From 8c44238f16c452484cbc1a4a53f9e8bc8dd8478a Mon Sep 17 00:00:00 2001 From: Scott R Charlton Date: Fri, 31 Jan 2014 00:51:04 +0000 Subject: [PATCH] currently working for subset of functions git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@8413 1feff8c3-07ed-0310-ac33-dd36852eb9cd --- R/Makefile | 230 +++++++++++++++++++++++++++++++++++++---------------- 1 file changed, 161 insertions(+), 69 deletions(-) diff --git a/R/Makefile b/R/Makefile index 608cf137..a4cef241 100644 --- a/R/Makefile +++ b/R/Makefile @@ -1,6 +1,9 @@ -DEST=phreeqc/src -SRC=../src/phreeqcpp CP=cp -f +IDEST=phreeqc/src +DEST=phreeqc/src/phreeqcpp +ISRC=../src +SRC=../src/phreeqcpp + PSRC = \ $(DEST)/advection.cpp \ @@ -10,59 +13,57 @@ PSRC = \ $(DEST)/ChartObject.cpp \ $(DEST)/ChartObject.h \ $(DEST)/cl1.cpp \ - $(DEST)/cl1mp.cpp \ - $(DEST)/class_main.cpp \ $(DEST)/CurveObject.cpp \ $(DEST)/CurveObject.h \ $(DEST)/cvdense.cpp \ $(DEST)/cvdense.h \ $(DEST)/cvode.cpp \ $(DEST)/cvode.h \ - $(DEST)/cxxKinetics.cxx \ + $(DEST)/cxxKinetics.cpp \ $(DEST)/cxxKinetics.h \ - $(DEST)/cxxMix.cxx \ + $(DEST)/cxxMix.cpp \ $(DEST)/cxxMix.h \ $(DEST)/dense.cpp \ $(DEST)/dense.h \ $(DEST)/dumper.cpp \ $(DEST)/dumper.h \ $(DEST)/dw.cpp \ - $(DEST)/Exchange.cxx \ + $(DEST)/Exchange.cpp \ $(DEST)/Exchange.h \ - $(DEST)/ExchComp.cxx \ + $(DEST)/ExchComp.cpp \ $(DEST)/ExchComp.h \ - $(DEST)/GasComp.cxx \ + $(DEST)/GasComp.cpp \ $(DEST)/GasComp.h \ $(DEST)/gases.cpp \ - $(DEST)/GasPhase.cxx \ + $(DEST)/GasPhase.cpp \ $(DEST)/GasPhase.h \ $(DEST)/global_structures.h \ $(DEST)/input.cpp \ $(DEST)/integrate.cpp \ $(DEST)/inverse.cpp \ - $(DEST)/ISolution.cxx \ + $(DEST)/ISolution.cpp \ $(DEST)/ISolution.h \ - $(DEST)/ISolutionComp.cxx \ + $(DEST)/ISolutionComp.cpp \ $(DEST)/ISolutionComp.h \ $(DEST)/isotopes.cpp \ $(DEST)/Keywords.cpp \ $(DEST)/Keywords.h \ $(DEST)/kinetics.cpp \ - $(DEST)/KineticsComp.cxx \ + $(DEST)/KineticsComp.cpp \ $(DEST)/KineticsComp.h \ $(DEST)/mainsubs.cpp \ $(DEST)/model.cpp \ $(DEST)/NA.h \ - $(DEST)/NameDouble.cxx \ + $(DEST)/NameDouble.cpp \ $(DEST)/NameDouble.h \ - $(DEST)/NumKeyword.cxx \ + $(DEST)/NumKeyword.cpp \ $(DEST)/NumKeyword.h \ $(DEST)/nvector.cpp \ $(DEST)/nvector.h \ $(DEST)/nvector_serial.cpp \ $(DEST)/nvector_serial.h \ $(DEST)/parse.cpp \ - $(DEST)/Parser.cxx \ + $(DEST)/Parser.cpp \ $(DEST)/Parser.h \ $(DEST)/PBasic.cpp \ $(DEST)/PBasic.h \ @@ -70,7 +71,7 @@ PSRC = \ $(DEST)/phqalloc.h \ $(DEST)/Phreeqc.cpp \ $(DEST)/Phreeqc.h \ - $(DEST)/PHRQ_base.cxx \ + $(DEST)/PHRQ_base.cpp \ $(DEST)/PHRQ_base.h \ $(DEST)/PHRQ_io.cpp \ $(DEST)/PHRQ_io.h \ @@ -78,18 +79,18 @@ PSRC = \ $(DEST)/phrqtype.h \ $(DEST)/pitzer.cpp \ $(DEST)/pitzer_structures.cpp \ - $(DEST)/PPassemblage.cxx \ + $(DEST)/PPassemblage.cpp \ $(DEST)/PPassemblage.h \ - $(DEST)/PPassemblageComp.cxx \ + $(DEST)/PPassemblageComp.cpp \ $(DEST)/PPassemblageComp.h \ $(DEST)/prep.cpp \ - $(DEST)/Pressure.cxx \ + $(DEST)/Pressure.cpp \ $(DEST)/Pressure.h \ $(DEST)/print.cpp \ - $(DEST)/Reaction.cxx \ + $(DEST)/Reaction.cpp \ $(DEST)/Reaction.h \ $(DEST)/read.cpp \ - $(DEST)/ReadClass.cxx \ + $(DEST)/ReadClass.cpp \ $(DEST)/readtr.cpp \ $(DEST)/runner.cpp \ $(DEST)/runner.h \ @@ -98,19 +99,19 @@ PSRC = \ $(DEST)/sit.cpp \ $(DEST)/smalldense.cpp \ $(DEST)/smalldense.h \ - $(DEST)/Solution.cxx \ + $(DEST)/Solution.cpp \ $(DEST)/Solution.h \ - $(DEST)/SolutionIsotope.cxx \ + $(DEST)/SolutionIsotope.cpp \ $(DEST)/SolutionIsotope.h \ $(DEST)/spread.cpp \ - $(DEST)/SS.cxx \ + $(DEST)/SS.cpp \ $(DEST)/SS.h \ - $(DEST)/SSassemblage.cxx \ + $(DEST)/SSassemblage.cpp \ $(DEST)/SSassemblage.h \ - $(DEST)/SScomp.cxx \ + $(DEST)/SScomp.cpp \ $(DEST)/SScomp.h \ $(DEST)/step.cpp \ - $(DEST)/StorageBin.cxx \ + $(DEST)/StorageBin.cpp \ $(DEST)/StorageBin.h \ $(DEST)/StorageBinList.cpp \ $(DEST)/StorageBinList.h \ @@ -118,16 +119,16 @@ PSRC = \ $(DEST)/sundialsmath.cpp \ $(DEST)/sundialsmath.h \ $(DEST)/sundialstypes.h \ - $(DEST)/Surface.cxx \ + $(DEST)/Surface.cpp \ $(DEST)/Surface.h \ - $(DEST)/SurfaceCharge.cxx \ + $(DEST)/SurfaceCharge.cpp \ $(DEST)/SurfaceCharge.h \ - $(DEST)/SurfaceComp.cxx \ + $(DEST)/SurfaceComp.cpp \ $(DEST)/SurfaceComp.h \ - $(DEST)/System.cxx \ + $(DEST)/System.cpp \ $(DEST)/System.h \ $(DEST)/tally.cpp \ - $(DEST)/Temperature.cxx \ + $(DEST)/Temperature.cpp \ $(DEST)/Temperature.h \ $(DEST)/tidy.cpp \ $(DEST)/transport.cpp \ @@ -136,11 +137,34 @@ PSRC = \ $(DEST)/UserPunch.cpp \ $(DEST)/UserPunch.h \ $(DEST)/utilities.cpp \ - $(DEST)/Utils.cxx \ + $(DEST)/Utils.cpp \ $(DEST)/Utils.h +XSRC = \ + $(IDEST)/CSelectedOutput.cpp \ + $(IDEST)/CSelectedOutput.hxx \ + $(IDEST)/CVar.hxx \ + $(IDEST)/Debug.h \ + $(IDEST)/ErrorReporter.hxx \ + $(IDEST)/IPhreeqcCallbacks.h \ + $(IDEST)/IPhreeqc.cpp \ + $(IDEST)/IPhreeqc.h \ + $(IDEST)/IPhreeqc.hpp \ + $(IDEST)/IPhreeqcLib.cpp \ + $(IDEST)/R.cpp \ + $(IDEST)/thread.h \ + $(IDEST)/Var.c \ + $(IDEST)/Var.h \ + $(IDEST)/Version.h \ + $(IDEST)/Makevars -all: $(PSRC) +all: $(PSRC) $(XSRC) + +##$(PSRC): $(DEST) + +##$(ISRC): $(IDEST) + +##$(DEST) : $(IDEST) $(DEST)/advection.cpp : $(SRC)/advection.cpp $(CP) $< $@ @@ -163,11 +187,11 @@ $(DEST)/ChartObject.h : $(SRC)/ChartObject.h $(DEST)/cl1.cpp : $(SRC)/cl1.cpp $(CP) $< $@ -$(DEST)/cl1mp.cpp : $(SRC)/cl1mp.cpp - $(CP) $< $@ +##$(DEST)/cl1mp.cpp : $(SRC)/cl1mp.cpp +## $(CP) $< $@ -$(DEST)/class_main.cpp : $(SRC)/class_main.cpp - $(CP) $< $@ +##$(DEST)/class_main.cpp : $(SRC)/class_main.cpp +## $(CP) $< $@ $(DEST)/CurveObject.cpp : $(SRC)/CurveObject.cpp $(CP) $< $@ @@ -187,13 +211,13 @@ $(DEST)/cvode.cpp : $(SRC)/cvode.cpp $(DEST)/cvode.h : $(SRC)/cvode.h $(CP) $< $@ -$(DEST)/cxxKinetics.cxx : $(SRC)/cxxKinetics.cxx +$(DEST)/cxxKinetics.cpp : $(SRC)/cxxKinetics.cxx $(CP) $< $@ $(DEST)/cxxKinetics.h : $(SRC)/cxxKinetics.h $(CP) $< $@ -$(DEST)/cxxMix.cxx : $(SRC)/cxxMix.cxx +$(DEST)/cxxMix.cpp : $(SRC)/cxxMix.cxx $(CP) $< $@ $(DEST)/cxxMix.h : $(SRC)/cxxMix.h @@ -214,19 +238,19 @@ $(DEST)/dumper.h : $(SRC)/dumper.h $(DEST)/dw.cpp : $(SRC)/dw.cpp $(CP) $< $@ -$(DEST)/Exchange.cxx : $(SRC)/Exchange.cxx +$(DEST)/Exchange.cpp : $(SRC)/Exchange.cxx $(CP) $< $@ $(DEST)/Exchange.h : $(SRC)/Exchange.h $(CP) $< $@ -$(DEST)/ExchComp.cxx : $(SRC)/ExchComp.cxx +$(DEST)/ExchComp.cpp : $(SRC)/ExchComp.cxx $(CP) $< $@ $(DEST)/ExchComp.h : $(SRC)/ExchComp.h $(CP) $< $@ -$(DEST)/GasComp.cxx : $(SRC)/GasComp.cxx +$(DEST)/GasComp.cpp : $(SRC)/GasComp.cxx $(CP) $< $@ $(DEST)/GasComp.h : $(SRC)/GasComp.h @@ -235,7 +259,7 @@ $(DEST)/GasComp.h : $(SRC)/GasComp.h $(DEST)/gases.cpp : $(SRC)/gases.cpp $(CP) $< $@ -$(DEST)/GasPhase.cxx : $(SRC)/GasPhase.cxx +$(DEST)/GasPhase.cpp : $(SRC)/GasPhase.cxx $(CP) $< $@ $(DEST)/GasPhase.h : $(SRC)/GasPhase.h @@ -253,13 +277,13 @@ $(DEST)/integrate.cpp : $(SRC)/integrate.cpp $(DEST)/inverse.cpp : $(SRC)/inverse.cpp $(CP) $< $@ -$(DEST)/ISolution.cxx : $(SRC)/ISolution.cxx +$(DEST)/ISolution.cpp : $(SRC)/ISolution.cxx $(CP) $< $@ $(DEST)/ISolution.h : $(SRC)/ISolution.h $(CP) $< $@ -$(DEST)/ISolutionComp.cxx : $(SRC)/ISolutionComp.cxx +$(DEST)/ISolutionComp.cpp : $(SRC)/ISolutionComp.cxx $(CP) $< $@ $(DEST)/ISolutionComp.h : $(SRC)/ISolutionComp.h @@ -277,7 +301,7 @@ $(DEST)/Keywords.h : $(SRC)/Keywords.h $(DEST)/kinetics.cpp : $(SRC)/kinetics.cpp $(CP) $< $@ -$(DEST)/KineticsComp.cxx : $(SRC)/KineticsComp.cxx +$(DEST)/KineticsComp.cpp : $(SRC)/KineticsComp.cxx $(CP) $< $@ $(DEST)/KineticsComp.h : $(SRC)/KineticsComp.h @@ -292,13 +316,13 @@ $(DEST)/model.cpp : $(SRC)/model.cpp $(DEST)/NA.h : $(SRC)/NA.h $(CP) $< $@ -$(DEST)/NameDouble.cxx : $(SRC)/NameDouble.cxx +$(DEST)/NameDouble.cpp : $(SRC)/NameDouble.cxx $(CP) $< $@ $(DEST)/NameDouble.h : $(SRC)/NameDouble.h $(CP) $< $@ -$(DEST)/NumKeyword.cxx : $(SRC)/NumKeyword.cxx +$(DEST)/NumKeyword.cpp : $(SRC)/NumKeyword.cxx $(CP) $< $@ $(DEST)/NumKeyword.h : $(SRC)/NumKeyword.h @@ -319,7 +343,7 @@ $(DEST)/nvector_serial.h : $(SRC)/nvector_serial.h $(DEST)/parse.cpp : $(SRC)/parse.cpp $(CP) $< $@ -$(DEST)/Parser.cxx : $(SRC)/Parser.cxx +$(DEST)/Parser.cpp : $(SRC)/Parser.cxx $(CP) $< $@ $(DEST)/Parser.h : $(SRC)/Parser.h @@ -343,7 +367,7 @@ $(DEST)/Phreeqc.cpp : $(SRC)/Phreeqc.cpp $(DEST)/Phreeqc.h : $(SRC)/Phreeqc.h $(CP) $< $@ -$(DEST)/PHRQ_base.cxx : $(SRC)/PHRQ_base.cxx +$(DEST)/PHRQ_base.cpp : $(SRC)/PHRQ_base.cxx $(CP) $< $@ $(DEST)/PHRQ_base.h : $(SRC)/PHRQ_base.h @@ -367,13 +391,13 @@ $(DEST)/pitzer.cpp : $(SRC)/pitzer.cpp $(DEST)/pitzer_structures.cpp : $(SRC)/pitzer_structures.cpp $(CP) $< $@ -$(DEST)/PPassemblage.cxx : $(SRC)/PPassemblage.cxx +$(DEST)/PPassemblage.cpp : $(SRC)/PPassemblage.cxx $(CP) $< $@ $(DEST)/PPassemblage.h : $(SRC)/PPassemblage.h $(CP) $< $@ -$(DEST)/PPassemblageComp.cxx : $(SRC)/PPassemblageComp.cxx +$(DEST)/PPassemblageComp.cpp : $(SRC)/PPassemblageComp.cxx $(CP) $< $@ $(DEST)/PPassemblageComp.h : $(SRC)/PPassemblageComp.h @@ -382,7 +406,7 @@ $(DEST)/PPassemblageComp.h : $(SRC)/PPassemblageComp.h $(DEST)/prep.cpp : $(SRC)/prep.cpp $(CP) $< $@ -$(DEST)/Pressure.cxx : $(SRC)/Pressure.cxx +$(DEST)/Pressure.cpp : $(SRC)/Pressure.cxx $(CP) $< $@ $(DEST)/Pressure.h : $(SRC)/Pressure.h @@ -391,7 +415,7 @@ $(DEST)/Pressure.h : $(SRC)/Pressure.h $(DEST)/print.cpp : $(SRC)/print.cpp $(CP) $< $@ -$(DEST)/Reaction.cxx : $(SRC)/Reaction.cxx +$(DEST)/Reaction.cpp : $(SRC)/Reaction.cxx $(CP) $< $@ $(DEST)/Reaction.h : $(SRC)/Reaction.h @@ -400,7 +424,7 @@ $(DEST)/Reaction.h : $(SRC)/Reaction.h $(DEST)/read.cpp : $(SRC)/read.cpp $(CP) $< $@ -$(DEST)/ReadClass.cxx : $(SRC)/ReadClass.cxx +$(DEST)/ReadClass.cpp : $(SRC)/ReadClass.cxx $(CP) $< $@ $(DEST)/readtr.cpp : $(SRC)/readtr.cpp @@ -427,13 +451,13 @@ $(DEST)/smalldense.cpp : $(SRC)/smalldense.cpp $(DEST)/smalldense.h : $(SRC)/smalldense.h $(CP) $< $@ -$(DEST)/Solution.cxx : $(SRC)/Solution.cxx +$(DEST)/Solution.cpp : $(SRC)/Solution.cxx $(CP) $< $@ $(DEST)/Solution.h : $(SRC)/Solution.h $(CP) $< $@ -$(DEST)/SolutionIsotope.cxx : $(SRC)/SolutionIsotope.cxx +$(DEST)/SolutionIsotope.cpp : $(SRC)/SolutionIsotope.cxx $(CP) $< $@ $(DEST)/SolutionIsotope.h : $(SRC)/SolutionIsotope.h @@ -442,19 +466,19 @@ $(DEST)/SolutionIsotope.h : $(SRC)/SolutionIsotope.h $(DEST)/spread.cpp : $(SRC)/spread.cpp $(CP) $< $@ -$(DEST)/SS.cxx : $(SRC)/SS.cxx +$(DEST)/SS.cpp : $(SRC)/SS.cxx $(CP) $< $@ $(DEST)/SS.h : $(SRC)/SS.h $(CP) $< $@ -$(DEST)/SSassemblage.cxx : $(SRC)/SSassemblage.cxx +$(DEST)/SSassemblage.cpp : $(SRC)/SSassemblage.cxx $(CP) $< $@ $(DEST)/SSassemblage.h : $(SRC)/SSassemblage.h $(CP) $< $@ -$(DEST)/SScomp.cxx : $(SRC)/SScomp.cxx +$(DEST)/SScomp.cpp : $(SRC)/SScomp.cxx $(CP) $< $@ $(DEST)/SScomp.h : $(SRC)/SScomp.h @@ -463,7 +487,7 @@ $(DEST)/SScomp.h : $(SRC)/SScomp.h $(DEST)/step.cpp : $(SRC)/step.cpp $(CP) $< $@ -$(DEST)/StorageBin.cxx : $(SRC)/StorageBin.cxx +$(DEST)/StorageBin.cpp : $(SRC)/StorageBin.cxx $(CP) $< $@ $(DEST)/StorageBin.h : $(SRC)/StorageBin.h @@ -487,25 +511,25 @@ $(DEST)/sundialsmath.h : $(SRC)/sundialsmath.h $(DEST)/sundialstypes.h : $(SRC)/sundialstypes.h $(CP) $< $@ -$(DEST)/Surface.cxx : $(SRC)/Surface.cxx +$(DEST)/Surface.cpp : $(SRC)/Surface.cxx $(CP) $< $@ $(DEST)/Surface.h : $(SRC)/Surface.h $(CP) $< $@ -$(DEST)/SurfaceCharge.cxx : $(SRC)/SurfaceCharge.cxx +$(DEST)/SurfaceCharge.cpp : $(SRC)/SurfaceCharge.cxx $(CP) $< $@ $(DEST)/SurfaceCharge.h : $(SRC)/SurfaceCharge.h $(CP) $< $@ -$(DEST)/SurfaceComp.cxx : $(SRC)/SurfaceComp.cxx +$(DEST)/SurfaceComp.cpp : $(SRC)/SurfaceComp.cxx $(CP) $< $@ $(DEST)/SurfaceComp.h : $(SRC)/SurfaceComp.h $(CP) $< $@ -$(DEST)/System.cxx : $(SRC)/System.cxx +$(DEST)/System.cpp : $(SRC)/System.cxx $(CP) $< $@ $(DEST)/System.h : $(SRC)/System.h @@ -514,7 +538,7 @@ $(DEST)/System.h : $(SRC)/System.h $(DEST)/tally.cpp : $(SRC)/tally.cpp $(CP) $< $@ -$(DEST)/Temperature.cxx : $(SRC)/Temperature.cxx +$(DEST)/Temperature.cpp : $(SRC)/Temperature.cxx $(CP) $< $@ $(DEST)/Temperature.h : $(SRC)/Temperature.h @@ -541,9 +565,77 @@ $(DEST)/UserPunch.h : $(SRC)/UserPunch.h $(DEST)/utilities.cpp : $(SRC)/utilities.cpp $(CP) $< $@ -$(DEST)/Utils.cxx : $(SRC)/Utils.cxx +$(DEST)/Utils.cpp : $(SRC)/Utils.cxx $(CP) $< $@ $(DEST)/Utils.h : $(SRC)/Utils.h $(CP) $< $@ +############################################### + + +$(IDEST)/CSelectedOutput.cpp : $(ISRC)/CSelectedOutput.cpp + $(CP) $< $@ + +$(IDEST)/CSelectedOutput.hxx : $(ISRC)/CSelectedOutput.hxx + $(CP) $< $@ + +$(IDEST)/CVar.hxx : $(ISRC)/CVar.hxx + $(CP) $< $@ + +$(IDEST)/Debug.h : $(ISRC)/Debug.h + $(CP) $< $@ + +$(IDEST)/ErrorReporter.hxx : $(ISRC)/ErrorReporter.hxx + $(CP) $< $@ + +$(IDEST)/IPhreeqcCallbacks.h : ../src/IPhreeqcCallbacks.h + $(CP) $< $@ + +$(IDEST)/IPhreeqc.cpp : $(ISRC)/IPhreeqc.cpp + $(CP) $< $@ + +$(IDEST)/IPhreeqc.h : $(ISRC)/IPhreeqc.h + $(CP) $< $@ + +$(IDEST)/IPhreeqc.hpp : $(ISRC)/IPhreeqc.hpp + $(CP) $< $@ + +$(IDEST)/IPhreeqcLib.cpp : $(ISRC)/IPhreeqcLib.cpp + $(CP) $< $@ + +$(IDEST)/thread.h : $(ISRC)/thread.h + $(CP) $< $@ + +$(IDEST)/Var.c : $(ISRC)/Var.c + $(CP) $< $@ + +$(IDEST)/Var.h : $(ISRC)/Var.h + $(CP) $< $@ + +$(IDEST)/Version.h : $(ISRC)/Version.h + $(CP) $< $@ + + +######################################## + +check : all + R CMD check phreeqc + +install : all + R CMD INSTALL phreeqc + +$(IDEST)/Makevars : Makevars + $(CP) $< $@ + +$(IDEST)/R.cpp : R.cpp + $(CP) $< $@ + +$(IDEST): + mkdir $(IDEST) + +$(DEST): + mkdir $(DEST) + +clean : + rm -f $(PSRC) $(ISRC) $(DEST)/*.o $(IDEST)/*.o $(DEST)/*.so \ No newline at end of file