Merge pull request #4 from YuriOku/gamer_plugin

added gamer plugin

README.md

@@ -11,7 +11,7 @@ To learn how to use MUSIC, please [read the Wiki](https://github.com/cosmo-sims/
 
 Current MUSIC key features include:
 
-- Supports output for RAMSES, ENZO, Arepo, Swift, Gadget-2/3, ART, Pkdgrav/Gasoline and NyX via plugins. New codes can be added.
+- Supports output for RAMSES, ENZO, Arepo, Swift, Gadget-2/3, ART, Pkdgrav/Gasoline, NyX, and GAMER-2 via plugins. New codes can be added.
 - Support for first (1LPT) and second order (2LPT) Lagrangian perturbation theory.
 - Full integration of the [PANPHASIA](https://arxiv.org/abs/1306.5968) hierarchical Gaussian random fields
 - Pluggable transfer functions, currently CAMB, Eisenstein&Hu, BBKS, Warm Dark Matter variants. Distinct baryon+CDM fields.

ics_example.conf

@@ -71,4 +71,8 @@ seed[12]		= 67890
 #format			= gadget2
 #filename		= ics_gadget.dat
 
+## GAMER-2 compatible output format
+#format     = gamer2
+#filename   = UM_IC
+#parfilename = PAR_IC
 

src/mesh.hh

@@ -1521,6 +1521,18 @@ public:
 			kr = ((kr % gridding_unit_) != 0) ? (kr / gridding_unit_ + 1) * gridding_unit_ : kr;
 		}
 
+		// require alighment with coarser block
+		if (blocking_factor_)
+		{
+			unsigned coarse_block = 2 * blocking_factor_;
+			il -= il % coarse_block;
+			jl -= jl % coarse_block;
+			kl -= kl % coarse_block;
+			ir += (nresmax - ir) % coarse_block;
+			jr += (nresmax - jr) % coarse_block;
+			kr += (nresmax - kr) % coarse_block;
+		}
+
 		// if doing unigrid, set region to whole box
 		if (levelmin_ == levelmax_)
 		{
@@ -1634,6 +1646,19 @@ public:
 				kr = ((kr % gridding_unit_) != 0) ? (kr / gridding_unit_ + 1) * gridding_unit_ : kr;
 			}
 
+			// require alighment with coarser block
+			if (blocking_factor_)
+			{
+				unsigned coarse_block = 2 * blocking_factor_;
+				int nres = 1 << ilevel;
+				il -= il % coarse_block;
+				jl -= jl % coarse_block;
+				kl -= kl % coarse_block;
+				ir += (nres - ir) % coarse_block;
+				jr += (nres - jr) % coarse_block;
+				kr += (nres - kr) % coarse_block;
+			}
+
 			if (il >= ir || jl >= jr || kl >= kr || il < 0 || jl < 0 || kl < 0)
 			{
 				music::elog.Print("Internal refinement bounding box error: [%d,%d]x[%d,%d]x[%d,%d], level=%d", il, ir, jl, jr, kl, kr, ilevel);