Three elements in principle work, but atomic density formula not for …

…some reason

mala/descriptors/bispectrum.py

@@ -132,10 +132,10 @@ def __calculate_lammps(self, outdir, **kwargs):
         # general LAMMPS import.
         from lammps import constants as lammps_constants
 
-        if len(set(self._atoms.numbers)) > 2:
+        if len(set(self._atoms.numbers)) > 3:
             raise ValueError(
-                "MALA can only compute bispectrum descriptors for 1- or "
-                "2-element systems currently."
+                "MALA can only compute bispectrum descriptors up to "
+                "3-element systems currently."
             )
 
         use_fp64 = kwargs.get("use_fp64", False)

mala/descriptors/in.bgrid_n3.python

@@ -0,0 +1,57 @@
+# Calculate bispectrum descriptors on a 3D grid
+
+# pass in values ngridx, ngridy, ngridz, twojmax, rcutfac, atom_config_fname 
+# using command-line -var option
+
+# Initialize simulation
+
+units		metal
+
+read_data ${atom_config_fname} 
+
+mass * 1.0
+
+# Needs to be defined for Kokkos
+run_style verlet
+
+# define grid compute and atom compute
+
+group 		snapgroup type 1 2 3
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+
+#variable 	radelem equal 0.5
+variable 	radelem1 equal 0.5
+variable 	radelem2 equal 0.5
+variable 	radelem3 equal 0.5
+
+variable 	bzero equal 0
+variable 	quadratic equal 0
+
+#variable        snap_options string &
+#"${rcutfac} ${rfac0} ${twojmax} ${radelem} ${wj} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
+
+#compute bgrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} ${snap_options}
+
+compute bgrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${radelem3} ${wj1} ${wj2} ${wj3} rmin0 ${rmin0} bzeroflag ${bzero} quadraticflag ${quadratic} switchflag ${switch}
+
+
+# create dummy potential for neighbor list
+
+
+# is this important? or does it just need to be big enough?
+variable rcutneigh equal 2.0*${rcutfac}*${radelem1}
+# for water
+#variable rcutneigh equal 4.0*${rcutfac}*${radelem1}
+
+pair_style zero ${rcutneigh}
+pair_coeff * *
+
+# define output
+
+thermo_style	custom step temp ke pe vol c_bgrid[1][1]
+thermo_modify norm yes
+
+# run
+
+run 0

mala/descriptors/in.bgridlocal_defaultproc_n2.python

@@ -13,7 +13,7 @@ mass * 1.0
 
 # define grid compute and atom compute
 
-group 		snapgroup type 1
+group 		snapgroup type 1 2
 variable 	rfac0 equal 0.99363
 variable 	rmin0 equal 0
 # variable 	wj1 equal 1

mala/descriptors/in.bgridlocal_defaultproc_n3.python

@@ -0,0 +1,41 @@
+# Calculate bispectrum descriptors on a 3D grid
+
+# pass in values ngridx, ngridy, ngridz, twojmax, rcutfac, atom_config_fname
+# using command-line -var option
+
+# Initialize simulation
+
+units		metal
+
+read_data ${atom_config_fname}
+
+mass * 1.0
+
+# define grid compute and atom compute
+
+group 		snapgroup type 1 2 3
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	wj1local equal ${wj1}-1.0e-15 # inject a bit of fuzz
+variable 	wj2local equal ${wj2}-1.0e-15 # inject a bit of fuzz
+variable 	wj3local equal ${wj2}-1.0e-15 # inject a bit of fuzz
+variable 	radelem1 equal 0.5
+variable 	radelem2 equal 0.5
+variable 	radelem3 equal 0.5
+variable 	bzero equal 0
+variable 	quadratic equal 0
+
+compute bgridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${radelem3} ${wj1local} ${wj2local} ${wj3local}  rmin0 ${rmin0} bzeroflag ${bzero} quadraticflag ${quadratic} switchflag ${switch}
+
+# is this important? or does it just need to be big enough?
+
+variable rcutneigh equal 2.0*${rcutfac}*${radelem1}
+
+pair_style zero ${rcutneigh}
+pair_coeff * *
+
+# define output
+
+thermo_modify norm yes
+
+run 0

mala/descriptors/in.bgridlocal_n3.python

@@ -0,0 +1,46 @@
+# Calculate bispectrum descriptors on a 3D grid
+
+# pass in values ngridx, ngridy, ngridz, twojmax, rcutfac, atom_config_fname 
+# using command-line -var option
+
+# set up processor grid to match QE
+${lammps_procs}
+
+# Initialize simulation
+
+units		metal
+
+read_data ${atom_config_fname}
+
+mass * 1.0
+
+# is this important? or does it just need to be big enough?
+
+variable 	radelem1 equal 0.5
+variable 	radelem2 equal 0.5
+variable 	radelem3 equal 0.5
+variable rcutneigh equal 2.0*${rcutfac}*${radelem1}
+
+pair_style zero ${rcutneigh}
+pair_coeff * *
+
+# set up plane cutoff values to evenly distribute grid points
+
+${zbal}
+
+# define grid compute and atom compute
+
+group 		snapgroup type 1 2 3
+variable 	rfac0 equal 0.99363
+variable 	rmin0 equal 0
+variable 	wj1local equal ${wj1}-1.0e-15 # inject a bit of fuzz
+variable 	wj2local equal ${wj2}-1.0e-15 # inject a bit of fuzz
+variable 	wj3local equal ${wj2}-1.0e-15 # inject a bit of fuzz
+variable 	bzero equal 0
+variable 	quadratic equal 0
+
+compute bgridlocal all sna/grid/local grid ${ngridx} ${ngridy} ${ngridz} ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${radelem3} ${wj1local} ${wj2local} ${wj3local} rmin0 ${rmin0} bzeroflag ${bzero} quadraticflag ${quadratic} switchflag ${switch}
+
+thermo_modify norm yes
+
+run 0

mala/descriptors/in.ggrid_defaultproc_n3.python

@@ -0,0 +1,26 @@
+# Calculate Gaussian atomic density descriptors on a 3D grid
+
+# pass in values ngridx, ngridy, ngridz, sigma, atom_config_fname
+# using command-line -var option
+
+# Initialize simulation
+
+units		metal
+read_data ${atom_config_fname}
+mass * 1.0
+
+
+# is this important? or does it just need to be big enough?
+variable	radelem1 equal 0.5
+variable	radelem2 equal 0.5
+variable	radelem3 equal 0.5
+variable rcutneigh equal 2.0*${rcutfac}*${radelem1}
+
+pair_style zero ${rcutneigh}
+pair_coeff * *
+
+compute ggrid all gaussian/grid/local  grid ${ngridx} ${ngridy} ${ngridz}  ${rcutfac}  ${radelem1}  ${radelem2} ${radelem3} ${sigma1} ${sigma2} ${sigma3}
+
+thermo_modify norm yes
+
+run 0

mala/descriptors/in.ggrid_n3.python

@@ -0,0 +1,33 @@
+# Calculate Gaussian atomic density descriptors on a 3D grid
+
+# pass in values ngridx, ngridy, ngridz, sigma, atom_config_fname
+# using command-line -var option
+
+# set up processor grid to match QE
+${lammps_procs}
+
+# Initialize simulation
+
+units		metal
+read_data ${atom_config_fname}
+mass * 1.0
+
+
+# is this important? or does it just need to be big enough?
+variable	radelem1 equal 0.5
+variable	radelem2 equal 0.5
+variable	radelem3 equal 0.5
+variable rcutneigh equal 2.0*${rcutfac}*${radelem}
+
+pair_style zero ${rcutneigh}
+pair_coeff * *
+
+# set up plane cutoff values to evenly distribute grid points
+${zbal}
+
+
+compute ggrid all gaussian/grid/local  grid ${ngridx} ${ngridy} ${ngridz}  ${rcutfac}  ${radelem1}  ${radelem2}  ${radelem3}  ${sigma1} ${sigma2} ${sigma3}
+
+thermo_modify norm yes
+
+run 0