new SNAP potentials and examples

doc/src/read_restart.txt

@@ -178,7 +178,7 @@ not the same and the current value is not the default.
 Note that some force field styles (pair, bond, angle, etc) do not
 store their coefficient info in restart files.  Typically these are
 many-body or tabulated potentials which read their parameters from
-separate files.  In these cases you will need to re-specify the "pair
+separate files.  In these cases you will need to re-specify the
 "pair_coeff"_pair_coeff.html, "bond_coeff"_bond_coeff.html, etc
 commands in your restart input script.  The doc pages for individual
 force field styles mention if this is the case.  This is also true of

examples/snap/Mo_Chen_PRM2017.snap

@@ -0,0 +1,7 @@
+
+# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# Generated by Materials Virtual Lab
+# Definition of SNAP potential.
+pair_style snap 
+pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
+

examples/snap/Mo_Chen_PRM2017.snapcoeff

@@ -0,0 +1,35 @@
+# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# Generated by Materials Virtual Lab
+1 31
+Mo 0.5 1
+-17.2757958404
+0.00431015861472
+0.0657685117891
+0.477733335702
+0.0152688837211
+0.77559888196
+0.284846429566
+0.148804982644
+0.0573702179736
+0.19281989434
+0.323441703578
+0.101324335724
+0.0139639846514
+-0.0324444749083
+0.0349797952779
+0.0613023441282
+0.0881078513046
+0.118716074611
+0.0069662975532
+-0.0174658914685
+-0.0178902177779
+0.0195993756659
+0.0719238160707
+0.0344832661036
+-0.0358616891662
+-0.0292380783172
+-0.0334933909866
+0.00595462520243
+0.0754556638328
+-0.000972545258845
+-0.0100170422751

examples/snap/Mo_Chen_PRM2017.snapparam

@@ -0,0 +1,4 @@
+# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# Generated by Materials Virtual Lab
+rcutfac 4.615858
+twojmax 6

examples/snap/in.snap.Mo_Chen

@@ -0,0 +1,45 @@
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.160
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary	p p p
+
+lattice         bcc $a
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box	1 box
+create_atoms	1 box
+
+mass 1 183.84
+
+# choose potential
+
+include Mo_Chen_PRM2017.snap
+
+# Setup output
+
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+

lib/voronoi/README

@@ -21,7 +21,7 @@ Instructions:
     tarball either in this /lib/voronoi directory
     or somewhere else on your system.
 
-2.  compile Voro++ from within its home directory
+2.  Compile Voro++ from within its home directory
     % make
 
 3.  There is no need to install Voro++ if you only wish

potentials/Mo_Chen_PRM2017.snap

@@ -0,0 +1,6 @@
+# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# Generated by Materials Virtual Lab
+# Definition of SNAP potential.
+pair_style snap 
+pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
+

potentials/Mo_Chen_PRM2017.snapcoeff

@@ -0,0 +1,35 @@
+# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# Generated by Materials Virtual Lab
+1 31
+Mo 0.5 1
+-17.2757958404
+0.00431015861472
+0.0657685117891
+0.477733335702
+0.0152688837211
+0.77559888196
+0.284846429566
+0.148804982644
+0.0573702179736
+0.19281989434
+0.323441703578
+0.101324335724
+0.0139639846514
+-0.0324444749083
+0.0349797952779
+0.0613023441282
+0.0881078513046
+0.118716074611
+0.0069662975532
+-0.0174658914685
+-0.0178902177779
+0.0195993756659
+0.0719238160707
+0.0344832661036
+-0.0358616891662
+-0.0292380783172
+-0.0334933909866
+0.00595462520243
+0.0754556638328
+-0.000972545258845
+-0.0100170422751

potentials/Mo_Chen_PRM2017.snapparam

@@ -0,0 +1,4 @@
+# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# Generated by Materials Virtual Lab
+rcutfac 4.615858
+twojmax 6

src/compute_centro_atom.cpp

@@ -39,7 +39,8 @@ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
   distsq(NULL), nearest(NULL), centro(NULL)
 {
-  if (narg < 4 || narg > 6) error->all(FLERR,"Illegal compute centro/atom command");
+  if (narg < 4 || narg > 6) 
+    error->all(FLERR,"Illegal compute centro/atom command");
 
   if (strcmp(arg[3],"fcc") == 0) nnn = 12;
   else if (strcmp(arg[3],"bcc") == 0) nnn = 8;
@@ -54,7 +55,8 @@ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
   int iarg = 4;
   while (iarg < narg) {
     if (strcmp(arg[iarg],"axes") == 0) {
-      if (iarg+2 > narg) error->all(FLERR,"Illegal compute centro/atom command3");
+      if (iarg+2 > narg) 
+        error->all(FLERR,"Illegal compute centro/atom command3");
       if (strcmp(arg[iarg+1],"yes") == 0) axes_flag = 1;
       else if (strcmp(arg[iarg+1],"no") == 0) axes_flag = 0;
       else error->all(FLERR,"Illegal compute centro/atom command2");
@@ -137,7 +139,8 @@ void ComputeCentroAtom::compute_peratom()
       memory->destroy(array_atom);
       nmax = atom->nmax;
       memory->create(centro,nmax,"centro/atom:centro");
-      memory->create(array_atom,nmax,size_peratom_cols,"centro/atom:array_atom");
+      memory->create(array_atom,nmax,size_peratom_cols,
+                     "centro/atom:array_atom");
     }
   }
 
@@ -320,6 +323,7 @@ void ComputeCentroAtom::compute_peratom()
     }
 }
 
+
 /* ----------------------------------------------------------------------
    2 select routines from Numerical Recipes (slightly modified)
    find k smallest values in array of length n
@@ -434,5 +438,6 @@ void ComputeCentroAtom::select2(int k, int n, double *arr, int *iarr)
 double ComputeCentroAtom::memory_usage()
 {
   double bytes = nmax * sizeof(double);
+  if (axes_flag) bytes += size_peratom_cols*nmax * sizeof(double);
   return bytes;
 }