Fix atom indices

Author: ericyuan00000

tests/000_P.xyz

@@ -6,13 +6,13 @@ C -1.2278682235707141 -0.795156965798265 -0.4432183279038852
 C -2.0921264024301207 0.3176621402769333 0.09334537173407473
 C 2.3023775671057063 1.32745759550386 -0.17248520260047165
 C 2.0684064033855525 0.1207003865216024 0.7236381973396382
-H 0.7831701727406736 -1.3461799398902923 -0.7974106982854509
 H 0.47551518860313274 0.3631877061845715 -1.1495875736140317
-H -1.486454321668363 -1.0467531948979716 -1.5062480723460925
+H 0.7831701727406736 -1.3461799398902923 -0.7974106982854509
 H -1.389625310873742 -1.7204756766551246 0.12998524585253302
-H -2.5102485859129042 0.030051843350409897 1.097502830276816
+H -1.486454321668363 -1.0467531948979716 -1.5062480723460925
+H -2.9587730905627216 0.4116902554652719 -0.6026348709098706
 H -1.5993809198749669 1.2897847257895312 0.13344740621889561
 H 1.6126174080090498 2.13649653535418 0.1376309609894206
-H -2.9587730905627216 0.4116902554652719 -0.6026348709098706
+H -2.5102485859129042 0.030051843350409897 1.097502830276816
 H 2.524381979112286 0.3027396265506924 1.7274513697747098
 H 2.5530163136758395 -0.7576444861190401 0.21669206414769768