From 0348a873a838d78c098e8709a197e130fcb84b18 Mon Sep 17 00:00:00 2001
From: Adam Grofe <agrofe1417@gmail.com>
Date: Wed, 5 Feb 2025 14:39:34 -0800
Subject: [PATCH] Convert angstrom to bohr for qcschema (#657)

Co-authored-by: Adam Grofe <adamgrofe@microsoft.com>
---
 .../target/microsoft/elements/dft/target.py   |   3 +-
 ...les_success_input_data0_input_params0_.yml | 360 ++++-----
 ...les_success_input_data0_input_params1_.yml | 360 ++++-----
 ...les_success_input_data1_input_params0_.yml | 720 +++++++++---------
 ...les_success_input_data1_input_params1_.yml | 720 +++++++++---------
 ...les_success_input_data0_input_params0_.yml | 360 ++++-----
 ...les_success_input_data0_input_params1_.yml | 360 ++++-----
 ...les_success_input_data1_input_params0_.yml | 720 +++++++++---------
 ...les_success_input_data1_input_params1_.yml | 720 +++++++++---------
 ...les_success_input_data0_input_params0_.yml | 360 ++++-----
 ...les_success_input_data0_input_params1_.yml | 360 ++++-----
 ...les_success_input_data0_input_params2_.yml | 360 ++++-----
 ...les_success_input_data0_input_params3_.yml | 360 ++++-----
 ...les_success_input_data0_input_params4_.yml | 360 ++++-----
 ...les_success_input_data0_input_params5_.yml | 360 ++++-----
 ...les_success_input_data1_input_params0_.yml | 720 +++++++++---------
 ...les_success_input_data1_input_params1_.yml | 720 +++++++++---------
 ...les_success_input_data1_input_params2_.yml | 720 +++++++++---------
 ...les_success_input_data1_input_params3_.yml | 720 +++++++++---------
 ...les_success_input_data1_input_params4_.yml | 720 +++++++++---------
 ...les_success_input_data1_input_params5_.yml | 720 +++++++++---------
 ..._0_00___nH___1_00___1_00___1_00___n_n_.yml |   8 +-
 ...0_00___0_00_nH___1_00___1_00___1_00_n_.yml |   8 +-
 ...00___0_00_nH___1_00___1_00___1_00_n_n_.yml |   8 +-
 24 files changed, 5414 insertions(+), 5413 deletions(-)

diff --git a/azure-quantum/azure/quantum/target/microsoft/elements/dft/target.py b/azure-quantum/azure/quantum/target/microsoft/elements/dft/target.py
index 351796dd..a8794a01 100644
--- a/azure-quantum/azure/quantum/target/microsoft/elements/dft/target.py
+++ b/azure-quantum/azure/quantum/target/microsoft/elements/dft/target.py
@@ -195,6 +195,7 @@ def _xyz_to_qcschema_mol(self, file_data: str ) -> Dict[str, Any]:
             "geometry": [],
             "symbols": [],
         }
+        bohr_to_angstrom = 0.52917721092
         for line in lines:
             if line:
                 elements = line.split()
@@ -202,7 +203,7 @@ def _xyz_to_qcschema_mol(self, file_data: str ) -> Dict[str, Any]:
                     raise ValueError("Invalid xyz format.")
                 symbol, x, y, z = elements
                 mol["symbols"].append(symbol)
-                mol["geometry"] += [float(x), float(y), float(z)]
+                mol["geometry"] += [float(x)/bohr_to_angstrom, float(y)/bohr_to_angstrom, float(z)/bohr_to_angstrom]
             else:
                 break
         
diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data0_input_params0_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data0_input_params0_.yml
index edf9068d..28e5ab50 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data0_input_params0_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data0_input_params0_.yml
@@ -1,185 +1,185 @@
 - initial_molecule:
     geometry:
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     symbols:
     - O
     - H
diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data0_input_params1_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data0_input_params1_.yml
index 391ff83b..81721143 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data0_input_params1_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data0_input_params1_.yml
@@ -1,185 +1,185 @@
 - initial_molecule:
     geometry:
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data1_input_params0_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data1_input_params0_.yml
index c1c533e4..50c3a16b 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data1_input_params0_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data1_input_params0_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data1_input_params1_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data1_input_params1_.yml
index ff57b432..bf4ff98b 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data1_input_params1_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_bomd_qcschema_from_files_success_input_data1_input_params1_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data0_input_params0_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data0_input_params0_.yml
index 14aa4303..005aea53 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data0_input_params0_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data0_input_params0_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data0_input_params1_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data0_input_params1_.yml
index 24b4839c..a54c3c23 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data0_input_params1_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data0_input_params1_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data1_input_params0_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data1_input_params0_.yml
index 6dbdbff7..40b60b9c 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data1_input_params0_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data1_input_params0_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data1_input_params1_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data1_input_params1_.yml
index 52146e86..cb29243f 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data1_input_params1_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_go_qcschema_from_files_success_input_data1_input_params1_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params0_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params0_.yml
index 56d6aeda..cbd0bb81 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params0_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params0_.yml
@@ -4,186 +4,186 @@
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params1_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params1_.yml
index e034b405..cce6eb82 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params1_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params1_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params2_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params2_.yml
index 1d405c18..2aec00dd 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params2_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params2_.yml
@@ -4,186 +4,186 @@
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params3_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params3_.yml
index 2a37a67f..95e2344a 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params3_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params3_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params4_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params4_.yml
index 31054a71..2fe03758 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params4_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params4_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params5_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params5_.yml
index 9ff8871e..4a4998d8 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params5_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data0_input_params5_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params0_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params0_.yml
index b9e43093..4ba3f47e 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params0_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params0_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params1_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params1_.yml
index 375b7d71..c1bb0420 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params1_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params1_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params2_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params2_.yml
index c2cc7f48..2255b56a 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params2_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params2_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params3_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params3_.yml
index 9c263726..ca65ff37 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params3_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params3_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params4_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params4_.yml
index 12e107b7..c45f2c96 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params4_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params4_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params5_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params5_.yml
index bc397d4e..54d13160 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params5_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_assemble_true_qcschema_from_files_success_input_data1_input_params5_.yml
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diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_xyz_parsing_correct_xyz_files_3_nwater_nO___0_00___0_00___0_00___nH___1_00___0_00___0_00___nH___1_00___1_00___1_00___n_n_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_xyz_parsing_correct_xyz_files_3_nwater_nO___0_00___0_00___0_00___nH___1_00___0_00___0_00___nH___1_00___1_00___1_00___n_n_.yml
index 2ac94ab4..662c5906 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_xyz_parsing_correct_xyz_files_3_nwater_nO___0_00___0_00___0_00___nH___1_00___0_00___0_00___nH___1_00___1_00___1_00___n_n_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_xyz_parsing_correct_xyz_files_3_nwater_nO___0_00___0_00___0_00___nH___1_00___0_00___0_00___nH___1_00___1_00___1_00___n_n_.yml
@@ -2,12 +2,12 @@ geometry:
 - 0.0
 - 0.0
 - 0.0
-- 1.0
+- 1.8897261245650618
 - 0.0
 - 0.0
-- -1.0
-- 1.0
-- 1.0
+- -1.8897261245650618
+- 1.8897261245650618
+- 1.8897261245650618
 symbols:
 - O
 - H
diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_xyz_parsing_correct_xyz_files_3_nwater_nO___0_00___0_00___0_00_nH___1_00___0_00___0_00_nH___1_00___1_00___1_00_n_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_xyz_parsing_correct_xyz_files_3_nwater_nO___0_00___0_00___0_00_nH___1_00___0_00___0_00_nH___1_00___1_00___1_00_n_.yml
index 2ac94ab4..662c5906 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_xyz_parsing_correct_xyz_files_3_nwater_nO___0_00___0_00___0_00_nH___1_00___0_00___0_00_nH___1_00___1_00___1_00_n_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_xyz_parsing_correct_xyz_files_3_nwater_nO___0_00___0_00___0_00_nH___1_00___0_00___0_00_nH___1_00___1_00___1_00_n_.yml
@@ -2,12 +2,12 @@ geometry:
 - 0.0
 - 0.0
 - 0.0
-- 1.0
+- 1.8897261245650618
 - 0.0
 - 0.0
-- -1.0
-- 1.0
-- 1.0
+- -1.8897261245650618
+- 1.8897261245650618
+- 1.8897261245650618
 symbols:
 - O
 - H
diff --git a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_xyz_parsing_correct_xyz_files_3_nwater_nO___0_00___0_00___0_00_nH___1_00___0_00___0_00_nH___1_00___1_00___1_00_n_n_.yml b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_xyz_parsing_correct_xyz_files_3_nwater_nO___0_00___0_00___0_00_nH___1_00___0_00___0_00_nH___1_00___1_00___1_00_n_n_.yml
index 2ac94ab4..662c5906 100644
--- a/azure-quantum/tests/unit/test_microsoft_elements_dft/test_xyz_parsing_correct_xyz_files_3_nwater_nO___0_00___0_00___0_00_nH___1_00___0_00___0_00_nH___1_00___1_00___1_00_n_n_.yml
+++ b/azure-quantum/tests/unit/test_microsoft_elements_dft/test_xyz_parsing_correct_xyz_files_3_nwater_nO___0_00___0_00___0_00_nH___1_00___0_00___0_00_nH___1_00___1_00___1_00_n_n_.yml
@@ -2,12 +2,12 @@ geometry:
 - 0.0
 - 0.0
 - 0.0
-- 1.0
+- 1.8897261245650618
 - 0.0
 - 0.0
-- -1.0
-- 1.0
-- 1.0
+- -1.8897261245650618
+- 1.8897261245650618
+- 1.8897261245650618
 symbols:
 - O
 - H