>From 11bfe8ad5031da2bba14f5331a40128aebcb6b5f Mon Sep 17 00:00:00 2001
From: Gerald Monard <Gerald.Monard@univ-lorraine.fr>
Date: Thu, 26 May 2016 22:04:02 +0200
Subject: [PATCH] libFpbsa (PBSA library for sander) dependency modifications

Makefile and makedepend were not up to date.
>From a search for #if...SANDER, makedepend now contains only the names
of F90 files that are dependent of sander compilation. Makefile is
modified accordingly (SANDERPBSAOBJS).
---
 AmberTools/src/pbsa/Makefile   | 16 +++++-----
 AmberTools/src/pbsa/depend     | 70 ++++++++++++++++--------------------------
 AmberTools/src/pbsa/makedepend | 18 +++++++----
 3 files changed, 46 insertions(+), 58 deletions(-)

diff --git a/AmberTools/src/pbsa/Makefile b/AmberTools/src/pbsa/Makefile
index 27ecd69..01d70f2 100644
--- a/AmberTools/src/pbsa/Makefile
+++ b/AmberTools/src/pbsa/Makefile
@@ -67,14 +67,14 @@ LIBPBSAOBJS= \
 	rgroup.o rfree.o memory_module.o gen_dx_file.LIBPBSA.o parms.LIBPBSA.o \
 	interface.o pbsaapi.LIBPBSA.o myopen.o pb_read.LIBPBSA.o 
 
-SANDERPBSAOBJS= density.SANDER.o pb_force.SANDER.o sa_driver.SANDER.o iimod.o \
-        pb_p3m.SANDER.o dsvdc.o svdcmp.o svbksb.o pythag.o miniop.o \
-        transf.o curv.o GrToPr.o phidev.o project.o interpX.SANDER.o \
-        pb_fddrv.o pb_nlsolver.o pb_lsolver.o pb_mpfrc.o \
-        pb_direct.o pb_crgview.SANDER.o np_force.SANDER.o \
-        pb_list.SANDER.o pb_read.SANDER.o pb_write.SANDER.o pb_init.SANDER.o \
-	timer.SANDER.o pbsa_lib.o gen_dx_file.o \
-        memory_module.o pb_bldsys.SANDER.o pb_fdfrc.SANDER.o
+# in alphabetical order (GM/2016-05-26)
+SANDERPBSAOBJS= curv.o density.o dsvdc.o gen_dx_file.o GrToPr.o \
+        iimod.o interpX.SANDER.o memory_module.o miniop.o np_force.SANDER.o  \
+        parms.SANDER.o pb_bldsys.o pb_crgview.o pb_direct.o pb_fddrv.o  \
+        pb_fdfrc.SANDER.o pb_force.SANDER.o pb_init.SANDER.o pb_list.o pb_lsolver.o  \
+        pb_mpfrc.o pb_nlsolver.o pb_p3m.SANDER.o pb_read.SANDER.o pbsa.SANDER.o \
+        pbsa_lib.o pb_write.SANDER.o phidev.o project.o pythag.o  \
+        sa_driver.SANDER.o svbksb.o svdcmp.o timer.SANDER.o transf.o
 
 install: install.$(INSTALLTYPE)
 
diff --git a/AmberTools/src/pbsa/depend b/AmberTools/src/pbsa/depend
index a185119..9b55727 100644
--- a/AmberTools/src/pbsa/depend
+++ b/AmberTools/src/pbsa/depend
@@ -37,8 +37,6 @@ decomp.o: \
 density.o: \
                     ../include/dprec.fh
 
-density.SANDER.o: \
-                    ../include/dprec.fh
 density.LIBPBSA.o: \
                     ../include/dprec.fh
 dsvdc.o: \
@@ -71,9 +69,6 @@ gen_dx_file.o: \
                     copyright.h\
                     ../include/dprec.fh
 
-gen_dx_file.SANDER.o: \
-                    copyright.h\
-                    ../include/dprec.fh
 gen_dx_file.LIBPBSA.o: \
                     copyright.h\
                     ../include/dprec.fh
@@ -92,15 +87,26 @@ gmresX.o: \
 GrToPr.o: \
                     ../include/dprec.fh
 
+IIM.o: \
+                    ../include/dprec.fh\
+                    pb_constants.h
+
 iimod.o: \
                     copyright.h\
                     ../include/dprec.fh
 
+indexg.o: \
+                    ../include/dprec.fh
+
 interpX.o: \
                     ../include/dprec.fh\
                     iimod.o\
                     pb_constants.h
 
+interpX.SANDER.o: \
+                    ../include/dprec.fh\
+                    iimod.o\
+                    pb_constants.h
 irre31.o: \
                     ../include/dprec.fh\
                     iimod.o
@@ -216,17 +222,6 @@ pb_bldsys.o: \
                     pb_constants.h\
                     ../include/md.h
 
-pb_bldsys.SANDER.o: \
-                    copyright.h\
-                    ../include/dprec.fh\
-                    pb_def.h\
-                    timer.h\
-                    pb_force.SANDER.o\
-                    density.SANDER.o\
-                    timer.SANDER.o\
-                    sa_driver.SANDER.o\
-                    pb_constants.h\
-                    ../include/md.h
 pb_bldsys.LIBPBSA.o: \
                     copyright.h\
                     ../include/dprec.fh\
@@ -256,13 +251,6 @@ pb_crgview.o: \
                     pb_force.o\
                     pb_constants.h
 
-pb_crgview.SANDER.o: \
-                    copyright.h\
-                    ../include/dprec.fh\
-                    pb_def.h\
-                    sa_driver.SANDER.o\
-                    pb_force.SANDER.o\
-                    pb_constants.h
 pb_crgview.LIBPBSA.o: \
                     copyright.h\
                     ../include/dprec.fh\
@@ -279,14 +267,6 @@ pb_direct.o: \
                     pb_force.o\
                     decomp.o
 
-pb_direct.SANDER.o: \
-                    copyright.h\
-                    ../include/dprec.fh\
-                    pb_def.h\
-                    pb_constants.h\
-                    flocntrl.h\
-                    pb_force.SANDER.o\
-                    decomp.o
 pb_direct.LIBPBSA.o: \
                     copyright.h\
                     ../include/dprec.fh\
@@ -461,14 +441,6 @@ pb_list.o: \
                     pb_constants.h\
                     extra.h
 
-pb_list.SANDER.o: \
-                    copyright.h\
-                    ../include/dprec.fh\
-                    pb_def.h\
-                    pb_force.SANDER.o\
-                    sa_driver.SANDER.o\
-                    pb_constants.h\
-                    extra.h
 pb_list.LIBPBSA.o: \
                     copyright.h\
                     ../include/dprec.fh\
@@ -501,7 +473,7 @@ pb_p3m.o: \
 
 pb_p3m.SANDER.o: \
                     ../include/dprec.fh\
-                    density.SANDER.o\
+                    density.o\
                     pb_constants.h\
                     iimod.o
 pb_p3m.LIBPBSA.o: \
@@ -601,6 +573,20 @@ pbsa.o: \
                     pb_md.h\
                     timer.h
 
+pbsa.SANDER.o: \
+                    copyright.h\
+                    ../include/dprec.fh\
+                    files.h\
+                    extra.h\
+                    parallel.h\
+                    timer.SANDER.o\
+                    decomp.o\
+                    memory_module.o\
+                    parms.SANDER.o\
+                    box.h\
+                    ../include/md.h\
+                    pb_md.h\
+                    timer.h
 pbsa_lib.o: \
                     copyright.h
 
@@ -633,10 +619,6 @@ problem.o: \
                     pb_force.o\
                     iimod.o
 
-problem.SANDER.o: \
-                    ../include/dprec.fh\
-                    pb_force.SANDER.o\
-                    iimod.o
 prodis.o: \
                     ../include/dprec.fh\
                     iimod.o
diff --git a/AmberTools/src/pbsa/makedepend b/AmberTools/src/pbsa/makedepend
index 68017af..7cf6b9f 100755
--- a/AmberTools/src/pbsa/makedepend
+++ b/AmberTools/src/pbsa/makedepend
@@ -16,12 +16,18 @@ printf <<EOF;
 #
 EOF
 
-$SANDER{"sa_driver"} = $SANDER{"pb_force"} = $SANDER{"np_force"} = 
-	$SANDER{"density"} = $SANDER{"pb_direct"} =
-	$SANDER{"pb_bldsys"} = $SANDER{"pb_read"} = $SANDER{"pb_write"} =
-	$SANDER{"pb_init"} = $SANDER{"timer"} = $SANDER{"problem"} =
-        $SANDER{"gen_dx_file"} = $SANDER{"pb_p3m"} = $SANDER{"pb_fdfrc"} = 
-        $SANDER{"pb_list"} = $SANDER{"pb_crgview"} = $SANDER{"parms"} = 1;
+# from grep '#.*SANDER' *.F90
+$SANDER{"interpX"} = $SANDER{"np_force"} = $SANDER{"parms"} =
+        $SANDER{"pb_fdfrc"} = $SANDER{"pb_force"} = $SANDER{"pb_init"} =
+        $SANDER{"pb_p3m"} = $SANDER{"pb_read"} = $SANDER{"pbsa"} =
+        $SANDER{"pb_write"} = $SANDER{"sa_driver"} = $SANDER{"timer"} = 1;
+# Commented out by Gerald Monard
+#$SANDER{"sa_driver"} = $SANDER{"pb_force"} = $SANDER{"np_force"} = 
+#	$SANDER{"density"} = $SANDER{"pb_direct"} =
+#	$SANDER{"pb_bldsys"} = $SANDER{"pb_read"} = $SANDER{"pb_write"} =
+#	$SANDER{"pb_init"} = $SANDER{"timer"} = $SANDER{"problem"} =
+#        $SANDER{"gen_dx_file"} = $SANDER{"pb_p3m"} = $SANDER{"pb_fdfrc"} = 
+#        $SANDER{"pb_list"} = $SANDER{"pb_crgview"} = $SANDER{"parms"} = 1;
 $LIBPBSA{"sa_driver"} = $LIBPBSA{"pb_force"} = $LIBPBSA{"np_force"} = 
         $LIBPBSA{"pb_p3m"} = $LIBPBSA{"pb_fdfrc"} = $LIBPBSA{"pb_direct"} =
 	$LIBPBSA{"pb_read"} = $LIBPBSA{"pb_write"} = $LIBPBSA{"pb_init"} = 
-- 
1.9.1