Plotting wavefunctions (molecular orbitals) in 3D

PR:             ports/8696
Submitted by:   Ryo MIYAMOTO rmiya@cc.hirosaki-u.ac.jp

9 files changed, 365 insertions, 0 deletions

diff --git a/biology/psi88/Makefile b/biology/psi88/Makefile
new file mode 100644
index 000000000000..81909bdad9e3
--- /dev/null
+++ b/biology/psi88/Makefile
@@ -0,0 +1,37 @@
+# New ports collection makefile for:	Psi88
+# Version required:	88-1.0
+# Date created:		1998-11-11
+# Whom:			Ryo MIYAMOTO
+#
+# $Id: Makefile,v 1.1.1.1 1999/04/01 08:09:45 taoka Exp $
+#
+
+DISTNAME=	psi88
+PKGNAME=	psi88-1.0
+CATEGORIES=	misc biology
+MASTER_SITES=	ftp://ccl.osc.edu/pub/chemistry/software/SOURCES/FORTRAN/psi88/
+EXTRACT_SUFX=	.tar.Z
+
+MAINTAINER=	rmiya@cc.hirosaki-u.ac.jp
+
+pre-patch:
+	${MV} ${WRKSRC}/src/makefile ${WRKSRC}/src/Makefile
+
+pre-build:
+	${CP} ${FILESDIR}/Makefile.top ${WRKSRC}/Makefile
+
+post-install:
+	ln -s ${PREFIX}/bin/PSI2PS ${PREFIX}/bin/PSI2
+	${INSTALL_SCRIPT} ${WRKDIR}/${DISTNAME}/unix/preplot ${PREFIX}/bin/
+	${INSTALL_SCRIPT} ${WRKDIR}/${DISTNAME}/unix/rpsi1 ${PREFIX}/bin/
+	${INSTALL_SCRIPT} ${WRKDIR}/${DISTNAME}/unix/rpsi2 ${PREFIX}/bin/
+	${INSTALL_SCRIPT} ${WRKDIR}/${DISTNAME}/unix/rpsicon ${PREFIX}/bin/
+.if !defined(NOPORTDOCS)
+	${MKDIR} ${PREFIX}/share/doc/psi88
+	${MKDIR} ${PREFIX}/share/doc/psi88/examples
+	${INSTALL_MAN} ${WRKDIR}/${DISTNAME}/README ${PREFIX}/share/doc/psi88
+	${INSTALL_MAN} ${WRKDIR}/${DISTNAME}/psi88.doc ${PREFIX}/share/doc/psi88
+	${INSTALL_MAN} ${WRKDIR}/${DISTNAME}/examples/* ${PREFIX}/share/doc/psi88/examples
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/psi88/distinfo b/biology/psi88/distinfo
new file mode 100644
index 000000000000..4fde2ad89d10
--- /dev/null
+++ b/biology/psi88/distinfo
@@ -0,0 +1 @@
+MD5 (psi88.tar.Z) = acccd40ac46430089ec053aa396da41c
diff --git a/biology/psi88/files/Makefile.top b/biology/psi88/files/Makefile.top
new file mode 100644
index 000000000000..8b1ab0338d92
--- /dev/null
+++ b/biology/psi88/files/Makefile.top
@@ -0,0 +1,9 @@
+all:
+	(cd src/ && make all)
+
+install:
+	(cd src/ && make install)
+
+clean:
+	(cd src/ && make clean)
+
diff --git a/biology/psi88/files/patch-aa b/biology/psi88/files/patch-aa
new file mode 100644
index 000000000000..0dbcb2dfa792
--- /dev/null
+++ b/biology/psi88/files/patch-aa
@@ -0,0 +1,116 @@
+*** src/Makefile.orig	Sat May 25 04:04:15 1991
+--- src/Makefile	Thu Nov 12 11:20:18 1998
+***************
+*** 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
+  #
+***************
+*** 60,66 ****
+  #  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
+--- 66,72 ----
+  #  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
+***************
+*** 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*
+  
diff --git a/biology/psi88/files/patch-ba b/biology/psi88/files/patch-ba
new file mode 100644
index 000000000000..494065d08251
--- /dev/null
+++ b/biology/psi88/files/patch-ba
@@ -0,0 +1,19 @@
+*** unix/rpsi1.orig	Sat May 25 03:50:02 1991
+--- unix/rpsi1	Thu Nov 12 11:25:41 1998
+***************
+*** 10,16 ****
+  #
+  # Run PSI1/88 using cmdlin.psi1 as input
+  #
+! time ./PSI1 < $1.psi1
+  #
+  # remove any old files with the target name
+  #
+--- 10,16 ----
+  #
+  # Run PSI1/88 using cmdlin.psi1 as input
+  #
+! time PSI1 < $1.psi1
+  #
+  # remove any old files with the target name
+  #
diff --git a/biology/psi88/files/patch-bb b/biology/psi88/files/patch-bb
new file mode 100644
index 000000000000..7ffeacd6497f
--- /dev/null
+++ b/biology/psi88/files/patch-bb
@@ -0,0 +1,143 @@
+*** unix/rpsi2.orig	Sat May 25 03:50:02 1991
+--- unix/rpsi2	Thu Nov 12 23:41:19 1998
+***************
+*** 13,79 ****
+     if ($1 == '-hp') goto noargs
+     if ($1 == '-ct') goto noargs
+     echo -n 'no [-ps][-pk][-hp][-ct] options - attempting to run PSI2 '
+!    /bin/time PSI2 < $1.psi2
+  else
+     if ($argv[1] == '-hp') then 
+        echo "Generating contours ... please wait."
+!       /bin/time PSI2HP < $2.psi2
+        echo -n "Renaming HP Plotter file to "$2".hpp"
+!       mv -f fort.10 $2.hpp
+        echo "Done"
+     else if ($argv[2] == '-hp') then 
+        echo "Generating contours ... please wait."
+!       /bin/time PSI2HP < $1.psi2
+        echo -n "Renaming HP Plotter file to "$1".hpp"
+!       mv -f fort.10 $1.hpp
+        echo "Done"
+     else if ($argv[1] == '-ct') then 
+        echo "Generating contours ... please wait."
+!       /bin/time PSI2CT < $2.psi2
+        echo -n "Plotting for ChemText ... "
+        echo -n "Renaming ChemText Metafile to "$2".met"
+!       mv -f fort.10 $2.met
+        echo "Done"
+     else if ($argv[2] == '-ct') then 
+        echo "Generating contours ... please wait."
+!       /bin/time PSI2CT < $1.psi2
+        echo -n "Renaming ChemText Metafile to "$1".met"
+        mv -f fort.10 $1.met
+        echo "Done"
+     else if ($argv[1] == '-pk') then 
+        echo "Generating contours ... please wait."
+  #      setenv OUTPUT_DEVICE PostScript
+!       /bin/time PSI2PS < $2.psi2
+        echo -n "Renaming PostScript file to "$2".ps"
+        mv -f psplot $argv[2].ps
+        echo "Done"
+     else if ($argv[2] == '-pk') then 
+        echo "Generating contours ... please wait."
+  #      setenv OUTPUT_DEVICE PostScript
+!       /bin/time PSI2PS < $1.psi2
+        echo -n "Renaming PostScript file to "$1".ps"
+        mv -f psplot $argv[1].ps
+        echo "Done"
+     else if ($argv[1] == '-ps') then 
+        echo "Generating contours ... please wait."
+        setenv OUTPUT_DEVICE PostScript
+!       /bin/time PSI2 < $2.psi2
+  #SYSV     echo -n "Plotting on the LaserWriter ... ";lp -c /tmp/ps_plot$USER
+  #SYSV     rm -f /tmp/ps_plot$USER
+! #BSD      echo -n "Plotting on the LaserWriter ... ";lpr -r /tmp/ps_plot$USER
+  
+! echo ' edit command file to choose print options, then remove this line'
+  
+        echo "Done"
+     else if ($argv[2] == '-ps') then 
+        echo "Generating contours ... please wait."
+        setenv OUTPUT_DEVICE PostScript
+!       /bin/time PSI2 < $1.psi2
+  #SYSV     echo -n "Plotting on the LaserWriter ... ";lp -c /tmp/ps_plot$USER
+  #SYSV     rm -f /tmp/ps_plot$USER
+! #BSD      echo -n "Plotting on the LaserWriter ... ";lpr -r /tmp/ps_plot$USER
+  
+! echo ' edit command file to choose print options, then remove this line'
+  
+        echo "Done"
+     else
+--- 13,83 ----
+     if ($1 == '-hp') goto noargs
+     if ($1 == '-ct') goto noargs
+     echo -n 'no [-ps][-pk][-hp][-ct] options - attempting to run PSI2 '
+!    time PSI2 < $1.psi2
+! # PSI2 is linked to PSI2PS, then output file `psplot' will moved to $argv[1].ps
+!    echo ': PSI2 is PSI2PS, now'
+!    mv -f psplot $argv[1].ps
+!    echo "Done"
+  else
+     if ($argv[1] == '-hp') then 
+        echo "Generating contours ... please wait."
+!       time PSI2HP < $2.psi2
+        echo -n "Renaming HP Plotter file to "$2".hpp"
+!       mv -f fort.66 $2.hpp
+        echo "Done"
+     else if ($argv[2] == '-hp') then 
+        echo "Generating contours ... please wait."
+!       time PSI2HP < $1.psi2
+        echo -n "Renaming HP Plotter file to "$1".hpp"
+!       mv -f fort.66 $1.hpp
+        echo "Done"
+     else if ($argv[1] == '-ct') then 
+        echo "Generating contours ... please wait."
+!       time PSI2CT < $2.psi2
+        echo -n "Plotting for ChemText ... "
+        echo -n "Renaming ChemText Metafile to "$2".met"
+!       mv -f fort.66 $2.met
+        echo "Done"
+     else if ($argv[2] == '-ct') then 
+        echo "Generating contours ... please wait."
+!       time PSI2CT < $1.psi2
+        echo -n "Renaming ChemText Metafile to "$1".met"
+        mv -f fort.10 $1.met
+        echo "Done"
+     else if ($argv[1] == '-pk') then 
+        echo "Generating contours ... please wait."
+  #      setenv OUTPUT_DEVICE PostScript
+!       time PSI2PS < $2.psi2
+        echo -n "Renaming PostScript file to "$2".ps"
+        mv -f psplot $argv[2].ps
+        echo "Done"
+     else if ($argv[2] == '-pk') then 
+        echo "Generating contours ... please wait."
+  #      setenv OUTPUT_DEVICE PostScript
+!       time PSI2PS < $1.psi2
+        echo -n "Renaming PostScript file to "$1".ps"
+        mv -f psplot $argv[1].ps
+        echo "Done"
+     else if ($argv[1] == '-ps') then 
+        echo "Generating contours ... please wait."
+        setenv OUTPUT_DEVICE PostScript
+!       time PSI2 < $2.psi2
+  #SYSV     echo -n "Plotting on the LaserWriter ... ";lp -c /tmp/ps_plot$USER
+  #SYSV     rm -f /tmp/ps_plot$USER
+!       echo -n "Plotting on the LaserWriter ... ";lpr -r /tmp/ps_plot$USER
+  
+! #echo ' edit command file to choose print options, then remove this line'
+  
+        echo "Done"
+     else if ($argv[2] == '-ps') then 
+        echo "Generating contours ... please wait."
+        setenv OUTPUT_DEVICE PostScript
+!       time PSI2 < $1.psi2
+  #SYSV     echo -n "Plotting on the LaserWriter ... ";lp -c /tmp/ps_plot$USER
+  #SYSV     rm -f /tmp/ps_plot$USER
+!       echo -n "Plotting on the LaserWriter ... ";lpr -r /tmp/ps_plot$USER
+  
+! #echo ' edit command file to choose print options, then remove this line'
+  
+        echo "Done"
+     else
diff --git a/biology/psi88/pkg-comment b/biology/psi88/pkg-comment
new file mode 100644
index 000000000000..00fcd0b7c031
--- /dev/null
+++ b/biology/psi88/pkg-comment
@@ -0,0 +1 @@
+Plotting wavefunctions (molecular orbitals) in 3D
diff --git a/biology/psi88/pkg-descr b/biology/psi88/pkg-descr
new file mode 100644
index 000000000000..21dfa84672c9
--- /dev/null
+++ b/biology/psi88/pkg-descr
@@ -0,0 +1,9 @@
+PSI/88 Version 1.0  by W. L. Jorgensen & D. L. Severance
+
+To plot wavefunctions in three dimensions from
+semi-empirical and most popular ab initio basis sets.
+Valence semi-empirical, STO-3G, 3-21++G(*) and
+6-31++G(d,p) basis sets are implemented for atoms
+H-Ar.
+
+WWW: http://zarbi.chem.yale.edu/programs/psi88.html
diff --git a/biology/psi88/pkg-plist b/biology/psi88/pkg-plist
new file mode 100644
index 000000000000..ce0007c57359
--- /dev/null
+++ b/biology/psi88/pkg-plist
@@ -0,0 +1,30 @@
+bin/PSI1
+bin/PSICON
+bin/PSI2CT
+bin/PSI2HP
+bin/PSI2PS
+bin/PSI2
+bin/PREPLOT
+bin/preplot
+bin/rpsi1
+bin/rpsi2
+bin/rpsicon
+share/doc/psi88/psi88.doc
+share/doc/psi88/README
+share/doc/psi88/examples/ad634a.psi1
+share/doc/psi88/examples/ad634a.psi2
+share/doc/psi88/examples/ad634a.psicon
+share/doc/psi88/examples/ad635a.psi1
+share/doc/psi88/examples/ad635a.psi2
+share/doc/psi88/examples/ad635a.psicon
+share/doc/psi88/examples/ad636a.psi1
+share/doc/psi88/examples/ad636a.psi2
+share/doc/psi88/examples/ad636a.psicon
+share/doc/psi88/examples/ch3cl.psi1
+share/doc/psi88/examples/ch3cl.psi2
+share/doc/psi88/examples/ch3cl.psicon
+share/doc/psi88/examples/test.psi1
+share/doc/psi88/examples/test.psi2
+share/doc/psi88/examples/test.psicon
+@dirrm share/doc/psi88/examples
+@dirrm share/doc/psi88