files missed in initial svn2git conversion.

SVN repository covered development from 2007 to 2017.  Some files were
completely unchanged and unmoved in last 10 years, and were not picked
up by the export to GIT.  These files are manually commited now.

Former-commit-id: 70aa60a31dc111b898001756152ac16b6a9176f9

NFsim_v1.11/VCell/src/VCellNFSim.cpp

@@ -50,7 +50,7 @@ int main(int argc, char **argv) {
 	vcell::JMSHolder holder; //we need to keep these strings in memory until end of program
 	try {
 		std::cout
-				<< "NFsim " << NETWORK_MESSAGING( "network","console" ) << " messaging version $URL$" VCELLSVNQUOTE(SVNVERSION)
+				<< "NFsim " << NETWORK_MESSAGING( "network","console" ) << " messaging version $URL: svn://code3.cam.uchc.edu/vcell/trunk/numerics/NFsim_v1.11/VCell/src/VCellNFSim.cpp $" VCELLSVNQUOTE(SVNVERSION)
 				<< std::endl;
 		bool isMessaging = startupMessaging(argc,argv,holder);
 		std::cout << " messaging is " << onOrOff(isMessaging) << std::endl;

PCGPack/Makefile

@@ -0,0 +1,112 @@
+
+# Version -- g(eneric), v(ector), c(ray)
+
+VERSION = g
+
+# Fortran Options
+
+# Standard Fortran options
+FOPT     = -fast
+# Special Fortran options
+SFOPT    = 
+FFLAGS   = ${FOPT} ${SFOPT}
+
+# Source Code Directories
+
+# Directories for routines that are the same in all versions
+# SDIR contains routines without external statements
+GDIR     = .
+# SEDIR contains routines with external statements
+GEDIR     = .
+
+# Directories for routines that change in all vector versions, but
+# do not have Cray-specific versions
+# VDIR contains routines without external statements
+VDIR     = .
+# VDIR contains routines with external statements
+VEDIR    = .
+
+# Directories for routines that change in all vector versions, and
+# do have Cray-specific versions
+# VCDIR contains routines without external statements
+VCDIR     = .
+# VCEDIR contains routines with external statements
+VCEDIR    = .
+
+# Directories for routines that change only in Cray versions
+# CDIR contains routines without external statements
+CDIR     = .
+# CEDIR contains routines with external statements
+CEDIR    = .
+
+# Library Name
+
+# LIBDIR contains PCGPAK2 library
+LIBDIR   = ../../lib
+# Precision options -- s(ingle), d(ouble), c(complex)
+PRECOPT  = d
+# Debug part of library name
+DB       =
+# Special options part of library name
+LBOPT    =
+# LIBRARY name is {s,d,c}{blank,v,c}pcglib{dbg option}{spec options}.
+LIBRARY  = ${LIBDIR}/${VERSION}${PRECOPT}pcglib${DB}${LBOPT}.a
+
+# Source File Names
+
+GNOEXTS  =  pc0v.o    pcijup.o  pcmlic.o  pcrdpt.o  pcsrfp.o \
+	    pc0vi.o   pcilu.o   pcmlir.o  pcric.o   pcsrij.o \
+	    pcaxpy.o  pcilu1.o  pcmlr.o   pcrilu.o  pcsrix.o \
+	    pcbtrc.o  pciluf.o  pcmuc.o   pcrsad.o  pcsriz.o \
+	    pccred.o  pcilus.o  pcmuic.o  pcrsbs.o  pcsro2.o \
+	    pcd2i.o   pciluz.o  pcmuir.o  pcrsfb.o  pcsrob.o \
+	    pcd2ii.o  pciprm.o  pcmur.o   pcrsfm.o  pcsrop.o \
+	    pcd2it.o  pciprp.o  pcmvc.o   pcrsfp.o  pcsrrb.o \
+	    pcdmv.o   pcirsw.o  pcmvr.o   pcrslu.o  pcsrrp.o \
+	    pcdmva.o  pclu1c.o  pcmvs.o   pcrspf.o  pcsrsb.o \
+	    pciabs.o  pclu1r.o  pcnegv.o  pcrsps.o  pcsrsp.o \
+	    pciblk.o  pclub1.o  pcnopr.o  pcrsrb.o  pcsrti.o \
+	    pcic.o    pclub2.o  pcpack.o  pcrsrp.o  pcsrzp.o \
+	    pcic1.o   pclub3.o  pcpaxp.o  pcsbge.o  pcsscl.o \
+	    pcicb.o   pclub4.o  pcpcnf.o  pcsbgp.o  pctran.o \
+	    pcicmc.o  pclub5.o  pcpcsf.o  pcsc1b.o  pcunpk.o \
+	    pcicmr.o  pclubf.o  pcprmb.o  pcsc1p.o  pcvadd.o \
+	    pcicms.o  pclup.o   pcprmp.o  pcsc2b.o  pcvdiv.o \
+	    pcicpr.o  pclup1.o  pcpunp.o  pcscal.o  pcverf.o \
+	    pcicpy.o  pclup2.o  pcrc1b.o  pcsd2f.o  pcvers.o \
+	    pcictr.o  pclup3.o  pcrc1p.o  pcsd2s.o  pcvmul.o \
+	    pcictx.o  pclup4.o  pcrc2b.o  pcsijb.o  pcvsma.o \
+	    pcicx.o   pclup5.o  pcrcpr.o  pcspfa.o  pcvsub.o \
+	    pciipr.o  pclupf.o  pcrcpy.o  pcspsl.o  pcvtm.o  \
+	    pcijab.o  pcmlc.o   pcrdpp.o  pcsrfb.o pcdslv.o
+
+GEXTS    =  pccg.o    pcgcr.o   pcop.o    pcsp.o   \
+	    pccgx.o   pcgmr.o   pcredb.o  pcspr.o  \
+	    pcdrv.o   pcity.o   pcredp.o  pcsrb.o  \
+	    pcend.o   pcomn.o   pcredu.o  pcsrp.o
+
+VNOEXTS  =  pcily.o   pclub.o   pcmv.o    pcvunp.o
+
+VEXTS    =  pcdrvx.o
+
+VCEXTS   =  pcgmrx.o
+
+CEXTS    =  pcitx.o
+
+pcgpak2:    ${LIBRARY}
+${LIBRARY}: ${GNOEXTS} ${GEXTS} ${VNOEXTS} ${VEXTS} ${VCEXTS} ${CEXTS}
+	  ar rv ${LIBRARY} *.o
+	  rm *.o
+	  ranlib ${LIBRARY}
+${GNOEXTS}:
+	  f77 $(FFLAGS) -c $(GDIR)/$*.f
+${GEXTS}:
+	  f77 $(FFLAGS) -c $(GEDIR)/$*.f
+${VNOEXTS}:
+	  f77 $(FFLAGS) -c $(VDIR)/$*.f
+${VEXTS}:
+	  f77 $(FFLAGS) -c $(VEDIR)/$*.f
+${VCEXTS}:
+	  f77 $(FFLAGS) -c $(VCEDIR)/$*.f
+${CEXTS}:
+	  f77 $(FFLAGS) -c $(CEDIR)/$*.f

PCGPack/Makefile.win32

@@ -0,0 +1,66 @@
+#####################################################
+# Makefile for the PCGPack double library for Windows 
+#
+# Date: July 14, 2001
+#####################################################
+#
+#Fortran compiler
+FC= ifort
+# Compilation options
+#FOPTIONS = /Gm /O3 /Qipo /Qprec-div- /QxN /compile_only /thread
+FOPTIONS = /O3 /Qprec-div- /QxN /compile_only /MT /nologo /names:lowercase 
+LIBTOOL = xilib
+
+.SUFFIXES: obj.f
+#
+.f.obj :
+	$(FC) $(FOPTIONS) $<
+#
+# Source File Names
+#
+GNOEXTS  =  pc0v.obj    pcijup.obj  pcmlic.obj  pcrdpt.obj  pcsrfp.obj \
+	    pc0vi.obj   pcilu.obj   pcmlir.obj  pcric.obj   pcsrij.obj \
+	    pcaxpy.obj  pcilu1.obj  pcmlr.obj   pcrilu.obj  pcsrix.obj \
+	    pcbtrc.obj  pciluf.obj  pcmuc.obj   pcrsad.obj  pcsriz.obj \
+	    pccred.obj  pcilus.obj  pcmuic.obj  pcrsbs.obj  pcsro2.obj \
+	    pcd2i.obj   pciluz.obj  pcmuir.obj  pcrsfb.obj  pcsrob.obj \
+	    pcd2ii.obj  pciprm.obj  pcmur.obj   pcrsfm.obj  pcsrop.obj \
+	    pcd2it.obj  pciprp.obj  pcmvc.obj   pcrsfp.obj  pcsrrb.obj \
+	    pcdmv.obj   pcirsw.obj  pcmvr.obj   pcrslu.obj  pcsrrp.obj \
+	    pcdmva.obj  pclu1c.obj  pcmvs.obj   pcrspf.obj  pcsrsb.obj \
+	    pciabs.obj  pclu1r.obj  pcnegv.obj  pcrsps.obj  pcsrsp.obj \
+	    pciblk.obj  pclub1.obj  pcnopr.obj  pcrsrb.obj  pcsrti.obj \
+	    pcic.obj    pclub2.obj  pcpack.obj  pcrsrp.obj  pcsrzp.obj \
+	    pcic1.obj   pclub3.obj  pcpaxp.obj  pcsbge.obj  pcsscl.obj \
+	    pcicb.obj   pclub4.obj  pcpcnf.obj  pcsbgp.obj  pctran.obj \
+	    pcicmc.obj  pclub5.obj  pcpcsf.obj  pcsc1b.obj  pcunpk.obj \
+	    pcicmr.obj  pclubf.obj  pcprmb.obj  pcsc1p.obj  pcvadd.obj \
+	    pcicms.obj  pclup.obj   pcprmp.obj  pcsc2b.obj  pcvdiv.obj \
+	    pcicpr.obj  pclup1.obj  pcpunp.obj  pcscal.obj  pcverf.obj \
+	    pcicpy.obj  pclup2.obj  pcrc1b.obj  pcsd2f.obj  pcvers.obj \
+	    pcictr.obj  pclup3.obj  pcrc1p.obj  pcsd2s.obj  pcvmul.obj \
+	    pcictx.obj  pclup4.obj  pcrc2b.obj  pcsijb.obj  pcvsma.obj \
+	    pcicx.obj   pclup5.obj  pcrcpr.obj  pcspfa.obj  pcvsub.obj \
+	    pciipr.obj  pclupf.obj  pcrcpy.obj  pcspsl.obj  pcvtm.obj  \
+	    pcijab.obj  pcmlc.obj   pcrdpp.obj  pcsrfb.obj pcdslv.obj
+#
+GEXTS    =  pccg.obj    pcgcr.obj   pcop.obj    pcsp.obj   \
+	    pccgx.obj   pcgmr.obj   pcredb.obj  pcspr.obj  \
+	    pcdrv.obj   pcity.obj   pcredp.obj  pcsrb.obj  \
+	    pcend.obj   pcomn.obj   pcredu.obj  pcsrp.obj
+#
+VNOEXTS  =  pcily.obj   pclub.obj   pcmv.obj    pcvunp.obj
+#
+VEXTS    =  pcdrvx.obj
+#
+VCEXTS   =  pcgmrx.obj
+#
+CEXTS    =  pcitx.obj
+#
+default all: pcgpack_dbl.lib
+#
+pcgpack_dbl.lib: $(GNOEXTS) $(GEXTS) $(VNOEXTS) $(VEXTS) $(VCEXTS) $(CEXTS)
+	$(LIBTOOL) $(GNOEXTS) $(GEXTS) $(VNOEXTS) $(VEXTS) $(VCEXTS) $(CEXTS) /out:pcgpack_dbl.lib
+
+clean:
+	del pcgpack_dbl.lib $(GNOEXTS) $(GEXTS) $(VNOEXTS) $(VEXTS) $(VCEXTS) $(CEXTS)

PCGPack/mssccprj.scc

@@ -0,0 +1,5 @@
+SCC = This is a Source Code Control file
+
+[pcgpack_dbl.dsp]
+SCC_Aux_Path = "\\Fs2\RAID\vss"
+SCC_Project_Name = "$/VCell/PCGPack", FCAAAAAA

PCGPack/pc0v.f

@@ -0,0 +1,10 @@
+      SUBROUTINEPC0V(N,V)
+      IMPLICITDOUBLEPRECISION(A-H,O-Z)
+      INTEGERN
+      DOUBLEPRECISIONV(*)
+      INTEGERI
+      DO1I=1,N
+      V(I)=0.0D0
+1     CONTINUE
+      RETURN
+      END

PCGPack/pc0vi.f

@@ -0,0 +1,9 @@
+      SUBROUTINEPC0VI(N,IV)
+      IMPLICITDOUBLEPRECISION(A-H,O-Z)
+      INTEGERN,IV(*)
+      INTEGERI
+      DO1I=1,N
+      IV(I)=0
+1     CONTINUE
+      RETURN
+      END

PCGPack/pcaxpy.f

@@ -0,0 +1,12 @@
+      SUBROUTINEPCAXPY(N,IJA,S,V,A)
+      IMPLICITDOUBLEPRECISION(A-H,O-Z)
+      INTEGERN,IJA(*)
+      DOUBLEPRECISIONS,A(*),V(*)
+      INTEGERK
+CVDIR IGNORE RECRDEPS
+CDIR$ IVDEP
+      DO1K=1,N
+      A(IJA(K))=A(IJA(K))+S*V(K)
+1     CONTINUE
+      RETURN
+      END

PCGPack/pcbtrc.f

@@ -0,0 +1,23 @@
+      SUBROUTINEPCBTRC(N,IBLKN,IBLK,IBLKS,IBTRM,IRTBM)
+      IMPLICITDOUBLEPRECISION(A-H,O-Z)
+      INTEGERN,IBLKN,IBLK,IBLKS(IBLKN),IBTRM(*),IRTBM(*)
+      INTEGERI,J,K
+      IBTRM(1)=1
+      DO1I=1,IBLKN
+      IBTRM(I+1)=IBTRM(I)+IBLKS(I)
+1     CONTINUE
+      IF(IBLK.GT.0)THEN
+      DO3I=1,N
+      IRTBM(I)=(I-1)/IBLK+1
+3     CONTINUE
+      ELSE
+      K=0
+      DO5I=1,IBLKN
+      DO7J=1,IBLKS(I)
+      K=K+1
+      IRTBM(K)=I
+7     CONTINUE
+5     CONTINUE
+      ENDIF
+      RETURN
+      END

PCGPack/pccg.f

@@ -0,0 +1,45 @@
+      SUBROUTINEPCCG(N,IJA,A,RHS,X,ISP,RSP,PRECON,PCSTOP,
+     *PCMV)
+      IMPLICITDOUBLEPRECISION(A-H,O-Z)
+      INTEGERN,IJA(*),ISP(*)
+      DOUBLEPRECISIONA(*),RHS(*),X(*),RSP(*)
+      EXTERNALPRECON,PCSTOP,PCMV
+      INTEGERIERR,ITMAX,ITEST,KMAX,IFL,IPRE,PBLK,LUDONE,IBLK,
+     *MNEED,ITS,RSDONE,NOVERF,RED1,RED2,IERR2,IFRMAT
+      COMMON/PCCOM1/IERR,ITMAX,ITEST,KMAX,IFL,IPRE,PBLK,
+     *LUDONE,IBLK,MNEED,ITS,RSDONE,NOVERF,RED1,RED2,IERR2,
+     *IFRMAT
+      SAVE/PCCOM1/
+      INTEGERISTOP,IRESD,INORM,ISAME,ISTATP,IRSDS,IOUT,JOUT,ISTATS,
+     *ISTAT1,ISTAT2
+      DOUBLEPRECISIONEPS1,EPS2
+      COMMON/PCSTIC/ISTOP,IRESD,INORM,ISAME,ISTATP,IRSDS,IOUT,JOUT,
+     *ISTATS,ISTAT1,ISTAT2
+      COMMON/PCSTRC/EPS1,EPS2
+      SAVE/PCSTIC/,/PCSTRC/
+      INTEGERNSP,RN,RP,P,ATP,NADR,NSP1
+      NADR=ISP(2)
+      NSP=ISP(1)
+      RN=NADR+NSP-N
+      IF(IPRE.NE.3)THEN
+      RP=RN-N
+      ATP=RP
+      ELSE
+      RP=RN
+      ATP=RP-N
+      ENDIF
+      P=ATP-N
+      NSP1=P-NADR
+      ISP(3)=NSP1
+      ISP(1)=NSP1
+      IF(NSP1.LT.0)THEN
+      RETURN
+      ENDIF
+      IF(IERR.NE.0)THEN
+      RETURN
+      ENDIF
+      IRESD=0
+      CALLPCCGX(N,IJA,A,RHS,X,RSP(RN),RSP(RP),RSP(P),RSP(ATP),ISP,
+     *RSP,PRECON,PCSTOP,PCMV)
+      RETURN
+      END

PCGPack/pccgx.f

@@ -0,0 +1,82 @@
+      SUBROUTINEPCCGX(N,IJA,A,RHS,X,RN,RP,P,ATP,ISP,RSP,
+     *PRECON,PCSTOP,PCMV)
+      IMPLICITDOUBLEPRECISION(A-H,O-Z)
+      INTEGERN,IJA(*),ISP(*)
+      DOUBLEPRECISIONA(*),RHS(*),X(*),RN(*),RP(*),P(*),
+     *ATP(*),RSP(*)
+      EXTERNALPRECON,PCSTOP,PCMV
+      INTEGERIERR,ITMAX,ITEST,KMAX,IFL,IPRE,PBLK,LUDONE,IBLK,
+     *MNEED,ITS,RSDONE,NOVERF,RED1,RED2,IERR2,IFRMAT
+      COMMON/PCCOM1/IERR,ITMAX,ITEST,KMAX,IFL,IPRE,PBLK,
+     *LUDONE,IBLK,MNEED,ITS,RSDONE,NOVERF,RED1,RED2,IERR2,
+     *IFRMAT
+      SAVE/PCCOM1/
+      INTEGERIPRE1,IPRE2,RATIO
+      COMMON/PCCOM3/IPRE1,IPRE2,RATIO
+      SAVE/PCCOM3/
+      INTEGERISRT,IJASGN,ISX0,IFORM
+      COMMON/PCVERI/ISRT,IJASGN,ISX0,IFORM
+      SAVE/PCVERI/
+      INTEGERONE,MTHREE
+      INTEGERLTEST
+      DOUBLEPRECISIONALPHA,BETA,RRP,NRRP,PAP
+      DOUBLEPRECISIONDDOT
+      ONE=1
+      MTHREE=-3
+      IF(ISX0.NE.1)THEN
+      CALLPCMV(N,IJA,A,X,RN)
+      CALLPCVSUB(N,RN,RHS)
+      ELSE
+      CALLDCOPY(N,RHS,ONE,RN,ONE)
+      ENDIF
+      CALLPCSTOP(ONE,N,IJA,A,RHS,X,RN,ISP,RSP,PRECON)
+      IF(IERR.GE.0)THEN
+      RETURN
+      ENDIF
+      IF(IPRE.NE.3)THEN
+      CALLDCOPY(N,RN,ONE,RP,ONE)
+      CALLPRECON(MTHREE,N,IJA,A,RP,ISP,RSP)
+      ENDIF
+      CALLDCOPY(N,RP,ONE,P,ONE)
+      RRP=DDOT(N,RP,ONE,RN,ONE)
+      LTEST=ITEST
+      DO1ITS=1,ITMAX-1
+      LTEST=LTEST-1
+      CALLPCMV(N,IJA,A,P,ATP)
+      PAP=DDOT(N,P,ONE,ATP,ONE)
+      IF(PAP.EQ.0.0D0)THEN
+      IERR=13
+      RETURN
+      ENDIF
+      ALPHA=RRP/PAP
+      CALLDAXPY(N,ALPHA,P,ONE,X,ONE)
+      CALLDAXPY(N,-ALPHA,ATP,ONE,RN,ONE)
+      IF(LTEST.EQ.0)THEN
+      LTEST=ITEST
+      CALLPCSTOP(ONE,N,IJA,A,RHS,X,RN,ISP,RSP,PRECON)
+      IF(IERR.GE.0)THEN
+      RETURN
+      ENDIF
+      ENDIF
+      IF(IPRE.NE.3)THEN
+      CALLDCOPY(N,RN,ONE,RP,ONE)
+      CALLPRECON(MTHREE,N,IJA,A,RP,ISP,RSP)
+      ENDIF
+      NRRP=DDOT(N,RN,ONE,RP,ONE)
+      BETA=NRRP/RRP
+      RRP=NRRP
+      CALLPCVSMA(N,BETA,P,RP,P)
+1     CONTINUE
+      CALLPCMV(N,IJA,A,P,ATP)
+      PAP=DDOT(N,P,ONE,ATP,ONE)
+      IF(PAP.EQ.0.0D0)THEN
+      IERR=13
+      RETURN
+      ENDIF
+      ALPHA=RRP/PAP
+      CALLDAXPY(N,ALPHA,P,ONE,X,ONE)
+      CALLDAXPY(N,-ALPHA,ATP,ONE,RN,ONE)
+      ITS=ITMAX
+      CALLPCSTOP(ONE,N,IJA,A,RHS,X,RN,ISP,RSP,PRECON)
+      RETURN
+      END