Merge pull request #490 from llaniewski/develop-refactor

Small mods to develop

example/heat/d2q9q9_Hot_Karman_Re100_Pr5.xml

@@ -1,7 +1,5 @@
-
-<!-- To be used with d2q9q9_cm_cht_OutFlowNeumann_AVG_IBB -->
-
 <?xml version="1.0"?>
+<!-- To be used with d2q9q9_cm_cht_OutFlowNeumann_AVG_IBB -->
 <CLBConfig version="2.0" output="output/d2q9q9_HotKarman_Re100_Pr5/">
     <Geometry nx="512" ny="100" > 
       <!-- <CM_HIGHER> <Box/> </CM_HIGHER>   -->

example/heat/d2q9q9_lid_driven_cavity.xml

@@ -1,7 +1,5 @@
-
-<!-- To be used with d2q9q9_cm_cht -->
-
 <?xml version="1.0"?>
+<!-- To be used with d2q9q9_cm_cht -->
 <CLBConfig version="2.0" output="output/d2q9q9_LidDrivenCavity/">
     <Geometry nx="256" ny="256" > 
         <CM_HIGHER> <Box/> </CM_HIGHER>  

example/heat/d3q27q27_Hot_Karman_Re100_Pr5.xml

@@ -1,7 +1,5 @@
-
-<!-- To be used with d3q27q27_cm_cht_OutFlowNeumann_AVG_IBB -->
-
 <?xml version="1.0"?>
+<!-- To be used with d3q27q27_cm_cht_OutFlowNeumann_AVG_IBB -->
 <CLBConfig version="2.0" output="output/d3q27q27_HotKarman_Re100_Pr5/">
     <Geometry nx="512" ny="100" nz="3" > 
       <BGK> <Box/> </BGK>  

example/heat/d3q27q7_Hot_Karman_Re100_Pr5.xml

@@ -1,7 +1,5 @@
-
-<!-- To be used with d3q27q27_cm_cht_OutFlowNeumann_AVG_IBB -->
-
 <?xml version="1.0"?>
+<!-- To be used with d3q27q27_cm_cht_OutFlowNeumann_AVG_IBB -->
 <CLBConfig version="2.0" output="output/d3q27q7_HotKarman_Re100_Pr5/">
     <Geometry nx="512" ny="100" nz="3" > 
       <CM> <Box/> </CM>  

example/multiphase/csf/cm_template_TaylorBubble.xml → example/multiphase/csf/cm_template_TaylorBubble.xml.Rt

@@ -103,5 +103,3 @@ for (i in 1:nrow(tab)) {
     detach()
 }
 ?>
-
-

src/Handlers.h

@@ -1,6 +1,7 @@
 #ifndef Handler_H
 #define Handler_H
 
+#include "Global.h"
 #include "Handlers/vHandler.h"
 #include "Handlers/NullHandler.h"
 #include "HandlerFactory.h"

src/Handlers/vHandler.h

@@ -1,7 +1,6 @@
 #ifndef VHANDLER_H
 #define VHANDLER_H
 
-#include "../Consts.h"
 #include "../pugixml.hpp"
 #include <math.h>
 #define HANDLER_CALLBACK  0x01

src/Lattice.hpp.Rt

@@ -9,6 +9,8 @@ c_header();
 #include <utility>
 
 #include "Global.h"
+#include "CartLattice.h"
+
 
 template <typename LatticeType>
 struct Lattice : public LatticeType {

src/Node.hpp.Rt

@@ -193,18 +193,17 @@ template < class LA > struct Node < LA, <?%s T1 ?>, <?%s T2 ?>, <?%s T3 ?> > {
 	CudaDeviceFunction void inline Glob() {
 		glob.Glob();
 	}
-	<?R
-		if (! tp$adjoint) { ?>
-	#include "Dynamics.h" <?R
-		} else { ?>
-	#undef DYNAMICS_B_LOADED <?R
-		} ?>
-//	#include "Dynamics.h"
+	<?R	for (n in c_table_decl(unique(c(Density$name,Fields$name)))) { ?>
+	real_t <?%s n ?>;
+	<?R } ?>
+
 #ifdef CALC_DOUBLE_PRECISION
 	#include "Dynamics.c"
 #else
 	#include "Dynamics_sp.c"
-#endif <?R
+#endif
+
+<?R
 		if (tp$adjoint) {
 		        if (tp$Globals == "Globs") { ?>
         #include "DynamicsS_b.c" <?R

src/RemoteForceInterface.hpp

@@ -12,8 +12,8 @@
  #define output printf
  #define RFI_DEF_output
 #endif
-#ifndef STRING_LEN
- #define STRING_LEN 1024*4
+#ifndef RFI_STRING_LEN
+ #define RFI_STRING_LEN 1024*4
 #endif
 
 namespace rfi {
@@ -148,7 +148,7 @@ void RemoteForceInterface < TYPE, ROT, STORAGE, rfi_real_t, tab_allocator >::all
    sizesStatsNum = 0;
    waitStats.resize(12, 0);
    waitStatsNum.resize(12, 0);
-   char fn[STRING_LEN];
+   char fn[RFI_STRING_LEN];
 
    if (stats_prefix == "") stats_prefix = "RFI";
    sprintf(fn, "%s_%s_P%02d.txt", stats_prefix.c_str(), name.c_str(), rank);
@@ -184,7 +184,7 @@ void RemoteForceInterface < TYPE, ROT, STORAGE, rfi_real_t, tab_allocator >::sav
 template < rfi_type_t TYPE, rfi_rot_t ROT, rfi_storage_t STORAGE, typename rfi_real_t, typename tab_allocator >
 void RemoteForceInterface < TYPE, ROT, STORAGE, rfi_real_t, tab_allocator >::printStats() {
   if (sizesStatsNum == stats_iter) {
-   char fn[STRING_LEN];
+   char fn[RFI_STRING_LEN];
    sprintf(fn, "RFI_stats_%s_%d.txt", name.c_str(), rank);
    FILE * f = fopen(stats_filename.c_str(), "a");
    fprintf(f,"%ld", sizesStatsNum);

src/SUMMARY.Rt

@@ -1,5 +1,5 @@
 <?R
-  plot.access=TRUE
+  plot_access=TRUE
   source("conf.R")
   save.image(file="SUMMARY.Rdata")
   options(width=4000)

src/ZoneSettings.h

@@ -1,7 +1,10 @@
 #include "Consts.h"
+#include "Global.h"
 #include "cross.h"
+#include "types.h"
 #include <stdlib.h>
 #include <assert.h>
+#include <vector>
 
 #ifndef ZONESETTINGS_H
 #define ZONESETTINGS_H

src/conf.R

@@ -16,15 +16,14 @@ if (!exists("SYMALGEBRA")) SYMALGEBRA=FALSE
 if (!exists("NEED_OFFSETS")) NEED_OFFSETS=TRUE
 if (!exists("X_MOD")) X_MOD=0
 if (!exists("CPU_LAYOUT")) CPU_LAYOUT=FALSE
-if (!exists("plot.access")) plot.access=FALSE
+if (!exists("plot_access")) plot_access=FALSE
 
 memory_arr_cpu = CPU_LAYOUT
 memory_arr_mod = X_MOD
 
 # SYMALGEBRA=TRUE
 
 options(stringsAsFactors=FALSE)
-format.list = function(x,...) sapply(x, class)
 
 if (! SYMALGEBRA) {
 	library(polyAlgebra,quietly=TRUE,warn.conflicts=FALSE)
@@ -63,7 +62,6 @@ SetOptions = function(...) {
 }
 
 AddDensity = function(name, dx=0, dy=0, dz=0, comment="", field=name, adjoint=F, group="", parameter=F, average=F, default=NA, sym=c("","",""), shift=NULL, ...) {
-	if (any((parameter) && (dx != 0) && (dy != 0) && (dz != 0))) stop("Parameters cannot be streamed (AddDensity)");
 	if (missing(name)) stop("Have to supply name in AddDensity!")
 	if (missing(group)) group = name
 	if (length(sym) != 3) stop("sym provided to AddDensity have to be a vector of length 3");
@@ -85,6 +83,7 @@ AddDensity = function(name, dx=0, dy=0, dz=0, comment="", field=name, adjoint=F,
 		symY=sym[2],
 		symZ=sym[3]
 	)
+	if (any((dd$parameter) & (dd$dx != 0) & (dd$dy != 0) & (dd$dz != 0))) stop("Parameters cannot be streamed (AddDensity)")
 	DensityAll <<- rbind(DensityAll,dd)
 	for (d in rows(dd)) {
 		AddField(name=d$field,
@@ -265,7 +264,7 @@ AddNodeType = function(name, group) {
 
 
 ## Description
-read.a.file = function(file) {
+read_a_file = function(file) {
 	pot = c(file, paste(include.dir,file,sep="/"))
 	sel = sapply(pot,file.exists)
 	sel = which(sel)
@@ -281,7 +280,7 @@ AddDescription = function(short, long) {
 		stop("Adding descripition twice!")
 	}
 	if (missing(long)) {
-		long = read.a.file("Description.md")
+		long = read_a_file("Description.md")
 		if (is.null(long)) long = short
 	}
 	Description <<- list(
@@ -430,7 +429,7 @@ if (any(duplicated(Stages$name))) stop ("Duplicated Stages' names\n")
 
 row.names(Stages)=Stages$name
 
-if (plot.access) {
+if (plot_access) {
 
 	pa_fi = Fields
 	pa_fi$index = seq_len(nrow(pa_fi))
@@ -475,7 +474,7 @@ for (a in rows(Actions)) {
 		bufout = rep(FALSE, nrow(Fields))
 		first = TRUE
 		pa_si = 0
-		if (plot.access) {
+		if (plot_access) {
 			pa_s = length(a$stages)
 			plot(NA,xlim=c(-0.5,pa_ws*pa_s+0.5),ylim=pa_frange,xaxt='n',yaxt='n',xlab="",ylab="",main=a$name,asp=1)
 			legend(par('usr')[2], par('usr')[3], xpd=TRUE, yjust=1, xjust=1, ncol=2, cex=0.7, bty = "n", bg="white",
@@ -498,7 +497,7 @@ for (a in rows(Actions)) {
 			sl = DensityAll[,s$loadtag]
 			sl = Fields$name %in% unique(DensityAll$field[sl])
 			sr[(!bufin) & is.na(sr)] = FALSE
-			if (plot.access) {
+			if (plot_access) {
 				pa_col = rep("white",nrow(pa_fi))
 				pa_col[bufout] = "darkgreen"
 				pa_col[ss] = "green"
@@ -540,7 +539,7 @@ for (a in rows(Actions)) {
 	}
 }
 
-if (plot.access) {
+if (plot_access) {
 	dev.off()
 }
 
@@ -559,9 +558,9 @@ if (nrow(NodeTypes) > 0) {
   NodeTypes = do.call(rbind, by(NodeTypes,NodeTypes$group,function(tab) {
           n = nrow(tab)
           l = ceiling(log2(n+1))
-          tab$index    = 1:n
+          tab$index    = seq_len(n)
           tab$Index    = paste("NODE",tab$name,sep="_")
-          tab$value    = NodeShift*(1:n)
+          tab$value    = NodeShift*(seq_len(n))
           tab$mask     = NodeShift*((2^l)-1)
           tab$max      = n
           tab$bits     = l
@@ -816,7 +815,7 @@ for (n in c("Settings","DensityAll","Density","DensityAD","Globals","Quantities"
 	if (is.null(v)) v = data.frame()
 	Consts = rbind(Consts, data.frame(name=toupper(n), value=nrow(v)));
 	if (nrow(v) > 0) {
-		v$index = 1:nrow(v)-1
+		v$index = seq_len(nrow(v))-1
 		v$nicename = gsub("[][ ]","",v$name)
 		v$Index = paste(" ",toupper(n), "_", v$nicename, " ", sep="")
 		row.names(v) = v$name
@@ -852,15 +851,11 @@ if (is.power.of.two(memory_arr_mod)) stop("memory_arr_mod has to be a power of 2
 offsets = function() {
   mw = PV(c("nx","ny","nz"))
   one = PV(c(1L,1L,1L))
-  bp = expand.grid(x=1:3,y=1:3,z=1:3)
   p = expand.grid(x=1:3*3-2,y=1:3*3-1,z=1:3*3)
-  tab1 = c(1,-1,0)
-  tab2 = c(0,-1,1)
-  get_tab = cbind(tab1[bp$x],tab1[bp$y],tab1[bp$z],tab2[bp$x],tab2[bp$y],tab2[bp$z])
   sizes = c(one,mw,one)
   size  =  sizes[p$x]  * sizes[p$y]  * sizes[p$z]
   MarginNSize = PV(rep(0L,27))
-  calc.functions = function(f) {
+  calc_functions = function(f) {
     mins = c(f$minx,f$miny,f$minz)
     maxs = c(f$maxx,f$maxy,f$maxz)
     tab1 = c(0,0,0,ifelse(mins == maxs & maxs > 0,-1,0),ifelse(maxs > 0,1,0))
@@ -874,7 +869,7 @@ offsets = function() {
     nsize = nsizes[p$x] * nsizes[p$y] * nsizes[p$z]
     mSize = MarginNSize
     MarginNSize <<- mSize + nsize
-    offset.p = function(positions) {
+    offset_p = function(positions) {
       positions[c(mins > -2, c(FALSE,FALSE,FALSE), maxs < 2)] = PV(0L)
       if (memory_arr_cpu) {
         offset =  (positions[p$x] +
@@ -927,13 +922,13 @@ offsets = function() {
 	mins = PV(as.integer(mins))
         get_tab = cbind(tab1[p$x],tab1[p$y],tab1[p$z],tab2[p$x],tab2[p$y],tab2[p$z])
         get_sel = tab3[p$x] & tab3[p$y] & tab3[p$z]
-        offset = offset.p(c(w+dw - mins,w+dw,w+dw - mw))
+        offset = offset_p(c(w+dw - mins,w+dw,w+dw - mw))
         cond = c(w+dw,mw-w-dw-one)
         list(Offset=offset,Conditions=cond,Table=get_tab,Selection=get_sel)
       },
       put_offsets = 
       function(w) {
-        offset = offset.p(c(w - mw - PV(as.integer(mins)),w,w))
+        offset = offset_p(c(w - mw - PV(as.integer(mins)),w,w))
         cond = c(w+PV(as.integer(-maxs)),mw-w+PV(as.integer(mins))-one)
         list(Offset=offset,Conditions=cond,Table=put_tab,Selection=put_sel)
       },
@@ -944,8 +939,8 @@ offsets = function() {
   ret$get_offsets = rep(list(NULL),nrow(ret))
   ret$put_offsets = rep(list(NULL),nrow(ret))
   ret$fOffset = rep(list(NULL),nrow(ret))
-  for (idx in 1:nrow(ret)) {
-      fun = calc.functions(ret[idx,])
+  for (idx in seq_len(nrow(ret))) {
+      fun = calc_functions(ret[idx,])
       ret$get_offsets[[idx]] = fun$get_offsets
       ret$put_offsets[[idx]] = fun$put_offsets
       ret$fOffset[[idx]] = fun$fOffset
@@ -956,7 +951,7 @@ offsets = function() {
 if (NEED_OFFSETS) {
     ret = offsets()
     Fields = ret$Fields
-    for (i in 1:length(Margin)) {
+    for (i in seq_along(Margin)) {
             Margin[[i]]$Size = ret$MarginSizes[i]
             if (! is.zero(Margin[[i]]$Size)) {
                      Margin[[i]]$size = 1L;

src/cuda.cu.Rt

@@ -8,7 +8,6 @@
         Here is nearly all of the CUDA C code. It includes:
           CartLatticeContainer.hpp
           Dynamics.c
-          Dynamics.h
           Dynamics_b.c (adjoint)
           Dynamics_adj.c (adjoint)
           ADTools.c (adjoint)

src/gpu_anim.h

@@ -8,6 +8,10 @@
 #ifndef __GPU_ANIM_H__
 #define __GPU_ANIM_H__
 
+#include "../config.h"
+
+#ifdef GRAPHICS
+
 #include "gl_helper.h"
 
 #include <cuda.h>
@@ -182,6 +186,6 @@ struct GPUAnimBitmap {
     }
 };
 
-
+#endif  // GRAPHICS
 #endif  // __GPU_ANIM_H__
 

src/makefile.main.Rt

@@ -25,7 +25,7 @@ SOURCE_PLAN+=main.cpp
 SOURCE_PLAN+=Global.h gpu_anim.h LatticeData.hpp LatticeBase.hpp LatticeBase.cpp cross.h cross.hpp StorageConversions.h
 SOURCE_PLAN+=CartLattice.h Region.h vtkLattice.h vtkOutput.h CartLatticeContainer.h CartLatticeLauncher.h CartLatticeLauncher.hpp CartConnectivity.hpp
 SOURCE_PLAN+=ArbLatticeAccess.hpp ArbLatticeContainer.hpp ArbLatticeLauncher.h ArbLatticeLauncher.hpp Lattice.hpp
-SOURCE_PLAN+=gl_helper.h Dynamics.h types.h Consts.h Solver.h pugixml.hpp pugiconfig.hpp Node.hpp
+SOURCE_PLAN+=gl_helper.h types.h Consts.h Solver.h pugixml.hpp pugiconfig.hpp Node.hpp
 SOURCE_PLAN+=Geometry.h utils.h utils.cpp unit.h ZoneSettings.h SyntheticTurbulence.h Sampler.h spline.h TCLBForceGroupCommon.h
 SOURCE_PLAN+=RemoteForceInterface.cpp RemoteForceInterface.h RemoteForceInterface.hpp
 SOURCE_PLAN+=TCLBForceGroupCommon.h MPMD.hpp empty.cpp Particle.hpp lammps.cpp

src/range_int.hpp

@@ -1,6 +1,8 @@
 #ifndef RANGE_INT_HPP
 #define RANGE_INT_HPP
 
+#include "cross.h"
+
 template <int A, int B=0, int C=A, int D=B>
 struct range_int {
   const int val;