From 1cff15163d52f73d6a4f035d69befc0ca08a25b7 Mon Sep 17 00:00:00 2001
From: Murat Keceli <keceli@gmail.com>
Date: Fri, 24 May 2024 06:27:24 +0000
Subject: [PATCH 1/5] Add ASE to elstruct reader program_modules

---
 .../elstruct/reader/program_modules.py        | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/autoio-interfaces/elstruct/reader/program_modules.py b/autoio-interfaces/elstruct/reader/program_modules.py
index 91e8023..bf60551 100644
--- a/autoio-interfaces/elstruct/reader/program_modules.py
+++ b/autoio-interfaces/elstruct/reader/program_modules.py
@@ -22,6 +22,8 @@ def _rename_prog(prog):
             prog = 'molpro2015'
         elif prog in ('gaussian03'):
             prog = 'gaussian09'
+        elif prog.startswith('ase'):
+            prog = 'ase'
         return prog
 
     new_name = _rename_prog(prog)
@@ -83,6 +85,27 @@ class Job():
 
 # Dictionaries that dictate what writer/reader functionality
 READER_MODULE_DCT = {
+   par.Program.ASE: (
+        Job.ENERGY, Job.GRADIENT,
+        Job.OPT_GEO, Job.OPT_ZMA,
+        Job.EXIT_MSG, Job.ERR_LST, Job.SUCCESS_LST,
+        Job.ERR_MSG, Job.CONV_MSG,
+        Job.PROG_NAME, Job.PROG_VERS
+   ),
+   par.Program.ASE_PSI4: (
+        Job.ENERGY, Job.GRADIENT,
+        Job.OPT_GEO, Job.OPT_ZMA,
+        Job.EXIT_MSG, Job.ERR_LST, Job.SUCCESS_LST,
+        Job.ERR_MSG, Job.CONV_MSG,
+        Job.PROG_NAME, Job.PROG_VERS
+   ),
+    par.Program.ASE_NWX: (
+        Job.ENERGY, Job.GRADIENT,
+        Job.OPT_GEO, Job.OPT_ZMA,
+        Job.EXIT_MSG, Job.ERR_LST, Job.SUCCESS_LST,
+        Job.ERR_MSG, Job.CONV_MSG,
+        Job.PROG_NAME, Job.PROG_VERS
+   ),
     par.Program.CFOUR2: (
         Job.ENERGY, Job.GRADIENT,
         Job.OPT_GEO, Job.OPT_ZMA,

From 2bf1ae8eae745d617f8fc24d085b817768443dcb Mon Sep 17 00:00:00 2001
From: Murat Keceli <keceli@gmail.com>
Date: Fri, 24 May 2024 06:28:57 +0000
Subject: [PATCH 2/5] Add ASE run into direct function

---
 autoio-interfaces/elstruct/par.py |  3 ++
 autoio-interfaces/elstruct/run.py | 50 ++++++++++++++++++++++++++-----
 2 files changed, 45 insertions(+), 8 deletions(-)

diff --git a/autoio-interfaces/elstruct/par.py b/autoio-interfaces/elstruct/par.py
index 04ceb98..179f8b9 100644
--- a/autoio-interfaces/elstruct/par.py
+++ b/autoio-interfaces/elstruct/par.py
@@ -24,6 +24,9 @@ class Module():
 
 class Program():
     """ Programs supported in elstruct """
+    ASE = 'ase'
+    ASE_PSI4 = 'ase_psi4'
+    ASE_NWX = 'ase_nwx'
     CFOUR2 = 'cfour2'
     GAUSSIAN09 = 'gaussian09'
     GAUSSIAN03 = 'gaussian03'
diff --git a/autoio-interfaces/elstruct/run.py b/autoio-interfaces/elstruct/run.py
index 9cca5b4..53b055e 100644
--- a/autoio-interfaces/elstruct/run.py
+++ b/autoio-interfaces/elstruct/run.py
@@ -1,8 +1,11 @@
 """ core run function
 """
 
+from email.mime import audio
 from autorun import from_input_string
-
+import automol
+import ase
+from ase.units import Hartree
 
 def direct(input_writer, script_str, run_dir, prog,
            geo, charge, mult, method, basis, **kwargs):
@@ -29,13 +32,44 @@ def direct(input_writer, script_str, run_dir, prog,
         :returns: the input string, the output string, and the run directory
         :rtype: (str, str)
     """
+    if prog.startswith('ase'):
+        atoms = geom_to_atoms(geo)
+        tokens = prog.split('_')
+        if len(tokens) > 1:
+            calculator = tokens[1]
+        else:
+            pass
+        if calculator == 'psi4':
+            from ase.calculators.psi4 import Psi4
+            calc = Psi4()
+            calc.parameters['basis'] = basis
+            calc.parameters['method'] = method
+            calc.parameters['multiplicity'] = mult
+            atoms.calc = calc
+            atoms.get_potential_energy()
+            version_str = f'ase_{ase.__version__}-psi4_{calc.psi4.__version__}'
+            calc.results['version'] = version_str
+            input_str = str(calc.parameters)
+            output_str = str(calc.results)
+    else:
+        input_str = input_writer(
+            prog=prog,
+            geo=geo, charge=charge, mult=mult, method=method, basis=basis,
+            **kwargs)
 
-    input_str = input_writer(
-        prog=prog,
-        geo=geo, charge=charge, mult=mult, method=method, basis=basis,
-        **kwargs)
-
-    output_strs = from_input_string(script_str, run_dir, input_str)
-    output_str = output_strs[0]
+        output_strs = from_input_string(script_str, run_dir, input_str)
+        output_str = output_strs[0]
 
     return input_str, output_str
+
+
+def geom_to_atoms(geo):
+    from ase import Atoms
+    if automol.zmat.is_valid(geo):
+        geo = automol.zmat.geometry(geo)
+    atoms = Atoms(symbols = automol.geom.symbols(geo), positions = automol.geom.coordinates(geo, angstrom=True) )
+    return atoms
+
+
+def atoms_to_geom(atoms):
+    pass
\ No newline at end of file

From 209dc92e43e302d37bcbf02446a3535970731aff Mon Sep 17 00:00:00 2001
From: Murat Keceli <keceli@gmail.com>
Date: Fri, 24 May 2024 06:35:09 +0000
Subject: [PATCH 3/5] Add ASE readers

---
 .../elstruct/reader/_ase/__init__.py          | 21 ++++++++++++++++
 .../elstruct/reader/_ase/status.py            | 25 +++++++++++++++++++
 2 files changed, 46 insertions(+)
 create mode 100644 autoio-interfaces/elstruct/reader/_ase/__init__.py
 create mode 100644 autoio-interfaces/elstruct/reader/_ase/status.py

diff --git a/autoio-interfaces/elstruct/reader/_ase/__init__.py b/autoio-interfaces/elstruct/reader/_ase/__init__.py
new file mode 100644
index 0000000..516cf6f
--- /dev/null
+++ b/autoio-interfaces/elstruct/reader/_ase/__init__.py
@@ -0,0 +1,21 @@
+from elstruct.reader._ase.status import has_normal_exit_message, check_convergence_messages
+from ase.units import Hartree
+import ase
+from ase.calculators.psi4 import Psi4
+
+def program_version(out_str):
+    import ast
+    results = ast.literal_eval(out_str)
+    return results['version']
+
+def energy(method, out_str):
+    import ast
+    results = ast.literal_eval(out_str)
+    return results['energy'] / Hartree
+
+__all__ = [
+
+    'has_normal_exit_message',
+    'check_convergence_messages',   
+'program_version'
+]
diff --git a/autoio-interfaces/elstruct/reader/_ase/status.py b/autoio-interfaces/elstruct/reader/_ase/status.py
new file mode 100644
index 0000000..cd566f9
--- /dev/null
+++ b/autoio-interfaces/elstruct/reader/_ase/status.py
@@ -0,0 +1,25 @@
+""" status checkers
+"""
+import autoparse.pattern as app
+import autoparse.find as apf
+import elstruct.par
+
+
+# Exit message for the program
+def has_normal_exit_message(output_str):
+    """ does this output string have a normal exit message?
+    """
+    return True
+    # pattern = app.escape('*** ASE exiting successfully.')
+    # return apf.has_match(pattern, output_str, case=False)
+
+def check_convergence_messages(error, success, output_str):
+    """ Assess whether the output file string contains messages
+        denoting all of the requested procedures in the job have converged.
+
+        :param output_str: string of the program's output file
+        :type output_str: str
+        :rtype: bool
+    """
+
+    return True
\ No newline at end of file

From 3528d0d72f6c0f792fe10020db7e9c7b945ae2b4 Mon Sep 17 00:00:00 2001
From: Murat Keceli <keceli@gmail.com>
Date: Fri, 24 May 2024 06:43:13 +0000
Subject: [PATCH 4/5] Move ev to Hartree conversion to run

---
 autoio-interfaces/elstruct/reader/_ase/__init__.py | 5 +----
 autoio-interfaces/elstruct/run.py                  | 1 +
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/autoio-interfaces/elstruct/reader/_ase/__init__.py b/autoio-interfaces/elstruct/reader/_ase/__init__.py
index 516cf6f..858b3a7 100644
--- a/autoio-interfaces/elstruct/reader/_ase/__init__.py
+++ b/autoio-interfaces/elstruct/reader/_ase/__init__.py
@@ -1,7 +1,4 @@
 from elstruct.reader._ase.status import has_normal_exit_message, check_convergence_messages
-from ase.units import Hartree
-import ase
-from ase.calculators.psi4 import Psi4
 
 def program_version(out_str):
     import ast
@@ -11,7 +8,7 @@ def program_version(out_str):
 def energy(method, out_str):
     import ast
     results = ast.literal_eval(out_str)
-    return results['energy'] / Hartree
+    return results['energy'] 
 
 __all__ = [
 
diff --git a/autoio-interfaces/elstruct/run.py b/autoio-interfaces/elstruct/run.py
index 53b055e..9b68a84 100644
--- a/autoio-interfaces/elstruct/run.py
+++ b/autoio-interfaces/elstruct/run.py
@@ -49,6 +49,7 @@ def direct(input_writer, script_str, run_dir, prog,
             atoms.get_potential_energy()
             version_str = f'ase_{ase.__version__}-psi4_{calc.psi4.__version__}'
             calc.results['version'] = version_str
+            calc.results['energy'] = calc.results['energy'] / Hartree
             input_str = str(calc.parameters)
             output_str = str(calc.results)
     else:

From 4e1d388ddaf15d1421f4c9f2566c1e1386e56a1e Mon Sep 17 00:00:00 2001
From: Murat Keceli <keceli@gmail.com>
Date: Fri, 24 May 2024 06:53:49 +0000
Subject: [PATCH 5/5] Remove import

---
 autoio-interfaces/elstruct/run.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/autoio-interfaces/elstruct/run.py b/autoio-interfaces/elstruct/run.py
index 9b68a84..fd8379b 100644
--- a/autoio-interfaces/elstruct/run.py
+++ b/autoio-interfaces/elstruct/run.py
@@ -1,7 +1,6 @@
 """ core run function
 """
 
-from email.mime import audio
 from autorun import from_input_string
 import automol
 import ase
@@ -73,4 +72,4 @@ def geom_to_atoms(geo):
 
 
 def atoms_to_geom(atoms):
-    pass
\ No newline at end of file
+    pass