doc

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/SNAP/pair_snap.cpp

@@ -165,6 +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]);