Added command line support for multiple files

ccinput/tests/test_cli.py

@@ -1,21 +1,19 @@
 import shlex
 import os
-from unittest import TestCase
 
 from ccinput.calculation import Calculation, Parameters
 from ccinput.wrapper import gen_input, get_input_from_args, get_parser
+from ccinput.tests.testing_utilities import InputTests
 
-class ManualCliTests(TestCase):
+class CliEquivalenceTests(InputTests):
     def are_equivalent(self, api_args, cmd_line):
         ref = gen_input(**api_args)
 
         parser = get_parser()
         args = parser.parse_args(shlex.split(cmd_line))
-        inp = get_input_from_args(args)
-        return ref == inp
-
-    def struct(self, name):
-        return os.path.join('/'.join(__file__.split('/')[:-1]), "structures/", name + '.xyz')
+        calcs, outputs = get_input_from_args(args)
+        inp = calcs[0].input_file
+        return self.is_equivalent(ref, inp)
 
     def test_basic(self):
         args = {
@@ -360,3 +358,128 @@ def test_d3bj_orca(self):
         line = "orca opt PBE0 -bs Def2SVP --xyz 'Cl 0 0 0' -n 1 --mem 1G -c -1 --d3bj"
         self.assertTrue(self.are_equivalent(args, line))
 
+class ManualCliTests(InputTests):
+    def test_multiple_files_no_output(self):
+        cmd_line = f"orca sp HF -bs Def2SVP -f {self.struct('ethanol')} {self.struct('CH4')} -n 1 --mem 1G"
+
+        parser = get_parser()
+        args = parser.parse_args(shlex.split(cmd_line))
+
+        objs, outputs = get_input_from_args(args)
+        assert len(objs) == 2
+        assert len(outputs) == 0
+
+        args1 = {
+            'software': "ORCA",
+            'type': "sp",
+            'method': "HF",
+            'basis_set': "Def2SVP",
+            'file': self.struct("ethanol"),
+            'nproc': 1,
+            'mem': "1G",
+        }
+        args2 = {
+            'software': "ORCA",
+            'type': "sp",
+            'method': "HF",
+            'basis_set': "Def2SVP",
+            'file': self.struct("CH4"),
+            'nproc': 1,
+            'mem': "1G",
+        }
+
+        inp1 = gen_input(**args1)
+        inp2 = gen_input(**args2)
+
+        assert self.is_equivalent(inp1, objs[0].input_file)
+        assert self.is_equivalent(inp2, objs[1].input_file)
+
+    def test_multiple_files_output(self):
+        cmd_line = f"orca sp HF -bs Def2SVP -f {self.struct('ethanol')} {self.struct('CH4')} -o test.inp -n 1 --mem 1G"
+
+        parser = get_parser()
+        args = parser.parse_args(shlex.split(cmd_line))
+
+        objs, outputs = get_input_from_args(args)
+        assert len(objs) == 2
+        assert len(outputs) == 2
+
+        assert os.path.basename(outputs[0]) == "test_ethanol.inp"
+        assert os.path.basename(outputs[1]) == "test_CH4.inp"
+
+        args1 = {
+            'software': "ORCA",
+            'type': "sp",
+            'method': "HF",
+            'basis_set': "Def2SVP",
+            'file': self.struct("ethanol"),
+            'nproc': 1,
+            'mem': "1G",
+        }
+        args2 = {
+            'software': "ORCA",
+            'type': "sp",
+            'method': "HF",
+            'basis_set': "Def2SVP",
+            'file': self.struct("CH4"),
+            'nproc': 1,
+            'mem': "1G",
+        }
+
+        inp1 = gen_input(**args1)
+        inp2 = gen_input(**args2)
+
+        assert self.is_equivalent(inp1, objs[0].input_file)
+        assert self.is_equivalent(inp2, objs[1].input_file)
+
+    def test_multiple_files_output_no_name(self):
+        cmd_line = f"orca sp HF -bs Def2SVP -f {self.struct('ethanol')} {self.struct('CH4')} -o .inp -n 1 --mem 1G"
+
+        parser = get_parser()
+        args = parser.parse_args(shlex.split(cmd_line))
+
+        objs, outputs = get_input_from_args(args)
+        assert len(objs) == 2
+        assert len(outputs) == 2
+
+        assert outputs[0] == "ethanol.inp"
+        assert outputs[1] == "CH4.inp"
+
+    def test_multiple_files_output_name_no_override(self):
+        cmd_line = f"orca sp HF -bs Def2SVP -f {self.struct('ethanol')} {self.struct('CH4')} -o .inp -n 1 --mem 1G --name test"
+
+        parser = get_parser()
+        args = parser.parse_args(shlex.split(cmd_line))
+
+        objs, outputs = get_input_from_args(args)
+        assert len(objs) == 2
+        assert len(outputs) == 2
+
+        assert outputs[0] == "ethanol.inp"
+        assert outputs[1] == "CH4.inp"
+
+    def test_multiple_files_output_directory(self):
+        cmd_line = f"orca sp HF -bs Def2SVP -f {self.struct('ethanol')} {self.struct('CH4')} -o calc_dir/.inp -n 1 --mem 1G"
+
+        parser = get_parser()
+        args = parser.parse_args(shlex.split(cmd_line))
+
+        objs, outputs = get_input_from_args(args)
+        assert len(objs) == 2
+        assert len(outputs) == 2
+
+        assert outputs[0] == "calc_dir/ethanol.inp"
+        assert outputs[1] == "calc_dir/CH4.inp"
+
+    def test_single_file_output(self):
+        cmd_line = f"orca sp HF -bs Def2SVP -f {self.struct('ethanol')} -o calc_dir/ethanol.inp -n 1 --mem 1G"
+
+        parser = get_parser()
+        args = parser.parse_args(shlex.split(cmd_line))
+
+        objs, outputs = get_input_from_args(args)
+        assert len(objs) == 1
+        assert len(outputs) == 1
+
+        assert outputs[0] == "calc_dir/ethanol.inp"
+

ccinput/tests/testing_utilities.py

@@ -1,12 +1,12 @@
 import os
 from unittest import TestCase
 
-from ccinput.wrapper import generate_calculation
+from ccinput.wrapper import gen_obj
 
 class InputTests(TestCase):
     def generate_calculation(self, **params):
         params['file'] = os.path.join('/'.join(__file__.split('/')[:-1]), "structures/", params['file'])
-        return generate_calculation(**params)
+        return gen_obj(**params)
 
     def is_equivalent(self, ref, res):
         ref_lines = [i.strip() for i in ref.strip().split('\n')]
@@ -58,3 +58,6 @@ def xyz_line_equivalent(self, line1, line2):
                 return False
         return True
 
+    def struct(self, name):
+        return os.path.join('/'.join(__file__.split('/')[:-1]), "structures/", name + '.xyz')
+

ccinput/wrapper.py

@@ -22,23 +22,21 @@ def process_calculation(calc):
 def generate_calculation(software=None, type=None, method="", basis_set="",
             solvent="", solvation_model="", solvation_radii="", custom_solvation_radii="",
             specifications="", freeze=[], scan=[], sfrom=[], sto=[], snsteps=[], sstep=[],
-            density_fitting="", custom_basis_sets="", xyz="", file="",
-            constraints="", nproc=0, mem="", charge=0, multiplicity=1, d3=False, d3bj=False,
-            aux_name="calc2", name="calc", header="File created by ccinput", **kwargs):
+            density_fitting="", custom_basis_sets="", xyz="", constraints="", nproc=0,
+            mem="", charge=0, multiplicity=1, d3=False, d3bj=False, aux_name="calc2",
+            name="calc", header="File created by ccinput", **kwargs):
 
     if software is None:
         raise InvalidParameter("Specify a software package to use (software=...)")
 
     if type is None:
         raise InvalidParameter("Specify a calculation type (type='...')")
 
-    if xyz != "":
-        xyz_structure = standardize_xyz(xyz)
-    elif file != "":
-        xyz_structure = parse_xyz_from_file(file)
-    else:
+    if xyz == "":
         raise InvalidParameter("No input structure")
 
+    xyz_structure = standardize_xyz(xyz)
+
     abs_software = get_abs_software(software)
 
     calc_type = get_abs_type(type)
@@ -58,11 +56,29 @@ def generate_calculation(software=None, type=None, method="", basis_set="",
 
     return process_calculation(calc)
 
+def gen_obj(**args):
+    if 'file' in args:
+        if isinstance(args['file'], list):
+            if len(args['file']) > 1:
+                print("file", args['file'])
+                raise UnimplementedError("No support for multiple input files at once except from the command line")
+            elif len(args['file']) == 0:
+                pass
+            else:
+                xyz = parse_xyz_from_file(args['file'][0])
+                args['xyz'] = xyz
+        else:
+            xyz = parse_xyz_from_file(args['file'])
+            args['xyz'] = xyz
+
+        del args['file']
+    return generate_calculation(**args)
+
 def gen_input(**args):
-    return generate_calculation(**args).input_file
+    return gen_obj(**args).input_file
 
 def write_input(filename, **args):
-    inp = generate_calculation(**args).input_file
+    inp = gen_input(**args)
     with open(filename, 'w') as out:
         out.write(inp)
 
@@ -101,11 +117,11 @@ def get_parser():
     parser.add_argument('--xyz', '-x', default="",
             type=str, help='XYZ structure as string')
 
-    parser.add_argument('--file', '-f', default="",
-            type=str, help='XYZ structure as file')
+    parser.add_argument('--file', '-f', default=[], nargs="+",
+            type=str, help='XYZ structure(s) as file(s)')
 
     parser.add_argument('--output', '-o', default="",
-            type=str, help='Write the result to the specified file')
+            type=str, help='Write the result to the specified file (single file) or using the specified pattern (multiple files)')
 
     parser.add_argument('--constraints', '-co', default="",
             type=str, help='String specification of constraints for certain calculations')
@@ -162,33 +178,67 @@ def cmd():
     parser = get_parser()
     args = parser.parse_args()
 
-    inp = get_input_from_args(args)
+    calcs, outputs = get_input_from_args(args)
     if args.output != "":
-        with open(args.output, 'w') as out:
-            out.write(inp)
-        print(f"Input file written to {args.output}")
+        for calc, outp in zip(calcs, outputs):
+            with open(outp, 'w') as out:
+                out.write(calc.input_file)
+            print(f"Input file written to {outp}")
     else:
-        print(inp)
+        if len(calcs) == 1:
+            print(calcs[0].input_file)
+        else:
+            for calc in calcs:
+                n = max(int((39 - len(calc.calc.name))/2), 4)
+                header = "-"*n + f" {calc.calc.name} " + "-"*n
+                print(header)
+                print(calc.input_file)
+                print("\n\n")
 
 def get_input_from_args(args):
-    if args.name == "calc" and args.file:
-        _name = os.path.basename(args.file).split('.')[0]
+    xyzs = []
+    names = []
+    outputs = []
+
+    if args.file:
+        xyzs = [parse_xyz_from_file(f) for f in args.file]
+        if len(args.file) > 1 or args.name == 'calc':
+            names = [os.path.basename(f).split('.')[0] for f in args.file]
+        else:
+            names = [args.name]
+
+        if args.output != "":
+            head, tail = os.path.split(args.output)
+            prefix, ext = tail.split('.')
+            if prefix != "":
+                prefix += '_'
+            if len(args.file) > 1:
+                outputs = [os.path.join(head, prefix+name+'.'+ext) for name in names]
+            else:
+                outputs = [os.path.join(head, name+'.'+ext) for name in names]
     else:
-        _name = args.name
-    try:
-        inp = gen_input(software=args.software, type=args.type, method=args.method,
-                basis_set=args.basis_set, solvent=args.solvent,
-                solvation_model=args.solvation_model, solvation_radii=args.solvation_radii,
-                custom_solvation_radii=args.custom_solvation_radii,
-                specifications=args.specifications, freeze=args.freeze,
-                scan=args.scan, sfrom=args.sfrom, sto=args.sto, snsteps=args.snsteps,
-                sstep=args.sstep, density_fitting=args.density_fitting,
-                custom_basis_sets=args.custom_basis_sets, xyz=args.xyz, file=args.file,
-                constraints=args.constraints, nproc=args.nproc, mem=args.mem,
-                charge=args.charge, multiplicity=args.mult, d3=args.d3, d3bj=args.d3bj,
-                aux_name=args.aux_name, name=_name, header=args.header)
-    except CCInputException as e:
-        print(f"*** {str(e)} ***")
-        return
-    return inp
+        xyzs = [args.xyz]
+        names = [args.name]
+        outputs = [args.output]
+
+    calcs = []
+    for name, xyz in zip(names, xyzs):
+        try:
+            calc = gen_obj(software=args.software, type=args.type, method=args.method,
+                    basis_set=args.basis_set, solvent=args.solvent,
+                    solvation_model=args.solvation_model, solvation_radii=args.solvation_radii,
+                    custom_solvation_radii=args.custom_solvation_radii,
+                    specifications=args.specifications, freeze=args.freeze,
+                    scan=args.scan, sfrom=args.sfrom, sto=args.sto, snsteps=args.snsteps,
+                    sstep=args.sstep, density_fitting=args.density_fitting,
+                    custom_basis_sets=args.custom_basis_sets, xyz=xyz,
+                    constraints=args.constraints, nproc=args.nproc, mem=args.mem,
+                    charge=args.charge, multiplicity=args.mult, d3=args.d3, d3bj=args.d3bj,
+                    aux_name=args.aux_name, name=name, header=args.header)
+        except CCInputException as e:
+            print(f"*** {str(e)} ***")
+            exit(0)
+        else:
+            calcs.append(calc)
+    return calcs, outputs
 

docs/source/usage.rst

@@ -115,6 +115,33 @@ Basis set to use for density fitting.
 
    Only available for Gaussian 16 for the moment
 
+Structure files
+^^^^^^^^^^^^^^^
+
+Structure file(s) to use in the input. Only XYZ files are currently supported.
+
+Multiple files can be specified at once when using from the command line:
+
+.. code-block:: console
+
+        $ ccinput [...] -f struct1.xyz struct2.xyz
+
+If no output pattern is specified, each input file will be printed to the console sequentially separated by a header. With an output pattern, the files will be created in the chosen directory with the given prefix and extension. When specifying only one file, the exact output path will be used.
+
+.. code-block:: console
+
+        $ ccinput [...] -f struct1.xyz struct2.xyz -o calc_dir/sp.inp
+        Input file written to calc_dir/sp_struct1.inp
+        Input file written to calc_dir/sp_struct2.inp
+
+        $ ccinput [...] -f struct1.xyz struct2.xyz -o .com
+        Input file written to struct1.com
+        Input file written to struct2.com
+
+        $ ccinput [...] -f struct1.xyz -o my_struct.com
+        Input file written to my_struct.com
+
+
 Solvent
 ^^^^^^^