h

@@ -12,9 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #ifdef PAIR_CLASS
-// clang-format off
 PairStyle(mesocnt, PairMesoCNT);
-// clang-format on
 #else
 
 #ifndef LMP_PAIR_MESOCNT_H
@@ -23,7 +21,7 @@ PairStyle(mesocnt, PairMesoCNT);
 #include "pair.h"
 
 namespace LAMMPS_NS {
-
+class PotentialFileReader;
 class PairMesoCNT : public Pair {
  public:
   PairMesoCNT(class LAMMPS *);
@@ -36,7 +34,6 @@ class PairMesoCNT : public Pair {
 
  protected:
   int uinf_points, gamma_points, phi_points, usemi_points;
-  int nlocal_size, reduced_neigh_size;
   int *reduced_nlist, *numchainlist;
   int **reduced_neighlist, **nchainlist, **endlist;
   int ***chainlist;
@@ -57,16 +54,18 @@ class PairMesoCNT : public Pair {
   double **uinf_coeff, **gamma_coeff, ****phi_coeff, ****usemi_coeff;
   double **flocal, **fglobal, **basis;
 
-  char *file;
+  int count_chains(int *, int);
 
   void allocate();
   void bond_neigh();
   void neigh_common(int, int, int &, int *);
-  void chain_split(int *, int, int &, int **, int *, int *);
+  void chain_lengths(int *, int, int *);
+  void chain_split(int *, int, int *, int **, int *);
   void sort(int *, int);
-  void read_file();
-  void read_data(FILE *, double *, double &, double &, int);
-  void read_data(FILE *, double **, double &, double &, double &, double &, int);
+  void read_file(const char *);
+  void read_data(PotentialFileReader &, double *, double &, double &, int);
+  void read_data(PotentialFileReader &, double **, double &, double &, double &, double &,
+                 int);
 
   void spline_coeff(double *, double **, double, int);
   void spline_coeff(double **, double ****, double, double, int);

src/memory.h

@@ -226,10 +226,38 @@ class Memory : protected Pointers {
   }
 
   template <typename TYPE>
-  TYPE ***create_ragged(TYPE ***& /*array*/, int /*n1*/, int * /*n2*/, const char *name)
+  TYPE ***create_ragged(TYPE ***& array, int n1, int *n2, int **n3, const char *name)
   {
-    fail(name);
-    return nullptr;
+    bigint size, nbytes;
+    int i, j;
+
+    size = 0;
+    for (i = 0; i < n1; i++)
+      for (j = 0; j < n2[i]; j++)
+        size += n3[i][j];
+    nbytes = ((bigint) sizeof(TYPE)) * size;
+    TYPE *data = (TYPE *) smalloc(nbytes, name);
+
+    size = 0;
+    for (i = 0; i < n1; i++) size += n2[i];
+    nbytes = ((bigint) sizeof(TYPE *)) * size;
+    TYPE **plane = (TYPE **) smalloc(nbytes, name);
+
+    nbytes = ((bigint) sizeof(TYPE **)) * n1;
+    array = (TYPE ***) smalloc(nbytes, name);
+
+    bigint m = 0;
+    bigint n = 0;
+    for (i = 0; i < n1; i++) {
+      array[i] = &plane[m];
+      for (j = 0; j < n2[i]; j++) {
+        plane[m + j] = &data[n];
+        n += n3[i][j];
+      }
+      m += n2[i];
+    }
+
+    return array;
   }
 
 /* ----------------------------------------------------------------------