Semi-empirical (MNDO, etc.) molecular orbital calculation

PR:             ports/8863
Submitted by:   Ryo MIYAMOTO rmiya@cc.hirosaki-u.ac.jp

6 files changed, 157 insertions, 0 deletions

diff --git a/biology/mopac/files/h2o.dat b/biology/mopac/files/h2o.dat
new file mode 100644
index 000000000000..79b255eaac49
--- /dev/null
+++ b/biology/mopac/files/h2o.dat
@@ -0,0 +1,6 @@
+ pm3 vector gnorm=0
+h2o.dat
+h2o.dat
+ O    0.0000000  0      0.000000  0      0.000000  0    0    0    0      0.0000
+ H    0.9730005  1      0.000000  0      0.000000  0    1    0    0      0.0000
+ H    0.9730879  1    104.580675  1      0.000000  0    1    2    0      0.0000
diff --git a/biology/mopac/files/patch-aa b/biology/mopac/files/patch-aa
new file mode 100644
index 000000000000..9b80aaaa373d
--- /dev/null
+++ b/biology/mopac/files/patch-aa
@@ -0,0 +1,20 @@
+*** matou1.f.2	Wed Apr 23 16:26:50 1997
+--- matou1.f	Wed Apr 23 16:32:56 1997
+***************
+*** 2,8 ****
+        IMPLICIT DOUBLE PRECISION (A-H,O-Z)
+        INCLUDE 'SIZES'
+        PARAMETER (MXDIM=MAXPAR+NUMATM)
+!       PARAMETER (MAXDIM=MAX(MAXORB,3*NUMATM))
+        DIMENSION A(NR,NR),B(NDIM)
+        COMMON /MOLKST/ NUMAT,NAT(NUMATM),NFIRST(NUMATM),NMIDLE(NUMATM),
+       1                NLAST(NUMATM), NORBS, NELECS,NALPHA,NBETA,
+--- 2,9 ----
+        IMPLICIT DOUBLE PRECISION (A-H,O-Z)
+        INCLUDE 'SIZES'
+        PARAMETER (MXDIM=MAXPAR+NUMATM)
+! C      PARAMETER (MAXDIM=MAX(MAXORB,3*NUMATM))
+!       PARAMETER (MAXDIM=(MAXORB+3*NUMATM))
+        DIMENSION A(NR,NR),B(NDIM)
+        COMMON /MOLKST/ NUMAT,NAT(NUMATM),NFIRST(NUMATM),NMIDLE(NUMATM),
+       1                NLAST(NUMATM), NORBS, NELECS,NALPHA,NBETA,
diff --git a/biology/mopac/files/patch-ab b/biology/mopac/files/patch-ab
new file mode 100644
index 000000000000..36e1c3ee0f53
--- /dev/null
+++ b/biology/mopac/files/patch-ab
@@ -0,0 +1,36 @@
+*** SIZES.2	Wed Apr 23 16:26:42 1997
+--- SIZES	Wed Apr 23 16:36:49 1997
+***************
+*** 10,16 ****
+  *     ISYBYL = 1 IF MOPAC IS TO BE USED IN THE SYBYL PACKAGE, =0 OTHERWISE
+  *     SEE ALSO NMECI, NPULAY AND MESP AT THE END OF THIS FILE
+  *                                                                       
+!       PARAMETER (MAXHEV=30, MAXLIT=30)
+        PARAMETER (MAXTIM=3600, MAXDMP=3600)
+        PARAMETER (ISYBYL=0)
+  *                                                                       
+--- 10,16 ----
+  *     ISYBYL = 1 IF MOPAC IS TO BE USED IN THE SYBYL PACKAGE, =0 OTHERWISE
+  *     SEE ALSO NMECI, NPULAY AND MESP AT THE END OF THIS FILE
+  *                                                                       
+!       PARAMETER (MAXHEV=50, MAXLIT=50)
+        PARAMETER (MAXTIM=3600, MAXDMP=3600)
+        PARAMETER (ISYBYL=0)
+  *                                                                       
+***************
+*** 32,38 ****
+  *     MAXHES         AREA OF HESSIAN MATRIX                             
+  *     MAXALL         LARGER THAN MAXORB OR MAXPAR.
+  ************************************************************************
+!       PARAMETER (VERSON=7.01D0)
+        PARAMETER (NUMATM=MAXHEV+MAXLIT)
+        PARAMETER (MAXORB=4*MAXHEV+MAXLIT)
+        PARAMETER (MAXPAR=3*NUMATM)
+--- 32,38 ----
+  *     MAXHES         AREA OF HESSIAN MATRIX                             
+  *     MAXALL         LARGER THAN MAXORB OR MAXPAR.
+  ************************************************************************
+!       PARAMETER (VERSON=7.02D0)
+        PARAMETER (NUMATM=MAXHEV+MAXLIT)
+        PARAMETER (MAXORB=4*MAXHEV+MAXLIT)
+        PARAMETER (MAXPAR=3*NUMATM)
diff --git a/biology/mopac/files/patch-ac b/biology/mopac/files/patch-ac
new file mode 100644
index 000000000000..cd2b71f24bd0
--- /dev/null
+++ b/biology/mopac/files/patch-ac
@@ -0,0 +1,25 @@
+*** readmo.f.2	Wed Apr 23 17:28:03 1997
+--- readmo.f	Wed Apr 23 17:30:15 1997
+***************
+*** 50,55 ****
+--- 50,56 ----
+  C
+        DIMENSION LOPT(3,NUMATM)
+        CHARACTER KEYWRD*241, KOMENT*81, TITLE*81, LINE*80, BANNER*80
++      * ,BANNR2*80
+        CHARACTER KEYS(80)*1, SPACE*1, SPACE2*2, CH*1, CH2*2
+        CHARACTER ELEMNT*2, IDATE*24, GETNAM*80, NAME*4, NAMO*4, ISTA*4
+        COMMON /KEYWRD/ KEYWRD
+***************
+*** 221,227 ****
+--- 222,231 ----
+  C
+        BANNER=' ** MOPAC FOR LINUX (PUBLIC DOMAIN VERSION) '//
+       1' MTA ATOMKI, Debrecen, 95-JUN-21  **'
++       BANNR2=' ** Porting to FreeBSD 2.1R  by Hiroki Minematu'//
++      1' and Ryo MIYAMOTO, 1997-04-23  **'
+        WRITE(6,'(A)')BANNER
++       WRITE(6,'(A)')BANNR2
+  C
+  C    THE BANNER DOES NOT APPEAR ANYWHERE ELSE.
+  C
diff --git a/biology/mopac/files/patch-ad b/biology/mopac/files/patch-ad
new file mode 100644
index 000000000000..2f95df01f162
--- /dev/null
+++ b/biology/mopac/files/patch-ad
@@ -0,0 +1,30 @@
+*** Makefile.2	Wed Apr 23 22:14:31 1997
+--- Makefile	Wed Apr 23 22:16:32 1997
+***************
+*** 15,21 ****
+  SIZEDEPSRC	:= $(shell grep -l -i '      INCLUDE ' *.f; true)
+  SIZEDEPEND	= $(SIZEDEPSRC:.f=.o)
+  MOPAC		= MOPAC7
+! MOPACSHELL	= mopac
+  BINDIR		= /usr/local/bin
+  OWNER		= root.bin
+  
+--- 15,21 ----
+  SIZEDEPSRC	:= $(shell grep -l -i '      INCLUDE ' *.f; true)
+  SIZEDEPEND	= $(SIZEDEPSRC:.f=.o)
+  MOPAC		= MOPAC7
+! MOPACSHELL	= rmopac
+  BINDIR		= /usr/local/bin
+  OWNER		= root.bin
+  
+***************
+*** 23,28 ****
+--- 23,30 ----
+  		@echo -n "Loading $@ ... "
+  		f77 -O $(OBJS) -o $@
+  		@echo "done"
++ 
++ all:          $(MOPAC)
+  
+  clean:
+  	 	$(RM) $(OBJS) *.trace core
diff --git a/biology/mopac/files/rmopac b/biology/mopac/files/rmopac
new file mode 100644
index 000000000000..597dc35c552a
--- /dev/null
+++ b/biology/mopac/files/rmopac
@@ -0,0 +1,40 @@
+#!/bin/csh -f
+#
+set job = $1
+set mopacdir = /usr/local/bin
+set smallmopac = MOPAC7
+#
+#  Check that prior copies of files do not exist
+foreach file (out log arc end)
+    if -e $job.$file mv $job.$file $job.$file.$$
+  end
+#
+#  Now, make all the necessary assignments
+#
+setenv FOR005 $job.dat
+setenv FOR006 $job.out
+setenv FOR009 $job.res
+setenv FOR010 $job.den
+setenv FOR011 $job.log
+setenv FOR012 $job.arc
+setenv FOR013 $job.gpt
+setenv FOR016 $job.syb
+setenv FOR020 $job.ump
+setenv SETUP  SETUP.DAT
+setenv SHUTDOWN $job.end
+if -e core rm core
+if -e fort.2 rm fort.2
+if -e fort.16 rm fort.16
+#
+time $mopacdir/$smallmopac >> $job.log  
+#
+echo job $job is finished
+head -3 $job.dat
+if -e core rm core
+if -e fort.2 rm fort.2
+if -e fort.16 rm fort.16
+#
+if -e SHUTDOWN rm SHUTDOWN
+if -e $job.end rm $job.end
+if -e nul      rm nul
+exit