Merge pull request #2634 from evoyiatzis/master

Small extension of extract method in Buckingham pair styles

doc/src/compute_fep.rst

@@ -163,7 +163,7 @@ the meaning of these parameters:
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`born <pair_born>`                                                      | a,b,c                   | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
-| :doc:`buck <pair_buck>`                                                      | a,c                     | type pairs |
+| :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm  <pair_buck>`       | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`buck/mdf <pair_mdf>`                                                   | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+

doc/src/fix_adapt.rst

@@ -128,9 +128,9 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`born/coul/long, born/coul/msm <pair_born>`                             | coulombic_cutoff                                 | type global |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
-| :doc:`buck <pair_buck>`                                                      | a,c                                              | type pairs  |
+| :doc:`buck, buck/coul/cut  <pair_buck>`                                      | a,c                                              | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
-| :doc:`buck/coul/long, buck/coul/msm <pair_buck>`                             | coulombic_cutoff                                 | type global |
+| :doc:`buck/coul/long, buck/coul/msm <pair_buck>`                             | a,c,coulombic_cutoff                             | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`buck/mdf <pair_mdf>`                                                   | a,c                                              | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+

doc/src/fix_adapt_fep.rst

@@ -120,7 +120,7 @@ styles and their energy formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`born <pair_born>`                                                      | a,b,c                   | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
-| :doc:`buck <pair_buck>`                                                      | a,c                     | type pairs |
+| :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm  <pair_buck>`       | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`buck/mdf <pair_mdf>`                                                   | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+

src/KSPACE/pair_buck_coul_long.cpp

@@ -558,5 +558,8 @@ void *PairBuckCoulLong::extract(const char *str, int &dim)
 {
   dim = 0;
   if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
+  dim = 2;
+  if (strcmp(str,"a") == 0) return (void *) a;
+  if (strcmp(str,"c") == 0) return (void *) c;
   return nullptr;
 }

src/KSPACE/pair_buck_coul_msm.cpp

@@ -246,5 +246,9 @@ void *PairBuckCoulMSM::extract(const char *str, int &dim)
 {
   dim = 0;
   if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
+  dim = 2;
+  if (strcmp(str,"a") == 0) return (void *) a;
+  if (strcmp(str,"c") == 0) return (void *) c;
+
   return nullptr;
 }

src/pair_buck_coul_cut.cpp

@@ -470,3 +470,13 @@ double PairBuckCoulCut::single(int i, int j, int itype, int jtype,
   }
   return eng;
 }
+
+/* ---------------------------------------------------------------------- */
+
+void *PairBuckCoulCut::extract(const char *str, int &dim)
+{
+  dim = 2;
+  if (strcmp(str,"a") == 0) return (void *) a;
+  if (strcmp(str,"c") == 0) return (void *) c;
+  return nullptr;
+}

src/pair_buck_coul_cut.h

@@ -40,6 +40,7 @@ class PairBuckCoulCut : public Pair {
   void write_data(FILE *);
   void write_data_all(FILE *);
   virtual double single(int, int, int, int, double, double, double, double &);
+  void *extract(const char *, int &);
 
  protected:
   double cut_lj_global,cut_coul_global;

unittest/force-styles/tests/mol-pair-buck_coul_cut.yaml

@@ -25,7 +25,9 @@ pair_coeff: ! |
   4 4 127198.698386798 0.207005479340455 37.2289658745028
   4 5 127198.698386798 0.207005479340455 37.2289658745028
   5 5 127198.698386798 0.207005479340455 37.2289658745028
-extract: ! ""
+extract: |
+  a 2
+  c 2
 natoms: 29
 init_vdwl: 143.749538808172
 init_coul: -127.494586297384

unittest/force-styles/tests/mol-pair-buck_coul_long.yaml

@@ -30,7 +30,9 @@ pair_coeff: ! |
   4 4 127198.698386798 0.207005479340455 37.2289658745028
   4 5 127198.698386798 0.207005479340455 37.2289658745028
   5 5 127198.698386798 0.207005479340455 37.2289658745028
-extract: ! ""
+extract: |
+  a 2
+  c 2
 natoms: 29
 init_vdwl: 143.749538808172
 init_coul: 225.821815126925

unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml

@@ -32,7 +32,9 @@ pair_coeff: ! |
   4 4 127198.698386798 0.207005479340455 37.2289658745028
   4 5 127198.698386798 0.207005479340455 37.2289658745028
   5 5 127198.698386798 0.207005479340455 37.2289658745028
-extract: ! ""
+extract: |
+  a 2
+  c 2
 natoms: 29
 init_vdwl: 143.749538808172
 init_coul: 226.465163473713

unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml

@@ -32,7 +32,9 @@ pair_coeff: ! |
   4 4 127198.698386798 0.207005479340455 37.2289658745028
   4 5 127198.698386798 0.207005479340455 37.2289658745028
   5 5 127198.698386798 0.207005479340455 37.2289658745028
-extract: ! ""
+extract: |
+  a 2
+  c 2
 natoms: 29
 init_vdwl: 143.749538808172
 init_coul: 226.465163473713

unittest/force-styles/tests/mol-pair-buck_coul_table.yaml

@@ -30,7 +30,9 @@ pair_coeff: ! |
   4 4 127198.698386798 0.207005479340455 37.2289658745028
   4 5 127198.698386798 0.207005479340455 37.2289658745028
   5 5 127198.698386798 0.207005479340455 37.2289658745028
-extract: ! ""
+extract: |
+  a 2
+  c 2
 natoms: 29
 init_vdwl: 143.749538808172
 init_coul: 225.821851347828