Date: Wed, 12 Sep 2018 03:00:47 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r479581 - in head/science: . openmx openmx/files Message-ID: <201809120300.w8C30lqi053571@repo.freebsd.org>
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Author: yuri Date: Wed Sep 12 03:00:46 2018 New Revision: 479581 URL: https://svnweb.freebsd.org/changeset/ports/479581 Log: New port: science/openmx: Nanoscale material simulations using density functional theories (DFT) Added: head/science/openmx/ head/science/openmx/Makefile (contents, props changed) head/science/openmx/distinfo (contents, props changed) head/science/openmx/files/ head/science/openmx/files/patch-Band__DFT__Col.c (contents, props changed) head/science/openmx/files/patch-Band__DFT__NonCol.c (contents, props changed) head/science/openmx/files/patch-Cluster__DFT.c (contents, props changed) head/science/openmx/files/patch-Cluster__DFT__ON2.c (contents, props changed) head/science/openmx/files/patch-Input__std.c (contents, props changed) head/science/openmx/files/patch-Mixing__H.c (contents, props changed) head/science/openmx/files/patch-Poisson.c (contents, props changed) head/science/openmx/files/patch-Poisson__ESM.c (contents, props changed) head/science/openmx/files/patch-bandgnu13.c (contents, props changed) head/science/openmx/files/patch-makefile (contents, props changed) head/science/openmx/files/patch-tran__variables.h (contents, props changed) head/science/openmx/pkg-descr (contents, props changed) Modified: head/science/Makefile Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Wed Sep 12 02:09:45 2018 (r479580) +++ head/science/Makefile Wed Sep 12 03:00:46 2018 (r479581) @@ -149,6 +149,7 @@ SUBDIR += octopus SUBDIR += openbabel SUBDIR += openkim + SUBDIR += openmx SUBDIR += openstructure SUBDIR += p5-Algorithm-SVMLight SUBDIR += p5-Chemistry-3DBuilder Added: head/science/openmx/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/Makefile Wed Sep 12 03:00:46 2018 (r479581) @@ -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 <bsd.port.mk> Added: head/science/openmx/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/distinfo Wed Sep 12 03:00:46 2018 (r479581) @@ -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 Added: head/science/openmx/files/patch-Band__DFT__Col.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/files/patch-Band__DFT__Col.c Wed Sep 12 03:00:46 2018 (r479581) @@ -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); Added: head/science/openmx/files/patch-Band__DFT__NonCol.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/files/patch-Band__DFT__NonCol.c Wed Sep 12 03:00:46 2018 (r479581) @@ -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); Added: head/science/openmx/files/patch-Cluster__DFT.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/files/patch-Cluster__DFT.c Wed Sep 12 03:00:46 2018 (r479581) @@ -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 */ + Added: head/science/openmx/files/patch-Cluster__DFT__ON2.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/files/patch-Cluster__DFT__ON2.c Wed Sep 12 03:00:46 2018 (r479581) @@ -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 <complex.h> + #include <stdio.h> + #include <stdlib.h> + #include <string.h> +@@ -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; Added: head/science/openmx/files/patch-Input__std.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/files/patch-Input__std.c Wed Sep 12 03:00:46 2018 (r479581) @@ -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 */ Added: head/science/openmx/files/patch-Mixing__H.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/files/patch-Mixing__H.c Wed Sep 12 03:00:46 2018 (r479581) @@ -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<Spe_Total_NO[Hwan]; j++){ + s = HisH1[0][spin][Mc_AN][h_AN][i][j] - HisH1[1][spin][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH1[0][spin][Mc_AN][h_AN][i][j] - ResidualH1[1][spin][Mc_AN][h_AN][i][j]; /* y */ +- or = ResidualH1[dim][spin][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- my_sum += (s-al*y)*or; ++ orx = ResidualH1[dim][spin][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ my_sum += (s-al*y)*orx; + } + } + } +@@ -1541,38 +1541,38 @@ 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 */ +- H[0][Mc_AN][h_AN][i][j] = h10 - alpha*(al*or + (s-al*y)*be); ++ orx = ResidualH1[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ H[0][Mc_AN][h_AN][i][j] = h10 - alpha*(al*orx + (s-al*y)*be); + + 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 */ +- H[1][Mc_AN][h_AN][i][j] = h11 - alpha*(al*or + (s-al*y)*be); ++ orx = ResidualH1[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ H[1][Mc_AN][h_AN][i][j] = h11 - alpha*(al*orx + (s-al*y)*be); + + 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 */ +- H[2][Mc_AN][h_AN][i][j] = h12 - alpha*(al*or + (s-al*y)*be); ++ orx = ResidualH1[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ H[2][Mc_AN][h_AN][i][j] = h12 - alpha*(al*orx + (s-al*y)*be); + + 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 */ +- H[3][Mc_AN][h_AN][i][j] = h13 - alpha*(al*or + (s-al*y)*be); ++ orx = ResidualH1[dim][3][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ H[3][Mc_AN][h_AN][i][j] = h13 - alpha*(al*orx + (s-al*y)*be); + + 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 */ +- iHNL[0][Mc_AN][h_AN][i][j] = h20 - alpha*(al*or + (s-al*y)*be); ++ orx = ResidualH2[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ iHNL[0][Mc_AN][h_AN][i][j] = h20 - alpha*(al*orx + (s-al*y)*be); + + 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 */ +- iHNL[1][Mc_AN][h_AN][i][j] = h21 - alpha*(al*or + (s-al*y)*be); ++ orx = ResidualH2[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ iHNL[1][Mc_AN][h_AN][i][j] = h21 - alpha*(al*orx + (s-al*y)*be); + + 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 */ +- iHNL[2][Mc_AN][h_AN][i][j] = h22 - alpha*(al*or + (s-al*y)*be); ++ orx = ResidualH2[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ iHNL[2][Mc_AN][h_AN][i][j] = h22 - alpha*(al*orx + (s-al*y)*be); + } + } + } +@@ -1599,8 +1599,8 @@ void Pulay_Mixing_H_with_One_Shot_Hessia + + s = HisH1[0][spin][Mc_AN][h_AN][i][j] - HisH1[1][spin][Mc_AN][h_AN][i][j]; /* s */ + y = ResidualH1[0][spin][Mc_AN][h_AN][i][j] - ResidualH1[1][spin][Mc_AN][h_AN][i][j]; /* y */ +- or = ResidualH1[dim][spin][Mc_AN][h_AN][i][j]; /* OptResidualH */ +- H[spin][Mc_AN][h_AN][i][j] = h - alpha*(al*or + (s-al*y)*be); ++ orx = ResidualH1[dim][spin][Mc_AN][h_AN][i][j]; /* OptResidualH */ ++ H[spin][Mc_AN][h_AN][i][j] = h - alpha*(al*orx + (s-al*y)*be); + + } + } Added: head/science/openmx/files/patch-Poisson.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/files/patch-Poisson.c Wed Sep 12 03:00:46 2018 (r479581) @@ -0,0 +1,84 @@ +--- Poisson.c.orig 2018-08-29 05:58:06 UTC ++++ Poisson.c +@@ -141,8 +141,8 @@ void FFT_Poisson(double *ReRhor, double + allocation of arrays: + ****************************************************/ + +- in = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); +- out = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); ++ in = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); ++ out = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); + + /*------------------ FFT along the C-axis in the AB partition ------------------*/ + +@@ -182,10 +182,10 @@ void FFT_Poisson(double *ReRhor, double + array0 = (double*)malloc(sizeof(double)*2*GP_B_AB2CA_S[NN_B_AB2CA_S]); + array1 = (double*)malloc(sizeof(double)*2*GP_B_AB2CA_R[NN_B_AB2CA_R]); + +- request_send = malloc(sizeof(MPI_Request)*NN_B_AB2CA_S); +- request_recv = malloc(sizeof(MPI_Request)*NN_B_AB2CA_R); +- stat_send = malloc(sizeof(MPI_Status)*NN_B_AB2CA_S); +- stat_recv = malloc(sizeof(MPI_Status)*NN_B_AB2CA_R); ++ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_AB2CA_S); ++ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_AB2CA_R); ++ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_AB2CA_S); ++ stat_recv = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_AB2CA_R); + + NN_S = 0; + NN_R = 0; +@@ -307,10 +307,10 @@ void FFT_Poisson(double *ReRhor, double + array0 = (double*)malloc(sizeof(double)*2*GP_B_CA2CB_S[NN_B_CA2CB_S]); + array1 = (double*)malloc(sizeof(double)*2*GP_B_CA2CB_R[NN_B_CA2CB_R]); + +- request_send = malloc(sizeof(MPI_Request)*NN_B_CA2CB_S); +- request_recv = malloc(sizeof(MPI_Request)*NN_B_CA2CB_R); +- stat_send = malloc(sizeof(MPI_Status)*NN_B_CA2CB_S); +- stat_recv = malloc(sizeof(MPI_Status)*NN_B_CA2CB_R); ++ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_CA2CB_S); ++ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_CA2CB_R); ++ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_CA2CB_S); ++ stat_recv = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_CA2CB_R); + + NN_S = 0; + NN_R = 0; +@@ -503,8 +503,8 @@ void Inverse_FFT_Poisson(double *ReRhor, + fftw_complex out[List_YOUSO[17]]; + ****************************************************/ + +- in = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); +- out = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); ++ in = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); ++ out = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); + + /*------------------ Inverse FFT along the A-axis in the CB partition ------------------*/ + +@@ -544,10 +544,10 @@ void Inverse_FFT_Poisson(double *ReRhor, + array0 = (double*)malloc(sizeof(double)*2*GP_B_CA2CB_R[NN_B_CA2CB_R]); + array1 = (double*)malloc(sizeof(double)*2*GP_B_CA2CB_S[NN_B_CA2CB_S]); + +- request_send = malloc(sizeof(MPI_Request)*NN_B_CA2CB_R); +- request_recv = malloc(sizeof(MPI_Request)*NN_B_CA2CB_S); +- stat_send = malloc(sizeof(MPI_Status)*NN_B_CA2CB_R); +- stat_recv = malloc(sizeof(MPI_Status)*NN_B_CA2CB_S); ++ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_CA2CB_R); ++ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_CA2CB_S); ++ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_CA2CB_R); ++ stat_recv = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_CA2CB_S); + + NN_S = 0; + NN_R = 0; +@@ -669,10 +669,10 @@ void Inverse_FFT_Poisson(double *ReRhor, + array0 = (double*)malloc(sizeof(double)*2*GP_B_AB2CA_R[NN_B_AB2CA_R]); + array1 = (double*)malloc(sizeof(double)*2*GP_B_AB2CA_S[NN_B_AB2CA_S]); + +- request_send = malloc(sizeof(MPI_Request)*NN_B_AB2CA_R); +- request_recv = malloc(sizeof(MPI_Request)*NN_B_AB2CA_S); +- stat_send = malloc(sizeof(MPI_Status)*NN_B_AB2CA_R); +- stat_recv = malloc(sizeof(MPI_Status)*NN_B_AB2CA_S); ++ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_AB2CA_R); ++ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_AB2CA_S); ++ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_AB2CA_R); ++ stat_recv = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_AB2CA_S); + + NN_S = 0; + NN_R = 0; Added: head/science/openmx/files/patch-Poisson__ESM.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/files/patch-Poisson__ESM.c Wed Sep 12 03:00:46 2018 (r479581) @@ -0,0 +1,24 @@ +--- Poisson_ESM.c.orig 2018-08-29 06:03:16 UTC ++++ Poisson_ESM.c +@@ -71,8 +71,8 @@ double Poisson_ESM(int fft_charge_flag, + fftw_complex out[List_YOUSO[17]]; + ****************************************************/ + +- in0 = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); +- out0 = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); ++ in0 = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); ++ out0 = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); + + + if (myid==Host_ID) { +@@ -908,8 +908,8 @@ void One_dim_FFT(FILE *fp, + fftw_complex out[List_YOUSO[17]]; + ****************************************************/ + +- in = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); +- out = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); ++ in = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); ++ out = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); + + p = fftw_plan_dft_1d(Ngrid1, in, out, sgn2, FFTW_ESTIMATE); + Added: head/science/openmx/files/patch-bandgnu13.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/files/patch-bandgnu13.c Wed Sep 12 03:00:46 2018 (r479581) @@ -0,0 +1,11 @@ +--- bandgnu13.c.orig 2018-09-11 19:33:10 UTC ++++ bandgnu13.c +@@ -75,7 +75,7 @@ void vk_rtv(double vk[4], double rtv[4][ + + #define MUNIT 2 + +-main(int argc, char **argv) ++int main(int argc, char **argv) + { + static double Unit0[MUNIT]={27.2,1.0}; /* Hartree-> eV */ + static char *Unitname0[MUNIT]={"eV","Hartree"}; Added: head/science/openmx/files/patch-makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/files/patch-makefile Wed Sep 12 03:00:46 2018 (r479581) @@ -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 + + Added: head/science/openmx/files/patch-tran__variables.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/files/patch-tran__variables.h Wed Sep 12 03:00:46 2018 (r479581) @@ -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]; Added: head/science/openmx/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/openmx/pkg-descr Wed Sep 12 03:00:46 2018 (r479581) @@ -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/
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