gnu: Add yaehmop.
* gnu/packages/chemistry.scm (yaehmop): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>master
David Elsing
Liliana Marie Prikler
parent
697f0c8a6a
commit
cfd62fdf86
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@ -43,6 +43,7 @@
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#:use-module (gnu packages documentation)
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#:use-module (gnu packages documentation)
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#:use-module (gnu packages flex)
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#:use-module (gnu packages flex)
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#:use-module (gnu packages fontutils)
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#:use-module (gnu packages fontutils)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages gl)
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#:use-module (gnu packages gl)
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#:use-module (gnu packages graphviz)
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#:use-module (gnu packages graphviz)
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#:use-module (gnu packages gv)
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#:use-module (gnu packages gv)
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@ -57,6 +58,7 @@
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#:use-module (gnu packages serialization)
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#:use-module (gnu packages serialization)
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#:use-module (gnu packages sphinx)
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#:use-module (gnu packages sphinx)
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#:use-module (gnu packages stb)
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#:use-module (gnu packages stb)
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#:use-module (gnu packages tex)
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#:use-module (gnu packages web)
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#:use-module (gnu packages web)
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#:use-module (gnu packages xml)
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#:use-module (gnu packages xml)
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#:use-module (guix build-system cmake)
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#:use-module (guix build-system cmake)
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@ -798,3 +800,108 @@ of the algorithms, the calculations give identical results.")
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coordinates of molecules including macrocycles and metal complexes. It has an
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coordinates of molecules including macrocycles and metal complexes. It has an
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emphasis on quality rather than speed.")
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emphasis on quality rather than speed.")
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(license license:bsd-3)))
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(license license:bsd-3)))
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(define-public yaehmop
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(package
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(name "yaehmop")
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(version "2022.09.1")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/greglandrum/yaehmop")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; Separate program
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(delete-file-recursively "viewkel")
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;; Remove example output (some are corrupted)
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(for-each delete-file (find-files "examples" "\\.Z$"))
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;; Documentation outputs
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(for-each delete-file (find-files "docs" "\\.(ps|pdf)$"))
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;; These are transpiled from Fortran to C, but we build the
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;; Fortran code instead
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(delete-file-recursively "tightbind/f2c_files")
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(with-directory-excursion "tightbind"
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(for-each delete-file '("abfns.c"
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"cboris.c"
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"diag.c"
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"lovlap.c")))))))
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(build-system cmake-build-system)
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(arguments
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(list
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#:configure-flags
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#~(list
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"-DUSE_BLAS_LAPACK=ON"
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(string-append "-DPARM_FILE_LOC=" #$output
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"/share/" #$name "-" #$version "/eht_parms.dat")
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"-DBIND_EXE_NAME=yaehmop-bind")
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'chdir
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(lambda _
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(chdir "tightbind")))
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(add-after 'chdir 'patch-fortran-functions
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(lambda _
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(substitute* '("mov.c" "prototypes.h")
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(("lovlap\\(") "lovlap_(")
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(("abfns\\(") "abfns_("))))
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(add-after 'chdir 'patch-cmake
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(lambda _
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(substitute* "CMakeLists.txt"
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(("project\\(yaehmop C\\)") "project(yaehmop C Fortran)")
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(("abfns.c") "fortran77/abfns.f")
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(("lovlap.c") "fortran77/lovlap.f")
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(("(set\\(PARM_FILE_LOC.*)\\)" all init)
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(string-append init " CACHE STRING \"\")"))
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(("add_library\\(yaehmop_eht" lib)
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(string-append lib " SHARED "))
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(("target_link_libraries\\(test_eht \\$\\{LAPACK_LIBRARIES\\}.*"
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all)
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(string-append all "\ntarget_link_libraries(yaehmop_eht "
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"${LAPACK_LIBRARIES})\n")))))
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(add-after 'build 'build-doc
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(lambda _
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(with-directory-excursion "../docs"
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(substitute* "bind_manual.tex"
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(("\\\\usepackage\\{bindpage\\}")
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(string-append
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"\\usepackage[left=2cm,right=2cm,top=4cm,bottom=2cm]"
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"{geometry}\n"
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"\\pdfsuppressptexinfo=-1\n")))
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(substitute* "Zmat_appendix.tex"
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(("file=dihedral\\.eps")
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"file=figs/dihedral.eps"))
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(setenv "FORCE_SOURCE_DATE" "1")
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(invoke "latexmk" "-pdf" "bind_manual.tex"))))
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(add-after 'install 'install-eht-parms
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(lambda _
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(install-file "../tightbind/eht_parms.dat"
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(string-append #$output "/share/"
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#$name "-" #$version))))
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(add-after 'install-eht-parms 'install-doc
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(lambda _
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(install-file "../docs/bind_manual.pdf"
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(string-append #$output "/share/doc/"
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#$name "-" #$version))))
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(delete 'check)
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(add-after 'install-doc 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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(invoke "./test_eht")))))))
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(inputs (list openblas))
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(native-inputs
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(list gfortran
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(texlive-updmap.cfg (list texlive-fonts-ec
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texlive-latex-graphics
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texlive-latex-geometry))))
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(home-page "https://github.com/greglandrum/yaehmop")
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(synopsis "Perform extended Hückel calculations")
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(description "@acronym{YAeHMOP, Yet Another extended Hueckel Molecular
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Orbital Package} contains a program and library for performing extended Hückel
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calculations and analyzing the results.")
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(license license:bsd-2)))
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