From ffe13c502e5c288efdc0515d60cefbabe3e54e2f Mon Sep 17 00:00:00 2001
From: Lenz Fiedler <l.fiedler@hzdr.de>
Date: Fri, 15 Nov 2024 11:17:31 +0100
Subject: [PATCH] Bispectrum descriptor calculation for two elements in
 principle works

---
 mala/descriptors/bispectrum.py                  | 17 ++++++++++++++++-
 .../{in.bgrid.python => in.bgrid_n1.python}     |  0
 ...id.twoelements.python => in.bgrid_n2.python} |  2 +-
 3 files changed, 17 insertions(+), 2 deletions(-)
 rename mala/descriptors/{in.bgrid.python => in.bgrid_n1.python} (100%)
 rename mala/descriptors/{in.bgrid.twoelements.python => in.bgrid_n2.python} (96%)

diff --git a/mala/descriptors/bispectrum.py b/mala/descriptors/bispectrum.py
index 207fac341..691012cff 100755
--- a/mala/descriptors/bispectrum.py
+++ b/mala/descriptors/bispectrum.py
@@ -137,6 +137,12 @@ def __calculate_lammps(self, outdir, **kwargs):
         # general LAMMPS import.
         from lammps import constants as lammps_constants
 
+        if len(set(self.atoms.numbers)) > 2:
+            raise ValueError(
+                "MALA can only compute bispectrum descriptors for 1- or "
+                "2-element systems currently."
+            )
+
         use_fp64 = kwargs.get("use_fp64", False)
         keep_logs = kwargs.get("keep_logs", False)
 
@@ -173,7 +179,10 @@ def __calculate_lammps(self, outdir, **kwargs):
                     )
             else:
                 self.parameters.lammps_compute_file = os.path.join(
-                    filepath, "in.bgrid.python"
+                    filepath,
+                    "in.bgrid_n{0}.python".format(
+                        len(set(self.atoms.numbers))
+                    ),
                 )
 
         # Do the LAMMPS calculation and clean up.
@@ -279,6 +288,12 @@ def __calculate_python(self, **kwargs):
             "large systems."
         )
 
+        if len(set(self.atoms.numbers)) > 1:
+            raise ValueError(
+                " MALA cannot compute bispectrum descriptors for "
+                "multi-element systems with python currently."
+            )
+
         # The entire bispectrum calculation may be extensively profiled.
         profile_calculation = kwargs.get("profile_calculation", False)
         if profile_calculation:
diff --git a/mala/descriptors/in.bgrid.python b/mala/descriptors/in.bgrid_n1.python
similarity index 100%
rename from mala/descriptors/in.bgrid.python
rename to mala/descriptors/in.bgrid_n1.python
diff --git a/mala/descriptors/in.bgrid.twoelements.python b/mala/descriptors/in.bgrid_n2.python
similarity index 96%
rename from mala/descriptors/in.bgrid.twoelements.python
rename to mala/descriptors/in.bgrid_n2.python
index 941948acd..82d22b7ab 100644
--- a/mala/descriptors/in.bgrid.twoelements.python
+++ b/mala/descriptors/in.bgrid_n2.python
@@ -43,7 +43,7 @@ compute bgrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} ${rcutfac} ${rfac0
 
 
 # is this important? or does it just need to be big enough?
-variable rcutneigh equal 2.0*${rcutfac}*${radelem}
+variable rcutneigh equal 2.0*${rcutfac}*${radelem1}
 # for water
 #variable rcutneigh equal 4.0*${rcutfac}*${radelem1}