diff --git a/doc/graphviz/Makefile b/doc/graphviz/Makefile index a8c424c540..a3e0c94c63 100644 --- a/doc/graphviz/Makefile +++ b/doc/graphviz/Makefile @@ -17,7 +17,7 @@ clean: ifeq ($(HAS_DOT),YES) $(IMGDIR)/%.png: %.dot - dot -Tpng -o $@ $< + dot -Tpng -Kneato -o $@ $< endif ifeq ($(HAS_DOT),NO) diff --git a/doc/graphviz/lammps-classes.dot b/doc/graphviz/lammps-classes.dot index 2573ff7c52..3c2d2f418d 100644 --- a/doc/graphviz/lammps-classes.dot +++ b/doc/graphviz/lammps-classes.dot @@ -1,7 +1,8 @@ // LAMMPS Class topology digraph lammps { - rankdir="LR" - La [shape=circle label="LAMMPS"] + overlap=false + splines=true + La [shape=circle label="LAMMPS" pos="0,0"] At [shape=box label="Atom" color=blue] Ci [shape=box label="CiteMe"] Co [shape=box label="Comm" color=blue] @@ -17,6 +18,7 @@ digraph lammps { Up [shape=box label="Update" color=blue] Un [shape=box label="Universe" color=blue] Ti [shape=box label="Timer" color=blue] + Lt [label="Lattice"] Rg [label="Region" color=red] Rb [shape=box label="RegionBlock"] Rs [shape=box label="RegionSphere"] @@ -59,6 +61,11 @@ digraph lammps { Fh [shape=box label="FixNH"] Fp [shape=box label="FixNPT"] Ft [shape=box label="FixNVT"] + Ce [shape=box label="ComputeTemp"] + Ca [shape=box label="ComputeTempAtom"] + Cr [shape=box label="ComputeReduce"] + Cg [shape=box label="ComputeReduceRegion"] + Ck [shape=box label="ComputeTempKokkos"] Da [shape=box label="DumpAtom"] Dc [shape=box label="DumpCustom"] Dg [shape=box label="DumpCFG"] @@ -67,10 +74,12 @@ digraph lammps { Pt [shape=box label="PPPMTIP4P"] Vs [shape=box label="VerletSplit"] Ro [shape=box label="RespaOMP"] + Mc [shape=box label="MinCG"] + Mf [shape=box label="MinFire"] La -> {At Ci Co Do Er Fo Gr In Me Mo Ne Ou Ti Up Un} [penwidth=2] - Do -> {Rg} [penwidth=2] - Co -> {Cb Ct} [style=dashed penwidth=2] + Do -> {Lt Rg} [penwidth=2] Rg -> {Rb Rs} [style=dashed penwidth=2] + Co -> {Cb Ct} [style=dashed penwidth=2] In -> Va [penwidth=2] Mo -> {Fi Cp} [penwidth=2] Fo -> {Pa Bo An Di Im Ks} [penwidth=2] @@ -91,7 +100,11 @@ digraph lammps { Bh -> Bp [style=dashed penwidth=2] Fi -> {Fa Fn Fh} [style=dashed penwidth=2] Fh -> {Fp Ft} [style=dashed penwidth=2] + Cp -> {Ce Ca Cr} [style=dashed penwidth=2] + Ce -> Ck [style=dashed penwidth=2] + Cr -> Cg [style=dashed penwidth=2] Ve -> Vs [style=dashed penwidth=2] Rr -> Ro [style=dashed penwidth=2] + Mi -> {Mc Mf} [style=dashed penwidth=2] } diff --git a/doc/src/Developer_org.rst b/doc/src/Developer_org.rst index abfe72260a..c234cd11cc 100644 --- a/doc/src/Developer_org.rst +++ b/doc/src/Developer_org.rst @@ -78,7 +78,7 @@ in the figure for demonstration purposes. the core is the :cpp:class:`LAMMPS ` class, which holds pointers to class instances with specific purposes. Those may hold instances of other classes, sometimes directly, or only - temporarily, sometimes as derived classes or derived classes or + temporarily, sometimes as derived classes or derived classes of derived classes, which may also hold instances of other classes. The :cpp:class:`LAMMPS_NS::LAMMPS` class is the topmost class and diff --git a/doc/src/JPG/lammps-classes.png b/doc/src/JPG/lammps-classes.png index cdf165350d..e401328783 100644 Binary files a/doc/src/JPG/lammps-classes.png and b/doc/src/JPG/lammps-classes.png differ