diff --git a/.gitignore b/.gitignore
index 6deec976380ada3d89b99a723abb1c4df20cf173..ecb83700cb4f01a8442484d33b4b02010c8592a6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
+build/include
build/cluster/*
build/sphere/*
build/trapping/*
diff --git a/doc/src/config.dox b/doc/src/config.dox
index d7006e0ad8550eb7c4604c605b8abaf8b5b1c19b..ee0f8baf7b73857b28611c48a3948ac67c512b16 100644
--- a/doc/src/config.dox
+++ b/doc/src/config.dox
@@ -342,7 +342,7 @@ OPTIMIZE_OUTPUT_SLICE = NO
#
# Note see also the list of default file extension mappings.
-EXTENSION_MAPPING =
+EXTENSION_MAPPING = f=FortranFixed f90=FortranFree
# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
# according to the Markdown format, which allows for more readable
@@ -984,6 +984,7 @@ INPUT_FILE_ENCODING =
# *.f18, *.f, *.for, *.vhd, *.vhdl, *.ucf, *.qsf and *.ice.
FILE_PATTERNS = *.cpp \
+ *.f \
*.h \
*.md
diff --git a/src/sphere/List.h b/src/include/List.h
similarity index 98%
rename from src/sphere/List.h
rename to src/include/List.h
index cb2911340cb3dad970d252eba1c69ec704bf9406..047616aaa574c6b9159600b043bdc2c46fc75065 100644
--- a/src/sphere/List.h
+++ b/src/include/List.h
@@ -154,8 +154,8 @@ template<class T> class List {
T* to_array() {
T *array = new T[size];
current = last;
- for (int i = size; i > 0; i--) {
- array[i - 1] = current->value;
+ for (int i = size - 1; i > -1; i--) {
+ array[i] = current->value;
current = current->p_prev;
}
return array;
diff --git a/src/include/file_io.h b/src/include/file_io.h
new file mode 100644
index 0000000000000000000000000000000000000000..24f2c5f0cff1165afacbea0b5d2ac443fd0f6df7
--- /dev/null
+++ b/src/include/file_io.h
@@ -0,0 +1,43 @@
+/*! \file file_io.h
+ *
+ * C++ wrapper of FORTRAN I/O operations with files.
+ */
+
+/*! \brief Open a file for subsequent access.
+ *
+ * \param uid: `int*` Pointer to the unit ID to be associated to the file.
+ * \param name: `char*` C-string for file name (max. length of 63).
+ * \param sta: `char*` C-string for file status (max. length of 7).
+ * \param mode: `char*` C-string for access mode (max. length of 11).
+ */
+extern "C" void open_file_(int* uid, const char* name, const char* sta, const char* mode);
+/*! \brief Close a previously opened file.
+ *
+ * \param uid: `int*` Pointer to the unit ID of the file.
+ */
+extern "C" void close_file_(int* uid);
+/*! \brief Read an integer value from a file.
+ *
+ * \param uid: `int*` Pointer to the unit ID of the file.
+ * \param value: `int*` Pointer of the variable to be updated.
+ */
+extern "C" void read_int_(int* uid, int* value);
+/*! \brief Write a complex value to a file.
+ *
+ * \param uid: `int*` Pointer to the unit ID of the file.
+ * \param real: `double*` Pointer to the real part of the value.
+ * \param imag: `double*` Pointer to the imaginary part of the value.
+ */
+extern "C" void write_complex_(int* uid, double* real, double* imag);
+/*! \brief Write a double precision float value to a file.
+ *
+ * \param uid: `int*` Pointer to the unit ID of the file.
+ * \param value: `double*` Pointer to the variable to be written.
+ */
+extern "C" void write_double_(int* uid, double* value);
+/*! \brief Write an integer value to a file.
+ *
+ * \param uid: `int*` Pointer to the unit ID of the file.
+ * \param value: `int*` Pointer to the variable to be written.
+ */
+extern "C" void write_int_(int* uid, int* value);
diff --git a/src/sphere/edfb.cpp b/src/sphere/edfb.cpp
index 574c089e6245b7e82eb7b0c24fbaf3875e8d9d4b..5858e70f6498008286a2b409c53698da4dcf604b 100644
--- a/src/sphere/edfb.cpp
+++ b/src/sphere/edfb.cpp
@@ -7,7 +7,8 @@
#include <cstring>
#include <iostream>
#include <fstream>
-#include "List.h"
+#include "../include/file_io.h"
+#include "../include/List.h"
using namespace std;
@@ -45,7 +46,6 @@ int main(int argc, char **argv) {
double *xiv, *wns, *wls, *pus, *evs, *vss;
string vns[5];
- int max_nsh = 0; // A helper variable to set the size of dc0m
int ici;
// Input file reading section
@@ -344,7 +344,7 @@ int main(int argc, char **argv) {
}
vss = xi_vector.to_array();
xiv = xi_vector.to_array();
- pu = xip + wp;
+ pu = xip * wp;
wn = pu / 3.0e8;
fprintf(output, " XIP WN WL PU EV\n");
fprintf(output, " %13.4lE", xip);
@@ -352,7 +352,7 @@ int main(int argc, char **argv) {
fprintf(output, "%13.4lE", pigt / wn);
fprintf(output, "%13.4lE", pu);
fprintf(output, "%13.4lE\n", pu * evc);
- fprintf(output, " SCALE FACTORS XI\n", pu * evc);
+ fprintf(output, " SCALE FACTORS XI\n");
for (int jxi6612 = 1; jxi6612 <= nxi; jxi6612++)
fprintf(output, "%5d%13.4lE\n", jxi6612, xiv[jxi6612 - 1]);
//INXI branch ends here.
@@ -361,7 +361,10 @@ int main(int argc, char **argv) {
last_read_line++;
iog = new int[nsph];
for (int i = 0; i < nsph; i++) {
- sscanf(file_lines[last_read_line].c_str(), " %d", (iog + i));
+ string read_format = "";
+ for (int j = 0; j < i; j++) read_format += " %*d";
+ read_format += " %d";
+ sscanf(file_lines[last_read_line].c_str(), read_format.c_str(), (iog + i));
}
nshl = new int[nsph];
ros = new double[nsph];
@@ -376,7 +379,6 @@ int main(int argc, char **argv) {
ros[i113 - 1] = ros_val * pow(10.0, ros_val_exp);
nsh = nshl[i113 -1];
if (i113 == 1) nsh += ies;
- if ((nsh + 1) / 2 + ies > max_nsh) max_nsh = (nsh + 1) / 2 + ies;
rcf[i113 - 1] = new double[nsh];
for (int ns = 0; ns < nsh; ns++) {
double ns_rcf;
@@ -388,28 +390,33 @@ int main(int argc, char **argv) {
// The FORTRAN code writes an auxiliary file in binary format. This should
// be avoided or possibly replaced with the use of standard file formats for
// scientific use (e.g. FITS).
- ofstream tedf_file;
- tedf_file.open("c_TEDF", ofstream::binary);
- tedf_file.write(reinterpret_cast<char *>(&nsph), sizeof(nsph));
+ int uid = 27;
+ string bin_file_name = "c_TEDF";
+ string status = "UNKNOWN";
+ string mode = "UNFORMATTED";
+ open_file_(&uid, bin_file_name.c_str(), status.c_str(), mode.c_str());
+ write_int_(&uid, &nsph);
for (int iogi = 0; iogi < nsph; iogi++)
- tedf_file.write(reinterpret_cast<char *>(iog + iogi), sizeof(iog[iogi]));
- tedf_file.write(reinterpret_cast<char *>(&exdc), sizeof(exdc));
- tedf_file.write(reinterpret_cast<char *>(&wp), sizeof(wp));
- tedf_file.write(reinterpret_cast<char *>(&xip), sizeof(xip));
- tedf_file.write(reinterpret_cast<char *>(&idfc), sizeof(idfc));
- tedf_file.write(reinterpret_cast<char *>(&nxi), sizeof(nxi));
+ write_int_(&uid, (iog + iogi));
+ write_double_(&uid, &exdc);
+ write_double_(&uid, &wp);
+ write_double_(&uid, &xip);
+ write_int_(&uid, &idfc);
+ write_int_(&uid, &nxi);
+ for (int xivi = 0; xivi < nxi; xivi++)
+ write_double_(&uid, (xiv + xivi));
for (int i115 = 1; i115 <= nsph; i115++) {
if (iog[i115 - 1] < i115) continue;
- tedf_file.write(reinterpret_cast<char *>(nshl + i115 - 1), sizeof(nshl[i115 - 1]));
- tedf_file.write(reinterpret_cast<char *>(ros + i115 - 1), sizeof(ros[i115 - 1]));
+ write_int_(&uid, (nshl + i115 -1));
+ write_double_(&uid, (ros + i115 - 1));
nsh = nshl[i115 - 1];
if (i115 == 1) nsh += ies;
for (int ins = 0; ins < nsh; ins++)
- tedf_file.write(reinterpret_cast<char *>(rcf[i115 - 1] + ins), sizeof(rcf[i115 - 1][ins]));
+ write_double_(&uid, (rcf[i115 - 1] + ins));
}
// Remake the dc0m matrix.
- dc0m = new complex<double>**[max_nsh];
- for (int dim1 = 0; dim1 < max_nsh; dim1++) {
+ dc0m = new complex<double>**[nsph];
+ for (int dim1 = 0; dim1 < nsph; dim1++) {
dc0m[dim1] = new complex<double>*[nsph];
for (int dim2 = 0; dim2 < nxi; dim2++) {
dc0m[dim1][dim2] = new complex<double>[nxi];
@@ -432,12 +439,11 @@ int main(int argc, char **argv) {
// The FORTRAN code writes the complex numbers as a 16-byte long binary stream.
// Here we assume that the 16 bytes are equally split in 8 bytes to represent the
// real part and 8 bytes to represent the imaginary one.
- tedf_file.write(reinterpret_cast<char *>(&dc0_real), sizeof(dc0_real));
- tedf_file.write(reinterpret_cast<char *>(&dc0_img), sizeof(dc0_img));
+ write_complex_(&uid, &dc0_real, &dc0_img);
}
}
}
- tedf_file.close();
+ close_file_(&uid);
if (idfc != 0) {
fprintf(output, " DIELECTRIC CONSTANTS\n");
for (int i473 = 1; i473 <= nsph; i473++) {
diff --git a/src/sphere/file_io.f b/src/sphere/file_io.f
new file mode 100644
index 0000000000000000000000000000000000000000..ebd708c5e50fb58d0dec7962cd8ff5391c19e0ef
--- /dev/null
+++ b/src/sphere/file_io.f
@@ -0,0 +1,33 @@
+ SUBROUTINE OPEN_FILE(UID,NAME,STA,MODE)
+ INTEGER, INTENT(IN):: UID
+ CHARACTER*64, INTENT(IN):: NAME
+ CHARACTER*8, INTENT(IN):: STA
+ CHARACTER*12, INTENT(IN):: MODE
+ OPEN(UNIT=UID, FILE=NAME, STATUS=STA(1:7), FORM=MODE(1:11))
+ END
+ SUBROUTINE CLOSE_FILE(UID)
+ INTEGER, INTENT(IN):: UID
+ CLOSE(UID)
+ END
+ SUBROUTINE READ_INT(UID, VALUE)
+ INTEGER, INTENT(IN):: UID
+ INTEGER, INTENT(OUT):: VALUE
+ READ(UID)VALUE
+ END
+ SUBROUTINE WRITE_COMPLEX(UID, RVAL, IVAL)
+ INTEGER, INTENT(IN):: UID
+ REAL*8, INTENT(IN):: RVAL, IVAL
+ COMPLEX*16:: VALUE
+ VALUE=COMPLEX(RVAL,IVAL)
+ WRITE(UID)VALUE
+ END
+ SUBROUTINE WRITE_DOUBLE(UID, VALUE)
+ INTEGER, INTENT(IN):: UID
+ REAL*8, INTENT(IN):: VALUE
+ WRITE(UID)VALUE
+ END
+ SUBROUTINE WRITE_INT(UID,VALUE)
+ INTEGER, INTENT(IN):: UID
+ INTEGER, INTENT(IN):: VALUE
+ WRITE(UID)VALUE
+ END