Add example for challenging SCF convergence

.gitignore

@@ -208,11 +208,9 @@ data/*/processed*
 data/misc
 
 # exclude some sample and reaction files for tests
-!data/GMTKN55/samples_ACONF.json
-!data/GMTKN55/reactions_ACONF.json
-
 !test/test_singlepoint/**/coord
-!test/test_singlepoint/**/.CHRG
+!examples/issues/**/coord
+!examples/issues/**/*.xyz
 
 !test/test_io/**/*.json
 !test/test_io/**/coord

examples/issues/123/coord

@@ -0,0 +1,13 @@
+$coord
+    0.03579425573719     -0.09112374056391      0.89335307999458      cr
+    5.42783204665614     -2.17294661121026      0.65916514368075      o
+    3.40375271909106     -1.38928570065300      0.82378719806096      c
+   -0.04074270812561     -0.17596705876656     -2.57265467283161      c
+   -0.08912415394703     -0.22969604472894     -4.75994430975133      o
+   -3.33299931144879      1.20626988769390      0.90894089019304      c
+   -5.36291624030506      1.98396405987989      0.79581613233819      o
+    1.33083886695733      3.27583741049000      0.75516281864174      c
+    2.10688687476585      5.29904198098028      0.54889443619263      o
+   -1.26102459345897     -3.45925462128772      0.97643580779788      c
+   -2.04398697392212     -5.48898687883367      0.90363185868314      o
+$end

examples/issues/123/run.py

@@ -0,0 +1,54 @@
+# This file is part of dxtb.
+#
+# SPDX-Identifier: Apache-2.0
+# Copyright (C) 2024 Grimme Group
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+https://github.com/grimme-lab/dxtb/issues/123
+"""
+from __future__ import annotations
+
+from pathlib import Path
+
+import torch
+from tad_mctc.io import read
+
+import dxtb
+
+
+def main() -> int:
+    dd = {"device": torch.device("cpu"), "dtype": torch.double}
+    dxtb.timer.cuda_sync = False
+
+    # read molecule from file
+    f = Path(__file__).parent / "coord"
+    numbers, positions = read.read_from_path(f, **dd)
+    charge = read.read_chrg_from_path(f, **dd)
+
+    opts = {"verbosity": 6, "scp_mode": dxtb.labels.SCP_MODE_CHARGE}
+    calc = dxtb.calculators.GFN1Calculator(numbers, opts=opts, **dd)
+
+    ref = -35.800705002354
+    energy = calc.get_energy(positions, chrg=charge)
+
+    print("\nComparison to xtb:")
+    print(f" - xtb (6.7.1) : {ref: .12f}")
+    print(f" - dxtb (0.1.0): {energy: .12f}")
+    print(f" - diff        : {energy - ref: .12f}")
+
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())