General fixes, improvements, and cleanup

.gitignore

@@ -0,0 +1 @@
+bin/

Makefile

@@ -0,0 +1,30 @@
+# Compiler and flags
+FC = gfortran
+FFLAGS = -std=legacy -fdefault-real-8 -fdefault-double-8 -fdefault-integer-8 -fbacktrace
+FDEBUG = -g -Wall -Wextra -O0 -fcheck=all -ffpe-trap=invalid,zero,overflow \
+         -finit-real=snan -finit-integer=-999999 -finit-logical=true \
+		 -fsanitize=address,undefined
+
+# Directories
+SRC_DIR = src
+BIN_DIR = bin
+
+# Files
+TARGET = $(BIN_DIR)/sources4d
+SRC    = src/sources4d.for
+
+.PHONY: all debug clean
+
+all: $(BIN_DIR) $(TARGET)
+
+debug: FFLAGS += $(FDEBUG)
+debug: $(BIN_DIR) $(TARGET)
+
+$(BIN_DIR):
+	mkdir -p $(BIN_DIR)
+
+$(TARGET): $(SRC)
+	$(FC) $(FFLAGS) $< -o $@
+
+clean:
+	rm -f $(TARGET)

README.md

@@ -4,12 +4,10 @@ SOURCES is a code for computing neutron source rates and spectra from spontaneou
 
 SOURCES4D has been built and tested only on a Linux platform with an Intel FORTRAN compiler.
 
-# Directory Contents
+## Directory Contents
 
 src--source code
 
-bin--executable code
-
 data--data files
 
 docs--documentation
@@ -24,15 +22,30 @@ User manual describing the new features in SOURCES4D.
 - mc2019.proc_v_n_pp2335-2347.pdf
 > Jeffrey A. Favorite, “Second Derivative of an (alpha,n) Neutron Source with Respect to Constituent Isotope Densities,” _Proceedings of the International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering (M&C 2019)_, 2335–2347, Portland, Oregon, August 25–29, 2019.
 
-samples--8 test inputs and outputs and utility scripts
+samples--10 test inputs and outputs and utility scripts
+
+## How to install
+
+To clone this repository and build the executable, please type the following commands:
+```bash
+git clone https://github.com/lanl/SOURCES4D.git
+cd SOURCES4D
+make
+```
+
+## Usage
+
+For usage instruction, refer to the manual included in the `docs` folder.
+
+The latest version of the code introduces an additional input parameter to enable or disable the sensitivity calculation. This parameter must be added in `card 2`, after the `idd`, `id`, `erg` parameters. It accepts two values: `0` to disable the sensitivity calculation and `1` to enable it. To ensure compatibility with older inputs, this parameter is optional and, if omitted, it defaults to `0`. The sensitivity calculation is only available for the homogeneous configuration and for the alpha beam configuration.
 
-# Copyright
+## Copyright
 
 © 2024. Triad National Security, LLC. All rights reserved.
 
 This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos National Laboratory (LANL), which is operated by Triad National Security, LLC for the U.S. Department of Energy/National Nuclear Security Administration. All rights in the program are reserved by Triad National Security, LLC, and the U.S. Department of Energy/National Nuclear Security Administration. The Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so. 
 
-# License
+## License
 
 GPLv3
 This software is open source under the GNU General Public License ; either version 3.0 of the License, or (at your option) any later version

samples/test1/tape1

@@ -1,5 +1,5 @@
 Sample 1 - PuBe13 Source (Stewart, 1953)
-1 2 1
+1 2 1 1
 2 0
     4 0.928571
    94 0.071429

samples/test10/outp

@@ -0,0 +1,256 @@
+SOURCES 4D Calculation
+<<<<<<<<<<<>>>>>>>>>>>
+
+
+
+                      Summary of Input
+                      ================
+
+Title: Three-Region Interface Problem Am-CO2-plastic                                
+
+Three region problem input (idd = 4)
+Magnitudes and spectra computed.
+
+ 2000 alpha energy groups used at each interface.
+Maximum energy for alpha spectra:  6.500E+00 MeV.
+Minimum energy for alpha spectra:  1.000E-07 MeV.
+
+Number of neutron spectrum energy groups:  20
+Maximum neutron energy is  1.00000E+01 MeV.
+Minimum neutron energy is  0.00000E+00 MeV.
+
+Neutron Energy Group Structure:
+
+  Group    Upper-Bound    Lower-Bound
+  -----    -----------    -----------
+     1     1.00000E+01    9.50000E+00
+     2     9.50000E+00    9.00000E+00
+     3     9.00000E+00    8.50000E+00
+     4     8.50000E+00    8.00000E+00
+     5     8.00000E+00    7.50000E+00
+     6     7.50000E+00    7.00000E+00
+     7     7.00000E+00    6.50000E+00
+     8     6.50000E+00    6.00000E+00
+     9     6.00000E+00    5.50000E+00
+    10     5.50000E+00    5.00000E+00
+    11     5.00000E+00    4.50000E+00
+    12     4.50000E+00    4.00000E+00
+    13     4.00000E+00    3.50000E+00
+    14     3.50000E+00    3.00000E+00
+    15     3.00000E+00    2.50000E+00
+    16     2.50000E+00    2.00000E+00
+    17     2.00000E+00    1.50000E+00
+    18     1.50000E+00    1.00000E+00
+    19     1.00000E+00    5.00000E-01
+    20     5.00000E-01    0.00000E+00
+
+Number of angular groups: 100
+
+Angular Group Structure:
+
+  Group    Upper-Bound    Lower-Bound
+  -----    -----------    -----------
+     1     1.57080E-02    0.00000E+00
+     2     3.14159E-02    1.57080E-02
+     3     4.71239E-02    3.14159E-02
+     4     6.28319E-02    4.71239E-02
+     5     7.85398E-02    6.28319E-02
+     6     9.42478E-02    7.85398E-02
+     7     1.09956E-01    9.42478E-02
+     8     1.25664E-01    1.09956E-01
+     9     1.41372E-01    1.25664E-01
+    10     1.57080E-01    1.41372E-01
+    11     1.72788E-01    1.57080E-01
+    12     1.88496E-01    1.72788E-01
+    13     2.04204E-01    1.88496E-01
+    14     2.19911E-01    2.04204E-01
+    15     2.35619E-01    2.19911E-01
+    16     2.51327E-01    2.35619E-01
+    17     2.67035E-01    2.51327E-01
+    18     2.82743E-01    2.67035E-01
+    19     2.98451E-01    2.82743E-01
+    20     3.14159E-01    2.98451E-01
+    21     3.29867E-01    3.14159E-01
+    22     3.45575E-01    3.29867E-01
+    23     3.61283E-01    3.45575E-01
+    24     3.76991E-01    3.61283E-01
+    25     3.92699E-01    3.76991E-01
+    26     4.08407E-01    3.92699E-01
+    27     4.24115E-01    4.08407E-01
+    28     4.39823E-01    4.24115E-01
+    29     4.55531E-01    4.39823E-01
+    30     4.71239E-01    4.55531E-01
+    31     4.86947E-01    4.71239E-01
+    32     5.02655E-01    4.86947E-01
+    33     5.18363E-01    5.02655E-01
+    34     5.34071E-01    5.18363E-01
+    35     5.49779E-01    5.34071E-01
+    36     5.65487E-01    5.49779E-01
+    37     5.81195E-01    5.65487E-01
+    38     5.96903E-01    5.81195E-01
+    39     6.12611E-01    5.96903E-01
+    40     6.28319E-01    6.12611E-01
+    41     6.44026E-01    6.28319E-01
+    42     6.59734E-01    6.44026E-01
+    43     6.75442E-01    6.59734E-01
+    44     6.91150E-01    6.75442E-01
+    45     7.06858E-01    6.91150E-01
+    46     7.22566E-01    7.06858E-01
+    47     7.38274E-01    7.22566E-01
+    48     7.53982E-01    7.38274E-01
+    49     7.69690E-01    7.53982E-01
+    50     7.85398E-01    7.69690E-01
+    51     8.01106E-01    7.85398E-01
+    52     8.16814E-01    8.01106E-01
+    53     8.32522E-01    8.16814E-01
+    54     8.48230E-01    8.32522E-01
+    55     8.63938E-01    8.48230E-01
+    56     8.79646E-01    8.63938E-01
+    57     8.95354E-01    8.79646E-01
+    58     9.11062E-01    8.95354E-01
+    59     9.26770E-01    9.11062E-01
+    60     9.42478E-01    9.26770E-01
+    61     9.58186E-01    9.42478E-01
+    62     9.73894E-01    9.58186E-01
+    63     9.89602E-01    9.73894E-01
+    64     1.00531E+00    9.89602E-01
+    65     1.02102E+00    1.00531E+00
+    66     1.03673E+00    1.02102E+00
+    67     1.05243E+00    1.03673E+00
+    68     1.06814E+00    1.05243E+00
+    69     1.08385E+00    1.06814E+00
+    70     1.09956E+00    1.08385E+00
+    71     1.11527E+00    1.09956E+00
+    72     1.13097E+00    1.11527E+00
+    73     1.14668E+00    1.13097E+00
+    74     1.16239E+00    1.14668E+00
+    75     1.17810E+00    1.16239E+00
+    76     1.19381E+00    1.17810E+00
+    77     1.20951E+00    1.19381E+00
+    78     1.22522E+00    1.20951E+00
+    79     1.24093E+00    1.22522E+00
+    80     1.25664E+00    1.24093E+00
+    81     1.27235E+00    1.25664E+00
+    82     1.28805E+00    1.27235E+00
+    83     1.30376E+00    1.28805E+00
+    84     1.31947E+00    1.30376E+00
+    85     1.33518E+00    1.31947E+00
+    86     1.35088E+00    1.33518E+00
+    87     1.36659E+00    1.35088E+00
+    88     1.38230E+00    1.36659E+00
+    89     1.39801E+00    1.38230E+00
+    90     1.41372E+00    1.39801E+00
+    91     1.42942E+00    1.41372E+00
+    92     1.44513E+00    1.42942E+00
+    93     1.46084E+00    1.44513E+00
+    94     1.47655E+00    1.46084E+00
+    95     1.49226E+00    1.47655E+00
+    96     1.50796E+00    1.49226E+00
+    97     1.52367E+00    1.50796E+00
+    98     1.53938E+00    1.52367E+00
+    99     1.55509E+00    1.53938E+00
+   100     1.57080E+00    1.55509E+00
+
+
+Region A Title: Am-241 in region A                                                           
+
+Number of elemental constituents in region A:  1
+Solid stopping cross-sections used (isga= 0) in region A.
+Elemental Constituents in Region A:
+
+  Z-value  Atom Fraction
+  -------  -------------
+     95     1.0000000000
+
+Number of source nuclides to be evaluated:  1
+
+Source Nuclides in Region A:
+
+    ZAID     Atom Fraction
+    ----     -------------
+   952410     1.000E+00
+
+
+Region B Title: CO2 in region B                                                              
+
+Number of elemental constituents in region B:  2
+Gas stopping cross-sections used (isgb= 1) in region B.
+Material B atom density:  1.00000E-05 atoms/b-cm.
+Interface region thickness:  2.00000E+00 cm.
+
+Elemental Constituents in Region B:
+
+  Z-value  Atom Fraction
+  -------  -------------
+      6     0.3330000000
+      8     0.6670000000
+
+Number of target nuclides in region B:  3
+
+Target Nuclides in Region B:
+
+    ZAID     Atom Fraction
+    ----     -------------
+    60130     7.333E-03
+    80170     2.667E-04
+    80180     1.333E-03
+
+
+Region C Title: Plastic in region C                                                          
+
+Number of elemental constituents in region C:  3
+Solid stopping cross-sections used (isgc= 0) in region C.
+
+Elemental Constituents in Region C:
+
+  Z-value  Atom Fraction
+  -------  -------------
+      6     0.4850000000
+      1     0.4240000000
+      8     0.0909481000
+
+Number of target nuclides in region C:  3
+
+Target Nuclides in Region C:
+
+    ZAID     Atom Fraction
+    ----     -------------
+    60130     5.189E-03
+    80170     3.458E-05
+    80180     1.866E-04
+
+
+
+
+                      Summary of Output
+                      =================
+
+Total (alpha,n) neutron source from all sources and targets:  1.62646E+01 n/sec-cm^2.
+
+Average (alpha,n) neutron energy:  3.78568E+00 MeV.
+
+Normalized Neutron Energy Spectrum by Energy Group for All Sources:
+(Note: group structure is independent of erg record!)
+
+          Group      Contribution
+          -----      ------------
+             1        0.00000E+00
+             2        0.00000E+00
+             3        0.00000E+00
+             4        0.00000E+00
+             5        5.33240E-10
+             6        2.75391E-03
+             7        1.35322E-02
+             8        2.29478E-02
+             9        3.32288E-02
+            10        7.97711E-02
+            11        1.24029E-01
+            12        1.82249E-01
+            13        1.86493E-01
+            14        1.24982E-01
+            15        6.35776E-02
+            16        6.72408E-02
+            17        4.72129E-02
+            18        2.40592E-02
+            19        1.20936E-02
+            20        1.58296E-02