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>
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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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