1.1 A reproducible executable and input tree
These are unexecuted teaching inputs and starting models. Original diagrams are schematics, not calculated results. Validate version-specific syntax, licensed or authorized data, numerical convergence and the scientific model before using this workflow.
1.1.1 Model, units and provenance
Keep basis/potential files and executable versions traceable. Grid controls use Ry; common energy/force outputs use hartree and hartree/bohr. Read the unit in each output heading.
Shared inputs, conventions and evidence
1.1.2 Unexecuted inputs and explicit deltas
Use the accompanying instructions to identify the parent calculation and placement of every delta; a snippet is not automatically a standalone input. Preserve all blank-line and file-provenance requirements.
1.1.2.1 Input block 1
cp2k.psmp --version > cp2k-version.txt
cp2k.psmp --help > cp2k-help.txt
export OMP_NUM_THREADS=1
cp2k.psmp -i water_A.inp -o water_A.out
sha256sum water_A.inp > inputs.sha256
1.1.3 Worked investigation
Intuition and prerequisites. A simulation has two inputs: the visible text and the software/data environment that interprets it. A correctly spelled basis name can resolve to a different data record after a package update; a binary built without an optional library may reject a method that appears in the online manual. Before studying chemistry, establish a small, reproducible calculation. You need shell access, an installed CP2K build approved by your computing center, and the matching data directory. Installing an arbitrary binary is outside this course; use an official release or a maintained site module.
Original operational example. The following shell commands inspect and run a locally installed program. Substitute the executable name provided by the installation. psmp conventionally denotes MPI plus OpenMP capability, but suffixes alone do not prove the linked libraries or accelerator support. On a cluster, obtain an allocation and use its documented launcher; do not start an MPI job on a login node.
See input block 1 above.
Workflow. 1. Save baseline A verbatim in a fresh directory, and locate the actual basis and potential files without editing them. Record absolute paths and checksums. 2. Read GLOBAL as the requested task, FORCE_EVAL as the energy/force engine, DFT as the electronic model and SUBSYS as atoms plus cell. Draw this tree before changing any keyword. 3. Run one small single-point calculation using one process. Inspect the opening banner, effective data paths, atom count, electron count and warnings before reading the final energy. 4. Require an explicit converged SCF and normal program termination. Preserve stderr even if the output file looks complete. 5. Repeat in a new directory with the same executable and files, then compare the observable at a tolerance appropriate to floating-point arithmetic.
Interpretation and tests. With O q6 and two H q1 potentials, neutral water has eight explicitly treated electrons, hence four doubly occupied orbitals for the restricted singlet. This electron-count arithmetic is a structural sanity check independent of the energy. A nonzero force is expected for the deliberately distorted starting geometry. A normal exit is necessary but not sufficient: a calculation can finish while warning that SCF convergence was not achieved. Record the parser's resolved settings when diagnosing defaults.
Pitfalls and limits. PROJECT controls many output prefixes; reusing it in the same directory can mix old and new data. A .wfn file is electronic state, not a universal portable record of an entire MD trajectory. A module name is not a full build specification. Do not put a proprietary path or username in a published teaching input. Do not remove warnings merely to make a tutorial look clean.
Exercise and deliverable. Deliberately misspell one KIND label in a copy, predict the failure, and record the earliest informative error. Restore it and prepare a manifest containing version, command, data hashes, input hash and success criteria. Explain why an energy number without that manifest is difficult to reproduce.