implement scale. spline5 as smoothing function. fix bug of empty region

Author: Han Wang

source/CMakeLists.txt

@@ -3,6 +3,12 @@ project(DeePMD)
 
 find_package(Git)
 if(GIT_FOUND)
+  execute_process(
+    COMMAND git describe --tags --dirty
+    WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+    OUTPUT_VARIABLE GIT_SUMM
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+    )
   execute_process(
     COMMAND git log -1 --format=%h
     WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}

source/lib/include/ComputeDescriptor.h

@@ -968,7 +968,7 @@ void compute_descriptor_norot (vector<double > &			descrpt_a,
       double inr4 = inr2 * inr2;
       double inr3 = inr4 * nr;
       double sw, dsw;
-      cos_switch(sw, dsw, nr, rmin, rmax);
+      spline5_switch(sw, dsw, nr, rmin, rmax);
       int idx_deriv = nei_iter * 4 * 3;	// 4 components time 3 directions
       int idx_value = nei_iter * 4;	// 4 components
       // 4 value components

source/lib/include/version.h.in

@@ -10,8 +10,9 @@ const string global_float_prec="float";
 #endif
 
 const string global_install_prefix="@CMAKE_INSTALL_PREFIX@";
+const string global_git_summ="@GIT_SUMM@";
 const string global_git_hash="@GIT_HASH@";
 const string global_git_date="@GIT_DATE@";
 const string global_git_branch="@GIT_BRANCH@";
 const string global_tf_include_dir="@TensorFlow_INCLUDE_DIRS@";
-const string global_tf_lib_dir="@TensorFlow_LIBRARY_PATH@";
+const string global_tf_lib="@TensorFlow_LIBRARY@";

source/lib/src/NNPInter.cc

@@ -293,6 +293,13 @@ run_model (ENERGYTYPE &			dener,
 {
   unsigned nloc = nnpmap.get_type().size();
   unsigned nall = nloc + nghost;
+  if (nloc == 0) {
+    dener = 0;
+    dforce_.clear();
+    dvirial.resize(9);
+    fill(dvirial.begin(), dvirial.end(), 0.0);
+    return;
+  }
 
   std::vector<Tensor> output_tensors;
 
@@ -335,6 +342,15 @@ run_model (ENERGYTYPE &			dener,
 {
   unsigned nloc = nnpmap.get_type().size();
   unsigned nall = nloc + nghost;
+  if (nloc == 0) {
+    dener = 0;
+    dforce_.clear();
+    dvirial.resize(9);
+    fill(dvirial.begin(), dvirial.end(), 0.0);
+    datom_energy_.clear();
+    datom_virial_.clear();    
+    return;
+  }
 
   std::vector<Tensor> output_tensors;
 
@@ -418,12 +434,13 @@ NNPInter::
 print_summary(const string &pre) const
 {
   cout << pre << "installed to:       " + global_install_prefix << endl;
+  cout << pre << "source:             " + global_git_summ << endl;
   cout << pre << "source brach:       " + global_git_branch << endl;
   cout << pre << "source commit:      " + global_git_hash << endl;
   cout << pre << "source commit at:   " + global_git_date << endl;
   cout << pre << "build float prec:   " + global_float_prec << endl;
   cout << pre << "build with tf inc:  " + global_tf_include_dir << endl;
-  cout << pre << "build with tf lib:  " + global_tf_lib_dir << endl;
+  cout << pre << "build with tf lib:  " + global_tf_lib << endl;
 }
 
 

source/lmp/pair_nnp.cpp

@@ -45,6 +45,7 @@ PairNNP::PairNNP(LAMMPS *lmp)
   cutoff = 0.;
   numb_models = 0;
   out_freq = 0;
+  scale = NULL;
 
   // set comm size needed by this Pair
   comm_reverse = 1;
@@ -61,12 +62,13 @@ PairNNP::print_summary(const string pre) const
     nnp_inter.print_summary(pre);
     cout << pre << ">>> Info of lammps module:" << endl;
     cout << pre << "use deepmd-kit at:  " << STR_DEEPMD_ROOT << endl;
+    cout << pre << "source:             " << STR_GIT_SUMM << endl;
     cout << pre << "source branch:      " << STR_GIT_BRANCH << endl;
     cout << pre << "source commit:      " << STR_GIT_HASH << endl;
     cout << pre << "source commit at:   " << STR_GIT_DATE << endl;
     cout << pre << "build float prec:   " << STR_FLOAT_PREC << endl;
     cout << pre << "build with tf inc:  " << STR_TensorFlow_INCLUDE_DIRS << endl;
-    cout << pre << "build with tf lib:  " << STR_TensorFlow_LIBRARY_PATH << endl;
+    cout << pre << "build with tf lib:  " << STR_TensorFlow_LIBRARY << endl;
   }
 }
 
@@ -76,6 +78,7 @@ PairNNP::~PairNNP()
   if (allocated) {
     memory->destroy(setflag);
     memory->destroy(cutsq);
+    memory->destroy(scale);
   }
 }
 
@@ -342,19 +345,19 @@ void PairNNP::compute(int eflag, int vflag)
   // get force
   for (int ii = 0; ii < nall; ++ii){
     for (int dd = 0; dd < 3; ++dd){
-      f[ii][dd] += dforce[3*ii+dd];
+      f[ii][dd] += scale[1][1] * dforce[3*ii+dd];
     }
   }
 
   // accumulate energy and virial
-  if (eflag) eng_vdwl += dener;
+  if (eflag) eng_vdwl += scale[1][1] * dener;
   if (vflag) {
-    virial[0] += 1.0 * dvirial[0];
-    virial[1] += 1.0 * dvirial[4];
-    virial[2] += 1.0 * dvirial[8];
-    virial[3] += 1.0 * dvirial[3];
-    virial[4] += 1.0 * dvirial[6];
-    virial[5] += 1.0 * dvirial[7];
+    virial[0] += 1.0 * dvirial[0] * scale[1][1];
+    virial[1] += 1.0 * dvirial[4] * scale[1][1];
+    virial[2] += 1.0 * dvirial[8] * scale[1][1];
+    virial[3] += 1.0 * dvirial[3] * scale[1][1];
+    virial[4] += 1.0 * dvirial[6] * scale[1][1];
+    virial[5] += 1.0 * dvirial[7] * scale[1][1];
   }
 }
 
@@ -372,6 +375,7 @@ void PairNNP::allocate()
     setflag[i][i] = 1;
 
   memory->create(cutsq,n+1,n+1,"pair:cutsq");
+  memory->create(scale,n+1,n+1,"pair:scale");
 }
 
 void PairNNP::settings(int narg, char **arg)
@@ -425,6 +429,28 @@ void PairNNP::coeff(int narg, char **arg)
   if (!allocated) {
     allocate();
   }
+
+  int n = atom->ntypes;
+  int ilo,ihi,jlo,jhi;
+  ilo = 0;
+  jlo = 0;
+  ihi = n;
+  jhi = n;
+  if (narg == 2) {
+    force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+    force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+    if (ilo != 0 || jlo != 0 || ihi != n || jhi != n) {
+      error->all(FLERR,"deepmd requires that the scale should be set to all atom types, i.e. pair_coeff * *.");
+    }
+  }  
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo,i); j <= jhi; j++) {
+      if (i == j) {
+        setflag[i][i] = 1;
+      }
+      scale[i][j] = 1.0;
+    }
+  }  
 }
 
 
@@ -439,6 +465,9 @@ void PairNNP::init_style()
 
 double PairNNP::init_one(int i, int j)
 {
+  if (setflag[i][j] == 0) scale[i][j] = 1.0;
+  scale[j][i] = scale[i][j];
+
   return cutoff;
 }
 
@@ -480,7 +509,13 @@ void PairNNP::unpack_reverse_comm(int n, int *list, double *buf)
 
 void *PairNNP::extract(const char *str, int &dim)
 {
-  dim = 0;
-  if (strcmp(str,"cut_coul") == 0) return (void *) &cutoff;
+  if (strcmp(str,"cut_coul") == 0) {
+    dim = 0;
+    return (void *) &cutoff;
+  }
+  if (strcmp(str,"scale") == 0) {
+    dim = 2;
+    return (void *) scale;
+  }
   return NULL;
 }

source/lmp/pair_nnp.h.in

@@ -25,6 +25,7 @@ PairStyle(deepmd,PairNNP)
 #include <iostream>
 #include <fstream>
 
+#define GIT_SUMM @GIT_SUMM@
 #define GIT_HASH @GIT_HASH@
 #define GIT_BRANCH @GIT_BRANCH@
 #define GIT_DATE @GIT_DATE@
@@ -35,16 +36,17 @@ PairStyle(deepmd,PairNNP)
 #endif
 #define DEEPMD_ROOT @CMAKE_INSTALL_PREFIX@
 #define TensorFlow_INCLUDE_DIRS @TensorFlow_INCLUDE_DIRS@
-#define TensorFlow_LIBRARY_PATH @TensorFlow_LIBRARY_PATH@
+#define TensorFlow_LIBRARY @TensorFlow_LIBRARY@
 #define DPMD_CVT_STR(x) #x
 #define DPMD_CVT_ASSTR(X) DPMD_CVT_STR(X)
+#define STR_GIT_SUMM DPMD_CVT_ASSTR(GIT_SUMM)
 #define STR_GIT_HASH DPMD_CVT_ASSTR(GIT_HASH)
 #define STR_GIT_BRANCH DPMD_CVT_ASSTR(GIT_BRANCH)
 #define STR_GIT_DATE DPMD_CVT_ASSTR(GIT_DATE)
 #define STR_FLOAT_PREC DPMD_CVT_ASSTR(FLOAT_PREC)
 #define STR_DEEPMD_ROOT DPMD_CVT_ASSTR(DEEPMD_ROOT)
 #define STR_TensorFlow_INCLUDE_DIRS DPMD_CVT_ASSTR(TensorFlow_INCLUDE_DIRS)
-#define STR_TensorFlow_LIBRARY_PATH DPMD_CVT_ASSTR(TensorFlow_LIBRARY_PATH)
+#define STR_TensorFlow_LIBRARY DPMD_CVT_ASSTR(TensorFlow_LIBRARY)
 
 namespace LAMMPS_NS {
 
@@ -55,7 +57,7 @@ class PairNNP : public Pair {
   virtual void compute(int, int);
   virtual void *extract(const char *, int &);
   void settings(int, char **);
-  void coeff(int, char **);
+  virtual void coeff(int, char **);
   void init_style();
   double init_one(int i, int j);
   int pack_reverse_comm(int, int, double *);
@@ -64,6 +66,7 @@ class PairNNP : public Pair {
 
  protected:  
   virtual void allocate();
+  double **scale;
 
 private:  
   NNPInter nnp_inter;

source/train/RunOptions.py.in

@@ -20,6 +20,7 @@ else :
     global_float_prec = 'float'
 
 global_install_prefix='@CMAKE_INSTALL_PREFIX@'
+global_git_summ='@GIT_SUMM@'
 global_git_hash='@GIT_HASH@'
 global_git_date='@GIT_DATE@'
 global_git_branch='@GIT_BRANCH@'
@@ -166,6 +167,7 @@ class RunOptions (object) :
         msg = ""
         msg += "---Summary of the training---------------------------------------\n"
         msg += 'installed to:       %s\n' % global_install_prefix
+        msg += 'source :            %s\n' % global_git_summ
         msg += 'source brach:       %s\n' % global_git_branch
         msg += 'source commit:      %s\n' % global_git_hash
         msg += 'source commit at:   %s\n' % global_git_date