Skip site navigation (1)Skip section navigation (2)
Date:      Mon, 25 Aug 2014 17:19:31 +0000 (UTC)
From:      Dmitry Marakasov <amdmi3@FreeBSD.org>
To:        ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org
Subject:   svn commit: r366104 - in head/biology/protomol: . files
Message-ID:  <201408251719.s7PHJVpT017298@svn.freebsd.org>

next in thread | raw e-mail | index | archive | help
Author: amdmi3
Date: Mon Aug 25 17:19:31 2014
New Revision: 366104
URL: http://svnweb.freebsd.org/changeset/ports/366104
QAT: https://qat.redports.org/buildarchive/r366104/

Log:
  - Stagify
  - Fix build

Added:
  head/biology/protomol/files/patch-applications__iSGProtomol-app__forces__iSGDihedralSystemForce.h   (contents, props changed)
  head/biology/protomol/files/patch-applications__iSGProtomol-app__forces__iSGImproperSystemForce.h   (contents, props changed)
  head/biology/protomol/files/patch-framework__forces__DihedralSystemForce.h   (contents, props changed)
  head/biology/protomol/files/patch-framework__forces__HarmDihedralSystemForce.h   (contents, props changed)
  head/biology/protomol/files/patch-framework__forces__ImproperSystemForce.h   (contents, props changed)
  head/biology/protomol/files/patch-framework__forces__NonbondedCutoffMollyForce.h   (contents, props changed)
  head/biology/protomol/files/patch-framework__forces__NonbondedCutoffSystemForce.h   (contents, props changed)
Modified:
  head/biology/protomol/Makefile

Modified: head/biology/protomol/Makefile
==============================================================================
--- head/biology/protomol/Makefile	Mon Aug 25 17:14:02 2014	(r366103)
+++ head/biology/protomol/Makefile	Mon Aug 25 17:19:31 2014	(r366104)
@@ -30,7 +30,6 @@ WRKSRC=		${WRKDIR}/${PORTNAME}
 OPTIONS_DEFINE=	GLUT
 OPTIONS_DEFAULT=	GLUT
 
-NO_STAGE=	yes
 .include <bsd.port.options.mk>
 
 .if ${PORT_OPTIONS:MGLUT}
@@ -42,9 +41,9 @@ CONFIGURE_ARGS+=	--with-glut=no
 
 .if ${PORT_OPTIONS:MEXAMPLES}
 post-install:
-	@${MKDIR} ${EXAMPLESDIR}
+	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	cd ${WRKSRC}/examples && ${FIND} . | ${EGREP} -v '\.cvsignore' | \
-		${CPIO} -pdmu -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
+		${CPIO} -pdmu -R ${SHAREOWN}:${SHAREGRP} ${STAGEDIR}${EXAMPLESDIR}
 .endif
 
 .include <bsd.port.mk>

Added: head/biology/protomol/files/patch-applications__iSGProtomol-app__forces__iSGDihedralSystemForce.h
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/protomol/files/patch-applications__iSGProtomol-app__forces__iSGDihedralSystemForce.h	Mon Aug 25 17:19:31 2014	(r366104)
@@ -0,0 +1,20 @@
+--- applications/iSGProtomol-app/forces/iSGDihedralSystemForce.h.orig	2005-05-07 18:40:20.000000000 +0400
++++ applications/iSGProtomol-app/forces/iSGDihedralSystemForce.h	2014-08-22 20:49:51.000000000 +0400
+@@ -71,7 +71,7 @@
+       (dynamic_cast<const SemiGenericTopology<TBoundaryConditions>& >(*topo)).boundaryConditions;
+ 
+     for (unsigned int i = 0; i < topo->dihedrals.size(); i++) 
+-      calcTorsion(boundary,topo->dihedrals[i], positions, forces,
++      this->calcTorsion(boundary,topo->dihedrals[i], positions, forces,
+       (*energies)[ScalarStructure::DIHEDRAL],
+       (*energies)[ScalarStructure::DIHEDRAL_DELTAMU],
+       energies);
+@@ -95,7 +95,7 @@
+ 	  to = n;
+ 	int from = (n*i)/count;
+ 	for (int j = from; j < to; j++)
+-	  calcTorsion(boundary, topo->dihedrals[j], positions, forces,
++	  this->calcTorsion(boundary, topo->dihedrals[j], positions, forces,
+           (*energies)[ScalarStructure::DIHEDRAL],
+           (*energies)[ScalarStructure::DIHEDRAL_DELTAMU],
+           energies);

Added: head/biology/protomol/files/patch-applications__iSGProtomol-app__forces__iSGImproperSystemForce.h
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/protomol/files/patch-applications__iSGProtomol-app__forces__iSGImproperSystemForce.h	Mon Aug 25 17:19:31 2014	(r366104)
@@ -0,0 +1,20 @@
+--- applications/iSGProtomol-app/forces/iSGImproperSystemForce.h.orig	2005-05-07 18:40:20.000000000 +0400
++++ applications/iSGProtomol-app/forces/iSGImproperSystemForce.h	2014-08-22 20:50:15.000000000 +0400
+@@ -67,7 +67,7 @@
+     const TBoundaryConditions &boundary = 
+       (dynamic_cast<const SemiGenericTopology<TBoundaryConditions>& >(*topo)).boundaryConditions;
+     for (unsigned int i = 0; i < topo->impropers.size(); i++)
+-      calcTorsion(boundary,topo->impropers[i], positions, forces,
++      this->calcTorsion(boundary,topo->impropers[i], positions, forces,
+       (*energies)[ScalarStructure::IMPROPER],
+       (*energies)[ScalarStructure::IMPROPER_DELTAMU],
+       energies);
+@@ -91,7 +91,7 @@
+ 	  to = n;
+ 	int from = (n*i)/count;
+ 	for (int j = from; j < to; j++)
+-	  calcTorsion(boundary, topo->impropers[j], positions, forces,
++	  this->calcTorsion(boundary, topo->impropers[j], positions, forces,
+           (*energies)[ScalarStructure::IMPROPER],
+           (*energies)[ScalarStructure::IMPROPER_DELTAMU],
+           energies);

Added: head/biology/protomol/files/patch-framework__forces__DihedralSystemForce.h
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/protomol/files/patch-framework__forces__DihedralSystemForce.h	Mon Aug 25 17:19:31 2014	(r366104)
@@ -0,0 +1,20 @@
+--- framework/forces/DihedralSystemForce.h.orig	2005-05-07 18:40:24.000000000 +0400
++++ framework/forces/DihedralSystemForce.h	2014-08-22 20:41:24.000000000 +0400
+@@ -72,7 +72,7 @@
+     const TBoundaryConditions &boundary = 
+       (dynamic_cast<const SemiGenericTopology<TBoundaryConditions>& >(*topo)).boundaryConditions;
+     for (unsigned int i = 0; i < topo->dihedrals.size(); i++) 
+-      calcTorsion(boundary,topo->dihedrals[i], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);
++      this->calcTorsion(boundary,topo->dihedrals[i], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);
+   }
+   template<class TBoundaryConditions> 
+   inline void DihedralSystemForce<TBoundaryConditions>::parallelEvaluate(const GenericTopology* topo,
+@@ -93,7 +93,7 @@
+ 	  to = n;
+ 	int from = (n*i)/count;
+ 	for (int j = from; j < to; j++)
+-	  calcTorsion(boundary, topo->dihedrals[j], positions, forces, (*energies)[ScalarStructure::DIHEDRAL],energies);
++	  this->calcTorsion(boundary, topo->dihedrals[j], positions, forces, (*energies)[ScalarStructure::DIHEDRAL],energies);
+       }
+     }
+   }

Added: head/biology/protomol/files/patch-framework__forces__HarmDihedralSystemForce.h
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/protomol/files/patch-framework__forces__HarmDihedralSystemForce.h	Mon Aug 25 17:19:31 2014	(r366104)
@@ -0,0 +1,20 @@
+--- framework/forces/HarmDihedralSystemForce.h.orig	2005-05-07 18:40:24.000000000 +0400
++++ framework/forces/HarmDihedralSystemForce.h	2014-08-22 20:42:13.000000000 +0400
+@@ -119,7 +119,7 @@
+       {
+ 	if (static_cast<int>(i) != myDihedral) {
+ 	  if(computeOthers) {
+-	    calcTorsion(boundary,topo->dihedrals[i], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);
++	    this->calcTorsion(boundary,topo->dihedrals[i], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);
+ 	  }
+ 	}
+ 	else {
+@@ -149,7 +149,7 @@
+ 	int from = (n*i)/count;
+ 	for (int j = from; j < to; j++){
+ 	  if (j != myDihedral) {
+-	    calcTorsion(boundary,topo->dihedrals[j], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);
++	    this->calcTorsion(boundary,topo->dihedrals[j], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);
+ 	  }
+ 	  else {
+ 	    harmCalcTorsion(topo,boundary,topo->dihedrals[j], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);

Added: head/biology/protomol/files/patch-framework__forces__ImproperSystemForce.h
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/protomol/files/patch-framework__forces__ImproperSystemForce.h	Mon Aug 25 17:19:31 2014	(r366104)
@@ -0,0 +1,20 @@
+--- framework/forces/ImproperSystemForce.h.orig	2005-05-07 18:40:24.000000000 +0400
++++ framework/forces/ImproperSystemForce.h	2014-08-22 20:52:46.000000000 +0400
+@@ -69,7 +69,7 @@
+     const TBoundaryConditions &boundary = 
+       (dynamic_cast<const SemiGenericTopology<TBoundaryConditions>& >(*topo)).boundaryConditions;
+     for (unsigned int i = 0; i < topo->impropers.size(); i++)
+-      calcTorsion(boundary,topo->impropers[i], positions, forces, (*energies)[ScalarStructure::IMPROPER],energies);
++      this->calcTorsion(boundary,topo->impropers[i], positions, forces, (*energies)[ScalarStructure::IMPROPER],energies);
+   }
+   template<class TBoundaryConditions> 
+   inline void ImproperSystemForce<TBoundaryConditions>::parallelEvaluate(const GenericTopology* topo,
+@@ -90,7 +90,7 @@
+ 	  to = n;
+ 	int from = (n*i)/count;
+ 	for (int j = from; j < to; j++)
+-	  calcTorsion(boundary, topo->impropers[j], positions, forces, (*energies)[ScalarStructure::IMPROPER],energies);
++	  this->calcTorsion(boundary, topo->impropers[j], positions, forces, (*energies)[ScalarStructure::IMPROPER],energies);
+       }
+     }
+   }

Added: head/biology/protomol/files/patch-framework__forces__NonbondedCutoffMollyForce.h
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/protomol/files/patch-framework__forces__NonbondedCutoffMollyForce.h	Mon Aug 25 17:19:31 2014	(r366104)
@@ -0,0 +1,11 @@
+--- framework/forces/NonbondedCutoffMollyForce.h.orig	2005-05-07 18:40:24.000000000 +0400
++++ framework/forces/NonbondedCutoffMollyForce.h	2014-08-22 20:42:42.000000000 +0400
+@@ -70,7 +70,7 @@
+     this->enumerator.initialize(realTopo, this->myCutoff);
+ 
+     unsigned int n = realTopo->cellLists.size();
+-    unsigned int count = numberOfBlocks(realTopo,positions);
++    unsigned int count = this->numberOfBlocks(realTopo,positions);
+ 
+     for(unsigned int i = 0;i<count;i++){
+       unsigned int l = (n*(i+1))/count - (n*i)/count;

Added: head/biology/protomol/files/patch-framework__forces__NonbondedCutoffSystemForce.h
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/protomol/files/patch-framework__forces__NonbondedCutoffSystemForce.h	Mon Aug 25 17:19:31 2014	(r366104)
@@ -0,0 +1,11 @@
+--- framework/forces/NonbondedCutoffSystemForce.h.orig	2005-05-07 18:40:24.000000000 +0400
++++ framework/forces/NonbondedCutoffSystemForce.h	2014-08-22 20:39:47.000000000 +0400
+@@ -76,7 +76,7 @@
+     this->enumerator.initialize(realTopo, this->myCutoff);
+ 
+     unsigned int n = realTopo->cellLists.size();
+-    unsigned int count = numberOfBlocks(realTopo,positions);
++    unsigned int count = this->numberOfBlocks(realTopo,positions);
+ 
+     for(unsigned int i = 0;i<count;i++){
+       unsigned int l = (n*(i+1))/count - (n*i)/count;



Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201408251719.s7PHJVpT017298>