Feature user manual (#102)

Resolves #16, resolves #89, resolves #91, resolves #92, resolves #93, resolves #94, resolves #95

This is a documentation update that should have no impact on the functionality of the underlying simulation code.

General:
- Updated Changelog to reflect all changes in this PR
- Added user manual explaining the different simulation tests and showing example data with detailed discussion of the physical models implemented and their parameters
- Added user_manual directory with all source data, images, and files used to produce the user manual
- Added User_Manual.pdf to the root repository directory a copy within the docs directory to easily open and view the pdf on the web through github pages
- Added Microsoft Visual Studio solution and project files to all users to easily build and run Excimontec on Windows machines
- Added install instructions for building Excimontec on Windows using Microsoft Visual Studio in the user manual
- Updated Readme to replace installation instruction with a link to the user manual
- Reorganized README and added citation info, recommended reading, and acknowledgement sections
- Updated gitignore file to ignore exacted example data subdirectories
- Updated gitignore file to not ignore the new Microsoft Visual Studio solution and project files but to still ignore the generated build directories
- Removed the googletest submodule because it was duplicating the one already located within the KMC_Lattice submodule
- Updated the gitmodules file to remove the googletest submodule entry
- Updated .travis.yml by removing exclude statement for googletest since it is no longer included as a submodule
- Updated .travis.yml file to reduce number of tested GCC 4.x versions and added GCC 9
- Updated Readme to show latest versions being testing with Travis CI
- Updated .travis.yml file copyright statement years
- Updated labeling of the parameter sections in parameters_default.txt

main:
- Updated version string
- Updated copyright statement years

.gitignore

@@ -28,14 +28,21 @@
 *.out
 *.app
 
-# Visual Studio files
-*.vcxproj*
-.vs*
-x64*
-*.sln
-packages*
+# Generated Visual Studio Files
+msvc/2019/.vs
+msvc/2019/x64*
+msvc/2019/Win32*
+
+# Generated Test Files
 test/energies.txt
 test/log.txt
 test/parameters_misspell*
 test/status.txt
 test/test_log.txt
+
+# Uncompressed example data files
+user_manual/example_data/Dynamics_test_data/set*/*/
+user_manual/example_data/Exciton_diffusion_test_data/set*/*/
+user_manual/example_data/IQE_test_data/set*/*/
+user_manual/example_data/Steady_transport_test_data/set*/*/
+user_manual/example_data/ToF_test_data/set*/*/

.gitmodules

@@ -1,6 +1,3 @@
 [submodule "KMC_Lattice"]
 	path = KMC_Lattice
 	url = https://github.com/MikeHeiber/KMC_Lattice
-[submodule "googletest"]
-	path = googletest
-	url = https://github.com/google/googletest

.travis.yml

@@ -1,4 +1,4 @@
-# Copyright (c) 2017-2019 Michael C. Heiber
+# Copyright (c) 2017-2020 Michael C. Heiber
 # This source file is part of the Excimontec project, which is subject to the MIT License.
 # For more information, see the LICENSE file that accompanies this software.
 # The Excimontec project can be found on Github at https://github.com/MikeHeiber/Excimontec
@@ -7,17 +7,12 @@
 language: cpp
 os: linux
 dist: trusty
-sudo: required
 
 compiler:
     - gcc
 
 env:
-    - OPTIONS="GCC_VERSION=4.7 && MPI=openmpi && TARGET=test_coverage"
-    - OPTIONS="GCC_VERSION=4.7 && MPI=mpich2 && TARGET=test"
-    - OPTIONS="GCC_VERSION=4.7 && MPI=openmpi && TARGET=test"
-    - OPTIONS="GCC_VERSION=4.8 && MPI=mpich2 && TARGET=test"
-    - OPTIONS="GCC_VERSION=4.8 && MPI=openmpi && TARGET=test"
+    - OPTIONS="GCC_VERSION=4.9 && MPI=openmpi && TARGET=test_coverage"
     - OPTIONS="GCC_VERSION=4.9 && MPI=mpich2 && TARGET=test"
     - OPTIONS="GCC_VERSION=4.9 && MPI=openmpi && TARGET=test"
     - OPTIONS="GCC_VERSION=5 && MPI=mpich2 && TARGET=test"
@@ -28,6 +23,8 @@ env:
     - OPTIONS="GCC_VERSION=7 && MPI=openmpi && TARGET=test"
     - OPTIONS="GCC_VERSION=8 && MPI=mpich2 && TARGET=test"
     - OPTIONS="GCC_VERSION=8 && MPI=openmpi && TARGET=test"
+    - OPTIONS="GCC_VERSION=9 && MPI=mpich2 && TARGET=test"
+    - OPTIONS="GCC_VERSION=9 && MPI=openmpi && TARGET=test"
 
 before_install:
     - eval "${OPTIONS}"
@@ -44,5 +41,5 @@ before_install:
 script:
     - make -j10 $TARGET
     - travis_wait 30 ./test/Excimontec_tests.exe
-    - if [[ "$TARGET" = test_coverage ]]; then coveralls --include src --exclude "googletest/*" --gcov-options '\-lp'; fi
+    - if [[ "$TARGET" = test_coverage ]]; then coveralls --include src --gcov-options '\-lp'; fi
     - if [[ "$TARGET" = test ]]; then make -j10 && mpiexec -n 4 ./Excimontec.exe parameters_default.txt; fi

CHANGELOG.md

@@ -6,11 +6,41 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 --------------------------------------------------------------------------------------------------------------------------------
 
+## [Unreleased]
+
+### Added
+- User_Manual.pdf - User manual PDF to the root directory including examples for each type of simulation test, a detailed description of the models implemented in the code and their parameters, and installation instructions
+- docs/User_Manual.pdf - Copy of user manual to the docs directory for easy linking and viewing on the web
+- user_manual - Directory with source files for the user manual including all of the simulation output data used for the examples
+- msvc - Directory with Microsoft Visual studio solution and project files for building Excimontec on Windows
+- README.md - Recommended reading, citation information, and acknowledgement sections
+
+### Changed
+- README.md - Replaced detailed installation and build instructions with link to new user manual
+- README.md - Reorganized sections to be more useful for new users
+- README.md - Updated information about Travis CI testing configuration
+- main.cpp - Version string to v1.0.0-rc.4
+- main.cpp - Updated copyright statement years
+- makefile - Updated googletest directory to the one located within the KMC_Lattice submodule
+- parameters_default.txt - Version string to v1.0.0
+- parameters_default.txt - Parameter section headings
+- .gitignore - Ignore statements for Microsoft Visual Studio files to not ignore the solution and project files but still ignore the build directories
+- .travis.yml - Updated copyright statement years
+- .travis.yml - Updating testing config by removing testing of GCC v4.7 and v4.8 and added testing of GCC v9
+
+### Removed
+- googletest - Duplicate googletest submodule with the intent to use the googletest submodule already within the KMC_Lattice submodule
+- .gitmodules - The googletest submodule entry
+- .travis.yml - Coveralls exlcude statement for the googletest directory
+- .travis.yml - sudo statement because it is no longer used by Travis CI
+
+### Fixed
+
 ## [v1.0.0-rc.3]- 2019-04-01 - Density of States Integration Bugfix
 
 ### Added
 - OSC_Sim - Steady_DOS_sampling_count and Steady_DOOS_sampling_counter to keep track of how many times the DOS and DOOS are sampled during the simulation
-- test.cpp (SteadyTransportTests) - tests to check the integral of the DOS and DOOS with and without including Coulomb interactions
+- test.cpp (SteadyTransportTests) - Tests to check the integral of the DOS and DOOS with and without including Coulomb interactions
 
 ### Changed
 - main.cpp - Version string to v1.0.0-rc.3
@@ -27,7 +57,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - OSC_Sim (getSteadyDOS) - To calculate the DOS using only one sample at call time because the DOS (without Coulomb) does not change during the simulation
 - OSC_Sim (getSteadyDOS_Coulomb) - To use the new sampling counter to avoid errors averaging over multiple samplings
 
-
 ## [v1.0.0-rc.2]- 2019-02-09 - Steady State Charge Transport Test Update
 
 ### Added