science/openmx: Re-add port: Nanoscale material simulations using den…

…sity functional theories (DFT)

It isn't unfetchable.

MOVED

@@ -14746,7 +14746,6 @@ russian/p5-cyrillic||2020-05-05|Has expired: Broken for more than 6 months
 russian/tidyup-mail||2020-05-05|Has expired: Broken for more than 6 months
 science/atom||2020-05-05|Has expired: Broken for more than 6 months
 science/esys-particle||2020-05-05|Has expired: Broken for more than 6 months
-science/openmx||2020-05-05|Has expired: Broken for more than 6 months
 science/p5-Geo-ReadGRIB||2020-05-05|Has expired: Broken for more than 6 months
 science/py-tensorflow-estimator||2020-05-05|Has expired: Broken for more than 6 months
 security/firewalk||2020-05-05|Has expired: Broken for more than 6 months

science/Makefile

@@ -174,6 +174,7 @@
     SUBDIR += openbabel
     SUBDIR += openkim
     SUBDIR += openkim-models
+    SUBDIR += openmx
     SUBDIR += opensim-core
     SUBDIR += opensph
     SUBDIR += opsin

science/openmx/Makefile

@@ -0,0 +1,74 @@
+# $FreeBSD$
+
+PORTNAME=	openmx
+DISTVERSION=	3.8.5 # the 18June12 patch upgrades 3.8 -> 3.8.5
+PORTREVISION=	7
+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
+
+BROKEN_i386=	undefined reference to `__atomic_load', see bug#229605 and https://reviews.llvm.org/D42154
+
+LIB_DEPENDS=	libblas.so:math/blas \
+		libfftw3.so:math/fftw3 \
+		liblapack.so:math/lapack \
+		libmpich.so:net/mpich
+
+USES=		dos2unix fortran gmake localbase:ldflags
+USE_CXXSTD=	c++11
+
+DOS2UNIX_FILES=	openmx_common.h
+
+MAKEFILE=	makefile
+
+WRKSRC=		${WRKDIR}/${PORTNAME}${DISTVERSION:R}
+
+CFLAGS+=	-Dkcomp -fcommon
+LDFLAGS+=	${LOCALBASE}/lib/gcc${GCC_DEFAULT}/libgcc_s.so ${LOCALBASE}/lib/libmpifort.so
+FFLAGS+=	-fallow-argument-mismatch
+
+WRKSRC_SUBDIR=	source
+
+MAKE_ENV=	MPICH_CC=${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>

science/openmx/distinfo

@@ -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

science/openmx/files/patch-Band__DFT__Col.c

@@ -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);

science/openmx/files/patch-Band__DFT__NonCol.c

@@ -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);

science/openmx/files/patch-Cluster__DFT.c

@@ -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 */
+

science/openmx/files/patch-Cluster__DFT__ON2.c

@@ -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;

science/openmx/files/patch-Input__std.c

@@ -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 */