From 148edc0a9b6fc151eeac7d3d20d5ba1139afccf3 Mon Sep 17 00:00:00 2001
From: Clara Fontaine <42681983+clarayfontaine@users.noreply.github.com>
Date: Wed, 26 Apr 2023 04:20:00 +0800
Subject: [PATCH] Correctly select a few modes in analyze_variation (#149)

* Fix mode selection in analyze_variation

Addressing issue #148: analyze_variation incorrectly chooses Pj, Sj, Om, PHI_zpf when passed a subset of modes

* Remove redundant frequency selection

The frequencies are already correctly selected outside of this if-statement, so this is not necessary
---
 pyEPR/core_quantum_analysis.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/pyEPR/core_quantum_analysis.py b/pyEPR/core_quantum_analysis.py
index 3b9b5af..1b936c5 100644
--- a/pyEPR/core_quantum_analysis.py
+++ b/pyEPR/core_quantum_analysis.py
@@ -664,11 +664,10 @@ def analyze_variation(self,
             PJ_cap = PJ_cap[:, junctions]
 
         if modes is not None:
-            freqs_hfss = freqs_hfss[range(len(self.modes[variation])), ]
-            PJ = PJ[range(len(modes)), :]
-            SJ = SJ[range(len(modes)), :]
-            Om = Om[range(len(modes)), :][:, range(len(modes))]
-            PHI_zpf = PHI_zpf[range(len(modes)), :]
+            PJ = PJ[modes, :]
+            SJ = SJ[modes, :]
+            Om = Om[modes, :][:, modes]
+            PHI_zpf = PHI_zpf[modes, :]
             PJ_cap = PJ_cap[:, junctions]
 
         # Analytic 4-th order