From 13fa49837182b4428f6b36acf812798d5e21620b Mon Sep 17 00:00:00 2001
From: qzhu2017 <alecfans@gmail.com>
Date: Sat, 10 Feb 2024 23:43:06 -0500
Subject: [PATCH] update the function of get_forcefield

---
 doc/Installation.rst   | 2 +-
 pyxtal/__init__.py     | 7 ++++++-
 requirements.txt       | 1 +
 scripts/pyxtal_main.py | 2 +-
 4 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/doc/Installation.rst b/doc/Installation.rst
index fffeec17..ee0c371b 100644
--- a/doc/Installation.rst
+++ b/doc/Installation.rst
@@ -53,7 +53,7 @@ or make a copy of the source code, and then install it manually.
 
     $ git clone https://github.com/qzhu2017/pyxtal
     $ cd pyxtal
-    $ python setup.py install
+    $ pip install .
 
 
 or update the code to our developing version
diff --git a/pyxtal/__init__.py b/pyxtal/__init__.py
index c48612a0..15ec4cf3 100644
--- a/pyxtal/__init__.py
+++ b/pyxtal/__init__.py
@@ -3002,7 +3002,7 @@ def to_atomic_xtal(self):
 
 
     def get_forcefield(self, ff_style='openff', code='lammps',
-                       chargemethod='am1bcc'):
+                       chargemethod='am1bcc', parameters=None):
         """
         An interface to create forcefield for molecular simulation with
         - Charmm
@@ -3014,6 +3014,7 @@ def get_forcefield(self, ff_style='openff', code='lammps',
             - ff_style: 'gaff' or 'openff'
             - code: 'lammps' or 'charmm'
             - charge_method: 'am1bcc', 'am1-mulliken', 'mmff94', 'gasteiger'
+            - parameters: 1D-array of user-specified FF parameters
 
         Returns:
             An ase_atoms_objects with force field information
@@ -3055,6 +3056,10 @@ def get_forcefield(self, ff_style='openff', code='lammps',
             # Initialize the forcefield instance from ost
             ff = forcefield(smiles, style=ff_style, chargemethod=chargemethod)
 
+            # update the parameters from the user
+            if parameters is not None:
+                ff.update_parameters(parameters)
+
             # Create the Parmed to handle FF parameters
             if sum(n_mols) == 1:
                 pd_struc = ff.molecules[0].copy(cls=ParmEdStructure)
diff --git a/requirements.txt b/requirements.txt
index 952858f6..39212b15 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,3 +5,4 @@ networkx>=2.3
 scipy>=1.7.3
 importlib_metadata>=1.4
 ase>=3.18.0
+monty==2023.11.3
diff --git a/scripts/pyxtal_main.py b/scripts/pyxtal_main.py
index 10f8678a..704fcd2d 100755
--- a/scripts/pyxtal_main.py
+++ b/scripts/pyxtal_main.py
@@ -140,7 +140,7 @@
             rand_crystal.from_random(3, sg, system, numIons0, factor, conventional=conventional)
         elif dimension == 2:
             rand_crystal.from_random(2, sg, system, numIons0, factor, thickness, conventional=conventional)
-        elif dimension == 1:                                             
+        elif dimension == 1:
             rand_crystal.from_random(1, sg, system, numIons0, factor, thickness, conventional=conventional)
         if dimension == 0:
             rand_crystal.from_random(0, sg, system, numIons0, factor)