Added a test for bgrid/local

examples/snap/grid.local.py

@@ -0,0 +1,119 @@
+#!/Users/athomps/miniconda3/bin/python3.7
+#
+# An example of SNAP grid from LAMMPS Python interface
+#
+# https://lammps.sandia.gov/doc/Python_library.html
+
+
+from lammps import lammps, LMP_STYLE_LOCAL, LMP_SIZE_ROWS, LMP_SIZE_COLS, LMP_TYPE_ARRAY
+import lammps_utils
+
+from mpi4py import MPI
+comm = MPI.COMM_WORLD
+me = comm.Get_rank()
+nprocs = comm.Get_size()
+
+# define command line input variables
+
+ngridx = 2
+ngridy = 3
+ngridz = nprocs
+twojmax = 2
+
+lmp_cmdargs = ["-echo","screen"]
+lmp_cmdargs = lammps_utils.set_cmdlinevars(lmp_cmdargs,
+    {
+        "ngridx":ngridx,
+        "ngridy":ngridy,
+        "ngridz":ngridz,
+        "twojmax":twojmax
+        }
+    )
+
+# launch LAMMPS instance
+
+lmp = lammps(cmdargs=lmp_cmdargs)
+
+# run LAMMPS input script
+
+lmp.file("in.grid.python.local")
+
+# get quantities from LAMMPS 
+
+num_atoms = lmp.get_natoms() 
+
+# set things not accessible from LAMMPS
+
+# first 3 cols are x, y, z, coords
+
+ncols0 = 3 
+
+# analytical relation
+
+ncoeff = (twojmax+2)*(twojmax+3)*(twojmax+4)
+ncoeff = ncoeff // 24 # integer division
+ncols = ncols0+ncoeff
+
+# get B_0 at position (0,0,0) in 4 different ways
+
+# 1. from comute sna/atom
+
+bptr = lmp.extract_compute("b", 1, 2) # 1 = per-atom data, 2 = array
+print("b = ",bptr[0][0])
+
+# 2. from compute sna/grid
+
+bgridptr = lmp.extract_compute("bgrid", 0, 2) # 0 = style global, 2 = type array
+print("bgrid = ",bgridptr[0][3])
+
+# 3. from Numpy array pointing to sna/atom array
+ 
+bptr_np = lammps_utils.extract_compute_np(lmp,"b",1,2,(num_atoms,ncoeff))
+print("b_np = ",bptr_np[0][0])
+
+# 4. from Numpy array pointing to sna/grid array
+
+bgridptr_np = lammps_utils.extract_compute_np(lmp,"bgrid",0,2,(ngridz,ngridy,ngridx,ncols))
+print("bgrid_np = ",bgridptr_np[0][0][0][ncols0+0])
+
+# 5. from sna/grid/local array
+
+bgridlocalnrows = lmp.extract_compute("bgridlocal", LMP_STYLE_LOCAL, LMP_SIZE_ROWS)
+print("bgridlocal nrows = ",bgridlocalnrows)
+bgridlocalncols = lmp.extract_compute("bgridlocal", LMP_STYLE_LOCAL, LMP_SIZE_COLS)
+print("bgridlocal ncols = ",bgridlocalncols)
+bgridlocalptr = lmp.extract_compute("bgridlocal", LMP_STYLE_LOCAL, LMP_TYPE_ARRAY)
+print("bgridlocal = ",bgridlocalptr)
+print("bgridlocal[0][0] = ",bgridlocalptr[5][10])
+
+# print out the LAMMPS array to a file
+
+outfile = open("bgrid.dat",'w')
+igrid = 0
+for iz in range(ngridz):
+    for iy in range(ngridy):
+        for ix in range(ngridx):
+            outfile.write("x, y, z = %g %g %g\n" % 
+                          (bgridptr[igrid][0],
+                           bgridptr[igrid][1],
+                           bgridptr[igrid][2]))
+            for icoeff in range(ncoeff):
+                outfile.write("%g " % bgridptr[igrid][ncols0+icoeff])
+            outfile.write("\n")
+            igrid += 1
+outfile.close()
+
+# print out the Numpy array to a file
+
+outfile = open("bgrid_np.dat",'w')
+for iz in range(ngridz):
+    for iy in range(ngridy):
+        for ix in range(ngridx):
+            outfile.write("x, y, z = %g %g %g\n" % 
+                          (bgridptr_np[iz][iy][ix][0],
+                           bgridptr_np[iz][iy][ix][1],
+                           bgridptr_np[iz][iy][ix][2]))
+            for icoeff in range(ncoeff):
+                outfile.write("%g " % bgridptr_np[iz][iy][ix][ncols0+icoeff])
+            outfile.write("\n")
+outfile.close()

examples/snap/in.grid.python.local

@@ -0,0 +1,69 @@
+# Demonstrate bispectrum per-atom and grid computes
+
+# Invoked from grid.py
+# pass in values for ngridx, ngridy, ngridz, twojmax
+
+# Initialize simulation
+
+variable nsteps equal 0
+variable nrep equal 1
+variable a equal 3.316
+
+units		metal
+
+# make processor grid equal to nz
+
+processors 1 1 ${ngridz}
+
+# 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		custom ${a} a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5
+
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box	1 box
+create_atoms	1 box
+
+mass 1 180.88
+
+# define grid compute and atom compute
+
+group 		snapgroup type 1
+variable 	rcutfac equal 4.67637
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	wj equal 1
+variable 	radelem equal 0.5
+variable 	bzero equal 0
+variable 	quad equal 0
+variable 	switch equal 1
+
+compute b all sna/atom ${rcutfac} ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} bzeroflag ${bzero} quadraticflag ${quad} switchflag ${switch}
+
+compute bgrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} ${rcutfac} ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} bzeroflag ${bzero}	quadraticflag ${quad} switchflag ${switch}
+
+compute bgridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} ${rcutfac} ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} bzeroflag ${bzero}	quadraticflag ${quad} switchflag ${switch}
+
+# create dummy potential for neighbor list
+
+variable rcutneigh equal 2.0*${rcutfac}*${radelem}
+pair_style zero ${rcutneigh}
+pair_coeff * *
+
+# define output
+
+thermo_style	custom step temp ke pe vol c_bgrid[1][1]
+thermo_modify norm yes
+
+dump mydump_b all custom 1000 dump_b id c_b[*]
+
+dump mydump_bgridlocal all local 1000 dump_bgridlocal index c_bgridlocal[*]
+
+# run
+
+run 0