1 files changed, 135 insertions, 126 deletions

diff --git a/biology/psi88/files/patch-aa b/biology/psi88/files/patch-aa
index 3c00f318a018..0a99544babac 100644
--- a/biology/psi88/files/patch-aa
+++ b/biology/psi88/files/patch-aa
@@ -1,126 +1,135 @@
-*** src/Makefile.orig  Fri May 24 21:04:15 1991
---- src/Makefile       Mon Jun 14 23:41:50 1999
-***************
-*** 27,37 ****
-  # level and when it is working, increase the optimization level.  So far
-  # optimization has never caused problems with this program.
-  #
-! # SGI 4D series flags
-  #
-  f77 = f77
-! FFLAGS = -w0 -O4 -G 64
-! LFLAGS = -lfastm -lfpe -s
-  #
-  # SUN Sparc series flags version 1.3 or later compiler
-  #
---- 27,43 ----
-  # level and when it is working, increase the optimization level.  So far
-  # optimization has never caused problems with this program.
-  #
-! # FreeBSD
-  #
-  f77 = f77
-! FFLAGS = -O3 -Wall
-! LFLAGS =
-! #
-! # SGI 4D series flags
-! #
-! #f77 = f77
-! #FFLAGS = -w0 -O4 -G 64
-! #LFLAGS = -lfastm -lfpe -s
-  #
-  # SUN Sparc series flags version 1.3 or later compiler
-  #
-***************
-*** 60,71 ****
-  #  Place your G88/G90 util library definition here if you wish to 
-  #  compile chk2psi
-  #
-! G90LIB = /usr/people/frisch/g90/libg90.a
-  #
-  # define the directory where the executables will reside
-  # usually /usr/local/bin or ~/bin to put it in your own directory
-  #
-! BIN = /usr/local/bin
-  #  
-  #**** Add PSI2 to this and the install lists if you have a user defined
-  #     Plotting library to plot to the screen, also remove any which you 
---- 66,77 ----
-  #  Place your G88/G90 util library definition here if you wish to 
-  #  compile chk2psi
-  #
-! #G90LIB = /usr/people/frisch/g90/libg90.a
-  #
-  # define the directory where the executables will reside
-  # usually /usr/local/bin or ~/bin to put it in your own directory
-  #
-! BIN = $(PREFIX)/bin
-  #  
-  #**** Add PSI2 to this and the install lists if you have a user defined
-  #     Plotting library to plot to the screen, also remove any which you 
-***************
-*** 84,96 ****
-  #######################################################################
-  #
-  
-!  all:  PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT chk2psi $(EXTRAS)
-  
-  #
-  # Install in the executable directory - may need to be superuser
-  # depending on where you decide to put it (/usr/local/bin for instance)
-  #
-! install: PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT chk2psi $(EXTRAS)
-  	mv PSI1 $(BIN)
-  	chmod +rx $(BIN)/PSI1
-  	mv PSICON $(BIN)
---- 90,104 ----
-  #######################################################################
-  #
-  
-! # all:  PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT chk2psi $(EXTRAS)
-!  all:  PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT $(EXTRAS)
-  
-  #
-  # Install in the executable directory - may need to be superuser
-  # depending on where you decide to put it (/usr/local/bin for instance)
-  #
-! #install: PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT chk2psi $(EXTRAS)
-! install: PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT $(EXTRAS)
-  	mv PSI1 $(BIN)
-  	chmod +rx $(BIN)/PSI1
-  	mv PSICON $(BIN)
-***************
-*** 99,106 ****
-  	chmod +rx $(BIN)/PREPLOT
-  	mv PSI2* $(BIN)
-  	chmod +rx $(BIN)/PSI2*
-! 	mv chk2psi $(BIN)
-! 	chmod +rx $(BIN)/chk2psi
-  
-  #
-  # This is the Density matrix generation program (PSI1/88)
---- 107,115 ----
-  	chmod +rx $(BIN)/PREPLOT
-  	mv PSI2* $(BIN)
-  	chmod +rx $(BIN)/PSI2*
-! 
-! #	mv chk2psi $(BIN)
-! #	chmod +rx $(BIN)/chk2psi
-  
-  #
-  # This is the Density matrix generation program (PSI1/88)
-***************
-*** 164,169 ****
-  # Clean up when done
-  #
-   clean :
-!         touch a.out foo.o core foo.u foo.f17 foo.22
-  	rm -f a.out *.o core *.u *.f17 *.f2*
-  
---- 173,178 ----
-  # Clean up when done
-  #
-   clean :
-! 	touch a.out foo.o core foo.u foo.f17 foo.22
-  	rm -f a.out *.o core *.u *.f17 *.f2*
-  
+--- src/Makefile.orig	Sat May 25 04:04:15 1991
++++ src/Makefile	Tue Jan  9 11:30:09 2007
+@@ -27,11 +27,11 @@
+ # level and when it is working, increase the optimization level.  So far
+ # optimization has never caused problems with this program.
+ #
+-# SGI 4D series flags
++# FreeBSD
+ #
+-f77 = f77
+-FFLAGS = -w0 -O4 -G 64
+-LFLAGS = -lfastm -lfpe -s
++FC = %%FC%%
++FFLAGS = %%FFLAGS%%
++#LFLAGS = -lfastm -lfpe -s
+ #
+ # SUN Sparc series flags version 1.3 or later compiler
+ #
+@@ -60,12 +60,12 @@
+ #  Place your G88/G90 util library definition here if you wish to 
+ #  compile chk2psi
+ #
+-G90LIB = /usr/people/frisch/g90/libg90.a
++#G90LIB = /usr/people/frisch/g90/libg90.a
+ #
+ # define the directory where the executables will reside
+ # usually /usr/local/bin or ~/bin to put it in your own directory
+ #
+-BIN = /usr/local/bin
++BIN = %%PREFIX%%/bin
+ #  
+ #**** Add PSI2 to this and the install lists if you have a user defined
+ #     Plotting library to plot to the screen, also remove any which you 
+@@ -84,13 +84,15 @@
+ #######################################################################
+ #
+ 
+- all:  PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT chk2psi $(EXTRAS)
++# all:  PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT chk2psi $(EXTRAS)
++ all:  PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT $(EXTRAS)
+ 
+ #
+ # Install in the executable directory - may need to be superuser
+ # depending on where you decide to put it (/usr/local/bin for instance)
+ #
+-install: PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT chk2psi $(EXTRAS)
++#install: PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT chk2psi $(EXTRAS)
++install: PSI1 PSICON PSI2CT PSI2HP PSI2PS PREPLOT $(EXTRAS)
+ 	mv PSI1 $(BIN)
+ 	chmod +rx $(BIN)/PSI1
+ 	mv PSICON $(BIN)
+@@ -99,71 +101,71 @@
+ 	chmod +rx $(BIN)/PREPLOT
+ 	mv PSI2* $(BIN)
+ 	chmod +rx $(BIN)/PSI2*
+-	mv chk2psi $(BIN)
+-	chmod +rx $(BIN)/chk2psi
++#	mv chk2psi $(BIN)
++#	chmod +rx $(BIN)/chk2psi
+ 
+ #
+ # This is the Density matrix generation program (PSI1/88)
+ #
+  PSI1: psi1.f 
+-	f77 $(FFLAGS) psi1.f -o PSI1 $(LFLAGS)
++	%%FC%% $(FFLAGS) psi1.f -o PSI1 $(LFLAGS)
+ 
+ #
+ # This is the contour generation program (PSICON/88)
+ # 
+  PSICON: psicon.f
+-	f77 $(FFLAGS) psicon.f -o PSICON $(LFLAGS)
++	%%FC%% $(FFLAGS) psicon.f -o PSICON $(LFLAGS)
+ 
+ #
+ # This is for the plotting routine (PSI2/88) to a user defined graphics lib
+ #
+  PSI2: psi2.f
+-	f77 $(FFLAGS) psi2.f -o PSI2 $(GRLIBS) $(LFLAGS)
++	%%FC%% $(FFLAGS) psi2.f -o PSI2 $(GRLIBS) $(LFLAGS)
+ 
+ #
+ #  This is for the plotting routine set up to plot to a GKS device
+ #  gksplot.f is a gks library that SHOULD work on any machine.....
+ #
+  PSI2GKS: psi2.f gksplot.f
+-	f77 $(FFLAGS) psi2.f gksplot.f -o PSI2GKS $(LFLAGS) $(GKSLIB)
++	%%FC%% $(FFLAGS) psi2.f gksplot.f -o PSI2GKS $(LFLAGS) $(GKSLIB)
+ 
+ #
+ #  This is for the plotting routine set up to plot to a ChemText Metafile
+ #
+  PSI2CT: psi2.f ctplot.f
+-	f77 $(FFLAGS) psi2.f ctplot.f -o PSI2CT $(LFLAGS)
++	%%FC%% $(FFLAGS) psi2.f ctplot.f -o PSI2CT $(LFLAGS)
+ 
+ #
+ #  This is for the plotting routine set up to plot to a PostScript device
+ #  psplot.f is a postscript library that SHOULD work on any machine.....
+ #
+  PSI2PS: psi2.f psplot.f
+-	f77 $(FFLAGS) psi2.f psplot.f -o PSI2PS $(LFLAGS)
++	%%FC%% $(FFLAGS) psi2.f psplot.f -o PSI2PS $(LFLAGS)
+ 
+ #
+ #  This is for the plotting routine set up to plot to a HP plotter
+ #  hpplot.f is a HP plotter library that SHOULD work on any machine.....
+ #
+  PSI2HP: psi2.f hpplot.f
+-	f77 $(FFLAGS) psi2.f hpplot.f -o PSI2HP $(LFLAGS)
++	%%FC%% $(FFLAGS) psi2.f hpplot.f -o PSI2HP $(LFLAGS)
+ 
+ #
+ # This is a program to convert MOPAC .GPT files (using the graph keyword)
+ # to PSI/88 input files.
+ #
+  PREPLOT: preplot.f 
+-	f77 $(FFLAGS) preplot.f -o PREPLOT $(LFLAGS)
++	%%FC%% $(FFLAGS) preplot.f -o PREPLOT $(LFLAGS)
+ 
+ #
+ # This is a program to read checkpoint files - 
+ #
+  chk2psi: chk2psi.f $(G90LIB)
+-	f77 $(FFLAGS) chk2psi.f $(G90LIB) -o chk2psi $(LFLAGS)
++	%%FC%% $(FFLAGS) chk2psi.f $(G90LIB) -o chk2psi $(LFLAGS)
+ 
+ #
+ # Clean up when done
+ #
+  clean :
+-        touch a.out foo.o core foo.u foo.f17 foo.22
++	touch a.out foo.o core foo.u foo.f17 foo.22
+ 	rm -f a.out *.o core *.u *.f17 *.f2*
+