Moltemplate2.22.5 graph/type/charge andgenerated-file examples
Own4-site A-B-A-B chain,masses1/2,reducedLJ coordinates;not a fitted chemical molecule.
3typed harmonicbondsK100r01.3;2automatic harmonicanglesK5theta090;1automatic OPLSdihedral0.2/0.1/0.05/0.
Three genuine LAMMPSrun0 branches:explicit nativechargepass;initialDATAq0withoutchargefile;angle105degree nonzero-force control.
NoMD,relaxation orCoulombenergy isclaimed:pair_style zero4.0 deliberately omitsnonbondinteractions.
Perbond A/B increments+0.2/-0.2 give+0.2,-0.4,+0.4,-0.2 withzero totalcharge.
Installed wrapper passes both finaltypedBonds and originalBondList andduplicates these increments.
assign-charges.sh invokes unmodifiednative charge_by_bond.py with onlythe finaltypedtable,then replaces system.in.charges before use.
native-auto-charges.in is a clearly documented version-boundary control,NOT the corrected runchargefile.
DATA qfields remain0;include system.in.charges after read_data andsettings to apply runtimecharges.
Generated setatomcharge commands assignvalues;do not assume they automaticallyadd nonzero initial DATAcharges.
Actual source wrapperfailure andallfailed-control evidence retained privately;originalnumericgates notrelaxed.
Source40checks;exactfresh ordinary/finalZIP workflows validate everycoordinate,topology,mass,charge,energycomponent andforcegradient.
RecalculateallocatedCPU resources:sbatch job.slurm;or bash run.sh withinallocation.
Viewrealreference:bash show-reference.sh;re-analyzeexistingwork:bash analyze-results.sh.
ExistingMoltemplate2.22.5Python3.11,LAMMPS30Sep2026oneAPI2024.2IntelMPI/MKL;plotPythonvia sisl0.16.4.
Sourceprivateexecutiontrace confirms15nativeentries;internalhelpers are not15newphysicalmethods.All32entrypoints notclaimedcomplete.
