From c525f4539b98512e0d7ef94cf254cd79098d9054 Mon Sep 17 00:00:00 2001
From: Pierre Beaujean <pierreb24@gmail.com>
Date: Thu, 14 Mar 2024 16:26:29 +0100
Subject: [PATCH] add command line option

---
 phonopy_vibspec/scripts/__init__.py      | 2 ++
 phonopy_vibspec/scripts/prepare_raman.py | 1 +
 phonopy_vibspec/scripts/spectrum_ir.py   | 3 ++-
 phonopy_vibspec/scripts/vesta_modes.py   | 1 +
 4 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/phonopy_vibspec/scripts/__init__.py b/phonopy_vibspec/scripts/__init__.py
index 377dd53..873f3ca 100644
--- a/phonopy_vibspec/scripts/__init__.py
+++ b/phonopy_vibspec/scripts/__init__.py
@@ -17,6 +17,8 @@ def add_common_args(parser: argparse.ArgumentParser):
 
     parser.add_argument('-m', '--modes', type=list_of_modes, help='List of modes (1-based)', default='')
 
+    parser.add_argument('-O', '--only', type=str, help='only consider certain atoms', default='')
+
 
 def interval(s_interval: str) -> Tuple[float, float]:
     """get interval
diff --git a/phonopy_vibspec/scripts/prepare_raman.py b/phonopy_vibspec/scripts/prepare_raman.py
index 796c070..00c801d 100644
--- a/phonopy_vibspec/scripts/prepare_raman.py
+++ b/phonopy_vibspec/scripts/prepare_raman.py
@@ -23,6 +23,7 @@ def main():
     phonons = PhononsAnalyzer.from_phonopy(
         phonopy_yaml=args.phonopy,
         force_constants_filename=args.fc,
+        only=args.only if args.only != '' else None
     )
 
     raman_spectrum = phonons.prepare_raman(
diff --git a/phonopy_vibspec/scripts/spectrum_ir.py b/phonopy_vibspec/scripts/spectrum_ir.py
index 83ca134..b2a4df0 100644
--- a/phonopy_vibspec/scripts/spectrum_ir.py
+++ b/phonopy_vibspec/scripts/spectrum_ir.py
@@ -21,7 +21,8 @@ def main():
     phonons = PhononsAnalyzer.from_phonopy(
         phonopy_yaml=args.phonopy,
         force_constants_filename=args.fc,
-        born_filename=args.born
+        born_filename=args.born,
+        only=args.only if args.only != '' else None
     )
 
     ir_spectrum = phonons.infrared_spectrum(modes=args.modes if len(args.modes) > 0 else None)
diff --git a/phonopy_vibspec/scripts/vesta_modes.py b/phonopy_vibspec/scripts/vesta_modes.py
index fccdc9c..90cdaea 100644
--- a/phonopy_vibspec/scripts/vesta_modes.py
+++ b/phonopy_vibspec/scripts/vesta_modes.py
@@ -47,6 +47,7 @@ def main():
     phonons = PhononsAnalyzer.from_phonopy(
         phonopy_yaml=args.phonopy,
         force_constants_filename=args.fc,
+        only=args.only if args.only != '' else None
     )
 
     phonons.make_vesta_for_modes(