Merge pull request #2828 from tomswinburne/snap-scale

Adding scale parameter to pair/snap for fix/adapt

doc/src/fix_adapt.rst

@@ -188,6 +188,8 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`reax/c <pair_reaxc>`                                                   | chi, eta, gamma                                  | type global |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`snap <pair_snap>`                                                      | scale                                            | type pairs  |
++------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`spin/dmi <pair_spin_dmi>`                                              | coulombic_cutoff                                 | type global |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`spin/exchange <pair_spin_exchange>`                                    | coulombic_cutoff                                 | type global |

doc/src/fix_adapt_fep.rst

@@ -173,10 +173,12 @@ styles and their energy formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>`                           | e0,r0,nn,mm             | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
-| :doc:`ufm <pair_ufm>`                                                        | epsilon,sigma,scale     | type pairs |
+| :doc:`snap <pair_snap>`                                                      | scale                   | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`soft <pair_soft>`                                                      | a                       | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
+| :doc:`ufm <pair_ufm>`                                                        | epsilon,sigma,scale     | type pairs |
++------------------------------------------------------------------------------+-------------------------+------------+
 
 .. note::
 

examples/snap/Ni_Zuo_JPCA2020.quadratic.snapcoeff

@@ -0,0 +1 @@
+../../potentials/Ni_Zuo_JPCA2020.quadratic.snapcoeff

examples/snap/Ni_Zuo_JPCA2020.quadratic.snapparam

@@ -0,0 +1 @@
+../../potentials/Ni_Zuo_JPCA2020.quadratic.snapparam

examples/snap/Ni_Zuo_JPCA2020.snapcoeff

@@ -0,0 +1 @@
+../../potentials/Ni_Zuo_JPCA2020.snapcoeff

examples/snap/Ni_Zuo_JPCA2020.snapparam

@@ -0,0 +1 @@
+../../potentials/Ni_Zuo_JPCA2020.snapparam

examples/snap/in.snap.scale.Ni_Zuo_JCPA2020

@@ -0,0 +1,53 @@
+# Toy demonstration of SNAP "scale" parameter, using fix/adapt and hybrid/overlay
+# Mixing linear and quadratic SNAP Ni potentials by Zuo et al. JCPA 2020
+
+# mixing parameter
+
+variable lambda equal 0.2
+
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 3
+variable a equal 3.52
+units           metal
+
+# generate the box and atom positions using a FCC lattice
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary        p p p
+
+lattice         fcc $a
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      1 box
+create_atoms    1 box
+
+mass 1 34.
+
+# choose bundled SNAP Ni potential from Zuo et al. JCPA 2020
+pair_style hybrid/overlay snap snap
+pair_coeff * * snap 1 Ni_Zuo_JPCA2020.snapcoeff Ni_Zuo_JPCA2020.snapparam Ni
+pair_coeff * * snap 2 Ni_Zuo_JPCA2020.quadratic.snapcoeff Ni_Zuo_JPCA2020.quadratic.snapparam Ni
+
+# scale according to mixing parameter
+variable l1 equal ${lambda}
+variable l2 equal 1.0-${lambda}
+fix scale1 all adapt 1 pair snap:1 scale * * v_l1
+fix scale2 all adapt 1 pair snap:2 scale * * v_l2
+
+# Setup output
+thermo          1
+thermo_modify norm yes
+
+# Set up NVE run
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+# Run MD
+velocity all create 300.0 4928459 loop geom
+fix 1 all nve
+run             ${nsteps}

src/ML-SNAP/pair_snap.cpp

@@ -70,6 +70,7 @@ PairSNAP::~PairSNAP()
   if (allocated) {
     memory->destroy(setflag);
     memory->destroy(cutsq);
+    memory->destroy(scale);
   }
 
 }
@@ -164,6 +165,7 @@ void PairSNAP::compute(int eflag, int vflag)
     // for neighbors of I within cutoff:
     // compute Fij = dEi/dRj = -dEi/dRi
     // add to Fi, subtract from Fj
+    // scaling is that for type I
 
     snaptr->compute_yi(beta[ii]);
 
@@ -178,12 +180,12 @@ void PairSNAP::compute(int eflag, int vflag)
 
       snaptr->compute_deidrj(fij);
 
-      f[i][0] += fij[0];
-      f[i][1] += fij[1];
-      f[i][2] += fij[2];
-      f[j][0] -= fij[0];
-      f[j][1] -= fij[1];
-      f[j][2] -= fij[2];
+      f[i][0] += fij[0]*scale[itype][itype];
+      f[i][1] += fij[1]*scale[itype][itype];
+      f[i][2] += fij[2]*scale[itype][itype];
+      f[j][0] -= fij[0]*scale[itype][itype];
+      f[j][1] -= fij[1]*scale[itype][itype];
+      f[j][2] -= fij[2]*scale[itype][itype];
 
       // tally per-atom virial contribution
 
@@ -224,6 +226,7 @@ void PairSNAP::compute(int eflag, int vflag)
           }
         }
       }
+      evdwl *= scale[itype][itype];
       ev_tally_full(i,2.0*evdwl,0.0,0.0,0.0,0.0,0.0);
     }
 
@@ -351,9 +354,9 @@ void PairSNAP::allocate()
 {
   allocated = 1;
   int n = atom->ntypes;
-
   memory->create(setflag,n+1,n+1,"pair:setflag");
   memory->create(cutsq,n+1,n+1,"pair:cutsq");
+  memory->create(scale,n+1,n+1,"pair:scale");
   map = new int[n+1];
 }
 
@@ -408,11 +411,16 @@ void PairSNAP::coeff(int narg, char **arg)
   }
 
   // Calculate maximum cutoff for all elements
-
   rcutmax = 0.0;
   for (int ielem = 0; ielem < nelements; ielem++)
     rcutmax = MAX(2.0*radelem[ielem]*rcutfac,rcutmax);
 
+  // set default scaling
+  int n = atom->ntypes;
+  for (int ii = 0; ii < n+1; ii++)
+    for (int jj = 0; jj < n+1; jj++)
+      scale[ii][jj] = 1.0;
+
 }
 
 /* ----------------------------------------------------------------------
@@ -441,6 +449,7 @@ void PairSNAP::init_style()
 double PairSNAP::init_one(int i, int j)
 {
   if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+  scale[j][i] = scale[i][j];
   return (radelem[map[i]] +
           radelem[map[j]])*rcutfac;
 }
@@ -711,6 +720,7 @@ double PairSNAP::memory_usage()
   int n = atom->ntypes+1;
   bytes += (double)n*n*sizeof(int);      // setflag
   bytes += (double)n*n*sizeof(double);   // cutsq
+  bytes += (double)n*n*sizeof(double);   // scale
   bytes += (double)n*sizeof(int);        // map
   bytes += (double)beta_max*ncoeff*sizeof(double); // bispectrum
   bytes += (double)beta_max*ncoeff*sizeof(double); // beta
@@ -720,3 +730,9 @@ double PairSNAP::memory_usage()
   return bytes;
 }
 
+void *PairSNAP::extract(const char *str, int &dim)
+{
+  dim = 2;
+  if (strcmp(str,"scale") == 0) return (void *) scale;
+  return nullptr;
+}

src/ML-SNAP/pair_snap.h

@@ -34,6 +34,7 @@ class PairSNAP : public Pair {
   virtual void init_style();
   virtual double init_one(int, int);
   virtual double memory_usage();
+  virtual void *extract(const char *, int &);
 
   double rcutfac, quadraticflag;    // declared public to workaround gcc 4.9
   int ncoeff;                       //  compiler bug, manifest in KOKKOS package
@@ -55,6 +56,7 @@ class PairSNAP : public Pair {
   double **coeffelem;     // element bispectrum coefficients
   double **beta;          // betas for all atoms in list
   double **bispectrum;    // bispectrum components for all atoms in list
+  double **scale;               // for thermodynamic integration
   int twojmax, switchflag, bzeroflag, bnormflag;
   int chemflag, wselfallflag;
   int chunksize;

unittest/force-styles/tests/manybody-pair-snap.yaml

@@ -14,7 +14,8 @@ pair_style: hybrid/overlay zbl 4.0 4.8 snap
 pair_coeff: ! |
   1*8 1*8 zbl 73 73
   * * snap Ta06A.snapcoeff Ta06A.snapparam Ta Ta Ta Ta Ta Ta Ta Ta
-extract: ! ""
+extract: ! |
+  scale 2
 natoms: 64
 init_vdwl: -473.569864629026
 init_coul: 0

unittest/force-styles/tests/manybody-pair-snap_chem.yaml

@@ -16,7 +16,8 @@ pair_coeff: ! |
   1*4 5*8 zbl 49 15
   5*8 5*8 zbl 15 15
   * * snap InP_JCPA2020.snapcoeff InP_JCPA2020.snapparam In In In In P P P P
-extract: ! ""
+extract: ! |
+  scale 2
 natoms: 64
 init_vdwl: -185.3871232982
 init_coul: 0