Update for multi cutoff and descriptors

CMakeLists.txt

@@ -112,6 +112,7 @@ FetchContent_Declare(
 FetchContent_MakeAvailable(Tadah.MD)
 
 add_library(tadah.lammps STATIC lammps_tadah.cpp)
+target_include_directories(tadah.lammps PRIVATE .)
 target_link_libraries(tadah.lammps PUBLIC tadah.md)
 target_link_libraries(tadah.lammps PUBLIC tadah.core)
 

ML-TADAH/Makefile.package.settings

@@ -13,4 +13,4 @@ models_src=$(dir)/_deps/tadah.models-src/include
 md_src=$(dir)/_deps/tadah.md-src/include
 cmrc_src=$(dir)/_cmrc/include
 
-tadah_inc=-I$(core_src) -I$(models_src) -I$(md_src) -I$(toml_src) -I$(cmrc_src)
\ No newline at end of file
+tadah_inc=-I$(core_src) -I$(models_src) -I$(md_src) -I$(toml_src) -I$(cmrc_src) -I../../lib/$(lib)

ML-TADAH/pair_tadah.h

@@ -11,6 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+/*----------------------------------------------------------------------*/
+/* Contributing author: Marcin Kirsz | marcin.kirsz@ed.ac.uk            */
+/* The University of Edinburgh       | https://git.ecdf.ed.ac.uk/tadah  */
+/*----------------------------------------------------------------------*/
+
 #ifdef PAIR_CLASS
 // clang-format off
 PairStyle(tadah,PairTadah)
@@ -21,7 +26,7 @@ PairStyle(tadah,PairTadah)
 #define LMP_PAIR_TADAH_H
 
 #include "pair.h"
-#include "../../lib/tadah.lammps/lammps_tadah.h"
+#include <lammps_tadah.h>
 
 namespace LAMMPS_NS {
 
@@ -38,7 +43,7 @@ namespace LAMMPS_NS {
       void compute_dimers(int eflag, int vflag);
       std::vector<std::pair<int,int>> midx;
 
-      TADAH::LammpsTadah lt;
+      TADAH::LammpsTadah *lt=nullptr;
       int nmax=0;
       void allocate();
 

lammps_tadah.cpp

-#include "lammps_tadah.h"
+#include <lammps_tadah.h>
+#include <tadah/core/periodic_table.h>
 
 using namespace TADAH;
 
-// // Const Assignment operator
-// LammpsTadah &LammpsTadah::operator=(const LammpsTadah& lt)
-// {
-//   c=lt.c;
-//   norm=lt.norm;
-//   bias=lt.bias;
-//   dsize=lt.dsize;
-//   cutoff_max_sq=lt.cutoff_max_sq;
-//   cutoff_max=lt.cutoff_max;
-//   linear=lt.linear;
-//   dimer=lt.dimer;
-//   dimer_r=lt.dimer_r;
-//   dimer_bond_bool=lt.dimer_bond_bool;
-//   init2b=lt.init2b;
-//   initmb=lt.initmb;
-//   watom=lt.watom;
-//   S=lt.S;
-//   // We need deep copy for fb and model.
-//   // For now we just init them the same way
-//   // as constructor does
-//   fb = CONFIG::factory<Function_Base,Config&>(
-//       c.get<std::string>("MODEL",1),c);
-//   model = CONFIG::factory<M_MD_Base,Function_Base&,Config&>(
-//       c.get<std::string>("MODEL",0),*fb,c);
-//   aeds=lt.aeds;
-//   rhos=lt.rhos;
-//   return *this;
-// }
-LammpsTadah &LammpsTadah::operator=(LammpsTadah& lt)
-{
-  std::swap(c,lt.c);
-  std::swap(norm , lt.norm);
-  std::swap(bias,lt.bias);
-  std::swap(dsize,lt.dsize);
-  std::swap(cutoff_max_sq,lt.cutoff_max_sq);
-  std::swap(cutoff_max,lt.cutoff_max);
-  std::swap(linear,lt.linear);
-  std::swap(dimer,lt.dimer);
-  std::swap(dimer_r,lt.dimer_r);
-  std::swap(dimer_bond_bool,lt.dimer_bond_bool);
-  std::swap(init2b,lt.init2b);
-  std::swap(initmb,lt.initmb);
-  std::swap(watom,lt.watom);
-  S=lt.S;
-  std::swap(fb,lt.fb);
-  std::swap(model,lt.model);
-  aeds=lt.aeds;
-  rhos=lt.rhos;
-  return *this;
-}
-LammpsTadah::LammpsTadah():
-  fb(nullptr),
-  model(nullptr)
-{}
-
 LammpsTadah::LammpsTadah(int narg, char **arg):
   c(arg[2]),
   norm(c.get<bool>("NORM") && !(c("MODEL")[1]=="BF_Linear" || c("MODEL")[1]=="Kern_Linear")),
-  //bias(c.get<bool>("BIAS")),
   cutoff_max_sq(pow(c.get<double>("RCUTMAX"),2)),
   cutoff_max(c.get<double>("RCUTMAX")),
   linear(c("MODEL")[1]=="BF_Linear" || c("MODEL")[1]=="Kern_Linear"),
@@ -70,26 +15,23 @@ LammpsTadah::LammpsTadah(int narg, char **arg):
   init2b(c.get<bool>("INIT2B")),
   initmb(c.get<bool>("INITMB")),
   S(c),
-  fb(nullptr),
-  model(nullptr)
+  fb(CONFIG::factory<Function_Base,Config&>(
+    c.get<std::string>("MODEL",1),c)),
+  model(CONFIG::factory<M_MD_Base,Function_Base&,Config&>(
+    c.get<std::string>("MODEL",0),*fb,c))
 {
-  // check does pot file exists
-  std::ifstream f(arg[2]);
-  if(!f.good())
-    throw std::runtime_error("Pot file does not exists.\n");
-
   // Map LAMMPS atom types to weight factors
   // e.g. pair_coaeff * * pot.tadah Ti Nb NULL
-  watom.resize(narg-3); // this includes NULL values
+  // watom.resize(narg-3); // this includes NULL values
+  Z.resize(narg-3); // this includes NULL values
                         // which want be set
-
   for (int i=3; i<narg; ++i) {
     std::string symbol=arg[i];
     if (symbol=="NULL") continue;
     size_t j=0;
     for (j=0; j<c.size("ATOMS"); ++j) {
       if (c.get<std::string>("ATOMS", j)==symbol) {
-        watom[i-3] = c.get<double>("WATOMS",j);
+        Z[i-3] = PeriodicTable::find_by_symbol(symbol).Z;
         break;
       }
     }
@@ -97,11 +39,6 @@ LammpsTadah::LammpsTadah(int narg, char **arg):
       throw std::runtime_error("Symbol not in potential file: "+symbol);
   }
 
-  fb = CONFIG::factory<Function_Base,Config&>(
-      c.get<std::string>("MODEL",1),c);
-  model = CONFIG::factory<M_MD_Base,Function_Base&,Config&>(
-      c.get<std::string>("MODEL",0),*fb,c);
-
   // bias affects position of fidx for descriptors
   if (c.get<bool>("BIAS"))
     bias++;
@@ -121,6 +58,7 @@ LammpsTadah::LammpsTadah(int narg, char **arg):
     c.add("SIZEMB",S.dmb->size());
     dsize+=S.dmb->size();
     S.dmb->set_fidx(bias+S.d2b->size());
+    rsize = S.dmb->rhoi_size()+ S.dmb->rhoip_size();
   }
   else {
     c.add("SIZEMB",0);

lammps_tadah.h

@@ -14,59 +14,50 @@
 #include <iostream>
 #include <string>
 
-/**
- * LAMMPS INTERFACE
- */
 namespace TADAH {
-  class LammpsTadah {
-
-    public:
-      Config c;
-      bool norm;
-      size_t bias=0;
-      size_t dsize=0;
-      double cutoff_max_sq;
-      double cutoff_max;
-      bool linear;
-      bool dimer;
-      double dimer_r;
-      bool dimer_bond_bool;
-
-      bool init2b;
-      bool initmb;
-      std::vector<double> watom;
-
-      DC_Selector S;
-      Function_Base *fb=nullptr;
-      M_MD_Base *model=nullptr;
-
-      aeds_type2 aeds;
-      rhos_type rhos;
-
-      // Const Assignment operator
-      //LammpsTadah& operator=(const LammpsTadah& lt);
-
-      // Assignment operator
-      LammpsTadah& operator=(LammpsTadah& lt);
-
-      // Constructor:
-      LammpsTadah();
-      LammpsTadah(int narg, char **arg);
-
-      ~LammpsTadah();
-
-      int pack_reverse_linear(int n, int first, double *buf);
-      void unpack_reverse_linear(int n, int *list, double *buf);
-      // Pack the derivative of the embedding func
-      int pack_forward_linear(int n, int *list, double *buf);
-      // Unpack the derivative of the embedding func
-      void unpack_forward_linear(int n, int first, double *buf);
-      // NONLINEAR
-      int pack_reverse_nonlinear(int n, int first, double *buf);
-      void unpack_reverse_nonlinear(int n, int *list, double *buf);
-      int pack_forward_nonlinear(int n, int *list, double *buf);
-      void unpack_forward_nonlinear(int n, int first, double *buf);
-
-  };
+class LammpsTadah {
+
+public:
+  Config c;
+  bool norm;
+  size_t bias=0;
+  size_t dsize=0; // descriptor dim inc bias
+  size_t rsize=0; // rho dim inc derivative
+  double cutoff_max_sq;
+  double cutoff_max;
+  bool linear;
+  bool dimer;
+  double dimer_r;
+  bool dimer_bond_bool;
+
+  bool init2b;
+  bool initmb;
+  std::vector<int> Z;
+
+  DC_Selector S;
+  Function_Base *fb=nullptr;
+  M_MD_Base *model=nullptr;
+
+  aeds_type2 aeds;
+  rhos_type rhos;
+
+  LammpsTadah(int narg, char **arg);
+  ~LammpsTadah();
+  LammpsTadah(const LammpsTadah&) = delete;
+  LammpsTadah& operator=(const LammpsTadah&) = delete;
+
+  int pack_reverse_linear(int n, int first, double *buf);
+  void unpack_reverse_linear(int n, int *list, double *buf);
+  // Pack the derivative of the embedding func
+  int pack_forward_linear(int n, int *list, double *buf);
+  // Unpack the derivative of the embedding func
+  void unpack_forward_linear(int n, int first, double *buf);
+  // NONLINEAR
+  int pack_reverse_nonlinear(int n, int first, double *buf);
+  void unpack_reverse_nonlinear(int n, int *list, double *buf);
+  int pack_forward_nonlinear(int n, int *list, double *buf);
+  void unpack_forward_nonlinear(int n, int first, double *buf);
+
+};
 }
 #endif