Parallelization for gp3_ipea (#109)

* initial work * new parallelization preliminary done * small fix in tests * commented unnecessary code * updated construction sites * hopefully fixed parallelization * small test fix * initial work * new parallelization preliminary done * small fix in tests * commented unnecessary code * updated construction sites * hopefully fixed parallelization * small test fix * only print when verbosity > 0, otherwise nothing is printed (bad) * pre-commit fixes * added ncores to config + implemented setting ncores for external programs * fixed tests * added check for number of cores available vs needed * pre-commit * Added support for Turbomole (#101) * Interface for the qm program turbomole Signed-off-by: Jonathan Schöps <[email protected]> * support for turbomole Signed-off-by: Jonathan Schöps <[email protected]> * corrected some typos Signed-off-by: Jonathan Schöps <[email protected]> * changed the PARNODES command Signed-off-by: Jonathan Schöps <[email protected]> * coord handling Signed-off-by: Jonathan Schöps <[email protected]> * requestet changes are build in Signed-off-by: Jonathan Schöps <[email protected]> * Implementation of the requested changes and the test of the read_mol_from_coord function Signed-off-by: Jonathan Schöps <[email protected]> * Implementation of two pathes for turbomole Signed-off-by: Jonathan Schöps <[email protected]> * Ignore HOMO-LUMO gap not implemented as refine engine for Orca and Trubomole Signed-off-by: Jonathan Schöps <[email protected]> * improve TURBOMOLE configuration Signed-off-by: Marcel Müller <[email protected]> * correct linting errors Signed-off-by: Marcel Mueller <[email protected]> * exclude more recent interfaces from coverage check Signed-off-by: Marcel Müller <[email protected]> * added a test for the 'write_coord_to_file' function Signed-off-by: Jonathan Schöps <[email protected]> * sync the lokal branch with the remote branch Signed-off-by: Jonathan Schöps <[email protected]> --------- Signed-off-by: Jonathan Schöps <[email protected]> Signed-off-by: Marcel Müller <[email protected]> Signed-off-by: Marcel Mueller <[email protected]> Co-authored-by: Marcel Müller <[email protected]> * test fix * fixed tm implementation * updated main.py * tqdm progress bar * updated dependencies * mypy types import * moved warnings in correct bracket * updated default config toml * added final output of molecules and timing * fixed time * better time info * print formatting * shift block setup to parallel.py Signed-off-by: Marcel Müller <[email protected]> * avoid UnboundLocalError Signed-off-by: Marcel Müller <[email protected]> * some code formatting and printout adjustments Signed-off-by: Marcel Müller <[email protected]> * shifted CHANGELOG entry to correct position Signed-off-by: Marcel Müller <[email protected]> * update CODEOWNERS file Signed-off-by: Marcel Müller <[email protected]> * New parallelization (#108) * initial work * new parallelization preliminary done * small fix in tests * commented unnecessary code * updated construction sites * hopefully fixed parallelization * small test fix * initial work * new parallelization preliminary done * small fix in tests * commented unnecessary code * updated construction sites * hopefully fixed parallelization * small test fix * only print when verbosity > 0, otherwise nothing is printed (bad) * pre-commit fixes * added ncores to config + implemented setting ncores for external programs * fixed tests * added check for number of cores available vs needed * pre-commit * test fix * fixed tm implementation * updated main.py * tqdm progress bar * updated dependencies * mypy types import * moved warnings in correct bracket * updated default config toml * added final output of molecules and timing * fixed time * better time info * print formatting * shift block setup to parallel.py Signed-off-by: Marcel Müller <[email protected]> * avoid UnboundLocalError Signed-off-by: Marcel Müller <[email protected]> * some code formatting and printout adjustments Signed-off-by: Marcel Müller <[email protected]> * shifted CHANGELOG entry to correct position Signed-off-by: Marcel Müller <[email protected]> * update CODEOWNERS file Signed-off-by: Marcel Müller <[email protected]> --------- Signed-off-by: Marcel Müller <[email protected]> Co-authored-by: Marcel Müller <[email protected]> * add IP/EA check with g-xTB for special purpose dev application only Signed-off-by: Marcel Müller <[email protected]> * rename gp3 to gxtb consistently Signed-off-by: Marcel Müller <[email protected]> * add simple SCF cycles check for molecule Signed-off-by: Marcel Mueller <[email protected]> * align variable names with g-xTB Signed-off-by: Marcel Mueller <[email protected]> * config is now loaded in dev mode; avoid redundant calculations Signed-off-by: Marcel Mueller <[email protected]> * hand over correct config and remove redundant config Signed-off-by: Marcel Mueller <[email protected]> * remove last rememnant of config for SCF cycles with g-xTB Signed-off-by: Marcel Mueller <[email protected]> * added ncores to gxtb calls * remove redundant config entry Signed-off-by: Marcel Mueller <[email protected]> --------- Signed-off-by: Jonathan Schöps <[email protected]> Signed-off-by: Marcel Müller <[email protected]> Signed-off-by: Marcel Mueller <[email protected]> Co-authored-by: Jonathan Schöps <[email protected]> Co-authored-by: Marcel Müller <[email protected]>
grimme-lab · Jan 20, 2025 · 8b82a86 · 8b82a86
1 parent 3a90201
commit 8b82a86
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diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -1,12 +1,12 @@
 # These owners will be the default owners for everything in
 # the repo. Unless a later match takes precedence,
-# @marcelmbn and @thfroitzheim will be requested for
+# the names mentioned after the '*' will be requested for
 # review when someone opens a pull request.
 *  @marcelmbn @jonathan-schoeps
 
 # These parts are specifically owned by some people
 /src/mindlessgen/cli @marcelmbn
-/src/mindlessgen/generator @marcelmbn
+/src/mindlessgen/generator @marcelmbn @lmseidler
 /src/mindlessgen/molecules @marcelmbn @jonathan-schoeps
-/src/mindlessgen/prog @marcelmbn @jonathan-schoeps
-/src/mindlessgen/qm @marcelmbn
+/src/mindlessgen/prog @marcelmbn @jonathan-schoeps @lmseidler
+/src/mindlessgen/qm @marcelmbn @jonathan-schoeps
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,9 +9,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - to set the elemental composition it is now possible to use dicts with not only int but also the element symbols (str)
 - dict keys for elemental compositions will now always be checked for validity
 - Renamed GP3-xTB to g-xTB
+- Nothing will be printed while multiple molecules are generated in parallel, tqdm-based progress bar instead
+- Some debugging statements from generate had to be removed (esp. w.r.t. early stopping)
 
 ### Added
 - `GXTBConfig` class for the g-xTB method, supporting SCF cycles check
+- support for TURBOMOLE as QM engine.
+- updated the parallelization to work over the number of molecules
 
 ### Fixed
 - version string is now correctly formatted and printed

diff --git a/environment.yml b/environment.yml
@@ -9,5 +9,6 @@ dependencies:
   - pre-commit
   - pytest
   - tox
+  - tqdm
   - pip:
       - covdefaults
diff --git a/mindlessgen.toml b/mindlessgen.toml
@@ -51,16 +51,18 @@ molecular_charge = "none"
 [refine]
 # > Maximum number of fragment optimization cycles. Options: <int>
 max_frag_cycles = 10
-# > Quantum Mechanics (QM) engine to use. Options: 'xtb', 'orca'
+# > Quantum Mechanics (QM) engine to use. Options: 'xtb', 'orca'. 'turbomole'
 engine = "xtb"
 # > HOMO-LUMO gap threshold applied at the end of the refinement step
 hlgap = 0.5
 # > Debug this step. Leads to more verbose output as soon as the refinement part is reached. Options: <bool>
 # > If `debug` is true, the process is terminated after the first (successful or not) refinement step.
 debug = false
+# > Number of cores to be used for geometry optimizations. Single-points will continue to use one core each.
+ncores = 4
 
 [postprocess]
-# > Engine for the post-processing part. Options: 'xtb', 'orca'
+# > Engine for the post-processing part. Options: 'xtb', 'orca', 'turbomole'
 engine = "orca"
 # > Optimize geometry in the post-processing part. If `false`, only a single-point is conducted. Options: <bool>
 optimize = true
@@ -70,6 +72,8 @@ opt_cycles = 5
 # > If `debug` is true, the process is terminated after the first (successful or not) post-processing step.
 # > Note: This option is only relevant if the 'postprocess' option in the 'general' section is set to 'true'.
 debug = false
+# > Number of cores to be used for both single-point calculations and geometry optimizations.
+ncores = 4
 
 [xtb]
 # > Path to the xtb executable. The names `xtb` and `xtb_dev` are automatically searched for. Options: <str | Path>
@@ -88,3 +92,15 @@ basis = "def2-SVP"
 gridsize = 1
 # > Maximum number of SCF cycles: Options: <int>
 scf_cycles = 100
+
+[turbomole]
+# > Path to the ridft executable. The name `ridft` is automatically searched for. Options: <str | Path>
+ridft_path = "/path/to/ridft"
+# > Path to the jobex executable. The name `jobex` is automatically searched for. Options: <str | Path>
+jobex_path = "/path/to/jobex"
+# > Functional/Method: Options: <str>
+functional = "PBE"
+# > Basis set: Options: <str>
+basis = "def2-SVP"
+# > Maximum number of SCF cycles: Options: <int>
+scf_cycles = 100
diff --git a/pyproject.toml b/pyproject.toml
@@ -22,7 +22,7 @@ classifiers = [
     "Topic :: Scientific/Engineering",
     "Typing :: Typed",
 ]
-dependencies = ["numpy", "networkx", "toml"]
+dependencies = ["numpy", "networkx", "toml", "tqdm"]
 dynamic = ["version"]
 
 [project.urls]
@@ -41,6 +41,7 @@ dev = [
     "tox",
     "setuptools_scm>=8",
     "types-toml",
+    "types-tqdm",
 ]
 
 [project.scripts]
@@ -59,7 +60,12 @@ markers = "optional: mark test as optional"
 plugins = ["covdefaults"]
 source = ["./src"]
 # Exclude interfaces to external programs from coverage
-omit = ["src/mindlessgen/qm/xtb.py", "src/mindlessgen/qm/orca.py"]
+omit = [
+    "src/mindlessgen/qm/xtb.py",
+    "src/mindlessgen/qm/orca.py",
+    "src/mindlessgen/qm/tm.py",
+    "src/mindlessgen/qm/gxtb.py",
+]
 
 [tool.coverage.report]
 fail_under = 50
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,5 +9,6 @@ dependencies: @@
       - pre-commit
       - pytest
       - tox
+      - tqdm
       - pip:
           - covdefaults