From 86dd213d32b9b7a33aff0c23f113a5bc9c4f8fd8 Mon Sep 17 00:00:00 2001
From: juliette1996 <48909188+juliette1996@users.noreply.github.com>
Date: Fri, 11 Sep 2020 12:52:02 +0200
Subject: [PATCH 01/10] Add elements coordination in schemas.py

Add an optional key to the dictionary input of COOP calculation that includes the coordination number to be considered for each of the two elements
---
 nanoqm/workflows/schemas.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/nanoqm/workflows/schemas.py b/nanoqm/workflows/schemas.py
index a1b347375..b8894defd 100644
--- a/nanoqm/workflows/schemas.py
+++ b/nanoqm/workflows/schemas.py
@@ -303,7 +303,10 @@ def merge(d1: Dict[str, Any], d2: Dict[str, Any]) -> Dict[str, Any]:
 #: Input for a Crystal Orbital Overlap Population calculation
 dict_coop = {
     # List of the two elements to calculate the COOP for
-    "coop_elements": list}
+    "coop_elements": list,
+    # Coordination number to be considered for each of the two elements
+    Optional("elements_coordination", default=None): Or(None, list)
+}
 
 
 dict_merged_single_points = merge(dict_general_options, dict_single_points)

From 4432fe321d0ccbca180c62251793e3f233a9ebeb Mon Sep 17 00:00:00 2001
From: juliette1996 <48909188+juliette1996@users.noreply.github.com>
Date: Fri, 11 Sep 2020 15:24:28 +0200
Subject: [PATCH 02/10] Update workflow_coop.py with coordination number

---
 nanoqm/workflows/workflow_coop.py | 27 ++++++++++++++++++++++-----
 1 file changed, 22 insertions(+), 5 deletions(-)

diff --git a/nanoqm/workflows/workflow_coop.py b/nanoqm/workflows/workflow_coop.py
index 9e115ed0c..faf563640 100644
--- a/nanoqm/workflows/workflow_coop.py
+++ b/nanoqm/workflows/workflow_coop.py
@@ -10,12 +10,16 @@
 __all__ = ['workflow_crystal_orbital_overlap_population']
 
 import logging
-from typing import List, Tuple
+from typing import List, Tuple, Union
 
 import numpy as np
 
+from scm.plams import Molecule
+
 from qmflows.parsers.xyzParser import readXYZ
 
+from nanoCAT.recipes import coordination_number
+
 from ..common import (DictConfig, MolXYZ, h2ev,
                       number_spherical_functions_per_atom, retrieve_hdf5_data)
 from ..integrals.multipole_matrices import compute_matrix_multipole
@@ -44,11 +48,14 @@ def workflow_crystal_orbital_overlap_population(config: DictConfig):
     # Converting the xyz-file to a mol-file
     mol = readXYZ(config.path_traj_xyz)
 
+    if config.elements_coordination is not None:
+        geometry = Molecule(config.path_traj_xyz)
+
     # Computing the indices of the atomic orbitals of the two selected
     # elements, and the overlap matrix that contains only elements related to
     # the two elements
     el_1_orbital_ind, el_2_orbital_ind, overlap_reduced = compute_overlap_and_atomic_orbitals(
-        mol, config)
+        mol, config, geometry)
 
     # Compute the crystal orbital overlap population between the two selected
     # elements
@@ -83,7 +90,8 @@ def get_eigenvalues_coefficients(config: DictConfig) -> Tuple[np.ndarray, np.nda
 
 
 def compute_overlap_and_atomic_orbitals(
-        mol: MolXYZ, config: DictConfig) -> Tuple[List[int], List[int], List[int]]:
+        mol: MolXYZ, config: DictConfig,
+        geometry: Union[Molecule, None]) -> Tuple[List[int], List[int], List[int]]:
     """Compute the indices of the atomic orbitals of the two selected elements.
 
     Computes the overlap matrix, containing only the elements related to those two elements.
@@ -102,8 +110,17 @@ def compute_overlap_and_atomic_orbitals(
     element_1 = config["coop_elements"][0]
     element_2 = config["coop_elements"][1]
 
-    element_1_index = [i for i, s in enumerate(mol) if element_1.lower() in s]
-    element_2_index = [i for i, s in enumerate(mol) if element_2.lower() in s]
+    if config["elements_coordination"] is None:
+        element_1_index = [i for i, s in enumerate(mol) if element_1.lower() in s]
+        element_2_index = [i for i, s in enumerate(mol) if element_2.lower() in s]
+
+    # For the two selected elements, only the indices corresponding to a given coordination number
+    else:
+        coord = coordination_number(geometry)
+        cn_1 = config["elements_coordination"][0]
+        cn_2 = config["elements_coordination"][1]
+        element_1_index = [i - 1 for i in coord[element_1][cn_1]]
+        element_2_index = [i - 1 for i in coord[element_2][cn_2]]
 
     # Making a list of the indices of the atomic orbitals for each of the two
     # elements

From 6541d2ac062072a1074fd1907b40dc96037e0279 Mon Sep 17 00:00:00 2001
From: juliette1996 <48909188+juliette1996@users.noreply.github.com>
Date: Mon, 14 Sep 2020 11:42:58 +0200
Subject: [PATCH 03/10] Add a description of elements_coordination option

---
 nanoqm/workflows/workflow_coop.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nanoqm/workflows/workflow_coop.py b/nanoqm/workflows/workflow_coop.py
index faf563640..d0d7d8e33 100644
--- a/nanoqm/workflows/workflow_coop.py
+++ b/nanoqm/workflows/workflow_coop.py
@@ -1,4 +1,7 @@
 """Crystal Orbital Overlap Population calculation.
+The COOP is calculated between two selected elements.
+For each element, a specific coordination number can optionally be selected 
+by using the "elements_coordination" key in the yaml input.
 
 Index
 -----

From d19ef5390282350b01ec40cc5db71045292d3ae0 Mon Sep 17 00:00:00 2001
From: juliette1996 <48909188+juliette1996@users.noreply.github.com>
Date: Mon, 14 Sep 2020 11:54:39 +0200
Subject: [PATCH 04/10] Add nano-CAT to setup.py

---
 setup.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 2b3c51e2a..c17105275 100644
--- a/setup.py
+++ b/setup.py
@@ -151,7 +151,8 @@ def build_extensions(self):
         'h5py', 'mendeleev', 'more-itertools', 'noodles==0.3.3', 'numpy', 'pybind11>=2.2.4',
         'scipy', 'schema', 'pyyaml>=5.1',
         'plams@git+https://github.com/SCM-NV/PLAMS@master',
-        'qmflows@git+https://github.com/SCM-NV/qmflows@master'
+        'qmflows@git+https://github.com/SCM-NV/qmflows@master',
+        'nano-CAT@git+https://github.com/nlesc-nano/nano-CAT@master'
     ],
     cmdclass={'build_ext': BuildExt},
     ext_modules=[ext_pybind],

From 472e2e7a5e83007bf408c6689ed0ced46a055b47 Mon Sep 17 00:00:00 2001
From: juliette1996 <48909188+juliette1996@users.noreply.github.com>
Date: Mon, 14 Sep 2020 12:10:55 +0200
Subject: [PATCH 05/10] Variable assignment in workflow_coop.py

---
 nanoqm/workflows/workflow_coop.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nanoqm/workflows/workflow_coop.py b/nanoqm/workflows/workflow_coop.py
index d0d7d8e33..34bf1ca6e 100644
--- a/nanoqm/workflows/workflow_coop.py
+++ b/nanoqm/workflows/workflow_coop.py
@@ -53,6 +53,8 @@ def workflow_crystal_orbital_overlap_population(config: DictConfig):
 
     if config.elements_coordination is not None:
         geometry = Molecule(config.path_traj_xyz)
+    else:
+        geometry = None
 
     # Computing the indices of the atomic orbitals of the two selected
     # elements, and the overlap matrix that contains only elements related to

From 6a4c11f682442a3a32f2d81b2732505987b8ddfc Mon Sep 17 00:00:00 2001
From: felipez <tifonzafel@gmail.com>
Date: Mon, 14 Sep 2020 15:04:00 +0200
Subject: [PATCH 06/10] fixed logger error

---
 test/test_distribute.py   | 13 ++++++++-----
 test/test_run_workflow.py |  4 +++-
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/test/test_distribute.py b/test/test_distribute.py
index 641e3053a..0f55ea7dc 100644
--- a/test/test_distribute.py
+++ b/test/test_distribute.py
@@ -1,10 +1,12 @@
 """Test the distribution script."""
-from qmflows.type_hints import PathLike
-from pathlib import Path
-from subprocess import (PIPE, Popen)
 import fnmatch
-import shutil
 import os
+import re
+import shutil
+from pathlib import Path
+from subprocess import PIPE, Popen
+
+from qmflows.type_hints import PathLike
 
 
 def test_distribute(tmp_path: PathLike) -> None:
@@ -20,7 +22,8 @@ def call_distribute(tmp_path: PathLike, cmd: str) -> None:
     try:
         p = Popen(cmd, stdin=PIPE, stdout=PIPE, stderr=PIPE, shell=True)
         _, err = p.communicate()
-        if err:
+        error = re.search("error", err.decode(), re.IGNORECASE)
+        if error is not None:
             raise RuntimeError(err.decode())
         check_scripts()
     finally:
diff --git a/test/test_run_workflow.py b/test/test_run_workflow.py
index 0735e1f90..cf53c7d55 100644
--- a/test/test_run_workflow.py
+++ b/test/test_run_workflow.py
@@ -1,6 +1,7 @@
 """Test the CLI to run a workflow."""
 
 import os
+import re
 import shutil
 from pathlib import Path
 from subprocess import PIPE, Popen
@@ -37,7 +38,8 @@ def test_run_workflow(tmp_path):
     try:
         p = Popen(cmd, stdin=PIPE, stdout=PIPE, stderr=PIPE, shell=True)
         out, err = p.communicate()
-        if err:
+        error = re.search("error", err.decode(), re.IGNORECASE)
+        if error is not None:
             print("output: ", out)
             print("err: ", err)
             raise RuntimeError(err.decode())

From 6058891c1e4cd043949283b9d9cc0438c8080251 Mon Sep 17 00:00:00 2001
From: felipez <tifonzafel@gmail.com>
Date: Mon, 14 Sep 2020 15:20:20 +0200
Subject: [PATCH 07/10] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 016c5d972..cfff42602 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,7 @@
 # 0.10.3 (Unreleased)
 ## New
 * Template to create B3LYP computations (#269)
+* Add nanoCAT dependency (#280)
 
 ## Fixed
 * Fix distribution error (#272)

From bb0820bfd25be51e5b67b1095da5769ab8ca000a Mon Sep 17 00:00:00 2001
From: juliette1996 <48909188+juliette1996@users.noreply.github.com>
Date: Mon, 14 Sep 2020 16:49:21 +0200
Subject: [PATCH 08/10] Create input_test_coop_coordination.yml

---
 .../input_test_coop_coordination.yml          | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 test/test_files/input_test_coop_coordination.yml

diff --git a/test/test_files/input_test_coop_coordination.yml b/test/test_files/input_test_coop_coordination.yml
new file mode 100644
index 000000000..149553c4f
--- /dev/null
+++ b/test/test_files/input_test_coop_coordination.yml
@@ -0,0 +1,26 @@
+workflow:
+  coop_calculation
+project_name: Cd33Se33
+
+active_space: [50, 50]
+path_hdf5: "test/test_files/Cd33Se33.hdf5"
+path_traj_xyz: "test/test_files/Cd33Se33.xyz"
+scratch_path: "/tmp/COOP"
+
+coop_elements: ["Cd", "Se"]
+elements_coordination: ["4", "3"]
+
+cp2k_general_settings:
+  basis:  "DZVP-MOLOPT-SR-GTH"
+  potential: "GTH-PBE"
+  cell_parameters: 20.0
+  periodic: none
+
+  cp2k_settings_main:
+    specific:
+      template: pbe_main
+
+  cp2k_settings_guess:
+    specific:
+      template:
+        pbe_guess

From 67c44f0e2a562471e10ee7e0f676f750c9d398cc Mon Sep 17 00:00:00 2001
From: juliette1996 <48909188+juliette1996@users.noreply.github.com>
Date: Mon, 14 Sep 2020 16:59:43 +0200
Subject: [PATCH 09/10] Test coordination functionality of coop workflow

---
 test/test_workflow_coop.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/test/test_workflow_coop.py b/test/test_workflow_coop.py
index 8c9d74571..1403a7afd 100644
--- a/test/test_workflow_coop.py
+++ b/test/test_workflow_coop.py
@@ -29,3 +29,21 @@ def test_workflow_coop(tmp_path: PathLike) -> None:
         print("scratch_path: ", tmp_path)
         print("Unexpected error:", sys.exc_info()[0])
         raise
+
+
+def test_workflow_coop_coordination(tmp_path: PathLike) -> None:
+    """Test the Crystal Orbital Overlap Population workflow."""
+    file_path = PATH_TEST / 'input_test_coop_coordination.yml'
+    config = process_input(file_path, 'coop_calculation')
+
+    # create scratch path
+    shutil.copy(config.path_hdf5, tmp_path)
+    config.path_hdf5 = join(tmp_path, "Cd33Se33.hdf5")
+    config.workdir = tmp_path
+    try:
+        workflow_crystal_orbital_overlap_population(config)
+        os.remove("COOP.txt")
+    except BaseException:
+        print("scratch_path: ", tmp_path)
+        print("Unexpected error:", sys.exc_info()[0])
+        raise

From c822be2c4e83913ad39f71bdc6ef1cb3b870afd4 Mon Sep 17 00:00:00 2001
From: juliette1996 <48909188+juliette1996@users.noreply.github.com>
Date: Thu, 15 Oct 2020 12:48:53 +0200
Subject: [PATCH 10/10] Update yml input test

---
 test/test_files/input_test_coop_coordination.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/test_files/input_test_coop_coordination.yml b/test/test_files/input_test_coop_coordination.yml
index 149553c4f..b6ccf3a7c 100644
--- a/test/test_files/input_test_coop_coordination.yml
+++ b/test/test_files/input_test_coop_coordination.yml
@@ -8,7 +8,7 @@ path_traj_xyz: "test/test_files/Cd33Se33.xyz"
 scratch_path: "/tmp/COOP"
 
 coop_elements: ["Cd", "Se"]
-elements_coordination: ["4", "3"]
+elements_coordination: [4, 3]
 
 cp2k_general_settings:
   basis:  "DZVP-MOLOPT-SR-GTH"