From 3aa6a640224b2d70ed98617c0b5d985a5a948839 Mon Sep 17 00:00:00 2001
From: nadyawilliams <nadya@sdsc.edu>
Date: Wed, 17 Feb 2016 18:14:09 -0800
Subject: [PATCH] create a separate GamD roll, mv notes there

---
 GaMD-diffs | 117 -----------------------------------------------------
 1 file changed, 117 deletions(-)
 delete mode 100644 GaMD-diffs

diff --git a/GaMD-diffs b/GaMD-diffs
deleted file mode 100644
index 41edccb..0000000
--- a/GaMD-diffs
+++ /dev/null
@@ -1,117 +0,0 @@
-diff --git a/src/amber-modules/amber.module.in b/src/amber-modules/amber.module.in
-index 2d5a1ef..b6399b7 100644
---- a/src/amber-modules/amber.module.in
-+++ b/src/amber-modules/amber.module.in
-@@ -7,17 +7,17 @@
- proc ModulesHelp { } {
-         global amberversion 
- 
--        puts stderr "\tAmber Tools from /opt/amber/@COMPILERNAME@/@ROLLNETWORK@"
-+        puts stderr "\tGaMD patched Amber Tools from /opt/amberGaMD/@COMPILERNAME@/@ROLLNETWORK@"
-         puts stderr "\tAmber Toolkit Version $amberversion\n"
- }
- 
--module-whatis   "Amber Toolkit Version @VERSION@"
-+module-whatis   "GaMD patched Amber Toolkit Version @VERSION@"
- module-whatis   "Compiled with @COMPILERNAME@ compiler"
- 
- # for Tcl script use only
- set     amberversion @VERSION@
- 
--set amberHome /opt/amber/@COMPILERNAME@/@ROLLNETWORK@
-+set amberHome /opt/amberGaMD/@COMPILERNAME@/@ROLLNETWORK@
- setenv AMBERHOME $amberHome
- prepend-path PATH $amberHome/bin
- prepend-path LD_LIBRARY_PATH $amberHome/lib
-
-diff --git a/src/amber-modules/version.mk b/src/amber-modules/version.mk
-index aaa0f1c..2d416e1 100644
---- a/src/amber-modules/version.mk
-+++ b/src/amber-modules/version.mk
-@@ -23,9 +23,9 @@ VERSION.MK.MASTER.DIR = ../amber
- VERSION.MK.INCLUDE = amber.version.mk
- include $(VERSION.MK.INCLUDE) 
- 
--PACKAGE     = amber
-+PACKAGE     = amberGaMD
- CATEGORY    = applications
--NAME        = amber-module-$(COMPILERNAME)-$(ROLLNETWORK)
-+NAME        = amberGaMD-module-$(COMPILERNAME)-$(ROLLNETWORK)
- RELEASE     = 0
- PKGROOT     = /opt/modulefiles/$(CATEGORY)/$(PACKAGE)$(VERSION)
- 
-diff --git a/src/amber/Makefile b/src/amber/Makefile
-index 6363d5a..fbeb2a9 100644
---- a/src/amber/Makefile
-+++ b/src/amber/Makefile
-@@ -42,6 +42,7 @@ build:
- 	  export AMBERHOME=`pwd`/$(SOURCE_DIR); \
- 	  cd $${AMBERHOME}; pwd ; \
- 	  ./update_amber --update ; \
-+	  patch -p0 < ../amber14_GaMD_patch_confidential.txt ; \
- 	  ./configure $(ROLLCOMPILER); \
- 	  make -j8 install;  make clean; \
- 	  ./configure -mpi $(ROLLCOMPILER); \
-
-diff --git a/src/amber/version.mk b/src/amber/version.mk
-index e5177ba..fb8972c 100644
---- a/src/amber/version.mk
-+++ b/src/amber/version.mk
-@@ -8,7 +8,7 @@ ifndef ROLLNETWORK
-   ROLLNETWORK = eth
- endif
- 
--NAME	    = amber-$(COMPILERNAME)-$(ROLLNETWORK)
-+NAME	    = amberGaMD-$(COMPILERNAME)-$(ROLLNETWORK)
- VERSION	    = 14
- RELEASE	    = 0
- SUFFIX      = tar.bz2
-@@ -22,7 +22,7 @@ TOOLSVERSION = 15
- TOOLS_PKG   = $(TOOLS_NAME)$(TOOLSVERSION).$(SUFFIX)
- TOOLS_DIR   = $(TOOLS_PKG:%.$(SUFFIX)=%)
- 
--PKGROOT     = /opt/amber/$(COMPILERNAME)/$(ROLLNETWORK)
-+PKGROOT     = /opt/amberGaMD/$(COMPILERNAME)/$(ROLLNETWORK)
- CUDAHOME    = /opt/cuda
- 
- RPM.EXTRAS = AutoReq:No
-
-diff --git a/version.mk b/version.mk
-index e940c46..f98e27a 100644
---- a/version.mk
-+++ b/version.mk
-@@ -1,4 +1,4 @@
--ROLLNAME = amber
-+ROLLNAME = amberGaMD
- RELEASE  = 0
- COLOR    = DarkTurquoise
- 
---- amber-common.xml.in	2015-11-06 13:10:46.860867993 -0800
-+++ amberGaMD-common.xml.in	2015-09-16 09:13:49.198369090 -0700
-@@ -15,9 +15,8 @@
- 	<changelog>
- 	</changelog>
- 
--	<package>amber-ROLLCOMPILER-ROLLNETWORK</package>
--	<package>amber-module-ROLLCOMPILER-ROLLNETWORK</package>
--	<package>amber-roll-test</package>
-+	<package>amberGaMD-ROLLCOMPILER-ROLLNETWORK</package>
-+	<package>amberGaMD-module-ROLLCOMPILER-ROLLNETWORK</package>
- 
- <post>
- </post>
-
---- amber.xml	2015-11-06 13:11:12.969386574 -0800
-+++ amberGaMD.xml	2015-09-16 10:21:23.816037723 -0700
-@@ -15,9 +15,9 @@
- 	<changelog>
- 	</changelog>
- 
--	<edge from="base" to="amber-common"/>
-+	<edge from="base" to="amberGaMD-common"/>
- 	<order head="base">
--		<tail>amber-common</tail>
-+		<tail>amberGaMD-common</tail>
- 	</order>
- 
- </graph>