Merge pull request #6 from pierre-24/fixups_and_upgrades

Fixups and upgrades

.github/workflows/tests.yml

@@ -26,7 +26,7 @@ jobs:
     - name: Install dependencies
       run: |
         pip3 install pip-tools
-        make init
+        make install-dev
     - name: Lint
       run: |
         make lint

Makefile

@@ -10,9 +10,9 @@ help:
 	@echo "  help                        to get this help"
 
 init:
-	pip-sync && pip3 install -e .
+	pip3 install -e .
 
-sync:
+install-dev:
 	pip-sync
 
 lint:

docs/install.rst

@@ -42,7 +42,7 @@ To contribute to the project,
 + Go in it: ``cd nachos``
 + Install pip-tools: ``pip3 install pip-tools``
 + Install virtualenv ``python3 -m venv venv; source venv/bin/activate``
-+ Install dependencies: ``make init``.
++ Install dependencies: ``make install-dev``.
 + Add upstream: ``git remote add upstream https://github.com/pierre-24/nachos.git``
 + Don't forget to create a separate branch to implement your changes: ``git checkout -b my_branch upstream/dev``.
 

docs/use.rst

@@ -521,6 +521,12 @@ By using ``-d``, you can decide where the input files should be generated, but k
 
 The ``-V 1`` option allows you to know how much files where generated.
 
+
+.. warning::
+
+    When using electric fields, Gaussian compute the fields in an opposite direction to what is expected by Nachos.
+    So, e.g., if the title card say that the field is computed in the +x direction it is the **normal behavior** that the x component of the electric field has a negative sign.
+
 .. note::
 
     To helps the dalton program, a file called ``inputs_matching.txt`` is created for this *flavor*, where each lines contains the combination of dal and mol file to launch (because there may be different dal files).

nachos/__init__.py

@@ -11,34 +11,6 @@
 __email__ = 'pierre.beaujean@unamur.be'
 __status__ = 'Development'
 
-# List of the scripts that are installed, without the .py extension. The name is used to give the command name.
-provide_scripts = [
-    'make',
-    'prepare',
-    'cook',
-    'bake',
-    'shake',
-    'analyze',
-    'peek'
-]
-
-
-def make_console_scripts(package_name='nachos'):
-    """Function used to generate the ``console_scripts`` list for ``setup.py``
-
-    :rtype: list
-    """
-
-    console_scripts = []
-    for script in provide_scripts:
-        path = os.path.join(package_name, script + '.py')
-        if not os.path.isfile(path):
-            raise FileNotFoundError(path)
-
-        console_scripts.append('{0} = {1}.{2}:main'.format('nachos_' + script, package_name, script))
-
-    return console_scripts
-
 
 def is_dir(dirname):
     """Checks if a path is an actual directory"""

nachos/core/__init__.py

@@ -86,6 +86,13 @@
     }
 }
 
+GAUSSIAN_DOUBLE_HYBRIDS = [
+    'B2PLYP', 'B2PLYPD', 'B2PLYPD3',
+    'mPW2PLYP', 'mPW2PLYPD',
+    'DSDPBEP86',
+    'PBE0DH', 'PBEQIDH'
+]
+
 
 def compute_numerical_derivative_of_tensor(
         recipe, basis, derivative_repr, tensor_func, frequency=None, dry_run=False, force_choice=None, **kwargs):

nachos/core/baking.py

@@ -261,10 +261,10 @@ def output_information(
                                 basis_name))
 
                         out.write('\n------------------------------------------------------\n')
-                        out.write(' F          V(F)              V(F)-V(0)\n')
+                        out.write(' F          V(F)                  V(F)-V(0)\n')
                         out.write('------------------------------------------------------\n')
                         zero_field_val = tensor_access(
-                            [0] * len(field), 0, initial_derivative, False, b_coo, final_result.frequency, recipe)
+                            [0] * len(field), 0, initial_derivative, b_coo, final_result.frequency, recipe)
 
                         for i, c in enumerate(all_fields):
                             k = i - recipe['k_max']
@@ -274,7 +274,7 @@ def output_information(
                                 field_val = recipe['min_field'] * recipe['ratio'] ** (abs(k) - 1) * (-1 if k < 0 else 1)
 
                             val = tensor_access(
-                                c, 0, initial_derivative, False, b_coo, final_result.frequency, recipe)
+                                c, 0, initial_derivative, b_coo, final_result.frequency, recipe)
                             dV = val - zero_field_val
                             out.write(
                                 '{: .7f} {: .14e} {: .14e}\n'.format(

nachos/core/cooking.py

@@ -7,7 +7,7 @@
 from qcip_tools import quantities, derivatives, derivatives_e
 from qcip_tools.chemistry_files import helpers, PropertyNotPresent, PropertyNotDefined
 
-from nachos.core import files, preparing
+from nachos.core import files, preparing, GAUSSIAN_DOUBLE_HYBRIDS
 from nachos.qcip_tools_ext import gaussian, qchem  # noqa
 
 
@@ -110,6 +110,11 @@ def almost_the_same(a, b, threshold=1e-3):
         if self.recipe['type'] == 'F':
             try:
                 real_fields = f.property('n:input_electric_field')[1:4]
+
+                if f.file_type in ['GAUSSIAN_FCHK', 'GAUSSIAN_LOG']:
+                    # Gaussian computes actually for the opposite field!
+                    real_fields = list(-x for x in real_fields)
+
             except PropertyNotPresent:
                 raise BadCooking('F derivative but not electric field for {}'.format(name))
         else:
@@ -143,6 +148,8 @@ def almost_the_same(a, b, threshold=1e-3):
                         key = self.recipe['method']
                         if key == 'DFT':
                             key = 'SCF/DFT'
+                            if self.recipe['flavor_extra']['XC'] in GAUSSIAN_DOUBLE_HYBRIDS:
+                                key = 'MP2'  # Gaussian puts the result in the MP2 field instead of SCF/DFT.
                         energy = energies[key]  # tries to catch the energy for the correct method
                     obtained.append('energy:' + self.recipe['method'])
                 else:  # ?!?

nachos/core/files.py

@@ -376,7 +376,7 @@ def read(self, path):
                     self.results[t_fields] = chemistry_datafile.ChemistryDataFile.read_derivatives_from_group(
                         fields_group[i], dof)
 
-    def tensor_element_access(self, fields, min_field, basis, inverse, component, frequency, recipe):
+    def tensor_element_access(self, fields, min_field, basis, component, frequency, recipe):
         t_fields = tuple(fields)
         if t_fields not in self.results:
             raise BadResult('fields {} is not available'.format(fields))
@@ -398,7 +398,7 @@ def tensor_element_access(self, fields, min_field, basis, inverse, component, fr
             if len(component) != results.representation.order():
                 raise BadResult('shape does not match for {}'.format(b_repr))
 
-        return (-1. if inverse else 1.) * results.components[component]
+        return results.components[component]
 
     @staticmethod
     def get_recipe_check_data(recipe):

nachos/core/preparing.py

@@ -240,6 +240,9 @@ def prepare_gaussian_inputs(self, dry_run=False):
                 fi.title = 'field({})='.format(level) + \
                     ','.join(Preparer.nonzero_fields(fields, self.recipe.geometry, self.recipe['type']))
 
+                if self.recipe['type'] == 'F':
+                    fi.title += '\nNote: E-field in the opposite direction is used.'
+
             fi.options['nprocshared'] = self.recipe['flavor_extra']['procs']
             fi.options['mem'] = self.recipe['flavor_extra']['memory']
             fi.options['chk'] = 'xxx'
@@ -281,7 +284,7 @@ def prepare_gaussian_inputs(self, dry_run=False):
                 fi.other_blocks.extend(extra_sections_before)
 
             if self.recipe['type'] == 'F':
-                fi.other_blocks.append(['\t'.join(['{: .10f}'.format(a) for a in real_fields])])
+                fi.other_blocks.append(['\t'.join(['{: .10f}'.format(-a) for a in real_fields])])
 
             if extra_sections:
                 fi.other_blocks.extend(extra_sections)

nachos/qcip_tools_ext/gaussian.py

@@ -46,81 +46,6 @@ def _find_in_links(obj, q, links):
         return -1
 
 
-@gaussian.Output.define_property('computed_energies')
-def gaussian__Output__get_computed_energies(obj, *args, **kwargs):
-    """Get the energies... Actually, "only"
-    + HF and DFT energy (in link 502/503/506/508)
-    + MP2 energy (in link 804/903/905/906)
-    + MP3, CCSD and CCSD(T) energy (in link 913)
-
-    :param obj: object
-    :type obj: qcip_tools.chemistry_files.gaussian.Output
-    :rtype: dict
-    """
-    energies = {}
-    modified_gaussian = False  # pristine Gaussian 16
-
-    # fetch HF or DFT energy
-    n = _find_in_links(obj, 'SCF Done:', [502, 503, 506, 508])
-    if n > 0:
-        chunks = obj.lines[n][12:].split()
-        e = float(chunks[2])
-        if (len(chunks[2]) - chunks[2].find('.')) != 9:
-            modified_gaussian = True
-        else:  # try to fetch more decimals above: "E = xxx" contains eleven of them
-            for line in reversed(obj.lines[:n]):
-                if 'Delta-E=' in line:
-                    e = float(line.split()[1])
-                    break
-                elif 'Cycle' in line:
-                    break
-
-        if 'HF' in chunks[0]:
-            energies['HF'] = e
-        else:
-            energies['SCF/DFT'] = e
-
-        energies['total'] = e
-
-    # fetch MP2 energies
-    n = _find_in_links(obj, 'EUMP2 =', [804, 903, 905, 906])
-    if n > 0:
-        chunk = obj.lines[n].split()[-1]
-        if not modified_gaussian:
-            chunk = chunk.replace('D', 'E')
-
-        energies['MP2'] = float(chunk)
-        energies['total'] = energies['MP2']
-
-    # fetch MP3 energies
-    n = _find_in_links(obj, 'EUMP3=', [913])
-    if n > 0:
-        chunk = obj.lines[n].split()[-1]
-        if not modified_gaussian:
-            chunk = chunk.replace('D', 'E')
-        energies['MP3'] = float(chunk)
-
-    # fetch CCSD energies
-    n = obj.search('Wavefunction amplitudes converged.', into=913)
-    if n > 0:
-        chunk = obj.lines[n - 3][:-16].split()[-1]
-        if not modified_gaussian:
-            chunk = chunk.replace('D', 'E')
-        energies['CCSD'] = float(chunk)
-        energies['total'] = energies['CCSD']
-
-    # fetch CCSD(T) energies
-    n = obj.search('CCSD(T)=', into=913)
-    if n > 0:
-        chunk = obj.lines[n].split()[-1]
-        if not modified_gaussian:
-            chunk = chunk.replace('D', 'E')
-        energies['CCSD(T)'] = float(chunk)
-        energies['total'] = energies['CCSD(T)']
-
-    return energies
-
-
 @gaussian.Output.define_property('n:spin_components_e2')
 def gaussian__Output__get_spin_component_e2(obj, *args, **kwargs):
     """Get the spin components of E(2) (link 906)

pyproject.toml

@@ -0,0 +1,51 @@
+[project]
+name = "nachos"
+dynamic = ["version"]
+authors = [
+    {name = "Pierre Beaujean", email = "pierre.beaujean@unamur.be"},
+]
+description = "NACHOS: numerical differentiation code"
+readme = "README.md"
+requires-python = ">=3.7"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "License :: OSI Approved :: MIT License",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+]
+dependencies = [
+    'pyyaml>=5.0',
+    'h5py',
+    'qcip-tools @ git+https://github.com/pierre-24/qcip_tools.git@v0.7.1',
+    'prompt_toolkit==1.0.15',
+    'pandas>=1.2',
+    'scipy>=1.7',
+    'numpy>=1.20'
+]
+
+
+[project.urls]
+documentation = "https://pierre-24.github.io/nachos/"
+repository = "https://github.com/pierre-24/nachos.git"
+
+[project.scripts]
+
+# keep that alphabetical
+nachos_make = 'nachos.make:main'
+nachos_prepare = 'nachos.prepare:main'
+nachos_cook = 'nachos.cook:main'
+nachos_bake = 'nachos.bake:main'
+nachos_shake = 'nachos.shake:main'
+nachos_analyze = 'nachos.analyze:main'
+nachos_peek = 'nachos.peek:main'
+
+[tool.setuptools]
+packages = ['nachos', 'nachos.core', 'nachos.qcip_tools_ext']
+
+[tool.setuptools.dynamic]
+version = {attr = "nachos.__version__"}

requirements/requirements.in → requirements.in

@@ -1,5 +1,5 @@
--r requirements-base.in
-flake8
+-e file:.  #egg=nachos
+flake8<6.0
 flake8-quotes
 autopep8
 sphinxcontrib-autoprogram