From a55d0316c38753587f561efc4af1e511a543e906 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rapha=C3=ABl=20Robidas?= <Raphael.Robidas@USherbrooke.ca>
Date: Mon, 21 Aug 2023 09:56:42 -0400
Subject: [PATCH] Added concerted xtb scans

---
 ccinput/packages/xtb.py   | 19 +++++++++
 ccinput/tests/test_xtb.py | 87 ++++++++++++++++++++++++++++++++++++++-
 2 files changed, 105 insertions(+), 1 deletion(-)

diff --git a/ccinput/packages/xtb.py b/ccinput/packages/xtb.py
index 62324b1..2ab927a 100644
--- a/ccinput/packages/xtb.py
+++ b/ccinput/packages/xtb.py
@@ -33,6 +33,7 @@ def __init__(self, calc):
         self.input_file = ""
         self.specifications = ""
         self.force_constant = 1.0
+        self.concerted_scan = False
         self.confirmed_specifications = ""
 
         if self.calc.type not in self.EXECUTABLES:
@@ -111,8 +112,17 @@ def handle_constraints_scan(self):
             if cmd.scan:
                 self.has_scan = True
 
+        if self.concerted_scan and (
+            not self.has_scan or len(self.calc.constraints) < 2
+        ):
+            raise InvalidParameter(
+                "The concerted mode only influences scans with multiple coordinates"
+            )
+
         if self.has_scan:
             self.input_file += "$scan\n"
+            if self.concerted_scan:
+                self.input_file += "mode=concerted\n"
             for counter, cmd in enumerate(self.calc.constraints):
                 if cmd.scan:
                     self.input_file += f"{counter+1}: {cmd.start_d:.2f}, {cmd.end_d:.2f}, {cmd.num_steps}\n"
@@ -217,6 +227,15 @@ def handle_specifications(self):
                     self.cmd_arguments += "--squick "
                 elif ss[0] == "mquick":
                     self.cmd_arguments += "--mquick "
+                elif ss[0] == "concerted":
+                    if self.calc.type not in [
+                        CalcType.CONSTR_OPT,
+                    ]:
+                        raise InvalidParameter(
+                            f"Invalid specification for calculation type: {ss[0]}"
+                        )
+                    self.concerted_scan = True
+
                 else:
                     raise InvalidParameter("Invalid specification")
             elif len(ss) == 2:
diff --git a/ccinput/tests/test_xtb.py b/ccinput/tests/test_xtb.py
index 1b877e1..15d73cb 100644
--- a/ccinput/tests/test_xtb.py
+++ b/ccinput/tests/test_xtb.py
@@ -258,6 +258,56 @@ def test_scan_auto(self):
         """
         self.assertTrue(self.is_equivalent(INPUT, xtb.input_file))
 
+    def test_scan_two_coordinates(self):
+        params = {
+            "type": "Constrained Optimisation",
+            "file": "ethanol.xyz",
+            "software": "xtb",
+            "constraints": "Scan_9_1.4_10/1_2;Scan_9_1.4_10/2_3",
+        }
+
+        xtb = self.generate_calculation(**params)
+
+        REF = "xtb ethanol.xyz --opt tight --input input"
+
+        self.assertTrue(self.is_equivalent(REF, xtb.command))
+
+        INPUT = """$constrain
+        force constant=1.0
+        distance: 1, 2, auto
+        distance: 2, 3, auto
+        $scan
+        1: 9.00, 1.40, 10
+        2: 9.00, 1.40, 10
+        """
+        self.assertTrue(self.is_equivalent(INPUT, xtb.input_file))
+
+    def test_scan_two_coordinates_concerted(self):
+        params = {
+            "type": "Constrained Optimisation",
+            "file": "ethanol.xyz",
+            "software": "xtb",
+            "constraints": "Scan_9_1.4_10/1_2;Scan_9_1.4_10/2_3",
+            "specifications": "--concerted",
+        }
+
+        xtb = self.generate_calculation(**params)
+
+        REF = "xtb ethanol.xyz --opt tight --input input"
+
+        self.assertTrue(self.is_equivalent(REF, xtb.command))
+
+        INPUT = """$constrain
+        force constant=1.0
+        distance: 1, 2, auto
+        distance: 2, 3, auto
+        $scan
+        mode=concerted
+        1: 9.00, 1.40, 10
+        2: 9.00, 1.40, 10
+        """
+        self.assertTrue(self.is_equivalent(INPUT, xtb.input_file))
+
     def test_constrained_opt_no_constraint(self):
         params = {
             "type": "Constrained Optimisation",
@@ -266,7 +316,42 @@ def test_constrained_opt_no_constraint(self):
         }
 
         with self.assertRaises(InvalidParameter):
-            xtb = self.generate_calculation(**params)
+            self.generate_calculation(**params)
+
+    def test_freeze_concerted_exception(self):
+        params = {
+            "type": "Constrained Optimisation",
+            "file": "ethanol.xyz",
+            "software": "xtb",
+            "constraints": "Freeze_9_1.4_10;Freeze_9_1.4_10",
+            "specifications": "--concerted",
+        }
+
+        with self.assertRaises(InvalidParameter):
+            self.generate_calculation(**params)
+
+    def test_scan_single_coordinate_concerted_exception(self):
+        params = {
+            "type": "Constrained Optimisation",
+            "file": "ethanol.xyz",
+            "software": "xtb",
+            "constraints": "Scan_9_1.4_10/1_2;",
+            "specifications": "--concerted",
+        }
+
+        with self.assertRaises(InvalidParameter):
+            self.generate_calculation(**params)
+
+    def test_opt_concerted_exception(self):
+        params = {
+            "type": "Geometrical Optimisation",
+            "file": "ethanol.xyz",
+            "software": "xtb",
+            "specifications": "--concerted",
+        }
+
+        with self.assertRaises(InvalidParameter):
+            self.generate_calculation(**params)
 
     def test_freeze(self):
         params = {