diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/chemistry.scm | 107 |
1 files changed, 107 insertions, 0 deletions
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index d005be5310..1242417c57 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -43,6 +43,7 @@ #:use-module (gnu packages documentation) #:use-module (gnu packages flex) #:use-module (gnu packages fontutils) + #:use-module (gnu packages gcc) #:use-module (gnu packages gl) #:use-module (gnu packages graphviz) #:use-module (gnu packages gv) @@ -57,6 +58,7 @@ #:use-module (gnu packages serialization) #:use-module (gnu packages sphinx) #:use-module (gnu packages stb) + #:use-module (gnu packages tex) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (guix build-system cmake) @@ -798,3 +800,108 @@ of the algorithms, the calculations give identical results.") coordinates of molecules including macrocycles and metal complexes. It has an emphasis on quality rather than speed.") (license license:bsd-3))) + +(define-public yaehmop + (package + (name "yaehmop") + (version "2022.09.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/greglandrum/yaehmop") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Separate program + (delete-file-recursively "viewkel") + ;; Remove example output (some are corrupted) + (for-each delete-file (find-files "examples" "\\.Z$")) + ;; Documentation outputs + (for-each delete-file (find-files "docs" "\\.(ps|pdf)$")) + ;; These are transpiled from Fortran to C, but we build the + ;; Fortran code instead + (delete-file-recursively "tightbind/f2c_files") + (with-directory-excursion "tightbind" + (for-each delete-file '("abfns.c" + "cboris.c" + "diag.c" + "lovlap.c"))))))) + (build-system cmake-build-system) + (arguments + (list + #:configure-flags + #~(list + "-DUSE_BLAS_LAPACK=ON" + (string-append "-DPARM_FILE_LOC=" #$output + "/share/" #$name "-" #$version "/eht_parms.dat") + "-DBIND_EXE_NAME=yaehmop-bind") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "tightbind"))) + (add-after 'chdir 'patch-fortran-functions + (lambda _ + (substitute* '("mov.c" "prototypes.h") + (("lovlap\\(") "lovlap_(") + (("abfns\\(") "abfns_(")))) + (add-after 'chdir 'patch-cmake + (lambda _ + (substitute* "CMakeLists.txt" + (("project\\(yaehmop C\\)") "project(yaehmop C Fortran)") + (("abfns.c") "fortran77/abfns.f") + (("lovlap.c") "fortran77/lovlap.f") + (("(set\\(PARM_FILE_LOC.*)\\)" all init) + (string-append init " CACHE STRING \"\")")) + (("add_library\\(yaehmop_eht" lib) + (string-append lib " SHARED ")) + (("target_link_libraries\\(test_eht \\$\\{LAPACK_LIBRARIES\\}.*" + all) + (string-append all "\ntarget_link_libraries(yaehmop_eht " + "${LAPACK_LIBRARIES})\n"))))) + (add-after 'build 'build-doc + (lambda _ + (with-directory-excursion "../docs" + (substitute* "bind_manual.tex" + (("\\\\usepackage\\{bindpage\\}") + (string-append + "\\usepackage[left=2cm,right=2cm,top=4cm,bottom=2cm]" + "{geometry}\n" + "\\pdfsuppressptexinfo=-1\n"))) + (substitute* "Zmat_appendix.tex" + (("file=dihedral\\.eps") + "file=figs/dihedral.eps")) + (setenv "FORCE_SOURCE_DATE" "1") + (invoke "latexmk" "-pdf" "bind_manual.tex")))) + (add-after 'install 'install-eht-parms + (lambda _ + (install-file "../tightbind/eht_parms.dat" + (string-append #$output "/share/" + #$name "-" #$version)))) + (add-after 'install-eht-parms 'install-doc + (lambda _ + (install-file "../docs/bind_manual.pdf" + (string-append #$output "/share/doc/" + #$name "-" #$version)))) + (delete 'check) + (add-after 'install-doc 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "./test_eht"))))))) + (inputs (list openblas)) + (native-inputs + (list gfortran + (texlive-updmap.cfg (list texlive-fonts-ec + texlive-latex-graphics + texlive-latex-geometry)))) + (home-page "https://github.com/greglandrum/yaehmop") + (synopsis "Perform extended Hückel calculations") + (description "@acronym{YAeHMOP, Yet Another extended Hueckel Molecular +Orbital Package} contains a program and library for performing extended Hückel +calculations and analyzing the results.") + (license license:bsd-2))) |