Add ORCA/Gaussian vmol2 plugins with view: selectors

.github/CHANGELOG.md

@@ -37,6 +37,7 @@
 ### Coming in the next version:
 * high-symmetry determination bugs (#21)
 * headless fallback build by @JamesOBrien2 (#44)
+* ORCA / Gaussian plugins for `vmol2`: prompt / `view:` selectors for frequencies, optimization, single point, scan, and IRC trajectories; frequency view builds a selectable mode-displacement trajectory (`mode:` / `scale:` / `npoints:`)
 
 **Full Changelog**: https://github.com/briling/v/compare/v2.0...v3.0rc7
 

README.md

@@ -10,14 +10,18 @@ A simple X11 molecular viewer.
 - [Priroda](http://rad.chem.msu.ru/~laikov) input and output files
 - [`.xyz`](https://en.wikipedia.org/wiki/XYZ_file_format) files
 - [extended `.xyz`](https://github.com/libAtoms/extxyz) files (currently the extra columns are ignored)
-- various quantum-chemical outputs with [cclib](https://github.com/cclib/cclib), see the Python wrapper [page](python/README.md).
+- various quantum-chemical outputs with [cclib](https://github.com/cclib/cclib), see the Python wrapper [page](python/README.md)
+  (`vmol2`; ORCA and Gaussian plugins for frequencies, optimization, single point, scan, and IRC)
 
 ## Python package (wrapper / API) available
 
 See python package page [here](python/README.md).
 
 Provides wrapper scripts with a simple installation and
-allows to open unsupported file formats with `cclib`.
+allows to open unsupported file formats with `cclib` (`vmol2`).
+For ORCA / Gaussian multi-job logs, `vmol2` can prompt (or take `view:` / `vib:`)
+for frequencies, optimization, single point, IRC, or scan
+(see [python/README.md](python/README.md)).
 
 ## Download
 ```bash

python/README.md

@@ -46,16 +46,33 @@ vmol ../mol/MOL_3525.xyz cell:8.93,0.0,0.0,4.2,8.9,0.0,0.48,2.32,10
 python -m vmol../mol/periodic.in bonds:0
 ```
 
-Unsupported quantum-chemical outputs, e.g., Orca:
+Unsupported quantum-chemical outputs, e.g., ORCA or Gaussian:
 ```bash
 vmol2 ../mol/CEHZOF_1_SPE.out
 python -m vmol.vmol2 ../mol/AJALIH_5_SPE.out
+vmol2 mol/Cat1_TSOA_CfA_Cf0.log
 ```
-or Gaussian:
+ORCA and Gaussian logs use dedicated plugins. When a file has several of
+frequencies, optimization, trailing single point (ORCA), scan, or IRC,
+`vmol2` prompts on a TTY (each choice opens in its own `v` session), or accepts:
 ```bash
-vmol2 mol/Cat1_TSOA_CfA_Cf0.log vib:0  #  geometry optimization
-vmol2 mol/Cat1_TSOA_CfA_Cf0.log        #  normal modes (default for files containing both)
+vmol2 job.out view:freq   #  pick a normal mode, then show a displacement path
+vmol2 job.out view:opt    #  geometry optimization frames
+vmol2 job.out view:sp     #  final single-point geometry / energy (ORCA multi-job)
+vmol2 job.out view:irc    #  IRC trajectory
+vmol2 job.out view:scan   #  relaxed surface scan
+vmol2 job.out vib:0       #  geometry path (opt, else SP, else IRC, else scan)
+vmol2 job.out vib:1       #  frequencies (same as view:freq)
+```
+Choosing frequencies (TTY) lists modes with their cm⁻¹ values, then asks for a
+mode number, displacement magnitude (Å), and number of frames. Non-interactive:
+```bash
+vmol2 job.out view:freq mode:1 scale:0.5 npoints:21
 ```
+ORCA IRC frames come from `basename_IRC_Full_trj.xyz` (or the path in the log's
+`Storing full IRC trajectory in ....` line). Gaussian IRC frames are read from
+the `.log` itself when an IRC job is detected. Other packages still use the
+generic cclib path.
 
 ### Library
 
@@ -154,8 +171,10 @@ out = vmol.capture(mols=mols)
 ```
 
 File formats which are not supported natively can be read with `cclib` and passed
-(see [example](https://github.com/briling/v/tree/master/python/examples/ex_cclib.py)
-and [vmol2 source](https://github.com/briling/v/tree/master/python/vmol/vmol2.py)).
+(see [example](https://github.com/briling/v/tree/master/python/examples/ex_cclib.py),
+[vmol2](https://github.com/briling/v/tree/master/python/vmol/vmol2.py), and the
+ORCA / Gaussian plugins under
+[python/vmol/plugins](https://github.com/briling/v/tree/master/python/vmol/plugins)).
 
 One can also pass normal modes data with
 ```python

python/pyproject.toml

@@ -46,4 +46,4 @@ Repository = "https://github.com/briling/v.git"
 "Bug Tracker" = "https://github.com/briling/v/issues"
 
 [tool.setuptools]
-packages = ["vmol"]
+packages = ["vmol", "vmol.plugins"]

python/ruff.toml

@@ -53,3 +53,5 @@ ignore = [
 [lint.per-file-ignores]
 "vmol/__main__.py" = ["D"]
 "examples/ex*.py"  = ["D"]
+"tests/*.py" = ["SLF", "PLC2701", "D"]
+"vmol/plugins/vibtraj.py" = ["PLC2701"]

python/tests/_plugin_fixtures.py

@@ -0,0 +1,20 @@
+"""Shared fixtures for ORCA / Gaussian plugin tests."""
+
+from __future__ import annotations
+
+from types import SimpleNamespace
+
+import numpy as np
+
+
+def coords(*frames):
+    return np.asarray(frames, dtype=float)
+
+
+def base_data(nframes=1):
+    frames = [[[0.0, 0.0, 0.0], [0.0, 0.0, 0.74 + 0.01 * i]] for i in range(nframes)]
+    return SimpleNamespace(
+        atomnos=np.array([1, 1]),
+        atomcoords=coords(*frames),
+        scfenergies=np.array([-27.2 - 0.01 * i for i in range(nframes)]),
+    )

python/tests/test_gaussian_plugin.py

@@ -0,0 +1,112 @@
+"""Unit tests for the Gaussian vmol2 plugin (no viewer / X11)."""
+
+from __future__ import annotations
+
+import os
+import tempfile
+import unittest
+from pathlib import Path
+
+import numpy as np
+
+from _plugin_fixtures import base_data
+from vmol import vmol2
+from vmol.plugins import plugin_for
+from vmol.plugins.gaussian import GaussianPlugin, _log_has_irc
+
+
+class TestGaussianInventory(unittest.TestCase):
+    """Inventory detection for Gaussian frequencies / optimization / IRC."""
+
+    def setUp(self):
+        """Create a temporary directory for fake log paths."""
+        self.tmpdir = tempfile.TemporaryDirectory()
+        self.addCleanup(self.tmpdir.cleanup)
+        self.log_path = os.path.join(self.tmpdir.name, "job.log")
+
+    def _write_log(self, text: str) -> str:
+        Path(self.log_path).write_text(text, encoding="utf-8")
+        return self.log_path
+
+    def test_opt_plus_freq(self):
+        """Opt+freq Link1 jobs expose both datasets."""
+        data = base_data(4)
+        data.geovalues = np.ones((4, 4))
+        data.optdone = True
+        data.vibfreqs = np.array([100.0, 200.0])
+        data.vibdisps = np.zeros((2, 2, 3))
+        data.vibdisps[:, 0, 0] = 1.0
+        self._write_log("Entering Gaussian System\n")
+
+        datasets = GaussianPlugin.inventory(self.log_path, data)
+        self.assertEqual([d.key for d in datasets], ["freq", "opt"])
+        self.assertEqual(len(datasets[1].mols), 4)
+        np.testing.assert_allclose(datasets[0].mols[0]["r"], data.atomcoords[3])
+
+    def test_irc_log_labeled_as_irc(self):
+        """IRC marker lines label the trajectory as irc, not opt."""
+        data = base_data(5)
+        data.geovalues = np.ones((5, 4))
+        data.optdone = True
+        self._write_log(
+            "Entering Gaussian System\nIRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC\n",
+        )
+        datasets = GaussianPlugin.inventory(self.log_path, data)
+        self.assertEqual([d.key for d in datasets], ["irc"])
+        self.assertEqual(len(datasets[0].mols), 5)
+
+    def test_single_point_geometry(self):
+        """A lone single-point job yields one geom dataset."""
+        data = base_data(1)
+        self._write_log("Entering Gaussian System\n")
+        datasets = GaussianPlugin.inventory(self.log_path, data)
+        self.assertEqual([d.key for d in datasets], ["geom"])
+
+    def test_log_has_irc_route(self):
+        """Route lines containing irc are detected."""
+        path = self._write_log("#p b3lyp/6-31g(d) irc=(calcfc,maxpoints=20)\n")
+        self.assertTrue(_log_has_irc(path))
+        path = self._write_log("#p b3lyp/6-31g(d) opt freq\n")
+        self.assertFalse(_log_has_irc(path))
+
+
+class TestGaussianSampleFile(unittest.TestCase):
+    """Integration check against the repo Gaussian opt+freq sample."""
+
+    @classmethod
+    def setUpClass(cls):
+        """Resolve the sample Gaussian logfile paths."""
+        mol = os.path.abspath(
+            os.path.join(os.path.dirname(__file__), "..", "..", "mol"),
+        )
+        cls.path = os.path.join(mol, "Cat1_TSOA_CfA_Cf0.log")
+        cls.spc = os.path.join(mol, "Cat1_TSOA_CfA_Cf0_SPC.log")
+
+    def test_parse_and_inventory_opt_freq(self):
+        """Sample opt+freq log exposes freq and opt selectors."""
+        if not os.path.isfile(self.path):
+            self.skipTest("sample Gaussian logfile not present")
+
+        parser, data = GaussianPlugin.parse(self.path)
+        self.assertEqual(parser.logname, "Gaussian")
+        self.assertIs(plugin_for(parser), GaussianPlugin)
+        datasets = GaussianPlugin.inventory(self.path, data)
+        self.assertEqual([d.key for d in datasets], ["freq", "opt"])
+        by_key = {d.key: d for d in datasets}
+        self.assertEqual(len(by_key["freq"].vib["freq"]), 123)
+        self.assertEqual(len(by_key["opt"].mols), 10)
+        chosen = vmol2._choose_datasets(datasets, ["opt"], None)
+        self.assertEqual(chosen[0].key, "opt")
+
+    def test_parse_spc(self):
+        """Separate single-point log is a single geometry."""
+        if not os.path.isfile(self.spc):
+            self.skipTest("sample Gaussian SPC logfile not present")
+        _parser, data = GaussianPlugin.parse(self.spc)
+        datasets = GaussianPlugin.inventory(self.spc, data)
+        self.assertEqual([d.key for d in datasets], ["geom"])
+        self.assertEqual(len(datasets[0].mols), 1)
+
+
+if __name__ == "__main__":
+    unittest.main()