Merge pull request #1973 from evoyiatzis/ext-fix-adapt

Small extension of bonds supported by fix adapt

doc/src/fix_adapt.rst

@@ -288,11 +288,19 @@ Currently *bond* does not support bond_style hybrid nor bond_style
 hybrid/overlay as bond styles. The only bonds that currently are
 working with fix_adapt are
 
-+---------------------------------+-------+------------+
-| :doc:`gromos <bond_gromos>`     | k, r0 | type bonds |
-+---------------------------------+-------+------------+
-| :doc:`harmonic <bond_harmonic>` | k,r0  | type bonds |
-+---------------------------------+-------+------------+
++------------------------------------+-------+------------+
+| :doc:`class2 <bond_class2>`        | r0    | type bonds |
++------------------------------------+-------+------------+
+| :doc:`fene <bond_fene>`            | k, r0 | type bonds |
++------------------------------------+-------+------------+
+| :doc:`gromos <bond_gromos>`        | k, r0 | type bonds |
++------------------------------------+-------+------------+
+| :doc:`harmonic <bond_harmonic>`    | k,r0  | type bonds |
++------------------------------------+-------+------------+
+| :doc:`morse <bond_morse>`          | r0    | type bonds |
++------------------------------------+-------+------------+
+| :doc:`nonlinear <bond_nonlinear>`  | r0    | type bonds |
++------------------------------------+-------+------------+
 
 ----------
 

src/CLASS2/bond_class2.cpp

@@ -15,6 +15,7 @@
    Contributing author: Eric Simon (Cray)
 ------------------------------------------------------------------------- */
 
+#include <cstring>
 #include "bond_class2.h"
 #include <mpi.h>
 #include <cmath>
@@ -220,3 +221,12 @@ double BondClass2::single(int type, double rsq, int /*i*/, int /*j*/, double &ff
   else fforce = 0.0;
   return (k2[type]*dr2 + k3[type]*dr3 + k4[type]*dr4);
 }
+
+/* ---------------------------------------------------------------------- */
+
+void *BondClass2::extract( char *str, int &dim )
+{
+  dim = 1;
+  if (strcmp(str,"r0")==0) return (void*) r0;
+  return NULL;
+}

src/CLASS2/bond_class2.h

@@ -35,6 +35,7 @@ class BondClass2 : public Bond {
   virtual void read_restart(FILE *);
   void write_data(FILE *);
   double single(int, double, int, int, double &);
+  virtual void *extract(char *, int &);
 
  protected:
   double *r0,*k2,*k3,*k4;

src/MOLECULE/bond_fene.cpp

@@ -14,6 +14,7 @@
 #include "bond_fene.h"
 #include <mpi.h>
 #include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "neighbor.h"
 #include "comm.h"
@@ -272,3 +273,13 @@ double BondFENE::single(int type, double rsq, int /*i*/, int /*j*/,
 
   return eng;
 }
+
+/* ---------------------------------------------------------------------- */
+
+void *BondFENE::extract( char *str, int &dim )
+{
+  dim = 1;
+  if (strcmp(str,"kappa")==0) return (void*) k;
+  if (strcmp(str,"r0")==0) return (void*) r0;
+  return NULL;
+}

src/MOLECULE/bond_fene.h

@@ -36,6 +36,7 @@ class BondFENE : public Bond {
   void read_restart(FILE *);
   void write_data(FILE *);
   double single(int, double, int, int, double &);
+  virtual void *extract(char *, int &);
 
  protected:
   double TWO_1_3;

src/MOLECULE/bond_morse.cpp

@@ -18,6 +18,7 @@
 #include "bond_morse.h"
 #include <mpi.h>
 #include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "neighbor.h"
 #include "comm.h"
@@ -205,3 +206,12 @@ double BondMorse::single(int type, double rsq, int /*i*/, int /*j*/,
   if (r > 0.0) fforce = -2.0*d0[type]*alpha[type]*(1-ralpha)*ralpha/r;
   return d0[type]*(1-ralpha)*(1-ralpha);
 }
+
+/* ---------------------------------------------------------------------- */
+
+void *BondMorse::extract(char *str, int &dim )
+{
+  dim = 1;
+  if (strcmp(str,"r0")==0) return (void*) r0;
+  return NULL;
+}

src/MOLECULE/bond_morse.h

@@ -35,6 +35,7 @@ class BondMorse : public Bond {
   void read_restart(FILE *);
   void write_data(FILE *);
   double single(int, double, int, int, double &);
+  virtual void *extract(char *, int &);
 
  protected:
   double *d0,*alpha,*r0;

src/MOLECULE/bond_nonlinear.cpp

@@ -14,6 +14,7 @@
 #include "bond_nonlinear.h"
 #include <mpi.h>
 #include <cmath>
+#include <cstring>
 #include "atom.h"
 #include "neighbor.h"
 #include "comm.h"
@@ -202,3 +203,13 @@ double BondNonlinear::single(int type, double rsq, int /*i*/, int /*j*/,
   fforce = -epsilon[type]/r * 2.0*dr*lamdasq/denomsq;
   return epsilon[type] * drsq / denom;
 }
+
+/* ---------------------------------------------------------------------- */
+
+void *BondNonlinear::extract( char *str, int &dim )
+{
+  dim = 1;
+  if (strcmp(str,"epsilon")==0) return (void*) epsilon;
+  if (strcmp(str,"r0")==0) return (void*) r0;
+  return NULL;
+}

src/MOLECULE/bond_nonlinear.h

@@ -35,6 +35,7 @@ class BondNonlinear : public Bond {
   void read_restart(FILE *);
   void write_data(FILE *);
   double single(int, double, int, int, double &);
+  virtual void *extract(char *, int &);
 
  protected:
   double *epsilon,*r0,*lamda;