svn commit: r366104 - in head/biology/protomol: . files
Dmitry Marakasov
amdmi3 at FreeBSD.org
Mon Aug 25 17:19:33 UTC 2014
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;
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