Index: head/science/Makefile =================================================================== --- head/science/Makefile (revision 479580) +++ head/science/Makefile (revision 479581) @@ -1,280 +1,281 @@ # $FreeBSD$ # COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += InsightToolkit SUBDIR += MOOSE-neural-simulator SUBDIR += PETSc SUBDIR += R-cran-AMORE SUBDIR += R-cran-DCluster SUBDIR += R-cran-Epi SUBDIR += R-cran-bayesm SUBDIR += R-cran-cmprsk SUBDIR += R-cran-e1071 SUBDIR += R-cran-eco SUBDIR += R-cran-epicalc SUBDIR += R-cran-etm SUBDIR += R-cran-fastICA SUBDIR += R-cran-kernlab SUBDIR += R-cran-snow SUBDIR += R-cran-som SUBDIR += R-cran-udunits2 SUBDIR += abinit SUBDIR += afni SUBDIR += aircraft-datcom SUBDIR += antioch SUBDIR += atom SUBDIR += atompaw SUBDIR += avogadro SUBDIR += bddsolve SUBDIR += bft SUBDIR += bodr SUBDIR += brian SUBDIR += buddy SUBDIR += cdcl SUBDIR += cdf SUBDIR += cdo SUBDIR += cgnslib SUBDIR += cgribex SUBDIR += checkmol SUBDIR += chemical-mime-data SUBDIR += chemps2 SUBDIR += chemtool SUBDIR += chemtool-devel SUBDIR += chrono SUBDIR += clhep SUBDIR += clipper SUBDIR += colt SUBDIR += coot SUBDIR += cp2k SUBDIR += crf++ SUBDIR += dalton SUBDIR += datawarrior SUBDIR += dcl SUBDIR += devisor SUBDIR += dft_tools SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += dlpoly-classic SUBDIR += eccodes SUBDIR += ecs SUBDIR += epte SUBDIR += erd SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fisicalab SUBDIR += fleur SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += fvm SUBDIR += gabedit SUBDIR += gchemutils SUBDIR += gdma SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gramps SUBDIR += grib_api SUBDIR += gromacs SUBDIR += gsmc SUBDIR += gtamsanalyzer SUBDIR += gwyddion SUBDIR += h5utils SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-18 SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jdftx SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kalzium-kde4 SUBDIR += kst2 SUBDIR += lammps SUBDIR += lamprop SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcint SUBDIR += libctl SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libghemical SUBDIR += libgridxc SUBDIR += libint SUBDIR += libint2 SUBDIR += libkml SUBDIR += liblinear SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libxc SUBDIR += linsmith SUBDIR += lm SUBDIR += madness SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += mdynamix SUBDIR += medit SUBDIR += meep SUBDIR += mei SUBDIR += metaf2xml SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mol2ps SUBDIR += mpb SUBDIR += mpqc SUBDIR += msms SUBDIR += multiwfn SUBDIR += namd SUBDIR += ncs SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nwchem SUBDIR += octopus SUBDIR += openbabel SUBDIR += openkim + SUBDIR += openmx SUBDIR += openstructure SUBDIR += p5-Algorithm-SVMLight SUBDIR += p5-Chemistry-3DBuilder SUBDIR += p5-Chemistry-Bond-Find SUBDIR += p5-Chemistry-Canonicalize SUBDIR += p5-Chemistry-Elements SUBDIR += p5-Chemistry-File-MDLMol SUBDIR += p5-Chemistry-File-Mopac SUBDIR += p5-Chemistry-File-PDB SUBDIR += p5-Chemistry-File-SLN SUBDIR += p5-Chemistry-File-SMARTS SUBDIR += p5-Chemistry-File-SMILES SUBDIR += p5-Chemistry-File-VRML SUBDIR += p5-Chemistry-File-XYZ SUBDIR += p5-Chemistry-FormulaPattern SUBDIR += p5-Chemistry-InternalCoords SUBDIR += p5-Chemistry-Isotope SUBDIR += p5-Chemistry-MacroMol SUBDIR += p5-Chemistry-MidasPattern SUBDIR += p5-Chemistry-Mok SUBDIR += p5-Chemistry-Mol SUBDIR += p5-Chemistry-Pattern SUBDIR += p5-Chemistry-Reaction SUBDIR += p5-Chemistry-Ring SUBDIR += p5-Geo-BUFR SUBDIR += p5-Geo-Coordinates-Converter SUBDIR += p5-Geo-Coordinates-Converter-iArea SUBDIR += p5-Geo-ReadGRIB SUBDIR += p5-Geo-WebService-Elevation-USGS SUBDIR += p5-Mcstas-Tools SUBDIR += p5-PerlMol SUBDIR += p5-Physics-Unit SUBDIR += paje SUBDIR += paraview SUBDIR += pcmsolver SUBDIR += pnetcdf SUBDIR += psychopy SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-PyQuante SUBDIR += py-ScientificPython SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-ase SUBDIR += py-cdo SUBDIR += py-coards SUBDIR += py-dlib SUBDIR += py-gpaw SUBDIR += py-gsd SUBDIR += py-h5py SUBDIR += py-hcluster SUBDIR += py-kinematics SUBDIR += py-mdp SUBDIR += py-mlpy SUBDIR += py-mmtf-python SUBDIR += py-netCDF4 SUBDIR += py-obspy SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pydicom SUBDIR += py-pymatgen SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pysal SUBDIR += py-pyteomics SUBDIR += py-pyteomics.biolccc SUBDIR += py-qspin SUBDIR += py-quantities SUBDIR += py-rmf SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-sparse SUBDIR += py-scimath SUBDIR += py-scipy SUBDIR += py-scoria SUBDIR += py-spglib SUBDIR += py-veusz SUBDIR += py-ws2300 SUBDIR += pybrain SUBDIR += pycdf SUBDIR += pynn SUBDIR += qbox SUBDIR += qcl SUBDIR += qmcpack SUBDIR += qtresistors SUBDIR += quantum-espresso SUBDIR += qwalk SUBDIR += rdkit SUBDIR += rmf SUBDIR += rubygem-ai4r SUBDIR += rubygem-cdo SUBDIR += rubygem-rgeo SUBDIR += rubygem-rgeo-geojson SUBDIR += rubygem-rgeo-proj4 SUBDIR += rubygem-rgeo-shapefile SUBDIR += rubygem-ruby-dcl SUBDIR += rubygem-ruby-netcdf SUBDIR += siesta SUBDIR += sigrok-cli SUBDIR += sigrok-firmware SUBDIR += sigrok-firmware-fx2lafw SUBDIR += sigrok-firmware-utils SUBDIR += silo SUBDIR += simlib SUBDIR += simsmith SUBDIR += spglib SUBDIR += step SUBDIR += step-kde4 SUBDIR += svmlight SUBDIR += szip SUBDIR += teem SUBDIR += tfel SUBDIR += triqs SUBDIR += udunits SUBDIR += v_sim SUBDIR += vmd SUBDIR += voro++ SUBDIR += wannier90 SUBDIR += xcrysden SUBDIR += xdrawchem SUBDIR += xfce4-equake-plugin SUBDIR += xmakemol .include Index: head/science/openmx/Makefile =================================================================== --- head/science/openmx/Makefile (nonexistent) +++ head/science/openmx/Makefile (revision 479581) @@ -0,0 +1,69 @@ +# $FreeBSD$ + +PORTNAME= openmx +DISTVERSION= 3.8.5 # the 18June12 patch upgrades 3.8 -> 3.8.5 +CATEGORIES= science +MASTER_SITES= http://www.openmx-square.org/ \ + http://www.openmx-square.org/bugfixed/18June12/:patch +DISTFILES= ${PORTNAME}${DISTVERSION:R}${EXTRACT_SUFX} \ + patch${DISTVERSION}${EXTRACT_SUFX}:patch # this patch isn't a patch, but a set of file updates +DIST_SUBDIR= ${PORTNAME} +EXTRACT_ONLY= ${PORTNAME}${DISTVERSION:R}${EXTRACT_SUFX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Nanoscale material simulations using density functional theories (DFT) + +LICENSE= GPLv2 + +LIB_DEPENDS= libblas.so:math/blas \ + libfftw3.so:math/fftw3 \ + liblapack.so:math/lapack \ + libmpich.so:net/mpich2 \ + libomp.so:devel/openmp + +USES= dos2unix fortran gmake localbase:ldflags +DOS2UNIX_FILES= openmx_common.h +USE_CXXSTD= c++11 +MAKEFILE= makefile + +WRKSRC= ${WRKDIR}/${PORTNAME}${DISTVERSION:R} + +CFLAGS+= -Dkcomp +LDFLAGS+= ${LOCALBASE}/lib/gcc${GCC_DEFAULT}/libgcc_s.so + +WRKSRC_SUBDIR= source + +MAKE_ENV= MPICH_CC=${CC} +MAKE_ARGS+= CFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}" LDFLAGS="${LDFLAGS}" GCC_LIB=${LOCALBASE}/lib/gcc${GCC_DEFAULT}/libgfortran.so + +BINARY_ALIAS= gcc=${CXX} gcc7=${CXX} + +UTIL_PROGS= DosMain jx analysis_example esp polB bandgnu13 bin2txt cube2xsf intensity_map md2axsf + +PLIST_FILES= bin/${PORTNAME} ${UTIL_PROGS:C/^/bin\//} + +OPTIONS_DEFINE_amd64= SIMD +OPTIONS_DEFINE_i386= SIMD +OPTIONS_DEFAULT_amd64= SIMD +OPTIONS_DEFAULT_i386= SIMD + +SIMD_CFLAGS= -msse -msse2 -mfpmath=sse +SIMD_CFLAGS_OFF= -Dnosse +CFLAGS+= ${ARCH:S/amd64//:S/i386//:S/${ARCH}/-Dnosse/} + +pre-patch: # overlay files before patching + @cd ${WRKSRC} && ${TAR} xzf ${DISTDIR}/${DIST_SUBDIR}/patch${DISTVERSION}${EXTRACT_SUFX} + +post-patch: + @cd ${WRKSRC} && ${REINPLACE_CMD} 's|DFT_DATA_PATH|"${DATADIR}/DFT_DATA13"|' Input_std.c check_lead.c SetPara_DFT.c OutData.c OutData_Binary.c + +post-install: +.for u in ${UTIL_PROGS} + ${INSTALL_PROGRAM} ${WRKSRC}/${u} ${STAGEDIR}${PREFIX}/bin +.endfor + cd ${WRKSRC}/.. && ${COPYTREE_SHARE} DFT_DATA13 ${STAGEDIR}${DATADIR} + # autoplist for potentials: about 500 files in DATADIR + @cd ${STAGEDIR}${PREFIX} && \ + ${FIND} ${DATADIR:S/^${PREFIX}\///} -type f >> ${TMPPLIST} + +.include Property changes on: head/science/openmx/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/openmx/distinfo =================================================================== --- head/science/openmx/distinfo (nonexistent) +++ head/science/openmx/distinfo (revision 479581) @@ -0,0 +1,5 @@ +TIMESTAMP = 1536713126 +SHA256 (openmx/openmx3.8.tar.gz) = 36ee10d8b1587b25a2ca1d57f110111be65c4fb4dc820e6d93e1ed2b562634a1 +SIZE (openmx/openmx3.8.tar.gz) = 143086177 +SHA256 (openmx/patch3.8.5.tar.gz) = d0fea2ce956d796a87a4bc9e9d580fb115ff2a22764650fffa78bb79a1b30468 +SIZE (openmx/patch3.8.5.tar.gz) = 316333 Property changes on: head/science/openmx/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/openmx/files/patch-Band__DFT__Col.c =================================================================== --- head/science/openmx/files/patch-Band__DFT__Col.c (nonexistent) +++ head/science/openmx/files/patch-Band__DFT__Col.c (revision 479581) @@ -0,0 +1,15 @@ +--- Band_DFT_Col.c.orig 2018-08-29 06:24:38 UTC ++++ Band_DFT_Col.c +@@ -483,9 +483,9 @@ double Band_DFT_Col(int SCF_iter, + + /* allocation */ + +- stat_send = malloc(sizeof(MPI_Status)*numprocs2); +- request_send = malloc(sizeof(MPI_Request)*numprocs2); +- request_recv = malloc(sizeof(MPI_Request)*numprocs2); ++ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*numprocs2); ++ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs2); ++ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs2); + + is1 = (int*)malloc(sizeof(int)*numprocs2); + ie1 = (int*)malloc(sizeof(int)*numprocs2); Property changes on: head/science/openmx/files/patch-Band__DFT__Col.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/openmx/files/patch-Band__DFT__NonCol.c =================================================================== --- head/science/openmx/files/patch-Band__DFT__NonCol.c (nonexistent) +++ head/science/openmx/files/patch-Band__DFT__NonCol.c (revision 479581) @@ -0,0 +1,15 @@ +--- Band_DFT_NonCol.c.orig 2018-08-29 06:26:10 UTC ++++ Band_DFT_NonCol.c +@@ -554,9 +554,9 @@ double Band_DFT_NonCol(int SCF_iter, + + /* allocation */ + +- stat_send = malloc(sizeof(MPI_Status)*numprocs1); +- request_send = malloc(sizeof(MPI_Request)*numprocs1); +- request_recv = malloc(sizeof(MPI_Request)*numprocs1); ++ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*numprocs1); ++ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs1); ++ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs1); + + is1 = (int*)malloc(sizeof(int)*numprocs1); + ie1 = (int*)malloc(sizeof(int)*numprocs1); Property changes on: head/science/openmx/files/patch-Band__DFT__NonCol.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/openmx/files/patch-Cluster__DFT.c =================================================================== --- head/science/openmx/files/patch-Cluster__DFT.c (nonexistent) +++ head/science/openmx/files/patch-Cluster__DFT.c (revision 479581) @@ -0,0 +1,46 @@ +--- Cluster_DFT.c.orig 2018-08-29 06:05:22 UTC ++++ Cluster_DFT.c +@@ -194,9 +194,9 @@ static double Cluster_collinear( + + Num_Comm_World1 = SpinP_switch + 1; + +- stat_send = malloc(sizeof(MPI_Status)*numprocs0); +- request_send = malloc(sizeof(MPI_Request)*numprocs0); +- request_recv = malloc(sizeof(MPI_Request)*numprocs0); ++ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*numprocs0); ++ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs0); ++ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs0); + + /*********************************************** + allocation of arrays for the first world +@@ -1541,9 +1541,9 @@ static double Cluster_non_collinear( + + /* allocation of arrays */ + +- stat_send = malloc(sizeof(MPI_Status)*numprocs); +- request_send = malloc(sizeof(MPI_Request)*numprocs); +- request_recv = malloc(sizeof(MPI_Request)*numprocs); ++ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*numprocs); ++ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs); ++ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs); + + /**************************************************** + calculation of the array size +@@ -2649,7 +2649,7 @@ void Save_DOS_Col(int n, int MaxN, int * + MPI_Comm_size(mpi_comm_level1,&numprocs); + MPI_Comm_rank(mpi_comm_level1,&myid); + +- request_recv = malloc(sizeof(MPI_Request)*numprocs); ++ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs); + + /* open file pointers */ + +@@ -2901,7 +2901,7 @@ void Save_DOS_NonCol(int n, int MaxN, in + MPI_Comm_size(mpi_comm_level1,&numprocs); + MPI_Comm_rank(mpi_comm_level1,&myid); + +- request_recv = malloc(sizeof(MPI_Request)*numprocs); ++ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs); + + /* open file pointers */ + Property changes on: head/science/openmx/files/patch-Cluster__DFT.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/openmx/files/patch-Cluster__DFT__ON2.c =================================================================== --- head/science/openmx/files/patch-Cluster__DFT__ON2.c (nonexistent) +++ head/science/openmx/files/patch-Cluster__DFT__ON2.c (revision 479581) @@ -0,0 +1,23 @@ +--- Cluster_DFT_ON2.c.orig 2016-03-27 06:53:28 UTC ++++ Cluster_DFT_ON2.c +@@ -10,6 +10,7 @@ + + ***********************************************************************/ + ++#include + #include + #include + #include +@@ -1275,9 +1276,9 @@ static void OND_Solver( + MPI_Request *request_send; + MPI_Request *request_recv; + +- stat_send = malloc(sizeof(MPI_Status)*numprocs2); +- request_send = malloc(sizeof(MPI_Request)*numprocs2); +- request_recv = malloc(sizeof(MPI_Request)*numprocs2); ++ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*numprocs2); ++ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs2); ++ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs2); + + al.r = 1.0; + al.i = 0.0; Property changes on: head/science/openmx/files/patch-Cluster__DFT__ON2.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/openmx/files/patch-Input__std.c =================================================================== --- head/science/openmx/files/patch-Input__std.c (nonexistent) +++ head/science/openmx/files/patch-Input__std.c (revision 479581) @@ -0,0 +1,11 @@ +--- Input_std.c.orig 2018-09-12 02:18:32 UTC ++++ Input_std.c +@@ -85,7 +85,7 @@ void Input_std(char *file) + + input_string("System.CurrrentDirectory",filepath,"./"); + input_string("System.Name",filename,"default"); +- input_string("DATA.PATH",DFT_DATA_PATH,"../DFT_DATA13"); ++ //input_string("DATA.PATH",DFT_DATA_PATH,"../DFT_DATA13"); + input_int("level.of.stdout", &level_stdout,1); + input_int("level.of.fileout",&level_fileout,1); + input_logical("memory.usage.fileout",&memoryusage_fileout,0); /* default=off */ Property changes on: head/science/openmx/files/patch-Input__std.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/openmx/files/patch-Mixing__H.c =================================================================== --- head/science/openmx/files/patch-Mixing__H.c (nonexistent) +++ head/science/openmx/files/patch-Mixing__H.c (revision 479581) @@ -0,0 +1,218 @@ +--- Mixing_H.c.orig 2018-08-29 05:53:55 UTC ++++ Mixing_H.c +@@ -74,7 +74,7 @@ void Pulay_Mixing_H_MultiSecant(int MD_i + double sum,my_sum,tmp1,tmp2,alpha; + double r,r10,r11,r12,r13,r20,r21,r22; + double h,h10,h11,h12,h13,h20,h21,h22; +- double my_sy,my_yy,sy,yy,norm,s,y,or,al,be; ++ double my_sy,my_yy,sy,yy,norm,s,y,orx,al,be; + double **A,**IA,*coes,*coes2,*ror; + char nanchar[300]; + +@@ -635,44 +635,44 @@ void Pulay_Mixing_H_MultiSecant(int MD_i + s = HisH1[m][0][Mc_AN][h_AN][i][j] - HisH1[m+1][0][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH1[m][0][Mc_AN][h_AN][i][j] - ResidualH1[m+1][0][Mc_AN][h_AN][i][j]; /* y */ + r = s - al*y; /* r */ +- or = ResidualH1[dim+1][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += r*or; ++ orx = ResidualH1[dim+1][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += r*orx; + + s = HisH1[m][1][Mc_AN][h_AN][i][j] - HisH1[m+1][1][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH1[m][1][Mc_AN][h_AN][i][j] - ResidualH1[m+1][1][Mc_AN][h_AN][i][j]; /* y */ + r = s - al*y; /* r */ +- or = ResidualH1[dim+1][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += r*or; ++ orx = ResidualH1[dim+1][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += r*orx; + + s = HisH1[m][2][Mc_AN][h_AN][i][j] - HisH1[m+1][2][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH1[m][2][Mc_AN][h_AN][i][j] - ResidualH1[m+1][2][Mc_AN][h_AN][i][j]; /* y */ + r = s - al*y; /* r */ +- or = ResidualH1[dim+1][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += r*or; ++ orx = ResidualH1[dim+1][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += r*orx; + + s = HisH1[m][3][Mc_AN][h_AN][i][j] - HisH1[m+1][3][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH1[m][3][Mc_AN][h_AN][i][j] - ResidualH1[m+1][3][Mc_AN][h_AN][i][j]; /* y */ + r = s - al*y; /* r */ +- or = ResidualH1[dim+1][3][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += r*or; ++ orx = ResidualH1[dim+1][3][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += r*orx; + + s = HisH2[m][0][Mc_AN][h_AN][i][j] - HisH2[m+1][0][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH2[m][0][Mc_AN][h_AN][i][j] - ResidualH2[m+1][0][Mc_AN][h_AN][i][j]; /* y */ + r = s - al*y; /* r */ +- or = ResidualH2[dim+1][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += r*or; ++ orx = ResidualH2[dim+1][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += r*orx; + + s = HisH2[m][1][Mc_AN][h_AN][i][j] - HisH2[m+1][1][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH2[m][1][Mc_AN][h_AN][i][j] - ResidualH2[m+1][1][Mc_AN][h_AN][i][j]; /* y */ + r = s - al*y; /* r */ +- or = ResidualH2[dim+1][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += r*or; ++ orx = ResidualH2[dim+1][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += r*orx; + + s = HisH2[m][2][Mc_AN][h_AN][i][j] - HisH2[m+1][2][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH2[m][2][Mc_AN][h_AN][i][j] - ResidualH2[m+1][2][Mc_AN][h_AN][i][j]; /* y */ + r = s - al*y; /* r */ +- or = ResidualH2[dim+1][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += r*or; ++ orx = ResidualH2[dim+1][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += r*orx; + + } + } +@@ -696,8 +696,8 @@ void Pulay_Mixing_H_MultiSecant(int MD_i + s = HisH1[m][spin][Mc_AN][h_AN][i][j] - HisH1[m+1][spin][Mc_AN][h_AN][i][j]; + y = ResidualH1[m][spin][Mc_AN][h_AN][i][j] - ResidualH1[m+1][spin][Mc_AN][h_AN][i][j]; + r = s - al*y; +- or = ResidualH1[dim+1][spin][Mc_AN][h_AN][i][j]; +- my_sum += r*or; ++ orx = ResidualH1[dim+1][spin][Mc_AN][h_AN][i][j]; ++ my_sum += r*orx; + } + } + } +@@ -986,7 +986,7 @@ void Pulay_Mixing_H_with_One_Shot_Hessia + double my_sum,tmp1,tmp2,alpha; + double r,r10,r11,r12,r13,r20,r21,r22; + double h,h10,h11,h12,h13,h20,h21,h22; +- double my_sy,my_yy,sy,yy,norm,s,y,or,al,be; ++ double my_sy,my_yy,sy,yy,norm,s,y,orx,al,be; + double **A,**IA,*coes; + char nanchar[300]; + +@@ -1427,38 +1427,38 @@ void Pulay_Mixing_H_with_One_Shot_Hessia + + s = HisH1[0][0][Mc_AN][h_AN][i][j] - HisH1[1][0][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH1[0][0][Mc_AN][h_AN][i][j] - ResidualH1[1][0][Mc_AN][h_AN][i][j]; /* y */ +- or = ResidualH1[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += (s-al*y)*or; ++ orx = ResidualH1[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += (s-al*y)*orx; + + s = HisH1[0][1][Mc_AN][h_AN][i][j] - HisH1[1][1][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH1[0][1][Mc_AN][h_AN][i][j] - ResidualH1[1][1][Mc_AN][h_AN][i][j]; /* y */ +- or = ResidualH1[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += (s-al*y)*or; ++ orx = ResidualH1[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += (s-al*y)*orx; + + s = HisH1[0][2][Mc_AN][h_AN][i][j] - HisH1[1][2][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH1[0][2][Mc_AN][h_AN][i][j] - ResidualH1[1][2][Mc_AN][h_AN][i][j]; /* y */ +- or = ResidualH1[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += (s-al*y)*or; ++ orx = ResidualH1[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += (s-al*y)*orx; + + s = HisH1[0][3][Mc_AN][h_AN][i][j] - HisH1[1][3][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH1[0][3][Mc_AN][h_AN][i][j] - ResidualH1[1][3][Mc_AN][h_AN][i][j]; /* y */ +- or = ResidualH1[dim][3][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += (s-al*y)*or; ++ orx = ResidualH1[dim][3][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += (s-al*y)*orx; + + s = HisH2[0][0][Mc_AN][h_AN][i][j] - HisH2[1][0][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH2[0][0][Mc_AN][h_AN][i][j] - ResidualH2[1][0][Mc_AN][h_AN][i][j]; /* y */ +- or = ResidualH2[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += (s-al*y)*or; ++ orx = ResidualH2[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += (s-al*y)*orx; + + s = HisH2[0][1][Mc_AN][h_AN][i][j] - HisH2[1][1][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH2[0][1][Mc_AN][h_AN][i][j] - ResidualH2[1][1][Mc_AN][h_AN][i][j]; /* y */ +- or = ResidualH2[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += (s-al*y)*or; ++ orx = ResidualH2[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += (s-al*y)*orx; + + s = HisH2[0][2][Mc_AN][h_AN][i][j] - HisH2[1][2][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH2[0][2][Mc_AN][h_AN][i][j] - ResidualH2[1][2][Mc_AN][h_AN][i][j]; /* y */ +- or = ResidualH2[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += (s-al*y)*or; ++ orx = ResidualH2[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += (s-al*y)*orx; + } + } + } +@@ -1479,8 +1479,8 @@ void Pulay_Mixing_H_with_One_Shot_Hessia + for (j=0; j eV */ + static char *Unitname0[MUNIT]={"eV","Hartree"}; Property changes on: head/science/openmx/files/patch-bandgnu13.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/openmx/files/patch-makefile =================================================================== --- head/science/openmx/files/patch-makefile (nonexistent) +++ head/science/openmx/files/patch-makefile (revision 479581) @@ -0,0 +1,43 @@ +--- makefile.orig 2016-04-02 12:43:42 UTC ++++ makefile +@@ -136,15 +136,15 @@ + # + + +-CC = mpicc -O3 -xHOST -ip -no-prec-div -openmp -I/opt/intel/mkl/include/fftw +-FC = mpif90 -O3 -xHOST -ip -no-prec-div -openmp +-LIB= -L/opt/intel/mkl/lib -mkl=parallel -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lifcore -lmpi -lmpi_f90 -lmpi_f77 ++CC = mpicc $(CFLAGS) -fopenmp ++FC = mpif90 $(FFLAGS) -fopenmp ++LIB= $(LDFLAGS) -lpthread -llapack -lblas -lgfortran -lfftw3 -liomp5 + + + + + +-CFLAGS = -g ++#CFLAGS = -g + + OBJS = openmx.o openmx_common.o Input_std.o Inputtools.o \ + init.o LU_inverse.o ReLU_inverse.o \ +@@ -661,7 +661,7 @@ Show_DFT_DATA.o: Show_DFT_DATA.c openmx_ + + install: $(PROG) + strip $(PROG) +- cp $(PROG) $(DESTDIR)/$(PROG) ++ install $(PROG) $(DESTDIR)$(PREFIX)/bin/$(PROG) + + # + # +@@ -889,9 +889,9 @@ TRAN_CDen_Main.o: TRAN_CDen_Main.c openm + + elpa1.o: elpa1.f90 + $(FC) -c elpa1.f90 +-solve_evp_real.o: solve_evp_real.f90 ++solve_evp_real.o: solve_evp_real.f90 elpa1.o + $(FC) -c solve_evp_real.f90 +-solve_evp_complex.o: solve_evp_complex.f90 ++solve_evp_complex.o: solve_evp_complex.f90 elpa1.o + $(FC) -c solve_evp_complex.f90 + + Property changes on: head/science/openmx/files/patch-makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/openmx/files/patch-tran__variables.h =================================================================== --- head/science/openmx/files/patch-tran__variables.h (nonexistent) +++ head/science/openmx/files/patch-tran__variables.h (revision 479581) @@ -0,0 +1,10 @@ +--- tran_variables.h.orig 2018-08-29 05:50:14 UTC ++++ tran_variables.h +@@ -46,7 +46,6 @@ double TRAN_Poisson_Gpara_Scaling; + double ScaleSize_e[2]; + int SpinP_switch_e[2], atomnum_e[2], SpeciesNum_e[2], Max_FSNAN_e[2]; + int TCpyCell_e[2], Matomnum_e[2], MatomnumF_e[2], MatomnumS_e[2]; +-int Latomnum,Ratomnum,Catomnum; + int *WhatSpecies_e[2]; + int *Spe_Total_CNO_e[2]; + int *Spe_Total_NO_e[2]; Property changes on: head/science/openmx/files/patch-tran__variables.h ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/openmx/pkg-descr =================================================================== --- head/science/openmx/pkg-descr (nonexistent) +++ head/science/openmx/pkg-descr (revision 479581) @@ -0,0 +1,24 @@ +OpenMX (Open source package for Material eXplorer) is a software package for +nano-scale material simulations based on density functional theories (DFT), +norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. +The methods and algorithms used in OpenMX and their implementation are carefully +designed for the realization of large-scale ab initio electronic structure +calculations on parallel computers based on the MPI or MPI/OpenMP hybrid +parallelism. The efficient implementation of DFT enables us to investigate +electronic, magnetic, and geometrical structures of a wide variety of materials +such as biological molecules, carbon-based materials, magnetic materials, and +nanoscale conductors. Systems consisting of 1000 atoms can be treated using the +conventional diagonalization method if several hundreds cores on a parallel +computer are used. Even ab initio electronic structure calculations for systems +consisting of more than 10000 atoms are possible with the O(N) method +implemented in OpenMX if several thousands cores on a parallel computer are +available. Since optimized pseudopotentials and basis functions, which are well +tested, are provided for many elements, users may be able to quickly start own +calculations without preparing those data by themselves. Considerable +functionalities have been implemented for calculations of physical properties +such as magnetic, dielectric, and electric transport properties. Thus, we expect +that OpenMX can be a useful and powerful theoretical tool for nano-scale +material sciences, leading to better and deeper understanding of complicated and +useful materials based on quantum mechanics. + +WWW: http://www.openmx-square.org/ Property changes on: head/science/openmx/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property