ENH: New structure.

.gitattributes

@@ -0,0 +1,12 @@
+*.f90 linguist-language=fortran
+*.fypp linguist-language=fortran
+
+doc/** linguist-documentation
+docs/** linguist-documentation
+example/** linguist-vendored
+include/** linguist-vendored
+capi/** linguist-vendored
+media/** linguist-vendored
+pywrapper/** linguist-vendored
+py/** linguist-vendored
+

.gitignore

@@ -1,34 +1,42 @@
-*.o
+#API: an (incompatible) API change
+#BENCH: changes to the benchmark suite
+#BLD: change related to building numpy
+#BUG: bug fix
+#DEP: deprecate something, or remove a deprecated object
+#DEV: development tool or utility
+#DOC: documentation
+#ENH: enhancement
+#MAINT: maintenance commit (refactoring, typos, etc.)
+#REV: revert an earlier commit
+#STY: style fix (whitespace, PEP8)
+#TST: addition or modification of tests
+#REL: related to releasing
+
+.idea/
+bin/
+build/
+docs/build/
+dist/
+local/
+API-doc/
+.vscode/
 *.obj
-*.exe
-*.out
-*.pyd
-*.lib
-*.cmake
+*.o
 *.mod
-*.dylib
-*.dll
+*.pyd
 *.dll.a
-*.so
 *.a
+*.dll
+*.so
+*.dylib
 
-.idea
-.vscode
-
-build/
 *.egg-info
-
-.DS_Store
-
-dist/
-
 __pycache__
+*.so
 
-generator*
+.DS_Store
 
-pywrapper/src/pyecx/ecx*.h
-pywrapper/src/pyecx/*.dylib
-pywrapper/src/pyecx/*.so
-pywrapper/src/pyecx/*.dll
-pywrapper/src/pyecx/*.dll.a
-pywrapper/wheelhouse/
+py/wheelhouse/
+py/src/pyecx/bin/
+py/src/pyecx/include/
+py/src/pyecx/lib/

API-doc-FORD-file.md

@@ -0,0 +1,41 @@
+---
+project: ecx
+summary: ECX - Electrochemistry
+project_github: https://github.com/MilanSkocic/ecx
+project_download: https://github.com/MilanSkocic/ecx/releases
+project_website: https://milanskocic.github.io/ecx/index.html
+author: Milan Skocic
+email: [email protected]
+github: https://github.com/MilanSkocic
+src_dir: ./src
+include: ./include
+media_dir: ./media
+page_dir: ./doc
+output_dir: API-doc
+exclude_dir: ./example
+             ./test
+display: public
+         protected
+source: true
+proc_internals: true
+sort: permission-alpha
+print_creation_date: true
+md_extensions: markdown.extensions.toc
+               markdown.extensions.smarty
+fpp_extensions: fypp
+preprocess: true
+preprocessor: fypp
+graph: true
+graph_maxnodes: 250
+graph_maxdepth: 5
+coloured_edges: true
+license: by-sa
+favicon: media/logo.ico
+---
+
+![ecx](./media/logo.png)
+
+[TOC]
+
+{!README.md!}
+

CHANGELOG.md

@@ -5,3 +5,5 @@
 * Documentation with sphinx.
 
 Full changelog available at [github](https://github.com/MilanSkocic/ecx/releases)
+
+**Note released yet**

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2021-2024 Milan Skocic
+Copyright (c) Milan Skocic
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

Makefile

@@ -10,19 +10,23 @@ else
 	btype=release
 endif
 
+SRC_FYPP=$(wildcard ./src/*.fypp)
+
+.PHONY: build doc docs
+
 all: $(LIBNAME)
 
 $(LIBNAME): build copy_a shared
 
-.PHONY: build
 build: 
 	fpm build --profile=$(btype)
 
 test: build
 	fpm test --profile=$(btype)
-	
+
 example: build
-	fpm run --profile=$(btype) --example example_in_f example_in_c
+	fpm run --profile=$(btype) --example example_in_f
+	fpm run --profile=$(btype) --example example_in_c
 
 copy_a: 
 	cp -f $(shell find ./build/gfortran* -type f -name $(LIBNAME).a) $(BUILD_DIR)
@@ -38,18 +42,14 @@ shared_darwin:
 shared_windows: 
 	$(FC) -shared $(FPM_LDFLAGS) -o $(BUILD_DIR)/$(LIBNAME).dll -Wl,--out-implib=$(BUILD_DIR)/$(LIBNAME).dll.a,--export-all-symbols,--enable-auto-import,--whole-archive $(BUILD_DIR)/$(LIBNAME).a -Wl,--no-whole-archive
 
-clean:
-	fpm clean --all
-	rm -f src/*.mod
-
 install: install_dirs install_$(PLATFORM)
 
 install_dirs: 
 	mkdir -p $(install_dir)/bin
 	mkdir -p $(install_dir)/include
 	mkdir -p $(install_dir)/lib
-	fpm install --prefix=$(install_dir)
-	cp -f ./include/*.h $(install_dir)/include
+	fpm install --prefix=$(install_dir) --profile=$(btype)
+	cp -f $(INCLUDE_DIR)/$(NAME)*.h $(install_dir)/include
 
 install_linux: 
 	cp -f $(BUILD_DIR)/$(LIBNAME).so $(install_dir)/lib
@@ -59,14 +59,31 @@ install_darwin:
 
 install_windows:
 	cp -f $(BUILD_DIR)/$(LIBNAME).dll.a $(install_dir)/lib
+	cp -f $(BUILD_DIR)/$(LIBNAME).dll $(install_dir)/lib
 	cp -f $(BUILD_DIR)/$(LIBNAME).dll $(install_dir)/bin
 
 uninstall:
-	rm -f $(install_dir)/include/$(HEADER_PREFIX)*.h
-	rm -f $(install_dir)/include/$(HEADER_PREFIX)*.mod
+	rm -f $(install_dir)/include/$(NAME)*.h
+	rm -f $(install_dir)/include/$(NAME)*.mod
 	rm -f $(install_dir)/lib/$(LIBNAME).a
 	rm -f $(install_dir)/lib/$(LIBNAME).so
 	rm -f $(install_dir)/lib/$(LIBNAME).dylib
 	rm -f $(install_dir)/lib/$(LIBNAME).dll.a
+	rm -f $(install_dir)/lib/$(LIBNAME).dll
 	rm -f $(install_dir)/bin/$(LIBNAME).dll
 
+clean:
+	fpm clean --all
+	make -C py clean
+	rm -rf API-doc/*
+
+doc:
+	ford API-doc-FORD-file.md
+
+docs:
+	rm -rf docs/*
+	cp -rf API-doc/* ./docs/
+
+logo:
+	make -C media
+

VERSION

@@ -0,0 +1 @@
+0.1.0

configure.sh

@@ -1,5 +1,9 @@
+#!/bin/bash
+
 LIBNAME="libecx"
-HEADER_PREFIX="ecx"
+NAME="ecx"
+PYNAME="py$NAME"
+PY_SRC="./src/$PYNAME"
 
 # environment variables
 FC=gfortran
@@ -10,21 +14,31 @@ FPM_CFLAGS="-std=c11 -pedantic -Wall -Wextra"
 FPM_LDFLAGS=""
 DEFAULT_INSTALL_DIR="$HOME/.local"
 PLATFORM="linux"
+EXT=".so"
 
 if [[ "$OSTYPE" == "msys" ]]; then
     DEFAULT_INSTALL_DIR="${APPDATA//\\//}/local"
     PLATFORM="windows"
+    ROOT=$ROOTWINDOWS
+    EXT=".dll"
+    LIBS=( "${LIBSWINDOWS[@]}" )
 fi
 
 if [[ "$OSTYPE" == "darwin"* ]];then
     PLATFORM="darwin"
+    ROOT=$ROOTDARWIN
+    EXT=".dylib"
+    LIBS=( "${LIBSDARWIN[@]}" )
 fi
 
+cp -f VERSION ./py/VERSION
+cp -f LICENSE ./py/LICENSE
+
 export LIBNAME
 echo "LIBNAME=" $LIBNAME
 
-export HEADER_PREFIX
-echo "HEADER_PREFIX=" $HEADER_PREFIX
+export NAME
+echo "NAME=" $NAME
 
 export PLATFORM
 echo "PLATFORM=" $PLATFORM
@@ -47,5 +61,9 @@ echo "BUILD DIR=" $BUILD_DIR
 export INCLUDE_DIR
 echo "INCLUDE_DIR=" $INCLUDE_DIR
 
+export PY_SRC
+echo "PY_SRC=" $PY_SRC
+
 export FC
 echo "FC=" $FC
+

fpm.toml

@@ -1,9 +1,9 @@
 name = "ecx"
 version = "0.1.0"
-license = "GNU General Public License v3 (GPLv3)"
+license = "MIT"
 author = "Milan Skocic"
 maintainer = "[email protected]"
-copyright = "Copyright 2021-2024, Milan Skocic"
+copyright = "Copyright, Milan Skocic"
 categories  =["Science"]
 keywords = ["electrochemistry", "impedance", "photoelectrochemistry"]
 homepage = "https://milanskocic.github.io/ecx/index.html"
@@ -28,11 +28,11 @@ library = true
 
 [[example]]
 name="example_in_f"
-main="example_in_f.f90"
+main="example.f90"
 
 [[example]]
 name="example_in_c"
-main="example_in_c.c"
+main="example.c"
 
 [[test]]
 name="test_core"

include/ecx.h

@@ -1,15 +1,53 @@
-/**
- * @file 
- * @brief C API - Main C header for the ecx library.
- */
 #ifndef ECX_H
 #define ECX_H
+#include <complex.h>
+#if _MSC_VER
+    #define ADD_IMPORT __declspec(dllimport)
+    typedef _Dcomplex ecx_cdouble; 
+    #define ecx_cbuild(real, imag) (_Cbuild(real, imag))
+#else
+    #define ADD_IMPORT
+    typedef double _Complex ecx_cdouble; 
+    #define ecx_cbuild(real, imag) (real+I*imag) 
+#endif
+
+extern char* ecx_get_version(void);
+
+
+/* ---------------------------------------------------------------------------------------------- */
+ADD_IMPORT extern const double ecx_core_PI; 
+ADD_IMPORT extern const double ecx_core_T_K; 
+void ecx_core_nm2eV(double *lambda, double *E, size_t n); 
+void ecx_core_kTe(double *U, double *kTE, size_t n); 
+/* ---------------------------------------------------------------------------------------------- */
+
+
+/* ---------------------------------------------------------------------------------------------- */
+extern double ecx_kinetics_capi_nernst(double E0, int z, 
+                                       double *aox, double *vox, size_t nox, 
+                                       double *ared, double *vred, size_t nred, 
+                                       double T);
+
+extern void ecx_kinetics_capi_sbv(double *U, double OCV, double j0, 
+                                  double aa, double ac, double za, double zc,
+                                  double A, double T, double *i, size_t n);
+
+extern void ecx_kinetics_capi_bv(double *U, double OCV, double j0, double jdla, double jdlc,
+                        double aa, double ac, double za, double zc,
+                        double A, double T, double *i, size_t n);
+/* ---------------------------------------------------------------------------------------------- */
+
 
-#include "ecx_core.h"
-#include "ecx_eis.h"
-#include "ecx_pec.h"
-#include "ecx_kinetics.h"
-#include "ecx_version.h"
+/* ---------------------------------------------------------------------------------------------- */
+extern void ecx_capi_zr(double *w, double R, size_t n, ecx_cdouble *Z);
+extern void ecx_capi_zc(double *w, double C, size_t n, ecx_cdouble *Z);
+extern void ecx_capi_zl(double *w, double L, size_t n, ecx_cdouble *Z);
+extern void ecx_capi_zcpe(double *w, double Q, double a, size_t n, ecx_cdouble *Z);
+extern void ecx_capi_zw(double *w, double s, size_t n, ecx_cdouble *Z);
+extern void ecx_eis_z(double *p, double *w, ecx_cdouble *z, 
+                      char e, size_t k, size_t n, 
+                      int *errstat, char *(*errmsg)); 
+/* ---------------------------------------------------------------------------------------------- */
 
 #endif